GapMind for catabolism of small carbon sources

 

Protein WP_095189148.1 in Pseudomonas baetica a390

Annotation: NCBI__GCF_003031005.1:WP_095189148.1

Length: 715 amino acids

Source: GCF_003031005.1 in NCBI

Candidate for 26 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism fadB hi Fatty acid oxidation complex subunit alpha; EC 4.2.1.17; EC 5.1.2.3; EC 5.3.3.8; EC 1.1.1.35 (characterized) 94% 100% 1322
4-hydroxybenzoate catabolism paaH hi Fatty acid oxidation complex subunit alpha; EC 4.2.1.17; EC 5.1.2.3; EC 5.3.3.8; EC 1.1.1.35 (characterized) 94% 100% 1322
L-arginine catabolism fadB hi Fatty acid oxidation complex subunit alpha; EC 4.2.1.17; EC 5.1.2.3; EC 5.3.3.8; EC 1.1.1.35 (characterized) 94% 100% 1322
L-citrulline catabolism fadB hi Fatty acid oxidation complex subunit alpha; EC 4.2.1.17; EC 5.1.2.3; EC 5.3.3.8; EC 1.1.1.35 (characterized) 94% 100% 1322
L-isoleucine catabolism ech hi Fatty acid oxidation complex subunit alpha; EC 4.2.1.17; EC 5.1.2.3; EC 5.3.3.8; EC 1.1.1.35 (characterized) 94% 100% 1322
L-lysine catabolism fadB hi Fatty acid oxidation complex subunit alpha; EC 4.2.1.17; EC 5.1.2.3; EC 5.3.3.8; EC 1.1.1.35 (characterized) 94% 100% 1322
phenylacetate catabolism fadB hi Fatty acid oxidation complex subunit alpha; EC 4.2.1.17; EC 5.1.2.3; EC 5.3.3.8; EC 1.1.1.35 (characterized) 94% 100% 1322
phenylacetate catabolism paaH hi Fatty acid oxidation complex subunit alpha; EC 4.2.1.17; EC 5.1.2.3; EC 5.3.3.8; EC 1.1.1.35 (characterized) 94% 100% 1322
L-phenylalanine catabolism fadB hi Fatty acid oxidation complex subunit alpha; EC 4.2.1.17; EC 5.1.2.3; EC 5.3.3.8; EC 1.1.1.35 (characterized) 94% 100% 1322
L-phenylalanine catabolism paaH hi Fatty acid oxidation complex subunit alpha; EC 4.2.1.17; EC 5.1.2.3; EC 5.3.3.8; EC 1.1.1.35 (characterized) 94% 100% 1322
L-proline catabolism fadB hi Fatty acid oxidation complex subunit alpha; EC 4.2.1.17; EC 5.1.2.3; EC 5.3.3.8; EC 1.1.1.35 (characterized) 94% 100% 1322
4-hydroxybenzoate catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 34% 80% 127.5
L-arginine catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 34% 80% 127.5
L-citrulline catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 34% 80% 127.5
L-lysine catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 34% 80% 127.5
phenylacetate catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 34% 80% 127.5
L-phenylalanine catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 34% 80% 127.5
L-proline catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 34% 80% 127.5
L-valine catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 34% 80% 127.5
4-hydroxybenzoate catabolism pimF lo 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 32% 98% 349 Fatty acid oxidation complex subunit alpha; EC 4.2.1.17; EC 5.1.2.3; EC 5.3.3.8; EC 1.1.1.35 94% 1322.0
phenylacetate catabolism pimF lo 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 32% 98% 349 Fatty acid oxidation complex subunit alpha; EC 4.2.1.17; EC 5.1.2.3; EC 5.3.3.8; EC 1.1.1.35 94% 1322.0
L-phenylalanine catabolism pimF lo 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 32% 98% 349 Fatty acid oxidation complex subunit alpha; EC 4.2.1.17; EC 5.1.2.3; EC 5.3.3.8; EC 1.1.1.35 94% 1322.0
L-leucine catabolism liuC lo Methylglutaconyl-CoA hydratase, mitochondrial; AU-specific RNA-binding enoyl-CoA hydratase; AU-binding enoyl-CoA hydratase; muAUH; Itaconyl-CoA hydratase; EC 4.2.1.18; EC 4.2.1.56 (characterized) 34% 75% 114 Fatty acid oxidation complex subunit alpha; EC 4.2.1.17; EC 5.1.2.3; EC 5.3.3.8; EC 1.1.1.35 94% 1322.0
4-hydroxybenzoate catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized) 30% 95% 82.8 Fatty acid oxidation complex subunit alpha; EC 4.2.1.17; EC 5.1.2.3; EC 5.3.3.8; EC 1.1.1.35 94% 1322.0
phenylacetate catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized) 30% 95% 82.8 Fatty acid oxidation complex subunit alpha; EC 4.2.1.17; EC 5.1.2.3; EC 5.3.3.8; EC 1.1.1.35 94% 1322.0
L-phenylalanine catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized) 30% 95% 82.8 Fatty acid oxidation complex subunit alpha; EC 4.2.1.17; EC 5.1.2.3; EC 5.3.3.8; EC 1.1.1.35 94% 1322.0

Sequence Analysis Tools

View WP_095189148.1 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

MIYEGKAITVKALESGIVELKFDLKGESVNKFNRLTLNELRQAVDTIKADASIKGVIVSS
GKDVFIVGADITEFVDNFKLPDAELVAGNLEANKIFSDFEDLNVPTVAAINGIALGGGLE
MCLAADYRVMSTKAKIGLPEVKLGIYPGFGGTVRLPRLIGVDNAIEWIAAGKENRPEDAL
KVSAVDAVVAPEKLQEAALELIKRAISGEFDYKAKRQPKLEKLKLNAIEQMMAFETAKGF
VAGQAGPNYPAPVEAIKTIQKAANFGRDKALEIEAAGFVKLAKTSAAQSLIGLFLNDQEL
KKKAKAYDEIAKDVKQAAVLGAGIMGGGIAYQSASKGTPILMKDINEHGIEQGLAEAAKL
LVGRVDKGRMTAAKMAEVLNAIRPTLSYGDFGHVDLVVEAVVENPKVKQAVLAEVEAQVK
EDTILASNTSTISISLLAKALKRPENFVGMHFFNPVHMMPLVEVIRGEKSSELAVATTVA
YAKKMGKNPIVVNDCPGFLVNRVLFPYFGGFAKLVSAGVDFVRIDKVMEKFGWPMGPAYL
MDVVGIDTGHHGRDVMAEGFPDRMKDDRRSAIDVLYEAKRLGQKNGKGFYAYEADKKGKQ
KKVADPSVLEVLKPIVYEQREVTDEDIINWMMIPLCLETVRCLEDGIVETAAEADMGLVY
GIGFPPFRGGALRYIDSIGVAEFVALADQYADLGALYHPTAKLREMAKNGQSFFG

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