GapMind for catabolism of small carbon sources

 

Protein HSERO_RS20640 in Herbaspirillum seropedicae SmR1

Annotation: HSERO_RS20640 enoyl-CoA hydratase

Length: 263 amino acids

Source: HerbieS in FitnessBrowser

Candidate for 19 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
phenylacetate catabolism paaG hi 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized) 58% 98% 300.1 BadK 41% 175.3
L-phenylalanine catabolism paaG hi 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized) 58% 98% 300.1 BadK 41% 175.3
L-isoleucine catabolism ech med Probable enoyl-CoA hydratase; EC 4.2.1.17 (uncharacterized) 50% 100% 247.7 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 58% 300.1
L-isoleucine catabolism ech med paaB: phenylacetate degradation probable enoyl-CoA hydratase PaaB (EC 4.2.1.17) (TIGR02280) 100% 411.8 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 58% 300.1
4-hydroxybenzoate catabolism badK med BadK (characterized) 41% 99% 175.3 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 58% 300.1
phenylacetate catabolism badK med BadK (characterized) 41% 99% 175.3 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 58% 300.1
L-phenylalanine catabolism badK med BadK (characterized) 41% 99% 175.3 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 58% 300.1
4-hydroxybenzoate catabolism ech lo trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 35% 99% 154.1 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 58% 300.1
4-hydroxybenzoate catabolism paaF lo trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 35% 99% 154.1 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 58% 300.1
L-arginine catabolism ech lo trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 35% 99% 154.1 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 58% 300.1
L-citrulline catabolism ech lo trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 35% 99% 154.1 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 58% 300.1
L-lysine catabolism ech lo trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 35% 99% 154.1 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 58% 300.1
phenylacetate catabolism ech lo trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 35% 99% 154.1 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 58% 300.1
phenylacetate catabolism paaF lo trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 35% 99% 154.1 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 58% 300.1
L-phenylalanine catabolism ech lo trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 35% 99% 154.1 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 58% 300.1
L-phenylalanine catabolism paaF lo trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 35% 99% 154.1 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 58% 300.1
L-proline catabolism ech lo trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 35% 99% 154.1 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 58% 300.1
L-valine catabolism ech lo trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 35% 99% 154.1 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 58% 300.1
phenylacetate catabolism paaZ1 lo Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale) 34% 98% 135.6 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 58% 300.1
L-phenylalanine catabolism paaZ1 lo Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale) 34% 98% 135.6 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 58% 300.1

Sequence Analysis Tools

View HSERO_RS20640 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MSSPSILLENRDGIAVITLNRPDKLNSFTVAMHLELRDAIATLQADPSVRVLLLTGAGRG
FCAGQDLGDRAVKPGDDGVDLGESIDKYYGPLVKSLRALPFPVICAVNGVAAGAGANLPL
ACDIVLAARSASFVEVFCKLGLIPDTGGTYFLPRLVGTARAMGMALLGEKISAEQAERWG
LIWKCVDDDQLMEEAHAMAAHFARAPTKGLAATKATLYASPAHTLPEQLDLERDTMRALG
RSRDYREGVTAFLEKRAPQFTGQ

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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