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 PfGW456L13_2984 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17)
Query= SwissProt::Q39TV7 (381 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2984 Length = 257 Score = 74.7 bits (182), Expect = 3e-18 Identities = 60/175 (34%), Positives = 84/175 (48%), Gaps = 12/175 (6%) Query: 57 IILDNPKQYNSYTTDMVKAIILAFRRASVDRSVNAVVFTGVGDKAFCTGGNTKEYAEYYA 116 I L+ P+ N+ +V + A D ++ +V TG KAF G + KE AE Sbjct: 17 ITLNRPQALNALNAQIVSELNQALDGFEADSNIGCIVLTG-SKKAFAAGADIKEMAELTY 75 Query: 117 GNPQEYRQYMRLFNDMVSAILGCDKAVISRVNGMRIGGGQEIGMACDFSIAQDLANFGQA 176 PQ Y LF+D + K +I+ VNG +GGG E+ + CDF +A D A FGQ Sbjct: 76 --PQIYID--DLFSDS-DRVANRRKPIIAAVNGFALGGGCELALMCDFILAGDNARFGQP 130 Query: 177 GPKHGSAAIGGATDFLPLMVGCEQAM---VSGTLCEPFSAHKAARLGIICDVVPA 228 G G T L VG +AM +SG L + A +A R GI+ +VP+ Sbjct: 131 EINLGVLPGMGGTQRLTRAVGKAKAMEMCLSGRLID---AVEAERCGIVARIVPS 182 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: 230 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: 381 Length of database: 257 Length adjustment: 27 Effective length of query: 354 Effective length of database: 230 Effective search space: 81420 Effective search space used: 81420 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