GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism

Analysis of pathway deoxyribose in 150 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 deoP, deoK, deoC, adh, acs
Acidithiobacillus ferrooxidans ATCC 23270 deoP, deoK, deoC, adh, acs
Alicycliphilus denitrificans K601 deoP, deoK, deoC, adh, acs
Allochromatium vinosum DSM 180 deoP, deoK, deoC, adh, ackA, pta
Ammonifex degensii KC4 deoP, deoK, deoC, adh, acs
Archaeoglobus veneficus SNP6 deoP, deoK, deoC, adh, acs
Arcobacter nitrofigilis DSM 7299 deoP, deoK, deoC, adh, ackA, pta
Azoarcus sp. BH72 deoP, deoK, deoC, adh, acs
Azohydromonas australica DSM 1124 drdehyd-alpha, drdehyd-beta, drdehyd-cytc, deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
Azorhizobium caulinodans ORS 571 drdehyd-alpha, drdehyd-beta, drdehyd-cytc, deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, aacS, atoB
Azospirillum lipoferum B510 deoP, deoK, deoC, adh, acs
Bacillus alkalinitrilicus DSM 22532 deoP, deoK, deoC, adh, ackA, pta
Beijerinckia indica ATCC 9039 drdehyd-alpha, drdehyd-beta, drdehyd-cytc, deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
Beijerinckia mobilis UQM 1969 drdehyd-alpha, drdehyd-beta, drdehyd-cytc, deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
Bradyrhizobium sp. BTAi1 deoP, deoK, deoC, adh, acs
Burkholderia vietnamiensis G4 drdehyd-alpha, drdehyd-beta, drdehyd-cytc, deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
Calditerrivibrio nitroreducens DSM 19672 deoP, deoK, deoC, adh, ackA, pta
Caminibacter mediatlanticus TB-2 deoP, deoK, deoC, adh, acs
Chlorobaculum parvum NCIB 8327 deoP, deoK, deoC, adh, acs
Chlorobaculum tepidum TLS deoP, deoK, deoC, adh, acs
Chlorobium limicola DSM 245 deoP, deoK, deoC, adh, acs
Chlorobium phaeobacteroides BS1 deoP, deoK, deoC, adh, acs
Clostridium acetobutylicum ATCC 824 deoP, deoK, deoC, adh, ackA, pta
Clostridium kluyveri DSM 555 deoP, deoK, deoC, adh, ackA, pta
Crocosphaera subtropica ATCC 51142 deoP, deoK, deoC, adh, ackA, pta
Dechloromonas agitata is5 deoP, deoK, deoC, adh, ackA, pta
Dehalococcoides mccartyi 195 deoP, deoK, deoC, ald-dh-CoA
Denitrovibrio acetiphilus DSM 12809 deoP, deoK, deoC, adh, ackA, pta
Derxia gummosa DSM 723 drdehyd-alpha, drdehyd-beta, drdehyd-cytc, deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
Desulfacinum hydrothermale DSM 13146 deoP, deoK, deoC, ald-dh-CoA
Desulfacinum infernum DSM 9756 deoP, deoK, deoC, ald-dh-CoA
Desulfallas geothermicus DSM 3669 deoP, deoK, deoC, ald-dh-CoA
Desulfarculus baarsii DSM 2075 deoP, deoK, deoC, adh, ackA, pta
Desulfatibacillum aliphaticivorans DSM 15576 deoP, deoK, deoC, adh, acs
Desulfatiglans anilini DSM 4660 deoP, deoK, deoC, adh, acs
Desulfitobacterium hafniense DCB-2 deoP, deoK, deoC, ald-dh-CoA
Desulfobacca acetoxidans DSM 11109 deoP, deoK, deoC, ald-dh-CoA
Desulfobacter vibrioformis DSM 8776 deoP, deoK, deoC, adh, ackA, pta
Desulfobulbus mediterraneus DSM 13871 deoP, deoK, deoC, adh, ackA, pta
Desulfotalea psychrophila LSv54 deoP, deoK, deoC, adh, ackA, pta
Desulfotomaculum ruminis DSM 2154 deoP, deoK, deoC, ald-dh-CoA
Desulfovibrio bastinii DSM 16055 deoP, deoK, deoC, adh, ackA, pta
Desulfovibrio gracilis DSM 16080 deoP, deoK, deoC, adh, ackA, pta
Desulfovibrio oxyclinae DSM 11498 deoP, deoK, deoC, adh, ackA, pta
Desulfovibrio zosterae DSM 11974 deoP, deoK, deoC, ald-dh-CoA*
Desulfurobacterium atlanticum DSM 15668 deoP, deoK, deoC, adh, acs
Desulfuromonas acetexigens deoP, deoK, deoC, adh, ackA, pta
Desulfuromusa kysingii DSM 7343 deoP, deoK, deoC, adh, ackA, pta
Ferroglobus placidus DSM 10642 deoP, deoK, deoC, ald-dh-CoA
Frankia alni ACN14A deoP, deoK, deoC, adh, acs
Geobacter lovleyi SZ deoP, deoK, deoC, adh, ackA, pta
Geobacter metallireducens GS-15 deoP, deoK, deoC, adh, ackA, pta
Geobacter uraniireducens Rf4 deoP, deoK, deoC, adh, ackA, pta
Haloechinothrix alba DSM 45207 deoP, deoK, deoC, adh, acs
Haloglycomyces albus DSM 45210 deoP, deoK, deoC, adh, ackA, pta
Halomonas desiderata SP1 deoP, deoK, deoC, adh, ackA, pta
Halorhodospira halophila SL1 deoP, deoK, deoC, adh, acs
Heliobacterium modesticaldum Ice1; ATCC 51547 deoP, deoK, deoC, ald-dh-CoA
Herbaspirillum autotrophicum IAM 14942 drdehyd-alpha, drdehyd-beta, drdehyd-cytc, deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
Hydrogenophaga taeniospiralis NBRC 102512 deoP, deoK, deoC, adh, acs
Hydrogenovibrio halophilus DSM 15072 deoP, deoK, deoC, adh, ackA, pta
Hydrogenovibrio kuenenii DSM 12350 deoP, deoK, deoC, adh, ackA, pta
Hydrogenovibrio marinus DSM 11271 deoP, deoK, deoC, adh, ackA, pta
Hyphomicrobium sulfonivorans WDL6 deoP, deoK, deoC, adh, acs
Klebsiella variicola At-22 deoP, deoK, deoC, adh, ackA, pta
Kyrpidia tusciae DSM 2912 deoP, deoK, deoC, adh, acs
Leptospirillum ferrooxidans C2-3 deoP, deoK, deoC, adh, acs
Malonomonas rubra DSM 5091 deoP, deoK, deoC, adh, ackA, pta
Mesorhizobium ciceri WSM1271 drdehyd-alpha, drdehyd-beta, drdehyd-cytc, deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, aacS, atoB
Methanobacterium lacus AL-21 deoP, deoK, deoC, adh, acs
Methanococcus aeolicus Nankai-3 deoP, deoK, deoC, ald-dh-CoA
Methanococcus maripaludis C5 deoP, deoK, deoC, ald-dh-CoA
Methanosarcina acetivorans C2A deoP, deoK, deoC, adh, ackA, pta
Methanosarcina barkeri Fusaro deoP, deoK, deoC, adh, ackA, pta
Methanosarcina mazei Go1 deoP, deoK, deoC, adh, ackA, pta
Methanothermobacter thermautotrophicus Delta H deoP, deoK, deoC, ald-dh-CoA
Methylobacterium nodulans ORS 2060 drdehyd-alpha, drdehyd-beta, drdehyd-cytc, deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
Methylobacterium sp. 4-46 drdehyd-alpha, drdehyd-beta, drdehyd-cytc, deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
Methylocapsa acidiphila B2 deoP, deoK, deoC, adh, acs
Methylocapsa aurea KYG T deoP, deoK, deoC, adh, acs
Methylocella silvestris BL2 deoP, deoK, deoC, adh, acs
Methylococcus capsulatus Bath deoP, deoK, deoC, adh, acs
Methylocystis bryophila S285 deoP, deoK, deoC, adh, acs
Methyloferula stellata AR4T deoP, deoK, deoC, adh, acs
Methylohalobius crimeensis 10Ki deoP, deoK, deoC, adh, acs
Methylomicrobium alcaliphilum 20Z deoP, deoK, deoC, adh, ackA, pta
Methylomonas methanica MC09 deoP, deoK, deoC, adh, ackA, pta
Methylosarcina fibrata AML-C10 deoP, deoK, deoC, adh, acs
Methylovulum miyakonense HT12 deoP, deoK, deoC, adh, acs
Mycolicibacterium vanbaalenii PYR-1 deoP, deoK, deoC, adh, ackA, pta
Nitratifractor salsuginis DSM 16511 deoP, deoK, deoC, adh, ackA, pta
Nitratiruptor tergarcus DSM 16512 deoP, deoK, deoC, adh, acs
Nitriliruptor alkaliphilus DSM 45188 deoP, deoK, deoC, adh, acs
Nocardiopsis lucentensis DSM 44048 deoP, deoK, deoC, adh, acs
Nostoc punctiforme ATCC 29133; PCC 73102 deoP, deoK, deoC, adh, acs
Novosphingobium aromaticivorans DSM 12444 deoP, deoK, deoC, adh, acs
Oleispira antarctica deoP, deoK, deoC, ald-dh-CoA
Paraburkholderia phymatum STM815 deoP, deoK, deoC, adh, ackA, pta
Paraburkholderia sp. CCGE1002 drdehyd-alpha, drdehyd-beta, drdehyd-cytc, deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
Pelobacter propionicus DSM 2379 deoP, deoK, deoC, adh, ackA, pta
Persephonella marina EX-H1 deoP, deoK, deoC, adh, acs
Polaromonas naphthalenivorans CJ2 deoP, deoK, deoC, adh, ackA, pta
Prosthecochloris aestuarii DSM 271 deoP, deoK, deoC, adh, acs
Pseudarthrobacter sulfonivorans Ar51 deoP, deoK, deoC, adh, ackA, pta
Pseudomonas benzenivorans DSM 8628 deoP, deoK, deoC, adh, ackA, pta
Pseudomonas stutzeri A1501 deoP, deoK, deoC, adh, ackA, pta
Pyrolobus fumarii 1A deoP, deoK, deoC, ald-dh-CoA
Rhizobium etli CFN 42 deoP, deoK, deoC, adh, acs
Rhizobium leguminosarum 3841 deoP, deoK, deoC, adh, acs
Rhizobium leguminosarum WSM1325 deoP, deoK, deoC, adh, acs
Rhodobacter sphaeroides ATCC 17029 deoP, deoK, deoC, adh, acs
Rhodomicrobium vannielii ATCC 17100 deoP, deoK, deoC, adh, acs
Rhodopseudomonas palustris CGA009 deoP, deoK, deoC, adh, acs
Rhodospirillum centenum SW; ATCC 51521 deoP, deoK, deoC, adh, acs
Rhodospirillum rubrum ATCC 11170 deoP, deoK, deoC, adh, ackA, pta
Saccharomonospora cyanea NA-134 deoP, deoK, deoC, adh, acs
Sedimenticola selenatireducens DSM 17993 deoP, deoK, deoC, adh, ackA, pta
Sinorhizobium fredii NGR234 deoP, deoK, deoC, adh, acs
Sinorhizobium medicae WSM419 deoP, deoK, deoC, adh, ackA, pta
Sphingomonas wittichii RW1 drdehyd-alpha, drdehyd-beta, drdehyd-cytc, deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
Stenotrophomonas chelatiphaga DSM 21508 deoP, deoK, deoC, adh, acs
Steroidobacter denitrificans DSM 18526 deoP, deoK, deoC, adh, ackA, pta
Sulfuricurvum kujiense DSM 16994 deoP, deoK, deoC, adh, ackA, pta
Sulfurihydrogenibium azorense Az-Fu1 deoP, deoK, deoC, adh, acs
Sulfurihydrogenibium subterraneum DSM 15120 deoP, deoK, deoC, adh, acs
Sulfurimonas denitrificans DSM 1251 deoP, deoK, deoC, adh, ackA, pta
Sulfuritalea hydrogenivorans DSM 22779 deoP, deoK, deoC, adh, acs
Sulfurivirga caldicuralii DSM 17737 deoP, deoK, deoC, adh, acs
Teredinibacter turnerae T7901 deoP, deoK, deoC, adh, ackA, pta
Thauera aminoaromatica S2 deoP, deoK, deoC, ald-dh-CoA
Thermithiobacillus tepidarius DSM 3134 deoP, deoK, deoC, adh, acs
Thermocrinis albus DSM 14484 deoP, deoK, deoC, adh, acs
Thermodesulforhabdus norvegica DSM 9990 drdehyd-alpha, drdehyd-beta, drdehyd-cytc, deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, aacS, atoB
Thermomonospora curvata DSM 43183 deoP, deoK, deoC, adh, acs
Thermovibrio ammonificans HB-1 deoP, deoK, deoC, adh, acs
Thioalkalivibrio denitrificans ALJD deoP, deoK, deoC, adh, ackA, pta
Thioalkalivibrio halophilus HL17 deoP, deoK, deoC, adh, acs
Thioalkalivibrio paradoxus ARh 1 deoP, deoK, deoC, adh, acs
Thioalkalivibrio thiocyanodenitrificans ARhD 1 deoP, deoK, deoC, adh, ackA, pta
Thiohalomonas denitrificans HLD2 deoP, deoK, deoC, adh, acs
Thiomicrorhabdus arctica DSM 13458 deoP, deoK, deoC, ald-dh-CoA
Thiomicrorhabdus chilensis DSM 12352 deoP, deoK, deoC, adh, acs
Thiomicrospira cyclica ALM1 deoP, deoK, deoC, adh, acs
Thiomicrospira microaerophila ASL8-2 deoP, deoK, deoC, adh, acs
Thiomicrospira pelophila DSM 1534 deoP, deoK, deoC, adh, acs
Thiothrix lacustris DSM 21227 deoP, deoK, deoC, adh, ackA, pta
Trichodesmium erythraeum IMS101 deoP, deoK, deoC, adh, acs
Trichormus variabilis ATCC 29413 deoP, deoK, deoC, adh, acs
Xanthobacter autotrophicus Py2 drdehyd-alpha, drdehyd-beta, drdehyd-cytc, deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
Xenophilus azovorans DSM 13620 deoP, deoK, 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 Sep 24 2021. 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