GapMind for catabolism of small carbon sources

 

thymidine catabolism

Analysis of pathway thymidine in 201 genomes

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

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