GapMind for catabolism of small carbon sources

 

D-ribose catabolism

Analysis of pathway ribose in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 rbsU, rbsK
Acidithiobacillus ferrooxidans ATCC 23270 rbsU, rbsK
Acidovorax sp. GW101-3H11 frcA, frcB, frcC, rbsK
Algiphilus aromaticivorans DG1253 rbsU, rbsK
Alicycliphilus denitrificans K601 rbsU, rbsK
Alkalihalobacterium alkalinitrilicum DSM 22532 rbsU, rbsK
Allochromatium vinosum DSM 180 rbsU, rbsK
Ammonifex degensii KC4 rbsU, rbsK
Anaerobutyricum hallii DSM 3353 rbsU, rbsK
Aquimarina longa SW024 rbsU, rbsK
Archaeoglobus veneficus SNP6 rbsU, rbsK
Arcobacter nitrofigilis DSM 7299 rbsU, rbsK
Azoarcus olearius BH72 rbsU, rbsK
Azohydromonas australica DSM 1124 rbsU, rbsK
Azorhizobium caulinodans ORS 571 rbsU, rbsK
Azospirillum brasilense Sp245 rbsU, rbsK
Azospirillum sp. B510 rbsA, rbsB, rbsC, rbsK
Bacteroides thetaiotaomicron VPI-5482 BT2809, rbsK
Beijerinckia indica ATCC 9039 rbsU, rbsK
Beijerinckia mobilis UQM 1969 rbsU, rbsK
Billgrantia desiderata SP1 rbsU, rbsK
Bradyrhizobium sp. BTAi1 rbsA, rbsB, rbsC, rbsK
Brevundimonas sp. GW460-12-10-14-LB2 rbsU, rbsK
Burkholderia phytofirmans PsJN rbsA, rbsB, rbsC, rbsK
Burkholderia vietnamiensis G4 rbsA, rbsB, rbsC, rbsK
Calditerrivibrio nitroreducens DSM 19672 rbsU, rbsK
Caminibacter mediatlanticus TB-2 rbsU, rbsK
Carboxydothermus pertinax Ug1 rbsU, rbsK
Caulobacter crescentus NA1000 rbsU, rbsK
Cereibacter sphaeroides ATCC 17029 frcA, frcB, frcC, rbsK
Chlorobaculum parvum NCIB 8327 rbsU, rbsK
Chlorobaculum tepidum TLS rbsU, rbsK
Chlorobium limicola DSM 245 rbsU, rbsK
Chlorobium phaeobacteroides BS1 rbsU, rbsK
Clostridium acetobutylicum ATCC 824 rbsU, rbsK
Clostridium kluyveri DSM 555 rbsU, rbsK
Clostridium tyrobutyricum FAM22553 rbsU, rbsK
Crocosphaera subtropica ATCC 51142 rbsU, rbsK
Cupriavidus basilensis FW507-4G11 rbsU, rbsK
Dechloromonas agitata is5 rbsU, rbsK
Dechlorosoma suillum PS rbsU, rbsK
Dehalococcoides mccartyi 195 rbsU, rbsK
Denitrovibrio acetiphilus DSM 12809 rbsA, rbsB, rbsC, rbsK
Derxia gummosa DSM 723 rbsA, rbsB, rbsC, rbsK
Desulfacinum hydrothermale DSM 13146 rbsU, rbsK
Desulfacinum infernum DSM 9756 rbsU, rbsK
Desulfarculus baarsii DSM 2075 rbsU, rbsK
Desulfatibacillum aliphaticivorans DSM 15576 rbsU, rbsK
Desulfatiglans anilini DSM 4660 rbsU, rbsK
Desulfitobacterium hafniense DCB-2 rbsU, rbsK
Desulfobacca acetoxidans DSM 11109 rbsU, rbsK
Desulfobacter vibrioformis DSM 8776 rbsU, rbsK
Desulfogranum mediterraneum DSM 13871 rbsU, rbsK
Desulforamulus ruminis DSM 2154 rbsA, rbsB, rbsC, rbsK
Desulfoscipio geothermicus DSM 3669 rbsU, rbsK
Desulfotalea psychrophila LSv54 rbsU, rbsK
Desulfovibrio oxyclinae DSM 11498 rbsU, rbsK
Desulfovibrio vulgaris Hildenborough JW710 rbsU, rbsK
Desulfovibrio vulgaris Miyazaki F rbsU, rbsK
Desulfurobacterium atlanticum DSM 15668 rbsU, rbsK
Desulfuromonas acetexigens rbsU, rbsK
Desulfuromusa kysingii DSM 7343 rbsU, rbsK
Dinoroseobacter shibae DFL-12 frcA, frcB, frcC, rbsK
Dyella japonica UNC79MFTsu3.2 rbsU, rbsK
Echinicola vietnamensis KMM 6221, DSM 17526 rbsA, rbsB, rbsC, rbsK
Escherichia coli BW25113 rbsA, rbsB, rbsC, rbsK
Ferroglobus placidus DSM 10642 rbsU, rbsK
Frankia alni ACN14a rbsU, rbsK
Geobacter metallireducens GS-15 rbsU, rbsK
Geotalea uraniireducens Rf4 rbsU, rbsK
Halococcus hamelinensis 100A6 rbsU, rbsK
Haloechinothrix alba DSM 45207 rbsU, rbsK
Haloferax volcanii DS2 rbsU, rbsK
Haloglycomyces albus DSM 45210 rbsU, rbsK
Halorhodospira halophila SL1 rbsU, rbsK
Heliomicrobium modesticaldum Ice1; ATCC 51547 rbsA, rbsB, rbsC, rbsK
Herbaspirillum autotrophicum IAM 14942 rbsU, rbsK
Herbaspirillum seropedicae SmR1 rbsA, rbsB, rbsC, rbsK
Hippea alviniae EP5-r rbsU, rbsK
Hydrogenophaga taeniospiralis NBRC 102512 frcA, frcB, frcC, rbsK
Hydrogenovibrio halophilus DSM 15072 rbsU, rbsK
Hydrogenovibrio kuenenii DSM 12350 rbsU, rbsK
Hydrogenovibrio marinus DSM 11271 rbsU, rbsK
Hyphomicrobium sulfonivorans WDL6 rbsU, rbsK
Klebsiella michiganensis M5al rbsA, rbsB, rbsC, rbsK
Klebsiella variicola At-22 rbsA, rbsB, rbsC, rbsK
Kyrpidia tusciae DSM 2912 rbsU, rbsK
Leptospirillum ferrooxidans C2-3 rbsU, rbsK
Magnetospirillum magneticum AMB-1 rbsU, rbsK
Malonomonas rubra DSM 5091 rbsU, rbsK
Maridesulfovibrio bastinii DSM 16055 rbsU, rbsK
Maridesulfovibrio zosterae DSM 11974 rbsU, rbsK
Marinobacter adhaerens HP15 rbsU, rbsK
Mesorhizobium ciceri WSM1271 frcA, frcB, frcC, rbsK
Methanobacterium lacus AL-21 rbsU, rbsK
Methanococcus aeolicus Nankai-3 rbsU, rbsK
Methanococcus maripaludis C5 rbsU, rbsK
Methanosarcina acetivorans C2A rbsU, rbsK
Methanosarcina mazei Go1 rbsU, rbsK
Methanospirillum lacunae Ki8-1 rbsU, rbsK
Methanothermobacter thermautotrophicus Delta H rbsU, rbsK
Methylobacterium nodulans ORS 2060 rbsU, rbsK
Methylobacterium sp. 4-46 Apr-46 rbsU, rbsK
Methylocapsa acidiphila B2 rbsU, rbsK
Methylocapsa aurea KYG rbsU, rbsK
Methylocella silvestris BL2 rbsU, rbsK
Methylococcus capsulatus Bath rbsU, rbsK
Methylocystis bryophila S285 rbsU, rbsK
Methyloferula stellata AR4T rbsU, rbsK
Methylohalobius crimeensis 10Ki rbsU, rbsK
Methylomonas methanica MC09 rbsU, rbsK
Methylosarcina fibrata AML-C10 rbsU, rbsK
Methylotuvimicrobium alcaliphilum 20Z rbsU, rbsK
Methylovulum miyakonense HT12 rbsU, rbsK
Mycolicibacterium vanbaalenii PYR-1 rbsU, rbsK
Nitratifractor salsuginis DSM 16511 rbsU, rbsK
Nitratiruptor tergarcus DSM 16512 rbsU, rbsK
Nitriliruptor alkaliphilus DSM 45188 rbsU, rbsK
Nocardioides dokdonensis FR1436 rbsU, rbsK
Nocardiopsis lucentensis DSM 44048 frcA, frcB, frcC, rbsK
Nostoc punctiforme ATCC 29133; PCC 73102 rbsU, rbsK
Novosphingobium aromaticivorans DSM 12444 rbsU, rbsK
Oleispira antarctica rbsU, rbsK
Paraburkholderia atlantica CCGE1002 rbsA, rbsB, rbsC, rbsK
Paraburkholderia bryophila 376MFSha3.1 rbsA, rbsB, rbsC, rbsK
Paraburkholderia phymatum STM815 rbsA, rbsB, rbsC, rbsK
Paucidesulfovibrio gracilis DSM 16080 rbsU, rbsK
Pedobacter sp. GW460-11-11-14-LB5 rbsU, rbsK
Pelobacter propionicus DSM 2379 rbsU, rbsK
Persephonella marina EX-H1 rbsU, rbsK
Phaeacidiphilus oryzae TH49 rbsA, rbsB, rbsC, rbsK
Phaeobacter inhibens BS107 frcA, frcB, frcC, rbsK
Polaromonas naphthalenivorans CJ2 frcA, frcB, frcC, rbsK
Prosthecochloris aestuarii DSM 271 rbsU, rbsK
Pseudarthrobacter sulfonivorans Ar51 frcA, frcB, frcC, rbsK
Pseudomonas benzenivorans DSM 8628 rbsU, rbsK
Pseudomonas fluorescens FW300-N1B4 rbsA, rbsB, rbsC, rbsK
Pseudomonas fluorescens FW300-N2C3 rbsA, rbsB, rbsC, rbsK
Pseudomonas fluorescens FW300-N2E2 rbsA, rbsB, rbsC, rbsK
Pseudomonas fluorescens FW300-N2E3 rbsA, rbsB, rbsC, rbsK
Pseudomonas fluorescens GW456-L13 rbsA, rbsB, rbsC, rbsK
Pseudomonas putida KT2440 rbsA, rbsB, rbsC, rbsK
Pseudomonas simiae WCS417 rbsA, rbsB, rbsC, rbsK
Pseudomonas stutzeri RCH2 rbsU, rbsK
Pyrolobus fumarii 1A rbsU, rbsK
Rhizobium etli CFN 42 frcA, frcB, frcC, rbsK
Rhizobium johnstonii 3841 frcA, frcB, frcC, rbsK
Rhizobium leguminosarum WSM1325 frcA, frcB, frcC, rbsK
Rhizorhabdus wittichii RW1 rbsU, rbsK
Rhodanobacter denitrificans FW104-10B01 rbsU, rbsK
Rhodomicrobium vannielii ATCC 17100 rbsU, rbsK
Rhodopseudomonas palustris CGA009 rbsU, rbsK
Rhodospirillum centenum SW; ATCC 51521 rbsU, rbsK
Rhodospirillum rubrum ATCC 11170 rbsU, rbsK
Roseburia faecis M72 rbsU, rbsK
Saccharomonospora cyanea NA-134 rbsU, rbsK
Sedimenticola selenatireducens DSM 17993 rbsU, rbsK
Shewanella amazonensis SB2B rbsU, rbsK
Shewanella loihica PV-4 rbsU, rbsK
Shewanella oneidensis MR-1 rbsU, rbsK
Shewanella sp. ANA-3 rbsU, rbsK
Sinorhizobium fredii NGR234 rbsA, rbsB, rbsC, rbsK
Sinorhizobium medicae WSM419 frcA, frcB, frcC, rbsK
Sinorhizobium meliloti 1021 frcA, frcB, frcC, rbsK
Sphingomonas koreensis DSMZ 15582 rbsU, rbsK
Stenotrophomonas chelatiphaga DSM 21508 rbsU, rbsK
Steroidobacter denitrificans DSM 18526 rbsU, rbsK
Stutzerimonas stutzeri A1501 rbsU, rbsK
Sulfuricurvum kujiense DSM 16994 rbsU, rbsK
Sulfurihydrogenibium azorense Az-Fu1 rbsU, rbsK
Sulfurihydrogenibium subterraneum DSM 15120 rbsU, rbsK
Sulfurimonas denitrificans DSM 1251 rbsU, rbsK
Sulfuritalea hydrogenivorans DSM 22779 rbsU, rbsK
Sulfurivirga caldicuralii DSM 17737 rbsU, rbsK
Synechococcus elongatus PCC 7942 rbsU, rbsK
Teredinibacter turnerae T7901 rbsU, rbsK
Thauera aminoaromatica S2 rbsU, rbsK
Thermithiobacillus tepidarius DSM 3134 rbsU, rbsK
Thermocrinis albus DSM 14484 rbsU, rbsK
Thermodesulforhabdus norvegica DSM 9990 rbsU, rbsK
Thermomonospora curvata DSM 43183 rbsU, rbsK
Thermovibrio ammonificans HB-1 rbsU, rbsK
Thermus aquaticus YT-1 rbsU, rbsK
Thioalkalivibrio denitrificans ALJD rbsU, rbsK
Thioalkalivibrio halophilus HL17 rbsU, rbsK
Thioalkalivibrio paradoxus ARh 1 rbsU, rbsK
Thioalkalivibrio thiocyanodenitrificans ARhD 1 rbsU, rbsK
Thiohalomonas denitrificans HLD2 rbsU, rbsK
Thiohalospira halophila HL 3 rbsU, rbsK
Thiomicrorhabdus arctica DSM 13458 rbsU, rbsK
Thiomicrorhabdus chilensis DSM 12352 rbsU, rbsK
Thiomicrospira cyclica ALM1 rbsU, rbsK
Thiomicrospira microaerophila ASL8-2 rbsU, rbsK
Thiomicrospira pelophila DSM 1534 rbsU, rbsK
Thiothrix lacustris DSM 21227 rbsU, rbsK
Tistlia consotensis USBA 355 frcA, frcB, frcC, rbsK
Trichlorobacter lovleyi SZ rbsU, rbsK
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome rbsU, rbsK
Trichormus variabilis ATCC 29413 rbsU, rbsK
Xanthobacter autotrophicus Py2 frcA, frcB, frcC, rbsK
Xenophilus azovorans DSM 13620 rbsA, rbsB, rbsC, rbsK

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