GapMind for catabolism of small carbon sources

 

Protein N515DRAFT_0416 in Dyella japonica UNC79MFTsu3.2

Annotation: FitnessBrowser__Dyella79:N515DRAFT_0416

Length: 686 amino acids

Source: Dyella79 in FitnessBrowser

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 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 42% 97% 183.3
4-hydroxybenzoate catabolism paaH hi 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 42% 97% 183.3
L-arginine catabolism fadB hi 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 42% 97% 183.3
L-citrulline catabolism fadB hi 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 42% 97% 183.3
L-lysine catabolism fadB hi 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 42% 97% 183.3
phenylacetate catabolism fadB hi 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 42% 97% 183.3
phenylacetate catabolism paaH hi 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 42% 97% 183.3
L-phenylalanine catabolism fadB hi 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 42% 97% 183.3
L-phenylalanine catabolism paaH hi 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 42% 97% 183.3
L-proline catabolism fadB hi 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 42% 97% 183.3
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) 37% 95% 390.6
L-leucine catabolism liuC med methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized) 42% 73% 126.7 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 37% 390.6
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) 32% 92% 345.5 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 37% 390.6
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) 33% 56% 184.1
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) 33% 56% 184.1
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) 33% 56% 184.1
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) 33% 56% 184.1
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) 33% 56% 184.1
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) 33% 56% 184.1
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) 33% 56% 184.1
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) 33% 56% 184.1
L-isoleucine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 37% 72% 120.9 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 37% 390.6
propionate catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 37% 72% 120.9 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 37% 390.6
L-threonine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 37% 72% 120.9 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 37% 390.6
L-valine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 37% 72% 120.9 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 37% 390.6
4-hydroxybenzoate catabolism paaF lo 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 38% 78% 107.1 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 37% 390.6
phenylacetate catabolism paaF lo 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 38% 78% 107.1 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 37% 390.6
L-phenylalanine catabolism paaF lo 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 38% 78% 107.1 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 37% 390.6
4-hydroxybenzoate catabolism badK lo BadK (characterized) 33% 76% 96.3 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 37% 390.6
phenylacetate catabolism badK lo BadK (characterized) 33% 76% 96.3 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 37% 390.6
L-phenylalanine catabolism badK lo BadK (characterized) 33% 76% 96.3 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 37% 390.6

Sequence Analysis Tools

View N515DRAFT_0416 at FitnessBrowser

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

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Sequence

MFEGLRFNHWKTSLDDSGIVTLTLDRANSSVNALSREVLDELGQIVERLSIEKPAGVLIH
SAKPGGFAVGADIKEFVEYARDGTVLQNIENGQRVFESLARLPCPTVAAIHGACMGGGTE
LVLACRQRIAADDEKTRIGLPEVMLGIHPGWGGTARLPRLIGALDALPVMLTGKALSARR
AAALGVVDRLAPPNELLAEARALLRRPHARPAARRLKAWATNTWPARQILAPMVLKQTAA
KVRKEHYPAPFALINVWQRGGSSIQQRLKLEARSVAKLAETSTARNLIRIFLLQERLKGQ
GSGVEHGIEHVHVVGAGVMGGDIAAWAAFKGFQVTLQDREMKFIQPALDRARALYEKKLK
TPEKVEETARRLRADVEGKGVAAADLAIEAIFENAEAKQALYASIEPQFQADEILATNTS
SIPLDELRRGLKAPQRFLGLHFFNPVAQMPLVEVVRHDGLDPEVEKRALAFCKAIGKLPV
AVKGTPGFLVNRILMPYLLEAIRLYNEGVPGPVLDKEAKKFGMPMGPIELADTVGLDVCA
SVGKELAPFLGLELPPGIEDKLAAGKRGKKDGQGFYVWQEGKPQKPEVDPDYAVPADLQE
RMLLPMVNEAVACLADGVVDDADLLDAGVIFGTGFAPFRGGPIQYVRSEGAAVIKGKLER
LAQRHGERFTPKQGWDLAILAQPPEA

This GapMind analysis is from Sep 17 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