Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate BPHYT_RS28020 BPHYT_RS28020 enoyl-CoA hydratase
Query= BRENDA::Q9I5I4 (272 letters) >FitnessBrowser__BFirm:BPHYT_RS28020 Length = 272 Score = 304 bits (779), Expect = 1e-87 Identities = 159/247 (64%), Positives = 184/247 (74%), Gaps = 1/247 (0%) Query: 25 GHTALITINHPPANTWDRDSLIGLRQLIEHLNRDDDIYALVVTGQGPKFFSAGADLNMFA 84 G A +T+ PPAN + + L+ L+Q +E LN + + A+V+TG GPKFFSAGADLN FA Sbjct: 10 GAVAQLTLKRPPANAFTPEGLLQLQQTVERLNGEARVRAIVITGDGPKFFSAGADLNTFA 69 Query: 85 DGDKARAREMARRFGEAFEALRDFRGVSIAAINGYAMGGGLECALACDIRIAERQAQMAL 144 DG++ AR A RFG AFE L++ R V IAAINGYAMGGGLECALACDIRIAE+ A +AL Sbjct: 70 DGNREVARTAAARFGAAFETLQNARPVVIAAINGYAMGGGLECALACDIRIAEQHALLAL 129 Query: 145 PEAAVGLLPCAGGTQALPWLVGEGWAKRMILCNERVDAETALRIGLVEQVVDSGEARGAA 204 PE AVGLLPC GTQ LPWLVGEGWAKRMIL ERVDA TALRIGLVE+VV+ G AR AA Sbjct: 130 PETAVGLLPCGCGTQTLPWLVGEGWAKRMILTGERVDAATALRIGLVEEVVEKGAARDAA 189 Query: 205 LLLAAKVARQSPVAIRTIKPLIQGARERAPN-TWLPEERERFVDLFDAQDTREGVNAFLE 263 L++AA+VA SP A+ K LI R P L ERERFVDLFD D REGVNAFLE Sbjct: 190 LVMAARVATLSPQAVGFSKTLIHQGRSGVPRAAALALERERFVDLFDGADQREGVNAFLE 249 Query: 264 KRDPKWR 270 KR P+W+ Sbjct: 250 KRPPRWQ 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: 240 Number of extensions: 8 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: 272 Length adjustment: 25 Effective length of query: 247 Effective length of database: 247 Effective search space: 61009 Effective search space used: 61009 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 17 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