Align cyclohexa-1,5-dienecarbonyl-CoA hydratase monomer (EC 4.2.1.100) (characterized)
to candidate WP_004514138.1 GMET_RS08635 enoyl-CoA hydratase
Query= metacyc::MONOMER-18320 (256 letters) >NCBI__GCF_000012925.1:WP_004514138.1 Length = 260 Score = 130 bits (326), Expect = 4e-35 Identities = 88/262 (33%), Positives = 132/262 (50%), Gaps = 8/262 (3%) Query: 1 MGFNTILFEKKDKVATITLNVPNS-NWLTIPMMKEINEALMDVKKDPTIQLLVFDHAGDK 59 M F +L E D VAT+T+N P + N L ++ E+ A ++ DP ++++V AG+K Sbjct: 1 MEFKNLLIETADGVATLTVNRPQALNALNSEVLTELASAFYQLEYDPAVRVVVLTGAGEK 60 Query: 60 AFCDGVDVADHVPEKVDE----MIDLFHGMFRNMAAMDVTSVCLVNGRSLGGGCELMAFC 115 AF G D+ + E + H M M M + VNG +LGGG EL C Sbjct: 61 AFVAGADIKEMAAMSSFEGHQFALKGQHCMMA-MEKMKTPVIAAVNGFALGGGLELALGC 119 Query: 116 DIVIASEKAKIGQPEINLAVFPPVAAAW-FPKIMGLKKAMELILTGKIISAKEAEAIGLV 174 D + ASEKAK+G PE+ L + P +++G +A ELI TG++I+A +A+A G+V Sbjct: 120 DFIYASEKAKLGFPEVTLGIIPGFGGTQNLARLIGKNRANELIFTGRMIAADKAQAWGIV 179 Query: 175 NVVLPVEGFREAAQKFMADFTSKSRPVAMWARRAIMAGLNLDFLQALKASEIIYMQGCMA 234 N V E A++ A +A+ AI GLN+ + ++ Sbjct: 180 NEVFAPEELLVKAKETAAAIAGVGPLGVTYAKNAIANGLNMGKEDGFRYEASLF-GVLFG 238 Query: 235 TEDANEGLASFLEKRKPVFKDK 256 T D EG+ +F+EKRK VF K Sbjct: 239 TADQKEGMGAFVEKRKAVFTGK 260 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: 160 Number of extensions: 10 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: 256 Length of database: 260 Length adjustment: 24 Effective length of query: 232 Effective length of database: 236 Effective search space: 54752 Effective search space used: 54752 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