Align Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized)
to candidate GFF2524 PS417_12870 enoyl-CoA hydratase
Query= reanno::psRCH2:GFF2389 (257 letters) >FitnessBrowser__WCS417:GFF2524 Length = 270 Score = 132 bits (332), Expect = 7e-36 Identities = 80/267 (29%), Positives = 138/267 (51%), Gaps = 13/267 (4%) Query: 3 FETLLVDIQERVALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTGSAKAFA 62 + +V++ VA + +NRP+ +NA+N +E+ +E + +VL+G+ K F+ Sbjct: 4 YHAFVVELIGNVAHVQINRPEKINAMNAAFWTEIIDIFQWIEDTDAVRAVVLSGAGKHFS 63 Query: 63 AGADIKEMAELTYP------------QIYLDDFFADADRIATRRKPLIAAVAGYALGGGC 110 +G D+ +A + + + + A + + RKP++AAV GY +GG Sbjct: 64 SGIDLMMLASVANEFGKDVGRNARLLRRKILELQASFNAVDNCRKPVLAAVQGYCIGGAI 123 Query: 111 ELALLCDMIFAADNARFGQPEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAEA 170 +L CDM +AA+ A+F E+++G+ +G QRL R +G ++ TGRQ A EA Sbjct: 124 DLISACDMRYAAEGAQFSIKEIDIGMAADVGTLQRLPRIIGDGMLRELAYTGRQFGAEEA 183 Query: 171 ERAGLVARVFP-AESLLEETLKAARVIAEKSLPATMMIKESVNRAFETTLAEGIRFERRV 229 GLV RV+P +SLL ++ A IA KS A K ++ + T+ +G+ + Sbjct: 184 RSIGLVNRVYPDQDSLLAGVMEIAHEIAAKSPIAVTGTKAMISYMRDHTVNDGLEYVATW 243 Query: 230 FHAVFATADQKEGMAAFSEKRKPEFTN 256 A+ + D + +AA K+KPEF + Sbjct: 244 NAAMLQSNDLRVAIAAHMSKQKPEFVD 270 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: 128 Number of extensions: 5 Number of successful extensions: 3 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: 270 Length adjustment: 25 Effective length of query: 232 Effective length of database: 245 Effective search space: 56840 Effective search space used: 56840 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 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