Align 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase; 6-OCH-CoA hydrolase; 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase; EC 3.7.1.21 (characterized)
to candidate GFF3595 PGA1_c36500 enoyl-CoA hydratase/isomerase
Query= SwissProt::Q39TV7 (381 letters) >FitnessBrowser__Phaeo:GFF3595 Length = 258 Score = 80.5 bits (197), Expect = 5e-20 Identities = 60/183 (32%), Positives = 87/183 (47%), Gaps = 21/183 (11%) Query: 57 IILDNPKQYNSYTTDMVKAIILAFRRASVDRSVNAVVFTGVGDKAFCTGGNTKE-----Y 111 I L+ P+ N+ ++++ + A A V ++ TG +KAF G + KE + Sbjct: 17 IKLNRPEALNALNSELLSELCTALEEADASDKVRCIILTG-SEKAFAAGADIKEMSDKSF 75 Query: 112 AEYYAGNPQEYRQYMRLF---NDMVSAILGCDKAVISRVNGMRIGGGQEIGMACDFSIAQ 168 E ++ N LF ND +SAI K +I+ V G +GGG E+ M CDF IA Sbjct: 76 TEVFSTN---------LFAGVNDRISAIR---KPIIAAVAGYALGGGCELAMLCDFIIAA 123 Query: 169 DLANFGQAGPKHGSAAIGGATDFLPLMVGCEQAMVSGTLCEPFSAHKAARLGIICDVVPA 228 D A FGQ G A G T L VG ++M +A +A R G++ VVPA Sbjct: 124 DTAKFGQPEINLGVIAGIGGTQRLTRFVGKSKSMDMNLTGRFMTAEEAERAGLVSRVVPA 183 Query: 229 LKV 231 K+ Sbjct: 184 KKL 186 Lambda K H 0.318 0.135 0.403 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: 218 Number of extensions: 5 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: 381 Length of database: 258 Length adjustment: 27 Effective length of query: 354 Effective length of database: 231 Effective search space: 81774 Effective search space used: 81774 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 (21.7 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