GapMind for catabolism of small carbon sources

 

Protein WP_003463745.1 in Gracilibacillus halophilus YIM-C55.5

Annotation: NCBI__GCF_000359605.1:WP_003463745.1

Length: 386 amino acids

Source: GCF_000359605.1 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
L-arabinose catabolism gguB hi GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 53% 95% 414.5 Probable ABC transport system permease protein for sugars, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 45% 319.3
D-cellobiose catabolism mglC hi GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 53% 95% 414.5 Probable ABC transport system permease protein for sugars, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 45% 319.3
D-galactose catabolism gguB hi GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 53% 95% 414.5 Probable ABC transport system permease protein for sugars, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 45% 319.3
D-glucose catabolism mglC hi GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 53% 95% 414.5 Probable ABC transport system permease protein for sugars, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 45% 319.3
lactose catabolism mglC hi GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 53% 95% 414.5 Probable ABC transport system permease protein for sugars, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 45% 319.3
D-maltose catabolism mglC hi GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 53% 95% 414.5 Probable ABC transport system permease protein for sugars, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 45% 319.3
sucrose catabolism mglC hi GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 53% 95% 414.5 Probable ABC transport system permease protein for sugars, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 45% 319.3
trehalose catabolism mglC hi GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 53% 95% 414.5 Probable ABC transport system permease protein for sugars, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 45% 319.3
D-xylose catabolism xylH hi GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 53% 95% 414.5 Probable ABC transport system permease protein for sugars, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 45% 319.3
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) 42% 61% 151.8 GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter 53% 414.5
D-ribose catabolism rbsC lo ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized) 36% 81% 146.4 GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter 53% 414.5
D-xylose catabolism xylF_Tm lo ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized) 31% 94% 125.2 GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter 53% 414.5

Sequence Analysis Tools

View WP_003463745.1 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

MQTIIHLFRNNLREYGMIIALVLITGLFWILTDGVTFTPLNLTNLILQNGFILVLAVGMV
LVIITGNIDLSVGSVVAFIGAIAGVLMINHDVPVWLAVVLSILAGAVIGVWQGFWIAYIG
IPSFIVTLAGMLIFRGLTLYLLNGQSLAPFPESFQNISGGFLPDLFGGSDIHILTLVFSA
VISLVLIYLEFNRRKTQLQYKFEVVPVWITLAKLAILVFVINWFAYQLALNEGMPMVLVI
VLFLIVIYTFIMKNTVMGRHIYATGGNKKAADLSGIKTKRVVFGVFVNNGILAALAGLMF
AARLNSATPAAGEMLELDAIAAVFIGGASMAGGVGTVIGAIVGGLVMGVMNNGMSLIGIG
IDWQQFIKGMVLLIAVGFDVYNKNKG

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