Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate WP_058860024.1 AS188_RS15810 enoyl-CoA hydratase
Query= BRENDA::D3RXI0 (252 letters) >NCBI__GCF_001482365.1:WP_058860024.1 Length = 264 Score = 123 bits (309), Expect = 3e-33 Identities = 86/246 (34%), Positives = 132/246 (53%), Gaps = 8/246 (3%) Query: 12 ERVARIKIANPPV-NVLDMETMKEIISAIDEVE---GVDVIVFSGEG-KSFSAGAEIKEH 66 +R+A + + P V N L+ + I +A+D E VD +VF+G G K+F AGA+I + Sbjct: 17 DRIAVVTVNRPEVRNALNFGVLDGIEAALDAFERREDVDAVVFTGAGEKAFVAGADISQL 76 Query: 67 FPDKAPEMIRWFTQ-LIDKVLRCKAITVAAVKGFALGGGFELAIACDFVLASKNAKLGVP 125 + +R Q L D++ + T+AAV GFALGGG ELA++CD +A+ NA+ G+P Sbjct: 77 IGYTLQDGLRARMQRLYDRIQDLELPTIAAVNGFALGGGNELAMSCDIRIAAANARFGLP 136 Query: 126 EITLAHYPPV-AIALLPRMIGWKNAYELILTGEAITAERAFEIGLVNKVFEDENFEESVN 184 E L P L R++G A E+ILTG I AE A IGLV V E ++ + Sbjct: 137 ETNLGILPGAGGTQRLSRLVGLGRAQEMILTGRIIDAEEALRIGLVTSVVPAEELMDTAH 196 Query: 185 DFVNSLLEKSSVALRLTKKALLFSTEKEYLSLFDVINDVYLSQLVKSEDAVEGLKAFLEK 244 ++L K +A+RL K + E + + ++ + S L +++ EG AFLEK Sbjct: 197 ATARTILAKGPLAVRLAKLVVRNGAETDQRTGL-LLERLAQSLLYAADEKAEGASAFLEK 255 Query: 245 RKPEWK 250 R ++ Sbjct: 256 RPARFR 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: 145 Number of extensions: 11 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: 264 Length adjustment: 24 Effective length of query: 228 Effective length of database: 240 Effective search space: 54720 Effective search space used: 54720 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