GapMind for catabolism of small carbon sources

 

2'-deoxyinosine catabolism

Analysis of pathway deoxyinosine in 150 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 nupC, deoD, deoB, deoC, adh, acs
Acidithiobacillus ferrooxidans ATCC 23270 nupC, deoD, deoB, deoC, adh, acs
Alicycliphilus denitrificans K601 nupC, deoD, deoB, deoC, adh, acs
Allochromatium vinosum DSM 180 nupC, deoD, deoB, deoC, adh, ackA, pta
Ammonifex degensii KC4 nupC, deoD, deoB, deoC, adh, acs
Archaeoglobus veneficus SNP6 nupC, deoD, deoB, deoC, adh, acs
Arcobacter nitrofigilis DSM 7299 nupC, deoD, deoB, deoC, adh, ackA, pta
Azoarcus sp. BH72 nupC, deoD, deoB, deoC, adh, acs
Azohydromonas australica DSM 1124 nupC, deoD, deoB, deoC, adh, ackA, pta
Azorhizobium caulinodans ORS 571 nupC, deoD, deoB, deoC, adh, acs
Azospirillum lipoferum B510 H281DRAFT_01115, H281DRAFT_01114, H281DRAFT_01113, H281DRAFT_01112, deoD, deoB, deoC, adh, acs
Bacillus alkalinitrilicus DSM 22532 nupA, nupB, nupC', bmpA, deoD, deoB, deoC, adh, ackA, pta
Beijerinckia indica ATCC 9039 nupC, deoD, deoB, deoC, adh, acs
Beijerinckia mobilis UQM 1969 nupC, deoD, deoB, deoC, adh, acs
Bradyrhizobium sp. BTAi1 nupC, deoD, deoB, deoC, adh, acs
Burkholderia vietnamiensis G4 nupC, deoD, deoB, deoC, adh, acs
Calditerrivibrio nitroreducens DSM 19672 nupC, deoD, deoB, deoC, adh, ackA, pta
Caminibacter mediatlanticus TB-2 nupC, deoD, deoB, deoC, adh, acs
Chlorobaculum parvum NCIB 8327 nupC, deoD, deoB, deoC, adh, acs
Chlorobaculum tepidum TLS nupC, deoD, deoB, deoC, adh, acs
Chlorobium limicola DSM 245 nupC, deoD, deoB, deoC, adh, acs
Chlorobium phaeobacteroides BS1 nupA, nupB, nupC', bmpA, deoD, deoB, deoC, adh, acs
Clostridium acetobutylicum ATCC 824 nupA, nupB, nupC', bmpA, deoD, deoB, deoC, adh, ackA, pta
Clostridium kluyveri DSM 555 nupC, deoD, deoB, deoC, adh, ackA, pta
Crocosphaera subtropica ATCC 51142 nupC, deoD, deoB, deoC, adh, ackA, pta
Dechloromonas agitata is5 nupC, deoD, deoB, deoC, adh, ackA, pta
Dehalococcoides mccartyi 195 nupC, deoD, deoB, deoC, ald-dh-CoA
Denitrovibrio acetiphilus DSM 12809 nupC, deoD, deoB, deoC, adh, ackA, pta
Derxia gummosa DSM 723 nupC, deoD, deoB, deoC, ald-dh-CoA
Desulfacinum hydrothermale DSM 13146 nupC, deoD, deoB, deoC, ald-dh-CoA
Desulfacinum infernum DSM 9756 nupC, deoD, deoB, deoC, ald-dh-CoA
Desulfallas geothermicus DSM 3669 nupC, deoD, deoB, deoC, ald-dh-CoA
Desulfarculus baarsii DSM 2075 nupC, deoD, deoB, deoC, adh, ackA, pta
Desulfatibacillum aliphaticivorans DSM 15576 nupC, deoD, deoB, deoC, adh, acs
Desulfatiglans anilini DSM 4660 nupC, deoD, deoB, deoC, adh, acs
Desulfitobacterium hafniense DCB-2 nupA, nupB, nupC', bmpA, deoD, deoB, deoC, ald-dh-CoA
Desulfobacca acetoxidans DSM 11109 nupC, deoD, deoB, deoC, ald-dh-CoA
Desulfobacter vibrioformis DSM 8776 nupC, deoD, deoB, deoC, adh, ackA, pta
Desulfobulbus mediterraneus DSM 13871 nupC, deoD, deoB, deoC, adh, ackA, pta
Desulfotalea psychrophila LSv54 nupC, deoD, deoB, deoC, adh, ackA, pta
Desulfotomaculum ruminis DSM 2154 nupC, deoD, deoB, deoC, ald-dh-CoA
Desulfovibrio bastinii DSM 16055 nupC, deoD, deoB, deoC, adh, ackA, pta
Desulfovibrio gracilis DSM 16080 nupC, deoD, deoB, deoC, adh, ackA, pta
Desulfovibrio oxyclinae DSM 11498 nupC, deoD, deoB, deoC, adh, ackA, pta
Desulfovibrio zosterae DSM 11974 nupC, deoD, deoB, deoC, ald-dh-CoA*
Desulfurobacterium atlanticum DSM 15668 nupC, deoD, deoB, deoC, adh, acs
Desulfuromonas acetexigens nupC, deoD, deoB, deoC, adh, ackA, pta
Desulfuromusa kysingii DSM 7343 nupC, deoD, deoB, deoC, adh, ackA, pta
Ferroglobus placidus DSM 10642 nupC, deoD, deoB, deoC, ald-dh-CoA
Frankia alni ACN14A nupC, deoD, deoB, deoC, adh, acs
Geobacter lovleyi SZ nupC, deoD, deoB, deoC, adh, ackA, pta
Geobacter metallireducens GS-15 nupC, deoD, deoB, deoC, adh, ackA, pta
Geobacter uraniireducens Rf4 nupC, deoD, deoB, deoC, adh, ackA, pta
Haloechinothrix alba DSM 45207 nupA, nupB, nupC', bmpA, deoD, deoB, deoC, adh, acs
Haloglycomyces albus DSM 45210 nupA, nupB, nupC', bmpA, deoD, deoB, deoC, adh, ackA, pta
Halomonas desiderata SP1 nupC, deoD, deoB, deoC, adh, ackA, pta
Halorhodospira halophila SL1 nupC, deoD, deoB, deoC, adh, acs
Heliobacterium modesticaldum Ice1; ATCC 51547 nupC, deoD, deoB, deoC, ald-dh-CoA
Herbaspirillum autotrophicum IAM 14942 nupC, deoD, deoB, deoC, adh, acs
Hydrogenophaga taeniospiralis NBRC 102512 nupC, deoD, deoB, deoC, adh, acs
Hydrogenovibrio halophilus DSM 15072 nupC, deoD, deoB, deoC, adh, ackA, pta
Hydrogenovibrio kuenenii DSM 12350 nupC, deoD, deoB, deoC, adh, ackA, pta
Hydrogenovibrio marinus DSM 11271 nupC, deoD, deoB, deoC, adh, ackA, pta
Hyphomicrobium sulfonivorans WDL6 nupC, deoD, deoB, deoC, adh, acs
Klebsiella variicola At-22 nupC, deoD, deoB, deoC, adh, ackA, pta
Kyrpidia tusciae DSM 2912 nupC, deoD, deoB, deoC, adh, acs
Leptospirillum ferrooxidans C2-3 nupC, deoD, deoB, deoC, adh, acs
Malonomonas rubra DSM 5091 nupC, deoD, deoB, deoC, adh, ackA, pta
Mesorhizobium ciceri WSM1271 nupA, nupB, nupC', bmpA, deoD, deoB, deoC, adh, acs
Methanobacterium lacus AL-21 nupC, deoD, deoB, deoC, adh, acs
Methanococcus aeolicus Nankai-3 nupC, deoD, deoB, deoC, ald-dh-CoA
Methanococcus maripaludis C5 nupC, deoD, deoB, deoC, ald-dh-CoA
Methanosarcina acetivorans C2A nupC, deoD, deoB, deoC, adh, ackA, pta
Methanosarcina barkeri Fusaro nupC, deoD, deoB, deoC, adh, ackA, pta
Methanosarcina mazei Go1 nupC, deoD, deoB, deoC, adh, ackA, pta
Methanothermobacter thermautotrophicus Delta H nupC, deoD, deoB, deoC, ald-dh-CoA
Methylobacterium nodulans ORS 2060 nupC, deoD, deoB, deoC, adh, acs
Methylobacterium sp. 4-46 nupC, deoD, deoB, deoC, adh, acs
Methylocapsa acidiphila B2 nupC, deoD, deoB, deoC, adh, acs
Methylocapsa aurea KYG T nupC, deoD, deoB, deoC, adh, acs
Methylocella silvestris BL2 nupC, deoD, deoB, deoC, adh, acs
Methylococcus capsulatus Bath nupC, deoD, deoB, deoC, adh, acs
Methylocystis bryophila S285 nupC, deoD, deoB, deoC, adh, acs
Methyloferula stellata AR4T nupC, deoD, deoB, deoC, adh, acs
Methylohalobius crimeensis 10Ki nupC, deoD, deoB, deoC, adh, acs
Methylomicrobium alcaliphilum 20Z nupC, deoD, deoB, deoC, adh, ackA, pta
Methylomonas methanica MC09 nupC, deoD, deoB, deoC, adh, ackA, pta
Methylosarcina fibrata AML-C10 nupC, deoD, deoB, deoC, adh, acs
Methylovulum miyakonense HT12 nupC, deoD, deoB, deoC, adh, acs
Mycolicibacterium vanbaalenii PYR-1 nupC, deoD, deoB, deoC, adh, ackA, pta
Nitratifractor salsuginis DSM 16511 nupC, deoD, deoB, deoC, adh, ackA, pta
Nitratiruptor tergarcus DSM 16512 nupC, deoD, deoB, deoC, adh, acs
Nitriliruptor alkaliphilus DSM 45188 nupA, nupB, nupC', bmpA, deoD, deoB, deoC, adh, acs
Nocardiopsis lucentensis DSM 44048 nupA, nupB, nupC', bmpA, deoD, deoB, deoC, adh, acs
Nostoc punctiforme ATCC 29133; PCC 73102 nupC, deoD, deoB, deoC, adh, acs
Novosphingobium aromaticivorans DSM 12444 nupC, deoD, deoB, deoC, adh, acs
Oleispira antarctica nupC, deoD, deoB, deoC, ald-dh-CoA
Paraburkholderia phymatum STM815 H281DRAFT_01115, H281DRAFT_01114, H281DRAFT_01113, H281DRAFT_01112, deoD, deoB, deoC, adh, ackA, pta
Paraburkholderia sp. CCGE1002 nupC, deoD, deoB, deoC, adh, acs
Pelobacter propionicus DSM 2379 nupC, deoD, deoB, deoC, adh, ackA, pta
Persephonella marina EX-H1 nupC, deoD, deoB, deoC, adh, acs
Polaromonas naphthalenivorans CJ2 nupC, deoD, deoB, deoC, adh, ackA, pta
Prosthecochloris aestuarii DSM 271 nupC, deoD, deoB, deoC, adh, acs
Pseudarthrobacter sulfonivorans Ar51 nupC, deoD, deoB, deoC, adh, ackA, pta
Pseudomonas benzenivorans DSM 8628 nupC, deoD, deoB, deoC, adh, ackA, pta
Pseudomonas stutzeri A1501 nupC, deoD, deoB, deoC, adh, ackA, pta
Pyrolobus fumarii 1A nupC, deoD, deoB, deoC, ald-dh-CoA
Rhizobium etli CFN 42 nupA, nupB, nupC', bmpA, deoD, deoB, deoC, adh, acs
Rhizobium leguminosarum 3841 H281DRAFT_01115, H281DRAFT_01114, H281DRAFT_01113, H281DRAFT_01112, deoD, deoB, deoC, adh, acs
Rhizobium leguminosarum WSM1325 H281DRAFT_01115, H281DRAFT_01114, H281DRAFT_01113, H281DRAFT_01112, deoD, deoB, deoC, adh, acs
Rhodobacter sphaeroides ATCC 17029 H281DRAFT_01115, H281DRAFT_01114, H281DRAFT_01113, H281DRAFT_01112, deoD, deoB, deoC, adh, acs
Rhodomicrobium vannielii ATCC 17100 nupC, deoD, deoB, deoC, adh, acs
Rhodopseudomonas palustris CGA009 nupC, deoD, deoB, deoC, adh, acs
Rhodospirillum centenum SW; ATCC 51521 nupC, deoD, deoB, deoC, adh, acs
Rhodospirillum rubrum ATCC 11170 H281DRAFT_01115, H281DRAFT_01114, H281DRAFT_01113, H281DRAFT_01112, deoD, deoB, deoC, adh, ackA, pta
Saccharomonospora cyanea NA-134 nupC, deoD, deoB, deoC, adh, acs
Sedimenticola selenatireducens DSM 17993 nupC, deoD, deoB, deoC, adh, ackA, pta
Sinorhizobium fredii NGR234 H281DRAFT_01115, H281DRAFT_01114, H281DRAFT_01113, H281DRAFT_01112, deoD, deoB, deoC, adh, acs
Sinorhizobium medicae WSM419 H281DRAFT_01115, H281DRAFT_01114, H281DRAFT_01113, H281DRAFT_01112, deoD, deoB, deoC, adh, ackA, pta
Sphingomonas wittichii RW1 nupC, deoD, deoB, deoC, adh, acs
Stenotrophomonas chelatiphaga DSM 21508 nupC, deoD, deoB, deoC, adh, acs
Steroidobacter denitrificans DSM 18526 nupC, deoD, deoB, deoC, adh, ackA, pta
Sulfuricurvum kujiense DSM 16994 nupC, deoD, deoB, deoC, adh, ackA, pta
Sulfurihydrogenibium azorense Az-Fu1 nupC, deoD, deoB, deoC, adh, acs
Sulfurihydrogenibium subterraneum DSM 15120 nupC, deoD, deoB, deoC, adh, acs
Sulfurimonas denitrificans DSM 1251 nupC, deoD, deoB, deoC, adh, ackA, pta
Sulfuritalea hydrogenivorans DSM 22779 nupC, deoD, deoB, deoC, adh, acs
Sulfurivirga caldicuralii DSM 17737 nupC, deoD, deoB, deoC, adh, acs
Teredinibacter turnerae T7901 nupC, deoD, deoB, deoC, adh, ackA, pta
Thauera aminoaromatica S2 nupC, deoD, deoB, deoC, ald-dh-CoA
Thermithiobacillus tepidarius DSM 3134 nupC, deoD, deoB, deoC, adh, acs
Thermocrinis albus DSM 14484 nupC, deoD, deoB, deoC, adh, acs
Thermodesulforhabdus norvegica DSM 9990 nupC, deoD, deoB, deoC, adh, acs
Thermomonospora curvata DSM 43183 nupA, nupB, nupC', bmpA, deoD, deoB, deoC, adh, acs
Thermovibrio ammonificans HB-1 nupC, deoD, deoB, deoC, adh, acs
Thioalkalivibrio denitrificans ALJD nupC, deoD, deoB, deoC, adh, ackA, pta
Thioalkalivibrio halophilus HL17 nupC, deoD, deoB, deoC, adh, acs
Thioalkalivibrio paradoxus ARh 1 nupC, deoD, deoB, deoC, adh, acs
Thioalkalivibrio thiocyanodenitrificans ARhD 1 nupC, deoD, deoB, deoC, adh, ackA, pta
Thiohalomonas denitrificans HLD2 nupC, deoD, deoB, deoC, adh, acs
Thiomicrorhabdus arctica DSM 13458 nupC, deoD, deoB, deoC, ald-dh-CoA
Thiomicrorhabdus chilensis DSM 12352 nupC, deoD, deoB, deoC, adh, acs
Thiomicrospira cyclica ALM1 nupC, deoD, deoB, deoC, adh, acs
Thiomicrospira microaerophila ASL8-2 nupC, deoD, deoB, deoC, adh, acs
Thiomicrospira pelophila DSM 1534 nupC, deoD, deoB, deoC, adh, acs
Thiothrix lacustris DSM 21227 nupC, deoD, deoB, deoC, adh, ackA, pta
Trichodesmium erythraeum IMS101 nupC, deoD, deoB, deoC, adh, acs
Trichormus variabilis ATCC 29413 nupC, deoD, deoB, deoC, adh, acs
Xanthobacter autotrophicus Py2 nupC, deoD, deoB, deoC, adh, acs
Xenophilus azovorans DSM 13620 nupC, deoD, 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 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