GapMind for catabolism of small carbon sources

 

Protein WP_085543671.1 in Dethiosulfovibrio salsuginis USBA 82

Annotation: NCBI__GCF_900177735.1:WP_085543671.1

Length: 252 amino acids

Source: GCF_900177735.1 in NCBI

Candidate for 12 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
myo-inositol catabolism PGA1_c07320 hi Inositol transport system ATP-binding protein (characterized) 41% 93% 181.8 Fructose import ATP-binding protein FrcA; EC 7.5.2.- 38% 161.0
L-arabinose catabolism xylGsa med Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 42% 94% 187.2 Inositol transport system ATP-binding protein 41% 181.8
D-fructose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 38% 95% 161 Inositol transport system ATP-binding protein 41% 181.8
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 38% 95% 161 Inositol transport system ATP-binding protein 41% 181.8
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 38% 95% 161 Inositol transport system ATP-binding protein 41% 181.8
sucrose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 38% 95% 161 Inositol transport system ATP-binding protein 41% 181.8
D-cellobiose catabolism mglA lo glucose transporter, ATPase component (characterized) 37% 91% 160.2 Inositol transport system ATP-binding protein 41% 181.8
D-glucose catabolism mglA lo glucose transporter, ATPase component (characterized) 37% 91% 160.2 Inositol transport system ATP-binding protein 41% 181.8
lactose catabolism mglA lo glucose transporter, ATPase component (characterized) 37% 91% 160.2 Inositol transport system ATP-binding protein 41% 181.8
D-maltose catabolism mglA lo glucose transporter, ATPase component (characterized) 37% 91% 160.2 Inositol transport system ATP-binding protein 41% 181.8
sucrose catabolism mglA lo glucose transporter, ATPase component (characterized) 37% 91% 160.2 Inositol transport system ATP-binding protein 41% 181.8
trehalose catabolism mglA lo glucose transporter, ATPase component (characterized) 37% 91% 160.2 Inositol transport system ATP-binding protein 41% 181.8

Sequence Analysis Tools

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

MEAMVEMKGIGKSFGSVEALRQVDFRLNPGEVVALLGDNGAGKSTLIKILSGFHSADRGS
MMVKGREIDFKAYDVTVARSLGVETVYQERSLGERQPLWRNVFIGRHRLNRWGLIDVKRE
KMETMELLSSVLGLRGAGLSPDASVETLSGGERQGLAIGRAMHFGADIIVLDEPTTALAL
SEVGKVLSFIGSIREDGRSCIVISHDLGHVYKVADRFVLMDRGSTVGDYRKGDITPEELM
ARMIGLNGEVKP

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