L-arabinose catabolism

GapMind for catabolism of small carbon sources

L-arabinose catabolism

Analysis of pathway arabinose in 150 genomes

Genome	Best path
Acidimicrobium ferrooxidans DSM 10331	araE, araA, araB, araD
Acidithiobacillus ferrooxidans ATCC 23270	araE, araA, araB, araD
Alicycliphilus denitrificans K601	araE, araA, araB, araD
Allochromatium vinosum DSM 180	araE, araA, araB, araD
Ammonifex degensii KC4	araE, araA, araB, araD
Archaeoglobus veneficus SNP6	araE, araA, araB, araD
Arcobacter nitrofigilis DSM 7299	araE, araA, araB, araD
Azoarcus sp. 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 lipoferum B510	gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Bacillus alkalinitrilicus DSM 22532	araE, 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
Bradyrhizobium sp. BTAi1	gguA, gguB, chvE, 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
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
Crocosphaera subtropica ATCC 51142	araE, araA, araB, araD
Dechloromonas agitata is5	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
Desulfallas geothermicus DSM 3669	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
Desulfobulbus mediterraneus DSM 13871	araE, araA, araB, araD
Desulfotalea psychrophila LSv54	araE, araA, araB, araD
Desulfotomaculum ruminis DSM 2154	araE, araA, araB, araD
Desulfovibrio bastinii DSM 16055	araE, araA, araB, araD
Desulfovibrio gracilis DSM 16080	araE, araA, araB, araD
Desulfovibrio oxyclinae DSM 11498	araE, araA, araB, araD
Desulfovibrio zosterae DSM 11974	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
Ferroglobus placidus DSM 10642	araE, araA, araB, araD
Frankia alni ACN14A	araE, xacB, xacC, xacD, xacE, xacF
Geobacter lovleyi SZ	araE, araA, araB, araD
Geobacter metallireducens GS-15	araE, araA, araB, araD
Geobacter uraniireducens Rf4	araE, araA, araB, araD
Haloechinothrix alba DSM 45207	araE, araA, araB, araD
Haloglycomyces albus DSM 45210	gguA, gguB, chvE, araA, araB, araD
Halomonas desiderata SP1	araF, araG, araH, xacB, xacC, xacD, xacE, xacF
Halorhodospira halophila SL1	araE, araA, araB, araD
Heliobacterium modesticaldum Ice1; ATCC 51547	araE, araA, araB, araD
Herbaspirillum autotrophicum IAM 14942	araE, xacB, xacC, xacD, xacE, xacF
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 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
Malonomonas rubra DSM 5091	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 barkeri Fusaro	araE, araA, araB, araD
Methanosarcina mazei Go1	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	araE, xacB, xacC, xacD, xacE, xacF
Methylocapsa acidiphila B2	araE, araA, araB, araD
Methylocapsa aurea KYG T	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
Methylomicrobium alcaliphilum 20Z	araE, araA, araB, araD
Methylomonas methanica MC09	araE, araA, araB, araD
Methylosarcina fibrata AML-C10	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
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 phymatum STM815	araF, araG, araH, xacB, xacC, xacD, xacE, xacF
Paraburkholderia sp. CCGE1002	araF, araG, araH, xacB, xacC, xacD, xacE, xacF
Pelobacter propionicus DSM 2379	araE, araA, araB, araD
Persephonella marina EX-H1	araE, araA, araB, araD
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 stutzeri A1501	araE, araA, araB, araD
Pyrolobus fumarii 1A	araE, araA, araB, araD
Rhizobium etli CFN 42	gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Rhizobium leguminosarum 3841	gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Rhizobium leguminosarum WSM1325	gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Rhodobacter sphaeroides ATCC 17029	araE, xacB, xacC, xacD, xacE, xacF
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
Saccharomonospora cyanea NA-134	araUsh, araVsh, araWsh, araZsh, xacB, xacC, xacD, xacE, xacF
Sedimenticola selenatireducens DSM 17993	araE, 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
Sphingomonas wittichii RW1	araE, araA, araB, araD
Stenotrophomonas chelatiphaga DSM 21508	Echvi_1880, xacB, xacC, xacD, KDG-aldolase, aldA, gyaR, glcB
Steroidobacter denitrificans DSM 18526	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
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
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
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
Trichodesmium erythraeum IMS101	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 Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources