GapMind for catabolism of small carbon sources


Protein 1936623 in Escherichia coli BW25113

Annotation: FitnessBrowser__Keio:1936623

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

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...



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:

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