Align Probable enoyl-CoA hydratase; EC 4.2.1.17 (characterized)
to candidate WP_078430086.1 BK574_RS21830 enoyl-CoA hydratase
Query= SwissProt::P94549 (258 letters) >NCBI__GCF_002019605.1:WP_078430086.1 Length = 254 Score = 197 bits (501), Expect = 2e-55 Identities = 109/256 (42%), Positives = 160/256 (62%), Gaps = 6/256 (2%) Query: 1 MNAISLAVDQFVAVLTIHNPPANALSSRILEELSSCLDQCETDAGVRSIIIHGEG-RFFS 59 M + V+ + ++TI +PP NAL +++LEEL+ ++ D V +II G G + F Sbjct: 1 MAKVKYEVENQIGLITIDSPPVNALETQVLEELAEIVNNISEDVNV--VIITGAGNKAFV 58 Query: 60 AGADIKEFTSLKGNEDSSLLAERGQQLMERIESFPKPIIAAIHGAALGGGLELAMACHIR 119 AGADIK+F +L E L ++GQQ+ ++IE +P+IAA+ G ALGGGLELA+AC R Sbjct: 59 AGADIKDFPNLT-KETGIELVKKGQQIFQQIEDLDQPVIAAVDGFALGGGLELALACDFR 117 Query: 120 IAAEDAKLGLPELNLGIIPGFAGTQRLPRYVGTAKALELIGSGEPISGKEALDLGLVSIG 179 IA + ++ GLPE+ LG+IPG+ GTQRLPR +G+ KA +LI SGE +S +EAL++G+V Sbjct: 118 IATKRSQFGLPEVKLGVIPGYGGTQRLPRLIGSGKAKQLIFSGEFLSAEEALNVGIVE-- 175 Query: 180 AKDEAEVIEKAKALAAKFAEKSPQTLASLLELLYSNKVYSYEGSLKLEAKRFGEAFESED 239 E +E A+ A K A++ P + + + + E L EA FG E+ED Sbjct: 176 EVTEGSALEAAQKWAEKIAQRGPLAVRAAKKAVNEGLNQMLEEGLNTEATYFGSIAETED 235 Query: 240 AKEGIQAFLEKRKPQF 255 EG+ AF EKR+P+F Sbjct: 236 MNEGVAAFFEKREPKF 251 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: 166 Number of extensions: 13 Number of successful extensions: 5 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: 254 Length adjustment: 24 Effective length of query: 234 Effective length of database: 230 Effective search space: 53820 Effective search space used: 53820 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