Align Probable enoyl-CoA hydratase; EC 4.2.1.17 (characterized)
to candidate WP_011842152.1 RSPH17029_RS16015 enoyl-CoA hydratase/isomerase family protein
Query= SwissProt::P94549 (258 letters) >NCBI__GCF_000015985.1:WP_011842152.1 Length = 655 Score = 145 bits (366), Expect = 2e-39 Identities = 83/183 (45%), Positives = 113/183 (61%), Gaps = 9/183 (4%) Query: 12 VAVLTIHNPPANALSSRILEELSSCLDQCETDAGVRSIIIHGEGRFFSAGADIKEFTSLK 71 +A+LT+ NPP NAL + + L++ + E D VR++++ EGR F GADI EF Sbjct: 14 IALLTLANPPVNALGLAVRQRLTALTAELEADESVRAVVLTAEGRVFVGGADIAEF---- 69 Query: 72 GNEDSSLLAERGQQLMERIESFPKPIIAAIHGAALGGGLELAMACHIRIAAEDAKLGLPE 131 D A ++ IE+ KP IAA++GAALGGG ELA+ CH RI A+ A+LGLPE Sbjct: 70 ---DRPPEAPHLPDVIAAIEASRKPWIAALNGAALGGGAELALGCHYRIFADTARLGLPE 126 Query: 132 LNLGIIPGFAGTQRLPRYVGTAKALELIGSGEPISGKEALDLGLVSIGAKDEAEVIEKAK 191 +LG+IPG GTQRLPR +G A A+E+I +G +S EA + GL A E+I +A Sbjct: 127 TSLGLIPGAGGTQRLPRRIGLAPAIEVITAGRTLSAAEAREAGLADRIA--AGELIPEAL 184 Query: 192 ALA 194 A A Sbjct: 185 AFA 187 Score = 28.5 bits (62), Expect = 4e-04 Identities = 34/123 (27%), Positives = 52/123 (42%), Gaps = 18/123 (14%) Query: 85 QLMERIESFPKPIIAAIHGAALGGGLELAMACHIRIAAEDAKLGLPELNLGIIPGFAGTQ 144 Q+M+ +E P +AA L G+ LA A+LG + G GF G + Sbjct: 433 QVMKLLEIVP---LAATAPRILATGVALA-----------ARLGKIPVQAGNGEGFIGNR 478 Query: 145 RLPRYVGTAKALELIGS--GEPISGKEALDLGLVSIGAKDEA--EVIEKAKALAAKFAEK 200 L RY A+AL L G+ E A LG+ +D A ++ +A+ A + Sbjct: 479 ILKRYRAEAEALLLAGATPTEIDEAMRAFGLGMGPFEMQDMAGLDIAFRAREAARALGQD 538 Query: 201 SPQ 203 P+ Sbjct: 539 LPE 541 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: 328 Number of extensions: 17 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 258 Length of database: 655 Length adjustment: 31 Effective length of query: 227 Effective length of database: 624 Effective search space: 141648 Effective search space used: 141648 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: 50 (23.9 bits)
This GapMind analysis is from Apr 10 2024. 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