GapMind for catabolism of small carbon sources

 

Protein WP_007155731.1 in Marinobacter algicola DG893

Annotation: NCBI__GCF_000170835.1:WP_007155731.1

Length: 697 amino acids

Source: GCF_000170835.1 in NCBI

Candidate for 22 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism pimF hi 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 54% 99% 718 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) 50% 653.7
phenylacetate catabolism pimF hi 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 54% 99% 718 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) 50% 653.7
L-phenylalanine catabolism pimF hi 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 54% 99% 718 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) 50% 653.7
4-hydroxybenzoate catabolism fadB med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 50% 99% 653.7 6-carboxyhex-2-enoyl-CoA hydratase 54% 718.0
4-hydroxybenzoate catabolism paaH med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 50% 99% 653.7 6-carboxyhex-2-enoyl-CoA hydratase 54% 718.0
L-arginine catabolism fadB med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 50% 99% 653.7 6-carboxyhex-2-enoyl-CoA hydratase 54% 718.0
L-citrulline catabolism fadB med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 50% 99% 653.7 6-carboxyhex-2-enoyl-CoA hydratase 54% 718.0
L-lysine catabolism fadB med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 50% 99% 653.7 6-carboxyhex-2-enoyl-CoA hydratase 54% 718.0
phenylacetate catabolism fadB med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 50% 99% 653.7 6-carboxyhex-2-enoyl-CoA hydratase 54% 718.0
phenylacetate catabolism paaH med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 50% 99% 653.7 6-carboxyhex-2-enoyl-CoA hydratase 54% 718.0
L-phenylalanine catabolism fadB med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 50% 99% 653.7 6-carboxyhex-2-enoyl-CoA hydratase 54% 718.0
L-phenylalanine catabolism paaH med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 50% 99% 653.7 6-carboxyhex-2-enoyl-CoA hydratase 54% 718.0
L-proline catabolism fadB med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 50% 99% 653.7 6-carboxyhex-2-enoyl-CoA hydratase 54% 718.0
L-isoleucine catabolism ech med enoyl-CoA hydratase (EC 4.2.1.17) (characterized) 42% 96% 525.8 6-carboxyhex-2-enoyl-CoA hydratase 54% 718.0
4-hydroxybenzoate catabolism ech lo 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); short-chain-enoyl-CoA hydratase (EC 4.2.1.150) (characterized) 35% 58% 209.1 6-carboxyhex-2-enoyl-CoA hydratase 54% 718.0
L-arginine catabolism ech lo 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); short-chain-enoyl-CoA hydratase (EC 4.2.1.150) (characterized) 35% 58% 209.1 6-carboxyhex-2-enoyl-CoA hydratase 54% 718.0
L-citrulline catabolism ech lo 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); short-chain-enoyl-CoA hydratase (EC 4.2.1.150) (characterized) 35% 58% 209.1 6-carboxyhex-2-enoyl-CoA hydratase 54% 718.0
L-lysine catabolism ech lo 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); short-chain-enoyl-CoA hydratase (EC 4.2.1.150) (characterized) 35% 58% 209.1 6-carboxyhex-2-enoyl-CoA hydratase 54% 718.0
phenylacetate catabolism ech lo 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); short-chain-enoyl-CoA hydratase (EC 4.2.1.150) (characterized) 35% 58% 209.1 6-carboxyhex-2-enoyl-CoA hydratase 54% 718.0
L-phenylalanine catabolism ech lo 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); short-chain-enoyl-CoA hydratase (EC 4.2.1.150) (characterized) 35% 58% 209.1 6-carboxyhex-2-enoyl-CoA hydratase 54% 718.0
L-proline catabolism ech lo 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); short-chain-enoyl-CoA hydratase (EC 4.2.1.150) (characterized) 35% 58% 209.1 6-carboxyhex-2-enoyl-CoA hydratase 54% 718.0
L-valine catabolism ech lo 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); short-chain-enoyl-CoA hydratase (EC 4.2.1.150) (characterized) 35% 58% 209.1 6-carboxyhex-2-enoyl-CoA hydratase 54% 718.0

Sequence Analysis Tools

View WP_007155731.1 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

MSEVVTYNREGSIGVITVNYPPVNALSHAVRSGLVAALEQGQKDADAKVLLLVCEGRTFI
AGADIREFGKPMQDPGLPSVVDQYENSDKPIIAAIHGTALGGGLETALGCHYRVALSSAK
VGLPEVKLGLLPGAGGTQRLPRLTGAQKALEMITTGEFVGAKDALALSIVDAVEDGSDIK
AAGLAYAQKVADEGKPVRRVRDLTDKLQADKGSDVFEQFRAGLQKKARGLFSPFKCVDAV
EAAFSLPFEDGVKRERELFMECMESPQRAGLVHSFFAEREVSKVKGLSKDTPVRDIRTVG
VIGAGTMGGGIAMNFANAGIPVTIAEVKQEALDKGLAVIRRNYENTAKKGRITQAQVEER
MSLISGTLTYDDFSDVDLVIEAVFESRDLKRKIFGQLDDACKPGAILASNTSTLSIDDIA
AATKRPQDVIGLHFFSPANVMKLLEIVRGEKTSDEVKATAMALAKKIRKVGVMVGNCYGF
VGNRMLHKRGAEAMALVNEGASPQQVDKVLTDLGFPMGQFAMSDLAGIDIGYSIRQERRK
AGEDVPASWMDKLAEQGRLGQKTQAGVYKYEEGNRKPIPDPEVDRVIAEFREEQGIKSRD
ITDQEILERCMYVMVNEGAKILEEGIADRSLDIDITWIYGYGFPAYRGGPMFWADQIGLD
IILGTVEQFYDDLGGEQWKPAALLQKLVSEGRKFSDL

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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