Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate GFF929 HP15_908 enoyl-CoA hydratase/isomerase
Query= BRENDA::D3RXI0 (252 letters) >FitnessBrowser__Marino:GFF929 Length = 259 Score = 119 bits (298), Expect = 6e-32 Identities = 79/257 (30%), Positives = 140/257 (54%), Gaps = 12/257 (4%) Query: 6 IKVEKDERVARIKIANPPVNVLDMETM---KEIISAIDEVEGVDVIVFSGEGKSF-SAGA 61 I++EK +A + I NPP N +++ I+ ++E + +V +G+G+ F SAGA Sbjct: 5 IQLEKRGHIAVLTINNPPANTWTKDSLIALTNIVKELNEDRDIFALVMTGQGEKFYSAGA 64 Query: 62 EIKEHFPD----KAPEMIRWFTQLIDKVLRCKAITVAAVKGFALGGGFELAIACDFVLAS 117 ++K F D +A EM + F + + R + +++AAV G+A+GGG E A+ACD +A Sbjct: 65 DLKT-FADGDKARANEMGQLFGEAFSTLQRFRGVSIAAVNGYAMGGGLECAMACDIRIAE 123 Query: 118 KNAKLGVPEITLAHYPPV-AIALLPRMIGWKNAYELILTGEAITAERAFEIGLVNKVFED 176 ++A++ +PE + P LP ++G A +IL GE + A+ A IGLV +V Sbjct: 124 EHAQMALPEAGVGLLPCAGGTQNLPWLVGEGWAKRMILCGERVKADTALRIGLVEEVVPS 183 Query: 177 ENFEESVNDFVNSLLEKSSVALRLTKKALLFSTE-KEYLSLFDVINDVYLSQLVKSEDAV 235 + + ++S + K ++ + + + + + + ++++ +L +ED Sbjct: 184 GQGLDKALELAEMACQQSPSSTARCKTLVMSARDGRSHDDGWRMERELFV-ELFSTEDQK 242 Query: 236 EGLKAFLEKRKPEWKGR 252 EG+ AFLEKRKPEWK R Sbjct: 243 EGVNAFLEKRKPEWKNR 259 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: 157 Number of extensions: 12 Number of successful extensions: 5 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: 259 Length adjustment: 24 Effective length of query: 228 Effective length of database: 235 Effective search space: 53580 Effective search space used: 53580 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