GapMind for catabolism of small carbon sources

 

D-sorbitol (glucitol) catabolism

Analysis of pathway sorbitol in 276 genomes

Genome Best path
Acidovorax caeni R-24608 mtlA, srlD
Actinokineospora bangkokensis 44EHW mtlE, mtlF, mtlG, mtlK, sdh, scrK
Actinomyces timonensis 7400942 SOT, sdh, scrK
Algiphilus aromaticivorans DG1253 SOT, sdh, scrK
Algoriphagus aquaeductus T4 SOT, sdh, scrK
Algoriphagus machipongonensis PR1 SOT, sdh, scrK
Alicyclobacillus ferrooxydans TC-34 SOT, sdh, scrK
Alishewanella agri BL06 SOT, sdh, scrK
Alistipes indistinctus YIT 12060 SOT, sdh, scrK
Alistipes shahii WAL 8301 mtlA, srlD
Alkalitalea saponilacus SC/BZ-SP2 mtlA, srlD
Amantichitinum ursilacus IGB-41 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Amphibacillus jilinensis Y1 srlA, srlB, srlE, srlD
Amphritea japonica JAMM 1866 mtlA, srlD
Amycolatopsis halophila YIM 93223 SOT, sdh, scrK
Amycolatopsis xylanica CPCC 202699 SOT, sdh, scrK
Aquimarina agarilytica ZC1 mtlA, srlD
Aquimarina longa SW024 mtlA, srlD
Aquimarina macrocephali JAMB N27 mtlA, srlD
Archaeoglobus sulfaticallidus PM70-1 mtlA, srlD
Arcticibacter svalbardensis MN12-7 mtlA, srlD
Ardenticatena maritima 110S SOT, sdh, scrK
Arenimonas metalli CF5-1 mtlA, srlD
Arenitalea lutea P7-3-5 SOT, sdh, scrK
Azospirillum humicireducens SgZ-5 SOT, sdh, scrK
Azospirillum thiophilum BV-S mtlE, mtlF, mtlG, mtlK, sdh, scrK
Bacillus altitudinis 41KF2b SOT, sdh, scrK
Bacillus coahuilensis m4-4 SOT, sdh, scrK
Bacillus cytotoxicus NVH 391-98 mtlA, srlD
Bacillus horneckiae 1P01SC SOT, sdh, scrK
Bacillus okhensis Kh10-101 SOT, sdh, scrK
Bacillus safensis FO-36b SOT, sdh, scrK
Bacillus velezensis CBMB205 SOT, sdh, scrK
Bacteroides clarus YIT 12056 SOT, sdh, scrK
Bacteroides faecis MAJ27 SOT, sdh, scrK
Bacteroides fluxus YIT 12057 SOT, sdh, scrK
Bacteroides oleiciplenus YIT 12058 SOT, sdh, scrK
Barnesiella intestinihominis YIT 11860 mtlA, srlD
Belnapia rosea CPCC 100156 SOT, sdh, scrK
Bizionia argentinensis JUB59 mtlA, srlD
Bradyrhizobium diazoefficiens USDA110 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Brevibacterium jeotgali SJ5-8 mtlA, srlD
Brucella inopinata BO1 SOT, sdh, scrK
Brucella microti CCM 4915 SOT, sdh, scrK
Bryobacter aggregatus MPL3 SOT, sdh, scrK
Caldicellulosiruptor hydrothermalis 108 mtlA, srlD
Caldicellulosiruptor kronotskyensis 2002 mtlA, srlD
Carboxydothermus pertinax Ug1 mtlA, srlD
Catellicoccus marimammalium M35/04/3 mtlA, srlD
Chromobacterium vaccinii MWU205 SOT, sdh, scrK
Chryseobacterium angstadtii KM SOT, sdh, scrK
Chryseobacterium arthrosphaerae CC-VM-7 SOT, sdh, scrK
Chryseobacterium viscerum 687B-08 SOT, sdh, scrK
Cloacibacillus porcorum CL-84 mtlA, srlD
Cobetia crustatorum JO1 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Collimonas arenae Ter10 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Collimonas pratensis Ter91 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Collinsella tanakaei YIT 12063 SOT, sdh, scrK
Coprobacter fastidiosus NSB1 SOT, sdh, scrK
Corynebacterium deserti GIMN1.010 mtlA, srlD
Corynebacterium frankenforstense ST18 SOT, sdh, scrK
Corynebacterium lactis RW2-5 mtlA, srlD
Croceitalea dokdonensis DOKDO 023 SOT, sdh, scrK
Cronobacter condimenti 1330 SOT, sdh, scrK
Cronobacter muytjensii ATCC 51329 mtlA, srlD
Cronobacter universalis NCTC 9529 mtlA, srlD
Desulfatitalea tepidiphila S28bF SOT, sdh, scrK
Desulfotomaculum hydrothermale Lam5 SOT, sdh, scrK
Dethiosulfovibrio salsuginis USBA 82 mtlA, srlD
Devosia chinhatensis IPL18 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Devriesea agamarum IMP2 mtlA, srlD
Dialister succinatiphilus YIT 11850 SOT, sdh, scrK
Dietzia timorensis ID05-A0528 mtlA, srlD
Dokdonella koreensis DS-123 mtlA, srlD
Domibacillus robiginosus WS 4628 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Duganella sacchari Sac-22 SOT, sdh, scrK
Dyadobacter tibetensis Y620-1 SOT, sdh, scrK
Dyella jiangningensis SBZ3-12 SOT, sdh, scrK
Endozoicomonas montiporae CL-33 mtlA, srlD
Enterococcus termitis LMG 8895 SOT, sdh, scrK
Enterorhabdus caecimuris B7 mtlA, srlD
Epibacterium ulvae U95 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Erythrobacter gangjinensis K7-2 mtlA, srlD
Erythrobacter marinus HWDM-33 SOT, sdh, scrK
Ethanoligenens harbinense YUAN-3 mtlA, srlD
Fervidicella metallireducens AeB mtlA, srlD
Fibrella aestuarina BUZ 2 SOT, sdh, scrK
Flammeovirga pacifica WPAGA1 mtlA, srlD
Flaviramulus ichthyoenteri Th78 mtlA, srlD
Flavobacterium beibuense F44-8 mtlA, srlD
Flavobacterium glycines Gm-149 SOT, sdh, scrK
Flavobacterium sp. LM5 mtlA, srlD
Flavobacterium ummariense DS-12 mtlA, srlD
Frischella perrara PEB0191 SOT, sdh, scrK
Galbibacter marinus ck-I2-15 mtlA, srlD
Gallaecimonas xiamenensis 3-C-1 mtlA, srlD
Geobacter daltonii FRC-32 mtlA, srlD
Gillisia marina CBA3202 mtlA, srlD
Gracilibacillus halophilus YIM-C55.5 mtlA, srlD
Granulicella mallensis MP5ACTX8 SOT, sdh, scrK
Granulicella tundricola MP5ACTX9 SOT, sdh, scrK
Hafnia paralvei ATCC 29927 mtlA, srlD
Haladaptatus cibarius D43 SOT, sdh, scrK
Halioglobus japonicus S1-36 mtlA, srlD
Halobacillus alkaliphilus FP5 SOT, sdh, scrK
Halococcus hamelinensis 100A6 SOT, sdh, scrK
Halomonas salina B6 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Halomonas smyrnensis AAD6 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Halomonas stevensii S18214 SOT, sdh, scrK
Halomonas titanicae BH1 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Halomonas xinjiangensis TRM 0175 SOT, sdh, scrK
Halopiger salifodinae KCY07-B2 SOT, sdh, scrK
Halostagnicola larsenii XH-48 SOT, sdh, scrK
Haloterrigena daqingensis JX313 mtlA, srlD
Herbaspirillum aquaticum IEH 4430 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Hippea alviniae EP5-r mtlA, srlD
Hippea jasoniae Mar08-272r mtlA, srlD
Hoeflea phototrophica DFL-43 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Hyphomicrobium nitrativorans NL23 SOT, sdh, scrK
Imtechella halotolerans K1 mtlA, srlD
Indibacter alkaliphilus LW1 SOT, sdh, scrK
Jannaschia aquimarina GSW-M26 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Jeotgalibacillus soli P9 SOT, sdh, scrK
Kangiella geojedonensis YCS-5 mtlA, srlD
Knoellia flava TL1 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Kocuria flava HO-9041 mtlA, srlD
Kocuria turfanensis HO-9042 mtlA, srlD
Laceyella sediminis RHA1 mtlA, srlD
Lacinutrix algicola AKS293 SOT, sdh, scrK
Lacinutrix himadriensis E4-9a SOT, sdh, scrK
Lacinutrix mariniflava AKS432 mtlA, srlD
Lactobacillus curieae CCTCC M 2011381 SOT, sdh, scrK
Lactobacillus delbrueckii ZN7a-9 SOT, sdh, scrK
Lactobacillus hokkaidonensis LOOC260 mtlA, srlD
Lactobacillus oryzae SG293 SOT, sdh, scrK
Lactobacillus pobuzihii E100301 SOT, sdh, scrK
Lactobacillus shenzhenensis LY-73 SOT, sdh, scrK
Lactobacillus silagei IWT126 SOT, sdh, scrK
Leeuwenhoekiella blandensis MED217 mtlA, srlD
Lentibacillus jeotgali Grbi srlA, srlB, srlE, srlD
Limnohabitans curvus MWH-C5 SOT, sdh, scrK
Limnohabitans parvus II-B4 SOT, sdh, scrK
Listeria fleischmannii LU2006-1 SOT, sdh, scrK
Luteimonas huabeiensis HB2 SOT, sdh, scrK
Luteipulveratus mongoliensis MN07-A0370 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Lutibaculum baratangense AMV1 SOT, sdh, scrK
Lysobacter daejeonensis GH1-9 mtlA, srlD
Magnetovibrio blakemorei MV-1 SOT, sdh, scrK
Marinicella litoralis KMM 3900 mtlA, srlD
Mariniradius saccharolyticus AK6 SOT, sdh, scrK
Marinobacter algicola DG893 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Marinobacter guineae M3B mtlA, srlD
Marinobacter psychrophilus 20041 SOT, sdh, scrK
Marinomonas arctica 328 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Marivita geojedonensis DPG-138 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Martelella endophytica YC6887 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Megamonas funiformis YIT 11815 mtlA, srlD
Mesorhizobium ciceri WSM1271 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Methanobacterium arcticum M2 mtlA, srlD
Methanobacterium veterum MK4 mtlA, srlD
Methanocella arvoryzae MRE50 mtlA, srlD
Methanococcus aeolicus Nankai-3 mtlA, srlD
Methanoculleus horonobensis T10 mtlA, srlD
Methanolinea tarda NOBI-1 mtlA, srlD
Methanosarcina soligelidi SMA-21 mtlA, srlD
Methanospirillum lacunae Ki8-1 mtlA, srlD
Methanospirillum stamsii Pt1 mtlA, srlD
Methylibium petroleiphilum PM1 SOT, sdh, scrK
Methylobacterium gossipiicola Gh-105 SOT, sdh, scrK
Methylocapsa aurea KYG SOT, sdh, scrK
Methylotenera versatilis 301 mtlA, srlD
Microbacterium profundi Shh49 mtlA, srlD
Microvirga lotononidis WSM3557 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Moritella dasanensis ArB 0140 mtlA, srlD
Mucilaginibacter gossypii Gh-67 SOT, sdh, scrK
Mucilaginibacter gossypiicola Gh-48 SOT, sdh, scrK
Mucilaginibacter mallensis MP1X4 SOT, sdh, scrK
Nafulsella turpanensis ZLM-10 mtlA, srlD
Natronomonas moolapensis 8.8.11 mtlA, srlD
Nautilia profundicola AmH mtlA, srlD
Neiella marina J221 SOT, sdh, scrK
Neptunomonas antarctica S3-22 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Nocardioides daejeonensis MJ31 SOT, sdh, scrK
Nocardioides dokdonensis FR1436 mtlA, srlD
Nocardiopsis baichengensis YIM 90130 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Nocardiopsis gilva YIM 90087 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Novosphingobium barchaimii LL02 SOT, sdh, scrK
Novosphingobium fuchskuhlense FNE08-7 SOT, sdh, scrK
Novosphingobium lindaniclasticum LE124 SOT, sdh, scrK
Oceanisphaera arctica V1-41 mtlA, srlD
Ochrobactrum rhizosphaerae PR17 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Ochrobactrum thiophenivorans DSM 7216 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Oscillibacter ruminantium GH1 SOT, sdh, scrK
Paenisporosarcina indica PN2 SOT, sdh, scrK
Palaeococcus pacificus DY20341 mtlA, srlD
Paludibacter propionicigenes WB4 mtlA, srlD
Pandoraea thiooxydans ATSB16 mtlA, srlD
Pantoea rwandensis LMG 26275 SOT, sdh, scrK
Pedobacter arcticus A12 mtlA, srlD
Photobacterium gaetbulicola Gung47 mtlA, srlD
Photobacterium jeanii R-40508 SOT, sdh, scrK
Phyllobacterium brassicacearum STM 196 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Phyllobacterium endophyticum PEPV15 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Phyllobacterium leguminum ORS 1419 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Planktomarina temperata RCA23 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Planococcus halocryophilus Or1 mtlA, srlD
Pleomorphomonas diazotrophica R5-392 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Polaribacter dokdonensis DSW-5 SOT, sdh, scrK
Pontibacillus litoralis JSM 072002 mtlA, srlD
Pontibacter lucknowensis DM9 mtlA, srlD
Pontibacter ramchanderi LP43 mtlA, srlD
Pontimonas salivibrio CL-TW6 mtlA, srlD
Porphyrobacter dokdonensis DSW-74 SOT, sdh, scrK
Pseudoalteromonas arctica A 37-1-2 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Pseudomonas baetica a390 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Pseudomonas litoralis 2SM5 mtlA, srlD
Pseudomonas taeanensis MS-3 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Pseudovibrio axinellae Ad2 SOT, sdh, scrK
Psychrobacter arcticus 273-4 mtlA, srlD
Psychrobacter cryohalolentis K5 mtlA, srlD
Psychromonas ingrahamii 37 mtlA, srlD
Psychromonas ossibalaenae JAMM 0738 SOT, sdh, scrK
Rhizobium freirei PRF 81 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Rhizobium grahamii CCGE 502 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Rhizobium subbaraonis JC85 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Rhodanobacter denitrificans 2APBS1 SOT, sdh, scrK
Rhodobacter johrii JA192 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Rhodobacter maris JA276 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Rhodobacter ovatus JA234 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Rhodobacter viridis JA737 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Rhodococcus qingshengii djl-6-2 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Rhodopseudomonas pseudopalustris DSM 123 mtlA, srlD
Roseateles aquatilis CCUG 48205 SOT, sdh, scrK
Roseivirga spongicola UST030701-084 SOT, sdh, scrK
Rubrivirga marina SAORIC-28 SOT, sdh, scrK
Ruegeria conchae TW15 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Saccharomonospora marina XMU15 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Salinicoccus carnicancri Crm srlA, srlB, srlE, srlD
Serinicoccus profundi MCCC 1A05965 SOT, sdh, scrK
Shewanella halifaxensis HAW-EB4 SOT, sdh, scrK
Skermanella stibiiresistens SB22 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Snodgrassella alvi wkB2 mtlA, srlD
Sphaerochaeta globosa Buddy mtlA, srlD
Sphaerochaeta pleomorpha Grapes mtlE, mtlF, mtlG, mtlK, sdh, scrK
Sphingobium baderi LL03 SOT, sdh, scrK
Sphingobium czechense LL01 SOT, sdh, scrK
Sphingobium quisquiliarum P25 SOT, sdh, scrK
Sphingomonas histidinilytica UM2 SOT, sdh, scrK
Sphingomonas indica Dd16 mtlA, srlD
Sphingomonas laterariae LNB2 mtlA, srlD
Sphingopyxis indica DS15 SOT, sdh, scrK
Sphingopyxis terrae UI2 SOT, sdh, scrK
Sporolactobacillus vineae SL153 srlA, srlB, srlE, srlD
Streptacidiphilus oryzae TH49 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Streptococcus anginosus CCUG 39159 SOT, sdh, scrK
Streptococcus massiliensis 4401825 SOT, sdh, scrK
Streptococcus oralis 7747 srlA, srlB, srlE, srlD
Streptococcus oralis AZ_3a SOT, sdh, scrK
Streptomyces kebangsaanensis SUK12 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Succinatimonas hippei YIT 12066 mtlA, srlD
Sulfurimonas gotlandica GD1 mtlA, srlD
Tatumella morbirosei LMG 23360 SOT, sdh, scrK
Thauera humireducens SgZ-1 SOT, sdh, scrK
Thermoactinomyces daqus H-18 mtlA, srlD
Thermobifida halotolerans YIM 90462 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Thermodesulfovibrio aggregans TGE-P1 mtlA, srlD
Thermophagus xiamenensis HS1 mtlA, srlD
Thermovenabulum gondwanense R270 mtlA, srlD
Thioclava dalianensis DLFJ1-1 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Thiohalospira halophila HL 3 SOT, sdh, scrK
Tistlia consotensis USBA 355 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Vagococcus penaei CD276 SOT, sdh, scrK
Verminephrobacter eiseniae EF01-2 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Weissella oryzae SG25 SOT, sdh, scrK
Williamsia sterculiae CPCC 203464 mtlE, mtlF, mtlG, mtlK, sdh, scrK
Yersinia intermedia Y228 srlA, srlB, srlE, srlD

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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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