Align Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized)
to candidate WP_068863803.1 I603_RS07850 enoyl-CoA hydratase
Query= reanno::psRCH2:GFF2389 (257 letters) >NCBI__GCF_001677335.1:WP_068863803.1 Length = 264 Score = 267 bits (682), Expect = 2e-76 Identities = 144/264 (54%), Positives = 184/264 (69%), Gaps = 7/264 (2%) Query: 1 MTFETLLVDIQER----VALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTG 56 MT+ET+ + V L+T+NRPQALNALN +++ EL A +AD C +LTG Sbjct: 1 MTYETITAETDAHGTKGVTLLTINRPQALNALNSKVLEELIDAFAAYQADATQLCAILTG 60 Query: 57 SA-KAFAAGADIKEMAELTYPQIYLDDFFAD--ADRIATRRKPLIAAVAGYALGGGCELA 113 S KAFAAGADIKEM+E YLDDFF+ ++ + RKP IAAV G+ALGGGCELA Sbjct: 61 SGDKAFAAGADIKEMSEKPAADFYLDDFFSPWTSEIVKKTRKPWIAAVNGFALGGGCELA 120 Query: 114 LLCDMIFAADNARFGQPEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAEAERA 173 ++ D I A+D A+FGQPE+ LGV PG+GG+QRLTRA+GK+K+M+MCLTGR M A EAER+ Sbjct: 121 MMADFIIASDKAKFGQPEIKLGVAPGMGGSQRLTRAIGKSKSMEMCLTGRMMGAEEAERS 180 Query: 174 GLVARVFPAESLLEETLKAARVIAEKSLPATMMIKESVNRAFETTLAEGIRFERRVFHAV 233 LVARV P + L+ ETLK A IA AT+ KE VN AFE TL +G+ ERR+F + Sbjct: 181 NLVARVVPHDELIAETLKTAATIAAMPPMATIANKEMVNSAFEMTLDQGLIVERRIFQIL 240 Query: 234 FATADQKEGMAAFSEKRKPEFTNR 257 A+ D+ EGMAAF EKR+ ++ R Sbjct: 241 TASEDKAEGMAAFIEKREGQWKGR 264 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: 197 Number of extensions: 8 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: 264 Length adjustment: 25 Effective length of query: 232 Effective length of database: 239 Effective search space: 55448 Effective search space used: 55448 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