D-maltose catabolism

GapMind for catabolism of small carbon sources

D-maltose catabolism

Analysis of pathway maltose in 150 genomes

Genome	Best path
Acidimicrobium ferrooxidans DSM 10331	thuE, thuF, thuG, thuK, susB, glk
Acidithiobacillus ferrooxidans ATCC 23270	susB, ptsG-crr
Alicycliphilus denitrificans K601	susB, ptsG-crr
Allochromatium vinosum DSM 180	MAL11, susB, glk
Ammonifex degensii KC4	malEIICBA, malA, glk
Archaeoglobus veneficus SNP6	susB, ptsG-crr
Arcobacter nitrofigilis DSM 7299	susB, ptsG-crr
Azoarcus sp. BH72	MAL11, susB, glk
Azohydromonas australica DSM 1124	susB, gtsA, gtsB, gtsC, gtsD, glk
Azorhizobium caulinodans ORS 571	susB, MFS-glucose, glk
Azospirillum lipoferum B510	susB, mglA, mglB, mglC, glk
Bacillus alkalinitrilicus DSM 22532	susB, ptsG-crr
Beijerinckia indica ATCC 9039	susB, mglA, mglB, mglC, glk
Beijerinckia mobilis UQM 1969	susB, MFS-glucose, glk
Bradyrhizobium sp. BTAi1	susB, mglA, mglB, mglC, glk
Burkholderia vietnamiensis G4	susB, gtsA, gtsB, gtsC, gtsD, glk
Calditerrivibrio nitroreducens DSM 19672	susB, ptsG-crr
Caminibacter mediatlanticus TB-2	susB, ptsG-crr
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
Crocosphaera subtropica ATCC 51142	malI, susB, glk
Dechloromonas agitata is5	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
Desulfallas geothermicus DSM 3669	malAP, susB, glk
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	malEIICBA, malA, glk
Desulfobacca acetoxidans DSM 11109	susB, ptsG-crr
Desulfobacter vibrioformis DSM 8776	malEIICBA, malA, glk
Desulfobulbus mediterraneus DSM 13871	susB, ptsG-crr
Desulfotalea psychrophila LSv54	malEIICBA, malA, glk
Desulfotomaculum ruminis DSM 2154	susB, ptsG-crr
Desulfovibrio bastinii DSM 16055	susB, ptsG-crr
Desulfovibrio gracilis DSM 16080	susB, ptsG-crr
Desulfovibrio oxyclinae DSM 11498	susB, ptsG-crr
Desulfovibrio zosterae DSM 11974	susB, MFS-glucose, glk
Desulfurobacterium atlanticum DSM 15668	susB, ptsG-crr
Desulfuromonas acetexigens	susB, ptsG-crr
Desulfuromusa kysingii DSM 7343	susB, ptsG-crr
Ferroglobus placidus DSM 10642	susB, ptsG-crr
Frankia alni ACN14A	MAL11, susB, glk
Geobacter lovleyi SZ	susB, ptsG-crr
Geobacter metallireducens GS-15	malEIICBA, malA, glk
Geobacter uraniireducens Rf4	malEIICBA, malA, glk
Haloechinothrix alba DSM 45207	MAL11, susB, glk
Haloglycomyces albus DSM 45210	susB, mglA, mglB, mglC, glk
Halomonas desiderata SP1	malE, malF, malG, malK, susB, glk
Halorhodospira halophila SL1	susB, ptsG-crr
Heliobacterium modesticaldum Ice1; ATCC 51547	susB, ptsG-crr
Herbaspirillum autotrophicum IAM 14942	malEIICBA, malA, glk
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 variicola At-22	malE, malF, malG, malK, susB, glk
Kyrpidia tusciae DSM 2912	malEIICBA, malA, glk
Leptospirillum ferrooxidans C2-3	susB, SemiSWEET, glk
Malonomonas rubra DSM 5091	malEIICBA, malA, 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 barkeri Fusaro	susB, ptsG-crr
Methanosarcina mazei Go1	susB, ptsG-crr
Methanothermobacter thermautotrophicus Delta H	susB, ptsG-crr
Methylobacterium nodulans ORS 2060	susB, ptsG-crr
Methylobacterium sp. 4-46	susB, ptsG-crr
Methylocapsa acidiphila B2	susB, ptsG-crr
Methylocapsa aurea KYG T	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
Methylomicrobium alcaliphilum 20Z	susB, SSS-glucose, glk
Methylomonas methanica MC09	susB, MFS-glucose, glk
Methylosarcina fibrata AML-C10	susB, MFS-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
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 phymatum STM815	susB, gtsA, gtsB, gtsC, gtsD, glk
Paraburkholderia sp. CCGE1002	susB, gtsA, gtsB, gtsC, gtsD, glk
Pelobacter propionicus DSM 2379	susB, SemiSWEET, glk
Persephonella marina EX-H1	susB, ptsG-crr
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 stutzeri A1501	malE, malF, malG, malK, susB, glk
Pyrolobus fumarii 1A	susB, ptsG-crr
Rhizobium etli CFN 42	thuE, thuF, thuG, thuK, susB, glk
Rhizobium leguminosarum 3841	thuE, thuF, thuG, thuK, susB, glk
Rhizobium leguminosarum WSM1325	aglE, aglF, aglG, aglK, susB, glk
Rhodobacter sphaeroides ATCC 17029	aglE, aglF, aglG, aglK, 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
Saccharomonospora cyanea NA-134	thuE, thuF, thuG, thuK, susB, glk
Sedimenticola selenatireducens DSM 17993	malEIICBA, malA, glk
Sinorhizobium fredii NGR234	thuE, thuF, thuG, thuK, susB, glk
Sinorhizobium medicae WSM419	thuE, thuF, thuG, thuK, susB, glk
Sphingomonas wittichii RW1	susB, ptsG-crr
Stenotrophomonas chelatiphaga DSM 21508	malI, susB, glk
Steroidobacter denitrificans DSM 18526	malEIICBA, malA, 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
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
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
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
Trichodesmium erythraeum IMS101	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 Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources