GapMind for catabolism of small carbon sources

 

D-mannitol catabolism

Analysis of pathway mannitol in 276 genomes

Genome Best path
Acidovorax caeni R-24608 mtlA, mtlD
Actinokineospora bangkokensis 44EHW PLT5, mt2d, scrK
Actinomyces timonensis 7400942 PLT5, mt2d, scrK
Algiphilus aromaticivorans DG1253 mtlA, mtlD
Algoriphagus aquaeductus T4 PLT5, mt2d, scrK
Algoriphagus machipongonensis PR1 PLT5, mt2d, scrK
Alicyclobacillus ferrooxydans TC-34 PLT5, mt2d, scrK
Alishewanella agri BL06 PLT5, mt2d, scrK
Alistipes indistinctus YIT 12060 mtlA, mtlD
Alistipes shahii WAL 8301 mtlA, mtlD
Alkalitalea saponilacus SC/BZ-SP2 mtlA, mtlD
Amantichitinum ursilacus IGB-41 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Amphibacillus jilinensis Y1 cmtA, cmtB, mtlD
Amphritea japonica JAMM 1866 mtlA, mtlD
Amycolatopsis halophila YIM 93223 mtlA, mtlD
Amycolatopsis xylanica CPCC 202699 cmtA*, cmtB, mtlD
Aquimarina agarilytica ZC1 mtlA, mtlD
Aquimarina longa SW024 mtlA, mtlD
Aquimarina macrocephali JAMB N27 mtlA, mtlD
Archaeoglobus sulfaticallidus PM70-1 mtlA, mtlD
Arcticibacter svalbardensis MN12-7 mtlA, mtlD
Ardenticatena maritima 110S PLT5, mt2d, scrK
Arenimonas metalli CF5-1 mtlA, mtlD
Arenitalea lutea P7-3-5 mtlA, mtlD
Azospirillum humicireducens SgZ-5 PLT5, mt2d, scrK
Azospirillum thiophilum BV-S mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Bacillus altitudinis 41KF2b cmtA, cmtB, mtlD
Bacillus coahuilensis m4-4 PLT5, mt2d, scrK
Bacillus cytotoxicus NVH 391-98 mtlA, mtlD
Bacillus horneckiae 1P01SC mtlA, mtlD
Bacillus okhensis Kh10-101 cmtA, cmtB, mtlD
Bacillus safensis FO-36b cmtA, cmtB, mtlD
Bacillus velezensis CBMB205 cmtA, cmtB, mtlD
Bacteroides clarus YIT 12056 PLT5, mt2d, scrK
Bacteroides faecis MAJ27 PLT5, mt2d, scrK
Bacteroides fluxus YIT 12057 PLT5, mt2d, scrK
Bacteroides oleiciplenus YIT 12058 PLT5, mt2d, scrK
Barnesiella intestinihominis YIT 11860 mtlA, mtlD
Belnapia rosea CPCC 100156 PLT5, mt1d, mak, manA
Bizionia argentinensis JUB59 mtlA, mtlD
Bradyrhizobium diazoefficiens USDA110 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Brevibacterium jeotgali SJ5-8 PLT5, mt1d, mak, manA
Brucella inopinata BO1 PLT5, mt2d, scrK
Brucella microti CCM 4915 PLT5, mt2d, scrK
Bryobacter aggregatus MPL3 PLT5, mt2d, scrK
Caldicellulosiruptor hydrothermalis 108 mtlA, mtlD
Caldicellulosiruptor kronotskyensis 2002 PLT5, mt2d, scrK
Carboxydothermus pertinax Ug1 mtlA, mtlD
Catellicoccus marimammalium M35/04/3 mtlA, mtlD
Chromobacterium vaccinii MWU205 PLT5, mt2d, scrK
Chryseobacterium angstadtii KM PLT5, mt2d, scrK
Chryseobacterium arthrosphaerae CC-VM-7 PLT5, mt2d, scrK
Chryseobacterium viscerum 687B-08 PLT5, mt2d, scrK
Cloacibacillus porcorum CL-84 mtlA, mtlD
Cobetia crustatorum JO1 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Collimonas arenae Ter10 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Collimonas pratensis Ter91 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Collinsella tanakaei YIT 12063 PLT5, mt2d, scrK
Coprobacter fastidiosus NSB1 PLT5, mt2d, scrK
Corynebacterium deserti GIMN1.010 PLT5, mt2d, scrK
Corynebacterium frankenforstense ST18 PLT5, mt2d, scrK
Corynebacterium lactis RW2-5 mtlA, mtlD
Croceitalea dokdonensis DOKDO 023 PLT5, mt2d, scrK
Cronobacter condimenti 1330 PLT5, mt1d, mak, manA
Cronobacter muytjensii ATCC 51329 mtlA, mtlD
Cronobacter universalis NCTC 9529 mtlA, mtlD
Desulfatitalea tepidiphila S28bF mtlA, mtlD
Desulfotomaculum hydrothermale Lam5 PLT5, mt2d, scrK
Dethiosulfovibrio salsuginis USBA 82 mtlA, mtlD
Devosia chinhatensis IPL18 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Devriesea agamarum IMP2 PLT5, mt1d, mak, manA
Dialister succinatiphilus YIT 11850 PLT5, mt2d, scrK
Dietzia timorensis ID05-A0528 PLT5, mt1d, mak, manA
Dokdonella koreensis DS-123 mtlA, mtlD
Domibacillus robiginosus WS 4628 mtlA, mtlD
Duganella sacchari Sac-22 PLT5, mt2d, scrK
Dyadobacter tibetensis Y620-1 PLT5, mt2d, scrK
Dyella jiangningensis SBZ3-12 PLT5, mt2d, scrK
Endozoicomonas montiporae CL-33 mtlA, mtlD
Enterococcus termitis LMG 8895 PLT5, mt2d, scrK
Enterorhabdus caecimuris B7 mtlA, mtlD
Epibacterium ulvae U95 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Erythrobacter gangjinensis K7-2 mtlA, mtlD
Erythrobacter marinus HWDM-33 PLT5, mt2d, scrK
Ethanoligenens harbinense YUAN-3 cmtA, cmtB, mtlD
Fervidicella metallireducens AeB mtlA, mtlD
Fibrella aestuarina BUZ 2 PLT5, mt1d, mak, manA
Flammeovirga pacifica WPAGA1 mtlA, mtlD
Flaviramulus ichthyoenteri Th78 mtlA, mtlD
Flavobacterium beibuense F44-8 PLT5, mt1d, mak, manA
Flavobacterium glycines Gm-149 PLT5, mt2d, scrK
Flavobacterium sp. LM5 mtlA, mtlD
Flavobacterium ummariense DS-12 mtlA, mtlD
Frischella perrara PEB0191 PLT5, mt1d, mak, manA
Galbibacter marinus ck-I2-15 mtlA, mtlD
Gallaecimonas xiamenensis 3-C-1 PLT5, mt2d, scrK
Geobacter daltonii FRC-32 mtlA, mtlD
Gillisia marina CBA3202 mtlA, mtlD
Gracilibacillus halophilus YIM-C55.5 cmtA, cmtB, mtlD
Granulicella mallensis MP5ACTX8 PLT5, mt1d, mak, manA
Granulicella tundricola MP5ACTX9 PLT5, mt1d, mak, manA
Hafnia paralvei ATCC 29927 mtlA, mtlD
Haladaptatus cibarius D43 mtlA, mtlD
Halioglobus japonicus S1-36 mtlA, mtlD
Halobacillus alkaliphilus FP5 cmtA, cmtB, mtlD
Halococcus hamelinensis 100A6 PLT5, mt2d, scrK
Halomonas salina B6 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Halomonas smyrnensis AAD6 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Halomonas stevensii S18214 PLT5, mt2d, scrK
Halomonas titanicae BH1 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Halomonas xinjiangensis TRM 0175 PLT5, mt2d, scrK
Halopiger salifodinae KCY07-B2 mtlA, mtlD
Halostagnicola larsenii XH-48 mtlA, mtlD
Haloterrigena daqingensis JX313 mtlA, mtlD
Herbaspirillum aquaticum IEH 4430 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Hippea alviniae EP5-r mtlA, mtlD
Hippea jasoniae Mar08-272r mtlA, mtlD
Hoeflea phototrophica DFL-43 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Hyphomicrobium nitrativorans NL23 mtlA, mtlD
Imtechella halotolerans K1 mtlA, mtlD
Indibacter alkaliphilus LW1 PLT5, mt2d, scrK
Jannaschia aquimarina GSW-M26 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Jeotgalibacillus soli P9 cmtA, cmtB, mtlD
Kangiella geojedonensis YCS-5 mtlA, mtlD
Knoellia flava TL1 PLT5, mt2d, scrK
Kocuria flava HO-9041 mtlA, mtlD
Kocuria turfanensis HO-9042 cmtA, cmtB, mtlD
Laceyella sediminis RHA1 cmtA, cmtB, mtlD
Lacinutrix algicola AKS293 PLT5, mt2d, scrK
Lacinutrix himadriensis E4-9a PLT5, mt2d, scrK
Lacinutrix mariniflava AKS432 PLT5, mt2d, scrK
Lactobacillus curieae CCTCC M 2011381 PLT5, mt2d, scrK
Lactobacillus delbrueckii ZN7a-9 PLT5, mt2d, scrK
Lactobacillus hokkaidonensis LOOC260 mtlA, mtlD
Lactobacillus oryzae SG293 PLT5, mt2d, scrK
Lactobacillus pobuzihii E100301 PLT5, mt2d, scrK
Lactobacillus shenzhenensis LY-73 PLT5, mt2d, scrK
Lactobacillus silagei IWT126 PLT5, mt2d, scrK
Leeuwenhoekiella blandensis MED217 mtlA, mtlD
Lentibacillus jeotgali Grbi cmtA, cmtB, mtlD
Limnohabitans curvus MWH-C5 mtlA, mtlD
Limnohabitans parvus II-B4 PLT5, mt2d, scrK
Listeria fleischmannii LU2006-1 cmtA, cmtB, mtlD
Luteimonas huabeiensis HB2 PLT5, mt2d, scrK
Luteipulveratus mongoliensis MN07-A0370 PLT5, mt2d, scrK
Lutibaculum baratangense AMV1 PLT5, mt2d, scrK
Lysobacter daejeonensis GH1-9 PLT5, mt1d, mak, manA
Magnetovibrio blakemorei MV-1 PLT5, mt1d, mak, manA
Marinicella litoralis KMM 3900 mtlA, mtlD
Mariniradius saccharolyticus AK6 PLT5, mt2d, scrK
Marinobacter algicola DG893 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Marinobacter guineae M3B mtlA, mtlD
Marinobacter psychrophilus 20041 PLT5, mt1d, mak, manA
Marinomonas arctica 328 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Marivita geojedonensis DPG-138 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Martelella endophytica YC6887 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Megamonas funiformis YIT 11815 mtlA, mtlD
Mesorhizobium ciceri WSM1271 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Methanobacterium arcticum M2 mtlA, mtlD
Methanobacterium veterum MK4 mtlA, mtlD
Methanocella arvoryzae MRE50 mtlA, mtlD
Methanococcus aeolicus Nankai-3 mtlA, mtlD
Methanoculleus horonobensis T10 mtlA, mtlD
Methanolinea tarda NOBI-1 mtlA, mtlD
Methanosarcina soligelidi SMA-21 mtlA, mtlD
Methanospirillum lacunae Ki8-1 mtlA, mtlD
Methanospirillum stamsii Pt1 mtlA, mtlD
Methylibium petroleiphilum PM1 mtlA, mtlD
Methylobacterium gossipiicola Gh-105 PLT5, mt2d, scrK
Methylocapsa aurea KYG mtlA, mtlD
Methylotenera versatilis 301 mtlA, mtlD
Microbacterium profundi Shh49 cmtA, cmtB, mtlD
Microvirga lotononidis WSM3557 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Moritella dasanensis ArB 0140 mtlA, mtlD
Mucilaginibacter gossypii Gh-67 PLT5, mt2d, scrK
Mucilaginibacter gossypiicola Gh-48 PLT5, mt2d, scrK
Mucilaginibacter mallensis MP1X4 PLT5, mt2d, scrK
Nafulsella turpanensis ZLM-10 mtlA, mtlD
Natronomonas moolapensis 8.8.11 mtlA, mtlD
Nautilia profundicola AmH mtlA, mtlD
Neiella marina J221 PLT5, mt2d, scrK
Neptunomonas antarctica S3-22 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Nocardioides daejeonensis MJ31 mtlA, mtlD
Nocardioides dokdonensis FR1436 mtlA, mtlD
Nocardiopsis baichengensis YIM 90130 PLT5, mt2d, scrK
Nocardiopsis gilva YIM 90087 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Novosphingobium barchaimii LL02 PLT5, mt2d, scrK
Novosphingobium fuchskuhlense FNE08-7 PLT5, mt2d, scrK
Novosphingobium lindaniclasticum LE124 PLT5, mt2d, scrK
Oceanisphaera arctica V1-41 mtlA, mtlD
Ochrobactrum rhizosphaerae PR17 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Ochrobactrum thiophenivorans DSM 7216 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Oscillibacter ruminantium GH1 PLT5, mt2d, scrK
Paenisporosarcina indica PN2 mtlA, mtlD
Palaeococcus pacificus DY20341 mtlA, mtlD
Paludibacter propionicigenes WB4 mtlA, mtlD
Pandoraea thiooxydans ATSB16 mtlA, mtlD
Pantoea rwandensis LMG 26275 mtlA, mtlD
Pedobacter arcticus A12 mtlA, mtlD
Photobacterium gaetbulicola Gung47 cmtA, cmtB, mtlD
Photobacterium jeanii R-40508 PLT5, mt2d, scrK
Phyllobacterium brassicacearum STM 196 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Phyllobacterium endophyticum PEPV15 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Phyllobacterium leguminum ORS 1419 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Planktomarina temperata RCA23 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Planococcus halocryophilus Or1 cmtA, cmtB, mtlD
Pleomorphomonas diazotrophica R5-392 mtlA, mtlD
Polaribacter dokdonensis DSW-5 PLT5, mt2d, scrK
Pontibacillus litoralis JSM 072002 mtlA, mtlD
Pontibacter lucknowensis DM9 mtlA, mtlD
Pontibacter ramchanderi LP43 mtlA, mtlD
Pontimonas salivibrio CL-TW6 PLT5, mt1d, mak, manA
Porphyrobacter dokdonensis DSW-74 PLT5, mt2d, scrK
Pseudoalteromonas arctica A 37-1-2 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Pseudomonas baetica a390 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Pseudomonas litoralis 2SM5 mtlA, mtlD
Pseudomonas taeanensis MS-3 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Pseudovibrio axinellae Ad2 PLT5, mt1d, mak, manA
Psychrobacter arcticus 273-4 mtlA, mtlD
Psychrobacter cryohalolentis K5 mtlA, mtlD
Psychromonas ingrahamii 37 mtlA, mtlD
Psychromonas ossibalaenae JAMM 0738 PLT5, mt2d, scrK
Rhizobium freirei PRF 81 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Rhizobium grahamii CCGE 502 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Rhizobium subbaraonis JC85 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Rhodanobacter denitrificans 2APBS1 PLT5, mt2d, scrK
Rhodobacter johrii JA192 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Rhodobacter maris JA276 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Rhodobacter ovatus JA234 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Rhodobacter viridis JA737 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Rhodococcus qingshengii djl-6-2 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Rhodopseudomonas pseudopalustris DSM 123 mtlA, mtlD
Roseateles aquatilis CCUG 48205 PLT5, mt2d, scrK
Roseivirga spongicola UST030701-084 mtlA, mtlD
Rubrivirga marina SAORIC-28 PLT5, mt2d, scrK
Ruegeria conchae TW15 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Saccharomonospora marina XMU15 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Salinicoccus carnicancri Crm cmtA, cmtB, mtlD
Serinicoccus profundi MCCC 1A05965 PLT5, mt1d, mak, manA
Shewanella halifaxensis HAW-EB4 mtlA, mtlD
Skermanella stibiiresistens SB22 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Snodgrassella alvi wkB2 mtlA, mtlD
Sphaerochaeta globosa Buddy mtlA, mtlD
Sphaerochaeta pleomorpha Grapes mtlA, mtlD
Sphingobium baderi LL03 mtlA, mtlD
Sphingobium czechense LL01 PLT5, mt2d, scrK
Sphingobium quisquiliarum P25 mtlA, mtlD
Sphingomonas histidinilytica UM2 PLT5, mt2d, scrK
Sphingomonas indica Dd16 PLT5, mt1d, mak, manA
Sphingomonas laterariae LNB2 mtlA, mtlD
Sphingopyxis indica DS15 PLT5, mt2d, scrK
Sphingopyxis terrae UI2 mtlA, mtlD
Sporolactobacillus vineae SL153 mtlA, mtlD
Streptacidiphilus oryzae TH49 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Streptococcus anginosus CCUG 39159 PLT5, mt2d, scrK
Streptococcus massiliensis 4401825 PLT5, mt2d, scrK
Streptococcus oralis 7747 gutB, gutE, gutA, mtlD
Streptococcus oralis AZ_3a PLT5, mt2d, scrK
Streptomyces kebangsaanensis SUK12 PLT5, mt2d, scrK
Succinatimonas hippei YIT 12066 mtlA, mtlD
Sulfurimonas gotlandica GD1 mtlA, mtlD
Tatumella morbirosei LMG 23360 cmtA, cmtB, mtlD
Thauera humireducens SgZ-1 PLT5, mt2d, scrK
Thermoactinomyces daqus H-18 cmtA, cmtB, mtlD
Thermobifida halotolerans YIM 90462 mtlA, mtlD
Thermodesulfovibrio aggregans TGE-P1 mtlA, mtlD
Thermophagus xiamenensis HS1 mtlA, mtlD
Thermovenabulum gondwanense R270 cmtA, cmtB, mtlD
Thioclava dalianensis DLFJ1-1 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Thiohalospira halophila HL 3 PLT5, mt2d, scrK
Tistlia consotensis USBA 355 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Vagococcus penaei CD276 PLT5, mt2d, scrK
Verminephrobacter eiseniae EF01-2 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Weissella oryzae SG25 PLT5, mt2d, scrK
Williamsia sterculiae CPCC 203464 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Yersinia intermedia Y228 gutB, gutE, gutA, mtlD

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