Align Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized)
to candidate WP_085770649.1 B1812_RS05255 enoyl-CoA hydratase
Query= reanno::psRCH2:GFF2389 (257 letters) >NCBI__GCF_002117405.1:WP_085770649.1 Length = 257 Score = 347 bits (890), Expect = e-100 Identities = 170/257 (66%), Positives = 209/257 (81%) Query: 1 MTFETLLVDIQERVALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTGSAKA 60 MTF+T+ ++ R ALI LNRP+ALNALN +LI+EL+ AL E+DP+IGC+VLTGS KA Sbjct: 1 MTFKTIEIERHGRAALIRLNRPEALNALNSELIAELDSALSDFESDPEIGCVVLTGSEKA 60 Query: 61 FAAGADIKEMAELTYPQIYLDDFFADADRIATRRKPLIAAVAGYALGGGCELALLCDMIF 120 FAAGADIKEM + + + L++F D +A RKP+IAAV+G+ALGGGCELA++CD I Sbjct: 61 FAAGADIKEMRDKNFAEALLENFLGRWDTVARARKPIIAAVSGFALGGGCELAMMCDFIL 120 Query: 121 AADNARFGQPEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAEAERAGLVARVF 180 A+++A+FGQPE+ LGV+PG GGTQRLTRAVGKAKAMD+CLTGR MDA EAERAGLVARV Sbjct: 121 ASESAQFGQPEIKLGVMPGAGGTQRLTRAVGKAKAMDLCLTGRMMDAQEAERAGLVARVL 180 Query: 181 PAESLLEETLKAARVIAEKSLPATMMIKESVNRAFETTLAEGIRFERRVFHAVFATADQK 240 PA LL E +K ++ IA S PA + +KE+VNRAFET+LAEG+RFERR FHA+FAT DQK Sbjct: 181 PAAELLPEAIKTSQRIAAMSAPAVLSVKEAVNRAFETSLAEGVRFERRAFHALFATHDQK 240 Query: 241 EGMAAFSEKRKPEFTNR 257 EGMAAF EKR P+F NR Sbjct: 241 EGMAAFIEKRPPQFQNR 257 Lambda K H 0.321 0.135 0.375 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: 241 Number of extensions: 7 Number of successful extensions: 1 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: 257 Length adjustment: 24 Effective length of query: 233 Effective length of database: 233 Effective search space: 54289 Effective search space used: 54289 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 Apr 09 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