GapMind for catabolism of small carbon sources

 

Protein WP_106712562.1 in Phyllobacterium brassicacearum STM 196

Annotation: NCBI__GCF_003010955.1:WP_106712562.1

Length: 259 amino acids

Source: GCF_003010955.1 in NCBI

Candidate for 19 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-isoleucine catabolism hpcD hi 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 42% 98% 186 crotonase (EC 4.2.1.150) 39% 172.2
propionate catabolism hpcD hi 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 42% 98% 186 crotonase (EC 4.2.1.150) 39% 172.2
L-threonine catabolism hpcD hi 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 42% 98% 186 crotonase (EC 4.2.1.150) 39% 172.2
L-valine catabolism hpcD hi 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 42% 98% 186 crotonase (EC 4.2.1.150) 39% 172.2
4-hydroxybenzoate catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 41% 93% 167.9 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 42% 186.0
L-arginine catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 41% 93% 167.9 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 42% 186.0
L-citrulline catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 41% 93% 167.9 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 42% 186.0
L-lysine catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 41% 93% 167.9 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 42% 186.0
phenylacetate catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 41% 93% 167.9 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 42% 186.0
L-phenylalanine catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 41% 93% 167.9 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 42% 186.0
L-proline catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 41% 93% 167.9 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 42% 186.0
L-valine catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 41% 93% 167.9 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 42% 186.0
4-hydroxybenzoate catabolism paaF lo 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 39% 95% 154.5 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 42% 186.0
L-isoleucine catabolism ech lo 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 39% 95% 154.5 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 42% 186.0
phenylacetate catabolism paaF lo 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 39% 95% 154.5 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 42% 186.0
L-phenylalanine catabolism paaF lo 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 39% 95% 154.5 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 42% 186.0
L-leucine catabolism liuC lo methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized) 38% 100% 151.4 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 42% 186.0
phenylacetate catabolism paaG lo 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized) 36% 96% 122.9 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 42% 186.0
L-phenylalanine catabolism paaG lo 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized) 36% 96% 122.9 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 42% 186.0

Sequence Analysis Tools

View WP_106712562.1 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

MAEPRIEVTFAGPVATITVSRPEKLNAFDIDMLKDLSAACDTVEANLDVRVTILTGAGKA
FSAGGDINAWAAMTPNEFGHAWVRFGHRVFERLATLRMPLIAALNGHALGGGLELAAAAD
IRIAETQIRLGLPETGLGMVPGWSGTQRLVRRFGAQVVRRMALGGEIFSATEGLGLGLID
HVVETGAAVNAAQTHAERIAKRGPAAVEVAKLMIAVANGEDNGTAVEALGSILVAKTADL
KEGVSAFAEKREPVFKGEW

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