GapMind for catabolism of small carbon sources

 

L-serine catabolism

Analysis of pathway serine in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 snatA, sdaB
Acidithiobacillus ferrooxidans ATCC 23270 snatA, sdaB
Acidovorax sp. GW101-3H11 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Algiphilus aromaticivorans DG1253 serP, sdaB
Alicycliphilus denitrificans K601 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Alkalihalobacterium alkalinitrilicum DSM 22532 serP, sdaB
Allochromatium vinosum DSM 180 serP, sdaB
Ammonifex degensii KC4 braC, braD*, braE, braF, braG, sdaB
Anaerobutyricum hallii DSM 3353 sstT, sdaB
Aquimarina longa SW024 serP, sdaB
Archaeoglobus veneficus SNP6 snatA, sdaB
Arcobacter nitrofigilis DSM 7299 snatA, sdaB
Azoarcus olearius BH72 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Azohydromonas australica DSM 1124 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Azorhizobium caulinodans ORS 571 braC, braD, braE, braF, braG, sdaB
Azospirillum brasilense Sp245 braC, braD, braE, braF, braG, sdaB
Azospirillum sp. B510 sdaC, sdaB
Bacteroides thetaiotaomicron VPI-5482 snatA, sdaB
Beijerinckia indica ATCC 9039 snatA, sdaB
Beijerinckia mobilis UQM 1969 snatA, sdaB
Billgrantia desiderata SP1 braC, braD, braE, braF, braG, sdaB
Bradyrhizobium sp. BTAi1 braC, braD, braE, braF, braG, sdaB
Brevundimonas sp. GW460-12-10-14-LB2 serP, sdaB
Burkholderia phytofirmans PsJN Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Burkholderia vietnamiensis G4 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Calditerrivibrio nitroreducens DSM 19672 serP, sdaB
Caminibacter mediatlanticus TB-2 snatA, sdaB
Carboxydothermus pertinax Ug1 serP, sdaB
Caulobacter crescentus NA1000 snatA, sdaB
Cereibacter sphaeroides ATCC 17029 snatA, sdaB
Chlorobaculum parvum NCIB 8327 snatA, sdaB
Chlorobaculum tepidum TLS snatA, sdaB
Chlorobium limicola DSM 245 serP, sdaB
Chlorobium phaeobacteroides BS1 snatA, sdaB
Clostridium acetobutylicum ATCC 824 serP, sdhA, sdhB
Clostridium kluyveri DSM 555 serP, sdhA, sdhB
Clostridium tyrobutyricum FAM22553 serP, sdhA, sdhB
Crocosphaera subtropica ATCC 51142 braC, braD, braE, braF, braG, sdaB
Cupriavidus basilensis FW507-4G11 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Dechloromonas agitata is5 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Dechlorosoma suillum PS Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Dehalococcoides mccartyi 195 snatA, sdaB
Denitrovibrio acetiphilus DSM 12809 braC, braD, braE, braF, braG, sdaB
Derxia gummosa DSM 723 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Desulfacinum hydrothermale DSM 13146 braC, braD, braE, braF, braG, sdaB
Desulfacinum infernum DSM 9756 braC, braD, braE, braF, braG, sdaB
Desulfarculus baarsii DSM 2075 snatA, sdaB
Desulfatibacillum aliphaticivorans DSM 15576 braC, braD, braE, braF, braG, sdaB
Desulfatiglans anilini DSM 4660 braC, braD, braE, braF, braG, sdaB
Desulfitobacterium hafniense DCB-2 sstT, sdaB
Desulfobacca acetoxidans DSM 11109 braC, braD, braE, braF, braG, sdaB
Desulfobacter vibrioformis DSM 8776 serP, sdaB
Desulfogranum mediterraneum DSM 13871 braC, braD, braE, braF, braG, sdaB
Desulforamulus ruminis DSM 2154 serP, sdaB
Desulfoscipio geothermicus DSM 3669 serP, sdaB
Desulfotalea psychrophila LSv54 sstT, sdaB
Desulfovibrio oxyclinae DSM 11498 braC, braD, braE, braF, braG, sdaB
Desulfovibrio vulgaris Hildenborough JW710 braC, braD, braE, braF, braG, sdaB
Desulfovibrio vulgaris Miyazaki F braC, braD, braE, braF, braG, sdaB
Desulfurobacterium atlanticum DSM 15668 braC, braD, braE, braF, braG, sdaB
Desulfuromonas acetexigens snatA, sdaB
Desulfuromusa kysingii DSM 7343 braC, braD, braE, braF, braG, sdaB
Dinoroseobacter shibae DFL-12 snatA, sdaB
Dyella japonica UNC79MFTsu3.2 serP, sdaB
Echinicola vietnamensis KMM 6221, DSM 17526 serP, sdaB
Escherichia coli BW25113 dlsT, sdaB
Ferroglobus placidus DSM 10642 serP, sdaB
Frankia alni ACN14a Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Geobacter metallireducens GS-15 serP, sdaB
Geotalea uraniireducens Rf4 snatA, sdaB
Halococcus hamelinensis 100A6 braC, braD, braE, braF, braG, sdaB
Haloechinothrix alba DSM 45207 braC, braD, braE, braF, braG, sdaB
Haloferax volcanii DS2 serP, sdaB
Haloglycomyces albus DSM 45210 serP, sdaB
Halorhodospira halophila SL1 serP, sdaB
Heliomicrobium modesticaldum Ice1; ATCC 51547 serP, sdaB
Herbaspirillum autotrophicum IAM 14942 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Herbaspirillum seropedicae SmR1 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Hippea alviniae EP5-r sdaC, sdaB
Hydrogenophaga taeniospiralis NBRC 102512 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Hydrogenovibrio halophilus DSM 15072 serP, sdaB
Hydrogenovibrio kuenenii DSM 12350 snatA, sdaB
Hydrogenovibrio marinus DSM 11271 snatA, sdaB
Hyphomicrobium sulfonivorans WDL6 braC, braD, braE, braF, braG, sdaB
Klebsiella michiganensis M5al Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Klebsiella variicola At-22 sdaC, sdaB
Kyrpidia tusciae DSM 2912 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Leptospirillum ferrooxidans C2-3 serP, sdaB
Magnetospirillum magneticum AMB-1 braC, braD, braE, braF, braG, sdaB
Malonomonas rubra DSM 5091 braC, braD, braE, braF, braG, sdaB
Maridesulfovibrio bastinii DSM 16055 sstT, sdaB
Maridesulfovibrio zosterae DSM 11974 sstT, sdaB
Marinobacter adhaerens HP15 braC, braD, braE, braF, braG, sdaB
Mesorhizobium ciceri WSM1271 braC, braD, braE, braF, braG, sdaB
Methanobacterium lacus AL-21 serP, sdaB
Methanococcus aeolicus Nankai-3 snatA, sdaB
Methanococcus maripaludis C5 snatA, sdaB
Methanosarcina acetivorans C2A snatA, sdaB
Methanosarcina mazei Go1 snatA, sdaB
Methanospirillum lacunae Ki8-1 snatA, sdaB
Methanothermobacter thermautotrophicus Delta H serP, sdaB
Methylobacterium nodulans ORS 2060 braC, braD, braE, braF, braG, sdaB
Methylobacterium sp. 4-46 Apr-46 braC, braD, braE, braF, braG, sdaB
Methylocapsa acidiphila B2 braC, braD, braE, braF, braG, sdaB
Methylocapsa aurea KYG braC, braD, braE, braF, braG, sdaB
Methylocella silvestris BL2 braC, braD, braE, braF, braG, sdaB
Methylococcus capsulatus Bath snatA, sdaB
Methylocystis bryophila S285 serP, sdaB
Methyloferula stellata AR4T braC, braD, braE, braF, braG, sdaB
Methylohalobius crimeensis 10Ki snatA, sdaB
Methylomonas methanica MC09 snatA, sdaB
Methylosarcina fibrata AML-C10 snatA, sdaB
Methylotuvimicrobium alcaliphilum 20Z snatA, sdaB
Methylovulum miyakonense HT12 snatA, sdaB
Mycolicibacterium vanbaalenii PYR-1 braC, braD, braE, braF, braG, sdaB
Nitratifractor salsuginis DSM 16511 snatA, sdaB
Nitratiruptor tergarcus DSM 16512 snatA, sdaB
Nitriliruptor alkaliphilus DSM 45188 braC, braD, braE, braF, braG, sdaB
Nocardioides dokdonensis FR1436 braC, braD, braE, braF, braG, sdaB
Nocardiopsis lucentensis DSM 44048 braC, braD, braE, braF, braG, sdaB
Nostoc punctiforme ATCC 29133; PCC 73102 braC, braD, braE, braF, braG, sdaB
Novosphingobium aromaticivorans DSM 12444 snatA, sdaB
Oleispira antarctica serP, sdaB
Paraburkholderia atlantica CCGE1002 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Paraburkholderia bryophila 376MFSha3.1 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Paraburkholderia phymatum STM815 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Paucidesulfovibrio gracilis DSM 16080 braC, braD, braE, braF, braG, sdaB
Pedobacter sp. GW460-11-11-14-LB5 serP, sdaB
Pelobacter propionicus DSM 2379 serP, sdaB
Persephonella marina EX-H1 serP, sdaB
Phaeacidiphilus oryzae TH49 braC, braD, braE, braF, braG, sdaB
Phaeobacter inhibens BS107 snatA, sdaB
Polaromonas naphthalenivorans CJ2 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Prosthecochloris aestuarii DSM 271 serP, sdaB
Pseudarthrobacter sulfonivorans Ar51 braC, braD, braE, braF, braG, sdaB
Pseudomonas benzenivorans DSM 8628 braC, braD, braE, braF, braG, sdaB
Pseudomonas fluorescens FW300-N1B4 braC, braD, braE, braF, braG, sdaB
Pseudomonas fluorescens FW300-N2C3 braC, braD, braE, braF, braG, sdaB
Pseudomonas fluorescens FW300-N2E2 braC, braD, braE, braF, braG, sdaB
Pseudomonas fluorescens FW300-N2E3 braC, braD, braE, braF, braG, sdaB
Pseudomonas fluorescens GW456-L13 braC, braD, braE, braF, braG, sdaB
Pseudomonas putida KT2440 braC, braD, braE, braF, braG, sdaB
Pseudomonas simiae WCS417 braC, braD, braE, braF, braG, sdaB
Pseudomonas stutzeri RCH2 braC, braD, braE, braF, braG, sdaB
Pyrolobus fumarii 1A snatA, sdaB
Rhizobium etli CFN 42 braC, braD, braE, braF, braG, sdaB
Rhizobium johnstonii 3841 braC, braD, braE, braF, braG, sdaB
Rhizobium leguminosarum WSM1325 braC, braD, braE, braF, braG, sdaB
Rhizorhabdus wittichii RW1 snatA, sdaB
Rhodanobacter denitrificans FW104-10B01 serP, sdaB
Rhodomicrobium vannielii ATCC 17100 snatA, sdaB
Rhodopseudomonas palustris CGA009 braC, braD, braE, braF, braG, sdaB
Rhodospirillum centenum SW; ATCC 51521 braC, braD, braE, braF, braG, sdaB
Rhodospirillum rubrum ATCC 11170 braC, braD, braE, braF, braG, sdaB
Roseburia faecis M72 serP, sdaB
Saccharomonospora cyanea NA-134 serP, sdaB
Sedimenticola selenatireducens DSM 17993 braC, braD, braE, braF, braG, sdaB
Shewanella amazonensis SB2B sdaC, sdaB
Shewanella loihica PV-4 sdaC, sdaB
Shewanella oneidensis MR-1 sdaC, sdaB
Shewanella sp. ANA-3 dlsT, sdaB
Sinorhizobium fredii NGR234 braC, braD, braE, braF, braG, sdaB
Sinorhizobium medicae WSM419 braC, braD, braE, braF, braG, sdaB
Sinorhizobium meliloti 1021 braC, braD, braE, braF, braG, sdaB
Sphingomonas koreensis DSMZ 15582 snatA, sdaB
Stenotrophomonas chelatiphaga DSM 21508 serP, sdaB
Steroidobacter denitrificans DSM 18526 snatA, sdaB
Stutzerimonas stutzeri A1501 braC, braD, braE, braF, braG, sdaB
Sulfuricurvum kujiense DSM 16994 serP, sdaB
Sulfurihydrogenibium azorense Az-Fu1 snatA, sdaB
Sulfurihydrogenibium subterraneum DSM 15120 snatA, sdaB
Sulfurimonas denitrificans DSM 1251 serP, sdaB
Sulfuritalea hydrogenivorans DSM 22779 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Sulfurivirga caldicuralii DSM 17737 serP, sdaB
Synechococcus elongatus PCC 7942 braC, braD, braE, braF, braG, sdaB
Teredinibacter turnerae T7901 snatA, sdaB
Thauera aminoaromatica S2 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Thermithiobacillus tepidarius DSM 3134 snatA, sdaB
Thermocrinis albus DSM 14484 serP, sdaB
Thermodesulforhabdus norvegica DSM 9990 snatA, sdaB
Thermomonospora curvata DSM 43183 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Thermovibrio ammonificans HB-1 serP, sdaB
Thermus aquaticus YT-1 snatA, sdaB
Thioalkalivibrio denitrificans ALJD snatA, sdaB
Thioalkalivibrio halophilus HL17 snatA, sdaB
Thioalkalivibrio paradoxus ARh 1 snatA, sdaB
Thioalkalivibrio thiocyanodenitrificans ARhD 1 snatA, sdaB
Thiohalomonas denitrificans HLD2 snatA, sdaB
Thiohalospira halophila HL 3 serP, sdaB
Thiomicrorhabdus arctica DSM 13458 snatA, sdaB
Thiomicrorhabdus chilensis DSM 12352 snatA, sdaB
Thiomicrospira cyclica ALM1 serP, sdaB
Thiomicrospira microaerophila ASL8-2 serP, sdaB
Thiomicrospira pelophila DSM 1534 serP, sdaB
Thiothrix lacustris DSM 21227 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
Tistlia consotensis USBA 355 braC, braD, braE, braF, braG, sdaB
Trichlorobacter lovleyi SZ serP, sdaB
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome serP, sdaB
Trichormus variabilis ATCC 29413 braC, braD, braE, braF, braG, sdaB
Xanthobacter autotrophicus Py2 braC, braD, braE, braF, braG, sdaB
Xenophilus azovorans DSM 13620 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB

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