GapMind for catabolism of small carbon sources


Protein 1936623 in Escherichia coli BW25113

Annotation: b4460 fused L-arabinose transporter subunits of ABC superfamily: membrane components (RefSeq)

Length: 328 amino acids

Source: Keio in FitnessBrowser

Candidate for 7 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arabinose catabolism araH hi L-arabinose ABC transporter, permease protein AraH (characterized) 100% 100% 629.8 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) 36% 216.5
D-galactose catabolism BPHYT_RS16925 med Arabinose ABC transporter permease (characterized, see rationale) 63% 94% 382.9 L-arabinose ABC transporter, permease protein AraH 100% 629.8
xylitol catabolism PS417_12060 lo ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale) 34% 99% 216.1 L-arabinose ABC transporter, permease protein AraH 100% 629.8
D-ribose catabolism rbsC lo Ribose import permease protein RbsC (characterized) 36% 97% 202.2 L-arabinose ABC transporter, permease protein AraH 100% 629.8
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) 36% 97% 199.9 L-arabinose ABC transporter, permease protein AraH 100% 629.8
myo-inositol catabolism PS417_11895 lo Inositol transport system permease protein (characterized) 37% 81% 183 L-arabinose ABC transporter, permease protein AraH 100% 629.8
L-rhamnose catabolism rhaQ lo RhaQ (characterized, see rationale) 31% 99% 169.9 L-arabinose ABC transporter, permease protein AraH 100% 629.8

Sequence Analysis Tools

View 1936623 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

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

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...



This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.



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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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