GapMind for catabolism of small carbon sources

 

Protein H281DRAFT_00427 in Paraburkholderia bryophila 376MFSha3.1

Annotation: H281DRAFT_00427 monosaccharide ABC transporter membrane protein, CUT2 family

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

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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