GapMind for catabolism of small carbon sources

 

Protein WP_084935212.1 in Pantoea rwandensis LMG 26275

Annotation: NCBI__GCF_002095475.1:WP_084935212.1

Length: 343 amino acids

Source: GCF_002095475.1 in NCBI

Candidate for 11 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 m-Inositol ABC transporter, permease component (iatP) (characterized) 67% 99% 459.9 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 40% 231.5
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) 43% 100% 255.4 m-Inositol ABC transporter, permease component (iatP) 67% 459.9
D-cellobiose catabolism mglC med 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) 40% 97% 231.5 m-Inositol ABC transporter, permease component (iatP) 67% 459.9
D-glucose catabolism mglC med 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) 40% 97% 231.5 m-Inositol ABC transporter, permease component (iatP) 67% 459.9
lactose catabolism mglC med 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) 40% 97% 231.5 m-Inositol ABC transporter, permease component (iatP) 67% 459.9
D-maltose catabolism mglC med 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) 40% 97% 231.5 m-Inositol ABC transporter, permease component (iatP) 67% 459.9
sucrose catabolism mglC med 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) 40% 97% 231.5 m-Inositol ABC transporter, permease component (iatP) 67% 459.9
trehalose catabolism mglC med 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) 40% 97% 231.5 m-Inositol ABC transporter, permease component (iatP) 67% 459.9
D-xylose catabolism xylH med 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) 40% 97% 231.5 m-Inositol ABC transporter, permease component (iatP) 67% 459.9
D-galactose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 38% 96% 219.2 m-Inositol ABC transporter, permease component (iatP) 67% 459.9
L-arabinose catabolism xylHsa lo Xylose/arabinose import permease protein XylH (characterized, see rationale) 31% 85% 145.6 m-Inositol ABC transporter, permease component (iatP) 67% 459.9

Sequence Analysis Tools

View WP_084935212.1 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

MSNVKITAPQAAESSSFFGNLRHKLPKDTGIFVVMLGIALIFEIAGWYVRDQSFLLNTNR
LVLIVLQVAIIGIIAVGVTQVIITTGIDLSSGSVIALTAVVAASLAQTSDSLTPMYPSLV
NLPAVIPIVAGIGVGLLCGLMNGFLITKTGIPPFIATLGMMVSARGLAQYYTQGNPISFL
SDGFTSIGQGAMPVIIFLVVAFLFHIALKHTRYGKYVYAIGGNMTSAKVSGINVNKYLII
VYTIAGALSGLAGVVLAARVSSGQSSMGVAYELDAIAAAVIGGSSLMGGVGRITGTLIGA
VILGLIKSGFTFVGVDAYVQDIIKGMIIVAAVSIDMHRNRKKR

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