GapMind for catabolism of small carbon sources

 

Protein H281DRAFT_02330 in Paraburkholderia bryophila 376MFSha3.1

Annotation: H281DRAFT_02330 L-arabinose ABC transporter membrane protein

Length: 334 amino acids

Source: Burk376 in FitnessBrowser

Candidate for 3 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-galactose catabolism BPHYT_RS16925 hi Monosaccharide-transporting ATPase; EC 3.6.3.17 (characterized, see rationale) 53% 92% 330.9 L-arabinose ABC transporter, permease protein AraH 50% 318.2
L-arabinose catabolism araH hi L-arabinose ABC transporter, permease protein AraH (characterized) 50% 98% 318.2 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) 35% 201.4
2'-deoxyinosine catabolism H281DRAFT_01112 lo deoxynucleoside transporter, permease component 2 (characterized) 31% 93% 145.6 L-arabinose ABC transporter, permease protein AraH 50% 318.2

Sequence Analysis Tools

View H281DRAFT_02330 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: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MHTPSTDPSTPAVASAGLSARAARTWDLINKSGIVMVFIILFAVLSFTVPDFLSSRNIQG
LLLSVTLIGSISVTMMFVLALGEVDLSVASIVAFAGVVASTLITVTHSVLLGVAAGVLAG
GAVGLVNGVLVARYKINSLIVTLAMMEVVRGLAFITSSGDAVMISEERFFDLGGGSFLGI
SYPIWSNIIGFVVFGFLLKKTVFGKNVLAVGGNSEAALLAGLPVTRIKITVFVLQGLVTG
FAGVMLASRMSLGDPKTSVGLELGVISACVLGGVSLTGGVATISGVLVGVLIMGSVQDAM
SLMNVPTFYQYLIRGGILLLAVLFDQFRRSKRVH

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, 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