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 354228 BT4702 dihydroxynapthoic acid synthetase (NCBI ptt file)
Query= SwissProt::Q39TV7 (381 letters) >FitnessBrowser__Btheta:354228 Length = 274 Score = 94.4 bits (233), Expect = 3e-24 Identities = 59/184 (32%), Positives = 92/184 (50%), Gaps = 6/184 (3%) Query: 55 AWIILDNPKQYNSYTTDMVKAIILAFRRASVDRSVNAVVFTGVGDKAFCTGG--NTKEYA 112 A I ++ + N++T + A R + ++ +V TG GDKAFC+GG N K Sbjct: 25 ARITINRERYRNAFTPTTTAEMSDALRICREEADIDVIVITGAGDKAFCSGGDQNVKGRG 84 Query: 113 EYYAGNPQEYRQYMRLFNDMVSAILGCDKAVISRVNGMRIGGGQEIGMACDFSIAQDLAN 172 Y + + D+ I K VI+ VNG IGGG + + CD SIA + A Sbjct: 85 GYIGKDGVPRLSVL----DVQKQIRSIPKPVIAAVNGFAIGGGHVLHVVCDLSIASENAI 140 Query: 173 FGQAGPKHGSAAIGGATDFLPLMVGCEQAMVSGTLCEPFSAHKAARLGIICDVVPALKVG 232 FGQ GP+ GS G +L +VG ++A LC ++A +A +G++ VVP ++ Sbjct: 141 FGQTGPRVGSFDAGFGASYLARVVGQKKAREIWFLCRKYNAQEALDMGLVNKVVPLEQLE 200 Query: 233 GKFV 236 ++V Sbjct: 201 DEYV 204 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: 262 Number of extensions: 10 Number of successful extensions: 2 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: 274 Length adjustment: 28 Effective length of query: 353 Effective length of database: 246 Effective search space: 86838 Effective search space used: 86838 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