RPSBLAST alignment for GI: 254781111 and conserved domain: cd00685

>gnl|CDD|173833 cd00685, Trans_IPPS_HT, Trans-Isoprenyl Diphosphate Synthases, head-to-tail. These trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) catalyze head-to-tail (HT) (1'-4) condensation reactions. This CD includes all-trans (E)-isoprenyl diphosphate synthases which synthesize various chain length (C10, C15, C20, C25, C30, C35, C40, C45, and C50) linear isoprenyl diphosphates from precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). They catalyze the successive 1'-4 condensation of the 5-carbon IPP to allylic substrates geranyl-, farnesyl-, or geranylgeranyl-diphosphate. Isoprenoid chain elongation reactions proceed via electrophilic alkylations in which a new carbon-carbon single bond is generated through interaction between a highly reactive electron-deficient allylic carbocation and an electron-rich carbon-carbon double bond. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions (DDXX(XX)D) located on opposite walls. These residues mediate binding of prenyl phosphates via bridging Mg2+ ions, inducing proposed conformational changes that close the active site to solvent, protecting and stabilizing reactive carbocation intermediates. Farnesyl diphosphate synthases produce the precursors of steroids, cholesterol, sesquiterpenes, farnsylated proteins, heme, and vitamin K12; and geranylgeranyl diphosphate and longer chain synthases produce the precursors of carotenoids, retinoids, diterpenes, geranylgeranylated chlorophylls, ubiquinone, and archaeal ether linked lipids. Isoprenyl diphosphate synthases are widely distributed among archaea, bacteria, and eukareya. Length = 259
 Score =  173 bits (440), Expect = 5e-44
 Identities = 80/205 (39%), Positives = 117/205 (57%), Gaps = 13/205 (6%)

Query: 34  QHNDRLLSAIRYALL-GGKKIRSFLVTECASLFNVNHL-TALRVGAAIECIHCYSLIHDD 91
              + L  A+RY LL GGK++R  LV   A       L  ALR+ AAIE +H  SL+HDD
Sbjct: 1   SEVELLREALRYLLLAGGKRLRPLLVLLAARALGGPELEAALRLAAAIELLHTASLVHDD 60

Query: 92  LPSMDNGYIRRGKPTVHIQYDEVTAIIAGNGLLTYAFEIISSPKTQLKDNIRSQLMLSLT 151
           +  MDN  +RRGKPTVH  +   TAI+AG+ LL  AFE+++    +L +    + +   +
Sbjct: 61  V--MDNSDLRRGKPTVHKVFGNATAILAGDYLLARAFELLA----RLGNPYYPRALELFS 114

Query: 152 HNIGLQGMLGGQMLDIQDEF---IDETQVFMIQKMKTGALMCFACESGAIMAHASQNEKE 208
               +  ++ GQ+LD+  E+   + E +   I ++KT AL   A   GA++A A + E E
Sbjct: 115 E--AILELVEGQLLDLLSEYDTDVTEEEYLRIIRLKTAALFAAAPLLGALLAGADEEEAE 172

Query: 209 RLRCFGENLGIIFQLADDLLDCEED 233
            L+ FG NLG+ FQ+ DD+LD   D
Sbjct: 173 ALKRFGRNLGLAFQIQDDILDLFGD 197