Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_046158881.1 VL52_RS21015 3-hydroxybutyryl-CoA dehydrogenase
Query= BRENDA::Q0KEY8 (284 letters) >NCBI__GCF_000971335.1:WP_046158881.1 Length = 282 Score = 308 bits (789), Expect = 9e-89 Identities = 153/278 (55%), Positives = 205/278 (73%) Query: 6 VGIVGAGTMGNGIAQACAVVGLNVVMVDISDAAVQKGVATVASSLDRLIKKEKLTEADKA 65 +G+VGAGTMGNGIAQ A+ G +VV+ D+SDAA+ KGVA + SL R+ KKE + EA+ Sbjct: 5 IGVVGAGTMGNGIAQVFAMKGFDVVLADVSDAALVKGVANINISLQRMAKKELIAEANIP 64 Query: 66 SALARIKGSTSYDDLKATDIVIEAATENYDLKVKILKQIDGIVGENVIIASNTSSISITK 125 +A I+ +T DL D+V+EAATEN ++K +I +++D VGE ++ASNTSSIS+T+ Sbjct: 65 GIVAHIRATTQLADLAGCDVVVEAATENAEIKERIFRELDAAVGEKCVLASNTSSISLTR 124 Query: 126 LAAVTSRADRFIGMHFFNPVPVMALVELIRGLQTSDTTHAAVEALSKQLGKYPITVKNSP 185 +A+ S +R +GMHF NPVP+M LVE+IR LQT D + V LS+ LGK P+TVK+ Sbjct: 125 IASWVSHPERVVGMHFMNPVPLMELVEIIRALQTGDEAYHTVFHLSQALGKTPVTVKDGA 184 Query: 186 GFVVNRILCPMINEAFCVLGEGLASPEEIDEGMKLGCNHPIGPLALADMIGLDTMLAVME 245 GFV NR+L PMINEA L E LA+ E+ID MKLG NHPIGPLALAD+IGLDT L++M+ Sbjct: 185 GFVSNRVLMPMINEAAFALYENLATAEDIDTVMKLGMNHPIGPLALADLIGLDTCLSIMD 244 Query: 246 VLYTEFADPKYRPAMLMREMVAAGYLGRKTGRGVYVYS 283 +L+ EF D KYR L+ ++V AG+LGRK+G+G Y Y+ Sbjct: 245 ILHREFRDSKYRACPLLVQLVQAGHLGRKSGKGFYSYN 282 Lambda K H 0.319 0.134 0.373 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: 221 Number of extensions: 4 Number of successful extensions: 1 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: 284 Length of database: 282 Length adjustment: 26 Effective length of query: 258 Effective length of database: 256 Effective search space: 66048 Effective search space used: 66048 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: 47 (22.7 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