Align cyclohexa-1,5-dienecarbonyl-CoA hydratase monomer (EC 4.2.1.100) (characterized)
to candidate WP_086511176.1 BZY95_RS17490 enoyl-CoA hydratase-related protein
Query= metacyc::MONOMER-18320 (256 letters) >NCBI__GCF_002151265.1:WP_086511176.1 Length = 257 Score = 123 bits (308), Expect = 4e-33 Identities = 79/245 (32%), Positives = 123/245 (50%), Gaps = 6/245 (2%) Query: 14 VATITLNVPNS-NWLTIPMMKEINEALMDVKKDPTIQLLVFDHAGDKAFCDGVDVAD--- 69 V +T+N P + N L ++ E+ L +++K ++ L+ AG+KAF G D+ + Sbjct: 14 VVRLTINRPKALNALNSAVLTELEALLTELEKRSDLRALLITGAGEKAFVAGADITEMRT 73 Query: 70 HVPEKVDEMIDLFHGMFRNMAAMDVTSVCLVNGRSLGGGCELMAFCDIVIASEKAKIGQP 129 PE+ + + + V V LVNG LGGGCEL CD +AS+ A GQP Sbjct: 74 KTPEEARAFASQALRTIKRLETLPVPVVALVNGFCLGGGCELALACDWAVASDNAIFGQP 133 Query: 130 EINLAVFPPVAAAW-FPKIMGLKKAMELILTGKIISAKEAEAIGLVNVVLPVEGFREAAQ 188 E+ L V P P+ +G A++L+ TG+ I A+EA IGLVN V+P A+ Sbjct: 134 EVLLGVIPGFGGTQRLPRRVGPAMALDLVTTGRKIDAQEALRIGLVNRVMPQAELEAYAE 193 Query: 189 KFMADFTSKSRPVAMWARRAIMAGLNLDFLQALKASEIIYMQGCMATEDANEGLASFLEK 248 + A++A+ G++ D AL ++ G A + EG+++F+EK Sbjct: 194 ELTKQLAGNGPLAVRSAKQAVHDGMDQDLDSALALETSLFALG-FAGSEQKEGMSAFVEK 252 Query: 249 RKPVF 253 RKP F Sbjct: 253 RKPNF 257 Lambda K H 0.322 0.136 0.401 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: 140 Number of extensions: 8 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: 256 Length of database: 257 Length adjustment: 24 Effective length of query: 232 Effective length of database: 233 Effective search space: 54056 Effective search space used: 54056 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 Apr 09 2024. 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