Align cyclohexa-1,5-dienecarbonyl-CoA hydratase monomer (EC 4.2.1.100) (characterized)
to candidate BPHYT_RS28015 BPHYT_RS28015 enoyl-CoA hydratase
Query= metacyc::MONOMER-18320 (256 letters) >FitnessBrowser__BFirm:BPHYT_RS28015 Length = 382 Score = 70.1 bits (170), Expect = 6e-17 Identities = 58/194 (29%), Positives = 91/194 (46%), Gaps = 10/194 (5%) Query: 6 ILFEKKDKVATITLNVPNS-NWLTIPMMKEINEALMDVKKDPTIQLLVFDHAGDKAFCDG 64 ILF ++VA ITLN P + N L+ M++E+ + + D I LV AG K FC G Sbjct: 19 ILFRVVNRVAIITLNRPAALNALSHAMVRELAVLVEHCRTDDGIVALVLKGAGAKGFCAG 78 Query: 65 VDVADH---VPEKVDEMIDLFHGMFRNMAAMDVTS---VCLVNGRSLGGGCELMAFCDIV 118 DV + + F +R A+ V L++G ++GGG L + Sbjct: 79 GDVREVQRLAKNNDSRWLAFFVDEYRLDYALHTFPKPVVALLDGIAMGGGMGLGQGARLR 138 Query: 119 IASEKAKIGQPEINLAVFPPVAAAWFPKIMGLKKAMELILTGKIISAKEAEAIGLVNVVL 178 I +E++KI PE + P V A F +M + + + LTG +S +A + L ++ + Sbjct: 139 IVTERSKIAMPETRIGFLPDVGATRFLSVMPAELELYVGLTGATLSGADALRLQLADLCV 198 Query: 179 PVE---GFREAAQK 189 P E F E Q+ Sbjct: 199 PAEWLASFEERLQR 212 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: 186 Number of extensions: 9 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: 382 Length adjustment: 27 Effective length of query: 229 Effective length of database: 355 Effective search space: 81295 Effective search space used: 81295 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: 48 (23.1 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