Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate 3610342 Dshi_3723 Enoyl-CoA hydratase/isomerase (RefSeq)
Query= BRENDA::D3RXI0 (252 letters) >FitnessBrowser__Dino:3610342 Length = 267 Score = 127 bits (319), Expect = 2e-34 Identities = 83/252 (32%), Positives = 131/252 (51%), Gaps = 6/252 (2%) Query: 5 KIKVEKDERVARIKIANPPVNVLDMETMKEI---ISAIDEVEGVDVIVFSGEGKSFSAGA 61 +I+V+ + I + P+NV+ M+ ++ A+D + V VIV EG+ FS+G Sbjct: 18 RIEVDAEAERGDIVLERAPMNVISMDQRDQLRAAFEALDADDAVRVIVLRAEGEHFSSGG 77 Query: 62 EIKEHFPDKAPEMIRWFTQLIDKVLRCKAITVAAVKGFALGGGFELAIACDFVLASKNAK 121 I F D +PE + + RC +AA KG+ G GFE+++ACDF +A+K+ Sbjct: 78 YI-HGFLDASPEHVSHLADNVAAPWRCAKPVIAANKGYTFGVGFEISLACDFRIAAKSTF 136 Query: 122 LGVPEITLAHYP-PVAIALLPRMIGWKNAYELILTGEAITAERAFEIGLVNKVFEDENFE 180 +PE L P A L +IG ++++ I+ ++AF+ G+ ++ ED+ E Sbjct: 137 YALPEQKLGQIPGSGGSARLQALIGLARTKDVVMRSRRISGQQAFDWGIAVELVEDDKLE 196 Query: 181 ESVNDFVNSLLEKSSVALRLTKKALLFSTEKEYLSLFDVINDVYLSQLVKSEDAVEGLKA 240 E+ VN L S +A R KK L S + ++ Y S+L +SED EG+KA Sbjct: 197 EATAKLVNELRSFSPMAQRTAKKLLNDSENATVATGIELEGHCY-SRLRQSEDFAEGVKA 255 Query: 241 FLEKRKPEWKGR 252 F EKRKP + GR Sbjct: 256 FHEKRKPTFVGR 267 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: 149 Number of extensions: 8 Number of successful extensions: 4 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: 267 Length adjustment: 24 Effective length of query: 228 Effective length of database: 243 Effective search space: 55404 Effective search space used: 55404 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 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