GapMind for catabolism of small carbon sources

 

Protein WP_106711278.1 in Phyllobacterium brassicacearum STM 196

Annotation: NCBI__GCF_003010955.1:WP_106711278.1

Length: 399 amino acids

Source: GCF_003010955.1 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
L-arabinose catabolism gguB hi GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 68% 96% 542 Probable ABC transport system permease protein for sugars, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 44% 332.8
D-cellobiose catabolism mglC hi GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 68% 96% 542 Probable ABC transport system permease protein for sugars, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 44% 332.8
D-galactose catabolism gguB hi GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 68% 96% 542 Probable ABC transport system permease protein for sugars, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 44% 332.8
D-glucose catabolism mglC hi GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 68% 96% 542 Probable ABC transport system permease protein for sugars, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 44% 332.8
lactose catabolism mglC hi GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 68% 96% 542 Probable ABC transport system permease protein for sugars, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 44% 332.8
D-maltose catabolism mglC hi GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 68% 96% 542 Probable ABC transport system permease protein for sugars, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 44% 332.8
sucrose catabolism mglC hi GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 68% 96% 542 Probable ABC transport system permease protein for sugars, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 44% 332.8
trehalose catabolism mglC hi GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 68% 96% 542 Probable ABC transport system permease protein for sugars, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 44% 332.8
D-xylose catabolism xylH hi GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 68% 96% 542 Probable ABC transport system permease protein for sugars, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 44% 332.8
myo-inositol catabolism PGA1_c07310 lo Inositol transport system permease protein (characterized) 30% 98% 144.1 GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter 68% 542.0

Sequence Analysis Tools

View WP_106711278.1 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

MTVETAATQGKKDFKTDGSALKGNYREYGLVLALILIMVFFQFTTNGVLFRPVNLTNLVL
QNSYIIIMALGMLLVIVAGHIDLSVGSVSGFIGGLAAVMMVRWQIHYIPATILCLAMGGA
IGAAQGYWIAYHKIPSFIVTLAGMLVFRGLALWLLGGQSVGPFPPQFQLLSSGFIPDVFG
YPGFNITSMLIGIILVALMIYFSVRGRAKREKHGYEGEPFALFVAKNLIIAGIVLFLAYL
LSSYKGLPNVLIVMSLLIALFVFVTKRMTVGRRIYAMGGNEKAAKLSGIKTERLTFLTFV
NMGVLAALAGLIFAARLNTATPKAGLGFELDVIAAVFIGGASAMGGVGQVMGAVIGAFIM
GVMNNGMSIMGVNIDWQQVIKGLVLLAAVIFDVYNKNKA

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