GapMind for catabolism of small carbon sources

 

Protein WP_084164990.1 in Skermanella stibiiresistens SB22

Annotation: NCBI__GCF_000576635.1:WP_084164990.1

Length: 377 amino acids

Source: GCF_000576635.1 in NCBI

Candidate for 14 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA med spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 47% 82% 269.6 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 46% 272.7
L-proline catabolism opuBA med BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) 41% 77% 198.4 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 46% 272.7
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 98% 227.3 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 46% 272.7
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 98% 227.3 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 46% 272.7
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 98% 227.3 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 46% 272.7
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 98% 227.3 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 46% 272.7
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 98% 227.3 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 46% 272.7
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 98% 227.3 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 46% 272.7
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 98% 227.3 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 46% 272.7
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 98% 227.3 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 46% 272.7
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 43% 69% 213 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 46% 272.7
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 43% 69% 213 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 46% 272.7
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 43% 69% 213 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 46% 272.7
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 43% 69% 213 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 46% 272.7

Sequence Analysis Tools

View WP_084164990.1 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

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Sequence

MTLAQRTLDPRPAHSAPAARPERGHLRLEGVTKRFAGDVNAVSDVNLDLERGKLLGLLGP
SGCGKTTTLRMIAGLLPITSGRILVDDDDISLRPPHQRDFGLVFQNYALFPHMTVAENVA
FGLDMRRVPKAEARRRVAEALELVRLPGYGERKPREMSGGQQQRVALARALVINPRILLL
DEPLSNLDAKLRDEMRREIREIQQRLGITTVFVTHDQVEALTMCDVVGVMSGGRLAQIGT
PEDIYERPASLFVADFVGRTNILDCEVLNGHRVRLGDGVYSCAATTIRPGKAKVAIRPHR
INLTPHRDRALLSTSTNSAEGRVLRTTYVGDIVQYDIDIGGPTLQVETPTHGRGLAVAVG
DKLLCEWRPDDMLVFER

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