D-mannose catabolism

GapMind for catabolism of small carbon sources

D-mannose catabolism

Analysis of pathway mannose in 276 genomes

Genome	Best path
Acidovorax caeni R-24608	manP, manA
Actinokineospora bangkokensis 44EHW	manP, manA
Actinomyces timonensis 7400942	manX, manY, manZ, manA
Algiphilus aromaticivorans DG1253	manP, manA
Algoriphagus aquaeductus T4	STP6, man-isomerase, scrK
Algoriphagus machipongonensis PR1	STP6, man-isomerase, scrK
Alicyclobacillus ferrooxydans TC-34	manP, manA
Alishewanella agri BL06	gluP, man-isomerase, scrK
Alistipes indistinctus YIT 12060	STP6, mannokinase, manA
Alistipes shahii WAL 8301	STP6, mannokinase, manA
Alkalitalea saponilacus SC/BZ-SP2	STP6, mannokinase, manA
Amantichitinum ursilacus IGB-41	HSERO_RS03635, HSERO_RS03640, HSERO_RS03645, man-isomerase, scrK
Amphibacillus jilinensis Y1	manX, manY, manZ, manA
Amphritea japonica JAMM 1866	manP, manA
Amycolatopsis halophila YIM 93223	manP, manA
Amycolatopsis xylanica CPCC 202699	frcA, frcB, frcC, mannokinase, manA
Aquimarina agarilytica ZC1	STP6, mannokinase, manA
Aquimarina longa SW024	manP, manA
Aquimarina macrocephali JAMB N27	manP, manA
Archaeoglobus sulfaticallidus PM70-1	manP, manA
Arcticibacter svalbardensis MN12-7	manP, manA
Ardenticatena maritima 110S	manP, manA
Arenimonas metalli CF5-1	manP, manA
Arenitalea lutea P7-3-5	manP, manA
Azospirillum humicireducens SgZ-5	manP, manA
Azospirillum thiophilum BV-S	manP, manA
Bacillus altitudinis 41KF2b	manP, manA
Bacillus coahuilensis m4-4	STP6, man-isomerase, scrK
Bacillus cytotoxicus NVH 391-98	manP, manA
Bacillus horneckiae 1P01SC	manP, manA
Bacillus okhensis Kh10-101	manP, manA
Bacillus safensis FO-36b	manP, manA
Bacillus velezensis CBMB205	manP, manA
Bacteroides clarus YIT 12056	gluP, mannokinase, manA
Bacteroides faecis MAJ27	STP6, mannokinase, manA
Bacteroides fluxus YIT 12057	STP6, mannokinase, manA
Bacteroides oleiciplenus YIT 12058	STP6, mannokinase, manA
Barnesiella intestinihominis YIT 11860	STP6, mannokinase, manA
Belnapia rosea CPCC 100156	manP, manA
Bizionia argentinensis JUB59	manP, manA
Bradyrhizobium diazoefficiens USDA110	HSERO_RS03635, HSERO_RS03640, HSERO_RS03645, man-isomerase, scrK
Brevibacterium jeotgali SJ5-8	manP, manA
Brucella inopinata BO1	manP, manA
Brucella microti CCM 4915	manP, manA
Bryobacter aggregatus MPL3	manMFS, man-isomerase, scrK
Caldicellulosiruptor hydrothermalis 108	manP, manA
Caldicellulosiruptor kronotskyensis 2002	manP, manA
Carboxydothermus pertinax Ug1	manP, manA
Catellicoccus marimammalium M35/04/3	manX, manY, manZ, manA
Chromobacterium vaccinii MWU205	manP, manA
Chryseobacterium angstadtii KM	gluP, mannokinase, manA
Chryseobacterium arthrosphaerae CC-VM-7	STP6, mannokinase, manA
Chryseobacterium viscerum 687B-08	gluP, mannokinase, manA
Cloacibacillus porcorum CL-84	manP, manA
Cobetia crustatorum JO1	STP6, man-isomerase, scrK
Collimonas arenae Ter10	HSERO_RS03635, HSERO_RS03640, HSERO_RS03645, man-isomerase, scrK
Collimonas pratensis Ter91	HSERO_RS03635, HSERO_RS03640, HSERO_RS03645, man-isomerase, scrK
Collinsella tanakaei YIT 12063	manX, manY, manZ, manA
Coprobacter fastidiosus NSB1	STP6, mannokinase, manA
Corynebacterium deserti GIMN1.010	manP, manA
Corynebacterium frankenforstense ST18	manP, manA
Corynebacterium lactis RW2-5	manP, manA
Croceitalea dokdonensis DOKDO 023	STP6, mannokinase, manA
Cronobacter condimenti 1330	manX, manY, manZ, manA
Cronobacter muytjensii ATCC 51329	manX, manY, manZ, manA
Cronobacter universalis NCTC 9529	manX, manY, manZ, manA
Desulfatitalea tepidiphila S28bF	manP, manA
Desulfotomaculum hydrothermale Lam5	manP, manA
Dethiosulfovibrio salsuginis USBA 82	manP, manA
Devosia chinhatensis IPL18	frcA, frcB, frcC, man-isomerase, scrK
Devriesea agamarum IMP2	manP, manA
Dialister succinatiphilus YIT 11850	STP6, man-isomerase, scrK
Dietzia timorensis ID05-A0528	manP, manA
Dokdonella koreensis DS-123	manP, manA
Domibacillus robiginosus WS 4628	STP6, man-isomerase, scrK
Duganella sacchari Sac-22	gluP, man-isomerase, scrK
Dyadobacter tibetensis Y620-1	manP, manA
Dyella jiangningensis SBZ3-12	STP6, man-isomerase, scrK
Endozoicomonas montiporae CL-33	manP, manA
Enterococcus termitis LMG 8895	manX, manY, manZ, manA
Enterorhabdus caecimuris B7	manP, manA
Epibacterium ulvae U95	manP, manA
Erythrobacter gangjinensis K7-2	manP, manA
Erythrobacter marinus HWDM-33	manP, manA
Ethanoligenens harbinense YUAN-3	manP, manA
Fervidicella metallireducens AeB	manP, manA
Fibrella aestuarina BUZ 2	gluP, mannokinase, manA
Flammeovirga pacifica WPAGA1	STP6, mannokinase, manA
Flaviramulus ichthyoenteri Th78	manP, manA
Flavobacterium beibuense F44-8	manP, manA
Flavobacterium glycines Gm-149	manP, manA
Flavobacterium sp. LM5	manP, manA
Flavobacterium ummariense DS-12	manP, manA
Frischella perrara PEB0191	manX, manY, manZ, manA
Galbibacter marinus ck-I2-15	manP, manA
Gallaecimonas xiamenensis 3-C-1	gluP, mannokinase, manA
Geobacter daltonii FRC-32	manP, manA
Gillisia marina CBA3202	manP, manA
Gracilibacillus halophilus YIM-C55.5	manP, manA
Granulicella mallensis MP5ACTX8	gluP, mannokinase, manA
Granulicella tundricola MP5ACTX9	gluP, mannokinase, manA
Hafnia paralvei ATCC 29927	manX, manY, manZ, manA
Haladaptatus cibarius D43	manP, manA
Halioglobus japonicus S1-36	manP, manA
Halobacillus alkaliphilus FP5	manP, manA
Halococcus hamelinensis 100A6	manP, manA
Halomonas salina B6	manP, manA
Halomonas smyrnensis AAD6	STP6, man-isomerase, scrK
Halomonas stevensii S18214	manP, manA
Halomonas titanicae BH1	HSERO_RS03635, HSERO_RS03640, HSERO_RS03645, man-isomerase, scrK
Halomonas xinjiangensis TRM 0175	manP, manA
Halopiger salifodinae KCY07-B2	TT_C0211, TT_C0327, TT_C0326, TT_C0328, man-isomerase, scrK
Halostagnicola larsenii XH-48	manP, manA
Haloterrigena daqingensis JX313	manP, manA
Herbaspirillum aquaticum IEH 4430	HSERO_RS03635, HSERO_RS03640, HSERO_RS03645, man-isomerase, scrK
Hippea alviniae EP5-r	manP, manA
Hippea jasoniae Mar08-272r	manP, manA
Hoeflea phototrophica DFL-43	frcA, frcB, frcC, man-isomerase, scrK
Hyphomicrobium nitrativorans NL23	manP, manA
Imtechella halotolerans K1	manP, manA
Indibacter alkaliphilus LW1	STP6, man-isomerase, scrK
Jannaschia aquimarina GSW-M26	frcA, frcB, frcC, mannokinase, manA
Jeotgalibacillus soli P9	manP, manA
Kangiella geojedonensis YCS-5	manP, manA
Knoellia flava TL1	frcA, frcB, frcC, mannokinase, manA
Kocuria flava HO-9041	manP, manA
Kocuria turfanensis HO-9042	manP, manA
Laceyella sediminis RHA1	manP, manA
Lacinutrix algicola AKS293	manP, manA
Lacinutrix himadriensis E4-9a	manP, manA
Lacinutrix mariniflava AKS432	manP, manA
Lactobacillus curieae CCTCC M 2011381	manP, manA
Lactobacillus delbrueckii ZN7a-9	manX, manY, manZ, manA
Lactobacillus hokkaidonensis LOOC260	manP, manA
Lactobacillus oryzae SG293	STP6, man-isomerase, scrK
Lactobacillus pobuzihii E100301	manX, manY, manZ, manA
Lactobacillus shenzhenensis LY-73	manP, manA
Lactobacillus silagei IWT126	STP6, man-isomerase, scrK
Leeuwenhoekiella blandensis MED217	manP, manA
Lentibacillus jeotgali Grbi	manP, manA
Limnohabitans curvus MWH-C5	frcA, frcB, frcC, man-isomerase, scrK
Limnohabitans parvus II-B4	manP, manA
Listeria fleischmannii LU2006-1	manX, manY, manZ, manA
Luteimonas huabeiensis HB2	gluP, man-isomerase, scrK
Luteipulveratus mongoliensis MN07-A0370	manP, manA
Lutibaculum baratangense AMV1	STP6, mannokinase, manA
Lysobacter daejeonensis GH1-9	manP, manA
Magnetovibrio blakemorei MV-1	STP6, mannokinase, manA
Marinicella litoralis KMM 3900	manP, manA
Mariniradius saccharolyticus AK6	STP6, man-isomerase, scrK
Marinobacter algicola DG893	manP, manA
Marinobacter guineae M3B	manP, manA
Marinobacter psychrophilus 20041	STP6, mannokinase, manA
Marinomonas arctica 328	frcA, frcB, frcC, man-isomerase, scrK
Marivita geojedonensis DPG-138	frcA, frcB, frcC, man-isomerase, scrK
Martelella endophytica YC6887	STP6, man-isomerase, scrK
Megamonas funiformis YIT 11815	manMFS, mannokinase, manA
Mesorhizobium ciceri WSM1271	frcA, frcB, frcC, man-isomerase, scrK
Methanobacterium arcticum M2	manP, manA
Methanobacterium veterum MK4	manP, manA
Methanocella arvoryzae MRE50	manP, manA
Methanococcus aeolicus Nankai-3	manP, manA
Methanoculleus horonobensis T10	manP, manA
Methanolinea tarda NOBI-1	manP, manA
Methanosarcina soligelidi SMA-21	manP, manA
Methanospirillum lacunae Ki8-1	manP, manA
Methanospirillum stamsii Pt1	manP, manA
Methylibium petroleiphilum PM1	manP, manA
Methylobacterium gossipiicola Gh-105	manP, manA
Methylocapsa aurea KYG	manP, manA
Methylotenera versatilis 301	manP, manA
Microbacterium profundi Shh49	manP, manA
Microvirga lotononidis WSM3557	HSERO_RS03635, HSERO_RS03640, HSERO_RS03645, man-isomerase, scrK
Moritella dasanensis ArB 0140	manP, manA
Mucilaginibacter gossypii Gh-67	manP, manA
Mucilaginibacter gossypiicola Gh-48	manP, manA
Mucilaginibacter mallensis MP1X4	manP, manA
Nafulsella turpanensis ZLM-10	manP, manA
Natronomonas moolapensis 8.8.11	manP, manA
Nautilia profundicola AmH	manP, manA
Neiella marina J221	STP6, mannokinase, manA
Neptunomonas antarctica S3-22	manP, manA
Nocardioides daejeonensis MJ31	manP, manA
Nocardioides dokdonensis FR1436	manP, manA
Nocardiopsis baichengensis YIM 90130	manP, manA
Nocardiopsis gilva YIM 90087	frcA, frcB, frcC, man-isomerase, scrK
Novosphingobium barchaimii LL02	manP, manA
Novosphingobium fuchskuhlense FNE08-7	manP, manA
Novosphingobium lindaniclasticum LE124	gluP, man-isomerase, scrK
Oceanisphaera arctica V1-41	manP, manA
Ochrobactrum rhizosphaerae PR17	frcA, frcB, frcC, man-isomerase, scrK
Ochrobactrum thiophenivorans DSM 7216	frcA, frcB, frcC, mannokinase, manA
Oscillibacter ruminantium GH1	STP6, man-isomerase, scrK
Paenisporosarcina indica PN2	manP, manA
Palaeococcus pacificus DY20341	manP, manA
Paludibacter propionicigenes WB4	STP6, mannokinase, manA
Pandoraea thiooxydans ATSB16	manP, manA
Pantoea rwandensis LMG 26275	HSERO_RS03635, HSERO_RS03640, HSERO_RS03645, mannokinase, manA
Pedobacter arcticus A12	gluP, mannokinase, manA
Photobacterium gaetbulicola Gung47	manP, manA
Photobacterium jeanii R-40508	manP, manA
Phyllobacterium brassicacearum STM 196	frcA, frcB, frcC, man-isomerase, scrK
Phyllobacterium endophyticum PEPV15	frcA, frcB, frcC, man-isomerase, scrK
Phyllobacterium leguminum ORS 1419	frcA, frcB, frcC, man-isomerase, scrK
Planktomarina temperata RCA23	frcA, frcB, frcC, man-isomerase, scrK
Planococcus halocryophilus Or1	manP, manA
Pleomorphomonas diazotrophica R5-392	frcA, frcB, frcC, mannokinase, manA
Polaribacter dokdonensis DSW-5	gluP, man-isomerase, scrK
Pontibacillus litoralis JSM 072002	manP, manA
Pontibacter lucknowensis DM9	manP, manA
Pontibacter ramchanderi LP43	manP, manA
Pontimonas salivibrio CL-TW6	manP, manA
Porphyrobacter dokdonensis DSW-74	gluP, man-isomerase, scrK
Pseudoalteromonas arctica A 37-1-2	gluP, man-isomerase, scrK
Pseudomonas baetica a390	manP, manA
Pseudomonas litoralis 2SM5	manP, manA
Pseudomonas taeanensis MS-3	manP, manA
Pseudovibrio axinellae Ad2	STP6, mannokinase, manA
Psychrobacter arcticus 273-4	manP, manA
Psychrobacter cryohalolentis K5	manP, manA
Psychromonas ingrahamii 37	manP, manA
Psychromonas ossibalaenae JAMM 0738	manP, manA
Rhizobium freirei PRF 81	frcA, frcB, frcC, man-isomerase, scrK
Rhizobium grahamii CCGE 502	frcA, frcB, frcC, man-isomerase, scrK
Rhizobium subbaraonis JC85	frcA, frcB, frcC, man-isomerase, scrK
Rhodanobacter denitrificans 2APBS1	gluP, man-isomerase, scrK
Rhodobacter johrii JA192	frcA, frcB, frcC, man-isomerase, scrK
Rhodobacter maris JA276	manP, manA
Rhodobacter ovatus JA234	frcA, frcB, frcC, man-isomerase, scrK
Rhodobacter viridis JA737	manP, manA
Rhodococcus qingshengii djl-6-2	manP, manA
Rhodopseudomonas pseudopalustris DSM 123	manP, manA
Roseateles aquatilis CCUG 48205	manP, manA
Roseivirga spongicola UST030701-084	STP6, mannokinase, manA
Rubrivirga marina SAORIC-28	gluP, mannokinase, manA
Ruegeria conchae TW15	frcA, frcB, frcC, man-isomerase, scrK
Saccharomonospora marina XMU15	manP, manA
Salinicoccus carnicancri Crm	manP, manA
Serinicoccus profundi MCCC 1A05965	manP, manA
Shewanella halifaxensis HAW-EB4	manP, manA
Skermanella stibiiresistens SB22	HSERO_RS03635, HSERO_RS03640, HSERO_RS03645, mannokinase, manA
Snodgrassella alvi wkB2	manP, manA
Sphaerochaeta globosa Buddy	manP, manA
Sphaerochaeta pleomorpha Grapes	TT_C0211, TT_C0327, TT_C0326, TT_C0328, mannokinase, manA
Sphingobium baderi LL03	manP, manA
Sphingobium czechense LL01	gluP, man-isomerase, scrK
Sphingobium quisquiliarum P25	manP, manA
Sphingomonas histidinilytica UM2	manP, manA
Sphingomonas indica Dd16	manP, manA
Sphingomonas laterariae LNB2	manP, manA
Sphingopyxis indica DS15	gluP, man-isomerase, scrK
Sphingopyxis terrae UI2	manP, manA
Sporolactobacillus vineae SL153	manX, manY, manZ, manA
Streptacidiphilus oryzae TH49	manP, manA
Streptococcus anginosus CCUG 39159	manX, manY, manZ, manA
Streptococcus massiliensis 4401825	manX, manY, manZ, manA
Streptococcus oralis 7747	manX, manY, manZ, manA
Streptococcus oralis AZ_3a	manX, manY, manZ, manA
Streptomyces kebangsaanensis SUK12	manP, manA
Succinatimonas hippei YIT 12066	HSERO_RS03635, HSERO_RS03640, HSERO_RS03645, mannokinase, manA
Sulfurimonas gotlandica GD1	manP, manA
Tatumella morbirosei LMG 23360	manX, manY, manZ, manA
Thauera humireducens SgZ-1	STP6, mannokinase, manA
Thermoactinomyces daqus H-18	manP, manA
Thermobifida halotolerans YIM 90462	manP, manA
Thermodesulfovibrio aggregans TGE-P1	manP, manA
Thermophagus xiamenensis HS1	STP6, mannokinase, manA
Thermovenabulum gondwanense R270	manP, manA
Thioclava dalianensis DLFJ1-1	frcA, frcB, frcC, man-isomerase, scrK
Thiohalospira halophila HL 3	manP, manA
Tistlia consotensis USBA 355	frcA, frcB, frcC, mannokinase, manA
Vagococcus penaei CD276	manX, manY, manZ, manA
Verminephrobacter eiseniae EF01-2	frcA, frcB, frcC, man-isomerase, scrK
Weissella oryzae SG25	manX, manY, manZ, manA
Williamsia sterculiae CPCC 203464	manP, manA
Yersinia intermedia Y228	manX, manY, manZ, 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.

Downloads

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