GapMind for catabolism of small carbon sources

 

L-arabinose catabolism

Analysis of pathway arabinose in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 araE, araA, araB, araD
Acidithiobacillus ferrooxidans ATCC 23270 araE, araA, araB, araD
Acidovorax sp. GW101-3H11 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Algiphilus aromaticivorans DG1253 BT0355, araA, araB, araD
Alicycliphilus denitrificans K601 araE, araA, araB, araD
Alkalihalobacterium alkalinitrilicum DSM 22532 araE, araA, araB, araD
Allochromatium vinosum DSM 180 araE, araA, araB, araD
Ammonifex degensii KC4 araE, araA, araB, araD
Anaerobutyricum hallii DSM 3353 araE, araA, araB, araD
Aquimarina longa SW024 Echvi_1880, araA, araB, araD
Archaeoglobus veneficus SNP6 araE, araA, araB, araD
Arcobacter nitrofigilis DSM 7299 araE, araA, araB, araD
Azoarcus olearius BH72 araE, araA, araB, araD
Azohydromonas australica DSM 1124 araE, xacB, xacC, xacD, xacE, xacF
Azorhizobium caulinodans ORS 571 araE, xacB, xacC, xacD, xacE, xacF
Azospirillum brasilense Sp245 gguA, gguB, chvE, xacB, xacC, xacD, KDG-aldolase, aldA, gyaR, glcB
Azospirillum sp. B510 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Bacteroides thetaiotaomicron VPI-5482 BT0355, araA, araB, araD
Beijerinckia indica ATCC 9039 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Beijerinckia mobilis UQM 1969 araE, xacB, xacC, xacD, KDG-aldolase, aldA, gyaR, glcB
Billgrantia desiderata SP1 araF, araG, araH, xacB, xacC, xacD, xacE, xacF
Bradyrhizobium sp. BTAi1 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Brevundimonas sp. GW460-12-10-14-LB2 Echvi_1880, xacB, xacC, xacD, xacE, xacF
Burkholderia phytofirmans PsJN araF, araG, araH, xacB, xacC, xacD, xacE, xacF
Burkholderia vietnamiensis G4 araF, araG, araH, xacB, xacC, xacD, xacE, xacF
Calditerrivibrio nitroreducens DSM 19672 araE, araA, araB, araD
Caminibacter mediatlanticus TB-2 araE, araA, araB, araD
Carboxydothermus pertinax Ug1 araE, araA, araB, araD
Caulobacter crescentus NA1000 araE, xacB, xacC, xacD, xacE, xacF
Cereibacter sphaeroides ATCC 17029 araE, xacB, xacC, xacD, xacE, xacF
Chlorobaculum parvum NCIB 8327 araE, araA, araB, araD
Chlorobaculum tepidum TLS araE, araA, araB, araD
Chlorobium limicola DSM 245 araE, araA, araB, araD
Chlorobium phaeobacteroides BS1 araE, araA, araB, araD
Clostridium acetobutylicum ATCC 824 araE, araA, araB, araD
Clostridium kluyveri DSM 555 araE, araA, araB, araD
Clostridium tyrobutyricum FAM22553 araE, araA, araB, araD
Crocosphaera subtropica ATCC 51142 araE, araA, araB, araD
Cupriavidus basilensis FW507-4G11 araE, xacB, xacC, xacD, xacE, xacF
Dechloromonas agitata is5 araE, araA, araB, araD
Dechlorosoma suillum PS araE, araA, araB, araD
Dehalococcoides mccartyi 195 araE, araA, araB, araD
Denitrovibrio acetiphilus DSM 12809 araE, araA, araB, araD
Derxia gummosa DSM 723 araE, araA, araB, araD
Desulfacinum hydrothermale DSM 13146 araE, araA, araB, araD
Desulfacinum infernum DSM 9756 araE, araA, araB, araD
Desulfarculus baarsii DSM 2075 araE, araA, araB, araD
Desulfatibacillum aliphaticivorans DSM 15576 araE, araA, araB, araD
Desulfatiglans anilini DSM 4660 araE, araA, araB, araD
Desulfitobacterium hafniense DCB-2 araE, araA, araB, araD
Desulfobacca acetoxidans DSM 11109 araE, araA, araB, araD
Desulfobacter vibrioformis DSM 8776 araE, araA, araB, araD
Desulfogranum mediterraneum DSM 13871 araE, araA, araB, araD
Desulforamulus ruminis DSM 2154 araE, araA, araB, araD
Desulfoscipio geothermicus DSM 3669 araE, araA, araB, araD
Desulfotalea psychrophila LSv54 araE, araA, araB, araD
Desulfovibrio oxyclinae DSM 11498 araE, araA, araB, araD
Desulfovibrio vulgaris Hildenborough JW710 araE, araA, araB, araD
Desulfovibrio vulgaris Miyazaki F araE, araA, araB, araD
Desulfurobacterium atlanticum DSM 15668 araE, araA, araB, araD
Desulfuromonas acetexigens araE, araA, araB, araD
Desulfuromusa kysingii DSM 7343 araE, araA, araB, araD
Dinoroseobacter shibae DFL-12 araE, xacB, xacC, xacD, xacE, xacF
Dyella japonica UNC79MFTsu3.2 araUsh, araVsh, araWsh, araZsh, xacB, xacC, xacD, xacE, xacF
Echinicola vietnamensis KMM 6221, DSM 17526 Echvi_1880, araA, araB, araD
Escherichia coli BW25113 araF, araG, araH, araA, araB, araD
Ferroglobus placidus DSM 10642 araE, araA, araB, araD
Frankia alni ACN14a araE, xacB, xacC, xacD, xacE, xacF
Geobacter metallireducens GS-15 araE, araA, araB, araD
Geotalea uraniireducens Rf4 araE, araA, araB, araD
Halococcus hamelinensis 100A6 xacG, xacH, xacI, xacJ, xacK, xacB, xacC, xacD, xacE, xacF
Haloechinothrix alba DSM 45207 araE, araA, araB, araD
Haloferax volcanii DS2 xacG, xacH, xacI, xacJ, xacK, xacB, xacC, xacD, xacE, xacF
Haloglycomyces albus DSM 45210 gguA, gguB, chvE, araA, araB, araD
Halorhodospira halophila SL1 araE, araA, araB, araD
Heliomicrobium modesticaldum Ice1; ATCC 51547 araE, araA, araB, araD
Herbaspirillum autotrophicum IAM 14942 araE, xacB, xacC, xacD, xacE, xacF
Herbaspirillum seropedicae SmR1 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Hippea alviniae EP5-r araE, araA, araB, araD
Hydrogenophaga taeniospiralis NBRC 102512 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Hydrogenovibrio halophilus DSM 15072 araE, araA, araB, araD
Hydrogenovibrio kuenenii DSM 12350 araE, araA, araB, araD
Hydrogenovibrio marinus DSM 11271 araE, araA, araB, araD
Hyphomicrobium sulfonivorans WDL6 araE, araA, araB, araD
Klebsiella michiganensis M5al araF, araG, araH, araA, araB, araD
Klebsiella variicola At-22 araF, araG, araH, araA, araB, araD
Kyrpidia tusciae DSM 2912 araE, araA, araB, araD
Leptospirillum ferrooxidans C2-3 araE, araA, araB, araD
Magnetospirillum magneticum AMB-1 araE, araA, araB, araD
Malonomonas rubra DSM 5091 araE, araA, araB, araD
Maridesulfovibrio bastinii DSM 16055 araE, araA, araB, araD
Maridesulfovibrio zosterae DSM 11974 araE, araA, araB, araD
Marinobacter adhaerens HP15 araE, araA, araB, araD
Mesorhizobium ciceri WSM1271 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Methanobacterium lacus AL-21 araE, araA, araB, araD
Methanococcus aeolicus Nankai-3 araE, araA, araB, araD
Methanococcus maripaludis C5 araE, araA, araB, araD
Methanosarcina acetivorans C2A araE, xacB, xacC, xacD, xacE, xacF
Methanosarcina mazei Go1 araE, araA, araB, araD
Methanospirillum lacunae Ki8-1 araE, araA, araB, araD
Methanothermobacter thermautotrophicus Delta H araE, araA, araB, araD
Methylobacterium nodulans ORS 2060 araE, xacB, xacC, xacD, xacE, xacF
Methylobacterium sp. 4-46 Apr-46 araE, xacB, xacC, xacD, xacE, xacF
Methylocapsa acidiphila B2 araE, araA, araB, araD
Methylocapsa aurea KYG araE, araA, araB, araD
Methylocella silvestris BL2 araE, araA, araB, araD
Methylococcus capsulatus Bath araE, araA, araB, araD
Methylocystis bryophila S285 araE, araA, araB, araD
Methyloferula stellata AR4T araE, araA, araB, araD
Methylohalobius crimeensis 10Ki araE, araA, araB, araD
Methylomonas methanica MC09 araE, araA, araB, araD
Methylosarcina fibrata AML-C10 araE, araA, araB, araD
Methylotuvimicrobium alcaliphilum 20Z araE, araA, araB, araD
Methylovulum miyakonense HT12 araE, araA, araB, araD
Mycolicibacterium vanbaalenii PYR-1 araE, araA, araB, araD
Nitratifractor salsuginis DSM 16511 araE, araA, araB, araD
Nitratiruptor tergarcus DSM 16512 araE, araA, araB, araD
Nitriliruptor alkaliphilus DSM 45188 gguA, gguB, chvE, araA, araB, araD
Nocardioides dokdonensis FR1436 araE, araA, araB, araD
Nocardiopsis lucentensis DSM 44048 araE, araA, araB, araD
Nostoc punctiforme ATCC 29133; PCC 73102 araE, xacB, xacC, xacD, xacE, xacF
Novosphingobium aromaticivorans DSM 12444 araE, araA, araB, araD
Oleispira antarctica araE, araA, araB, araD
Paraburkholderia atlantica CCGE1002 araF, araG, araH, xacB, xacC, xacD, xacE, xacF
Paraburkholderia bryophila 376MFSha3.1 araF, araG, araH, xacB, xacC, xacD, xacE, xacF
Paraburkholderia phymatum STM815 araF, araG, araH, xacB, xacC, xacD, xacE, xacF
Paucidesulfovibrio gracilis DSM 16080 araE, araA, araB, araD
Pedobacter sp. GW460-11-11-14-LB5 araE, araA, araB, araD
Pelobacter propionicus DSM 2379 araE, araA, araB, araD
Persephonella marina EX-H1 araE, araA, araB, araD
Phaeacidiphilus oryzae TH49 xylFsa, xylGsa, xylHsa, araA, araB, araD
Phaeobacter inhibens BS107 araE, xacB, xacC, xacD, xacE, xacF
Polaromonas naphthalenivorans CJ2 araE, xacB, xacC, xacD, xacE, xacF
Prosthecochloris aestuarii DSM 271 araE, araA, araB, araD
Pseudarthrobacter sulfonivorans Ar51 gguA, gguB, chvE, araA, araB, araD
Pseudomonas benzenivorans DSM 8628 araE, araA, araB, araD
Pseudomonas fluorescens FW300-N1B4 araF, araG, araH, xacB, xacC, xacD, xacE, xacF
Pseudomonas fluorescens FW300-N2C3 araF, araG, araH, xacB, xacC, xacD, xacE, xacF
Pseudomonas fluorescens FW300-N2E2 araF, araG, araH, xacB, xacC, xacD, xacE, xacF
Pseudomonas fluorescens FW300-N2E3 araE, xacB, xacC, xacD, xacE, xacF
Pseudomonas fluorescens GW456-L13 araF, araG, araH, xacB, xacC, xacD, xacE, xacF
Pseudomonas putida KT2440 araE, araA, araB, araD
Pseudomonas simiae WCS417 araF, araG, araH, xacB, xacC, xacD, xacE, xacF
Pseudomonas stutzeri RCH2 araE, araA, araB, araD
Pyrolobus fumarii 1A araE, araA, araB, araD
Rhizobium etli CFN 42 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Rhizobium johnstonii 3841 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Rhizobium leguminosarum WSM1325 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Rhizorhabdus wittichii RW1 araE, araA, araB, araD
Rhodanobacter denitrificans FW104-10B01 araE, araA, araB, araD
Rhodomicrobium vannielii ATCC 17100 araE, araA, araB, araD
Rhodopseudomonas palustris CGA009 araE, xacB, xacC, xacD, xacE, xacF
Rhodospirillum centenum SW; ATCC 51521 araE, araA, araB, araD
Rhodospirillum rubrum ATCC 11170 araE, araA, araB, araD
Roseburia faecis M72 araUsh, araVsh, araWsh, araZsh, araA, araB, araD
Saccharomonospora cyanea NA-134 araUsh, araVsh, araWsh, araZsh, xacB, xacC, xacD, xacE, xacF
Sedimenticola selenatireducens DSM 17993 araE, araA, araB, araD
Shewanella amazonensis SB2B araE, araA, araB, araD
Shewanella loihica PV-4 Echvi_1880, araA, araB, araD
Shewanella oneidensis MR-1 araE, araA, araB, araD
Shewanella sp. ANA-3 araUsh, araVsh, araWsh, araZsh, araA, araB, araD
Sinorhizobium fredii NGR234 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Sinorhizobium medicae WSM419 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Sinorhizobium meliloti 1021 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Sphingomonas koreensis DSMZ 15582 araE, xacB, xacC, xacD, xacE, xacF
Stenotrophomonas chelatiphaga DSM 21508 Echvi_1880, xacB, xacC, xacD, KDG-aldolase, aldA, gyaR, glcB
Steroidobacter denitrificans DSM 18526 araE, araA, araB, araD
Stutzerimonas stutzeri A1501 araE, araA, araB, araD
Sulfuricurvum kujiense DSM 16994 araE, araA, araB, araD
Sulfurihydrogenibium azorense Az-Fu1 araE, araA, araB, araD
Sulfurihydrogenibium subterraneum DSM 15120 araE, araA, araB, araD
Sulfurimonas denitrificans DSM 1251 araE, araA, araB, araD
Sulfuritalea hydrogenivorans DSM 22779 araE, araA, araB, araD
Sulfurivirga caldicuralii DSM 17737 araE, araA, araB, araD
Synechococcus elongatus PCC 7942 araE, araA, araB, araD
Teredinibacter turnerae T7901 araE, araA, araB, araD
Thauera aminoaromatica S2 araE, araA, araB, araD
Thermithiobacillus tepidarius DSM 3134 araE, araA, araB, araD
Thermocrinis albus DSM 14484 araE, araA, araB, araD
Thermodesulforhabdus norvegica DSM 9990 araE, araA, araB, araD
Thermomonospora curvata DSM 43183 araE, araA, araB, araD
Thermovibrio ammonificans HB-1 araE, araA, araB, araD
Thermus aquaticus YT-1 araE, araA, araB, araD
Thioalkalivibrio denitrificans ALJD araE, araA, araB, araD
Thioalkalivibrio halophilus HL17 araE, araA, araB, araD
Thioalkalivibrio paradoxus ARh 1 araE, araA, araB, araD
Thioalkalivibrio thiocyanodenitrificans ARhD 1 araE, araA, araB, araD
Thiohalomonas denitrificans HLD2 araE, araA, araB, araD
Thiohalospira halophila HL 3 araE, araA, araB, araD
Thiomicrorhabdus arctica DSM 13458 araE, araA, araB, araD
Thiomicrorhabdus chilensis DSM 12352 araE, araA, araB, araD
Thiomicrospira cyclica ALM1 araE, araA, araB, araD
Thiomicrospira microaerophila ASL8-2 araE, araA, araB, araD
Thiomicrospira pelophila DSM 1534 araE, araA, araB, araD
Thiothrix lacustris DSM 21227 araE, araA, araB, araD
Tistlia consotensis USBA 355 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Trichlorobacter lovleyi SZ araE, araA, araB, araD
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome araE, araA, araB, araD
Trichormus variabilis ATCC 29413 araE, araA, araB, araD
Xanthobacter autotrophicus Py2 araE, xacB, xacC, xacD, xacE, xacF
Xenophilus azovorans DSM 13620 araE, xacB, xacC, xacD, xacE, xacF

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