Align Probable enoyl-CoA hydratase; EC 4.2.1.17 (characterized)
to candidate CA265_RS20005 CA265_RS20005 enoyl-CoA hydratase
Query= SwissProt::P94549 (258 letters) >FitnessBrowser__Pedo557:CA265_RS20005 Length = 259 Score = 177 bits (449), Expect = 2e-49 Identities = 106/259 (40%), Positives = 159/259 (61%), Gaps = 6/259 (2%) Query: 2 NAISLAVDQFVAVLTIHNPPANALSSRILEELSSCLDQCETDAGVRSIIIHGEG-RFFSA 60 N IS + + V NAL+ L EL+ + VR +I+ G G + F A Sbjct: 5 NLISEIKENILYVTINREKALNALNKDTLAELADVIAFAGRTDEVRGVILTGAGEKAFVA 64 Query: 61 GADIKEFTSLKGNEDSSLLAERGQQLM-ERIESFPKPIIAAIHGAALGGGLELAMACHIR 119 GADIKEF+ G + L A+RG +L+ IE+ KP IAAI+G ALGGGLELAMACHIR Sbjct: 65 GADIKEFSDYSGKQGEEL-AKRGHELVFNAIENSSKPFIAAINGFALGGGLELAMACHIR 123 Query: 120 IAAEDAKLGLPELNLGIIPGFAGTQRLPRYVGTAKALELIGSGEPISGKEALDLGLVSIG 179 IA+++AKLGLPE+ LG+IPG+ GTQRL + VG KA+E+I + I+ +A +GLV++ Sbjct: 124 IASDNAKLGLPEVTLGLIPGYGGTQRLTQLVGKGKAIEMITTANMITATDAEKIGLVNV- 182 Query: 180 AKDEAEVIEKAKALAAKFAEKSPQTLASLLELLYSNKVYSYEGSLKLEAKRFGEAFESED 239 +A++I KA+ + +++P +++ ++ + ++ + E + FG+ FE+ D Sbjct: 183 VVPQADLIGKAEEMLNVIKQRAPLAISAAIKSVIAS--INNTNGYATEIEEFGKCFETAD 240 Query: 240 AKEGIQAFLEKRKPQFKGE 258 KEG+ AF+EKRK F G+ Sbjct: 241 FKEGVTAFVEKRKAIFTGK 259 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: 155 Number of extensions: 9 Number of successful extensions: 4 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: 259 Length adjustment: 24 Effective length of query: 234 Effective length of database: 235 Effective search space: 54990 Effective search space used: 54990 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