GapMind for catabolism of small carbon sources

 

Protein WP_110754194.1 in Phyllobacterium leguminum ORS 1419

Annotation: NCBI__GCF_003217235.1:WP_110754194.1

Length: 740 amino acids

Source: GCF_003217235.1 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 med fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 35% 98% 426 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) 34% 377.5
4-hydroxybenzoate catabolism paaH med fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 35% 98% 426 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) 34% 377.5
L-arginine catabolism fadB med fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 35% 98% 426 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) 34% 377.5
L-citrulline catabolism fadB med fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 35% 98% 426 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) 34% 377.5
L-isoleucine catabolism ech med fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 35% 98% 426
L-lysine catabolism fadB med fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 35% 98% 426 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) 34% 377.5
phenylacetate catabolism fadB med fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 35% 98% 426 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) 34% 377.5
phenylacetate catabolism paaH med fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 35% 98% 426 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) 34% 377.5
L-phenylalanine catabolism fadB med fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 35% 98% 426 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) 34% 377.5
L-phenylalanine catabolism paaH med fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 35% 98% 426 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) 34% 377.5
L-proline catabolism fadB med fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 35% 98% 426 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) 34% 377.5
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) 34% 95% 376.3 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 35% 426.0
4-hydroxybenzoate catabolism pimF lo 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 31% 98% 318.5 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 35% 426.0
phenylacetate catabolism pimF lo 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 31% 98% 318.5 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 35% 426.0
L-phenylalanine catabolism pimF lo 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 31% 98% 318.5 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 35% 426.0
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) 34% 61% 184.9
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) 34% 61% 184.9
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) 34% 61% 184.9
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) 34% 61% 184.9
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) 34% 61% 184.9
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) 34% 61% 184.9
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) 34% 61% 184.9
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) 34% 61% 184.9
L-isoleucine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 33% 69% 116.3 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 35% 426.0
propionate catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 33% 69% 116.3 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 35% 426.0
L-threonine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 33% 69% 116.3 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 35% 426.0
L-valine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 33% 69% 116.3 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 35% 426.0
L-leucine catabolism liuC lo methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized) 33% 75% 104.4 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 35% 426.0
4-hydroxybenzoate catabolism paaF lo enoyl-CoA hydratase (EC 4.2.1.17) (characterized) 30% 70% 94 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 35% 426.0
phenylacetate catabolism paaF lo enoyl-CoA hydratase (EC 4.2.1.17) (characterized) 30% 70% 94 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 35% 426.0
L-phenylalanine catabolism paaF lo enoyl-CoA hydratase (EC 4.2.1.17) (characterized) 30% 70% 94 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 35% 426.0

Sequence Analysis Tools

View WP_110754194.1 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

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Fitness BLAST: loading...

Sequence

MADYKNFKFDVDADGIALVTWDMPDKSMNVFTEEVMDELETIVDRVAGDAAIKGAVITSG
KDSFSGGADLTMLKRMFQLFQEEKAKDSQKAVELLFKSSGRMGGLFRKLETSGKPWVSAI
NGTCMGGAFEMSLACHARVASDAPGVKMALPEVKVGIFPGAGGTQRVPRLTNQQDALQMM
TTGQSLTPQRAKAMGLITEIAPAKKLVETAKKLIKGGLKPVQPWDEKGFKLPGAPIYSAA
GANLWPAASAILRRETYGNYPAAAAILKCVYEGLLVPFDTGLKIEQRYFTQILQTLEAGM
MIRSLFVSLQELNKGARRPADIKPTKFTKIGVIGAGFMGAGIAYVTAKSGIPVVLIDRDV
EAAEKGKAHAADLIAKEMQKGRMSEEDKQKLLSLIIPTADYADLEGADLVIEAVFEDREV
KRQATEKAEAVLKSSAIFASNTSTLPISGLAKVSERPKNFIGIHFFSPVDKMMLVEVILG
KKTGDKALAVALDYVRAIKKTPIVVNDTRGFYVNRCVLRYMSEAYNMLIEGVPPAMIENA
ARMAGMPVGPLALNDETAIDLSQKILKAALADLGPKAVDPRHVELVDKLVNEFDRKGRKN
GKGFYDYPAKPAKKHLWPELKTLYPQQDPDKVNVEELKERFLFTIALEAARVMEEGIVTD
PREADVGSILAFGFAPYTGGTLSYIDGMGAKKFVRRAKELQKKYGAQFKAPKLLTDMADN
GETFYQRFDPYKAETQKQAA

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