D-alanine catabolism

GapMind for catabolism of small carbon sources

D-alanine catabolism

Analysis of pathway D-alanine in 150 genomes

Genome	Best path
Acidimicrobium ferrooxidans DSM 10331	cycA, dadA
Acidithiobacillus ferrooxidans ATCC 23270	cycA, dadA
Alicycliphilus denitrificans K601	cycA, dadA
Allochromatium vinosum DSM 180	cycA, dadA
Ammonifex degensii KC4	cycA, dadA
Archaeoglobus veneficus SNP6	cycA, dadA
Arcobacter nitrofigilis DSM 7299	Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Azoarcus sp. BH72	cycA, dadA
Azohydromonas australica DSM 1124	cycA, dadA
Azorhizobium caulinodans ORS 571	mctP, dadA
Azospirillum lipoferum B510	AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
Bacillus alkalinitrilicus DSM 22532	cycA, dadA
Beijerinckia indica ATCC 9039	mctP, dadA
Beijerinckia mobilis UQM 1969	mctP, dadA
Bradyrhizobium sp. BTAi1	Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Burkholderia vietnamiensis G4	cycA, dadA
Calditerrivibrio nitroreducens DSM 19672	cycA, dadA
Caminibacter mediatlanticus TB-2	cycA, dadA
Chlorobaculum parvum NCIB 8327	cycA, dadA
Chlorobaculum tepidum TLS	cycA, dadA
Chlorobium limicola DSM 245	cycA, dadA
Chlorobium phaeobacteroides BS1	cycA, dadA
Clostridium acetobutylicum ATCC 824	cycA, dadA
Clostridium kluyveri DSM 555	cycA, dadA
Crocosphaera subtropica ATCC 51142	Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Dechloromonas agitata is5	cycA, dadA
Dehalococcoides mccartyi 195	cycA, dadA
Denitrovibrio acetiphilus DSM 12809	cycA, dadA
Derxia gummosa DSM 723	AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
Desulfacinum hydrothermale DSM 13146	Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Desulfacinum infernum DSM 9756	Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Desulfallas geothermicus DSM 3669	cycA, dadA
Desulfarculus baarsii DSM 2075	cycA, dadA
Desulfatibacillum aliphaticivorans DSM 15576	AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
Desulfatiglans anilini DSM 4660	cycA, dadA
Desulfitobacterium hafniense DCB-2	cycA, dadA
Desulfobacca acetoxidans DSM 11109	cycA, dadA
Desulfobacter vibrioformis DSM 8776	cycA, dadA
Desulfobulbus mediterraneus DSM 13871	AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
Desulfotalea psychrophila LSv54	cycA, dadA
Desulfotomaculum ruminis DSM 2154	cycA, dadA
Desulfovibrio bastinii DSM 16055	Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Desulfovibrio gracilis DSM 16080	cycA, dadA
Desulfovibrio oxyclinae DSM 11498	cycA, dadA
Desulfovibrio zosterae DSM 11974	AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
Desulfurobacterium atlanticum DSM 15668	cycA, dadA
Desulfuromonas acetexigens	cycA, dadA
Desulfuromusa kysingii DSM 7343	Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Ferroglobus placidus DSM 10642	cycA, dadA
Frankia alni ACN14A	mctP, dadA
Geobacter lovleyi SZ	cycA, dadA
Geobacter metallireducens GS-15	cycA, dadA
Geobacter uraniireducens Rf4	cycA, dadA
Haloechinothrix alba DSM 45207	cycA, dadA
Haloglycomyces albus DSM 45210	cycA, dadA
Halomonas desiderata SP1	Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Halorhodospira halophila SL1	cycA, dadA
Heliobacterium modesticaldum Ice1; ATCC 51547	cycA, dadA
Herbaspirillum autotrophicum IAM 14942	AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
Hydrogenophaga taeniospiralis NBRC 102512	Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Hydrogenovibrio halophilus DSM 15072	cycA, dadA
Hydrogenovibrio kuenenii DSM 12350	cycA, dadA
Hydrogenovibrio marinus DSM 11271	cycA, dadA
Hyphomicrobium sulfonivorans WDL6	AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
Klebsiella variicola At-22	cycA, dadA
Kyrpidia tusciae DSM 2912	cycA, dadA
Leptospirillum ferrooxidans C2-3	cycA, dadA
Malonomonas rubra DSM 5091	Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Mesorhizobium ciceri WSM1271	Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Methanobacterium lacus AL-21	cycA, dadA
Methanococcus aeolicus Nankai-3	cycA, dadA
Methanococcus maripaludis C5	cycA, dadA
Methanosarcina acetivorans C2A	cycA, dadA
Methanosarcina barkeri Fusaro	cycA, dadA
Methanosarcina mazei Go1	cycA, dadA
Methanothermobacter thermautotrophicus Delta H	cycA, dadA
Methylobacterium nodulans ORS 2060	cycA, dadA
Methylobacterium sp. 4-46	AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
Methylocapsa acidiphila B2	mctP, dadA
Methylocapsa aurea KYG T	mctP, dadA
Methylocella silvestris BL2	AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
Methylococcus capsulatus Bath	cycA, dadA
Methylocystis bryophila S285	cycA, dadA
Methyloferula stellata AR4T	mctP, dadA
Methylohalobius crimeensis 10Ki	cycA, dadA
Methylomicrobium alcaliphilum 20Z	cycA, dadA
Methylomonas methanica MC09	cycA, dadA
Methylosarcina fibrata AML-C10	cycA, dadA
Methylovulum miyakonense HT12	cycA, dadA
Mycolicibacterium vanbaalenii PYR-1	cycA, dadA
Nitratifractor salsuginis DSM 16511	Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Nitratiruptor tergarcus DSM 16512	cycA, dadA
Nitriliruptor alkaliphilus DSM 45188	cycA, dadA
Nocardiopsis lucentensis DSM 44048	cycA, dadA
Nostoc punctiforme ATCC 29133; PCC 73102	cycA, dadA
Novosphingobium aromaticivorans DSM 12444	cycA, dadA
Oleispira antarctica	cycA, dadA
Paraburkholderia phymatum STM815	mctP, dadA
Paraburkholderia sp. CCGE1002	mctP, dadA
Pelobacter propionicus DSM 2379	cycA, dadA
Persephonella marina EX-H1	cycA, dadA
Polaromonas naphthalenivorans CJ2	cycA, dadA
Prosthecochloris aestuarii DSM 271	cycA, dadA
Pseudarthrobacter sulfonivorans Ar51	cycA, dadA
Pseudomonas benzenivorans DSM 8628	Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Pseudomonas stutzeri A1501	cycA, dadA
Pyrolobus fumarii 1A	cycA, dadA
Rhizobium etli CFN 42	AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
Rhizobium leguminosarum 3841	mctP, dadA
Rhizobium leguminosarum WSM1325	mctP, dadA
Rhodobacter sphaeroides ATCC 17029	Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Rhodomicrobium vannielii ATCC 17100	AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
Rhodopseudomonas palustris CGA009	Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Rhodospirillum centenum SW; ATCC 51521	AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
Rhodospirillum rubrum ATCC 11170	AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
Saccharomonospora cyanea NA-134	cycA, dadA
Sedimenticola selenatireducens DSM 17993	AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
Sinorhizobium fredii NGR234	mctP, dadA
Sinorhizobium medicae WSM419	Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Sphingomonas wittichii RW1	cycA, dadA
Stenotrophomonas chelatiphaga DSM 21508	cycA, dadA
Steroidobacter denitrificans DSM 18526	cycA, dadA
Sulfuricurvum kujiense DSM 16994	cycA, dadA
Sulfurihydrogenibium azorense Az-Fu1	cycA, dadA
Sulfurihydrogenibium subterraneum DSM 15120	cycA, dadA
Sulfurimonas denitrificans DSM 1251	cycA, dadA
Sulfuritalea hydrogenivorans DSM 22779	cycA, dadA
Sulfurivirga caldicuralii DSM 17737	cycA, dadA
Teredinibacter turnerae T7901	cycA, dadA
Thauera aminoaromatica S2	AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
Thermithiobacillus tepidarius DSM 3134	cycA, dadA
Thermocrinis albus DSM 14484	cycA, dadA
Thermodesulforhabdus norvegica DSM 9990	Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Thermomonospora curvata DSM 43183	cycA, dadA
Thermovibrio ammonificans HB-1	cycA, dadA
Thioalkalivibrio denitrificans ALJD	cycA, dadA
Thioalkalivibrio halophilus HL17	cycA, dadA
Thioalkalivibrio paradoxus ARh 1	cycA, dadA
Thioalkalivibrio thiocyanodenitrificans ARhD 1	cycA, dadA
Thiohalomonas denitrificans HLD2	cycA, dadA
Thiomicrorhabdus arctica DSM 13458	cycA, dadA
Thiomicrorhabdus chilensis DSM 12352	cycA, dadA
Thiomicrospira cyclica ALM1	cycA, dadA
Thiomicrospira microaerophila ASL8-2	cycA, dadA
Thiomicrospira pelophila DSM 1534	cycA, dadA
Thiothrix lacustris DSM 21227	Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Trichodesmium erythraeum IMS101	cycA, dadA
Trichormus variabilis ATCC 29413	cycA, dadA
Xanthobacter autotrophicus Py2	AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
Xenophilus azovorans DSM 13620	Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA

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

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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:

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