Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_015799170.1 AFER_RS09185 enoyl-CoA hydratase
Query= BRENDA::P76082 (255 letters) >NCBI__GCF_000023265.1:WP_015799170.1 Length = 257 Score = 156 bits (395), Expect = 3e-43 Identities = 110/260 (42%), Positives = 145/260 (55%), Gaps = 30/260 (11%) Query: 1 MSELI-VSRQQR-VLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISV---CVITGN 55 MSE + V R V + L+RP A NAL+ A+L EL AAA+D + V+TG Sbjct: 1 MSEFVHVERDDAGVATVRLDRPKA-NALSGAVLA----ELAAAASDLERDLPRAVVVTGG 55 Query: 56 ARFFAAGADLNEMAEKDLAATLNDTRPQLWARLQAFNKPL----------IAAVNGYALG 105 R FAAGAD+ E D RP W +AF++ L IAA+ GYALG Sbjct: 56 DRIFAAGADIAEF----------DERPVGWETARAFHRALGAIAALPRVVIAAIEGYALG 105 Query: 106 AGCELALLCDVVVAGENARFGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITA 165 G ELAL CD+ VA +A+ GLPEI+LG++PG GGTQRL R VG ++A ++VL+GE +TA Sbjct: 106 GGLELALACDLRVASSSAKLGLPEISLGLIPGGGGTQRLPRLVGLAVAKRLVLTGEPLTA 165 Query: 166 QQAQQAGLVSDVFPSDLTLEYALQLASKMARHSPLALQAAKQALRQSQEVALQAGLAQER 225 +A GLV V E A A + A AL AK AL + + +L+ GLA E+ Sbjct: 166 AEALGVGLVDRVVEPGQATEAARAWAQRFASGPLAALAFAKVALAEGTQGSLEEGLALEQ 225 Query: 226 QLFTLLAATEDRHEGISAFL 245 LF + TED G+ +FL Sbjct: 226 ALFAQVFTTEDARIGVRSFL 245 Lambda K H 0.318 0.130 0.356 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: 127 Number of extensions: 8 Number of successful extensions: 2 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: 255 Length of database: 257 Length adjustment: 24 Effective length of query: 231 Effective length of database: 233 Effective search space: 53823 Effective search space used: 53823 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: 41 (21.8 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