L-glutamate catabolism

GapMind for catabolism of small carbon sources

L-glutamate catabolism

Analysis of pathway glutamate in 150 genomes

Genome	Best path
Acidimicrobium ferrooxidans DSM 10331	yveA, gdhA
Acidithiobacillus ferrooxidans ATCC 23270	yveA, aspA
Alicycliphilus denitrificans K601	gltI, gltJ, gltK, gltL, aspA
Allochromatium vinosum DSM 180	gltP, gdhA
Ammonifex degensii KC4	gltP, aspA
Archaeoglobus veneficus SNP6	gltS, gdhA
Arcobacter nitrofigilis DSM 7299	gltP, aspA
Azoarcus sp. 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 lipoferum B510	braC, braD, braE, braF, braG, gdhA
Bacillus alkalinitrilicus DSM 22532	dmeA, gdhA
Beijerinckia indica ATCC 9039	aapJ, aapQ, aapM, aapP, gdhA
Beijerinckia mobilis UQM 1969	aapJ, aapQ, aapM, aapP, aspA
Bradyrhizobium sp. BTAi1	braC, braD, braE, braF, braG, gdhA
Burkholderia vietnamiensis G4	gltI, gltJ, gltK, gltL, gdhA
Calditerrivibrio nitroreducens DSM 19672	gltS, gdhA
Caminibacter mediatlanticus TB-2	gltS, 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
Crocosphaera subtropica ATCC 51142	gltS, gdhA
Dechloromonas agitata is5	dmeA, gdhA
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
Desulfallas geothermicus DSM 3669	gltL, glnP, aspA
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
Desulfobulbus mediterraneus DSM 13871	dmeA, aspA
Desulfotalea psychrophila LSv54	gltP, aspA
Desulfotomaculum ruminis DSM 2154	gltP, gdhA
Desulfovibrio bastinii DSM 16055	aapJ, aapQ, aapM, aapP, aspA
Desulfovibrio gracilis DSM 16080	dmeA, gdhA
Desulfovibrio oxyclinae DSM 11498	dmeA, aspA
Desulfovibrio zosterae DSM 11974	aapJ, aapQ, aapM, aapP, aspA
Desulfurobacterium atlanticum DSM 15668	gltS, aspA
Desulfuromonas acetexigens	gltS, gdhA
Desulfuromusa kysingii DSM 7343	dmeA, aspA
Ferroglobus placidus DSM 10642	gltS, gdhA
Frankia alni ACN14A	yveA, gdhA
Geobacter lovleyi SZ	gltS, gdhA
Geobacter metallireducens GS-15	gltS, aspA
Geobacter uraniireducens Rf4	gltP, aspA
Haloechinothrix alba DSM 45207	gltL, gluB, gluC, gluD, gdhA
Haloglycomyces albus DSM 45210	gltP, gdhA
Halomonas desiderata SP1	gltS_Syn, gdhA
Halorhodospira halophila SL1	gltS_Syn, gdhA
Heliobacterium modesticaldum Ice1; ATCC 51547	gltS, gdhA
Herbaspirillum autotrophicum IAM 14942	gltI, gltJ, gltK, gltL, 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 variicola At-22	gltI, gltJ, gltK, gltL, gdhA
Kyrpidia tusciae DSM 2912	dmeA, gdhA
Leptospirillum ferrooxidans C2-3	gltS, aspA
Malonomonas rubra DSM 5091	aapJ, aapQ, aapM, aapP, 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 barkeri Fusaro	gltS, gdhA
Methanosarcina mazei Go1	gltP, gdhA
Methanothermobacter thermautotrophicus Delta H	gltS, gdhA
Methylobacterium nodulans ORS 2060	braC, braD, braE, braF, braG, gdhA
Methylobacterium sp. 4-46	braC, braD, braE, braF, braG, gdhA
Methylocapsa acidiphila B2	braC, braD, braE, braF, braG, aspA
Methylocapsa aurea KYG T	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
Methylomicrobium alcaliphilum 20Z	gltP, gdhA
Methylomonas methanica MC09	gltP, gdhA
Methylosarcina fibrata AML-C10	gltP, aspA
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
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 phymatum STM815	gltI, gltJ, gltK, gltL, gdhA
Paraburkholderia sp. CCGE1002	gltI, gltJ, gltK, gltL, gdhA
Pelobacter propionicus DSM 2379	dmeA, aspA
Persephonella marina EX-H1	gltP, gdhA
Polaromonas naphthalenivorans CJ2	gltP, gdhA
Prosthecochloris aestuarii DSM 271	gltP, gdhA
Pseudarthrobacter sulfonivorans Ar51	gltL, glnP, gdhA
Pseudomonas benzenivorans DSM 8628	gltI, gltJ, gltK, gltL, gdhA
Pseudomonas stutzeri A1501	gltS, gdhA
Pyrolobus fumarii 1A	gltS, gdhA
Rhizobium etli CFN 42	braC, braD, braE, braF, braG, gdhA
Rhizobium leguminosarum 3841	braC, braD, braE, braF, braG, gdhA
Rhizobium leguminosarum WSM1325	braC, braD, braE, braF, braG, gdhA
Rhodobacter sphaeroides ATCC 17029	bztA, bztB, bztC, gltL, 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
Saccharomonospora cyanea NA-134	gltL, gluB, gluC, gluD, gdhA
Sedimenticola selenatireducens DSM 17993	braC, braD, braE, braF, braG, gdhA
Sinorhizobium fredii NGR234	braC, braD, braE, braF, braG, gdhA
Sinorhizobium medicae WSM419	braC, braD, braE, braF, braG, gdhA
Sphingomonas wittichii RW1	gltP, gdhA
Stenotrophomonas chelatiphaga DSM 21508	gltP, gdhA
Steroidobacter denitrificans DSM 18526	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
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
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
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
Trichodesmium erythraeum IMS101	gltS, gdhA
Trichormus variabilis ATCC 29413	gtrA, gtrB, gtrC, gdhA
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 Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources