Align Probable enoyl-CoA hydratase; EC 4.2.1.17 (characterized)
to candidate WP_078430958.1 BK574_RS22580 enoyl-CoA hydratase
Query= SwissProt::P94549 (258 letters) >NCBI__GCF_002019605.1:WP_078430958.1 Length = 258 Score = 286 bits (733), Expect = 2e-82 Identities = 148/258 (57%), Positives = 193/258 (74%) Query: 1 MNAISLAVDQFVAVLTIHNPPANALSSRILEELSSCLDQCETDAGVRSIIIHGEGRFFSA 60 M IS+ V+Q +A +T++ PPANALSS +L+EL+ ++ E + V II+HGEGRFF+A Sbjct: 1 METISVKVEQQIATITLNRPPANALSSLLLQELAQAFNEVEHNEDVSVIILHGEGRFFAA 60 Query: 61 GADIKEFTSLKGNEDSSLLAERGQQLMERIESFPKPIIAAIHGAALGGGLELAMACHIRI 120 GADIKEFT+L+ + LA +GQ+L+ RIE+FPKP+IAAIHGAALGGGLE+AMACHIR+ Sbjct: 61 GADIKEFTTLESGNKFAELARKGQELLNRIEAFPKPVIAAIHGAALGGGLEIAMACHIRL 120 Query: 121 AAEDAKLGLPELNLGIIPGFAGTQRLPRYVGTAKALELIGSGEPISGKEALDLGLVSIGA 180 A ED LGLPEL LG+IPGFAGTQRLPR +G AKA ELI + EPI+G EAL LGL++ Sbjct: 121 ATEDTMLGLPELQLGLIPGFAGTQRLPRIIGKAKATELILTSEPITGSEALSLGLINSVY 180 Query: 181 KDEAEVIEKAKALAAKFAEKSPQTLASLLELLYSNKVYSYEGSLKLEAKRFGEAFESEDA 240 + A ++E+A LA K A+KS T+ LE L + ++ L+ EA+ FG A ES D+ Sbjct: 181 SERALMMEEAYKLAGKIAKKSRYTMKLALEALSYAQDSNFTEGLEKEAELFGFAGESHDS 240 Query: 241 KEGIQAFLEKRKPQFKGE 258 KEGIQAFLEKRKP+F+ + Sbjct: 241 KEGIQAFLEKRKPEFQNK 258 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: 207 Number of extensions: 8 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: 258 Length of database: 258 Length adjustment: 24 Effective length of query: 234 Effective length of database: 234 Effective search space: 54756 Effective search space used: 54756 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