HHsearch alignment for GI: 254780755 and conserved domain: cd00683
>cd00683 Trans_IPPS_HH Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS), head-to-head (HH) (1'-1) condensation reaction. This CD includes squalene and phytoene synthases which catalyze the 1'-1 condensation of two 15-carbon (farnesyl) and 20-carbon (geranylgeranyl) isoprenyl diphosphates, respectively. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions (DXXXD) located on opposite walls. These residues mediate binding of prenyl phosphates. A two-step reaction has been proposed for squalene synthase (farnesyl-diphosphate farnesyltransferase) in which, two molecules of FPP react to form a stable cyclopropylcarbinyl diphosphate intermediate, and then the intermediate undergoes heterolysis, isomerization, and reduction with NADPH to form squalene, a precursor of cholestrol. The carotenoid biosynthesis enzyme, phytoene synthase (CrtB), catalyzes the condensation reaction of two molecules of geranylgeranyl diphosp
Probab=97.61 E-value=0.0029 Score=39.83 Aligned_cols=135 Identities=23% Similarity=0.161 Sum_probs=82.0
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHC
Q ss_conf 34567777775456554213221035789899864335555443210001122221015799999731116898876411
Q gi|254780755|r 134 SLVACTLAEGELRQLSLSKNLDVTEEDYLHVIKSKTAVLFSAALEVSSLIAGVQNSVRQALKSYGMNLGIAFQLVDDVLD 213 (322)
Q Consensus 134 ~~~~~~l~~Gq~~d~~~~~~~~~s~~~y~~ii~~KTa~Lf~~~~~~ga~lag~~~~~~~~l~~fG~~lG~afQI~DD~ld 213 (322)
T Consensus 92 ~~~~~~li~g~~~Dl~~~~--~~t~~eL~~Yc~~vAg~VG~l~~~i---~g-~--~~~~~~~~~A~~lG~AlQltNilRD 163 (265)
T cd00683 92 REPFRDLLAGMAMDLDKRR--YETLDELDEYCYYVAGVVGLMLLRV---FG-A--SSDEAALERARALGLALQLTNILRD 163 (265)
T ss_pred HHHHHHHHHHHHHHCCCCC--CCCHHHHHHHHHHHHHHHHHHHHHH---HC-C--CCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 8999999999998756789--9999999999997117999999999---58-7--8818899999998899999989987
Q ss_pred CCCCCCCCCCHHHHHHHHCCCCCCCCHHHHCCCCCCCHHHHHHCCCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHH
Q ss_conf 23670003840123454213653210011014311000134320368999899999999999749699999999999999
Q gi|254780755|r 214 YRGEVNEMGKNIGEDFRNGKPTLPVILAFQRGTKREKNFWKSTINDGKISVENLKKAFIIMRENRALVDTEYRAYSYGQK 293 (322)
Q Consensus 214 ~~g~~~~~GK~~g~Dl~egk~Tlpii~al~~~~~~~~~~l~~~~~~~~~~~~~~~~i~~ll~~~gai~~~~~~~~~~~~~ 293 (322)
T Consensus 164 i-----------~eD~~~gRiYlP~~~l~~~gv~-~----~dl~-~~~~~-~~~~~~---------~~~~~~~A~~~~~~ 216 (265)
T cd00683 164 V-----------GEDARRGRIYLPREELARFGVT-L----EDLL-APENS-PAFRAL---------LRRLIARARAHYRE 216 (265)
T ss_pred H-----------HHHHHCCCEECCHHHHHHCCCC-H----HHHH-CCCCC-HHHHHH---------HHHHHHHHHHHHHH
T ss_conf 9-----------9999589157889999884999-9----9984-76688-999999---------99999999999999
Q ss_pred HHHHHHCCCC
Q ss_conf 9998420899
Q gi|254780755|r 294 AKDSLRCLPD 303 (322)
Q Consensus 294 A~~~L~~lp~ 303 (322)
T Consensus 217 a~~~~~~lp~ 226 (265)
T cd00683 217 ALAGLAALPR 226 (265)
T ss_pred HHHHHHHCCH
T ss_conf 9998986999