D-mannose catabolism

GapMind for catabolism of small carbon sources

D-mannose catabolism

Analysis of pathway mannose in 150 genomes

Genome	Best path
Acidimicrobium ferrooxidans DSM 10331	manP, manA
Acidithiobacillus ferrooxidans ATCC 23270	manP, manA
Alicycliphilus denitrificans K601	manP, manA
Allochromatium vinosum DSM 180	manP, manA
Ammonifex degensii KC4	manP, manA
Archaeoglobus veneficus SNP6	manP, manA
Arcobacter nitrofigilis DSM 7299	manP, manA
Azoarcus sp. BH72	manP, manA
Azohydromonas australica DSM 1124	manP, manA
Azorhizobium caulinodans ORS 571	manP, manA
Azospirillum lipoferum B510	manP, manA
Bacillus alkalinitrilicus DSM 22532	manP, manA
Beijerinckia indica ATCC 9039	HSERO_RS03635, HSERO_RS03640, HSERO_RS03645, man-isomerase, scrK
Beijerinckia mobilis UQM 1969	gluP, man-isomerase, scrK
Bradyrhizobium sp. BTAi1	HSERO_RS03635, HSERO_RS03640, HSERO_RS03645, man-isomerase, scrK
Burkholderia vietnamiensis G4	HSERO_RS03635, HSERO_RS03640, HSERO_RS03645, man-isomerase, scrK
Calditerrivibrio nitroreducens DSM 19672	manP, manA
Caminibacter mediatlanticus TB-2	manP, manA
Chlorobaculum parvum NCIB 8327	manP, manA
Chlorobaculum tepidum TLS	manP, manA
Chlorobium limicola DSM 245	manP, manA
Chlorobium phaeobacteroides BS1	manP, manA
Clostridium acetobutylicum ATCC 824	manX, manY, manZ, manA
Clostridium kluyveri DSM 555	manP, manA
Crocosphaera subtropica ATCC 51142	manP, manA
Dechloromonas agitata is5	manP, manA
Dehalococcoides mccartyi 195	manP, manA
Denitrovibrio acetiphilus DSM 12809	manP, manA
Derxia gummosa DSM 723	HSERO_RS03635, HSERO_RS03640, HSERO_RS03645, man-isomerase, scrK
Desulfacinum hydrothermale DSM 13146	manP, manA
Desulfacinum infernum DSM 9756	manP, manA
Desulfallas geothermicus DSM 3669	manP, manA
Desulfarculus baarsii DSM 2075	manP, manA
Desulfatibacillum aliphaticivorans DSM 15576	manP, manA
Desulfatiglans anilini DSM 4660	manP, manA
Desulfitobacterium hafniense DCB-2	manP, manA
Desulfobacca acetoxidans DSM 11109	manP, manA
Desulfobacter vibrioformis DSM 8776	manP, manA
Desulfobulbus mediterraneus DSM 13871	manP, manA
Desulfotalea psychrophila LSv54	manP, manA
Desulfotomaculum ruminis DSM 2154	manP, manA
Desulfovibrio bastinii DSM 16055	manP, manA
Desulfovibrio gracilis DSM 16080	manP, manA
Desulfovibrio oxyclinae DSM 11498	manP, manA
Desulfovibrio zosterae DSM 11974	manP, manA
Desulfurobacterium atlanticum DSM 15668	manP, manA
Desulfuromonas acetexigens	manP, manA
Desulfuromusa kysingii DSM 7343	manP, manA
Ferroglobus placidus DSM 10642	manP, manA
Frankia alni ACN14A	manP, manA
Geobacter lovleyi SZ	manP, manA
Geobacter metallireducens GS-15	manP, manA
Geobacter uraniireducens Rf4	STP6, mannokinase, manA
Haloechinothrix alba DSM 45207	manP, manA
Haloglycomyces albus DSM 45210	manP, manA
Halomonas desiderata SP1	manP, manA
Halorhodospira halophila SL1	manP, manA
Heliobacterium modesticaldum Ice1; ATCC 51547	manP, manA
Herbaspirillum autotrophicum IAM 14942	manP, manA
Hydrogenophaga taeniospiralis NBRC 102512	frcA, frcB, frcC, man-isomerase, scrK
Hydrogenovibrio halophilus DSM 15072	manP, manA
Hydrogenovibrio kuenenii DSM 12350	STP6, mannokinase, manA
Hydrogenovibrio marinus DSM 11271	STP6, mannokinase, manA
Hyphomicrobium sulfonivorans WDL6	manP, manA
Klebsiella variicola At-22	HSERO_RS03635, HSERO_RS03640, HSERO_RS03645, mannokinase, manA
Kyrpidia tusciae DSM 2912	manP, manA
Leptospirillum ferrooxidans C2-3	manP, manA
Malonomonas rubra DSM 5091	manP, manA
Mesorhizobium ciceri WSM1271	frcA, frcB, frcC, man-isomerase, scrK
Methanobacterium lacus AL-21	manP, manA
Methanococcus aeolicus Nankai-3	manP, manA
Methanococcus maripaludis C5	manP, manA
Methanosarcina acetivorans C2A	manP, manA
Methanosarcina barkeri Fusaro	manP, manA
Methanosarcina mazei Go1	manP, manA
Methanothermobacter thermautotrophicus Delta H	manP, manA
Methylobacterium nodulans ORS 2060	manMFS, mannokinase, manA
Methylobacterium sp. 4-46	STP6, mannokinase, manA
Methylocapsa acidiphila B2	manP, manA
Methylocapsa aurea KYG T	manP, manA
Methylocella silvestris BL2	STP6, mannokinase, manA
Methylococcus capsulatus Bath	STP6, mannokinase, manA
Methylocystis bryophila S285	manP, manA
Methyloferula stellata AR4T	manP, manA
Methylohalobius crimeensis 10Ki	manP, manA
Methylomicrobium alcaliphilum 20Z	manP, manA
Methylomonas methanica MC09	gluP, man-isomerase, scrK
Methylosarcina fibrata AML-C10	gluP, man-isomerase, scrK
Methylovulum miyakonense HT12	manP, manA
Mycolicibacterium vanbaalenii PYR-1	manP, manA
Nitratifractor salsuginis DSM 16511	manP, manA
Nitratiruptor tergarcus DSM 16512	manP, manA
Nitriliruptor alkaliphilus DSM 45188	TM1746, TM1747, TM1748, TM1749, TM1750, mannokinase, manA
Nocardiopsis lucentensis DSM 44048	frcA, frcB, frcC, mannokinase, manA
Nostoc punctiforme ATCC 29133; PCC 73102	HSERO_RS03635, HSERO_RS03640, HSERO_RS03645, man-isomerase, scrK
Novosphingobium aromaticivorans DSM 12444	gluP, man-isomerase, scrK
Oleispira antarctica	manP, manA
Paraburkholderia phymatum STM815	frcA, frcB, frcC, man-isomerase, scrK
Paraburkholderia sp. CCGE1002	frcA, frcB, frcC, man-isomerase, scrK
Pelobacter propionicus DSM 2379	manP, manA
Persephonella marina EX-H1	manP, manA
Polaromonas naphthalenivorans CJ2	frcA, frcB, frcC, man-isomerase, scrK
Prosthecochloris aestuarii DSM 271	STP6, mannokinase, manA
Pseudarthrobacter sulfonivorans Ar51	manP, manA
Pseudomonas benzenivorans DSM 8628	manP, manA
Pseudomonas stutzeri A1501	manP, manA
Pyrolobus fumarii 1A	manP, manA
Rhizobium etli CFN 42	frcA, frcB, frcC, man-isomerase, scrK
Rhizobium leguminosarum 3841	frcA, frcB, frcC, man-isomerase, scrK
Rhizobium leguminosarum WSM1325	frcA, frcB, frcC, man-isomerase, scrK
Rhodobacter sphaeroides ATCC 17029	frcA, frcB, frcC, man-isomerase, scrK
Rhodomicrobium vannielii ATCC 17100	STP6, mannokinase, manA
Rhodopseudomonas palustris CGA009	manP, manA
Rhodospirillum centenum SW; ATCC 51521	STP6, mannokinase, manA
Rhodospirillum rubrum ATCC 11170	manP, manA
Saccharomonospora cyanea NA-134	manP, manA
Sedimenticola selenatireducens DSM 17993	STP6, mannokinase, manA
Sinorhizobium fredii NGR234	frcA, frcB, frcC, mannokinase, manA
Sinorhizobium medicae WSM419	frcA, frcB, frcC, mannokinase, manA
Sphingomonas wittichii RW1	manP, manA
Stenotrophomonas chelatiphaga DSM 21508	gluP, man-isomerase, scrK
Steroidobacter denitrificans DSM 18526	manP, manA
Sulfuricurvum kujiense DSM 16994	manP, manA
Sulfurihydrogenibium azorense Az-Fu1	manP, manA
Sulfurihydrogenibium subterraneum DSM 15120	manP, manA
Sulfurimonas denitrificans DSM 1251	manP, manA
Sulfuritalea hydrogenivorans DSM 22779	STP6, mannokinase, manA
Sulfurivirga caldicuralii DSM 17737	STP6, mannokinase, manA
Teredinibacter turnerae T7901	manP, manA
Thauera aminoaromatica S2	STP6, mannokinase, manA
Thermithiobacillus tepidarius DSM 3134	manP, manA
Thermocrinis albus DSM 14484	manP, manA
Thermodesulforhabdus norvegica DSM 9990	manP, manA
Thermomonospora curvata DSM 43183	manP, manA
Thermovibrio ammonificans HB-1	manP, manA
Thioalkalivibrio denitrificans ALJD	manP, manA
Thioalkalivibrio halophilus HL17	manP, manA
Thioalkalivibrio paradoxus ARh 1	manP, manA
Thioalkalivibrio thiocyanodenitrificans ARhD 1	STP6, mannokinase, manA
Thiohalomonas denitrificans HLD2	manP, manA
Thiomicrorhabdus arctica DSM 13458	manP, manA
Thiomicrorhabdus chilensis DSM 12352	STP6, mannokinase, manA
Thiomicrospira cyclica ALM1	manP, manA
Thiomicrospira microaerophila ASL8-2	manP, manA
Thiomicrospira pelophila DSM 1534	STP6, man-isomerase, scrK
Thiothrix lacustris DSM 21227	STP6, mannokinase, manA
Trichodesmium erythraeum IMS101	manP, manA
Trichormus variabilis ATCC 29413	HSERO_RS03635, HSERO_RS03640, HSERO_RS03645, man-isomerase, scrK
Xanthobacter autotrophicus Py2	frcA, frcB, frcC, mannokinase, manA
Xenophilus azovorans DSM 13620	manP, manA

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

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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:

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