GapMind for catabolism of small carbon sources

 

Protein WP_023433147.1 in Lutibaculum baratangense AMV1

Annotation: NCBI__GCF_000496075.1:WP_023433147.1

Length: 388 amino acids

Source: GCF_000496075.1 in NCBI

Candidate for 7 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-lysine catabolism bcd med butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (subunit 1/2) (EC 1.3.8.1) (characterized) 42% 97% 279.6 Short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) 40% 278.1
L-isoleucine catabolism acdH med Short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized) 40% 99% 278.1 butanal dehydrogenase (EC 1.2.1.57) 44% 298.5
L-valine catabolism acdH med 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized) 40% 99% 271.2 butanal dehydrogenase (EC 1.2.1.57) 44% 298.5
4-hydroxybenzoate catabolism Ch1CoA med cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized) 40% 98% 247.3 butanal dehydrogenase (EC 1.2.1.57) 44% 298.5
phenylacetate catabolism Ch1CoA med cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized) 40% 98% 247.3 butanal dehydrogenase (EC 1.2.1.57) 44% 298.5
L-phenylalanine catabolism Ch1CoA med cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized) 40% 98% 247.3 butanal dehydrogenase (EC 1.2.1.57) 44% 298.5
L-leucine catabolism liuA lo Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized) 37% 97% 223 butanal dehydrogenase (EC 1.2.1.57) 44% 298.5

Sequence Analysis Tools

View WP_023433147.1 at NCBI

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

MRIFEQLERRRGWSEDEQMVLDQVRRCAAEVIEPNAERFDREHAFPWDNVHAINELGLNA
IFVPEEYGGARMSYRLYLEVVKVISAACASTGIIYATNFHSMKPLIDLGTEEQKQRLLPC
IAEGGLGSLAITEPDAGSDATGMKTRFTLDGDEIVVDGGKIFITNGDVADRILLFGKWSG
IEDPKKAISVLVLEKGTPGLEVVRLEEKMGHRASSTAALAFTGCRVPRANLIGEPGEGLK
ILLSSLNKSRPSIAAHALGIARAAFTDMVEYTNERQQGGRRIIDFQGNQFAIADMAAELA
LAELWLDYVGGLVDDGADDFGLEASVAKLRASDLAMKISSEAVQLFGGYGYCGDYRVERL
MRDAKITQIWEGANQIHRQLIGRSFIAK

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