Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate N515DRAFT_1164 N515DRAFT_1164 enoyl-CoA hydratase
Query= BRENDA::D3RXI0 (252 letters) >FitnessBrowser__Dyella79:N515DRAFT_1164 Length = 260 Score = 120 bits (300), Expect = 4e-32 Identities = 89/261 (34%), Positives = 134/261 (51%), Gaps = 10/261 (3%) Query: 1 MEYKKIKVEKDERVARIKIANPP-VNVLDMETMKEIISAIDEV---EGVDVIVFSGEG-K 55 M Y+ + + V I + P +N L+ +T+ E+ A + + V +V +G G K Sbjct: 1 MAYRNLDIGNRGAVRIITVNRPDKLNALNRDTLNELTLAFAQAAQDDAVRTVVLAGAGDK 60 Query: 56 SFSAGAEIKE---HFPDKAPEMIRWFTQLIDKVLRCKAITVAAVKGFALGGGFELAIACD 112 +F AGA+I E + P +A R +L+ + R VA ++GFALGGG ELA+AC Sbjct: 61 AFVAGADIAEMNGYTPVQAQGFSRAGQRLMSSIERLGKPVVARIQGFALGGGMELAMACH 120 Query: 113 FVLASKNAKLGVPEITLAHYPPV-AIALLPRMIGWKNAYELILTGEAITAERAFEIGLVN 171 +AS+ A+ G PEI L P L R+ G A EL LTG + A+RA+E+G+VN Sbjct: 121 LRVASEKARFGQPEINLGLIPGFGGTQRLLRLAGRGAALELCLTGAMVGAQRAYELGVVN 180 Query: 172 KVFEDENFEESVNDFVNSLLEKSSVALRLTKKALLFSTEKEYLSLFDVINDVYLSQLVKS 231 +V E +E+V+ + L + +A A+L E + + + + Sbjct: 181 RVVAPEALDETVDALADQLAASAPLAAAGILDAILQGGEMALDQGLEFETQAF-ALAFST 239 Query: 232 EDAVEGLKAFLEKRKPEWKGR 252 ED EG AFLEKRK E+KGR Sbjct: 240 EDMREGTTAFLEKRKAEFKGR 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: 150 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 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