RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 018156
(360 letters)
>gnl|CDD|178478 PLN02890, PLN02890, geranyl diphosphate synthase.
Length = 422
Score = 470 bits (1212), Expect = e-166
Identities = 229/355 (64%), Positives = 278/355 (78%), Gaps = 27/355 (7%)
Query: 33 HQPTFRNSNENKKHLDPFSLVGDELSLISMRLRSMVVAEVPELASAAGYFFKEGVEGKKL 92
+Q ++S+ ++ LDPFSLV DELSL++ +LRSMVVAEVP+LASAA YFFK GVEGK+
Sbjct: 68 YQVRHQSSSLVEEQLDPFSLVADELSLLANKLRSMVVAEVPKLASAAEYFFKVGVEGKRF 127
Query: 93 CPTVILLMATALNVCTPELSPNVLGNTLILDLRRRQQCIAEITEMIHVASLIHDDVLDDA 152
PTV+LLMATALNV PE + + + + +LR RQQ IAEITEMIHVASL+HDDVLDDA
Sbjct: 128 RPTVLLLMATALNVPLPESTEGGVLDIVASELRTRQQNIAEITEMIHVASLLHDDVLDDA 187
Query: 153 DTRRGIGSLSSVMGNKLAILAGDLLISRALVALASLKHTEVI------------------ 194
DTRRG+GSL+ VMGNKL++LAGD L+SRA VALA+LK+TEV+
Sbjct: 188 DTRRGVGSLNVVMGNKLSVLAGDFLLSRACVALAALKNTEVVSLLATAVEHLVTGETMQI 247
Query: 195 ---------MECYMQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLI 245
M+ YMQKTY KTA+L+SNSCKAVA L+GQ EVA LAFEYG+NLGLA+QLI
Sbjct: 248 TSSREQRRSMDYYMQKTYYKTASLISNSCKAVAILAGQTAEVAVLAFEYGRNLGLAFQLI 307
Query: 246 DDILDFTGTSASLGKASLTDLRNGIITAPILFAMEEFPQLRAFINSSSDNPANVDVILEY 305
DD+LDFTGTSASLGK SL+D+R+G+ITAPILFAMEEFPQLR ++ DNPANVD+ LEY
Sbjct: 308 DDVLDFTGTSASLGKGSLSDIRHGVITAPILFAMEEFPQLREVVDRGFDNPANVDIALEY 367
Query: 306 LGKSHGIQRTTELALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITRNK 360
LGKS GIQRT ELA +HA+LAAAAI+SLPET D D +R AL+ +T+++ITRNK
Sbjct: 368 LGKSRGIQRTRELAREHANLAAAAIESLPETDDEDVLTSRRALIDLTERVITRNK 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 = 241 bits (618), Expect = 5e-78
Identities = 127/336 (37%), Positives = 194/336 (57%), Gaps = 49/336 (14%)
Query: 50 FSLVGDELSLISMRLRSMVVAEVPELASAAGYFFKEGVEGKKLCPTVILLMATALNVCTP 109
F+ V D+L L++ L+S+V A P L +AA + F G GK+L P ++LL++ A
Sbjct: 7 FAPVEDDLYLLTDNLKSLVGARHPILYAAAEHLFSAG--GKRLRPAIVLLVSRAT----- 59
Query: 110 ELSPNVLGNTLILDLRRRQQCIAEITEMIHVASLIHDDVLDDADTRRGIGSLSSVMGNKL 169
+L R + +AEITEMIH ASL+HDDV+D++DTRRGI ++ S+ G ++
Sbjct: 60 ---------AEQQELTPRHRRLAEITEMIHTASLVHDDVIDESDTRRGIETVHSLFGTRV 110
Query: 170 AILAGDLLISRALVALASLKHTEVI---------------------------MECYMQKT 202
A+LAGD L ++A LA+L++ EV+ +E Y++K+
Sbjct: 111 AVLAGDFLFAQASWYLANLENLEVVKLISKVITDFAEGEIKQGLNQFDSDLSLEDYLEKS 170
Query: 203 YNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKAS 262
+ KTA+LV+ S KA A LS +VA +EYGK+LGLA+Q++DDILDFTG++ LGK +
Sbjct: 171 FYKTASLVAASSKAAAVLSDVPSQVANDLYEYGKHLGLAFQVVDDILDFTGSTEQLGKPA 230
Query: 263 LTDLRNGIITAPILFAMEEFPQLRAFINSSSDNPANVDVILEYLGKSHGIQRTTELALKH 322
+DL G +TAP+LFA+EE P+L I +++ L + KS GI++ ELA +
Sbjct: 231 GSDLMKGNLTAPVLFALEEEPKLSELIEREFSQKGDLEQALSLVRKSGGIKKARELAKEQ 290
Query: 323 ASLAAAAIDSLPETHDVDATNARTALVHITQKIITR 358
A LA ++ LP + R AL + +++R
Sbjct: 291 AQLALQSLSFLPP------SPPREALKELVHFVLSR 320
>gnl|CDD|215462 PLN02857, PLN02857, octaprenyl-diphosphate synthase.
Length = 416
Score = 232 bits (594), Expect = 4e-73
Identities = 127/380 (33%), Positives = 200/380 (52%), Gaps = 49/380 (12%)
Query: 9 RIAARTPRNSLPSCRWILSHRRYGHQPTFRNSNENKKHL---DPFSLVGDELSLISMRLR 65
R R S +++ G E+K+ + + F V D+L ++ L+
Sbjct: 54 RDIGRCRVVSPSPETSLVNGIGQGPTVALDLKAESKEPISLSELFEPVADDLQQLNDNLQ 113
Query: 66 SMVVAEVPELASAAGYFFKEGVEGKKLCPTVILLMATALNVCTPELSPNVLGNTLILDLR 125
S+V AE P L SAA F G GK++ P ++ L++ A T EL+ + +L
Sbjct: 114 SIVGAENPVLMSAAEQIFGAG--GKRMRPALVFLVSRA----TAELAG-------LKELT 160
Query: 126 RRQQCIAEITEMIHVASLIHDDVLDDADTRRGIGSLSSVMGNKLAILAGDLLISRALVAL 185
+ +AEITEMIH ASLIHDDVLD++D RRG ++ + G ++A+LAGD + +++ L
Sbjct: 161 TEHRRLAEITEMIHTASLIHDDVLDESDMRRGKETVHQLYGTRVAVLAGDFMFAQSSWYL 220
Query: 186 ASLKHTEVI---------------------------MECYMQKTYNKTAALVSNSCKAVA 218
A+L + EVI ++ Y+ K+Y KTA+L++ S K+ A
Sbjct: 221 ANLDNLEVIKLISQVIKDFASGEIKQASSLFDCDVTLDEYLLKSYYKTASLIAASTKSAA 280
Query: 219 YLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGIITAPILFA 278
SG V +EYGKNLGLA+Q++DDILDFT ++ LGK + +DL G +TAP++FA
Sbjct: 281 IFSGVDSSVKEQMYEYGKNLGLAFQVVDDILDFTQSTEQLGKPAGSDLAKGNLTAPVIFA 340
Query: 279 MEEFPQLRAFINSSSDNPANVDVILEYLGKSHGIQRTTELALKHASLAAAAIDSLPETHD 338
+E+ P+LR I S +++ +E + + GI+R ELA + A LA ++ LP
Sbjct: 341 LEKEPELREIIESEFCEEGSLEEAIELVNEGGGIERAQELAKEKADLAIQNLECLPR--- 397
Query: 339 VDATNARTALVHITQKIITR 358
R++L + + R
Sbjct: 398 ---GAFRSSLEDMVDYNLER 414
>gnl|CDD|164542 CHL00151, preA, prenyl transferase; Reviewed.
Length = 323
Score = 210 bits (537), Expect = 8e-66
Identities = 111/338 (32%), Positives = 183/338 (54%), Gaps = 49/338 (14%)
Query: 50 FSLVGDELSLISMRLRSMVVAEVPELASAAGYFFKEGVEGKKLCPTVILLMATALNVCTP 109
+ + +EL ++ L+ ++ + P L +AA + F G GK++ P ++LL+A A
Sbjct: 8 LTPIEEELLILEDNLKKLIGSGHPILYAAAKHLFSAG--GKRIRPAIVLLVAKAT----- 60
Query: 110 ELSPNVLGNTLILDLRRRQQCIAEITEMIHVASLIHDDVLDDADTRRGIGSLSSVMGNKL 169
G + + QQ +AEITE+IH ASL+HDDV+D+ RRGI ++ + G K+
Sbjct: 61 -------GGNMEIKTS--QQRLAEITEIIHTASLVHDDVIDECSIRRGIPTVHKIFGTKI 111
Query: 170 AILAGDLLISRALVALASLKHTEVI---------------------------MECYMQKT 202
A+LAGD L +++ LA+L + EV+ + Y++K+
Sbjct: 112 AVLAGDFLFAQSSWYLANLNNLEVVKLISKVITDFAEGEIRQGLVQFDTTLSILNYIEKS 171
Query: 203 YNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKAS 262
+ KTA+L++ SCKA A LS E+ + YGK+LGLA+Q+IDD+LD T ++ SLGK
Sbjct: 172 FYKTASLIAASCKAAALLSDADEKDHNDFYLYGKHLGLAFQIIDDVLDITSSTESLGKPI 231
Query: 263 LTDLRNGIITAPILFAMEEFPQLRAFINSSSDNPANVDVILEYLGKSHGIQRTTELALKH 322
+DL+NG +TAP+LFA+ + +L I ++ L+ + +++GI++ +LAL+H
Sbjct: 232 GSDLKNGNLTAPVLFALTQNSKLAKLIEREFCETKDISQALQIIKETNGIEKAKDLALEH 291
Query: 323 ASLAAAAIDSLPETHDVDATNARTALVHITQKIITRNK 360
A + LP + D +L+ I II R
Sbjct: 292 MQAAIQCLKFLPPSSAKD------SLIEIANFIINRLN 323
>gnl|CDD|223220 COG0142, IspA, Geranylgeranyl pyrophosphate synthase [Coenzyme
metabolism].
Length = 322
Score = 208 bits (532), Expect = 4e-65
Identities = 105/342 (30%), Positives = 159/342 (46%), Gaps = 50/342 (14%)
Query: 48 DPFSLVGDELSLISMRLRSMV-VAEVPELASAAGYFFKEGVEGKKLCPTVILLMATALNV 106
D +L+ L+ I L ++ ++ L A Y G GK+L P ++LL A AL +
Sbjct: 2 DLLALLLKRLARIEELLSELLSGSDPELLLEAMRYLLLAG--GKRLRPLLVLLAAEALGI 59
Query: 107 CTPELSPNVLGNTLILDLRRRQQCIAEITEMIHVASLIHDDVLDDADTRRGIGSLSSVMG 166
+ L +A E+IH ASLIHDD++DD D RRG ++ + G
Sbjct: 60 DLETGGNDALD-------------LAAAIELIHTASLIHDDLMDDDDLRRGKPTVHAKFG 106
Query: 167 NKLAILAGDLLISRALVALASL----------------------------KHTEVIMECY 198
AILAGD L++ A L+ L ++ V +E Y
Sbjct: 107 EATAILAGDALLAAAFELLSKLGSEALEAIKALAEAINGLCGGQALDLAFENKPVTLEEY 166
Query: 199 MQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASL 258
++ KTAAL + + A L+G EE+ +YG+NLGLA+Q+ DDILD TG L
Sbjct: 167 LRVIELKTAALFAAAAVLGAILAGADEELLEALEDYGRNLGLAFQIQDDILDITGDEEEL 226
Query: 259 GKASLTDLRNGIITAPILFAMEEFPQLRAFINSSSDNPANVDVILEYLGKSHGIQRTTEL 318
GK +DL+ G T P+L A+E+ + + + + V+ LE L KS I+ L
Sbjct: 227 GKPVGSDLKEGKPTLPVLLALEKANEDQKLLRILLEGGGEVEEALELLRKSGAIEYAKNL 286
Query: 319 ALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITRNK 360
A + A A++ LP++ A+ AL+ + II R
Sbjct: 287 AKTYVEKAKEALEKLPDSE------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 = 193 bits (494), Expect = 4e-60
Identities = 98/319 (30%), Positives = 136/319 (42%), Gaps = 90/319 (28%)
Query: 70 AEVPELASAAGYFFKEGVEGKKLCPTVILLMATALNVCTPELSPNVLGNTLILDLRRRQQ 129
+EV L A Y G GK+L P ++LL A AL
Sbjct: 1 SEVELLREALRYLLLAG--GKRLRPLLVLLAARALGG----------------PELEAAL 42
Query: 130 CIAEITEMIHVASLIHDDVLDDADTRRGIGSLSSVMGNKLAILAGDLLISRALVALASLK 189
+A E++H ASL+HDDV+D++D RRG ++ V GN AILAGD L++RA LA L
Sbjct: 43 RLAAAIELLHTASLVHDDVMDNSDLRRGKPTVHKVFGNATAILAGDYLLARAFELLARLG 102
Query: 190 H----------TEVIMEC--------------------YMQKTYNKTAALVSNSCKAVAY 219
+ +E I+E Y++ KTAAL + + A
Sbjct: 103 NPYYPRALELFSEAILELVEGQLLDLLSEYDTDVTEEEYLRIIRLKTAALFAAAPLLGAL 162
Query: 220 LSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGIITAPILFAM 279
L+G EE A +G+NLGLA+Q+ DDILD G +LGK +DLR G T P+L A+
Sbjct: 163 LAGADEEEAEALKRFGRNLGLAFQIQDDILDLFGDPETLGKPVGSDLREGKCTLPVLLAL 222
Query: 280 EEFPQLRAFINSSSDNPANVDVILEYLGKSHGIQRTTELALKHASLAAAAIDSLPETHDV 339
ELA ++ A A+ +LPE
Sbjct: 223 R------------------------------------ELAREYEEKALEALKALPE---- 242
Query: 340 DATNARTALVHITQKIITR 358
+ AR AL + I+ R
Sbjct: 243 --SPAREALRALADFILER 259
>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 = 148 bits (376), Expect = 5e-42
Identities = 99/340 (29%), Positives = 161/340 (47%), Gaps = 53/340 (15%)
Query: 48 DPFSLVGDELSLISMRLRSMVVAEVPELASAAGYFFKEGVEGKKLCPTVILLMATALNVC 107
D +S + ++ I L V AE P L+ A+ + + G GK++ P +LL
Sbjct: 4 DIYSFLQKDIDSIEKELEKAVQAEHPVLSEASLHLLEAG--GKRIRPVFVLLAGK----- 56
Query: 108 TPELSPNVLGNTLILDLRRRQQCIAEITEMIHVASLIHDDVLDDADTRRGIGSLSSVMGN 167
G+ DL + +A E+IH+ASL+HDDV+DDAD RRG ++ S GN
Sbjct: 57 --------FGD---YDLDAIKH-VAVALELIHMASLVHDDVIDDADLRRGRPTIKSKWGN 104
Query: 168 KLAILAGDLLISRALVALASLK----HT---EVIME-C-------------------YMQ 200
++A+ GD L +++L + +K H I+E C Y++
Sbjct: 105 RIAMYTGDYLFAKSLETMTEIKDPRAHQILSHTIVEVCRGEIEQIKDKYNFDQNLRTYLR 164
Query: 201 KTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGK 260
+ KTA L++ SC+ A SG E + + +G +G++YQ+ DDILDF GT LGK
Sbjct: 165 RIKRKTALLIAASCQLGAIASGANEAIVKKLYWFGYYVGMSYQITDDILDFVGTEEELGK 224
Query: 261 ASLTDLRNGIITAPILFAMEEFPQLRAFINSSSDNPAN-VDVILEYLGKSHGIQRTTELA 319
+ DL G +T P+L+AME+ + + A ++ ++E + KS I+ ++
Sbjct: 225 PAGGDLLQGNVTLPVLYAMEDPFLKKRIEQVLEETTAEEMEPLIEEVKKSDAIEYAYAVS 284
Query: 320 LKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITRN 359
++ A +D LP A+ L I + I R
Sbjct: 285 DRYLKKALELLDGLP------DGRAKKPLQEIAKYIGKRK 318
>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 = 144 bits (366), Expect = 2e-41
Identities = 69/196 (35%), Positives = 96/196 (48%), Gaps = 29/196 (14%)
Query: 115 VLGNTLILDLRRRQQCIAEITEMIHVASLIHDDVLDDADTRRGIGSLSSV-MGNKLAILA 173
+L + +A E++H ASL+HDD++DD+D RRG + GN LAILA
Sbjct: 7 LLLARALGGDLEAALRLAAAVELLHAASLVHDDIVDDSDLRRGKPTAHLRRFGNALAILA 66
Query: 174 GDLLISRALVALASLKHTEVI---------------------------MECYMQKTYNKT 206
GD L++RA LA L + + ++ Y++ KT
Sbjct: 67 GDYLLARAFQLLARLGYPRALELFAEALRELLEGQALDLEFERDTYETLDEYLEYCRYKT 126
Query: 207 AALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDL 266
A LV C A LSG +E A +YG+ LGLA+QL DD+LD G + LGK +DL
Sbjct: 127 AGLVGLLCLLGAGLSGADDEQAEALKDYGRALGLAFQLTDDLLDVFGDAEELGKV-GSDL 185
Query: 267 RNGIITAPILFAMEEF 282
R G IT P++ A E
Sbjct: 186 REGRITLPVILARERA 201
>gnl|CDD|215873 pfam00348, polyprenyl_synt, Polyprenyl synthetase.
Length = 260
Score = 143 bits (363), Expect = 1e-40
Identities = 77/225 (34%), Positives = 107/225 (47%), Gaps = 50/225 (22%)
Query: 89 GKKLCPTVILLMATALNVCTPELSPNVLGNTLILDLRRRQQCIAEITEMIHVASLIHDDV 148
GK++ P +++L A AL V L +A EMIH ASL+HDD+
Sbjct: 13 GKRIRPLLVVLAARALGVEPETLLY-----------------LACAIEMIHTASLVHDDL 55
Query: 149 LDDADTRRGIGSLSSVMGNKLAILAGDLLISRALVALASLKH--------------TEVI 194
+D++D RRG + G AILAGD L+SRA LA L H V
Sbjct: 56 MDNSDLRRGKPTCHKKFGEAGAILAGDALLSRAFQLLALLGHVRPEPKYILISELANAVG 115
Query: 195 MEC-------------------YMQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYG 235
+ Y++ KTAAL S + A ++G EE +++G
Sbjct: 116 AQGEVGQLMDLETEGKDITLEEYLRIVSYKTAALFYASVQLGAIVAGADEEDEKDLYDFG 175
Query: 236 KNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGIITAPILFAME 280
++LGLA+Q+ DDILD TG + LGK TDL+ G T P+L A+E
Sbjct: 176 RDLGLAFQIQDDILDLTGDTEELGKPVGTDLQEGKSTLPVLLALE 220
>gnl|CDD|182813 PRK10888, PRK10888, octaprenyl diphosphate synthase; Provisional.
Length = 323
Score = 116 bits (291), Expect = 8e-30
Identities = 92/303 (30%), Positives = 142/303 (46%), Gaps = 52/303 (17%)
Query: 80 GYFFKEGVEGKKLCPTVILLMATALNVCTPELSPNVLGNTLILDLRRRQQCIAEITEMIH 139
GY+ G GK++ P + +L A A+ GN + IA + E IH
Sbjct: 36 GYYIISG-GGKRIRPMIAVLAARAVGY---------QGNAHV--------TIAALIEFIH 77
Query: 140 VASLIHDDVLDDADTRRGIGSLSSVMGNKLAILAGDLLISRA---LVALASLKHTEV--- 193
A+L+HDDV+D++D RRG + ++ GN ++L GD + +RA + +L SLK EV
Sbjct: 78 TATLLHDDVVDESDMRRGKATANAAFGNAASVLVGDFIYTRAFQMMTSLGSLKVLEVMSE 137
Query: 194 ------------IMEC---------YMQKTYNKTAALVSNSCKAVAYLSGQREEVATLAF 232
+M YM+ Y+KTA L + + L+G E
Sbjct: 138 AVNVIAEGEVLQLMNVNDPDITEENYMRVIYSKTARLFEAAAQCSGILAGCTPEQEKGLQ 197
Query: 233 EYGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGIITAPILFAMEE-FPQLRAFINS 291
+YG+ LG A+QLIDD+LD++ +LGK DL G T P+L AM P+ A I +
Sbjct: 198 DYGRYLGTAFQLIDDLLDYSADGETLGKNVGDDLNEGKPTLPLLHAMHHGTPEQAAMIRT 257
Query: 292 SSDNPAN---VDVILEYLGKSHGIQRTTELALKHASLAAAAIDSLPETHDVDATNARTAL 348
+ + ++ +LE + ++ T + A + A A AA+ LP+T A L
Sbjct: 258 AIEQGNGRHLLEPVLEAMNACGSLEWTRQRAEEEADKAIAALQVLPDT---PWREALIGL 314
Query: 349 VHI 351
HI
Sbjct: 315 AHI 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 = 107 bits (269), Expect = 3e-27
Identities = 66/256 (25%), Positives = 102/256 (39%), Gaps = 58/256 (22%)
Query: 131 IAEITEMIHVASLIHDDVLDDADTRRGIGSLSSVM---GNKLAILAGDLLISRALVALAS 187
+ E +H ASL+HDD++DD+ TRRG+ + + G AILAGDLL++ A LA
Sbjct: 15 LRAAVEKLHAASLVHDDIVDDSGTRRGLPTAHLAVAIDGLPEAILAGDLLLADAFEELAR 74
Query: 188 LKHTEVI---------------------------MECYMQKTYNKTAALVSNSCKAVAYL 220
E + +E Y++ KTA LV C A L
Sbjct: 75 EGSPEALEILAEALLDLLEGQLLDLKWRREYVPTLEEYLEYCRYKTAGLVGALCLLGAGL 134
Query: 221 SGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGIITAPILFAME 280
SG E+ + G+ LGLA+QL +D+LD+ G + G T P+L+A+E
Sbjct: 135 SGGEAELLEALRKLGRALGLAFQLTNDLLDYEGDAERG---------EGKCTLPVLYALE 185
Query: 281 EFPQLRAFINSSSDNPANVDVILEYLGKSHGIQRTTELALKHASLAAAAIDSLPETHDVD 340
+ + KS ++ E K A A ++ L +
Sbjct: 186 YGVPAEDLL---------------LVEKSGSLEEALEELAKLAEEALKELNELILSLPD- 229
Query: 341 ATNARTALVHITQKII 356
AL+ + +
Sbjct: 230 ---VPRALLALALNLY 242
>gnl|CDD|182567 PRK10581, PRK10581, geranyltranstransferase; Provisional.
Length = 299
Score = 68.3 bits (167), Expect = 6e-13
Identities = 58/189 (30%), Positives = 82/189 (43%), Gaps = 39/189 (20%)
Query: 132 AEITEMIHVASLIHDDV--LDDADTRRGIGSLSSVMGNKLAILAGDLLISRALVALASLK 189
A E IH SLIHDD+ +DD D RRG+ + G AILAGD L + A L+
Sbjct: 70 AAAVECIHAYSLIHDDLPAMDDDDLRRGLPTCHVKFGEANAILAGDALQTLAFSILSDAP 129
Query: 190 HTEV--------IMECYM----------------------------QKTYNKTAALVSNS 213
EV I E + +KT AL+ +
Sbjct: 130 MPEVSDRDRISMISELASASGIAGMCGGQALDLEAEGKQVPLDALERIHRHKTGALIRAA 189
Query: 214 CKAVAYLSGQREEVATLAFE-YGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGIIT 272
+ A +G + A + Y +++GLA+Q+ DDILD G +A+LGK D + G T
Sbjct: 190 VRLGALSAGDKGRRALPVLDRYAESIGLAFQVQDDILDVVGDTATLGKRQGADQQLGKST 249
Query: 273 APILFAMEE 281
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 = 32.3 bits (74), Expect = 0.40
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 5/47 (10%)
Query: 270 IITAPILFAMEEFPQLRAFIN--SSSDNPAN--VDVILEYLGKSHGI 312
++ 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 = 29.7 bits (67), Expect = 2.1
Identities = 15/61 (24%), Positives = 22/61 (36%), Gaps = 9/61 (14%)
Query: 221 SGQREEVATLAFE------YGKNLGLAYQLID--DILDFTGTSASLGKASLTDLR-NGII 271
R A L YG+N G+ Y + D L G A+L + R + +
Sbjct: 94 LFTRLAFAGLKGADFGSLDYGRNYGVLYDVAGWTDPLPEFGGDATLVDDNFMTGRADNVA 153
Query: 272 T 272
T
Sbjct: 154 T 154
>gnl|CDD|234826 PRK00730, rnpA, ribonuclease P; Reviewed.
Length = 138
Score = 28.0 bits (62), Expect = 4.4
Identities = 13/36 (36%), Positives = 21/36 (58%), Gaps = 2/36 (5%)
Query: 3 FSQLVYRIAARTPRNSLPSCRWILSHRRYGHQPTFR 38
F ++V R A R R++LP C+ ++S + QP F
Sbjct: 65 FKRIV-REAFRHVRHNLPGCQIVVSPKG-NSQPDFL 98
>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 = 5.2
Identities = 16/71 (22%), Positives = 30/71 (42%), Gaps = 2/71 (2%)
Query: 280 EEFPQLRAFINSSSDNPANVDVILEYLGKSHGIQRTTELALKHASLAAAAI-DSLPETHD 338
FP R IN SD+ A +++ E L + +R L + AA+ + P+
Sbjct: 150 AAFPDRRFLINFKSDDAAEGELLAEKL-ATLPRKRLQVLTVYGGDKPIAALRELTPDLRT 208
Query: 339 VDATNARTALV 349
+ + + L+
Sbjct: 209 LSKASMKDCLI 219
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
0.320 0.133 0.375
Gapped
Lambda K H
0.267 0.0756 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,183,652
Number of extensions: 1782791
Number of successful extensions: 1503
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1480
Number of HSP's successfully gapped: 28
Length of query: 360
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 262
Effective length of database: 6,590,910
Effective search space: 1726818420
Effective search space used: 1726818420
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: 60 (26.8 bits)