GapMind for catabolism of small carbon sources

 

D-glucosamine (chitosamine) catabolism

Analysis of pathway glucosamine in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 gamP, nagB
Acidithiobacillus ferrooxidans ATCC 23270 gamP, nagB
Acidovorax sp. GW101-3H11 SLC2A2, glc-kinase, nagB
Algiphilus aromaticivorans DG1253 gamP, nagB
Alicycliphilus denitrificans K601 gamP, nagB
Alkalihalobacterium alkalinitrilicum DSM 22532 gamP, nagB
Allochromatium vinosum DSM 180 gamP, nagB
Ammonifex degensii KC4 gamP, nagB
Anaerobutyricum hallii DSM 3353 gamP, nagB
Aquimarina longa SW024 gamP, nagB
Archaeoglobus veneficus SNP6 gamP, nagB
Arcobacter nitrofigilis DSM 7299 gamP, nagB
Azoarcus olearius BH72 gamP, nagB
Azohydromonas australica DSM 1124 SLC2A2, glc-kinase, nagB
Azorhizobium caulinodans ORS 571 gamP, nagB
Azospirillum brasilense Sp245 SLC2A2, glc-kinase, nagB
Azospirillum sp. B510 gamP, nagB
Bacteroides thetaiotaomicron VPI-5482 nagX, nagP, nagK, nagA, nagB
Beijerinckia indica ATCC 9039 gamP, nagB
Beijerinckia mobilis UQM 1969 gamP, nagB
Billgrantia desiderata SP1 gamP, nagB
Bradyrhizobium sp. BTAi1 gdh, AO353_21715, AO353_21720, AO353_21725, AO353_21710, glucosaminate-lyase, kdgK, kdgA
Brevundimonas sp. GW460-12-10-14-LB2 gamP, nagB
Burkholderia phytofirmans PsJN gamP, nagB
Burkholderia vietnamiensis G4 gamP, nagB
Calditerrivibrio nitroreducens DSM 19672 gamP, nagB
Caminibacter mediatlanticus TB-2 gamP, nagB
Carboxydothermus pertinax Ug1 SM_b21216, SM_b21219, SM_b21220, SM_b21221, glc-kinase, nagB
Caulobacter crescentus NA1000 nagX, nagF, nagEcb, nagA, nagB
Cereibacter sphaeroides ATCC 17029 gamP, nagB
Chlorobaculum parvum NCIB 8327 gamP, nagB
Chlorobaculum tepidum TLS gamP, nagB
Chlorobium limicola DSM 245 gamP, nagB
Chlorobium phaeobacteroides BS1 gamP, nagB
Clostridium acetobutylicum ATCC 824 gamP, nagB
Clostridium kluyveri DSM 555 gamP, nagB
Clostridium tyrobutyricum FAM22553 gamP, nagB
Crocosphaera subtropica ATCC 51142 gamP, nagB
Cupriavidus basilensis FW507-4G11 SLC2A2, glc-kinase, nagB
Dechloromonas agitata is5 gamP, nagB
Dechlorosoma suillum PS gamP, nagB
Dehalococcoides mccartyi 195 gamP, nagB
Denitrovibrio acetiphilus DSM 12809 gamP, nagB
Derxia gummosa DSM 723 SLC2A2, glc-kinase, nagB
Desulfacinum hydrothermale DSM 13146 gamP, nagB
Desulfacinum infernum DSM 9756 gamP, nagB
Desulfarculus baarsii DSM 2075 gamP, nagB
Desulfatibacillum aliphaticivorans DSM 15576 gamP, nagB
Desulfatiglans anilini DSM 4660 gamP, nagB
Desulfitobacterium hafniense DCB-2 gamP, nagB
Desulfobacca acetoxidans DSM 11109 gamP, nagB
Desulfobacter vibrioformis DSM 8776 gamP, nagB
Desulfogranum mediterraneum DSM 13871 gamP, nagB
Desulforamulus ruminis DSM 2154 gamP, nagB
Desulfoscipio geothermicus DSM 3669 gamP, nagB
Desulfotalea psychrophila LSv54 gamP, nagB
Desulfovibrio oxyclinae DSM 11498 gamP, nagB
Desulfovibrio vulgaris Hildenborough JW710 gamP, nagB
Desulfovibrio vulgaris Miyazaki F gamP, nagB
Desulfurobacterium atlanticum DSM 15668 gamP, nagB
Desulfuromonas acetexigens gamP, nagB
Desulfuromusa kysingii DSM 7343 gamP, nagB
Dinoroseobacter shibae DFL-12 gamP, nagB
Dyella japonica UNC79MFTsu3.2 nagX, nagP, nagK, nagA, nagB
Echinicola vietnamensis KMM 6221, DSM 17526 nagX, nagEcba, nagA, nagB
Escherichia coli BW25113 manX, manY, manZ, nagB
Ferroglobus placidus DSM 10642 gamP, nagB
Frankia alni ACN14a gamP, nagB
Geobacter metallireducens GS-15 gamP, nagB
Geotalea uraniireducens Rf4 gamP, nagB
Halococcus hamelinensis 100A6 gamP, nagB
Haloechinothrix alba DSM 45207 gamP, nagB
Haloferax volcanii DS2 gamP, nagB
Haloglycomyces albus DSM 45210 nagX, crr, ptsB, ptsC, nagA, nagB
Halorhodospira halophila SL1 gamP, nagB
Heliomicrobium modesticaldum Ice1; ATCC 51547 gamP, nagB
Herbaspirillum autotrophicum IAM 14942 SLC2A2, glc-kinase, nagB
Herbaspirillum seropedicae SmR1 nagX, SMc02869, SMc02872, SMc02871, SMc02873, nagK, nagA, nagB
Hippea alviniae EP5-r gamP, nagB
Hydrogenophaga taeniospiralis NBRC 102512 gamP, nagB
Hydrogenovibrio halophilus DSM 15072 gamP, nagB
Hydrogenovibrio kuenenii DSM 12350 gamP, nagB
Hydrogenovibrio marinus DSM 11271 gamP, nagB
Hyphomicrobium sulfonivorans WDL6 SLC2A2, glc-kinase, nagB
Klebsiella michiganensis M5al manX, manY, manZ, nagB
Klebsiella variicola At-22 manX, manY, manZ, nagB
Kyrpidia tusciae DSM 2912 gamP, nagB
Leptospirillum ferrooxidans C2-3 gamP, nagB
Magnetospirillum magneticum AMB-1 SLC2A2, glc-kinase, nagB
Malonomonas rubra DSM 5091 gamP, nagB
Maridesulfovibrio bastinii DSM 16055 gamP, nagB
Maridesulfovibrio zosterae DSM 11974 gamP, nagB
Marinobacter adhaerens HP15 SLC2A2, glc-kinase, nagB
Mesorhizobium ciceri WSM1271 nagX, SMc02869, SMc02872, SMc02871, SMc02873, nagK, nagA, nagB
Methanobacterium lacus AL-21 gamP, nagB
Methanococcus aeolicus Nankai-3 SLC2A2, glc-kinase, nagB
Methanococcus maripaludis C5 SLC2A2, glc-kinase, nagB
Methanosarcina acetivorans C2A gamP, nagB
Methanosarcina mazei Go1 gamP, nagB
Methanospirillum lacunae Ki8-1 gamP, nagB
Methanothermobacter thermautotrophicus Delta H gamP, nagB
Methylobacterium nodulans ORS 2060 gamP, nagB
Methylobacterium sp. 4-46 Apr-46 gamP, nagB
Methylocapsa acidiphila B2 gamP, nagB
Methylocapsa aurea KYG gamP, nagB
Methylocella silvestris BL2 gamP, nagB
Methylococcus capsulatus Bath gamP, nagB
Methylocystis bryophila S285 SLC2A2, glc-kinase, nagB
Methyloferula stellata AR4T gamP, nagB
Methylohalobius crimeensis 10Ki gamP, nagB
Methylomonas methanica MC09 gamP, nagB
Methylosarcina fibrata AML-C10 gamP, nagB
Methylotuvimicrobium alcaliphilum 20Z gamP, nagB
Methylovulum miyakonense HT12 gamP, nagB
Mycolicibacterium vanbaalenii PYR-1 gamP, nagB
Nitratifractor salsuginis DSM 16511 gamP, nagB
Nitratiruptor tergarcus DSM 16512 gamP, nagB
Nitriliruptor alkaliphilus DSM 45188 nagX, SMc02869, SMc02872, SMc02871, SMc02873, nagK, nagA, nagB
Nocardioides dokdonensis FR1436 gamP, nagB
Nocardiopsis lucentensis DSM 44048 nagX, crr, ptsB, ptsC, nagA, nagB
Nostoc punctiforme ATCC 29133; PCC 73102 nagX, nagEcba, nagA, nagB
Novosphingobium aromaticivorans DSM 12444 gamP, nagB
Oleispira antarctica gamP, nagB
Paraburkholderia atlantica CCGE1002 gamP, nagB
Paraburkholderia bryophila 376MFSha3.1 gamP, nagB
Paraburkholderia phymatum STM815 gamP, nagB
Paucidesulfovibrio gracilis DSM 16080 gamP, nagB
Pedobacter sp. GW460-11-11-14-LB5 nagX, nagP, nagK, nagA, nagB
Pelobacter propionicus DSM 2379 gamP, nagB
Persephonella marina EX-H1 gamP, nagB
Phaeacidiphilus oryzae TH49 nagX, crr, ptsB, ptsC, nagA, nagB
Phaeobacter inhibens BS107 nagX, SMc02869, SMc02872, SMc02871, SMc02873, nagK, nagA, nagB
Polaromonas naphthalenivorans CJ2 SLC2A2, glc-kinase, nagB
Prosthecochloris aestuarii DSM 271 gamP, nagB
Pseudarthrobacter sulfonivorans Ar51 nagX, crr, ptsB, ptsC, nagA, nagB
Pseudomonas benzenivorans DSM 8628 gamP, nagB
Pseudomonas fluorescens FW300-N1B4 gdh, AO353_21715, AO353_21720, AO353_21725, AO353_21710, glucosaminate-lyase, kdgK, kdgA
Pseudomonas fluorescens FW300-N2C3 gdh, AO353_21715, AO353_21720, AO353_21725, AO353_21710, glucosaminate-lyase, kdgK, kdgA
Pseudomonas fluorescens FW300-N2E2 gdh, AO353_21715, AO353_21720, AO353_21725, AO353_21710, glucosaminate-lyase, kdgK, kdgA
Pseudomonas fluorescens FW300-N2E3 gdh, AO353_21715, AO353_21720, AO353_21725, AO353_21710, glucosaminate-lyase, kdgK, kdgA
Pseudomonas fluorescens GW456-L13 gamP, nagB
Pseudomonas putida KT2440 gamP, nagB
Pseudomonas simiae WCS417 gdh, AO353_21715, AO353_21720, AO353_21725, AO353_21710, glucosaminate-lyase, kdgK, kdgA
Pseudomonas stutzeri RCH2 gamP, nagB
Pyrolobus fumarii 1A gamP, nagB
Rhizobium etli CFN 42 SM_b21216, SM_b21219, SM_b21220, SM_b21221, glc-kinase, nagB
Rhizobium johnstonii 3841 SM_b21216, SM_b21219, SM_b21220, SM_b21221, glc-kinase, nagB
Rhizobium leguminosarum WSM1325 SM_b21216, SM_b21219, SM_b21220, SM_b21221, glc-kinase, nagB
Rhizorhabdus wittichii RW1 gamP, nagB
Rhodanobacter denitrificans FW104-10B01 nagX, nagP, nagK, nagA, nagB
Rhodomicrobium vannielii ATCC 17100 gamP, nagB
Rhodopseudomonas palustris CGA009 gamP, nagB
Rhodospirillum centenum SW; ATCC 51521 SLC2A2, glc-kinase, nagB
Rhodospirillum rubrum ATCC 11170 SLC2A2, glc-kinase, nagB
Roseburia faecis M72 SLC2A2, glc-kinase, nagB
Saccharomonospora cyanea NA-134 nagX, crr, ptsB, ptsC, nagA, nagB
Sedimenticola selenatireducens DSM 17993 gamP, nagB
Shewanella amazonensis SB2B nagX, nagP, nagK, nagA, nagB
Shewanella loihica PV-4 nagX, nagP, nagK, nagA, nagB
Shewanella oneidensis MR-1 nagX, nagP, nagK, nagA, nagB
Shewanella sp. ANA-3 nagX, nagP, nagK, nagA, nagB
Sinorhizobium fredii NGR234 SM_b21216, SM_b21219, SM_b21220, SM_b21221, glc-kinase, nagB
Sinorhizobium medicae WSM419 SM_b21216, SM_b21219, SM_b21220, SM_b21221, glc-kinase, nagB
Sinorhizobium meliloti 1021 SM_b21216, SM_b21219, SM_b21220, SM_b21221, glc-kinase, nagB
Sphingomonas koreensis DSMZ 15582 nagX, nagF, nagEcb, nagA, nagB
Stenotrophomonas chelatiphaga DSM 21508 nagX, nagP, nagK, nagA, nagB
Steroidobacter denitrificans DSM 18526 SLC2A2, glc-kinase, nagB
Stutzerimonas stutzeri A1501 gamP, nagB
Sulfuricurvum kujiense DSM 16994 gamP, nagB
Sulfurihydrogenibium azorense Az-Fu1 gamP, nagB
Sulfurihydrogenibium subterraneum DSM 15120 gamP, nagB
Sulfurimonas denitrificans DSM 1251 gamP, nagB
Sulfuritalea hydrogenivorans DSM 22779 gamP, nagB
Sulfurivirga caldicuralii DSM 17737 gamP, nagB
Synechococcus elongatus PCC 7942 gamP, nagB
Teredinibacter turnerae T7901 nagX, nagP, nagK, nagA, nagB
Thauera aminoaromatica S2 gamP, nagB
Thermithiobacillus tepidarius DSM 3134 gamP, nagB
Thermocrinis albus DSM 14484 gamP, nagB
Thermodesulforhabdus norvegica DSM 9990 gamP, nagB
Thermomonospora curvata DSM 43183 nagX, crr, ptsB, ptsC, nagA, nagB
Thermovibrio ammonificans HB-1 gamP, nagB
Thermus aquaticus YT-1 gamP, nagB
Thioalkalivibrio denitrificans ALJD gamP, nagB
Thioalkalivibrio halophilus HL17 gamP, nagB
Thioalkalivibrio paradoxus ARh 1 gamP, nagB
Thioalkalivibrio thiocyanodenitrificans ARhD 1 gamP, nagB
Thiohalomonas denitrificans HLD2 gamP, nagB
Thiohalospira halophila HL 3 gamP, nagB
Thiomicrorhabdus arctica DSM 13458 gamP, nagB
Thiomicrorhabdus chilensis DSM 12352 gamP, nagB
Thiomicrospira cyclica ALM1 gamP, nagB
Thiomicrospira microaerophila ASL8-2 gamP, nagB
Thiomicrospira pelophila DSM 1534 gamP, nagB
Thiothrix lacustris DSM 21227 gamP, nagB
Tistlia consotensis USBA 355 gdh, AO353_21715, AO353_21720, AO353_21725, AO353_21710, glucosaminate-lyase, kdgK, kdgA
Trichlorobacter lovleyi SZ gamP, nagB
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome nagX, nagEcba, nagA, nagB
Trichormus variabilis ATCC 29413 nagX, nagEcba, nagA, nagB
Xanthobacter autotrophicus Py2 gamP, nagB
Xenophilus azovorans DSM 13620 gdh, AO353_21715, AO353_21720, AO353_21725, AO353_21710, glucosaminate-lyase, kdgK, kdgA

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