Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_003940434.1 C1M55_RS25285 3-hydroxybutyryl-CoA dehydrogenase
Query= BRENDA::P9WNP7 (286 letters) >NCBI__GCF_002893965.1:WP_003940434.1 Length = 282 Score = 307 bits (787), Expect = 2e-88 Identities = 151/282 (53%), Positives = 200/282 (70%), Gaps = 1/282 (0%) Query: 5 IQRVGVVGAGQMGSGIAEVSARAGVEVTVFEPAEALITAGRNRIVKSLERAVSAGKVTER 64 ++ VGV+G G MG+GIAEV A+AG V V E E A R RI KS+ R V+ GK+T+ Sbjct: 1 MELVGVIGGGTMGAGIAEVCAKAGSSVLVLETKEEFAAAARERIAKSINRGVAKGKITQE 60 Query: 65 ERDRALGLLTFTTDLNDLSDRQLVIEAVVEDEAVKSEIFAELDRVVTDPDAVLASNTSSI 124 E D A+ + T D+ + +DR LVIEA E EA+K EIF +LD++V P +LA+NTSSI Sbjct: 61 EADAAIARVRVTLDMEEFADRDLVIEAAPEIEALKYEIFGKLDKIVK-PAGILATNTSSI 119 Query: 125 PIMKVAAATKQPQRVLGLHFFNPVPVLPLVELVRTLVTDEAAAARTEEFASTVLGKQVVR 184 P++K+A AT +P +V+G+HFFNPVPV+PLVE+V +L T E ++A L K+ VR Sbjct: 120 PVIKIAKATSRPGQVVGVHFFNPVPVMPLVEIVVSLTTSEETVLAVTDYAKNTLRKKTVR 179 Query: 185 CSDRSGFVVNALLVPYLLSAIRMVEAGFATVEDVDKAVVAGLSHPMGPLRLSDLVGLDTL 244 DRSGF+VNALL+PYL A+RM+E+G+AT ED+D+A+ G +PMGPL L D VGLD Sbjct: 180 AGDRSGFIVNALLIPYLCQAVRMLESGYATAEDIDEAMKGGCGYPMGPLTLLDTVGLDIA 239 Query: 245 KLIADKMFEEFKEPHYGPPPLLLRMVEAGQLGKKSGRGFYTY 286 A+ ++ EF EPHY PP LL RMV+AG+LGKK+GRGFY Y Sbjct: 240 LAAAESLYAEFAEPHYAPPALLRRMVDAGRLGKKTGRGFYEY 281 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: 249 Number of extensions: 7 Number of successful extensions: 2 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: 282 Length adjustment: 26 Effective length of query: 260 Effective length of database: 256 Effective search space: 66560 Effective search space used: 66560 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