Align cyclohexa-1,5-dienecarbonyl-CoA hydratase monomer (EC 4.2.1.100) (characterized)
to candidate WP_011383294.1 AMB_RS04340 enoyl-CoA hydratase
Query= metacyc::MONOMER-18320 (256 letters) >NCBI__GCF_000009985.1:WP_011383294.1 Length = 261 Score = 108 bits (271), Expect = 8e-29 Identities = 78/256 (30%), Positives = 129/256 (50%), Gaps = 8/256 (3%) Query: 5 TILFEKKDK-VATITLNVPNS-NWLTIPMMKEINEALMDVKKDPTIQLLVFDHAGDKAFC 62 TIL + + VAT+TLN P + N L++ +M E++ L + +DP ++++V A AFC Sbjct: 6 TILLRRDEAGVATLTLNRPEARNALSVALMSELDSELARIARDPAVRVVVLA-ANGPAFC 64 Query: 63 DGVDVAD-HVPEKVDEMIDLFHGMFRNMAA---MDVTSVCLVNGRSLGGGCELMAFCDIV 118 G D+ + + DE+ +F R M A + + V+ + GC+L+A CD+ Sbjct: 65 AGHDLKEMRALQGRDEVAAVFALCSRVMTAIVRLPQPVIAKVHAMATAAGCQLVASCDLA 124 Query: 119 IASEKAKIGQPEINLAVFPPVAAAWFPKIMGLKKAMELILTGKIISAKEAEAIGLVNVVL 178 A+ +AK P +N+ +F + +G K+AME++L+G+ I+A AE GLVN V+ Sbjct: 125 YAATEAKFATPGVNIGLFCSTPMVALSRGVGRKQAMEMLLSGRPINAGTAERWGLVNHVV 184 Query: 179 PVEGFREAAQKFMADFTSKSRPVAMWARRAIMAGLNLDFLQALKASEIIYMQGCMATEDA 238 E SKS + A L + A + + + +A DA Sbjct: 185 AAEALDSEVASMARLIASKSAHTLKVGKEAFYRQLEMGLDDAYALASKVMTENMLAM-DA 243 Query: 239 NEGLASFLEKRKPVFK 254 EG+ +FLEKR PV++ Sbjct: 244 AEGIDAFLEKRPPVWR 259 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: 152 Number of extensions: 9 Number of successful extensions: 2 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: 261 Length adjustment: 24 Effective length of query: 232 Effective length of database: 237 Effective search space: 54984 Effective search space used: 54984 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 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