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 RR42_RS11095 RR42_RS11095 3-hydroxyacyl-CoA dehydrogenase
Query= SwissProt::Q39TV7 (381 letters) >FitnessBrowser__Cup4G11:RR42_RS11095 Length = 693 Score = 63.9 bits (154), Expect = 1e-14 Identities = 60/198 (30%), Positives = 90/198 (45%), Gaps = 17/198 (8%) Query: 48 VAEGIYNAWIILDNPKQYNSYTTDMVKAIILAFRRASVDRSVNAVVFTGVGDKAFCTGGN 107 V +G+ A I LDNP N I+ RA D +V A+V TG G KAF G + Sbjct: 7 VQDGV--AVITLDNPP-VNGLGLSTRLGIVEGMTRALDDAAVKAIVITGAG-KAFSGGAD 62 Query: 108 TKEYAEYYAGNPQEYRQYMRLFNDMVSAILGCDKAVISRVNGMRIGGGQEIGMACDFSIA 167 +E+ N + Q L + ++ + G K V++ ++ + +GGG E+ + C++ +A Sbjct: 63 IREF------NTPKATQEPTL-HSVIKVVEGSSKPVVAAIHSVAMGGGLELALGCNYRVA 115 Query: 168 QDLANFGQAGPKHGSAAIGGATDFLPLMVGCEQAM---VSGTL--CEPFSAHKAARLGII 222 A K G G T LP ++G E A+ VSG E F+ K + Sbjct: 116 SKGAQIALPEVKLGLLPGAGGTQRLPRVIGLEAALNMIVSGNAIPSEKFAGTKLFDEIVD 175 Query: 223 CDVVPALKVGGK-FVANP 239 DV+PA K ANP Sbjct: 176 GDVLPAAVAFAKTAAANP 193 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: 652 Number of extensions: 40 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: 693 Length adjustment: 35 Effective length of query: 346 Effective length of database: 658 Effective search space: 227668 Effective search space used: 227668 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: 52 (24.6 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