GapMind for catabolism of small carbon sources

 

D-maltose catabolism

Analysis of pathway maltose in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 thuE, thuF, thuG, thuK, susB, glk
Acidithiobacillus ferrooxidans ATCC 23270 susB, ptsG-crr
Acidovorax sp. GW101-3H11 susB, gtsA, gtsB, gtsC, gtsD, glk
Algiphilus aromaticivorans DG1253 susB, SSS-glucose, glk
Alicycliphilus denitrificans K601 susB, ptsG-crr
Alkalihalobacterium alkalinitrilicum DSM 22532 susB, ptsG-crr
Allochromatium vinosum DSM 180 MAL11, susB, glk
Ammonifex degensii KC4 malEIICBA, malA, glk
Anaerobutyricum hallii DSM 3353 susB, manX, manY, manZ
Aquimarina longa SW024 susB, ptsG-crr
Archaeoglobus veneficus SNP6 susB, ptsG-crr
Arcobacter nitrofigilis DSM 7299 susB, ptsG-crr
Azoarcus olearius BH72 MAL11, susB, glk
Azohydromonas australica DSM 1124 susB, gtsA, gtsB, gtsC, gtsD, glk
Azorhizobium caulinodans ORS 571 susB, MFS-glucose, glk
Azospirillum brasilense Sp245 susB, mglA, mglB, mglC, glk
Azospirillum sp. B510 susB, mglA, mglB, mglC, glk
Bacteroides thetaiotaomicron VPI-5482 susB, SSS-glucose, glk
Beijerinckia indica ATCC 9039 susB, mglA, mglB, mglC, glk
Beijerinckia mobilis UQM 1969 susB, MFS-glucose, glk
Billgrantia desiderata SP1 malE, malF, malG, malK, susB, glk
Bradyrhizobium sp. BTAi1 susB, mglA, mglB, mglC, glk
Brevundimonas sp. GW460-12-10-14-LB2 malI, susB, glk*
Burkholderia phytofirmans PsJN susB, gtsA, gtsB, gtsC, gtsD, glk
Burkholderia vietnamiensis G4 susB, gtsA, gtsB, gtsC, gtsD, glk
Calditerrivibrio nitroreducens DSM 19672 susB, ptsG-crr
Caminibacter mediatlanticus TB-2 susB, ptsG-crr
Carboxydothermus pertinax Ug1 malEIICBA, malA, glk
Caulobacter crescentus NA1000 malI, susB, glk
Cereibacter sphaeroides ATCC 17029 aglE, aglF, aglG, aglK, susB, glk
Chlorobaculum parvum NCIB 8327 susB, SemiSWEET, glk
Chlorobaculum tepidum TLS susB, SemiSWEET, glk
Chlorobium limicola DSM 245 susB, SemiSWEET, glk
Chlorobium phaeobacteroides BS1 susB, SemiSWEET, glk
Clostridium acetobutylicum ATCC 824 MAL11, malP, pgmB, glk
Clostridium kluyveri DSM 555 MAL11, susB, glk
Clostridium tyrobutyricum FAM22553 susB, ptsG-crr
Crocosphaera subtropica ATCC 51142 malI, susB, glk
Cupriavidus basilensis FW507-4G11 susB, mglA, mglB, mglC, glk
Dechloromonas agitata is5 susB, ptsG-crr
Dechlorosoma suillum PS susB, ptsG-crr
Dehalococcoides mccartyi 195 susB, ptsG-crr
Denitrovibrio acetiphilus DSM 12809 susB, ptsG-crr
Derxia gummosa DSM 723 susB, gtsA, gtsB, gtsC, gtsD, glk
Desulfacinum hydrothermale DSM 13146 susB, ptsG-crr
Desulfacinum infernum DSM 9756 susB, ptsG-crr
Desulfarculus baarsii DSM 2075 susB, ptsG-crr
Desulfatibacillum aliphaticivorans DSM 15576 susB, ptsG-crr
Desulfatiglans anilini DSM 4660 malEIICBA, malA, glk
Desulfitobacterium hafniense DCB-2 susB, MFS-glucose, glk
Desulfobacca acetoxidans DSM 11109 susB, ptsG-crr
Desulfobacter vibrioformis DSM 8776 malEIICBA, malA, glk
Desulfogranum mediterraneum DSM 13871 susB, ptsG-crr
Desulforamulus ruminis DSM 2154 susB, ptsG-crr
Desulfoscipio geothermicus DSM 3669 malAP, susB, glk
Desulfotalea psychrophila LSv54 malEIICBA, malA, glk
Desulfovibrio oxyclinae DSM 11498 susB, ptsG-crr
Desulfovibrio vulgaris Hildenborough JW710 susB, ptsG-crr
Desulfovibrio vulgaris Miyazaki F susB, ptsG-crr
Desulfurobacterium atlanticum DSM 15668 susB, ptsG-crr
Desulfuromonas acetexigens susB, ptsG-crr
Desulfuromusa kysingii DSM 7343 susB, ptsG-crr
Dinoroseobacter shibae DFL-12 aglE, aglF, aglG, aglK, susB, glk
Dyella japonica UNC79MFTsu3.2 malI, susB, glk
Echinicola vietnamensis KMM 6221, DSM 17526 malI, susB, glk
Escherichia coli BW25113 malE, malF, malG, malK, susB, glk
Ferroglobus placidus DSM 10642 susB, ptsG-crr
Frankia alni ACN14a MAL11, susB, glk
Geobacter metallireducens GS-15 malEIICBA, malA, glk
Geotalea uraniireducens Rf4 malEIICBA, malA, glk
Halococcus hamelinensis 100A6 susB, MFS-glucose, glk
Haloechinothrix alba DSM 45207 MAL11, susB, glk
Haloferax volcanii DS2 susB, MFS-glucose, glk
Haloglycomyces albus DSM 45210 susB, mglA, mglB, mglC, glk
Halorhodospira halophila SL1 susB, ptsG-crr
Heliomicrobium modesticaldum Ice1; ATCC 51547 susB, ptsG-crr
Herbaspirillum autotrophicum IAM 14942 malEIICBA, malA, glk
Herbaspirillum seropedicae SmR1 susB, mglA, mglB, mglC, glk
Hippea alviniae EP5-r susB, ptsG-crr
Hydrogenophaga taeniospiralis NBRC 102512 susB, gtsA, gtsB, gtsC, gtsD, glk
Hydrogenovibrio halophilus DSM 15072 malEIICBA, malA, glk
Hydrogenovibrio kuenenii DSM 12350 malEIICBA, malA, glk
Hydrogenovibrio marinus DSM 11271 malEIICBA, malA, glk
Hyphomicrobium sulfonivorans WDL6 malEIICBA, malA, glk
Klebsiella michiganensis M5al malE, malF, malG, malK, susB, glk
Klebsiella variicola At-22 malE, malF, malG, malK, susB, glk
Kyrpidia tusciae DSM 2912 malEIICBA, malA, glk
Leptospirillum ferrooxidans C2-3 susB, SemiSWEET, glk
Magnetospirillum magneticum AMB-1 susB, SemiSWEET, glk
Malonomonas rubra DSM 5091 malEIICBA, malA, glk
Maridesulfovibrio bastinii DSM 16055 susB, ptsG-crr
Maridesulfovibrio zosterae DSM 11974 susB, MFS-glucose, glk
Marinobacter adhaerens HP15 susB, gtsA, gtsB, gtsC, gtsD, glk
Mesorhizobium ciceri WSM1271 thuE, thuF, thuG, thuK, susB, glk
Methanobacterium lacus AL-21 susB, ptsG-crr
Methanococcus aeolicus Nankai-3 susB, ptsG-crr
Methanococcus maripaludis C5 susB, ptsG-crr
Methanosarcina acetivorans C2A susB, ptsG-crr
Methanosarcina mazei Go1 susB, ptsG-crr
Methanospirillum lacunae Ki8-1 susB, SemiSWEET, glk
Methanothermobacter thermautotrophicus Delta H susB, ptsG-crr
Methylobacterium nodulans ORS 2060 susB, ptsG-crr
Methylobacterium sp. 4-46 Apr-46 susB, ptsG-crr
Methylocapsa acidiphila B2 susB, ptsG-crr
Methylocapsa aurea KYG MAL11, susB, glk
Methylocella silvestris BL2 susB, ptsG-crr
Methylococcus capsulatus Bath MAL11, susB, glk
Methylocystis bryophila S285 susB, SemiSWEET, glk
Methyloferula stellata AR4T susB, ptsG-crr
Methylohalobius crimeensis 10Ki MAL11, susB, glk
Methylomonas methanica MC09 susB, MFS-glucose, glk
Methylosarcina fibrata AML-C10 susB, MFS-glucose, glk
Methylotuvimicrobium alcaliphilum 20Z susB, SSS-glucose, glk
Methylovulum miyakonense HT12 susB, SemiSWEET, glk
Mycolicibacterium vanbaalenii PYR-1 susB, MFS-glucose, glk
Nitratifractor salsuginis DSM 16511 susB, ptsG-crr
Nitratiruptor tergarcus DSM 16512 susB, ptsG-crr
Nitriliruptor alkaliphilus DSM 45188 susB, mglA, mglB, mglC, glk
Nocardioides dokdonensis FR1436 MAL11, susB, glk
Nocardiopsis lucentensis DSM 44048 susB, MFS-glucose, glk
Nostoc punctiforme ATCC 29133; PCC 73102 susB, MFS-glucose, glk
Novosphingobium aromaticivorans DSM 12444 malI, susB, glk
Oleispira antarctica susB, ptsG-crr
Paraburkholderia atlantica CCGE1002 susB, gtsA, gtsB, gtsC, gtsD, glk
Paraburkholderia bryophila 376MFSha3.1 susB, gtsA, gtsB, gtsC, gtsD, glk
Paraburkholderia phymatum STM815 susB, gtsA, gtsB, gtsC, gtsD, glk
Paucidesulfovibrio gracilis DSM 16080 susB, ptsG-crr
Pedobacter sp. GW460-11-11-14-LB5 malI, malP, pgmB, glk
Pelobacter propionicus DSM 2379 susB, SemiSWEET, glk
Persephonella marina EX-H1 susB, ptsG-crr
Phaeacidiphilus oryzae TH49 susB, MFS-glucose, glk
Phaeobacter inhibens BS107 aglE, aglF, aglG, aglK, susB, glk
Polaromonas naphthalenivorans CJ2 susB, gtsA, gtsB, gtsC, gtsD, glk
Prosthecochloris aestuarii DSM 271 susB, SemiSWEET, glk
Pseudarthrobacter sulfonivorans Ar51 susB, mglA, mglB, mglC, glk
Pseudomonas benzenivorans DSM 8628 malE, malF, malG, malK, susB, glk
Pseudomonas fluorescens FW300-N1B4 susB, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas fluorescens FW300-N2C3 susB, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas fluorescens FW300-N2E2 susB, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas fluorescens FW300-N2E3 susB, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas fluorescens GW456-L13 susB, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas putida KT2440 susB, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas simiae WCS417 susB, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas stutzeri RCH2 malE, malF, malG, malK, susB, glk
Pyrolobus fumarii 1A susB, ptsG-crr
Rhizobium etli CFN 42 thuE, thuF, thuG, thuK, susB, glk
Rhizobium johnstonii 3841 thuE, thuF, thuG, thuK, susB, glk
Rhizobium leguminosarum WSM1325 aglE, aglF, aglG, aglK, susB, glk
Rhizorhabdus wittichii RW1 susB, ptsG-crr
Rhodanobacter denitrificans FW104-10B01 malI, susB, glk
Rhodomicrobium vannielii ATCC 17100 susB, ptsG-crr
Rhodopseudomonas palustris CGA009 susB, ptsG-crr
Rhodospirillum centenum SW; ATCC 51521 thuE, thuF, thuG, thuK, susB, glk
Rhodospirillum rubrum ATCC 11170 susB, gtsA, gtsB, gtsC, gtsD, glk
Roseburia faecis M72 malE_Aa, malF_Aa, malG_Aa, malK_Aa, susB, glk
Saccharomonospora cyanea NA-134 thuE, thuF, thuG, thuK, susB, glk
Sedimenticola selenatireducens DSM 17993 malEIICBA, malA, glk
Shewanella amazonensis SB2B malI, susB, glk
Shewanella loihica PV-4 malI, susB, glk
Shewanella oneidensis MR-1 malI, susB, glk
Shewanella sp. ANA-3 malI, susB, glk
Sinorhizobium fredii NGR234 thuE, thuF, thuG, thuK, susB, glk
Sinorhizobium medicae WSM419 thuE, thuF, thuG, thuK, susB, glk
Sinorhizobium meliloti 1021 thuE, thuF, thuG, thuK, susB, glk
Sphingomonas koreensis DSMZ 15582 malI, susB, glk
Stenotrophomonas chelatiphaga DSM 21508 malI, susB, glk
Steroidobacter denitrificans DSM 18526 malEIICBA, malA, glk
Stutzerimonas stutzeri A1501 malE, malF, malG, malK, susB, glk
Sulfuricurvum kujiense DSM 16994 susB, ptsG-crr
Sulfurihydrogenibium azorense Az-Fu1 susB, ptsG-crr
Sulfurihydrogenibium subterraneum DSM 15120 susB, ptsG-crr
Sulfurimonas denitrificans DSM 1251 susB, ptsG-crr
Sulfuritalea hydrogenivorans DSM 22779 malEIICBA, malA, glk
Sulfurivirga caldicuralii DSM 17737 susB, ptsG-crr
Synechococcus elongatus PCC 7942 thuE, thuF, thuG, thuK, susB, glk
Teredinibacter turnerae T7901 susB, MFS-glucose, glk
Thauera aminoaromatica S2 susB, ptsG-crr
Thermithiobacillus tepidarius DSM 3134 susB, ptsG-crr
Thermocrinis albus DSM 14484 susB, ptsG-crr
Thermodesulforhabdus norvegica DSM 9990 susB, ptsG-crr
Thermomonospora curvata DSM 43183 susB, MFS-glucose, glk
Thermovibrio ammonificans HB-1 susB, ptsG-crr
Thermus aquaticus YT-1 susB, gtsA, gtsB, gtsC, gtsD, glk
Thioalkalivibrio denitrificans ALJD malEIICBA, malA, glk
Thioalkalivibrio halophilus HL17 susB, ptsG-crr
Thioalkalivibrio paradoxus ARh 1 malAP, susB, glk
Thioalkalivibrio thiocyanodenitrificans ARhD 1 malEIICBA, malA, glk
Thiohalomonas denitrificans HLD2 thuE, thuF, thuG, thuK, susB, glk
Thiohalospira halophila HL 3 malEIICBA, malA, glk
Thiomicrorhabdus arctica DSM 13458 susB, ptsG-crr
Thiomicrorhabdus chilensis DSM 12352 susB, ptsG-crr
Thiomicrospira cyclica ALM1 susB, ptsG-crr
Thiomicrospira microaerophila ASL8-2 susB, ptsG-crr
Thiomicrospira pelophila DSM 1534 malEIICBA, malA, glk
Thiothrix lacustris DSM 21227 malEIICBA, malA, glk
Tistlia consotensis USBA 355 susB, mglA, mglB, mglC, glk
Trichlorobacter lovleyi SZ susB, ptsG-crr
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome susB, mglA, mglB, mglC, glk
Trichormus variabilis ATCC 29413 susB, SemiSWEET, glk
Xanthobacter autotrophicus Py2 susB, MFS-glucose, glk
Xenophilus azovorans DSM 13620 susB, ptsG-crr

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