GapMind for catabolism of small carbon sources

 

L-glutamate catabolism

Analysis of pathway glutamate in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 yveA, gdhA
Acidithiobacillus ferrooxidans ATCC 23270 yveA, aspA
Acidovorax sp. GW101-3H11 gltI, gltJ, gltK, gltL, gdhA
Algiphilus aromaticivorans DG1253 gltP, gdhA
Alicycliphilus denitrificans K601 gltI, gltJ, gltK, gltL, aspA
Alkalihalobacterium alkalinitrilicum DSM 22532 dmeA, gdhA
Allochromatium vinosum DSM 180 gltP, gdhA
Ammonifex degensii KC4 gltP, aspA
Anaerobutyricum hallii DSM 3353 gltP, aspA
Aquimarina longa SW024 gltP, gdhA
Archaeoglobus veneficus SNP6 gltS, gdhA
Arcobacter nitrofigilis DSM 7299 gltP, aspA
Azoarcus olearius BH72 gltI, gltJ, gltK, gltL, aspA
Azohydromonas australica DSM 1124 gltI, gltJ, gltK, gltL, aspA
Azorhizobium caulinodans ORS 571 braC, braD, braE, braF, braG, gdhA
Azospirillum brasilense Sp245 braC, braD, braE, braF, braG, gdhA
Azospirillum sp. B510 braC, braD, braE, braF, braG, gdhA
Bacteroides thetaiotaomicron VPI-5482 gltS, gdhA
Beijerinckia indica ATCC 9039 aapJ, aapQ, aapM, aapP, gdhA
Beijerinckia mobilis UQM 1969 aapJ, aapQ, aapM, aapP, aspA
Billgrantia desiderata SP1 gltS_Syn, gdhA
Bradyrhizobium sp. BTAi1 braC, braD, braE, braF, braG, gdhA
Brevundimonas sp. GW460-12-10-14-LB2 gltP, gdhA
Burkholderia phytofirmans PsJN gltI, gltJ, gltK, gltL, gdhA
Burkholderia vietnamiensis G4 gltI, gltJ, gltK, gltL, gdhA
Calditerrivibrio nitroreducens DSM 19672 gltS, gdhA
Caminibacter mediatlanticus TB-2 gltS, gdhA
Carboxydothermus pertinax Ug1 gltP, glmS, glmE, mal, fumD*, mcl
Caulobacter crescentus NA1000 gltP, gdhA
Cereibacter sphaeroides ATCC 17029 bztA, bztB, bztC, gltL, gdhA
Chlorobaculum parvum NCIB 8327 gltS, gdhA
Chlorobaculum tepidum TLS gltS, gdhA
Chlorobium limicola DSM 245 gltS, gdhA
Chlorobium phaeobacteroides BS1 gltS, aspA
Clostridium acetobutylicum ATCC 824 gltP, aspA
Clostridium kluyveri DSM 555 gltS, aspA
Clostridium tyrobutyricum FAM22553 gltP, aspA
Crocosphaera subtropica ATCC 51142 gltS, gdhA
Cupriavidus basilensis FW507-4G11 gltI, gltJ, gltK, gltL, gdhA
Dechloromonas agitata is5 dmeA, gdhA
Dechlorosoma suillum PS gltI, gltJ, gltK, gltL, aspA
Dehalococcoides mccartyi 195 dmeA, gdhA
Denitrovibrio acetiphilus DSM 12809 gltS, aspA
Derxia gummosa DSM 723 gltI, gltJ, gltK, gltL, aspA
Desulfacinum hydrothermale DSM 13146 aapJ, aapQ, aapM, aapP, gdhA
Desulfacinum infernum DSM 9756 aapJ, aapQ, aapM, aapP, gdhA
Desulfarculus baarsii DSM 2075 gltS, gdhA
Desulfatibacillum aliphaticivorans DSM 15576 dmeA, gdhA
Desulfatiglans anilini DSM 4660 gltS, gdhA
Desulfitobacterium hafniense DCB-2 peb1A, peb1B, gltL, aspA
Desulfobacca acetoxidans DSM 11109 gltS, gdhA
Desulfobacter vibrioformis DSM 8776 gltS, aspA
Desulfogranum mediterraneum DSM 13871 dmeA, aspA
Desulforamulus ruminis DSM 2154 gltP, gdhA
Desulfoscipio geothermicus DSM 3669 gltL, glnP, aspA
Desulfotalea psychrophila LSv54 gltP, aspA
Desulfovibrio oxyclinae DSM 11498 dmeA, aspA
Desulfovibrio vulgaris Hildenborough JW710 dmeA, aspA
Desulfovibrio vulgaris Miyazaki F dmeA, aspA
Desulfurobacterium atlanticum DSM 15668 gltS, aspA
Desulfuromonas acetexigens gltS, gdhA
Desulfuromusa kysingii DSM 7343 dmeA, aspA
Dinoroseobacter shibae DFL-12 bztA, bztB, bztC, gltL, gdhA
Dyella japonica UNC79MFTsu3.2 gltP, gdhA
Echinicola vietnamensis KMM 6221, DSM 17526 gltP, gdhA
Escherichia coli BW25113 gltI, gltJ, gltK, gltL, aspA
Ferroglobus placidus DSM 10642 gltS, gdhA
Frankia alni ACN14a yveA, gdhA
Geobacter metallireducens GS-15 gltS, aspA
Geotalea uraniireducens Rf4 gltP, aspA
Halococcus hamelinensis 100A6 gltP, gdhA
Haloechinothrix alba DSM 45207 gltL, gluB, gluC, gluD, gdhA
Haloferax volcanii DS2 gltP, gdhA
Haloglycomyces albus DSM 45210 gltP, gdhA
Halorhodospira halophila SL1 gltS_Syn, gdhA
Heliomicrobium modesticaldum Ice1; ATCC 51547 gltS, gdhA
Herbaspirillum autotrophicum IAM 14942 gltI, gltJ, gltK, gltL, gdhA
Herbaspirillum seropedicae SmR1 gltI, gltJ, gltK, gltL, gdhA
Hippea alviniae EP5-r gltS, gdhA
Hydrogenophaga taeniospiralis NBRC 102512 gltI, gltJ, gltK, gltL, gdhA
Hydrogenovibrio halophilus DSM 15072 gltP, gdhA
Hydrogenovibrio kuenenii DSM 12350 gltP, aspA
Hydrogenovibrio marinus DSM 11271 gltP, aspA
Hyphomicrobium sulfonivorans WDL6 braC, braD, braE, braF, braG, gdhA
Klebsiella michiganensis M5al gltI, gltJ, gltK, gltL, aspA
Klebsiella variicola At-22 gltI, gltJ, gltK, gltL, gdhA
Kyrpidia tusciae DSM 2912 dmeA, gdhA
Leptospirillum ferrooxidans C2-3 gltS, aspA
Magnetospirillum magneticum AMB-1 braC, braD, braE, braF, braG, gdhA
Malonomonas rubra DSM 5091 aapJ, aapQ, aapM, aapP, gdhA
Maridesulfovibrio bastinii DSM 16055 aapJ, aapQ, aapM, aapP, aspA
Maridesulfovibrio zosterae DSM 11974 aapJ, aapQ, aapM, aapP, aspA
Marinobacter adhaerens HP15 gltP, gdhA
Mesorhizobium ciceri WSM1271 aapJ, aapQ, aapM, aapP, gdhA
Methanobacterium lacus AL-21 gltS, aspA
Methanococcus aeolicus Nankai-3 gltS, gdhA
Methanococcus maripaludis C5 gltS, gdhA
Methanosarcina acetivorans C2A gltP, gdhA
Methanosarcina mazei Go1 gltP, gdhA
Methanospirillum lacunae Ki8-1 gltS, gdhA
Methanothermobacter thermautotrophicus Delta H gltS, gdhA
Methylobacterium nodulans ORS 2060 braC, braD, braE, braF, braG, gdhA
Methylobacterium sp. 4-46 Apr-46 braC, braD, braE, braF, braG, gdhA
Methylocapsa acidiphila B2 braC, braD, braE, braF, braG, aspA
Methylocapsa aurea KYG braC, braD, braE, braF, braG, aspA
Methylocella silvestris BL2 gltS, aspA
Methylococcus capsulatus Bath gltP, aspA
Methylocystis bryophila S285 gltS, aspA
Methyloferula stellata AR4T braC, braD, braE, braF, braG, gdhA
Methylohalobius crimeensis 10Ki gltP, gdhA
Methylomonas methanica MC09 gltP, gdhA
Methylosarcina fibrata AML-C10 gltP, aspA
Methylotuvimicrobium alcaliphilum 20Z gltP, gdhA
Methylovulum miyakonense HT12 gltP, aspA
Mycolicibacterium vanbaalenii PYR-1 gltL, gluB, gluC, gluD, gdhA
Nitratifractor salsuginis DSM 16511 gltP, gdhA
Nitratiruptor tergarcus DSM 16512 gltP, gdhA
Nitriliruptor alkaliphilus DSM 45188 gltS_Syn, gdhA
Nocardioides dokdonensis FR1436 gltP, gdhA
Nocardiopsis lucentensis DSM 44048 gltP, gdhA
Nostoc punctiforme ATCC 29133; PCC 73102 gltP, gdhA
Novosphingobium aromaticivorans DSM 12444 gltP, gdhA
Oleispira antarctica gltP, gdhA
Paraburkholderia atlantica CCGE1002 gltI, gltJ, gltK, gltL, gdhA
Paraburkholderia bryophila 376MFSha3.1 gltI, gltJ, gltK, gltL, gdhA
Paraburkholderia phymatum STM815 gltI, gltJ, gltK, gltL, gdhA
Paucidesulfovibrio gracilis DSM 16080 dmeA, gdhA
Pedobacter sp. GW460-11-11-14-LB5 gltP, gdhA
Pelobacter propionicus DSM 2379 dmeA, aspA
Persephonella marina EX-H1 gltP, gdhA
Phaeacidiphilus oryzae TH49 yveA, gdhA
Phaeobacter inhibens BS107 bztA, bztB, bztC, gltL, gdhA
Polaromonas naphthalenivorans CJ2 gltP, gdhA
Prosthecochloris aestuarii DSM 271 gltP, gdhA
Pseudarthrobacter sulfonivorans Ar51 gltP, gdhA
Pseudomonas benzenivorans DSM 8628 gltI, gltJ, gltK, gltL, gdhA
Pseudomonas fluorescens FW300-N1B4 gltI, gltJ, gltK, gltL, gdhA
Pseudomonas fluorescens FW300-N2C3 gltI, gltJ, gltK, gltL, gdhA
Pseudomonas fluorescens FW300-N2E2 gltI, gltJ, gltK, gltL, gdhA
Pseudomonas fluorescens FW300-N2E3 gltI, gltJ, gltK, gltL, gdhA
Pseudomonas fluorescens GW456-L13 gltI, gltJ, gltK, gltL, gdhA
Pseudomonas putida KT2440 gltI, gltJ, gltK, gltL, gdhA
Pseudomonas simiae WCS417 gltI, gltJ, gltK, gltL, gdhA
Pseudomonas stutzeri RCH2 gltP, gdhA
Pyrolobus fumarii 1A gltS, gdhA
Rhizobium etli CFN 42 braC, braD, braE, braF, braG, gdhA
Rhizobium johnstonii 3841 braC, braD, braE, braF, braG, gdhA
Rhizobium leguminosarum WSM1325 braC, braD, braE, braF, braG, gdhA
Rhizorhabdus wittichii RW1 gltP, gdhA
Rhodanobacter denitrificans FW104-10B01 gltP, gdhA
Rhodomicrobium vannielii ATCC 17100 gltI, gltJ, gltK, gltL, gdhA
Rhodopseudomonas palustris CGA009 gltS, aspA
Rhodospirillum centenum SW; ATCC 51521 braC, braD, braE, braF, braG, gdhA
Rhodospirillum rubrum ATCC 11170 gltI, gltJ, gltK, gltL, gdhA
Roseburia faecis M72 gltS, aspA
Saccharomonospora cyanea NA-134 gltL, gluB, gluC, gluD, gdhA
Sedimenticola selenatireducens DSM 17993 braC, braD, braE, braF, braG, gdhA
Shewanella amazonensis SB2B gltP, gdhA
Shewanella loihica PV-4 gltS, gdhA
Shewanella oneidensis MR-1 gltS, gdhA
Shewanella sp. ANA-3 gltS, gdhA
Sinorhizobium fredii NGR234 braC, braD, braE, braF, braG, gdhA
Sinorhizobium medicae WSM419 braC, braD, braE, braF, braG, gdhA
Sinorhizobium meliloti 1021 braC, braD, braE, braF, braG, gdhA
Sphingomonas koreensis DSMZ 15582 gltP, gdhA
Stenotrophomonas chelatiphaga DSM 21508 gltP, gdhA
Steroidobacter denitrificans DSM 18526 gltS, gdhA
Stutzerimonas stutzeri A1501 gltS, gdhA
Sulfuricurvum kujiense DSM 16994 gltS, gdhA
Sulfurihydrogenibium azorense Az-Fu1 gltS, gdhA
Sulfurihydrogenibium subterraneum DSM 15120 gltS, gdhA
Sulfurimonas denitrificans DSM 1251 gltP, gdhA
Sulfuritalea hydrogenivorans DSM 22779 gltI, gltJ, gltK, gltL, gdhA
Sulfurivirga caldicuralii DSM 17737 gltP, aspA
Synechococcus elongatus PCC 7942 dmeA, aspA
Teredinibacter turnerae T7901 gltP, gdhA
Thauera aminoaromatica S2 braC, braD, braE, braF, braG, gdhA
Thermithiobacillus tepidarius DSM 3134 gltP, aspA
Thermocrinis albus DSM 14484 gltS, gdhA
Thermodesulforhabdus norvegica DSM 9990 aapJ, aapQ, aapM, aapP, gdhA
Thermomonospora curvata DSM 43183 gltL, gluB, gluC, gluD, gdhA
Thermovibrio ammonificans HB-1 gltP, gdhA
Thermus aquaticus YT-1 dmeA, gdhA
Thioalkalivibrio denitrificans ALJD gltS_Syn, gdhA
Thioalkalivibrio halophilus HL17 gltS, gdhA
Thioalkalivibrio paradoxus ARh 1 gltS, gdhA
Thioalkalivibrio thiocyanodenitrificans ARhD 1 gltS, gdhA
Thiohalomonas denitrificans HLD2 gltP, gdhA
Thiohalospira halophila HL 3 gltP, gdhA
Thiomicrorhabdus arctica DSM 13458 gltP, aspA
Thiomicrorhabdus chilensis DSM 12352 gltP, gdhA
Thiomicrospira cyclica ALM1 gltP, gdhA
Thiomicrospira microaerophila ASL8-2 gltP, gdhA
Thiomicrospira pelophila DSM 1534 gltP, aspA
Thiothrix lacustris DSM 21227 gltP, aspA
Tistlia consotensis USBA 355 dmeA, gdhA
Trichlorobacter lovleyi SZ gltS, gdhA
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome gltS, gdhA
Trichormus variabilis ATCC 29413 gtrA, gtrB, gtrC, aspA
Xanthobacter autotrophicus Py2 braC, braD, braE, braF, braG, gdhA
Xenophilus azovorans DSM 13620 gltI, gltJ, gltK, gltL, gdhA

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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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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