GapMind for catabolism of small carbon sources

 

Protein BWI76_RS06145 in Klebsiella michiganensis M5al

Annotation: BWI76_RS06145 MFS transporter

Length: 428 amino acids

Source: Koxy 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
D-cellobiose catabolism kguT hi KguT (characterized, see rationale) 66% 99% 580.9
D-gluconate catabolism kguT hi KguT (characterized, see rationale) 66% 99% 580.9
D-glucose catabolism kguT hi KguT (characterized, see rationale) 66% 99% 580.9
lactose catabolism kguT hi KguT (characterized, see rationale) 66% 99% 580.9
D-maltose catabolism kguT hi KguT (characterized, see rationale) 66% 99% 580.9
sucrose catabolism kguT hi KguT (characterized, see rationale) 66% 99% 580.9
trehalose catabolism kguT hi KguT (characterized, see rationale) 66% 99% 580.9

Sequence Analysis Tools

View BWI76_RS06145 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

MHMLAKLPARRWWYLMPIIFITYSLAYLDRANYGFAAAAGIESDLGITKGTASLIGALFF
LGYFFFQVPGAIYAVKRSVRKMIFCSLILWGFCAAATGFVSNIPMLMAIRFTLGVVEAAV
MPAMLIYISNWFTKTERSRANTFLILGNPVTVLWMSIVSGYLIQAWGWREMFIIEGIPAV
LWAVCWWILVRDKPSEVSWLNEQEKETLQKVMDSEQSHIKPVRNYGEALRSRNVIMLCAV
HALWSIGVYGFMMWMPSILKNAAQMDIVAVGWLAAVPYLAAIILMLTVSWLSDKFQNRKL
FIWPLLLIAAIAFFGSWMVGNQAFWLSYALLVIAAACMYAPYGPFFALIPELLPRNVSGV
SMGLINSFGALGAFLGAWLVGYLNGITGGPGVSYTFMAVALLSSVVLMFNVRANPQSSSP
AVAKRVVG

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 (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 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