GapMind for catabolism of small carbon sources

 

Protein 201386 in Shewanella oneidensis MR-1

Annotation: FitnessBrowser__MR1:201386

Length: 169 amino acids

Source: MR1 in FitnessBrowser

Candidate for 10 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-cellobiose catabolism crr hi PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 62% 99% 216.9 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 47% 153.3
D-glucose catabolism crr hi PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 62% 99% 216.9 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 47% 153.3
lactose catabolism crr hi PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 62% 99% 216.9 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 47% 153.3
D-maltose catabolism crr hi PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 62% 99% 216.9 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 47% 153.3
sucrose catabolism crr hi PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 62% 99% 216.9 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 47% 153.3
trehalose catabolism crr hi PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 62% 99% 216.9 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 47% 153.3
trehalose catabolism treEIIA hi glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 61% 99% 213.4 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 47% 153.3
N-acetyl-D-glucosamine catabolism nagEIIA lo Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) 37% 88% 125.2 PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component 62% 216.9
D-glucosamine (chitosamine) catabolism nagEIIA lo Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) 37% 88% 125.2 PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component 62% 216.9
D-maltose catabolism malEIIA lo Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) 37% 88% 125.2 PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component 62% 216.9

Sequence Analysis Tools

View 201386 at FitnessBrowser

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

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Sequence

MGFLSRIRRLVSGQPQLAGGIMVYAPVNGEIVAIEKVPDVVFAEKIVGDGIAIAPTGSTI
VAPIDGTIGKIFETNHAFSIESPQGLELFVHFGVGTVELRGRGFSRLAEEGQEVKVGDPI
LSFDLEYLKDQVDSLLTPVVLANMEDVKYLDKAQGSVTAGKDPIFTVQL

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:

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