Align Probable enoyl-CoA hydratase; EC 4.2.1.17 (uncharacterized)
to candidate WP_111392290.1 CLV31_RS07705 enoyl-CoA hydratase/isomerase family protein
Query= curated2:Q52995 (257 letters) >NCBI__GCF_003253485.1:WP_111392290.1 Length = 260 Score = 112 bits (280), Expect = 8e-30 Identities = 84/260 (32%), Positives = 131/260 (50%), Gaps = 12/260 (4%) Query: 1 MSYETLLVETQGRVGLITLNRPQALNALNAVLMRELDAALKAFDADRAVGAIVLAGSEKA 60 M +T+L + ++G ITLNRP+ NAL+ L+ EL A AD++V ++L KA Sbjct: 1 MMEKTVLTHVENQLGFITLNRPEKRNALSPQLIGELSEAFAQMKADKSVKLVILQAKGKA 60 Query: 61 FAAGADIKEMQGL-------DFVDGYLADFLGGWEHVANARKPMIAAVSGFALGGGCELA 113 F AGAD++ +Q L + D + L + + K +IA V G AL GGC L Sbjct: 61 FCAGADLEYLQELQQFSYEENLEDSHRLKRL--FSQIYEFPKVVIAKVQGHALAGGCGLV 118 Query: 114 MMCDFIIASETAKFGQPEITLGVIPGMGGSQRLTRAVGKAKAMDLILTGRMMDAAEAERS 173 +CDF A A FG E +G +P + S L +G +A +L+++G M+ A +A+ Sbjct: 119 TVCDFAFADSEALFGYTEAKIGFVPAL-VSVFLAEQIGHYRAGELLISGEMISAKKADEF 177 Query: 174 GLVSRVVAPDRLLEEALGA-AEKIASFSLPAAMMAKEAVNRSL-ELTLAEGLRFERRLFQ 231 GL++ + L L A K+ + +M + + RSL ++T + L Sbjct: 178 GLITGYMDGASLDHWVLNEFALKLIRDNSAFSMGETKRLLRSLGKVTRDQALDAAAEANA 237 Query: 232 SLFATEDQKEGMAAFVAKRK 251 A ED K+G+AAF+ K K Sbjct: 238 RARAHEDCKKGIAAFLQKTK 257 Lambda K H 0.321 0.134 0.371 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: 159 Number of extensions: 10 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: 257 Length of database: 260 Length adjustment: 24 Effective length of query: 233 Effective length of database: 236 Effective search space: 54988 Effective search space used: 54988 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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