Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_076478390.1 BW971_RS08035 3-hydroxybutyryl-CoA dehydrogenase
Query= BRENDA::P9WNP7 (286 letters) >NCBI__GCF_900156495.1:WP_076478390.1 Length = 288 Score = 400 bits (1028), Expect = e-116 Identities = 204/285 (71%), Positives = 237/285 (83%) Query: 2 SDAIQRVGVVGAGQMGSGIAEVSARAGVEVTVFEPAEALITAGRNRIVKSLERAVSAGKV 61 S+ I RVGVVGAGQMG+GIAEV ARA +V V+E L AGR+RI++SL+R VS+GK+ Sbjct: 3 SEKISRVGVVGAGQMGAGIAEVCARAHTDVLVYETTRELAAAGRSRILRSLDRGVSSGKL 62 Query: 62 TERERDRALGLLTFTTDLNDLSDRQLVIEAVVEDEAVKSEIFAELDRVVTDPDAVLASNT 121 TERER++A L FT+DL D +DRQLV EA VEDEA+K+EIF LD+VVTDP+AVLASNT Sbjct: 63 TEREREQASWRLRFTSDLGDFADRQLVCEAAVEDEAIKTEIFKSLDKVVTDPNAVLASNT 122 Query: 122 SSIPIMKVAAATKQPQRVLGLHFFNPVPVLPLVELVRTLVTDEAAAARTEEFASTVLGKQ 181 SSIPIMK+ AT+ +RV+G+HFFNPVPVLPLVELV TL+T R E FA VLGKQ Sbjct: 123 SSIPIMKLGMATQHAERVVGMHFFNPVPVLPLVELVTTLMTSPEVTERAEHFAGEVLGKQ 182 Query: 182 VVRCSDRSGFVVNALLVPYLLSAIRMVEAGFATVEDVDKAVVAGLSHPMGPLRLSDLVGL 241 VVR +DRSGFVVNALLVPYLLSAIRMVE+GFAT ED+DKA+V G +HPMGPL+LSDLVGL Sbjct: 183 VVRSADRSGFVVNALLVPYLLSAIRMVESGFATKEDIDKAMVLGTAHPMGPLKLSDLVGL 242 Query: 242 DTLKLIADKMFEEFKEPHYGPPPLLLRMVEAGQLGKKSGRGFYTY 286 DT+K IADKM+EEFKEP Y PPPLLLRMVEAG+LGKK G GFY Y Sbjct: 243 DTVKAIADKMYEEFKEPLYSPPPLLLRMVEAGRLGKKVGHGFYQY 287 Lambda K H 0.318 0.135 0.369 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: 332 Number of extensions: 7 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: 286 Length of database: 288 Length adjustment: 26 Effective length of query: 260 Effective length of database: 262 Effective search space: 68120 Effective search space used: 68120 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