GapMind for catabolism of small carbon sources

 

N-acetyl-D-glucosamine catabolism

Analysis of pathway NAG in 201 genomes

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