GapMind for catabolism of small carbon sources

 

Protein H281DRAFT_00427 in Paraburkholderia bryophila 376MFSha3.1

Annotation: FitnessBrowser__Burk376:H281DRAFT_00427

Length: 341 amino acids

Source: Burk376 in FitnessBrowser

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-fucose catabolism HSERO_RS05255 hi ABC-type sugar transport system, permease component protein (characterized, see rationale) 74% 96% 482.3 Ribose import permease protein RbsC 41% 241.5
D-ribose catabolism rbsC hi Ribose import permease protein RbsC (characterized) 41% 96% 241.5 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) 41% 228.0
D-fructose catabolism frcC med Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 40% 97% 226.9 Ribose import permease protein RbsC 41% 241.5
sucrose catabolism frcC med Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 40% 97% 226.9 Ribose import permease protein RbsC 41% 241.5
D-mannose catabolism frcC med Fructose import permease protein FrcC (characterized) 41% 85% 221.1 Ribose import permease protein RbsC 41% 241.5
D-ribose catabolism frcC med Fructose import permease protein FrcC (characterized) 41% 85% 221.1 Ribose import permease protein RbsC 41% 241.5
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) 39% 98% 218.4 Ribose import permease protein RbsC 41% 241.5
myo-inositol catabolism PS417_11895 lo m-Inositol ABC transporter, permease component (iatP) (characterized) 36% 99% 209.9 Ribose import permease protein RbsC 41% 241.5
D-fructose catabolism fruG lo Fructose import permease protein FruG (characterized) 32% 91% 162.9 Ribose import permease protein RbsC 41% 241.5
sucrose catabolism fruG lo Fructose import permease protein FruG (characterized) 32% 91% 162.9 Ribose import permease protein RbsC 41% 241.5
L-arabinose catabolism gguB lo GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 31% 79% 144.8 Ribose import permease protein RbsC 41% 241.5
D-galactose catabolism gguB lo GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 31% 79% 144.8 Ribose import permease protein RbsC 41% 241.5

Sequence Analysis Tools

View H281DRAFT_00427 at FitnessBrowser

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Find functional residues: SitesBLAST

Search for conserved domains

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

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Sequence

MTMQPDSSALTGQRRLTGLRARIFSPTALQKLLAFASLILLLVFFSFASPAFMQMDNILG
ILQATAVNGVLAIASTFVIITGGIDLSVGTLMTFTAVICGVFLTYWHLPMWLGVIAAIGT
GAICGTISGTLTAKMKIPPFIATLGMMLLLKGLSLVVSADKPIYFTDTENFYMISQDSLI
GYLVPSLPIPNAVLILFFLAIVSSVTLNRTALGRYTFALGSNEEAVRLSGVNVDRWKIAI
YGLGGAICGIAGLLIASRLNSAQPALGQGYELEAIAAVVIGGTSLSGGSGTILGTIIGAF
IMSVLTNGLRIMSVAQEWQIVVTGLIIILAVYADILRRRKS

This GapMind analysis is from Sep 17 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