GapMind for catabolism of small carbon sources

 

L-glutamate catabolism

Analysis of pathway glutamate in 276 genomes

Genome Best path
Acidovorax caeni R-24608 gltI, gltJ, gltK, gltL, gdhA
Actinokineospora bangkokensis 44EHW gltL, gluB, gluC, gluD, gdhA
Actinomyces timonensis 7400942 gltL, glnP, aspA
Algiphilus aromaticivorans DG1253 gltP, gdhA
Algoriphagus aquaeductus T4 gltP, gdhA
Algoriphagus machipongonensis PR1 gltP, gdhA
Alicyclobacillus ferrooxydans TC-34 gltP, gdhA
Alishewanella agri BL06 gltP, gdhA
Alistipes indistinctus YIT 12060 gltS, gdhA
Alistipes shahii WAL 8301 gltS, gdhA
Alkalitalea saponilacus SC/BZ-SP2 gltS, gdhA
Amantichitinum ursilacus IGB-41 gltI, gltJ, gltK, gltL, gdhA
Amphibacillus jilinensis Y1 gltS_Syn, gdhA
Amphritea japonica JAMM 1866 aapJ, aapQ, aapM, aapP, gdhA
Amycolatopsis halophila YIM 93223 gltL, gluB, gluC, gluD, gdhA
Amycolatopsis xylanica CPCC 202699 gltL, gluB, gluC, gluD, gdhA
Aquimarina agarilytica ZC1 gltP, aspA
Aquimarina longa SW024 gltP, gdhA
Aquimarina macrocephali JAMB N27 gltP, aspA
Archaeoglobus sulfaticallidus PM70-1 gltS, gdhA
Arcticibacter svalbardensis MN12-7 gltS, gdhA
Ardenticatena maritima 110S dmeA, gdhA
Arenimonas metalli CF5-1 gltP, gdhA
Arenitalea lutea P7-3-5 gltP, gdhA
Azospirillum humicireducens SgZ-5 braC, braD, braE, braF, braG, gdhA
Azospirillum thiophilum BV-S braC, braD, braE, braF, braG, gdhA
Bacillus altitudinis 41KF2b gltP, gdhA
Bacillus coahuilensis m4-4 gltS, gdhA
Bacillus cytotoxicus NVH 391-98 gltP, gdhA
Bacillus horneckiae 1P01SC gltS, gdhA
Bacillus okhensis Kh10-101 gltP, gdhA
Bacillus safensis FO-36b gltP, gdhA
Bacillus velezensis CBMB205 gltP, gdhA
Bacteroides clarus YIT 12056 gltS, gdhA
Bacteroides faecis MAJ27 gltS, gdhA
Bacteroides fluxus YIT 12057 gltS, gdhA
Bacteroides oleiciplenus YIT 12058 gltP, gdhA
Barnesiella intestinihominis YIT 11860 gltS, gdhA
Belnapia rosea CPCC 100156 gltP, gdhA
Bizionia argentinensis JUB59 gltP, gdhA
Bradyrhizobium diazoefficiens USDA110 gltI, gltJ, gltK, gltL, gdhA
Brevibacterium jeotgali SJ5-8 gltL, gluB, gluC, gluD, gdhA
Brucella inopinata BO1 braC, braD, braE, braF, braG, gdhA
Brucella microti CCM 4915 braC, braD, braE, braF, braG, gdhA
Bryobacter aggregatus MPL3 gltP, gdhA
Caldicellulosiruptor hydrothermalis 108 gltS, aspA
Caldicellulosiruptor kronotskyensis 2002 gltS, aspA
Carboxydothermus pertinax Ug1 gltP, glmS, glmE, mal, fumD*, mcl
Catellicoccus marimammalium M35/04/3 acaP, gdhA
Chromobacterium vaccinii MWU205 gltI, gltJ, gltK, gltL, gdhA
Chryseobacterium angstadtii KM gltP, gdhA
Chryseobacterium arthrosphaerae CC-VM-7 gltP, gdhA
Chryseobacterium viscerum 687B-08 gltP, gdhA
Cloacibacillus porcorum CL-84 gltS, gdhA
Cobetia crustatorum JO1 gltS, gdhA
Collimonas arenae Ter10 gltI, gltJ, gltK, gltL, gdhA
Collimonas pratensis Ter91 gltI, gltJ, gltK, gltL, gdhA
Collinsella tanakaei YIT 12063 peb1A, peb1B, gltL, gdhA
Coprobacter fastidiosus NSB1 gltS, gdhA
Corynebacterium deserti GIMN1.010 gltL, gluB, gluC, gluD, aspA
Corynebacterium frankenforstense ST18 gltP, aspA
Corynebacterium lactis RW2-5 gltP, aspA
Croceitalea dokdonensis DOKDO 023 gltP, gdhA
Cronobacter condimenti 1330 gltI, gltJ, gltK, gltL, aspA
Cronobacter muytjensii ATCC 51329 gltI, gltJ, gltK, gltL, aspA
Cronobacter universalis NCTC 9529 gltI, gltJ, gltK, gltL, aspA
Desulfatitalea tepidiphila S28bF dmeA, gdhA
Desulfotomaculum hydrothermale Lam5 gltP, aspA
Dethiosulfovibrio salsuginis USBA 82 gltS, gdhA
Devosia chinhatensis IPL18 aapJ, aapQ, aapM, aapP, gdhA
Devriesea agamarum IMP2 gltP, aspA
Dialister succinatiphilus YIT 11850 gltP, aspA
Dietzia timorensis ID05-A0528 gltL, gluB, gluC, gluD, aspA
Dokdonella koreensis DS-123 gltP, gdhA
Domibacillus robiginosus WS 4628 gltP, gdhA
Duganella sacchari Sac-22 gltP, gdhA
Dyadobacter tibetensis Y620-1 gltP, gdhA
Dyella jiangningensis SBZ3-12 gltP, gdhA
Endozoicomonas montiporae CL-33 gltP, gdhA
Enterococcus termitis LMG 8895 peb1A, peb1B, gltL, gdhA
Enterorhabdus caecimuris B7 gltP, gdhA
Epibacterium ulvae U95 bztA, bztB, bztC, gltL, gdhA
Erythrobacter gangjinensis K7-2 gltP, gdhA
Erythrobacter marinus HWDM-33 gltP, gdhA
Ethanoligenens harbinense YUAN-3 gltS, aspA
Fervidicella metallireducens AeB gltS, gdhA
Fibrella aestuarina BUZ 2 gltS, gdhA
Flammeovirga pacifica WPAGA1 gltP, gdhA
Flaviramulus ichthyoenteri Th78 gltP, gdhA
Flavobacterium beibuense F44-8 gltP, gdhA
Flavobacterium glycines Gm-149 gltP, gdhA
Flavobacterium sp. LM5 gltP, gdhA
Flavobacterium ummariense DS-12 gltP, aspA
Frischella perrara PEB0191 gltI, gltJ, gltK, gltL, gdhA
Galbibacter marinus ck-I2-15 gltP, gdhA
Gallaecimonas xiamenensis 3-C-1 gltP, gdhA
Geobacter daltonii FRC-32 gltP, aspA
Gillisia marina CBA3202 gltP, gdhA
Gracilibacillus halophilus YIM-C55.5 gltS, gdhA
Granulicella mallensis MP5ACTX8 gltP, gdhA
Granulicella tundricola MP5ACTX9 gltP, gdhA
Hafnia paralvei ATCC 29927 gltI, gltJ, gltK, gltL, aspA
Haladaptatus cibarius D43 gltP, gdhA
Halioglobus japonicus S1-36 gltS, gdhA
Halobacillus alkaliphilus FP5 gltP, gdhA
Halococcus hamelinensis 100A6 gltP, gdhA
Halomonas salina B6 gltP, gdhA
Halomonas smyrnensis AAD6 gltP, gdhA
Halomonas stevensii S18214 gltS_Syn, gdhA
Halomonas titanicae BH1 gltP, gdhA
Halomonas xinjiangensis TRM 0175 aapJ, aapQ, aapM, aapP, gdhA
Halopiger salifodinae KCY07-B2 gltP, gdhA
Halostagnicola larsenii XH-48 gltP, gdhA
Haloterrigena daqingensis JX313 gltS, gdhA
Herbaspirillum aquaticum IEH 4430 gltI, gltJ, gltK, gltL, gdhA
Hippea alviniae EP5-r gltS, gdhA
Hippea jasoniae Mar08-272r gltS, gdhA
Hoeflea phototrophica DFL-43 aapJ, aapQ, aapM, aapP, gdhA
Hyphomicrobium nitrativorans NL23 braC, braD, braE, braF, braG, gdhA
Imtechella halotolerans K1 gltP, gdhA
Indibacter alkaliphilus LW1 gltP, gdhA
Jannaschia aquimarina GSW-M26 bztA, bztB, bztC, gltL, gdhA
Jeotgalibacillus soli P9 gltP, gdhA
Kangiella geojedonensis YCS-5 gltP, gdhA
Knoellia flava TL1 gltL, gluB, gluC, gluD, gdhA
Kocuria flava HO-9041 gltL, gluB, gluC, gluD, gdhA
Kocuria turfanensis HO-9042 gltL, gluB, gluC, gluD, gdhA
Laceyella sediminis RHA1 gltP, gdhA
Lacinutrix algicola AKS293 gltP, gdhA
Lacinutrix himadriensis E4-9a gltP, gdhA
Lacinutrix mariniflava AKS432 gltP, gdhA
Lactobacillus curieae CCTCC M 2011381 gltL, glnP, gdhA
Lactobacillus delbrueckii ZN7a-9 acaP, aspA
Lactobacillus hokkaidonensis LOOC260 gltP, gdhA
Lactobacillus oryzae SG293 gltP, gdhA
Lactobacillus pobuzihii E100301 acaP, gdhA
Lactobacillus shenzhenensis LY-73 acaP, gdhA
Lactobacillus silagei IWT126 gltP, gdhA
Leeuwenhoekiella blandensis MED217 gltP, gdhA
Lentibacillus jeotgali Grbi gltP, gdhA
Limnohabitans curvus MWH-C5 gltI, gltJ, gltK, gltL, aspA
Limnohabitans parvus II-B4 aapJ, aapQ, aapM, aapP, gdhA
Listeria fleischmannii LU2006-1 gltL, glnP, aspA
Luteimonas huabeiensis HB2 gltS, gdhA
Luteipulveratus mongoliensis MN07-A0370 gltL, gluB, gluC, gluD, gdhA
Lutibaculum baratangense AMV1 aapJ, aapQ, aapM, aapP, gdhA
Lysobacter daejeonensis GH1-9 gltP, gdhA
Magnetovibrio blakemorei MV-1 aapJ, aapQ, aapM, aapP, gdhA
Marinicella litoralis KMM 3900 gltP, aspA
Mariniradius saccharolyticus AK6 gltP, gdhA
Marinobacter algicola DG893 gltP, gdhA
Marinobacter guineae M3B gltP, gdhA
Marinobacter psychrophilus 20041 gltP, gdhA
Marinomonas arctica 328 gltP, gdhA
Marivita geojedonensis DPG-138 bztA, bztB, bztC, gltL, gdhA
Martelella endophytica YC6887 aapJ, aapQ, aapM, aapP, gdhA
Megamonas funiformis YIT 11815 gltP, aspA
Mesorhizobium ciceri WSM1271 aapJ, aapQ, aapM, aapP, gdhA
Methanobacterium arcticum M2 gltS, aspA
Methanobacterium veterum MK4 gltS, aspA
Methanocella arvoryzae MRE50 gltS, gdhA
Methanococcus aeolicus Nankai-3 gltS, gdhA
Methanoculleus horonobensis T10 gltS, gdhA
Methanolinea tarda NOBI-1 gltS, gdhA
Methanosarcina soligelidi SMA-21 gltP, gdhA
Methanospirillum lacunae Ki8-1 gltS, gdhA
Methanospirillum stamsii Pt1 gltS, gdhA
Methylibium petroleiphilum PM1 gltI, gltJ, gltK, gltL, gdhA
Methylobacterium gossipiicola Gh-105 braC, braD, braE, braF, braG, gdhA
Methylocapsa aurea KYG braC, braD, braE, braF, braG, aspA
Methylotenera versatilis 301 gltP, gdhA
Microbacterium profundi Shh49 gltL, gluB, gluC, gluD, aspA
Microvirga lotononidis WSM3557 braC, braD, braE, braF, braG, gdhA
Moritella dasanensis ArB 0140 gltS, gdhA
Mucilaginibacter gossypii Gh-67 gltP, gdhA
Mucilaginibacter gossypiicola Gh-48 gltP, gdhA
Mucilaginibacter mallensis MP1X4 gltP, gdhA
Nafulsella turpanensis ZLM-10 gltP, gdhA
Natronomonas moolapensis 8.8.11 dmeA, gdhA
Nautilia profundicola AmH gltS, gdhA
Neiella marina J221 gltS, gdhA
Neptunomonas antarctica S3-22 aapJ, aapQ, aapM, aapP, aspA
Nocardioides daejeonensis MJ31 gltP, gdhA
Nocardioides dokdonensis FR1436 gltP, gdhA
Nocardiopsis baichengensis YIM 90130 gltP, gdhA
Nocardiopsis gilva YIM 90087 gltL, gluB, gluC, gluD, gdhA
Novosphingobium barchaimii LL02 gltP, gdhA
Novosphingobium fuchskuhlense FNE08-7 gltP, gdhA
Novosphingobium lindaniclasticum LE124 gltP, aspA
Oceanisphaera arctica V1-41 gltS, gdhA
Ochrobactrum rhizosphaerae PR17 braC, braD, braE, braF, braG, gdhA
Ochrobactrum thiophenivorans DSM 7216 braC, braD, braE, braF, braG, gdhA
Oscillibacter ruminantium GH1 gltS, gdhA
Paenisporosarcina indica PN2 gltP, gdhA
Palaeococcus pacificus DY20341 gltP, gdhA
Paludibacter propionicigenes WB4 gltS, gdhA
Pandoraea thiooxydans ATSB16 gltP, gdhA
Pantoea rwandensis LMG 26275 gltI, gltJ, gltK, gltL, gdhA
Pedobacter arcticus A12 gltS, gdhA
Photobacterium gaetbulicola Gung47 gltS, gdhA
Photobacterium jeanii R-40508 gltS, gdhA
Phyllobacterium brassicacearum STM 196 braC, braD, braE, braF, braG, gdhA
Phyllobacterium endophyticum PEPV15 braC, braD, braE, braF, braG, gdhA
Phyllobacterium leguminum ORS 1419 braC, braD, braE, braF, braG, gdhA
Planktomarina temperata RCA23 bztA, bztB, bztC, gltL, gdhA
Planococcus halocryophilus Or1 gltP, gdhA
Pleomorphomonas diazotrophica R5-392 braC, braD, braE, braF, braG, gdhA
Polaribacter dokdonensis DSW-5 gltP, gdhA
Pontibacillus litoralis JSM 072002 gltP, gdhA
Pontibacter lucknowensis DM9 gltP, gdhA
Pontibacter ramchanderi LP43 gltP, gdhA
Pontimonas salivibrio CL-TW6 gltS, aspA
Porphyrobacter dokdonensis DSW-74 gltP, gdhA
Pseudoalteromonas arctica A 37-1-2 gltP, gdhA
Pseudomonas baetica a390 gltI, gltJ, gltK, gltL, gdhA
Pseudomonas litoralis 2SM5 gltP, gdhA
Pseudomonas taeanensis MS-3 gltP, gdhA
Pseudovibrio axinellae Ad2 gltS, gdhA
Psychrobacter arcticus 273-4 gltI, gltJ, gltK, gltL, gdhA
Psychrobacter cryohalolentis K5 gltI, gltJ, gltK, gltL, gdhA
Psychromonas ingrahamii 37 gltP, gdhA
Psychromonas ossibalaenae JAMM 0738 gltS, gdhA
Rhizobium freirei PRF 81 braC, braD, braE, braF, braG, gdhA
Rhizobium grahamii CCGE 502 braC, braD, braE, braF, braG, gdhA
Rhizobium subbaraonis JC85 braC, braD, braE, braF, braG, gdhA
Rhodanobacter denitrificans 2APBS1 gltP, gdhA
Rhodobacter johrii JA192 bztA, bztB, bztC, gltL, gdhA
Rhodobacter maris JA276 bztA, bztB, bztC, gltL, aspA
Rhodobacter ovatus JA234 bztA, bztB, bztC, gltL, gdhA
Rhodobacter viridis JA737 bztA, bztB, bztC, gltL, aspA
Rhodococcus qingshengii djl-6-2 gltL, gluB, gluC, gluD, gdhA
Rhodopseudomonas pseudopalustris DSM 123 braC, braD, braE, braF, braG, aspA
Roseateles aquatilis CCUG 48205 gltI, gltJ, gltK, gltL, gdhA
Roseivirga spongicola UST030701-084 gltS, gdhA
Rubrivirga marina SAORIC-28 gltP, gdhA
Ruegeria conchae TW15 bztA, bztB, bztC, gltL, gdhA
Saccharomonospora marina XMU15 gltL, gluB, gluC, gluD, gdhA
Salinicoccus carnicancri Crm gltP, gdhA
Serinicoccus profundi MCCC 1A05965 gltL, gluB, gluC, gluD, gdhA
Shewanella halifaxensis HAW-EB4 gltS, gdhA
Skermanella stibiiresistens SB22 gltS, gdhA
Snodgrassella alvi wkB2 gltP, aspA
Sphaerochaeta globosa Buddy peb1A, peb1B, gltL, gdhA
Sphaerochaeta pleomorpha Grapes peb1A, peb1B, gltL, gdhA
Sphingobium baderi LL03 gltP, gdhA
Sphingobium czechense LL01 gltP, gdhA
Sphingobium quisquiliarum P25 gltP, gdhA
Sphingomonas histidinilytica UM2 gltP, gdhA
Sphingomonas indica Dd16 gltP, gdhA
Sphingomonas laterariae LNB2 gltS, gdhA
Sphingopyxis indica DS15 gltP, gdhA
Sphingopyxis terrae UI2 gltP, gdhA
Sporolactobacillus vineae SL153 yveA, aspA
Streptacidiphilus oryzae TH49 yveA, gdhA
Streptococcus anginosus CCUG 39159 gltL, glnP, gdhA
Streptococcus massiliensis 4401825 gltL, glnP, gdhA
Streptococcus oralis 7747 peb1A, peb1B, gltL, gdhA
Streptococcus oralis AZ_3a peb1A, peb1B, gltL, gdhA
Streptomyces kebangsaanensis SUK12 gltL, gluB, gluC, gluD, gdhA
Succinatimonas hippei YIT 12066 gltS, gdhA
Sulfurimonas gotlandica GD1 gltS, gdhA
Tatumella morbirosei LMG 23360 gltI, gltJ, gltK, gltL, aspA
Thauera humireducens SgZ-1 gltS, gdhA
Thermoactinomyces daqus H-18 gltP, gdhA
Thermobifida halotolerans YIM 90462 gltL, gluB, gluC, gluD, gdhA
Thermodesulfovibrio aggregans TGE-P1 gltS, gdhA
Thermophagus xiamenensis HS1 gltS, gdhA
Thermovenabulum gondwanense R270 gltP, gdhA
Thioclava dalianensis DLFJ1-1 bztA, bztB, bztC, gltL, aspA
Thiohalospira halophila HL 3 gltP, gdhA
Tistlia consotensis USBA 355 aapJ, aapQ, aapM, aapP, gdhA
Vagococcus penaei CD276 acaP, gdhA
Verminephrobacter eiseniae EF01-2 gltI, gltJ, gltK, gltL, gdhA
Weissella oryzae SG25 gltL, glnP, gdhA
Williamsia sterculiae CPCC 203464 gltL, gluB, gluC, gluD, gdhA
Yersinia intermedia Y228 gltI, gltJ, gltK, gltL, aspA

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory