GapMind for catabolism of small carbon sources

 

D-mannose catabolism

Analysis of pathway mannose in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 manP, manA
Acidithiobacillus ferrooxidans ATCC 23270 manP, manA
Acidovorax sp. GW101-3H11 frcA, frcB, frcC, man-isomerase, scrK
Algiphilus aromaticivorans DG1253 manP, manA
Alicycliphilus denitrificans K601 manP, manA
Alkalihalobacterium alkalinitrilicum DSM 22532 manP, manA
Allochromatium vinosum DSM 180 manP, manA
Ammonifex degensii KC4 manP, manA
Anaerobutyricum hallii DSM 3353 manX, manY, manZ, manA
Aquimarina longa SW024 manP, manA
Archaeoglobus veneficus SNP6 manP, manA
Arcobacter nitrofigilis DSM 7299 manP, manA
Azoarcus olearius BH72 manP, manA
Azohydromonas australica DSM 1124 manP, manA
Azorhizobium caulinodans ORS 571 manP, manA
Azospirillum brasilense Sp245 manP, manA
Azospirillum sp. B510 manP, manA
Bacteroides thetaiotaomicron VPI-5482 STP6, mannokinase, manA
Beijerinckia indica ATCC 9039 HSERO_RS03635, HSERO_RS03640, HSERO_RS03645, man-isomerase, scrK
Beijerinckia mobilis UQM 1969 gluP, man-isomerase, scrK
Billgrantia desiderata SP1 manP, manA
Bradyrhizobium sp. BTAi1 HSERO_RS03635, HSERO_RS03640, HSERO_RS03645, man-isomerase, scrK
Brevundimonas sp. GW460-12-10-14-LB2 gluP, man-isomerase, scrK
Burkholderia phytofirmans PsJN frcA, frcB, frcC, 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
Carboxydothermus pertinax Ug1 manP, manA
Caulobacter crescentus NA1000 manP, manA
Cereibacter sphaeroides ATCC 17029 frcA, frcB, frcC, man-isomerase, scrK
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
Clostridium tyrobutyricum FAM22553 manP, manA
Crocosphaera subtropica ATCC 51142 manP, manA
Cupriavidus basilensis FW507-4G11 HSERO_RS03635, HSERO_RS03640, HSERO_RS03645, man-isomerase, scrK
Dechloromonas agitata is5 manP, manA
Dechlorosoma suillum PS 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
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
Desulfogranum mediterraneum DSM 13871 manP, manA
Desulforamulus ruminis DSM 2154 manP, manA
Desulfoscipio geothermicus DSM 3669 manP, manA
Desulfotalea psychrophila LSv54 manP, manA
Desulfovibrio oxyclinae DSM 11498 manP, manA
Desulfovibrio vulgaris Hildenborough JW710 manP, manA
Desulfovibrio vulgaris Miyazaki F manP, manA
Desulfurobacterium atlanticum DSM 15668 manP, manA
Desulfuromonas acetexigens manP, manA
Desulfuromusa kysingii DSM 7343 manP, manA
Dinoroseobacter shibae DFL-12 frcA, frcB, frcC, man-isomerase, scrK
Dyella japonica UNC79MFTsu3.2 gluP, man-isomerase, scrK
Echinicola vietnamensis KMM 6221, DSM 17526 gluP, man-isomerase, scrK
Escherichia coli BW25113 manX, manY, manZ, manA
Ferroglobus placidus DSM 10642 manP, manA
Frankia alni ACN14a manP, manA
Geobacter metallireducens GS-15 manP, manA
Geotalea uraniireducens Rf4 STP6, mannokinase, manA
Halococcus hamelinensis 100A6 manP, manA
Haloechinothrix alba DSM 45207 manP, manA
Haloferax volcanii DS2 manP, manA
Haloglycomyces albus DSM 45210 manP, manA
Halorhodospira halophila SL1 manP, manA
Heliomicrobium modesticaldum Ice1; ATCC 51547 manP, manA
Herbaspirillum autotrophicum IAM 14942 manP, manA
Herbaspirillum seropedicae SmR1 HSERO_RS03635, HSERO_RS03640, HSERO_RS03645, man-isomerase, scrK
Hippea alviniae EP5-r 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 michiganensis M5al manX, manY, manZ, 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
Magnetospirillum magneticum AMB-1 STP6, mannokinase, manA
Malonomonas rubra DSM 5091 manP, manA
Maridesulfovibrio bastinii DSM 16055 manP, manA
Maridesulfovibrio zosterae DSM 11974 manP, manA
Marinobacter adhaerens HP15 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 mazei Go1 manP, manA
Methanospirillum lacunae Ki8-1 manP, manA
Methanothermobacter thermautotrophicus Delta H manP, manA
Methylobacterium nodulans ORS 2060 manMFS, mannokinase, manA
Methylobacterium sp. 4-46 Apr-46 STP6, mannokinase, manA
Methylocapsa acidiphila B2 manP, manA
Methylocapsa aurea KYG 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
Methylomonas methanica MC09 gluP, man-isomerase, scrK
Methylosarcina fibrata AML-C10 gluP, man-isomerase, scrK
Methylotuvimicrobium alcaliphilum 20Z manP, manA
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
Nocardioides dokdonensis FR1436 manP, 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 atlantica CCGE1002 frcA, frcB, frcC, man-isomerase, scrK
Paraburkholderia bryophila 376MFSha3.1 frcA, frcB, frcC, man-isomerase, scrK
Paraburkholderia phymatum STM815 frcA, frcB, frcC, man-isomerase, scrK
Paucidesulfovibrio gracilis DSM 16080 manP, manA
Pedobacter sp. GW460-11-11-14-LB5 gluP, man-isomerase, scrK
Pelobacter propionicus DSM 2379 manP, manA
Persephonella marina EX-H1 manP, manA
Phaeacidiphilus oryzae TH49 manP, manA
Phaeobacter inhibens BS107 frcA, frcB, frcC, man-isomerase, scrK
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 fluorescens FW300-N1B4 manP, manA
Pseudomonas fluorescens FW300-N2C3 manMFS, man-isomerase, scrK
Pseudomonas fluorescens FW300-N2E2 manP, manA
Pseudomonas fluorescens FW300-N2E3 gluP, man-isomerase, scrK
Pseudomonas fluorescens GW456-L13 manP, manA
Pseudomonas putida KT2440 manP, manA
Pseudomonas simiae WCS417 HSERO_RS03635, HSERO_RS03640, HSERO_RS03645, man-isomerase, scrK
Pseudomonas stutzeri RCH2 manP, manA
Pyrolobus fumarii 1A manP, manA
Rhizobium etli CFN 42 frcA, frcB, frcC, man-isomerase, scrK
Rhizobium johnstonii 3841 frcA, frcB, frcC, man-isomerase, scrK
Rhizobium leguminosarum WSM1325 frcA, frcB, frcC, man-isomerase, scrK
Rhizorhabdus wittichii RW1 manP, manA
Rhodanobacter denitrificans FW104-10B01 gluP, 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
Roseburia faecis M72 manP, manA
Saccharomonospora cyanea NA-134 manP, manA
Sedimenticola selenatireducens DSM 17993 STP6, mannokinase, manA
Shewanella amazonensis SB2B gluP, man-isomerase, scrK
Shewanella loihica PV-4 gluP, mannokinase, manA
Shewanella oneidensis MR-1 manP, manA
Shewanella sp. ANA-3 gluP, man-isomerase, scrK
Sinorhizobium fredii NGR234 frcA, frcB, frcC, mannokinase, manA
Sinorhizobium medicae WSM419 frcA, frcB, frcC, mannokinase, manA
Sinorhizobium meliloti 1021 frcA, frcB, frcC, mannokinase, manA
Sphingomonas koreensis DSMZ 15582 gluP, man-isomerase, scrK
Stenotrophomonas chelatiphaga DSM 21508 gluP, man-isomerase, scrK
Steroidobacter denitrificans DSM 18526 manP, manA
Stutzerimonas stutzeri A1501 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
Synechococcus elongatus PCC 7942 manP, 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
Thermus aquaticus YT-1 TT_C0211, TT_C0327, TT_C0326, TT_C0328, mannokinase, 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
Thiohalospira halophila HL 3 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
Tistlia consotensis USBA 355 frcA, frcB, frcC, mannokinase, manA
Trichlorobacter lovleyi SZ manP, manA
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome 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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

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:

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