GapMind for catabolism of small carbon sources

 

Protein 14809 in Escherichia coli BW25113

Annotation: b0679 fused N-acetyl glucosamine specific PTS enzyme: IIC, IIB , and IIA components (NCBI)

Length: 648 amino acids

Source: Keio in FitnessBrowser

Candidate for 37 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
N-acetyl-D-glucosamine catabolism nagEcba hi protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized) 100% 100% 1263.4 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 53% 545.8
D-glucosamine (chitosamine) catabolism gamP hi protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized) 100% 100% 1263.4 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 53% 545.8
D-glucosamine (chitosamine) catabolism nagEcba hi protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized) 100% 100% 1263.4 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 53% 545.8
N-acetyl-D-glucosamine catabolism nagEcb med N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized) 53% 88% 545.8 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 100% 1263.4
D-glucosamine (chitosamine) catabolism nagEcb med N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized) 53% 88% 545.8 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 100% 1263.4
N-acetyl-D-glucosamine catabolism nagEIIA med Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) 43% 97% 488.8 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 100% 1263.4
D-glucosamine (chitosamine) catabolism nagEIIA med Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) 43% 97% 488.8 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 100% 1263.4
D-maltose catabolism malEIIA med Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) 43% 97% 488.8 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 100% 1263.4
trehalose catabolism treEIIA med Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) 43% 97% 488.8 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 100% 1263.4
D-cellobiose catabolism ptsG-crr med PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized) 42% 96% 481.9 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 100% 1263.4
D-glucose catabolism ptsG-crr med PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized) 42% 96% 481.9 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 100% 1263.4
lactose catabolism ptsG-crr med PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized) 42% 96% 481.9 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 100% 1263.4
D-maltose catabolism ptsG-crr med PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized) 42% 96% 481.9 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 100% 1263.4
sucrose catabolism ptsG-crr med PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized) 42% 96% 481.9 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 100% 1263.4
trehalose catabolism ptsG-crr med PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized) 42% 96% 481.9 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 100% 1263.4
N-acetyl-D-glucosamine catabolism nagPcb med PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized) 50% 100% 477.2 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 100% 1263.4
D-glucosamine (chitosamine) catabolism nagPcb med PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized) 50% 100% 477.2 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 100% 1263.4
D-cellobiose catabolism ptsG med PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized) 42% 99% 380.6 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 100% 1263.4
D-glucose catabolism ptsG med PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized) 42% 99% 380.6 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 100% 1263.4
lactose catabolism ptsG med PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized) 42% 99% 380.6 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 100% 1263.4
D-maltose catabolism ptsG med PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized) 42% 99% 380.6 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 100% 1263.4
sucrose catabolism ptsG med PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized) 42% 99% 380.6 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 100% 1263.4
trehalose catabolism ptsG med PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized) 42% 99% 380.6 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 100% 1263.4
N-acetyl-D-glucosamine catabolism ptsC med PTS system N-acetylglucosamine-specific EIIC component; PTS system GlcNAc-specific EIIC component; GlcNAc-specific transporter; N-acetylglucosamine permease IIC component; GlcNAc permease IIC component (characterized) 49% 94% 373.6 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 100% 1263.4
D-glucosamine (chitosamine) catabolism ptsC med PTS system N-acetylglucosamine-specific EIIC component; PTS system GlcNAc-specific EIIC component; GlcNAc-specific transporter; N-acetylglucosamine permease IIC component; GlcNAc permease IIC component (characterized) 49% 94% 373.6 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 100% 1263.4
D-cellobiose catabolism crr med PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 51% 88% 163.7 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 100% 1263.4
D-glucose catabolism crr med PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 51% 88% 163.7 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 100% 1263.4
lactose catabolism crr med PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 51% 88% 163.7 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 100% 1263.4
D-maltose catabolism crr med PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 51% 88% 163.7 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 100% 1263.4
sucrose catabolism crr med PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 51% 88% 163.7 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 100% 1263.4
trehalose catabolism crr med PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 51% 88% 163.7 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 100% 1263.4
D-maltose catabolism malEIICBA lo PTS system, IIABC components (characterized, see rationale) 33% 88% 298.1 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 100% 1263.4
D-maltose catabolism malEIICB lo The Maltose group translocator, MalT of 470 aas and 10 TMSs. Takes up extracellular maltose, releasing maltose-phosphate into the cytoplasm (characterized) 34% 84% 221.1 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 100% 1263.4
N-acetyl-D-glucosamine catabolism crr lo Putative PTS system sugar phosphotransferase component IIA (characterized, see rationale) 34% 93% 82.8 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 100% 1263.4
D-glucosamine (chitosamine) catabolism crr lo Putative PTS system sugar phosphotransferase component IIA (characterized, see rationale) 34% 93% 82.8 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 100% 1263.4
N-acetyl-D-glucosamine catabolism ptsB lo IIB aka PtsB, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized) 31% 95% 60.5 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 100% 1263.4
D-glucosamine (chitosamine) catabolism ptsB lo IIB aka PtsB, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized) 31% 95% 60.5 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 100% 1263.4

Sequence Analysis Tools

View 14809 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MNILGFFQRLGRALQLPIAVLPVAALLLRFGQPDLLNVAFIAQAGGAIFDNLALIFAIGV
ASSWSKDSAGAAALAGAVGYFVLTKAMVTINPEINMGVLAGIITGLVGGAAYNRWSDIKL
PDFLSFFGGKRFVPIATGFFCLVLAAIFGYVWPPVQHAIHAGGEWIVSAGALGSGIFGFI
NRLLIPTGLHQVLNTIAWFQIGEFTNAAGTVFHGDINRFYAGDGTAGMFMSGFFPIMMFG
LPGAALAMYFAAPKERRPMVGGMLLSVAVTAFLTGVTEPLEFLFMFLAPLLYLLHALLTG
ISLFVATLLGIHAGFSFSAGAIDYALMYNLPAASQNVWMLLVMGVIFFAIYFVVFSLVIR
MFNLKTPGREDKEDEIVTEEANSNTEEGLTQLATNYIAAVGGTDNLKAIDACITRLRLTV
ADSARVNDTMCKRLGASGVVKLNKQTIQVIVGAKAESIGDAMKKVVARGPVAAASAEATP
ATAAPVAKPQAVPNAVSIAELVSPITGDVVALDQVPDEAFASKAVGDGVAVKPTDKIVVS
PAAGTIVKIFNTNHAFCLETEKGAEIVVHMGIDTVALEGKGFKRLVEEGAQVSAGQPILE
MDLDYLNANARSMISPVVCSNIDDFSGLIIKAQGHIVAGQTPLYEIKK

This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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