GapMind for catabolism of small carbon sources

 

Protein WP_041416478.1 in Shewanella halifaxensis HAW-EB4

Annotation: NCBI__GCF_000019185.1:WP_041416478.1

Length: 235 amino acids

Source: GCF_000019185.1 in NCBI

Candidate for 8 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism pcaI hi 3-oxoadipate CoA-transferase subunit A; EC 2.8.3.6 (characterized) 57% 97% 250.4 acetyl-CoA:acetoacetate CoA transferase, A subunit (EC 2.8.3.8) 47% 200.7
L-tryptophan catabolism pcaI hi 3-oxoadipate CoA-transferase subunit A; EC 2.8.3.6 (characterized) 57% 97% 250.4 acetyl-CoA:acetoacetate CoA transferase, A subunit (EC 2.8.3.8) 47% 200.7
2-deoxy-D-ribonate catabolism atoA med acetyl-CoA:acetoacetate CoA transferase, A subunit (EC 2.8.3.8) (characterized) 47% 97% 200.7 3-oxoadipate CoA-transferase subunit A; EC 2.8.3.6 57% 250.4
2-deoxy-D-ribose catabolism atoA med acetyl-CoA:acetoacetate CoA transferase, A subunit (EC 2.8.3.8) (characterized) 47% 97% 200.7 3-oxoadipate CoA-transferase subunit A; EC 2.8.3.6 57% 250.4
L-leucine catabolism atoA med acetyl-CoA:acetoacetate CoA transferase, A subunit (EC 2.8.3.8) (characterized) 47% 97% 200.7 3-oxoadipate CoA-transferase subunit A; EC 2.8.3.6 57% 250.4
L-phenylalanine catabolism atoA med acetyl-CoA:acetoacetate CoA transferase, A subunit (EC 2.8.3.8) (characterized) 47% 97% 200.7 3-oxoadipate CoA-transferase subunit A; EC 2.8.3.6 57% 250.4
L-tyrosine catabolism atoA med acetyl-CoA:acetoacetate CoA transferase, A subunit (EC 2.8.3.8) (characterized) 47% 97% 200.7 3-oxoadipate CoA-transferase subunit A; EC 2.8.3.6 57% 250.4
L-lysine catabolism ctfA med Butyrate--acetoacetate CoA-transferase subunit A; Short=Coat A; EC 2.8.3.9 (characterized, see rationale) 44% 93% 157.9 3-oxoadipate CoA-transferase subunit A; EC 2.8.3.6 57% 250.4

Sequence Analysis Tools

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

MNKLMATPAQAVADIFDGATVMIGGFGESGSPIELIHALIDQGAKNLTVINNNTGSGHVG
LAALIENGQVGKMICSFPRTANSTVFPDLYRAGKIELELVPQGTLAERIRAGGAGIPAFY
TATSVGTPLADGKKHEIFDGREHVQELGLKADFALIKSLQADRLGNLRYNKTARNFAPIM
AMAANYTIVQTQEYVEAGAIDPEIVVTPGIFVDRIVTVKQPAQESKLVAAGVSYP

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