GapMind for catabolism of small carbon sources

 

D-glucosamine (chitosamine) catabolism

Analysis of pathway glucosamine in 276 genomes

Genome Best path
Acidovorax caeni R-24608 gamP, nagB
Actinokineospora bangkokensis 44EHW gamP, nagB
Actinomyces timonensis 7400942 nagX, crr, ptsB, ptsC, nagA, nagB
Algiphilus aromaticivorans DG1253 gamP, nagB
Algoriphagus aquaeductus T4 gamP, nagB
Algoriphagus machipongonensis PR1 gamP, nagB
Alicyclobacillus ferrooxydans TC-34 gamP, nagB
Alishewanella agri BL06 nagX, nagP, nagK, nagA, nagB
Alistipes indistinctus YIT 12060 nagX, nagP, nagK, nagA, nagB
Alistipes shahii WAL 8301 nagX, nagP, nagK, nagA, nagB
Alkalitalea saponilacus SC/BZ-SP2 gamP, nagB
Amantichitinum ursilacus IGB-41 gamP, nagB
Amphibacillus jilinensis Y1 gamP, nagB
Amphritea japonica JAMM 1866 gamP, nagB
Amycolatopsis halophila YIM 93223 gamP, nagB
Amycolatopsis xylanica CPCC 202699 nagX, crr, ptsB, ptsC, nagA, nagB
Aquimarina agarilytica ZC1 gamP, nagB
Aquimarina longa SW024 gamP, nagB
Aquimarina macrocephali JAMB N27 gamP, nagB
Archaeoglobus sulfaticallidus PM70-1 gamP, nagB
Arcticibacter svalbardensis MN12-7 nagX, nagP, nagK, nagA, nagB
Ardenticatena maritima 110S gamP, nagB
Arenimonas metalli CF5-1 gamP, nagB
Arenitalea lutea P7-3-5 gamP, nagB
Azospirillum humicireducens SgZ-5 gamP, nagB
Azospirillum thiophilum BV-S gdh, AO353_21715, AO353_21720, AO353_21725, AO353_21710, glucosaminate-lyase, kdgK, kdgA
Bacillus altitudinis 41KF2b gamP, nagB
Bacillus coahuilensis m4-4 gamP, nagB
Bacillus cytotoxicus NVH 391-98 gamP, nagB
Bacillus horneckiae 1P01SC gamP, nagB
Bacillus okhensis Kh10-101 nagX, nagEIIA, nagPcb, nagA, nagB
Bacillus safensis FO-36b gamP, nagB
Bacillus velezensis CBMB205 gamP, nagB
Bacteroides clarus YIT 12056 nagX, nagP, nagK, nagA, nagB
Bacteroides faecis MAJ27 nagX, nagP, nagK, nagA, nagB
Bacteroides fluxus YIT 12057 nagX, nagP, nagK, nagA, nagB
Bacteroides oleiciplenus YIT 12058 gamP, nagB
Barnesiella intestinihominis YIT 11860 gamP, nagB
Belnapia rosea CPCC 100156 gdh, AO353_21715, AO353_21720, AO353_21725, AO353_21710, glucosaminate-lyase, kdgK, kdgA
Bizionia argentinensis JUB59 gamP, nagB
Bradyrhizobium diazoefficiens USDA110 gdh, AO353_21715, AO353_21720, AO353_21725, AO353_21710, glucosaminate-lyase, kdgK, kdgA
Brevibacterium jeotgali SJ5-8 gamP, nagB
Brucella inopinata BO1 nagX, SMc02869, SMc02872, SMc02871, SMc02873, nagK, nagA, nagB
Brucella microti CCM 4915 nagX, SMc02869, SMc02872, SMc02871, SMc02873, nagK, nagA, nagB
Bryobacter aggregatus MPL3 nagX, nagEcba, nagA, nagB
Caldicellulosiruptor hydrothermalis 108 SLC2A2, glc-kinase, nagB
Caldicellulosiruptor kronotskyensis 2002 SLC2A2, glc-kinase, nagB
Carboxydothermus pertinax Ug1 SM_b21216, SM_b21219, SM_b21220, SM_b21221, glc-kinase, nagB
Catellicoccus marimammalium M35/04/3 manX, manY, manZ, nagB
Chromobacterium vaccinii MWU205 gamP, nagB
Chryseobacterium angstadtii KM gamP, nagB
Chryseobacterium arthrosphaerae CC-VM-7 gamP, nagB
Chryseobacterium viscerum 687B-08 gamP, nagB
Cloacibacillus porcorum CL-84 gamP, nagB
Cobetia crustatorum JO1 gamP, nagB
Collimonas arenae Ter10 nagX, SMc02869, SMc02872, SMc02871, SMc02873, nagK, nagA, nagB
Collimonas pratensis Ter91 nagX, SMc02869, SMc02872, SMc02871, SMc02873, nagK, nagA, nagB
Collinsella tanakaei YIT 12063 manX, manY, manZ, nagB
Coprobacter fastidiosus NSB1 gamP, nagB
Corynebacterium deserti GIMN1.010 gamP, nagB
Corynebacterium frankenforstense ST18 gamP, nagB
Corynebacterium lactis RW2-5 gamP, nagB
Croceitalea dokdonensis DOKDO 023 nagX, nagP, nagK, nagA, nagB
Cronobacter condimenti 1330 manX, manY, manZ, nagB
Cronobacter muytjensii ATCC 51329 manX, manY, manZ, nagB
Cronobacter universalis NCTC 9529 manX, manY, manZ, nagB
Desulfatitalea tepidiphila S28bF gamP, nagB
Desulfotomaculum hydrothermale Lam5 gamP, nagB
Dethiosulfovibrio salsuginis USBA 82 gamP, nagB
Devosia chinhatensis IPL18 gamP, nagB
Devriesea agamarum IMP2 nagX, crr, ptsB, ptsC, nagA, nagB
Dialister succinatiphilus YIT 11850 gamP, nagB
Dietzia timorensis ID05-A0528 gamP, nagB
Dokdonella koreensis DS-123 gamP, nagB
Domibacillus robiginosus WS 4628 gamP, nagB
Duganella sacchari Sac-22 nagX, SMc02869, SMc02872, SMc02871, SMc02873, nagK, nagA, nagB
Dyadobacter tibetensis Y620-1 nagX, nagP, nagK, nagA, nagB
Dyella jiangningensis SBZ3-12 nagX, nagP, nagK, nagA, nagB
Endozoicomonas montiporae CL-33 gamP, nagB
Enterococcus termitis LMG 8895 gamP, nagB
Enterorhabdus caecimuris B7 gamP, nagB
Epibacterium ulvae U95 gamP, nagB
Erythrobacter gangjinensis K7-2 gamP, nagB
Erythrobacter marinus HWDM-33 gamP, nagB
Ethanoligenens harbinense YUAN-3 gamP, nagB
Fervidicella metallireducens AeB gamP, nagB
Fibrella aestuarina BUZ 2 nagX, nagEcba, nagA, nagB
Flammeovirga pacifica WPAGA1 nagX, nagP, nagK, nagA, nagB
Flaviramulus ichthyoenteri Th78 nagX, nagP, nagK, nagA, nagB
Flavobacterium beibuense F44-8 gamP, nagB
Flavobacterium glycines Gm-149 gamP, nagB
Flavobacterium sp. LM5 nagX, nagEcba, nagA, nagB
Flavobacterium ummariense DS-12 gamP, nagB
Frischella perrara PEB0191 gamP, nagB
Galbibacter marinus ck-I2-15 gamP, nagB
Gallaecimonas xiamenensis 3-C-1 nagX, nagP, nagK, nagA, nagB
Geobacter daltonii FRC-32 gamP, nagB
Gillisia marina CBA3202 gamP, nagB
Gracilibacillus halophilus YIM-C55.5 gamP, nagB
Granulicella mallensis MP5ACTX8 nagX, nagEcba, nagA, nagB
Granulicella tundricola MP5ACTX9 nagX, nagEcba, nagA, nagB
Hafnia paralvei ATCC 29927 manX, manY, manZ, nagB
Haladaptatus cibarius D43 gamP, nagB
Halioglobus japonicus S1-36 nagX, nagP, nagK, nagA, nagB
Halobacillus alkaliphilus FP5 gamP, nagB
Halococcus hamelinensis 100A6 gamP, nagB
Halomonas salina B6 gamP, nagB
Halomonas smyrnensis AAD6 gdh, AO353_21715, AO353_21720, AO353_21725, AO353_21710, glucosaminate-lyase, kdgK, kdgA
Halomonas stevensii S18214 gamP, nagB
Halomonas titanicae BH1 gamP, nagB
Halomonas xinjiangensis TRM 0175 gamP, nagB
Halopiger salifodinae KCY07-B2 gamP, nagB
Halostagnicola larsenii XH-48 gamP, nagB
Haloterrigena daqingensis JX313 gamP, nagB
Herbaspirillum aquaticum IEH 4430 nagX, SMc02869, SMc02872, SMc02871, SMc02873, nagK, nagA, nagB
Hippea alviniae EP5-r gamP, nagB
Hippea jasoniae Mar08-272r gamP, nagB
Hoeflea phototrophica DFL-43 gamP, nagB
Hyphomicrobium nitrativorans NL23 gamP, nagB
Imtechella halotolerans K1 gamP, nagB
Indibacter alkaliphilus LW1 gamP, nagB
Jannaschia aquimarina GSW-M26 gamP, nagB
Jeotgalibacillus soli P9 gamP, nagB
Kangiella geojedonensis YCS-5 gamP, nagB
Knoellia flava TL1 gamP, nagB
Kocuria flava HO-9041 gamP, nagB
Kocuria turfanensis HO-9042 gamP, nagB
Laceyella sediminis RHA1 gamP, nagB
Lacinutrix algicola AKS293 gamP, nagB
Lacinutrix himadriensis E4-9a gamP, nagB
Lacinutrix mariniflava AKS432 gamP, nagB
Lactobacillus curieae CCTCC M 2011381 gamP, nagB
Lactobacillus delbrueckii ZN7a-9 gamP, nagB
Lactobacillus hokkaidonensis LOOC260 gamP, nagB
Lactobacillus oryzae SG293 gamP, nagB
Lactobacillus pobuzihii E100301 manX, manY, manZ, nagB
Lactobacillus shenzhenensis LY-73 gamP, nagB
Lactobacillus silagei IWT126 gamP, nagB
Leeuwenhoekiella blandensis MED217 gamP, nagB
Lentibacillus jeotgali Grbi gamP, nagB
Limnohabitans curvus MWH-C5 gamP, nagB
Limnohabitans parvus II-B4 SLC2A2, glc-kinase, nagB
Listeria fleischmannii LU2006-1 manX, manY, manZ, nagB
Luteimonas huabeiensis HB2 nagX, nagP, nagK, nagA, nagB
Luteipulveratus mongoliensis MN07-A0370 gamP, nagB
Lutibaculum baratangense AMV1 gdh, AO353_21715, AO353_21720, AO353_21725, AO353_21710, glucosaminate-lyase, kdgK, kdgA
Lysobacter daejeonensis GH1-9 SLC2A2, glc-kinase, nagB
Magnetovibrio blakemorei MV-1 gamP, nagB
Marinicella litoralis KMM 3900 gamP, nagB
Mariniradius saccharolyticus AK6 gamP, nagB
Marinobacter algicola DG893 gamP, nagB
Marinobacter guineae M3B SLC2A2, glc-kinase, nagB
Marinobacter psychrophilus 20041 gamP, nagB
Marinomonas arctica 328 nagX, SMc02869, SMc02872, SMc02871, SMc02873, nagK, nagA, nagB
Marivita geojedonensis DPG-138 gamP, nagB
Martelella endophytica YC6887 gamP, nagB
Megamonas funiformis YIT 11815 gamP, nagB
Mesorhizobium ciceri WSM1271 nagX, SMc02869, SMc02872, SMc02871, SMc02873, nagK, nagA, nagB
Methanobacterium arcticum M2 gamP, nagB
Methanobacterium veterum MK4 gamP, nagB
Methanocella arvoryzae MRE50 gamP, nagB
Methanococcus aeolicus Nankai-3 SLC2A2, glc-kinase, nagB
Methanoculleus horonobensis T10 gamP, nagB
Methanolinea tarda NOBI-1 gamP, nagB
Methanosarcina soligelidi SMA-21 gamP, nagB
Methanospirillum lacunae Ki8-1 gamP, nagB
Methanospirillum stamsii Pt1 gamP, nagB
Methylibium petroleiphilum PM1 gamP, nagB
Methylobacterium gossipiicola Gh-105 gamP, nagB
Methylocapsa aurea KYG gamP, nagB
Methylotenera versatilis 301 gamP, nagB
Microbacterium profundi Shh49 gamP, nagB
Microvirga lotononidis WSM3557 gdh, AO353_21715, AO353_21720, AO353_21725, AO353_21710, glucosaminate-lyase, kdgK, kdgA
Moritella dasanensis ArB 0140 gamP, nagB
Mucilaginibacter gossypii Gh-67 nagX, nagP, nagK, nagA, nagB
Mucilaginibacter gossypiicola Gh-48 nagX, nagP, nagK, nagA, nagB
Mucilaginibacter mallensis MP1X4 nagX, nagP, nagK, nagA, nagB
Nafulsella turpanensis ZLM-10 gamP, nagB
Natronomonas moolapensis 8.8.11 gamP, nagB
Nautilia profundicola AmH gamP, nagB
Neiella marina J221 gamP, nagB
Neptunomonas antarctica S3-22 gamP, nagB
Nocardioides daejeonensis MJ31 gamP, nagB
Nocardioides dokdonensis FR1436 gamP, nagB
Nocardiopsis baichengensis YIM 90130 nagX, crr, ptsB, ptsC, nagA, nagB
Nocardiopsis gilva YIM 90087 nagX, crr, ptsB, ptsC, nagA, nagB
Novosphingobium barchaimii LL02 gamP, nagB
Novosphingobium fuchskuhlense FNE08-7 gamP, nagB
Novosphingobium lindaniclasticum LE124 gamP, nagB
Oceanisphaera arctica V1-41 nagX, nagP, nagK, nagA, nagB
Ochrobactrum rhizosphaerae PR17 gamP, nagB
Ochrobactrum thiophenivorans DSM 7216 nagX, nagP, nagK, nagA, nagB
Oscillibacter ruminantium GH1 SLC2A2, glc-kinase, nagB
Paenisporosarcina indica PN2 gamP, nagB
Palaeococcus pacificus DY20341 SLC2A2, glc-kinase, nagB
Paludibacter propionicigenes WB4 gamP, nagB
Pandoraea thiooxydans ATSB16 SLC2A2, glc-kinase, nagB
Pantoea rwandensis LMG 26275 manX, manY, manZ, nagB
Pedobacter arcticus A12 nagX, nagP, nagK, nagA, nagB
Photobacterium gaetbulicola Gung47 gamP, nagB
Photobacterium jeanii R-40508 gamP, nagB
Phyllobacterium brassicacearum STM 196 SM_b21216, SM_b21219, SM_b21220, SM_b21221, glc-kinase, nagB
Phyllobacterium endophyticum PEPV15 SM_b21216, SM_b21219, SM_b21220, SM_b21221, glc-kinase, nagB
Phyllobacterium leguminum ORS 1419 nagX, SMc02869, SMc02872, SMc02871, SMc02873, nagK, nagA, nagB
Planktomarina temperata RCA23 gamP, nagB
Planococcus halocryophilus Or1 gamP, nagB
Pleomorphomonas diazotrophica R5-392 SM_b21216, SM_b21219, SM_b21220, SM_b21221, glc-kinase, nagB
Polaribacter dokdonensis DSW-5 gamP, nagB
Pontibacillus litoralis JSM 072002 gamP, nagB
Pontibacter lucknowensis DM9 gamP, nagB
Pontibacter ramchanderi LP43 gamP, nagB
Pontimonas salivibrio CL-TW6 gamP, nagB
Porphyrobacter dokdonensis DSW-74 gamP, nagB
Pseudoalteromonas arctica A 37-1-2 gamP, nagB
Pseudomonas baetica a390 gdh, AO353_21715, AO353_21720, AO353_21725, AO353_21710, glucosaminate-lyase, kdgK, kdgA
Pseudomonas litoralis 2SM5 gamP, nagB
Pseudomonas taeanensis MS-3 gamP, nagB
Pseudovibrio axinellae Ad2 gamP, nagB
Psychrobacter arcticus 273-4 gamP, nagB
Psychrobacter cryohalolentis K5 gamP, nagB
Psychromonas ingrahamii 37 gamP, nagB
Psychromonas ossibalaenae JAMM 0738 gamP, nagB
Rhizobium freirei PRF 81 SM_b21216, SM_b21219, SM_b21220, SM_b21221, glc-kinase, nagB
Rhizobium grahamii CCGE 502 SM_b21216, SM_b21219, SM_b21220, SM_b21221, glc-kinase, nagB
Rhizobium subbaraonis JC85 nagX, SMc02869, SMc02872, SMc02871, SMc02873, nagK, nagA, nagB
Rhodanobacter denitrificans 2APBS1 nagX, nagP, nagK, nagA, nagB
Rhodobacter johrii JA192 gamP, nagB
Rhodobacter maris JA276 gamP, nagB
Rhodobacter ovatus JA234 gamP, nagB
Rhodobacter viridis JA737 gamP, nagB
Rhodococcus qingshengii djl-6-2 nagX, crr, ptsB, ptsC, nagA, nagB
Rhodopseudomonas pseudopalustris DSM 123 gamP, nagB
Roseateles aquatilis CCUG 48205 SLC2A2, glc-kinase, nagB
Roseivirga spongicola UST030701-084 gamP, nagB
Rubrivirga marina SAORIC-28 gamP, nagB
Ruegeria conchae TW15 nagX, SMc02869, SMc02872, SMc02871, SMc02873, nagK, nagA, nagB
Saccharomonospora marina XMU15 nagX, crr, ptsB, ptsC, nagA, nagB
Salinicoccus carnicancri Crm gamP, nagB
Serinicoccus profundi MCCC 1A05965 gamP, nagB
Shewanella halifaxensis HAW-EB4 nagX, nagP, nagK, nagA, nagB
Skermanella stibiiresistens SB22 SLC2A2, glc-kinase, nagB
Snodgrassella alvi wkB2 gamP, nagB
Sphaerochaeta globosa Buddy SM_b21216, SM_b21219, SM_b21220, SM_b21221, glc-kinase, nagB
Sphaerochaeta pleomorpha Grapes nagX, SMc02869, SMc02872, SMc02871, SMc02873, nagK, nagA, nagB
Sphingobium baderi LL03 gamP, nagB
Sphingobium czechense LL01 gamP, nagB
Sphingobium quisquiliarum P25 gamP, nagB
Sphingomonas histidinilytica UM2 gamP, nagB
Sphingomonas indica Dd16 gamP, nagB
Sphingomonas laterariae LNB2 gamP, nagB
Sphingopyxis indica DS15 gamP, nagB
Sphingopyxis terrae UI2 gamP, nagB
Sporolactobacillus vineae SL153 gamP, nagB
Streptacidiphilus oryzae TH49 nagX, crr, ptsB, ptsC, nagA, nagB
Streptococcus anginosus CCUG 39159 manX, manY, manZ, nagB
Streptococcus massiliensis 4401825 gamP, nagB
Streptococcus oralis 7747 gamP, nagB
Streptococcus oralis AZ_3a manX, manY, manZ, nagB
Streptomyces kebangsaanensis SUK12 nagX, crr, ptsB, ptsC, nagA, nagB
Succinatimonas hippei YIT 12066 SLC2A2, glc-kinase, nagB
Sulfurimonas gotlandica GD1 gamP, nagB
Tatumella morbirosei LMG 23360 manX, manY, manZ, nagB
Thauera humireducens SgZ-1 SLC2A2, glc-kinase, nagB
Thermoactinomyces daqus H-18 gamP, nagB
Thermobifida halotolerans YIM 90462 gamP, nagB
Thermodesulfovibrio aggregans TGE-P1 gamP, nagB
Thermophagus xiamenensis HS1 nagX, nagP, nagK, nagA, nagB
Thermovenabulum gondwanense R270 gamP, nagB
Thioclava dalianensis DLFJ1-1 nagX, SMc02869, SMc02872, SMc02871, SMc02873, nagK, nagA, nagB
Thiohalospira halophila HL 3 gamP, nagB
Tistlia consotensis USBA 355 gdh, AO353_21715, AO353_21720, AO353_21725, AO353_21710, glucosaminate-lyase, kdgK, kdgA
Vagococcus penaei CD276 manX, manY, manZ, nagB
Verminephrobacter eiseniae EF01-2 SLC2A2, glc-kinase, nagB
Weissella oryzae SG25 manX, manY, manZ, nagB
Williamsia sterculiae CPCC 203464 gamP, nagB
Yersinia intermedia Y228 manX, manY, manZ, nagB

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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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