Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate WP_086511947.1 BZY95_RS21580 enoyl-CoA hydratase-related protein
Query= BRENDA::O87873 (258 letters) >NCBI__GCF_002151265.1:WP_086511947.1 Length = 298 Score = 95.1 bits (235), Expect = 1e-24 Identities = 64/184 (34%), Positives = 96/184 (52%), Gaps = 7/184 (3%) Query: 10 VWLERDGSLLRLRLARPKANIVDAAMIAAMRQALGEHLQAPALRAVLLDAEGPHFSFGAS 69 V L R G+ + L P N + A+ + + AL L+ P + +LL + G FS GA Sbjct: 5 VTLTRHGNCGLITLFSPPVNALSQAVRSGLVAALDAALEDPQVAWILLQSGGRCFSAGAD 64 Query: 70 VDEHMPDQCAQMLKSLHGLVREMLDSPVPILVALRGQCLGGGLEVAAAGNLLFAAPDAKF 129 + E + +L + + DSP P++ L G LGGGLE+A A + AAPDA+F Sbjct: 65 IKEFGKPPQSPVLPEVIDAIE---DSPKPVVAWLHGVSLGGGLELAMACHYRLAAPDARF 121 Query: 130 GQPEIRLGVFAPAASC-LLPPRVGQACAEDLLWSGRSIDGAEGHRIGLIDVLAED---PE 185 G PE++LG+ A LP +G A +++ SG I + H +GL+D +A+ PE Sbjct: 122 GLPEVKLGLIPGAGGTQRLPRLIGLEAALEMILSGEPIGTRQAHELGLVDGVADQGHTPE 181 Query: 186 AAAL 189 AA L Sbjct: 182 AARL 185 Lambda K H 0.321 0.135 0.402 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: 221 Number of extensions: 9 Number of successful extensions: 1 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: 258 Length of database: 298 Length adjustment: 25 Effective length of query: 233 Effective length of database: 273 Effective search space: 63609 Effective search space used: 63609 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