D-serine catabolism

GapMind for catabolism of small carbon sources

D-serine catabolism

Analysis of pathway D-serine in 201 genomes

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

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.

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