Align 3-hydroxybutyryl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate BPHYT_RS06760 BPHYT_RS06760 3-hydroxyacyl-CoA dehydrogenase
Query= SwissProt::Q0AVM2 (279 letters) >FitnessBrowser__BFirm:BPHYT_RS06760 Length = 521 Score = 216 bits (551), Expect = 6e-61 Identities = 112/278 (40%), Positives = 166/278 (59%), Gaps = 1/278 (0%) Query: 3 IMVLGAGTMGAGIVQTAAQAGFEVVVRDIKQEFVDRGIAGIDKLLSKNVDKGRMTAEDKA 62 I ++G G MG GI Q AA AG V + D + + + +K KG++ Sbjct: 11 IGIVGTGAMGRGIAQIAALAGLTVRLYDTNPAAIGAARDYLAETFAKLTAKGKLDQARSL 70 Query: 63 AVMGRISGTVDMGAAADCDLVIEAALEVMDIKKAIFKELDSICKPECILASNTSALSVTE 122 A + +SG +G A CDLV+EA +E +D+K+A+F+EL+++ C+LASNTS+LS+T Sbjct: 71 AALANVSGAQSIGELAGCDLVVEAIVEKLDVKQALFRELETVVSGRCVLASNTSSLSITA 130 Query: 123 IAAATGRADKVIGMHFFNPVPAMKLVEVIRGASTSQATYDAIKDLSVKMGKSPVEINEAP 182 IAA +V+G HFFNPVP MK+VEVI G + A DA+ +L+ +MG +PV + P Sbjct: 131 IAAGCSDPSRVVGYHFFNPVPLMKVVEVIDGLRSDPAAGDALMNLARRMGHTPVRAKDMP 190 Query: 183 GFVVNRLLIPMLNEGMYCLMEGVANAADIDTSMKFGAGHPMGPLALADMIGLDICLKIME 242 GF+VN M EG+ EGVA+ ADID ++ AG +GP L D+ LD+ +ME Sbjct: 191 GFIVNHAGRGMNTEGLRVAGEGVASFADIDRIVREQAGFRLGPFELLDLTALDVSHPVME 250 Query: 243 TLYKEF-GDPKYRPCPLLAKMVRANKLGRKTGEGFFAY 279 ++Y +F +P++ P P+ + +GRKTGEGF+ Y Sbjct: 251 SIYHQFYEEPRFTPSPITGTRLAGGLIGRKTGEGFYRY 288 Score = 72.4 bits (176), Expect = 2e-17 Identities = 38/132 (28%), Positives = 65/132 (49%) Query: 130 ADKVIGMHFFNPVPAMKLVEVIRGASTSQATYDAIKDLSVKMGKSPVEINEAPGFVVNRL 189 A +V+ + P+ + ++ +T++ D L G I ++ GFV R+ Sbjct: 365 ATRVVAIDALFPLVGAQRRTLMTTPATTRTARDTAHALFAADGVPVTVIRDSTGFVAQRV 424 Query: 190 LIPMLNEGMYCLMEGVANAADIDTSMKFGAGHPMGPLALADMIGLDICLKIMETLYKEFG 249 + ++N G + +A DID ++ G G+P GPL L D +G L I+ ++ G Sbjct: 425 VATIVNIGCDIAQKQIATPQDIDLAVTLGLGYPRGPLGLGDALGSTTILTILRNMFSVLG 484 Query: 250 DPKYRPCPLLAK 261 DP+YRP P LA+ Sbjct: 485 DPRYRPSPWLAR 496 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: 376 Number of extensions: 20 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 279 Length of database: 521 Length adjustment: 30 Effective length of query: 249 Effective length of database: 491 Effective search space: 122259 Effective search space used: 122259 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: 50 (23.9 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