L-alanine catabolism

GapMind for catabolism of small carbon sources

L-alanine catabolism

Analysis of pathway alanine in 150 genomes

Genome	Best path
Acidimicrobium ferrooxidans DSM 10331	snatA
Acidithiobacillus ferrooxidans ATCC 23270	snatA
Alicycliphilus denitrificans K601	cycA
Allochromatium vinosum DSM 180	alsT
Ammonifex degensii KC4	braC, braD *, braE, braF, braG
Archaeoglobus veneficus SNP6	snatA
Arcobacter nitrofigilis DSM 7299	alsT
Azoarcus sp. BH72	TRIC
Azohydromonas australica DSM 1124	alsT
Azorhizobium caulinodans ORS 571	braC, braD, braE, braF, braG
Azospirillum lipoferum B510	braC, braD, braE, braF, braG
Bacillus alkalinitrilicus DSM 22532	alsT
Beijerinckia indica ATCC 9039	snatA
Beijerinckia mobilis UQM 1969	snatA
Bradyrhizobium sp. BTAi1	braC, braD, braE, braF, braG
Burkholderia vietnamiensis G4	cycA
Calditerrivibrio nitroreducens DSM 19672	alsT
Caminibacter mediatlanticus TB-2	snatA
Chlorobaculum parvum NCIB 8327	snatA
Chlorobaculum tepidum TLS	alsT
Chlorobium limicola DSM 245	alsT
Chlorobium phaeobacteroides BS1	alsT
Clostridium acetobutylicum ATCC 824	cycA
Clostridium kluyveri DSM 555	cycA
Crocosphaera subtropica ATCC 51142	braC, braD, braE, braF, braG
Dechloromonas agitata is5	TRIC
Dehalococcoides mccartyi 195	snatA
Denitrovibrio acetiphilus DSM 12809	braC, braD, braE, braF, braG
Derxia gummosa DSM 723	braC, braD, braE, braF, braG
Desulfacinum hydrothermale DSM 13146	alsT
Desulfacinum infernum DSM 9756	alsT
Desulfallas geothermicus DSM 3669	cycA
Desulfarculus baarsii DSM 2075	snatA
Desulfatibacillum aliphaticivorans DSM 15576	braC, braD, braE, braF, braG
Desulfatiglans anilini DSM 4660	braC, braD, braE, braF, braG
Desulfitobacterium hafniense DCB-2	alsT
Desulfobacca acetoxidans DSM 11109	braC, braD, braE, braF, braG
Desulfobacter vibrioformis DSM 8776	cycA
Desulfobulbus mediterraneus DSM 13871	alsT
Desulfotalea psychrophila LSv54	alsT
Desulfotomaculum ruminis DSM 2154	cycA
Desulfovibrio bastinii DSM 16055	alsT
Desulfovibrio gracilis DSM 16080	braC, braD, braE, braF, braG
Desulfovibrio oxyclinae DSM 11498	braC, braD, braE, braF, braG
Desulfovibrio zosterae DSM 11974	alsT
Desulfurobacterium atlanticum DSM 15668	braC, braD, braE, braF, braG
Desulfuromonas acetexigens	snatA
Desulfuromusa kysingii DSM 7343	braC, braD, braE, braF, braG
Ferroglobus placidus DSM 10642	cycA
Frankia alni ACN14A	cycA
Geobacter lovleyi SZ	cycA
Geobacter metallireducens GS-15	cycA
Geobacter uraniireducens Rf4	TRIC
Haloechinothrix alba DSM 45207	alsT
Haloglycomyces albus DSM 45210	alsT
Halomonas desiderata SP1	alsT
Halorhodospira halophila SL1	alsT
Heliobacterium modesticaldum Ice1; ATCC 51547	alsT
Herbaspirillum autotrophicum IAM 14942	braC, braD, braE, braF, braG
Hydrogenophaga taeniospiralis NBRC 102512	alsT
Hydrogenovibrio halophilus DSM 15072	alsT
Hydrogenovibrio kuenenii DSM 12350	alsT
Hydrogenovibrio marinus DSM 11271	alsT
Hyphomicrobium sulfonivorans WDL6	braC, braD, braE, braF, braG
Klebsiella variicola At-22	cycA
Kyrpidia tusciae DSM 2912	cycA
Leptospirillum ferrooxidans C2-3	cycA
Malonomonas rubra DSM 5091	braC, braD, braE, braF, braG
Mesorhizobium ciceri WSM1271	braC, braD, braE, braF, braG
Methanobacterium lacus AL-21	cycA
Methanococcus aeolicus Nankai-3	snatA
Methanococcus maripaludis C5	alsT
Methanosarcina acetivorans C2A	alsT
Methanosarcina barkeri Fusaro	alsT
Methanosarcina mazei Go1	alsT
Methanothermobacter thermautotrophicus Delta H	cycA
Methylobacterium nodulans ORS 2060	cycA
Methylobacterium sp. 4-46	braC, braD, braE, braF, braG
Methylocapsa acidiphila B2	braC, braD, braE, braF, braG
Methylocapsa aurea KYG T	braC, braD, braE, braF, braG
Methylocella silvestris BL2	braC, braD, braE, braF, braG
Methylococcus capsulatus Bath	snatA
Methylocystis bryophila S285	cycA
Methyloferula stellata AR4T	braC, braD, braE, braF, braG
Methylohalobius crimeensis 10Ki	alsT
Methylomicrobium alcaliphilum 20Z	alsT
Methylomonas methanica MC09	alsT
Methylosarcina fibrata AML-C10	alsT
Methylovulum miyakonense HT12	snatA
Mycolicibacterium vanbaalenii PYR-1	alsT
Nitratifractor salsuginis DSM 16511	snatA
Nitratiruptor tergarcus DSM 16512	snatA
Nitriliruptor alkaliphilus DSM 45188	braC, braD, braE, braF, braG
Nocardiopsis lucentensis DSM 44048	alsT
Nostoc punctiforme ATCC 29133; PCC 73102	braC, braD, braE, braF, braG
Novosphingobium aromaticivorans DSM 12444	snatA
Oleispira antarctica	alsT
Paraburkholderia phymatum STM815	braC, braD, braE, braF, braG
Paraburkholderia sp. CCGE1002	cycA
Pelobacter propionicus DSM 2379	alsT
Persephonella marina EX-H1	cycA
Polaromonas naphthalenivorans CJ2	braC, braD, braE, braF, braG
Prosthecochloris aestuarii DSM 271	alsT
Pseudarthrobacter sulfonivorans Ar51	cycA
Pseudomonas benzenivorans DSM 8628	braC, braD, braE, braF, braG
Pseudomonas stutzeri A1501	braC, braD, braE, braF, braG
Pyrolobus fumarii 1A	snatA
Rhizobium etli CFN 42	braC, braD, braE, braF, braG
Rhizobium leguminosarum 3841	braC, braD, braE, braF, braG
Rhizobium leguminosarum WSM1325	braC, braD, braE, braF, braG
Rhodobacter sphaeroides ATCC 17029	snatA
Rhodomicrobium vannielii ATCC 17100	snatA
Rhodopseudomonas palustris CGA009	braC, braD, braE, braF, braG
Rhodospirillum centenum SW; ATCC 51521	braC, braD, braE, braF, braG
Rhodospirillum rubrum ATCC 11170	braC, braD, braE, braF, braG
Saccharomonospora cyanea NA-134	alsT
Sedimenticola selenatireducens DSM 17993	braC, braD, braE, braF, braG
Sinorhizobium fredii NGR234	braC, braD, braE, braF, braG
Sinorhizobium medicae WSM419	alsT
Sphingomonas wittichii RW1	cycA
Stenotrophomonas chelatiphaga DSM 21508	alsT
Steroidobacter denitrificans DSM 18526	alsT
Sulfuricurvum kujiense DSM 16994	cycA
Sulfurihydrogenibium azorense Az-Fu1	snatA
Sulfurihydrogenibium subterraneum DSM 15120	snatA
Sulfurimonas denitrificans DSM 1251	alsT
Sulfuritalea hydrogenivorans DSM 22779	braC, braD, braE, braF, braG
Sulfurivirga caldicuralii DSM 17737	cycA
Teredinibacter turnerae T7901	alsT
Thauera aminoaromatica S2	alsT
Thermithiobacillus tepidarius DSM 3134	snatA
Thermocrinis albus DSM 14484	cycA
Thermodesulforhabdus norvegica DSM 9990	snatA
Thermomonospora curvata DSM 43183	cycA
Thermovibrio ammonificans HB-1	cycA
Thioalkalivibrio denitrificans ALJD	snatA
Thioalkalivibrio halophilus HL17	snatA
Thioalkalivibrio paradoxus ARh 1	alsT
Thioalkalivibrio thiocyanodenitrificans ARhD 1	snatA
Thiohalomonas denitrificans HLD2	alsT
Thiomicrorhabdus arctica DSM 13458	alsT
Thiomicrorhabdus chilensis DSM 12352	alsT
Thiomicrospira cyclica ALM1	TRIC
Thiomicrospira microaerophila ASL8-2	TRIC
Thiomicrospira pelophila DSM 1534	TRIC
Thiothrix lacustris DSM 21227	braC, braD, braE, braF, braG
Trichodesmium erythraeum IMS101	alsT
Trichormus variabilis ATCC 29413	braC, braD, braE, braF, braG
Xanthobacter autotrophicus Py2	braC, braD, braE, braF, braG
Xenophilus azovorans DSM 13620	snatA

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.

Downloads

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