Align Probable enoyl-CoA hydratase; EC 4.2.1.17 (characterized)
to candidate WP_015799170.1 AFER_RS09185 enoyl-CoA hydratase
Query= SwissProt::P94549 (258 letters) >NCBI__GCF_000023265.1:WP_015799170.1 Length = 257 Score = 167 bits (424), Expect = 2e-46 Identities = 101/240 (42%), Positives = 140/240 (58%), Gaps = 5/240 (2%) Query: 9 DQFVAVLTIHNPPANALSSRILEELSSCLDQCETDAGVRSIIIHGEGRFFSAGADIKEFT 68 D VA + + P ANALS +L EL++ E D R++++ G R F+AGADI EF Sbjct: 11 DAGVATVRLDRPKANALSGAVLAELAAAASDLERDLP-RAVVVTGGDRIFAAGADIAEFD 69 Query: 69 SLKGNEDSSLLAERGQQLMERIESFPKPIIAAIHGAALGGGLELAMACHIRIAAEDAKLG 128 +++ R + I + P+ +IAAI G ALGGGLELA+AC +R+A+ AKLG Sbjct: 70 ERPVGWETARAFHRA---LGAIAALPRVVIAAIEGYALGGGLELALACDLRVASSSAKLG 126 Query: 129 LPELNLGIIPGFAGTQRLPRYVGTAKALELIGSGEPISGKEALDLGLVSIGAKDEAEVIE 188 LPE++LG+IPG GTQRLPR VG A A L+ +GEP++ EAL +GLV + + E Sbjct: 127 LPEISLGLIPGGGGTQRLPRLVGLAVAKRLVLTGEPLTAAEALGVGLVD-RVVEPGQATE 185 Query: 189 KAKALAAKFAEKSPQTLASLLELLYSNKVYSYEGSLKLEAKRFGEAFESEDAKEGIQAFL 248 A+A A +FA LA L S E L LE F + F +EDA+ G+++FL Sbjct: 186 AARAWAQRFASGPLAALAFAKVALAEGTQGSLEEGLALEQALFAQVFTTEDARIGVRSFL 245 Lambda K H 0.315 0.134 0.366 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: 139 Number of extensions: 11 Number of successful extensions: 3 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: 258 Length of database: 257 Length adjustment: 24 Effective length of query: 234 Effective length of database: 233 Effective search space: 54522 Effective search space used: 54522 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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