GapMind for catabolism of small carbon sources

 

Protein WP_038858639.1 in Cronobacter universalis NCTC 9529

Annotation: NCBI__GCF_001277175.1:WP_038858639.1

Length: 396 amino acids

Source: GCF_001277175.1 in NCBI

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-xylose catabolism xylH hi D-xylose ABC transporter, permease protein (characterized) 87% 100% 676.4 Probable ABC transport system permease protein for sugars, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 39% 255.4
L-arabinose catabolism gguB lo GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 37% 100% 268.1 D-xylose ABC transporter, permease protein 87% 676.4
D-cellobiose catabolism mglC lo GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 37% 100% 268.1 D-xylose ABC transporter, permease protein 87% 676.4
D-galactose catabolism gguB lo GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 37% 100% 268.1 D-xylose ABC transporter, permease protein 87% 676.4
D-glucose catabolism mglC lo GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 37% 100% 268.1 D-xylose ABC transporter, permease protein 87% 676.4
lactose catabolism mglC lo GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 37% 100% 268.1 D-xylose ABC transporter, permease protein 87% 676.4
D-maltose catabolism mglC lo GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 37% 100% 268.1 D-xylose ABC transporter, permease protein 87% 676.4
sucrose catabolism mglC lo GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 37% 100% 268.1 D-xylose ABC transporter, permease protein 87% 676.4
trehalose catabolism mglC lo GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 37% 100% 268.1 D-xylose ABC transporter, permease protein 87% 676.4
L-rhamnose catabolism rhaQ lo RhaQ (characterized, see rationale) 30% 91% 99.4 D-xylose ABC transporter, permease protein 87% 676.4

Sequence Analysis Tools

View WP_038858639.1 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

MSKSNPSEIKLAAPSASSPVSFRALNKINVQVFVMIAAIVVIMLFFTFMTDGAYLSARNI
SNLLRQTAITGILAVGMVFVIISAEIDLSVGSMMGLLGGAAAIFDVWLGWPLPLTIVVTL
LLGLLLGAWNGWWVAYRKVPSFIVTLAGMLAFRGVLIGITNGTTVSPTSPAMSQIGQSYL
PGGVGFAIGALGLALFIFWQWRGRMRRQALGLTSTPSSAVAGKQALTAVIVLGAIWLLND
YRGVPTPVLILTFLLLAGMFMALHTAFGRRIYAIGGNIDAARLSGINVERTKLAVFAING
VMVAIAGLILSSRLGAGSPSAGNIAELDAIAACVIGGTSLAGGVGSVAGAVMGAFIMASL
DNGMSMMDVPTFWQYIVKGAILLLAVWMDSATRRRA

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