GapMind for catabolism of small carbon sources

 

Protein Synpcc7942_0597 in Synechococcus elongatus PCC 7942

Annotation: Synpcc7942_0597 naphthoate synthase

Length: 279 amino acids

Source: SynE in FitnessBrowser

Candidate for 28 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) 49% 99% 243 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) 80% 464.5
phenylacetate catabolism badI med BadI (characterized) 49% 99% 243 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) 80% 464.5
L-phenylalanine catabolism badI med BadI (characterized) 49% 99% 243 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) 80% 464.5
L-isoleucine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 36% 99% 136 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) 80% 464.5
propionate catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 36% 99% 136 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) 80% 464.5
L-threonine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 36% 99% 136 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) 80% 464.5
L-valine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 36% 99% 136 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) 80% 464.5
4-hydroxybenzoate catabolism ech lo Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 38% 98% 135.2 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) 80% 464.5
L-arginine catabolism ech lo Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 38% 98% 135.2 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) 80% 464.5
L-citrulline catabolism ech lo Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 38% 98% 135.2 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) 80% 464.5
L-lysine catabolism ech lo Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 38% 98% 135.2 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) 80% 464.5
phenylacetate catabolism ech lo Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 38% 98% 135.2 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) 80% 464.5
L-phenylalanine catabolism ech lo Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 38% 98% 135.2 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) 80% 464.5
L-proline catabolism ech lo Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 38% 98% 135.2 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) 80% 464.5
L-valine catabolism ech lo Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 38% 98% 135.2 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) 80% 464.5
L-isoleucine catabolism ech lo Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized) 38% 95% 126.7 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) 80% 464.5
4-hydroxybenzoate catabolism paaF lo trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 34% 99% 122.1 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) 80% 464.5
phenylacetate catabolism paaF lo trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 34% 99% 122.1 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) 80% 464.5
L-phenylalanine catabolism paaF lo trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 34% 99% 122.1 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) 80% 464.5
L-leucine catabolism liuC lo methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized) 35% 97% 113.6 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) 80% 464.5
4-hydroxybenzoate catabolism badK lo BadK (characterized) 34% 94% 106.3 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) 80% 464.5
phenylacetate catabolism badK lo BadK (characterized) 34% 94% 106.3 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) 80% 464.5
L-phenylalanine catabolism badK lo BadK (characterized) 34% 94% 106.3 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) 80% 464.5
phenylacetate catabolism paaG lo 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized) 34% 96% 101.7 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) 80% 464.5
L-phenylalanine catabolism paaG lo 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized) 34% 96% 101.7 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) 80% 464.5
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) 33% 54% 87.4 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) 80% 464.5
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) 33% 54% 87.4 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) 80% 464.5
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) 33% 54% 87.4 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) 80% 464.5

Sequence Analysis Tools

View Synpcc7942_0597 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

VAQVQWQSVREYEDIRYEKCAEGIAKITINRPHKRNAFRPKTVVELYDAFCDAREDIAIG
VILLTGAGPHTDGRYAFCAGGDQSVRGAGGYIDEEGLPRLNVLDLQRLIRTIPKVVIALV
AGYAIGGGHVLHILCDLTIAADNAVFGQTGPKVGSFDGGFGASYLARLVGQKKAREIWFL
CRQYGAKEALQMGLVNTVVPVEELEAEGIRWALEILEKSPIAIRCLKAAFNAELDGMAGI
QELAGHATHLYYLTEEGSEGKQAFLEKRSPDFRQYPWLP

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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