Align 3-hydroxybutyryl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate WP_051301816.1 A3GO_RS22465 3-hydroxyacyl-CoA dehydrogenase
Query= SwissProt::Q0AVM2 (279 letters) >NCBI__GCF_000428045.1:WP_051301816.1 Length = 525 Score = 216 bits (550), Expect = 8e-61 Identities = 115/276 (41%), Positives = 167/276 (60%), Gaps = 1/276 (0%) Query: 5 VLGAGTMGAGIVQTAAQAGFEVVVRDIKQEFVDRGIAGIDKLLSKNVDKGRMTAEDKAAV 64 V+GAG MG GIVQ AAQAG +VV+ D E V I I + + +K ++T E Sbjct: 20 VVGAGVMGRGIVQVAAQAGIDVVLYDANSEAVSVAIEEIAHIFDRLQNKKKLTPEQVVQA 79 Query: 65 MGRISGTVDMGAAADCDLVIEAALEVMDIKKAIFKELDSICKPECILASNTSALSVTEIA 124 + RIS D+ A + C +VIEA +E +D K+ + L+ + +CILA+NTS+LSVT IA Sbjct: 80 LSRISCASDLDAFSSCAVVIEAIVERLDAKQGLLGSLERVVADDCILATNTSSLSVTSIA 139 Query: 125 AATGRADKVIGMHFFNPVPAMKLVEVIRGASTSQATYDAIKDLSVKMGKSPVEINEAPGF 184 A R ++V G H FNPVP MKLVEVI G T D + L+ ++G + V + PGF Sbjct: 140 AGCTRPERVGGFHCFNPVPLMKLVEVIEGVQTEPRVTDKLTALAQQVGHTAVRAQDTPGF 199 Query: 185 VVNRLLIPMLNEGMYCLMEGVANAADIDTSMKFGAGHPMGPLALADMIGLDICLKIMETL 244 VVN M+ E + EGVA+ +D ++ G G +GP L D+ GLD+ +ME++ Sbjct: 200 VVNHAGRGMITESLRLHSEGVADFRAVDDILRDGVGFRLGPFELMDLTGLDVSQPVMESI 259 Query: 245 YKE-FGDPKYRPCPLLAKMVRANKLGRKTGEGFFAY 279 Y++ + +P+YRP PL + ++A LGRK+G+GF+ Y Sbjct: 260 YQQYYQEPRYRPTPLALQRLQAGLLGRKSGKGFYTY 295 Score = 70.9 bits (172), Expect = 6e-17 Identities = 40/118 (33%), Positives = 66/118 (55%), Gaps = 4/118 (3%) Query: 151 IRGASTSQATYDAIKDLSVKMGKSP----VEINEAPGFVVNRLLIPMLNEGMYCLMEGVA 206 +R + AT +AIK + + S V I E+ GFV R+L ++N G + +A Sbjct: 387 LRTLMATPATGEAIKRAAYCLFSSDKVPVVMIRESAGFVAQRVLATIINIGCDMAQQRIA 446 Query: 207 NAADIDTSMKFGAGHPMGPLALADMIGLDICLKIMETLYKEFGDPKYRPCPLLAKMVR 264 + ADID ++ G G+P GPLA D++G + +KI+ +++ DP+YR P L++ R Sbjct: 447 SPADIDRAVTLGLGYPHGPLAWGDILGANKVVKILTNMHQASQDPRYRVSPWLSRRAR 504 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: 374 Number of extensions: 15 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 279 Length of database: 525 Length adjustment: 30 Effective length of query: 249 Effective length of database: 495 Effective search space: 123255 Effective search space used: 123255 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