Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate 5209192 Shew_1670 enoyl-CoA hydratase (RefSeq)
Query= BRENDA::Q9I5I4 (272 letters) >FitnessBrowser__PV4:5209192 Length = 257 Score = 324 bits (830), Expect = 1e-93 Identities = 166/247 (67%), Positives = 187/247 (75%) Query: 25 GHTALITINHPPANTWDRDSLIGLRQLIEHLNRDDDIYALVVTGQGPKFFSAGADLNMFA 84 GHTA++T+N+PPANTW DSL L+Q + LN + +IYALV+TG+G KFFSAGADL +FA Sbjct: 10 GHTAVLTMNNPPANTWTADSLALLKQKVTELNANKEIYALVLTGEGEKFFSAGADLKLFA 69 Query: 85 DGDKARAREMARRFGEAFEALRDFRGVSIAAINGYAMGGGLECALACDIRIAERQAQMAL 144 DGDK A MA+ FGEAFEAL FRGVSIAAINGYAMGGGLE ALACDIRIAE QA MAL Sbjct: 70 DGDKGNAATMAKHFGEAFEALSGFRGVSIAAINGYAMGGGLEVALACDIRIAEAQAVMAL 129 Query: 145 PEAAVGLLPCAGGTQALPWLVGEGWAKRMILCNERVDAETALRIGLVEQVVDSGEARGAA 204 PEA VGLLPCAGGTQ L +VGEGWAKRMILC ERV A+ AL IGL+E+VVD G A A Sbjct: 130 PEATVGLLPCAGGTQNLTAMVGEGWAKRMILCGERVGADKALSIGLIEEVVDKGAALDTA 189 Query: 205 LLLAAKVARQSPVAIRTIKPLIQGARERAPNTWLPEERERFVDLFDAQDTREGVNAFLEK 264 + LA KVA QSP ++ K LIQ R LP ERE FV LFD +D EGVNAFLEK Sbjct: 190 MALAEKVANQSPSSVTVCKQLIQSGRAMPRTQALPLERELFVGLFDTEDQAEGVNAFLEK 249 Query: 265 RDPKWRN 271 R W+N Sbjct: 250 RKANWKN 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: 238 Number of extensions: 5 Number of successful extensions: 1 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: 257 Length adjustment: 25 Effective length of query: 247 Effective length of database: 232 Effective search space: 57304 Effective search space used: 57304 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