GapMind for catabolism of small carbon sources

 

D-sorbitol (glucitol) catabolism

Analysis of pathway sorbitol in 201 genomes

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

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.

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