Align Probable enoyl-CoA hydratase; EC 4.2.1.17 (characterized)
to candidate Echvi_4069 Echvi_4069 Enoyl-CoA hydratase/carnithine racemase
Query= SwissProt::P94549 (258 letters) >FitnessBrowser__Cola:Echvi_4069 Length = 261 Score = 188 bits (478), Expect = 9e-53 Identities = 106/239 (44%), Positives = 150/239 (62%), Gaps = 7/239 (2%) Query: 23 NALSSRILEELSSCLDQCETDAGVRSIIIHGEG-RFFSAGADIKEFTSLKGNE-DSSLLA 80 NA++ LEEL + ++ + +R +++ G G + F AGADI E L NE ++ + Sbjct: 27 NAINFDTLEELKNIFNEVSDNKSIRGVVLTGSGEKAFVAGADISEIAEL--NELNARKFS 84 Query: 81 ERGQQLMERIESFPKPIIAAIHGAALGGGLELAMACHIRIAAEDAKLGLPELNLGIIPGF 140 E GQ++ IES KP+IA ++G ALGGG EL+MACH+RIA +AK G PE+NLGIIPG+ Sbjct: 85 ENGQEVFSLIESCHKPVIAVVNGFALGGGCELSMACHMRIATSNAKFGQPEVNLGIIPGY 144 Query: 141 AGTQRLPRYVGTAKALELIGSGEPISGKEALDLGLVSIGAKDEAEVIEKAKALAAKFAEK 200 GTQRL +G KA EL+ +G+ + EA LGLV+ + +AE I+KA+ + K K Sbjct: 145 GGTQRLTFLIGRTKANELLMTGDMVDAAEAKALGLVNYVTQTKAEAIQKAEEILQKIMTK 204 Query: 201 SPQTLASLLELLYSNKVYSY-EGSLKLEAKRFGEAFESEDAKEGIQAFLEKRKPQFKGE 258 +P ++ +++ + N VYS E +EA F +SED EG AFLEKRKP FKGE Sbjct: 205 APLSIGMIIDCV--NAVYSNDENGYLIEANSFARCVKSEDYSEGTSAFLEKRKPNFKGE 261 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: 151 Number of extensions: 8 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: 261 Length adjustment: 24 Effective length of query: 234 Effective length of database: 237 Effective search space: 55458 Effective search space used: 55458 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 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