Category organism orgId locusId sysName locus_tag protein_id uniprotId new_annotation comment original_description SEED_description KEGG_description protein_sequence catabolism Acidovorax sp. GW101-3H11 acidovorax_3H11 Ac3H11_2078 A1D30_RS07410 WP_063460136.1 tr|A0A165KQE5|A0A165KQE5_9BURK D-mannose isomerase (EC 5.3.1.7) Specifically important for: D-Mannitol; D-Mannose. Often annotated as N-acylglucosamine 2-epimerase instead (SEED_correct) D-mannose isomerase (EC 5.3.1.7) D-mannose isomerase (EC 5.3.1.7) MAIPPYPDFRSAAFLRQHLRATMAFYDPVATDASGGQFHFFLDDGTVYNTHTRHLVSATRFVVTHAMLYRTTGEARYQVGMRHALEFLRTAFLDPATGGYAWLIDWQDGRATVQDTTRHCYGMAFVMLAYARAYEAGVPEARVWLAEAFDTAEQHFWQPAAGLYADEASPDWQLTSYRGQNANMHACEAMISAFRATGERRYIERAEQLAQGICQRQAALSDRTHAPAAEGWVWEHFHADWSVDWDYNRHDRSNIFRPWGYQVGHQTEWAKLLLQLDALLPADWHLPCAQRLFDTAVERGWDAEHGGLYYGMAPDGSICDDGKYHWVQAESMAAAAVLAVRTGDARYWQWYDRIWAYCWAHFVDHEHGAWFRILHRDNRNTTREKSNAGKVDYHNMGACYDVLLWALDAPGFSKESRSAALGRP transporters Acidovorax sp. GW101-3H11 acidovorax_3H11 Ac3H11_2554 A1D30_RS09780 WP_063460535.1 tr|A0A162DKX0|A0A162DKX0_9BURK ABC transporter for L-Histidine, permease component 1 Specific phenotypes on L-Histidine. In a gene cluster that also includes hutD and imidazolonepropionase. Some subunits are annotated as transporting glutamine. Amino acid ABC transporter, permease protein Amino acid ABC transporter, permease protein polar amino acid transport system permease protein MELDFSPVWAGVPQLLAGALVTVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALCTAYVAAIRGTPLLVQLFILFFGLPQFGILLPAFVCGVIGLGIYSGAYVSEVVRGAIQSIDKGQMEAARSIGMSSGLAMRTVVLPQAVVRMIPPLGNEFIALIKNSALVSLLTIHDLMHEGQKIISVSYRSLEVYLAIAVVYFILTGATTLVLRRIELRLRAGGMVQ transporters Acidovorax sp. GW101-3H11 acidovorax_3H11 Ac3H11_2555 A1D30_RS09785 WP_063460536.1 tr|A0A165KWF3|A0A165KWF3_9BURK ABC transporter for L-Histidine, periplasmic substrate-binding component 1 Specific phenotype on L-Histidine. Do not understand why there seem to be two substrate binding proteins for this ABC transporter. Both SBPs have signal peptides, so they seem unlikely to be involved in efflux of a waste product instead. Glutamine ABC transporter, periplasmic glutamine-binding protein (TC 3.A.1.3.2) Glutamine ABC transporter, periplasmic glutamine-binding protein (TC 3.A.1.3.2) polar amino acid transport system substrate-binding protein MNLRRNLLLASLAAAAFCTTGAQAQDNVLRVGTDATFPPMEFVENGKRTGFDIELVEAIAKTMGKQVEWVDIDFKGLIPGLISKRFDMAVSAIYITDERKKVVDFTDSYYAGGLVVMVKADNKAINKLADLDGKKVSVQVGTKSVSYLTEKFPKVQRVEVEKNQEMFNLVDIGRADAAVTGKPAAFQYVRTRPGLRVLDEQLTTEEYGMALRKDTPELTKAVNGAITKLKADGTYAAIVKKWFSNSAAK transporters Acidovorax sp. GW101-3H11 acidovorax_3H11 Ac3H11_2560 A1D30_RS09810 WP_063460541.1 tr|A0A165KWL1|A0A165KWL1_9BURK ABC transporter for L-Histidine, ATPase component Specific phenotype on L-Histidine. There may also be a second ATPase component, Ac3H11_2553, but it has no fitness data Urea carboxylase-related ABC transporter, ATPase protein Urea carboxylase-related ABC transporter, ATPase protein sulfonate/nitrate/taurine transport system ATP-binding protein MSSVSIQAVSRVFETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSGRVLLDGAPVEGPGAERGMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAAYFIAKVGLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLGIWEAERKTVLFVTHDIDEAIFMANRVAVFSARPGRIKTELAVDLPHPRHYTIKTSPEFMDLKARLTEEIRAESMAADLH transporters Acidovorax sp. GW101-3H11 acidovorax_3H11 Ac3H11_2561 A1D30_RS09815 WP_063460542.1 tr|A0A165KWL8|A0A165KWL8_9BURK ABC transporter for L-Histidine, permease component 2 Specific phenotypes on L-Histidine. In a gene cluster that also includes hutD and imidazolonepropionase. Some subunits are annotated as transporting glutamine. ABC transporter, permease protein ABC transporter, permease protein sulfonate/nitrate/taurine transport system permease protein VSARARWMLGLAFFVVFVAVWAFFTLGGFVSPTFLASPITMAKEGWLLFTEYGFIKDIGMTIWRVVGGFVLAAVIAVPLGIAMGAYKGIEAFFEPFISFCRYLPASAFIPLLILWAGIGEAQKILVIFIGSVFQITLMVAVTVGGARRDLVEAAYTLGAGHKGIVTRVLIPGAAPEIAETLRLVLGWAWTYVIVAELIGSSSGIGHMITDSQSLLNTGQIIFGIIIIGLIGLVSDFAFKALNHRLFAWSFVR transporters Acidovorax sp. GW101-3H11 acidovorax_3H11 Ac3H11_2562 A1D30_RS09820 WP_082836420.1 tr|A0A165KWM6|A0A165KWM6_9BURK ABC transporter for L-Histidine, periplasmic substrate-binding component 2 Specific phenotype on L-Histidine. Do not understand why there seem to be two substrate binding proteins for this ABC transporter. Both SBPs have signal peptides, so they seem unlikely to be involved in efflux of a waste product instead. ABC transporter substrate-binding protein ABC transporter substrate-binding protein sulfonate/nitrate/taurine transport system substrate-binding protein MTRSVVKWTSLAAAAACVMALAAPAQAQDTKIVLGMSGWTGFAPLTLADKAGIFKKNGLDVEIKMIPQKDRHLALASKSIQCAATTVETHVAWNANGVPIVQIFQMDKSYGADGIAVRGDIKSFADLKGKTIGVDAPGTAPYFGLAWMLSKNGMSLKDVKTTTLSPQAAAQAFVAGQNDAAMTYEPYLSTVRDNPAAGKILATTLDYPMVMDTVGCDPTWLKANGKAAQALANSYFQALDMIKADPAKSNEIMGAAVKQTGEQFAKSSSFLRWQDKAANQKFFAGELTTFMKDATAILLEAGIIRKANEDLAVTFDASFIK catabolism Acidovorax sp. GW101-3H11 acidovorax_3H11 Ac3H11_2940 A1D30_RS11765 WP_063460789.1 tr|A0A165L336|A0A165L336_9BURK D-sorbitol 2-dehydrogenase (EC 1.1.1.14) Specifically important for: D-Sorbitol. Annotated as ribitol dehydrogenase; it could well have both activities, as with AT5G51970 Ribitol 2-dehydrogenase (EC 1.1.1.56) Ribitol 2-dehydrogenase (EC 1.1.1.56) ribitol 2-dehydrogenase MSAARNLQGQVAAITGAASGIGFASAQTMADAGARVVLIDRDEAALAKACATIGPNALPLVLDLLDARQCASLLQRTLALAGQLDIFHANAGLYVGGDLVDADPDAIDRMLNLNVNVVMKNVHNVLPHMIERGTGDIIVTSSLAAHFPTPWEPVYASSKWAVNCFVQTVRRQVFKHGIRVGSISPGPVITSLLADWPAEKLAEAKASGSLIEAAEVAEVVLFMLTRPRGMTIRDVVMMPTNFDL transporters Acidovorax sp. GW101-3H11 acidovorax_3H11 Ac3H11_2941 A1D30_RS11770 WP_063460790.1 tr|A0A165L344|A0A165L344_9BURK ABC transporter for D-Sorbitol, ATPase component Specific phenotypes on D-Sorbitol. Various polyols ABC transporter, ATP-binding component Various polyols ABC transporter, ATP-binding component MAYLQLRGIEKFFGEHRAIKGIDLTIQQGEFIVFVGPSGCGKSTLLRLIAGLEAIDGGSLMLDGRDITDQPSSKRDLAMVFQSYALYPHMSVYENMSFALKLAKVDKQVIDEKVQNAARILNLTQYLQRTPKELSGGQRQRVAIGRAIVRAPKVFLFDEPLSNLDAALRGQTRVEIAKLHRDLGATTIYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDKPANQFVAQFIGTPQMNVVPVDKLPQPVQQQAPAAPAGAAVGAIGLRPENITVRTTGATPVGGQVDLIEALGAETLIYVTTPGGAQFVSRQNDRTDLRVGDAVSLDIDASQAHWFDTAGRVVAGHAA transporters Acidovorax sp. GW101-3H11 acidovorax_3H11 Ac3H11_2942 A1D30_RS11775 WP_063460791.1 tr|A0A165L353|A0A165L353_9BURK ABC transporter for D-Sorbitol, permease component 1 Specific phenotypes on D-Sorbitol. homolog in P. simiae WCS417 is important for mannitol and mannose as well, but in acidovorax, no phenotype on mannitol Various polyols ABC transporter, permease component 2 Various polyols ABC transporter, permease component 2 sorbitol/mannitol transport system permease protein MTVRRRSNFPLGLLALRTAAAWGVALLLFFPLGWLFLTAFKTELQAIAVPPLFVFTPTLENFHEVQERSDYLLYAKNSVITSVLSTVLGLMLAAPAAYAMAFFKGKYTKDILMWMLSTKMMPAVGALVPIYVLAQKSHLLDTQLALIIVFALSNLPIMVWMLYSHFKDIPHEILEAARMDGATLWQEVRLVLLPLGMGGLASTGLLCLVLSWNEAFWSLNLSAAKAGTLATLIASYSSPEGLFWAKLSAASLMAIAPIVVFGWFSQKQLVQGLTFGAVK transporters Acidovorax sp. GW101-3H11 acidovorax_3H11 Ac3H11_2943 A1D30_RS11780 WP_063460792.1 tr|A0A165L360|A0A165L360_9BURK ABC transporter for D-Sorbitol, permease component 2 Specific phenotypes on D-Sorbitol. homolog in P. simiae WCS417 is important for mannitol and mannose as well, but in acidovorax, no phenotype on mannitol Various polyols ABC transporter, permease component 1 Various polyols ABC transporter, permease component 1 sorbitol/mannitol transport system permease protein VELRTSPPIAHATACPFSAAFFRCFDGLSMNRRLLPRLLLTPAMATLFLWMIVPLVMTIYFSLIRYNLMQPDQTGFAGLENFEFFVTDPSFGTAVVNTILLLGSVILITVVLGVAIALLINEPFPGRGIVRVLLISPFFVMPTVNALMWKNMMMNPIYGVLAQVWIFFGAAPVDWLTDHPLFSVIVMVSWQWLPFATLIFMTALQSMNHEQLEASRMDGANYLQQLRYLYVPHLGRSVAVVVMIELIFLLSIFAEIYTTTAGGPGDASTNVTFLIFKQALLNFDAGVASAGALFAVVLANIAAVFLIRMVGKNLDK transporters Acidovorax sp. GW101-3H11 acidovorax_3H11 Ac3H11_2944 A1D30_RS11785 WP_063460793.1 tr|A0A165L365|A0A165L365_9BURK ABC transporter for D-Sorbitol, periplasmic substrate-binding component Specific phenotype on D-Sorbitol. Various polyols ABC transporter, periplasmic substrate-binding protein Various polyols ABC transporter, periplasmic substrate-binding protein sorbitol/mannitol transport system substrate-binding protein MPRSTRPHTRLALAAAALAASLCGAAAHAQTELVIATVNNGHMIEMQKLSKNFEQAHPDIKLKWVTLEEGVLRQRVTTDIATKGGQFDVMTIGMYEAPIWGKKGWLQELKTDAAYDVDDLLPAVRNGLSIDGKLFAAPFYGESSMLMYRKDLADKAGVQVPERPTWPQIKDLAAKIHDPKNGVYGICLRGKPGWGDNMAFLSTLVNTFGGQWFDMQWKPQLESKPWKEAITFYVDLLKNYGPPGSSANSFNEILALTNSGKCGMWIDATIAASFVSDPKQSKVADQMAFAQAPTMNTPKGANWLWSWNLAIPAGSKKVDAAQKFITWSTSKEYVQLVAKTNGWANVPTGTRKSTYASPEFQKAARFAAAEKVAIDSANPTDSTLPKSPYVGVQFAAIPEFQAIGIAVGQQMSAALAGKTTVDAALKASQVSADREMKKAGYYK catabolism Acidovorax sp. GW101-3H11 acidovorax_3H11 Ac3H11_603 A1D30_RS22575 WP_063462980.1 tr|A0A165IRK1|A0A165IRK1_9BURK L-2-keto-3-deoxyarabonate dehydratase (EC 4.2.1.43) Specifically important for L-arabinose utilization and 80% similar to araD from A. brasilense (KDADA_AZOBR, PMID:16950779). This gene is also important for D-galactose utilization, which might be due to polar effects. SEED_correct L-2-keto-3-deoxyarabonate dehydratase (EC 4.2.1.43) L-2-keto-3-deoxyarabonate dehydratase (EC 4.2.1.43) dihydrodipicolinate synthase VPTTFHEDGTLDLDSQKRCLDFMIDAGVDGVCILANFSEQFSLSDAEREVLTRTSLEHVAGRVPVIVTTTHYGTRVCAERSRAAQDMGAAMVMVMPPYHGATFRVPEAQIYEFYARVSDAIRIPIMVQDAPASGTVLSAPFLARMAQEIENLAYFKIEVPGAASKLRELIRLGGDAIEGPWDGEEAITLLADLDAGATGAMTGGAFPDGIRPIIEAHRQGDMDQAFALYQRWLPLINHENRQGGILTAKALMKEGGVIACEAGRHPFPAMHPEVRRGLVDIARRLDPLVLRWAR catabolism Acidovorax sp. GW101-3H11 acidovorax_3H11 Ac3H11_614 A1D30_RS22630 WP_063462990.1 tr|A0A165IRU8|A0A165IRU8_9BURK L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) Specifically important for: D-Galactose; L-Arabinose. Some other dehydrogenases are known to act on both of these substrates Putative oxidoreductase in arabinose utilization cluster Putative oxidoreductase in arabinose utilization cluster LIDCNIDMTQLFAPSSSSTDATGAPQGLAKFPSLQGRAVFVTGGGSGIGAAIVAAFAEQGARVAFVDVAREASEALAQHIADAGLPRPWWRVCDVRDVQALQACMADAAAELGSDFAVLVNNVASDDRHTLESVTPEYYDERMAINERPAFFAIQAVVPGMRRLGAGSVINLGSTGWQGKGTGYPCYAIAKSSVNGLTRGLAKTLGQDRIRINTVSPGWVMTERQIKLWLDAEGEKELARNQCLPDKLRPHDIARMVLFLASDDAAMCTAQEFKVDAGWV transporters Acidovorax sp. GW101-3H11 acidovorax_3H11 Ac3H11_791 A1D30_RS19405 WP_063462373.1 tr|A0A165JCN6|A0A165JCN6_9BURK ABC transporter for Glycerol, ATPase component 1 Specific phenotype on Glycerol; D-Galactose. Has a TOBE domain after the ATPase domain. The phenotype on galactose is not explained. Glycerol-3-phosphate ABC transporter, ATP-binding protein UgpC (TC 3.A.1.1.3) Glycerol-3-phosphate ABC transporter, ATP-binding protein UgpC (TC 3.A.1.1.3) multiple sugar transport system ATP-binding protein MQLALDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTVDGKDVTGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKLRGEKNIDARVREIASRLHIDMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFAAGQSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPMNLMAASATAQGVRLQGGAELTLPLPQGAATAAGLTVGVRASALRVHARPGDVSVAGVVELAEISGSDTFVHASTPWGDLVAQLTGVHYFELGTAITLHLDPAQAYVFGADGRLAQAPARPVTAQGGR transporters Acidovorax sp. GW101-3H11 acidovorax_3H11 Ac3H11_792 A1D30_RS19410 WP_063462374.1 tr|A0A165JCR1|A0A165JCR1_9BURK ABC transporter for Glycerol, ATPase component 2 Specific phenotype on Glycerol. Has a TOBE domain after the ATPase domain. Also mildly important on phenotype on galactose, which is not explained. Glycerol-3-phosphate ABC transporter, ATP-binding protein UgpC (TC 3.A.1.1.3) Glycerol-3-phosphate ABC transporter, ATP-binding protein UgpC (TC 3.A.1.1.3) multiple sugar transport system ATP-binding protein MARISLDLAHSYKPNPQQDSDYALLPLKMEFEDGGAYALLGPSGCGKTTMLNIMSGLLVPSHGKVLFDGRDVTRASPQERNIAQVFQFPVIYDTMTVAENLAFPLRNRKVPEGQIKQRVGVIAEMLEMSGQLNQRAAGLAADAKQKISLGRGLVRADVAAVLFDEPLTVIDPHLKWQLRRKLKQIHHELKLTLIYVTHDQVEALTFADQVVVMTRGKAVQVGSADALFERPAHTFVGHFIGSPGMNFLPAHRDGENLSVAGHRLASPVGRALPAGALQVGIRPEYLALAQPQQAGALPGTVVQVQDIGTYQMLTAKVGEHTVKARFTPETRLPSSGDTAWLQVLGEHTCYYKNEELLA transporters Acidovorax sp. GW101-3H11 acidovorax_3H11 Ac3H11_793 A1D30_RS19415 WP_063462375.1 tr|A0A165JCS4|A0A165JCS4_9BURK ABC transporter for Glycerol, permease component 1 Specific phenotypes on Glycerol. in a gene cluster for glycerol utilization; see phenotype on both strands Glycerol-3-phosphate ABC transporter, permease protein UgpA (TC 3.A.1.1.3) Glycerol-3-phosphate ABC transporter, permease protein UgpA (TC 3.A.1.1.3) multiple sugar transport system permease protein MSTTTKPVNQKAWFLILPVIICVAFSAILPLMTVVNYSVQDIISPERRVFVGTEWFAAVMRDEELHAALWRQLTFSLAVLAVEIPLGILLALSMPAQGWKSSAVLVVVALSLLIPWNVVGTIWQIYGRADIGLMGRMLQEMGIEYSYTGNATQAWLTVLLMDVWHWTPLVALLAFAGLRSIPDAYYQAARIDGASKFAVFRYIQLPKMRGVLMIAVLLRFMDSFMIYTEPFVLTGGGPGNATTFLSQYLTTKAVGQFDLGPAAAFSLIYFFIILLLCFILYNWMQRVGTVSDEGAGHE transporters Acidovorax sp. GW101-3H11 acidovorax_3H11 Ac3H11_794 A1D30_RS19420 WP_063462376.1 tr|A0A165JCS9|A0A165JCS9_9BURK ABC transporter for Glycerol, permease component 2 Specific phenotype on Glycerol. Glycerol-3-phosphate ABC transporter, permease protein UgpE (TC 3.A.1.1.3) Glycerol-3-phosphate ABC transporter, permease protein UgpE (TC 3.A.1.1.3) multiple sugar transport system permease protein MNEKRFQKRTLFLIAYLLFALLPIYWMVNMSFKTNAEILSTFSFFPQHFTWDNYKTIFTDESWYSGYINSLIYVSINMVITLTVALPAAYAFSRYSFLGDKHVFFWLLTNRMTPPAVFLLPFFQLYTTVGLMDTHIAVALAHLLFSVPLAVWILEGFMSGIPREIDETAYIDGYSFPRFFMTIFLPLIKAGVGVAAFFCFMFSWVELLLARTLTSVNAKPIVATMTRTVSASGMDWATLAAAGVLTIVPGAIVIWFVRHYIAKGFAMGRV transporters Acidovorax sp. GW101-3H11 acidovorax_3H11 Ac3H11_796 A1D30_RS19430 WP_063462378.1 tr|A0A165JCU2|A0A165JCU2_9BURK ABC transporter for Glycerol, periplasmic substrate-binding component Specific phenotype on Glycerol. Has signal peptide but not transmembrane helices, and CDD confirms it in the SBP family, not a permease as sometimes annotated Glycerol-3-phosphate ABC transporter, permease protein UgpA (TC 3.A.1.1.3) Glycerol-3-phosphate ABC transporter, permease protein UgpA (TC 3.A.1.1.3) multiple sugar transport system substrate-binding protein MKMQFKAIAFAAAALAMGQAAWAGEAEAKKWIDSEFQPSTLNKDQQMAEMKWFIDAAKKLQAKGVKEISVVSETITTHEYESKTLAKAFEEITGIKVKHDLIQEGDVVEKLQTSMQSGKSIYDGWISDSDLIGTHYRYGKIMNLTDYMGGAGKEWTNPGIDLKDYIGTKFTTGPDGKLYQLPDQQFANLYWFRADLFDRKDIKDKFKAKYGYDLGVPLNWSAYEDIAEFFTNDVKNIDGKPIYGHMDYGKKDPSLGWRFTDAWLSMAGTADIGAPNGLPIDEWGIRVADDKCTPVGASVARGGATNSPAAVYALTKYVDWMKKYAPKEATGMTFGEAGPVPAQGQIAQQIFWYTAFTADMTKPGLPVVNADGTPKWRMAPGPNGPYWKQGMQNGYQDVGSWTFFKDHDANKTAAAWLYAQFVTAKTTSLKKTMVGLTPIRESDIQSKAMTDMAPKLGGLVEFYRSPARVAWSPTGTNVPDYPKLAQLWWKNVAQAVTGEKTPQGAMDTLADEMDQVMARLERAGMAHCAPKLNAKSDPNKWLSDKQAPWKKLANEKPKGETIAYGTLLQAWKDGKTR transporters Shewanella sp. ANA-3 ANA3 7022816 Shewana3_0067 SHEWANA3_RS00365 WP_011715352.1 tr|A0KR93|A0KR93_SHESA sucrose permease scrT specific phenotype on sucrose; 82% identical to the sucrose transporter scrTII or Sfri_3989, which was validated by complementation (PMCID:PMC2996990); SEED_correct major facilitator transporter (RefSeq) Predicted sucrose permease, MFS family, FucP subfamily MVSDSNSVENRHHTRIRVLTYLMFFMFAMTSDAVGVIIPQLISEFGLSLSQASAFHYMPMIFIAISGLFLGFLADKIGRKLTILLGLLLFAIACFLFALGESFYYFLLLLALVGLAIGVFKTGALALIGDISRSTKQHSSTMNTVEGFFGVGAMVGPAIVSYLLISGVSWKYLYFGAGVFCLLLCWLAFRADYPQVKRSSTETINLTNTFSMMKNPYALGFSLAIGLYVATEVAIYVWMPSLLQEYQGDYTVLAAYALTIFFTLRAGGRFLGGWILNHFSWQQVMFWFSLAISLCYLGSMLYGVEAAVILLPLSGLFMSMMYPTLNSKGISCFPVAQHGSVAGVILFFTAVSAALAPLCMGLVGDIFGHVKYGFYLATGFAVLLCLLAGVNLIKDPSQALLSRETA catabolism Shewanella sp. ANA-3 ANA3 7024896 Shewana3_2070 SHEWANA3_RS10895 WP_041412631.1 tr|A0KWY1|A0KWY1_SHESA L-arabonate dehydratase (EC 4.2.1.25) Specifically important for: L-Arabinose. L-arabonate is an intermediate in the oxidation of L-arabinose (SEED_correct) dihydroxy-acid dehydratase (RefSeq) L-arabonate dehydratase (EC 4.2.1.25) dihydroxy-acid dehydratase MCLGRRRCHMNNKKPKTLRSASWFGSDDKNGFMYRSWMKNQGIPEHHFQNKPVIGICNTWSELTPCNGHLRELAQRVKNGIREAGGIPVEFPVFSNGESNLRPSAMLTRNLAAMDTEEAIRGNPIDGVVLLVGCDKTTPALLMGAASCDLPTIVVTGGPMLNGKHKGKDVGSGTLVWELHQEYKAGNISLAAFMNAEADMSRSTGTCNTMGTASTMACMVETLGVSLPHNATIPAVDSRRQVLAHMSGMRIVDMVKEDLTLSKILSRDAFINAIKVNAAIGGSTNAVIHLKAIAGRIGVELSLDDWRHGYTVPTIVNLKPSGQYLMEDFYYAGGLPAVLRQLFEHDLLSKNTLTVNAASLWDNVKEAPCYNQEVIMSLENPLVENGGIRVLRGNLAPRGAVIKPSAASAHLMQHRGKAVVFESFDDYNARIGDPELDIDENSIMVLKNCGPKGYPGMAEVGNMGLPPKLLKKGIKDMVRISDARMSGTAFGTVVLHVAPEAQALGPLAAVQNGDMIALDTYAGTLQLEISDQELQARLAKLATVKSIPVNGGYLSLFKEHVLQADEGCDFDFLVGCRGAEIPAHSH catabolism Shewanella sp. ANA-3 ANA3 7024897 Shewana3_2071 SHEWANA3_RS10900 WP_011717047.1 tr|A0KWY2|A0KWY2_SHESA L-arabinose 1-dehydrogenase (EC 1.1.1.46) Specifically important for: L-Arabinose. Also, was correctly annotated by PMID:20836887 short-chain dehydrogenase/reductase SDR (RefSeq) Putative oxidoreductase in arabinose utilization cluster MKLTNQYPSLQGKTIFISGGATGIGACLVNAFLEQGAKVAFVDILVEESTQLVADLKQTQPEASVTFYHCDLVDIAALKRVIAQVEDDLGPISVLINNAACDQRHSIDEVTPEYWDQCLNTNLRHYFFAVQAVRPQMQRLGGGSVINLGSMSWHNRQAGMAGYTASKAGAMGLTRGLAADLGKDKIRINTLTPGWVMTKRQLTHWVDKDTAKHIENNQCIKEYVMPEDIAAMALFLAADDSKLCTAQNFIVDGGWI catabolism Shewanella sp. ANA-3 ANA3 7024898 Shewana3_2072 SHEWANA3_RS10905 WP_011717048.1 tr|A0KWY3|A0KWY3_SHESA L-arabinose 1-epimerase (mutarotase) (EC 5.1.3.3) Specifically important for: L-Arabinose. Was correctly annotated by PMID:20836887 (more specific than EC number); (SEED_correct) aldose 1-epimerase (RefSeq) L-arabinose-specific 1-epimerase (mutarotase) aldose 1-epimerase MQLSVTQKSLQHAAFADELQLVTLTNSHGLEVVLSNYGASIWSVKLYGQAQEPISLSLGYQDIKDWVTNPYYFGITAGRVANRIGKAQFPLAGKTIQLVANEGNNQLHGGPKGLSHCTWQVEMLQDNDSVAAVFSITSPDGDQGFPGNLAITLEYRLNENNELTLNYQAVCDQTTPVCLTNHAYWNLASNKQQGILGHELSIQASHFLALDNEQIPTGELILVDDGAYDFKQPKLIATDIKQLTNGYDHYFVMDRNPDNKNSLQTIAVLKDPLSGRELEISTTEVGVQFYSGNFLDGSHIDDEGYSINQFHGLCLETHGYPNAVNIDHFPSVMLEANTQYQQITVHKFKNI catabolism Shewanella sp. ANA-3 ANA3 7024914 Shewana3_2088 SHEWANA3_RS10985 WP_011717064.1 tr|A0KWZ9|A0KWZ9_SHESA L-arabinolactonase (EC 3.1.1.15) Important on L-arabinose; Was correctly annotated by PMID:20836887 (SEED_correct) hypothetical protein (RefSeq) L-arabinolactonase (EC 3.1.1.15) MQTVTVGELLMTIPVGNRLGEGVLWDDLHQSIWWTDILSSVIYRFHLASRSLETFPMPHRVGSFGLTAKPTTLIVAFDIGIAIYDIEDQSLTWLAQPESHFAGNRFNDGRIDRQGRFWAGTMVEQRDTLQQTAALYCLDEKGHCHQHLTNLEISNGLCWSVDGRTLYHADSPKHQIYQYDFDIEQGLLSRKRLFASTSHHIFPDGSDVDAAGYLWNAQWGGGQVVRYRPDGEVDLILKLPVTHPTSIAFGGEKRDLLIVTSAKHSLDASQLDQEPQAGDVFIYPLQGIYGVNSPRFCGQL catabolism Shewanella sp. ANA-3 ANA3 7025618 Shewana3_2769 SHEWANA3_RS14565 WP_011717648.1 tr|A0KYX7|A0KYX7_SHESA Branched-chain acyl-CoA dehydrogenase (EC 1.3.99.12) Specifically important for: L-Isoleucine. specificity for isoleucine indicates that 2-methylbutanoyl-CoA is a substrate (SEED_correct) acyl-CoA dehydrogenase domain-containing protein (RefSeq) Branched-chain acyl-CoA dehydrogenase (EC 1.3.99.12) MDFNFNEDQRQFADLARQFAADELAPFAAKWDEEHHFPKDVIQKAGELGFCSLYSPESEGGMGLSRLDASIIFEELSKGCTATTAMLTIHNMATWMVTTWGTDTLRQAWSEPLTTGQMLASYCLTEPGAGSDAASLQTKAVREGDEYVVSGSKMFISGAGSTELLVVMCRTGQAGPKGISAIAIPADSEGIIYGKAEDKMGWNAQPTRLVTFDNVRVPVANLLGEEGQGFTFAMKGLDGGRINIATCSVGTAQAALERATQYMNERQQFGKPLAAFQALQFKLADMATELVAARQMVRLAAFKLDSGDPEATAYCAMAKRFATDVGFQVCDAALQIHGGYGYIREYPLERHFRDVRVHQILEGTNEIMRLIIARRLLDENAGQIL transporters Shewanella sp. ANA-3 ANA3 7025962 Shewana3_3110 SHEWANA3_RS16315 WP_011717943.1 tr|A0KZW5|A0KZW5_SHESA N-acetylglucosamine transporter nagP specific phenotype on NAG and D-glucosamine. This protein is similar to SO3503, which was named nagP (PMID:16857666). There is another putative glucosamine transporter (nagX, Shewana3_3111) but the phenotype of 3110 on glucosamine does not seem to be a polar effect. (It is observed on both strands, conserved in S. amazonensis SB2B, and 3110 is downstream of nagX). It apears that both nagP and nagX might be required for glucosamine utilization. NagX has weak similarity to acyltransferases (Q3UDW8, or possibly opgC from Rhodobacter sphaeroides) so nagX might convert glucosamine into another compound before transport by nagP. (SEED_correct) glucose/galactose transporter (RefSeq) N-acetyl glucosamine transporter, NagP MTLDKSQQKSSFLPMAIVAALFFILGFATWLNGSLMPYLKQILQLNPFQASLILFSFYIAVTFTALPSAWVIRKVGYKNGMALGMGIMMLAGLLFIPAAKTQIFGLFLCAQLVMGTGQTLLQTAVNPYVVRLGPEESAAARVSVMGILNKGAGVIAPLVFSALILDSFKDRIGTTLTQVQIDEMANSLVFPYLGMAIFIGVLALAVKKSPLPELSNEDEVAEHTDKGQIKAALSHPNLAFGVIALFVYVAVEVIAGDTIGTFALSLGVEHYGVMTSYTMVCMVLGYTLGIILIPRFISQPTALMISAILGLLLTLAILFGDNNSYAIANALLVPFGGVALPDTLLFIAFLGLANAIVWPAVWPLALSGLGKLTSTGSALLIMGIAGGAFGPLFWGLTSSATDMGQQGGYMVMLPCYLFILFYAVKGHKMRHW catabolism Shewanella sp. ANA-3 ANA3 7025966 Shewana3_3114 SHEWANA3_RS16335 WP_011717945.1 tr|A0KZW9|A0KZW9_SHESA N-acetylglucosamine kinase (EC 2.7.1.59) Specifically important for: D-Glucosamine Hydrochloride; N-Acetyl-D-Glucosamine. The first step in NAG catabolism. The phenotype on glucosamine is strong and is present on both strands, but is not conserved. It may be a polar effect. (SEED_correct) ATPase, BadF/BadG/BcrA/BcrD type (RefSeq) N-acetylglucosamine kinase of eukaryotic type (EC 2.7.1.59) MGLVQTKDQQLFIGVDGGGSKCRATIYTADGTVLGTGVAGRANPLHGLAQTFASIEASTRQALLDAGMKETDSHLLVAGLGLAGVNVPRLYQDVISWQHPFAAMYVTTDLHTACIGAHRGADGAVIITGTGSCGYAHVGDDSLSIGGHGFALGDKGSGAWLGLKAAEHVLLALDGFATPTALTEMLLKHFGVSDALGIVEHLAGKSSSCYAELARSVLDCANAGDEVARGIVQEGADYISEMARKLFSLNPVRFSMIGGLAEPLQAWLGSDVVAKISETLAPPELGAMYFAQQQFNSVNINE transporters Shewanella sp. ANA-3 ANA3 7026137 Shewana3_3279 SHEWANA3_RS17205 WP_011718086.1 tr|A0L0D4|A0L0D4_SHESA Vitamin B12 transporter, permease component (fecCD-like) This protein is cofit with the B12-dependent methionine synthase MetH and is FecCD-like. It probably works with Shewana3_3280 (ABC transporter domain protein with similar phenotypes) and Shewana3_3272 (periplasmic binding protein). This protein is similar to SO_1033 which is also involved in B12 uptake (it is strongly cofit with metH; also see PMCid:PMC3219624) transport system permease protein (RefSeq) ABC transporter (iron.B12.siderophore.hemin) , permease component iron complex transport system permease protein MIDTLKLVTMNFFSHIFTPLTRQQWLILGLAGFALLTPIAAASFGAANISFLDVLQVFINKLSHLFMADEAVSTSMTERIVMELRLPRIILAFVAGAGLSLAGSVLQTVTRNPLADPYLFGISSGASFGAVVMLTLFTGSGLFGNAGTIANSGIFSGSGTFAGLLWFSLPFGAFIGASLSVLIVLALAGLGLKSQVERMLLSGVATSFMFSALTSLLLYFASPQATASVLFWSLGSFAKASWSLLVLPSLVVLLSFFIILGWKRQIMALQAGDETAHTLGVNVPKLRLNMLLLCSLITAILVATCGGIGFVGLMIPHTVRLLFPGRQPILLTALVGGLFMVWIDVLARCLLGNQELPVGIITAAIGSFFFLLILRRRKLSN catabolism Azospirillum brasilense Sp245 azobra AZOBR_RS05755 AZOBR_RS05755 AZOBR_RS05755 WP_014239822.1 tr|G8AJX1|G8AJX1_AZOBR Butyryl-CoA dehydrogenase (EC 1.3.8.7) Specifically important for: Sodium butyrate. KEGG's annotation of azl:AZL_005040 has been updated to 3-(methylthio)propanoyl-CoA dehydrogenase [EC:1.3.8.-], which is questionable; phenotype indicates that butyryl-CoA is a substrate (SEED_correct) acyl-CoA dehydrogenase Acyl-CoA dehydrogenase (EC 1.3.8.7) MIPYTAPVDDLRFVLNEVVGLETVAALPNCDSAAPDLVDAVLEEAGKFASGVLAPLNRVGDKEGSVLENGVVRTPTGWKDAYSQFTESGWNSLPFEPEYGGQGLPWTVAFAVNEMWQAANLSFGLCPLLTQGAVDLLTEHASAEQKALYLPKMIAGEWNGTMNLTEPQAGSDLAAVRTRAVRADDGTYRITGQKIFITYGEHDLTDNIVHLVLARLPDAPPGIKGISLFIVPKFLPNADGTPGARNDLRCASLEHKLGIMASPTAVMAFGDDGGAVGFLVGQENRGIEYMFTMMNNARLGVGIQGVAIAERAYQQARDYAKGRVQSKDLADPKGSGVAIIRHPDVRRMLLDMRAKTEAARALALYAGTQLDVSRHHEDATVRAAATARVDILTPIVKAWSTDIGCDVASTGVQIHGGMGFIEETGAAQHYRDARITPIYEGTNGIHANDLTFRKTGRDGGESARTFIAEMRATVAELESIPGDDMEAIRTNLSAGLDALEQAVAWVVKTQADGDLRAAAAGAVNYLKLWGTVAGGWMLARSAAKALEGLRQPGANAPFLEAKLVTARFYAEQILAQGPGLLLPILTAHRTVMALSEDQF transporters Azospirillum brasilense Sp245 azobra AZOBR_RS08235 AZOBR_RS08235 AZOBR_RS08235 WP_014240349.1 tr|G8ALI8|G8ALI8_AZOBR L-proline and D-alanine ABC transporter, permease component 1 specific phenotype on L-proline and D-alanine and cofit with other subunits nearby branched-chain amino acid transporter permease subunit LivH High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1) MEYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLGITWVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQILQGARSKPLQPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRACEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAAVLGGIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLLGRPEIEKV transporters Azospirillum brasilense Sp245 azobra AZOBR_RS15920 AZOBR_RS15920 AZOBR_RS15920 WP_014197389.1 tr|G8AR25|G8AR25_AZOBR Large component of TRAP-type D-gluconate transporter specific phenotype on D-gluconic acid and cofit with other components nearby; 56% identical to SMa0250 of S. meliloti, which is required for gluconate utilization (PMCid:PMC2631997). Also is 56% identical to Atu2743 of A. tumefaciens, which takes up galacturonate (PMCid:PMC4751846), so this might also be a galacturonate transporter (we did not study galacturonate utilizaton in this organism) dehydroascorbate transporter TRAP-type C4-dicarboxylate transport system, large permease component MALAVFLSSLFGLMLLGMPIAFALMLTGVALMVHLDFFDAQLVAQNMLSGADNYPLMAVPFFILAGELMNAGGISQRIINLAVSLVGHIRGGLGYVTIGASVMLASLSGSAIADTAALATLLIPMMRDNGYPVPRSAGLIASGGIIAPIIPPSMPFIIFGVTTNTSISGLFMAGIVPGLLMGAGLVITWMFVVRGMTVKLQPKASWGERRTALVEGVWALALPVIIIGGLRGGIFTPTEAAVVAAVYSLVVALFVYRQVTLKDLVPLLVQAARTTSTVMFLCAAALVSSYMVTLADLPQQMNEMLAPLLHEPKLLMVAITLLLLAVGTVMDLTPTILVLGPVLTPLAAAAGIDPTYFGVMFVLTGTLGLIHPPVCTVLNVVCGVARISLESATRGIWPFLLTYLLLLCLLIAVPEIVTAPLAFFRH transporters Azospirillum brasilense Sp245 azobra AZOBR_RS18550 AZOBR_RS18550 AZOBR_RS18550 WP_014197980.1 tr|G8AST9|G8AST9_AZOBR ABC transporter for nitrate, ATPase component Specific phenotype on Sodium nitrate. (SEED_correct) ABC transporter ATPase Nitrate ABC transporter, ATP-binding protein MAILELKNVAKSYGGTEVLRGIDLSIAEGEFVAIVGFSGAGKTTLVNLMGGLAAPDAGTVLFRGAPVRGPGAERGVVFQNYSLMPWLSVKDNVALAVDAVHKGKPSPERGVLTRRAVETVGLGHATDRRPKELSGGMRQRVGFARALAMSPEMLLLDEPLSALDALTRAKLQDEIEAIWRKDRKTVVLITNDVDEAILLADRIIPLTPGPGATLGPAFAVDLPRPRDRTAVNHDPDFKRLRAEVTAWLMEAGASRAAAAVDESLTMPAATPITAAPPPKAYLAGQPGGLSDDRYVEFSRVTKTFATPKGPLTVVDGFDLKMRKGEFISLIGHSGCGKSTVLSMVAGLADVSSGGIVLDGKEVVGAGPDRAVVFQAPSLFPWLTALENVMLGVDRVYPQAGRGERNDIARYYLSRVGLGNAMHKTAAELSNGMKQRVGIARAFALSPKLLLLDEPFGMLDSLTRWELQEVLMEVWARTQVTAICVTHDVDEAILLADRVVMMSNGPNARIGHILEVDIPHPRTRQALLEHPRYYAYREELLNFLEGGHHGTVKAA transporters Azospirillum brasilense Sp245 azobra AZOBR_RS18555 AZOBR_RS18555 AZOBR_RS18555 WP_014197981.1 tr|G8ASU0|G8ASU0_AZOBR ABC transporter for nitrate, permease component Specific phenotypes on Sodium nitrate; Sodium nitrate. Other substrates proposed by KEGG )sulfonate and taurine) were not tested. (KEGG_correct) nitrate ABC transporter permease sulfonate/nitrate/taurine transport system permease protein MTSVTEASTLSSAEAMRARRKARLAHALNRTAATLQIVGLGWLSPLLRMAAGDSPRQQGQELWQQMGVPLTALMLFLAAWAWLAPQVNTSLGAIPGPAQVWEQIGILHADHKAERAKEAAFYDRQAKRNAELLAKDPAAEVKTRPYAGKPTYLDQILTSLKTVFTGFLLGALVAVPLGVACGLSRTVNAAMNPLIQIFKPVSPLAWLPLVTMVVSATVSSDNPTFEKSFLTSAVTVTLCSLWPTLINTAVGVSSIDKDLMNVGKVLQLSGPTMVRRLVLPSALPYIFTGLRLSLGVGWMVLIAAEMLAQNPGLGKFVWDEFQNGSSSSLARIMVAVFTIGLIGFLLDRVMLAFQAAVSHTGTR transporters Azospirillum brasilense Sp245 azobra AZOBR_RS18560 AZOBR_RS18560 AZOBR_RS18560 WP_082188256.1 tr|G8ASU1|G8ASU1_AZOBR ABC transporter for nitrate, periplasmic substrate-binding component Specific phenotype on Sodium nitrate. (SEED_correct) nitrate ABC transporter substrate-binding protein Nitrate ABC transporter, nitrate-binding protein sulfonate/nitrate/taurine transport system ATP-binding protein IRLPASPRTALLSAAATLALMLGSAQAAPLDVEKDQLKLGFIKLTDMAPLAIAAEKGFFEDEGLSVTLEPQANWKVLLDRVISGELDGAHMLAGQPLGATIGFGTQANVVTAFSMDLNGNGITLSNEVWERMKPNLPKGPDGKPLHPIKADALKPVIAQYRAEGKPFTMGMVFPVSTHNYELRYWLAAGGINPGYYAPNDVSGQIQADALLSVTPPPQMPATLEAGTIFGYSVGEPWNQQAVMKGIGVPVITDTEIWKNNPEKVFGVTEGWAAKNPKTHLALVKALIRAAMWLDENGNANRAEAVKILAKSEYVGADAKVIANSMTGTFEYEKGDKRAVPDFNVFFRYNATYPFYSDAVWYLTQMRRWGQIAEAKPDAWYDETARKVYKPEIYLKAARLLVEEGKAKEADFPWTSDGYKPLDNGFIDGIAYDGRKPNEYLTKLPIGLKGGQAVQGGQLVGG catabolism Burkholderia phytofirmans PsJN BFirm BPHYT_RS02015 BPHYT_RS02015 BPHYT_RS02015 WP_012431485.1 tr|B2SWP8|B2SWP8_PARPJ phenylpyruvate ferredoxin oxidoreductase (EC 1.2.7.8) Specifically important for: L-Phenylalanine. Annotated as indolepyruvate ferredoxin oxidoreductase, which has the same EC number; alternatively, could be a decarboxylase, but did not identify a separate aldehyde dehydrogenase MFS transporter Indolepyruvate ferredoxin oxidoreductase, alpha and beta subunits indolepyruvate ferredoxin oxidoreductase MTARLPIDGTPALADYKLSDNLTATRGRIFLTGTQALVRLVLMQRAADKARGMNTAGFISGYRGSPLGMVDQQLWKAKKLLAASDIRFLPAINEELGGTAVLGTQRVESDPERTVEGVFAMWYGKGPGVDRAGDALKHGNAYGSSPHGGVLVVAGDDHGCVSSSMPHQSDFAMMAWHMPVVNPSNIADMLEFGLYGWELSRFSGAWVGYKAISETVESGSTVDLDALRTDWTMPQDFEVPAGGLHNRWPDLPSLTIESRMHAKLDAVRHFARVNSIDKWIAPSPHANVGIVTCGKAHLDLMETLRRLDLTVADLEAAGVRIYKVGLSFPLEMTRIDAFVSGLSEVLVIEEKGPVIEQQIKDYLYNRTQGTRPIVVGKNAEDGTLLLSSLGELRPSRILPVFANWLAKHKPALDRRERVVDLVAPQILSNAADSVKRTPYFCSGCPHNTSTKVPEGSIAHAGIGCHFMASWMERDTTGLIQMGGEGVDWASHSMFTKTRHVFQNLGDGTYFHSGILAIRQAVAAKATITYKILYNDAVAMTGGQPVDGSISVPQIARQVEAEGVSRFVVVSDEPEKYDGHHDQFPKGTTFHHRSEMDTVQRQLRDTDGVTVLIYDQTCAAEKRRRRKKGEFPDPDKRLFINEEVCEGCGDCGVQSNCLSVEPVETALGRKRRIDQSSCNKDYSCVNGFCPSFVTVEGGKLKKAAGAAFDPQALAARVEALPIPATHLDAAPYDILVTGVGGTGVVTVGALISMAAHLEGKSASVLDFMGFAQKGGSVLSFVRFAARDEWLNQVRIDTQQADVLLACDMVVGASADALQTVRHGRTRIVVNTHAIPNATFVTNPDATLHADALLDKMRHAAGAERMSTCDAQALATRFLGDTIGANILMLGYAWQLGLVPVSFGAMMRAIELNNVAVQMNQLAFSIGRLAAEDPAALEALWQARHLAKQSVRVDTLDELIAHREGRLQTYGGASYVKRYRALVDAARRAETSVDAKSERVTRAVATTFYRLLAVKDEYEVARLHTDAVFREALEAQFEGVAGKDFGIKFNLAPPTLTRPEPGKNPVKKTFGQWMWPVLGTLAKFSSLRGTMLDPFGRTLERKMERELAGDYETTLQRALARLDAGNLEDVAKLADLHARVRGYGHVKLANLAGVKRGERDLAARLQIEAATGESVRKSLEEMKGAGQLRGIPVVVAK catabolism Burkholderia phytofirmans PsJN BFirm BPHYT_RS02050 BPHYT_RS02050 BPHYT_RS02050 WP_012431492.1 tr|B2SWQ5|B2SWQ5_PARPJ D-mannose isomerase (EC 5.3.1.7) Specifically important for: D-Mannose; D-Sorbitol; D-Mannitol; D-Fructose. Often annotated as N-acylglucosamine 2-epimerase, but phenotype on mannose, mannitol is consistent with annotation as mannose isomerase. Its role on sorbitol (which is probably oxidized to sorbose or fructose by BPHYT_RS16120) or fructose is unclear - this might be a polar effect on fructokinase (BPHYT_RS02045), as there is a stronger phenotype for insertions with the antibiotic resistance marker in the non-coding orientation (SEED_correct) N-acylglucosamine 2-epimerase D-mannose isomerase (EC 5.3.1.7) MTQSDPLHPANGAAAAPPVESFRSRDFLLSHVQDTLRFYAPNVFDPSGGFFHFFRDDGSVYDKTTRHLVSSCRYVFNYAMAYRQFGDPQHLEYARHGLRFLREAHWDAQHEGYDWEIEWRDGKKRTLDATRHCYGLAFVLLAYSHAAMAGIEEAKPMIGATFELMEHRFWDAAAGLYADEASPDWRVSSYRGQNANMHTTEALLAAHEATRHLVYLDRAERVASNITLRQAKLSQGLVWEHFHADWSVDWHYNEEDSSNIFRPWGFQPGHQTEWAKLLLILERFRPLPWLLPRAIELFDAAMAHAWDEDHGGLYYGFGPDGTVCDHDKYFWVQAETFATAALLGKRTGNERFWDWYDEIWRYSWAHFVDHEYGAWYRILTCDNRKYSDEKSPAGKTDYHTMGACYEVLAHALPDGAAAAPESAEQTK transporters Burkholderia phytofirmans PsJN BFirm BPHYT_RS02740 BPHYT_RS02740 BPHYT_RS02740 WP_085966699.1 tr|B2SXE3|B2SXE3_PARPJ N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) Specifically important on NAG and cofit with the IIBC component nearby (BPHYT_RS02745). 58% identical to nagF or H16_A0311 of R. eutropha, which is important for NAG utilization (PMCid:PMC3127587). 58% similar to PA3760, which is required for NAG utilization in P. aeruginosa (PMCid:PMC2542419) PTS glucose transporter subunit IIA Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9) / PTS system, glucose-specific IIA component PTS system, fructose-specific IIA component ; phosphotransferase system, enzyme I, PtsI ; phosphocarrier protein FPr MSHSEGHIVLLAPMTGPVVPLANVPDPVFSGGMFGDGIGVDPLEGRLVAPCDATVTHLARTGHAVTLATAEGAEILLHIGIDTVELNGKGFAPMVAQGAHVRAGDVLIEFDQDQVALNAPSLVSVIAIANSDAFEIVERVQGGLLKAGETPLLVLRARDGAAAEASRQLSSTNVTEEARQQVTLVHAGGLHARPAARAREAARGFDARVEVRYEGRKAAIESVVGLLGLGAGEGATVELLGMGPQAAAAVAAIANELTREAHGEVEEKPARQSSPAPQAVARPAGETLAPNTLAGVCAAPGVAVGKLVRWDDADIDPPEKANGTSAAESRLLDKAIATVDADLDTTVRDASQRGAVGEAGIFSVHRVLLEDPTLLDAARDLISLGKSAGFAWREAIRAQIAILTNIEDALLAERAADLRDIEKRVLRALGYTSATARTLPEEAVLAAEEFTPSDLSTLDRSRVTALVMARGGATSHAAILARQAGIPALVAVGDALHAIPEGTQVVVNATTGRLEFAPTELDVERARLERTRLADVREANRRTSQQAAVTSDGRAIEVAANIATLDDAKTAVENGADSVGLLRTELLFIHRAAAPTTDEHRQSYQAIVDALSGRTAIIRTLDVGADKEVDYLTLPPEPNPALGLRGIRLAQVRPDLLDDQLRGLLAVQPLGAVRILLPMVTDVGELIRIRKRIDEFARELGRTEPIEVGVMIEVPSAALLADQLAQHADFLSIGTNDLTQYTLAMDRCQADLAAQADGLHPAVLRLIAATVQGADKHGKWVGVCGALAGDPLAMPLLVGLGVTELSVDPVSVPGIKARVRNLDYQLCRQRAQDALALESAQAVRAASRETWPLD transporters Burkholderia phytofirmans PsJN BFirm BPHYT_RS02745 BPHYT_RS02745 BPHYT_RS02745 WP_012431627.1 tr|B2SXE4|B2SXE4_PARPJ N-acetylglucosamine-specific PTS system, IIBC components (nagE) Specifically important on NAG and cofit with the I-HPr-IIA component nearby (BPHYT_RS02740). CDD or PFam do not show any sign of this gene containing a IIA component, so the SEED annotation is misleading. 62% similar to H16_A0312 (nagE) and 58% similar to PA3761, which are both involved in NAG utilization (PMCid:PMC3127587, PMCid:PMC2542419). KEGG_correct. PTS system N-acetylglucosamine-specific transporter subunit IIBC PTS system, N-acetylglucosamine-specific IIA component / PTS system, N-acetylglucosamine-specific IIB component (EC 2.7.1.69) / PTS system, N-acetylglucosamine-specific IIC component PTS system, N-acetylglucosamine-specific IIB component ; PTS system, N-acetylglucosamine-specific IIC component MDGNPFLKIQRLGRALMLPIAVLPVAGLLLRLGQPDVFNIKMIADAGGAIFDNLPLLFAIGVAVGFAKDNNGVAGLAGAIGYLIEVAVMKDINDKLNMGVLSGIVAGIVAGLLYNRYKDIKLPDYLAFFGGKRFVPIVTGVVCLVLGIAFGYVWQPVQAVIDTAGHWLTTAGALGAFVFGVLNRLLLVTGLHHILNSLTWFVFGTFTPPGGAAVTGDLHRFFAGDPTAGTFMTGFFPVMMFGLPAACLAMFHEAPKERRAVVGGLLFSMALTSFLTGVTEPIEFSFMFLAPVLYVIHALLTGISLAICSALGIHLGFTFSAGAIDYVLNYGLSTRGWWAIPIGLVYMVVYYGLFRFFIRKFNMATPGREPAAADEQVDSFAAGGFVSPVAGTAVPRAQRYIAALGGASNLSVVDACTTRLRLSVVDSNKVSENELKTIGARGVLKRGSTNVQVIIGPEADIIADEIRTVIAQGGGDAVKPAAAAPAQVVAAAPVAASVAQGSGPLDPDPLRWLAVFGGAGNVLSLDAIAATRLRIVVRDPSAVDRQRLATLDTAWISADTFHIVVGDAAQRYAEKLATRTTQSGGATPLPA catabolism Burkholderia phytofirmans PsJN BFirm BPHYT_RS03220 BPHYT_RS03220 BPHYT_RS03220 WP_012431722.1 tr|B2SX46|B2SX46_PARPJ Acyl-CoA dehydrogenase (EC 1.3.8.7) Specifically important for: Tween 20; Trisodium citrate dihydrate. Tween 20 hydrolyzes to a mix of C12, C14, and C16 fatty acids; this is probably part of beta oxidation. The phenotype on citrate is milder and is not explained, but it is conserved. (SEED_correct) acyl-CoA dehydrogenase Acyl-CoA dehydrogenase (EC 1.3.8.7) MGQYAAPLRDMQFVLHELLNVEAEIKQMPKHADLDADTINAVLEEAGKFCSEVLFPLNHSGDQEGCTYVGDGVVTTPKGFKEAYAQYVEAGWPALGCDPEYGGQGLPAFVNNALYEMLNSANQAWTMYPGLSHGAYECLHAHGTPELQQRYLPKLVAGVWTGTMCLTEPHCGTDLGILRTKAEPNSDGSYAISGTKIFISSGEHDLAENIVHLVLARLPGAPNGTKGISLFIVPKFVPNEAGEPGERNGVKCGSIEHKMGIHGNATCVINLDNAKGWLVGEPNKGLNAMFVMMNAARLGVGMQSLGLTEIGYQNSLTYAKERLQMRSLTGPKAPEKAADPIIVHPDVRRMLLTQKAYAEAARAFSYWSALHIDKELSHADESVRKEAADLVALLTPILKAFLSDNAFESTNHAMQIYGGHGFIAEWGMEQYVRDARINMIYEGTNAIQALDLLGRKILGDMGAKMKKFGKLVSDFVEAEGVKPEMQEFINPLADIGEKVQKLTMEIGMKAMQNPDEVGAAAVPYLRTVGHLVFSYFWARMARVALDKEASGDPFYKAKLATARFYFAKLLPETAMTIRQARAGSKSLMDVEEALF transporters Burkholderia phytofirmans PsJN BFirm BPHYT_RS07675 BPHYT_RS07675 BPHYT_RS07675 WP_012432581.1 tr|B2T306|B2T306_PARPJ ABC transporter for L-Arginine, permease component 2 Very important for utilization of L-arginine histidine/lysine/arginine/ornithine ABC transporter permease HisQ Histidine ABC transporter, permease protein HisQ (TC 3.A.1.3.1) histidine transport system permease protein MFLYGFGPVLLAGTIQTIELSVLSLAAAVLLGLAGAAAKLSFNRPLRAIATGYTTLIRSVPDLVLMLLLFYSIQIAVNNLTDALNLPQFDIDPFVAGVLTLGFIYGAYFTETFRGAFLAVPRGQLEAGSAYGMSGARVFTRILFPQMMRFALPGIGNNWQVLVKATALVSIIGLADVVKAAQDAGKSTFNMFFFILVAALIYLAITTASNLVLIWLEKRYSIGVRHAEL transporters Burkholderia phytofirmans PsJN BFirm BPHYT_RS07680 BPHYT_RS07680 BPHYT_RS07680 WP_012432582.1 tr|B2T307|B2T307_PARPJ ABC transporter for L-Arginine, permease component 1 Specific phenotypes on L-Arginine. no phenotype on histidine histidine/lysine/arginine/ornithine ABC transporter permease HisM Histidine ABC transporter, permease protein HisM (TC 3.A.1.3.1) histidine transport system permease protein MIDILNQFWRAFLYWDGQRMSGLAVTLWLLVASVGIGFCAAIPLAVARVSKKRWLSTPVRLYTYVFRGTPLYVQLLLIYTGMYSLEFVRSHQLLDAFFRSGFHCAILAFALNTCAYTTEIFAGAIRSTSHGEVEAARAYGMSWFTMYRRIVIPSALRRALPLYSNEVILMLHATTVAFTATVPDILKVARDANSATYQSFDAFGLAALIYLVVSFVLVALFRRAERHWLGYLAVRTH transporters Burkholderia phytofirmans PsJN BFirm BPHYT_RS07735 BPHYT_RS07735 BPHYT_RS07735 WP_012432593.1 tr|B2T318|B2T318_PARPJ ABC transporter for L-Arginine, periplasmic substrate-binding component Specific phenotype on L-Arginine. Not near the permease components ABC transporter substrate-binding protein Lysine-arginine-ornithine-binding periplasmic protein precursor (TC 3.A.1.3.1) lysine/arginine/ornithine transport system substrate-binding protein MKMNWRNIAALALFAAASATAGTAAAADIKEVHFGVEASYAPFESKSPSGELQGFDIDVGNAVCAKLKAKCVWVENSFDGLIPALQARKFNAINSDMTITDQRRQAVDFTDPIYTIPNQMIAKKGSGLLPTPASLKGKHVGVLQGTIQETYAKARWAPAGVDVVPYQTQDQIYADLASGRLDAAFQDAEAASKGFLKKPQGAGFEFAGPAVTDEKLLGAGVGFGVRKGDKALKDALNQALKELKADGTIDRFAAKYFDVKVVLK catabolism Burkholderia phytofirmans PsJN BFirm BPHYT_RS11290 BPHYT_RS11290 BPHYT_RS11290 WP_012433273.1 tr|B2T518|B2T518_PARPJ 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) Specifically important for: D-Gluconic Acid sodium salt. Gluconate is probably primarily catabolized via gluconate kinase (BPHYT_RS16720) and the Entner-Doudoroff pathway (starting with phosphogluconate dehydratase, BPHYT_RS16735). However it appears that there is a side pathway involving gluconate 2-dehydrogenase (BPHYT_RS14520, which has no phenotype because this side path is not beneficial), 2-ketogluconate kinase (BPHYT_RS11300, no fitness data), and 2-ketogluconate-6-P reductase (this gene). A similar side path is known in P. putida (PMCID:PMC4646247) and this gene is similar to the P. putida 2-ketoglutarate-6-phosphate reductase (PP3376). (SEED_correct) bifunctional glyoxylate/hydroxypyruvate reductase B 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) gluconate 2-dehydrogenase MKKIVAWKSLPEDVLAYLQQHAQVVQVDATQHDAFVAALKDADGGIGSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAAENLVAALDGTLTSNIVNREVLSK catabolism Burkholderia phytofirmans PsJN BFirm BPHYT_RS16050 BPHYT_RS16050 BPHYT_RS16050 WP_012434194.1 tr|B2SY89|B2SY89_PARPJ xylitol 2-dehydrogenase (EC 1.1.1.9) Specifically important for: Xylitol. (SEED_correct) iditol 2-dehydrogenase Xylitol dehydrogenase (EC 1.1.1.9) L-iditol 2-dehydrogenase MTTQSTDHDQQNMTAIVCHAPKDYRVEQVSKPRAGAHELVIRIAACGICASDCKCHSGAKMFWGGPSPWVKAPVIPGHEFFGFVEEIGEGAADHFGVKMGDRVIAEQIVPCGKCRYCKSGQYWMCEVHNIFGFQREVADGGMAEYMRIPPTAIVHKIPDGISLEDAAIIEPLACAIHTVNRGEVQLDDVVVIAGAGPLGLMMTQIAHLKTPKKLVVIDLVEERLALAREYGADVTINPKQDDALAIIHSLTDGYGCDVYIETTGAPIGVNQGMDLIRKLGRFVEFSVFGADTTLDWSVIGDRKELDVRGAHLGPYCYPIAIDLLARGLVTSKGIVTHGFSLEEWDEAIKIANSLDSIKVLLKPRA transporters Burkholderia phytofirmans PsJN BFirm BPHYT_RS16095 BPHYT_RS16095 BPHYT_RS16095 WP_012434203.1 tr|B2SY98|B2SY98_PARPJ ABC transporter for D-Sorbitol, ATPase component Specific phenotype on D-Sorbitol. sugar ABC transporter ATP-binding protein Various polyols ABC transporter, ATP-binding component sorbitol/mannitol transport system ATP-binding protein MASVTLRNIRKAYDENEVMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGGDLTIDGMRVNDVAPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNAAKILHIDHLLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFARLHDELKTTMIYVTHDQVEAMTLADKIVVLSAGNLEQVGSPTMLYHAPANRFVAGFIGSPKMNFMEGVVQSVTHDGVTVRYETGETQRVAVEPAAVKQGDKVTVGIRPEHLHVGMAEDGISARTMAVESLGDAAYLYAESSVAPDGLIARIPPLERHTKGETQKLGATPEHCHLFDSAGKAFQRKIVEVLAA transporters Burkholderia phytofirmans PsJN BFirm BPHYT_RS16105 BPHYT_RS16105 BPHYT_RS16105 WP_012434205.1 tr|B2SYA0|B2SYA0_PARPJ ABC transporter for D-Sorbitol, permease component 1 Specific phenotypes on D-Sorbitol. no phenotype on mannitol; fitness data identifies a different mannitol transporter mannitol ABC transporter permease Various polyols ABC transporter, permease component 2 sorbitol/mannitol transport system permease protein MSQVASTPVSNPTAMTVPAKSPFAAIRRGIPGVIAWLVALLLFFPIFWMTITAFKTEQQAYASSLFFIPTLDSFREVFARSNYFSFAWNSILISAGVTILCLILAVPAAYAMAFFPTRRTQKVLLWMLSTKMMPSVGVLVPIYLLWKNSGLLDSVSGLVIVYTLINLPIAVWMSFTYFAEIPRDILEAGRIDGAATWQEIVYLLMPMSLPGLASTALLLVILSWNEAFWSINLSSSNAAPLTVFIASYSSPEGLFWAKLSAASLLAVAPILIVGWLSQKQLVRGLTFGAVK transporters Burkholderia phytofirmans PsJN BFirm BPHYT_RS16110 BPHYT_RS16110 BPHYT_RS16110 WP_012434206.1 tr|B2SYA1|B2SYA1_PARPJ ABC transporter for D-Sorbitol, permease component 2 Specific phenotypes on D-Sorbitol. no phenotype on mannitol; fitness data identifies a different mannitol transporter sugar ABC transporter permease Various polyols ABC transporter, permease component 1 sorbitol/mannitol transport system permease protein MRPLRLPIMHAHPQTEKERETRKANSARWLATPSVAVLVLWMAIPLAMTIWFSFSRYNLLNPDLKGFAGFDNYKYLASDPSFGPSIGHTLELIISVLVITVVGGVLMAILFDRKFYGQGIARLLAIAPFFVMPTVSALIWKNMILHPVYGLIAQGMRAMGMQPIDWFAEYPLTAVIMIVAWQWLPFAFLILFTAIQSLDQEQKEAARIDGAGPFSMFFYITLPHLKRAIAVVVMMETIFLLSIFAEIYTTTGGGPGTATTNLSYLIYSLGLQQFDVGLASAGGILAVVLANIVSFFLVRMLAKNLKGEYEK transporters Burkholderia phytofirmans PsJN BFirm BPHYT_RS16115 BPHYT_RS16115 BPHYT_RS16115 WP_012434207.1 tr|B2SYA2|B2SYA2_PARPJ ABC transporter for D-Sorbitol, periplasmic substrate-binding component Specific phenotype on D-Sorbitol. sugar ABC transporter substrate-binding protein Various polyols ABC transporter, periplasmic substrate-binding protein sorbitol/mannitol transport system substrate-binding protein MKPALKSTLKAVSAGAVACFALSASAATVTIATLNNPDMIELKKLSPEFEKANPDIKLNWVILEENVLRQRATTDITTGSGQFDVMTIGAYETPQWGKRGWLTPLTNLPADYDLNDVVKTARDGLSSGGQLYALPFYVESSMTYYRKDLFEKAGLKMPDQPTYDQIKQFADKLTDKANGIYGICLRGKAGWGENMAYGTTVVNTFGGRWFDEKWNAQLTSPEWKKAMTFYVDLLKKDGPPGASSNGFNENLTLMSSGKCAMWIDATVAAGMLYNKQQSQIADKVGFAAAPVAVTPKGSHWLWAWALAIPKSSKQADAAKKFITWATSKQYIELVAKDEGWASVPPGTRKSTYARAEYKQAAPFGDFVLKAIETADPEHPTLKPVPYTGVQFVGIPEFQSFGTVVGQSISGAIAGQMTIDQALAAGNATADRAVKQAGYQK catabolism Burkholderia phytofirmans PsJN BFirm BPHYT_RS16120 BPHYT_RS16120 BPHYT_RS16120 WP_012434208.1 tr|B2SYA3|B2SYA3_PARPJ sorbitol dehydrogenase, D-fructose forming (EC 1.1.1.14) Specifically important for: D-Sorbitol. The KEGG EC number implies that sorbose would be the product, but it is not clear how sorbose would be consumed. The only other genes with specific phenotypes on sorbitol are an ABC transporter, the fructokinase BPHYT_RS02045, and an apparent polar effect on mannose isomerase BPHYT_RS02050. Also this protein is 60% similar to DHSO_RHOSH (polS), which is annotated in UniProt as forming sorbose but is believed to form D-fructose, see PMID: 15805591 (SEED_correct) sorbitol dehydrogenase Sorbitol dehydrogenase (EC 1.1.1.14) D-sorbitol dehydrogenase (acceptor) MAARLQDKVAILTGAASGIGEAVARRYLDEGARCVLVDVKPADSFGDSLRATYGDRVLTVSADVTRRDDIQRIVASTLERFGQIDILFNNAALFDMRPILEESWDVFDRLFAVNVKGMFFLMQAVAQKMVEQGCGGKIINMSSQAGRRGEALVSHYCATKAAVLSYTQSAALALAPHKINVNGIAPGVVDTPMWNEVDALFARYENRPLGEKKRLVGEAVPLGRMGVPDDLTGAALFLASADADYITAQTLNVDGGNWMS catabolism Burkholderia phytofirmans PsJN BFirm BPHYT_RS16405 BPHYT_RS16405 BPHYT_RS16405 WP_012434262.1 tr|B2SYF9|B2SYF9_PARPJ galactonate dehydratase [EC: 4.2.1.6] Specifically important for: D-Galactose. galactonate is an intermediate in galactose oxidation (KEGG_correct) galactonate dehydratase Gluconate dehydratase (EC 4.2.1.39) galactonate dehydratase MKITKLETFIVPPRWCFLKIETDEGIVGWGEPVVEGRAHTVAAAVEELSDYLIGKDPLLIEDHWQVMYRSGFYRGGPITMSAIAGVDQALWDIKGKHHGVPIHALLGGQVRDKIKVYSWIGGDRPSDVANNARAVVERGFKAVKMNGSEELQIIDTFDKVQGVINNVAAVREAVGPNIGIGVDFHGRVHKPMAKVLAKELDPYKLLFIEEPVLSENAEALRDIVNQTNTPIALGERLYSRWDFKHILSGGYVDIIQPDASHAGGITECRKIASMAEAYDVALALHCPLGPIALATCLQIDAVSYNAFIQEQSLGIHYNQGNDLLDYIKNPEVFKYEDGFVSIPQGPGLGIEVNEEKVREMAKVGHRWRNPVWRHEDGSVAEW transporters Burkholderia phytofirmans PsJN BFirm BPHYT_RS16725 BPHYT_RS16725 BPHYT_RS16725 WP_012434323.1 tr|B2SYM4|B2SYM4_PARPJ gluconate:H+ symporter (gntT) Specific phenotype on gluconate and 72% identical to the gluconate permease (gntT, ACIAD0544) of A. baylayi ADP1 (PMCid:PMC4254613). KEGG_correct permease Gluconate transporter family protein gluconate:H+ symporter, GntP family MEAVHGSTLLVFAVIAIALLILLITRYKVYPFLVLIIVSLLLGLASGMPMATIVKSFETGNGNTLGHIAIVVGLGTMLGKMMAESGGAERIATTLIDFFGEKNIHWAMMIVAIIVGLPVFFEVGFVLLIPIAFNVAKRTNKSLLLVGLPMVAGLSVVHGLLPPHPAAMLAVQAYHADIGRTIAYGLIVGVPTAIVAGPLFALMISRYIKLPKENALAAQFLGHGDETKNGAQTAAQNVAPKRELPSFGITLLTILLPVILMLVGSWADLFTTPKTLPNDLLHFAGNSDVALLIAVLVSFWTFGASRGFTREQIQKFCGDCLAPIAGITLIVGAGGGFGRVLMDSGISKEIVNVATAMHLSPLLFGWLVAALIRLATGSATVAMTTACGIVAPIASASGVHVEPELLVLATGSGSLIFSHVNDGGFWLIKEYFGMTVGQTFKTWSLLETIISLMGLGLTFALAAVV catabolism Burkholderia phytofirmans PsJN BFirm BPHYT_RS16920 BPHYT_RS16920 BPHYT_RS16920 WP_012434361.1 tr|B2SYR3|B2SYR3_PARPJ L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) # Specifically important in carbon source L-Arabinose; carbon source D-Galactose. Some other dehydrogenases are known to act on both of these substrates. 3-oxoacyl-ACP reductase Putative oxidoreductase in arabinose utilization cluster MSSPANANVRLADSAFARYPSLVDRTVLITGGATGIGASFVEHFAAQGARVAFFDIDASAGEALADELGDSKHKPLFLSCDLTDIDALQKAIADVKAALGPIQVLVNNAANDKRHTIGEVTRESFDAGIAVNIRHQFFAAQAVMEDMKAANSGSIINLGSISWMLKNGGYPVYVMSKSAVQGLTRGLARDLGHFNIRVNTLVPGWVMTEKQKRLWLDDAGRRSIKEGQCIDAELEPADLARMALFLAADDSRMITAQDIVVDGGWA catabolism Burkholderia phytofirmans PsJN BFirm BPHYT_RS17340 BPHYT_RS17340 BPHYT_RS17340 WP_012434437.1 tr|B2SYZ1|B2SYZ1_PARPJ Phenylacetaldehyde dehydrogenase PaaZ (EC 1.2.1.3) Specifically important for: L-Phenylalanine. phenylalanine is transaminated to phenylpyruvate, decarboxylated to phenylacetaldehyde, and this converts it to phenylacetate (SEED_correct) aldehyde dehydrogenase Aldehyde dehydrogenase (EC 1.2.1.3), PaaZ MTHPLFTKHEDTLQKALTAVETRGYWSPFVEMPSPKVYGETANADGEAAFKAHLNATFQLDQPSTGETVGAEVSPFGFPLGVRYPKAEPAALIAAAAAAQRDWRAAGPQAWIGVCLEILARVNRASFEIGYSVMHTTGQAFMMAFQAGGPHAQDRALEAVVYAWDQLRRIPGDTHWEKPQGKNPPLAMHKRYTVVPRGTGLVLGCCTFPTWNGYPGLFADLATGNTVIVKPHPGAILPLALTVRIARDVLREAGFDPNVVTLLATEPNDGALVQDLALRPEIKLIDFTGSTQNGTWLERNAHQAQVYTEKAGVNQIVIDSVDDIKAAARNVAFSLALYSGQMCTAPQNIYVPRGGIRTAEGTLSFDEVAQAIAGAVQKLVADPARAVELLGAIQNEGVTQRIDEAAKLGRVLVESLTLEHPAFAGARVRTPLVLQLDAATDHAQFTKEWFGPISFVIATDSTAQSLDLAGAIASEHGALTLSVYSTDEAVLDDAHEASIRGGVALSINLTGGVFVNQSAAFSDFHGTGANPAANAALADAAFVANRFRVVQSRVHVEPKAAPAVAG catabolism Burkholderia phytofirmans PsJN BFirm BPHYT_RS19730 BPHYT_RS19730 BPHYT_RS19730 WP_012434865.1 tr|B2T7R9|B2T7R9_PARPJ L-arabonate dehydratase (EC 4.2.1.25) Specifically important for: L-Arabinose. L-arabonate is an intermediate in the oxidation of L-arabinose (SEED_correct) dihydroxy-acid dehydratase L-arabonate dehydratase (EC 4.2.1.25) dihydroxy-acid dehydratase MADSNQTKKPLRSQAWFGLKDRDGFLHRSWMKNQGIPHDEFDGRPVIGICNTWSELTPCNAHFRELAEYVKKGVHEAGGLPLEFPVMSLGETNLRPTAMLFRNLASMDVEESIRGNPMDGVILLVGCDKTTPALLMGAASCNLPALAVSGGPMLNGRFRGKNIGSGTGVWQMSEEVRAGTMTQEEFTEAESCMNRSRGHCMTMGTASTMASMVESLGMGLPHNAAIPAVDARRQVLAHLAGRRIVDMVREDLTMDKILTRQAFENAIRTNAAIGGSTNAVVHLIALAKRIGVELSLEDWELGSNVPCLVNLQPSGEYLMEDFYYAGGLPAVLKQLGEQGLLHKEALTVNGKTLWDNVRNAANYDEKVITTFAEPFKPKAGIAVLKGNLAPNGAVIKPSAATASLLKHRGRAVVFENIEELHAKIDDESLDIDEHCIMVLKGAGPKGYPGFAEVGNMPLPKKVLQKGITDMVRISDGRMSGTAYGAVVLHVSPEAAAGGPLAFVQTGDMIELDVEERRLHLDVTDEELARRRAAWQAPEAPKRGYYKLYVEHVLQADQGADLDFLVGSSGAPVPRDSH catabolism Burkholderia phytofirmans PsJN BFirm BPHYT_RS22715 BPHYT_RS22715 BPHYT_RS22715 WP_012426462.1 tr|B2TD34|B2TD34_PARPJ L-2-keto-3-deoxyarabonate dehydratase (EC 4.2.1.43) important for L-arabinose utilization and 70% similar to araD from A. brasilense (KDADA_AZOBR, PMID:16950779). SEED_correct cytochrome C biogenesis protein CcdA L-2-keto-3-deoxyarabonate dehydratase (EC 4.2.1.43) dihydrodipicolinate synthase MTQSSHPAAMRGVFPVAPTIFDDAGRLDLEGQKRCIDFMIDAGSNGLCILANFSEQFALSDDERNTLMHVVLEHVAGRVPVIVTTTHFSSYQCAERSRSAQAAGAAMVMVMPPYHGATIRIGERGIYEFYRTVSDAIGIPIMIQDAPVSGTPLSAPFLARMAREIDNVSYFKIEVPQAANKLRELIELGGDAIVGPWDGEEAITLMADLDAGATGSMTGGGYADGIRLIVDAYAAGDTEAAAAHYQQWLPLINYENRQGGLASCKALMKEGGVIRSDAVRHPLPQMHPATREGLLKVARRLDPLVLRWGR catabolism Burkholderia phytofirmans PsJN BFirm BPHYT_RS23155 BPHYT_RS23155 BPHYT_RS23155 WP_012426549.1 tr|B2TDJ5|B2TDJ5_PARPJ Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) Important for utilization of putrescine as C or N source. This is the only transamination reaction in putrescine catabolism via gamma-glutamylputrescine (formed by BPHYT_RS23160), gamma-glutamylpurescine oxidase (possibly redundant, BPHYT_RS23125 or BPHYT_RS22700, neither has a phenotype), gamma-glutamylbutyraldehyde dehydrogenase (BPHYT_RS23175), and gamma-glutamyl-gamma-aminobutyrate hydrolase (probably BPHYT_RS23165, but no fitness data). Another gene (BPHYT_RS22435) likely has this activity as well, and is important (but with a weaker phenotype) on putresine as a carbon source. However that gene is not important with putrescine as a nitrogen source, which suggests that this gene is providing the activity. aminotransferase Omega-amino acid--pyruvate aminotransferase (EC 2.6.1.18) putrescine aminotransferase MSYRTEEVAYVQPAQPAASAQASQAAQQQRSTAEYRALDAAHHIHPFSDMGSLNRSGSRVIVKAQGVYLWDSEGNKVIDGMAGLWCVNVGYGRKELADAAYKQMQELPYYNTFFKTTHPPVIELSALLAELAPEAFNHFFYCNSGSEGNDTVLRIVHQYWATQGKHSKKFVISRKNGYHGSTIAGGTLGGMGYMHEQMPSKVENIVHIDQPYFFGEAQGNLTPEEFALARAQQLEAKILEIGADNVAAFIGEPFQGAGGVIFPASTYWPEIQRICRKYDILLVADEVIGGFGRTGEWFAHQHFGFEPDLITLAKGLTSGYVPMGAVGLHDRVAKAIIENGDFNHGLTYSGHPVAAAVAVANLKLLRDEKIVDRVKNDTGPYFQKQLRETFANHPIIGEISGTGLVAGLQLAQDPKARKRFANGGDVGTICRDFCFNGNLIMRATGDRMLLSPPLVINKLEIDEIVSKAKKAIDATAQQLGIS catabolism Burkholderia phytofirmans PsJN BFirm BPHYT_RS23160 BPHYT_RS23160 BPHYT_RS23160 WP_012426550.1 tr|B2TDJ6|B2TDJ6_PARPJ Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) Specifically important for: Putrescine Dihydrochloride. The first step in putrescine catabolism via gamma-glutamyl-putrescine (SEED_correct) glutamine synthetase Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) glutamine synthetase MHDIDDFLKKNRVTEIEAIIPDMAGIARGKIIPRSKFESGESMRLPQAVMIQTVTGDYPEDGTLTGVTDPDMVCVPDASTIRMIPWAVDPTAQVIHDCVHFDGTPVAISPRRVLRRVLELYKAKGWKPVIAPELEFYLVDMNKDPDLPLQPPIGRTGRPETGRQAYSIEAVNEFDPLFEDIYEYCEVQELEVDTLIHEVGAAQMEINFMHGDPLKLADSVFLFKRTVREAALRHKMYATFMAKPMEGEPGSAMHMHQSLVDEETGHNLFTGPDGKPTSLFTSYIAGLQKYTPALMPIFAPYINSYRRLSRFMAAPINVAWGYDNRTVGFRIPHSGPAARRIENRIPGVDCNPYLAIAATLAAGYLGMTQKLEATEPLLSDGYELPYQLPRNLEEGLTLMGACEPIAEVLGEKFVKAYLALKETEYEAFFRVISSWERRHLLLHV catabolism Burkholderia phytofirmans PsJN BFirm BPHYT_RS34210 BPHYT_RS34210 BPHYT_RS34210 WP_012428702.1 tr|B2T9V2|B2T9V2_PARPJ 2,4-diketo-3-deoxy-L-rhamnonate hydrolase (EC 3.7.1.-) Specifically important for: L-Fucose; L-Rhamnose monohydrate. The substrate is also known as 2,4-diketo-3-deoxy-L-fuconate, and is an intermediate in both L-rhamnose and L-fucose degradation (SEED_correct) ureidoglycolate lyase 2,4-diketo-3-deoxy-L-fuconate hydrolase MKLLRYGPKGQEKPGLLDAQGKIRDLSKVVADIDGAALTDEGLAKLRALDPASLPLVEGNPRMGPCVGKIGKFICIGLNYADHAAESNLPVPAEPVIFNKWTSAISGPNDDVEIPRGSKKTDWEVELGVVIGKPAKYIDEANALDYVAGYCVINDVSEREWQIEKGGTWDKGKGFDTFGPIGPWVVTRDEVADPQNLSLWLEVDGHRYQNGSTKTMVFGVAKLVSYVSQCMSLQPGDVISTGTPPGVGMGVKPNPVFLKPGQTIRLGIEGLGEQTQKTYAAE catabolism Burkholderia phytofirmans PsJN BFirm BPHYT_RS34225 BPHYT_RS34225 BPHYT_RS34225 WP_012428705.1 tr|B2T9V5|B2T9V5_PARPJ L-fucose dehydrogenase; L-rhamnose 1-dehydrogenase (EC 1.1.1.122; EC 1.1.1.173) Specifically important for: L-Rhamnose monohydrate; L-Fucose. Annotated by SEED for the fucose dehydrogenase activity only aldo/keto reductase L-fuco-beta-pyranose dehydrogenase (EC 1.1.1.122) MTATIGSKIGQRRRIGRGPLQVTGLGLGTAPLGGLYRDLSDEEAHATIAAAWDAGVRYFDTAPHYGNTKAEHRLGDALRRYPRADYVLSTKVGRRFVPRTTPFDDKEGWQNPLPFEAIYDYTHDGILRSFEDSQQRLGIVDIDILLVHDIGRVTHGDNHPHYWRQLTEGGGFRALDALRSSGAIKAVGLGVNEGAAILDAMAEFDIDCALLAGRYTLLEQTTLDDLLPACEKRGVSILLGGAFNSGILARGVQGDLKFNYGEAPPEVIERVARLEAVCRTHGVPLAAAALQFPYAHPTVATVLTGARSADELRENAASFELPIPAALWFALREEGLLDSRAPAPED catabolism Burkholderia phytofirmans PsJN BFirm BPHYT_RS34230 BPHYT_RS34230 BPHYT_RS34230 WP_012428706.1 tr|B2T9V6|B2T9V6_PARPJ L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) Specifically important for: L-Rhamnose monohydrate; L-Fucose. annotated by SEED for fuconate activity only hydrolase L-fuconate dehydratase (EC 4.2.1.68), type 2 altronate hydrolase MPVAAQQPTLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFREPLDAFDDPSAEREPPVHLIGFPGCYPNGYAEKMLERLTTHPNVGAVLFVSLGCESMNKHYLVDVVRASGRPVEVLTIQEKGGTRSTIQYGVDWIRGAREQLAAQQKVPMALSELVIGTICGGSDGTSGITANPAVGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAARPALGDEIVACVAKAARYYSILGHGSFAVGNADGGLTTQEEKSLGAYAKSGASPIVGIIKPGDIPPTGGLYLLDVVPDGEPRFGFPNISDNAEIGELIACGAHVILFTTGRGSVVGSAISPVIKVCANPATYRNLSGDMDVDAGRILEGRGTLDEVGREVFEQTVAVSRGAASKSETLGHQEFILTYKTFEPVGPACLPSSAAAQHRVVAIEPH catabolism Burkholderia phytofirmans PsJN BFirm BPHYT_RS34235 BPHYT_RS34235 BPHYT_RS34235 WP_085966746.1 tr|B2T9V7|B2T9V7_PARPJ putative accessory domain for L-fuconate/L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) Important for L-fucose and perhaps L-rhamnose catabolism, but seems to have milder phenotypes than the adjacent dehydratase _RS34230. CDD suggests (see cd11613) that it might be a dimerization domain for the dehydratase, but that wouldn't make sense for a separate ORF. Some homologs of this gene are fused to the dehydratase (which has a GD_AH_C domain). hydrolase Altronate dehydratase (EC 4.2.1.7) altronate hydrolase MTSRLLPLQTDPRLILLSPADNCLIAAARLDCGTQVEIEGERVTLTRTIDLGHKVARHELAKDDKVLRYGAVIGHVTEAVARGAHLHTHNLESDYLPTYTHDAGHEFVHH catabolism Burkholderia phytofirmans PsJN BFirm BPHYT_RS35445 BPHYT_RS35445 BPHYT_RS35445 WP_012428943.1 tr|B2TAE5|B2TAE5_PARPJ 2-aminobenzoate-CoA ligase [EC: 6.2.1.32] Specifically important for: L-Tryptophan. B. phytofirmans catabolizes tryptophan via 2-aminobenzoyl-CoA (KEGG_correct) 2-aminobenzoate-CoA ligase Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases 2-aminobenzoate-CoA ligase MEPSAHVDTFARDNLPPQDQWPVFLLDNPDVAYPARLNCASELLDRTIDAGHRDDPAIWSDVDGAPRATTYGELLALVNRSAHVLVDEMGLQPGNRVLLRGPNTLHMAVTALAALKVGLVVVPTMPLLRAKELKQIIDKAQVGAALCDARLTAELARCSDPEDEFYCAGLMQTRLFHDDSPDSLDTLAVNKPDHFTACDTAADDVCLIAFTSGTTGAPKGCMHFHRDVVAMCDLFPRHVLKPTSSDIFCGTPPLAFTFGLGGLLCFPLRVGASTVLIEKLTPETLLQTVERFHATVMFTAPTFYRQMAPLVAHHDVSSLKKTVSAGEALPDSTRRLWRDATGIDMIDGIGGTELIHIFISAQGDEIRPNAIGRAVPGYAVQAVDDDMQPVAPGTIGKLAVRGPTGCRYLADERQMKFVRDGWNLPGDSVYLDEDGYVFYQARADDMIVSAGYNISGPEVESVLLQHDAVSECGVIGVPDETRGQIVKAFVVVNPGYERDDKLVAQLQEFVKNSVAPYKYPRDIVFVDSLPRTETGKLKRFELRTMA transporters Cupriavidus basilensis 4G11 Cup4G11 RR42_RS03025 RR42_RS03025 RR42_RS03025 WP_052494419.1 tr|A0A0C4YBR9|A0A0C4YBR9_9BURK Inner membrane protein (FUSC-like) required for 4-hydroxybenzoate transport, together with NodT, MFP, and DUF1656 proteins (RR42_RS03040, RR42_RS03035, and RR42_RS03030) specific phenotype on 4-hydroxybenzoate and cofit with other nearby components. Not clear if this is primarily an efflux pump (because of the high and potentially toxic concentration of hydroxybenzoate) or for uptake transporter Inner membrane component of tripartite multidrug resistance system MVSWPTGRDWIFSLKAFAAAMLALFIALYLGLPRPYWAMASVYIVAHPLTGATRSKALYRVLGTLLGAAASVAIVPPLVNAPVLLMAAVALWTGILLYVALLHRTPRSYVFMLAAYTLPMVALPSVSDPSGVFDIAVARAEEICLGIVCASIVGSTIFPAKVATVLGQKSAQWLADAALWATDMLSAHPAAKVSRHHSRHRLAADILALDQLISHLSYDAESAARVKHAQELRGRMTMLLPVLSSLASVVDALHQHAAGIPQRLSHNMALVSAWISAGAQAPLPALQLSQDAPIDDAGLEPGSAGPDWHAALAATAEGRLRELMELWQDCVSLQRRIGEAAPQGDWAPVFRRWGVGAARHYDHGMLLFSTATTALAIFSMGMVWIWTGWADGAGAVALGAVSCCFFAAMDEPAPMIRSFFRWNVVCLVLATIYLFVVLPNAHDFEMLVLMFAVPYLIIGVMMAQPRLALIAMPLAVVTANDIGIQGAYNADFNAFFNGNVAGIAGILFALVWTLVARPFGTRAAVRRLVRASWGDIARNATGREPGEHAHLRARMLDRLAQLVPRLAASEDETTGDGFTEVRVELSTLALQRELSALAPEHQHSVRRVLQGVASYYQARLDARAEAPPQVLRDRLAKAIRKVASRADQASREAFAALVEMHVALF transporters Cupriavidus basilensis 4G11 Cup4G11 RR42_RS03040 RR42_RS03040 RR42_RS03040 WP_043343879.1 tr|A0A0C4Y7B9|A0A0C4Y7B9_9BURK Outer membrane protein (NodT-like) required for 4-hydroxybenzoate transport, together with FUSC, MFP, and DUF1656 proteins (RR42_RS03025, RR42_RS03035, and RR42_RS03030) specific phenotype on 4-hydroxybenzoate and cofit with other nearby components. Not clear if this is primarily an efflux pump (because of the high and potentially toxic concentration of hydroxybenzoate) or for uptake RND transporter Outer membrane component of tripartite multidrug resistance system MNTLRKALLPALVPLLFAACTTVGPDYHVPDNAAVKAQAANGPLLGTNNPAVSIAEVPDGWWRLYDDPKLDQLVQQALVANTDLRVAAANLKRAIAVYHEVEAENLPEARLSAGAERGQIAGEPLLKEEKIPVMNFGDVGFKVSYLIDFFGKLARADEAALAGAQASQAALDQARIGVVAETVRAYVQGCAATHELTVAEHQLALQSRGVELARKMVDAGRGQPLDLLRAQAQADVLRAALPRFKAEQEGAAYRLAVMLGKPPSATSQAEYACHEEPRLRQALPVGDGAALLKRRPDVRQAERELASATAKIGVATADLYPSIRIGASAGFTGILDHLGQAPTAHWGYGPLITWNIPTSGTRARVHGTEAGAEAALAHFDGVVLKALRETQSALSSYTRELERTQALRDARDKANEVARQNRQLYQAGRSPYLSSLDADRTLASTEASLAASESQVALDQINLFLALGGGWQNAPKVESRTMSEQAH catabolism Cupriavidus basilensis 4G11 Cup4G11 RR42_RS13535 RR42_RS13535 RR42_RS13535 WP_043352074.1 tr|A0A0C4Y492|A0A0C4Y492_9BURK 2-aminobenzoate-CoA ligase (EC 6.2.1.32) Specifically important for: L-Tryptophan. This bacterium catabolizes tryptophan via 2-aminobenzoyl-CoA; (KEGG_correct); SEED has a very broad annotation (Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases) 2-aminobenzoate-CoA ligase Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases 2-aminobenzoate-CoA ligase MASTAHLDTYALDRLPPPQQWPAFLFNADTRYPERMNCALELVERHVREGRGERVAIRYEQDGAHRTVSYAELAALSNRIAHVLTGDMKLVPGSRVLLRGPNNLMMAACWLAVVKAGLIAVPTMPLLRAKELKQVIDRAAVSAALCDERLREELEANLKPGGEHHCPSLTQALYFNSSGAGSVEAAMANKPDGFEACDTAADDICLIAFTSGTTGQPKGTVHFHRDVIAMCDLFPRHVLKPGPDDIFCGTPPLAFTFGLGGILCFPLRVGASTVLAERLTPESLLALIQSWRATIVFTAPTFYRQMAALAPGYDLSSLQKSVSAGEALPDATRQSWKAATGIEMTDGIGGTEMMHIFISSAGADVRPGAIGKVVPGYIAQIVDEQMQPVPHGTVGKLAVRGPTGCRYLDDPRQANYVKDGWNLPGDTFKADADGYYYYQARSDDMIVSAGYNIAGPEVESALMRHEAVAECGVVGMPDPERGQIVAAYVVLRPGVAASDETCAALQSYVKAEIAPYKYPRKVIFVDALPRTETGKLQRFRLRQMAEQSGAPEGARQP catabolism Cupriavidus basilensis 4G11 Cup4G11 RR42_RS13555 RR42_RS13555 RR42_RS13555 WP_043347637.1 tr|A0A0C4YHI0|A0A0C4YHI0_9BURK anthraniloyl-CoA monooxygenase (EC 1.14.13.40) Specifically important for: L-Tryptophan. Antrhanioyl-CoA is a synonym for 2-aminobenzoyl-CoA, an intermediate in the degradation of Trp via 2-aminobenzoate (KEGG_correct) salicylyl-CoA 5-hydroxylase probable bifunctional hydroxylase/oxidoreductase anthraniloyl-CoA monooxygenase MRVLCIGGGPSGLYFGLLMKLRDPSSEVYVVERNRPYDTFGWGVVFSDATMDNLKQADPVSAEQINAAFNHWDDIDIHIGGRTLRSGGHGFIGIGRKRLLNILQARCEALGVHLVFETDVTDDQALAQQYQADIVIASDGINSRVRGRYAETFQPDIDTRLCRFVWLGTRKLFDAFTFAFEKTEHGWFQAHAYRFDDNTSTFIVEAPEPVWRAAGIEQMSQEEGVAFCERLFARYLDGNALISNATHLRGSANWIRFPRVICGTWVHWNTLAGGRRVPVVLMGDAAHTAHFSIGSGTKLALEDAIDLANNIRDAGPGGADVLPQALERYQATRSVEVLKIQNAARNSTEWFENVERYAGLAPEQFAYSLLTRSQRISHENLRVRDPGYVEGFERWLAGQAAANVANATSTGQAAEARVVPPMFTPLRVRNVTLKNRVVVSPMAMYSCEDGVPGDFHLTHLGARALGGAGMVVAEMTCTSPDARITPGCPGLWNDEQRDAWRRIVDFVHANSDARIAMQIGHAGRKGSTQLGWEQMDYPLAEGNWPVLSASPLPYMPGISQVPREMSRADMDAVRDDFVASARRAAQAGFDWLELHCAHGYLLSSFISPLTNQRSDEYGGSLQARLRYPLEVFAAVRAVWPQERPMSVRISAHDWVEGGITPDDAIEIARAFKAAGADMIDCSSGQVSPDQAPVYGRMYQTPFADRIRNEAGIATIAVGAIFEADHVDSIIAAGRADLCAIARPHLADPAWTIHEAARLGHRDLAWPKQYQAGKRQLETNLERAAQQARQARQPEDH catabolism Cupriavidus basilensis 4G11 Cup4G11 RR42_RS17300 RR42_RS17300 RR42_RS17300 WP_043349422.1 tr|A0A0C4Y642|A0A0C4Y642_9BURK D-lactate oxidase, FAD-linked subunit (EC 1.1.3.15) Specifically important for: Sodium D-Lactate. KEGG has the correct EC # but describes it as glycolate oxidase; SEED has it as 1.1.99.14 (glycolate dehydrogenase) glycolate oxidase Glycolate dehydrogenase (EC 1.1.99.14), subunit GlcD glycolate oxidase MNAPHEVSLVADDARRSALLAGLAKILPDAALLWKPEDTVPYECDGLAAYRQVPMAVALPDNEDQVCAILRLCHSLQVPVVPRGAGTSLSGGAMPIATGLVLSLAKFKRIVSVDVRSRTAVVQPGVRNLAISEAAAQYNLYYAPDPSSQIACTIGGNVSENSGGVHCLKYGLTVHNVLRVRAVTMEGDVVEFGSEAPDAPGLDLLAAVIGSEGMLAVVTEVSVKLIPKPQLAQVIMASFDDVAKGGNAVADVIGAGIIPAGLEMMDKPATAAVEEFVRAGYDLDAAAILLCESDGTPEEVAEEVERMSEVLRASGASRIQVSQSEPERLRFWSGRKNAFPAAGRISPDYYCMDGTIPRKHIGTLLKRIEEMERKYGLRCMNVFHAGDGNMHPLILFDGADQDEWHRAELFGSDILESCVELGGTVTGEHGVGVEKLNSMCVQFSAQERDLFFGVKAAFDPARLLNPDKAIPTLARCAEYGRMHVKRGLLPHPDLPRF catabolism Cupriavidus basilensis 4G11 Cup4G11 RR42_RS17310 RR42_RS17310 RR42_RS17310 WP_043349427.1 tr|A0A0C4YFX9|A0A0C4YFX9_9BURK D-lactate oxidase, FAD binding subunit (EC 1.1.3.15) Important on D-lactate; KEGG oddly has no EC #; SEED has it as 1.1.99.14 (glycolate dehydrogenase) glycolate oxidase Glycolate dehydrogenase (EC 1.1.99.14), FAD-binding subunit GlcE glycolate oxidase FAD binding subunit MPATPADQQATLTAFRDAIRHATGTRTPLRLRGGGSKDFYGQHPQGTLLDTRAYSGIVDYDPPELVITARCGTPLAQIEAALAERRQMLAFEPPHFSTGADGSDVATIGGAVAAGLSGPRRQAVGALRDFVLGTRVMDGRGDVLSFGGQVMKNVAGYDVSRLMSGSLGTLGLILEVSLKVLPVPFDDATLRFALDEAAALDRLNDWGGQPLPIAASAWHDGVLHLRLSGAAAALRAARARLGGEAVDAAQADALWRALREHSHAFFAPVQAGRALWRIAVPTTAAPLALPGGQLIEWGGGQRWWLGGSDSAADSAIVRAAAKAAGGHATLFRNGDKAVGVFTPLSAPVAAIHQRLKATFDPAGIFNPQRMYAGL catabolism Cupriavidus basilensis 4G11 Cup4G11 RR42_RS17315 RR42_RS17315 RR42_RS17315 WP_043349430.1 tr|A0A0C4YDN4|A0A0C4YDN4_9BURK D-lactate oxidase, iron-sulfur subunit (EC 1.1.3.15) Important on D-lactate; KEGG oddly has no EC #; SEED has it as 1.1.99.14 (glycolate dehydrogenase) glycolate oxidase Glycolate dehydrogenase (EC 1.1.99.14), iron-sulfur subunit GlcF glycolate oxidase iron-sulfur subunit MQTTLAEFLRDTPDGEEAKSIVGKCVHCGFCTATCPTYQLLGDELDGPRGRIYLMKQVLEGQPVTQSTRLHLDRCLTCRNCESTCPSGVKYGRLVDIGRKVVDDRLEAQGIQRPARERFARWALRETMTRPALFGTAMRMGQRVRPLLPQALRNKVPQAVDAGAWPRTTHARKMLLLDGCVQPSMSPNINAATARVFDRLGVQLVMAREAGCCGAVRYHTGDHDGGLDNMRRNIDAWWPAVQAGAEAIVMTASGCGVMVKEYGHLLRNDAHYADRARQISALTKDLSELLPNFADALQDAAAEAGSSKGTNGTDGQRVAYHPPCTLQHGQQIRGKVEALLTGLGVDVKLCADSHLCCGSAGTYSVLQPALSYRLRDEKLANLQALKPEAIVSANIGCITHLQSGTGTPVMHWIELVDRMLG catabolism Cupriavidus basilensis 4G11 Cup4G11 RR42_RS25930 RR42_RS25930 RR42_RS25930 WP_043354222.1 tr|A0A0C4YL05|A0A0C4YL05_9BURK glycine dehydrogenase (deaminating) (EC 1.4.1.10) Specifically important for: L-Threonine. Annotated as D-amino acid dehydrogenase; SEED has it as the small subunit but do not see why another subunit is expected (i.e. E. coli dadA). Important on Thr as well as Gly because Thr is cleaved (via the threonine dehydrogenase and kbl) to glycine. The electron acceptor is uncertain -- the given EC number implies that NAD is the electron acceptor, which is consistent with an N-terminal NAD binding domain (PF13450). amino acid dehydrogenase D-amino acid dehydrogenase small subunit (EC 1.4.99.1) D-amino-acid dehydrogenase MKTIAVIGGGITGVTTAYALAKRGFSVTLLEKHRYAAMETSFANGGQLSASNAEVWTHWSTILKGIKWMLKSDAPLLVNPRPSWHKLSWFAEFIAAIPHYRKNTIETTRLAIAARDHLFSWAAAEGIDFDLKKEGILHIYRDKAGFEHAGRVSKLLAEGGLARHAVTPEEMRAIEPTLAGQYYGGYFTQSDSTGDIHKFTSGMAAAIDRLGVRCLYNQDVQSVSTDGRQVTIVSGDGRQAESRVFDGVVVCAGTASRALAASLGDRVNIYPVKGYSITVNLNDAQSQAAAPVVSLLDDETKLVTSRLGVDRFRVAGTAEFNGYNRDIRADRIRPLVEWVNQCFPGVSTRSVVPWAGLRPMMPTMLPRVGRGRASCVFYNTGHGHLGWTLSAVTADMIGDVVQQAMGARRAHGVQEPVALVTP catabolism Cupriavidus basilensis 4G11 Cup4G11 RR42_RS28300 RR42_RS28300 RR42_RS28300 WP_043354857.1 tr|A0A0C4YKU6|A0A0C4YKU6_9BURK L-threonine 3-dehydrogenase (EC 1.1.1.103) Specifically important for: L-Threonine. The first step in Thr catabolism (SEED_correct) NAD-dependent epimerase L-threonine 3-dehydrogenase (EC 1.1.1.103) MTKPARVLIIGANGQLGTELASALADRYGKQNVVTSDMVPHGRHLHLTHEMLDVTDRAHLRDVIERHGITQIYHLAAALSATGEKSPTWAWQLNMNGLLNVLEAARHQKLDKVFWPSSIAAFGPTTPPDGTPQSTIMEPKTVYGISKLAGEGWCRWYFENHGVDVRSLRYPGLISYKTPPGGGTTDYAIDIFHSALRAQPYACFLEKDEALPMMYMPDAVRATMELMEAPRASISERGSYNLAGLSFTPGEIANEIRRHCPGFDVRYEPDFRQEIAAGWPDSIDDSVARRDWNWRPEFGLKEMVADMLKNLATLNQGSALECVS transporters Cupriavidus basilensis 4G11 Cup4G11 RR42_RS28835 RR42_RS28835 RR42_RS28835 WP_043355010.1 tr|A0A0C4YJP4|A0A0C4YJP4_9BURK gluconate:H+ symporter (gntT) 67% identical to the gluconate permease (gntT, ACIAD0544) of A. baylayi ADP1 (PMCid:PMC4254613). KEGG_correct permease DsdX Gluconate transporter family protein gluconate:H+ symporter, GntP family MGAVTGTTLLLYALIAVIALVVLIAKFKLNPFITLVVVSVLLGFAVGMPMGDIVKSFEAGVGGTLGHIALVVGLGTMLGKMMAESGGAERIARTLIDAFGEKNVHWAMVTIAFIVGLPVFFEVGFVLLVPIAFNVAKRTGTSMVLVGIPMVAGLSVVHGLIPPHPAALLAVTAYKADIGKTILYALIVGIPTAAIAGPLFAKLMTRYVTLPDVNPLAAQFTEEDEGVKASHELPGFGITLFTILLPVILMLIGSWADLITTPKTFANDFLKLIGNSVIALLIAALVSFYTFGKRRGFTRENILRFTNECVAPTAIITLVVGAGGGFGRVLRDSGISNAIVDVATGAHVSVLLLGWLVAVLIRIATGSATVAMTTAAGIVAPIAASVPGTRPELLVLTTGAGSLILSHVNDGGFWLVKEYFNMTVAQTFKTWSVCETLISVIALLLTLALATVV transporters Dinoroseobacter shibae DFL-12 Dino 3607124 Dshi_0546 DSHI_RS02765 WP_012177224.1 tr|A8LPG9|A8LPG9_DINSH ABC transporter for Xylitol, ATPase component Specific phenotype on Xylitol. ABC transporter related (RefSeq) Various polyols ABC transporter, ATP-binding component multiple sugar transport system ATP-binding protein MAGIKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRIEIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARVLQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLHKQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAMNVFSSDVGLQDISLDASAAFVGCRPEHIEIVPDGDGHIAATVHVKERLGGESLLYLGLKGGGQIVARVGGDDETKVGAAVSLRFSRHRLHQFDEAGRAI transporters Dinoroseobacter shibae DFL-12 Dino 3607125 Dshi_0547 DSHI_RS02770 WP_012177225.1 tr|A8LPH0|A8LPH0_DINSH ABC transporter for Xylitol, periplasmic substrate-binding component Specific phenotype on Xylitol. extracellular solute-binding protein family 1 (RefSeq) Various polyols ABC transporter, periplasmic substrate-binding protein multiple sugar transport system substrate-binding protein MKTLRNLLCSAAVASVMASGAMADGHGWSLKDAAAPYAGTTVDVVFLLRPGYEAIEAMLPAFEEETGIKVNVIKHPYENALGEQVRDFVAGGDLDVALIDLVWIGSFAENEWILPLADVQAKFPDAVDPDLDIDDFFPLVLNAFGGWNDTIYGLPFDNYSGLMFYNRCMLEEAGFDGPPSTWEELKDVYGPALTKDGKYAFALQSKRNETQSADSFARMLWPFGGSFLNEEFRSNLMSEGSQAGLKFRQELMEYMPDGIVAYDHAETVNAFSQGDVAMITEWSAFYSSVVSPETSRVADCVEIAPEPMGPAGRKPALGGFSLAVASQADEAEQAAAYLFIQWATSKANAREYLERGGVPARQSVYQQDGLEEFKFVPALVESWQDGVPEFRPRFAEWPEITEIVQEWGTKMMLGEVTTEEGAQEIGTRMEEVLDAAGYYSGEKPLAQ transporters Dinoroseobacter shibae DFL-12 Dino 3607126 Dshi_0548 DSHI_RS02775 WP_012177226.1 tr|A8LPH1|A8LPH1_DINSH ABC transporter for Xylitol, permease component 1 Specific phenotypes on Xylitol; Xylitol. Phenotype is very specific binding-protein-dependent transport systems inner membrane component (RefSeq) Various polyols ABC transporter, permease component 1 multiple sugar transport system permease protein MSGQVPRKTVFAFIGPAVIGLALVGIAPLLYALWTSLHFYNLTKLRRVEFIGLENYWTVLTDEVFWQAMGRTFFLLGTALPLQIALGLGIALVLHQPGLTLVKTLARLSLVLPMATTYAVVGLLGQVMFNQKFGVVNQLLGGADINWIGDPENAFAMIIFWDVWQWTPFVALVLLAGLTMVPGEVEEAARLETKSKWTVLRYVQLPFLLPGLVAVLILRTADTLKLFDMVFTLTRGGPGSSTEFISLMIQRVGFRGFDQGLASAQAIILLIITIVLAQIYIRVFYKEV transporters Dinoroseobacter shibae DFL-12 Dino 3607127 Dshi_0549 DSHI_RS02780 WP_012177227.1 tr|A8LPH2|A8LPH2_DINSH ABC transporter for Xylitol, permease component 2 Specific phenotypes on Xylitol; Xylitol. Phenotype is very specific binding-protein-dependent transport systems inner membrane component (RefSeq) Various polyols ABC transporter, permease component 2 multiple sugar transport system permease protein MTSTRSLFSQIALLVLIITVCVFPFYWMVTTSLKTQIVALEAPPVWIFEPTLSNYREALFEDGVLRTLINSLIIAISTTFLALVLGVPAAFALARFEFRGKKDLWFWFITNRMISPIVLALPFFLIARNLGLLDKHITLILIYLTFNLPIVIWIVTDQFRGIPYDLDEAARLEGASQFTIMRKICLPLAMPGVAVSAIFSFIFSWNELMFGLILTRSEAKTAPAMAVSFMEGYNLPYGKIMATSTLIVIPVLIFALIASKQLVRGLTMGAVK catabolism Dinoroseobacter shibae DFL-12 Dino 3609040 Dshi_2429 DSHI_RS12360 WP_012179094.1 tr|A8LS70|A8LS70_DINSH Rhamnulokinase RhaK in alpha-proteobacteria (EC 2.7.1.5) Specifically important for: L-Rhamnose monohydrate. The second step in rhamnose catabolism (SEED_correct) carbohydrate kinase FGGY (RefSeq) Rhamnulokinase RhaK in alpha-proteobacteria (EC 2.7.1.5) MTRHVAVIDIGKTNAKLALVDRQSLTEISVITRPNTVLPGPPWPHFDVDGHWAFLLDGLRDFQARHGIDAISITTHGACAALLQKDGALAAPILDYEHPGPDDTALAYDALRPPFSETGSPRLAGGLNIGAQLFWQFHTDPALRDRTRQIVTYPQFWGAKLTGVTATDVTSLGCHTDLWNPHAGAVSSLVDRLGLTGKLAPVRKPHDILGPVLPAVAAQTGLAPGTPVHCGIHDSNASLLPYVLTQTSPFSVISTGTWVVAMSVGGRPVVLDPDLDTLINVTALGQPAPSARFMGGREHDLATEGTGPPPSAQDLDHILSRQILLLPAVVPDTGPFKGQASRWEGDAPAPGTGARGAAVALYLALVTAECLSNIGHAGKIIVEGPFAGNRLYLEMLSVAMEADVVRASGTTGTSAGAALLAGGDAGAPPRPDSLVALPAASKTRLRHYAAHWRQRARRRTP catabolism Dinoroseobacter shibae DFL-12 Dino 3609047 Dshi_2436 DSHI_RS12395 WP_012179101.1 tr|A8LS77|A8LS77_DINSH rhamnulose-1-phosphate aldolase (EC 4.1.2.19) / lactaldehyde dehydrogenase (EC 1.2.1.22) Specifically important for: L-Rhamnose monohydrate. Part of rhamnose catabolism via rhamnulose. TIGR annotates the C terminal part as alcohol dehydrogenase rather than as lactaldehyde dehydrogenase but do not see why (SEED_correct) rhamnulose-1-phosphate aldolase/alcohol dehydrogenase (RefSeq) Predicted rhamnulose-1-phosphate aldolase (EC 4.1.2.19) / Predicted lactaldehyde dehydrogenase (EC 1.2.1.22) MLKSLETQLLESRWDDEVAKGMSESELLLYRSNILGADKRVTNYGGGNTSAKVMEADPLTGAQVEVLWVKGSGGDIGSIKMDGFATLYMDKLRALKGLYRGVAFEDEMVSYLPHCTFRLNPRAASIDTPLHAYVPRKHVDHVHADAIIAIAASDNSKELTQEIFGNRIGWLPWKRPGFELGLWLEKFCRENPEADGVVLESHGLFTWADTAKECYDQTIDVINVATRWLAERSAGVPAFGGAIHESLPAAARREVAARLMPAIRGFVSDNQHMVGHFNDSDAVLEFVNARDMEALAALGTSCPDHFLRTKIRPLVVPFDPAQNNILAVLSELPDQVAAYREAYAAYYARCKHDDSPALRDPNAVVYLVPGVGMITFAKDKATARISGEFYVNAINVMRGASAVSTYQGLPEQEAFDIEYWLLEEAKLQRMPKPKSLAGRVALVTGGAGGIGAATAERFLAEGACVVLADINEDSLASTQERLSERFGADVVRSVVMNVTREEAVAAAFAEASVEFGGVDILVSNAGIASSAPIEETSLALWNKNMDILSTGYFLVSRAAFKLMRVQDMGGAVVFVASKNGLAASPNAAAYCTAKASEIHLARCLALEGAEAGIRVNVVNPDAVLRGSKIWEGDWLEQRAGTYGTDKDGLEEMYRQRSLLKRSVLPEDIAEACYFFAADASSKSTGNIINVDAGNVQAFTR transporters Dinoroseobacter shibae DFL-12 Dino 3609738 Dshi_3121 DSHI_RS15825 WP_012179782.1 tr|A8LLA5|A8LLA5_DINSH Tricarboxylate transport membrane protein TctA specific phenotype on citrate and cofit with other nearby components; SEED_correct protein of unknown function DUF112 transmembrane (RefSeq) Tricarboxylate transport membrane protein TctA putative tricarboxylic transport membrane protein MLEGLLIGLQTAFSIQNLAMVIGGCLIGTFIGMLPGLGPMSIIAIMIPVAISLGDPSAALILLAGVYYGAIFGGSTSSILLNAPGVAGTVATSFDGYPMAQQGKAGKALTIAAIASFAGGTIGAILLMVFAPALSSVALLFHSAEYFALMVVGLSAIAAFAGTGQVAKALLMTILGLIMATVGEGALFASPRFTMGLMDLQSGFGFITLAMAMFALPEALFLVMNPLRAASGQGGGEIKDLRITRAEARSIAPVIGRQSVQGFFIGVLPGAGATIASFLGYAVERNIASKDEQAEFGKGSVKGLAAPETANNAACTGSFVPLLTLGIPGSGTTAILLGALLALNVSPGPRLMIDAPEIFWAVIMSMFIGNLVLLILNLPLIPYIAKILSVPRNYLIPFILFFTLMGAYIGQNNATELLLLVGFGICATILKFADYPLAPLLIGFILGGLLENNFSRAMQLYDGISFIWERPMTLGLLVIAALLIILPSYRNRRAKARAAGVADGD transporters Dinoroseobacter shibae DFL-12 Dino 3609739 Dshi_3122 DSHI_RS15830 WP_012179783.1 tr|A8LLA6|A8LLA6_DINSH Tricarboxylate transport protein TctB specific phenotype on citrate and cofit with other nearby components; SEED_correct hypothetical protein (RefSeq) Tricarboxylate transport protein TctB putative tricarboxylic transport membrane protein MALDRWIALVLLGVCLIYGYTAWFTMDADLAPFMRRNPIWPSTFPKVLSVLGAVAALVILLGLEGPQKPPKAGDIDYRRLGDYKIGQAALLLGLMVGYALLLRPAGFLVSTTSFLILGSVILGERNWPVMIGVAVVATGAIWYLVQEVLGIFLRPLPMFMGV transporters Dinoroseobacter shibae DFL-12 Dino 3609740 Dshi_3123 DSHI_RS15835 WP_012179784.1 tr|A8LLA7|A8LLA7_DINSH Tricarboxylate transport protein TctC specific phenotype on citrate and cofit with other nearby components; SEED_correct hypothetical protein (RefSeq) Tricarboxylate transport protein TctC putative tricarboxylic transport membrane protein MTLEFTRRTLIAAAAALAMTGGAHAEGEQMLESIHFLIPGGAGGGWDGTARGTGEALTKAGLVGSASYENMSGGGGGKAIAYLIENANSSHGTLMVNSTPIVIRSLTGEISQSFRDLTLVAGTIGDYAAIVVGKDSPINSMADLIAAYDADPNATAVGGGSVPGGMDHLVAAMVMEAAGKDALGVKYIPYDAGGKAMAALLSGEIAALSTGFSEAIDLAEAGEVKIIGVTAPERVAAYDSAPTMVEQGIDTTFVNWRGFFAAPGLPEEQLAAYQATLEKMYDTPEWEEVRARNGWVNIHNSGADFQSFLEAQEAQIGDLMKKLGFL transporters Escherichia coli BW25113 Keio 17022 b2943 BW25113_RS15285 WP_001112301.1 sp|P0AEP1|GALP_ECOLI galactose:H+ symporter (galP) A characterized E. coli protein, see EcoCyc. Not sure why SEED has it as transporting arabinose. KEGG_correct. D-galactose transporter (NCBI) Arabinose-proton symporter MFS transporter, SP family, galactose:H+ symporter MPDAKKQGRSNKAMTFFVCFLAALAGLLFGLDIGVIAGALPFIADEFQITSHTQEWVVSSMMFGAAVGAVGSGWLSFKLGRKKSLMIGAILFVAGSLFSAAAPNVEVLILSRVLLGLAVGVASYTAPLYLSEIAPEKIRGSMISMYQLMITIGILGAYLSDTAFSYTGAWRWMLGVIIIPAILLLIGVFFLPDSPRWFAAKRRFVDAERVLLRLRDTSAEAKRELDEIRESLQVKQSGWALFKENSNFRRAVFLGVLLQVMQQFTGMNVIMYYAPKIFELAGYTNTTEQMWGTVIVGLTNVLATFIAIGLVDRWGRKPTLTLGFLVMAAGMGVLGTMMHIGIHSPSAQYFAIAMLLMFIVGFAMSAGPLIWVLCSEIQPLKGRDFGITCSTATNWIANMIVGATFLTMLNTLGNANTFWVYAALNVLFILLTLWLVPETKHVSLEHIERNLMKGRKLREIGAHD transporters Escherichia coli BW25113 Keio 17664 b3603 BW25113_RS18715 WP_001295233.1 sp|P33231|LLDP_ECOLI (R)-lactate / (S)-lactate / glycolate:H+ symporter LldP This protein is annotated by EcoCyc as transporting both stereoisomers of lactate and glycolate, which is consistent with our genetic data and a more detailed study (PMID:11785976). The previous study found that yghK (glcA) also transported glycolate and was important for glycolyate utilization. We instead observed a very subtle defect of the glcA mutant during growth on glycolate (fitness = -0.5). L-lactate permease (NCBI) L-lactate permease L-lactate permease MNLWQQNYDPAGNIWLSSLIASLPILFFFFALIKLKLKGYVAASWTVAIALAVALLFYKMPVANALASVVYGFFYGLWPIAWIIIAAVFVYKISVKTGQFDIIRSSILSITPDQRLQMLIVGFCFGAFLEGAAGFGAPVAITAALLVGLGFKPLYAAGLCLIVNTAPVAFGAMGIPILVAGQVTGIDSFEIGQMVGRQLPFMTIIVLFWIMAIMDGWRGIKETWPAVVVAGGSFAIAQYLSSNFIGPELPDIISSLVSLLCLTLFLKRWQPVRVFRFGDLGASQVDMTLAHTGYTAGQVLRAWTPFLFLTATVTLWSIPPFKALFASGGALYEWVINIPVPYLDKLVARMPPVVSEATAYAAVFKFDWFSATGTAILFAALLSIVWLKMKPSDAISTFGSTLKELALPIYSIGMVLAFAFISNYSGLSSTLALALAHTGHAFTFFSPFLGWLGVFLTGSDTSSNALFAALQATAAQQIGVSDLLLVAANTTGGVTGKMISPQSIAIACAAVGLVGKESDLFRFTVKHSLIFTCIVGVITTLQAYVLTWMIP transporters Escherichia coli BW25113 Keio 17808 b3748 BW25113_RS19480 WP_001301979.1 sp|P04982|RBSD_ECOLI D-ribose pyranase [EC:5.4.99.62] This is a ribose pyranase, not a transporter, see PMID:15060078 or UniProt:RBSD_ECOLI (KEGG_correct) D-ribose high-affinity transport system; membrane-associated protein (VIMSS) Ribose ABC transport system, high affinity permease RbsD (TC 3.A.1.2.1) D-ribose pyranase MKKGTVLNSDISSVISRLGHTDTLVVCDAGLPIPKSTTRIDMALTQGVPSFMQVLGVVTNEMQVEAAIIAEEIKHHNPQLHETLLTHLEQLQKHQGNTIEIRYTTHEQFKQQTAESQAVIRSGECSPYANIILCAGVTF transporters Sphingomonas koreensis DSMZ 15582 Korea Ga0059261_1577 Ga0059261_1577 SKO01S_RS16465 WP_066580458.1 L-glutamine and L-histidine transporter Specific phenotype on glutamine; also important for histidine utilization; detrimental to fitness on some other amino acids (proline, alanine) which may indicate that it likes these amino acids amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3) amino acid transporter basic amino acid/polyamine antiporter, APA family MAGGLFRTKRVKDAAEQAPEHRLAATLSWPHLVALGVGAIVGTGILTLIGVGAGKAGPAVIMSFVIAGAICACAALAYAEMATMMPASGSAYAYSYAVLGEIIAWVVGWSLILEYSLVVSTVAVGWSGYAAPLLHAWTGMPLELMAGPHANGIVNLPAIFIIAVVAGLLCLGTKESATLNAALVVVKIIALAVFVAVALPYFNGANLEPFAPFGFAKTISPDGVERGVMAAAAIIFFAFYGFDAISTAAEETKNPGRDLAIGIVGSMIACVAIYMLVAVAAVGATPFTHFANSPEPLALILRDLGRPGFATFLAVSAIIALPTVLLGFLFGQSRIFFTMARDGMLPIGLAKVSKRGSPVRITLFTAAIVAVIAGLLPIDEIAALANAGTLAAFTAVAVCMMVLRVRAPDMPRMFRTPLWWLVGAIAVLGCIYLFFSLPVKTQLWFLAWNALGVVIYFAYARPRVSAKGIE catabolism Sphingomonas koreensis DSMZ 15582 Korea Ga0059261_1581 Ga0059261_1581 SKO01S_RS16485 WP_066580460.1 Maltose or maltodextrin glucosidase (EC 3.2.1.20) Specifically important for: D-Maltose monohydrate; a-Cyclodextrin. The first step in catabolism of maltose or longer maltodextrin polymers. The phenotype on maltose implies that maltose is also a substrate, which was ambiguous with the original SEED annotation (SEED_correct) Glycosidases Maltodextrin glucosidase (EC 3.2.1.20) MRSLAFALTLLAGTVASAQTAAPAELRARAAETEVLYFLLPDRFENGDPSNDRGGLRGDRLTTGFDPAHKGFFHGGDLKGLIRRLDYIQSLGASAIWLGPIYKNKPVQGGPGQETAGYHGYWITDFTRVDPHFGTNDEMKAFVDAAHARGIKVYLDIITNHTADVIQYRECPKSACDYRSRADYPYQRKGGVKGAAINPGFAGDGVQTPENFAKLSDPNYAYTTVVPEAERTVKVPAWLNDPIHYHNRGNTTFRNESSTMGDFVGLDDLMTESPRVLQGFIDIYGAWIDQFGIDGFRIDTARHVNPEFWQGFSKAMIERAKARGIPNFHIFGEVANEGDVGDLALHTRVHQLPSVLDFGFRAAVQHTVAGEKGPDMLAAMFDRDALYEGGAEAALRLPTFISNHDHGRFSTDVRKAFPKASDDEVLARVKLAHAMLLLLRGVPTIYSGDEQGFVSDGNDQDAREDMFPSKVAIYNDNRLLGTDKTTADSNFDTGHPLYMEISKLSAIRKATPALSRGRQVTRAYDEKPGLFAVSRFDPASGAEVLVAFNTSAAPITRQVEVGVSSTAFAPLVGQCAASASAPGSVTVTLPAFGYVACVAAGGAK transporters Sphingomonas koreensis DSMZ 15582 Korea Ga0059261_1777 Ga0059261_1777 SKO01S_RS20290 WP_083954491.1 D-fructose transporter, sugar porter family Specific phenotype on fructose and raffinose; during growth on raffinose, it is probably cleaved to sucrose in the periplasm (by Ga0059261_1166), so this probably is important on raffinose because of the fructose uptake MFS transporter, sugar porter (SP) family MHSVSASFAGAPDEEARATVAIILSAAGAALGGLLFGFDTAVISGATQALQLQFGLTDAMLGFTVASALIGTVLGSLIAGAPADRFGRKGVMLTVAIAYVVSSLGTGLAPDLNAFLVFRFMGGLAIGAASVVTPIYIAEVSPARFRGRLVAMNQLNIVLGILIAFLSNYIIAGLVQYDVAWRWMFGIVAVPSTIFLLVTLLLPESPRWLAIHGQADRARDVMQRLGFADPRAELARIELAEAREEAAGKPRLFQRSHFTPVACAIAIAMFNQLSGINALLYYAPRIFELAGAGADSALLQSIAVGGTNLVFTVAALFLIDRFGRRPLLFVGSVICAATLLLVGWQLESAKPDGTLILFGLLGFIAAFAMSQGAVIWVFISEVFPSAVRGKGQALGSTTHWVMAAAITWAFPVFAASVGGWVFAFFGAMMLLQLLWTWKFMPETNGIALEDMNLGSARA catabolism Sphingomonas koreensis DSMZ 15582 Korea Ga0059261_1778 Ga0059261_1778 SKO01S_RS20285 WP_066581977.1 beta-fructosidase for D-raffinose catabolism (EC 3.2.1.26) Specifically important for: D-Raffinose pentahydrate. Uncertain if it acts on raffinose or sucrose (raffinose could be cleaved to galactose + sucrose first). Alternatively, SEED suggests that it hydrolyzes sucrose-6-phosphate, but the basis for this is unclear. Beta-fructosidases (levanase/invertase) Sucrose-6-phosphate hydrolase (EC 3.2.1.B3) MKKLAILLTAAAVLASAASAQQADVRPGYHYGPARNWMNDPNGLVYYDGEYHLFYQYNPHGDRWGHMNWGHAVSRDLVNWEELPVAIPETDVMAFSGTAVIDWNNTTGFGKNGKPPMIAIYTGHDPKTERQSQYLAYSNDRGRTFTIHGEVLNAGNEKHFRDPKVFWHAPTRRWVMVVLKAAANTAEIYTSPNLKDWTHRSSFGPAGGRGKFWECPDLFELPVEGGAPGETRWVLSINLGDNAIGGGSGGQYFVGDFDGEKFTLVPGWPAAPQWMDYGADFYATISWNDMPKGDPRRVWMGWANDWRYAEAIPTWPARGIMTVARTVALRKTAEGYHLLQAPVRELATLRGTPQRAPALALSETPVPLPIEGGKADIELELDTGTADQVSIALTDGQGWQTRIGVNPTVNEVFVDRTRSGPHFHDGFANRHVAPVDLKSRKVKLRVLADESIVEVFVNDGRQTITDRFYRGGGALTWSATARGGKATMNLTAWPMRSMESRK catabolism Sphingomonas koreensis DSMZ 15582 Korea Ga0059261_1893 Ga0059261_1893 SKO01S_RS12770 WP_066578889.1 Xylonolactonase (EC 3.1.1.68) Specifically important for: D-Xylose. xylonolactone is an intermediate in the oxidation of xylose (SEED_correct) Gluconolactonase Xylonolactonase (EC 3.1.1.68) MGVVLTAPEPVWALGAPLLEGPVWVQRDAALWFVDIKSHRIHRFDPASGERRSWDAPAQVGFCLPAANGKFVAGLQTGLAIFDPADRSFTPLTDPEPALPGNRLNDGTVDPAGRLWFGTMDDGESEATGRIYRLGGDGRCVAETAAVSISNGPAVSPDGRTLYHVDTLGGVIHSAAIGDDGILGDSRVFATIPNSEGFPDGPAVDAEGCVWIGLYNGAAVRRYSPAGELLDVVAFPVGAITKVAFGGPDLRTVYATTASKHLDADGRAEEPHAGDLFAFRVSVPGMPGTEVSVGL catabolism Sphingomonas koreensis DSMZ 15582 Korea Ga0059261_1894 Ga0059261_1894 SKO01S_RS12775 WP_066578892.1 D-xylose 1-dehydrogenase (EC 1.1.1.175) Specifically important for: D-Xylose. the first step in xylose oxidation (SEED_correct) Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) D-xylose 1-dehydrogenase (EC 1.1.1.175) MTQPAAASAAAVYPSLKGKRVLVTGGGSGIGAGIVEGFARQGADVTFFDIAGAESQLLVERLSADGHKACFERVDLTDVASLQAVIARLIKGAGGFDILVNNAANDDRHAIDEITEAYWDERLSVNLKHIFFCAQAVVPAMRARGGGAIVNLGSISWHLGLSDLVLYQTCKAAIEGLTRSLARDLGRDGIRATCVIPGNVRTPRQLKWYSPEGEAEIVAAQCLDGRLAPEDVAAMVLFLASDDARLVTGHSYFVDAGWR catabolism Sphingomonas koreensis DSMZ 15582 Korea Ga0059261_1895 Ga0059261_1895 SKO01S_RS12780 WP_083629275.1 2-keto-3-deoxyxylonate dehydratase # Specifically important in carbon source D-Xylose. 31% identical to HVO_B0027, which is 2-keto-3-deoxyxylonate dehydratase (see PMC2785657). Ga0059261_1895 is also 61% identical to xylX from Caulobacter crescentus, which is also required for xylose utilization (PMC1855722) and is believed to have this activity as well (ibid.). Fumarylacetoacetate (FAA) hydrolase family protein Fumarylacetoacetate hydrolase family protein VPEAFDVSALPEDAGQATLAGRVMLAEGPVPVIVREGRVHDVSTVAATTADLFDLPDPASAAGKYLCDVTDLTIGGGAYALLAPIDLQCVKACGVTFAVSALERVIEERARGDAGQAAAIRAELEEKIGGGIRSVVPGSADAAKLKAVLIDAGMWSQYLEVAIGPDAEVFTKAPVLSSVGWGAEIGIRSDSSWNNPEPEVVVIANAAGKVIGATLGNDVNLRDFEGRSALLLGKAKDNNAACAIGPFVRLFDAQFGIDDVRNAELDLLIEGPEGYRLEGHSSMNQISRDPLELVRQTLSEHQYPDGFALFLGTLFAPVQDRDDPGRGFTHKIGDTVRIRSRKLGTLTNRVTTSKDAAPWTFGIRELYRSIAARTAA catabolism Sphingomonas koreensis DSMZ 15582 Korea Ga0059261_1896 Ga0059261_1896 SKO01S_RS12785 WP_066578896.1 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) Specifically important for: D-Xylose. The KEGG annotation is vague; xylose is oxidized to alpha-ketoglutarate semialdehyde (SEED_correct) NAD-dependent aldehyde dehydrogenases Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) NADP-dependent aldehyde dehydrogenase MELTGGLFIGGERRQSDARFHAYDPAAGADIADAGFASASEQDVADACAAAEAAFLPYSTKPLEARARFLETIADEIEALGDVLIERACRESGLPAARITGERGRTVGQLRLFAKEVRDGAWQKLRIDHADRERTPPRPDLRLRMVPLGPVAVFGASNFPLAFSTAGGDTASAFAAGCPVVVKGHRAHPGTAELIATAIIRAVETCGMPAGTFGMVNGTSRKVGETLVADPRIQAVGFTGSRGGGEALMRIAAARPRPIPVYAEMAAINPVILMPQALKARGPALAEAFVASLAMGAGQFCTNPGLVMGIDGPELDAFVARAGEVLSGQAAQVMLTDGIWEAFESGKAKLAGSAFVTKVAEGVEADGPNRGRAALFSVAGKDFLADPVHLHEVFGVSSVVVRCASLEELKAVLGELEGQLTATLQVDEGDYPEAQALLPVLERTVGRVIANGWPTGVEVTHAMVHGGPYPSTSDPRSTSVGTLAIDRFLRPVSYQDLPEALLPAALRENAQAGTVARIDGSWTI catabolism Marinobacter adhaerens HP15 Marino GFF2534 HP15_2478 HP15_RS12360 WP_041645374.1 tr|E4PHV4|E4PHV4_MARAH Acyl-CoA dehydrogenase (EC 1.3.8.7) Specifically important for: Tween 20. tween 20 hydrolyzes to a mix of C12, C14, and C16 fatty acids; this is probably part of beta oxidation (SEED_correct) acyl-CoA dehydrogenase family protein Acyl-CoA dehydrogenase (EC 1.3.8.7) MRFVLNEVFDAPALWASLPKVAEHVDPETADAILEEAGKISSGVLAPLNREGDEQGCKWNDGEVTSPEGFKEAYQTIVEGGWNGLGGNPDFGGMGMPKTLVAQFEEMMQGANMAFGLAPMLTAGACLALDAHGSDELKEKYLPNMYSGVWSGAMDLTEPHAGTDLGIIRTKAEPNDDGSFNVTGTKIFITWGEHDMAENIIHLVLAKLPDAPKGPKGISMFLVPKFLVNDDGSLGERNSFSCGSLEKKMGIKGSATCVMNFDGAKGWLVGEENKGLAAMFTMMNYERLGVGIQGIGAAEASLQSAREYALDRIQSRAPTGAQQPEKAADPILVHPDVRRMLLTMKSYVEGGRTFSTYVAQWLDIAKFAEDDERRKHAEGMVALLTPVAKAFLTDRGLDTCIMGQQVFGGHGFIREWGQEQLVRDCRITQIYEGTNGIQALDLMGRKVVGTQGKLYELFAQDVANFLEENSGNDHLRPFLEPLAAAVERLDDVTEHVIKQAGDNPNAIGAASVDYLDLFGLTALGYMWAKIVKAAAPQADSDTSGFYSGKLKTARFYFDRLLPKTVSLAEGIRSGSDSMMALTAEEF catabolism Marinobacter adhaerens HP15 Marino GFF2749 HP15_2693 HP15_RS13380 WP_014577963.1 tr|E4PKI1|E4PKI1_MARAH 3-hydroxyacyl-CoA dehydrogenase PaaC (EC 1.1.1.-) Specifically important for: L-Phenylalanine. Part of phenylalanine catabolism via phenylacetate (SEED_correct) 3-hydroxybutyryl-CoA dehydrogenase 3-hydroxyacyl-CoA dehydrogenase PaaC (EC 1.1.1.-) 3-hydroxybutyryl-CoA dehydrogenase MPALDTQTKVAVVGAGAMGSGIAQVAAQAGHQVYLHDQREGAAEAGRDGIAKQLQRRVDKGKMQQQELDDVIGRIHPVAKLDDVADAGLVIEAIIEDLQIKRQLLASLEDLCTADAILATNTSSISVTALGADMSKPERLVGMHFFNPAPLMALVEVVMGLATSKTVADTVHATATAWGKKPVYATSTPGFIVNRVARPFYAESLRLLQEQATDAATLDAIIREAGQFRMGAFELTDLIGHDVNYAVTSSVFNSYYQDPRFLPSLIQKELVEAGRLGRKSGQGFYPYGESAEKPQPKTEPAHQSDESVIIAEGNPGVAAPLLERLKAAGLTIIERDGPGQIRFGDAVLALTDGRMATERAACEGVANLVLFDLAFDYSKASRLALAPADQASDAAVSCACALLQKAGIEVSLIADRPGLVIMRTVAMLANEAADAALHGVATVADIDLAMKAGLNYPDGPLSWSDRLGAGHVFKVLTNIQTSYAEDRYRPALLLRKNAFAQKGFYS catabolism Marinobacter adhaerens HP15 Marino GFF2751 HP15_2695 HP15_RS13390 WP_041646301.1 tr|E4PKI3|E4PKI3_MARAH Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) Specifically important for: L-Phenylalanine. The second SEED annotation (beta-ketoadipyl-CoA thiolase) is part of phenylalanine catabolism via phenylacetate. Not clear if the acetyl-CoA acetyltransferase annotation is correct, so it was removed, but it remains plausible (SEED_correct) acetyl-CoA acetyltransferase Acetyl-CoA acetyltransferase (EC 2.3.1.9) @ Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) MSADNILKDAYIVDAIRTPIGRYGGALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLYGCANQAGEDNRDVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGVESMSRAPFVMGKADSAFSRKAEIFDTTIGWRFVNPVLKKQYGIDSMPETAENVAADFGISREDQDAFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPLVVDTDEHPRETSLEKLASLPTPFRENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGVEPRIMGFGPAPATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNGGAIALGHPLGMSGARLVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIERMDAVA catabolism Marinobacter adhaerens HP15 Marino GFF3193 HP15_3135 HP15_RS15560 WP_014578345.1 tr|E4PPM8|E4PPM8_MARAH ethanol oxidation regulatory protein ercA Specifically important for: Ethanol; D-Trehalose dihydrate. Similar to ercA (PA1991) which apparently has a regulatory role (PMCID: PMC3754586) rather than being directly involved in catabolism. Also this gene is adjacent to an apparent ercS (HP15_3134). Do not see why SEED annotates it as aldehyde dehydrogenase. HP15_3164 is probably the ethanol dehydrogenase and HP15_3144 the acetaldehyde dehydrogenase. iron-containing alcohol dehydrogenase Alcohol dehydrogenase (EC 1.1.1.1); Acetaldehyde dehydrogenase (EC 1.2.1.10) MSHDISSLRKFVSPEIVFGAGSRKSVANFASNFGARHVFLVSDPGVAAAGWVDEIVTLLTDAGIRSTVYTGVSPNPKVDEVMTGAELYKSNECDVIVAIGGGSPMDCAKGIGIVATHGRSILEFEGVDTITNPSPPLILIPTTAGTSADVSQFAIISDPNRRFKFSIISKAVVPDVSLIDPEVTETMDAYLTACTGVDALVHAIEAYVSTGSGPLTDTHALEAIRLINRNLEPLVDNTADPYLREQIMLASMQAGLAFSNAILGAVHAMSHSLGGFLDLPHGLCNALLLEHVVAYNFQSAEDRFRRVAEAMDIDTRGMAKPEIKKRLMNRIVELKRRVGLEARLAQLGVSVSDIPHLSGFALQDPCILTNPRKSSLRDVQVVYEEAL catabolism Marinobacter adhaerens HP15 Marino GFF879 HP15_858 HP15_RS04300 WP_014576347.1 tr|E4PR87|E4PR87_MARAH phenylalanine aminotransferase (EC 2.6.1.57) Specifically important for: L-Phenylalanine. The donor for the amine group is uncertain, but this gene is specifically involved in catabolism of phenylalanine via phenylpyruvate (the product of this enzyme) aspartate aminotransferase Aspartate aminotransferase (EC 2.6.1.1) aspartate aminotransferase MFEALQPLPQDPILQLMQTFLEDDRPDKVDLGIGVYKDDAGNTPIMAAVHEAERRLLEGETTKSYVGPAGSAGFNSAMAELILGSNSPLVRDGRVSVIQTPGGCGALRMAAEFLRLCKADTKVWVSTPTWANHLPLLGGAGLTIREYPYLNPETLQVDFGAMLETLERADAGDVVLLHGCCHNPSGADLSLAQWQEVTSLIQRKGLLPFVDMAYQGLGEGLDADAAGLRHLASAVPEMLIAASCSKNFGLYRERTGALALVSETATVNAAATSQLLSVIRSHYSMPPAHGASIVETILGDDDLRAQWQQELNGMCKRILHLRHAFADALSPVGDFDFIARQRGMFSFLGISPEQVGRLRKEHGIHMLESSRVNVAGLNDHVLPQVASALREVLGK catabolism Marinobacter adhaerens HP15 Marino GFF880 HP15_859 HP15_RS04305 WP_014576348.1 tr|E4PR88|E4PR88_MARAH phenylpyruvate ferredoxin oxidoreductase (EC 1.2.7.8) Specifically important for: L-Phenylalanine. This is the second step in phenylalanine catabolism (to phenylacetyl-CoA). Alternatively, could be a decarboxylase (forming phenylacetaldehyde), but we did not identify a separate aldehyde dehydrogenase. Annotated as indolepyruvate ferredoxin oxidoreductase, which has the same EC number but is part of tryptophan catabolism.. pyruvate ferredoxin/flavodoxin oxidoreductase Indolepyruvate ferredoxin oxidoreductase, alpha and beta subunits MSADTPQLDDYKLEDRYLRESGRVFLTGTQALVRIPLMQAALDRKQGLNTAGLVSGYRGSPLGAVDQALWQAKDLLDENRIDFVPAINEDLAATILLGTQQVETDEDRQVEGVFGLWYGKGPGVDRAGDALKHGTTYGSSPHGGVLVVAGDDHGCVSSSMPHQSDVAFMSFFMPTINPANIAEYLEFGLWGYALSRYSGCWVGFKAISETVESAASVEIPPAPDFVTPDDFTAPESGLHYRWPDLPGPQLETRIEHKLAAVQAFARANRIDRCLFDNKEARFGIVTTGKGHLDLLEALDLLGIDEDKARDMGLDIYKVGMVWPLERRGILDFVHGKEEVLVIEEKRGIIESQIKEYMSEPDRPGEVLITGKQDELGRPLIPYVGELSPKLVAGFLAARLGRFFEVDFSERMAEISAMTTAQDPGGVKRMPYFCSGCPHNTSTKVPEGSKALAGIGCHFMASWMGRNTESLIQMGGEGVNWIGKSRYTGNPHVFQNLGEGTYFHSGSMAIRQAVAAGINITYKILFNDAVAMTGGQPVDGQITVDRIAQQMAAEGVNRVVVLSDEPEKYDGHHDLFPKDVTFHDRSELDQVQRELRDIPGCTVLIYDQTCAAEKRRRRKRKQFPDPAKRAFINHHVCEGCGDCSVQSNCLSVVPRKTELGRKRKIDQSSCNKDFSCVNGFCPSFVTIEGGQLRKSRGVDTGSVLTRKLADIPAPKLPEMTGSYDLLVGGVGGTGVVTVGQLITMAAHLESRGASVLDFMGFAQKGGTVLSYVRMAPSPDKLHQVRISNGQADAVIACDLVVASSQKALSVLRPNHTRIVANEAELPTADYVLFRDADMKADKRLGLLKNAVGEDHFDQLDANGIAEKLMGDTVFSNVMMLGFAWQKGLLPLSEAALMKAIELNGVAIDRNKEAFGWGRLSAVDPSAVTDLLDDSNAQVVEVKPEPTLDELINTRHKHLVNYQNQRWADQYRDAVAGVRKAEESLGETNLLLTRAVAQQLYRFMAYKDEYEVARLFAETDFMKEVNETFEGDFKVHFHLAPPLLSGETDAQGRPKKRRFGPWMFRAFRLLAKLRGLRGTAIDPFRYSADRKLDRAMLKDYQSLVDRIGRELNASNYETFLQLAELPADVRGYGPVREQAAESIREKQTQLIKALDTGRPTLIRTQQANEEANHV catabolism Shewanella oneidensis MR-1 MR1 200453 SO1275 SO_1275 NP_716898.1 tr|Q8EHE8|Q8EHE8_SHEON succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] Specifically important for: L-Isoleucine. Also very important with putrescine as the N source. The more specific KEGG annotation is consistent its role on N putrescine (which is converted to 4-aminobutyrate and then to succinate semialdehyde). Its role on isoleucine is unclear but a close homolog, Shewana3_3092, also has this phenotype (albeit milder). Also note that isoleucine is catabolized to propionyl-CoA and Shewana3_3092 is very important for propionate utilization. The annotation of son:SO_1275 in KEGG has been updated to list glutarate-semialdehyde as an additional substrate. (KEGG_correct) succinate-semialdehyde dehydrogenase (NCBI ptt file) Aldehyde dehydrogenase B (EC 1.2.1.22) succinate-semialdehyde dehydrogenase (NADP+) MLLNDPSLLRQQCYINGQWCDANSKETVAITNPATGAVIACVPVMGQAETQAAIAAAEAALPAWRALTAKERGAKLRRWFELLNENSDDLALLMTSEQGKPLTEAKGEVTYAASFIEWFAEEAKRIYGDTIPGHQGDKRIMVIKQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMVVKPAPQTPFTALALAVLAERAGIPAGVFSVITGDAIAIGNEMCTNPIVRKLSFTGSTNVGIKLMAQCAPTLKKLSLELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANRIYVQAGVYDEFAEKLSMAVAKLKVGEGIIAGVTTGPLINAAAVEKVQSHLEDAIKKGATVLAGGKVHELGGNFFEPTVLTNADKSMRVAREETFGPLAPLFKFNDVDDVIKQANDTEFGLAAYFYGRDISLVWKVAESLEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKYGIEEYLEIKYICMSV catabolism Shewanella oneidensis MR-1 MR1 201633 SO2492 SO_2492 NP_718079.1 tr|Q8EE95|Q8EE95_SHEON acyl-CoA dehydrogenase (1.3.8.-) Specifically important for: Tween 20. Tween 20 hydrolyzes to a mix of C12, C14, and C16 fatty acids; this is probably part of beta oxidation. Similar to fadE from E. coli. The specific SEED annotation as butyryl-CoA dehydrogenase seems questionable but could still be correct oxidoreductase, acyl-CoA dehydrogenase family (NCBI ptt file) Butyryl-CoA dehydrogenase (EC 1.3.99.2) MLTIIIIALIAIIALFAVKSLRMQFITQPVFHFFKKVLPPLSDTEREAMEAGDVWWEGELFRGNPNWNTLHSYGKPTLTAEEKDFIDNQVMTALTMIDDFDIVHNRKDLPPELWDYFKKEGFFALIIPKKFGGKAFSAYANSTIVSKLASRSVSAAVTVMVPNSLGPGELLTHYGTEEQKERWLPALAKGDEIPCFALTGPEAGSDAGAIPDVGIVCRGEFNGEEVLGLKLTWNKRYITLAPVATVLGLAFQMRDPDGLLGEKKNLGITCALIPTDHPGVVIGRRHNPLNMAFMNGTTQGDEVFIPLDWIIGGPEFAGRGWRMLVECLSAGRGISLPALATASGHMATKTTTAYSYVRHQFGMAIGQFEGVQEALARIIANTYQLEAARRLTTTGIDLKVKPSVVTAIAKFHMTELGRAVMNDAMDIQSGKGIQLGPKNYLGHPYMSNPISITVEGANILTRSLMIFGQGATRCHPYVLAEMEAAAMENQHDALTRFDSLLMGHMGYATRNAFSALFNALTASRFGNAPVSGETKQYYKDMSRLSSALAFMTDISMLIMGGDLKRKEMLSARMGDVLSQLYLGSATLKLFEDNGRQQDDLPAVRYVMANRLHLAAKALEDVIRNFPNRPVAWLLRALIFPIGNHFNAPSDKMATELVSGMLKPSPARERITFLCPEFEGDVGGIAEVEQAFVAQYACKEIYKKLKKAQRSGELPAKVPNLVLFAKALEQGTISNDEHQTLLHADKLRLAAINVNDFEAL transporters Shewanella oneidensis MR-1 MR1 202564 SO3461 SO_3461 NP_719010.1 tr|Q8EBP8|Q8EBP8_SHEON Fatty acid transporter Specific phenotype on Tween-20, which is hydrolyzed extracellularly to fatty acids (typically around 12 carbons). This protein is distantly related (PF03547) to auxin efflux transporters in plants and to the malate permease mleT of Lactobacillus casei (PMID: 23835171) transporter, putative (NCBI ptt file) TRANSPORTER MTILTPLFAVFGIMLLGTLVQKLRFLPVETDQVLNQYVYYIAFPAVLLIALAQQPIEEILQWRFIAGYSAAMLVIYLMCIGISLLVNPKQHAIAAVRALNATFGNTAFIGIPLLVIIFPEQQSALVAAIASLLSVLMFAVALVSLELTTNKHRQHHAVVIMCLAITKNPIVIGCFIGISISALGITLPSGVALMIQQIGNTSSPCALFAVGMVLAKAMRYQKDSKLFSLTNFVELCLINLFKLILQPALVFFMLKSIGVTGDYLVMGVILSALPTAASVYLLAQRYNTQASTCAQGILFGTIVTFFSLPILEQLVKTYS transporters Shewanella oneidensis MR-1 MR1 202604 SO3503 SO_3503 NP_719050.1 tr|Q8EBL0|Q8EBL0_SHEON N-acetyl glucosamine transporter, NagP Specific phenotype on NAG. Also see PMID:16857666 (SEED_correct) glucose/galactose transporter (NCBI ptt file) N-acetyl glucosamine transporter, NagP MTLDKSQQKSSFLPMAIVAALFFILGFATWLNGSLMPYLKQILQLNPFQASLILFSFYIAVTFTALPSAWVIRKVGYKNGMALGMGVMMIAGLLFIPAAKTQVFALFLFAQLVMGAGQTLLQTAVNPYVVRLGPEESAAARVSVMGILNKGAGVIAPLVFSALILDSFKDRIGTTLTQVQIDEMANGLVLPYLGMAVFIGILALAVKKSPLPELSNEDEVADHTDKSQIKAALSHPNLALGVLALFVYVAVEVIAGDTIGTFALSLGIDHYGVMTSYTMVCMVLGYILGILLIPRVISQPTALMISAILGLLLTLGILFGDNNSYAIANLLLVPFGGVALPDTLLLIAFLGLANAIVWPAVWPLALSGMGKLTSTGSALLIMGIAGGAFGPVSWGLMSSATDMGQQGGYMVMLPCYLFILFYAVKGHKMRSWSAK catabolism Shewanella oneidensis MR-1 MR1 202608 SO3507 SO_3507 NP_719054.1 tr|Q8EBK6|Q8EBK6_SHEON N-acetylglucosamine kinase (EC 2.7.1.59) Specifically important for: N-Acetyl-D-Glucosamine. First step in NAG catabolism; (SEED_correct); see PMID 16857666 conserved hypothetical protein (NCBI ptt file) N-acetylglucosamine kinase of eukaryotic type (EC 2.7.1.59) MGLVQTNDQQLFIGVDGGGSKCRATIYTADGTVLGTGVAGRANPLHGLAQTFESIEASAHQALLDAGMKATDSHLLVAGLGLAGVNVPRLYQDVVNWQHPFAAMYVTTDLHTACIGAHRGADGAVIITGTGSCGYAHVGDASLSIGGHGFALGDKGSGAWLGLKAAEHVLLALDGFATPTALTEMLLSHLGVKDALGIVEHLAGKSSSCYAQLARNVLDCANAGDQVAIAIVQEGADYISEMARKLFMLNPVRFSMIGGLAEPLQAWLGSDVVAKISETLAPPELGAMYYAQQQFNSATV transporters Phaeobacter inhibens BS107 Phaeo GFF1248 PGA1_c12640 PGA1_RS06295 WP_014874390.1 tr|I7DPJ2|I7DPJ2_PHAIB D-lactate transporter, ATP-binding component Specific phenotype on D-lactate and D,L-lactate and cofit with other components putative high-affinity branched-chain amino acid transport ATP-binding protein InterPro IPR001687:IPR003439:IPR003593 COGs COG0411 MGILEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMFDGKSVLGRAPYEINQMGISRVFQTPEIFGDLSVLENMMIPCFAKRDGAFEMNAISAVSGQRDILEKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPTAGMARADTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQGTPLVEDDPQNIKGNPKVREAYLGESA transporters Phaeobacter inhibens BS107 Phaeo GFF1249 PGA1_c12650 PGA1_RS06300 WP_014874391.1 tr|I7EW25|I7EW25_PHAIB D-lactate transporter, permease component 1 Specific phenotype on D-lactate and D,L-lactate and cofit with other components putative high-affinity branched-chain amino acid transport system permease protein Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1) MFTLNKKDKTLLLVVAILTLFAPFILNPFPTGSALAQFNAGYPDLMQRFVIFGIFAIGFNILFGLTGYLSFGHAAFLGVGSYSAVWMFKLLSMNVVPAIVLSVIVAGLFALVIGYVSLRRSGIYFSILTLAFAQMSFNLAYSVLTPITNGETGLQLTLDDPRVLGVSATADGSIPVTSLFGLEMRSTFEMVVGPWAFQFNAGYYLCALILLAAFYLSIRIFRSPFGLMLKAVKSNQQRMNYTGLNTRPYTLAAFVISGMYAGLAGGLMASMDPLAGAERMQWTASGEVVLMTILGGAGTLIGPVLGAGFIKYFENIFSKINDNVLHSWFSFMPDGIEDAMVFIVHPFIGKGWHLTLGILFMLVVIFLPGGLVEGGQKLRGWIQGRKAKKDGPSGKTEPAE transporters Phaeobacter inhibens BS107 Phaeo GFF1250 PGA1_c12660 PGA1_RS06305 WP_014874392.1 tr|I7EL66|I7EL66_PHAIB D-lactate transporter, permease component 2 Specific phenotype on D-lactate and D,L-lactate and cofit with other components putative high-affinity branched-chain amino acid transport system permease protein Possible ABC transporter subunit MDAILLQILNGLDKGSAYALIALGLTLIFGTLGVVNFAHGALFMIGAFCAVTVQRVLSLSFETVDETQKDFLGNPLKVKTPYVESWFGPEVGGAIIDWAVPLAILFAIPIMIGVGYVMERGLIKHFYKRPHADQILVTFGLAIVLQEVVKYFYGANPIQTPAPDALNGVVNLGSIIGMDIVYPVWRVVYFFFAVVIIGGIFSFLQFTTFGMVVRAGMADRETVGLLGINIDRRFTIMFGIAAAVAGLAGVMYTPINSPNYHMGMDFLVLSFVVVVVGGMGSLPGAVLAGFLLGVLESFASMNEIKSLIPGIDQIIIYVVAIIILLTRPRGLMGRKGVMED transporters Phaeobacter inhibens BS107 Phaeo GFF1251 PGA1_c12670 PGA1_RS06310 WP_014874393.1 tr|I7DZT5|I7DZT5_PHAIB D-lactate transporter, substrate binding component Cofit with the other components and important for growth in various D-lactate and D,L-lactate media ABC-type branched-chain amino acid transport systems, periplasmic component Branched-chain amino acid ABC transporter, periplasmic substrate- binding protein MSKTDVSRRGVLKTGAIAGAGVALPTIFTASSAAAFTNEPTGSTVTLGFNVPQTGPYADEGADELRAYQLAVEHLNGGGDGGMMNTFSSKALQGNGIMGKEVKFVTGDTQTKSDAARASAKSMIEKDGAVMITGGSSSGVAIAVQGLCQEAGVIFMAGLTHSNDTTGKDKKANGFRHFFNGYMSGAALAPVLKNLYGTDRNAYHLTADYTWGWTQEESIAAATEALGWNTVNKVRTPLAATDFSSYIAPVLNSGADVLVLNHYGGNMVNSLTNAVQFGLREKVVNGKNFEIVVPLYSRLMAKGAGANVKGIHGSTNWHWSLQDEGSQAFVRSFGSKYGFPPSQAAHTVYCQTLLYADAVERAGSFNPCAVVEALEGFEFDGLGNGKTLYRAEDHQCFKDVLVVRGKENPTSEFDLLEVVEVTPAEQVTYAPDHPMFAGGALGTCNSGA catabolism Phaeobacter inhibens BS107 Phaeo GFF1301 PGA1_c13170 PGA1_RS06560 WP_014879812.1 tr|I7ELB3|I7ELB3_PHAIB Sorbitol dehydrogenase (EC 1.1.1.14) Specifically important for: D-Sorbitol. First step is sorbitol catabolism; (SEED_correct) sorbitol dehydrogenase PolS Sorbitol dehydrogenase (EC 1.1.1.14) MKRLSGKRALITGAARGIGAAFAEAYANEGARVVIADIDTARAEATAAQIGAAAIAVELDVTDQASIDRALSRTVECFGGLDILINNAAVFTAAPLVEVTREAYQRTFDINVSGTLFMMQAAAQQMITQGTGGKIINMASQAGRRGEPLVSVYCATKAAVISLTQSAGLNLISHGINVNAIAPGVVDGEHWDGVDAFFAKYEGKAPGQKKAEVAQSVPYGRMGTAADLTGMAVFLASEDADYVVAQTYNVDGGQWMS transporters Phaeobacter inhibens BS107 Phaeo GFF1302 PGA1_c13180 PGA1_RS06565 WP_014879813.1 tr|I7DZW6|I7DZW6_PHAIB ABC transporter for D-Sorbitol, ATPase component Specific phenotype on D-Sorbitol. ABC transporter, ATP binding protein Various polyols ABC transporter, ATP-binding component sorbitol/mannitol transport system ATP-binding protein MGQIKLESVTKNFGPVEVIPPLDLTIEDGEFTVFVGPSGCGKSTLLRLIAGLEDITSGTIRIDGEDATNIPPAKRGLAMVFQSYALYPHMSVRKNIAFPMKMAGIPADEQKRRIDNAAAALNLTDYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVGMRLEISELHKRLATTMIYVTHDQVEAMTMADKIVVLQAGVIEQVGSPMELYRAPRNVFVAGFIGSPKMNLLTGPQAAQHNAATIGIRPEHLSISETEGMWAGTIGVSEHLGSDTFFHVQCDAFDDPLTVRASGELDLGYGERVFLTPDMTHLHRFGSDGLRIE transporters Phaeobacter inhibens BS107 Phaeo GFF1303 PGA1_c13190 PGA1_RS06570 WP_014874441.1 tr|I7EYP2|I7EYP2_PHAIB ABC transporter for D-Sorbitol, permease component 1 Specific phenotypes on D-Sorbitol; D-Sorbitol. Not important on mannitol. ABC transporter permease protein Various polyols ABC transporter, permease component 2 sorbitol/mannitol transport system permease protein MARAVTPRRKAINTALAWAVGLLIFFPILWTILTSFKTEAQAISDPPVFLFFDWTLENYSVVQERSDYMRFLWNSVIIAGGSTILGIIIAVPAAWSMAFVPSKRTKDILLWMLSTKMLPAVGVLYPIYILFIKMGLLDNRFGLVVVLMLINLPIIVWMLYTYFKEIPGEILEAARMDGATLKEEILYVLTPMAIPGIASTLLLNIILAWNEAFWTLNLTAAKAAPLTAFIASYSSPEGLFYAKLSAASTMAIAPILILGWFSQKQLVSGLTFGAVK transporters Phaeobacter inhibens BS107 Phaeo GFF1304 PGA1_c13200 PGA1_RS06575 WP_014874442.1 tr|I7DPP3|I7DPP3_PHAIB ABC transporter for D-Sorbitol, permease component 2 Specific phenotypes on D-Sorbitol; D-Sorbitol. Not important on mannitol. ABC transporter permease protein Various polyols ABC transporter, permease component 1 sorbitol/mannitol transport system permease protein MATQHSRSAARIMMAPAVILLLGWMLVPLTMTLYFSFKKYLPLRGGDLGWVGFDNYARFLSSSAFWPSVQATLVIVGGVLAITVILGVFLALLLNQPMWGQGIVRILVIAPFFVMPTVSALVWKNMFMDPVNGLFAHLWKAFGAEPVSWLSEASLQSIILIVSWQWLPFATLILLTAIQSLDSEQLEAAEMDGAPPVARFGYITLPHLSRAITVVVLIQTIFLLSIFAEIFVTTQGSFGTKTLTYLIYQRVLESQNVGLGSAGGVYAIILANIVAIFLMRIVGKNLDA transporters Phaeobacter inhibens BS107 Phaeo GFF1305 PGA1_c13210 PGA1_RS06580 WP_014879814.1 tr|I7EW74|I7EW74_PHAIB ABC transporter for D-Sorbitol, periplasmic substrate-binding component Specific phenotype on D-Sorbitol. extracellular solute-binding protein Various polyols ABC transporter, periplasmic substrate-binding protein sorbitol/mannitol transport system substrate-binding protein MYLKSALRAATALTVFASTAAFADTITIATVNNGDMIRMQGLTEDFTAKTGHEVEWVTLEENVLRQRVTTDISAKGGQFDIMTIGMYETPIWGKNGWLVPLNDLPADYDVDDILPAMRGGLSHDGTLFAAPFYGESSMIMYRTDLMEKAGLEMPAAPTWDFVADAARQMTDKDNETYGICLRGKAGWGENAAFITAMSNSFGARWFDENWAPQFDSEAWSNTLNFYINLLNDAGPPGASNNGFNENLSLFQQGKCGMWIDATVAASFVTNPNDSTVADKVGFALAPDTGLGKRSNWLWAWALAIPAGTQKEAAAKEFIQWATSKDYIELVAENEGWANVPPGARISLYENANYKDIPFAKMTLESILSADPNNPTVDPVPYVGIQFAAIPEFAGIATQVGQEFSAALAGQQTAEEALAKAQALTADEMEAAGY catabolism Phaeobacter inhibens BS107 Phaeo GFF1382 PGA1_c13990 PGA1_RS06965 WP_014879881.1 tr|I7EWE4|I7EWE4_PHAIB Novel Xylose regulator from LacI family # Specifically important in carbon source D-Xylose. Also see expression evidence (PMC4148808). (SEED_correct) putative transcriptional regulator, iacl family Novel Xylose regulator from LacI family LacI family transcriptional regulator MGKPTLHDVAAAAGVSYATADRVLNNRGGVAKKSQDRVRAAIADLGYQRDITAANLSRRRRYRFAVLMPAAQEGFFATLHADLEQEVAARSQARQQITLTQVPPFDAAALTCALEACAAEGYDGVCLVAVQDPSVDAALTGLRAQGVAVVTLVADSAAQARDTYVGIDNRRAGRTAGDLMRLAHRGSAASLGQILPITGSLNARDHADRYAGFCDVVSADLHILPPLETGDDPEILEQALRRTLRANPNITGIYNLGAGIPGLISALAAIQPDDRPVVISHELCPATRDAVAHGLIDAVIDQKPAQEITAALAALVALSDGQSVDPLAGQITPAVHFKHNMPPQSAVGPEEGA catabolism Phaeobacter inhibens BS107 Phaeo GFF1469 PGA1_c14880 PGA1_RS07390 WP_014879948.1 tr|I7E0E8|I7E0E8_PHAIB 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60) Specifically important for: L-Serine. probably important for serine utilization because L-serine can be transaminated to 2-hydroxy-3-oxopropionate, which then needs to be dealt with somehow (SEED_correct) putative 3-hydroxyisobutyrate dehydrogenase 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60) 3-hydroxyisobutyrate dehydrogenase MAKVAFLGLGVMGYPMAGHLAAAGHEVTVYNRTAAKAEAWAKEHGGTAAATPREAAAGAEFVMACVGNDDDLRSVCLGDTGAFGGMGAGAIFVDHTTVSAKVTRELNAAAADLGLSFVDAPISGGQAGAENGVLSVMCGGDQAAYDKAEPVIGSYARICRRIGDSGAGQMTKMCNQIAIAGLVQGLSEALHFAEKAGLDGRAVVEVISQGAAGSWQMANRHETMLDDHFDHGFAVDWMRKDLGICLDAAEETGASLPVTALVDQFYKDVQKLGGGRWDTSSLFKRLKAFE catabolism Phaeobacter inhibens BS107 Phaeo GFF1616 PGA1_c16380 PGA1_RS08130 WP_014880051.1 tr|I7EX15|I7EX15_PHAIB arginine deiminase (EC 3.5.3.6) Specifically important for: L-Citrulline. Citrulline is catabolized via arginine by this reaction in reverse; this is distantly related to characterized arginine deiminases (see PF02274) Uncharacterized protein conserved in bacteria containing a pentein-type domain Amidinotransferase family protein MSQLQAPGAVVMIRPHHFCSNPETRDDNAFQTLADDTADVTSAQAQAEFDGAVTALRGAGVSVHVFDDTGTETPDSVFPNNWFSTHAGGHVAVYPMYAANRRKERRWDVIELLKRDYRVQDVIDYSGLEQDGLALEGTGAMVLDHIGRIAYTVKSNRADPVLLERFCTHFNFEPMVFEARDAQGRDVYHTNVLMGIGTDYALICLDMITDPTRRAEVAARLEETGRRVIDLTPEQIAGFAGNALELTGHSRLLALSSRAAEVLRADQITIIERSATLLPLSIPTIETAGGSVRCMLAAIHLSPRERTQS catabolism Phaeobacter inhibens BS107 Phaeo GFF1644 PGA1_c16670 PGA1_RS08270 WP_014880077.1 tr|I7E0Z4|I7E0Z4_PHAIB D-mannose isomerase (EC 5.3.1.7) Specifically important for: D-Mannitol; D-Mannose. often annotated as N-acylglucosamine 2-epimerase, but the phenotypes confirm that it is mannose isomerase. (Mannitol is catabolized via mannose.) putative N-acylglucosamine 2-epimerase N-acylglucosamine 2-epimerase (EC 5.1.3.8) MSTHSAVGDLSAPGVWLEDTGHQAYLIADARRQLDFFAGSLRAEPGFHTLDAAGRPLPDDKQELHTTTRLVHSYALAHICGYAGAEQMIDHGMAYLNSHHRDQIHGGYLWALSGDAIADDRKLAYGHVFVLLAAASAKLAGHPGADALLSDVAEVLDQRFWETGPKRFADEWNRDWTPFSTYRGMNANMHGVEALLTAYEATGETVFLDRAGHILDFFVDEVAAAESWRLPEHYTETWQIDRTYAGDPMFRPAGTTPGHSFELGRLMLQHWDLAGRRDTGAPTRARSLIEQALADAWLVDGGFAYTLDFEGKVAMRNRFWWPVTEAIGAVATLVKLDGRVEDEQWYRRLWGFAQAHFIDEDRGGWYPEIDGNGQVTRTIFTGKPDIYHALQACLLPLGALPLGHVAGLKKLSAPLLS catabolism Phaeobacter inhibens BS107 Phaeo GFF2748 PGA1_c27910 PGA1_RS13875 WP_014880980.1 tr|I7EZT8|I7EZT8_PHAIB N-acetylglucosamine kinase (EC 2.7.1.59) Specifically important for: D-Glucose; N-Acetyl-D-Glucosamine. This is the first step in NAG catabolism. The next step is expected to be N-acetylglucosamine-6-phosphate deacetylase (PGA1_c27880, no data). The phenotype on D-glucose is consistent across replicates and is not explained. It does not seem to be due to polar effects. There is a glucokinase that is important for glucose utilization (PGA1_c05420 ) so we don't expect that this is glucokinase. (SEED_correct) putative ATPase, BadF/BadG/BcrA/BcrD type N-acetylglucosamine kinase of eukaryotic type (EC 2.7.1.59) MTDSRFPYLIAVDGGGTSCRFALLKSGATPPQQLVVTGGSANVYTAPDQAVETLSAGLADLQRQSGLTDEVFHQIPVYAGLAGVIDGESAARVAEALPQAHVRVEDDRMPAVVGALGEDTASLIGVGTGSFLGRQVAGQVTLIGGHGTVLGDEASGGWLGRRALQLTLQAAEGIEPMTPLLRSCLRDFSNETAKIVRFAQTARPVAFGAYAPRVAKAAVEGDAAGRRLMAEGAEYLCNGLQALGRRPEEPVYHIGGVAAQYAAYLPADVADYLRGAEGSPLDGALELARRFAREIAQEVV transporters Phaeobacter inhibens BS107 Phaeo GFF2750 PGA1_c27930 PGA1_RS13885 WP_014880982.1 tr|I7E3W0|I7E3W0_PHAIB N-Acetyl-D-glucosamine ABC transport system, periplasmic substrate-binding component Specific phenotype on N-Acetyl-D-Glucosamine. (SEED_correct) putative sugar ABC transporter, periplasmic binding protein N-Acetyl-D-glucosamine ABC transport system, sugar-binding protein multiple sugar transport system substrate-binding protein MTRKLFTLALLGSTMIGGAAAAEDVTLTIESWRNDDLALWQDKIIPAFEAANPGIKLKFTPSAPAEYNAVLNSKLDAGSAGDLITCRPFDASLGLYDKGQLADLSDLDAMGSFSNVAKSAWQTDDGSATFCVPIASVIHGFIYNKDAFAELGVNVPETEDEFFAALEKIKEDGNYVPLAMGTNDQWEAATMGYNNIGPNYWKGEEGRLALIAGEQKLTDDQWVAPYETLSKWGAYMGDGYEAQTYPDSQNIFTLGRAAIYPAGSWEISGFNTQADFAMGAFKPPVKAAGDTCYISDHTDIAVGLNAASPNAEAAKTFLNWVGSAEFASIYANALPGFFSLSNHEVAMEDPLAQEFVSWRGECESTIRSTYQILSRGTPNLENETWGASVAAIKGTKAPADLGAELQEGLASWYEPQK transporters Phaeobacter inhibens BS107 Phaeo GFF2751 PGA1_c27940 PGA1_RS13890 WP_014875690.1 tr|I7F282|I7F282_PHAIB N-Acetyl-D-glucosamine ABC transport system, permease component 1 Specific phenotypes on N-Acetyl-D-Glucosamine. (SEED_correct) ABC transporter permease protein N-Acetyl-D-glucosamine ABC transport system, permease protein 1 multiple sugar transport system permease protein MQNTPHKPRRRWHIAVFLAPAVLVYTAIMIFPLFNTLRLALYSESDQIRQFVGLANFETLFGNPNWSEQFWNALGNNFWFFFVHMLVQNPIGVALAAILSHPRLRFAALYRTAIFVPTILSFVIVGFAWKLILSPIWGITPDLLDAIGLKWLFAPWLGKEDYALTTLALISVWQFVGIPMMLIYAALLSIPEEVIEAGEVDGITGMSAFWKIKLPLILPSIGIISILTFVGNFNAFDLIYTTQGALAGPDFSTDILGTFMYRTFFGFQLQLGDPHMGSAIATAMFAIILIGVCIYLFGIQTRLRRYQF transporters Phaeobacter inhibens BS107 Phaeo GFF2752 PGA1_c27950 PGA1_RS13895 WP_044040979.1 tr|I7DTQ0|I7DTQ0_PHAIB N-Acetyl-D-glucosamine ABC transport system, permease component 2 Specific phenotypes on N-Acetyl-D-Glucosamine. (SEED_correct) ABC transporter permease protein N-Acetyl-D-glucosamine ABC transport system, permease protein 2 multiple sugar transport system permease protein MMHKSRSNPFNSILAHGALITYTLIALFPVFVILVNSFKTRKAIFRDPLGLPTSDTFSLVGYQTVLKQGDFFLYFQNSMIVTVVSLALVLLFGAMAAFALAEYRFKGNMLLGLYLALGIMIPIRIGTVAILELMVDTGLVNTLTALILVYTAQGLPLAVFILSEFMKQVSDDLKNAGRIDGLSEYTIFFRLVLPLVRPAMATVAVFNMIPIWNDLWFPLILAPAEETKTLTLGSQVFIGQFVTDWNAVLSALSMAILPVMVLYVIFSRQLIRGITSGAVK transporters Phaeobacter inhibens BS107 Phaeo GFF2754 PGA1_c27970 PGA1_RS13905 WP_014880984.1 tr|I7EQ92|I7EQ92_PHAIB N-Acetyl-D-glucosamine ABC transport system, ATPase component Specific phenotype on N-Acetyl-D-Glucosamine. (SEED_correct) ATP-binding transport protein SmoK N-Acetyl-D-glucosamine ABC transport system ATP-binding protein sorbitol/mannitol transport system ATP-binding protein MTALQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEISIGGQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRMLSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLHRQLSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGAPAMNFVPAQRLGGNPGQFIGIRPEYARISPVGPLAGEVIHVEKLGGDTNILVDMGEDLTFTARLFGQHDTNVGETLQFDFDPANCLSFDEAGQRI catabolism Phaeobacter inhibens BS107 Phaeo GFF2923 PGA1_c29700 PGA1_RS14755 WP_014881125.1 tr|I7DU71|I7DU71_PHAIB D-lactate oxidase, iron-sulfur subunit (EC 1.1.3.15) Specifically important for: Sodium D,L-Lactate; Sodium D-Lactate. KEGG oddly has no EC #; SEED has it as 1.1.99.14 (glycolate dehydrogenase) glycolate oxidase iron-sulfur subunit Glycolate dehydrogenase (EC 1.1.99.14), iron-sulfur subunit GlcF glycolate oxidase iron-sulfur subunit MQTTFSEKQLRDPGTQRANEILRSCVHCGFCTATCPTYQVLGDELDSPRGRIYLIKDMLENERVPDAKTVKHIDRCLSCLACMTTCPSGVHYMHLVDHARAYIDKHYNRPWSDRALRWLLARILPYPGRFRLALIGAKLAQPFKRLVPDARLRAMLDMAPRHIPPVSRNDDPQSFAAKAPRRKRVALMTGCAQKALNTDINDATIRLLTRLGCEVVVAAGAGCCGALTHHMGREEESHATAAKNIRAWTDEIDGQGLDAIVINTSGCGTTVKDYGHMFRNDALAEDAARVSAIAMDISELLMQLDLPEGEDKETTVAYHAACSLQHGQQIKTHPKTLLKRAGFTVVEPADSHLCCGSAGTYNLLQPEISAELKARKVTSLEARQPDLIAAGNIGCMMQIGSATDIPILHTVELLDWATGGPKPRALVAGGPGADPRAGEIPILR catabolism Phaeobacter inhibens BS107 Phaeo GFF2924 PGA1_c29710 PGA1_RS14760 WP_014881126.1 tr|I7F093|I7F093_PHAIB D-lactate oxidase, FAD binding subunit (EC 1.1.3.15) Specifically important for: Sodium D-Lactate; Sodium D,L-Lactate. KEGG oddly has no EC #; SEED has it as 1.1.99.14 (glycolate dehydrogenase) glycolate oxidase subunit GlcE Glycolate dehydrogenase (EC 1.1.99.14), FAD-binding subunit GlcE glycolate oxidase FAD binding subunit MTPQSEAELAQIIVGATAPLAVSGGGTRGLSTGGETLSVAGLNGVTLYEPGALTLVVQAGTSVEEVQALLAGENQRLAFEPMDHRGLLGTKGTPTIGGVFAANVSGPRRIQCGAARDFLLGVRFVDGRGDVLSNGGRVMKNVTGYDLVKLMAGSHGTLGVLSEVSLKVLPCSEACATVTVHVADLTSAVAAMSTALGSPYDVTGAAYDPEAGAVYIRVEGFEASVTYRAEALKMALGKFGEVSLALGAGDALWEGIRNVAAFHDRPGDVWRISVKPSDAVALAPALEAEGLLFDWGGGLIWALVPAGRDLRFRLTVPGHATLVRASAQTRAELGQFQPQPGPLAAISGGLRRQFDPRGILNPGLMG catabolism Phaeobacter inhibens BS107 Phaeo GFF2925 PGA1_c29720 PGA1_RS14765 WP_014881127.1 tr|I7EQM9|I7EQM9_PHAIB D-lactate oxidase, FAD-linked subunit (EC 1.1.3.15) Specifically important for: Sodium D,L-Lactate; Sodium D-Lactate. KEGG has the correct EC # but describes it as glycolate oxidase; SEED has it as 1.1.99.14 (glycolate dehydrogenase) glycolate oxidase subunit GlcD Glycolate dehydrogenase (EC 1.1.99.14), subunit GlcD glycolate oxidase MEMPIPDQTVLSQKTELALRLAAVLPDDALVQDPAETRAYECDALTAYKCPPMLVVLPRTTKEVSDVLRICHAAGVPVVPRGAGTSLAGGALPTADCVILGVARMNAVLETDYDNRIIRVQTGRTNLSVSGAVEEEEFFYAPDPSSQLACAIAGNIAMNSGGAHCLKYGVTTNNLMGVTMVMMDGTVVEIGGAHLDAGGLDLLGVICGSEGQLGVVTEATLRILRKPEGARPVLIGYDSNEVAGACVSDIIKAGVLPVAIEFMDRPCIEACEAFAKAGYPMCEALLIVEVEGSDAEIDHQLRLITEIARSHNPVELREARDSDEAARIWLGRKSAFGAMGQINDYMCLDGTIPVTSLPHVLRRIGEMSKEFGLDVANVFHAGDGNMHPLILFDANKPGDLETCEAFGAEILKLCVEVGGCLTGEHGVGIEKRDLMLDQYGVADIEAQLRVKDVFDPKWLLNPAKVFPLSTTQSRRTPAVTPL catabolism Phaeobacter inhibens BS107 Phaeo GFF357 PGA1_c03680 PGA1_RS01815 WP_014879056.1 tr|I7ETR9|I7ETR9_PHAIB (3S)-malyl-CoA thioesterase [EC:3.1.2.30] Specifically important for: L-Threonine; Potassium acetate. This is part of the ethylmalonyl-CoA cycle for acetate assimilation, and hence is important on threonine (cleaved to glycine and acetate via the PGA1_c34330 or kbl) and acetate (where it has a milder phenotype). The annotation of sit:TM1040_3520 has been updated to (3S)-malyl-CoA thioesterase [EC:3.1.2.30]. 69% similar to MCTE_RHOS4 (consistent with the KEGG annotation). SEED suggests that this is the malyl-CoA/methylmalyl-CoA lyase but that activity is probably provided by PGA1_c30490. (KEGG_correct) putative citrate lyase subunit beta L-malyl-CoA/beta-methylmalyl-CoA lyase (EC 4.1.3.-) (3S)-malyl-CoA thioesterase MDPRIRPYRSVLYIPGSKLRALEKARSLPVDAIIFDLEDAVSAEEKVNARQTLEEALRAGGYGARMKIVRINGLDTVWGRADAAAAARMDCDAILLPKVSSPEDLDALAVITGDKPLWAMMETPRGMLNAAAIAAHPLLQGMVMGTNDLAKELQTRFRPDRLPLMAGLGQCLLAAKAKGIIIVDGVYNAFKDAEGLEAECDQGRDMGFDGKTLIHPAQVDVANSAFAPSEDEIDLARRQIAAFDAAEAEGQGVAVVDGKIVENLHVATAREILAKADAIAAVSA transporters Phaeobacter inhibens BS107 Phaeo GFF3639 PGA1_262p00430 PGA1_RS18345 WP_014881674.1 tr|I7F4G1|I7F4G1_PHAIB glucose transporter, periplasmic substrate-binding component specific phenotype on glucose and cofit with other nearby components. This is similar (65% identity) to gxyS (Atu3576) of Agrobacterium tumefaciens, which is involved in the transport of glucose, glucosamine, and xylose (PMCID: PMC4135649). It is not clear if the Phaeobacter system transports xylose, as it is not required for utilizing xylose, but no other xylose transport system was identified either. D-xylose-binding periplasmic protein XylF Xylose ABC transporter, periplasmic xylose-binding protein XylF D-xylose transport system substrate-binding protein MKFLSGVSALAFAATASMAFAEDVTVGVSWSNFQEERWKTDEAAIKAALEAKGATYVSADAQSSSAKQLSDIESLIAQGVDALIVLAQDAQAIGPAVQAAADEGIPVVAYDRLIEDGRAFYLTFDNVEVGRMQARAVLEAQPSGNYVMIKGSPTDPNADFLRGGQQEIIQAAIDSGDIKIVGEAYTDGWLPANAQRNMEQILTANDNKVDAVVASNDGTAGGVVAALTAQGMEGIAVSGQDGDHAALNRVAKGTQTVSVWKDARDLGKAAANIAVEMAEGAVMGDVAGGAAWTSPAGTELTARFLEPIPVTADNLSVVVDAGWITKEALCQGVTNGPAPCN transporters Phaeobacter inhibens BS107 Phaeo GFF3640 PGA1_262p00440 PGA1_RS18350 WP_014881675.1 tr|I7DWB0|I7DWB0_PHAIB glucose transporter, permease component specific phenotype on glucose and cofit with nearby xylF (PGA1_262p00430) and xylG (PGA1_262p00450). This is similar to the gxyB (Atu3575) of Agrobacterium tumefaciens, which is involved in the transport of glucose, glucosamine, and xylose (PMCID: PMC4135649). It is not clear if the Phaeobacter system transports xylose, as it is not required for utilizing xylose, but no other xylose transport system was identified either. xylose transport system permease protein XylH Xylose ABC transporter, permease protein XylH D-xylose transport system permease protein MTETTSQPIPEHSKRGLFQQLELDVRLLGMIGAFVILCIGFNILTDGRFLTPRNIFNLTIQTVSVAIMATGMVFVIVTRHIDLSVGALLATCSAVMAVVQTDVLPDMFGLGLNHPATWIITVAVGLAIGTLIGAFQGWMVGFLTIPAFIVTLGGFLVWRNVAWYLTDGQTIGPLDSTFLVFGGTSGTLGTTLSWVVGIVATLLALAALWNSRRAKQGHGFPVKPAWAEAVIAGSIAASILGFVAILNAYQIPARRLKRMMEAQGETMPEGLVVGYGLPISVLILIATAVVMTIIARRTRLGRYIFATGGNPDAAELSGINTRLLTVKIFALMGFLCALSAVVASARLANHSNDIGTLDELRVIAAAVIGGTALSGGFGTIYGAILGALIMQSLQSGMAMVGVDAPFQNIVVGTVLVAAVWIDILYRKRVGARI transporters Phaeobacter inhibens BS107 Phaeo GFF3641 PGA1_262p00450 PGA1_RS18355 WP_014881676.1 tr|I7F276|I7F276_PHAIB glucose transporter, ATPase component Important for utilizing glucose and cofit with the other components. This is similar (68% identity) to gxyA (Atu3574) of Agrobacterium tumefaciens, which is involved in the transport of glucose, glucosamine, and xylose (PMCID: PMC4135649). It is not clear if the Phaeobacter system transports xylose, as it is not required for utilizing xylose, but no other xylose transport system was identified either. sugar ABC transporter, ATP-binding protein D-xylose transport ATP-binding protein XylG D-xylose transport system ATP-binding protein MSTAKELRAAGATPLVEMKDISISFGGIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEIRVNGDKVEITNPRDARSHNIETIYQTLALADNLDAASNLFLGRELVTPFGLVDDSAMEAECRKIMNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALGPHETQMVAELIQQLKAQGIGIFLIDHDVNAVMELCDRASVMKNGQLVGTVDIDDVTDDDLLSMIILGKRPGEAAA catabolism Phaeobacter inhibens BS107 Phaeo GFF707 PGA1_c07220 PGA1_RS03580 WP_014879336.1 tr|I7EX64|I7EX64_PHAIB 5-keto-2-deoxy-D-gluconate-6 phosphate aldolase (EC 4.1.2.29) Specifically important for: m-Inositol. Part of inositol catabolism via 5-deoxyglucuronate (SEED_correct) putative 6-phospho-5-dehydro-2-deoxy-D-gluconate aldolase 5-keto-2-deoxy-D-gluconate-6 phosphate aldolase (EC 4.1.2.29) fructose-bisphosphate aldolase, class II MTIATLAEVLQPALRDGYAVAGLVTLGWEDMRAYVAAAEAEGVPVILQAGPSCRVHTPLPILGKMFRHLAEGASVPVVAHLDHGYTAEDCRIAIDSGFTSVMFDGSRNALDDNIAETAAIAGMAHAAGVSCEGEIGFVGYSGGEGSAGTDPEEARRFAQETGVDAMAISVGNVHLQQDKEGGLDIDRIRAIEAITEVPLVIHGGSGVPVAQRRMLARESRICKFNIGTELRMVFGAAMRDAVNSDPDRFDRVSILSETHDPVVAAARSVLRAFKGETQC catabolism Phaeobacter inhibens BS107 Phaeo GFF711 PGA1_c07260 PGA1_RS03600 WP_014879339.1 tr|I7DYC7|I7DYC7_PHAIB Myo-inositol 2-dehydrogenase (EC 1.1.1.18) Specifically important for: m-Inositol. The first step in inositol catabolism (SEED_correct) putative inositol 2-dehydrogenase Myo-inositol 2-dehydrogenase (EC 1.1.1.18) MVCGRVDLILRDVESQDTSFATGCKLNLMVWEARMTEIGIGILGGGYMGKAHAVAMAAVGAVFDTALRPRLEMVCATSPVSAERYRKAYGFQRATDDWQVLVNDPKVEAIVIASPQQTHRVVAEAAFALGKPVFCEKPLGASLADSRAMVAAAQSSGCPNMVGFNYIRTPASQYARQLIADGLIGEVTWFRGEHTEDFYADPDAPATWRTEGEANGTMGDLAPHMINGAMALIGPIAELIAEVETVHTDRPGGRVTNDDQGQLMCRFANGAMGQMFFSRIATGRKMGYAYEITGTKGAIRFDQEDQNALWLYLSEGDEATRGFRKILTGPAHPDYLPFCQGPGHGTGYQDQILIEARDFLRAIETQTPVWPTFEDGMAVNQVIAAAMAASEARSWQTVSTF transporters Phaeobacter inhibens BS107 Phaeo GFF715 PGA1_c07300 PGA1_RS03620 WP_014873819.1 tr|I7EJU1|I7EJU1_PHAIB Inositol transport system sugar-binding protein Specific phenotype on inositol and cofit with other nearby components (SEED_correct) ABC-type sugar transport system, periplasmic component Inositol transport system sugar-binding protein simple sugar transport system substrate-binding protein MTSIFKTFMLATTVAAAPMMLATTASAEGEKYILVSHAPDSDSWWNTIKNGIALAGEQMNVEVEYRNPPTGDLADMARIIEQAAASGPNGIITTLSDYDVLSGPIKAAVDSGVDVIIMNSGTPDQAREVGALMYVGQPEYDAGHAAGMRAKADGVGSFLCVNHYISSPSSTERCQGFADGLGVDLGDQMIDSGQDPAEIKNRVLAYLNTNPETDAILTLGPTSADPTLLALDENGMAGDIYFGTFDLGEEIVKGLKSGVINWGIDQQPFLQAYLPVVVLTNYHRYGVLPGNNINSGPGFVTKDGLEKVEEFAGEYR transporters Phaeobacter inhibens BS107 Phaeo GFF716 PGA1_c07310 PGA1_RS03625 WP_014873820.1 tr|I7DYD2|I7DYD2_PHAIB Inositol transport system permease protein Specific phenotype on inositol and cofit with other nearby components (SEED_correct) binding protein dependent transport system permease Inositol transport system permease protein simple sugar transport system permease protein MSDAPTQFAEDERIKTRSKFREAMIRPELGGIIGTITVFAMFLIFAGDSGMFNSQGVMNWSQISAQFMIIAVGACLLMIAGEFDLSVGSMIGFAGMLIAIFSVTLGWPVWLAILVTFAIATAIGALNGFIVVRTGLPSFIVTLAFLFILRGFAIYLPQTIERKTIIGGVADAAEGDWLAALFGGKILTGLFQWFGDNGWIAVFERGTRKGQPVVEGLPMLIVWAILLVIIGHVILTKTRFGNWIFAAGGDAEAARNSGVPVNRVKILMFMFTAFCATVFATCQVMEFGGAGSDRGLLKEFEAIIAVVIGGALLTGGYGSVLGAALGALIFGVVQQGLFFAGVESSLFRVFLGLILLFAVILNTYIRRVITGER transporters Phaeobacter inhibens BS107 Phaeo GFF717 PGA1_c07320 PGA1_RS03630 WP_014873821.1 tr|I7EX72|I7EX72_PHAIB Inositol transport system ATP-binding protein Specific phenotype on inositol and cofit with other nearby components (SEED_correct) sugar ABC transporter, ATP-binding protein Inositol transport system ATP-binding protein simple sugar transport system ATP-binding protein MSMSQPLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMMAGGQELATLEGSLGGTV catabolism Dechlorosoma suillum PS PS Dsui_0512 Dsui_0512 DSUI_RS02475 WP_014235627.1 tr|G8QFB6|G8QFB6_DECSP Methylmalonyl-CoA epimerase (EC 5.1.99.1) Important on proprionate; this makes sense because of the utilization of the (S)-methylmalonyl-CoA formed by propionyl-CoA carboxylase (SEED_correct) hypothetical protein Methylmalonyl-CoA epimerase (EC 5.1.99.1) lactoylglutathione lyase MSQRPFKVLGIQQIAIGGPSKDKLKTLWVDMLGLEVTGNFVSERENVDEDICAMGKGPFKVEVDLMQPLDPEKKPAVHTTPLNHVGLWIDDLPKAVEWLTANGVRFAPGGIRKGAAGFDICFLHPKGNEESPIGGEGVLIELVQAPAEVVDAFAKLAG catabolism Pseudomonas fluorescens FW300-N1B4 pseudo1_N1B4 Pf1N1B4_1109 A1D17_RS10255 WP_063341556.1 tr|A0A166N099|A0A166N099_PSEFL 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) Specifically important for: D-Galacturonic Acid monohydrate. ketoglutarate semialdehyde is an intermedate in the oxidation of galacturonate (SEED_correct) 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) aldehyde dehydrogenase (NAD+) VADAKRYDNYINGEWVSGADYSANINPSELTDTIGDYAKADLAQVHAAIDAARAAFPAWSTSGIQARHDSLDKVGTEILARREELGTLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLRLSGDYLPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVLKPADLVPGCAWALAEIISRAGFPAGVFNLVMGSGRVVGDALVQSPKVDGISFTGSVGVGRQIAVSCVSRQAKVQLEMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRFIVTAGIHDKFVEAMAERMKSIKVGHALKTGTDIGPVVSQAQLEQDLKYIDIGQSEGARLVSGGGLVACDTEGYFLAPTLFADSTAAMRISREEIFGPVANIVRVADYEAALAMANDTEFGLSAGIATTSLKYANHFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEFYTVVKTSYIGS catabolism Pseudomonas fluorescens FW300-N1B4 pseudo1_N1B4 Pf1N1B4_2254 A1D17_RS15975 WP_007897683.1 tr|A0A166NMU2|A0A166NMU2_PSEFL Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) Specifically important for: Putrescine Dihydrochloride. This is the first step in putrescine catabolism. Some close homologs are annotated as this by SEED, so not sure why it was missed. Also, another gene is annotated as this activity (Pf1N1B4_4354) but has no phenotype. Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) glutamine synthetase MNGVVRGKRIERTSLHKVYEKGINLPASLFALDINGSTVESTGLGLDIGDADRICYPIPDTLCNEPWQKRPTAQLLMTMHELEGDPFFADPREVLRQVVAKFDEMGLTICAAFELEFYLIDQENVNGRPQPPRSPISGKRPHSTQVYLIDDLDEYVDCLQDILEGAKEQGIPADAIVKESAPAQFEVNLHHVADPIKACDYAVLLKRLIKNIAYDHEMDTTFMAKPYPGQAGNGLHVHISILDKDGKNIFASEDPEQNAALRHAIGGVLETLPAQMAFLCPNVNSYRRFGAQFYVPNSPCWGLDNRTVAIRVPTGSSDAVRIEHRVAGADANPYLLMASVLAGVHHGLTNKIEPGAPVEGNSYEQNEQSLPNNLRDALRELDDSEVMAKYIDPKYIDIFVACKESELEEFEHSISDLEYNWYLHTV transporters Pseudomonas fluorescens FW300-N1B4 pseudo1_N1B4 Pf1N1B4_3431 A1D17_RS21835 WP_063342827.1 tr|A0A166PAW1|A0A166PAW1_PSEFL ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component Specific phenotype on L-Arginine; L-Citrulline. Arginine/ornithine ABC transporter, periplasmic arginine/ornithine binding protein Arginine/ornithine ABC transporter, periplasmic arginine/ornithine binding protein MKKLVLLGALALSVLSLPTFADEKPLKIGIEAAYPPFASKAPDGSIVGFDYDIGNALCEEMKVKCVWVEQEFDGLIPALKVRKIDAILSSMSITEDRKKSVDFTNKYYNTPARLVMKAGTAVSENLAELKGKNIGVQRGSIHERFAREVLAPLGAEIKPYGSQNEIYLDVAAGRLDGTVADATLLDDGFLKTDAGKGFAFVGPAFTDVKYFGDGVGIAVRKGDALKDKINTAIAAIRENGKYKQIQDKYFAFDIYGK transporters Pseudomonas fluorescens FW300-N1B4 pseudo1_N1B4 Pf1N1B4_3432 A1D17_RS21840 WP_063342828.1 tr|A0A162AX92|A0A162AX92_PSEFL ABC transporter for L-Arginine and L-Citrulline, permease component 1 Specific phenotypes on L-Arginine; L-Citrulline. Arginine/ornithine ABC transporter, permease protein AotQ Arginine/ornithine ABC transporter, permease protein AotQ arginine/ornithine transport system permease protein MLKGYGAVILDGVWLTLQLALSSMVLAIVLGLIGVALRLSPIRWLAWLGDLYSTVIRGIPDLVLILLIFYGGQDLLNRVAPMFGYDDYIDLNPLAAGIGTLGFIFGAYLSETFRGAFMAIPKGQAEAGMAYGMSSFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKAKQAADATREPFTFFLAVAAMYLVITSVSLLALRHLEKRYSVGVRAADL transporters Pseudomonas fluorescens FW300-N1B4 pseudo1_N1B4 Pf1N1B4_3433 A1D17_RS21845 WP_063342829.1 tr|A0A161Z5M0|A0A161Z5M0_PSEFL ABC transporter for L-Arginine and L-Citrulline, permease component 2 Specific phenotypes on L-Arginine; L-Citrulline. Arginine/ornithine ABC transporter, permease protein AotM Arginine/ornithine ABC transporter, permease protein AotM arginine/ornithine transport system permease protein MIFDYNVIWEALPLYLGGLVTTLKLLALSLFFGLLAALPLGLMRVSKQPVVNMSAWLFTYVIRGTPMLVQLFLIYYGLAQFEAVRESFLWPWLSSATFCACLAFAINTSAYTAEIIAGSLRATPNGEIEAAKAMGMSRIKMYKRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITGAARTVNAQFYLPFEAYITAGVFYLCLTFILVRLFKMAEHRWLGYLAPRKH transporters Pseudomonas fluorescens FW300-N1B4 pseudo1_N1B4 Pf1N1B4_3435 A1D17_RS21855 WP_007904680.1 tr|A0A166PAY4|A0A166PAY4_PSEFL ABC transporter for L-Arginine and L-Citrulline, ATPase component Very important for utilization of L-Arginine or L-Citrulline. Detrimental to fitness in some other minimal media experiments. Arginine/ornithine ABC transporter, ATP-binding protein AotP Arginine/ornithine ABC transporter, ATP-binding protein AotP MYKLEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLNNEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMSKTEAREKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPELVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQSERLQQFLSGSLK catabolism Pseudomonas fluorescens FW300-N1B4 pseudo1_N1B4 Pf1N1B4_412 A1D17_RS06770 WP_063341172.1 tr|A0A166MLN9|A0A166MLN9_PSEFL L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) Both of these sugars are catabolized via a 1-dehydrogenase followed by lactonase and dehydratase reactions. This is the only dehydrogenase is specifically important for either of these carbon sources in several Pseudomonas, apart from a alpha-ketoglutarate semialdehyde dehydrogenase that is expected to be the last dedicated step in L-arabinose catabolism (i.e., Pf6N2E2_612). L-arabinose and D-galactose are chemically similar and some dehydrogenases are already known to act on both substrates. 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100) 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100) MAEPLSLPPVPEPPKGERLKNKVVLLTGAAQGIGEAIVATFASQQARLVISDIQGEKVEKVAAHWREQGADVVAIKADVSRQQDLHAMARLAIELHGRIDVLVNCAGVNVFRDPLQMTEEDWHRCFAIDLDGAWYGCKAVLPQMIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGIRVNAIAPGYIETQLNVDYWNGFADPHAERQRAFDLHPPRRIGQPIEVAMTAVFLASDEAPFINASCITIDGGRSVMYHD catabolism Pseudomonas fluorescens FW300-N1B4 pseudo1_N1B4 Pf1N1B4_4511 A1D17_RS27145 WP_063343423.1 tr|A0A166Q345|A0A166Q345_PSEFL D-galacturonate dehydrogenase (EC 1.1.1.203) Important on D-galacturonate; KEGG now has pfo:Pfl01_3452 as uronate dehydrogenase which is correct but less specific (KEGG_correct) UDP-glucose 4-epimerase (EC 5.1.3.2) UDP-glucose 4-epimerase (EC 5.1.3.2) MTNTSPFNRLLLTGAAGGLGKVLRERLRPYANVLRLSDIANMAPAIDDREEVVPCDLADKQAVHQLVEGVDAILHFGGVSVERPFEEILGANICGVFHIYEAARRHGVKRVIFASSNHVIGFYKQDKTLDAHSPRRPDSYYGLSKSYGEDMASFYFDRYGIETVSIRIGSSFPEPQNRRMMSTWLSFDDMTQLLERALYTPNVGHTVVYGMSANKSVWWDNRFAAHLGFAPQDTSEVFREKVEAQPMPAEDDPARVYQGGAFVAAGPFGD catabolism Pseudomonas fluorescens FW300-N1B4 pseudo1_N1B4 Pf1N1B4_4623 A1D17_RS27665 WP_063343491.1 tr|A0A161Z7Y9|A0A161Z7Y9_PSEFL 2-dehydro-3-deoxy-L-arabinonate dehydratase (EC 4.2.1.43) # Specifically important in carbon source L-Arabinose. Similar to PA2216 from Pseudomonas aeruginosa (see PMC:PMC4038344) and to gguC or araD1 (Atu2345) from Agrobacterium tumefaciens (see PMC: PMC3232879), which also have this activity. In Agrobacterium, this reaction is proposed to be a step in L-arabinose oxidation. (Note that 2-keto-3-deoxy-L-lyxonate and 2-keto-3-deoxy-L-arabinonate are the same compound.) SUGAR TRANSPORTER SUGAR TRANSPORTER MRLVQFELSHGERRVGVVEDGLVREVRDARSVRDLALAAIEAGVNLEQQVQTLGLGISHDYSALLANLQILPPLDHPDPAHMLVSGTGLTHLGSASARDKMHQQAGDETAMTDTMRIFKWGVEGGKPATGQVGVQPEWFYKGDGSIVVRPGKPFPLPPFAEDAGEEPELSGLYVIGHDGKPYRLGFAVGNEFSDHVMERKNYLYLAHSKLRSCSYGPELRVGELPQHLAGTSRILRDGEVLWQNEFLSGEANMCHSLENLEYHHFKYSQFLRPGDVHIHFFGTATLSFADGIRTQPGDVFEISQAEFGAPLINGIEPVEAAFEPGTVGTL catabolism Pseudomonas fluorescens FW300-N1B4 pseudo1_N1B4 Pf1N1B4_597 A1D17_RS07755 WP_063341295.1 tr|A0A161YYW9|A0A161YYW9_PSEFL Isomerase for D-mannose and D-mannitol catabolism (probably D-mannose-6-phosphate or D-mannose isomerase) Specifically important for: D-Mannitol; D-Mannose. Often annotated as N-acylglucosamine 2-epimerase, but some homologs are annotated as D-mannose isomerase or D-mannose-6-phosphate isomerase, which would fit its phenotypes. (Mannitol is probably converted to mannose or mannose-6-phosphate.) The organism has a fructokinase (Pf1N1B4_4844, no data) which probably utilizes the resulting fructose if this is D-mannose isomerase. However data for close homologs suggests a phosphorylated substrate instead, so the substrate is uncertain. N-acylglucosamine 2-epimerase (EC 5.1.3.8) N-acylglucosamine 2-epimerase (EC 5.1.3.8) MDTFQPAFSSWLNAPAHQQWLAAEGLRLLAFAKAAKLAEGFGNLDEKGRLAANAQAETMNTARMTHSFAMAHIQGLPGFAELVDHGIQALSGPLRDAEHGGWFATPEHRDGNTGKAAYLHAFVALAASSAVVAQRPGAQALLDDAIHIIDSHFWSEEEGAMRESFNRDWSVEEAYRGANSNMHATEAFLALADVTEDNRWLIRAQRIVERVIHDHAAVNDYLVVEHFDRDWQPLRDYNYDNPADGFRPYGTTPGHGFEWARLLLHLEAARVQAGILTPGWLATDAQKLFDHNCRHGWDVDGAPGIVYTLDWDNRAVVRHRLHWTHAEASAAASALLKRTGDEQYERWYRLFWEFCDSHFIDRCDGSWHHELDPLNRPSADIWAGKPDLYHAWQAVLIPRLPLAPSMAIALAQLSQSVAV catabolism Pseudomonas fluorescens FW300-N1B4 pseudo1_N1B4 Pf1N1B4_6029 A1D17_RS02225 WP_063340417.1 tr|A0A166R3Y5|A0A166R3Y5_PSEFL uridine nucleosidase (EC 3.2.2.3) Important on uridine; annotated by SEED as for uridine and inosine; close homologs are important for utilizing uridine (SEED_correct) Inosine-uridine preferring nucleoside hydrolase (EC 3.2.2.1) Inosine-uridine preferring nucleoside hydrolase (EC 3.2.2.1) MQRYAQKLHHLLRSLLLLSLITATSAQAAEKIDLIIDTDPGADDVVALLFALASPDELNIRALTTVAGNVRLDKTSRNARLAREWAGREEVPVYAGAPKPMMRTPIYAENIHGKEGLSGVTVHEPKKGLAEGNAVNYLIDTLKTAKPHSITIAMLGPQTNLALALIQEPEIVQGIKEVVIMGGAHFNGGNITPVAEFNLFADPQAAEVVLKSGVKLTYLPLDVTHKILTSEARLKQIAALNNNASKLVGDILNEYVKGDMEHYGIPGGPVHDATVIAYLLKPELFTGRSVNVVVDSREGPTFGQTIVDWYDGLKAPKNAFWVESGDAQGFFDLLTQRLSRLK transporters Pseudomonas fluorescens FW300-N1B4 pseudo1_N1B4 Pf1N1B4_771 A1D17_RS08645 WP_063341404.1 tr|A0A162BIP5|A0A162BIP5_PSEFL ABC transporter for L-asparagine and L-glutamate, periplasmic substrate-binding component # Specifically important in carbon source L-Asparagine. Also important for glutamate utilization. Glutamate Aspartate periplasmic binding protein precursor GltI (TC 3.A.1.3.4) Glutamate Aspartate periplasmic binding protein precursor GltI (TC 3.A.1.3.4) glutamate/aspartate transport system substrate-binding protein MRIVPHILGAAIAAALISTPVFAAELTGTLKKIKESGTITLGHRDASIPFSYIADASGKPVGYSHDIQLKIVEAIKKDLDMPNLQVKYNLVTSQTRIPLVQNGTVDVECGSTTNNVERQQQVDFSVGIFEIGTKLLSKKDSAYKDFADLKGKNVVTTAGTTSERILKSMNADKQMGMNVISAKDHGESFQMLETGRAVAFMMDDALLAGEMAKAKKPTDWAVTGTAQSNEIYGCMVRKGDAPFKKAVDDAIIATYKSGEINKIYEKWFMQPIPPKGLNLMFPMSEELKALIANPTDKAADEKKS transporters Pseudomonas fluorescens FW300-N1B4 pseudo1_N1B4 Pf1N1B4_772 A1D17_RS08650 WP_008069477.1 tr|A0A166MU26|A0A166MU26_PSEFL ABC transporter for L-asparagine and L-glutamate, permease component 1 # Specifically important in carbon source L-Asparagine. Also important for glutamate utilization. We do not have fitness data for aspartate utilization - it may well transport aspartate as well. Also note that the aspariganase (Pf1N1B4_2023) is predicted to be cytoplasmic and is important for asparagine utilization, so we do not think that asparagine is converted to aspartate before uptake. Glutamate Aspartate transport system permease protein GltJ (TC 3.A.1.3.4) Glutamate Aspartate transport system permease protein GltJ (TC 3.A.1.3.4) glutamate/aspartate transport system permease protein MNYNWDWGVFFKSTGVGSEIYFDWYLSGLGWTIAIAVAAWIIALLLGSILGVMRTVPNRIVSGIATCYVELFRNVPLLVQLFIWYFLVPDLLPADIQEWYKQDLNPTTSAFLSVVVCLGLFTTARVCEQVRTGIQALPRGQEAAARAMGFKLPQIYWNVLLPQAYRIIIPPLTSEFLNVFKNSSVASLIGLMELLAQTKQTAEFSANLFEAFTLATLIYFTLNMSLMLLMRSVEKKVAVPGLISVGGK transporters Pseudomonas fluorescens FW300-N1B4 pseudo1_N1B4 Pf1N1B4_773 A1D17_RS08655 WP_063341405.1 tr|A0A166MU41|A0A166MU41_PSEFL ABC transporter for L-asparagine and L-glutamate, permease subunit 2 # Important for glutamate and asparagine utilization and cofit with other components Glutamate Aspartate transport system permease protein GltK (TC 3.A.1.3.4) Glutamate Aspartate transport system permease protein GltK (TC 3.A.1.3.4) glutamate/aspartate transport system permease protein MEFDFSGIIPSLPGLWNGMIMTLKLMALGVIGGIILGTILALMRLSHNKLLSNIAGAYVNYFRSIPLLLVITWFYLAVPFVLRWITGEDTPIGAFASCIVAFMMFEAAYFCEIVRAGVQSIPKGQMGAAQALGMEYGQMMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYAVGLVDFLNASRASGDIIGRSNEFLIFAGLTYFTISFAASLLVKRLQKRFAV transporters Pseudomonas fluorescens GW456-L13 pseudo13_GW456_L13 PfGW456L13_1894 AO361_RS09435 WP_057713549.1 ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component Specific phenotype on D-Fructose; L-Aspartic Acid; D-Galactose; L-Lysine. The nitrogen source phenotypes for aspartate and lysine are with glucose as the carbon source. May also transport fructose. Glucose ABC transport system, periplasmic sugar-binding protein Glucose ABC transport system, periplasmic sugar-binding protein multiple sugar transport system substrate-binding protein MNAISRLATVISLASLSALPLSVLAAESKGSVEVVHWWTSGGEKAAVDVLKAQVEKDGFTWKDGAVAGGGGSTAMTVLKSRAVAGNPPGVAQIKGPDIQEWGSTGLLSTDALKDVSKAENWDGLLSKKVSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGIEKAPTTLEEFYAAGDKLKAAGFIALAHGGQPWQDSTVFEDVVLSVMGADGYKKALVDLDQKTLSGPEMTKSFAELKKITGYMDPNRAGRDWNIAAADVISGKAGMQMMGDWAKSEWTAAKKIAGKDYQCVAFPGTEKAFTYNIDSMAVFKLKADRKGDIAAQQDLAKVALGTDFQKVFSMNKGSIPVRNDMLNEMDKLGFDECAQKSAKDFIADDKTGGLQPSMAHNMATSLAVQGAIFDVVTNFMNDKDADPAKASAQLASAVKAAQ transporters Pseudomonas fluorescens GW456-L13 pseudo13_GW456_L13 PfGW456L13_1895 AO361_RS09440 WP_057713550.1 ABC transporter for D-Galactose and D-Glucose, permease component 1 Specific phenotypes on D-Galactose; N L-Lysine. glucose is the C source for the N source experiments with a phenotype (i.e. lysine); may also transport fructose. Glucose ABC transport system, inner membrane component 1 Glucose ABC transport system, inner membrane component 1 multiple sugar transport system permease protein MSSVAVFSKASPFDALQRWLPKLVLAPSMLIVLVGFYGYIIWTFILSFTNSSFMPSYKWVGLQQYMRLMDNDRWWVASKNLALFGGMFISISLVLGVFLAVLLDQRIRKEGFIRTVYLYPMALSMIVTGTAWKWLLNPGLGLDKMLRDWGWEGFRLDWLVDQDRVVYCLVIAAVWQASGFVMAMFLAGLRGVDQSIIRAAQVDGASLPTIYLKIVLPSLRPVFFSAFMILAHIAIKSFDLVAAMTAGGPGYSSDLPAMFMYSFTFSRGQMGIGSASAMLMLGAVLTILVPYLYSELRGKRHD transporters Pseudomonas fluorescens GW456-L13 pseudo13_GW456_L13 PfGW456L13_1896 AO361_RS09445 WP_007974434.1 ABC transporter for D-Galactose and D-Glucose, permease component 2 Specific phenotypes on D-Galactose; N L-Lysine. glucose is the C source for the N source experiments with a phenotype (i.e. lysine); may also transport fructose. Glucose ABC transport system, inner membrane component 2 Glucose ABC transport system, inner membrane component 2 multiple sugar transport system permease protein MTNQLGKSGISFSRIAIYATLLLAAAVYLIPLVVMLLTSFKSPEDIRTGNLLSWPTVIDGIGWIKAWDVVGGYFWNSVKITVPAVLISTFIGAMNGYVLSMWRFRGSQLFFGLLLFGCFLPFQTVLLPASFTLGKFGLANTTTGLVLVHVVYGLAFTTLFFRNYYVSIPDALVKAARLDGAGFFTIFLKILLPMSIPIVMVCLIWQFTQIWNDFLFGVVFASGDAQPITVALNNLVNTSTGAKEYNVDMAAAMIAGLPTLLVYIFAGKYFLRGLTSGAVKG transporters Pseudomonas fluorescens GW456-L13 pseudo13_GW456_L13 PfGW456L13_1897 AO361_RS09450 WP_057713551.1 ABC transporter for D-Galactose and D-Glucose, ATPase component Specific phenotype on D-Galactose; L-Lysine; L-Aspartic Acid. The nitrogen source phenotypes for aspartate and lysine are with glucose as the carbon source. May also transport fructose. Glucose ABC transporter, ATP-binding subunit (EC 3.6.3.-) Glucose ABC transporter, ATP-binding subunit (EC 3.6.3.-) multiple sugar transport system ATP-binding protein MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSKLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPPMNFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQIILANGEANGLPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVGETLTLQFDPAKVLLFDAKTGERLGVAGVPKAEAHADNVAQFKGR catabolism Pseudomonas fluorescens GW456-L13 pseudo13_GW456_L13 PfGW456L13_2119 AO361_RS10555 WP_057713727.1 L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) Specifically important for: D-Galactose; L-Arabinose. Both of these sugars are catabolized via a 1-dehydrogenase followed by lactonase and dehydratase reactions. This is the only dehydrogenase is specifically important for either of these carbon sources in several Pseudomonas, except for an alpha-ketoglutarate semialdehyde dehydrogenase that is expected to be the last dedicated step in L-arabinose catabolism (i.e., Pf6N2E2_612). L-arabinose and D-galactose are chemically similar and some dehydrogenases are already known to act on both substrates. 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100) 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100) MAEPLSLPPVPEPPRGERLKNKVVLLTGAAQGIGEAIVATFASQQARLIISDIQGEKVEKVAAHWRDQGADVVAIKADVSRQQDLHAMARLAIDLHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYGCKAVLPQMIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVNAIAPGYIETQLNVDYWNGFADPHAERQRAFDLHPPRRIGQPIEVAMTAVFLASDEAPFINASCITIDGGRSVMYHD catabolism Pseudomonas fluorescens GW456-L13 pseudo13_GW456_L13 PfGW456L13_2867 AO361_RS14290 WP_057714593.1 D-glucosaminate dehydratase (EC 4.3.1.9) Specifically important for: D-Glucosamine Hydrochloride. This enzyme had not previously been linked to a gene. This is the second step in catabolism of glucosamine, and the 'beta' form of the enzyme was expected to be PLP-dependent and about this size. Iwamoto et al (2003) purified a non-specific 'alpha' enzyme for this reaction (PMID: 12686150) D-serine deaminase (EC 4.3.1.18) D-serine deaminase (EC 4.3.1.18) MSSAPNTAAVEKGTAPKGASLVRDVSLPALVLHREALEHNIRWMQAFVSDSGAELAPHGKTSMTPALFRRQLDAGAWGITLASATQTRAAYAHGVRRVLMANQLVGTPNMALIADLLADPTFDFYCMVDHPDNVADLGAYFASRGVRLNVMIEYGVVGGRCGCRSEQQVLDLAKAIAAQPALALTGIEGYEGVIHGDHAVTGIRDFAASLVRLAVQLQDSGAFAIPKPIITASGSAWYDLIAESFEAQNAAGRFLSVLRPGSYVAHDHGIYKEAQCCVLDRRSDLHEGLRPALEVWAHVQSLPEPGFAVIALGKRDVAYDAGLPVPLLRYKAGVVPAEGDDVSVCKVTAVMDQHAFMTVAPGVDLRVGDIISFGTSHPCLTFDKWRVGCLVDEQLNVIETMETCF catabolism Pseudomonas fluorescens GW456-L13 pseudo13_GW456_L13 PfGW456L13_2985 AO361_RS14885 WP_057714718.1 isobutyrl-CoA dehydrogenase (EC 1.3.8.1) Specifically important for: L-Valine. Isobutyryl-CoA is an intermediate in valine degradation. SEED annotates it as butyryl-CoA dehydrogenase, which is also expected to perform this reaction Butyryl-CoA dehydrogenase (EC 1.3.99.2) Butyryl-CoA dehydrogenase (EC 1.3.99.2) MHDIELSEEQVMIRDMARDFARGEIAPHAQAWEKAGWIDDGLVAKMGELGLLGMVVPEEWGGTYVDYVAYALAVEEISAGDGATGAFMSIHNSVGCGPVLNYGSEEQKQTWLADLASGQVIGCFCLTEPQAGSEAHNLRTRAELRDGQWVINGAKQFVSNGKRAKLAIVFAVTDPDLGKRGISAFLVPTDTAGFIVDRTEHKMGIRASDTCAVTLNNCTIPEANLLGERGKGLAIALSNLEGGRIGIAAQALGIARAAFEAALAYSRDRVQFGKAINEHQSIANLLADMHMQLNAARLMILHAARLRTAGKPCLSEASQAKLFASEMAEKVCSSAIQIHGGYGYLEDYPVEKYYRDARITQIYEGSSEIQRMVIARELKNYLI transporters Pseudomonas fluorescens GW456-L13 pseudo13_GW456_L13 PfGW456L13_3039 AO361_RS15130 WP_057714764.1 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component Specific phenotype on D-Mannitol; D-Mannose. Various polyols ABC transporter, ATP-binding component Various polyols ABC transporter, ATP-binding component sorbitol/mannitol transport system ATP-binding protein MANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGGTIELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVSEAARILELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLRLHKELQATMIYVTHDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPKMGFLKGKITRVDSQGCEVQLDAGTRVSLPLGGRHLSVGSAVTLGIRPEHLELAKPGDCALQVTADVSERLGSDTFCHVRTASGEALTMRVRGDLASRYGETLSLHLDAQHCHLFDADGVALTRPLRVAA transporters Pseudomonas fluorescens GW456-L13 pseudo13_GW456_L13 PfGW456L13_3040 AO361_RS15135 WP_057714765.1 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, permease component 1 Specific phenotypes on D-Mannitol; D-Mannose; D-Mannose Various polyols ABC transporter, permease component 2 Various polyols ABC transporter, permease component 2 sorbitol/mannitol transport system permease protein MTLQQSRRLQSLLLGTLAWAIAILIFFPIFWMVLTSFKTEIDAFATPPQFIFMPTLENYLHINERSDYFSFAWNSVVISFSATALCLLIAVPAAYSMAFYETQRTRGTLLWMLSTKMLPPVGVLMPIYLLAKSFGLLDTRIALIVIYTLINLPIVVWMIYTYFKDIPRDILEAARLDGATLAQEMLRVLLPIAKGGLASTVLLSLILCWNEAFWSLNLTSSKAAPLTALIASYSSPEGLFWAKLSAVSTLACAPILIFGWISQKQLVRGLSFGAVK transporters Pseudomonas fluorescens GW456-L13 pseudo13_GW456_L13 PfGW456L13_3041 AO361_RS15140 WP_046042047.1 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, permease component 2 Specific phenotypes on D-Mannitol; D-Mannose; D-Mannose Various polyols ABC transporter, permease component 1 Various polyols ABC transporter, permease component 1 sorbitol/mannitol transport system permease protein MDIAQPQRKSRVANPGWFLVSPSVALLLLWMIVPLGMTVYFSTIRYNLLNPGENEFVGLENFTYFLTDSGFLPGATNTLLLVGSVLLISVVFGVLISALLEASEFFGRGIVRVMLISPFFIMPTVGALIWKNLIFHPVSGILAYVWKLFGAQPVDWLAHYPLLSIIIIVSWQWLPFAILILMTAMQSLDQEQKEAARLDGAGPIAIFWHLTLPHLARPIAVVVMIETIFLLSVFAEIFTTTNGGPGYASTNLAYLIYNQALVQFDVGMASAGGLIAVVIANIAAIILVRMIGKNLTDKA transporters Pseudomonas fluorescens GW456-L13 pseudo13_GW456_L13 PfGW456L13_3042 AO361_RS15145 WP_057714766.1 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, periplasmic substrate-binding component Specific phenotype on D-Mannose; D-Mannitol. Various polyols ABC transporter, periplasmic substrate-binding protein Various polyols ABC transporter, periplasmic substrate-binding protein sorbitol/mannitol transport system substrate-binding protein MQPSVKALLALTCMTLSSVSLGAQTLTIATVNNSDMIRMQKLSKTFEAEHPDIKLNWVVLEENVLRQRLTTDIATQGGQFDVLTIGMYEAALWGAKGWLEPMKDLPAGYALDDVFASVREGLSVKGQLYALPFYAESSITYYRTDLFKDAGLTMPERPTWEQIGEFAAKLNKPEQEQYGICLRGKAGWGENIALISTVANAYGARWFDEKWQPEFNGPEWKNALNFYVDTMKKSGPPGASSNGFNENLALFNSGKCAIWVDASVAGSFVTDKSQSKVTDHVGFTYAPHQVTDKGSAWLYSWALAIPTSSKAKDAAKTFSAWATSKEYGALVAEKDGIANVPPGTRASTYSEAYMSAAPFARVTLESLKAADPSKPGTRPVPYIGIQLVTIPEFQGIGTQVGKSFSAALIGQTTVDQALAAAQQTTEREMKRAGYPK catabolism Pseudomonas fluorescens GW456-L13 pseudo13_GW456_L13 PfGW456L13_3314 AO361_RS16495 WP_057715013.1 D-galactono-lactonase (EC 3.1.1.-) Specifically important for: D-Galactose. A 1,5-lactone is probably the product of D-galactose dehydrogenase (PfGW456L13_2119), althought it might rearrange to a 1,4-lactone. Related to E. coli ybhE or pgl, which is 6-phospho-D-glucono-1,5-lactonase. 3-carboxymuconate cyclase 3-carboxymuconate cyclase MRNLWPLLMAGSIGAMGVQVASAEDYQLLVGSYTAGQSQGIYRLAFDSRTGQIDASPLQVIKSANPSWLTLSKDQRHLFVVNENGPGQTDPVGRVSSFAIDPKTHALSLISQVQSLGNEPTHSSLSIDGSHLFVSNYSVAEDPGGTLAVLPVAADGKLKAVVQMSSHPASRVNPERQASAHVHSTIPSPDGRYVFANDLGADKVFAYRFDPKANPELPLTPATPAFVQLPPGSGPRHLLFSADGKHAWLTMEMSAQVAVFDYHDGQLEQTQMVDLAAGQPVSDKAAAALHASADGKFLYVSNRGTANQLLVFAIDPATGHLSELQRRAVEGDHPREFSLDPSGKFLLIANQKSNQIVVVERDARTGLLGKTVQKLPMDAPSDLRFLLRQ catabolism Pseudomonas fluorescens GW456-L13 pseudo13_GW456_L13 PfGW456L13_3317 AO361_RS16510 WP_057715016.1 2-dehydro-3-deoxy-L-arabinonate dehydratase (EC 4.2.1.43) # Specifically important in carbon source L-Arabinose. Similar to PA2216 from Pseudomonas aeruginosa (see PMC:PMC4038344) and to gguC or araD1 (Atu2345) from Agrobacterium tumefaciens (see PMC: PMC3232879), which also have this activity. In Agrobacterium, this reaction is proposed to be a step in L-arabinose oxidation. (Note that 2-keto-3-deoxy-L-lyxonate and 2-keto-3-deoxy-L-arabinonate are the same compound.) SUGAR TRANSPORTER SUGAR TRANSPORTER MRLVQFELSNGERRVGVVEAGLVREVQDTRTVRDLALAAIEASASLEQQVQSLGLGISHDYAELLTQRRILPPLDHADPAHMLVSGTGLTHLGSASARDKMHQQSGDETAMTDTMRIFKWGVEGGKPAVDEAGVQPEWFYKGDGGIVVRPGQPFPLPPFAEDAGEEPEIAGLYVIGHDGKPYRLGFAVGNEFSDHVMERKNYLYLAHSKLRSCSYGPELRVGELPQHLAGTSRILRDGEVLWQNEFLSGEANMCHSLANLEFHHFKYSQFLRPGDVHIHFFGTATLSFADGIRTQPGDVFEITQAEFGAPLINGIAPVAAAFEPGTVGTL catabolism Pseudomonas fluorescens GW456-L13 pseudo13_GW456_L13 PfGW456L13_4396 AO361_RS21975 WP_057715924.1 tyrosine aminotransferase (EC 2.6.1.57) Specifically important for: L-Phenylalanine. Phenylalanine is hydroxylated to tyrosine (by PfGW456L13_4394) before deamination. KEGG has same EC# but less specific Aspartate aminotransferase (EC 2.6.1.1) Aspartate aminotransferase (EC 2.6.1.1) aromatic-amino-acid transaminase MHFDAIGRVPGDPILGLMEAYAQDPNPRKFDLGVGVYKDAQGLTPILESVKLAEQRLVDHQSTKTYIGGHGEPAFGKAINELVLGADSKLISAQRAGATQTPGGTGALRLSADFIAQCLPGRGVWLSNPTWPIHETIFAAAKVKVSHYPYVGSDNRLDVDGMLAALNEAPKGDVVLLHACCHNPTGFDLSQDDWQRVLEVVRKRELLPLIDFAYQGFGDGLEQDAWSTRLFAAELPELLITSSCSKNFGLYRDRTGALIVCAKTADKLVDIRSQLANIARNLWSTPPDHGAAVVATILGDPELKRLWADEVEAMRLRIAQLRSGLVEALEPHGLRERFAHIGVQRGMFSYTGLSPEQVKNLRDHHSVYMVSSGRANVAGIDATRLDLLAEAIASVCK transporters Pseudomonas fluorescens GW456-L13 pseudo13_GW456_L13 PfGW456L13_4770 AO361_RS23845 WP_046041277.1 ABC transporter for L-Asparagine and possibly other L-amino acids, periplasmic substrate-binding component Specific phenotype on L-Asparagine; Sodium octanoate. Detrimental on glutamine and might leak it. The mild phenotype on octanoate is not explained. Glutamate Aspartate periplasmic binding protein precursor GltI (TC 3.A.1.3.4) Glutamate Aspartate periplasmic binding protein precursor GltI (TC 3.A.1.3.4) glutamate/aspartate transport system substrate-binding protein MRIVPHILGAAIAAALISTPVFAAELTGTLKKIKESGTITLGHRDASIPFSYIADASGKPVGYSHDIQLKVVEALKKDLDMPNLQVKYNLVTSQTRIPLVQNGTVDLECGSTTNNVERQQQVDFSVGIFEIGTRLLSKADSKYKDFPDLAGKNVVTTAGTTSERILKAMNADKQMGMNVISAKDHGESFQMLETGRAVAFMMDDALLAGEAAKAKKASDWAVTGTPQSYEIYGCMVRKGDEPFKKAVDDAIKATYASGEINKIYEKWFMQPIPPKGLNLNFPMSDELKALIAKPTDKAADDKKS transporters Pseudomonas fluorescens GW456-L13 pseudo13_GW456_L13 PfGW456L13_4771 AO361_RS23850 WP_057716225.1 ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 1 Specific phenotypes on L-Asparagine; L-Asparagine. also has weak phenotypes on other a.a., but not on aspartate; weak phenotype on glutamate; also is detrimental during growth on glutamine (along with a downstream HK-RR), which could imply that it leaks glutamate; ko:K10003 : glutamate/aspartate transport system permease protein Glutamate Aspartate transport system permease protein GltJ (TC 3.A.1.3.4) Glutamate Aspartate transport system permease protein GltJ (TC 3.A.1.3.4) glutamate/aspartate transport system permease protein MNYNWDWGVFFKSTGVGSETYFDWYVTGLAWTIGIAIAAWIIALTLGSILGVMRTVPNRIVSGIATCYVELFRNVPLLVQLFIWYFLVPDLLPADLQEWYKQDLNPTTSAFLSVVVCLGLFTTARVCEQVRTGIQALPKGQESAARAMGFKLPQIYWNVLLPQAYRIIIPPLTSEFLNVFKNTSVASLIGLMELLAQTKQTAEFSANLFEAFTLATLIYFTLNMSLMLLMRVVEKKVAVPGLISVGGK transporters Pseudomonas fluorescens GW456-L13 pseudo13_GW456_L13 PfGW456L13_4772 AO361_RS23855 WP_057716226.1 ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 2 Specific phenotypes on L-Asparagine; L-Asparagine. also has weak phenotypes on other a.a., but not on aspartate; weak phenotype on glutamate; also is detrimental during growth on glutamine (along with a downstream HK-RR), which could imply that it leaks glutamate; K10002 : glutamate/aspartate transport system permease protein Glutamate Aspartate transport system permease protein GltK (TC 3.A.1.3.4) Glutamate Aspartate transport system permease protein GltK (TC 3.A.1.3.4) glutamate/aspartate transport system permease protein MEFDFSGIIPSLPGLWNGMIMTLKLMAMGVIGGIILGTILALMRLSHNKVLSNIAGAYVNYFRSIPLLLVITWFYLAVPFVLRWITGEDTPIGAFASCIVAFMMFEAAYFCEIVRAGVQSIPKGQMGAAQALGMSYGQMMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYAVGLVDFLNASRASGDIIGRSNEFLIFAGLVYFIISFAASQLVKRLQKRFAV catabolism Pseudomonas fluorescens GW456-L13 pseudo13_GW456_L13 PfGW456L13_805 AO361_RS03965 WP_057712751.1 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) Specifically important for: Putrescine Dihydrochloride. Part of the gamma-glutamyl-putrescine pathway. Annotated as aldehyde dehydrogenase in SEED and as the 4-guanidino enzyme in KEGG (based on studies of PA5312 = kauB). Since this enzyme is closely related to kauB it is probably flexible. Aldehyde dehydrogenase (EC 1.2.1.3) Aldehyde dehydrogenase (EC 1.2.1.3) 4-guanidinobutyraldehyde dehydrogenase / NAD-dependent aldehyde dehydrogenase MTTLTRADWEQRARDLKIEGRAYINGEYTDAVSGETFECISPVDGRLLGKIASCDAADAQRAVENARATFNSGVWSRLAPTKRKSTMIRFAGLLKQHAEELALLETLDMGKPISDSLYIDVPGAAQALSWSGEAIDKIYDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVILKPSEKSPLTAIRIAELAVEAGIPKGVLNVLPGYGHTVGKALALHNDVDTLVFTGSTKIAKQLLIYSGESNMKRVWLEAGGKSPNIVFADAPNLQDAAEAAAGAIAFNQGEVCTAGSRLLVERSIKDKFLPLVIEALKAWKPGNPLDPATNVGALVDTQQMNTVLSYIESGHADGARLVAGGKRTLQETGGTYVEPTIFDGVSNAMKIAQEEIFGPVLSVIEFDSAEEAIAIANDTPYGLAAAVWTADISKAHLTARALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFDKYTELKATWIKL catabolism Pseudomonas fluorescens GW456-L13 pseudo13_GW456_L13 PfGW456L13_925 AO361_RS04565 WP_053163627.1 Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) Specifically important for: Putrescine Dihydrochloride. The first step in putrescine catabolism. (SEED_correct) Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) glutamine synthetase MSVPPRAVQLNEANAFLKEHPEVLYVDLLIADMNGVVRGKRIERTSLHKVYEKGINLPASLFALDINGSTVESTGLGLDIGDADRICYPIPDTLCNEPWQKRPTAQLLMTMHELEGEPFFADPREVLANVVRKFDEMGLTICAAFELEFYLIDQENVNGRPQPPRSPVSGKRPHSTQVYLIDDLDEYVDCLQDILEGAKEQGIPADAIVKESAPAQFEVNLHHVADPIKACDYAVLLKRLIKNIAYDHEMDTTFMAKPYPGQAGNGLHVHISILDKDGKNIFASEDPEQNAALRHAIGGVLETLPAQMAFLCPNVNSYRRFGAQFYVPNSPCWGLDNRTVAIRVPTGSADAVRIEHRVAGADANPYLLMASVLAGVHHGLTNKIEPGAPVEGNSYEQNEQSLPNNLRDALRELDDSEVMAKYIDPKYIDIFVACKESELEEFEHSISDLEYNWYLHTV transporters Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_03040 AO353_03040 AO353_RS03040 WP_019693166.1 tr|A0A0N9W776|A0A0N9W776_PSEFL ABC transporter for L-Arginine and L-Citrulline, ATPase component Specific phenotype on L-Arginine. Also important on citrulline. amino acid transporter Arginine/ornithine ABC transporter, ATP-binding protein AotP MYKLEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLNNEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMSKAEAREKAELYLAKVGVSHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPELVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQSERLQQFLSGSLK transporters Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_03045 AO353_03045 AO353_RS03045 WP_019693167.1 tr|A0A0N9W128|A0A0N9W128_PSEFL ABC transporter for L-Arginine and L-Citrulline, permease component 1 Specific phenotypes on L-Arginine; L-Arginine. also important for citrulline amino acid ABC transporter permease Arginine/ornithine ABC transporter, permease protein AotM arginine/ornithine transport system permease protein MIFDYNVIWEALPLYFGGLVTTLKLLALSLLFGLLAALPLGLMRVSKQPIVNMSAWLYTYVIRGTPMLVQLFLIYYGLAQFEAVRESFLWPWLSSATFCACLAFAINTSAYTAEIIAGSLRATPNGEIEAAKAMGMSRFKMYKRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITGAARTVNAQYYLPFEAYITAGVFYLCMTFILVRLFKMAEHRWLGYLAPRKH transporters Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_03050 AO353_03050 AO353_RS03050 WP_019693168.1 tr|A0A0N9WAY7|A0A0N9WAY7_PSEFL ABC transporter for L-Arginine and L-Citrulline, permease component 2 Specific phenotypes on L-Arginine; L-Arginine; L-Arginine. possibly citrulline as well ABC transporter Arginine/ornithine ABC transporter, permease protein AotQ MLKGYGAVILDGAWLTLQLALSSMALAIVLGLIGVALRLSPIRWLARLGDLYSTVIRGIPDLVLILLIFYGGQDLLNRVAPLLGYDDYIDLNPLVAGIGTLGFIFGAYLSETFRGAFMAIPKGQAEAGAAYGMSSFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKAKQAADATREPFTFFLAVAAMYLVITSVSLLALRHLEKRYSVGVRAADL transporters Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_03055 AO353_03055 AO353_RS03055 WP_054593623.1 tr|A0A0N7GZD9|A0A0N7GZD9_PSEFL ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component Specific phenotype on L-Arginine; L-Citrulline. ABC transporter substrate-binding protein Arginine/ornithine ABC transporter, periplasmic arginine/ornithine binding protein arginine/ornithine transport system substrate-binding protein MKKLVLLGALALSVLSLPTFADEKPLKIGIEAAYPPFASKAPDGSIVGFDYDIGNALCEEMKVKCVWVEQEFDGLIPALKVRKIDAILSSMSITDDRKKSVDFTNKYYNTPARLVMKAGTQVSDNLAELKGKKIGVQRGSIHNRFAEEVLKPLGAEIKPYGSQNEIYLDVAAGRLDGTVADATLLDDGFLKTDSGKGFAFVGPAFTDEKYFGDGIGIAVRKGDKAELDKINAAIVAIRANGKYKQIQDKYFNFDIYGK catabolism Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_03400 AO353_03400 AO353_RS03400 WP_054593685.1 tr|A0A0N9WB79|A0A0N9WB79_PSEFL Isomerase for D-mannose and D-mannitol catabolism (probably D-mannose-6-phosphate isomerase or D-mannose isomerase) Specifically important for: D-Mannitol; D-Mannose. This has a conserved phenotype on mannose and mannitol (which is probably catabolized via mannose or mannose-6-P, although we did not identify the dehydrogenase). Some homologs are annotated as D-mannose isomerase or D-mannose-6-P isomerase. We suspect that the putative fructokinase (AO353_25910) is actually mannose kinase, which would complete the pathway for mannose utilization if this is D-mannose-6-P isomerase (forming fructose-6-phosphate). Also, some close homologs of the 'fructokinase' are detrimental during growth on fructose, which suggests that it is not actually fructokinase. However, data for close homologs suggests D-mannose as the substrate of this enzyme, so the exact role is uncertain. (Also, another gene is annotated as a potential mannose-6-P isomerase (AO353_13390) but is not important for utilizing mannose or mannitol.) sugar isomerase N-acylglucosamine 2-epimerase (EC 5.1.3.8) MNTAPPAFSSWLNAPAHQQWLADEGLRLLAFAKASKLPEGFGNLDEHGQLPADAQAHTMNTARMTHSFAMAHIQGLPGFAELVDHGINALNGLLRDAEFGGWFAAPDHRDGDTGKAAYLHAFVALAASSAVIAQRPGAEALLNDAIAIIEQHFWSEEEGAMRESFNRDWSEEEPYRGANSNMHATEAFLALADVTQDSRWLNRALRIVERVIHRHAASNDHLVVEHFDRDWQPLRDYNQANPADHFRPYGTTPGHGFEWSRLLLHLEAARGQAGMLTPGWLLSDAQQLFANNCLHGWDVDGAPGIVYTLDWDNRPVVRQRLHWVHCEASAAASVLLKRTGEAQYETWYRRFWEFSDRCLIDRIHGSWHHELDPQNRPSTEIWGGKPDLYHAWQAVLIPRLPLAPSMASALAQGSVSVLM transporters Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_03810 AO353_03810 AO353_RS03810 WP_054593749.1 tr|A0A0N9WF03|A0A0N9WF03_PSEFL Alpha-ketoglutarate permease, MFS superfamily Specific phenotype on a-ketoglutarate. 86% identical to the a-ketoglutarate transporter in P. aeruginosa (PA5530, see PMCID: PMC4097582) and 56% similar to E. coli kgtP. (KEGG_correct) MFS transporter Dicarboxylate MFS transporter MFS transporter, MHS family, alpha-ketoglutarate permease MDNSQTLPLGSAAVPAKEKTTASRIKSIFSGSVGNMVEWYDWYVYAAFSLYFAKAFFPKGDTTAQLLNTAAIFAVGFLMRPIGGWLMGLYADRAGRKAALMASVYLMCFGSLIIALSPGYETIGVGAPILLVFARLLQGLSVGGEYGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALGVLIVLQQTLTTEQLYDWGWRIPFAIGALCAIVALYLRRGMEETESFAKKEKSKESAMRTLLRHPKELMTVVGLTMGGTLAFYTYTTYMQKYLVNTVGMSISDSTTISAATLFLFMCLQPIIGGLSDKVGRRPILIAFGILGTLFTVPILTTLHTIQTWWGAFFLIMAALIIVSGYTSINAVVKAELFPTEIRALGVGLPYALTVSIFGGTAEYIALWFKSIGMETGYYWYVTACIAVSLLVYVTMKDTRKHSRIETD transporters Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_04460 AO353_04460 AO353_RS04460 WP_054593864.1 tr|A0A0N9WFD8|A0A0N9WFD8_PSEFL N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) Specifically important for NAG utilization. (SEED_correct) PTS N-acetyl-D-glucosamine transporter PTS system, glucose-specific IIA component / Phosphotransferase system, phosphocarrier protein HPr / Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9) phosphocarrier protein MHNNNKDLTLSAPLSGPVLTLAKVPDPVFASGAMGDGIAIDPLNNTLHAPCAGVVVHVARTGHAVTLRADNGAELLLHLGLDTVELQGEGFSMLVKEGTRVSNGQALLRFDLDQVAQGCKSLVSLLVLTNSEDFQVLPITLKSVKVGEPLLHIVPRTTHSAQVEADSSGAEVHGHIRIIHRGGLHARPAALIRQTAHLFNSKSQLHFAGKSASCDSLIGLMGLGIGEQDEVQVSCKGADAKAALQALLNALSTAVNDDSHAAAPTPIAQRTRTAEAGVLNGVCAAPGLVGGPLFQLAAIPLPEDTGKHNAEEQLQALDRALEQVRSEIRETLSHAKKHKHTEEEQIFAAHLALLEDPALLEAAIQSIDQGSAATHAWSQSIEAQCEVLQQLGNPLLAERANDLRDLRQRVLRALLGQDWHYDVPAGAIVAAHELTPSDLLQLSQQGVAGLCMAEGGATSHVAILARGKGLPCLVALSASLLQQPQGQSVVLDADGGRLELTPDSQRLEQVAQAQREHLQRRERQQAQAHTPAHTRDGLRIEVAANVASSNEAADALKGGADGVGLLRTEFLFVDRQTAPDEQEQRQAYQAVLDAMGDKSVIIRTIDVGGDKQLDYLPLPAEANPVLGLRGIRMAQVRPELLDQQLRALLQVSPLQRCRILLPMVTEVDELLYIRQRLDALCAELALTQRLELGVMIEVPAAALLAEQLAEHADFLSIGTNDLSQYTLAMDRDHAGLAARVDALHPALLRLIAQTCIGAAKHQRWVGVCGALASDPLATPVLIGLGISELSVSPPQVGEIKERVRQLDAADCRRFSATLLNLSSATAVRHACHQHWPLS transporters Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_04465 AO353_04465 AO353_RS04465 WP_054593865.1 tr|A0A0N9VKH1|A0A0N9VKH1_PSEFL N-acetylglucosamine-specific PTS system, IIBC components (nagE) Specifically important for NAG utilization. SEED incorrectly implies that this contains the IIA component as well. (KEGG_correct) PTS N-acetyl-D-glucosamine transporter PTS system, N-acetylglucosamine-specific IIA component (EC 2.7.1.69) / PTS system, N-acetylglucosamine-specific IIB component (EC 2.7.1.69) / PTS system, N-acetylglucosamine-specific IIC component (EC 2.7.1.69) PTS system, N-acetylglucosamine-specific IIB component ; PTS system, N-acetylglucosamine-specific IIC component MYQLFIEGLQRLGRALMLPIAILPIAGLLLRLGDTDLLNIAIIHDAGQVIFANLALIFAIGIAVGFARDNNGTAGLAGAIGYLVMVSTLKVLDASINMGMLAGIISGLMAGALYNRFKDIKLPEYLAFFGGRRFVPIATGFSAVGLGVIFGLIWPPIQHGINSFGQLLLESGSIGAFVFGVFNRLLIVTGLHHILNNMAWFIFGSFTDPTTGAIVTGDLARYFAGDPKGGQFMTGMFPMMIFGLPAACLAMYRNALPERRKVMGGIFLSMALTSFLTGVTEPIEFAFMFLAPLLYLLHVLLTGMAMAITNALNIHLGFTFSGGAIDMALGWGKSTNGWLVFPVGLAYAVIYYVVFDFCIRRFNLKTPGREGVVVGEKVVLSENQRAGAYIQALGGAENLITVGACTTRLRLEMVDRNKASDSELKALGAMAVVRPGKGGSLQVVVGPLADSIADEIRQAMPTAGSALVAAVVVTEEAPKAAPVETPEAQKWLNAVGGSDNVLQLDCVAMTRIRLQLADGKALSECQLKDLGCQGVSALDGGVWHLLIGDKALSLSEALEGLVNRSEVSAKV transporters Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_05485 AO353_05485 AO353_RS05485 WP_054594049.1 tr|A0A0N9W2F2|A0A0N9W2F2_PSEFL Fructose-specific PTS system, I, HPr, and IIA components Specifically important for fructose utilization. The enzyme II B/C components of this PTS system are in AO353_05475 which is cofit and is correctly annotated. AO353_05485 is 73% identical to PA3562, which is also part of a fructose-specific system (PMC:PMC2542419) PTS fructose transporter subunit IIA Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9) phosphocarrier protein MLELTIEQISMGQSAVDKAAALHLLADTLVNDGLVAEGYLSGLQAREAQGSTFLGQGIAIPHGTPDTRDLVHTTGVRLLQFPEGVDWGDGHIVYLAIGIAAKSDEHLRLLQLLTRALGETDLGQALRRASSAEALLKLLQGAPQELALDAQMIGLGVSADDFEELVWRGARLLRQADCVSNGFSAVLQQVEALPLGDGLWWLHSEQTVKRPGLAFVTPDKPIRYLGQPLSGLFCLASLGEAHQALLERLCALLIEGRGHELGRATSRRAVLEVLGGELPADWPSARIALANAHGLHARPAKILAQLAKSFEGEIRIRIVDGQDSAVSVKSLSKLLSLGARRGQVLELIAEPSIAADALPALLRAIEEGLGEDIEPLPTVSAQSEVIDEITDVVVAPASGCVIQAVAAAPGIAIGPAHIQVLQAIDYPLRGESTAIERERLKTSLADVRRDIEGLIQRSKAKAIREIFITHQEMLDDPELTDEVDTRLKQGESAEAAWMAVIDAAARQQESLQDALLAERAADLRDIGRRVLAQLCGIETPSEPDQPYILVMDEVGPSDVARLDPTRVAGILTARGGATAHSAIVARALGIPALVGAGAAVLRLASGTPLLLDGQRGRLHVDADAATLQRAAEERDNREQRLQAAAAQRHQPALTTDGHAVEVFANIGESAGVVSAVEQGAEGIGLLRTELIFMAHQQAPDEATQEVEYRRVLDGLAGRPLVVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQRPQIMEAQLRALLRAADNRPLRIMFPMVGSVDEWRQARDMTERLRLEIPVADLQLGIMIEVPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSARSIGEVKARVRELSLAQVKHLAQLALAVGSANEVRALVEAL catabolism Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_07485 AO353_07485 AO353_RS07485 WP_054594340.1 tr|A0A0N9WH75|A0A0N9WH75_PSEFL Acyl-CoA dehydrogenase (EC 1.3.8.7) Specifically important for: Sodium butyrate; Tween 20. The phenotype on Tween 20 suggests that it has activity on longer substrates as well as on butyryl-CoA (SEED_correct) acyl-CoA dehydrogenase Acyl-CoA dehydrogenase (EC 1.3.8.7) MADYKAPLRDMRFVLNEVFEVAKLWAELPALADTVDAETVEAILEEAGKVTSKSIAPLSRAADEEGCHWSDGAVTTPAGFPQAYQTYAEGGWVGVGGDPSYGGMGMPKAVSAQVEEMVNSASLSFGLYPMLTAGACLSINAHASEELKAAYLPNMYAGVWAGSMCLTEPHAGTDLGIIRTKAEPQADGSYKVSGTKIFITGGEHDLTENIIHLVLAKLPDAPAGPKGISLFLVPKFMVNADGSLGARNPANCGSIEHKMGIQASATCVMNFDEAVGYLVGEPNKGLAAMFTMMNYERLGVGIQGLASGERSYQNAVEYARDRLQSRSPTGAQNKDKVADPIIVHPDVRRMLLTMKASNEGGRAFSTYVAMQLDTAKFSEDATIRKRAEDLVALLTPVAKAFLTDLGLETTIHGQQVFGGHGYIREWGQEQLVRDVRITQIYEGTNGIQALDLVGRKIVGSGGAYYKLFADEIRHFTATASADLAEFTKPLNDAVDTLDELTAWLLDRVKNNPNEIGAASVEYLQVFGYVSYAYMWALMAKAAFGKEAQDDFYASKLGTARFYFARLLPRFHSLSASVKAGSESLFLLDAAQF catabolism Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_07705 AO353_07705 AO353_RS07705 WP_054594379.1 tr|A0A0N7GZP8|A0A0N7GZP8_PSEFL DgcB Dimethylglycine demethylase subunit B (EC 1.5.3.-) Specifically important for: Carnitine Hydrochloride. Dimethylglycine is an intermediate in L-carnitine metabolism; this gene is similar to PA5399 or dgcB (PMCID: PMC2293255) (Fe-S)-binding protein Predicted L-lactate dehydrogenase, Iron-sulfur cluster-binding subunit YkgF MLNTLLPILLFAALGLAVLGALRRVAMWRRGRASKVDLIGGLLAMPKRYMVDLHHVVARDKYIANTHVATAGGAVASIVLAILVHGFGLHNRFLGYALLLMTAVMFVGAIFVYLRRRNPPARLSKGPWMRLPKSLLAFSASFFLVTLPVAGILPENFGGWLLAAILGVGVLWGVSELFFGMTWGGPMKHAFAGALHLAWHRRAERFGGGRSTGLKPLDLNDPQAPLGVEKPKDFTWNQLLGFDACVQCGKCEAACPAFAAGQPLNPKKLIQDMVVGLAGGTDAKFAGSPYPGKAIGEHAGNPHQPIVNGLVDAETLWSCTTCRACVEECPMMIEHVDAIVDMRRHLTLEKGATPNKGAEVLENLIATDNPGGFAPGGRMNWAADLNLTLLSEKKSTDVLFWVGDGAFDMRNQRTLRAFVKVLKAAKVDFAVLGLEERDSGDVARRLGDEATFQLLAKRNIQTLAKYSFNRIVTCDPHSFHVLKNEYGAFDGNYLVQHHSTYMAEIIDAGALNLGQHKGDSVTYHDPCYLGRYNGEYEAPRQVLRALGIEVKEMQRSGFRSRCCGGGGGAPITDIPGKQRIPDMRMDDIRETGAELVAVGCPQCTAMLEGVVEPRPLIKDIAELVADALLEDAAPSKSPAPTKRQPAEAH catabolism Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_07710 AO353_07710 AO353_RS07710 WP_054594380.1 tr|A0A0N9WSS7|A0A0N9WSS7_PSEFL DgcA Dimethylglycine demethylase subunit A Specifically important for: Carnitine Hydrochloride. Carnitine is catabolized via glycine betaine (trimethylglycine) and then demethylated twice to sarcosine (N-methylglycine) (PMCID: PMC2293255) (SEED_correct) N-methylproline demethylase DgcA Dimethylglycine demethylase subunit A MAFEAMFQPIQIGKLTIRNRVLSTAHAEVYATDGGMTTDRYVKYYEEKAKGGIGLAICGGSSSVAIDSPQGWWKSVNLADDRIIPHFQNLADAMHKHGAKIMIQITHMGRRSRWDGEHWPTLLSPSGIREPVHRATCKTIEPEEIWRVIGNYASAAARAKAGGLDGVELSAVHQHMIDQFWSPRVNKRTDEWGGSFENRMRFGLEVIKAVRKEVGPDFCVGIRICGDEFHPDGLSHEDMKQIAKYYDDTGMIDFIGVVGSGCDTHNTLANVIPNMSYPPEPFLHLAAGIKEVVKAPVLHAQNIKDPNQATRILEGGYVDMVGMTRAHIADPHLIAKIKMGQIDQIKQCVGANYCIDRQYQGLDVLCIQNAATSREYMGVPHIIEKSTGVKRKVVVVGAGPAGMEAARVAAERGHDVTLFEKKEFIGGQITTASKAPQRDQIAGITRWFQLELARLKVDLRLGVAADAATILDLRPDIVVLAVGGHPFLEQNEHWGAAEGLVVSSWDVLDGKVLPGKNVLVYDTICEFTGMSVADYLADKGSQVEIVTDDIKPGVAIGGTSFPTYYRSMYPKEVIMTGDMMLDKVYREGDKLVAVLENEYTGAKEERVVDQVVVENGVRPDEEIYYALKEGSRNKGQMDIEALFAIKPQPSLSQAGDGYLLFRIGDCVAQRNTHAAIYDALRLCKDF transporters Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_07740 AO353_07740 AO353_RS07740 WP_054594384.1 tr|A0A0N9WDQ6|A0A0N9WDQ6_PSEFL ABC transporter for Carnitine, substrate-binding component Specific phenotypes on Carnitine Hydrochloride. Similar to CaiX (see PMID:19919675). This transporter may also have a second SBP, AO353_07780, similar to CbcX, which is reported to be an alternate SBP for choline or glycine utilization (ibid). However _07780 is also important for carnitine utilization - it might be an additional necessary subunit of this transporter. glycine/betaine ABC transporter substrate-binding protein L-proline glycine betaine binding ABC transporter protein ProX (TC 3.A.1.12.1) glycine betaine/proline transport system substrate-binding protein MKRLISSCVLALSGTAFLSSGAMAADPAACQNVRMGVVNWTDVIATSAMTQVLLDGLGYKTKQTSASQQIIFAGIRDQRLDMFLGYWNPLMTQTITPFVAGKQVTVLSEPSLKDARATLAVPTYLADKGLKTFADIAKFEKELGGKIYGIEPGSGANTQIKEMIAKNQFGLGKFQLVESSEAGMLAAVDRAVRRNEAVVFFGWAPHPMNVNVKMTYLTGSQDALGPNEGSATVWTVTAPNYASQCPNVSRLLSNLTFTAEDESRMMQPLLDHKDAFESAKQWLKDHPQDKQRWLEGVTTFDGKPAAENLQLSSQ catabolism Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_07750 AO353_07750 AO353_RS07750 WP_054594385.1 tr|A0A0N9VS13|A0A0N9VS13_PSEFL carnitine 3-dehydrogenase [EC:1.1.1.108] Specifically important for: Carnitine Hydrochloride. Not sure why SEED missed this: some very similar proteins are annotated correctly. pba:PSEBR_a5237 has been updated in KEGG and is now annotated as the carnitine dehydrogenase. (KEGG_correct) 3-hydroxybutyryl-CoA dehydrogenase 3-hydroxybutyryl-CoA dehydrogenase MSFITEIKTFAALGSGVIGSGWVSRALAHGLDVVAWDPAPGAEVALRKRVANAWGALEKQGLAPGASQDRLRFVATIEECVRDADFIQESAPERLELKLELHSKISAAAKPNALIGSSTSGLLPSEFYEGSTHPERCVVGHPFNPVYLLPLVEVVGGKNTAPEAVQAAMKVYESLGMRPLHVRKEVPGFIADRLLEALWREALHLVNDGVATTGEIDDAIRFGAGLRWSFMGTFLTYTLAGGDAGMRHFMAQFGPALQLPWTYLPAPELTDKLIDDVVDGTSDQLGKHSISALERYRDDCLLAVLEAVKTTKAKHGMTFSE catabolism Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_07755 AO353_07755 AO353_RS07755 WP_054594386.1 tr|A0A0N9WGA2|A0A0N9WGA2_PSEFL betainyl-CoA thiolase (EC 3.1.2.-) Specifically important for: Carnitine Hydrochloride. This is part of the degradation of carnitine (K. Bastard et al, Nature Chem Biol. 2014). Since KEGG had this EC number you could argue that it is correct, but it made a very vague prediction. 4-hydroxybenzoyl-CoA thioesterase acyl-CoA thioester hydrolase MPALTTYTTKIIPDWVDYNGHLRDAFYLLIFSYATDALMDQLGMDSNNREASGNSLFTLELHLNYLHEVKLGAEVEVHTQIIGHDRKRLHLYHSLHLVGEEQELAGNEQMLLHVDLAGPRSAPFSESVLNKLRAMSALQSDLPTPAYIGRVIALPPEK transporters Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_07785 AO353_07785 AO353_RS07785 WP_054594390.1 tr|A0A0N7GZQ0|A0A0N7GZQ0_PSEFL ABC transporter for Carnitine, permease component Specific phenotypes on Carnitine Hydrochloride. no phenotype in choline stress; annotated as glycine betaine or proline transport. Another issue is that carnitine might be oxidized to choline which is then excreted (MetaCyc Pathway: L-carnitine degradation II) but this would not support growth with carnitine as either C or N source (no C or N extracted). Note that both carnitine and choline are catabolized via glycine betaine and this is clustered with glycine betaine degradation genes. This ABC transporter might also transport choline or glycine betaine with a different SBP (AO353_07780). choline ABC transporter permease subunit L-proline glycine betaine ABC transport system permease protein ProW (TC 3.A.1.12.1) glycine betaine/proline transport system permease protein MLIDQKIPLGQYIAAFVEWLTQHGASTFDAIATTLETMIHGVTFALTWFNPLALIGLIALLAHFIQRKWGLTAFVIASFLLILNLGYWQETMETLAQVLFATFVCVIIGVPLGIVAAHKPMFYTMMRPVLDLMQTVPTFVYLIPTLTLFGLGVVPGLISTVVFAIAAPIRLTYLGIRDVPQELMDAGKAFGCSRRQLLSRIELPHAMPSIAAGITQCIMLSLSMVVIAALVGADGLGKPVVNALNTADIALGFEAGLAIVLLAIMLDRICKQPDAKVGGDA transporters Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_07790 AO353_07790 AO353_RS07790 WP_054594391.1 tr|A0A0N9WA42|A0A0N9WA42_PSEFL ABC transporter for Carnitine, ATPase component Specific phenotypes on Carnitine Hydrochloride. Note that both carnitine and choline are catabolized via glycine betaine and this is clustered with glycine betaine degradation genes. This ABC transporter might also transport choline or glycine betaine with a different SBP (AO353_07780). choline ABC transporter ATP-binding protein L-proline glycine betaine ABC transport system permease protein ProV (TC 3.A.1.12.1) glycine betaine/proline transport system ATP-binding protein MSIIRFDNVDVIFSKDPREALKLLDQGMTRDQILKKTGQIVGVEKASLDIEKGEICVLMGLSGSGKSSLLRCINGLNTVSRGKLFVEHEGRQIDIASCTPAELKMMRTKRIAMVFQKFALMPWLTVRENISFGLEMQGRPEKERRQLVDEKLELVGLTQWRNKKPDELSGGMQQRVGLARALAMDADILLMDEPFSALDPLIRQGLQDELLELQRKLHKTIVFVSHDLDEALKLGSRIAIMKDGRIIQYSKPEEIVLNPADDYVRTFVAHTNPLNVLCGRSLMRTLDNCKRINGSVCLDPGGDSWLDLAEGNTIKGARQNGSSLDLQNWVPGQAVEGLGRRPTLVDSNIGMRDALQIRYQTGNKLVLHDNNKVVGILGDSELYHALLGKNLG catabolism Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_08585 AO353_08585 AO353_RS08585 WP_054594536.1 tr|A0A0N9VTA1|A0A0N9VTA1_PSEFL Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) Specifically important for: Putrescine Dihydrochloride. KEGG annotates this as putrescine aminotransferase, probably based on similarity to spuC (PA0299) of P. aeruginosa, but it is believed that only the g-glutamyl- pathway operates in P. aeruginosa (X. Yao et al 2011, PMC:3147493) aminotransferase Omega-amino acid--pyruvate aminotransferase (EC 2.6.1.18) putrescine aminotransferase MTSKNPQTREWQTLSSEHHLAPFSDFKQLKEKGPRIITNAKGVYLWDSEGNKILDGMAGLWCVAIGYGRDELADAASKQMRELPYYNLFFQTAHPPVLELAKAISDIAPEGMNHVFFTGSGSEGNDTMLRMVRHYWAIKGQPNKKVIISRINGYHGSTVAGASLGGMTYMHEQGDLPIPGIVHIPQPYWFGEGGDMTPEEFGIWAANQLEEKILELGVDTVGAFIAEPIQGAGGVIIPPDSYWPRIKEILAKYDILFVADEVICGFGRTGEWFGSDFYGLKPDMMTIAKGLTSGYIPMGGLIVRDEVVEVLNEGGDFNHGFTYSGHPVAAAVALENIRILREEKIIEHVRAETAPYLQKRLRELNDHPLVGEVRGVGLLGAIELVQDKATRARYVGKGVGMICRQFCFDNGLIMRAVGDTMIIAPPLVITKAEIDELVTKARKCLDLTLSALQS catabolism Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_08595 AO353_08595 AO353_RS08595 WP_054594538.1 tr|A0A0N9VMN1|A0A0N9VMN1_PSEFL Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) Specifically important for: Potassium acetate; L-Arginine; Putrescine Dihydrochloride; L-Citrulline. This is the first step in putrescine degradation and is important for the usage of putrescine as either C or N source. The phenotypes on citrulline and arginine might indicate a side pathway where they are converted to putrescine via ornithine decarboxylase (SEED_correct) gamma-glutamylputrescine synthetase Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) glutamine synthetase MSVPPRAVQLNEANAFLKEHPEVLYVDLLIADMNGVVRGKRIERTSLHKVYEKGINLPASLFALDINGSTVESTGLGLDIGDADRICYPIPNTLCNEPWQKRPTAQLLMTMHELEGEPFFADPREVLANVVRKFDDMGLTICAAFELEFYLIDQENVNGRPQPPRSPVSGKRPHSTQVYLIDDLDEYVDCLQDILEGAKEQGIPADAIVKESAPAQFEVNLHHVADPIKACDYAVLLKRLIKNIAYDHEMDTTFMAKPYPGQAGNGLHVHISILDKDGKNIFASEDPEQNAALRHAIGGVLETLPAQMAFLCPNVNSYRRFGAQFYVPNSPCWGLDNRTVAIRVPTGSADAVRIEHRVAGADANPYLLMASVLAGVHHGLTNKIEPGAPVEGNSYEQNEQSLPNNLRDALRELDDSEVMAKYIDPKYIDIFVACKESELEEFEHSISDLEYNWYLHTV catabolism Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_11505 AO353_11505 AO353_RS11505 WP_054595050.1 tr|A0A0N9WI11|A0A0N9WI11_PSEFL succinate-semialdehyde dehydrogenase (EC 1.2.1.16) Specifically important for: L-Citrulline; L-Arginine; Putrescine Dihydrochloride. succinate semialdehyde is an intermediate in putrescine catabolism. KEGG has updated its annotation (K00135, see pman:OU5_3276) to include both succinate semialdehyde and glutarate semialdehyde as substrates. The other phenotypes are milder and might indicate a side pathway of conversion of citrulline and arginine to putrescine via ornithine decarboxylase. (KEGG_correct) succinate-semialdehyde dehydrogenase glutarate semialdehyde dehydrogenase MQLKDTLLFRQQAFIDGAWVDADNGQTINVTNPATGEILGTVPKMGAAETRRAIEAADKALPAWRALTAKERANKLRRWFELIIENQDDLARLMTLEQGKPLAEAKGEIVYAASFIEWFAEEAKRIYGDVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPYSAFALAELAQRAGIPKGVLSVVTGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMAECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDSVYDAFAEKLKVAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIADALSKGATLLAGGKVMEGNFFEPTILTNVPKSAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDLGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLGI transporters Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_12275 AO353_12275 AO353_RS12275 WP_054595190.1 tr|A0A0N9VTP5|A0A0N9VTP5_PSEFL histidine permease Specific phenotype on histidine. 86% identical to PFLU0368, which is required for histidine utilization (PMCID: PMC1950622). SEED_correct proline-specific permease Histidine transport protein (permease) amino acid transporter, AAT family MQKPANGLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALGEMAVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPEVSRWIWVLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPGQVTDISNLWTQGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINAVPLRILLFYVLTMLVLMSIFPWQQIGSQGSPFVQIFDKLGISSAATILNIVVITAAISAINSDIFGAGRMMFGLAQQGHAPKGFAHLSRNGVPWMTVVVMSVALLLGVLLNYLIPENVFLLIASIATFATVWVWLMILFTQVAMRRSMTAEQVAQLKFPVPFWPYAPMAAIAFMLFVFGVLGYFPDTQAALIVGVVWIVLLVLAYLMWVKPAAGQAALVARDPSFSNR catabolism Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_12285 AO353_12285 AO353_RS12285 WP_054595192.1 tr|A0A0N9WHL9|A0A0N9WHL9_PSEFL N-formylglutamate deformylase (EC 3.5.1.68) Specifically important for: L-Histidine. KEGG suggests formimidoyl-L-glutamate as the substrate, while SEED suggests N-formylglutamate. This gene is cofit with iminohydrolase (which produces N-formylglutamate) which suggests that the SEED annotation is correct. (SEED_correct) N-formylglutamate deformylase N-formylglutamate deformylase (EC 3.5.1.68) formiminoglutamase VDKVLNFKQGRVPLLISMPHAGVRLTPAVEAGLIPEAKSLPDTDWHIPTLYEFAAELGASTLAAEYSRFVIDLNRPSDDKPMYVGATTGLYPATLFDGVPLFREGLEPSAEERASYLEKVWTPYHSTLQQELARLKAEFGYALLFDAHSIRSVIPHLFDGKLPDFNLGTFNGASCDPQLASQLEAICARHTDYSHVLNGRFKGGHITRHYGNPAENIHAVQLELGQCTYMEEVEPFRYRPDLAAPTQVVLKELLQGLLAWGQKHYA transporters Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_15995 AO353_15995 AO353_RS15995 WP_054595825.1 tr|A0A0N9WH78|A0A0N9WH78_PSEFL trehalose-specific PTS system, I, HPr, and IIA components Specific phenotype on trehalose. The IIB/IIC components are provided by AO353_15980. 45% similar to a NAG PTS system (PA3760, PMC:PMC2542419) PTS mannose transporter subunit IIC PTS system, glucose-specific IIA component / Phosphotransferase system, phosphocarrier protein HPr / Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9) PTS system, fructose-specific IIA component ; phosphotransferase system, enzyme I, PtsI ; phosphocarrier protein FPr MTLTQPLQLLAPLSGVLMPLDHVPDPVFASRVIGDGLCIDPTSQVLCAPLAGVVSNLQHSGHAISITDDSGVQVLLHIGLDTVNLKGQGFSALVEQGQRVEAGQPLIEFDADYVALHARSLLTLMLVVSGEPFSLLTPDSGLVACAQPVLRLSLGDPRTVVAQEEGEALFSKPVHLPNPNGLHARPAAVFAQAAKGFAASICLHKQQDSANAKSLVAIMALQTVHGDALQVSAVGEDAELAISTLAQLLADGCGEAVTPVAVVAPVVEAQEVSTKLLRGVCASAGSAFGYVVQVAERTLEMPEFAADQQLERESLERALMHATQALQRLRDNAAGEAQADIFKAHQELLEDPSLLEQAQALIAEGKSAAFAWNSATEATATLFKSLGSTLLAERALDLMDVGQRVLKLILGVPDGVWELPDQAILIAEQLTPSQTAALDTGKVLGFATVGGGATSHVAILARALGLPAVCGLPLQVLSLASGTRVLLDADKGELHLDPAVSVIEQLHAKRQQQRQRHQHELENAARAAVTRDGHHFEVTANVASLAETEQAMSLGAEGIGLLRSEFLYQQRSVAPSHDEQAGTYSAIARALGPQRNLVVRTLDVGGDKPLAYVPMDSEANPFLGMRGIRLCLERPQLLREQFRAILSSAGLARLHIMLPMVSQLSELRLARLMLEEEALALGLRELPKLGIMIEVPAAALMADLFAPEVDFFSIGTNDLTQYTLAMDRDHPRLASQADSFHPSVLRLIASTVKAAHAHGKWVGVCGALASETLAVPLLLGLGVDELSVSVPLIPAIKAAIREVELSDCQAIAHQVLGLESAEQVREALSVQQQAMVETSQVLES transporters Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_16120 AO353_16120 AO353_RS16120 WP_054595847.1 tr|A0A0N9WH98|A0A0N9WH98_PSEFL D-alanine and L-alanine transporter Specific phenotype on D-alanine as the carbon source. Also important for utilizing L-alanine as a carbon source. Both of these phenotypes are conserved. For D-alanine as a nitrogen source, there is a mild phenotype, and it may be partly redundant with another amino acid transporter (AO353_04615:04600). Sometimes annotated as a glycine transporter, but neither it nor its orthologs are important on glycine. D-alanine/D-serine/glycine permease D-serine/D-alanine/glycine transporter amino acid transporter, AAT family MTVGNHLPHGETAQGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWFPEVPRWIWALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVVGGVGVIAFGFGNDGVALGISNLWSHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSVFWRILLFYVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIFSTGRMLYSLAQNGQAPAGFAKTSNGVPRRALLLSIGALLLGVLLNYLVPEKVFVWVTAIATFGAIWTWVMILLAQLKFRKGLSPAERAALKYRMWLYPVSSYLALAFLVMVVGLMAYFPDTRVALYVGPAFLVLLTVLFYVFKLQPTGVPQAAVRTAS transporters Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_16280 AO353_16280 AO353_RS16280 WP_054595877.1 tr|A0A0N7H0A0|A0A0N7H0A0_PSEFL ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1 # Specifically important in carbon source L-Aspartic Acid; pH ; carbon source L-Asparagine; carbon source L-Glutamic acid monopotassium salt monohydrate; carbon source L-Glutamine amino acid ABC transporter permease Glutamate Aspartate transport system permease protein GltK (TC 3.A.1.3.4) glutamate/aspartate transport system permease protein MDLDFSGVVQAVPGMWNGMVMTLQLTVLGVVGGIILGTLLALMRLSHSKLLSNIAGAYVNYFRSIPLLLVITWFYLAVPFVLRWITGEDTPIGAFTSCIVAFMMFEAAYFCEIVRAGVQSIPKGQMGAAKALGMGYGQMMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLVDFLNATRASGDIIGRANEFLIIAGLVYFTISFAASRLVKRLQKRFAV transporters Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_16285 AO353_16285 AO353_RS16285 WP_054595878.1 tr|A0A0N9WDU0|A0A0N9WDU0_PSEFL ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 2 # Specifically important in carbon source L-Aspartic Acid; pH ; carbon source L-Asparagine; carbon source L-Glutamic acid monopotassium salt monohydrate; carbon source L-Glutamine amino acid ABC transporter permease Glutamate Aspartate transport system permease protein GltJ (TC 3.A.1.3.4) glutamate/aspartate transport system permease protein MNYNWDWGVFFKSTGVGSETYLDWFITGLGWTIAIAIVAWIIALMLGSVLGVMRTVPNRLVSGIATCYVELFRNVPLLVQLFIWYFLVPDLLPQNLQDWYKQDLNPTTSAYLSVVVCLGLFTAARVCEQVRTGIQALPRGQESAARAMGFKLPQIYWNVLLPQAYRIVIPPLTSEFLNVFKNSSVASLIGLMELLAQTKQTAEFSANLFEAFTLATLIYFTLNMSLMLLMRMVEKKVAVPGLISVGGK transporters Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_16290 AO353_16290 AO353_RS16290 WP_054595879.1 tr|A0A0N9W726|A0A0N9W726_PSEFL ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, periplasmic substrate-binding component # Specifically important in carbon source L-Aspartic Acid; carbon source L-Asparagine; pH ; carbon source L-Glutamic acid monopotassium salt monohydrate; carbon source L-Glutamine ABC transporter Glutamate Aspartate periplasmic binding protein precursor GltI (TC 3.A.1.3.4) glutamate/aspartate transport system substrate-binding protein MRIVPHILGAAITAALISTPVFAAELTGTLKKIKESGTITLGHRDASIPFSYIADASGVPVGYSHDIQLKIVEAIKKDLDMPNLKVKYNLVTSQTRIPLVQNGTVDVECGSTTNNTERQQQVDFSVGIFEIGTKLLSKKDSTYKDFADLKGKNVVTTAGTTSERILKSMNADKQMGMNVISAKDHGESFQMLESGRAVAFMMDDALLAGEMAKAKSPTDWAVTGTAQSYEIYGCMVRKGDAPFKKAVDDAIVATYKSGEINTIYGKWFTQPIPPKNLNLMFPMSDELKALISNPTDKAAEEKKS catabolism Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_18575 AO353_18575 AO353_RS18575 WP_054596267.1 tr|A0A0N9WXT8|A0A0N9WXT8_PSEFL tyrosine aminotransferase (EC 2.6.1.57) Specifically important for: L-Phenylalanine. Phenylalanine is catabolized via tyrosine and transamination to 4-hydroxyphenylpyruvate, so tyrosine is the relevant substrate. (KEGG_correct) aromatic amino acid aminotransferase Aspartate aminotransferase (EC 2.6.1.1) aromatic-amino-acid transaminase MHFDAIGRVPGDPILGLMEAYAQDSNPCKFDLGVGVYKDAQGLTPIPQSVKLAELRLVDRQTTKTYIGGHGDPAFGKVINELVLGADSALIAEQRVGATQTPGGTGALRLSADFIAHCLPGRGIWLSNPTWPIHETIYATAGLKVSHYPYVGSDNRLDVEAMLATLNLIPKGDVVLLHACCHNPTGFDLSHDDWRRVLEVVRSRELLPLIDFAYQGFGDGLEQDAWAVRLFAAELPELLITSSCSKNFGLYRDRTGALIVCAKDAEKLVDIRSQLANIARNLWSTPPDHGAAVVATILGDPELKQLWADEVEAMRLRIAQLRSGLVEALEPHGLGERFAHIGVQRGMFSYTGLTPAQVKNLRDHHSVYMVSSGRANVAGIDATRLDLLAQAFADVCK catabolism Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_20845 AO353_20845 AO353_RS20845 WP_054596656.1 tr|A0A0N9WN92|A0A0N9WN92_PSEFL uridine/adenosine nucleosidase (EC 3.2.2.3; EC 3.2.2.7) Important on adenosine and uridine; annotated by SEED as for uridine and inosine; fitness defect on uridine is subtle but is confirmed by observations for close homologs (SEED_correct) nucleoside hydrolase Inosine-uridine preferring nucleoside hydrolase (EC 3.2.2.1) purine nucleosidase MYRYAQRLHHLIRSLLLLSLLTATGAHAAEKIDLIIDTDPGADDVVALLFALASPEELNIRALTTVAGNVRLDKTSRNARLAREWAGREDVPVYAGAPKPLMRTPIYAENIHGKEGLSGVTVHEPKKGLAKGDAVSYLIDTLRAAKPHSITIAMLGPQTNLALALIQDPEITQGIKEVVIMGGAHFNGGNITPVAEFNLFADPHAAEVVLKSGVKLTYLPLDVTHKILTSDARLKQIAALNNNASKLVGDILNEYVKGDMEHYGIPGGPVHDATVIAYLLKPELFTGRAVNVVVDSREGPTFGQTVVDWYDGLKAPKNAFWVANGDAQGFFDLLTARLARLK transporters Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_21385 AO353_21385 AO353_RS21385 WP_054598296.1 tr|A0A0N9WNW1|A0A0N9WNW1_PSEFL m-Inositol ABC transporter, ATPase component (itaA) Specific phenotype on m-Inositol and 63% identical to SMb20173 or itaA, which also has this function (see PMC2597717). The periplasmic substrate-binding component (AO353_21380) is not included in this table because it was annotated correclty in both resources. SEED_correct D-ribose transporter ATP-binding protein Inositol transport system ATP-binding protein simple sugar transport system ATP-binding protein MFASATASSIPLVGVQPNAIPVDEPYLLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREMHRCTAQLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRELSQLFPVREKPIGDLLMSVRDLRLDGVFKGVSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYAGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASGMSVRH transporters Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_21390 AO353_21390 AO353_RS21390 WP_054596742.1 tr|A0A0N7H0L7|A0A0N7H0L7_PSEFL m-Inositol ABC transporter, permease component (iatP) Specific phenotype on m-Inositol and 71% identical to SMb20174 or itaP, which also has this function (see PMC2597717). The periplasmic substrate-binding component (AO353_21380) is not included in this table because it was annotated correclty in both resources. SEED_correct ABC transporter Inositol transport system permease protein simple sugar transport system permease protein MNAILENKPAMAPAKSRRRLPTELSIFLVLIGIGLVFEMFGWIVRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQVIITTGIDLSSGSVLALSAMIAASLAQTSDFARAVFPSLTDLPVWIPVIAGLGVGLLAGAINGSIIAVTGIPPFIATLGMMVSARGLARYYTEGQPVSMLSDSYTAIGHGAMPVIIFLVVAVIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLVIVYSIAGLLAGLAGVVASARAATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGALILGVMASGFTFVGVDAYIQDIIKGLIIVIAVVIDQYRNKRKLKR transporters Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_21710 AO353_21710 AO353_RS21710 WP_054596801.1 tr|A0A0N9WMM3|A0A0N9WMM3_PSEFL ABC transporter for D-glucosamine, periplasmic substrate-binding component # Specifically important in nitrogen source D-Glucosamine Hydrochloride; carbon source D-Glucosamine Hydrochloride ABC transporter substrate-binding protein Glutamine ABC transporter, periplasmic glutamine-binding protein (TC 3.A.1.3.2) MQRRLSLFTACVFLFAATASAVGIAQAADSRLDNVLKRGHLIVGTGSTNAPWHFQGADGKLQGFDIDIGRMVAKGLFNDPSKVEFVVQSSDARIPNLLTDKVDMSCQFITVTASRAQQVAFTLPYYREGVGLLLPANSKYKEIEDLKAAGDSVTVAVLQNVYAEELVHQALPKAKVDQYDSVDLMYQAVNSGRADTAATDQSSVKYLMVQNPGRYRSPTYAWSPQTYACAVKRGDQDWLNFVNTVLHEAMTGVEFPTYAASFKQWFGVDLPSPAIGFPVEFK transporters Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_21715 AO353_21715 AO353_RS21715 WP_054596802.1 tr|A0A0N7H0M5|A0A0N7H0M5_PSEFL ABC transporter for D-glucosamine, permease component 1 # Specifically important in nitrogen source D-Glucosamine Hydrochloride; carbon source D-Glucosamine Hydrochloride amino acid ABC transporter permease amino acid ABC transporter, permease protein polar amino acid transport system permease protein MNYQLNFAAVWRDFDTLLAGLGLGLELALVSIAIGCVIGLLMAFALLSKHRALRVLASVYVTVIRNTPILVLILLIYFALPSLGIRLDKLPSFIITLSLYAGAYLTEVFRGGLLSIPKGLREAGLAIGLGEWQVKAYVTVPVMLRNVLPALSNNFISLFKDTSLAAAIAVPELTYYARKINVESYRVIETWLVTTALYVAACYLIAMLLRYLEQRLAIRR transporters Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_21720 AO353_21720 AO353_RS21720 WP_054596803.1 tr|A0A0N9WLR5|A0A0N9WLR5_PSEFL ABC transporter for D-glucosamine, permease component 2 # Specifically important in nitrogen source D-Glucosamine Hydrochloride; carbon source D-Glucosamine Hydrochloride ABC transporter permease Amino acid ABC transporter, permease protein polar amino acid transport system permease protein MYESPSWLHELWVARDTLWSGFLTSVQCSVLAIMLGTLIGIVAGLVLTYGTLWMRAPFRFYVDLIRGTPVFVLVLACFYMAPALGWQIDAFQAGVLGLTLFCGSHVAEIVRGALQALPRGQMEASKAIGLTFYQALAYVLLPQALRQILPTWVNSSTEIVKASTLLSVIGVAELLLSTQQIIARTFMTLEFYLFAGFLFFIINYAIELLGRHIEKRVALP catabolism Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_21740 AO353_21740 AO353_RS21740 WP_054596807.1 tr|A0A0N9VSJ9|A0A0N9VSJ9_PSEFL D-glucosaminate dehydratase (EC 4.3.1.9) Specifically important for: D-Glucosamine Hydrochloride. This enzyme had not previously been linked to a gene. This is the second step in catabolism of glucosamine, and the 'beta' form of the enzyme was expected to be PLP-dependent and about this size. Iwamoto et al (2003) purified a non-specific 'alpha' enzyme for this reaction (PMID: 12686150) amino acid deaminase D-serine deaminase (EC 4.3.1.18) MSSALNIAAVEKGAGQPGANLVRDVSLPALVLHREALEHNIHWMQAFVSHSGAELAPHGKTSMTPSLFRRQLEAGAWGITLATVVQTRAAYAHGVRRVLMANQLVGAPNMALIAELLADPSFDFYCMVDHPDNVADLGVFFAARGLRLNVMIEYGVVGGRCGCRSEAEVLALAEAIKAQPGLALTGIEGYEGVIHGDQAVSGIREFAASLVRLAVQLQDSGAFAISKPIITASGSAWYDLIAESFEAQNAGGRFLSVLRPGSYVAHDHGIYKEAQCCVLDRRSDLHEGLRPALEVWAHVQSLPEPGFAVIALGKRDVAYDAGLPVPLLRYRAGVLPAVGDDVSACTVTAVMDQHAFMTVAPGVQLRVGDIISFGTSHPCLTFDKWRTGCLVDEQLNVIESMETCF catabolism Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_25635 AO353_25635 AO353_RS25635 WP_054597481.1 tr|A0A0N9VZU6|A0A0N9VZU6_PSEFL arginine deiminase (EC 3.5.3.6) Specifically important for: L-Citrulline. Distantly related to characterized arginine deiminases (PF02274); this reaction (in reverse) is the first step of citrulline catabolism, followed by the N2-succinyl-arginine pathway amidinotransferase MQTTNTVLMIRPTRFSFNQDTAANNRFQRPAAAAEDVQLKALQEFDGYVAALREHGVEVMVHNDSEAPHTPDSIFPNNWWSSHPDGTLVLYPMQGHNRRLERDKGVLDWLRDAYRIEQLLDLSDLEQQEVFLEGTGSMVLDREQRICYAGYSTRTHAKALDQVVEHLGYELCAFNAVDRHGVPIYHTNVMMSVGRQLAVVCLESVSDLDERNALRSRLECSGKQVLTLSFDQLESFAGNMLEVHNAAGEPLLVMSRTAWRSLHADQRRMVEAYAKPLPVNIDTIERIGGGSARCMLAEVYLPKRVSPQEQH catabolism Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_25665 AO353_25665 AO353_RS25665 WP_054597487.1 tr|A0A0N9WLS4|A0A0N9WLS4_PSEFL 3-hydroxy-isobutyryl-CoA hydro-lyase (EC 4.2.1.17) Specifically important for: L-Valine. Hydroxyisobutyryl-CoA is an intermediate in valine degradation. But is this the hydrolase (forming 3-hydroxyisobutyrate) as suggested by SEED, or is it the hydratase (or hydro-lyase in reverse) converting methylacrylyl-CoA to (S)-3-hydroxy-isobutanoyl-CoA, as suggested by KEGG? It belongs to the ECH_2 (PF16113) family, which should be a hydratase. No other genes for either step are apparent, but a CoA-transferase (AO353_11105) could replace the hydrolase. (KEGG_correct) crotonase 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) enoyl-CoA hydratase MTAQVSSQATHGIDASANDVLAEVRNHIGHLTLNRPAGLNAITLDMVRSLHRQLDAWSKDPHIHAVVLRGAGEKAFCAGGDIRSLYDSFKSGGTLHEDFFVEEYALDLAIHHYRKPVLALMDGFVLGGGMGLVQGADLRVVTERSRLAMPEVAIGYFPDVGGSYFLPRIPGELGIYLGVSGVQIRAADALYCGLADWYLESQKLAELDQHLDSLEWHDTPLKDLQGLLAKLALQQLPDAPLQALRPTIDHFFALPDVPSIVEQLRTVTVADSHDWAMTTADLLDSRSPLAMGVTLEMLRRGRQLSLENCFALELHLDRQWFERGDLIEGVRALLIDKDKSPRWNPPTVQALDAKHVASFFSGFDQSGS catabolism Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_25670 AO353_25670 AO353_RS25670 WP_054597488.1 tr|A0A0N9VZC5|A0A0N9VZC5_PSEFL isobutyrl-CoA dehydrogenase (EC 1.3.8.1) Specifically important for: L-Valine. SEED has it as butyryl-CoA dehydrogenase, which is also expected to perform this reaction in valine catabolism acyl-CoA dehydrogenase Butyryl-CoA dehydrogenase (EC 1.3.99.2) MHDIELTEEQVMIRDMARDFARGEIAPHAQAWEKAGWIDDALVAKMGELGLLGMVVPEEWGGTYVDYVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGTEEQKQTWLADLASGQAIGCFCLTEPQAGSEAHNLRTRAELRDGQWVINGAKQFVSNGRRAKLAIVFAVTDPDLGKKGLSAFLVPTDTPGFIVDRSEHKMGIRASDTCAVTLNNCTIPEANLLGERGKGLAIALSNLEGGRIGIAAQALGIARAAFEAALAYARDRVQFDKPIIEHQSVANMLADMHTRLNAARLLILHAARLRSAGKPCLSEASQAKLFASEMAEKVCSSAIQIHGGYGYLEDYPVERYYRDARITQIYEGSSEIQRMVIARELKNYLV catabolism Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_25680 AO353_25680 AO353_RS25680 WP_054597490.1 tr|A0A0N9WNL1|A0A0N9WNL1_PSEFL 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1) Specifically important for: Sodium butyrate. SEED has it as butyryl-CoA dehydrogenase. Also important on isoleucine and valine, which implies that it acts on the other substrates as well acyl-CoA dehydrogenase Butyryl-CoA dehydrogenase (EC 1.3.99.2) MLPTDEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTGYLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFALTEPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIVPTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRVGIASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALRDSGKPALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEGTSDIQRMVISRNL catabolism Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_25685 AO353_25685 AO353_RS25685 WP_054597491.1 tr|A0A0N9X119|A0A0N9X119_PSEFL acetyl-CoA:acetyl-CoA C-acetyltransferase / acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase (EC 2.3.1.9) Specifically important for: Sodium butyrate; L-Isoleucine. Degradation of acetoacetyl-CoA is consistent with a role in butyrate degradation. The role in Ile degradation suggests that 2-methylacetoacetyl-CoA is also a substrate (conversion to propionyl-CoA + acetyl-CoA). This is included in EC 2.3.1.9. The SEED annotation is more vague. (KEGG_correct) acetyl-CoA acetyltransferase 3-ketoacyl-CoA thiolase (EC 2.3.1.16) acetyl-CoA C-acetyltransferase MTMSHDPIVIVSAVRTPMGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAVEEVLFGCVLSAGLGQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESMSNAPYLLDRARSGYRMGHGKVLDHMFLDGLEDAYDKGRLMGTFAEDCAEANGFTREAQDEFAIASTTRAQQAIKDGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLKPAFRDGGTVTAANSSSISDGAAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAPVGAIKKLLKKTGWSLDEVELFEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGASGARILVTLLSALRQKGLKRGVAAICIGGGEATAMAVECLY transporters Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_25880 AO353_25880 AO353_RS25880 WP_054597528.1 tr|A0A0N9WQM3|A0A0N9WQM3_PSEFL ABC transporter for D-mannitol and D-mannose, periplasmic substrate-binding component # Specifically important in carbon source D-Mannitol; carbon source D-Mannose sugar ABC transporter substrate-binding protein Various polyols ABC transporter, periplasmic substrate-binding protein sorbitol/mannitol transport system substrate-binding protein MKPTVKALLACTCMTLSSVSLGAQTLTIATVNNSDMIRMQKLSKTFEAEHPEIKLNWVVLEENVLRQRLTTDIATQGGQFDVLTIGMYEAALWGAKGWLEPMKDLPAGYALDDVFPSVREGLSVKGTLYALPFYAESSMTYYRTDLFKDAGLAMPEHPTWEQIGEFAGKLNKPDQEQYGICLRGKAGWGENMALITTIANAYGARWFDEKWQPEFSGPEWKNALSFYADTMKKSGPPGASSNGFNENLALFNSGKCAIWVDASVAGSFVTDKTQSKVSEHVGFTYAPHQVTDKGSAWLYSWALAIPTSSKAKDAAKTFSAWATSKEYGALVAEKDGIANVPPGTRASTYSEAYMNAAPFAKVTLESLKVADPGKPTLKPVPYIGIQLVTIPEFQAVGTQVGKLFSAALIGQTTVDQALAAAQQTTEREMKRAGYPK transporters Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_25885 AO353_25885 AO353_RS25885 WP_054597529.1 tr|A0A0N9VUK6|A0A0N9VUK6_PSEFL ABC transporter for D-mannitol and D-mannose, permease component 1 # Specifically important in carbon source D-Mannose; also important for using D-mannitol sugar ABC transporter permease Various polyols ABC transporter, permease component 1 sorbitol/mannitol transport system permease protein MNTSTLKAQMDIPAPLRKSRLANPGWFLVSPSVALLLLWMIVPLGMTLYFSLIRYNLLYPGDNAFVGLENFSYFLTDSGFLPGATNTLLLVGSVLLISVVFGVLISALLEASEFLGRGIVRVMLISPFFIMPTVGALIWKNLIFHPVSGILAAVWKLFGAQPVDWLAHYPLLSIIIIVSWQWLPFAILILMTAMQSLDQEQKEAARLDGAGPIAIFWHLTLPHLARPIAVVVMIETIFLLSVFAEIFTTTNGGPGYASTNLAYLIYNQALVQFDVGMASAGGLIAVVIANIAAIILVRMLGKNLTDKA transporters Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_25890 AO353_25890 AO353_RS25890 WP_054597530.1 tr|A0A0N9WHV6|A0A0N9WHV6_PSEFL ABC transporter for D-mannitol and D-mannose, permease component 2 # Specifically important in carbon source D-Mannose; also important for using D-mannitol sugar ABC transporter permease Various polyols ABC transporter, permease component 2 sorbitol/mannitol transport system permease protein MTLQQTRRLQSLLLGTLAWAIAILIFFPIFWMVLTSFKTEIDAFATPPQFIFTPTLENYLHVNERSGYFSFAWNSVVISFSATALCLLIAVPAAYSMAFYETQRTKGTLLWMLSTKMLPPVGVLMPIYLLAKSFGLLDTRIALIIIYTLINLPIVVWMIYTYFKDIPKDILEAARLDGATLWQEMVRVLLPIAKGGLASTVLLSLILCWNEAFWSLNLTSSKAAPLTALIASYSSPEGLFWAKLSAVSTLACAPILIFGWISQKQLVRGLSFGAVK transporters Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_25895 AO353_25895 AO353_RS25895 WP_054597531.1 tr|A0A0N9WAL6|A0A0N9WAL6_PSEFL ABC transporter for D-mannitol and D-mannose, ATPase component # Specifically important in carbon source D-Mannose; carbon source D-Mannitol ABC transporter ATP-binding protein Various polyols ABC transporter, ATP-binding component sorbitol/mannitol transport system ATP-binding protein MAHLKIKNLQKGFEGFSIIKGIDLEVNDREFVVFVGPSGCGKSTLLRLIAGLEEVTAGTIELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVNKAEVEKKVNEAARILELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLHKELQATMIYVTHDQVEAMTLADKVVVLNGGRIEQVGSPLELYHQPANLFVAGFLGTPKMGFLKGKVTRVERQNCEVLLDAGTRITLPLSGANLSIGGAVTLGIRPEHLNLALPGDCTLQVTADVSERLGSDTFCHVLTASGEALTMRIRGDLASRYGEQLSLHLDAEHCHLFDANGVAVARPLRAAA transporters Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_26685 AO353_26685 AO353_RS26685 WP_054598350.1 tr|A0A0N9W1L7|A0A0N9W1L7_PSEFL cobalt efflux pump Strong phenotypes on citrate (as a carbon source) but also on cobalt stress. The citrate phenotype may be due to iron deprivation (via chelation by the citrate) leading to heavy metal stress. The cobalt phenotype is more conserved. It is possible that nickel is also a substrate of this efflux pump, as a slight defect in nickel stress was observed, and this protein is 49% identical to the cobalt and nickel exporter dmeF (Atu0891) of Agrobacterium tumefaciens (PMID:27235438). AO353_26685 is annotated as performing zinc or cadium efflux as well (czcD), but unfortunately, we do not have data for those heavy metal stresses. However a role in zinc stress seems doubtful, as a close homolog in strain GW456-L13 is not important for resisting zinc. cation transporter Cobalt-zinc-cadmium resistance protein CzcD MRSTPQVSRYSHDHMFLGATHDENARRTLWVVALTFVMMVGEIIAGYITGSMALLADGFHMATHVGALGITAIAYGFARRNAGNARYSFGTGKVGDLAGFASAMVLGLVSIFIAVESVMRLFQPTTVAFTEATLIAVLGLAVNIVSALLLAGNSAHHDHGHGHGHGHGHGHGHHHDNNLRSAYVHVLADAMTSVLAIAALLAGRYLGWVWLDPVMGIVGAIVIANWAYGLMRDSAAVLLDTTDEHVAAEVRELLESTGDVSITDLHVWRVGPQARAAIVSVVTSAAVTADTIRERLAPVHELSHLTVEYRNA catabolism Pseudomonas fluorescens FW300-N2E3 pseudo3_N2E3 AO353_29305 AO353_29305 AO353_RS29305 WP_054598124.1 tr|A0A0N9WJH3|A0A0N9WJH3_PSEFL Gamma-glutamyl-GABA hydrolase (EC 3.5.1.94) Specifically important for: Putrescine Dihydrochloride. part of the gamma-glutamyl-putrescine pathway for degrading putrescine (SEED_correct) gamma-glutamyl-gamma-aminobutyrate hydrolase Gamma-glutamyl-GABA hydrolase (EC 3.5.1.94) putative glutamine amidotransferase MALKPLIGVTACVKQIGLHPYHVSGDKYLRAVSVAALGLPVVIPSLGELTEIDELLAHLDGLLLTGSPSNVEPFHYQGPASAPGTDHDPARDSTTLPLLRAAIAAGVPVLGICRGFQEMNVAFGGSLHQKVHELPGMLDHREADHPDLAVQYAPAHAVSVQPGGVFQALELPPVFQVNSIHSQGIDRLAPGLRAEAIAPDGLIEAISVEHSKAFALGVQWHPEWQVLANPPYLSIFQAFGDACRQRAALRNTR transporters Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_00010 AO356_00010 AO356_RS00010 WP_060738036.1 tr|A0A0N9WSQ8|A0A0N9WSQ8_PSEFL ABC transporter for D-Sorbitol, ATPase component Specific phenotype on D-Sorbitol. ABC transporter ATP-binding protein Various polyols ABC transporter, ATP-binding component MATLKIENLKKGFEGLSIIKGIDLEVKDKEFVVFVGPSGCGKSTLLRLIAGLEDVTSGTIELDGRDITEVTPAKRDLAMVFQTYALYPHMTVRKNLSFALDLAGEKKPDVERKVAEAARILELGSLLDRKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQTRLELSRLHKELQATMIYVTHDQVEAMTLATKVVVLNAGRIEQIGSPLELYHHPANLFVAGFLGTPKMGFLQATVHAVHASGVEVRFASGTTLLIPRDSSALSVGQSVTIGIRPEHLTLGAEGQVLVTTDVTERLGSDTFCHVNVDSGESLTVRVQGDCEVPYAARRYLTLDVAHCHLFDESGLSVSPAASRAA transporters Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_00015 AO356_00015 AO356_RS00015 WP_013692786.1 tr|A0A0N9VWQ6|A0A0N9VWQ6_PSEFL ABC transporter for D-Sorbitol, permease component 1 Specific phenotypes on D-Sorbitol; D-Sorbitol. (no phenotype on mannitol) sugar ABC transporter permease Various polyols ABC transporter, permease component 2 sorbitol/mannitol transport system permease protein MMTLKQSRSLQSVLLGTLAWVTALLLFFPIFWMVLTSFKTEIDAFATPPQFIFMPTLENYLHIQERSDYFHFAWNSVLISFSATALCMLIAVPAAYSMAFYETKRTKQTLLWMLSTKMLPPVGVLMPIYLLAKGAGLLDTRIALIVIYTLINLPIVVWMIYTYFKDIPREILEAARLDGATLGQEMLRVLLPISKGGLASTMLLSMILCWNEAFWSLNLTSSSAAPLTALIASYSSPEGLFWAKLSAVSTLACAPILIFGWISQKQLVRGLSFGAVK transporters Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_00020 AO356_00020 AO356_RS00020 WP_013692785.1 tr|A0A0N9WK88|A0A0N9WK88_PSEFL ABC transporter for D-Sorbitol, permease component 2 Specific phenotypes on D-Sorbitol; D-Sorbitol. (no phenotype on mannitol) sugar ABC transporter permease Various polyols ABC transporter, permease component 1 MNTSIIRAQLAASAPSRARRLINPGWFLVSPSVALLLLWMIVPLAMTVYFSVIRYNLLNPGENEFVGLENFAYFVTDSGFLPGALNTLILVGSVLLISVIFGVLIAALLEASEFFGRGIVRVLLISPFFIMPTVGSLIFKNLIFHPVSGILAAVWKFFGAQPVDWLAHYPLFSIIVIVSWQWLPFAILLLMTAMQSLDQEQKEAARLDGAGALAIFWHLTLPHLARPIAVVVMIETIFLLSVFAEIFTTTNGGPGFASTNLAYLIYNQALVQFDVGMASAGGLIAVVIANIAAIVLVRMIGKNLTDKA transporters Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_00025 AO356_00025 AO356_RS00025 WP_060738037.1 tr|A0A0N9WC97|A0A0N9WC97_PSEFL ABC transporter for D-Sorbitol, periplasmic substrate-binding component Specific phenotype on D-Sorbitol. sugar ABC transporter substrate-binding protein Various polyols ABC transporter, periplasmic substrate-binding protein MKITNALILSTGLSFALASHAAETLTIATVNNGDMIRMQRLSKVFEQQHPDIKLNWVVLEENVLRQRLTTDIATQGGQFDVLTIGTYETPMWGAKNWLEPMKDLPAGYDVDDIFPAVRQGLSVNDTLYALPFYGESTITYYRTDLFKAAGLTMPGQPTWSQLGEFAAKLNDPSKDQYGMCLRGKAGWGENMALLTTMANAFGARWFDEKWQPELNGPEWKAAATFYVDTLKKYGPPGVSSNGFNETLALFNSGKCAIWVDASVAGSFTTDKEQSRVVDSVGFAPAPIEVTDKGSSWLYAWSLAIPATSKHKEAAKSFVTWATSKEYIQLVTDKDGITNVPPGTRISTYSDAYLKAAPFAQVTLQMMKHADPSQPSAKPVPYVGIQYVVIPEFQSIGTSVGKLFSAALTGQMSVEQALASAQSTTEREMKRAGYPKK catabolism Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_00450 AO356_00450 AO356_RS00450 WP_060738105.1 tr|A0A0N9WKE9|A0A0N9WKE9_PSEFL D-glucosaminate dehydratase (EC 4.3.1.9) Specifically important for: D-Glucosamine Hydrochloride. This enzyme had not previously been linked to a gene. This is the second step in catabolism of glucosamine, and the 'beta' form of the enzyme was expected to be PLP-dependent and about this size. Iwamoto et al (2003) purified a non-specific 'alpha' enzyme for this reaction (PMID: 12686150) amino acid deaminase D-serine deaminase (EC 4.3.1.18) MSSVIPNAGVEKGAATVGAHLLKDVSLPALVLHRAALEHNIRWMQAFVTDSGAELAPHGKTSMTPALFRRQLDAGAWGLTLATAVQTRAAYAHGVRRVLMANQLVGTPNMALIADLLADPAFEFHCMVDHPDNVADLGAFFASRGMKLNVMIEYGVVGGRCGCRTEAEVLALAEAIRSQPALALTGIEGYEGVIHGDHAISGIRAFAASLVRLAVQLQDDDAFAIDKPIITASGSAWYDLIAESFEAQNAHGRFLSVLRPGSYVAHDHGIYKEAQCCVLERRSDLHEGLRPALEVWAHVQSLPEPGFAVIALGKRDVAYDAGLPVPLKRYTPGSDSVPGDDVSGCKVTAVMDQHAFMSVAAGVELRVGDIIAFGTSHPCLTFDKWRVGCLVDEQLRVVESMETCF transporters Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_00470 AO356_00470 AO356_RS00470 WP_028236639.1 tr|A0A0N9WS63|A0A0N9WS63_PSEFL ABC transporter for D-Glucosamine, permease component 1 Specific phenotypes on D-Glucosamine Hydrochloride. Detrimental on D-serine as N source ABC transporter permease Amino acid ABC transporter, permease protein polar amino acid transport system permease protein MYESPSWLHELWVARDTLWAGFLTSVQCSLLAIVLGTLIGLVAGLVLTYGRTWMRAPFRFYVDLIRGTPVFVLVLACFYMAPALGWQIGAFQAGVLGLTLFCGSHVAEIVRGALQALPRGQMEASQAIGLTFYQSLGYVLLPQALRQILPTWVNSSTEIVKASTLLSVIGVAELLLSTQQIIARTFMTLEFYLFAGFLFFIINYAIELLGRHIEKRVALP transporters Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_00475 AO356_00475 AO356_RS00475 WP_018608019.1 tr|A0A0N7H195|A0A0N7H195_PSEFL ABC transporter for D-Glucosamine, permease component 2 Specific phenotypes on D-Glucosamine Hydrochloride. Detrimental on D-serine as N source amino acid ABC transporter permease amino acid ABC transporter, permease protein polar amino acid transport system permease protein MNYQLNFAAVWRDFDTLLAGLGLGLSLALVSIAIGCVIGLAMAFALLSKHRVLRVLASVYVTVIRNTPILVLILLIYFALPSLGIRLDKLPSFVITLSLYAGAYLTEVFRGGLLSIHKGQREAGLAIGLGEWQVKAYVTVPVMLRNVLPALSNNFISLFKDTSLAAAIAVPELTYYARKINVESYRVIETWLVTTALYVAACYLIAMVLRYFEQRLAIRR transporters Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_00480 AO356_00480 AO356_RS00480 WP_060738109.1 tr|A0A0N9WRG0|A0A0N9WRG0_PSEFL ABC transporter for D-Glucosamine, periplasmic substrate-binding component Specific phenotype on D-Glucosamine Hydrochloride. ABC transporter substrate-binding protein Glutamine ABC transporter, periplasmic glutamine-binding protein (TC 3.A.1.3.2) MQRRPSLFKACVFLFAATTAAMGVAQAADSKLDSVLQRGKLIVGTGSTNAPWHFQGADGKLQGFDIDIARMVAKGLFNDPEKVEFVVQSSDARIPNLLTDKVDMSCQFITVTASRAQQVAFTLPYYREGVGLLLPANSKYKEIEDLKAAGDDVTVAVLQNVYAEELVHQALPKAKVDQYDSVDLMYQAVNSGRADAAATDQSSVKYLMVQNPGRYRSPAYAWSPQTYACAVKRGDQDWLNFVNTTLHEAMTGVEFPTYAASFKQWFGVELPSPAIGFPVEFK catabolism Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_00940 AO356_00940 AO356_RS00940 WP_060738180.1 tr|A0A0N9WKN2|A0A0N9WKN2_PSEFL uridine/adenosine nucleosidase (EC 3.2.2.3; EC 3.2.2.7) Specifically important for: Uridine. Also important on adenosine. Annotated by SEED as acting on uridine and inosine, and the fitness data suggests that it might also act on inosine (subtle phenotype) nucleoside hydrolase Inosine-uridine preferring nucleoside hydrolase (EC 3.2.2.1) MHRYAEKMHQLIRSLLLLSLITATSAQAAEKIDLIIDTDPGADDVVALLFALASPEELHIRALTTVAGNVRLDKTSRNARLAREWAGREDVPVYAGAPKPLMRTPIYAENIHGKEGLSGVTVHEPKKGLAEGNAVNYLIDTLKAAKPHSITIAMLGPQTNLALALVQEPDIVQGIKEVVIMGGAHFNGGNITPVAEFNLFADPQAAEVVAKSSVKLTYLPLDVTHKILTSEARLKQIAALNNNASKLVGDILNEYVKGDMEHYGMTGGPVHDATVIAYLLKPQLFTGRSVNVVVDSREGPTFGQTIVDWYDGLKAPKNAFWVENGDAQGFFDLLTERLARLK catabolism Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_05200 AO356_05200 AO356_RS05210 WP_060738871.1 tr|A0A0N9WVA7|A0A0N9WVA7_PSEFL Isomerase for D-mannose and D-mannitol catabolism (probably D-mannose-6-phosphate isomerase or D-mannose isomerase) Specifically important for: D-Mannitol; D-Mannose. Often annotated as N-acylglucosamine 2-epimerase, but some homologs are annotated as D-mannose isomerase or D-mannose-6-phosphate isomerase, which would fit its phenotypes. (Mannitol is probably converted to mannose or mannose-6-phosphate.) A fructokinase AO356_00035 also seems to be required for consuming these substrates, which suggests that this converts D-mannose to D-fructose, but data for close homologs suggests a phosphorylated substrate instead, so the substrate is uncertain. sugar isomerase N-acylglucosamine 2-epimerase (EC 5.1.3.8) MDTFQPAFSSWLNAPAHQQWLAAEGLRLLAFAKASKLPDGFGNLDELGRLPADARAETMNTARMTHSFAMAHIQGLPGFAELVDHGIQALNGRLRDAEHGGWFATTRPDEDGAGKAAYLHAFVALAASSAVVAQRPGAAALLDEAVRIIDEHFWCEEEGALRESFNRDWSEEEAYRGANSNMHATEAFLALADATDDPRWLVRALRIVERVIHGHAAANDYLVVEHFDRHWQPLHEYNQDNPADGFRPYGTTPGHGFEWARLLLHLEAARVQIGMLTPGWLAQDAQKLFDQNCRHGWDVDGAPGIVYTLDWDNRAVVRHRLHWVHAEAAAAASALLKRTDEAKYEAWYRCFWEFCDKHFIDRCNGSWHHELDPQNRPSADIWPGKPDLYHAWQAVLIPRLPLAPSMASALARLSSPAPV transporters Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_05495 AO356_05495 AO356_RS05505 WP_060738925.1 tr|A0A0N9WVJ0|A0A0N9WVJ0_PSEFL ABC transporter for L-Lysine, periplasmic substrate-binding component Specific phenotype on L-Lysine. Note that this organism has a second ABC transporter that is also important for lysine utilization, which is not explained. ABC transporter substrate-binding protein Lysine-arginine-ornithine-binding periplasmic protein precursor (TC 3.A.1.3.1) lysine/arginine/ornithine transport system substrate-binding protein MKKALLTLSALALCMAAGVATAKEYKELRFGVDPSYAPFESKAADGSLVGFDIDLGNAICAELKVKCKWVESDFDGMIPGLKANKFDGVISSMTVTPAREKVIDFSSELFSGPTAYVFKKGSGLSEDVASLKGKTIGYEQGTIQEAYAKAVLDKAGVKTQAYQNQDQVYADLTSGRLDAAIQDMLQAELGFLKSPKGEGYEVSKPVDSELLPAKTAIGIKKGNSELKALLDKGIKALHDDGKYAEIQKKHFGDLNLYSGK transporters Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_05500 AO356_05500 AO356_RS05510 WP_060743074.1 tr|A0A0N9X3H8|A0A0N9X3H8_PSEFL ABC transporter for L-Lysine, permease component 1 Specific phenotypes on L-Lysine; L-Lysine. Note that this organism has a second ABC transporter operon that is important for lysine utilization, which is not explained. amino acid ABC transporter permease Histidine ABC transporter, permease protein HisQ (TC 3.A.1.3.1) histidine transport system permease protein MFEQLLQNLGLSAFSLQGFGPLLMQGTWMTIKLSALSLLLSVLLGLLGASAKLSRVKLLRIPAQLYTTLIRGVPDLVLMLLIFYSLQTWLTSFTDFMEWEYIEIDPFGAGVITLGFIYGAYFTETFRGAILAVPRGQVEAATAYGLKRGQRFRFVVFPQMMRFALPGIGNNWMVMLKATALVSIIGLADLVKAAQDAGKSTYQLFYFLVLAALIYLLITSASNFILRWLERRYAAGAREAVR transporters Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_05505 AO356_05505 AO356_RS05515 WP_060738926.1 tr|A0A0N9VZB6|A0A0N9VZB6_PSEFL ABC transporter for L-Lysine, permease component 2 Specific phenotypes on L-Lysine; L-Lysine. Note that this organism has a second ABC transporter operon that is also important for lysine utilization, which is not explained. amino acid ABC transporter permease Histidine ABC transporter, permease protein HisM (TC 3.A.1.3.1) histidine transport system permease protein MIELLQEYWRPFLYSDGVNITGLAMTLWLLSASLLIGFVVSIPLSIARVSPKFYVRWPVQFYTYLFRGTPLYIQLLICYTGIYSIAAVRAQPMLDSFFRDAMNCTILAFALNTCAYTTEIFAGAIRSMNHGEVEAAKAYGLTGWKLYAYVIMPSALRRSLPYYSNEVILMLHSTTVAFTATVPDVLKVARDANSATFLTFQSFGIAALIYLTVTFALVGLFRLAERRWLAFLGPTH transporters Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_05515 AO356_05515 AO356_RS05525 WP_060738928.1 tr|A0A0N9WEE5|A0A0N9WEE5_PSEFL ABC transporter for L-Lysine, ATPase component Specific phenotype on L-Lysine. Note that this organism has a second ABC transporter operon that is also important for lysine utilization, which is not explained. amino acid transporter Histidine ABC transporter, ATP-binding protein HisP (TC 3.A.1.3.1) histidine transport system ATP-binding protein MYKLTIEGLHKSYGEHEVLKGVSLKAKTGDVISLIGASGSGKSTFLRCINFLEQPNDGAMTLDGQPVQMIKDRHGMHVADADELQRIRTRLAMVFQHFNLWSHMTVLENITMAPRRVLGVSKQEADDRARRYLDKVGLPARVAEQYPAFLSGGQQQRVAIARALAMEPEVMLFDEPTSALDPELVGEVLKVIQGLAEEGRTMIMVTHEMSFARKVSNQVLFLHQGLVEEEGAPEDVLGNPKSERLKQFLSGNLK transporters Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_07550 AO356_07550 AO356_RS07560 WP_060743082.1 tr|A0A0N9WGP9|A0A0N9WGP9_PSEFL L-lactate and D-lactate permease (lctP family) This gene is often annotated as a L-lactate transporter but has a specific phenotype on D-lactate as well. Although it is difficult to rule out polar effects on the lactate dehydrogenase genes downstream, this gene's phenotype on D-lactate is conserved and is observed on both strands, and no other D-lactate transporter was identified by the mutant fitness data. (There is a zinc ABC transporter with a specific defect on D-lactate, but it is very similar to znuABC of P. aeruginosa, i.e. AO356_11480 is 65% identical to PA5498, so it is unlikely to be a lactate transporter.) Furthermore, the annotation as lactate permease seems to be derived from E. coli glcA or yghK, which transports both isomers of lactate (PMID:11283302). (KEGG_correct) L-lactate permease L-lactate permease lactate transporter, LctP family MQTWQQLYSPLGSLGLSALAAVIPIVFFFLALAVFRLKGHVAGSITLALAIAVAIFAFNMPADMAFAAAGYGFAYGLWPIAWIIVAAVFLYKLTVKSGQFEVIRSSVLSITDDQRLQVLLIGFCFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGALGIPIIVAGQVTGIDAFKIGAMTGRQLPLLSLFVPFWLVFMMDGLRGVRETWPAALVAGLSFAITQYFTSNFIGPELPDITSALASLISLTLFLKVWQPKRTAGAQIAGATSSATVTASVGGFGQPRSTVASPYSLGEIIKAWSPFLILTVLVTIWTLKPFKAMFAAGGSMYGWVFNFAIPHLDQMVIKVAPIVINPTAIPAVFKLDPISATGTAIFFSALISMLVLKINIKTGLTTFKETLFELRWPILSIGMVLAFAFVTNYSGMSSTMALVLAGTGAAFPFFSPFLGWLGVFLTGSDTSSNALFSSLQATTAHQIGVNDTLLVAANTSGGVTGKMISPQSIAVACAATGLVGKESDLFRFTLKHSLFFATIVGLITLAQAYWFTGMLVH catabolism Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_09590 AO356_09590 AO356_RS09605 WP_060739584.1 tr|A0A0N9W738|A0A0N9W738_PSEFL N-formylglutamate deformylase (EC 3.5.1.68) Specifically important for: L-Histidine. KEGG suggests formimidoyl-L-glutamate as the substrate, while SEED suggests N-formylglutamate. This gene is cofit with iminohydrolase (which produces N-formylglutamate) which suggests that the SEED annotation is correct. (SEED_correct) N-formylglutamate deformylase N-formylglutamate deformylase (EC 3.5.1.68) formiminoglutamase VEKVLNFKQGRVPLLVSMPHAGLRLTPAVKAGLIPEAQSLPDTDWHIPQLYEFANELGASTLAAEYSRFVVDLNRPSDDKPMYVGATTGLYPATLFDGVPLFREGLEPSAEERATYLQQVWMPYHQALRQELARLKAEFGYALLFDAHSIRSVIPHLFDGKLPDFNLGTFNGASCDPTLASQLEAICARHGQFTHVLNGRFKGGHITRHYGNPAEDIHAVQLELCQSTYMEEFEPFNYRPDLAAPTQVVLRELLEGFLAWGQKTYKH transporters Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_09610 AO356_09610 AO356_RS09625 WP_050586211.1 tr|A0A0N9X7T0|A0A0N9X7T0_PSEFL ABC transporter for L-Histidine, ATPase component Specific phenotype on L-Histidine. This gene cluster also includes a permease of the nucleobase-cation-symport family (AO356_09625) that is important for histidine utilization but whose role is unclear. (SEED_correct) hypothetical protein Histidine ABC transporter, ATP-binding protein (TC 3.A.1) glycine betaine/proline transport system ATP-binding protein MSNAAISKIEVKNVFKIFGNRSKEALELIRQNKTKDQVLAETGCVVGVNDLSLSIGTGEIFVIMGLSGSGKSTLVRHFNRLIDPTSGAILVDGEDILQLDMDALREFRRHKISMVFQSFGLLPHKSVLDNVAYGLKVRGESKQVCAERALHWINTVGLKGYENKYPHQLSGGMRQRVGLARALAADTDIILMDEAFSALDPLIRAEMQDQLLELQKTLHKTIVFITHDLDEAVRIGNRIAILKDGKLIQVGTPREILHSPADEYVDRFVQRRAAVV transporters Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_09615 AO356_09615 AO356_RS09630 WP_060739588.1 tr|A0A0N9W6X3|A0A0N9W6X3_PSEFL ABC transporter for L-Histidine, permease component Specific phenotypes on L-Histidine. ABC transporter permease Histidine ABC transporter, permease protein (TC 3.A.1) glycine betaine/proline transport system permease protein MFPESFTFSIADWVNGWVDSLVTNYGDVFRHISDTLLWAIVNLEGLLRMAPWWLMLAIVGGIAWHATRKVLATAVIVGLLFLVGAVGLWDKLMQTLALMLVATLISVLIGIPLGILSARSNRLRSVLMPLLDIMQTMPSFVYLIPVLMLFGLGKVPAIFATVIYAAPPLIRLTDLGIRQVDGEVMEAINAFGANRWQQLFGVQLPLALPSIMAGINQTTMMALSMVVIASMIGARGLGEDVLVGIQTLNVGRGLEAGLAIVILAVVIDRITQAYGRPRHEVSK transporters Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_09620 AO356_09620 AO356_RS09635 WP_014336129.1 tr|A0A0N9WXL6|A0A0N9WXL6_PSEFL ABC transporter for L-Histidine, periplasmic substrate-binding component Specific phenotype on L-Histidine. This gene cluster also includes a permease of the nucleobase-cation-symport family (AO356_09625) that is important for histidine utilization but whose role is unclear histidine ABC transporter substrate-binding protein Histidine ABC transporter, histidine-binding protein (TC 3.A.1) glycine betaine/proline transport system substrate-binding protein MKSNKTLLTTLLSMGLLASAGATQAAGWCESGKPVKFAGLNWESGMLLTDVLQVVLEKGYDCKTDSLPGNSITMENALSSNDIQVFAEEWVGRSEVWNKAEKAGKVVGVGAPVVGAIEGWYVPRYVVEGDAKRKLEAKAPGLKNIADLGQYAAVFKDPEEPSKGRFYNCPAGWTCELDNSEMLKSYGLEKTYTNFRPGTGPALDAAVLSSYKRGEPILFYYWSPTPLMGQVDLVKLEEKPGVDKSVSIKVGLSKTFHDEAPELVAVLEKVNLPIDILNQNLGRMAKERIESPKLAKIFLKEHPEVWHAWVSEDAAKKIDAAL catabolism Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_09635 AO356_09635 AO356_RS09650 WP_060739590.1 tr|A0A0N7H1W3|A0A0N7H1W3_PSEFL histidine utilization regulatory protein hutD Specifically important for: L-Histidine. Believed to prevent overexpression of the hut operon (not an enzyme) (PMC:1950622) hypothetical protein Conserved hypothetical protein (perhaps related to histidine degradation) hypothetical protein MSQLKVLRAADYPRMPWKNGGGSTEEITRDAGTGLEGFGWRLSIADIGESGGFSTFAGYERIISVLQGDGMTLNVDGQATGPLRPLDPFAFSGESHVHCTLLGGPIRDFNLIYAPQRYRARLQWVGGQQRFFSEAETLLVFSAAPGLTIRIGESAVILGLYDCLQLSGNTGLLDITSHGQCCVIELTAR transporters Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_09895 AO356_09895 AO356_RS09910 WP_014336086.1 tr|A0A0N9WX98|A0A0N9WX98_PSEFL ABC transporter for L-Lysine, ATPase component Has weaker phenotypes on lysine than the other components, but is in an apparent operon and has the correct domain. Note that this organism has a second ABC transporter operon that is also important for lysine utilization, which is not explained. amino acid transporter Histidine ABC transporter, ATP-binding protein HisP (TC 3.A.1.3.1) MAQATPALEIRNLHKRYGQLEVLKGVSLTARDGDVISILGSSGSGKSTFLRCINLLENPNQGQILVAGEELKLKAAKNGELVAADGKQINRLRSEIGFVFQNFNLWPHMSVLDNIIEAPRRVLGQSKAEAVEVAEALLAKVGIADKRHAYPAELSGGQQQRAAIARTLAMQPKVILFDEPTSALDPEMVQEVLSVIRALAEEGRTMLLVTHEMGFARQVSSEVVFLHQGLVEEQGSPQQVFENPLSARCKQFMSSNR transporters Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_09900 AO356_09900 AO356_RS09915 WP_060739627.1 tr|A0A0N9WVY2|A0A0N9WVY2_PSEFL ABC transporter for L-Lysine, periplasmic substrate-binding component Specific phenotypes on L-Lysine; L-Lysine. Note that this organism has a second ABC transporter operon that is also important for lysine utilization, which is not explained. amino acid ABC transporter Lysine-arginine-ornithine-binding periplasmic protein precursor (TC 3.A.1.3.1) MQTYKKFLLAAAVSLVFSANAMAADKLKMGIEAAYPPFNNKDASGQVVGFDKDIGDALCAKMKVECEVVTSDWDGIIPALNAKKFDFLISSLSITEERKQAVDFTDPYYSNKLQFIAPKSAEFKTDKDSLKGKVIGAQRATLAGTWLEDELGSDITTKLYDTQENAYLDLTSGRVDAILADKYVNYDWLKTEAGRAYEFKGDPVVESDKIGIAVRKGDNELRNKLNAALKEIVADGTYKKINDKYFPFNIY transporters Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_09905 AO356_09905 AO356_RS09920 WP_060739628.1 tr|A0A0N9X7X5|A0A0N9X7X5_PSEFL ABC transporter for L-Lysine, permease component 1 Specific phenotypes on L-Lysine; L-Lysine. Note that this organism has a second ABC transporter operon that is also important for lysine utilization, which is not explained. ABC transporter permease Arginine ABC transporter, permease protein ArtQ polar amino acid transport system permease protein MMIDLHGFGPALAAGALMTVKLALSALCLGLVLGLLGALAKTSPYKPLQWLGGTYSTLVRGIPELLWVLLIYFGTVNLMRALGEYLGMPDLALNAFAAGVIALGLCFGAYATEVFRGAILAIPKGHREAGVALGLSKWRIFTRLIMPQMWRIALPGLGNLFMILMKDTALVSVIGLEEIMRHAQIGVTVSKQPFTFYMVAALMYLGLTVLAMLGMHLLERRAARGFARSTQ transporters Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_09910 AO356_09910 AO356_RS09925 WP_060739629.1 tr|A0A0N9W704|A0A0N9W704_PSEFL ABC transporter for L-Lysine, permease component 2 Specific phenotype on L-Lysine. Note that this organism has a second ABC transporter operon that is also important for lysine utilization, which is not explained. ABC transporter permease Amino acid ABC transporter, permease protein polar amino acid transport system permease protein MNWDVIIKWLPKLAQGATLTLELVAIAVIAGLLLAIPLGIARSSRLWQVRALPYAYIFFFRGTPLLVQLFLVYYGLAQFDAVRSSALWPYLRDPFWCATVTMTLHTAAYIAEILRGAIQAIPKGEIEAARALGMSRPKALFYIMLPRAARIGLPAYSNEVILMLKASALASTVTLLELTGMARTIIARTYLPVEIFFAAGMFYLLMSFLLVQGFKQLERWLRVDACQGR catabolism Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_10715 AO356_10715 AO356_RS10730 WP_060739768.1 tr|A0A0N9WQQ6|A0A0N9WQQ6_PSEFL 2-aminoadipate:2-oxoglutarate aminotransferase (EC 2.6.1.39) Specifically important for: L-Lysine. This is required for catabolism of lysine on the way to glutarate. The amino group donor is uncertain 4-aminobutyrate aminotransferase 5-aminovalerate aminotransferase (EC 2.6.1.48) / Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) MSKTNADLMARRTAAVPRGVGQIHPIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTAQLNKLTHTCFQVLAYEPYVEVCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSIDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTFFAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQKKYPVIGEVRALGAMIAVELFENGDTHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDEQLDKGLAIIEECFSEL catabolism Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_10845 AO356_10845 AO356_RS10860 WP_060739786.1 tr|A0A0N7H1Z1|A0A0N7H1Z1_PSEFL succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) Specifically important for: L-Lysine. Glutaryl-CoA is an intermediate in lysine catabolism and this reaction would be a way to form it from glutarate before oxidation by AO356_10850. Other reactions in this pathway were also found but the only candidate for glutarate semialdehyde dehydrogenase, AO356_26740, had little phenotype.) Note that this EC number is primarily associated with forming (S)-3-hydroxy-methylglutaryl-CoA. CoA-transferase L-carnitine dehydratase/bile acid-inducible protein F MGALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTGLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPNIVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIRQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVASPIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL catabolism Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_12580 AO356_12580 AO356_RS12595 WP_060740066.1 tr|A0A0N9W2U4|A0A0N9W2U4_PSEFL gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) Specifically important for: Putrescine Dihydrochloride; L-Arginine. Part of the gamma-glutamyl-putrescine pathway. The phenotype on arginine is mild and might reflect a side pathway from arginine to putrescine via ornithine decarboxylase. KEGG now annotates it as acting on the 4-guanidino form, and it probably also acts on the 4-amino form (see studies of PA5312 = kauB). Since this enzyme is closely related to kauB it is probably flexible. aldehyde dehydrogenase Aldehyde dehydrogenase (EC 1.2.1.3) MTTLTRTDWEQRARDLKIEGRAFINGEYTDAVSGETFDCLSPVDGRLLGKIASCDVADAQRAVENARATFNSGVWSRLAPSKRKTTMIRFAGLLKQHAEELALLETLDMGKPISDSLNIDVPGAAQALSWSGEAIDKLYDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVVLKPSEKSPLTAIRIAALAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIYSGESNMKRIWLEAGGKSPNIVFADAPDLQAAAESAASAIAFNQGEVCTAGSRLLVERSIKDTFLPLVIEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAGHSDGAKLVAGGKRILEETGGTYVEPTIFDGVSNAMKIAQEEIFGPVLSVIAFDTAEQAIEIANDTPYGLAAAVWTKDISKAHLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFDKYTELKSTWIKL catabolism Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_13135 AO356_13135 AO356_RS13155 WP_025216023.1 tr|A0A0N9WZ72|A0A0N9WZ72_PSEFL Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) Specifically important for: Putrescine Dihydrochloride. This is the first step in putrescine catabolism gamma-glutamylputrescine synthetase glutamine synthetase MSVPPRAVQLNEANAFLKEHPEVLYVDLLIADMNGVVRGKRIERTSLHKVYEKGINLPASLFALDINGSTVESTGLGLDIGDADRICYPIPDTLCNEPWQKRPTAQLLMTMHELEGEPFFADPREVLRQVVTKFDELGLTICAAFELEFYLIDQENVNGRPQPPRSPISGKRPHSTQVYLIDDLDEYVDCLQDILEGAKEQGIPADAIVKESAPAQFEVNLHHVADPIKACDYAVLLKRLIKNIAYDHEMDTTFMAKPYPGQAGNGLHVHISILDKDGKNIFASEDPEQNAALRHAIGGVLETLPAQMAFLCPNVNSYRRFGAQFYVPNSPTWGLDNRTVALRVPTGSADAVRLEHRVAGADANPYLLMAAVLAGVHHGLVNKIEPGAPVEGNSYEQNEQSLPNNLRDALRELDDSEVMAKYIDPKYIDIFVACKESELEEFEHSISDLEYNWYLHTV catabolism Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_13140 AO356_13140 AO356_RS13160 WP_060740154.1 tr|A0A0N9W325|A0A0N9W325_PSEFL Gamma-glutamyl-GABA hydrolase (EC 3.5.1.94) Specifically important for: Putrescine Dihydrochloride. this is part of the gamma-glutamyl-putrescine pathway for putrescine catabolism (SEED_correct) gamma-glutamyl-gamma-aminobutyrate hydrolase Gamma-glutamyl-GABA hydrolase (EC 3.5.1.94) putative glutamine amidotransferase MSRLPLIGVTTCSRQMGLHAYHTSGDKYARAVATAAKGLPVLVPSLADLFPPSDILDALDGILLTGSPSNVEPFHYQGPASAPGTAHDPARDATTLPLIRAAVEAGVPVLGICRGFQEMNVAFGGSLHQKVHEVGTFIDHREDDTQAVEVQYGPAHAVDIQPGGILAGLGLPQSIEVNSIHSQGIERLAPGLRAEAVAPDGLIEAVSVPEGKAFALGVQWHPEWEVSSNPHYLAIFQAFGDACRARATQRDADASNNA catabolism Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_13150 AO356_13150 AO356_RS13170 WP_060740156.1 tr|A0A0N9WHY7|A0A0N9WHY7_PSEFL Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) Specifically important for: Putrescine Dihydrochloride. KEGG annotates this as putrescine aminotransferase, probably based on similarity to spuC (PA0299) of P. aeruginosa, but it is believed that only the g-glutamyl- pathway operates in P. aeruginosa (X. Yao et al 2011, PMC3147493) aminotransferase Omega-amino acid--pyruvate aminotransferase (EC 2.6.1.18) putrescine aminotransferase MTRNNPQTREWQALSNDHHLAPFSDFKQLKEKGPRIITHAKGVYLWDSEGNKILDGMAGLWCVAVGYGREELADAASQQMRELPYYNLFFQTAHPPVLELSKAIADIAPEGMNHVFFTGSGSEGNDTMLRMVRHYWAIKGQPNKKVIISRKNGYHGSTVAGASLGGMTYMHEQGDLPIPGIVHIAQPYWFGEGGDMSPEEFGVWAANQLEEKILEIGVDNVGAFIAEPIQGAGGVIVPPDSYWPRMKEILAKYDILFVADEVICGFGRTGEWFGTDHYGLKPHMMTIAKGLTSGYIPMGGLIVRDDVVAVLNEGGDFNHGFTYSGHPVAAAVALENIRILRDEKIIERVHSETAPYLQKRLRELNDHPLVGEVRGVGLLGAIELVQDKATRKRYEGKGVGMICRQFCFDNGLIMRAVGDTMIIAPPLVISKAEIDELVTKARHCLDLTLSALQG transporters Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_13805 AO356_13805 AO356_RS13825 WP_060740268.1 tr|A0A0N9WRY0|A0A0N9WRY0_PSEFL ABC transporter for Carnitine, ATPase component Specific phenotype on Carnitine Hydrochloride. Likely to be a choline or glycine betaine transporter as well (with AO356_13855 as the SBP) choline ABC transporter ATP-binding protein L-proline glycine betaine ABC transport system permease protein ProV (TC 3.A.1.12.1) glycine betaine/proline transport system ATP-binding protein MSIIRFEDVDVIFSNRPKAALDLLDKGFSRPEILQQTGLIVGVEKASLSIEKGEICVLMGLSGSGKSSLLRCINGLNTVSRGKLFVEHEGRQIDIASCSPAELKMMRTKRIAMVFQKFALMPWLTVRENISFGLEMQGRPEKERRKLVDEKLELVGLTQWRNKKPDELSGGMQQRVGLARALAMDADILLMDEPFSALDPLIRQGLQDELLELQRKLQKTIVFVSHDLDEALKLGTRIAIMKDGKIIQYSKPEEIVLNPADDYVRTFVAHTNPLNVLCGRSLMRTLDNCKRINGSVCLDPGGDSWLDLAEGNTIKGARQNGAVLDLQNWAPGQSVEELGRRPTLVDSNIGMRDALQIRYQTGNKLVLHDNQKVVGILGDSELYHALLGKNLG transporters Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_13810 AO356_13810 AO356_RS13830 WP_060740269.1 tr|A0A0N9WI93|A0A0N9WI93_PSEFL ABC transporter for Carnitine, permease component Specific phenotypes on Carnitine Hydrochloride; Carnitine Hydrochloride. choline ABC transporter permease subunit L-proline glycine betaine ABC transport system permease protein ProW (TC 3.A.1.12.1) glycine betaine/proline transport system permease protein MLIDQKIPLGQYIAGFVEWLTQNGASTFDAIALFLETMIHGVTFALTWFNPLALIGLIALLAHFIQRKWGLTVFVIASFLLILNLGYWQETMETLAQVLFATLVCVLIGVPLGIVAAHKPMFYTMMRPVLDLMQTVPTFVYLIPTLTLFGLGVVPGLISTVVFAIAAPIRLTYLGIRDVPDELMDAGKAFGCSRRQLLSRIELPHAMPSIAAGITQCIMLSLSMVVIAALVGADGLGKPVVNALNTADIALGFEAGLAIVLLAIMLDRICKQPDAKVGGDA transporters Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_13815 AO356_13815 AO356_RS13835 WP_060740270.1 tr|A0A0N9WVR6|A0A0N9WVR6_PSEFL ABC transporter for Carnitine, periplasmic substrate-binding component 1 Specific phenotype on Carnitine Hydrochloride. This protein is similar to CaiX of P. syringae or P. aeruginosa (Psyr_2916 and PA5388) which has been shown to be a L-carnitine SBP (see PMID:19919675). Another gene in the cluster, AO356_13855, is also a SBP and is specifically important for L-carnitine utilization. AO356_13855 is similar to CbcX of P. aeruginosa or P. syringae (PA5378 or Psyr_4709) which is specific for choline or glycine betaine (ibid). Nevertheless, insertions in _13855 have a specific defect for carnitine utilization. It is possible that these insertions are polar on the beta-cleavage enzyme (_13850) which is required for carnitine catabolism. However insertions in _13855 in either orientation have a strong phenotype. glycine/betaine ABC transporter substrate-binding protein L-proline glycine betaine binding ABC transporter protein ProX (TC 3.A.1.12.1) glycine betaine/proline transport system substrate-binding protein MKGSKPLLLAAMLSLPMLANAADPEKCSTVNFSDVGWTDITVTTATTSVVLDALGYKTKTTMISVPVTYKSLADGKNMDVFLGNWMPTMENDIKAYREAGTVETVRTNLKGAKYTLAVPQALYDKGLHDFADIPKFKKELDGKIYGIEPGNDGNRLIQSMIEKNAFGLKDAGFKVVESSEAGMLSQVDRASKRGTDVVFLGWAPHPMNTRFKIQYLTGGDDFFGPDFGAATVATNTRKGYSQECSNVGQLLKNLEFTVDMESQLMGNVLDDKMKPEAAAKAWLKKNPQVLDTWLAGVTTIDGKPGLEAVKAKLAQ catabolism Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_13840 AO356_13840 AO356_RS13860 WP_060740275.1 tr|A0A0N9X9G0|A0A0N9X9G0_PSEFL L-carnitine 3-dehydrogenase, thioesterase-like subunit CdhB (EC 1.1.1.108) Specifically important for: Carnitine Hydrochloride. This is CdhB (PA5385), a subunit of L-carnitine 3-dehydrogenase. See PMC2857723. 4-hydroxybenzoyl-CoA thioesterase acyl-CoA thioester hydrolase MPTLTTYQTRILPEWVDYNGHLRDAFYLLIFSYATDALMDRLGLDSQNREASGHSLFTLELHLNYLHEVKLGAEVQVHTQIIGHDAKRLHLYHSLHLVGGDKELAGNEQMLLHVDLAGPRSAPFTEQTLARLDALLDEQSDLPPPAYIGRVIALPPAR catabolism Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_14165 AO356_14165 AO356_RS14185 WP_060740332.1 tr|A0A0N9WIE7|A0A0N9WIE7_PSEFL Acyl-CoA dehydrogenase (EC 1.3.8.7) Specifically important for: Tween 20. tween 20 hydrolyzes to a mix of C12, C14, and C16 fatty acids; this is probably part of beta oxidation (SEED_correct) acyl-CoA dehydrogenase Acyl-CoA dehydrogenase (EC 1.3.8.7) MPDYKAPLRDIRFVRDELLGYEAHYQSLPACQDATPDMVDAILEEGAKFCEQVLAPLNRVGDIEGCTWSESGVKTPAGFKEAYKQFVEGGWPSLAHDVEHGGQGLPESLGLAVSEMVGEANWSWGMYPGLSHGAMNTISEHGTPEQQEAYLTKLVSGEWTGTMCLTEPHCGTDLGMLRTKAEPQADGSYKVSGTKIFISAGEHDMADNIVHIVLARLPDAPAGTKGISLFIVPKFLPNADGSIGQRNAVSCGSLEHKMGIHGNATCVMNFDAATGYLIGPANKGLNCMFTFMNTARLGTALQGLAHAEIGFQGGLKYARDRLQMRSLTGPKAPDKAADPIIVHPDVRRMLLTMKAFAEGNRAMVYFTAKQVDIVKYGVDEEEKKKADALLAFMTPIAKAFMTEVGFESANHGVQIYGGHGFIAEWGMEQNVRDSRISMLYEGTTGIQALDLLGRKVLMTQGEALKGFTKIVHKFCQSNEGNEAVKEFVEPLAALNKEWGELTMKVGMAAMKDREEVGAASVDYLMYSGYACLAYFWADMARLAAEKLAAGTTEEAFYTAKLQTARFYFQRILPRTRTHVATMLSGANNLMDMKEEDFALGY catabolism Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_14190 AO356_14190 AO356_RS14210 WP_060740336.1 tr|A0A0N9WXM3|A0A0N9WXM3_PSEFL Acyl-CoA dehydrogenase (EC 1.3.8.7) Specifically important for: Tween 20. tween 20 hydrolyzes to a mix of C12, C14, and C16 fatty acids; this is probably part of beta oxidation (SEED_correct) acyl-CoA dehydrogenase Acyl-CoA dehydrogenase (EC 1.3.8.7) MADYKAPLRDMRFVLNEVFEVAKLWAQLPVLADTVDAETVEAILEEAGKVTSKSIAPLSRAADEEGCHWANGAVTTPAGFPQAYKTYAEGGWVGVGGDPVYGGMGMPKAVSAQVEEMVNSASLSFGLYPMLTAGACLSINAHASEELKAAYLPNMYAGVWAGSMCLTEPHAGTDLGIIRTKAEPQADGSYKVSGTKIFITGGEHDLTENIIHLVLAKLPDAPAGPKGISLFLVPKFMVNADGSLGARNAANCGSIEHKMGIQASATCVMNFDEAVGYLVGEPNKGLAAMFTMMNYERLGVGIQGLASGERSYQNAVEYARDRLQSRSPTGAQNKDKVADPIIVHPDVRRMLLTMKASNEGGRAFSTYVAMQLDTAKFSEDPVTRKRAEDLVALLTPVAKAFLTDLGLETTVHGQQVFGGHGYIREWGQEQLVRDVRITQIYEGTNGIQALDLVGRKIVGSGGAFYRLFADEIRHFTATASSDLAEFTKPLNDAVGTLDELTDWLLDRAKNNPNEIGAASVEYLQAFGYTAYAYMWALMAKAAFGKENQDDFYASKLGTARFYFARLLPRIHSLSASVKAGSESLFLLEPGQF catabolism Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_14225 AO356_14225 AO356_RS14245 WP_060740343.1 tr|A0A0N9WIF6|A0A0N9WIF6_PSEFL 5-aminopentanamidase (EC 3.5.1.30) Specifically important for: L-Lysine. this is an early step in the oxidation of lysine (SEED_correct) carbon-nitrogen hydrolase 5-aminopentanamidase (EC 3.5.1.30) MRVALYQCPPLPLDPAGNLHRLHQVALEARGADVLVLPEMFMTGYNIGVDAVNVLAEVYNGEWAQQIGRIAKAANLAIVYGYPERGEDGQIYNAVQLIDAQGERLANYRKSHLFGDLDHAMFSAGDSALPIVELNGWKLGLLICYDLEFPENARRLALAGAELILVPTANMQPYEFIADVTVRARAIENQCFVAYANYCGHEAELQYCGQSSIAAPNGSRPALAGLDEALIVGELDRQLLDDSRAAYNYLHDRRPELYDDLHKH catabolism Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_14230 AO356_14230 AO356_RS14250 WP_060740344.1 tr|A0A0N9WVY4|A0A0N9WVY4_PSEFL lysine 2-monooxygenase (EC 1.13.12.2) Specifically important for: L-Lysine. this is the first step in the oxidation of lysine (SEED_correct) amine oxidase Lysine 2-monooxygenase (EC 1.13.12.2) tryptophan 2-monooxygenase MNKNNRHPADGKKPITIFGPDFPFAFDDWIEHPAGLGSIPAHNHGTEVAIVGAGIAGLVAAYELMKLGLKPVVYEASKMGGRLRSQAFNGAEGVIAELGGMRFPVSSTAFYHYVDKLGLETKPFPNPLTPASGSTVIDLEGQTYYAQKLADLPALFQEVADAWADALEDGSRFGDIQQAIRDRDVPRLKELWNTLVPLWDDRTFYDFVATSKAFAKLSFQHREVFGQVGFGTGGWDSDFPNSMLEIFRVVMTNCDDHQHLVVGGVEQVPHGIWNHVPERCAHWPEGTSLNSLHLGAPRSGVKRIARSADGRFSVTDVWENTREYAAVLVTCQSWLLTTQIECEEALFSQKMWMALDRTRYMQSSKTFVMVDRPFWKDKDPETGRDLMSMTLTDRLTRGTYLFDNGDDKPGVICLSYSWMSDALKMLPHPVEKRVKLALDALKKIYPKVDIAARIIGDPITVSWEADPHFLGAFKGALPGHYRYNQRMYAHFMQDDMPAEQRGIFIAGDDVSWTPAWVEGAVQTSLNAVWGIMKHFGGETHAENPGPGDVFHEIGPIALPE transporters Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_17535 AO356_17535 AO356_RS17560 WP_060740818.1 tr|A0A0N7H2E9|A0A0N7H2E9_PSEFL N-acetylglucosamine-specific PTS system, IIBC components (nagE) Specific phenotype on NAG as a carbon source. Not sure why SEED think s this includes the IIA component. (KEGG_correct) PTS N-acetyl-D-glucosamine transporter PTS system, N-acetylglucosamine-specific IIA component (EC 2.7.1.69) / PTS system, N-acetylglucosamine-specific IIB component (EC 2.7.1.69) / PTS system, N-acetylglucosamine-specific IIC component (EC 2.7.1.69) PTS system, N-acetylglucosamine-specific IIB component ; PTS system, N-acetylglucosamine-specific IIC component MYQHFIEGLQRLGRALMLPIAILPIAGLLLRLGDTDLLDIAIIHDAGQAIFANLAMIFAIGIAVGFARDNNGTAGLAGAIGYLVMIATLKVLDASINMGMLAGIISGLLAGALYNRFKDIKLPEYLAFFGGRRFVPIVTGFSAVGLGVVFGLIWPPIQQGINGFGALLMESGSFGAFVFGVFNRLLIVTGLHHILNNMAWFIFGSFTDPATGAVVTGDLSRYFAGDPKGGQFMTGMFPVMLFGLPAACLAMYRNALPQRRKVMGGILLSMALTSFLTGVTEPIEFAFMFLAPLLFLVHALLTGVSMAVTNLLGIHLGFTFSGGFIDMVLGWGKSTNGWLVVPVGLAYAAIYYLVFDFCIRRFDLKTPGREEVPAGDKPAIAENQRAAAYIQALGGADNLITIGACTTRLRLDMVDRNKASDAQLKALGAMAVVRPGNGGSLQVVVGPMADSIADEIRLAVPSSLRPVTAPVPNAPAPTTPAALSSTEAQQWLDALGGQDNVLQLECVATSRLRVRLADDKGLSESRLKGLGCQGMSSLEDGVWHLLLGEKAPRLWQALDGLAHGRKVDAGA transporters Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_17540 AO356_17540 AO356_RS17565 WP_060740819.1 tr|A0A0N9WA75|A0A0N9WA75_PSEFL N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) Specific phenotype on NAG as a carbon source. Not sure why SEED think s this includes the IIA component. (KEGG_correct) PTS N-acetyl-D-glucosamine transporter PTS system, fructose-specific IIA component ; phosphotransferase system, enzyme I, PtsI ; phosphocarrier protein FPr MPNNNKELILSAPLSGPVLTLANVPDAVFASGAMGDGIAIDPLNDTLYAPCDAEVIHVARTGHAVTLRADNGAELLLHLGLDTVELQGEGFSMLVKEGARVSHGQPLLRYDVDKVALRCKSLVSLLVITNGEHFQARPITLKGVKVGEPLLHILAKAVGQAEHHDQDSGIEVFGQVRIAHRGGLHARPAALVRQTAQGFKSRSQLHFSGKSASCDSVMGMMGLAITEQAQVHVSCRGSDAEAALQALLTTLSTALVEEAHASAPPPEPPRANAEEGVLHGVCAAPGLVTGPLVRLSGIQLPEDIGGHAIEEQRQRLSDALAQVRGEIHLTLEHARARQHRDEEAIFSAHLALLEDPVLLDAADLFIEQGSAAPHAWSRSIDTQCQVLQQLGSTLLAERANDLRDLRQRVLRVLLGEAWQFDVAAGAIVAAQELTPSDLLQLSAQGVAGVCMVEGGATSHVAILARGKGLPCLVALGDELLAQEQGQAVVLDADGGRLELTPTVERLAQVRQAQTRRTALRAQQQSLAHTPARTVDGVEVEVAANVASSAEAGESLANGADGVGLLRTEFLFVDRHTAPDEEEQRQAYQAVLEAMGDKPVIIRTIDVGGDKQLDYLPLPSEANPVLGLRGIRLAQVRPDLLDQQLRALLQTRPLDRCRILLPMVTEVDELLHIRKRLDALGSELGLSERPQLGVMVEVPAAALLAEQLAEHADFLSIGTNDLSQYTLAMDRDHAGLAARVDALHPALLRLIAQTCAGAAKHGRWVGVCGALASDPLATPVLIGLGVRELSVSPPQIGEIKDRVRHLDAAQCARLSNELLNLGSALAVRRACHRHWPLG transporters Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_17670 AO356_17670 AO356_RS17695 WP_060740842.1 tr|A0A0N9XB41|A0A0N9XB41_PSEFL L-alanine and D-alanine permease Specific phenotype on D-alanine and L-alanine D-alanine/D-serine/glycine permease D-serine/D-alanine/glycine transporter amino acid transporter, AAT family MPVGNHLPHGETAQGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWFPDVPRWIWALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGNDGVALGISNLWAHGGFMPNGVSGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSVFWRILLFYVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIFSTGRMLYSLAQNGQAPAGFAKTSTNGVPRRALLLSIAALLLGVLLNYLVPEKVFVWVTSIATFGAIWTWVMILLAQLKFRKSLSASERAALKYRMWLYPVSSYLALAFLVLVVGLMAYFPDTRVALYVGPAFLVLLTVLFYTFKLQPTGDVQRAVRSAS transporters Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_17790 AO356_17790 AO356_RS17815 WP_060740863.1 tr|A0A0N9WZ17|A0A0N9WZ17_PSEFL alpha-ketoglutarate permease (MHS family) Specific phenotype on a-ketoglutarate. Not important for the utilization of other dicarboxylates (succinate or malate). 83% identical to PA5530, which is reported to transport a-ketoglutarate and also glutarate (PMC4097582). KEGG_correct MFS transporter Dicarboxylate MFS transporter MFS transporter, MHS family, alpha-ketoglutarate permease MDNSNALPIGSAAVPARERTTASRIKSIFSGSVGNMVEWYDWYVYAAFSLYFAKVFFPKGDTTAQLLNTAAIFAVGFLMRPIGGWLMGLYADRAGRKRALMASVYLMCFGSLIIALSPSYETIGVGAPILLVFARLLQGLSVGGEYGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALGVLIVLQQFLTTEQLYAWGWRIPFAIGALCAVVALYLRRGMEETESFTKKEKSKESAMRTLLRHPKELMTVVGLTMGGTLAFYTYTTYMQKYLVNTVGMSISDSTTISAATLFLFMCLQPVIGGLSDKIGRRPILIAFGILGTLFTVPILTTLHTIQTWWGAFFLIMAALIIVSGYTSINAVVKAELFPTEIRALGVGLPYALTVSIFGGTAEYIALWFKSIGMETGYYWYVTACIAVSLLVYITMKDTRKHSRIVTD transporters Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_18530 AO356_18530 AO356_RS18555 WP_060740975.1 tr|A0A0N9WU01|A0A0N9WU01_PSEFL L-tyrosine transporter Specific phenotype with tyrosine as the nitrogen source. Not important if phenylalanine is the nitrogen source. aromatic amino acid transporter Aromatic amino acid transport protein AroP amino acid transporter, AAT family MSGQNSHSGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAFMIMRQLGEMIVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHYWAPDIPTWVSAAAFFILINAINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGHGGPQASVTNLWSHGGFFPNGVSGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTVIPKAINQVIYRILIFYIGALVVLLSLTPWDSLLATLNASGDAYSGSPFVQVFSMLGSNTAAHILNFVVLTAALSVYNSGTYCNSRMLLGMAEQGDAPKALSRIDKRGVPVRSILASAAVTLVAVLLNYLVPQHALELLMSLVVATLVINWAMISYSHFKFRQHMNQTQQTPLFKALWYPYGNYICLAFVVFILGVMLLIPGIQISVYAIPVWVVFMWVCYVIKNKRSARQELAVAAAK transporters Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_18700 AO356_18700 AO356_RS18725 WP_060741003.1 tr|A0A0N9WZF1|A0A0N9WZF1_PSEFL L-Arginine ABC transporter, periplasmic substrate-binding component Specific phenotype on L-Arginine. (SEED_correct) ABC transporter substrate-binding protein Arginine/ornithine ABC transporter, periplasmic arginine/ornithine binding protein MKKLVLLGALALSVLSLPTFADEKPLKIGIEAAYPPFASKAPDGSIVGFDYDIGNALCEEMKVKCVWVEQEFDGLIPALKVRKIDAILSSMSITEDRKKSVDFTNKYYNTPARLVMKAGTQVSDNLAELKGKNIGVQRGSIHERFAREVLAPLGAEIKPYGSQNEIYLDVAAGRLDGTVADATLLDDGFLKTDAGKGFAFVGPAFTDEKYFGDGIGIAVRKGDALKDKINGAITALRENGKYKQIQDKYFAFDIYGK transporters Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_18705 AO356_18705 AO356_RS18730 WP_060741004.1 tr|A0A0N9XBK6|A0A0N9XBK6_PSEFL L-Arginine ABC transporter, permease component 2 Specific phenotype on L-Arginine. (SEED_correct) ABC transporter Arginine/ornithine ABC transporter, permease protein AotQ arginine/ornithine transport system permease protein MLKGYGAVILDGAWLTLELALSSMALAIVLGLIGVALRLSPVRWLAWLGDLYSTVIRGIPDLVLILLIFYGGQDLLNRVAPMLGYDDYIDLNPLAAGIGTLGFIFGAYLSETFRGAFMAIPKGQAEAGMAYGMSGFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKAKQAADATREPFTFFLAVAAMYLVITSVSLLALRHLEKRYSVGVRAADL transporters Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_18710 AO356_18710 AO356_RS18735 WP_060741005.1 tr|A0A0N9WA12|A0A0N9WA12_PSEFL L-Arginine ABC transporter, permease component 1 Specific phenotypes on L-Arginine; L-Arginine. (SEED_correct) amino acid ABC transporter permease Arginine/ornithine ABC transporter, permease protein AotM MIFDYNVIYEALPLYFSGLLTTLKLLALSLFFGLLAALPLGLMRVSKQPIVNMTAWLYTYVIRGTPMLVQLFLIYYGLAQFAIVRESFLWPWLSSATFCACLAFAINTSAYTAEIIAGSLRATPNGEIEAAKAMGMSRYKLYRRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITGAARTVNAQYYLPFEAYITAGAFYLCLTFILVRLFKLAERRWLGYLAPRKH transporters Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_18715 AO356_18715 AO356_RS18740 WP_060741006.1 tr|A0A0N9X1K7|A0A0N9X1K7_PSEFL L-Arginine ABC transporter, ATPase component Important for utiliizing L-arginine. Detrimental on L-lysine which might indicate that it leaks lysine. (SEED_correct) amino acid transporter Arginine/ornithine ABC transporter, ATP-binding protein AotP MYKLEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLNNEELKLVAGKDGAMKAADPKQLQRMRSRLSMVFQHFNLWSHMTALENIMEAPVHVLGVAKAEAREKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPELVGDVLKVMQALAVEGRTMVVVTHEMGFAREVSNQLVFLHKGIVEESGNPREVLVNPQSERLQQFLSGSLK transporters Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_18980 AO356_18980 AO356_RS19005 WP_060741049.1 tr|A0A0N9WU67|A0A0N9WU67_PSEFL sodium:C4-dicarboxylate symporter (dctA) Important for utilization of malate, succinate, or fumarate (all C4 dicarboxylates) as carbon sources. 81% identical to PA1183 from P. aeruginosa (PMC3165536), which is also involved in growth with these substrates. KEGG_correct C4-dicarboxylate transporter aerobic C4-dicarboxylate transport protein MTTRQPLYKSLYFQVIVAIAIGILLGHFYPQTGVALKPFGDGFIKLIKMVIAPIIFCTVVSGIGGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGAGMHIDVSTLDTSKIAGFISAGKDQSIIAFILNVIPNTIVGAFANGDILQVLMFSVLFGFALHRLGAYGKPVLDFIDRFAHVMFIIINMIMKLAPLGAFGAMAFTIGAYGVGSLVQLGQLMICFYITCVVFVLVVLGAICRAHGFSVIKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSFNLDGTSIYLTMAAVFIAQATDTPMDLTHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAVGHLPVAGLALILGIDRFMSEARALTNLVGNAVATIVVAKWVKELDEDQLQTELASGGRGISDVREDDEQIAAAQIAAAETSAPGTVK catabolism Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_19460 AO356_19460 AO356_RS19485 WP_060741122.1 tr|A0A0N9W5Z8|A0A0N9W5Z8_PSEFL allantoinase (EC 3.5.2.5) Specifically important for: Inosine. This protein is similar to hpxB from Klebsiella, which is allantoinase, an step in the degradation of purines such as adenine or hypoxanthine (inosine is the nucleoside of hypoxanthine). See PMID:19060149 allantoinase Uricase (urate oxidase) (EC 1.7.3.3) VSADYPRDLIGYGNNPPHPQWPGNARIALSFVLNYEEGGERNVLHGDKESEAFLSEMVAAQPLQGERNMSMESLYEYGSRAGVWRVLKLFKAFDIPLTIFAVAMAAQRHPDVIRAMVAAGHEICSHGYRWIDYQYMDEAQEREHMLEAIRILTEITGERPLGWYTGRTGPNTRRLVMEEGGFLYDSDTYDDDLPYWEPNTPNGKPHLVIPYTLDTNDMRFTQVQGFNKGDDFFQYLKDAFDVLYAEGAEAPKMLSIGLHCRLIGRPARLASLKRFLEYVKGHEHVWFSRRVDIARHWQQAHPYQGASNPGASK catabolism Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_19465 AO356_19465 AO356_RS19490 WP_060741123.1 tr|A0A0N9WUD7|A0A0N9WUD7_PSEFL 5-hydroxyisourate hydrolase [EC: 3.5.2.17] Specifically important for: Inosine. 5-hydroxyisourate is an intermediate in purine degradation (KEGG_correct) 5-hydroxyisourate hydrolase 5-hydroxyisourate hydrolase MGRLTTHVLDAAHGCPGSAIKVELYRVEGSQLQLVASAQTNSDGRCDAPLLQGEDYRSGVYQLQFHAGDYYRARGVQLPEPAFLDVVVLRFGISAEQEHYHVPLLISPYAYSTYRGS catabolism Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_20235 AO356_20235 AO356_RS20260 WP_060741243.1 tr|A0A0N9WBN8|A0A0N9WBN8_PSEFL L-arabinolactonase (EC 3.1.1.15) / D-galactonolactonase (EC 3.1.1.25) Specifically important for: L-Arabinose; D-Galactose. The SEED prediction explains the phenotype on L-arabinose but not on D-galactose. L-arabinose and D-galactose are chemically similar and some dehydrogenases act on both substrates, so it is not surprising that a lactonase would hydrolase both of their products. The dehydrogenase is probably AO356_20240. (SEED_correct) gluconolaconase L-arabinolactonase (EC 3.1.1.15) MKWTAVTEHRAKLGEGPFWDAPTQALYWVDIAGKQALRLIGANVEIWQMPEHVSAFIPTQSGDALVTLSSGVYRLDLDSPGLEPRLTLLCMADPQPGNRANEARCDPQGQLWLGTMQNNIGAEGEDLPIEHRSGGLFRVGSDGRVLPLLRGLGIPNTLLWSPDGTTVYFGDSLDGTVYRHFIYPEGNLAPAEVWFGPHPRGGPDGSAMDARGYIWNARWDGSCLLRLTPDGQVDRVIELPVSRPTSCVFGGEDLKTLYITSAASPLGHPLDGAVLSMRVDVPGVACTRFAG catabolism Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_20240 AO356_20240 AO356_RS20265 WP_060741244.1 tr|A0A0N7H2L2|A0A0N7H2L2_PSEFL L-arabinose 1-dehydrogenase (EC 1.1.1.46) This is specifically important for L-arabinose utilization. Some closely related proteins in other Pseudomonas are important for D-galactose utilization as well, so this is probably also a D-galactose 1-dehydrogenase. However mutants in this gene had little phenotype in D-galactose (two replicates). No other dehydrogenase was identified as specifically important on D-galactose. short-chain dehydrogenase 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100) MAEPLVLPPVPEPPKGERLKDKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAQKVEAVAAHWRERGADVHALQADVSKQQDLQAMARRAVELHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYGCKAVLPQMIEQGVGSIINIASVHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVNAIAPGYIETQLNVDYWNGFADPHAERQRALDLHPPRRVGQPIEVAMTAVFLASDEAPFINASCITIDGGRSVMYHD catabolism Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_21495 AO356_21495 AO356_RS21520 WP_060741450.1 tr|A0A0N9WV93|A0A0N9WV93_PSEFL gamma-glutamylputrescine oxidase (EC 1.4.3.-) Specifically important for: Putrescine Dihydrochloride. part of the pathway for oxidizing putrescine via gamma-glutamyl-putrescine (KEGG_correct) gamma-glutamylputrescine oxidoreductase Nucleoside-diphosphate-sugar epimerases gamma-glutamylputrescine oxidase MANTPYPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAAKVGFGASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCDLKDGGVFAALTAKQMGHLESQKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSGGHIHPLNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYLGNLVPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGGGVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYYSQGCSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYGLRDKLGF catabolism Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_21640 AO356_21640 AO356_RS21665 WP_060741475.1 tr|A0A0N9WCD3|A0A0N9WCD3_PSEFL acetyl-CoA C-acetyltransferase [EC: 2.3.1.9] Specifically important for: L-Lysine; Carnitine Hydrochloride. acetyl-CoA acetyltransferase is required for the breakdown of acetoacetyl-CoA, which is an intermediate in lysine degradation (via glutaryl-CoA) and in carnitine degradation (from the beta cleavage enzyme, see PMID: 24240508) (KEGG_correct) acetyl-CoA acetyltransferase acetyl-CoA C-acetyltransferase MQEVVIVAATRTAIGSFQGSLAAIPAPELGAAVIRRLLEQTGLSGEQVDEVILGQVLTAGSGQNPARQASILAGLPHAVPALTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSLAPYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREEQDAFAAASQQKAVAAIEGGRFADEITPILIPQRKGDPVAFATDEQPRAGTTAESLGKLKPAFKKDGSVTAGNASSLNDGAAAVILMSAEKAKALGLPVLAKISAYANAGVDPAIMGIGPVSATRRCLDKAGWSLEQLDLIEANEAFAAQSLAVARELKWDMDKVNVNGGAIALGHPIGASGCRVLVSLLHEMIKRDAKKGLATLCIGGGQGVALALERA catabolism Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_23175 AO356_23175 AO356_RS23200 WP_060741734.1 tr|A0A0N9X3S4|A0A0N9X3S4_PSEFL malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) Specifically important for: m-Inositol. 3-oxopropionate or malonate semialdehyde is an intermediate in myo-inositol catabolism (SEED_correct, although the name and EC number are confusing) methylmalonate-semialdehyde dehydrogenase Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) methylmalonate-semialdehyde dehydrogenase MSDAPVVGHYIDGRIQASDNARLSNVFNPATGAVQARVALAEPSTVDAAVASALAAFPAWSEQSSLRRSRVMFKFKELLDRHHDELAQIISREHGKVLSDAHGEVTRGIEIVEYACGAPNLLKTDFSDNIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERDPSASLLMARLLTEAGLPDGVFNVVQGDKVAVDALLQHPDIEAISFVGSTPIAEYIHQQGTAQGKRVQALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAVAVGDVGDELIAKLLPRIDQLKIGNGQQPGTDMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRGFKVPGAEQGFFVGATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFTRDGGIARAFARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGLRFYSRYKSVMQRWPDSIAKGPEFSMPTAQ catabolism Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_24585 AO356_24585 AO356_RS24610 WP_060741989.1 tr|A0A0N9WWL3|A0A0N9WWL3_PSEFL L-arabonate dehydratase (EC 4.2.1.25) Specifically important for: L-Arabinose. L-arabonate is an intermediate in the oxidation of L-arabinose (SEED_correct) dihydroxy-acid dehydratase L-arabonate dehydratase (EC 4.2.1.25) dihydroxy-acid dehydratase MSDKKPSLRSAQWFGTADKNGFMYRSWMKNQGIADHQFHGKPIIGICNTWSELTPCNAHFRQIAEHVKRGVIEAGGFPVEFPVFSNGESNLRPTAMLTRNLASMDVEEAIRGNPIDGVVLLTGCDKTTPALLMGAASCDVPAIVVTGGPMLNGKHKGQDIGSGTVVWQLSEQVKAGTITIDDFLAAEGGMSRSAGTCNTMGTASTMACMAEALGTSLPHNAAIPAVDARRYVLAHMSGMRAVEMVREDLKLSKILTKEAFENAIRVNAAIGGSTNAVIHLKAIAGRIGVQLDLDDWTRIGRGMPTIVDLQPSGRFLMEEFYYAGGLPAVLRRLGEANLIPNPNALTVNGKSLGENTKDAPIYGQDEVIRTLDNPIRADGGICVLRGNLAPLGAVLKPSAATAELMQHRGRAVVFENFDEYKARINDPELDVDANSILVMKNCGPKGYPGMAEVGNMGLPAKLLAQGVTDMVRISDARMSGTAYGTVVLHVAPEAAAGGPLAAVKEGDWIELDCASGRLHLDIPDAELAARLADLAPPQQLLVGGYRQLYIDHVLQADQGCDFDFLVGCRGAEVPRHSH catabolism Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_24595 AO356_24595 AO356_RS24620 WP_060741991.1 tr|A0A0N9WN17|A0A0N9WN17_PSEFL 2-dehydro-3-deoxy-L-arabinonate dehydratase (EC 4.2.1.43) # Specifically important in carbon source L-Arabinose. Similar to PA2216 from Pseudomonas aeruginosa (see PMC:PMC4038344) and to gguC or araD1 (Atu2345) from Agrobacterium tumefaciens (see PMC: PMC3232879), which also have this activity. In Agrobacterium, this reaction is proposed to be a step in L-arabinose oxidation. (Note that 2-keto-3-deoxy-L-lyxonate and 2-keto-3-deoxy-L-arabinonate are the same compound.) FAH family protein SUGAR TRANSPORTER MRLVQFELSNGERRVGVVDGDQVREVQGAGSVRELALAAIEAGVKLEQQVDSLGLGTGHDYARLLGELRILPPLDHPDPAHLLVSGTGLTHLGSASARDKMHQQAGDEATMTDTMRIFKWGVEGGKPQAGQTGVQPEWFYKGDGSIVVRPGHPFPLPPFAEDAGEEPEISGLYVIGHDGKPYRLGFAVGNEFSDHVMERKNYLYLAHSKLRSCSFGPELRVGELPQHLSGTSRILRNGEVLWQNEFLSGEANMCHSLENLEFHHFKYSQFLRPGDVHVHFFGTATLSFADGIRTQPGDVFEISQAEFGAPLVNGIAPVDAVFNPGTIGTL catabolism Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_28020 AO356_28020 AO356_RS28045 WP_060742590.1 tr|A0A0N7H343|A0A0N7H343_PSEFL ethanol oxidation regulatory protein ercA Specifically important for: Ethanol. Similar to ercA (PA1991) which apparently has a regulatory role (PMCID: PMC3754586) rather than being directly involved in catabolism. AO356_28055 is probably the main ethanol dehydrogenase. (not an enzyme) alcohol dehydrogenase Alcohol dehydrogenase (EC 1.1.1.1); Acetaldehyde dehydrogenase (EC 1.2.1.10) MSHVTEKMSLSPLRKFVSPEIMFGAGCRHNVGNYAKTFGARKVLIVTDPGVIAAGWVADVEASLQAQGIDYCIYSAVSPNPRVEEVMLGADLYRENHCDVIVAVGGGSPMDCGKGIGIVVAHGRSILEFEGVDTLNVPSPPLILIPTTAGTSADVSQFVIISNQQERMKFSIVSKAAVPDVSLIDPETTLSMDPFLSACTGIDALVHAIEAFVSTGHGPLTDPHALEAMRLINGNLVQMIANPADIALREKIMLGSMQAGLAFSNAILGAVHAMSHSLGGFLDLPHGLCNAVLVEHVVAFNYNSAPERFKVIAETLGIDCRGLNHREIRTRLVEHLIALKHTIGFHETLGLHGVSTSDIPFLSQHAMHDPCILTNPRESSQRDVEVVYGEAL transporters Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_28540 AO356_28540 AO356_RS28565 WP_060742692.1 tr|A0A0N9WPT3|A0A0N9WPT3_PSEFL D-mannose and D-mannitol transporter Specific phenotype on D-mannose and D-mannitol as carbon sources. No other transporter for these substrates was apparent in the fitnes data. hexuronate transporter Hexuronate transporter MFGQGRSLIIIMLFLAGVINYLDRSALSVAAPFIQKDYGLSTGEMGMIFSSFFVGYAAFNFIGGWAADRYGAKTTLLLAMVLWSLFSGLTVLTVGFASLVLIRILFGMGEGPLSVTTSKMVNNWYTPKRRARAIGASMSGTPLGGAISGPVVGFIAVTYGWKISFIIIMLIGLVWAAVWFKFVKERPEGEGAEDILRAEGQGELAAQPVFPLRFYLKQPTVLFTSLAFFSYNYTLFFFLTWFPSYLTMAHGLNVKDMSIATVIPWVLGFLGLALGGFISDFVFKKTGRMMFSRKVVLVTCLLACAVCIACAGMVTTLYPAVILVALAVFFLYLTGAIYWAIIQDTVPAARVGGVSGFMHFLANTSGIVGPTLTGFLVQFTGSFTSAFLLAGLLTVIGAVCVARYVKPLSVADTGNAAAQSPQPVSALGRS catabolism Pseudomonas fluorescens FW300-N2C3 pseudo5_N2C3_1 AO356_28590 AO356_28590 AO356_RS28615 WP_060742701.1 tr|A0A0N7H357|A0A0N7H357_PSEFL Sucrose-6-phosphate hydrolase (EC 3.2.1.B3) Specifically important for: Sucrose. This gene is cofit with a sugar PTS system (AO356_07325; annotated as fructose specific but also apparently active on sucrose), which suggests that sucrose-6-phosphate is the correct substrate. The KEGG annotation (beta-fructofuranosidase) is broader but also includes this activity. (SEED_correct) glycosyl hydrolase family 32 Sucrose-6-phosphate hydrolase (EC 3.2.1.B3) beta-fructofuranosidase MTLSLNSLSNPMPASLEHAQQALRDGLSRLIHDYRPDYHLAPPTGWMNDPNGVVFFRGEYHVFYQHHPFDAKWGPMYWGHAKSADLVHWQHLPIALAPGDDFDRDGCFSGSAVVCGDTLALIYTGHTWLGEVGDERLIRQVQCLATSVDGVRFVKHGAVIEDAPQAAIMHFRDPKVWQEDGYWYLIAGARLGDTPLLPLYRSTDLRAWEFLDYVSRGTDGDGYMWECPDLFRLDGRDVLLYSPQGMQPAGYERLNKYQTGYRIGHLDSEWHFSGGPFIELDNGHDFYAAQTLVAADGRRLVWAWLDMWESPMPSQAHHWCGMLGLPRELELQGDRLGVFPARELVALRQAPLPSIAPWGESGSRWVPQVSGDRLEIHVHLDLLDCTEGHLGIALRCSADEQEQTLLYYDASLRRLVLDRSRSGAQVSGQRSVPIEPAQTQLHLRVFLDRSSIEVFEQSGRFSLSSRLYPRPDSLGVKLLASGTGGHVAISNAWPLASGWL catabolism Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_1146 TK06_RS05765 WP_063321224.1 tr|A0A159ZWN4|A0A159ZWN4_PSEFL 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.1) Specifically important for: L-Isoleucine. 2-methylbutanoyl-CoA is an intermediate in isoleucine catabolism. Butyryl-CoA dehydrogenase (EC 1.3.99.2) Butyryl-CoA dehydrogenase (EC 1.3.99.2) MLATEEQTQIRDMARQFAEERLKPFAAEWDREHRFPREAIDEMAELGFFGMLVPEQWGGCDTGYLAYAMTLEEIAAGDGACSTIMSVHNSVGCVPILKFGNDEQKAKFLTPLASGAMLGAFALTEPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIVPTDSPGYSVARVEDKLGQHASDTCQILFEDLKVPVGNRLGEEGEGYKIALANLEGGRVGIAAQAVGMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALRDSGQPALVEASMAKLFASEMAEKVCSMALQTLGGYGYLNDFPLERIYRDVRVCQIYEGTSDIQRMVISRNL transporters Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_1960 TK06_RS09830 WP_063321903.1 tr|A0A159ZWP3|A0A159ZWP3_PSEFL ABC transporter for D-sorbitol, ATPase component # Specifically important in carbon source D-Sorbitol Various polyols ABC transporter, ATP-binding component Various polyols ABC transporter, ATP-binding component MATLKIENLKKGFEGLSIIKGIDLEVKDKEFVVFVGPSGCGKSTLLRLIAGLEDVTSGTIELDGRDITEVTPAKRDLAMVFQTYALYPHMTVRKNLSFALDLAGEKKPDVERKVAEAARILELGSLLDRKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQTRLELSRLHKELQATMIYVTHDQVEAMTLATKVVVLNAGRIEQIGSPLELYHHPANLFVAGFLGTPKMGFLQATVHAVHASGVEVRFASGTTLLIPRDSSALSVGQSVTIGIRPEHLTLSAEGQVPVTTDVTERLGSDTFCHVNVDSGESLTVRVQGDCEVPYAARRYLTLDVAHCHLFDESGLSVSPAASRAA transporters Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_1961 TK06_RS09835 WP_063321904.1 tr|A0A159ZW38|A0A159ZW38_PSEFL ABC transporter for D-sorbitol, permease component 2 # Specifically important in carbon source D-Sorbitol. We do not have fitness data for the putative first subunit Pf6N2E2_1962. Various polyols ABC transporter, permease component 2 Various polyols ABC transporter, permease component 2 sorbitol/mannitol transport system permease protein MMTLKQSRSLQSLLLGTLAWVAALLLFFPIFWMVLTSFKTEIDAFATPPQFIFMPTLENYLHIQERSDYFHFAWNSVLISFSATALCMLIAVPAAYSMAFYETKRTKQTLLWMLSTKMLPPVGVLMPIYLLAKGAGLLDTRIALIVIYTLINLPIVVWMIYTYFKDIPREILEAARLDGATLGQEMLRVLLPISKGGLASTMLLSMILCWNEAFWSLNLTSSSAAPLTALIASYSSPEGLFWAKLSAVSTLACAPILIFGWISQKQLVRGLSFGAVK transporters Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_1963 TK06_RS09845 WP_063321905.1 tr|A0A159ZYG7|A0A159ZYG7_PSEFL ABC transporter for D-sorbitol, periplasmic substrate-binding component # Specifically important in carbon source D-Sorbitol Various polyols ABC transporter, periplasmic substrate-binding protein Various polyols ABC transporter, periplasmic substrate-binding protein MKITNALILSTGLSFALASHAAETLTIATVNNGDMIRMQRLSKVFEQQHPDIKLSWVVLEENVLRQRLTTDIATQGGQFDVLTIGTYETPMWGAKNWLEPMKDLPAGYDVDDIFPAVRQGLSVNDTLYALPFYGESTITYYRTDLFKAAGLTMPAQPTWSQLGEFAAKLNDPSKDQYGMCLRGKAGWGENMALLTTMANAFGARWFDEKWQPELNGPEWKAAATFYVDTLKKYGPPGVSSNGFNETLALFNSGKCAIWVDASVAGSFTTDKEQSRVVDSVGFAPAPTEVTDKGSSWLYAWSLAIPATSKHKEAAKSFVTWATSKEYIQLVTDKDGITNVPPGTRISTYSDAYLKAAPFAQVTLQMMKHADPSQPSAKPVPYVGIQYVVIPEFQSIGTSVGKLFSAALTGQMSVEQALASAQSTTEREMKRAGYPKK catabolism Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_2047 TK06_RS10360 WP_063321988.1 tr|A0A159ZWW4|A0A159ZWW4_PSEFL D-glucosaminate dehydratase (EC 4.3.1.9) Specifically important for: D-Glucosamine Hydrochloride. This enzyme had not previously been linked to a gene. This is the second step in catabolism of glucosamine, and the 'beta' form of the enzyme was expected to be PLP-dependent and about this size. Iwamoto et al (2003) purified a non-specific 'alpha' enzyme for this reaction (PMID: 12686150) D-serine deaminase (EC 4.3.1.18) D-serine deaminase (EC 4.3.1.18) MSSVIPNAGVEKGAATVGAHLLKDVSLPALVLHRAALEHNIRWMQAFVTDSGAELAPHGKTSMTPALFRRQLDAGAWGLTLASAVQTRAAYAHGVRRVLMANQLVGTPNMALIADLLADPAFEFHCMVDHPDNVADLGAFFASRGMKLNVMIEYGVVGGRCGCRTEAEVLALAEAIQAQPALALTGIEGYEGVIHGDHAISGIRAFAASLVRLAVQLQDNGAFAIDKPIITASGSAWYDLIAESFEAQNAHGRFLSVLRPGSYVAHDHGIYKEAQCCVLERRSDLHEGLRPALEVWAHVQSLPEPGFAVIALGKRDVAYDAGLPVPLKRYTPGSDSVTGDDVSGCKVTAVMDQHAFMNVAAGVELRVGDIISFGTSHPCLTFDKWRVGCLVDEQLRVVESMETCF transporters Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_2051 TK06_RS10380 WP_028236639.1 tr|A0A0N9WS63|A0A0N9WS63_PSEFL ABC transporter for D-Glucosamine Hydrochloride, permease component 1 Specific phenotypes on D-Glucosamine Hydrochloride. Amino acid ABC transporter, permease protein Amino acid ABC transporter, permease protein polar amino acid transport system permease protein MYESPSWLHELWVARDTLWAGFLTSVQCSLLAIVLGTLIGLVAGLVLTYGRTWMRAPFRFYVDLIRGTPVFVLVLACFYMAPALGWQIGAFQAGVLGLTLFCGSHVAEIVRGALQALPRGQMEASQAIGLTFYQSLGYVLLPQALRQILPTWVNSSTEIVKASTLLSVIGVAELLLSTQQIIARTFMTLEFYLFAGFLFFIINYAIELLGRHIEKRVALP transporters Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_2052 TK06_RS10385 WP_014338685.1 tr|A0A159ZWH7|A0A159ZWH7_PSEFL ABC transporter for D-Glucosamine Hydrochloride, permease component 2 Specific phenotypes on D-Glucosamine Hydrochloride; D-Glucosamine Hydrochloride. ko:K02029 : polar amino acid transport system permease protein amino acid ABC transporter, permease protein amino acid ABC transporter, permease protein polar amino acid transport system permease protein MNYQLNFAAVWRDFDTLLAGLGLGLSLALVSIAIGCVIGLAMAFALLSKHRVLRVLASVYVTVIRNTPILVLILLIYFALPSLGIRLDKLPSFVITLSLYAGAYLTEVFRGGLLSIHKGQREAGLAIGLGEWQVKAYVTVPVMLRNVLPALSNNFISLFKDTSLAAAIAVPELTYYARKINVESYRVIETWLVTTALYVAACYLIAMLLRYFEQRLAIRR transporters Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_2053 TK06_RS10390 WP_063321992.1 tr|A0A159ZUY1|A0A159ZUY1_PSEFL ABC transporter for D-Glucosamine, periplasmic substrate-binding component Specific phenotype on D-Glucosamine Hydrochloride. Glutamine ABC transporter, periplasmic glutamine-binding protein (TC 3.A.1.3.2) Glutamine ABC transporter, periplasmic glutamine-binding protein (TC 3.A.1.3.2) MQRRPSLFKTCVFLFAATVAAVGVAQAADSKLDSVLQRGKLIVGTGSTNAPWHFQGADGKLQGFDIDIARMVAKGLFNDPEKVEFVVQSSDARIPNLLTDKVDMSCQFITVTASRAQQVAFTLPYYREGVGLLLPANSKYKEIEDLKAAGDDVTVAVLQNVYAEELVHQALPKAKVDQYDSVDLMYQAVNSGRADAAATDQSSVKYLMVQNPGRYRSPAYAWSPQTYACAVKRGDQDWLNFVNTTLHEAMTGVEFPTYAASFKQWFGVELPSPAIGFPVEFK catabolism Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_2111 TK06_RS10665 WP_063322042.1 tr|A0A159ZX12|A0A159ZX12_PSEFL Dehydrocarnitine CoA-transferase and acetoacetate CoA-transferase, subunit A Very important on cartinine and also important on L-phenylalanine and L-leucine. Acts on dehydrocarnitine during carnitine catabolism to give dehydrocarnitine-CoA. Probably also acts on acetoacetate, which is an intermediate in the degradation of phenylalanine (via tyrosine and homogentistate) and leucine (from HMG-CoA lyase). Both substrates are 3-oxoacids, but not sure if succinyl-CoA is the source of the CoA as annotated. Note that acetoacetyl-CoA is probably cleaved to acetyl-CoA by _2113 (downstream). Similar to DhcA = PA1999. Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit A (EC 2.8.3.5) Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit A (EC 2.8.3.5) 3-oxoacid CoA-transferase subunit A MAGFDKRVSSYEEALEGLKDGMTVIAGGFGLCGIPENLIAEIKRKGIRDLTVVSNNCGVDGFGLGVLLEDRQIRKVVASYVGENALFEQQLLSGEIEVVLTPQGTLAEKMRAGGAGIPAFFTATGVGTPVAEGKEVREFHGRQYLMEESITGDFAIVKGWKADHFGNVIYRHTAQNFNPLAATAGKITVVEVEEIVEPGELDPTQIHTPGIYVDRVICGTFEKRIEQRTVRK catabolism Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_2112 TK06_RS10670 WP_003180355.1 tr|A0A0D9AX93|A0A0D9AX93_PSEFL Dehydrocarnitine CoA-transferase and acetoacetate CoA-transferase, subunit B Specifically important for: Carnitine Hydrochloride; L-Phenylalanine. Also important on L-leucine. Converts dehydrocarnitine to dehydrocarnitine-CoA during carnitine catabolism. Probably also acts on acetoacetate, which is an intermediate in the degradation of phenylalanine (via tyrosine and homogentistate) and leucine (from HMG-CoA lyase). Both substrates are 3-oxoacids, but not sure if succinyl-CoA is the source of the CoA as annotated. Similar to DhcB = PA2000. Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit B (EC 2.8.3.5) Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit B (EC 2.8.3.5) 3-oxoacid CoA-transferase subunit B MALSREQMAQRVAREMQDGYYVNLGIGIPTLVANYIPEGMEVMLQSENGLLGMGAFPTEAEVDADMINAGKQTVTARIGASIFSSAESFAMIRGGHIDLTVLGAFEVDVEGNIASWMIPGKLVKGMGGAMDLVAGAENIIVTMTHASKDGESKLLPRCSLPLTGAGCIKRVLTDLAYLEIQDGAFILKERAPGVSVEEIVAKTAGKLIVPDHVPEMQFAAQ catabolism Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_2632 TK06_RS13235 WP_063322430.1 tr|A0A159ZXT3|A0A159ZXT3_PSEFL tyrosine aminotransferase (EC 2.6.1.57) Specifically important for: L-Phenylalanine. Phenylalanine is first hydroxylated to tyrosine (Pf6N2E2_2630) and then transaminated. KEGG has same EC# but less specific. (KEGG_correct) Aspartate aminotransferase (EC 2.6.1.1) Aspartate aminotransferase (EC 2.6.1.1) aromatic-amino-acid transaminase MHFDAIGRVPGDPILGLMEAYGADANPSKFDLGVGVYKDAQGLTPILQSVKQAEQRLVDRQTTKTYIGGHGDAAFGQLINELVLGADSPLISAKRAGATQTPGGTGALRLSADFIAQCLPGRGVWLSNPTWPIHETIFAAAGVKVGHYPYVGADNRLDFEAMLATLNQAPKGDVVLLHACCHNPTGFDLSHEQWRQVLEVVRDRDLLPLIDFAYQGFGDGLEQDAWAVRLFAQALPEVLVTSSCSKNFGLYRDRTGALIVCARDAEKLVDIRSQLANIARNLWSTPPDHGAAVVATILGNPELKSLWADEVQAMRLRIAQLRSGLLEALEPHGLRERFAHIGVQRGMFSYTGLTPEQVKHLRERHSVYMVGTGRANVAGIDATRLDLLAEAIADACK transporters Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_2958 TK06_RS14820 WP_063322689.1 tr|A0A159ZWV1|A0A159ZWV1_PSEFL ABC transporter for L-Lysine, periplasmic substrate-binding component Specific phenotype on L-Lysine; Gly-Glu. There is another dedicated transporter for the dipeptide gly-glu so the basis of that phenotype is unclear. Lysine-arginine-ornithine-binding periplasmic protein precursor (TC 3.A.1.3.1) Lysine-arginine-ornithine-binding periplasmic protein precursor (TC 3.A.1.3.1) lysine/arginine/ornithine transport system substrate-binding protein MKKALLTLSALALCMAAGVATAKEYKELRFGVDPSYAPFESKAADGSLVGFDIDLGNAICAELKVKCKWVESDFDGMIPGLKANKFDGVISSMTVTPAREKAIDFSSELFSGPTAYVFKKGSGLSEDVASLKGKTVGYEQGTIQEAYAKAVLDKAGVKTQAYQNQDQVYADLTSGRLDAAIQDMLQAELGFLKSPKGEGYEVSKPVDSELLPSKTAIGIRKGNSELKALLNKGIKALHDDGKYAEIQKKHFGDLNLYSGK transporters Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_2959 TK06_RS14825 WP_063322690.1 tr|A0A159ZWN7|A0A159ZWN7_PSEFL ABC transporter for L-Lysine, permease component 1 Specific phenotypes on L-Lysine. Also important on gly-glu. There is another dedicated transporter for the dipeptide gly-glu so the basis of that phenotype is unclear. Histidine ABC transporter, permease protein HisQ (TC 3.A.1.3.1) Histidine ABC transporter, permease protein HisQ (TC 3.A.1.3.1) histidine transport system permease protein MFEQLLQNLGLSAFSLQGFGPLLMQGTWMTIKLSALSLLLSVLLGLLGASAKLSSVKLLRIPAQLYTTLIRGVPDLVLMLLIFYSLQTWLTSLTDFMEWEYIEIDPFGAGVITLGFIYGAYFTETFRGAILSVPRGQVEAATAYGLKRGQRFRFVVFPQMMRFALPGIGNNWMVMLKATALVSIIGLADLVKAAQDAGKSTYQLFYFLVLAALIYLLITSASNFILRWLERRYAAGAREAVR transporters Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_2960 TK06_RS14830 WP_063322691.1 tr|A0A165ZC74|A0A165ZC74_PSEFL ABC transporter for L-Lysine, permease component 2 Specific phenotype on Gly-Glu; L-Lysine. There is another dedicated transporter for the dipeptide gly-glu so the basis of that phenotype is unclear. Histidine ABC transporter, permease protein HisM (TC 3.A.1.3.1) Histidine ABC transporter, permease protein HisM (TC 3.A.1.3.1) histidine transport system permease protein MIELLQEYWRPFLYSDGVNVTGLAMTLWLLSASLLIGFLVSIPLSIARVSPKFYVRWPVQFYTYLFRGTPLYIQLLICYTGIYSIAAVRAQPLLDSFFRDAMNCTILAFALNTCAYTTEIFAGAIRSMNHGEVEAAKAYGLTGWRLYTYVIMPSALRRSLPYYSNEVILMLHSTTVAFTATVPDVLKVARDANSATFLTFQSFGIAALIYLTVTFALVGLFRLAERRWLAFLGPTH transporters Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_2962 TK06_RS14840 WP_003198401.1 tr|A0A159ZYQ4|A0A159ZYQ4_PSEFL ABC transporter for L-Lysine, ATPase component Very important for L-lysine and gly-glu utilization. There is another dedicated transporter for the dipeptide gly-glu so the basis of that phenotype is unclear. Histidine ABC transporter, ATP-binding protein HisP (TC 3.A.1.3.1) Histidine ABC transporter, ATP-binding protein HisP (TC 3.A.1.3.1) histidine transport system ATP-binding protein MYKLTIEGLHKSYGEHEVLKGVSLKAKTGDVISLIGASGSGKSTFLRCINFLEQPNDGAMSLDGQPIQMIKDRHGMHVADADELQRIRTRLAMVFQHFNLWSHMTVLENITMAPRRVLGVSKQEADDRARRYLDKVGLPARVAEQYPAFLSGGQQQRVAIARALAMEPEVMLFDEPTSALDPELVGEVLKVIQGLAEEGRTMIMVTHEMSFARKVSNQVLFLHQGLVEEEGRPEDVLGNPTSERLKQFLSGNLK catabolism Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_4383 TK06_RS21985 WP_063323808.1 tr|A0A159ZZQ3|A0A159ZZQ3_PSEFL gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) Important on putrescine; this is the dehydrogenase reaction in the gamma-glutamyl-putrescine pathway. KEGG now annotates it as acting on the 4-guanidino form and it may also act on 4-aminobutyraldehyde (based on studies of PA5312 = kauB). Since this enzyme is closely related to kauB it is probably flexible. Aldehyde dehydrogenase (EC 1.2.1.3) Aldehyde dehydrogenase (EC 1.2.1.3) MTTLTRADWEQRARDLKIEGRAFINGEYTDAVSGETFDCLSPVDGRLLGKIASCDVADAQRAVENARATFSSGVWSRLAPSKRKATMIRFAGLLKQHAEELALLETLDMGKPISDSLNIDVPGAAQALSWSGEAIDKLYDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVVLKPSEKSPLTALRIAALAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIYSGESNMKRIWLEAGGKSPNIVFADAPDLQAAAESAASAIAFNQGEVCTAGSRLLVERSIKDTFLPLVIEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAGHSDGAKLVAGGKRILEETGGTYVEPTIFDGVSNAMKIAQEEIFGPVLSVIAFDTAEQAIEIANDTPYGLAAAVWTKDISKAHLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFDKYTELKSTWIKL catabolism Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_4509 TK06_RS22580 WP_014340747.1 tr|A0A161H3M9|A0A161H3M9_PSEFL Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) Specifically important for: Putrescine Dihydrochloride. This synthetase reaction is the first step in putrescine catabolism glutamine synthetase family protein glutamine synthetase VVRGKRIERTSLHKVYEKGINLPASLFALDINGSTVESTGLGLDIGDADRICYPIPDTLCNEPWQKRPTAQLLMTMHELEGEPFFADPREVLRQVVTKFDELGLTICAAFELEFYLIDQENVNGRPQPPRSPISGKRPHSTQVYLIDDLDEYVDCLQDILEGAKEQGIPADAIVKESAPAQFEVNLHHVADPIKACDYAVLLKRLIKNIAYDHEMDTTFMAKPYPGQAGNGLHVHISILDKDGKNIFASEDPEQNAALRHAIGGVLETLPAQMAFLCPNVNSYRRFGAQFYVPNSPTWGLDNRTVALRVPTGSADAVRLEHRVAGADANPYLLMASVLAGVHHGLVNKIEPGAPVEGNSYEQNEQSLPNNLRDALRELDDSEVMAKYIDPKYIDIFVACKESELEEFEHSISDLEYNWYLHTV catabolism Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_4510 TK06_RS31160 WP_086936699.1 Gamma-glutamyl-GABA hydrolase (EC 3.5.1.94) Specifically important for: Putrescine Dihydrochloride. part of putrescine catabolism via gamma-glutamyl-putrescine (SEED_correct) Gamma-glutamyl-GABA hydrolase (EC 3.5.1.94) Gamma-glutamyl-GABA hydrolase (EC 3.5.1.94) putative glutamine amidotransferase MSRLPLIGVTTCSRQIGLHAYHISGEKYSRAVATAAKGLPVLIPSLADLFPPSDILDALDGILLTGSPSNVEPFHYQGPASAPGTAHDPARDATTLPLIRAAVDAGIPVLGICRGFQEMNVAFGGSLHQKVHEVGTFIDHREDDTQAVDVQYGPAHAVHIQPGGVLAGLGLPQRIEVNSIHSQGIERLAPGLRAEAVAPDGLIEAVSVPGGKAFALGVQWHPEWEVSSNPHYLAIFQAFGDACRARAAQRDADASNNA catabolism Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_4512 TK06_RS22595 WP_063323898.1 tr|A0A159ZZY6|A0A159ZZY6_PSEFL Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) Specifically important for: Putrescine Dihydrochloride. KEGG annotates this as putrescine aminotransferase, probably based on similarity to spuC (PA0299) of P. aeruginosa, but it is believed that only the g-glutamyl- pathway operates in P. aeruginosa (X. Yao et al 2011, PMC3147493) Omega-amino acid--pyruvate aminotransferase (EC 2.6.1.18) Omega-amino acid--pyruvate aminotransferase (EC 2.6.1.18) putrescine aminotransferase MTRNNPQTREWQALSNDHHLAPFSDFKQLKEKGPRIITHAKGVYLWDSEGNKILDGMAGLWCVAVGYGREELADAASQQMRELPYYNLFFQTAHPPVLELSKAIADIAPEGMNHVFFTGSGSEGNDTMLRMVRHYWAIKGQPNKKVIISRKNGYHGSTVAGASLGGMTYMHEQGDLPIPGIVHIAQPYWFGEGGDMSPEEFGVWAANQLEEKILELGVDNVGAFIAEPIQGAGGVIVPPDSYWPRMKEILAKYDILFVADEVICGFGRTGEWFGTDHYELKPHMMTIAKGLTSGYIPMGGLIVRDDVVAVLNEGGDFNHGFTYSGHPVAAAVALENIRILRDEKIIERVHSETAPYLQKRLRELNDHPLVGEVRGVGLLGAIELVQDKATRKRYEGKGVGMICRQFCFDNGLIMRAVGDTMIIAPPLVISKAEIDELVAKARQCLDLTLSALQG transporters Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_4681 TK06_RS23410 WP_063324024.1 tr|A0A160A3C6|A0A160A3C6_PSEFL ABC transporter for Carnitine, ATPase component Specific phenotype on Carnitine Hydrochloride. This ABC transporter might also take up choline or glycine-betaine, in conjunction with another SBP, Pf6N2E2_4683 L-proline glycine betaine ABC transport system permease protein ProV (TC 3.A.1.12.1) L-proline glycine betaine ABC transport system permease protein ProV (TC 3.A.1.12.1) glycine betaine/proline transport system ATP-binding protein MSIIRFEDVDVIFSNRPKAALDLLDKGLSRPEILQQTGLIVGVEKASLSIEKGEICVLMGLSGSGKSSLLRCINGLNTVSRGKLFVEHEGRQIDIASCSPAELKMMRTKRIAMVFQKFALMPWLTVRENISFGLEMQGRPEKERRKLVDEKLELVGLTQWRNKKPDELSGGMQQRVGLARALAMDADILLMDEPFSALDPLIRQGLQDELLELQRKLQKTIVFVSHDLDEALKLGTRIAIMKDGKIIQYSKPEEIVLNPADDYVRTFVAHTNPLNVLCGRSLMRTLDNCKRINGSVCLDPGGDSWLDLAEGNTIKGARQNGAALDLQNWVPGQAVEDLGRRPTLVDSNIGMRDALQIRYQTGNKLVLHDNQQVVGILGDSELYHALLGKNLG transporters Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_4682 TK06_RS23415 WP_063324025.1 tr|A0A160A470|A0A160A470_PSEFL ABC transporter for Carnitine, permease component Specific phenotypes on Carnitine Hydrochloride. This ABC transporter might also take up choline or glycine-betaine, in conjunction with another SBP, Pf6N2E2_4683 L-proline glycine betaine ABC transport system permease protein ProW (TC 3.A.1.12.1) L-proline glycine betaine ABC transport system permease protein ProW (TC 3.A.1.12.1) glycine betaine/proline transport system permease protein MLIDQKIPLGQYIAGFVEWLTQNGANTFDAIALFLETMIHGVTFALTWFNPLALIGLIALLAHFIQRKWGLTIFVIASFLLILNLGYWQETMETLAQVLFATLVCVLIGVPLGIVAAHKPMFYTMMRPVLDLMQTVPTFVYLIPTLTLFGLGVVPGLISTVVFAIAAPIRLTYLGIRDVPDELMDAGKAFGCSRRQLLSRIELPHAMPSIAAGITQCIMLSLSMVVIAALVGADGLGKPVVNALNTADIALGFEAGLAIVLLAIMLDRICKQPDAKVGGDA catabolism Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_4689 TK06_RS23445 WP_063324030.1 tr|A0A160A4C1|A0A160A4C1_PSEFL L-carnitine 3-dehydrogenase, B subunit (EC 1.1.1.108) Specifically important for: Carnitine Hydrochloride. Similar to CdhB = PA5385 FIG143042: Thioesterase-like protein acyl-CoA thioester hydrolase MPTLTTYQTRILPEWVDYNGHLRDAFYLLIFSYATDALMDRLGMDSQNREASGHSLFTLELHLNYLHEVKLDAQVEVHTHIIGHDAKRLHLYHSLHLVGGDKELAGNEQMLLHVDLAGPRSAPFTEQTLDRLSALLDEQSDLPPPLYIGRIIALPLPR catabolism Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_4690 TK06_RS23450 WP_063324031.1 tr|A0A160A2B4|A0A160A2B4_PSEFL L-carnitine 3-dehydrogenase, A subunit (EC 1.1.1.108) Specifically important for: Carnitine Hydrochloride. Similar to CdhA = PA5386 Carnitine 3-dehydrogenase (EC 1.1.1.108) @ 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157) @ 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) Carnitine 3-dehydrogenase (EC 1.1.1.108) @ 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157) @ 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) 3-hydroxybutyryl-CoA dehydrogenase MSFITDIKTFAALGSGVIGSGWISRALAHGLDVIAWDPAPGAEAALRKRVANAWGALEKQGLAPGASQDRLRFVATIEECVRDADFIQESAPERLELKLELHGQISAAAKPNALIGSSTSGLLPSEFYEGATHPERCVVGHPFNPVYLLPLVEVVGGKNTAPEAVQAAMQVYESLGMRPLHVRKEVPGFIADRLLEALWREALHLVNDGVATTGEIDDAIRFGAGLRWSFMGTFLTYTLAGGDAGMRHFMAQFGPALQLPWTYLPAPELTEKLIDDVVDGTSAQLGSHSISALERYRDDCLLAVLEAVKATKAKHGMAFSE catabolism Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_4692 TK06_RS23455 WP_063324032.1 tr|A0A160A201|A0A160A201_PSEFL dehydrocarnitine cleavage enzyme (EC 2.3.1.-) Specifically important for: Carnitine Hydrochloride. Similar to CdhC = PA5387 FIG004891: hypothetical protein in carnitine cluster FIG004891: hypothetical protein in carnitine cluster MNHDVIITCALTGAGDTTAKSPHVPVTPKQIADAAIEAAKAGATVVHCHVRDPQTGKFSRDVALYREVMERIREADVDIIVNLTAGMGGDLEIGAGEQPMEFGPNTDLVGPLTRLAHVEELLPEICTLDCGTLNFGDGDTIYVSTPAQLRAGAKRITELGVKAELEIFDTGHLWFAKQLIKEGLLDNPLFQLCLGIPWGAPADTTTMKAMVDNLPADAVWAGFGIGRMQMPMAAQAVLLGGNVRVGLEDNLWLDKGVLATNGQLVERAGEILSRLGARVLTPAEGRKKMGLTQRG transporters Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_4693 TK06_RS23460 WP_063324033.1 tr|A0A160A3D7|A0A160A3D7_PSEFL ABC transporter for Carnitine Hydrochloride, periplasmic substrate-binding component Specific phenotype on Carnitine Hydrochloride. Similar to CaiX. There might also be another SBP, Pf6N2E2_4683 (similar to CbcX) that is expected to be specific for choline and glycine-betaine. However _4683 is important for carnitine utilization as well and it does not appear to be a polar effect, so it could be another subunit. L-proline glycine betaine binding ABC transporter protein ProX (TC 3.A.1.12.1) L-proline glycine betaine binding ABC transporter protein ProX (TC 3.A.1.12.1) glycine betaine/proline transport system substrate-binding protein MKRLISSCVLALCGTTFLNGTAMAAEPAACQNVRLGVVNWTDVIATSALTQVMLDGLGYKTKQTSASQQIIFAGIRDQRLDLFLGYWNPLMTQTITPFVEAKQVKVLEQPSLKDARATLAVPTYLADKGLKTFADIAKFEKELGGKIYGIEPGSGANTQIKAMIAKNQFGLGKFQLVESSEAGMLAAVDRAVRRKEAVVFFGWAPHPMNVNVQMTYLTGSDDALGPNEGMATVWTVTAPDYAQQCPNVGRLLSNLTFSAEDESRMMQPLLDHKDPLESARQWLKDHPQDKQRWLEGVTTFDGKPAADNLKLTSN catabolism Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_515 TK06_RS02565 WP_063320678.1 tr|A0A159ZT15|A0A159ZT15_PSEFL malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) Specifically important for: m-Inositol. 3-oxopropionate or malonate semialdehyde is an intermediate in myo-inositol catabolism (SEED_correct, although the name and EC number are confusing) Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) methylmalonate-semialdehyde dehydrogenase MSDAPVVGHYLNGHVQDHDSTRFSNVFNPATGAVQARVALAEPGTVDAAVASALAAFPAWSEQSSLRRSRVMFKFKELLDRHHDELAQIISREHGKVLSDAHGEVTRGIEIVEYACGAPNLLKTDFSDNIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERDPSASLLMARLLTEAGLPDGVFNVVQGDKVAVDALLQHPDIEAISFVGSTPIAEYIHQQGTAHGKRVQALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAVAVGDVGDELIAKLLPRIDQLKIGNGQQPGTDMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRSFKVPGAEQGFFVGATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFTRDGGIARAFARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGLRFYSRYKSVMQRWPDSIAKGPEFSMPTAQ transporters Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_5402 TK06_RS26960 WP_003205302.1 tr|A0A160A3S6|A0A160A3S6_PSEFL ABC transporter for D-Alanine, periplasmic substrate-binding component Very important for D-alanine utilization. This transporter may also uptake L-histidine. Glutamate Aspartate periplasmic binding protein precursor GltI (TC 3.A.1.3.4) Glutamate Aspartate periplasmic binding protein precursor GltI (TC 3.A.1.3.4) general L-amino acid transport system substrate-binding protein MKLLKSTLAVMTAAAVLGVSGFAQAGATLDAVQKKGFVQCGVSDGLPGFSVPDSTGKIVGIDADFCRAVAAAVFGDATKVKFSQLNAKERFTALQSGEIDMLSRNSTMTSSRDAGMGLKFPGFITYYDGIGFLANNKLGVKSAKELDGATICIQAGTTTELNVSDYFRANGLKYTPITFDTSDESAKSLESGRCDVLTSDKSQLFAQRSKLASPKDYVVLPETISKEPLGPVVRNGDDEWLAIVRWTGYALLNAEEAGVTSKNVEAEAKSTKNPDVARMLGADGEYGKDLKLPKDWVVQIVKQVGNYGEMFERNLGKGTPLEIDRGLNALWNAGGIQYAPPVR transporters Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_5403 TK06_RS26965 WP_063324518.1 tr|A0A160A3G2|A0A160A3G2_PSEFL ABC transporter for D-Alanine, permease component 2 Very important for D-alanine utilization. This transporter may also uptake L-histidine. Glutamate Aspartate transport system permease protein GltJ (TC 3.A.1.3.4) Glutamate Aspartate transport system permease protein GltJ (TC 3.A.1.3.4) general L-amino acid transport system permease protein VRAWVFQVVTVVAVIALGWFLFDNTQTNLQHRGITSGFGFLERSAGFGIAQHLIDYTEADSYARVFLIGLLNTLLVTFIGVILATILGFIIGVARLSQNWIISKLATVYVEVFRNIPPLLQILFWYFAVFLSMPGPRAAHNFGDTFFVSSRGLNMPAALVAEGFWPFVISVVLAIVAIVLMTRWANKRFEATGEPFHKFWVGLALFLVIPALSALLFGAPVHWEMPELKGFNFVGGWVLIPELLALTLALTVYTAAFIAEIVRSGIKSVSHGQTEAARSLGLRNGPTLRKVIIPQALRVIIPPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAISISISLLMNWYNKRIALIER transporters Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_5404 TK06_RS26970 WP_063324519.1 tr|A0A160A4M7|A0A160A4M7_PSEFL ABC transporter for D-Alanine, permease component 1 Specific phenotypes on D-Alanine. Also important for histidine utilization, so this may also take up L-histidine Glutamate Aspartate transport system permease protein GltK (TC 3.A.1.3.4) Glutamate Aspartate transport system permease protein GltK (TC 3.A.1.3.4) general L-amino acid transport system permease protein MTTHTFKPDMPPPGSSIGVVAWMRANMFSSWINTLLTLFAFYLIYLIVPPLVQWAILDANWVGTTRADCTKEGACWVFIQQRFGQFMYGYYPADLRWRVDLTVWLAVIGVAPLFISRFPRKAIYGLSFLVLYPISAWCLLHGGVFGLDAVATSQWGGLMLTLVIATVGIVGALPLGIVLALGRRSNMPAIRVVCVTFIEFWRGVPLITVLFMSSVMLPLFLPEGMNFDKLLRALIGVILFQSAYIAEVVRGGLQAIPKGQYEAAAAMGLGYWRSMGLVILPQALKLVIPGIVNTFIALFKDTSLVIIIGLFDLLNSVKQAAADPKWLGMATEGYVFAALVFWIFCFGMSRYSMHLERKLDTGHKR transporters Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_5405 TK06_RS26975 WP_003178331.1 tr|A0A0D9AS17|A0A0D9AS17_PSEFL ABC transporter for D-Alanine, ATPase component Very important for D-alanine utilization. This transporter may also uptake L-histidine. ABC-type polar amino acid transport system, ATPase component ABC-type polar amino acid transport system, ATPase component general L-amino acid transport system ATP-binding protein MSEAIKQPVSPEGIIQMQGVNKWYGQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQGRIVVDGVELTNDLKQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAEEIAMHYLERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKEVLDTMIGLAEDGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPNDFFDNPQNDRTKLFLSQILH transporters Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_5660 TK06_RS28180 WP_063324706.1 tr|A0A160A465|A0A160A465_PSEFL L-Arginine ABC transporter, periplasmic substrate-binding component Specific phenotype on L-Arginine. (SEED_correct) Arginine/ornithine ABC transporter, periplasmic arginine/ornithine binding protein Arginine/ornithine ABC transporter, periplasmic arginine/ornithine binding protein MKKLVLLGALALSVLSLPTFADEKPLKIGIEAAYPPFASKAPDGSIVGFDYDIGNALCEEMKVKCVWVEQEFDGLIPALKVRKIDAILSSMSITEDRKKSVDFTNKYYNTPARLVMKAGTQVSDNLAELKGKNIGVQRGSIHERFAREVLAPLGAEIKPYGSQNEIYLDVSAGRLDGTVADATLLDDGFLKTDAGKGFAFVGPAFTDEKYFGDGIGIAVRKGDALKDKINGAITAIRENGKYKQIQDKYFAFDIYGK transporters Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_5661 TK06_RS28185 WP_003204800.1 tr|A0A160A3X7|A0A160A3X7_PSEFL L-Arginine ABC transporter, permease protein AotQ Specific phenotypes on L-Arginine; L-Arginine. no data for ornithine (SEED_correct) Arginine/ornithine ABC transporter, permease protein AotQ Arginine/ornithine ABC transporter, permease protein AotQ MLKGYGAVILDGAWLTLELALSSMALAIVLGLIGVALRLSPVRWLAWLGDLYATVIRGIPDLVLILLIFYGGQDLLNRVAPMLGYDDYIDLNPLAAGIGTLGFIFGAYLSETFRGAFMAIPKGQAEAGMAYGMNGFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKAKQAADATREPFTFFLAVAAMYLVITSVSLLALRHLEKRYSVGVRAADL transporters Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_5662 TK06_RS28190 WP_063324707.1 tr|A0A160A563|A0A160A563_PSEFL L-Arginine ABC transporter, permease protein AotM Specific phenotypes on L-Arginine; L-Arginine. (SEED_correct) Arginine/ornithine ABC transporter, permease protein AotM Arginine/ornithine ABC transporter, permease protein AotM MIFDYNVIYEALPLYFSGLLTTLKLLALSLFFGLLAALPLGLMRVSKQPIVNMTAWLYTYVIRGTPMLVQLFLIYYGLAQFAIVRESFLWPWLSSATFCACLAFAINTSAYTAEIIAGSLRATSNGEIEAAKAMGMSRYKLYRRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITGAARTVNAQYYLPFEAYITAGVFYLCLTFILVRLFKLAERRWLGYLAPRKH transporters Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_5663 TK06_RS28195 WP_063324708.1 tr|A0A160A5V6|A0A160A5V6_PSEFL L-Arginine ABC transporter, ATPase component Very important for utilizing L-arginine. (SEED_correct) Arginine/ornithine ABC transporter, ATP-binding protein AotP Arginine/ornithine ABC transporter, ATP-binding protein AotP MYKLEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLNNEELKLVAGKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTALENIMEAPVHVLGVTKAQAREKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPELVGDVLKVMQGLALEGRTMVVVTHEMGFAREVSNQLVFLHKGIVEESGNPREVLVNPQSERLQQFLSGSLK catabolism Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_5967 TK06_RS29720 WP_063324926.1 tr|A0A165ZSW6|A0A165ZSW6_PSEFL L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) Important for utilization of L-arabinose and D-galactose in several Pseudomonas. Both of these sugars are catabolized via a 1-dehydrogenase followed by lactonase and dehydratase reactions. This is the only dehydrogenase is specifically important for either of these carbon sources in several Pseudomonas, except for an alpha-ketoglutarate semialdehyde dehydrogenase that is expected to be the last dedicated step in L-arabinose catabolism (i.e., Pf6N2E2_612). L-arabinose and D-galactose are chemically similar and some dehydrogenases are already known to act on both substrates. This gene might also be involved in D-gluconate utilization. 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100) 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100) MAEPLSLPPVPEPPKGERLKNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAAHWRERGADVHALKADVSNQQDLHAMARHAVERHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYGCKAVLPQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVNAIAPGYIETQLNVDYWNGFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASDEAPFINASCITIDGGRSVMYHD catabolism Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_611 TK06_RS03025 WP_063320756.1 tr|A0A159ZTV2|A0A159ZTV2_PSEFL 2-dehydro-3-deoxy-L-arabinonate dehydratase (EC 4.2.1.43) # Specifically important in carbon source L-Arabinose. Similar to PA2216 from Pseudomonas aeruginosa (see PMC:PMC4038344) and to gguC or araD1 (Atu2345) from Agrobacterium tumefaciens (see PMC: PMC3232879), which also have this activity. In Agrobacterium, this reaction is proposed to be a step in L-arabinose oxidation. (Note that 2-keto-3-deoxy-L-lyxonate and 2-keto-3-deoxy-L-arabinonate are the same compound.) SUGAR TRANSPORTER SUGAR TRANSPORTER MRLVQFELPNGERRVGVVDGDQVREVQGAASVRDLALAAIEAGVKLEEQVNSLGLGAGHDYARLLSELRILPPLDHPDPAHLLVSGTGLTHLGSASARDKMHQQAGDESAMTDTMRIFKWGVEGGKPQAGQAGVQPEWFYKGDGSIVVRPGHPFPLPPFAEDAGEEPEISGLYVIGHDGKPYRLGFAVGNEFSDHVMERKNYLYLAHSKLRSCSFGPELRVGELPQHLSGTSRILRNGEVLWQNEFLSGEANMCHSLENLEFHHFKYSQFLRPGDVHVHFFGTATLSFADGIRTQPGDVFEISQAEFGAPLVNGIAPVDAVFNPGTIGTL catabolism Pseudomonas fluorescens FW300-N2E2 pseudo6_N2E2 Pf6N2E2_80 TK06_RS00420 WP_063320323.1 tr|A0A165YII0|A0A165YII0_PSEFL gamma-glutamylputrescine oxidase (EC 1.4.3.-) Specifically important for: Putrescine Dihydrochloride. This is part of the gamma-glutamyl-putrescine pathway. (KEGG_correct) Nucleoside-diphosphate-sugar epimerases Nucleoside-diphosphate-sugar epimerases gamma-glutamylputrescine oxidase VIGAGYTGLSSALFLLENGFKVTVLEAAKVGFGASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCDLKDGGVFAALTAKQMGHLESQKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSGGHIHPLNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYLGNLVPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGGGVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYYSQGCSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYGLRDKLGF catabolism Pseudomonas stutzeri RCH2 psRCH2 GFF1044 Psest_1077 PSEST_RS05235 WP_003280093.1 tr|L0GFY2|L0GFY2_PSEST acetyl-CoA:acetoacetate CoA transferase, B subunit (EC 2.8.3.8) Specifically important for: L-tyrosine disodium salt; L-Leucine. This role makes sense because of its involvement in acetoacetate catabolism (from tyrosine or leucine). It had been annotated as succinyl-CoA:3-ketoacid-coenzyme A transferase (a broader range of substrates and with succinyl-CoA not acetyl-CoA as donor). Similar to E. coli atoA (52% identical), which has this activity. 3-oxoacid CoA-transferase, B subunit Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit B (EC 2.8.3.5) 3-oxoacid CoA-transferase subunit B MAWTREQMAQRAAQELQDGFYVNLGIGLPTLVANYIPEGMDVWLQSENGLLGIGPFPTEEEIDPDLINAGKQTVTALPGSSFFDNAQSFAMIRGGHINLAILGAMQVSEKGDLANWMIPGKMVKGMGGAMDLVAGVKRVVVLMEHTAKGGAHKILPACDLPLTGLGVVDRIITDLGVLDVTEQGLKLVELAEGVSFDELQEATGSPIQR catabolism Pseudomonas stutzeri RCH2 psRCH2 GFF1045 Psest_1078 PSEST_RS05240 WP_003294550.1 tr|L0GK00|L0GK00_PSEST acetyl-CoA:acetoacetate CoA transferase, A subunit (EC 2.8.3.8) Specifically important for: L-Leucine. Important on tyrosine as well. This role makes sense because of its involvement in acetoacetate catabolism (from tyrosine or leucine). It had been annotated as succinyl-CoA:3-ketoacid-coenzyme A transferase (a broader range of substrates and with succinyl-CoA not acetyl-CoA as donor). Similar to E. coli atoD (46% identical), which has the same activity. 3-oxoacid CoA-transferase, A subunit Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit A (EC 2.8.3.5) 3-oxoacid CoA-transferase subunit A MNKIYPSAAHALEGLVEDGMTIAVGGFGLCGIPEQLIAALRDSGKKDLTAISNNAGVDGFGLGLLLETRQISKMVSSYVGENKEFERQYLAGELALEFTPQGTLAEKLRAGGAGIPAFYTKTGYGTLVAEGKETRQFNGEWYVMEESLTADLALVKAWKADKAGNLLFRKTARNFNPLAAMAGEVCVVEVEEIVETGELDPDQIHLPGIYVHRIVHNPNPEKRIEKRTVRS catabolism Pseudomonas stutzeri RCH2 psRCH2 GFF1145 Psest_1178 PSEST_RS05740 WP_015276062.1 tr|L0GIY0|L0GIY0_PSEST D-glycerate 2-kinase (EC 2.7.1.-) Specifically important for: Glycolic Acid. Either glycerate kinase or hydroxypyruvate reductase could be involved in glycolate utilization (via glyoxylate and tartronate-semialdehyde, which can be converted to glycerate, perhaps via hydroxypyruvate). However this protein is similar to TM1585 (also PDB:2b8nA or GCK_THEMA), which is a glycerate kinase. We were not able to find a rationale for KEGG's annotation as hydroxypyruvate reductase. (SEED_correct) Putative glycerate kinase D-glycerate 2-kinase (EC 2.7.1.-) hydroxypyruvate reductase MTLDPQALLRQLFDSAIEAAHPRHVLADHLPEDRSGRAIVIGAGKAAAAMAEAIEKVWEGELSGLVVTRYEHHADCKRIEVVEAAHPVPDDAGERVARRVLELVSNLEESDRVIFLLSGGGSSLLALPAEGISLADKQAINKALLRSGAHIGEMNCVRKHLSAIKGGRLAKACWPASVYTYAISDVPGDEATVIASGPTVADPTTSEQALEILERYHIEVPANVRAWLEDPRSETLKPGDPMLSRSHFRLIATPQQSLDAAAEVARAAGITPLILGDLEGEAREVAKVHAGIARQVVLHGQPIAAPCVILSGGETTVTVRGNGRGGRNAEFLLALTENLQGLPNVYALAGDTDGIDGSEDNAGALMMPDSYARAETLGLRAADALANNDGYGYFAALDDLIVTGPTRTNVNDFRAILILPPSA transporters Pseudomonas stutzeri RCH2 psRCH2 GFF2080 Psest_2123 PSEST_RS10360 WP_015276942.1 tr|L0GLK1|L0GLK1_PSEST fusion of gluconokinase and the small permease component of the D-gluconate TRAP transporter This protein has pleiotropic phenotypes which are not explained, but it is most important for fitness with D-gluconate as the carbon source, consistent with its putative roles as part of the tripartite gluconate transport system and as gluconate kinase. Also, the N-terminal part is 49% identical to PP3416 or gnuK from P. putida, which is the catabolic gluconate kinase (PMC1951859). The SEED and KEGG annotations ignore the dctQ-like C-terminal portion carbohydrate kinase, thermoresistant glucokinase family Gluconokinase (EC 2.7.1.12) gluconokinase MPSVHTSKASALPVLVVMGVSGSGKTETSHAVADALGLPHIEADNFHPAENVARMRAGTPLSDADRMEWLHALIAEMQRTLAAGSGFVLACSALKRSYRELLRSAVPELRFAHLAIDYETAVQRVGGRAGHFMPISLVDSQFATLESPEGEPGVLTVDASQPREGVLRQIVEWMQGSGLDELIETRVDLSSRPFDSATTAPPLTNEPIYSGRVAQHFDRLTDWLMAALMAFMVIVVFSSVVLRYAFGTGWTGAEELSRLAFVWLVFVGVASSMRRGELMSFSMLRDRFPRLFRRVVDSLSWLLVAAASCLAAWGGWNQMQFGWTINSPVVGYPLGLAMLPVAASMVALAVLALLQLVNVWRRDQPSATAAANVTAD transporters Pseudomonas stutzeri RCH2 psRCH2 GFF2081 Psest_2124 PSEST_RS10365 WP_014820165.1 tr|L0GIU4|L0GIU4_PSEST D-gluconate TRAP transporter, large permease component specific phenotype on D-gluconate and no other transporter is apparent in the fitness data. TRAP transporter, DctM subunit TRAP-type C4-dicarboxylate transport system, large permease component MTVVVFLSSLLGFMTLGMPIAFALLLTGSVLMWYLDFWDVQLLAQNLQAGADSFPLLAVPFFILAGELMNAGGISRRIIAMAQAYFGHKRGGLGYVAIAASVLLASMSGSALADTAALATLLLPMMRERGYPLSSSSGLVAAGGIIAPIIPPSMPFVIYGVVTGTSISQLFLAGMVPGLIMGMGLIVAWTLIARRIDEPKQEKASAAERRRVLVDGAAALMLPVIIVGGLRGGLFTPTEAAVVAAVYALAVSTLLYRELNWAGLVEVLTRASRTTASVMFLCAAATVSAYMITLAQLPDEIAAMLGPLAQDPKLLMVAIMLLMIAVGMVLDLTPTILILGPVLAPIAIKAGIDPVYFGVMFVLIGSIGLITPPVGTVLNVVGGIGRLRMETLVRGVMPFFLIYLVIVGLLIAVPSIITVPLAWLR transporters Pseudomonas stutzeri RCH2 psRCH2 GFF2082 Psest_2125 PSEST_RS10370 WP_015276943.1 tr|L0GMV7|L0GMV7_PSEST D-gluconate TRAP transporter, periplasmic component specific phenotype on D-gluconate and no other transporter is apparent in the fitness data tripartite ATP-independent periplasmic transporter solute receptor, DctP family TRAP-type transport system, periplasmic component, predicted N-acetylneuraminate-binding protein MKRLLISTLAAALLGSTLSLGYAQAADDIRPRMIRFGYGLNEDSNQGRAAKLLAEEVAKASGGKLKVRTFASASLGSDDQMQNALIGGAQEMMVGSTATLVGISKEMAVWDTPFLFTDPRQADQVLDGPVGRQVMDKLEEKGLVGLVYWENGFRNVTNSARPIEKLEDFNGVKLRVMPNPVFIDTFKRMGANAVPLPFSELFTALETKAVDGQENPFNTILSSKFYEVQKYLSVTNHVYSPWIVTVSKRWWDGLSATEQGILMEAAEKARDAEREDTRREASQALAALKERGMQINEVSPDEIQRMREKAQPAIQTVIDAVGQELFDQVQAEVEKAAP catabolism Pseudomonas stutzeri RCH2 psRCH2 GFF2392 Psest_2440 PSEST_RS11895 WP_015277224.1 tr|L0GMF3|L0GMF3_PSEST isobutyrl-CoA dehydrogenase (EC 1.3.8.1) Important for valine utilization as N source, and isobutyrl-CoA is an intermediate in valine catabolism. SEED annotated it as butyryl-CoA dehydrogenase, which is also expected to perform this reaction Acyl-CoA dehydrogenases Butyryl-CoA dehydrogenase (EC 1.3.99.2) MHDLELSEDQRMIRDMARDFARREIAPHAQAWEKAGWIDDTLVAQMGELGLLGMVVPEEWGGSYIDYVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGSQAQKDEWLTELASGRAIGCFALTEPQAGSEAHNLRTRAELVDGHWVLNGSKQFCSNAKRSKLAIVFAVTDPELGKKGLSAFLVPTDTPGFAVERSEHKMGIRASDTCGVSLSDCRIPEANLLGERGKGLAIALSNLEGGRIGIGAQALGIARAAFEAALLYARERVQFGKPIAEHQSIANMLADMQTQLNAARLLILHAARLKSAGLPCLSEASQAKLFASEMAEKVCSQAVQIHGGYGYLEDYPVERYYRDARITQIYEGSSEIQRLLIARELANYAL catabolism Pseudomonas stutzeri RCH2 psRCH2 GFF2397 Psest_2445 PSEST_RS11915 WP_015277229.1 tr|L0GMG4|L0GMG4_PSEST 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.1) Specifically important for: L-Isoleucine. SEED has it as butyryl-CoA dehydrogenase, which is also expected to perform this reaction. 2-methylbutanoyl-CoA is an intermediate in isoleucine catabolism Acyl-CoA dehydrogenases Butyryl-CoA dehydrogenase (EC 1.3.99.2) MLPNEDQNAIAEMARQFAQERLKPFAEQWSREHRYPAEAIGEMAALGFFGMLVPEQWGGSDTGYLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKSDFLTPLARGEQIGAFALTEPQAGSDASSLRTRARRDGDHYVLNGAKQFITSGKHAGTVIVFAVTDPDAGKGGISAFIVPTDSPGYQVVRVEDKLGQHASDTCQIAFEDLRVPVANRLGEEGEGYRIALANLEGGRIGIAAQAVGMARAAFEAARDYARDRETFGKPIIEHQAVAFRLADMATQIAVARQMVHHAAALREVGRPALVEASMAKLFASEMAEKVCSAAIQTLGGYGYLADFPVERIYRDVRVCQIYEGTSDIQRLVISRNLGGPV catabolism Pseudomonas stutzeri RCH2 psRCH2 GFF3447 Psest_3512 PSEST_RS17065 WP_015278222.1 tr|L0GPV2|L0GPV2_PSEST fumarylacetoacetate (FAA) hydrolase (EC 3.7.1.2) Specifically important for: L-tyrosine disodium salt; casamino acids. The annotation of psa:PST_0871 has been updated to fumarylacetoacetate (FAA) hydrolase [EC:3.7.1.2], which is a step in tyrosine catabolism (KEGG_correct) 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) Fumarylacetoacetate hydrolase family protein MKLATLNQGRDGVLVVVSRDLAQAVKVPQIAATLQAALDDWNYCKPKLEAVYQRLNDGLEEGAFAFDQTACHSPLPRAYHWADGSAYVNHVELVRKARGAEMPESFWHDPLMYQGGADAFIPPHSPIRLADEAWGIDLEGELAVITDDVPMGATPAEAASHIQLLMLVNDVSLRNLIPGELAKGFGFYQSKPSSSFSPVAVTPDELGETWRDGKVHRPLVSHINGELFGQPDAGTDMTFNFPTLVAHAARTRPLGAGTIIGSGTVSNYDRSAGSSCLAEKRMLEVVEHGEAKTPFLKFGDRVRIEMFDAAGQSIFGAIDQQVERYGH catabolism Pseudomonas stutzeri RCH2 psRCH2 GFF3452 Psest_3517 PSEST_RS17090 WP_015278227.1 tr|L0GPV5|L0GPV5_PSEST branched-chain ketoacid ferredoxin reductase (EC 1.2.7.7) active on 4-methyl-2-oxopentanoate, (S)-3-methyl-2-oxopentanoate, or 3-methyl-2-oxobutanoate Specifically important for: L-Leucine; L-Isoleucine. This oxidizes and decarboxylates the alpha-keto acid that is produced by a branched chain amino acid dehydrogenase (4-methyl-2-oxopentanoate or (S)-3-methyl-2-oxopentanoate). This is also improtant for utilization of valine as a nitrogen source implying a third substrate (3-methyl-2-oxobutanoate). Indolepyruvate ferredoxin oxidoreductase, alpha and beta subunits Indolepyruvate ferredoxin oxidoreductase, alpha and beta subunits indolepyruvate ferredoxin oxidoreductase MSLAEIRLDDKYRLATGHLYLTGTQALTRLPMLQHQRDQARGLNTGGFISGYRGSPLGGLDKSLWEARDYLKQHAIHFQPGVNEELAATAVWGSQQTNLFPGAKYDGVFAMWYGKGPGVDRAGDVFKHANAAGVSPQGGVLLLAGDDHGCKSSTLPHQSEHAFIAASIPVLNPANVQEILDYGIIGWELSRYSGCWVALKTIAENVDSSAVVEVDPLRVQTRIPEDFELPEDGVHIRWPDPPLAQEKRLNLYKIYAARAFARANNLNRVMLDSPNPRLGIITTGKSYLDVRQALDDLGLDEALCASVGLRVLKVGMSWPLEPVSVHEFAQGLDEILVVEEKRSIIEDQLTGQLYNWPVSKRPRVVGEFDEQGNSLLPNLSELTPAMIARVIAKRLAPIYTSDSIQARLAFLAAKEKALAARSYSTVRTPHYCSGCPHNSSTKVPEGSRASAGIGCHYMVQWMDRRTETFTQMGGEGVNWIGQAPFTDTPHMFQNLGDGTYFHSGSLAVRAAVAAGVNVTYKILYNDAVAMTGGQPIDGELRVDQLSRQIFHEGVKRIALVSDEPDKYPSRDTFAPITSFHHRRELDAVQRELREFKGVSVIIYDQTCATEKRRRRKRGKMEDPAKRAFINPAVCEGCGDCGEKSNCLAVLPLETELGRKREIDQNACNKDFSCVEGFCPSFVTVHGGGLRKPEAVAGGIEAATLPEPQHPTLDRPWNVLIPGVGGSGVTTLGALLGMAAHLEGKGCTVLDQAGLAQKFGPVTTHVRIAAKQSDIYAVRIAAGEADLLLGCDLIVAAGDESLTRLNEQISNAVVNSHESATAEFTRNPDAQVPGAAMRQAISDAVGADKTHFVDATRLATRLLGDSIATNLFLLGFAYQQGLLPISAEAIEKAIELNGVSAKLNLQAFRWGRRAVLEREAVEQLARPVDMVEPICKTLEEIVDWRVDFLTRYQSAGLARRYRQLVERVRDADSADDLALSKAVARYYFKLLAYKDEYEVARLYSEPEFRQQLEAQFEGDYKLQFHLAPAWLAKRDPVTGEPRKRELGPWVLNLFGVLAKFRFLRGTPLDPFGYGHDRRVERQLISEYEKTVDELLAQLKPTNYRTAVAIAALPEQIRGYGPVKERSIAKARQQEKLLREQLAKGDEVQSVRLFQPAA catabolism Pseudomonas stutzeri RCH2 psRCH2 GFF3770 Psest_3839 PSEST_RS18675 WP_015278495.1 tr|L0GSM3|L0GSM3_PSEST D-lactate oxidase and glycolate oxidase, iron-sulfur subunit (EC 1.1.3.15) Specifically important for: Glycolic Acid; Sodium D-Lactate. This is the first step in both D-lactate and glycolate oxidation. KEGG oddly has no EC #; SEED has it as 1.1.99.14 (glycolate dehydrogenase) Fe-S oxidoreductase Glycolate dehydrogenase (EC 1.1.99.14), iron-sulfur subunit GlcF glycolate oxidase iron-sulfur subunit MQTNLSEAAKKLPRAEEAESILRSCVHCGFCNATCPTYQLLGDELDGPRGRIYLMKQMFEGGEVTESTQLHLDRCLTCRNCETTCPSGVKYHNLLDIGRDFIEQQVQRPLGERVVRGGLRTVIPRPGLFKALLGAGNALKPLMPASLKDHLPREIRPAKPRPQVMHSRRVLILEGCVQPSLSPSTNAAAARVLDRLGISVSPAREAGCCGAVDYHLNAQDAGLDRARRNIDAWWPAIEAGAEAIVQTASGCGAFVKEYGHLLKDDPAYAAKAARVSELAKDLVEVLRSAELEKLNVRADKRMAFHCPCTLQHAQKLGGAVEDVLTRLGYQLTAVPDAHLCCGSAGSYSITQPEISHQLRDNKLNALESGKPEVIVTANIGCQTHLDGAGRTPVKHWIEVVEESMQ catabolism Pseudomonas stutzeri RCH2 psRCH2 GFF3771 Psest_3840 PSEST_RS18680 WP_015278496.1 tr|L0GSF4|L0GSF4_PSEST D-lactate oxidase and glycolate oxidase, FAD binding subunit (EC 1.1.3.15) Specifically important for: Sodium D-Lactate; Glycolic Acid. This is the first step in both D-lactate and glycolate oxidation. KEGG oddly has no EC #; SEED has it as 1.1.99.14 (glycolate dehydrogenase) FAD/FMN-containing dehydrogenases Glycolate dehydrogenase (EC 1.1.99.14), FAD-binding subunit GlcE glycolate oxidase FAD binding subunit MSVIANDASAQLLDQVNQALAANTPLRIQGSGSKSFLGLQADGVLLDTREHRGIVSYDPTELVVTVRAGTPLTELETALDEAGQMLPCEPPHFGEGATVGGMIAAGLSGPRRPWSGSVRDFVLGSRVITGQGKHLRFGGEVMKNVAGYDLSRLMAGSFGCLGVLTEVSLKVLPKPRLCTSLRLEIDLERALLKLAEWGQQPIPISAASHDGQALHLRLEGGEGSVGAARERIGGEDLDPGYWNDLREQRLAFFADPRPLWRLSLPNNTPALGLPGDQLVDWAGAQRWLKSDADAVTIRGIAIEVGGHATCFTAGATTNPFQPLAAPLLRYHRQLKAALDPQGIFNPGRMYSEV catabolism Pseudomonas stutzeri RCH2 psRCH2 GFF3772 Psest_3841 PSEST_RS18685 WP_015278497.1 tr|L0GQM8|L0GQM8_PSEST D-lactate oxidase and glycolate oxidase, FAD-linked subunit (EC 1.1.3.15) Specifically important for: Sodium D-Lactate; Glycolic Acid. This is the first step in both D-lactate and glycolate oxidation. KEGG has the correct EC # but describes it as glycolate oxidase; SEED has it as 1.1.99.14 (glycolate dehydrogenase) glycolate oxidase, subunit GlcD Glycolate dehydrogenase (EC 1.1.99.14), subunit GlcD glycolate oxidase MNILYDERVDGALPKVDKAALLAELQAQLPDLDILHRSEDLKPYECDGLSAYRTTPLLVVLPERIEQVETLLKLCHQRGVPVVARGAGTGLSGGALPLEQGILLVMARFNKILEVDPAGRFARVQPGVRNLAISQAAAPYELYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHNLLKVDILTVEGERMTLGSDALDSPGFDLLALFTGSEGMLGIVTEVTVKLLPKPQVAKVLLAAFDSVEKAGRAVGDIIAAGIIPGGLEMMDNLSIRAAEDFIHAGYPVDAEAILLCELDGVEADVHDDCARVSEVLKLAGATEVRLAKDEAERVRFWAGRKNAFPAVGRISPDYYCMDGTIPRRELPGVLKGISDLSEQFGLRVANVFHAGDGNMHPLILFDANQPGELERAEDLGGKILELCVKVGGSITGEHGVGREKINQMCSQFNADELTLFHAVKAAFDPSGLLNPGKNIPTLHRCAEFGRMHIHNGQLPFPELERF transporters Pseudomonas stutzeri RCH2 psRCH2 GFF4058 Psest_4131 PSEST_RS20130 WP_015278763.1 tr|L0GRH7|L0GRH7_PSEST alpha-ketoglutarate sensor protein (mifS) Specific phenotype on a-ketoglutarate and 56% identical to PA5512 (mifS), which regulates a-ketoglutarate transport in P. aeruginosa (PMC4482717). The transporter in this organism is Psest_0084:0085. Signal transduction histidine kinase regulating C4-dicarboxylate transport system C4-dicarboxylate transport sensor protein two-component system, NtrC family, C4-dicarboxylate transport sensor histidine kinase DctB MPALPNRLRVTLIVALILVGLLLSMHWAGRLAEQRAWAERSQESQGQLELYAQAIHTQVERFRSVPALLALDSDIQGLLADPGNRALRRELNQRLEQQNHAAGSSVLYLLDRNGETIAASNWRDWSSFVGNNYAFRPYFRDAVAHDSGRYFAVGVTTGIPGYFLSSSVKSATGEVLGVLVVKLELEDMQRDWVGQPGILLIADSLDIVILTNRPAWRFRYLRPLSDEVRSRLIDVRRYAEQTLQPLQSSRVQQLSESSERRLVDGPDGRREYLWQRLALPEEDWTLHLLHDPQMVVASVRSYRLAAAGVWMTLAFLLLYLAQRRKTRRVEMRSRSELEHLVHERTRELHTAQDELVHAARMAALGQMSAALAHEINQPLTALRMQLASLRLLLDSGRDGEVREGLGHVEGLLERMAALTGHLKTFARKSPAGLRQRLSLAEVLEQALQLLSPRIRSEQVEVFRQVPAEAMVSGDAIRLEQVLINLLHNALDAMAGRPQRRLRILCQLNGDSWQLSVGDNGGGIASEHLDQVFEPFFTTKPVGQGLGLGLAVSYGIVRDMGGTLEVSNDAHGAVFTLTLLAVEGHAAE transporters Pseudomonas stutzeri RCH2 psRCH2 GFF4059 Psest_4132 PSEST_RS20135 WP_015278764.1 tr|L0GS32|L0GS32_PSEST alpha-ketoglutarate DNA-binding response regulator (mifR) Specific phenotype on a-ketoglutarate and 75% identical to PA5511 (mifR), which regulates a-ketoglutarate transport in P. aeruginosa (PMC4482717). The transporter in this organism is Psest_0084:0085. Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains Nitrogen regulation protein NtrX two-component system, NtrC family, C4-dicarboxylate transport response regulator DctD MSGQVIFIDDEAAIRQAVQQWLELSGFQVRTFSRAREALTALDRDFPGVLISDVRMPDLDGLGLLEQLVALDADLPVIMVTGHGDVPMAVQALRQGAYDFIEKPFTPERLLDSVRRAMDKRRLVCENRQLREQFARKGRIESQLLGVSRAMDNLRRQVLELAGTDVNVLIRGETGSGKEQVARCLHDFSPRAGGPFVALNCAAIPETIFESELFGHESGAFTGAQGKRIGRIEHAAGGTLFLDEIESMPLAQQVKLLRVLQEKTLERLGSNRSIEVDLRVISAAKPDLLEEVRGGRFREDLLYRLNVAELHIPPLRERREDIPLLFEHFASQAAQRHGRAAPPVTPGELTQLLAHDWPGNVRELINAAERHALGLSAPAPASSGGQSLAEQMEAFEAQCLHNALQQCKGNITEVMTQLQLPRRTLNEKMQRHGLSRSDYLPAGSADS catabolism Pseudomonas stutzeri RCH2 psRCH2 GFF418 Psest_0419 PSEST_RS02075 WP_015275423.1 tr|L0GI16|L0GI16_PSEST Acyl-CoA dehydrogenase (EC 1.3.8.7) Specifically important for: L-tyrosine disodium salt; Sodium butyrate; Tween 20. tween 20 hydrolyzes to a mix of C12, C14, and C16 fatty acids; this is probably part of beta oxidation (SEED_correct) Acyl-CoA dehydrogenases Acyl-CoA dehydrogenase (EC 1.3.8.7) MADYQAPLRDMRFVLNEVFDAPKLWQALPALAEVVDAETADAILEEAGKITANSIAPLNRSGDEEGCRWDAGAVSTPAGYREAYQLYAKGGWVGVGGDPAFGGMGMPKVISAQVEEMMNSASLAFGLYPMLTSGACLSIYAHASEELKQKYLPNMYAGVWSGSMCLTEPHAGTDLGIIRTKAEPQADGSYKVSGTKIFITGGEHDLTENIIHLVLAKLPDAPAGSRGISLFLVPKVMVNEDGSLGERNSLSCGSIEHKMGIQASATCVMNFDGAVGWMVGEPNKGLAAMFTMMNYERLGVGIQGLATGERSYQSAIEYARDRIQSRAPTGPVAQDKAADPIIVHPDVRRMLLTMKALNEGGRAFSSYVALQLDIAKFSDDDEARQRAEAQVALLTPVAKAFLTDMGLETTVHGQQVFGGHGFIREWGQEQLVRDCRITQIYEGTNGIQALDLVGRKIVGSGGTMYQAFVDEIRAFIADAGPELTEFAEPLKAAMDNLDELTAWVIDQAKANPNEIGAASVEYLHVFGYTAYAYMWARMAAVAVAKREEGDFYQSKLGTARFYFARLLPRIHSLSASVKAGSESLYLLDAAQF transporters Pseudomonas stutzeri RCH2 psRCH2 GFF4196 Psest_4269 PSEST_RS20825 WP_015278892.1 tr|L0GPQ3|L0GPQ3_PSEST C4-dicarboxylate transporter, DctQ subunit Important for succinate and fumarate utilization (KEGG_correct). The other components (Psest_4268 and Psest_4270) were already annotated correctly TRAP-type C4-dicarboxylate transport system, small permease component TRAP-type transport system, small permease component, predicted N-acetylneuraminate transporter C4-dicarboxylate transporter, DctQ subunit MNALWRVWDHFEEGFIAFLLAAMTLVTFVYVILNNLYTLFYNLGDRFEGSADFWFAIGDFIIGLAQAMTWSTALTKALFAWLIFSGLAYGVRTAGHIGVDALVKLAPRHIQRIIGIIACLLCLGYAGLLTVASFEWIQTLFIANIGAEDLGHIGVKQWHIGMIVPFGFAMVFIRFAEIFVRILRNEQTGLGLADEAADALKHGEEEPK catabolism Pseudomonas stutzeri RCH2 psRCH2 GFF765 Psest_0779 PSEST_RS03815 WP_015275719.1 tr|L0GHV7|L0GHV7_PSEST tyrosine aminotransferase (EC 2.6.1.57) Specifically important for: L-tyrosine disodium salt. This is cofit with 4-hydroxyphenylpyruvate dioxygenase (Psest_0779) which would be the second step in tyrosine catabolism (KEGG_correct) Aspartate/tyrosine/aromatic aminotransferase Aspartate aminotransferase (EC 2.6.1.1) aromatic-amino-acid transaminase MHFGQIPRVPGDPILGLMDLYRADPNPAKLDLGVGVYKDAQGLTPIPRAVKLAEQRLVDGEQSKSYIGGHGDAQFGALLLRQALGSRAIALGEQRAGCTQAPGGTGALRLAGEFIAKCLPGRSIWLSDPTWPIHETLFAAAGLRVQHYPYVGADNRLDVEGMLAALQQVPPGDVVLLHACCHNPTGFDLNHDDWLRVLEVVRARELLPLFDFAYQGFGDGLEEDAWAVRLFAETLPEMLITTSCSKNFGLYRERTGALIAVTSDAERLLDVRSQLASLARNLWSTPPAHGAAVVATILADEPLRQIWQGEVERMRRRIASLRQGLVEALMPYGLAERFAHIAQQRGMFSYTGLTAEQVRRLRAEDSVYLVESGRANVAGLDAERLDALAKAIARVVSN transporters Pseudomonas stutzeri RCH2 psRCH2 GFF84 Psest_0084 PSEST_RS00420 WP_015275111.1 tr|L0GG09|L0GG09_PSEST alpha-ketoglutarate TRAP transporter, 4TM/12TM components specific phenotype on a-ketoglutarate and no other transporter for this substrate is apparent in the fitness data. (Mutants in another TRAP system, Psest_4268:Psest_4270, have a much milder defect in a-ketoglutarate utilization). TRAP transporter, 4TM/12TM fusion protein TRAP transporter, 4TM/12TM fusion protein, unknown substrate 1 MSESQGLHASPSEWPRALFYVALLFSIYQIVTAAFHPVSSQVLRAGHVGFLLLLVFLCYPARGNGKPFQPVAWLLGLAGFATFFYQWYFEADLIQRSGDMTTADMVVGLTLIVLVFEAARRVMGIALPIICALFLAYGLLGEYLPGDLAHRGYYLDQIVNQLSFGTEGLYGTPTYVSATYIFLFILFGSFLEQAGMIKLFTDFAMGLFGHKLGGPAKVSVVSSALMGTITGSGVANVVTTGQFTIPLMKRFGYRPAFAGGVEATSSMGSQIMPPVMGAVAFIMAETINVPFVEIAKAALIPALLYFGSVFWMVHLEAKRAGLKGLPKDECPSAMAAVKERWYLLIPLVVLVWLLFSGRTPMFAGTIGLALTAIVILGSAIILKVSNFALRIAFWIALGLLCAGFFQLGIGVIFGVIAALVAVCWFIKGGRDTLVICLHALVEGARHAVPVGIACALVGVIIGVVSLTGVASTFAGYILAVGENNLFLSLLLTMLTCLVLGMGIPTIPNYIITSSIAAPALLDLGVPLIVSHMFVFYFGIMADLTPPVALACFAAAPIAKERGLKISMWAIRIAIAGFIVPFMAVYNPALMMQGGDWGATLYMLFKAAFAVGLWGAVFTGYLQRPMALWEKVLAFAAAASMVLAMPISDEIGFALGALFLIQHIWRARRAEPATA transporters Pseudomonas stutzeri RCH2 psRCH2 GFF85 Psest_0085 PSEST_RS00425 WP_015275112.1 tr|L0GD92|L0GD92_PSEST alpha-ketoglutarate TRAP transporter, solute receptor component specific phenotype on a-ketoglutarate and no other transporter for this substrate is apparent in the fitness data. (Mutants in another TRAP system, Psest_4268:Psest_4270, have a much milder defect in a-ketoglutarate utilization). TRAP transporter solute receptor, TAXI family TRAP transporter solute receptor, unknown substrate 1 MRLTKRLGLLAAAAAFTASTAAVAAPTFINILTGGTSGVYYPIGVALSQQYNKIDGAKTSVQATKASVENLNLLQAGRGELAFSLGDSVEDAWNGVEDAGFKAPLKRLRAIAGTYNNYIQIVASAESGIKTLDDLKGKRISVGAPKSGTELNARAIFKAAGLDYKDMGRVEFLPYAESVELIKNRQLDATLQSSGLGMAAIRDLASTMPVTFVEIPAEVVEKIESDAYLAGVIPAGTYDGQDADVPTVAITNILVTHEKVSDEVAYQMTKLMFDNLAALGNAHSAAKDIKLENATKNLPIPLHPGAERFYKEAGVLK catabolism Shewanella loihica PV-4 PV4 5208605 Shew_1116 SHEW_RS05745 WP_011864920.1 tr|A3QBY9|A3QBY9_SHELP N-acetylglucosamine kinase (EC 2.7.1.59) Specifically important for: N-Acetyl-D-Glucosamine. The first step in NAG utilization (SEED_correct) ATPase, BadF/BadG/BcrA/BcrD type (RefSeq) N-acetylglucosamine kinase of eukaryotic type (EC 2.7.1.59) MGFNQTEEQALVIGIDGGGSKCRATIYAADDSVLGTGVAGRANPLYGLTHTFDSISRATELALQDAGLKAGDGKTMVAGVGLAGVNVAHLYQAIKAWQHPFAEMYVTTDLHTACIGAHKGGDGAVIITGTGSCGYAHVGEQSLSLGGHGFALGDKGSGAWLGLQAAQQVLLDLDGFGPATQLTERLLEHFKVNDAMGIVEHLAGKSSGCYATLARTVLSCAQAQDEVAKAIVVEGAEYISALAHKLFEIHPPRFSMIGGLAEPLAPWLDKRVVDKISPILAPPELGAAYFARQQLGFSS transporters Shewanella loihica PV-4 PV4 5208943 Shew_1444 SHEW_RS07400 WP_011865243.1 tr|A3QCW3|A3QCW3_SHELP dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component Important for utilizing succinate, fumarate, and L-malate, as expected, and also for utilizing a-ketoglutarate TRAP dicarboxylate transporter, DctM subunit (RefSeq) TRAP-type C4-dicarboxylate transport system, large permease component C4-dicarboxylate transporter, DctM subunit MTIATLFISLFLCMLLGMPIAIALGFSSMLTILLFSDDSLASVALKLYESTSEHYTLLAIPFFILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIGSIVIVGMVRAGYPEKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIPGLMMGLLLMLAIYIVARIKKLPSRPFPGFRPLAISSAKAMGGLALIVIVLGSIYGGIASPTEAAAVACVYAYFIAVFGYRDIGPLKNVSWRDSGEPLIRAILRNLGFMVLAVFKTPADKEIRHVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHLIAETIVGMGLPVWGFLIIVNLLLLAAGNFMEPSAILLIMAPILFPIATQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTAGITGRSMGWVIHSCIPWLALLLFFLALITYIPQISLFLPEYIDKLNGY transporters Shewanella loihica PV-4 PV4 5208944 Shew_1445 SHEW_RS07405 WP_011865244.1 tr|A3QCW4|A3QCW4_SHELP dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), small permease component Important for utilizing succinate, fumarate, and L-malate, as expected, and also for utilizing a-ketoglutarate tripartite ATP-independent periplasmic transporter DctQ (RefSeq) C4-dicarboxylate transporter, DctQ subunit MMSRFFSHIEEVVLNALITAMTLLVFVEVIARFFFNTGFLWIQELTLTICGWFVLFGMSYGVKVGAHIGVDAFVKKLPAQGRKYTAILAVAICLIYCGMFLVGSWDYLAKMYQIGVPMEDIDLPHFLIGGLDGDFAWEYLRIDVEEPAVPLWTSQSILLIGFILLTWRFLQLALAIITNKTDGFAFADEAKESMHLIDQEAQADDKQPGDKK transporters Shewanella loihica PV-4 PV4 5208945 Shew_1446 SHEW_RS07410 WP_011865245.1 sp|A3QCW5|DCTP_SHELP dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), solute receptor component Important for utilizing succinate, fumarate, and L-malate, as expected, and also for utilizing a-ketoglutarate TRAP dicarboxylate transporter, DctP subunit (RefSeq) TRAP-type C4-dicarboxylate transport system, periplasmic component C4-dicarboxylate-binding protein DctP MTRLNTCTFIKQIVKMTSIAALLGASLNSWAAPTEIKFSHVVAENTPKGQMALKFKQLVEERLPGEYQVNVFPNSQLFGDNNELSALLLNDVQFVAPSLSKFERYTKKLQLFDLPFLFKDMDAVNRFQQSDAGQQLLNSMKRKGVVGLGYLHNGMKQFSASSPLVLPEDAQGKKFRIMASDVLAAQFQAVEAIPVKKPFSEVFTLLQTRAIDGQENTWSNIYSKKFYEVQSNITESNHGVLDYMVVTSNTFWKSLPADKRKVIKASLDEAIAYGNEIAAAKVNKDKQAIIDSKRSEVTYLTPEQRAAWVNAMKPVWAQFEDKIGKDLIDAAVASNE catabolism Shewanella amazonensis SB2B SB2B 6936372 Sama_0560 SAMA_RS02985 WP_011758678.1 tr|A1S312|A1S312_SHEAM D-mannose isomerase (EC 5.3.1.7) Specifically important for: D-Mannose; D-Mannitol. This is the first step in D-mannose catabolism. D-mannitol is probably oxidized to mannose first. (SEED_correct) hypothetical protein (RefSeq) D-mannose isomerase (EC 5.3.1.7) MKFYNRDFLLSHSQSILDFYDPRVLDASGGYFHNYYDDGSLFEPGFRQLVSSCRITVNYARAADILDKPEYLAHARHGLNYLLNVHLQADERFAWTLKSHRPEDMTQQAYGYAFALLAFAACRKSGILKDNNKLLWIYNLLEQRFWQPEYGLYADEIGADGVLSDYRGQNANMHLCEAMIAAFEASGEGRFLDRAMEIADKIANRQAALTGGIIWEHFTPGFAINWEYNKDDPKNLYRPWGFQGGHQTEWAKLLLSLARHSHQPWLISRAKTLFDTAFEKSWDKEHGGMVYGFGPNGDWCDDDKYFWVQAESFAAAAMLYQQTGEQKYLDAYNALWNYAWQHFVDHEHGAWFRVLYRDNRKYSNEKSTAGAKCDYHTLGACFDSLRDLT transporters Shewanella amazonensis SB2B SB2B 6936374 Sama_0562 SAMA_RS02995 WP_011758680.1 tr|A1S314|A1S314_SHEAM D-mannitol and D-mannose transporter (MFS superfamily) Specific phenotype on mannitol and mannose and no other transporter for these compounds is apparent in the fitness data. SEED_correct glucose/galactose transporter (RefSeq) Predicted mannose transporter, GGP family MAFVSSTTPQNGSAAPAQSHQQLLFGAMTSLFFIWGFITALNDILIPHLKGIFDLSYTQAMLVQFCFFGAYFLVSPLAGVLIARIGYLRGIIFGLSTMATGCLLFYPASSLEQYALFLLALFVLASGITILQVSANPFVARLGPERTAASRLNLAQALNSLGHTLGPLFGSLLIFGAAAGTHEAVQLPYLLLAAVIGIIAVGFIFLGGKVKHADMGVDHRHKGSLLSHKRLLLGALAIFLYVGAEVSIGSFLVNYFAEPSIGGLDEKSAAELVSWYWGGAMIGRFAGAALTRRFNPAMVLAANAVFANLLLMLTIVSSGELALVAVLAVGFFNSIMFPTIFTLAIEGLGELTSRGSGLLCQAIVGGALLPVIQGVVADNVGVQLSFIVPTFCYFYICWYAFFARNRMNGETAS catabolism Shewanella amazonensis SB2B SB2B 6936606 Sama_0794 SAMA_RS04165 WP_011758911.1 tr|A1S3P5|A1S3P5_SHEAM gamma-glutamyl-gamma-aminobutyrate hydrolase [EC: 3.5.1.94] Specifically important for: Putrescine Dihydrochloride. Similar to puuD (PUUD_ECO57), a step in putrescine catabolism. Also, is cofit with other genes from the gamma-glutamyl-putrescine pathway. hypothetical protein (RefSeq) Para-aminobenzoate synthase, amidotransferase component (EC 2.6.1.85) putative glutamine amidotransferase MPLQQESARQERKPVILMSMGQQDRNGHAYQVMTHKYMQPVVDISDCIPLLIPTCFGVADIEQYLDMADGVYLSGAASNIDPSLYGQENLTPEKKQDLARDLVDIALIKGAVKRGLPILGICRGMQEMNIAFGGDLYQKVHDEDHLNDHREDPDTPPDVQYGASHSISMVKGSWLHKLLGDTIEVNSLHGQGIKTLGKGLEALALAEDGLVEALHAPYLPQFTLGVQWHPEWKALENPDSIKIFKAFGEACRRRAGSALDLRIDKAS catabolism Shewanella amazonensis SB2B SB2B 6936757 Sama_0944 SAMA_RS04925 WP_011759060.1 tr|A1S445|A1S445_SHEAM N-acetylglucosamine kinase (EC 2.7.1.59) Specifically important for: N-Acetyl-D-Glucosamine. This is the first step in NAG utilization (SEED_correct) hypothetical protein (RefSeq) N-acetylglucosamine kinase of eukaryotic type (EC 2.7.1.59) MAFDQTLEGQLYLGIDGGGSKCRATLYNNKLDVLGTGVAGRANPLFGLEQTFESILASTEMALRDAGLSLNDASLLVAGLGLAGVNVPRLLADVQAWQHPFKTMYVTSDLHTACIGAHQGGDGAVIITGTGSCGYVHVGDESLSLGGHGFALGDKGSGAWLGLRAAEHVLLQLDGFAEPTALTERLFANLGVSDALGIVENLAGRSSSCYATLAREVFAAADEGDKVAVGILREGAAYISEMARKLFTLEPARFSMIGGLAEPLQKWLDADVVARLEPSLAAPETGAVLFAIQQHNKQSAA transporters Shewanella amazonensis SB2B SB2B 6937231 Sama_1401 SAMA_RS07300 WP_011759516.1 tr|A1S5F2|A1S5F2_SHEAM D-cellobiose transporter (MFS superfamily) Specific phenotype on cellobiose and no other transporter for this compound was apparent in the fitness data. Also, this protein is 70% identical to bglT from S. fridgimarina, which is a cellobiose transporter (PMC2996990). sugar (glycoside-Pentoside-hexuronide) transporter (RefSeq) Predicted beta-glucoside transporter, GPH family glycoside/pentoside/hexuronide:cation symporter, GPH family MLSVREKIAYGLGDTASNIVFQTVMLFLTFFYTDIFGISAAYVGTMFLAVRIMDAVTDPLMGYLADRTNTRWGRYRPYLLWFAFPFAAISVLAFTTPDLSESGKEWYAFATYALLMLAYTAINIPYCALGAALTTNPAERVSVQSYRFVFAMLGGVMVSALTLPLVDFFGQGDKAKGYQLTILAMSIVGTVMFLLCFIGTKERDFSSDDNSGNFKAASKALWANDQWRVLSAAAIFLLTGLVLKSTLAIYYVKYFLGREDMISVFVTSGVVGNIFGVALAKKLADKMCKVKAYIRLQLIAAALCMAAWFVPADQYVLALVFYIAWNFTINMGTPLLWAKMADTVDYGQFKTGVRTTGLVYSSVIFFIKLGLAIGGALGGWLLAAYGYQPDVAQTEETRAGILLCFTLYPALASIAVAFVMRHYTLDSQRVAEISVSLQQKHSGT catabolism Shewanella amazonensis SB2B SB2B 6937235 Sama_1405 SAMA_RS07320 WP_011759520.1 tr|A1S5F6|A1S5F6_SHEAM glucokinase (EC 2.7.1.2) Specifically important for: D-Cellobiose. After cellobiose is cleaved to 2 glucose (by Sama_1404), it would be phosphorylated to enter glycolysis (SEED_correct) fructokinase (RefSeq) Glucokinase, ROK family (EC 2.7.1.2) fructokinase MYRSGIDLGGTKIELVTLNEKGEEVFRKRVPTPKDYRATLEAVAGLVHDSEKETGQVSSVGIGIPGVVSAVTGRVKNSNAVWLNGQPMDKDLGAMLGREVRIANDANCFAVSESVDGGGAGKTLVFGAILGTGCGAGIAINHKVHGGGNGIGGEWGHNPLPWMTADEFNSTRCFCGNADCIETFVSGTGFVRDFRAHGGEAASGIEIVALMGKGEPLAEAAFGRFIDRLARALAHVINLLDPDVIVLGGGVSNIDEIYEYLPALLPKYVLGGECATKVVKNHHGASSGVRGAAWLWAPGEQAALPGLQEL catabolism Shewanella amazonensis SB2B SB2B 6937966 Sama_2099 SAMA_RS10975 WP_011760212.1 tr|A1S7E8|A1S7E8_SHEAM UMP phosphatase (EC 3.1.3.5) Specifically important for: Thymidine. Probably required for thymidine utilization because it allows overflow metabolism of pyrimidine intermediates, as with umpH from E. coli (which is 72% identical), see PMID 23903661 UMP phosphatase (RefSeq) Phosphatase NagD predicted to act in N-acetylglucosamine utilization subsystem NagD protein MKNIICDIDGVLLHDNKLVPGSDKFIHRVLEQGNPLVILTNYPVQTGKDLQNRLDAAGINVPEECFYTAAMATADFLKHQEGSKAFVIGEGALTHELYKAGFTITDINPDFVIVGETRSYNWDMIHKAARFVADGARFIATNPDTHGPAFSPACGALCAPIERITGRKPFYVGKPSSWIVRSALNHINGHSENTVIIGDNMRTDILAGFQAGLETILVLTGVSRLEDIEKEPFRPNHVFNCAGDIDIF transporters Shewanella amazonensis SB2B SB2B 6938088 Sama_2209 SAMA_RS11590 WP_011760322.1 tr|A1S7Q8|A1S7Q8_SHEAM alpha-ketoglutarate TRAP transporter, solute receptor component specific phenotype on a-ketoglutarate. A putrescine ABC transporter (Sama_2642:Sama_2638) is also important in this condition, which is not explained. This organism can also utilize succinate or fumarate (but not L-malate), which we do not have fitness data for these under aerobic conditions. This could also transport some C4 compounds. C4-dicarboxylate-binding periplasmic protein (RefSeq) TRAP-type C4-dicarboxylate transport system, periplasmic component C4-dicarboxylate-binding protein DctP MKVSKPATLQSLFTLGKASLLATVLGFSFGAVAEPVEIKFSHVVAENTPKGQMALKFKELVESRLPGEYKVSVFPNSQLFGDNNELAALLLNDVQLVAPSLSKFERYTKKLQVFDLPFLFEDMDAVDRFQQSEAGQQLLNSMSRKGLVGLGYLHNGMKQFSANNALSLPGDAAGKKFRIMPSDVIAAQFEAVGAIPVKKPFSEVFTLLQTRAIDGQENTWSNIYSKKFYEVQTHITESNHGVLDYMLVTSETFWKSLPKDKREIIKQSMDEAVALGNKLALEKANEDRQLILDSKRVELVTLTPEQRQAWVNAMRPVWSQFEDKIGKDLIEAAESANKP transporters Shewanella amazonensis SB2B SB2B 6938089 Sama_2210 SAMA_RS11595 WP_011760323.1 tr|A1S7Q9|A1S7Q9_SHEAM alpha-ketoglutarate TRAP transporter, small permease component specific phenotype on a-ketoglutarate. A putrescine ABC transporter (Sama_2642:Sama_2638) is also important in this condition, which is not explained. This organism can also utilize succinate or fumarate (but not L-malate), which we do not have fitness data for these under aerobic conditions. This could also transport some C4 compounds. C4-dicarboxylate transporter, putative (RefSeq) C4-dicarboxylate transporter, DctQ subunit MISRIFGYFEEGVLNLLITLMTLLVFMEVIARFFFNTGFLWIQELTLTFCGWFVLFGMSYGIKVGAHIGVDAFVKKLKPGARRISALLAVSICLIYCAMFLKGTWDYLSQIYHIGIGMEDLDVPSVLMKQMSEDFAWDVMRIDPEDPAIPLWISQSILLLGFVMLTWRFLELAVAIFRGTSNGFSFHDEAKESMHLADEQSGANDNNNDGAKS transporters Shewanella amazonensis SB2B SB2B 6938090 Sama_2211 SAMA_RS11600 WP_011760324.1 tr|A1S7R0|A1S7R0_SHEAM alpha-ketoglutarate TRAP transporter, large permease component specific phenotype on a-ketoglutarate. A putrescine ABC transporter (Sama_2642:Sama_2638) is also important in this condition, which is not explained. This organism can also utilize succinate or fumarate (but not L-malate), which we do not have fitness data for these under aerobic conditions. This could also transport some C4 compounds. C4-dicarboxylate transport protein (RefSeq) TRAP-type C4-dicarboxylate transport system, large permease component C4-dicarboxylate transporter, DctM subunit MTIATLFLTLFLCMLLGMPIAIALGFSSMLTILLFSNDSLASVALKLYEATSEHYTLLAIPFFILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIGSIVIVGMVRAGYPQKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIPGLLMGVLLMVAIYIVARIKNLPSRPFPGVKALSLSSAKAMGGLALIFIVLGSIYGGVASPTEAAAVACVYAYLVAVFGYRDIGPLKEVPWRKEGEAILAAIVRNLLHVGLGLIKTPTDKEIRNVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHIIAETIVGWGLPPWGFLIIVNLLLLAAGNFMEPSAILLIMAPILFPIAVQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTAGITGRSIGWVIHACLPWLLLLLGFLVLITYVPQISLFLPEYLDSLRGFK catabolism Shewanella amazonensis SB2B SB2B 6938110 Sama_2231 SAMA_RS11700 WP_011760344.1 tr|A1S7T0|A1S7T0_SHEAM glucokinase (EC 2.7.1.2) Specifically important for: D-Maltose monohydrate. Maltose is presumably cleaved to glucose, so the annotation as glucokinase (but not as fructokinase) fits. The other glucokinase (Sama_1405) is not important on maltose. (SEED_correct) fructokinase (RefSeq) Glucokinase, ROK family (EC 2.7.1.2) fructokinase MMRMGVDLGGTKIELVALGEDGSELFRKRIATPREYQGTLNAVVTLVNEAEATLGTQGSLGIGIPGVISPYTGLVKNANSTWINGHPLDRDLGALLNREVRVANDANCFAVSEAVDGAAAGKRVVFGAILGTGCGAGLAFDGRVHEGGNGIGGEWGHNPLPWMRPDEFNTTECFCGNKDCIETFVSGTGFVRDFRNSGGTAQNGAEIMSLVDAGDELANLVFDRYLDRLARSLAHVINMLDPDAIVLGGGMSNVQAIYARLPAILPKYVVGRECRTPVVQNLYGCSSGVRGAAWLWEKR catabolism Shewanella amazonensis SB2B SB2B 6938540 Sama_2643 SAMA_RS13845 WP_011760751.1 tr|A1S8Y9|A1S8Y9_SHEAM Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) Specifically important for: Putrescine Dihydrochloride. Putrescine is catabolized via gamma-aminobutyrate (SEED_correct) putative aminotransferase (RefSeq) Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) putrescine aminotransferase MQQQQQDTISALQAMDAAHHLHPFTDSADLAKRGTRVIERAEGVYIWDAKGNKLLDAMAGLWCVNVGYGRKSIADAAYAQLQTLPFYNNFFQCTHEPAIRLASKIASLAPGHMNRVFFTGSGSEANDTNLRMVRRYWDLKGMPSKKTIISRKNAYHGSTVAGASLGGMGFMHQQGDLPIPGIVHIDQPYWFGEGRDMSPEAFGIKTAQALEAKILELGEDKVAAFIAEPFQGAGGVIIPPDSYWNEIKRILEKYNILFILDEVISGFGRTGNWFAAQTLGLKPDLITIAKGMTSGYIPMGGVIVSDRVADVLISDGGEFAHGFTYSGHPVAAAVALENIRILEEERLVDKVRTDTGPYLQDRLQTLSAHPLVGEVRGMGMVGAIELVADKHSMVRFGSEISAGMLCREACIESGLVMRAVGDTMIISPPLCITRDEIDELIFKASQALSLTLEKIAARGN catabolism Shewanella amazonensis SB2B SB2B 6938542 Sama_2645 SAMA_RS13855 WP_011760753.1 tr|A1S8Z1|A1S8Z1_SHEAM Gamma-glutamyl-GABA hydrolase (EC 3.5.1.94) Specifically important for: Putrescine Dihydrochloride. Part of the gamma-glutamyl-putrescine pathway for putrescine catabolism (SEED_correct) glutamine amidotransferase (RefSeq) Gamma-glutamyl-GABA hydrolase (EC 3.5.1.94) putative glutamine amidotransferase MSDATIPLIGVSACNTPIGLQTFNTVGEKYLLGVINGTGGWPLIIPSIGDGMPTELLLERLDGILFTGSPSNVEPHHYSGPASEPGTHHDPRRDATTLPLIKAAIAAGVPVLGICRGFQEMNVAFGGSLHQKLHETGVFEEHREDRTAPLEVQYGLAHTVTLEPGGVIFEAWGRSSAEVNSVHTQGVERLGNGLRPEAYAPDGLIEAFSVTDAKNFALGVQFHPEWKVADNAFYLSIFNAFGDACRRRAQERAR transporters Sinorhizobium meliloti 1021 Smeli SM_b20002 SM_b20002 SM_b20002 NP_436545.1 tr|Q92XF6|Q92XF6_RHIME ABC transporter for Lactose, ATPase component Specific phenotype on Beta-Lactose. (KEGG_correct) sugar ABC transporter ATP-binding protein Various polyols ABC transporter, ATP-binding component lactose/L-arabinose transport system ATP-binding protein MSELQLSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDLTIDDVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHILELGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLHKQLATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKMNFLKGVIEIDEDQAYARLPDYGDAKIPVTLQAAAGTAVTIGIRPEHFDEAGPAALDLAIDMLEHLGGETFAYARHHGNGELIVVETKNGRGLKTGDRLTARFDPVSVLVFDGEGKRLRS transporters Sinorhizobium meliloti 1021 Smeli SM_b20325 SM_b20325 SM_b20325 NP_436851.1 tr|Q7ANS2|Q7ANS2_RHIME ABC transporter for D-Trehalose, periplasmic substrate-binding component Specific phenotype on D-Trehalose dihydrate. trehalosemaltose-binding protein Maltose/maltodextrin ABC transporter, substrate binding periplasmic protein MalE MNVKPFVRTLISCAAIAGAIDLAAAAELSMAANSTGKNLSFLRDQIARFEKETGHKVNLVTMPASSSEQFSQYRLWLAAGNKDVDVYQTDVIWAPQLAEQFVDLTEATKDVVGEHFPSIIQSQTVNGKLVALPFYTDAPALYYRKDLLDKYGKTPPKTWDELAATAKEVQDKERAAGSADIWGFVFQGNAYEGLTCNALEWIKSSGGGQIIEPDGTISVNNEKAAAAVEKVKEWIGTIAPKGVLAYQEEESRGVWQTGNAVFMRNWPYAYALGNGDDSAVKGKFEVAPLPAATDGDQPSSTLGGWNLAVSKYSDEQEAAIAFVKFLGSAETQKVRAIELSNLPTIAALYDDPEVAAAQPFMPHWKPIFQSAVPRPSAVAKVKYNEVSSKFWSAVHNTLSGNGTAAENLELLEVELTELKGDAW transporters Sinorhizobium meliloti 1021 Smeli SM_b20326 SM_b20326 SM_b20326 NP_436852.1 tr|Q7ANS1|Q7ANS1_RHIME ABC transporter for D-Trehalose, permease component 1 Specific phenotypes on D-Trehalose dihydrate. no phenotype on maltose, and there is an alpha-glucoside transporter with specific phenotype on maltose. trehalosemaltose transporter permease Maltose/maltodextrin ABC transporter, permease protein MalF trehalose/maltose transport system permease protein MTDLSLADRPAALAHGGRIGSDLQAQRVRSAWLFLAPTFLVLALVAGWPLIRTIYFSFTNASLTNLSGAEFVGFANYLSWITLKSGRTIYRGLLADPAWWNAVWNTLKFTVLSVSIETALGLIVALVLNAQFPGRGLVRAAILIPWAIPTIVSAKMWAWMLNDQFGILNDMLIGLGLIGEKIAWTASPDTAMIAELIVDVWKTTPFMALLILAGLQMVPGDIYEAAKIDGVHPVRVFWRVTLPLIRPALMVAVIFRMLDALRIFDLIYVLTPNNAQTKTMSVMARENLFDFDKFAYGAAASTMLFLIIATITILYMWLGRLNLSGGER transporters Sinorhizobium meliloti 1021 Smeli SM_b20327 SM_b20327 SM_b20327 NP_436853.1 tr|Q7ANS0|Q7ANS0_RHIME ABC transporter for D-Trehalose, permease component 2 Specific phenotypes on D-Trehalose dihydrate. no phenotype on maltose, and there is an alpha-glucoside transporter with specific phenotype on maltose. trehalosemaltose transporter permease Maltose/maltodextrin ABC transporter, permease protein MalG trehalose/maltose transport system permease protein MVVAIAKRTAFYALVAVIILVAVFPFYYAILTSLKSGTALFRIDYWPTDISLANYAGIFSHGTFVRNLGNSLLVATLVVAISLLLAVTAAYALARVRFRGRGLLLLTILSVSMFPQIAVLAGLFELIRFVGIFNTPLALIFSYMIFTLPFTVWVLTTFMRDLPIEIEEAAIVDGASPWVVITRVFMPLMWPALVTTGLLAFIAAWNEFLFALTFTSSNTQRTVPVAIALLSGGSQFEIPWGNIMAASVIVTVPLVVLVLIFQRRIISGLTAGGVKG transporters Sinorhizobium meliloti 1021 Smeli SM_b20328 SM_b20328 SM_b20328 NP_436854.1 tr|Q7ANR9|Q7ANR9_RHIME ABC transporter for D-Trehalose, ATPase component Specific phenotype on D-Trehalose dihydrate. trehalosemaltose transporter ATP-binding protein Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19) trehalose/maltose transport system ATP-binding protein MAELQLRDIRKSFGAFDVIKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTLAFDGQIVNQLTPSRRGIAMVFQSYALYPHMTVYENMAFGMQLAGKDKQQCRKRVEAAAEMLQLTPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIAKLHRSMHKTTMIYVTHDQVEAMTLADRICVLRDGLVEQIGTPLELYETPNSVFVAGFIGSPKMNFLSGAFAEPYKADTIGIRAEHLEIDEQGGEWSGTVIHSEMLGSDSYIYLDIGTGEPVIVRESGIAKHQPGQTIRISPAAGQVHRFDAGGRALGRMQMRGAA catabolism Sinorhizobium meliloti 1021 Smeli SM_b20329 SM_b20329 SM_b20329 NP_436855.1 tr|Q7ANR8|Q7ANR8_RHIME required for glucoside 3-dehydrogenase activity on raffinose or trehalose (thuA) (EC 1.1.99.13) Specifically important for: D-Raffinose pentahydrate; D-Trehalose dihydrate. a close homolog is described by PMID 23772075; (SEED_correct) ThuA protein, function Trehalose utilization protein ThuA MPQITRRMTLSINAIVWGENIHEQTNAVVREIYPDGMHNTIAAALNSDPGIDATTATLQEPEHGLSETRLAAADVLLWWGHKDHGAVDDAIVERVAKRVWEGMGLIVLHSGHFSKVFKRLMGTPCALKWREAGERERVWVVNPRHPIAEGLGENFVIENEEMYGEQFSVPEPLETVFISWFAGGEVFRSGLTWRRGAGNIFYFRPGHETYPTYHDATVHKVLRNAVKWAYNPQGTYKAIHDAPNVPVEKALEPIVERGPRLHRAGEAGYR catabolism Sinorhizobium meliloti 1021 Smeli SM_b20330 SM_b20330 SM_b20330 NP_436856.1 tr|Q7ANR7|Q7ANR7_RHIME glucoside 3-dehydrogenase; active on raffinose or trehalose (thuB) (EC 1.1.99.13) Specifically important for: D-Raffinose pentahydrate; D-Trehalose dihydrate. a close homolog is described by PMID 23772075 trehalosemaltose utilization protein, function Nucleoside-diphosphate-sugar epimerases MKGTPMRLLILGTGGMANSHAKAFAEIEGVEMVGAVDVDPSRAKAFAVTHGIENTFTSLDDAIAWGEFDAATNVTPDKAHHPTTLALIAAGKHVLCEKPLAENYEKAAEMAAAAERAGLVTMVNLTYRNVAPLQKARELVVAGEIGRVRHLEASYLQSWLVSRAWGDWASESKWLWRLSTKHGSNGVLGDVGIHILDFAGYGANSSVERVFARLKAFDKAPDNRIGEYDLDANDSFAMTAEFENGAMAVIHASRWATGHLNELRLRLHGDRGALEVIHTPDGSSLRGCMGPDVEKAVWRTVDAGTVPTNYQRFVEAVKAGRTVEPGFRHAADLQRVLDLAIETERSRRELGVPDIDAVVQERAVG catabolism Sinorhizobium meliloti 1021 Smeli SM_b20890 SM_b20890 SM_b20890 NP_437724.1 tr|Q92UE7|Q92UE7_RHIME L-arabonate dehydratase (EC 4.2.1.25) Specifically important for: L-Arabinose. L-arabonate is an intermediate in the oxidation of L-arabinose (SEED_correct) dihydroxy-acid dehydratase L-arabonate dehydratase (EC 4.2.1.25) dihydroxy-acid dehydratase MKKKAEWPRKLRSQEWFGGTGKNAIMHRSWMKNQGLPADTFDGRPIIGICNTWSELTPCNAHLRDLAERVKRGVYEAGGFPVEFPVFSTGESTLRPTAMMFRNLAAMDVEESIRGNPVDGVVLLGGCDKTTPSLLMGAASVDIPAIVVSGGPMLNGKWRGKDVGSGTAIWQFSEMVKSGEMSLEEFMDAEQGMARSAGSCMTMGTASTMASMAEALGMTLSGNAAIPAVDARRRVISQLTGRRIVEMVKEDLKPSDILTKEAFENAIRVNGAVGGSTNAVLHLLALAGRVGVDLSLDDWDRLGRDVPTIVNLQPSGKYLMEEFYYAGGLPVVIKAVAEMGLLHNDAITVSGDTIWNDVKGVVNYNEDVILPREKALTKSGGIAVLRGNLAPRGAVLKPSAASPHLMQHKGRAVVFESIEDYHARINREDLDIDETCIMVLKYCGPKGYPGMAEVGNMGLPPKVLKKGITDMIRISDARMSGTAYGTVILHTAPEAAEGGPLALVENGDLIEVDIPNRTLHLHVSDEELARRRAAWVSPVKPLTGGYGGLYIKTVMQADAGADLDFLVGARGSVVERDSH catabolism Sinorhizobium meliloti 1021 Smeli SM_b20891 SM_b20891 SM_b20891 NP_437725.1 tr|Q92UE6|Q92UE6_RHIME Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) Specifically important for: L-Arabinose. The only dehydrogenase steps in the arabinose catabolism pathway are L-arabinose 1-dehydrogenase (which is SMc00588) and a-ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26). So, this is the semialdehyde dehydrogenase. dehydrogenase Aldehyde dehydrogenase B (EC 1.2.1.22) MTLHQNLIAGEWVGGDGVANINPSNTDDVVGEYARASAEDAKAAIAAAKAAFPAWSRSGILERHAILKKTADEILARKDELGRLLSREEGKTLAEGIGETVRAGQIFEFFAGETLRLAGEVVPSVRPGIGVEITREPAGVVGIITPWNFPIAIPAWKLAPALCYGNTIVFKPAELVPGCSWAIVDILHRAGLPKGVLNLVMGKGSVVGQAMLDSPDVQAITFTGSTATGKRVAVASVEHNRKYQLEMGGKNPFVVLDDADLSVAVEAAVNSAFFSTGQRCTASSRIIVTEGIHDRFVAAMGERIKGLVVDDALKPGTHIGPVVDQSQLNQDTDYIAIGKQEGAKLAFGGEVISRDTPGFYLQPALFTEATNEMRISREEIFGPVAAVIRVKDYDEALAVANDTPFGLSSGIATTSLKHATHFKRNAEAGMVMVNLPTAGVDFHVPFGGRKASSYGPREQGKYAAEFYTNVKTAYTLA catabolism Sinorhizobium meliloti 1021 Smeli SM_b20892 SM_b20892 SM_b20892 NP_437726.1 tr|Q92UE5|Q92UE5_RHIME 2-dehydro-3-deoxy-L-arabinonate dehydratase (EC 4.2.1.43) # Specifically important in carbon source L-Arabinose. Similar to PA2216 from Pseudomonas aeruginosa (see PMC:PMC4038344) and to gguC or araD1 (Atu2345) from Agrobacterium tumefaciens (see PMC: PMC3232879), which also have this activity. In Agrobacterium, this reaction is proposed to be a step in L-arabinose oxidation. (Note that 2-keto-3-deoxy-L-lyxonate and 2-keto-3-deoxy-L-arabinonate are the same compound.) hypothetical protein SUGAR TRANSPORTER MLISQVRKEDGSVIVAVRAPGETARAVRGAESVYALAMEAANSRRSLRDVVDAKGFGETIDLEEAYSQGRLLSPITHPDPAHLHLTGTGLTHLGSAATRDAMHKKATEATEETLTDSMKMFRMGLEGGKPKSGEKGVQPEWFYKGNGTTAVAPGEPLVSPSFAEDGGEEPEMAGIYVISDKGVPFRLGFAVANEFSDHKTERVNYLWLAHSKLRQASFGPEIRIGAAPEDIRGASRILRGGKVLWEKPFLSGEANMSHSFANLEYHHFKYGLFRAPGDIHVHMFGTATLSFGDGIRTEEGDVFEIEAKEFGLPLRNPLAIAAEEEVAVHQL catabolism Sinorhizobium meliloti 1021 Smeli SM_b21101 SM_b21101 SM_b21101 NP_437220.1 tr|Q92VM0|Q92VM0_RHIME L-fucono-1,5-lactonase; D-arabinolactonase # Specifically important in carbon source D-Arabinose; carbon source L-Fucose. A related protein (29% identical) was shown by Hobbs et al (2013) to be a L-fucono-1,5-lactonase. Note that D-arabinolactone is chemically similar to L-fuconolactone, with one methyl group replaced with a hydrogen. hypothetical protein L-fuconolactone hydrolase MIIDTHLHLIDKSALNYPWLAGVPALDRDFLYATYAAEAKRVGVAASLHMEVDVDPAEIELETREVARLAGEPGSLLKGAIAACRPEDEGFAAYLERQEENAFVKGFRRVLHVVTDDLSEQPLFRENVKRLSGTRFTFDLCVLPHQIPKAIALADLAPDVQFILDHCGVPDIKGHAEHPWRDHMTEIARHPNVVAKISGVVAYAEEDWALDSIRPYVEHTISVFGWDRVVWGSDWPVCTLGGNLSTWVAATQALIEGCSPQERRKLLSGNAQRIWNLI transporters Sinorhizobium meliloti 1021 Smeli SM_b21103 SM_b21103 SM_b21103 NP_437222.1 tr|Q926H4|Q926H4_RHIME ABC transporter for L-Fucose, periplasmic substrate-binding protein Specific phenotype on L-Fucose. sugar ABC transporter substrate-binding protein Maltose/maltodextrin ABC transporter, substrate binding periplasmic protein MalE multiple sugar transport system substrate-binding protein MNRLLSGVSAGVIMLACAMGAAKAADLPGKFEGVTIDAKLIGGQQYEKLYERIGEWEKATGAKVNILSKKNHFELDKEIKSDIATGGLTWCVGSNHSSFAPQYPDIYADLFGLIPSEEVAKFVPAVIDASTLEGKLVMLPRAQFDVSALYFQKSLYQDEAKKTEFKAKYGYDLAPPDTWAQVSDQAEFFAAPPNFYGTQFAGKEEAINGRFYEMLVAEGGEYLDKDGRPAFNSDAGVRALEWFVKLYKDKAVPPGTTNYLWDDLGQGFASGSIAVNLDWPGWASFFNDPKSSKVAGNVGVKVQPAGSSGKRTGWSGHHGFSVTESCADKEAAASLVWWLTNEDSQKLESAAGPLPTRSAVWDFNIKAAEGDAYKTEVLQAFQEAAKHAFPVPQTAEWIEISNAVYPELQAAILGDKTSKEALDAAAEKATGILEDAGKL transporters Sinorhizobium meliloti 1021 Smeli SM_b21104 SM_b21104 SM_b21104 NP_437223.2 tr|Q92VL8|Q92VL8_RHIME ABC transporter for L-Fucose, permease component 1 Specific phenotypes on L-Fucose. sugar ABC transporter permease Maltose/maltodextrin ABC transporter, permease protein MalF MKLSKLSAPTLLLLPAFIVLAVFIVLPLIFSLYSSFTPFRLTKPDSLWVFIGFRNYVNVLTNAEFWVAFGRTVLLLTVALNAEMFLGLGLALLVNKATYGQRALRTAMMFPMMFSPVLVGFQFKFLFNDNIGFVNNALQSLGLTDRAIPWLIDGNLALFSIIVAEVWSSTAVFAILILAGLLAMPKDPVEAAHVDGCTPWQTFRYVTWPYLMPFAFIAMTIRSLDVARAYDIVKIMTDGGPAKRTELLWTLIGRTAYGDARMGMANAMAYVAILLSIFFTVYFFRKLAAARQQIGAEW transporters Sinorhizobium meliloti 1021 Smeli SM_b21105 SM_b21105 SM_b21105 NP_437224.1 tr|Q92VL7|Q92VL7_RHIME ABC transporter for L-Fucose, permease component 2 Specific phenotypes on L-Fucose. sugar ABC transporter permease Maltose/maltodextrin ABC transporter, permease protein MalG multiple sugar transport system permease protein MDTNASHRLRRRLLKVAHLAGLFLAMLVICLPGLWIVLSSLRPTVEIMAKPPVWIPETLSLDAYRAMFSGAGQGGVPVWDYFRNSLIVSVTSTVIALAIGLSGGYAFARYRFKAKSAIFLGFMLTRAVPGIALSLPLFMLYARTGIIDTHFSLILTYVALNVPFTIWLIDGFFRQVPKDLAEAAQIDGCTPWQAFWQVEFPLAGPGIASAGIFAFLTSWNEYALASQITRSVNSKTLPVGLLDYTAEFTIDWRGMCALAVVMIVPALTLTFIIQKHLVSGLTFGAVKG transporters Sinorhizobium meliloti 1021 Smeli SM_b21106 SM_b21106 SM_b21106 NP_437225.1 tr|Q92VL6|Q92VL6_RHIME ABC transporter for L-Fucose, ATPase component Specific phenotype on L-Fucose. sugar ABC transporter ATP-binding protein Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19) multiple sugar transport system ATP-binding protein MAPVTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAIEIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAILDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLHARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPMNMEEAVLTDGKLAFASGATLPLPPRFRSLVREGQKVTFGLRPDDVYPSGHGLHAGDADAVHEIELPVTITEPLGNETLVFTQFNGRDWVSRMLNPRPLRPGEAVPMSFDLARAHLFDGETGRALAS catabolism Sinorhizobium meliloti 1021 Smeli SM_b21107 SM_b21107 SM_b21107 NP_437226.1 tr|Q92VL5|Q92VL5_RHIME dehydratase involved in L-fucose catabolism # Specifically important in carbon source L-Fucose. T. Lukk's 2009 thesis reported that this protein had weak activity as a L-fuconate dehydratase, which was the expected substrate. The fitness data shows that two other dehydratases are involved in fucose catabolism as well (see SMc02776 and SM_b21110), so the pathway is probably more complicated. mandelate racemase or evolutionary related enzyme of the mandelate racemase muconate lactonizing enzyme family protein mandelate racemase/muconate lactonizing enzyme family protein MARIEKTELRMVDLPPKNKRTDAIQSFVSQETPIVTITDADGATGTGYSYTIGTGGSSVMRLLSDHLVPILLGEDADCIEALWQKMEFATHATTIGAITALALAAVDTALWDLRAKKQKLPLWKLAGGAKESCPLYTTEGGWLHIEKQALVDDALQAKANGFSGSKVKIGKPSGAEDYDRLSAMRAALGDGFEIMTDCNQGFTVDEAIRRAARLRELDLAWIEEPLPADDLDGHIRLTRSTPTPIAVGESIYSIRHFREYMQKGACSIVQVDVARIGGITPWLKVAHAAEAFDIPVCPHFLMELHVSLVCAVPNGKYVEYIPQLDDLTQMGMEIREGRAIAPSNPGIGIAWDWEAVKARSVAEFTREFRR catabolism Sinorhizobium meliloti 1021 Smeli SM_b21108 SM_b21108 SM_b21108 NP_437227.1 tr|Q92VL4|Q92VL4_RHIME L-fucose mutarotase (EC 5.1.3.29) Specifically important for: L-Fucose. The first step in fucose catabolism. This protein is related to XCC4070 (FUCM_XANCP) hypothetical protein MQRMGMVIGLEPSKIAEYKRLHAAVWPEILALISECNITNYSIFLKEPENLLFGYWEYVGEDFEADMTKMAAHPKNQEWWSVCMPCQKPLESRRQGEWWAMMEEVFHHD catabolism Sinorhizobium meliloti 1021 Smeli SM_b21109 SM_b21109 SM_b21109 NP_437228.1 tr|Q92VL3|Q92VL3_RHIME L-fucose dehydrogenase (EC 1.1.1.122) Specifically important for: L-Fucose. The second step in fucose catabolism. oxidoreductase oxidoreductase, Gfo/Idh/MocA family MTETFDPSSLRQWWPKPVAPRPIVIFGAGSIVGDAHLPAYRNAGFPVAGIFDPDAGKAAALARASDVMAFTSEEEALSAENAIFDLATPPAAHASILSKLPKGSFALIQKPLGSDLAAATGILEICRERNIRAAANFQLRFAPMMLALKDAIATGYLGEVVDFDAWLALATPWGLWPFLKGLPRIEIAMHSIHYLDLVRSLLGDPRGVHAKTIGHPNHDVAQTRTAAILDYGDAVRCVLSVNHDHDFGRRFQACEFRICGTRGAAYVKLGVNLDYPRGEPDELWIRPAGGADWIQVPLEGSWFPDAFANRMANLQRHAGGEDDELIGSVEDAWRTMALVEAAYQSSARPATPIAALPLEN catabolism Sinorhizobium meliloti 1021 Smeli SM_b21110 SM_b21110 SM_b21110 NP_437229.1 tr|Q92VL2|Q92VL2_RHIME dehydratase involved in L-fucose catabolism # Specifically important in carbon source L-Fucose. This protein is similar to the (R)-enoyl-CoA hydratase portion of E. coli maoC (36% identical). It is one of three dehydratases involved in L-fucose catabolism (see SMc02776 and SM_b21107) MaoC-like (monoamine oxidase-like) protein, NodN Aldehyde dehydrogenase (EC 1.2.1.3) MSEQTIYYEDYEQGHVRLTSGRTITETDFVVHAGHTGDFFPHHMDAEFAKTLPGGQRIAHGTMIFSIGVGLTASLINPVAFSYGYDRLRFVRPVHIGDTIRTRVTIAAKEDDPKRPGAGRVVERCEVINQRGEVVLAADHILIVERKPEGTIQ catabolism Sinorhizobium meliloti 1021 Smeli SM_b21112 SM_b21112 SM_b21112 NP_437231.1 tr|Q92VL0|Q92VL0_RHIME L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase # Specifically important in carbon source L-Fucose; carbon source D-Arabinose. SM_b21112 is 58% identical to LRA6, which is L-2,4-diketo-3-deoxyrhamnonate hydrolase (PMID:19187228). This reaction is also proposed to be involved in L-fucose catabolism (PMID:17144652), which explains the phenotype on L-fucose. Its role in D-arabinose catabolism suggests that it also acts on a five-carbon substrate such as 2,4-dioxopentanoate. This protein belongs to the fumarylacetoacetate hydrolase family, which hydrolyses substrates of the form R-CO-CH2-CO-R'. Both keto groups are involved in the catalytic mechanism (Bateman et al 2001) so we propose that 2,4-dioxopentanoate is the intermediate in D-arabinose catabolism. This would be formed from D-arabinoate by two successive dehydratase reactions (see SMa0247 and SM_b21112). bifunctional 2-hydroxyhepta-2,4-diene-1, 7-dioatesomerase/5-carboxymethyl-2-oxo-hex-3-ene-1, 7-dioatedecarboxylase 2,4-diketo-3-deoxy-L-fuconate hydrolase MKLLRYGEPGQEKPGLLGSDGIIRDLSGHVSDLAAGALDPSKLDELANLDVETLPAVSGNPRLGPCVAGTGKFICIGLNYSDHAAETGATVPPEPIIFMKATSAIVGPNDDLVLPRGSEKTDWEVELGIVIGKTAKYVSEAEALDYVAGYCTVHDVSERAFQTERHGQWTKGKSCDTFGPTGPWLVTKDEVADPQDLAMWLKVNGETMQDGSTKTMVYGAAHLVSYLSQFMSLRPGDIISTGTPPGVGMGMKPPRYLKAGDVVELGIEGLGSQKQRVRADA catabolism Sinorhizobium meliloti 1021 Smeli SM_b21164 SM_b21164 SM_b21164 NP_437370.1 tr|Q92V79|Q92V79_RHIME N-formylglutamate deformylase (EC 3.5.1.68) Specifically important for: L-Histidine. KEGG suggests formimidoyl-L-glutamate as the substrate, while SEED suggests N-formylglutamate. This gene is cofit with a deiminase or iminohydrolase (which produces N-formylglutamate) which suggests that the SEED annotation is correct. (SEED_correct) formiminoglutamase N-formylglutamate deformylase (EC 3.5.1.68) formiminoglutamase MAVFEVRQGSSPVILGFPHTGTDVPASIRERLNDNGRILADTDWHIHDLYQGLLPDATAVRATFHRYVIDANRDPAGVSLYPGQNTTGLVPETDFDGLPIWKEGEGPTEVDITERLRDFHAPYHAALSAEIARVKAIHGVVVLYDCHSIRSHIPFLFEGRLPDFNIGTDMGKTCATEIERAAAEIAAGAECYSHILNGRFKGGWTTRHYGRPEQGVHAIQMELAQSTHLATEAPPFALDRAKADRLRRPLKAILERIETVAKELKRTGSEA transporters Sinorhizobium meliloti 1021 Smeli SM_b21216 SM_b21216 SM_b21216 NP_437260.1 tr|Q92VI3|Q92VI3_RHIME ABC transporter for D-Glucosamine, ATPase component Specific phenotype on D-Glucosamine Hydrochloride. sugar ABC transporter ATP-binding protein Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19) MSALEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDILIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARLLQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLHQMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMNILDAEMTANGLKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSEAQRLTASVEVVELTGPELVTTATVGSQRITACLPPRTAVGMGSAHAFTFDGTALHLFDPESGRSLRME transporters Sinorhizobium meliloti 1021 Smeli SM_b21219 SM_b21219 SM_b21219 NP_437263.1 tr|Q92VI0|Q92VI0_RHIME ABC transporter for D-Glucosamine, permease component 1 Specific phenotypes on D-Glucosamine Hydrochloride. sugar ABC transporter permease Glycerol-3-phosphate ABC transporter, permease protein UgpE (TC 3.A.1.1.3) multiple sugar transport system permease protein MERQSPLFSVFIHASALLLAVVILAPVAWLLIMSISPAADLSAKPLAWWPSDIDLSRYRTLLSAVENSAGAAFIASLLNSIKVAGMATLAAVVVAVPAAWAVSRTPAVAWSLYAVIATYMLPPVALAVPLYMGLAYFGLLNSVFGLALVYLTILAPFTTWLLKSGFDSIPREIESAAMIDGARLDQILRILTLPLAAPVMATSALFAFLLAWDEFFYALLFTSDQRAKTLTVAIADLAGGRVSDYGLIATAGVLAALPPVLIGLIMQRALISGLTSGGVKG transporters Sinorhizobium meliloti 1021 Smeli SM_b21220 SM_b21220 SM_b21220 NP_437264.2 tr|Q92VH9|Q92VH9_RHIME ABC transporter for D-Glucosamine, permease component 2 Specific phenotypes on D-Glucosamine Hydrochloride. sugar ABC transporter permease Glycerol-3-phosphate ABC transporter, permease protein UgpA (TC 3.A.1.1.3) multiple sugar transport system permease protein MTGTWISTRAWLLMLPLLVVMTAVIGWPLVDTVRLSFTDAKLVGTEGGFVGTANYIKMLGGSNFQRALVTTTWFAVISVAAEMVLGVLAALLLNQQFRGRTALRALMILPWALPTVVNATLWRLIYNPEYGALNAALTQLGLLDSYRSWLGEPGTALAALIVADCWKNFPLVALIALAALQAVPRDITAASLVDGAGPFNRFRFVIMPYLAGPLLVALVLRTIEAFKVFDIIWVMTRGGPANSTRTLSILVYQEAFSFQRAGSGASLALIVTLLVTILAAAYAALLRKAAGAS transporters Sinorhizobium meliloti 1021 Smeli SM_b21221 SM_b21221 SM_b21221 NP_437265.1 tr|Q926H2|Q926H2_RHIME ABC transporter for D-Glucosamine, periplasmic substrate-binding protein Specific phenotype on D-Glucosamine Hydrochloride. (SEED_correct) sugar uptake ABC transporter substrate-binding protein precursor Glucosamine ABC transport system, periplasmic sugar-binding protein multiple sugar transport system substrate-binding protein MLKSTRNALIGATLIGAGFTGHAQAETTLNALFMAQAAYSEADVRAMTDAFAKANPDIKVNLEFVPYEGLHDKTVLAQGSGGGYDVVLFDVIWPAEYAANNVLLDVTDRVTDEMNKGVLPGAWTTVEYDGKRYGMPWILDTKYLFYNKEILEKAGIKQPPKTWEELSEQATAIKDKGLLESPIAWSWSQAEAAICDYTTLVSAYGGKFLDGGKPAFTTGGGLDALNYMVTSYTSGLTNPNSKEFLEEDVRKVFQNGEAAFALNWTYMYNLANDPKESKVAGKVGVVPAPGAAGKSEVSAVNGSMGLGITATSKHPEEAWKYIVHMTSQETQNAYAKLSLPIWASSYENPNVTKGQEELIAAAKRGLAAMYPRPTTPKYQELSTALQQAIQEALLGQSSAEDALKSAAENSGL catabolism Sinorhizobium meliloti 1021 Smeli SM_b21373 SM_b21373 SM_b21373 NP_437491.1 tr|Q92UY3|Q92UY3_RHIME tagatose 6-phosphate kinase [EC: 2.7.1.144] Specifically important for: D-Tagatose. annotated as 6-phosphofructokinase by SEED, but tagatose 1,6-bisphosphate is the relevant intermediate for tagatose catabolism (KEGG_correct) sugar kinase 6-phosphofructokinase (EC 2.7.1.11), PF08013 family tagatose 6-phosphate kinase MQENHLIDIARWSERPGPRGIPSICSAHPLVIEAAMLRAHREKAPVLIEATCNQVNQDGGYTGMTPEDFTRFVGAIADRIEFPREKILLGGDHLGPNPWKHLPADEAMAKAEAMITAYAKAGFTKLHLDTSMGCAGEPTALPDATTAARAARLAAVAEDAVGGRGGVLPVYIIGTEVPIPGGALEELDTLEVTAPEAAIETVRVHRAAFEEAGAAGAFSRVVGAVVQPGVEFGNENVIAYDRARAEKLSATLGQLHGMVFEAHSTDYQTPDALRELVADGFAILKVGPGLTFALREALYGLDQIAAFLFPAARERTLAEVTEAVMREEPANWAKYYHGSAEEQRLQRHFSYSDRIRYYWPHPKAAAAVDELMSLLDGVAIPETLISQFLAGSYARVRNGEVAPQAKPLALAAVDAVLQDYFAACRV catabolism Sinorhizobium meliloti 1021 Smeli SM_b21374 SM_b21374 SM_b21374 NP_437492.1 tr|Q92UY2|Q92UY2_RHIME tagatose kinase (EC 2.7.1.101) Important on tagatose. This is the first step in tagatose catabolism. sugar kinase Fructokinase (EC 2.7.1.4) MHKILTIGEILVEIIATEKGDGFRKATPLIGPFPSGAPAIFIDQAGKLGQPCAIISRVGGDDFGTVNLERLKRDGVDISGIEVDPLATTGSAFVRYRPDGSRAFVFNIRDSACGKITLDERMTRLVGECSHVHVMGSSLYAPSVVESILAAIGIVKAGGGTVSFDPNLRPEILKSPGMREALLTVLAETDLFLPSGDELFLFTEAKTESQAVAELLASGIKAVVVKRGAAGASYFDAGAALSLPGFPVEEIDPTGAGDCFGATFVSFWLNGASPREALEFAAASGARAVMHFGPMEGASTRAELERFISEQQA transporters Sinorhizobium meliloti 1021 Smeli SM_b21644 SM_b21644 SM_b21644 NP_438103.1 tr|Q92TF7|Q92TF7_RHIME ABC transporter for D-Raffinose, ATPase component Specific phenotype on D-Raffinose pentahydrate. ABC transporter ATP-binding protein Oligopeptide transport system permease protein OppB (TC 3.A.1.5.1) peptide/nickel transport system ATP-binding protein; peptide/nickel transport system ATP-binding protein MVTIESIVPAPEERRDRDMKDERPVIDARKVAVSFKVENGTVQAVKDVSFQLYRGETVAIVGESGSGKSVTARTVMGLLSKRATIAPQARIEYDGRDVLKFSKRERRALRGDRISMIFQEPMSSLNPVYTIGSQIIEAIRAHRRVSRRAAAERALELLRHVQIPDPEARLNQYPHQLSGGQRQRVMIAMALANDPDVLIADEPTTALDVTVQAQILNLIRKLQQELGMAVILITHDLTVVRQFSDYVYVMQLGEVKEHNTTEALFADPQHAYTRRLLSSEPSGSANPLPDDAPILLDGRNVRVSFTLKKGGFFRPEFKELVAVDGLSLNLRRHETLGLVGESGSGKTTFGQALIRLLNTDGGEIYFEGEPIHDKDRKGMRPLRSKIQIVFQDPFSSLNPRMSVGQIIEEGLIVNGMGENRKDRLKRVEDALVSAGMPSNILSRFPHEFSGGQRQRIAIARAVALEPEFILLDEPTSALDLSVQAQIIELLRRLQDERGLSYLVISHDLKVVRALCHRVVVMQDGKIVEEGPVSEVLNNPKTAYTERLVKAAFEVAA transporters Sinorhizobium meliloti 1021 Smeli SM_b21645 SM_b21645 SM_b21645 NP_438104.1 tr|Q92TF6|Q92TF6_RHIME ABC transporter for D-Raffinose, permease component 1 Specific phenotypes on D-Raffinose pentahydrate. ABC transporter permease ABC transporter, permease protein peptide/nickel transport system permease protein MTIEAESTLPVAIEPEEKHHHESYSALVWRRLKRSWTGLLGLVLVCLLILMAVFAEFLSPVDPKATDVAFAQPQTISFRDKEGNFVFPPRSYPVRETEELDPVTFQPIIGPDYDNPQVLGFFVKGAPYRLFGLIPAERHLFGAVDGTPVHLLGTDKFGRDVLSRILYGSRISLMIALTVVFIVTVVGTTVGMVSGYFGGRFDAWVQRFVELVLAFPQLPLYLALASLIPVTAPTNVFLAFVIIVMSALGWAQMSREVRGKTLALARIEYVRAAIAIGATDRRIIFQHIFPNVMSHVIVAVTLAIPHVVLLESFLGFLGFAVKPPLISWGLMLQDTANYSAIGSYPWILSPVAFVLVTVFAFNALGDGLRDAIDPY transporters Sinorhizobium meliloti 1021 Smeli SM_b21646 SM_b21646 SM_b21646 NP_438105.1 tr|Q92TF5|Q92TF5_RHIME ABC transporter for D-Raffinose, permease component 2 Specific phenotypes on D-Raffinose pentahydrate. ABC transporter permease ABC transporter, permease protein peptide/nickel transport system permease protein MFRFLLVRIASAIPVLLVLSVVTFGIIQAPPGDYSDYIRSQLINQGGASFEEADAQAQAYRKEHGLDKPLPIQYVNWITGIVTRGDFGHSLYYNKPVADVVGERLPRTLALALVCHILASVIGIAFGIIAATRQYSWIDSLLSTVSFLGMTVPRFLMALIIVYILVFHFNVSEINSFHSARYGGAPWSWDKFVDLIKHVWPVVAIATFGGLAYNMRVMRGNLLDTLNAQYVETARAKGLSEGAVVMRHAVPNALHPLIMYQGVVLPYMLTGEIETAIIFALPTVGPAIVGSMWVGDVYVTATFMLVLSATLIVGNIIADMMLAALDPRVRMGGGVYA transporters Sinorhizobium meliloti 1021 Smeli SM_b21647 SM_b21647 SM_b21647 NP_438106.1 sp|Q9X4Y1|AGPA_RHIME ABC transporter for D-Raffinose, periplasmic substrate-binding protein Specific phenotype on D-Raffinose pentahydrate. alpha-galactoside ABC transporter substrate-binding protein precursor Periplasmic alpha-galactoside-binding protein precursor peptide/nickel transport system substrate-binding protein MKTHRLNMTASLLIGISAFAVQAFASEPTVVPEQPPFPAQGKITYVSRDSILEFKALREYREPEWVTEKFVKAGKLPPVAERLPKEPMVFKAGNMPDGMGVYGDVMRHVIGGRPEGWNYSAGQTQGWGGIDIGMFECLTRTAPLFQVEADDMEPLPNLAKSWDWSEDGRKLTMHLIEGAKWSDGDPFDADDVMFYWEDNVLDSSVSPLNGATPETFGEGTTLKKIDQYTVEWTFKEAFPRQHLFAMAYGTFCPGPSHILKTKHPKYAGTTYNEYKNGFPAEYMNLPVMGAWVPVAYRPDDIIVLRRNPYYWKVDEAGNQLPYLNELHYKLSTWADRDVQAIAGSGDISNLEQPENFVESLKRAANESAPARLAFGPRVIGYNMHMNFSGNGWGDPDERAKAVRELNRNLDFRKAVTMAVDRKKLGEALVKGPFTAIYPGGLSSGTSFYDRNSTIYYPHDLEGAKVLLEKVGLKDTDGNGFVNFPAGKLGGRDVEIVLLVNSDYSTDRNLAEGMVGQMEKLGLRVVLNALDGKQRDAANYAGRFDWMIHRNTAEFASVVQNTPQLAPTGPRTSWHHRAPEGGEVDVMPHEQELVDIVNKFIASNDNDERTELMKQYQKVATTNVDTVGLTEYPGALIINKRFSNIPPGAPIFMFNWAEDTIIRERVFVAADKQGDYELYPEQLPGKPGESGPIN transporters Sinorhizobium meliloti 1021 Smeli SM_b21652 SM_b21652 SM_b21652 NP_436541.1 tr|Q926I0|Q926I0_RHIME ABC transporter for Lactose, periplasmic substrate-binding component Specific phenotype on Beta-Lactose. (KEGG_correct) lactose ABC transporter substrate-binding protein ABC transporter sugar binding protein lactose/L-arabinose transport system substrate-binding protein MDIQTRAYLPRIAGLALAGASFLGVTAAQAKEITIWCWDPNFNVAIMKEAGARYTKTHPDVTFNIVDFAKLDVEQKLQTGLSSGTADALPDIVLIEDYGAQKYLQSFPGAFAPLSGTVDYSGFAPYKVELMTLDGQVYGMPFDSGVTGLYYRKDYLEAAGFKPEDMQDLTWDRFIEIGKQVEEKTGKKMMGLDPNDAGLVRIIMQSAGQWYFDKEGKPNIAGNAALKAALETIGKIMQANIYKPANGWSDWVGTFTSGDVATVVTGVWITGTVKAQPDQSGNWGVAPIPALSIEGATHASNLGGSSWYVLESSEEKAEAIDFLNEIYAKDIDFYQKILQDRGAVGSLLAARGGAAYEAADPFFGGEKVWQNFSDWLAKVPSVNYGIFTNEADLAVTAQLPAVTQGTPVDEVLQAIEAEVSAQIQ transporters Sinorhizobium meliloti 1021 Smeli SM_b21653 SM_b21653 SM_b21653 NP_436542.1 tr|Q92XF9|Q92XF9_RHIME ABC transporter for Lactose, permease component 1 Specific phenotypes on Beta-Lactose. Not important for arabinose utilization but there is no other clear arabinose tranpsorter so who knows (KEGG_correct) lactose ABC transporter permease Inositol transport system permease protein lactose/L-arabinose transport system permease protein MVRARRGIGRYYDVNGWLFVAPALGLITLFMVYPIAWSLWMSFQSGRGMTLKFAGFANIVRLWNDPVFIKALTNTMTYFVVQVPIMILLALILASLLNNPRLVGRGVFRTAIFLPCVSSLVAYSVLFKGMFATDGIVNSTLQAIGLAASPIPWLTHPFWAKVLVILAITWRWTGYNMIFYLAALQNIDKSIYEVARIDGVPAWARLTHLTIPLLKPVILFTTVISTIGTLQLFDEVYNLTEGKGGPSNATLTLSLYIYNLTFRFMPNLGYAATVSYVIVVLVALLAFVQFFAARERDR transporters Sinorhizobium meliloti 1021 Smeli SM_b21654 SM_b21654 SM_b21654 NP_436543.1 tr|Q92XF8|Q92XF8_RHIME ABC transporter for Lactose, permease component 2 Specific phenotypes on Beta-Lactose. Not important for arabinose utilization but there is no other clear arabinose tranpsorter so who knows (KEGG_correct) lactose ABC transporter permease Glycerol-3-phosphate ABC transporter, permease protein UgpE (TC 3.A.1.1.3) lactose/L-arabinose transport system permease protein MNGFGRFAAMAATYGFLGLMAFLSVFPFIWMVLGATNSSIDIIKGKLLPGAAFATNVANFFTLVNVPLVFWNSAKIAIVATVLTLAVSSLAGYGFEMFRSRRRERVYRAMLLTLMIPFAALMIPLFVMMGKAGLINTHLAVVLPSIGSAFVIFYFRQSTKAFPSELRDAAKVDGLKEWQIFLFIYVPVMRSTYAAAFVIVFMTAWNNYLWPLIVLQTNETKTITLVISSLASAYYPDYGVVMVGTILATLPTLAVFFFMQRQFVQGMLGSVK catabolism Sinorhizobium meliloti 1021 Smeli SMa0247 SMa0247 SMa0247 NP_435377.1 tr|Q930R4|Q930R4_RHIME 2-dehydro-3-deoxy-D-arabinonate dehydratase, 2,4-dioxopentanoate forming # Specifically important in carbon source D-Arabinose. SMa0247 is related to 2-keto-3-deoxyxylonate dehydratase (xylX), which acts on the same substrate. Furthermore, a close homolog (HSERO_RS19360, 59% identical) is important for D-xylose utilization. However, the product of XylX is 2,5-dioxopentanoate, but in S. meliloti the pathway probably proceeds via 2,4-dioxopentanoate (see SM_b21112). hypothetical protein Fumarylacetoacetate hydrolase family protein MSGGFLVSFEQALSAESIQPADASSAMLVGRVWSKTAGGPCPVLISEGEVFDLTPLAATISALLEIDGLVDALRDPSRFASLGSLDAFLRGEAGDLLAPADLQAVKAAGVTFADSMLERVIEEQAKGDPLRAQEIRGRLAPVLGDNLKGLVAGSDKAAEVKKLLQELGLWSQYLEVGIGPDAEIFTKAQPMSSVGCGAYIGIHPKSDWNNPEPEVVLAVTSKGKIVGATLGNDVNLRDFEGRSALLLSKAKDNNASCSIGPFIRLFDGAFTIEDVKQAEVSLVVDGKEGFKMTGISPMSAISRSPEDLVSQLLNDNHQYPDGVVFFLGTMFAPVKDRRGTGLGFTHEIGDRVEISTPRLGRLVNWVDHSDRCPKWSFGLGALMKNLAERGLLQAKREG catabolism Sinorhizobium meliloti 1021 Smeli SMc00588 SMc00588 SMc00588 NP_385263.1 tr|Q92QY5|Q92QY5_RHIME L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) Important on L-arabinose and D-galactose; may also act on D-glucose, given phenotype with some N sources with glucose as C source; 55% identical to ARAA_AZOBR, which has L-arabinose and D-galactose 1-dehydrogenase activity in vitro D-galactose 1-dehydrogenase Uncharacterized oxidoreductase ydgJ (EC 1.-.-.-) D-galactose 1-dehydrogenase MSPINIAIVGVGKIVRDQHLPALAKNADYRLIAAASRHGTVDGIDNFKSIEAMIDAVPAVEAVSLCMPPQYRYEAARTALAAGKHVFLEKPPGATLSEVADLEALAEEKGVSLFASWHSRYAPAVEAAKTFLASAAIRNVRIIWKEDVRHWHPNQEWIWAAGGLGVFDPGINALSIMTHILPRPVFITSATLEFPENRDAPIAATIAFSDAEKLDVAAEFDWRQTGKQSWDIVAETDAGGMVLSEGGAKLAIDGKIVHEEPEQEYPMLYRRFAEIIKAGRSDVDLAPLRHVADAFMLGRRKFVEAFHD catabolism Sinorhizobium meliloti 1021 Smeli SMc00781 SMc00781 SMc00781 NP_384832.1 tr|Q92RW4|Q92RW4_RHIME malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) Specifically important for: m-Inositol; Uridine. 3-oxopropionate or malonate semialdehyde is an intermediate in myo-inositol catabolism and also in pyrimidine catabolism malonic semialdehyde oxidative decarboxylase Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) methylmalonate-semialdehyde dehydrogenase MYELGHFIDGKRVAGTSGRVSNIFNPATGEVQGTVALASDADLAAAVESAKAAQPKWAATNPQRRARVFMKFVQLLNDNMNELAEMLSREHGKTIDDAKGDIVRGLEVCEFVIGIPHLQKSEFTEGAGPGIDMYSIRQPVGIGAGITPFNFPGMIPMWMFAPAIACGNAFILKPSERDPSVPIRLAELMIEAGLPAGILNVVNGDKGAVDAILTHPDIAAVSFVGSTPIARYVYGTAAMNGKRAQCFGGAKNHMIIMPDADLDQAANALIGAGYGSAGERCMAISVAVPVGEETANRLIDKLVPMVESLRIGPYTDEKADMGPVVTKEAEQRIRSLIDSGIEQGAKLVVDGRDFKLQGYENGHFIGGCLFDDVTPDMDIYKTEIFGPVLSVVRARNYEEALSLPMKHEYGNGVAIYTRDGDAARDFASRINIGMVGVNVPIPVPLAYHSFGGWKSSSFGDLNQHGTDSIKFWTRTKTITSRWPSGIKDGAEFSIPTMR catabolism Sinorhizobium meliloti 1021 Smeli SMc00832 SMc00832 SMc00832 NP_384883.1 tr|Q92RS3|Q92RS3_RHIME D-lactate oxidase, FAD-linked subunit (EC 1.1.3.15) Specifically important for: Sodium D,L-Lactate. This is the first step in D-lactate oxidation. KEGG has the correct EC # but describes it as glycolate oxidase; SEED has it as 1.1.99.14 (glycolate dehydrogenase) glycolate oxidase subunit protein Glycolate dehydrogenase (EC 1.1.99.14), subunit GlcD MPETIGFLKPRQAVLDRRREIVADLADLLPEGGLISDERGLKPFETDAFIAYRRMPLAVVLPETTEHVAAVLKYCSRYGIPIVPRGAGTSLSGGAIPQEDAIVVGLSKMSRTLDIDLFNRTATVQAGVTNLNISDAVSADGFFYAPDPSSQLACTIGGNIGMNSGGAHCLKYGVTTNNLLGVKMVLFDGTVIELGGKALDAPGYDLLGLVCGSEGQLGIVTEATVRLIAKPEGARPVLFGFASSESAGSCVADIIGSGIIPVAIEFMDRPAIEICEAFAQAGYPLDVEALLIVEVEGSEAEMDATLAGIIEIARRHGVMTIRESQSALEAALIWKGRKSAFGATGRIADYICMDGTVPLSQLSHVLRRTGEIVAGYGLRVANVFHAGDGNMHPLILYNINDPEEAARAEAAGNDILKLCVEAGGCLTGEHGVGIEKRDLMLHQYSRADLGQQMAARAAFDPQWLMNPSKVFPLEGRPAA catabolism Sinorhizobium meliloti 1021 Smeli SMc00833 SMc00833 SMc00833 NP_384884.1 tr|Q92RS2|Q92RS2_RHIME D-lactate oxidase, FAD binding subunit (EC 1.1.3.15) Specifically important for: Sodium D,L-Lactate. This is the first step in D-lactate oxidation. KEGG oddly has no EC #; SEED has it as 1.1.99.14 (glycolate dehydrogenase) glycolate oxidase subunit protein Glycolate dehydrogenase (EC 1.1.99.14), FAD-binding subunit GlcE glycolate oxidase FAD binding subunit MIVHFEPASEEGIASVVRSAAAERVTLAVVGGGTRAGLGNPVRADRTLSTRRLSGIVTYDPAEMTMSALAGTPVAEVEAALHAKGQMLSFEPMDHRPIFATTGEPTIGGVFAANVSGPRRYVAGAARDSLLGVRFVNGRGEPIKAGGRVMKNVTGLDLVKLMAGSYGTLGILTEVTFKVLPLPPAAATVVVSGLNDAEAAAVMAEAMAQPVEVSGASHLPESVRSRFLDGALPDGAATVLRLEGLAASVAIRAEKLGEKLSRFGRISQLDEAQTRTLWAEIRDVKPYADGTRRPLWRISVAPSAGHQLVAALRLQTGVDAFYDWQGGLVWLRMEADPEAELLRRYIGAVGGGHAALLRAGEEARGRIPAFEPQPPAVARLSERIRAQFDPSGIFNPGRAAALVRN catabolism Sinorhizobium meliloti 1021 Smeli SMc00926 SMc00926 SMc00926 NP_384885.2 tr|Q92RS1|Q92RS1_RHIME D-lactate oxidase, iron-sulfur subunit (EC 1.1.3.15) Specifically important for: Sodium D,L-Lactate. This is the first step in D-lactate oxidation. KEGG oddly has no EC #; SEED has it as 1.1.99.14 (glycolate dehydrogenase) glycolate oxidase iron-sulfur subunit protein Glycolate dehydrogenase (EC 1.1.99.14), iron-sulfur subunit GlcF glycolate oxidase iron-sulfur subunit MIQRPQGATWSTRLQTNFSPEQLADPHVAESETILRKCVHCGFCTATCPTYVVLGDELDSPRGRIYLIKDMLENGRAADSETVTHIDRCLSCLSCLTTCPSGVDYMHLVDHARAHIEKTYKRPFKDRLARSVIAATLPYPSRFRLALGAAGLARPLAGLLKRVPFLRTLGVMLDLAPSALPAARGAKPAVYAAKGTPRARVALLTGCAQPVLRPEINDATIRLLTGQGVEVVVSAGEGCCGALVHHMGRDEQALQAGRHNIDVWLKAAEEDGLDAIIITASGCGTTIKDYGHMLRLDPAYAEKAARVSALAKDVTEYLATLDLPEQGARNLTVAYHSACSMQHGQKITSAPKQLLKRAGFSVREPAEGHLCCGSAGTYNILQPEISAKLKARKVRNIEATKPEVIATGNIGCITQIASGTEIPILHTVELLDWAYGGPKPAGL catabolism Sinorhizobium meliloti 1021 Smeli SMc01105 SMc01105 SMc01105 NP_384521.1 tr|Q92SI0|Q92SI0_RHIME uridine nucleosidase (EC 3.2.2.3) Specifically important for: Uridine. annotated by SEED as acting on uridine and inosine nucleoside hydrolase (SEED_correct) Inosine-uridine preferring nucleoside hydrolase (EC 3.2.2.1) purine nucleosidase MSSARKIIIDTDPGQDDAAAIMLALGSPEEIEVLGITAVAGNVPLTLTARNARIVCELCNRTDVKIFAGAERPVARPLVTAEHVHGKTGLDGPALDEPTMPLQEQHAVDFIVETLRAEAPGAVTLCTLGPLTNIALALTKAPEIAPSVRELVMMGGGFFEGGNITPAAEFNIYVDPEAAEIVFRSGIPIVMMPLDVTHRVLTRKTRVEKIRAIGSPAAVALAEMLEFFERFDIEKYGTDGGPLHDPTVIAYILRPELFTGRDCNVEIETASPLTTGMTVVDWWQVTGRAHNAKVMRHIDDEGFFELLAERLARI transporters Sinorhizobium meliloti 1021 Smeli SMc02118 SMc02118 SMc02118 NP_385584.1 tr|Q92Q71|Q92Q71_RHIME ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, periplasmic substrate-binding component Specific phenotype on L-Histidine; L-Glutamine. general L-amino acid-binding periplasmic ABC transporter protein Glutamate Aspartate periplasmic binding protein precursor GltI (TC 3.A.1.3.4) general L-amino acid transport system substrate-binding protein MARRILTALVGAAVVGIGTHAASAATLDDVKAKGFVQCGVNTGLAGFAAPDASGNWSGFDVDYCKAIAAAIFGDGSKVKYTPLSAKERFPALQSGEVDVLARNTTWSINRDTALGFNFRPVNYYDGQGFMVRKELDVKSALELSGAAVCVQTGTTTELNLADYFKANNLQYNPVVFEKLEEVNAAYDAGRCDVYTTDQSGLYSLRLTLSKPDDHIVLPEIISKEPLAPAVRQGDDQWFDIVSWVHYALVQAEEFGVTQANLEEMKKSTNPDVQRFLGVEADSKIGTDLGLTNEWAVNIVKAVGNYGEVFDRNIGAGSPLKIERGLNALWNKGGLQYAPPVR transporters Sinorhizobium meliloti 1021 Smeli SMc02119 SMc02119 SMc02119 NP_385583.1 tr|Q92Q72|Q92Q72_RHIME ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1 Specific phenotypes on L-Glutamine; L-Histidine. Mild phenotypes on proline or lysine (KEGG_correct) general L-amino acid transport permease ABC transporter protein Glutamate Aspartate transport system permease protein GltJ (TC 3.A.1.3.4) general L-amino acid transport system permease protein MAIGVTNAPERSRSSGSIINDPQVRGIFYQAITIIILAALIYWIVDNTVDNLRRANIASGYDFVRSRAGFDVGQSLISFTSDSTYGRALLVGFINTLLVAITGIITATIIGFIVGIGRLSHNWIIAKLSLAYVEVFRNIPPLLVIFFWYSGVLSILPQARDALALPFDIFLSNRGVAFPRPIAEEGAEYTLLAFVIAVAASVFFARYARKRQLATGERLPVLWTVLGLIIGLPLVTFLVTGAPITFDIPVAGKFNLTGGSVVGPEFMSLFLALSFYTAAFIAEIVRAGIRGVSKGQTEAAHALGIRPALTTRLVVVPQAMRIIIPPLTSQYLNLTKNSSLAVAIGYADLVAVGGTILNQTGQSIEIVSIWLIVYLSLSLATSLFMNWYNARMALVER transporters Sinorhizobium meliloti 1021 Smeli SMc02120 SMc02120 SMc02120 NP_385582.1 tr|Q92Q73|Q92Q73_RHIME ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 Specific phenotypes on L-Glutamine; L-Histidine. Mild phenotypes on proline or lysine (KEGG_correct) general L-amino acid transport permease ABC transporter protein Glutamate Aspartate transport system permease protein GltK (TC 3.A.1.3.4) general L-amino acid transport system permease protein MSTNQASFVRASMIEASPAPSLESGAVSWLRKNLFATPKDTALTIISLLILAWLVPPAIQWLFIDAAWSGGGRGVCATLSQGGSQPEGWSGACWAFVNAKFAQFLFGRYPLDERWRPALVGILFVLLLVPMLIPRIPYKGLNALLLLVALPILSAILLPGGWFGLTYVETPLWGGLMVTLVLSFVGIAVSLPLGILLALGRRSNMPVIKMLCTVFIEVIRGVPLITVLFMASVMLPLFLPQGVTFDKFLRALIGVSLFASAYMAEVVRGGLQAIPKGQYEGADSLGLSFWQKMGFIVLPQALKLVIPGIVNTFIGLFKDTSLVSIIGMFDLLGIVRLNFSDTNWATAVTPLTGLIFAGFVFWLFCFGMSRYSGFMERLLDRSQR transporters Sinorhizobium meliloti 1021 Smeli SMc02121 SMc02121 SMc02121 NP_385581.1 tr|Q92Q74|Q92Q74_RHIME ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component Very important for histidine and glutamine utilization and also for lysine utilization. It could be the ATPase component for lysine transport by Smc00140:Smc00138 as well (as there is no ATPase component in that gene cluster or other ATPase component identified in the fitness data) general L-amino acid transport ATP-binding ABC transporter protein ABC-type polar amino acid transport system, ATPase component general L-amino acid transport system ATP-binding protein MANTATAPKLAVSTTDVAIEITNMNKWYGDFHVLRDINLRVMRGERIVVAGPSGSGKSTMIRCINRLEEHQKGKIVVDGIELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKEAEQVAMHFLERVKIPEQALKYPGQLSGGQQQRVAIARSLCMRPKILLFDEPTSALDPEMVKEVLDTMVGLAEEGMTMICVTHEMGFARQVANRVIFMDQGQIVEQNSPAEFFDNPQHERTKLFLSQILH catabolism Sinorhizobium meliloti 1021 Smeli SMc02321 SMc02321 SMc02321 NP_384733.1 sp|Q92S14|RHAL_RHIME L-rhamnose isomerase (EC 5.3.1.14) Specifically important for: L-Rhamnose monohydrate. KEGG now annotates it as L-rhamnose isomerase, which is correct. The gene is cofit with SMc03003 (rhaK), which is probably rhamnulose kinase. It had been suggested that rhaK might be rhamnose kinase and that the isomerase might act on L-rhamnose 1-phosphate, but the S. meliloti rhaK is not a rhamnose kinase. See the PhD thesis of Damien M. R. Rivers (2015). (KEGG_correct) sugar isomerase MTLMISTSVLDAENASRRDALTRDYESLGDRLARRGIDIDAVKAKVAAYGVAVPSWGVGTGGTRFARFPGPGEPRNIFDKLEDCAVIQQLTRATPAVSLHIPWDKVSDLGALKEKGSALGLSFDAMNSNTFSDAPGQAHSYKFGSLSHTDSATRRQAIEHNLECVEIGKALGSKALTVWVGDGSNFPGQSNFTRAFERYLDSMKAVYAALPDDWRIFTEHKMFEPAFYSTVVQDWGTNYLIAQELGPKAFCLVDLGHHAPNVNIEMIVARLIQFKKLGGFHFNDSKYGDDDLDTGSIDPYRLFLVFNELVDAETRAANGFDPAHMLDQSHNVTDPIESLMTSAMEVGRAYAQALIVDRKALAGYQEENDALMASETLKTAFRTDVEPILATARLENDGAIAPVAAYRASGYRARVAAERPAVAGGGGGIV catabolism Sinorhizobium meliloti 1021 Smeli SMc02322 SMc02322 SMc02322 NP_384734.1 tr|Q92S13|Q92S13_RHIME rhamnulose-1-phosphate aldolase (EC 4.1.2.19) / lactaldehyde dehydrogenase (EC 1.2.1.22) Specifically important for: L-Rhamnose monohydrate. These are the steps after the L-rhamnose 1-phosphate isomerase (SEED_correct) short chain dehydrogenase Predicted rhamnulose-1-phosphate aldolase (EC 4.1.2.19) / Predicted lactaldehyde dehydrogenase (EC 1.2.1.22) MLDKHQGARLANLWDDGKAAGMTEPEKLLYRSNLLGSDKRITNYGGGNTSAKVMEKDPLTGEIVEVLWVKGSGGDVGTIKMDGFSTLYMDKLRALKGIYRGVEFEDEMVGYLPHCTFNLNPRAASIDTPLHAYVPKPHVDHMHPDAIIAIAASKNSRELTSKIFGDEIGWLPWKRPGYELGLWLEKFCQENPDARGVVLESHGLFTWGDTAKEAYETTIEIINRAIAWFETENTGPAFGGRSKPVLAAADRAAIAKKLMPVIRGLISAGESKVGHFDDSQAVLDFVTSTSLEPLAALGTSCPDHFLRTKIRPLVVDFDPAQPDVGNTLAGLPEAIATYRADYAAYYERCKRADSPAMRDPNAVVYLVPGVGMITFAKDKATARISAEFYVNAINVMRGASGVSTYVGLPEQEAFDIEYWLLEEAKLQRMPKPKSLAGRIALVTGGAGGIGKATANRLMQEGACVVLADIDETALEAAQTELSTRYGKDFVRSVNMNVTSEAAVESGFGDALLAFGGLDILVSNAGLATSAAVEDTTLALWNKNMDILATGYFLVSREAFRIFRNQKAGGNVVFVASKNGLAASPGASAYCTAKAAEIHLARCLALEGASAQIRVNVVNPDAVLRGSKIWTGEWKEQRAAAYKMDVDELEAHYRERSMLKLSVFPEDIAEAIYFLASDMSAKSTGNIVNVDAGNAQSFTR catabolism Sinorhizobium meliloti 1021 Smeli SMc02775 SMc02775 SMc02775 NP_384125.1 tr|Q92TD8|Q92TD8_RHIME D-arabinose 1-dehydrogenase # Specifically important in carbon source D-Arabinose. This is the first step in the oxidation of D-arabinose. (The fucose dehydrogenase is SM_b21109.) The product is probably the 1,5-lactone, not the 1,4-lactone, see SM_b21101. L-fucose dehydrogenase (D-threo aldose 1-dehydrogenase) protein L-fuco-beta-pyranose dehydrogenase (EC 1.1.1.122) D-threo-aldose 1-dehydrogenase MQTRRIGRTALAVTEYSFGTAGLGGLYRECTREAAMATLDAAWEAGIRYFDTAPFYGLGLAERRVGDFLRDKPRDSFVLSTKVGRLLHPVPENQVPDYSYVKPLNFDVTYDYGYDAIMRSVEMSYARLGLNRIDILYVHDIGGYTHGAAKNAVYLRQLLDSGLKALDELKSSGVISAYGLGVNEVPVCLDVMRQADIDCILLAGRYTLLDRSAVAELLPLCAKKDTSLVVGGVFNSGILATGPVEGAHFDYMPATGEVRAKVAAMERIAGERGMPLAAPALQFPLANPHVASVLLGTAKPSSLTRNMELTRYGIAPEDYAAFEPHTLVAPELGPEAVRA catabolism Sinorhizobium meliloti 1021 Smeli SMc02776 SMc02776 SMc02776 NP_384124.1 tr|Q92TD9|Q92TD9_RHIME D-arabinoate dehydratase (EC 4.2.1.5); also involved in L-fucose catabolism # Specifically important in carbon source D-Arabinose; carbon source L-Fucose. SMc02776 is 36% identical to D-galactarate dehydratase (garD) from E. coli, which is a similar reaction. The product (2-dehydro-3-deoxy-D-arabinonate) is consumed by SMa0247. The role of SMc02776 role in L-fucose catabolism is unclear because two other dehydratases (SM_b21107 and SM_b21110) are also required but the pathway requires only one dehydratase reaction (PMID:17144652). Probably two of these dehydratases act together (with one of them in reverse) to switch the stereochemistry of a chiral center. altronate hydrolase altronate hydrolase MPAPSSILLSPDDNVVVATAAIAPGDRLAGGVSAVARIEPGHKAAIRRIDVGEPVVKYGQAIGRATSPIAPGEHVHSHNLAFDQGRLAVGAAVPPEAASEADKARTFLGYRRADGRAATRNYIGIVASVNCSTTVCRAIADEANRRILPKYEGIDGFVPIVHDQGCGMSSTGDGMKNLHRTLAGYARHANFGGVLMVGLGCEVNQLTLYGQSGAGAEKRHFNIQEAGGSRRSVERALGILDEIAKEVAAARRVPIPVSEIIVGLQCGGSDGLSGITANPALGAAVDILAAAGGTAILSETSEIYGAEHLLRSRAVNETVAVKLDGLIAWWEDYVAMHGASLDNNPSPGNKRGGLTTILEKSLGAVAKGGRSPLTAVYNYAERVTEPGLVFMDTPGYDPVSATGQVAGGANVIAFTTGRGSCFGCRPAPSIKLTSNTALYRAMEEDMDIDCGVIASGETTIADLGRGIFELIIETASGRKTKSELFGYGDNEFVPWHLGATL transporters Sinorhizobium meliloti 1021 Smeli SMc02869 SMc02869 SMc02869 NP_384300.2 tr|Q92T01|Q92T01_RHIME N-Acetyl-D-glucosamine ABC transport system, ATPase component Specific phenotype on N-Acetyl-D-Glucosamine. (SEED_correct) ABC transporter ATP-binding protein N-Acetyl-D-glucosamine ABC transport system ATP-binding protein multiple sugar transport system ATP-binding protein MCAPASRSSFNPRGRHVGSLQLKTIRKAFGSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSVQIDGVEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAGMLSLEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARLHRSLKATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIGSPQMNFIEAAKLGDGEAKTIGIRPEHIGLSRESGDWKGKVIHVEHLGADTIIYIESETVGLLTVRLFGEHRYATDDIVHATPVIGSMHRFDADGRVIKSGQ transporters Sinorhizobium meliloti 1021 Smeli SMc02871 SMc02871 SMc02871 NP_384302.1 tr|Q92SZ9|Q92SZ9_RHIME ABC transporter for N-Acetyl-D-glucosamine, permease protein 2 Specific phenotypes on N-Acetyl-D-Glucosamine; N-Acetyl-D-Glucosamine. (SEED_correct) ABC transporter permease N-Acetyl-D-glucosamine ABC transport system, permease protein 2 multiple sugar transport system permease protein MSKARASFMRTGAVHAALIAYTLIALFPVFLTIVNSFKSRNAIFREPLAVPTPETFSLIGYETVLKQGDFIGYFQNSIIVTVVSIALVLLFGAMAAFALSEYRFRGNTLMGLYLALGIMIPIRLGTVAILQGMVATGLVNTLTALILVYTAQGLPLAVFILSEFMRTVSDDLKNAGRIDGLSEYAIFLRLVLPLIRPAMATVAVFTMIPIWNDLWFPLILAPAEATKTVTLGSQIFIGQFVTNWNAVLSALSLAIFPVLVLYVIFSRQLIRGITAGAVK transporters Sinorhizobium meliloti 1021 Smeli SMc02872 SMc02872 SMc02872 NP_384303.1 tr|Q92SZ8|Q92SZ8_RHIME ABC transporter for N-Acetyl-D-glucosamine, permease protein 1 Specific phenotypes on N-Acetyl-D-Glucosamine; N-Acetyl-D-Glucosamine. (SEED_correct) ABC transporter permease N-Acetyl-D-glucosamine ABC transport system, permease protein 1 multiple sugar transport system permease protein MNPREITTYVTEIKRPRRWHILVFLLPALVVYTAVMILPLFETLRQSFYNTVDGQLTFVGLGNFKVLFGDPRWAADFWNALKNNFVFFLIHMAVQNPIGIALAAMLSVPKLRFGAFYRTAIFLPTLLSFVIVGFIWKLILSPIWGVAPYLLDTVGLRSLFGPWLGKPDTALIAVSLISVWQYIGIPMMLIYAALLNIPDEVTEAAELDGVTGWSQFWKIKLPLILPAIGIVSILTFVGNFNAFDLIYTVQGALAGPDKSTDILGTLLYRTFFGFQLQLGDRSMGATIAAIMFLIILAGVALYLFGIQRRMRRYQF transporters Sinorhizobium meliloti 1021 Smeli SMc02873 SMc02873 SMc02873 NP_384304.1 tr|Q92SZ7|Q92SZ7_RHIME N-Acetyl-D-glucosamine ABC transport system, periplasmic substrate-binding component Specific phenotype on N-Acetyl-D-Glucosamine. (SEED_correct) periplasmic binding (signal peptide) ABC transporter protein N-Acetyl-D-glucosamine ABC transport system, sugar-binding protein multiple sugar transport system substrate-binding protein MTRTTMKGLLLASSILGSAGLAQAQDATLTIESWRNDDLAIWQEKLIPAFEAKNPGIKVVFAPSAPTEYNAALNAKLDAGSAGDLITCRPFDASLELYNKKHLADLTGLSGMENFSDVAKSAWTTDDGKATFCVPMASVIHGFIYNKDAFDQLGLSVPATEEEFFAVLEKIKADGNYIPMAMGTKDLWEAATMGYQNIGPNYWKGEEGRLALLKGEQKLTDEPWVEPFRVLAKWKDYLGDGFEAQTYPDSQNLFTLGRAAIYPAGSWEISGFNTQAEFKMGAFPPPVKKAGDTCYISDHNDIGIGLNAKSKNADAAKTFLTWVASPEFAEIYANALPGFFSLNSTAVKMSDPLAQEFVSWREKCKPTIRSTYQILSRGTPNLENETWVMSANVINGTDTPEAAAKKLQDGLDSWFKPVK catabolism Sinorhizobium meliloti 1021 Smeli SMc02875 SMc02875 SMc02875 NP_384306.1 tr|Q92SZ5|Q92SZ5_RHIME N-acetylglucosamine kinase (EC 2.7.1.59) Specifically important for: N-Acetyl-D-Glucosamine. The first step in NAG catabolism (SEED_correct) hypothetical protein N-acetylglucosamine kinase of eukaryotic type (EC 2.7.1.59) MTFYLIGIDGGGTSCRAAVAALDGRILGRGKAGAANILTDPETALQNITDAARDAFGDAGLDPAGIGASRAIVGVAGHNVGDAVHYVKRRLPFAQADIESDGLIALQGALGDGDGAVAILGTGTIYIARRGDEVSYVGGWGFTIGDHGSGARIGHALLQESLLAYDGIHQGSGVTDAVLAEFNDDPRDIVDFARLAKPGEFGRYAPRVFEFAERGDPVAISLLKAAAATVDEALDVVVSRGSEKLCLLGGLAPLYRRWLADRHQPRFVEARADALTGAVALAAARFGSHSGVSA catabolism Sinorhizobium meliloti 1021 Smeli SMc03003 SMc03003 SMc03003 NP_384741.1 tr|Q92S06|Q92S06_RHIME Rhamnulokinase RhaK in alpha-proteobacteria (EC 2.7.1.5) Specifically important for: L-Rhamnose monohydrate. Also see comment on SMc02321; this is the first step in L-rhamnose degradation. (SEED_correct) hypothetical protein Rhamnulokinase RhaK in alpha-proteobacteria (EC 2.7.1.5) MMMKTVAVIDIGKTNAKVALVDLERFEEIAVRKSGNGVSDDGPYPHFDTERLWRFVLDSLAALHREHPVDAISVTTHGATAVLLDEAGELALPVLDYEFTGPDALAEEYEKARPPFTETGSARLPMGLNVGAQLFWQQRMFPEHFARVATILTYAQYWSYRLTGVRTNELTSLGCHTDLWNPKAATFSSMVDEQGWRHLFAPVRRAGDVLGPLLRQVADETGLPPETPVHCGIHDSNASLLPHLITRQAPFSVASTGTWVVMLAVGAEPVKLDERRDTLINVNALGDPVPSARFMGGRAYSLLIGDDPPTASPEAEASVLEQGHMLLPSLPGGSGPFPAARPHWTADEDKLAPAERLAVVSFHLALMTATCLDLIGARGEILVEGPFALNDAYLRMLAAATGRPVLANRLNSTGTSLGAACLVAGARVRTGAEAIPAAKPDAYAAYAEAWRRRTAAHVRSDP transporters Sinorhizobium meliloti 1021 Smeli SMc03061 SMc03061 SMc03061 NP_384801.1 sp|Q9Z3R5|AGLE_RHIME ABC transporter for D-Maltose and D-Trehalose, ATPase component Specific phenotype on D-Maltose monohydrate; D-Trehalose dihydrate. Also mildly important for D-cellobiose utilization, which has its own ABC transporter, so the cause is unclear. (SEED_correct) alpha-glucoside ABC transporter periplasmic-binding protein Alpha-glucosides-binding periplasmic protein AglE precursor alpha-glucoside transport system substrate-binding protein MKRSLLIGVAAFALLAGTAGLAGTAGAADLKFKPGEDSRFNWASLEEFKKGHDLKGQTLTIFGPWRGEDEALFKSVYAYFVEATGVELKYSSSENYEQQIVIDTQAGSPPDVAILPQPGLIADLAAKGLLTPLGDETKQWLLDNYAAGQSWVDLSTYNGKDGTSALYAFPYKIDVKSLVWYVPENFEDAGYEVPKTMEELKALTEKIAEDGEKPWCIGLGSGGATGWPATDWVEDLMLRTQPAETYDKWVKNEIPFTDAAVTGALEEFGWFARNDAFVDGGAAAVASTDFRDSPKGLFSSPPKCYLHHQASFIPSFFPEGKVVGEDADFFYMPPYESKKELGNPVLGAGTLAMITKDTPAARAFIEFLKTPIAHEVWMAQTSFLTPYKSVNVDVYGNPPLKKQGEILLNATTFRFDGSDLMPGKIGAGAFWTGMVDFVGGKSSADVAAGVQKAWDSIK transporters Sinorhizobium meliloti 1021 Smeli SMc03062 SMc03062 SMc03062 NP_384802.1 sp|Q9Z3R6|AGLF_RHIME ABC transporter for D-Maltose and D-Trehalose, permease component 1 Specific phenotypes on D-Maltose monohydrate; D-Trehalose dihydrate. Also possibly important for cellobiose (but that has its own transporter) or raffinose; note cellobiose and maltose are beta glucosides not alpha glucosides permease protein alpha-glucoside ABC transporter permease ABC alpha-glucoside transporter, inner membrane subunit AglF alpha-glucoside transport system permease protein MEQLIAAILTMVAGVLVCAAYFWSTNLVLDWIFPSKGKFGAVASRNLRIANSIRPWLFLAPALLALTLYLVYPVVQSVWLSLHGRGGQNFVGLSNYSWMINDGEFRQSIFNNFLWLLVVPALSTFFGLIIAALTDRIWWGNIAKTLIFMPMAISFVGAAVIWKFIYDYRAAGSEQIGLLNAIVVALGGEPQAWITLPFWNNFFLMVILIWIQTGFAMVILSAALRGIPEETIEAAVIDGANGWQIFFKIMVPQIWGTIAVVWTTITILVLKVFDIVLAMTNGQWQSQVLANLMFDWMFRGGGDFGRGAAIAVVIMILVVPIMIWNIRNATRESGGH transporters Sinorhizobium meliloti 1021 Smeli SMc03063 SMc03063 SMc03063 NP_384803.1 sp|Q9Z3R7|AGLG_RHIME ABC transporter for D-Maltose and D-Trehalose, permease component 2 Specific phenotypes on D-Maltose monohydrate; D-Trehalose dihydrate. Also possibly important for cellobiose (but that has its own transporter) or raffinose; note cellobiose and maltose are beta glucosides not alpha glucosides permease protein alpha-glucoside ABC transporter permease Alpha-glucoside transport system permease protein AglG alpha-glucoside transport system permease protein MNPSRRSPLTWAVHLSVLLLVLLWTLPTAGLLISSLRDKDQLAVSGWWTALSSSSRNAVVRAPSAEDQVERDGKFVISGNLLEGRGEVSAFGFSSREPTKFKPGETAELNDGERLTVQSDGSFEIVSDQRMEGSRGQRIFFTATTPPRFTLDNYAEVLSAAGIGRSFLNSLTVAVPSTVIPILIAAFAAYALAWMPFPGRAVLLAVVVGLLVVPLQMSLIPLLQLYNGVGAFFGVSAKTYMGIWLAHTGFGLPLAIYLLRNYMAGLPREIMESARVDGASDFDIFVKIILPLSFPALASFAIFQFLWTWNDLLVAIVFLGAGDDKLVLTGRLVNLLGSRGGNWEILTASAFITIVVPLIVFFALQRYLVRGLLAGSVKGG transporters Sinorhizobium meliloti 1021 Smeli SMc03065 SMc03065 SMc03065 NP_384805.1 sp|Q9Z3R9|AGLK_RHIME ABC transporter for D-Maltose and D-Trehalose, ATPase component Specific phenotype on D-Trehalose dihydrate; D-Cellobiose; D-Maltose monohydrate. Mildly important for D-cellobiose utilization, which has its own ABC transporter, so the cause is unclear. (SEED_correct) alpha-glucoside ABC transporter ATP-binding protein Alpha-glucoside transport ATP-binding protein AglK alpha-glucoside transport system ATP-binding protein MTGLLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDMFIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADMLQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLSERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAMNVIPATITATGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEADDFLFEGTVSIVEALGEVTLLYIEGLVENEPIIAKMPGIARVGRGDKVRFTADKAKLHLFDTNGQSYRA catabolism Sinorhizobium meliloti 1021 Smeli SMc03162 SMc03162 SMc03162 NP_386999.1 tr|Q92LX0|Q92LX0_RHIME epimerase involved in beta-glucoside degradation Specifically important for: D-Salicin; D-Cellobiose. The SEED prediction (for a step in myo-inositol degradation) is not consistent with the phenotypes on D-salicin and D-cellobiose (which are both beta-glucosides). Because it is cofit with a beta-mannosidase (SMc04255), we suspect that it converts beta-glucosides to beta-mannosides. However this pathway also seems to involve two oxidoreductases (SMc03161, SMc04253) so its exact role is uncertain. hypothetical protein Inosose isomerase (EC 5.3.99.-) MKTIKGPGLFLAQFAGDAAPFNSWDSITKWAADCGYKGVQVPSWDGRLFDLKKAAESKTYCDEVAGKARDNGVEITELATHLQGQLVAAHPAYDEAFDGFAVPQVRGNPRARQEWAVEQVKLALTASKNLGLGAMASFSGALAWPFVYPWPQRPAGLVETAFDELARRWKPILDHAEDCGVDVCYEIHPGEDLHDGITYEMFLERTGNHARACMLYDPSHYVLQCLDYLENIDIYKDRIRMFHVKDAEFNPTGRQGVYGGYQSWVNRAGRFRSLGDGQVDFGAVFSKMAANDFAGWAVVEWECCLKHPEDGAREGSEFVKAHIIRVTEKAFDDFADSGTDEAANRRMLGI catabolism Sinorhizobium meliloti 1021 Smeli SMc03165 SMc03165 SMc03165 NP_387002.1 tr|Q92LW7|Q92LW7_RHIME Novel Xylose regulator from LacI family # Specifically important in carbon source D-Xylose. Also see expression evidence for the putative ortholog from Phaeobacter, PGA1_c13990, which is 41% identical (PMC4148808). (SEED_correct) transcriptional regulator Novel Xylose regulator from LacI family LacI family transcriptional regulator MRPTVHDIAAEAGVSLATVDRVLNNRPGVRSVTRGKVERAIATLGYVRDVAAANLAKSRSYPLIFILPAGENSFMRGLEAEVRSAMSRSATERLDITILSVPVFDAPALAAALHDARERRPAGVAVVAVDAPEVTEAVKRLREDGIAVVTLVSDLPGSGRDHFAGVDNVAAGRTAGSLMGRFLGGGEGPVAVLAGSMLVRDHRDRLEGFQAVMSEDFAWRRILPVIEGQDNPSLVETLVGALLGQHPDLAGIYSLGAGNRGLVAALEKAGKGRAVCTIAHELTPHSRAGLLSGTIDALLNQNAGHEVRSAIRVLKAKADGLPVIAAQERIRIDIFLKDNLPLEQE transporters Sinorhizobium meliloti 1021 Smeli SMc04256 SMc04256 SMc04256 NP_386032.1 tr|Q92P67|Q92P67_RHIME ABC transporter for D-Cellobiose and D-Salicin, ATPase component Specific phenotype on D-Salicin; D-Cellobiose. ABC transporter ATP-binding protein Nucleoside ABC transporter, permease protein 1 multiple sugar transport system ATP-binding protein MTSVSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMNFFRGEVEPKDGRSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEARDGEPTHQAVVDIEEPMGADNLLWLTFAGQSMSVRIAGQRRYPPGSTVRLSFDMGVASIFDAESENRL transporters Sinorhizobium meliloti 1021 Smeli SMc04257 SMc04257 SMc04257 NP_386033.2 tr|Q92P66|Q92P66_RHIME ABC transporter for D-Cellobiose and D-Salicin, permease component 1 Specific phenotypes on D-Cellobiose; D-Salicin. ABC transporter permease ABC-type sugar transport system, permease component multiple sugar transport system permease protein MAAAYETAPGGPMAGPRGRKPRRTLSRRNIIVYGTLIVVALYYLLPLYVMIVTSLKGMPEIRVGNIFAPPLEITFEPWVKAWAEACTGLNCDGLSRGFWNSVRITVPSVIISIAIASVNGYALANWRFKGADLFFTILIVGAFIPYQVMIYPIVIVLREMGVYGTLTGLIIVHTIFGMPILTLLFRNYFAGLPEELFKAARVDGAGFWTIYFKIMLPMSLPIFVVAMILQVTGIWNDFLFGVVFTRPEYYPMTVQLNNIVNSVQGVKEYNVNMAATILTGLVPLTVYFVSGRLFVRGIAAGAVKG transporters Sinorhizobium meliloti 1021 Smeli SMc04258 SMc04258 SMc04258 NP_386034.1 tr|Q92P65|Q92P65_RHIME ABC transporter for D-Cellobiose and D-Salicin, permease component 2 Specific phenotypes on D-Cellobiose; D-Salicin. ABC transporter permease ABC transporter, permease protein multiple sugar transport system permease protein MTGLTRGSARPNQWLRNLNAKIASIPMILTAMVIFVGGTAWTVVYSFTNSKLLPRLAFVGFDQYERLWAAPRWLVSIQNLAVFGCLSLVFSLVIGFVLAALMDQKIRFENTFRTIMLYPFALSFIVTGLVWQWLLNPQYGIQSIVRSLGWTSFSFDPLYNSNIVIYGILIAALWQGTGLVMCLMLAGLRGIDEDIWKAARVDGIPMWKTYVLIIIPMMRGVFITTLVIIASGIVKVYDLVVAQTSGGPGIASEVPAKYVYDYMFQAQNLGQGFAASTMMLVTVAIIIVPWAYLEFGGGRKRG transporters Sinorhizobium meliloti 1021 Smeli SMc04259 SMc04259 SMc04259 NP_386035.1 tr|Q92P64|Q92P64_RHIME ABC transporter for D-Cellobiose and D-Salicin, periplasmic substrate-binding protein Specific phenotype on D-Salicin; D-Cellobiose. periplasmic binding ABC transporter signal peptide protein ABC-type sugar transport system, periplasmic component multiple sugar transport system substrate-binding protein MNLRFLAAALGATAALPFGAASATDLEVTHWWTSGGEAAAVAELAKAFDATGNKWVDGAIAGSGGTARPIMISRITGGDPMAATQFNHGRQAEELVQAGLMRDLTDIATKENWKEIVKPSSLLDSCTIEGKIYCAPVNIHSWQWLWLSNAAFKQAGVEVPKNWDEFVAAAPALEKAGIVPLAVGGQPWQANGAFDVLMVAIAGKENFEKVFAQKDEEVAAGPEIAKVFKAADDARRMSKGTNVQDWNQATNMVITGKAGGQIMGDWAQGEFQLAGQKAGVDYTCLPGLGVNEVISTGGDAFYFPLLEDEEKSKAQEVLASTLLKPETQVAFNLKKGSLPVRGDVDLAAANDCMKKGLDILAKGNVIQGTDQLLSADSQKQKEDLFSEFFANHSMTPEDAQKRFADIIAAAD catabolism Sinorhizobium meliloti 1021 Smeli SMc04386 SMc04386 SMc04386 NP_387397.1 sp|P58350|AATB_RHIME 2-aminoadipate:2-oxoglutarate aminotransferase (EC 2.6.1.39) Specifically important for: L-Lysine. This is required for catabolism of lysine on the way to glutarate. The amino group donor is uncertain aspartate aminotransferase B protein Aspartate aminotransferase (EC 2.6.1.1) aspartate aminotransferase MTINATVKEAGFQPASRISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKYTALDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPYWTSYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAADYRPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMTGWRIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDLVVNGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVPGSAFGLSPFFRISYATSEAELKEALERIAAACDRLS transporters Pseudomonas simiae WCS417 WCS417 GFF1004 PS417_05090 PS417_RS22700 WP_029529237.1 UPI000496EDA7 ferric citrate outer membrane transporter (fecA) Specific phenotype on citrate; 63% identical to E. coli fecA; SEED_correct transporter Iron(III) dicitrate transport protein FecA @ Iron siderophore receptor protein iron complex outermembrane recepter protein MPQQPTLLARTLRQLLLGASLSLTALPPVMAADAKPYHIAPTSLEAALNQFGREAGVLISFGSEVTAGMQSRGLSGNYGAADGLQKLLEGTGLQARAEGDNAYSLQPATAPASIELGTSSVVGDWLGDAAQTHVFEHPGARDVIRREEFERQGATQAKDVLNRIPGVNAPDNNGTGSHDMALNFGIRGLNPRLASRSTVLMDGIPVPFAPYGQPQLSFAPISMGNMDAVDVVRGGGAVRYGPQNVGGVVNFVTRAIPDAPTVKGGLQTETSPSSSHDGFKTTGNLLAGGTADNGLGGAILYSGTRGGDWRENSNTRIDDLILKGKYQLDDANSFNAMAQYYEGQADMPGGLNVADYKADPYQSTRPYDKFWGRRTMFNVGYRYEQDRREFTVNSFFTKTLRSGYLDQGTFLSLSPREYWVRGIETRFAQGFDLGPTSHEVGVGYRYINEAGHELRYRTPIAANQQIPTTNSRNDRDTRGGTEANAFFVDDRIDIGKWTITPGIRYEIIESQQTNNLTNVKYKGDYNTALPALNVLYHLTDNWNLYANTEGSFGSVQYSQMPNRVTSGEVKPEKARTWELGTRYDDGTLRAEIGAFLINFDNQYESNQTNDSVIARGETRHQGIETSINYALDGLSPALAGFDVYATYAYVDATIREDGPNKGNRVPFSSKHKGTLGVGYTEGRWKLNLDSSYQSSQFADNANTEKETANGANGRIPGYMLFSSRAAYDFGPQLSDLNVAVGVKNIFNTQYFTRSFDDNNKGKYVGEPRTVYVQTSIAF transporters Pseudomonas simiae WCS417 WCS417 GFF1065 PS417_05405 PS417_RS22395 WP_010212811.1 UPI000299F6F4 L-alanine and D-alanine permease Important for utilizing both isomers of alanine, and no other transporter is apparent. Both phenotypes are conserved. D-alanine/D-serine/glycine permease D-serine/D-alanine/glycine transporter amino acid transporter, AAT family MPVGNHLPHGETAQGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGVWFPDTPRWIWALAALISMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGNDGVALGISNLWAHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPSAIGSVFWRILLFYVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIFSTGRMLYSLAQNGQAPATFAKTSSNGVPRKALLLSIFALLLGVLLNYLVPEKVFVWVTSIATFGAIWTWLMILLAQLKFRKSLSPAEQAGLKYRMWLYPVSSYLALAFLLLVVGLMAYFPDTRIALYVGPVFLVLLTVLFYVFKLQPTQVAQGEARPV transporters Pseudomonas simiae WCS417 WCS417 GFF1579 PS417_08035 PS417_RS19860 WP_010211991.1 UPI00029A6093 adenine transporter (MFS superfamily) specific phenotype on adenine and no other transporter was identified by the fitness data. Also mildly important on adenosine, which could reflect extracellular conversion to adenine transporter Putative transport protein MKNSFGFTWYLAGLSMLGYLAMDMYLPAFGAMGEQLQIGAGAVGASLSIFLAGFAVGQLLWGPLSDRLGRKPILLAGLSLFVLGCAGMFWVETAPQLLALRFIQAIGVCSAAVSWQALVIDRYPADKAHRVFASIMPLMSLSPALAPLLGAMVLNHFGWQAIFGVLLGVSVLLLLPTVFLRGMPKRPTEGREPVRLGYGQLLTSRVFTGNVMIFAACSASFFAWLTASPFILGGMGYSPNDIGLSYVLPTLAFLVGGYSCRSALQRFQGKTLLPWLLLAYCISMVALYLVATLTVPTLTTLLIPFCLMALCNGASYPIVVANALMPFSENSGKAAALQNTLQLGLCFLSSLVVSSMLDQPLLITAIVMLATAPLAVLGYWLARPKADNSVLAPNLK catabolism Pseudomonas simiae WCS417 WCS417 GFF2142 PS417_10925 PS417_RS17080 WP_038453112.1 UPI00049A49C0 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) Specifically important for: m-Inositol. 3-oxopropionate or malonate semialdehyde is an intermediate in myo-inositol catabolism (SEED_correct, although the name and EC number are confusing) methylmalonate-semialdehyde dehydrogenase Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) methylmalonate-semialdehyde dehydrogenase MTTTIEHYINDQRVSRDDRYQDVFNPATGEKTGRVALASRQTVSEAVAAAQAAFAGWADTPPIRRARVLFEYLHLLRERKDDLARIIVAEHGKVFTDAQGEVDRGIDILEFACGIPNLLKGEHSDQVSRGMDNWTMRQPLGVVAGVTPFNFPVMVPMWMYPIAIAAGNTFILKPSPTDPSASLFMAELLREAGLPKGVFNVVQGDKESVDALIEHPDVKAVSFVGSTPIAQYIYETGARNGKRVQGLGGAKNHMVVMPDADIEKTVDALMGAAYGSAGERCMAISVAVLVGDVGDKVIAALTERAKHLRITDGRDLKAEMGPIVSRAALERISGYIEQGVQAGAQLLLDGRDYVPTEPGLENGFWLGATLFDHVTEEMSIYREEIFGPVLACVRVNDFAEAIKLVNAHEFGNGVSCFTRDGNIAREFARRIEVGMVGINVPISVPMAWHGFGGWKKSLFGDMHAYGTEGVRFYTKQKSIMQRWSESIEQGAEFAMPVSK catabolism Pseudomonas simiae WCS417 WCS417 GFF2156 PS417_11000 PS417_RS17010 WP_010211220.1 UPI00029AE918 L-arabonate dehydratase (EC 4.2.1.25) Specifically important for: L-Arabinose. L-arabonate is an intermediate in the oxidation of L-arabinose (SEED_correct) dihydroxy-acid dehydratase L-arabonate dehydratase (EC 4.2.1.25) dihydroxy-acid dehydratase MPDKKPGLRSAQWFGTADKNGFMYRSWMKNQGIADHQFHGKPIIGICNTWSELTPCNAHFRQIAEHVKRGVIEAGGFPVEFPVFSNGESNLRPTAMLTRNLASMDVEEAIRGNPIDGVVLLTGCDKTTPALLMGAASCDVPAIVVTGGPMLNGKHKGQDIGSGTVVWQLSEQVKAGTITLDDFLAAEGGMSRSAGTCNTMGTASTMACMAEALGTSLPHNAAIPAVDARRYVLAHMSGMRAVEMVREDLKLSKILTKEAFENAIRVNAAIGGSTNAVIHLKAIAGRIGVELDLDDWTRIGRGMPTIVDLQPSGRFLMEEFYYAGGLPAVLRRLGEANLIPHPNALTVNGKSLGENTQDSPIYGQDEVIRTLDNPIRADGGICVLRGNLAPLGAVLKPSAASPALMQHRGRAVVFENFDMYKARINDPELDVDANSILVMKNCGPKGYPGMAEVGNMGLPAKLLAQGVTDMVRISDARMSGTAYGTVVLHVAPEAAAGGPLATVKEGDWIELDCANGRLHLDIPDAELAARMADLAPPQKLIVGGYRQLYIDHVLQADQGCDFDFLVGCRGAEVPRHSH catabolism Pseudomonas simiae WCS417 WCS417 GFF2159 PS417_11015 PS417_RS16995 WP_010211217.1 UPI00029B5717 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) Specifically important for: L-Arabinose. alpha-ketoglutarate semialdehyde is an intermediate in the oxidation of L-arabinose (SEED_correct) ketoglutarate semialdehyde dehydrogenase Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) NADP-dependent aldehyde dehydrogenase MTSFLGHNYIGGQRSANGSVTLQSVDATSGEALPQHFYQATPQEVDAAAKAAAQAYPAYRALSAARRAQFLDAVADELDALGDEFVELVCRETALPAARIKGERGRTSGQMRLFATVLRRGDFYGARIDKALPDRQPMPRPDLRQYRIGLGPVAVFGASNFPLAFSTAGGDTAAALAAGCPVVFKAHSGHMATAERVADAIIRAAEATEMPAGVFNMIFGGGVGEALVKHPAIQAVGFTGSLKGGRALCDMAAARPQPIPVFAEMSSINPVIVLPQALKARAESVARDLTASVVQGCGQFCTNPGLVIGVASPEFTAFTQQVAQLIGDQPAQTMLNAGTLSSYGKGLEKLLAHPGIQHLAGSQQAGNQAQPQLFKADVRLLIDGDEVLQEEVFGPTTVFVEVADQAQLSAALHGLHGQLTATIIGEPADLQQFAELTPLLEQKVGRILLNGYPTGVEVCDSMVHGGPYPATSDARGTSVGTLAIDRFLRPVCFQNYPDSLLPDALKNANPLRIQRLVDGTPSRDPL catabolism Pseudomonas simiae WCS417 WCS417 GFF2160 PS417_11020 PS417_RS16990 WP_010211216.1 UPI00029AF246 L-arabinolactonase (EC 3.1.1.15) Specifically important for: L-Arabinose. a step in L-arabinose oxidation (SEED_correct) gluconolaconase L-arabinolactonase (EC 3.1.1.15) MSCIAVTPHRAQLGEGPFWDAPTQALYWVNIAGKQALRLMGGQLQVWQLPEHVSAFIPCESGDALVTLSSGVYRLDLATEALTLLCVADPQPGNRGNEARCDASGRLWLGTMQNNIGEQGEDLPITRRSGGLFRIDADAQVTPLLSGLGIPNTLLWSDDGRHVHFGDSLDGTLYRHAIQPDGQLDPAQTWFGPHERGGPDGSAMDVDGYIWNARWDGSCLLRLTPDGEVDRIVELPVSRPTSCVLGGPNLTTLYITSAASPLDHPLDGAVLAMEVDVPGKPCHRFAG catabolism Pseudomonas simiae WCS417 WCS417 GFF2259 PS417_11520 PS417_RS16495 WP_010211099.1 UPI000299D29F Sorbitol dehydrogenase (EC 1.1.1.14) Specifically important for: D-Sorbitol. The first step in sorbitol degradation (SEED_correct) sorbitol dehydrogenase Sorbitol dehydrogenase (EC 1.1.1.14) MKRLEGKSALITGSARGIGRAFAQAYIAEGATVAIADIDLQRAQATAAELGPQAYAVAMDVTDQASIDGAITAVVAQAGKLDILINNAALFDLAPIVDITRDSYDRLFSINVAGTLFTLQAAARQMIRQGHGGKIINMASQAGRRGEPLVAIYCATKAAVISLTQSAGLNLIKQGINVNAIAPGVVDGEHWDGVDALFAKHEGLAPGEKKQRVGAEVPFGRMGTAEDLTGMAIFLASKEADYVVAQTYNVDGGNWMN transporters Pseudomonas simiae WCS417 WCS417 GFF2331 PS417_11885 PS417_RS16140 WP_010211018.1 UPI00029B1E87 Inositol transport system sugar-binding protein specific phenotype on inositol. SEED_correct rhizopine-binding protein Inositol transport system sugar-binding protein simple sugar transport system substrate-binding protein MKTPIRFTALALSMLLASGVASAADLKIGVSMSAFDDTFLTYLREDMDKQAKSYPKGDGVQLQFEDARADVVKQLSQVENFISQKVDAIIVNPVDTASTANIIKAATAAKIPLVFVNRRPDSQTLAPGVAAVTSDDVEAGKLQMQYIAEKLGGKGNIVILLGDLANNSTTNRTKGVKEVLTKYPGIKIEQEQTGIWLRDRGMTLVNDWLTQGRDFQAVLSNNDEMAIGAAMALKSAGKKGVLIAGVDGTPDGLNAITKGDMTVSAFQDAKGQADKSVETARKMAKNEPIEQNVVIPFQLITPDNVKDFK transporters Pseudomonas simiae WCS417 WCS417 GFF2332 PS417_11890 PS417_RS16135 WP_010211017.1 UPI00029B1B5E Inositol transport system ATP-binding protein specific phenotype on inositol. SEED_correct D-ribose transporter ATP-binding protein Inositol transport system ATP-binding protein simple sugar transport system ATP-binding protein MLAQATVSQPPSLQPQTLEEPYLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRLRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTAELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRELSQLFPLRETPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVMQLASGMTAVH transporters Pseudomonas simiae WCS417 WCS417 GFF2333 PS417_11895 PS417_RS16130 WP_010211015.1 UPI00029AEE01 Inositol transport system permease protein specific phenotype on inositol. SEED_correct ABC transporter Inositol transport system permease protein simple sugar transport system permease protein MNAITDNKPATVPTKSRRRLPTELSIFLVLIGIGLVFELFGWIVRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQVIITTGIDLSSGSVLALSAMIAASLAQTSDFSRAVFPSLTDLPVWIPVAMGLGVGLLAGAINGSIIAVTGIPPFIATLGMMVSARGLARYYTEGQPVSMLSDSYTAIGHGAMPVIIFLVVAVIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLIIVYSIAGLLAGLAGVVASARAATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGALILGVMASGFTFVGVDAYIQDIIKGLIIVVAVVIDQYRNKRKLKR catabolism Pseudomonas simiae WCS417 WCS417 GFF2378 PS417_12125 PS417_RS15905 WP_010210955.1 UPI00029B06D9 D-glucosaminate dehydratase (EC 4.3.1.9) Specifically important for: D-Glucosamine Hydrochloride. This enzyme had not previously been linked to a gene. This is the second step in catabolism of glucosamine, and the 'beta' form of the enzyme was expected to be PLP-dependent and about this size. Iwamoto et al (2003) purified a non-specific 'alpha' enzyme for this reaction (PMID: 12686150) amino acid deaminase D-serine deaminase (EC 4.3.1.18) MSAINAVEKGAAAVGAHLVRDVSLPALVLHRDALEHNIRWMQDFVSNSGAELAPHGKTSMMPALFQRQIEAGAWGITLANAVQTRAAYAGGVRRVLMANQLVGAPNMALIADLLADKDFDFHCMVDHPDNVADLGLFFAARGLRLNVMIEYGVVGGRCGCRTEQEVRDLARAIKAQPALALTGIEGYEGVIHGEHAISGIRDFAASLVRLAVDLQNNGSFDLPKPIVTASGSAWYDLIAESFEQQNAAGRFLSVLRPGSYVAHDHGIYKEAQCCVLDRRSDLNEGLRPALEVWAHVQSLPEPGFAVIALGKRDVAYDAGLPVPLKRYKAGILPAEGDDVTACKVTAVMDQHAFMTVAPGVELRIGDIISFGTSHPCLTFDKWQVGCLVDEQLQVIESLETRF transporters Pseudomonas simiae WCS417 WCS417 GFF2490 PS417_12700 PS417_RS15345 WP_010210760.1 UPI00029A7CFC ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component Specific phenotype on D-Sorbitol; D-Mannitol. Also important for D-mannose utilization. ABC transporter ATP-binding protein Various polyols ABC transporter, ATP-binding component sorbitol/mannitol transport system ATP-binding protein MANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGTIELDGRDITEVTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKKLVESKVSEAARILELGPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLHKELQATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAGFLGTPKMGFLKGKVTRVESQSCEVQLDAGTLINLPLSGATLSVGSAVTLGIRPEHLEIASPGQTTLTVTADVGERLGSDTFCHVITANGEPLTMRIRGDMASQYGETLHLHLDPAHCHLFDTDGVAVARPLRAAA transporters Pseudomonas simiae WCS417 WCS417 GFF2491 PS417_12705 PS417_RS15340 WP_010210759.1 UPI00029ADD6A ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, permease component 1 Specific phenotypes on D-Mannitol; D-Mannose; D-Mannose; D-Sorbitol; D-Sorbitol. mannitol ABC transporter permease Various polyols ABC transporter, permease component 2 sorbitol/mannitol transport system permease protein MTLQQSRRLQSLLLGTLAWAIAILIFFPIFWMVLTSFKTEIDAFATPPQFIFTPTLENYLHINERSNYFSYAWNSVLISFSATALCLLISVPAAYSMAFYETQRTKGTLLWMLSTKMLPPVGVLMPIYLLAKSFGLLDTRIALIIIYTLINLPIVVWMVYTYFKDIPKDILEAARLDGATLWQEMVRVLLPIAKGGLASTVLLSLILCWNEAFWSLNLTSSSAAPLTALIASYSSPEGLFWAKLSAVSTLACAPILIFGWISQKQLVRGLSFGAVK transporters Pseudomonas simiae WCS417 WCS417 GFF2492 PS417_12710 PS417_RS15335 WP_029529156.1 UPI000403AE5C ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, permease component 2 Very important for utilization of D-sorbitol, D-mannitol, and D-mannose. sugar ABC transporter permease Various polyols ABC transporter, permease component 1 sorbitol/mannitol transport system permease protein MNTTTPKNRLANPGWFLVSPSVALLLLWMIVPLGMTLYFSLIRYNLLYPGENEFVGLENFTYFITDSGFLPGATNTLLLVGSVLLISVVFGVLISALLEASEFLGRGLVRVLLISPFFIMPTVGALIWKNLIFHPVSGILAAVWKFFGAEPVDWLAHYPLLSIIIIVSWQWLPFAILLLMTAMQSLDQEQKEAARLDGAGAIAIFWHLTLPHLARPIAVVVMIETIFLLSVFAEIFTTTNGGPGYASTNLAYLIYNQALVQFDVGMASAGGLIAVVIANIAAIILVRMIGKNLTDKP transporters Pseudomonas simiae WCS417 WCS417 GFF2493 PS417_12715 PS417_RS15330 WP_010210754.1 UPI00029A3EE3 ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, periplasmic substrate-binding protein Specific phenotype on D-Mannose; D-Sorbitol; D-Mannitol. sugar ABC transporter substrate-binding protein Various polyols ABC transporter, periplasmic substrate-binding protein sorbitol/mannitol transport system substrate-binding protein MKFTAKALLASTCMMTCMTLSAVSFGAQTLTIATVNNSDMIRMQKLSKTFEAEHPEIKLNWVVLEENVLRQRLTTDIATQGGQFDVLTIGMYEAALWGAKGWLEPMKDLPASYDLDDVFPSVRDGLSVKGSLYALPFYAESSITYYRTDLFKDAGLTMPEHPTWTQIGEFASKLTDKTKEQYGLCLRGKAGWGENMALITTLANGYGARWFDEKWQPEFNGPEWKDALNFYVDNMKKSGPPGASSNGFNENLALFNSGKCAIWVDASVAGSFVTDKTQSKVADHVGFTFAPHEKTDKGTSWLYSWSLAIPTSSKAKDAAKVFTSWATSKEYGELVAKTDGIANVPPGTRKSTYNDEYMKAAPFAKVTLESLKVADPTKPTLKPVPYIGIQLVTIPEFQAIGTQVGKFFSGALTGQQTVDAALTAAQTTTEREMKRAGYPK catabolism Pseudomonas simiae WCS417 WCS417 GFF2712 PS417_13835 PS417_RS14240 WP_010210414.1 UPI00029AC8B2 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) Specifically important for: L-Valine. KEGG no longer makes any prediction (see pfo:Pfl01_2864). 3-hydroxy-isobutanoyl-CoA is an intermediate in valine degradation. (SEED_correct) crotonase 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) enoyl-CoA hydratase MTAQVSSEASHAETLQDEVLAEVRNHIGHLTLNRPAGLNAITLNMVRRLASQLKAWADDPQVYAVVLRGAGEKAFCAGGDIRSLYDSFKNGDTLHQDFFVEEYALDLAIHHYRKPVLALMDGFVLGGGMGLVQGADLRVVTERSRLAMPEVAIGYFPDVGGSYFLPRIPGELGIYLGVTGVQIRAADALYCGLADWYLESSKLADLDNKLDRLQWHDSPLKDLQGVLAKLAVQQLPDAPLAVLRPAIDHFFALPDVPSIVEQLQQVTVADSHEWALTTAHLMQTRSPLAMAVTLEMLRRGRRLPLEQCFALELHLDRQWFERGDLIEGVRALIIDKDKAPRWNPPTLHGLALSHVESFFHNFKKVAN catabolism Pseudomonas simiae WCS417 WCS417 GFF2713 PS417_13840 PS417_RS14235 WP_010210413.1 UPI00029B4FAD isobutyrl-CoA dehydrogenase (EC 1.3.8.1) Specifically important for: L-Valine. SEED annotates it as butyryl-CoA dehydrogenase, which is also expected to perform this reaction in valine catabolism acyl-CoA dehydrogenase Butyryl-CoA dehydrogenase (EC 1.3.99.2) MQDIEYTEEQVMIRDMARDFARGEIAPYAQAWEKAGWIDDALVAKMGELGLLGMVVPEEWGGTYVDYVAYALAVEEISAGDGATGALMSIHNSVGCGPILNYGTESQKQTWLADLASGQAIGCFCLTEPQAGSEAHNLRTRAELRDGHWVITGAKQFVSNGKRAKLAIVFAITDPELGKKGISAFLVPTATPGFVVDRTEHKMGIRASDTCAVTLNQCTVPEANLLGERGKGLAIALSNLEGGRIGIAAQALGIARAAFEAALAYARDRVQFDKAIIEHQSVANLLADMQTQLNAARLLILHAARLRSAGKPCLSEASQAKLFASEMAEKVCSSAMQIHGGYGYLEDYPVERYYRDARITQIYEGTSEIQRMVIARELKHYQL catabolism Pseudomonas simiae WCS417 WCS417 GFF2715 PS417_13850 PS417_RS14225 WP_010210411.1 UPI00029AB5F1 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.1) Specifically important for: L-Isoleucine. SEED has it as butyryl-CoA dehydrogenase, which is also expected to perform this reaction in isoleucine catabolism acyl-CoA dehydrogenase Butyryl-CoA dehydrogenase (EC 1.3.99.2) MLPNEEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTGYLAYAMALEEIAAGDGACSTIMSVHNSVGCVPVLKFGNDQQKEQFLKPLASGAMLGAFALTEPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPAAGKRGISAFIVPTDSPGYSVARVEDKLGQHASDTCQILFEDVKVPVANRLGEEGEGYKIALANLEGGRVGIASQAVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALRDSGKPALVEASMAKLFASEMAEKVCSAALQTLGGYGYLSDFPLERIYRDVRVCQIYEGTSDIQRMVISRNL catabolism Pseudomonas simiae WCS417 WCS417 GFF3392 PS417_17360 PS417_RS10860 WP_010209382.1 UPI000299FAF3 D-galacturonate dehydrogenase (EC 1.1.1.203) Specifically important for: D-Galacturonic Acid monohydrate. KEGG now annotates it as uronate dehydrogenase which is correct (although less specific) (KEGG_correct) NAD-dependent dehydratase UDP-glucose 4-epimerase (EC 5.1.3.2) MTTTPTTPVPFNRLLLTGAAGGLGKVLRERLRPYAQVLRLSDIANMAPAADASEEVQPCDLADKQAVHHLVEGVDAILHFGGVSVERSFEEVLGANISGIFHIYEAARRHGVKRVIFASSNHVIGFYKQGEKLDAHSPRRPDSYYGLSKSYGEDMASFYFDRYGIETVSIRIGSSFPEPQNRRMMHTWLSFDDLTQLLERALYTPNVGHTVVYGMSDNLDTWWDNRYAAHLGFAPKDSSEVFRAQVETQPPVSDNDPAKVYQGGAFCAAGPFGD catabolism Pseudomonas simiae WCS417 WCS417 GFF3393 PS417_17365 PS417_RS10855 WP_010209380.1 UPI00029A69C7 galactaro-1,5-lactonase # Specifically important in carbon source D-Galacturonic Acid monohydrate. This is the second step after D-galacturonate dehydrogenase (PS417_17360) and forms meso-galactarate, which is the substrate of PS417_04210. The substrate is probably the 1,5-lactone, not the 1,4-lactone, given the characterization of the D-galacturonate dehydrogenase from Agrobacterium tumefaciens (PMID:24450804), which is 51% identical to PS417_17360. gluconolactonase Gluconolactonase (EC 3.1.1.17) MNAELIVDARNAVGECPVWVPGENALYWVDIPKGGLQRWSAATGHVAAWTAPQMLACIARTDAGNWVAGMETGFFQLTPHNDGSLDTTLLAAVEHPRQDMRLNDGRCDRQGRFWAGSMVLNMGLNAAEGTLYRYTSGAAPHAQLDGFITLNGLAFSPDGRTMYASDSHPLVQQIWAFDYDIDTGTPSNRRVFVDMHKHLGRPDGAAVDADGCYWICANDAGLIHRFSPDGRLDRSLTVPVKKPTMCAFGGSRLDTLFVTSIRDDQSEQSLSGGVFALNPGVVGLPEPTFTL catabolism Pseudomonas simiae WCS417 WCS417 GFF3404 PS417_17420 PS417_RS10800 WP_010209365.1 UPI00029A62DC ethanol oxidation regulatory protein ercA Strongest phenotype is on ethanol. Similar to ercA (PA1991) which apparently has a regulatory role (PMCID: PMC3754586) rather than being directly involved in catabolism. Consistent with a regulatory role, this gene has pleiotropic phenotypes. The main ethanol dehydrogenase is probably PS417_17460. alcohol dehydrogenase Alcohol dehydrogenase (EC 1.1.1.1); Acetaldehyde dehydrogenase (EC 1.2.1.10) MSPNLSLLRKFVSPEIIFGAGCRHNVGNYAKTFGARKVLVVSDPGVIAAGWVADVEASLQAIGIDYCLYSAVSPNPRVEEVMLGAEVYRENHCDVIVAIGGGSPMDCGKAIGIVVAHGRCILEFEGVDTIRVPSPPLILIPTTAGTSADVSQFVIISNQQERMKFSIVSKAVVPDVSLIDPETTASMDPFLSACTGIDALVHAIEAFVSTGHGPLTDPHALEAMRLINGNLVQMIANPGDIALREKIMLGSMQAGLAFSNAILGAVHAMSHSLGGFLDLPHGLCNAVLVEHVVAFNYNSAPERFKVIAETFGIDCRGLSHRQVCARLVEHLIALKHAIGFHETLGLHGVRVADIPFLSRHAMHDPCILTNPRESSQRDVEVVYGEAL catabolism Pseudomonas simiae WCS417 WCS417 GFF3434 PS417_17580 PS417_RS10650 WP_010209327.1 UPI00029A57C7 arginine deiminase (EC 3.5.3.6) Important on citrulline, which is catabolized via arginine by this reaction in reverse; distantly related to characterized arginine deiminases (PF02274) amidinotransferase MQTTNTVLMIRPARFAFNPDTAINNRFQRQPLDPLGAQQKALEEFDGYVDTLRRHGVEVLVVQDTPAPHTPDSIFPNNWWSSHADGSLVLYPMEGQNRRLERNKGVLQVLEQRFAINSTIDLSHLEQQNIFLEGTGSMVLDRQHRISYACHSGRTHQDALRQFAERLDYQLCVFHAVDRHHAPIYHSNVMMSVGRDLSVVCLQALPDASERQGLERSLRDTGKDILALDFDQLEGFAGNMLEIHDRDGQPLLVMSASAWGALQPAQRQHVERHTRPVVVNIDNIERIGGGSARCMLAEVHLPARATVQ catabolism Pseudomonas simiae WCS417 WCS417 GFF3461 PS417_17720 PS417_RS10515 WP_010209291.1 UPI00029A5520 xylitol 2-dehydrogenase (EC 1.1.1.9) Specifically important for: Xylitol. This is the first step in xylitol degradation (SEED_correct) iditol 2-dehydrogenase Xylitol dehydrogenase (EC 1.1.1.9) L-iditol 2-dehydrogenase MDKHTEMQAVVCHGPKDYRLERIGKPQARANELVIRIAACGICASDCKCHSGAAMFWGGDNPWVKAPVVPGHEFFGYVVEAGEGAEEHFEVAVGDKVIAEQIVPCGKCRFCKSGKYWMCEVHNIFGFQREVAEGGMAQYMRIPKTAIVHKIPESVSLEDSALVEPMACSIHTVNRGDIQLDDVVVIAGAGTLGLCMVQVAALKTPKKLVVIDMVDERLELAKKFGADVVINPSRDNAREIINGLTDNYGCDVYIETTGVPAGVTQGLDLIRKLGRFVEFSVFGAETSVDWSIIGDRKELDVRGAHLGPYCYPIAIDLFERGLVTSKGIVTHDFPLDDWAEAFELANSTKSIKVLLKPVV transporters Pseudomonas simiae WCS417 WCS417 GFF4091 PS417_20960 PS417_RS07405 WP_010208503.1 UPI00029A64B9 Nitrate-binding regulatory protein (nasS) This protein is specifically important for the utilization of nitrate as a nitrogen source, but this may be a polar effect. It is74% identical to the nasS/PA1786 protein from P. aeruginosa (PMID:22493305) and to nasS from Azotobacter vinelandii (PMID:8748040), which binds nitrate and suppresses the activity of the transcriptional activator nasT. It is also more distantly related to the periplasmic substrate-binding components of nitrate ABC transporters (i.e., 37% identity to the N terminal part of ntrC/sll1452 and 36% identity to ntrA/sll1450), hence the misannotation as a transporter. nitrate transporter Nitrate ABC transporter, nitrate-binding protein sulfonate/nitrate/taurine transport system substrate-binding protein MNDSDGNSPMNDPLAWVNGSDAPEKSSLDLGFMALSDCASMVVAATQGFAQPYGLTLNLKRQTSWANLRDKLVSGELDAAHSLYGLIYAVHLGIGGVAPTDMAVLMGLNQNGQSINLSRGLQQQGVITPEALDRHVHQSRTKLTFAQTFPTGTHAMWLYYWLASQGIHPLQDVDSVVVPPPQMVAHLQAGRIDGFCVGEPWCASAVKQNQGFTLATTQAIWPDHPEKVLGCTQAFVDQYPNTARVLVMAILEASRFIEESSENRRSTAQLLSGREYLDAPLDCIEPRLLGTYDDGLGNHWQDPHALRFFADGEVNLPYLSDGMWFMTQFRRWGLLREDPDYLGVARQVQQLPLYRQAAAALGIATKHPDMRSSQLIDGKVWDGSDPADYARSFRLHALADTTHRQALR catabolism Pseudomonas simiae WCS417 WCS417 GFF4238 PS417_21710 PS417_RS06670 WP_010208316.1 UPI00029ACDDF Succinylornithine transaminase (EC 2.6.1.81) Specifically important for: L-Arginine. succinylornithine transaminase is involved in L-arginine degradation via N-succinylarginine. Also this gene is cofit with other putative steps in that pathway (N-succinylarginine dihydrolase, succinylglutamate-semialdehyde dehydrogenase, succinylglutamate desuccinylase). In contrast, neither of the functions proposed by KEGG have an obvious relationship to arginine catabolism. (SEED_correct) acetylornithine aminotransferase Succinylornithine transaminase (EC 2.6.1.81) acetylornithine/N-succinyldiaminopimelate aminotransferase MSVEQAPVQRADFDQVMVPNYAPAAFIPVRGEGSRVWDQAGRELIDFAGGIAVNVLGHAHPALVGALTEQAHKLWHVSNVFTNEPALRLAHKLIDATFAERVFFCNSGAEANEAAFKLARRVAFDRFGSEKYEIIAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLDALKAAVSDKTCAVVLEPIQGEGGVLPAELAYLQGARDLCDANNALLVFDEVQTGMGRSGHLFAYQHYGVTPDILTSAKSLGGGFPIAAMLTTEALAKHLVVGTHGTTYGGNPLACAVAEAVIDVINTPEVLAGVNAKHDLFKARLEQIGKQYGIFTEVRGMGLLLGCVLSDAFKGKAKDVFNAAEKENLMILQAGPDVVRFAPSLVVEDADIKEGLDRFERAVKALTQA transporters Pseudomonas simiae WCS417 WCS417 GFF4244 PS417_21740 PS417_RS06640 WP_010208305.1 UPI00029A6D5A ABC transporter for L-Arginine, permease component 1 Specific phenotypes on L-Arginine; L-Arginine. KEGG annotation has been updated since the last public release (KEGG_correct) ABC transporter MLKGYGAVILDGAWLTLQLALSSMALAIVLGLIGVALRLSPVRWLAWLGDLYSTVIRGIPDLVLILLIFYGGQDLLNRVAPMLGYDDYIDLNPLAAGIGTLGFIFGAYLSETFRGAFMAIPKGQAEAGLAYGMSSFQVFFRVMVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKAKQAADATREPFTFFLAVAAMYLVITSVSLLALRHLEKRYSVGVRAADL transporters Pseudomonas simiae WCS417 WCS417 GFF4321 PS417_22130 PS417_RS06255 WP_010208189.1 UPI00029B0C82 ABC transporter for D-Glucose-6-Phosphate, ATPase component Specific phenotype on D-Xylose; D-Glucose-6-Phosphate sodium salt. Xylose has its own transporter so the reason for a phenotype on xylose is unclear. sugar ABC transporter ATPase Glucose ABC transporter, ATP-binding subunit (EC 3.6.3.-) multiple sugar transport system ATP-binding protein MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGAIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVAKLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPPMNFVPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEGDSASSIRAEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDVAPQVGETLTLQFDPSKVLLFDANTGERLGTASSLPAQGHADNVAQFKGR transporters Pseudomonas simiae WCS417 WCS417 GFF4322 PS417_22135 PS417_RS06250 WP_010208187.1 UPI00029A8D08 ABC transporter for D-Glucose-6-Phosphate, permease component 1 Specific phenotypes on D-Glucose-6-Phosphate sodium salt; D-Glucose-6-Phosphate sodium salt. Also somewhat important on D-xylose but that has its own transporter so the interpretation is unclear. sugar ABC transporter permease Glucose ABC transport system, inner membrane component 2 multiple sugar transport system permease protein MTSLASKPAISLSRIAIYAVLILAVLLYLVPLVVMLLTSFKTPEDISSGNLLSWPTVVTGIGWVKAWATVDGYFWNSIKITVPAVLISTAIGALNGYVLSFWRFKGSQLFFGLLLFGCFLPFQTVLLPASFTLGKMGLASTTTGLVFVHVVYGLAFTTLFFRNYYVSIPDALIKAARLDGAGFFTIFRQIILPMSTPIIMVCLIWQFTQIWNDFLFGVVFSSGDSQPITVALNNLVNTSTGAKEYNVDMAAAMIAGLPTLLVYVIAGKYFVRGLTAGAVKG transporters Pseudomonas simiae WCS417 WCS417 GFF4323 PS417_22140 PS417_RS06245 WP_010208185.1 UPI000299D5D4 ABC transporter for D-Glucose-6-Phosphate, permease component 2 Specific phenotypes on D-Glucose-6-Phosphate sodium salt; D-Glucose-6-Phosphate sodium salt. Also somewhat important on D-xylose but that has its own transporter so the interpretation is unclear. sugar ABC transporter permease Glucose ABC transport system, inner membrane component 1 multiple sugar transport system permease protein MSSVAVFSKASPFDALQRWLPKLVLAPSMFIVLVGFYGYILWTFVLSFTNSTFLPTYKWAGLAQYARLFDNDRWWVASKNLAVFGGMFIGITLVIGVTLAIFLDQKIRREGFIRTIYLYPMALSMIVTGTAWKWLLNPGMGLDKLLRDWGWEGFRLDWLIDPDRVVYCLVIAAVWQASGFIMAMFLAGLRGVDQSIVRAAQIDGASMPRIYWSVVLPSLRPVFFSAVMILAHIAIKSFDLVAAMTAGGPGYSSDLPAMFMYSFTFSRGQMGMGSASAILMLGAILAIIVPYLYSELRTKRND transporters Pseudomonas simiae WCS417 WCS417 GFF4324 PS417_22145 PS417_RS06240 WP_010208183.1 UPI00029A56A3 ABC transporter for D-Glucose-6-Phosphate, periplasmic substrate-binding component Specific phenotype on D-Xylose; D-Glucose-6-Phosphate sodium salt. Probably also the main transporter for D-xylose. sugar ABC transporter substrate-binding protein Glucose ABC transport system, periplasmic sugar-binding protein multiple sugar transport system substrate-binding protein MNAINRLAVAISIASLFPLSAFAADSKGTVEVVHWWTSGGEKAAVDVLKAQVEKDGFVWKDGAVAGGGGATAMTVLKSRAVAGNPPGVAQIKGPDIQEWASTGLLDTDVLKDVAKEEKWDSLLDKKVSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGITKNPTTLQEFYAAGDKLKAAGFIPLAHGGQPWQDSTVFEAVVLSVMGADGYKKALVDLDNGALTGPEMVKALTELKKVATYMDVDGKGQDWNLEAGKVINGKAGMQIMGDWAKSEWTAAKKVAGKDYECVAFPGTDKAFTYNIDSLAVFKQKDKGTAAGQQDIAKVVLGENFQKVFSINKGSIPVRNDMLNKMDSYGFDSCAQTAAKDFLADAKTGGLQPSMAHNMATTLAVQGAFFDVVTNYINDPKADPADTAKKLGAAIKSAK catabolism Pseudomonas simiae WCS417 WCS417 GFF4325 PS417_22150 PS417_RS06235 WP_038453710.1 UPI00049AFFAB D-mannose isomerase (EC 5.3.1.7) Specifically important for: D-Mannitol; D-Mannose. D-mannose isomerase is the first step in mannose catabolism, and the second step in mannitol catabolism. This gene is similar to the putative mannose isomerase Sama_0560 (PMID:20836887, PMCID: PMC4436071). sugar isomerase N-acylglucosamine 2-epimerase (EC 5.1.3.8) MITQPLPASSWLNAPAHYVWLAAEGQRLLAFAKASRLPDGFGNLDDKGQLPADAHAETMNTARMTHSFAMAHALGLPGYAELVAHGVAALSGALRDSEHGGWFAAPHALDGNRGKAAYLHAFVALAASSAVVAGAPGASTLLNDAIHIIDHFFWSEEEGVMLESFAQDWSGVEAYRGANSNMHATEAFLALADVTGDTRWLDRALRIVERVIHTHAAGNQFMVIEHFDTHWHPLLGYNEDNPADGFRPYGITPGHGFEWARLVLHLEAARLQAGLVTPEWLVADAKRLFASACEYAWSVDGAPGIVYTLDWNHRPVVRERLHWTHAEASAAAQALLKRTGELHYETWYRRFWEFCETHFIDRLHGSWHHELSPHNQPSSNIWGGKPDLYHAWQAVLLPALPLAPSMASAIGTGRYVTNW transporters Pseudomonas simiae WCS417 WCS417 GFF4500 PS417_23035 PS417_RS05360 WP_010207948.1 UPI00029A7B26 D-trehalose PTS system, I, HPr, and IIA components Specific phenotype for trehalose and no other trehalose transporter is apparent in the fitness data. The IIB and IIC components are provided by PS417_23050 PTS mannose transporter subunit IIC PTS system, glucose-specific IIA component (EC 2.7.1.69) / Phosphotransferase system, phosphocarrier protein HPr / Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9) PTS system, fructose-specific IIA component ; phosphotransferase system, enzyme I, PtsI ; phosphocarrier protein FPr MTTTQPLELLAPLSGVLLALDKVPDPVFSSRLIGDGLCIDPTSQTLCAPLAGVISNIQDSGHAVSITDDNGVQVLMHIGLDTVNLAGQGFTRLVQEGQRVEAGQPLIEFDADYVALNARSLLTLMLVVSGEPFSLLADGLVETGQPLLQLSPSGAVEAVDEEEGDALFSKPLTLPNANGLHARPAAVFAQAAKGFNASIYLHKQTQSANAKSLVAIMALQTVQGDTLQVSAAGEDAEAAIKALVALLAEGCGEAVVNVAEPVATQSSATLLRGVCASPGSAFGQVVQVTDPELVITEQGTGGATERAALTRGLLAANEALQVLQDKAAGSAQAEIFRAHQELLEDPTLLEHAHRLLGEGKSAAFAWNSATLATVTLFQGLGNALIAERAADLADVGQRVLKLILGIQDSAWDLPERAILIAEQLTPSQTASLDTRKVLGFVTVAGGATSHVAILARALGLPAICGVPAQVLALANGKQVLLDADKGELHLEPNLAEIEQLEAARKHQVLRHQRDVAQASLPATTRDGHHVEVTANVASLQEVEHALTLGGEGVGLLRSEFLYLDRNRAPSPEEQAGTYTAIARALGTERNLVVRTLDVGGDKPLAYVPMDAETNPFLGLRGIRLCLERPQLLREQFRAILASAGFARLHIMLPMVSLLSELHLARKILEEEALALGLTELPKLGIMIEVPSAALMADVFAPHVDFFSIGTNDLTQYTLAMDRDHPRLANQADSFHPAVLRLIATTVKAAHAHGKWVGVCGALASEALAVPVLIGLGVDELSVSVPLIPTIKATVRELDLADCQIIARQVLGLEEAAEVREALRQYHAATVESSPVVEH transporters Pseudomonas simiae WCS417 WCS417 GFF4501 PS417_23040 PS417_RS05355 WP_010207947.1 UPI00029ADD78 D-trehalose outer membrane porin Specific phenotype for trehalose (and conserved) maltoporin Maltoporin (maltose/maltodextrin high-affinity receptor, phage lambda receptor protein) maltoporin MKTTIKLGLVASCLGLPFGAQALEFAGYLRSGAGTSTGSGPQQCFQLPGAQTKYRLGNECEQYAELELRQDLLTLDDGSVLSVDAMASLYNKYDRALKFQGENNGSARMPQMYAQWSNLPSLNGGSLWAGRRYYKRNDIHISDFYYWNQSATGGGIEDVLIGDLKYSYAISRKDNLYQKEYATRHDFNVAGFKTNPGGELELGLSYIEKAGGRDTNSGWALTAQHVQKPFLGGKNKFALQYGEGPGTGLGYTGNTFLDKSSKSYRAVEFFDWQVTPRFGGQIEAVYQKDIRPGSQDQTWMSLGVRPAYAISEQFKLVTELGHDQVDATGGTRKLSKFTFAPTWSPKGPEFWARPEVRLYYTYATWNKAAKRAANELAAGSALSDTGSYGTARHGSNVGVQVEYWWK catabolism Pseudomonas simiae WCS417 WCS417 GFF4629 PS417_23685 PS417_RS04715 WP_010206526.1 UPI00029B3552 anthranilate 1,2-dioxygenase (deaminating, decarboxylating) large subunit [EC: 1.14.12.1] Specifically important for: L-Tryptophan. anthranilate is an intermediate in the breakdown of tryptophan (via kynurenine) (KEGG_correct) anthranilate 1,2-dioxygenase Benzoate 1,2-dioxygenase alpha subunit (EC 1.14.12.10) anthranilate 1,2-dioxygenase (deaminating, decarboxylating) large subunit MSGARSVEQWKTFIEGCLDFRPADEVFRIARDMFTEPQLFDLEMELIFEKNWIYACHESELANNHDFVTMRAGRQPMIITRDGEGQLNALINACQHRGTTLTRVGKGNQSTFTCPFHAWCYKSDGRLVKVKAPGEYPDGFDKATRGLKKARIESYKGFVFISLDVAGTDSLEDFLGDAKVFFDMMVAQSATGELEVLPGKSAYTYDGNWKLQNENGLDGYHVSTVHYNYVATVQHRQQVNTENGAGAGSTLDYSKLGAGDANTDDGWFAFNNGHSVLFSDMPNPSVRSGYATIMPRLVEEHGQQKAEWMMHRLRNLNIYPSLFFLDQISSQLRIIRPVAWNKTEIISQCLGVKGESDADRENRIRQFEDFFNVSGMGTPDDLVEFREAQRGFQGRLERWSDISRGSHRWETGPTPNSEAIGIQPAMTGTEFTHEGLYVNQHRNWQQFLLNGLDRQALTLREVK transporters Pseudomonas simiae WCS417 WCS417 GFF4712 PS417_24105 PS417_RS04300 WP_010206633.1 UPI00029B168E D-lactate transporter (lctP family) specific phenotype for D-lactate and no other transporter for D-lactate was apparent in the fitness data. Also important for utilization of D,L-lactate. Not clear if it transports L-lactate as well or not, but since it is in an apparent operon with a D-lactate dehydrogenase (PS417_24110), its main role is probably for transport of D-lactate. L-lactate permease L-lactate permease lactate transporter, LctP family MQTWQQLYSPLGSLGLSAMAAVIPIVFFFLALAVFRLKGHVAGSITLALSILVAIFAFQMPVDMALAAAGYGFAYGLWPIAWIIVAAVFLYKLTVKSGQFEIIRSSVLSITDDQRLQVLLIGFCFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGALGIPIIVAGQVTGIDAFKIGAMTGRQLPLLSLFVPFWLVFMMDGVRGVRETWPAALVAGLSFAITQYFTSNFIGPELPDITSALASLISLTLFLKVWQPKRTAGAQIAGATSSAAVTASAGGFGLPRNTIVSPYSLGQIFKAWSPFLILTVLVTIWTLKPFKAMFAAGGSMYSWVFNFAIPHLDQLVIKVAPIVTNPTAIPAVFKLDPISATGTAIFFSALISMLVLKIDIKTGLTTLKETFYELRWPILSIGMVLAFAFVTNYSGMSSTMALVLAGTGAAFPFFSPFLGWLGVFLTGSDTSSNALFSSLQATTAHQIGVNDTLLVAANTSGGVTGKMISPQSIAVACAATGLVGKESDLFRFTLKHSLFFATIVGLITLAQAYWFTGMLVH catabolism Pseudomonas simiae WCS417 WCS417 GFF5067 PS417_25960 PS417_RS02565 WP_010207013.1 UPI00029A3054 Acyl-CoA dehydrogenase (EC 1.3.8.7) Specifically important for: Sodium octanoate. presumably part of beta oxidation, but not sure why 2 different ones are required (could relate to different chain lengths) (SEED_correct) acyl-CoA dehydrogenase Acyl-CoA dehydrogenase (EC 1.3.8.7) MADYKAPLRDMRFVLNEVFEVATTWAQLPALADTVDAETVEAILEEAGKVTAKSIAPLSRGGDEQGCRWDNTAVFTPDGFPQAYATYAQGGWVGVGGDPIFGGMGMPKAVSAQVEEMINSSSLAFGLYPMLTSGACVSINTHASEALKATYLPKMYSGEWSGSMCLTEAHAGTDLGIIRTKAEPQADGSYKVSGTKIFITGGEHDLTDNIIHLVLAKLPDAPAGPKGISLFLVPKFMVNADGSLGARNTVSCGSIEHKMGIQASATCVMNFDEAVGYLVGEPNRGLAAMFTMMNYERLGVGIQGLASGERSYQNAIEYARDRLQSRAPTGAQAQDKMADPIIVHPDVRRMLLTMKAANEGGRAFSTYVATQLDIAKFSDDAAARERADNLVALLTPVAKAFLSDLGLETTVLGQQVFGGHGYIREWGQEQLVRDVRITQIYEGTNGIQALDLMGRKIVGSGGAFYTLFADEIRGFIASSGTELAEFTKPLSAAVDNLDELTAWVLDRAKTNPNEIGAASVEYLHAFGYMAYAYMWARMAKAALGKESEEDFYASKLGTARFYFARLLPRIHSLSASVKAGSESLFLLDEALF catabolism Pseudomonas simiae WCS417 WCS417 GFF5070 PS417_25975 PS417_RS02550 WP_010207016.1 UPI00029AE91F Acyl-CoA dehydrogenase (EC 1.3.8.7) Specifically important for: Sodium octanoate. presumably part of beta oxidation, but not sure why 2 different ones are required (could relate to different chain lengths) (SEED_correct) acyl-CoA dehydrogenase Acyl-CoA dehydrogenase (EC 1.3.8.7) MPDYKAPLRDIRFVRDELLGYEAHYQSLPACQDATPDMVDAILEEGAKFCEQVLAPLNRVGDIEGCTWSESGVKTPTGFKEAYKQFVEGGWPSLAHDVEHGGQGLPESLGLAVSEMVGEANWSWGMYPGLSHGAMNTISEHGTPEQQEAYLTKLVSGEWTGTMCLTEPHCGTDLGMLRTKAEPQADGTYKVSGTKIFISAGEHDMADNIVHIVLARLPDAPAGTKGISLFIVPKFLPNADGSIGARNAVTCGSLEHKMGIHGNATCVMNFDAATGFLIGPANKGLNCMFTFMNTARLGTALQGLAHAEIGFQGGLKYARDRLQMRSLTGPKAPDKAADPIIVHPDVRRMLLTMKAFAEGNRAMVYFTAKQVDIVKYGTDDEAKKQADGLLAFMTPIAKAFMTEVGFESANHGVQIYGGHGFIAEWGMEQNVRDSRISMLYEGTTGIQALDLLGRKVLMTQGEALKGFTKIVHKFCQANEGNEAVKEFVAPLAALNKEWGELTMKVGMAAMKDREEVGAASVDYLMYSGYACLAYFWADMARLAAEKLAAGTTEEAFYTAKLQTARFYFQRILPRTRTHVATMLSGANNLMDMKEEDFGLAY catabolism Pseudomonas simiae WCS417 WCS417 GFF5299 PS417_27130 PS417_RS01405 WP_010207340.1 UPI000299D157 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) Specifically important for: Putrescine Dihydrochloride. KEGG annotates this as putrescine aminotransferase, probably based on similarity to spuC (PA0299) of P. aeruginosa, but it is believed that only the g-glutamyl- pathway operates in P. aeruginosa (X. Yao et al 2011, PMC3147493) aminotransferase Omega-amino acid--pyruvate aminotransferase (EC 2.6.1.18) putrescine aminotransferase MSSNNPQTREWQALSSDHHLAPFSDFKQLKEKGPRIITKAHGVYLWDSEGNKILDGMAGLWCVAIGYGRDELADAAAKQMKELPYYNLFFQTAHPPVLELAKAISDIAPAGMNHVFFTGSGSEGNDTMLRMVRHYWAIKGQPNKKTIISRKNGYHGSTVAGASLGGMTYMHEQGDLPIPGITHIAQPYWFGEGGDMSPEEFGVWAANQLEEKILELGVDNVGAFIAEPIQGAGGVIVPPATYWPRIKEILAKYDILFIADEVICGFGRTGEWFGSDFYDLKPHMMTIAKGLTSGYIPMGGLIVRDEVVEVLNEGGDFNHGFTYSGHPVAAAVALENIRIMRDEKIVNRVHDETAPYLQKRLRELADHPLVGEVRGVGMLGAIELVQDKATRKRYEGKGVGMICRTFCFENGLIMRAVGDTMIISPPLVISKAEIDELVTKARQCLDLTLAALQG catabolism Pseudomonas simiae WCS417 WCS417 GFF5301 PS417_27140 PS417_RS01395 WP_010207341.1 UPI00029A5BC8 Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) Specifically important for: Putrescine Dihydrochloride; L-Arginine. The first step in the gamma-glutamyl-putrescine pathway gamma-glutamylputrescine synthetase glutamine synthetase family protein glutamine synthetase MSVPPRAVQLNEANAFLKDHPEVLYVDLLIADMNGVVRGKRIERTSLHKVYEKGINLPASLFALDINGSTVESTGLGLDIGDADRICYPIPDTLCNEPWQKRPTAQLLMTMHELEGEPFFADPREVLRQVVSKFDDLGLTICAAFELEFYLIDQENVNGRPQPPRSPISGKRPHSTQVYLIDDLDEYVDCLQDILEGAKEQGIPADAIVKESAPAQFEVNLHHVADPIKACDYAVLLKRLIKNIAYDHEMDTTFMAKPYPGQAGNGLHVHISILDKDGKNIFASEDPEQNAALRHAIGGVLETLPAQMAFLCPNVNSYRRFGAQFYVPNSPCWGLDNRTVAIRVPTGSSDAVRIEHRVAGADANPYLLMASVLAGVHHGLTNKIEPNAPVEGNSYEQNEQSLPNNLRDALRELDDSEVMAKYIDPKYIDIFVACKESELEEFEHSISDLEYNWYLHTV catabolism Pseudomonas simiae WCS417 WCS417 GFF5420 PS417_27745 PS417_RS00800 WP_010207491.1 UPI00029B3B75 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) Specifically important for: Putrescine Dihydrochloride. This is part of the gamma-glutamylputrescine pathway. Annotated as the 4-guanidino enzyme in KEGG (based on studies of PA5312 = kauB). Since this enzyme is closely related to kauB it is probably flexible. aldehyde dehydrogenase Aldehyde dehydrogenase (EC 1.2.1.3) 4-guanidinobutyraldehyde dehydrogenase / NAD-dependent aldehyde dehydrogenase MTTLTRADWEQRAKDLKIEGRAYINGEYTAAVSGDTFECISPVDGRLLATVASCDAADAQRAVENARATFNSGVWSRLAPAKRKSAMLRFAALLKANAEELALLETLDMGKPISDSLNIDVPGAANALSWSGEAIDKIYDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVILKPSEKSPLTAIRIAALAVEAGIPKGVFNVLPGYGHTVGNALALHMDVDTLVFTGSTKIAKQLLIRSGESNMKRVWLEAGGKSPNIVFADAPDLQAAAESAAGAIAFNQGEVCTAGSRLLVERSIKDKFLPLVIEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAGHADGAKLVAGGKRTLEETGGTYVEPTIFDGVTNAMKIAKEEIFGPVLSVITFDSAEEAVAIANDTIYGLAAAVWTADISKAHLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFDKYTELKATWIKL catabolism Pseudomonas simiae WCS417 WCS417 GFF5490 PS417_28100 PS417_RS00450 WP_010207589.1 UPI000299DEB1 glucose-6-phosphate 1-epimerase [EC: 5.1.3.15] Specifically important for: D-Trehalose dihydrate; N-Acetyl-D-Glucosamine. NAG is phosphorylated by a PTS system, deacetylated (PS417_22985), and converted to fructose-6-phosphate by an aminotranferase (PS417_22990). One might expect the fructose-6-P to be converted to fructose-1,6-bisphosphate, but no gene for that is apparent in this organism or many other Pseudomonas (nor did the fitness data highlight any kinase). Instead, the fructose-6-phosphate is apparently converted to glucose-6-phosphate by the glucose-6-phosphate isomerase (PS417_23920) and oxidized by G6P dehydrogenase (PS417_22110). (Both of these genes are essential so we cannot confirm this.) G6P dehydrogenase is reportedly specific for the beta form, while G6P isomerase produces the alpha form of G6P, so it makes sense for a glucose-6-P epimerase to be involved (even though the reaction can occur spontaneously). This gene is also mildly important for trehalose utilization, which involves the hydrolysis of trehalose 6-phosphate to glucose-6-phosphate. Because trehalose has an alpha 1->1 linkage, the product is probably alpha-G6P. Thus, this gene's phenotypes are consistent with KEGG's annotation as glucose-6-phosphate 1-epimerase. (KEGG_correct) aldose epimerase Aldose 1-epimerase glucose-6-phosphate 1-epimerase MPTPHVETVKIDELDCWRIRHNGAELIVAQQGAHLFSYGRDGEQPLIWPNPEAVFKKGKGIRTGVPVCWPWFGVFDRNPQSVKAMRQSEQPAGAHGFVRTALWELAATELEGEALRVDLVLPVPAGGFPGWPHQVDLTLSLLLDEQLHIRLTSHNRGTDTVTLSQALHTYFAVSDVRNAQVEGLDGRAYIDTADGWTEKTQSGLLHFTAETDRIYLDTPSQLTIVDKDWQRRIQLTSEGSKSTVIWNPWTERAKAFDDMADDGWTGMLCIETANVLDDVVSLAPGESHTLGVSIAAIAL catabolism Pseudomonas simiae WCS417 WCS417 GFF827 PS417_04200 PS417_RS23585 WP_010213153.1 UPI00029AA936 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) Specifically important for: D-Galacturonic Acid monohydrate. alpha-ketoglutarate semialdehyde is an intermediate in the oxidation of galacturonate (SEED_correct) aldehyde dehydrogenase 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) aldehyde dehydrogenase (NAD+) MSQAQRFDNYINGQWVAGADYCVNLNPSELSDVIGEYAKADVTQVNAAIDAARAAFPAWSTSGIQARHDALDKVGSEILARREELGTLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLRLSGDYVPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAELVPGCAWALAEIISRAGFPAGVFNLVMGSGRVVGDVLVNSPKVDGISFTGSVGVGRQIAVSCVSRQAKVQLEMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRLIVTAGIHDQFVAAMAERMKSIKVGHALKSGTDIGPVVSQAQLDQDLKYIDIGQSEGARLVSGGGLVTCDTEGYYLAPTLFADSEAAMRISREEIFGPVANVVRVADYEAALAMANDTEFGLSAGIATTSLKYANHFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEFYTVVKTSYIGS transporters Pseudomonas simiae WCS417 WCS417 GFF828 PS417_04205 PS417_RS23580 WP_010213152.1 UPI00029A5E75 D-galacturonate transporter (MFS superfamily) Specific phenotype on galacturonate. This phenotype is conserved. There is also another putative hexuronate transporter that has a weaker phenotype on galacturonate (PS417_14775). glucarate transporter D-galactarate permease MFS transporter, ACS family, glucarate transporter MQATKPTHVRYLILLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAYVAGQIPGGWLLDRFGSKKVYALSIFTWSLFTVLQGYVGEFGVSTAVVALFMLRFMVGLAEAPSFPGNARIVAAWFPTAERGTASAIFNSAQYFATVLFAPLMGWIVYSFGWQHVFIVMGVIGIIFSLIWLKVIHSPRQHPMINEAEFNHIAANGAMVDMDQDKGKGKKTDGPKWDYIRQLLTNRMMLGVYLGQYCINGITYFFLTWFPVYLVQDRGMTILKAGFIASLPAICGFIGGVLGGVISDYLLRKGHSLTFARKAPIIGGLLISSSIVACNYVDIEWMVVGFMALAFFGKGVGALGWAVVSDTSPKQIAGLSGGLFNTFGNLASITTPIVIGYIISTTGSFKWALVFVGANALVAVFSYLVIVGPIKRVVLKEPPTQGPELTRLTEAHS