GapMind for catabolism of small carbon sources

 

Protein WP_084938412.1 in Pantoea rwandensis LMG 26275

Annotation: NCBI__GCF_002095475.1:WP_084938412.1

Length: 727 amino acids

Source: GCF_002095475.1 in NCBI

Candidate for 31 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) 75% 99% 1085.5
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) 75% 99% 1085.5
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) 75% 99% 1085.5
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) 75% 99% 1085.5
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) 75% 99% 1085.5
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) 75% 99% 1085.5
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) 75% 99% 1085.5
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) 75% 99% 1085.5
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) 75% 99% 1085.5
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) 75% 99% 1085.5
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) 75% 99% 1085.5
4-hydroxybenzoate catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 33% 82% 127.5
L-arginine catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 33% 82% 127.5
L-citrulline catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 33% 82% 127.5
L-lysine catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 33% 82% 127.5
phenylacetate catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 33% 82% 127.5
L-phenylalanine catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 33% 82% 127.5
L-proline catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 33% 82% 127.5
L-valine catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 33% 82% 127.5
L-isoleucine catabolism fadA lo long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized) 35% 93% 386 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 75% 1085.5
4-hydroxybenzoate catabolism pimF lo 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 33% 99% 354.8 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 75% 1085.5
phenylacetate catabolism pimF lo 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 33% 99% 354.8 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 75% 1085.5
L-phenylalanine catabolism pimF lo 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 33% 99% 354.8 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 75% 1085.5
L-isoleucine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 40% 72% 127.9 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 75% 1085.5
propionate catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 40% 72% 127.9 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 75% 1085.5
L-threonine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 40% 72% 127.9 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 75% 1085.5
L-valine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 40% 72% 127.9 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 75% 1085.5
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% 77% 122.5 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 75% 1085.5
4-hydroxybenzoate catabolism paaF lo 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 31% 90% 115.2 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 75% 1085.5
phenylacetate catabolism paaF lo 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 31% 90% 115.2 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 75% 1085.5
L-phenylalanine catabolism paaF lo 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 31% 90% 115.2 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 75% 1085.5

Sequence Analysis Tools

View WP_084938412.1 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

MLYQGDTLSVHWLDDGIAELVFDAPGSVNKLDTKTVASLGEALGILEQQPALRGLLLSSA
KPAFIVGADITEFLSLFDAPEEKLSQWLAFANSIFNRLEDLPVPTVAAIDGYALGGGCEC
VLATDFRIATPTARIGLPETKLGIMPGFGGSVRLPRLLGADSALEIIAAGKDIDGNSALK
LGLIDAVVSSDKLRAAALTMLQDAIAQGSWQVRRAPKLNPLKLSPIEAAMSFTIAKSMVM
QTAGKHYPAPITAVKTIEAAASLHRDDALKLETAAFVPLAQSDVARALVGIFLNDQYVKG
LAKKHSSAAGAPQQAAVLGAGIMGGGIAYQSAWKGVPVKMKDINPQALTLGMTEASKLLN
KQLERGKIDGAKLASVLTTIQPTLDYAGFERTDVVVEAVVENPQIKAKVLAETEQHLRED
AILASNTSTIPISLLAQSLQRPENFCGMHFFNPVPRMPLVEVIRGEKTSEATISKVVAWA
SKMGKTPIVVNDCPGFFVNRVLFPYFAAFSLLLRDGADFRQIDKVMEKQFGWPMGPAWLL
DVVGIDTAHHAQKVMAQGFPTRMQKDYRDAIDVLFDAQRFGQKNGKGFYLWEQDKKGKAQ
KKADPAVDALLEPICEPKRVFSDEDIANRMMLPMLNEVVRCLEENIIASPAEADMALVYG
LGFPPFRGGAFRYMDTLGNSNVVDQAKRYIALGPLYTLPEQLVQKAHQHQSWYPAVQPID
EAALQSA

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