Align cyclohexa-1,5-dienecarbonyl-CoA hydratase monomer (EC 4.2.1.100) (characterized)
to candidate WP_058930224.1 AU252_RS07800 enoyl-CoA hydratase
Query= metacyc::MONOMER-18320 (256 letters) >NCBI__GCF_001484605.1:WP_058930224.1 Length = 258 Score = 149 bits (377), Expect = 4e-41 Identities = 94/255 (36%), Positives = 138/255 (54%), Gaps = 7/255 (2%) Query: 3 FNTILFEKKDKVATITLNVPNS-NWLTIPMMKEINEALMDVKKDPTIQLLVFDHAGDKAF 61 + IL E++ +V +TLN P + N L M ++ A+ + DP + +V KAF Sbjct: 4 YTNILVEQRGRVGLVTLNRPEALNALDKATMDQLVAAVTAMDADPGVGAVVIT-GSSKAF 62 Query: 62 CDGVDVADHVPEKVDEMI--DLFHGMFRNMAAMDVTSVCLVNGRSLGGGCELMAFCDIVI 119 G D+ + + +M D F G + + + + + V+G +LGGGCEL CD +I Sbjct: 63 AAGADIKEMASQGYMDMYAADWFRG-WEDFTRLRIPVIAAVSGFALGGGCELAMMCDFII 121 Query: 120 ASEKAKIGQPEINLAVFPPVAAAW-FPKIMGLKKAMELILTGKIISAKEAEAIGLVNVVL 178 A + AK GQPEINL V P + + + +G KAM++ILTG+ I A+EAE GLV+ V+ Sbjct: 122 AGDNAKFGQPEINLGVLPGMGGSQRLTRAVGKAKAMDMILTGRFIGAEEAERSGLVSRVV 181 Query: 179 PVEGFREAAQKFMADFTSKSRPVAMWARRAIMAGLNLDFLQALKASEIIYMQGCMATEDA 238 P E E A K SKS+PVAM A+ A+ A Q + I+ A+ED Sbjct: 182 PAENVVEEALKAAEVIASKSKPVAMLAKEAVNAAFETGLAQGVLFERRIF-HSLFASEDQ 240 Query: 239 NEGLASFLEKRKPVF 253 EG+A+F EKR+P F Sbjct: 241 KEGMAAFTEKRQPEF 255 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: 177 Number of extensions: 10 Number of successful extensions: 3 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: 258 Length adjustment: 24 Effective length of query: 232 Effective length of database: 234 Effective search space: 54288 Effective search space used: 54288 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