GapMind for catabolism of small carbon sources

 

Protein WP_038856233.1 in Cronobacter universalis NCTC 9529

Annotation: NCBI__GCF_001277175.1:WP_038856233.1

Length: 340 amino acids

Source: GCF_001277175.1 in NCBI

Candidate for 8 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-galactose catabolism ytfT hi Galactofuranose transporter permease protein YtfT (characterized) 86% 100% 570.1 Fructose import permease protein FruF 42% 228.0
L-arabinose catabolism araWsh med Inner-membrane translocator (characterized, see rationale) 59% 79% 333.6 Galactofuranose transporter permease protein YtfT 86% 570.1
D-fructose catabolism fruF med Fructose import permease protein FruF (characterized) 42% 90% 228 Galactofuranose transporter permease protein YtfT 86% 570.1
sucrose catabolism fruF med Fructose import permease protein FruF (characterized) 42% 90% 228 Galactofuranose transporter permease protein YtfT 86% 570.1
D-ribose catabolism rbsC med ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized) 43% 84% 186.8 Galactofuranose transporter permease protein YtfT 86% 570.1
D-mannose catabolism HSERO_RS03645 med ABC-type sugar transport system, permease component protein (characterized, see rationale) 40% 78% 181.8 Galactofuranose transporter permease protein YtfT 86% 570.1
xylitol catabolism PS417_12060 lo ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale) 35% 96% 189.1 Galactofuranose transporter permease protein YtfT 86% 570.1
myo-inositol catabolism PS417_11895 lo m-Inositol ABC transporter, permease component (iatP) (characterized) 36% 96% 182.6 Galactofuranose transporter permease protein YtfT 86% 570.1

Sequence Analysis Tools

View WP_038856233.1 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

MPRSLPDTGAPKRRLRFPPGMPQIAALMLVLLVDGLVADHFFQIVLQDGRLFGSPIDILN
RAAPVALLAIGMTLVIATGGIDLSVGAVMAIAGATAATLTVSGHSLAVVILASLGVGVLA
GLWNGILVAVLKIQPFVATLILMVAGRGVAQLITSGQIVTFNSPSLAWLGSGSLFFFPTP
VIIAIVTLLAFWLFTRKTALGMFIEAVGINIRAAKNAGVSTRLIVMLTYMLSGLCAAIAG
IIVAADIRGADANNAGLWLELDAILAVVIGGASLMGGRFNLALSVVGALIIQGMNTGILL
SGFPPELNQVVKAVVVLCVLVVQSPRFIGLIKGVRRHDKT

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