Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate WP_012277951.1 SHAL_RS14880 enoyl-CoA hydratase
Query= BRENDA::D3RXI0 (252 letters) >NCBI__GCF_000019185.1:WP_012277951.1 Length = 269 Score = 115 bits (288), Expect = 9e-31 Identities = 74/244 (30%), Positives = 128/244 (52%), Gaps = 9/244 (3%) Query: 15 ARIKIANPPVNVLDMETMKEI---ISAIDEVEGVDVIVFSGEG-KSFSAGAEIK---EHF 67 A I + NPP N ++++E+ + A++E + V +V + EG K FSAGA++K + Sbjct: 25 AVISMNNPPANTWTAQSLQELKQKVLALNENKEVYALVITAEGDKFFSAGADLKLFADGD 84 Query: 68 PDKAPEMIRWFTQLIDKVLRCKAITVAAVKGFALGGGFELAIACDFVLASKNAKLGVPEI 127 A +M R+F + + + +++AA+ G+A+GGG E+A+ACD + + A++ +PE Sbjct: 85 KQNAADMARYFGEAFETLSTFHGVSIAAINGYAMGGGLEVALACDLRICEEQAQMALPEA 144 Query: 128 TLAHYPPV-AIALLPRMIGWKNAYELILTGEAITAERAFEIGLVNKVFEDENFEESVNDF 186 T+ P L ++G A +IL GE I AE+A +IGLV +V N + Sbjct: 145 TVGLLPCAGGTQNLTALVGEGWAKRMILCGERINAEKAEKIGLVEEVVVQGNAFNAAMAL 204 Query: 187 VNSLLEKSSVALRLTKKALLFSTEKEYLSLFDVINDVYLSQLVKSEDAVEGLKAFLEKRK 246 + +S +++ K+ + + + + Y + L +ED EG+ AFL KRK Sbjct: 205 AEKVANQSPSSVKACKQLVQAGRSMPRSQVLPLERE-YFANLFDTEDQAEGVSAFLNKRK 263 Query: 247 PEWK 250 WK Sbjct: 264 ANWK 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: 164 Number of extensions: 12 Number of successful extensions: 6 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: 269 Length adjustment: 24 Effective length of query: 228 Effective length of database: 245 Effective search space: 55860 Effective search space used: 55860 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