Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_003941541.1 C1M55_RS07980 3-hydroxybutyryl-CoA dehydrogenase
Query= BRENDA::P9WNP7 (286 letters) >NCBI__GCF_002893965.1:WP_003941541.1 Length = 298 Score = 407 bits (1046), Expect = e-118 Identities = 208/285 (72%), Positives = 240/285 (84%) Query: 2 SDAIQRVGVVGAGQMGSGIAEVSARAGVEVTVFEPAEALITAGRNRIVKSLERAVSAGKV 61 S+ IQRVGV+GAG MG+GIAEV ARA V+V VFE L AGR+RI++SL+R VS+GK+ Sbjct: 3 SEKIQRVGVIGAGIMGAGIAEVCARAHVDVLVFEQTRELAAAGRSRILRSLDRGVSSGKI 62 Query: 62 TERERDRALGLLTFTTDLNDLSDRQLVIEAVVEDEAVKSEIFAELDRVVTDPDAVLASNT 121 TERER++A L FT+DL D +DRQLV+EAVVEDE +KSEIFAELD VVTDPDAVLASNT Sbjct: 63 TEREREQAAWRLRFTSDLGDFADRQLVVEAVVEDEKIKSEIFAELDAVVTDPDAVLASNT 122 Query: 122 SSIPIMKVAAATKQPQRVLGLHFFNPVPVLPLVELVRTLVTDEAAAARTEEFASTVLGKQ 181 SSIPIMK+ +TK+P+RV+G+HFFNPVPVLPLVELV TL T + + R E FAS +LGKQ Sbjct: 123 SSIPIMKLGISTKRPERVIGMHFFNPVPVLPLVELVTTLKTSASVSQRAEAFASDILGKQ 182 Query: 182 VVRCSDRSGFVVNALLVPYLLSAIRMVEAGFATVEDVDKAVVAGLSHPMGPLRLSDLVGL 241 VVR +DRSGFVVNALLVPYLLSAIRMVE+GFAT ED+DKA V GL+HPMGPL L+DLVGL Sbjct: 183 VVRSADRSGFVVNALLVPYLLSAIRMVESGFATKEDIDKATVLGLAHPMGPLALTDLVGL 242 Query: 242 DTLKLIADKMFEEFKEPHYGPPPLLLRMVEAGQLGKKSGRGFYTY 286 DT+K IAD M+EEFKEP Y PPLLLRMVEAG GKKSG GFY Y Sbjct: 243 DTVKSIADSMYEEFKEPLYSAPPLLLRMVEAGLTGKKSGAGFYEY 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: 335 Number of extensions: 10 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: 298 Length adjustment: 26 Effective length of query: 260 Effective length of database: 272 Effective search space: 70720 Effective search space used: 70720 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: 48 (23.1 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