GapMind for catabolism of small carbon sources

 

Protein WP_157035422.1 in Psychromonas ingrahamii 37

Annotation: NCBI__GCF_000015285.1:WP_157035422.1

Length: 244 amino acids

Source: GCF_000015285.1 in NCBI

Candidate for 23 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism paaF hi enoyl-CoA hydratase (EC 4.2.1.17) (characterized) 55% 95% 255 enoyl-CoA hydratase (EC 4.2.1.17); DELTA3,5-DELTA2,4-dienoyl-CoA isomerase (EC 5.3.3.21) 45% 204.5
L-isoleucine catabolism ech hi enoyl-CoA hydratase (EC 4.2.1.17) (characterized) 55% 95% 255 AcuK 40% 178.7
phenylacetate catabolism paaF hi enoyl-CoA hydratase (EC 4.2.1.17) (characterized) 55% 95% 255 enoyl-CoA hydratase (EC 4.2.1.17); DELTA3,5-DELTA2,4-dienoyl-CoA isomerase (EC 5.3.3.21) 45% 204.5
L-phenylalanine catabolism paaF hi enoyl-CoA hydratase (EC 4.2.1.17) (characterized) 55% 95% 255 enoyl-CoA hydratase (EC 4.2.1.17); DELTA3,5-DELTA2,4-dienoyl-CoA isomerase (EC 5.3.3.21) 45% 204.5
4-hydroxybenzoate catabolism badK med BadK (characterized) 41% 93% 172.6 enoyl-CoA hydratase (EC 4.2.1.17) 55% 255.0
phenylacetate catabolism badK med BadK (characterized) 41% 93% 172.6 enoyl-CoA hydratase (EC 4.2.1.17) 55% 255.0
L-phenylalanine catabolism badK med BadK (characterized) 41% 93% 172.6 enoyl-CoA hydratase (EC 4.2.1.17) 55% 255.0
4-hydroxybenzoate catabolism ech lo crotonase (EC 4.2.1.150) (characterized) 38% 90% 171.8 AcuK 40% 178.7
L-arginine catabolism ech lo crotonase (EC 4.2.1.150) (characterized) 38% 90% 171.8 AcuK 40% 178.7
L-citrulline catabolism ech lo crotonase (EC 4.2.1.150) (characterized) 38% 90% 171.8 AcuK 40% 178.7
L-lysine catabolism ech lo crotonase (EC 4.2.1.150) (characterized) 38% 90% 171.8 AcuK 40% 178.7
phenylacetate catabolism ech lo crotonase (EC 4.2.1.150) (characterized) 38% 90% 171.8 AcuK 40% 178.7
L-phenylalanine catabolism ech lo crotonase (EC 4.2.1.150) (characterized) 38% 90% 171.8 AcuK 40% 178.7
L-proline catabolism ech lo crotonase (EC 4.2.1.150) (characterized) 38% 90% 171.8 AcuK 40% 178.7
L-valine catabolism ech lo crotonase (EC 4.2.1.150) (characterized) 38% 90% 171.8 AcuK 40% 178.7
L-isoleucine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 39% 95% 170.2 enoyl-CoA hydratase (EC 4.2.1.17) 55% 255.0
propionate catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 39% 95% 170.2 enoyl-CoA hydratase (EC 4.2.1.17) 55% 255.0
L-threonine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 39% 95% 170.2 enoyl-CoA hydratase (EC 4.2.1.17) 55% 255.0
L-valine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 39% 95% 170.2 enoyl-CoA hydratase (EC 4.2.1.17) 55% 255.0
L-leucine catabolism liuC lo methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized) 37% 78% 160.6 enoyl-CoA hydratase (EC 4.2.1.17) 55% 255.0
phenylacetate catabolism paaZ1 lo Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale) 31% 94% 120.2 enoyl-CoA hydratase (EC 4.2.1.17) 55% 255.0
L-phenylalanine catabolism paaZ1 lo Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale) 31% 94% 120.2 enoyl-CoA hydratase (EC 4.2.1.17) 55% 255.0
L-valine catabolism bch lo 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized) 30% 50% 72.4 enoyl-CoA hydratase (EC 4.2.1.17) 55% 255.0

Sequence Analysis Tools

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MLLIQFTHYEKRNALSNDCLNELAGVLDKAEQQNHIAAVVLTGGQRCFAAGADLNELATQ
GAIDTWLNPRPELWARLNKFSKPLLAAVNGYALGAGLELVLLCDIAISGQKALFGLPEIT
LGLIPGAGGTQRLARTVGKSLTNQMVLTGLPITAERALQAGLISEVVIPELTLERTIIIA
ETIAKRAPLAIKAAKQSLQQVPNSSLDQGLKFERQLFVTLAASNDRKEGIDAFFNKRQPT
YKGS

This GapMind analysis is from Sep 24 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