GapMind for catabolism of small carbon sources

 

Protein GFF32 in Pseudomonas simiae WCS417

Annotation: FitnessBrowser__WCS417:GFF32

Length: 382 amino acids

Source: WCS417 in FitnessBrowser

Candidate for 9 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-galactose catabolism dgoD hi galactonate dehydratase [EC: 4.2.1.6] (characterized) 78% 100% 631.7 gluconate dehydratase (EC 4.2.1.39) 37% 216.5
lactose catabolism dgoD hi galactonate dehydratase [EC: 4.2.1.6] (characterized) 78% 100% 631.7 gluconate dehydratase (EC 4.2.1.39) 37% 216.5
L-arabinose catabolism xacD lo D-xylonate dehydratase subunit (EC 4.2.1.25; EC 4.2.1.82) (characterized) 36% 97% 211.1 galactonate dehydratase [EC: 4.2.1.6] 78% 631.7
D-xylose catabolism xad lo D-xylonate dehydratase subunit (EC 4.2.1.25; EC 4.2.1.82) (characterized) 36% 97% 211.1 galactonate dehydratase [EC: 4.2.1.6] 78% 631.7
D-glucuronate catabolism uxuA lo D-mannonate dehydratase; ManD; EC 4.2.1.8 (characterized) 32% 100% 199.1 galactonate dehydratase [EC: 4.2.1.6] 78% 631.7
myo-inositol catabolism uxuA lo D-mannonate dehydratase; ManD; EC 4.2.1.8 (characterized) 32% 100% 199.1 galactonate dehydratase [EC: 4.2.1.6] 78% 631.7
D-galacturonate catabolism gci lo D-galactarolactone cycloisomerase (EC 5.5.1.27) (characterized) 36% 90% 180.3 galactonate dehydratase [EC: 4.2.1.6] 78% 631.7
D-glucuronate catabolism gci lo D-galactarolactone cycloisomerase (EC 5.5.1.27) (characterized) 36% 90% 180.3 galactonate dehydratase [EC: 4.2.1.6] 78% 631.7
L-rhamnose catabolism LRA3 lo Putative L-rhamnonate dehydratase; RhamD; EC 4.2.1.90 (uncharacterized) 33% 65% 124.8 galactonate dehydratase [EC: 4.2.1.6] 78% 631.7

Sequence Analysis Tools

View GFF32 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...

Sequence

MKITKLTTFIVPPRWCFLKVETDQGVTGWGEPVVEGRAHTVAAAVEELSDYLIGKDPRNI
EDIWTVLYRGGFYRGGAVHMSALAGIDQALWDIKGKALGVSVSDLLGGQVRDKIRVYSWI
GGDRPADTARAAKEAVARGFTAVKMNGTEELQFVDSFEKVDLALANVAAVRDAVGPNVGI
GVDFHGRVHKPMAKVLMKELDPYKLMFIEEPVLSENYEALKELAPLTSTPIALGERLFSR
WDFKRVLSEGYVDIIQPDASHAGGITETRKIANMAEAYDVALALHCPLGPIALAACLQLD
AVCYNAFIQEQSLGIHYNESNDLLDYVRDPGVFDYDQGFVKIPNGPGLGIEINEEYVIER
AAIGHRWRNPIWRHADGSFAEW

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:

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