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 WP_111606238.1 DK187_RS04960 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase
Query= SwissProt::Q39TV7 (381 letters) >NCBI__GCF_003259225.1:WP_111606238.1 Length = 263 Score = 82.0 bits (201), Expect = 2e-20 Identities = 61/181 (33%), Positives = 84/181 (46%), Gaps = 4/181 (2%) Query: 47 SVAEGIYNAWIILDNPKQYNSYTTDMVKAIILAFRRASVDRSVNAVVFTGVGDKAFCTGG 106 SV G+ A + L+ PK NS+ M + A + A D+ V A+V T G + FC G Sbjct: 9 SVDSGV--ALLSLNRPKALNSFNEAMHLEVQQALKSALKDKQVRALVLTAEG-RGFCAGQ 65 Query: 107 NTKEY-AEYYAGNPQEYRQYMRLFNDMVSAILGCDKAVISRVNGMRIGGGQEIGMACDFS 165 + + + A +P R +N ++ + VI VNG+ G G I +ACD Sbjct: 66 DLSDRNVDPNAASPDLGISIERFYNPLIKQLQAFPMPVICAVNGVAAGAGANIPLACDLV 125 Query: 166 IAQDLANFGQAGPKHGSAAIGGATDFLPLMVGCEQAMVSGTLCEPFSAHKAARLGIICDV 225 IA A F QA K G G T FLP ++G +A L EP A KA G+I V Sbjct: 126 IAARSAKFIQAFCKIGLIPDSGGTWFLPRLIGMAKAKELALLGEPLMAEKALEWGMIYKV 185 Query: 226 V 226 V Sbjct: 186 V 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: 225 Number of extensions: 7 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: 263 Length adjustment: 27 Effective length of query: 354 Effective length of database: 236 Effective search space: 83544 Effective search space used: 83544 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 24 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