Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_015798929.1 AFER_RS07900 3-hydroxybutyryl-CoA dehydrogenase
Query= BRENDA::P9WNP7 (286 letters) >NCBI__GCF_000023265.1:WP_015798929.1 Length = 294 Score = 336 bits (861), Expect = 4e-97 Identities = 164/282 (58%), Positives = 215/282 (76%) Query: 5 IQRVGVVGAGQMGSGIAEVSARAGVEVTVFEPAEALITAGRNRIVKSLERAVSAGKVTER 64 + ++GVVG G MGSGIAEV+AR G++V V E + A RI +S+ R + + K++E Sbjct: 3 VTQLGVVGGGLMGSGIAEVAARRGIDVVVVEATDDAAKAALGRIERSIARGLRSSKLSEA 62 Query: 65 ERDRALGLLTFTTDLNDLSDRQLVIEAVVEDEAVKSEIFAELDRVVTDPDAVLASNTSSI 124 E + ALG ++ T+DL L DR VIEAV+EDEA K +FA+LD VVT DA+LASNTSSI Sbjct: 63 EAEAALGRISVTSDLEALGDRDAVIEAVIEDEATKLAVFAKLDHVVTRADALLASNTSSI 122 Query: 125 PIMKVAAATKQPQRVLGLHFFNPVPVLPLVELVRTLVTDEAAAARTEEFASTVLGKQVVR 184 PIMK+A AT++P+ V+G+HFFNPVPV+PLVELV +L+T EA R FA+ LGK V++ Sbjct: 123 PIMKLAMATQRPEYVIGIHFFNPVPVMPLVELVPSLLTSEATQERAHAFAADQLGKHVIK 182 Query: 185 CSDRSGFVVNALLVPYLLSAIRMVEAGFATVEDVDKAVVAGLSHPMGPLRLSDLVGLDTL 244 DR+GF+VNALL+PY+LSA+RM+E+GFAT ED+D +V G +HPMGPL L+DL+GLDT Sbjct: 183 AKDRAGFIVNALLIPYILSAVRMLESGFATAEDIDTGMVDGCAHPMGPLALADLIGLDTT 242 Query: 245 KLIADKMFEEFKEPHYGPPPLLLRMVEAGQLGKKSGRGFYTY 286 +A+ ++EEFKEP + PPPLL RM EAG LG+KSGRGFY Y Sbjct: 243 MAVAESLYEEFKEPLFAPPPLLSRMCEAGLLGRKSGRGFYRY 284 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: 277 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: 294 Length adjustment: 26 Effective length of query: 260 Effective length of database: 268 Effective search space: 69680 Effective search space used: 69680 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