Align 3-hydroxybutyryl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate WP_090275047.1 BLU11_RS15865 3-hydroxyacyl-CoA dehydrogenase
Query= SwissProt::Q0AVM2 (279 letters) >NCBI__GCF_900105005.1:WP_090275047.1 Length = 504 Score = 218 bits (556), Expect = 2e-61 Identities = 113/279 (40%), Positives = 171/279 (61%), Gaps = 1/279 (0%) Query: 2 KIMVLGAGTMGAGIVQTAAQAGFEVVVRDIKQEFVDRGIAGIDKLLSKNVDKGRMTAEDK 61 +I V+GAG MG GI Q A +G +V++ D + E ++ +A LL + V KG+++ + Sbjct: 4 RIGVIGAGAMGRGIAQLFASSGQQVLLFDTRAEAIEDALAFNRNLLQRQVAKGKLSEAEF 63 Query: 62 AAVMGRISGTVDMGAAADCDLVIEAALEVMDIKKAIFKELDSICKPECILASNTSALSVT 121 AV R+ ++ DCDL+IEA +E++++K+ +F +L++I C+LA+NTS+LSVT Sbjct: 64 EAVNARMQPAAELEQLKDCDLIIEAIVEILEVKQKLFTDLEAIVSEACLLATNTSSLSVT 123 Query: 122 EIAAATGRADKVIGMHFFNPVPAMKLVEVIRGASTSQATYDAIKDLSVKMGKSPVEINEA 181 IAA R ++V G HFFNPV MK+VEV+RG+ T + + +L+ K G P + Sbjct: 124 RIAAGCNRPERVAGFHFFNPVTLMKIVEVVRGSRTDERYIQGLVELAEKAGHFPAITPDT 183 Query: 182 PGFVVNRLLIPMLNEGMYCLMEGVANAADIDTSMKFGAGHPMGPLALADMIGLDICLKIM 241 PGF+VN E + L EGVA A ID ++ G G MGP L D+ GLD+ +M Sbjct: 184 PGFLVNHAGRAFGTEALRMLSEGVATAQQIDRILRDGPGFRMGPFELFDLTGLDVSHAVM 243 Query: 242 ETLYKEF-GDPKYRPCPLLAKMVRANKLGRKTGEGFFAY 279 E++Y++F DP+Y P + + V A LGRKTG+GF+ Y Sbjct: 244 ESVYEQFYHDPRYTPSFIAGQRVAAGLLGRKTGQGFYRY 282 Score = 68.9 bits (167), Expect = 2e-16 Identities = 31/91 (34%), Positives = 52/91 (57%), Gaps = 1/91 (1%) Query: 175 PVE-INEAPGFVVNRLLIPMLNEGMYCLMEGVANAADIDTSMKFGAGHPMGPLALADMIG 233 PVE IN++PGFV+ RL+ + N G +G+A +D +++ G+P GPLA + G Sbjct: 402 PVEVINDSPGFVIQRLIASVTNLGCEIAQKGIATPETLDRAIQLALGYPKGPLAFGEHYG 461 Query: 234 LDICLKIMETLYKEFGDPKYRPCPLLAKMVR 264 ++ + +G+P+YRP P L + V+ Sbjct: 462 KQALFTVLNNMQATYGEPRYRPSPWLRRRVQ 492 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: 311 Number of extensions: 12 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: 504 Length adjustment: 30 Effective length of query: 249 Effective length of database: 474 Effective search space: 118026 Effective search space used: 118026 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 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