GapMind for catabolism of small carbon sources

 

Protein WP_012756382.1 in Rhizobium leguminosarum bv. trifolii WSM1325

Annotation: NCBI__GCF_000023185.1:WP_012756382.1

Length: 310 amino acids

Source: GCF_000023185.1 in NCBI

Candidate for 13 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
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) 44% 92% 250.8 Ribose import permease protein RbsC 45% 248.1
D-ribose catabolism rbsC med Ribose import permease protein RbsC (characterized) 45% 91% 248.1 RbsC, component of The probable autoinducer-2 (AI-2;, a furanosyl borate diester: 3aS,6S,6aR)-2,2,6,6a-tetrahydroxy-3a-methyltetrahydrofuro[3,2-d][1,3,2]dioxaborolan-2-uide) uptake porter (Shao et al., 2007) (50-70% identical to RbsABC of E. coli; TC# 3.A.1.2.1) 44% 242.3
D-xylose catabolism xylF_Tm med ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized) 43% 95% 221.9 Ribose import permease protein RbsC 45% 248.1
D-mannose catabolism HSERO_RS03645 med ABC-type sugar transport system, permease component protein (characterized, see rationale) 44% 82% 215.7 Ribose import permease protein RbsC 45% 248.1
D-galactose catabolism BPHYT_RS16925 lo Arabinose ABC transporter permease (characterized, see rationale) 38% 90% 204.9 Ribose import permease protein RbsC 45% 248.1
myo-inositol catabolism PS417_11895 lo m-Inositol ABC transporter, permease component (iatP) (characterized) 39% 85% 204.5 Ribose import permease protein RbsC 45% 248.1
L-arabinose catabolism araH lo L-arabinose ABC transporter, permease protein AraH (characterized) 37% 91% 202.2 Ribose import permease protein RbsC 45% 248.1
L-fucose catabolism BPHYT_RS34240 lo Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) 34% 86% 182.6 Ribose import permease protein RbsC 45% 248.1
L-rhamnose catabolism BPHYT_RS34240 lo Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) 34% 86% 182.6 Ribose import permease protein RbsC 45% 248.1
D-galactose catabolism ytfT lo Galactofuranose transporter permease protein YtfT (characterized) 37% 91% 180.3 Ribose import permease protein RbsC 45% 248.1
D-fructose catabolism fruF lo Fructose import permease protein FruF (characterized) 32% 86% 166 Ribose import permease protein RbsC 45% 248.1
sucrose catabolism fruF lo Fructose import permease protein FruF (characterized) 32% 86% 166 Ribose import permease protein RbsC 45% 248.1
2'-deoxyinosine catabolism H281DRAFT_01115 lo deoxynucleoside transporter, permease component 1 (characterized) 30% 85% 140.2 Ribose import permease protein RbsC 45% 248.1

Sequence Analysis Tools

View WP_012756382.1 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

MKYLPRGTGLAGALIVLIIAASLISPHFLNPINILNVLRQVALYGILGIGMTFVILTKGI
DLSVGSIVALVGVTGAVLMEQGVPIPLMVLICLSIGALVGCVNGLGISYFRIPAFIMTLG
CMVMVRGFALMIADGGTVNPGKLADSFFVLGGGYMLGVPTPIYVFAAVCIIAAVVLSFTQ
FGRAIYAVGSNEEAARLSGINVPLVIFSVYIICGVLAALSGLIFLSRLSVGDPNSGLGLE
LEAITIAVIGGTSLFGGEGTVLGTIGGAMVLAIIANILNLAGVSPFSQQVVKGAIIVLAV
LLEAGRKPRK

This GapMind analysis is from Apr 09 2024. 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