RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 024463
(267 letters)
>gnl|CDD|178478 PLN02890, PLN02890, geranyl diphosphate synthase.
Length = 422
Score = 386 bits (992), Expect = e-134
Identities = 189/292 (64%), Positives = 227/292 (77%), Gaps = 27/292 (9%)
Query: 3 VILLMATALNVCTPELSPNVLGNTLILDLRRRQQCIAEITEMIHVASLIHDDVLDDADTR 62
V+LLMATALNV PE + + + + +LR RQQ IAEITEMIHVASL+HDDVLDDADTR
Sbjct: 131 VLLLMATALNVPLPESTEGGVLDIVASELRTRQQNIAEITEMIHVASLLHDDVLDDADTR 190
Query: 63 RGIGSLSSVMGNKLAILAGDLLISRALVALASLKHTEVI--------------------- 101
RG+GSL+ VMGNKL++LAGD L+SRA VALA+LK+TEV+
Sbjct: 191 RGVGSLNVVMGNKLSVLAGDFLLSRACVALAALKNTEVVSLLATAVEHLVTGETMQITSS 250
Query: 102 ------MECYMQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDI 155
M+ YMQKTY KTA+L+SNSCKAVA L+GQ EVA LAFEYG+NLGLA+QLIDD+
Sbjct: 251 REQRRSMDYYMQKTYYKTASLISNSCKAVAILAGQTAEVAVLAFEYGRNLGLAFQLIDDV 310
Query: 156 LDFTGTSASLGKASLTDLRNGIITAPILFAMEEFPQLRAFINSSSDNPANVDVILEYLGK 215
LDFTGTSASLGK SL+D+R+G+ITAPILFAMEEFPQLR ++ DNPANVD+ LEYLGK
Sbjct: 311 LDFTGTSASLGKGSLSDIRHGVITAPILFAMEEFPQLREVVDRGFDNPANVDIALEYLGK 370
Query: 216 SHGIQRTTELALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITRNK 267
S GIQRT ELA +HA+LAAAAI+SLPET D D +R AL+ +T+++ITRNK
Sbjct: 371 SRGIQRTRELAREHANLAAAAIESLPETDDEDVLTSRRALIDLTERVITRNK 422
>gnl|CDD|131796 TIGR02749, prenyl_cyano, solanesyl diphosphate synthase. Members
of this family all are from cyanobacteria or
plastid-containing eukaryotes. A member from Arabidopsis
(where both plastoquinone and ubiquinone contain the
C(45) prenyl moiety) was characterized by heterologous
expression as a solanesyl diphosphate synthase
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Menaquinone and ubiquinone].
Length = 322
Score = 214 bits (548), Expect = 1e-68
Identities = 105/263 (39%), Positives = 159/263 (60%), Gaps = 33/263 (12%)
Query: 30 DLRRRQQCIAEITEMIHVASLIHDDVLDDADTRRGIGSLSSVMGNKLAILAGDLLISRAL 89
+L R + +AEITEMIH ASL+HDDV+D++DTRRGI ++ S+ G ++A+LAGD L ++A
Sbjct: 64 ELTPRHRRLAEITEMIHTASLVHDDVIDESDTRRGIETVHSLFGTRVAVLAGDFLFAQAS 123
Query: 90 VALASLKHTEVI---------------------------MECYMQKTYNKTAALVSNSCK 122
LA+L++ EV+ +E Y++K++ KTA+LV+ S K
Sbjct: 124 WYLANLENLEVVKLISKVITDFAEGEIKQGLNQFDSDLSLEDYLEKSFYKTASLVAASSK 183
Query: 123 AVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGIITAPI 182
A A LS +VA +EYGK+LGLA+Q++DDILDFTG++ LGK + +DL G +TAP+
Sbjct: 184 AAAVLSDVPSQVANDLYEYGKHLGLAFQVVDDILDFTGSTEQLGKPAGSDLMKGNLTAPV 243
Query: 183 LFAMEEFPQLRAFINSSSDNPANVDVILEYLGKSHGIQRTTELALKHASLAAAAIDSLPE 242
LFA+EE P+L I +++ L + KS GI++ ELA + A LA ++ LP
Sbjct: 244 LFALEEEPKLSELIEREFSQKGDLEQALSLVRKSGGIKKARELAKEQAQLALQSLSFLPP 303
Query: 243 THDVDATNARTALVHITQKIITR 265
+ R AL + +++R
Sbjct: 304 ------SPPREALKELVHFVLSR 320
>gnl|CDD|215462 PLN02857, PLN02857, octaprenyl-diphosphate synthase.
Length = 416
Score = 204 bits (521), Expect = 1e-63
Identities = 97/265 (36%), Positives = 151/265 (56%), Gaps = 33/265 (12%)
Query: 28 ILDLRRRQQCIAEITEMIHVASLIHDDVLDDADTRRGIGSLSSVMGNKLAILAGDLLISR 87
+ +L + +AEITEMIH ASLIHDDVLD++D RRG ++ + G ++A+LAGD + ++
Sbjct: 156 LKELTTEHRRLAEITEMIHTASLIHDDVLDESDMRRGKETVHQLYGTRVAVLAGDFMFAQ 215
Query: 88 ALVALASLKHTEVI---------------------------MECYMQKTYNKTAALVSNS 120
+ LA+L + EVI ++ Y+ K+Y KTA+L++ S
Sbjct: 216 SSWYLANLDNLEVIKLISQVIKDFASGEIKQASSLFDCDVTLDEYLLKSYYKTASLIAAS 275
Query: 121 CKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGIITA 180
K+ A SG V +EYGKNLGLA+Q++DDILDFT ++ LGK + +DL G +TA
Sbjct: 276 TKSAAIFSGVDSSVKEQMYEYGKNLGLAFQVVDDILDFTQSTEQLGKPAGSDLAKGNLTA 335
Query: 181 PILFAMEEFPQLRAFINSSSDNPANVDVILEYLGKSHGIQRTTELALKHASLAAAAIDSL 240
P++FA+E+ P+LR I S +++ +E + + GI+R ELA + A LA ++ L
Sbjct: 336 PVIFALEKEPELREIIESEFCEEGSLEEAIELVNEGGGIERAQELAKEKADLAIQNLECL 395
Query: 241 PETHDVDATNARTALVHITQKIITR 265
P R++L + + R
Sbjct: 396 PR------GAFRSSLEDMVDYNLER 414
>gnl|CDD|164542 CHL00151, preA, prenyl transferase; Reviewed.
Length = 323
Score = 189 bits (482), Expect = 7e-59
Identities = 94/266 (35%), Positives = 152/266 (57%), Gaps = 33/266 (12%)
Query: 29 LDLRRRQQCIAEITEMIHVASLIHDDVLDDADTRRGIGSLSSVMGNKLAILAGDLLISRA 88
++++ QQ +AEITE+IH ASL+HDDV+D+ RRGI ++ + G K+A+LAGD L +++
Sbjct: 64 MEIKTSQQRLAEITEIIHTASLVHDDVIDECSIRRGIPTVHKIFGTKIAVLAGDFLFAQS 123
Query: 89 LVALASLKHTEVI---------------------------MECYMQKTYNKTAALVSNSC 121
LA+L + EV+ + Y++K++ KTA+L++ SC
Sbjct: 124 SWYLANLNNLEVVKLISKVITDFAEGEIRQGLVQFDTTLSILNYIEKSFYKTASLIAASC 183
Query: 122 KAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGIITAP 181
KA A LS E+ + YGK+LGLA+Q+IDD+LD T ++ SLGK +DL+NG +TAP
Sbjct: 184 KAAALLSDADEKDHNDFYLYGKHLGLAFQIIDDVLDITSSTESLGKPIGSDLKNGNLTAP 243
Query: 182 ILFAMEEFPQLRAFINSSSDNPANVDVILEYLGKSHGIQRTTELALKHASLAAAAIDSLP 241
+LFA+ + +L I ++ L+ + +++GI++ +LAL+H A + LP
Sbjct: 244 VLFALTQNSKLAKLIEREFCETKDISQALQIIKETNGIEKAKDLALEHMQAAIQCLKFLP 303
Query: 242 ETHDVDATNARTALVHITQKIITRNK 267
+ D +L+ I II R
Sbjct: 304 PSSAKD------SLIEIANFIINRLN 323
>gnl|CDD|223220 COG0142, IspA, Geranylgeranyl pyrophosphate synthase [Coenzyme
metabolism].
Length = 322
Score = 188 bits (480), Expect = 2e-58
Identities = 92/291 (31%), Positives = 136/291 (46%), Gaps = 47/291 (16%)
Query: 5 LLMATALNVCTPELSPNVLGNTLILDLRRRQQCIAEITEMIHVASLIHDDVLDDADTRRG 64
LL A AL + + L +A E+IH ASLIHDD++DD D RRG
Sbjct: 51 LLAAEALGIDLETGGNDALD-------------LAAAIELIHTASLIHDDLMDDDDLRRG 97
Query: 65 IGSLSSVMGNKLAILAGDLLISRALVALASL----------------------------K 96
++ + G AILAGD L++ A L+ L +
Sbjct: 98 KPTVHAKFGEATAILAGDALLAAAFELLSKLGSEALEAIKALAEAINGLCGGQALDLAFE 157
Query: 97 HTEVIMECYMQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDIL 156
+ V +E Y++ KTAAL + + A L+G EE+ +YG+NLGLA+Q+ DDIL
Sbjct: 158 NKPVTLEEYLRVIELKTAALFAAAAVLGAILAGADEELLEALEDYGRNLGLAFQIQDDIL 217
Query: 157 DFTGTSASLGKASLTDLRNGIITAPILFAMEEFPQLRAFINSSSDNPANVDVILEYLGKS 216
D TG LGK +DL+ G T P+L A+E+ + + + + V+ LE L KS
Sbjct: 218 DITGDEEELGKPVGSDLKEGKPTLPVLLALEKANEDQKLLRILLEGGGEVEEALELLRKS 277
Query: 217 HGIQRTTELALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITRNK 267
I+ LA + A A++ LP++ A+ AL+ + II R
Sbjct: 278 GAIEYAKNLAKTYVEKAKEALEKLPDSE------AKEALLELADFIIKRKY 322
>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 = 181 bits (463), Expect = 1e-56
Identities = 83/266 (31%), Positives = 117/266 (43%), Gaps = 72/266 (27%)
Query: 30 DLRRRQQCIAEITEMIHVASLIHDDVLDDADTRRGIGSLSSVMGNKLAILAGDLLISRAL 89
+A E++H ASL+HDDV+D++D RRG ++ V GN AILAGD L++RA
Sbjct: 36 PELEAALRLAAAIELLHTASLVHDDVMDNSDLRRGKPTVHKVFGNATAILAGDYLLARAF 95
Query: 90 VALASLKH----------TEVIMEC--------------------YMQKTYNKTAALVSN 119
LA L + +E I+E Y++ KTAAL +
Sbjct: 96 ELLARLGNPYYPRALELFSEAILELVEGQLLDLLSEYDTDVTEEEYLRIIRLKTAALFAA 155
Query: 120 SCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGIIT 179
+ A L+G EE A +G+NLGLA+Q+ DDILD G +LGK +DLR G T
Sbjct: 156 APLLGALLAGADEEEAEALKRFGRNLGLAFQIQDDILDLFGDPETLGKPVGSDLREGKCT 215
Query: 180 APILFAMEEFPQLRAFINSSSDNPANVDVILEYLGKSHGIQRTTELALKHASLAAAAIDS 239
P+L A+ ELA ++ A A+ +
Sbjct: 216 LPVLLALR------------------------------------ELAREYEEKALEALKA 239
Query: 240 LPETHDVDATNARTALVHITQKIITR 265
LPE + AR AL + I+ R
Sbjct: 240 LPE------SPAREALRALADFILER 259
>gnl|CDD|173836 cd00867, Trans_IPPS, Trans-Isoprenyl Diphosphate Synthases.
Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) of
class 1 isoprenoid biosynthesis enzymes which either
synthesis geranyl/farnesyl diphosphates (GPP/FPP) or
longer chained products from isoprene precursors,
isopentenyl diphosphate (IPP) and dimethylallyl
diphosphate (DMAPP), or use geranyl (C10)-, farnesyl
(C15)-, or geranylgeranyl (C20)-diphosphate as
substrate. These enzymes produce a myriad of precursors
for such end products as steroids, cholesterol,
sesquiterpenes, heme, carotenoids, retinoids,
diterpenes, ubiquinone, and archaeal ether linked
lipids; and are widely distributed among archaea,
bacteria, and eukareya. The enzymes in this family share
the same 'isoprenoid synthase fold' and include the
head-to-tail (HT) IPPS which catalyze the successive
1'-4 condensation of the 5-carbon IPP to the growing
isoprene chain to form linear, all-trans, C10-, C15-,
C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid
diphosphates. The head-to-head (HH) IPPS catalyze the
successive 1'-1 condensation of 2 farnesyl or 2
geranylgeranyl isoprenoid diphosphates. 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 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, stabilizing reactive
carbocation intermediates. Mechanistically and
structurally distinct, cis-IPPS are not included in this
CD.
Length = 236
Score = 139 bits (353), Expect = 2e-40
Identities = 69/196 (35%), Positives = 96/196 (48%), Gaps = 29/196 (14%)
Query: 22 VLGNTLILDLRRRQQCIAEITEMIHVASLIHDDVLDDADTRRGIGSLSSV-MGNKLAILA 80
+L + +A E++H ASL+HDD++DD+D RRG + GN LAILA
Sbjct: 7 LLLARALGGDLEAALRLAAAVELLHAASLVHDDIVDDSDLRRGKPTAHLRRFGNALAILA 66
Query: 81 GDLLISRALVALASLKHTEVI---------------------------MECYMQKTYNKT 113
GD L++RA LA L + + ++ Y++ KT
Sbjct: 67 GDYLLARAFQLLARLGYPRALELFAEALRELLEGQALDLEFERDTYETLDEYLEYCRYKT 126
Query: 114 AALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDL 173
A LV C A LSG +E A +YG+ LGLA+QL DD+LD G + LGK +DL
Sbjct: 127 AGLVGLLCLLGAGLSGADDEQAEALKDYGRALGLAFQLTDDLLDVFGDAEELGKV-GSDL 185
Query: 174 RNGIITAPILFAMEEF 189
R G IT P++ A E
Sbjct: 186 REGRITLPVILARERA 201
>gnl|CDD|131795 TIGR02748, GerC3_HepT, heptaprenyl diphosphate synthase component
II. Members of this family are component II of the
heterodimeric heptaprenyl diphosphate synthase. The
trusted cutoff was set such that all members identified
are encoded near to a recognizable gene for component I
(in Pfam family pfam07307). This enzyme acts in
menaquinone-7 isoprenoid side chain biosynthesis
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Menaquinone and ubiquinone].
Length = 319
Score = 140 bits (354), Expect = 7e-40
Identities = 79/257 (30%), Positives = 128/257 (49%), Gaps = 34/257 (13%)
Query: 38 IAEITEMIHVASLIHDDVLDDADTRRGIGSLSSVMGNKLAILAGDLLISRALVALASLK- 96
+A E+IH+ASL+HDDV+DDAD RRG ++ S GN++A+ GD L +++L + +K
Sbjct: 68 VAVALELIHMASLVHDDVIDDADLRRGRPTIKSKWGNRIAMYTGDYLFAKSLETMTEIKD 127
Query: 97 ---HT---EVIMEC--------------------YMQKTYNKTAALVSNSCKAVAYLSGQ 130
H I+E Y+++ KTA L++ SC+ A SG
Sbjct: 128 PRAHQILSHTIVEVCRGEIEQIKDKYNFDQNLRTYLRRIKRKTALLIAASCQLGAIASGA 187
Query: 131 REEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGIITAPILFAMEEFP 190
E + + +G +G++YQ+ DDILDF GT LGK + DL G +T P+L+AME+
Sbjct: 188 NEAIVKKLYWFGYYVGMSYQITDDILDFVGTEEELGKPAGGDLLQGNVTLPVLYAMEDPF 247
Query: 191 QLRAFINSSSDNPAN-VDVILEYLGKSHGIQRTTELALKHASLAAAAIDSLPETHDVDAT 249
+ + A ++ ++E + KS I+ ++ ++ A +D LP
Sbjct: 248 LKKRIEQVLEETTAEEMEPLIEEVKKSDAIEYAYAVSDRYLKKALELLDGLP------DG 301
Query: 250 NARTALVHITQKIITRN 266
A+ L I + I R
Sbjct: 302 RAKKPLQEIAKYIGKRK 318
>gnl|CDD|215873 pfam00348, polyprenyl_synt, Polyprenyl synthetase.
Length = 260
Score = 138 bits (349), Expect = 1e-39
Identities = 68/183 (37%), Positives = 93/183 (50%), Gaps = 33/183 (18%)
Query: 38 IAEITEMIHVASLIHDDVLDDADTRRGIGSLSSVMGNKLAILAGDLLISRALVALASLKH 97
+A EMIH ASL+HDD++D++D RRG + G AILAGD L+SRA LA L H
Sbjct: 38 LACAIEMIHTASLVHDDLMDNSDLRRGKPTCHKKFGEAGAILAGDALLSRAFQLLALLGH 97
Query: 98 --------------TEVIMEC-------------------YMQKTYNKTAALVSNSCKAV 124
V + Y++ KTAAL S +
Sbjct: 98 VRPEPKYILISELANAVGAQGEVGQLMDLETEGKDITLEEYLRIVSYKTAALFYASVQLG 157
Query: 125 AYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGIITAPILF 184
A ++G EE +++G++LGLA+Q+ DDILD TG + LGK TDL+ G T P+L
Sbjct: 158 AIVAGADEEDEKDLYDFGRDLGLAFQIQDDILDLTGDTEELGKPVGTDLQEGKSTLPVLL 217
Query: 185 AME 187
A+E
Sbjct: 218 ALE 220
>gnl|CDD|182813 PRK10888, PRK10888, octaprenyl diphosphate synthase; Provisional.
Length = 323
Score = 111 bits (280), Expect = 5e-29
Identities = 81/252 (32%), Positives = 124/252 (49%), Gaps = 34/252 (13%)
Query: 38 IAEITEMIHVASLIHDDVLDDADTRRGIGSLSSVMGNKLAILAGDLLISRA---LVALAS 94
IA + E IH A+L+HDDV+D++D RRG + ++ GN ++L GD + +RA + +L S
Sbjct: 69 IAALIEFIHTATLLHDDVVDESDMRRGKATANAAFGNAASVLVGDFIYTRAFQMMTSLGS 128
Query: 95 LKHTEV---------------IMEC---------YMQKTYNKTAALVSNSCKAVAYLSGQ 130
LK EV +M YM+ Y+KTA L + + L+G
Sbjct: 129 LKVLEVMSEAVNVIAEGEVLQLMNVNDPDITEENYMRVIYSKTARLFEAAAQCSGILAGC 188
Query: 131 REEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGIITAPILFAMEE-F 189
E +YG+ LG A+QLIDD+LD++ +LGK DL G T P+L AM
Sbjct: 189 TPEQEKGLQDYGRYLGTAFQLIDDLLDYSADGETLGKNVGDDLNEGKPTLPLLHAMHHGT 248
Query: 190 PQLRAFINSSSDNPAN---VDVILEYLGKSHGIQRTTELALKHASLAAAAIDSLPETHDV 246
P+ A I ++ + ++ +LE + ++ T + A + A A AA+ LP+T
Sbjct: 249 PEQAAMIRTAIEQGNGRHLLEPVLEAMNACGSLEWTRQRAEEEADKAIAALQVLPDT--- 305
Query: 247 DATNARTALVHI 258
A L HI
Sbjct: 306 PWREALIGLAHI 317
>gnl|CDD|173830 cd00385, Isoprenoid_Biosyn_C1, Isoprenoid Biosynthesis enzymes,
Class 1. Superfamily of trans-isoprenyl diphosphate
synthases (IPPS) and class I terpene cyclases which
either synthesis geranyl/farnesyl diphosphates (GPP/FPP)
or longer chained products from isoprene precursors,
isopentenyl diphosphate (IPP) and dimethylallyl
diphosphate (DMAPP), or use geranyl (C10)-, farnesyl
(C15)-, or geranylgeranyl (C20)-diphosphate as
substrate. These enzymes produce a myriad of precursors
for such end products as steroids, cholesterol,
sesquiterpenes, heme, carotenoids, retinoids, and
diterpenes; and are widely distributed among archaea,
bacteria, and eukaryota.The enzymes in this superfamily
share the same 'isoprenoid synthase fold' and include
several subgroups. The head-to-tail (HT) IPPS catalyze
the successive 1'-4 condensation of the 5-carbon IPP to
the growing isoprene chain to form linear, all-trans,
C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or
C50-isoprenoid diphosphates. Cyclic monoterpenes,
diterpenes, and sesquiterpenes, are formed from their
respective linear isoprenoid diphosphates by class I
terpene cyclases. The head-to-head (HH) IPPS catalyze
the successive 1'-1 condensation of 2 farnesyl or 2
geranylgeranyl isoprenoid diphosphates. Cyclization of
these 30- and 40-carbon linear forms are catalyzed by
class II cyclases. Both the isoprenoid chain elongation
reactions and the class I terpene cyclization 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 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, stabilizing reactive carbocation intermediates.
Generally, the enzymes in this family exhibit an
all-trans reaction pathway, an exception, is the
cis-trans terpene cyclase, trichodiene synthase.
Mechanistically and structurally distinct, class II
terpene cyclases and cis-IPPS are not included in this
CD.
Length = 243
Score = 102 bits (257), Expect = 2e-26
Identities = 66/256 (25%), Positives = 102/256 (39%), Gaps = 58/256 (22%)
Query: 38 IAEITEMIHVASLIHDDVLDDADTRRGIGSLSSVM---GNKLAILAGDLLISRALVALAS 94
+ E +H ASL+HDD++DD+ TRRG+ + + G AILAGDLL++ A LA
Sbjct: 15 LRAAVEKLHAASLVHDDIVDDSGTRRGLPTAHLAVAIDGLPEAILAGDLLLADAFEELAR 74
Query: 95 LKHTEVI---------------------------MECYMQKTYNKTAALVSNSCKAVAYL 127
E + +E Y++ KTA LV C A L
Sbjct: 75 EGSPEALEILAEALLDLLEGQLLDLKWRREYVPTLEEYLEYCRYKTAGLVGALCLLGAGL 134
Query: 128 SGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGIITAPILFAME 187
SG E+ + G+ LGLA+QL +D+LD+ G + G T P+L+A+E
Sbjct: 135 SGGEAELLEALRKLGRALGLAFQLTNDLLDYEGDAERG---------EGKCTLPVLYALE 185
Query: 188 EFPQLRAFINSSSDNPANVDVILEYLGKSHGIQRTTELALKHASLAAAAIDSLPETHDVD 247
+ + KS ++ E K A A ++ L +
Sbjct: 186 YGVPAEDLL---------------LVEKSGSLEEALEELAKLAEEALKELNELILSLPD- 229
Query: 248 ATNARTALVHITQKII 263
AL+ + +
Sbjct: 230 ---VPRALLALALNLY 242
>gnl|CDD|182567 PRK10581, PRK10581, geranyltranstransferase; Provisional.
Length = 299
Score = 65.9 bits (161), Expect = 1e-12
Identities = 58/189 (30%), Positives = 82/189 (43%), Gaps = 39/189 (20%)
Query: 39 AEITEMIHVASLIHDDV--LDDADTRRGIGSLSSVMGNKLAILAGDLLISRALVALASLK 96
A E IH SLIHDD+ +DD D RRG+ + G AILAGD L + A L+
Sbjct: 70 AAAVECIHAYSLIHDDLPAMDDDDLRRGLPTCHVKFGEANAILAGDALQTLAFSILSDAP 129
Query: 97 HTEV--------IMECYM----------------------------QKTYNKTAALVSNS 120
EV I E + +KT AL+ +
Sbjct: 130 MPEVSDRDRISMISELASASGIAGMCGGQALDLEAEGKQVPLDALERIHRHKTGALIRAA 189
Query: 121 CKAVAYLSGQREEVATLAFE-YGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGIIT 179
+ A +G + A + Y +++GLA+Q+ DDILD G +A+LGK D + G T
Sbjct: 190 VRLGALSAGDKGRRALPVLDRYAESIGLAFQVQDDILDVVGDTATLGKRQGADQQLGKST 249
Query: 180 APILFAMEE 188
P L +E+
Sbjct: 250 YPALLGLEQ 258
>gnl|CDD|233139 TIGR00814, stp, serine transporter. The Hydroxy/Aromatic Amino
Acid Permease (HAAAP) Family- serine/threonine subfamily
(TC 2.A.42.2) The HAAAP family includes well
characterized aromatic amino acid:H+ symport permeases
and hydroxy amino acid permeases. This subfamily is
specific for hydroxy amino acid transporters and
includes the serine permease, SdaC, of E. coli, and the
threonine permease, TdcC, of E. coli.//added GO terms,
none avaialbelf or ser/thr specifically [SS 2/6/05]
[Transport and binding proteins, Amino acids, peptides
and amines].
Length = 397
Score = 31.9 bits (73), Expect = 0.35
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 5/47 (10%)
Query: 177 IITAPILFAMEEFPQLRAFIN--SSSDNPAN--VDVILEYLGKSHGI 219
++ A I + + F RA SS NP +V+ E+ GK+ GI
Sbjct: 37 VLMAIIAYPLTYFGH-RALARFLLSSKNPCEDITEVVEEHFGKNWGI 82
>gnl|CDD|225744 COG3203, OmpC, Outer membrane protein (porin) [Cell envelope
biogenesis, outer membrane].
Length = 354
Score = 28.9 bits (65), Expect = 2.5
Identities = 15/61 (24%), Positives = 22/61 (36%), Gaps = 9/61 (14%)
Query: 128 SGQREEVATLAFE------YGKNLGLAYQLID--DILDFTGTSASLGKASLTDLR-NGII 178
R A L YG+N G+ Y + D L G A+L + R + +
Sbjct: 94 LFTRLAFAGLKGADFGSLDYGRNYGVLYDVAGWTDPLPEFGGDATLVDDNFMTGRADNVA 153
Query: 179 T 179
T
Sbjct: 154 T 154
>gnl|CDD|176554 cd08613, GDPD_GDE4_like_1, Glycerophosphodiester phosphodiesterase
domain of uncharacterized bacterial homologs of
mammalian glycerophosphodiester phosphodiesterase GDE4.
This subfamily corresponds to the glycerophosphodiester
phosphodiesterase domain (GDPD) present in
uncharacterized bacterial homologs of mammalian GDE4, a
transmembrane protein whose cellular function has not
been elucidated yet.
Length = 309
Score = 28.5 bits (64), Expect = 3.3
Identities = 16/71 (22%), Positives = 30/71 (42%), Gaps = 2/71 (2%)
Query: 187 EEFPQLRAFINSSSDNPANVDVILEYLGKSHGIQRTTELALKHASLAAAAI-DSLPETHD 245
FP R IN SD+ A +++ E L + +R L + AA+ + P+
Sbjct: 150 AAFPDRRFLINFKSDDAAEGELLAEKL-ATLPRKRLQVLTVYGGDKPIAALRELTPDLRT 208
Query: 246 VDATNARTALV 256
+ + + L+
Sbjct: 209 LSKASMKDCLI 219
>gnl|CDD|151200 pfam10707, YrbL-PhoP_reg, PhoP regulatory network protein YrbL.
This is a family of proteins that are activated by PhoP.
PhoP protein controls the expression of a large number
of genes that mediate adaptation to low Mg2+
environments and/or virulence in several bacterial
species. YbrL is proposed to be acting in a loop
activity with PhoP and PrmA analogous to the
multicomponent loop in Salmonella where the
PhoP-dependent PmrD protein activates the regulatory
protein PmrA, and the activated PmrA then represses
transcription from the PmrD promoter which harbours
binding sites for both the PhoP and PmrA proteins.
Expression of YrbL is induced in low Mg2+ in a
PhoP-dependent fashion and repressed by Fe3+ in a
PmrA-dependent manner.
Length = 199
Score = 27.6 bits (62), Expect = 5.2
Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 8/66 (12%)
Query: 144 NLGLAYQLIDDILDFTGTSASLGKASLTDL-RNGIITAPILFAMEEFPQ--LRAFINSSS 200
+LGL + + I D G + +L DL +NG +TA + A+ EF + L I +
Sbjct: 89 DLGLGL-VTERIRDADGNISP----TLEDLLKNGGLTAALREALNEFKRYLLDNHIVARD 143
Query: 201 DNPANV 206
NP N+
Sbjct: 144 LNPHNI 149
>gnl|CDD|236601 PRK09637, PRK09637, RNA polymerase sigma factor SigZ; Provisional.
Length = 181
Score = 26.9 bits (60), Expect = 8.7
Identities = 14/29 (48%), Positives = 20/29 (68%), Gaps = 1/29 (3%)
Query: 191 QLRAFINSSSDNPANVDVIL-EYLGKSHG 218
QL+AF++S N A+VD +L E L K+H
Sbjct: 13 QLKAFLHSRVSNEADVDDLLQEVLIKTHS 41
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.132 0.361
Gapped
Lambda K H
0.267 0.0724 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,334,055
Number of extensions: 1291529
Number of successful extensions: 1183
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1165
Number of HSP's successfully gapped: 26
Length of query: 267
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 172
Effective length of database: 6,723,972
Effective search space: 1156523184
Effective search space used: 1156523184
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 (21.8 bits)
S2: 58 (26.1 bits)