GapMind for catabolism of small carbon sources

 

Protein WP_110806514.1 in Rhodobacter viridis JA737

Annotation: NCBI__GCF_003217355.1:WP_110806514.1

Length: 339 amino acids

Source: GCF_003217355.1 in NCBI

Candidate for 28 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
myo-inositol catabolism PS417_11895 hi Inositol transport system permease protein (characterized) 62% 95% 402.5 ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 39% 218.0
xylitol catabolism PS417_12060 med ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale) 40% 99% 235.7 Inositol transport system permease protein 62% 402.5
D-ribose catabolism rbsC lo ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized) 39% 91% 218 Inositol transport system permease protein 62% 402.5
D-cellobiose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 38% 94% 201.8 Inositol transport system permease protein 62% 402.5
D-galactose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 38% 94% 201.8 Inositol transport system permease protein 62% 402.5
D-glucose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 38% 94% 201.8 Inositol transport system permease protein 62% 402.5
lactose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 38% 94% 201.8 Inositol transport system permease protein 62% 402.5
D-maltose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 38% 94% 201.8 Inositol transport system permease protein 62% 402.5
sucrose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 38% 94% 201.8 Inositol transport system permease protein 62% 402.5
trehalose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 38% 94% 201.8 Inositol transport system permease protein 62% 402.5
myo-inositol catabolism iatP lo Inositol ABC transport system, permease protein IatP, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized) 39% 92% 201.4 Inositol transport system permease protein 62% 402.5
D-xylose catabolism xylH lo Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 38% 97% 199.9 Inositol transport system permease protein 62% 402.5
D-fructose catabolism frcC lo Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 39% 96% 198 Inositol transport system permease protein 62% 402.5
sucrose catabolism frcC lo Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 39% 96% 198 Inositol transport system permease protein 62% 402.5
L-fucose catabolism HSERO_RS05255 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 36% 90% 189.1 Inositol transport system permease protein 62% 402.5
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) 36% 98% 183 Inositol transport system permease protein 62% 402.5
D-mannose catabolism HSERO_RS03645 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 37% 91% 178.7 Inositol transport system permease protein 62% 402.5
D-galactose catabolism BPHYT_RS16925 lo Monosaccharide-transporting ATPase; EC 3.6.3.17 (characterized, see rationale) 33% 83% 164.5 Inositol transport system permease protein 62% 402.5
L-arabinose catabolism araH lo L-arabinose ABC transporter, permease protein AraH (characterized) 34% 92% 160.2 Inositol transport system permease protein 62% 402.5
D-galactose catabolism ytfT lo Galactofuranose transporter permease protein YtfT (characterized) 34% 94% 157.9 Inositol transport system permease protein 62% 402.5
D-mannose catabolism frcC lo Fructose import permease protein FrcC (characterized) 33% 88% 155.6 Inositol transport system permease protein 62% 402.5
D-ribose catabolism frcC lo Fructose import permease protein FrcC (characterized) 33% 88% 155.6 Inositol transport system permease protein 62% 402.5
L-arabinose catabolism araWsh lo Inner-membrane translocator (characterized, see rationale) 32% 85% 152.9 Inositol transport system permease protein 62% 402.5
L-arabinose catabolism xylHsa lo Xylose/arabinose import permease protein XylH (characterized, see rationale) 32% 87% 149.4 Inositol transport system permease protein 62% 402.5
L-arabinose catabolism araZsh lo Inner-membrane translocator (characterized, see rationale) 33% 98% 142.5 Inositol transport system permease protein 62% 402.5
L-fucose catabolism BPHYT_RS34240 lo Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) 31% 86% 137.9 Inositol transport system permease protein 62% 402.5
L-rhamnose catabolism BPHYT_RS34240 lo Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) 31% 86% 137.9 Inositol transport system permease protein 62% 402.5
D-galactose catabolism yjtF lo Inner membrane ABC transporter permease protein YjfF (characterized) 32% 90% 134.4 Inositol transport system permease protein 62% 402.5

Sequence Analysis Tools

View WP_110806514.1 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

MQDTYTTGAEIKAAPRRLPPEVNILFVLVGIALVFEILGWIFQGQSFLMSIDRLKIMILQ
VSVIGIISVGVTQVIIAGGIDLSSGSVVGAVAMFAMSFAQVSTYARAVYPDLTDLPAIVP
IALGLMAGALVGLINGALIAYAKIPPFIATLGTMVTARGFAKWYTKGQPISFPTDDFAFI
GKGMMPVAIFLAVAAIFHVAMKYTRYGKFTYAIGANQQAARVSGINVEHHLIKVYVVAAT
LAALAGMVVAARGQTAQAGMGLAYELDAIAMAVIGGVSLTGGRGSILGTMIGMVIFGVII
SGFTFLRLDAYYQEMIKGVIIVAAVVADVYRQKKRTKKS

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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