GapMind for catabolism of small carbon sources

 

D-mannitol catabolism

Analysis of pathway mannitol in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 mtlA, mtlD
Acidithiobacillus ferrooxidans ATCC 23270 PLT5, mt1d, mak, manA
Acidovorax sp. GW101-3H11 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Algiphilus aromaticivorans DG1253 mtlA, mtlD
Alicycliphilus denitrificans K601 mtlA, mtlD
Alkalihalobacterium alkalinitrilicum DSM 22532 PLT5, mt2d, scrK
Allochromatium vinosum DSM 180 PLT5, mt2d, scrK
Ammonifex degensii KC4 mtlA, mtlD
Anaerobutyricum hallii DSM 3353 mtlA, mtlD
Aquimarina longa SW024 mtlA, mtlD
Archaeoglobus veneficus SNP6 mtlA, mtlD
Arcobacter nitrofigilis DSM 7299 mtlA, mtlD
Azoarcus olearius BH72 mtlA, mtlD
Azohydromonas australica DSM 1124 mtlA, mtlD
Azorhizobium caulinodans ORS 571 mtlA, mtlD
Azospirillum brasilense Sp245 PLT5, mt2d, scrK
Azospirillum sp. B510 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Bacteroides thetaiotaomicron VPI-5482 PLT5, mt2d, scrK
Beijerinckia indica ATCC 9039 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Beijerinckia mobilis UQM 1969 PLT5, mt2d, scrK
Billgrantia desiderata SP1 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Bradyrhizobium sp. BTAi1 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Brevundimonas sp. GW460-12-10-14-LB2 PLT5, mt2d, scrK
Burkholderia phytofirmans PsJN mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Burkholderia vietnamiensis G4 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Calditerrivibrio nitroreducens DSM 19672 mtlA, mtlD
Caminibacter mediatlanticus TB-2 mtlA, mtlD
Carboxydothermus pertinax Ug1 mtlA, mtlD
Caulobacter crescentus NA1000 PLT5, mt2d, scrK
Cereibacter sphaeroides ATCC 17029 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Chlorobaculum parvum NCIB 8327 mtlA, mtlD
Chlorobaculum tepidum TLS mtlA, mtlD
Chlorobium limicola DSM 245 mtlA, mtlD
Chlorobium phaeobacteroides BS1 mtlA, mtlD
Clostridium acetobutylicum ATCC 824 cmtA, cmtB, mtlD
Clostridium kluyveri DSM 555 mtlA, mtlD
Clostridium tyrobutyricum FAM22553 cmtA, cmtB, mtlD
Crocosphaera subtropica ATCC 51142 mtlA, mtlD
Cupriavidus basilensis FW507-4G11 PLT5, mt2d, scrK
Dechloromonas agitata is5 mtlA, mtlD
Dechlorosoma suillum PS mtlA, mtlD
Dehalococcoides mccartyi 195 mtlA, mtlD
Denitrovibrio acetiphilus DSM 12809 mtlA, mtlD
Derxia gummosa DSM 723 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Desulfacinum hydrothermale DSM 13146 mtlA, mtlD
Desulfacinum infernum DSM 9756 mtlA, mtlD
Desulfarculus baarsii DSM 2075 mtlA, mtlD
Desulfatibacillum aliphaticivorans DSM 15576 mtlA, mtlD
Desulfatiglans anilini DSM 4660 mtlA, mtlD
Desulfitobacterium hafniense DCB-2 mtlA, mtlD
Desulfobacca acetoxidans DSM 11109 mtlA, mtlD
Desulfobacter vibrioformis DSM 8776 PLT5, mt2d, scrK
Desulfogranum mediterraneum DSM 13871 PLT5, mt2d, scrK
Desulforamulus ruminis DSM 2154 PLT5, mt2d, scrK
Desulfoscipio geothermicus DSM 3669 mtlA, mtlD
Desulfotalea psychrophila LSv54 mtlA, mtlD
Desulfovibrio oxyclinae DSM 11498 mtlA, mtlD
Desulfovibrio vulgaris Hildenborough JW710 mtlA, mtlD
Desulfovibrio vulgaris Miyazaki F mtlA, mtlD
Desulfurobacterium atlanticum DSM 15668 mtlA, mtlD
Desulfuromonas acetexigens mtlA, mtlD
Desulfuromusa kysingii DSM 7343 mtlA, mtlD
Dinoroseobacter shibae DFL-12 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Dyella japonica UNC79MFTsu3.2 PLT5, mt2d, scrK
Echinicola vietnamensis KMM 6221, DSM 17526 PLT5, mt2d, scrK
Escherichia coli BW25113 gutB, gutE, gutA, mtlD
Ferroglobus placidus DSM 10642 mtlA, mtlD
Frankia alni ACN14a mtlA, mtlD
Geobacter metallireducens GS-15 mtlA, mtlD
Geotalea uraniireducens Rf4 mtlA, mtlD
Halococcus hamelinensis 100A6 PLT5, mt2d, scrK
Haloechinothrix alba DSM 45207 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Haloferax volcanii DS2 mtlA, mtlD
Haloglycomyces albus DSM 45210 mtlA, mtlD
Halorhodospira halophila SL1 mtlA, mtlD
Heliomicrobium modesticaldum Ice1; ATCC 51547 mtlA, mtlD
Herbaspirillum autotrophicum IAM 14942 mtlA, mtlD
Herbaspirillum seropedicae SmR1 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Hippea alviniae EP5-r mtlA, mtlD
Hydrogenophaga taeniospiralis NBRC 102512 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Hydrogenovibrio halophilus DSM 15072 PLT5, mt2d, scrK
Hydrogenovibrio kuenenii DSM 12350 PLT5, mt2d, scrK
Hydrogenovibrio marinus DSM 11271 PLT5, mt1d, mak, manA
Hyphomicrobium sulfonivorans WDL6 mtlA, mtlD
Klebsiella michiganensis M5al gutB, gutE, gutA, mtlD
Klebsiella variicola At-22 gutB, gutE, gutA, mtlD
Kyrpidia tusciae DSM 2912 PLT5, mt2d, scrK
Leptospirillum ferrooxidans C2-3 mtlA, mtlD
Magnetospirillum magneticum AMB-1 PLT5, mt2d, scrK
Malonomonas rubra DSM 5091 mtlA, mtlD
Maridesulfovibrio bastinii DSM 16055 mtlA, mtlD
Maridesulfovibrio zosterae DSM 11974 PLT5, mt2d, scrK
Marinobacter adhaerens HP15 mtlA, mtlD
Mesorhizobium ciceri WSM1271 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Methanobacterium lacus AL-21 mtlA, mtlD
Methanococcus aeolicus Nankai-3 mtlA, mtlD
Methanococcus maripaludis C5 mtlA, mtlD
Methanosarcina acetivorans C2A PLT5, mt1d, mak, manA
Methanosarcina mazei Go1 mtlA, mtlD
Methanospirillum lacunae Ki8-1 mtlA, mtlD
Methanothermobacter thermautotrophicus Delta H mtlA, mtlD
Methylobacterium nodulans ORS 2060 PLT5, mt1d, mak, manA
Methylobacterium sp. 4-46 Apr-46 PLT5, mt2d, scrK
Methylocapsa acidiphila B2 PLT5, mt1d, mak, manA
Methylocapsa aurea KYG mtlA, mtlD
Methylocella silvestris BL2 PLT5, mt1d, mak, manA
Methylococcus capsulatus Bath PLT5, mt1d, mak, manA
Methylocystis bryophila S285 PLT5, mt1d, mak, manA
Methyloferula stellata AR4T mtlA, mtlD
Methylohalobius crimeensis 10Ki PLT5, mt2d, scrK
Methylomonas methanica MC09 PLT5, mt2d, scrK
Methylosarcina fibrata AML-C10 PLT5, mt2d, scrK
Methylotuvimicrobium alcaliphilum 20Z PLT5, mt2d, scrK
Methylovulum miyakonense HT12 PLT5, mt2d, scrK
Mycolicibacterium vanbaalenii PYR-1 mtlA, mtlD
Nitratifractor salsuginis DSM 16511 mtlA, mtlD
Nitratiruptor tergarcus DSM 16512 mtlA, mtlD
Nitriliruptor alkaliphilus DSM 45188 PLT5, mt2d, scrK
Nocardioides dokdonensis FR1436 mtlA, mtlD
Nocardiopsis lucentensis DSM 44048 cmtA*, cmtB, mtlD
Nostoc punctiforme ATCC 29133; PCC 73102 PLT5, mt2d, scrK
Novosphingobium aromaticivorans DSM 12444 PLT5, mt2d, scrK
Oleispira antarctica mtlA, mtlD
Paraburkholderia atlantica CCGE1002 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Paraburkholderia bryophila 376MFSha3.1 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Paraburkholderia phymatum STM815 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Paucidesulfovibrio gracilis DSM 16080 mtlA, mtlD
Pedobacter sp. GW460-11-11-14-LB5 mtlA, mtlD
Pelobacter propionicus DSM 2379 mtlA, mtlD
Persephonella marina EX-H1 mtlA, mtlD
Phaeacidiphilus oryzae TH49 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Phaeobacter inhibens BS107 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Polaromonas naphthalenivorans CJ2 PLT5, mt2d, scrK
Prosthecochloris aestuarii DSM 271 PLT5, mt2d, scrK
Pseudarthrobacter sulfonivorans Ar51 cmtA, cmtB, mtlD
Pseudomonas benzenivorans DSM 8628 mtlA, mtlD
Pseudomonas fluorescens FW300-N1B4 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Pseudomonas fluorescens FW300-N2C3 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Pseudomonas fluorescens FW300-N2E2 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Pseudomonas fluorescens FW300-N2E3 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Pseudomonas fluorescens GW456-L13 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Pseudomonas putida KT2440 mtlA, mtlD
Pseudomonas simiae WCS417 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Pseudomonas stutzeri RCH2 PLT5, mt1d, mak, manA
Pyrolobus fumarii 1A mtlA, mtlD
Rhizobium etli CFN 42 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Rhizobium johnstonii 3841 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Rhizobium leguminosarum WSM1325 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Rhizorhabdus wittichii RW1 PLT5, mt2d, scrK
Rhodanobacter denitrificans FW104-10B01 PLT5, mt2d, scrK
Rhodomicrobium vannielii ATCC 17100 PLT5, mt1d, mak, manA
Rhodopseudomonas palustris CGA009 mtlA, mtlD
Rhodospirillum centenum SW; ATCC 51521 PLT5, mt1d, mak, manA
Rhodospirillum rubrum ATCC 11170 PLT5, mt1d, mak, manA
Roseburia faecis M72 PLT5, mt2d, scrK
Saccharomonospora cyanea NA-134 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Sedimenticola selenatireducens DSM 17993 PLT5, mt2d, scrK
Shewanella amazonensis SB2B PLT5, mt2d, scrK
Shewanella loihica PV-4 mtlA, mtlD
Shewanella oneidensis MR-1 mtlA, mtlD
Shewanella sp. ANA-3 PLT5, mt2d, scrK
Sinorhizobium fredii NGR234 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Sinorhizobium medicae WSM419 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Sinorhizobium meliloti 1021 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Sphingomonas koreensis DSMZ 15582 PLT5, mt2d, scrK
Stenotrophomonas chelatiphaga DSM 21508 PLT5, mt2d, scrK
Steroidobacter denitrificans DSM 18526 mtlA, mtlD
Stutzerimonas stutzeri A1501 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Sulfuricurvum kujiense DSM 16994 mtlA, mtlD
Sulfurihydrogenibium azorense Az-Fu1 mtlA, mtlD
Sulfurihydrogenibium subterraneum DSM 15120 mtlA, mtlD
Sulfurimonas denitrificans DSM 1251 mtlA, mtlD
Sulfuritalea hydrogenivorans DSM 22779 PLT5, mt2d, scrK
Sulfurivirga caldicuralii DSM 17737 PLT5, mt2d, scrK
Synechococcus elongatus PCC 7942 mtlA, mtlD
Teredinibacter turnerae T7901 PLT5, mt2d, scrK
Thauera aminoaromatica S2 PLT5, mt1d, mak, manA
Thermithiobacillus tepidarius DSM 3134 mtlA, mtlD
Thermocrinis albus DSM 14484 mtlA, mtlD
Thermodesulforhabdus norvegica DSM 9990 mtlA, mtlD
Thermomonospora curvata DSM 43183 mtlA, mtlD
Thermovibrio ammonificans HB-1 mtlA, mtlD
Thermus aquaticus YT-1 mtlA, mtlD
Thioalkalivibrio denitrificans ALJD PLT5, mt2d, scrK
Thioalkalivibrio halophilus HL17 PLT5, mt2d, scrK
Thioalkalivibrio paradoxus ARh 1 PLT5, mt2d, scrK
Thioalkalivibrio thiocyanodenitrificans ARhD 1 PLT5, mt2d, scrK
Thiohalomonas denitrificans HLD2 PLT5, mt2d, scrK
Thiohalospira halophila HL 3 PLT5, mt2d, scrK
Thiomicrorhabdus arctica DSM 13458 PLT5, mt2d, scrK
Thiomicrorhabdus chilensis DSM 12352 PLT5, mt1d, mak, manA
Thiomicrospira cyclica ALM1 mtlA, mtlD
Thiomicrospira microaerophila ASL8-2 PLT5, mt1d, mak, manA
Thiomicrospira pelophila DSM 1534 PLT5, mt2d, scrK
Thiothrix lacustris DSM 21227 mtlE, mtlF, mtlG, mtlK, mt1d, mak, manA
Tistlia consotensis USBA 355 mtlE, mtlF, mtlG, mtlK, mt2d, scrK
Trichlorobacter lovleyi SZ mtlA, mtlD
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome mtlA, mtlD
Trichormus variabilis ATCC 29413 PLT5, mt2d, scrK
Xanthobacter autotrophicus Py2 PLT5, mt2d, scrK
Xenophilus azovorans DSM 13620 mtlE, mtlF, mtlG, mtlK, mt2d, 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.

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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