GapMind for catabolism of small carbon sources

 

Protein WP_007706749.1 in Cronobacter universalis NCTC 9529

Annotation: NCBI__GCF_001277175.1:WP_007706749.1

Length: 674 amino acids

Source: GCF_001277175.1 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) 55% 100% 691.4 PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 39% 462.6
D-glucosamine (chitosamine) catabolism gamP hi protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized) 55% 100% 691.4 PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 39% 462.6
D-glucosamine (chitosamine) catabolism nagEcba hi protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized) 55% 100% 691.4 PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 39% 462.6
N-acetyl-D-glucosamine catabolism nagEcb med N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized) 42% 88% 369.4 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 55% 691.4
D-glucosamine (chitosamine) catabolism nagEcb med N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized) 42% 88% 369.4 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 55% 691.4
N-acetyl-D-glucosamine catabolism nagPcb med PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized) 42% 100% 359.4 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 55% 691.4
D-glucosamine (chitosamine) catabolism nagPcb med PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized) 42% 100% 359.4 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 55% 691.4
N-acetyl-D-glucosamine catabolism ptsC med IIC' aka PtsC2, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized) 45% 97% 325.1 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 55% 691.4
D-glucosamine (chitosamine) catabolism ptsC med IIC' aka PtsC2, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized) 45% 97% 325.1 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 55% 691.4
D-cellobiose catabolism crr med PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 52% 86% 156.4 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 55% 691.4
D-glucose catabolism crr med PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 52% 86% 156.4 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 55% 691.4
lactose catabolism crr med PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 52% 86% 156.4 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 55% 691.4
D-maltose catabolism crr med PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 52% 86% 156.4 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 55% 691.4
sucrose catabolism crr med PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 52% 86% 156.4 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 55% 691.4
trehalose catabolism crr med PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 52% 86% 156.4 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 55% 691.4
trehalose catabolism treEIIA med glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 50% 86% 153.3 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 55% 691.4
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) 44% 90% 62.4 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 55% 691.4
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) 44% 90% 62.4 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 55% 691.4
N-acetyl-D-glucosamine catabolism nagEIIA lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 39% 99% 462.6 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 55% 691.4
D-cellobiose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 39% 99% 462.6 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 55% 691.4
D-glucosamine (chitosamine) catabolism nagEIIA lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 39% 99% 462.6 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 55% 691.4
D-glucose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 39% 99% 462.6 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 55% 691.4
lactose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 39% 99% 462.6 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 55% 691.4
D-maltose catabolism malEIIA lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 39% 99% 462.6 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 55% 691.4
D-maltose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 39% 99% 462.6 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 55% 691.4
sucrose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 39% 99% 462.6 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 55% 691.4
trehalose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 39% 99% 462.6 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 55% 691.4
D-cellobiose catabolism ptsG lo protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 37% 97% 316.2 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 55% 691.4
D-glucose catabolism ptsG lo protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 37% 97% 316.2 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 55% 691.4
lactose catabolism ptsG lo protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 37% 97% 316.2 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 55% 691.4
D-maltose catabolism ptsG lo protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 37% 97% 316.2 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 55% 691.4
sucrose catabolism ptsG lo protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 37% 97% 316.2 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 55% 691.4
trehalose catabolism ptsG lo protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 37% 97% 316.2 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 55% 691.4
D-maltose catabolism malEIICBA lo PTS system, IIABC components (characterized, see rationale) 32% 98% 295 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 55% 691.4
N-acetyl-D-glucosamine catabolism crr lo Putative PTS system sugar phosphotransferase component IIA (characterized, see rationale) 38% 97% 90.9 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 55% 691.4
D-glucosamine (chitosamine) catabolism crr lo Putative PTS system sugar phosphotransferase component IIA (characterized, see rationale) 38% 97% 90.9 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 55% 691.4

Sequence Analysis Tools

View WP_007706749.1 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

MSILGYLQRVGRALMVPVATLPAAAILMGVGYWLDPTGWGGSNALAAFFIQSGSAIIDNM
GVLFAVGVAYGMSKDKDGAAALAGFVGFLVLTTLCSPAAVAMIMKIPADQVPAAFGKIKN
QFVGIMVGIIAAELYNRFSAVELPKALSFFSGRRLVPILTSFVMIVVAFIMMYIWPVVFG
GLVDFGEQIQKLGSVGAGVYAFFNRLLIPVGLHHALNSVFWFDVAGINDIPNFLGGAQSI
ESGKAVVGITGRYQAGFFPIMMFGLPGAALAIYHCARPENKAKVLGIMMAGAFAAFFTGI
TEPLEFSFMFVAPVLYVIHAVLTGISVFIAATMHWIAGFGFSAGLVDMVLSSRNPLATHW
YMLIPQGLVFFVIYYAVFRFTITKFNLMTPGRELAVAGSEADGVDVNVSDEKDLDAAGLA
RQYIAAVGGSDNLTGIDACITRLRLNVKDSARVDEAMAKRLGATGVIRLNKTSVQIIVGF
VAEKIANAMKTTGHVDASAPKAQTAAPVAPAVKPQAVANAKTIAALVSPVTGEVVALDAV
PDEAFASKAVGDGVAIKPTDKLVVAPAAGTIVKIFNTNHAFCLETENGAEIVVHMGIDTV
ALNGQGFKRLVEEGAQVTAGQPVLELDLDYLNANARSMISPVVCSNIDDFGGLVIQAQGA
VVAGQSALYEIKGK

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