Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_012404381.1 BPHY_RS25715 enoyl-CoA hydratase
Query= BRENDA::Q9I5I4 (272 letters) >NCBI__GCF_000020045.1:WP_012404381.1 Length = 268 Score = 301 bits (770), Expect = 1e-86 Identities = 159/247 (64%), Positives = 184/247 (74%), Gaps = 1/247 (0%) Query: 25 GHTALITINHPPANTWDRDSLIGLRQLIEHLNRDDDIYALVVTGQGPKFFSAGADLNMFA 84 G AL+T+ PPAN + D L+ L+Q + LN + ++ A+V+TG GPKFFSAGADLN FA Sbjct: 10 GSVALLTLRRPPANAFTPDGLLQLQQTVLRLNGEVNVRAIVITGDGPKFFSAGADLNTFA 69 Query: 85 DGDKARAREMARRFGEAFEALRDFRGVSIAAINGYAMGGGLECALACDIRIAERQAQMAL 144 DG+K AR A RFG AFE L++ R V IAAINGYAMGGGLECALACDIR+AE+ A MAL Sbjct: 70 DGNKEVARLAATRFGAAFETLQNARPVVIAAINGYAMGGGLECALACDIRVAEQHAVMAL 129 Query: 145 PEAAVGLLPCAGGTQALPWLVGEGWAKRMILCNERVDAETALRIGLVEQVVDSGEARGAA 204 PE AVGLLPC GTQ LP LVGEGWAKR++L ERVDA TALRIGLVE+VV+ G AR A Sbjct: 130 PETAVGLLPCGCGTQTLPSLVGEGWAKRIVLTGERVDAPTALRIGLVEEVVEKGAARSFA 189 Query: 205 LLLAAKVARQSPVAIRTIKPLIQGARERAPN-TWLPEERERFVDLFDAQDTREGVNAFLE 263 L +AA+VA SP A+ K LIQ AR P L ERERFVDLFD D REGVNAFLE Sbjct: 190 LAMAARVAGLSPQAVTFSKELIQQARNGVPRPAALAVERERFVDLFDGADQREGVNAFLE 249 Query: 264 KRDPKWR 270 KR P+W+ Sbjct: 250 KRAPRWQ 256 Lambda K H 0.321 0.136 0.412 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 223 Number of extensions: 7 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 272 Length of database: 268 Length adjustment: 25 Effective length of query: 247 Effective length of database: 243 Effective search space: 60021 Effective search space used: 60021 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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:
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