RPSBLAST alignment for GI: 254780755 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 =  268 bits (688), Expect = 1e-72
 Identities = 115/300 (38%), Positives = 168/300 (56%), Gaps = 45/300 (15%)

Query: 25  SDVEMIPDVVKYLIFSGGKRLRPMLTLATALMLEYRGDNHVL-LACAIEFIHTATLLHDD 83
           S+VE++ + ++YL+ +GGKRLRP+L L  A  L        L LA AIE +HTA+L+HDD
Sbjct: 1   SEVELLREALRYLLLAGGKRLRPLLVLLAARALGGPELEAALRLAAAIELLHTASLVHDD 60

Query: 84  VVDDSALRRGKVAARLVWGNQTSVLVGDFLLSQAFCMVIETKSQEALEALSLVACT---L 140
           V+D+S LRRGK     V+GN T++L GD+LL++AF ++    +     AL L +     L
Sbjct: 61  VMDNSDLRRGKPTVHKVFGNATAILAGDYLLARAFELLARLGNPYYPRALELFSEAILEL 120

Query: 141 AEGELRQLSLSKNLDVTEEDYLHVIKSKTAVLFSAALEVSSLIAGVQNSVRQALKSYGMN 200
            EG+L  L    + DVTEE+YL +I+ KTA LF+AA  + +L+AG      +ALK +G N
Sbjct: 121 VEGQLLDLLSEYDTDVTEEEYLRIIRLKTAALFAAAPLLGALLAGADEEEAEALKRFGRN 180

Query: 201 LGIAFQLVDDVLDYRGEVNEMGKNIGEDFRNGKPTLPVILAFQRGTKREKNFWKSTINDG 260
           LG+AFQ+ DD+LD  G+   +GK +G D R GK TLPV+LA +                 
Sbjct: 181 LGLAFQIQDDILDLFGDPETLGKPVGSDLREGKCTLPVLLALRE---------------- 224

Query: 261 KISVENLKKAFIIMRENRALVDTEYRAYSYGQKAKDSLRCLPDSSWKKSLMEVVDFCLQR 320
                                     A  Y +KA ++L+ LP+S  +++L  + DF L+R
Sbjct: 225 -------------------------LAREYEEKALEALKALPESPAREALRALADFILER 259