GapMind for catabolism of small carbon sources

 

Protein BWI76_RS20065 in Klebsiella michiganensis M5al

Annotation: FitnessBrowser__Koxy:BWI76_RS20065

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

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

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:

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