GapMind for catabolism of small carbon sources

 

L-rhamnose catabolism

Analysis of pathway rhamnose in 150 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Acidithiobacillus ferrooxidans ATCC 23270 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Alicycliphilus denitrificans K601 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Allochromatium vinosum DSM 180 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Ammonifex degensii KC4 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Archaeoglobus veneficus SNP6 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Arcobacter nitrofigilis DSM 7299 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Azoarcus sp. BH72 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Azohydromonas australica DSM 1124 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Azorhizobium caulinodans ORS 571 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Azospirillum lipoferum B510 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Bacillus alkalinitrilicus DSM 22532 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Beijerinckia indica ATCC 9039 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, fucO
Beijerinckia mobilis UQM 1969 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Bradyrhizobium sp. BTAi1 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Burkholderia vietnamiensis G4 rhaT, LRA1, LRA2, LRA3, LRA4, fucO
Calditerrivibrio nitroreducens DSM 19672 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Caminibacter mediatlanticus TB-2 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Chlorobaculum parvum NCIB 8327 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Chlorobaculum tepidum TLS rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Chlorobium limicola DSM 245 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Chlorobium phaeobacteroides BS1 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Clostridium acetobutylicum ATCC 824 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Clostridium kluyveri DSM 555 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Crocosphaera subtropica ATCC 51142 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Dechloromonas agitata is5 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Dehalococcoides mccartyi 195 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Denitrovibrio acetiphilus DSM 12809 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Derxia gummosa DSM 723 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Desulfacinum hydrothermale DSM 13146 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, fucO
Desulfacinum infernum DSM 9756 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, fucO
Desulfallas geothermicus DSM 3669 rhaT, LRA1, LRA2, LRA3, LRA4, fucO
Desulfarculus baarsii DSM 2075 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Desulfatibacillum aliphaticivorans DSM 15576 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Desulfatiglans anilini DSM 4660 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Desulfitobacterium hafniense DCB-2 rhaT, LRA1, LRA2, LRA3, LRA4, fucO
Desulfobacca acetoxidans DSM 11109 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Desulfobacter vibrioformis DSM 8776 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Desulfobulbus mediterraneus DSM 13871 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, fucO
Desulfotalea psychrophila LSv54 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, fucO
Desulfotomaculum ruminis DSM 2154 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Desulfovibrio bastinii DSM 16055 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Desulfovibrio gracilis DSM 16080 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, fucO
Desulfovibrio oxyclinae DSM 11498 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Desulfovibrio zosterae DSM 11974 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Desulfurobacterium atlanticum DSM 15668 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Desulfuromonas acetexigens rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Desulfuromusa kysingii DSM 7343 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Ferroglobus placidus DSM 10642 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Frankia alni ACN14A rhaT, LRA1, LRA2, LRA3, LRA4, fucO
Geobacter lovleyi SZ rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Geobacter metallireducens GS-15 rhaT, LRA1, LRA2, LRA3, LRA4, fucO
Geobacter uraniireducens Rf4 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Haloechinothrix alba DSM 45207 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Haloglycomyces albus DSM 45210 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Halomonas desiderata SP1 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Halorhodospira halophila SL1 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Heliobacterium modesticaldum Ice1; ATCC 51547 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Herbaspirillum autotrophicum IAM 14942 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Hydrogenophaga taeniospiralis NBRC 102512 rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Hydrogenovibrio halophilus DSM 15072 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Hydrogenovibrio kuenenii DSM 12350 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Hydrogenovibrio marinus DSM 11271 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Hyphomicrobium sulfonivorans WDL6 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Klebsiella variicola At-22 rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Kyrpidia tusciae DSM 2912 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Leptospirillum ferrooxidans C2-3 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Malonomonas rubra DSM 5091 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Mesorhizobium ciceri WSM1271 rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Methanobacterium lacus AL-21 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Methanococcus aeolicus Nankai-3 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Methanococcus maripaludis C5 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Methanosarcina acetivorans C2A rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Methanosarcina barkeri Fusaro rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Methanosarcina mazei Go1 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Methanothermobacter thermautotrophicus Delta H rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Methylobacterium nodulans ORS 2060 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Methylobacterium sp. 4-46 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Methylocapsa acidiphila B2 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, fucO
Methylocapsa aurea KYG T rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Methylocella silvestris BL2 rhaT, LRA1, LRA2, LRA3, LRA4, fucO
Methylococcus capsulatus Bath rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Methylocystis bryophila S285 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Methyloferula stellata AR4T rhaT, rhaM, rhaA, rhaB, rhaD, tpi, fucO
Methylohalobius crimeensis 10Ki rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Methylomicrobium alcaliphilum 20Z rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Methylomonas methanica MC09 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Methylosarcina fibrata AML-C10 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Methylovulum miyakonense HT12 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Mycolicibacterium vanbaalenii PYR-1 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Nitratifractor salsuginis DSM 16511 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Nitratiruptor tergarcus DSM 16512 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Nitriliruptor alkaliphilus DSM 45188 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Nocardiopsis lucentensis DSM 44048 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Nostoc punctiforme ATCC 29133; PCC 73102 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Novosphingobium aromaticivorans DSM 12444 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Oleispira antarctica rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Paraburkholderia phymatum STM815 BPHYT_RS34250, BPHYT_RS34245, BPHYT_RS34240, LRA1, LRA2, LRA3, LRA5, LRA6
Paraburkholderia sp. CCGE1002 rhaP, rhaQ, rhaS, rhaT', LRA1, LRA2, LRA3, LRA5, LRA6
Pelobacter propionicus DSM 2379 rhaT, LRA1, LRA2, LRA3, LRA4, fucO
Persephonella marina EX-H1 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Polaromonas naphthalenivorans CJ2 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Prosthecochloris aestuarii DSM 271 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Pseudarthrobacter sulfonivorans Ar51 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Pseudomonas benzenivorans DSM 8628 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Pseudomonas stutzeri A1501 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Pyrolobus fumarii 1A rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Rhizobium etli CFN 42 rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Rhizobium leguminosarum 3841 rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Rhizobium leguminosarum WSM1325 rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Rhodobacter sphaeroides ATCC 17029 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Rhodomicrobium vannielii ATCC 17100 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Rhodopseudomonas palustris CGA009 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Rhodospirillum centenum SW; ATCC 51521 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Rhodospirillum rubrum ATCC 11170 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Saccharomonospora cyanea NA-134 rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Sedimenticola selenatireducens DSM 17993 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Sinorhizobium fredii NGR234 rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Sinorhizobium medicae WSM419 rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Sphingomonas wittichii RW1 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Stenotrophomonas chelatiphaga DSM 21508 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Steroidobacter denitrificans DSM 18526 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Sulfuricurvum kujiense DSM 16994 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Sulfurihydrogenibium azorense Az-Fu1 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Sulfurihydrogenibium subterraneum DSM 15120 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Sulfurimonas denitrificans DSM 1251 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Sulfuritalea hydrogenivorans DSM 22779 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Sulfurivirga caldicuralii DSM 17737 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Teredinibacter turnerae T7901 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Thauera aminoaromatica S2 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Thermithiobacillus tepidarius DSM 3134 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Thermocrinis albus DSM 14484 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Thermodesulforhabdus norvegica DSM 9990 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, fucO
Thermomonospora curvata DSM 43183 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Thermovibrio ammonificans HB-1 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Thioalkalivibrio denitrificans ALJD rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Thioalkalivibrio halophilus HL17 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Thioalkalivibrio paradoxus ARh 1 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Thioalkalivibrio thiocyanodenitrificans ARhD 1 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Thiohalomonas denitrificans HLD2 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Thiomicrorhabdus arctica DSM 13458 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Thiomicrorhabdus chilensis DSM 12352 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Thiomicrospira cyclica ALM1 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Thiomicrospira microaerophila ASL8-2 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Thiomicrospira pelophila DSM 1534 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Thiothrix lacustris DSM 21227 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Trichodesmium erythraeum IMS101 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Trichormus variabilis ATCC 29413 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Xanthobacter autotrophicus Py2 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Xenophilus azovorans DSM 13620 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6

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.

Links

Downloads

Related tools

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