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.



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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