GapMind for catabolism of small carbon sources

 

Protein BWI76_RS20065 in Klebsiella michiganensis M5al

Annotation: BWI76_RS20065 1,4-dihydroxy-2-naphthoyl-CoA synthase

Length: 285 amino acids

Source: Koxy in FitnessBrowser

Candidate for 15 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism badI med BadI (characterized) 47% 98% 240.4 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 97% 573.9
phenylacetate catabolism badI med BadI (characterized) 47% 98% 240.4 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 97% 573.9
L-phenylalanine catabolism badI med BadI (characterized) 47% 98% 240.4 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 97% 573.9
L-isoleucine catabolism ech lo Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized) 37% 95% 132.5 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 97% 573.9
4-hydroxybenzoate catabolism paaF lo enoyl-CoA hydratase (EC 4.2.1.17) (characterized) 33% 95% 116.3 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 97% 573.9
phenylacetate catabolism paaF lo enoyl-CoA hydratase (EC 4.2.1.17) (characterized) 33% 95% 116.3 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 97% 573.9
L-phenylalanine catabolism paaF lo enoyl-CoA hydratase (EC 4.2.1.17) (characterized) 33% 95% 116.3 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 97% 573.9
4-hydroxybenzoate catabolism badK lo BadK (characterized) 34% 94% 105.9 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 97% 573.9
phenylacetate catabolism badK lo BadK (characterized) 34% 94% 105.9 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 97% 573.9
L-phenylalanine catabolism badK lo BadK (characterized) 34% 94% 105.9 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 97% 573.9
4-hydroxybenzoate catabolism oah lo 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase; 6-OCH-CoA hydrolase; 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase; EC 3.7.1.21 (characterized) 34% 51% 104.8 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 97% 573.9
phenylacetate catabolism oah lo 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase; 6-OCH-CoA hydrolase; 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase; EC 3.7.1.21 (characterized) 34% 51% 104.8 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 97% 573.9
L-phenylalanine catabolism oah lo 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase; 6-OCH-CoA hydrolase; 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase; EC 3.7.1.21 (characterized) 34% 51% 104.8 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 97% 573.9
L-leucine catabolism liuC lo Methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized) 33% 72% 91.7 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 97% 573.9
L-valine catabolism bch lo 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized) 30% 57% 72 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 97% 573.9

Sequence Analysis Tools

View BWI76_RS20065 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...

Sequence

MISLDEAMLYAPIEWQDCSEGYTDIRYQKSADGIAKITINRPQVRNAFRPLTVKEMIQAL
ADARYDDNIGVIVLTGEGDKAFCAGGDQKVRGDYGGYQDDSGVHHLNVLDFQRQIRTCPK
PVLAMVAGYSIGGGHVLHMMCDLTIAAENAIFGQTGPKVGSFDGGWGASYMARIVGQKKA
REIWFLCRQYDAQQALDMGLVNTVVPLADLEKETVRWCREMLQNSPMALRCLKAALNADC
DGQAGLQELAGNATMLFYMTEEGQEGRNAFNQKRQPDFSKFKRNP

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 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