Align Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized)
to candidate WP_035218954.1 G491_RS0114180 enoyl-CoA hydratase
Query= reanno::psRCH2:GFF2389 (257 letters) >NCBI__GCF_000429905.1:WP_035218954.1 Length = 260 Score = 223 bits (568), Expect = 3e-63 Identities = 121/256 (47%), Positives = 162/256 (63%), Gaps = 6/256 (2%) Query: 3 FETLLVDIQERVALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTGSAKAFA 62 ++ L V + + +A IT+NRPQA+NALN +I+EL A+ +L A+ + IV+TG+ KAF Sbjct: 4 YQDLEVTVADYIATITMNRPQAMNALNSNVIAELEAAVTELGANDDVRVIVITGAGKAFV 63 Query: 63 AGADIKEMAELTYPQIYLDDFFADADR----IATRRKPLIAAVAGYALGGGCELALLCDM 118 AGADIK+M L F A+ + I KP+IAA+ G+ALGGGCELAL CD Sbjct: 64 AGADIKQMNSLELQDFRA--FIANGQKAMYAIDLCEKPVIAAINGFALGGGCELALACDF 121 Query: 119 IFAADNARFGQPEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAEAERAGLVAR 178 A++ A+FG PEVNLG+ PG GGTQR R +G+ A +M TG +DAAEA R GLV Sbjct: 122 RVASEKAKFGFPEVNLGLFPGFGGTQRAPRFIGRGYASEMTFTGEMIDAAEALRVGLVNH 181 Query: 179 VFPAESLLEETLKAARVIAEKSLPATMMIKESVNRAFETTLAEGIRFERRVFHAVFATAD 238 V+PA+ L++ +K A+ IA K+ A K ++ A +TTL G+ FER VF T D Sbjct: 182 VYPADELMDSVMKIAKTIASKAPIAVARSKTAIKMAGDTTLEAGLAFERESMSMVFPTKD 241 Query: 239 QKEGMAAFSEKRKPEF 254 + EGM AF KRK EF Sbjct: 242 RAEGMDAFINKRKAEF 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: 174 Number of extensions: 5 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: 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