GapMind for catabolism of small carbon sources


Protein BWI76_RS22410 in Klebsiella michiganensis M5al

Annotation: FitnessBrowser__Koxy:BWI76_RS22410

Length: 104 amino acids

Source: Koxy 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-cellobiose catabolism celEIIA med PTS system N,N'-diacetylchitobiose-specific EIIA component; EIIA-Chb; EIII-Chb; IIIcel; N,N'-diacetylchitobiose-specific phosphotransferase enzyme IIA component (characterized) 62% 84% 117.9 VC_1283 aka IIA, component of Glucosamine β(1→4) glucosamine (GlcN)2 (glucosamine dimer) transporter, VC1281-1283 (IIB; IIC; IIA, respectively) 59% 115.9
lactose catabolism lacIIA med PTS lactose transporter subunit IIA, component of PTS-type lactose transporter, IIC-IIB-IIA (characterized) 45% 96% 99.4 PEP-dependent phosphotransferase enzyme III, component of N,N'-diacetylchitobiose (cellobiose) PTS permease, CelABC (IIABC) 63% 124.8
D-galactose catabolism ptcA med PTS system galactose-specific EIIA component (characterized) 43% 83% 73.6 PEP-dependent phosphotransferase enzyme III, component of N,N'-diacetylchitobiose (cellobiose) PTS permease, CelABC (IIABC) 63% 124.8

Sequence Analysis Tools

View BWI76_RS22410 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