Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate 5210229 Shew_2672 carnitinyl-CoA dehydratase (RefSeq)
Query= BRENDA::D3RXI0 (252 letters) >FitnessBrowser__PV4:5210229 Length = 261 Score = 111 bits (277), Expect = 2e-29 Identities = 81/264 (30%), Positives = 131/264 (49%), Gaps = 20/264 (7%) Query: 4 KKIKVEKDERVARIKIANPPVNVLDMET---MKEIISAIDEVEGVDVIVFSGEG-KSFSA 59 + + V ++ + I + P N +D +T M E+ A + + V + +G G + FSA Sbjct: 3 ESLHVTRNGSILEIVLDRPKANAIDAKTSYEMGEVFLAFRDDPELRVAIITGAGARFFSA 62 Query: 60 GAEIKEHFPDKAPEM------IRWFTQLIDKVLRCKAITVAAVKGFALGGGFELAIACDF 113 G ++K +AP+ T+L D +AAV G+A GGGFELA+A D Sbjct: 63 GWDLKAAAEGEAPDADFGPGGFAGLTELFD----LDKPVIAAVNGYAFGGGFELALAADL 118 Query: 114 VLASKNAKLGVPEITLAHYPPVAIAL-LPRMIGWKNAYELILTGEAITAERAFEIGLVNK 172 ++ + NA +PE L P L LP+++ EL++TG ++ A+ A G+VN+ Sbjct: 119 IVCADNASFALPEAKLGIVPDSGGMLRLPKLLPAPIVNELMMTGRSMDAQEALRWGVVNR 178 Query: 173 VFEDENFEESVNDFVNSLLEKSSVALRLTKKALL----FSTEKEYLSLFDVINDVYLSQL 228 V E E E+ + N + + + +AL K+ S E+ Y + Y S + Sbjct: 179 VVEQEALMETARELANEISQSAPLALAAIKEIYRETGELSVEQGYAHIRGGQLKHYPS-V 237 Query: 229 VKSEDAVEGLKAFLEKRKPEWKGR 252 + SEDA+EG AF EKR P W+G+ Sbjct: 238 LHSEDALEGPAAFAEKRDPVWQGK 261 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: 152 Number of extensions: 14 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: 261 Length adjustment: 24 Effective length of query: 228 Effective length of database: 237 Effective search space: 54036 Effective search space used: 54036 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