Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate WP_013076734.1 BTUS_RS14055 enoyl-CoA hydratase
Query= BRENDA::O87873 (258 letters) >NCBI__GCF_000092905.1:WP_013076734.1 Length = 258 Score = 94.0 bits (232), Expect = 3e-24 Identities = 76/246 (30%), Positives = 122/246 (49%), Gaps = 10/246 (4%) Query: 21 LRLARPKA-NIVDAAMIAAMRQALGEHLQAPALRAVLLDAEGPHFSFGASVDEHMPDQCA 79 + L RP+ N + ++A++R+AL Q +R+VLL G F G + P Sbjct: 15 ITLNRPEVLNALTDQVLASLREALIRAEQDEGVRSVLLTGAGKGFCAGLDLKSVDPGMLG 74 Query: 80 QM----LKSLHGLVREMLDSPVPILVALRGQCLGGGLEVAAAGNLLFAAPDAKFGQPEIR 135 ++ + + L+ +M P PIL A+ G G GL +A A +L A+ DA+F IR Sbjct: 75 RIDMHVRRDFNPLILKMQQLPKPILAAVGGVAAGAGLSLALAADLRIASEDARFVSAFIR 134 Query: 136 LGVFAPA-ASCLLPPRVGQACAEDLLWSGRSIDGAEGHRIGLID--VLAEDPEAAALRWF 192 +G+ + AS LP +G + A +L +G S+D + + GL++ V E E A+L W Sbjct: 135 IGLVPDSGASYFLPRLIGVSRAMELALTGESLDAEKALQAGLVNRVVPREQLEEASLAW- 193 Query: 193 DEHIARLSASSLRFAVRAARCDSVPRIKQKLDTVEALYLEELMASHDAVEGLKAFLEKRS 252 + +A A ++ R + + + LD EA Y S D EG++AFLEKR Sbjct: 194 AQQLAEGPAYAMALTKRMIYEGAAGSLAEALDR-EATYQGWAAGSADFTEGMQAFLEKRK 252 Query: 253 ANWENR 258 A ++ R Sbjct: 253 ARFQGR 258 Lambda K H 0.321 0.135 0.402 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: 136 Number of extensions: 10 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: 258 Length of database: 258 Length adjustment: 24 Effective length of query: 234 Effective length of database: 234 Effective search space: 54756 Effective search space used: 54756 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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