Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate WP_035704417.1 BA79_RS18210 enoyl-CoA hydratase
Query= BRENDA::D3RXI0 (252 letters) >NCBI__GCF_000691145.1:WP_035704417.1 Length = 260 Score = 119 bits (299), Expect = 5e-32 Identities = 79/252 (31%), Positives = 129/252 (51%), Gaps = 10/252 (3%) Query: 10 KDERVARIKIANPP-VNVLDMETMKEIISAIDEVE---GVDVIVFSGEG-KSFSAGAEIK 64 +D+ + + + P N L ++EI I E++ + ++ +G G K F AGA++K Sbjct: 10 QDDYIGIMTLNRPAQANALSAAMLEEINQTIQEIKHDANIRCLLMTGAGAKVFCAGADLK 69 Query: 65 EH---FPDKAPEMIRWFTQLIDKVLRCKAITVAAVKGFALGGGFELAIACDFVLASKNAK 121 E +A E + Q + +A + G ALGGG ELA+ACD +A A Sbjct: 70 ERRLMTEQEAKEAVLTIQQTFTDIESLPVPVIAVINGHALGGGLELALACDLRIARAGAA 129 Query: 122 LGVPEITLAHYPPV-AIALLPRMIGWKNAYELILTGEAITAERAFEIGLVNKVFEDENFE 180 LG+PE LA P LPR+IG A E+I TG ++ AE A +IGL+ ++ ++ Sbjct: 130 LGLPETGLAILPGAGGTQRLPRLIGPGKAKEMIFTGTSLRAEEAVQIGLIERISTADSLM 189 Query: 181 ESVNDFVNSLLEKSSVALRLTKKALLFSTEKEYLSLFDVINDVYLSQLVKSEDAVEGLKA 240 + + +AL+ K+A+ S + + + + YL +L+ +ED +EGLKA Sbjct: 190 NDAITLAKQITKNGPIALKEAKQAIQSSLDHDLQTGLTKEYEAYL-RLIHTEDRLEGLKA 248 Query: 241 FLEKRKPEWKGR 252 F EKR P ++G+ Sbjct: 249 FQEKRTPHYRGK 260 Lambda K H 0.318 0.136 0.382 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: 147 Number of extensions: 9 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: 252 Length of database: 260 Length adjustment: 24 Effective length of query: 228 Effective length of database: 236 Effective search space: 53808 Effective search space used: 53808 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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