Align 3-hydroxybutyryl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate CA265_RS07715 CA265_RS07715 3-hydroxybutyryl-CoA dehydrogenase
Query= SwissProt::Q0AVM2 (279 letters) >FitnessBrowser__Pedo557:CA265_RS07715 Length = 297 Score = 290 bits (741), Expect = 3e-83 Identities = 149/279 (53%), Positives = 187/279 (67%), Gaps = 1/279 (0%) Query: 2 KIMVLGAGTMGAGIVQTAAQAGFEVVVRDIKQEFVDRGIAGIDKLLSKNVDKGRMTAEDK 61 +I V+G+GTMG GI T AQ ++V + DI Q+ +D+ I I K L + V KG +TA+ K Sbjct: 3 QIAVIGSGTMGNGIAHTFAQFNYQVNLIDINQDALDKAIQTITKNLDRQVAKGTLTADQK 62 Query: 62 AAVMGRISG-TVDMGAAADCDLVIEAALEVMDIKKAIFKELDSICKPECILASNTSALSV 120 A + I+ T DL++EAA E +D+K IF++LD ILASNTS++S+ Sbjct: 63 ATTLNNITTYTSTKDGVQQADLIVEAATENVDLKLKIFRDLDDYAPAHAILASNTSSISI 122 Query: 121 TEIAAATGRADKVIGMHFFNPVPAMKLVEVIRGASTSQATYDAIKDLSVKMGKSPVEINE 180 T+IAA T R DKVIGMHF NPVP MKLVEVIRG +TS T I LS + K PVE+N+ Sbjct: 123 TQIAAVTNRGDKVIGMHFMNPVPVMKLVEVIRGYATSDETTSTIMTLSQNLEKVPVEVND 182 Query: 181 APGFVVNRLLIPMLNEGMYCLMEGVANAADIDTSMKFGAGHPMGPLALADMIGLDICLKI 240 PGFV NR+L+PM+NE +Y L EGVA +IDT MK G HPMGPL LAD IGLD+CL I Sbjct: 183 YPGFVANRILMPMINEAIYTLYEGVAGVYEIDTVMKLGMAHPMGPLQLADFIGLDVCLAI 242 Query: 241 METLYKEFGDPKYRPCPLLAKMVRANKLGRKTGEGFFAY 279 ++ L FG+PKY PCPLL MV A K G KT EGF+ Y Sbjct: 243 LKVLNDGFGNPKYAPCPLLVNMVAAGKKGVKTSEGFYKY 281 Lambda K H 0.321 0.137 0.389 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: 256 Number of extensions: 8 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: 279 Length of database: 297 Length adjustment: 26 Effective length of query: 253 Effective length of database: 271 Effective search space: 68563 Effective search space used: 68563 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 (21.8 bits) S2: 47 (22.7 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