GapMind for catabolism of small carbon sources

 

Protein WP_007670388.1 in Cronobacter condimenti 1330

Annotation: NCBI__GCF_000319285.1:WP_007670388.1

Length: 650 amino acids

Source: GCF_000319285.1 in NCBI

Candidate for 36 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) 92% 100% 1178.3 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 55% 541.6
D-glucosamine (chitosamine) catabolism gamP hi protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized) 92% 100% 1178.3 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 55% 541.6
D-glucosamine (chitosamine) catabolism nagEcba hi protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized) 92% 100% 1178.3 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 55% 541.6
N-acetyl-D-glucosamine catabolism nagEcb med N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized) 55% 88% 541.6 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 92% 1178.3
D-glucosamine (chitosamine) catabolism nagEcb med N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized) 55% 88% 541.6 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 92% 1178.3
N-acetyl-D-glucosamine catabolism nagEIIA med Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) 43% 97% 490 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 92% 1178.3
D-glucosamine (chitosamine) catabolism nagEIIA med Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) 43% 97% 490 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 92% 1178.3
D-maltose catabolism malEIIA med Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) 43% 97% 490 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 92% 1178.3
trehalose catabolism treEIIA med Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) 43% 97% 490 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 92% 1178.3
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) 40% 99% 473 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 92% 1178.3
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) 40% 99% 473 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 92% 1178.3
lactose catabolism ptsG-crr med PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized) 40% 99% 473 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 92% 1178.3
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) 40% 99% 473 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 92% 1178.3
sucrose catabolism ptsG-crr med PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized) 40% 99% 473 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 92% 1178.3
trehalose catabolism ptsG-crr med PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized) 40% 99% 473 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 92% 1178.3
N-acetyl-D-glucosamine catabolism nagPcb med PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized) 51% 100% 472.6 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 92% 1178.3
D-glucosamine (chitosamine) catabolism nagPcb med PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized) 51% 100% 472.6 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 92% 1178.3
D-cellobiose catabolism ptsG med PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized) 42% 99% 382.9 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 92% 1178.3
D-glucose catabolism ptsG med PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized) 42% 99% 382.9 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 92% 1178.3
lactose catabolism ptsG med PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized) 42% 99% 382.9 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 92% 1178.3
D-maltose catabolism ptsG med PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized) 42% 99% 382.9 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 92% 1178.3
sucrose catabolism ptsG med PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized) 42% 99% 382.9 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 92% 1178.3
trehalose catabolism ptsG med PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized) 42% 99% 382.9 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 92% 1178.3
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) 50% 94% 370.5 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 92% 1178.3
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) 50% 94% 370.5 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 92% 1178.3
D-cellobiose catabolism crr med PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 54% 86% 163.7 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 92% 1178.3
D-glucose catabolism crr med PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 54% 86% 163.7 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 92% 1178.3
lactose catabolism crr med PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 54% 86% 163.7 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 92% 1178.3
D-maltose catabolism crr med PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 54% 86% 163.7 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 92% 1178.3
sucrose catabolism crr med PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 54% 86% 163.7 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 92% 1178.3
trehalose catabolism crr med PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 54% 86% 163.7 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 92% 1178.3
N-acetyl-D-glucosamine catabolism ptsB med PTS system N-acetylglucosamine-specific EIIB component; PTS system GlcNAc-specific EIIB component; N-acetylglucosamine-specific phosphotransferase enzyme IIB component; GlcNAc-specific phosphotransferase enzyme IIB component; EC 2.7.1.193 (characterized) 46% 100% 68.6 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 92% 1178.3
D-glucosamine (chitosamine) catabolism ptsB med PTS system N-acetylglucosamine-specific EIIB component; PTS system GlcNAc-specific EIIB component; N-acetylglucosamine-specific phosphotransferase enzyme IIB component; GlcNAc-specific phosphotransferase enzyme IIB component; EC 2.7.1.193 (characterized) 46% 100% 68.6 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 92% 1178.3
D-maltose catabolism malEIICBA lo PTS system, IIABC components (characterized, see rationale) 33% 88% 295.8 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 92% 1178.3
N-acetyl-D-glucosamine catabolism crr lo Putative PTS system sugar phosphotransferase component IIA (characterized, see rationale) 35% 97% 87 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 92% 1178.3
D-glucosamine (chitosamine) catabolism crr lo Putative PTS system sugar phosphotransferase component IIA (characterized, see rationale) 35% 97% 87 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 92% 1178.3

Sequence Analysis Tools

View WP_007670388.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MNILGFFQRLGRALQLPIAVLPVAALLLRFGQPDLLNVAFIAQAGGAIFDNLALIFAIGV
ASSWSKDSAGAAALAGAVGYFVLTKAMVTINPEINMGVLAGIITGLVGGAVYNRWSAIKL
PDFLSFFGGKRFVPIATGFFCLVLAAVFGYVWPPVQHAIHAGGEWIVSAGALGSGIFGFI
NRLLIPTGLHQVLNTIAWFQIGEFTNAAGTVFHGDINRFYAGDGTAGMFMSGFFPIMMFG
LPGAALAMYFAAPKARRPMVGGMLLSVAITAFLTGVTEPLEFLFMFLAPVLYLLHALLTG
ISLFVATLLGIHAGFSFSAGAIDYALMYSLPAASKNVWMLLVMGLVFFVIYFVLFSAVIR
MFNLKTPGREDKENEIVADEANSNTEEGLAQLATSYVAAVGGTDNLKAIDACITRLRLTV
GDSALVSDAACKRLGASGVVKLNKQTIQVIVGAKAESIGDEMKKVVARGPVAAVAANVTP
LNAVTPAAKPQAVTGAQTIAALVSPVTGEVVALDAVPDEAFASKAVGDGVAIKPTDKLVV
SPAAGTIVKIFNTNHAFCLETENGAEIVVHMGIDTVALKGQGFKRLVEEGAQVSAGQPVL
EMDLDYLNANARSMVSPVVCSNIDDFSGLVIKAQGQVVAGQTPLYEIKGK

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