RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 020685
(322 letters)
>gnl|CDD|178478 PLN02890, PLN02890, geranyl diphosphate synthase.
Length = 422
Score = 594 bits (1532), Expect = 0.0
Identities = 274/322 (85%), Positives = 302/322 (93%), Gaps = 1/322 (0%)
Query: 1 MVVAEVPKLASAAEYFFKMGVEGKRFRPTVLLLMATALNVRVPEPLHDGVEDALATELRT 60
MVVAEVPKLASAAEYFFK+GVEGKRFRPTVLLLMATALNV +PE GV D +A+ELRT
Sbjct: 102 MVVAEVPKLASAAEYFFKVGVEGKRFRPTVLLLMATALNVPLPESTEGGVLDIVASELRT 161
Query: 61 RQQCIAEITEMIHVASLLHDDVLDDADTRRGIGSLNFVMGNKVLAVLAGDFLLSRACVAL 120
RQQ IAEITEMIHVASLLHDDVLDDADTRRG+GSLN VMGNK L+VLAGDFLLSRACVAL
Sbjct: 162 RQQNIAEITEMIHVASLLHDDVLDDADTRRGVGSLNVVMGNK-LSVLAGDFLLSRACVAL 220
Query: 121 ASLKNTEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIA 180
A+LKNTEVV+LLAT VEHLVTGETMQ+T+S +QR SMDYYMQKTYYKTASLISNSCKA+A
Sbjct: 221 AALKNTEVVSLLATAVEHLVTGETMQITSSREQRRSMDYYMQKTYYKTASLISNSCKAVA 280
Query: 181 LLAGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFA 240
+LAGQTAEVA+LAF+YG+NLGLA+QLIDDVLDFTGTSASLGKGSLSDIRHG+ITAPILFA
Sbjct: 281 ILAGQTAEVAVLAFEYGRNLGLAFQLIDDVLDFTGTSASLGKGSLSDIRHGVITAPILFA 340
Query: 241 MEEFPQLRTVVEQGFEDSSNVDIALEYLGKSRGIQKTRELAVKHANLAAAAIDSLPENND 300
MEEFPQLR VV++GF++ +NVDIALEYLGKSRGIQ+TRELA +HANLAAAAI+SLPE +D
Sbjct: 341 MEEFPQLREVVDRGFDNPANVDIALEYLGKSRGIQRTRELAREHANLAAAAIESLPETDD 400
Query: 301 EDVTKSRRALLDLTHRVITRNK 322
EDV SRRAL+DLT RVITRNK
Sbjct: 401 EDVLTSRRALIDLTERVITRNK 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 = 283 bits (726), Expect = 9e-95
Identities = 139/320 (43%), Positives = 206/320 (64%), Gaps = 23/320 (7%)
Query: 1 MVVAEVPKLASAAEYFFKMGVEGKRFRPTVLLLMATALNVRVPEPLHDGVEDALATELRT 60
+V A P L +AAE+ F G GKR RP ++LL++ A A EL
Sbjct: 24 LVGARHPILYAAAEHLFSAG--GKRLRPAIVLLVSRAT--------------AEQQELTP 67
Query: 61 RQQCIAEITEMIHVASLLHDDVLDDADTRRGIGSLNFVMGNKVLAVLAGDFLLSRACVAL 120
R + +AEITEMIH ASL+HDDV+D++DTRRGI +++ + G +V AVLAGDFL ++A L
Sbjct: 68 RHRRLAEITEMIHTASLVHDDVIDESDTRRGIETVHSLFGTRV-AVLAGDFLFAQASWYL 126
Query: 121 ASLKNTEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIA 180
A+L+N EVV L++ V+ GE Q D S++ Y++K++YKTASL++ S KA A
Sbjct: 127 ANLENLEVVKLISKVITDFAEGEIKQGLNQFDSDLSLEDYLEKSFYKTASLVAASSKAAA 186
Query: 181 LLAGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFA 240
+L+ ++VA ++YGK+LGLA+Q++DD+LDFTG++ LGK + SD+ G +TAP+LFA
Sbjct: 187 VLSDVPSQVANDLYEYGKHLGLAFQVVDDILDFTGSTEQLGKPAGSDLMKGNLTAPVLFA 246
Query: 241 MEEFPQLRTVVEQGFEDSSNVDIALEYLGKSRGIQKTRELAVKHANLAAAAIDSLPENND 300
+EE P+L ++E+ F +++ AL + KS GI+K RELA + A LA ++ LP
Sbjct: 247 LEEEPKLSELIEREFSQKGDLEQALSLVRKSGGIKKARELAKEQAQLALQSLSFLPP--- 303
Query: 301 EDVTKSRRALLDLTHRVITR 320
+ R AL +L H V++R
Sbjct: 304 ---SPPREALKELVHFVLSR 320
>gnl|CDD|215462 PLN02857, PLN02857, octaprenyl-diphosphate synthase.
Length = 416
Score = 257 bits (659), Expect = 2e-83
Identities = 129/320 (40%), Positives = 201/320 (62%), Gaps = 20/320 (6%)
Query: 1 MVVAEVPKLASAAEYFFKMGVEGKRFRPTVLLLMATALNVRVPEPLHDGVEDALATELRT 60
+V AE P L SAAE F G GKR RP ++ L++ A E A EL T
Sbjct: 115 IVGAENPVLMSAAEQIFGAG--GKRMRPALVFLVSRAT-----------AELAGLKELTT 161
Query: 61 RQQCIAEITEMIHVASLLHDDVLDDADTRRGIGSLNFVMGNKVLAVLAGDFLLSRACVAL 120
+ +AEITEMIH ASL+HDDVLD++D RRG +++ + G +V AVLAGDF+ +++ L
Sbjct: 162 EHRRLAEITEMIHTASLIHDDVLDESDMRRGKETVHQLYGTRV-AVLAGDFMFAQSSWYL 220
Query: 121 ASLKNTEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIA 180
A+L N EV+ L++ V++ +GE Q ++ D ++D Y+ K+YYKTASLI+ S K+ A
Sbjct: 221 ANLDNLEVIKLISQVIKDFASGEIKQASSLFDCDVTLDEYLLKSYYKTASLIAASTKSAA 280
Query: 181 LLAGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFA 240
+ +G + V ++YGKNLGLA+Q++DD+LDFT ++ LGK + SD+ G +TAP++FA
Sbjct: 281 IFSGVDSSVKEQMYEYGKNLGLAFQVVDDILDFTQSTEQLGKPAGSDLAKGNLTAPVIFA 340
Query: 241 MEEFPQLRTVVEQGFEDSSNVDIALEYLGKSRGIQKTRELAVKHANLAAAAIDSLPENND 300
+E+ P+LR ++E F + +++ A+E + + GI++ +ELA + A+LA ++ LP
Sbjct: 341 LEKEPELREIIESEFCEEGSLEEAIELVNEGGGIERAQELAKEKADLAIQNLECLPR--- 397
Query: 301 EDVTKSRRALLDLTHRVITR 320
R +L D+ + R
Sbjct: 398 ---GAFRSSLEDMVDYNLER 414
>gnl|CDD|164542 CHL00151, preA, prenyl transferase; Reviewed.
Length = 323
Score = 253 bits (649), Expect = 3e-83
Identities = 124/316 (39%), Positives = 197/316 (62%), Gaps = 23/316 (7%)
Query: 7 PKLASAAEYFFKMGVEGKRFRPTVLLLMATALNVRVPEPLHDGVEDALATELRTRQQCIA 66
P L +AA++ F G GKR RP ++LL+A A E++T QQ +A
Sbjct: 31 PILYAAAKHLFSAG--GKRIRPAIVLLVAKATGG--------------NMEIKTSQQRLA 74
Query: 67 EITEMIHVASLLHDDVLDDADTRRGIGSLNFVMGNKVLAVLAGDFLLSRACVALASLKNT 126
EITE+IH ASL+HDDV+D+ RRGI +++ + G K +AVLAGDFL +++ LA+L N
Sbjct: 75 EITEIIHTASLVHDDVIDECSIRRGIPTVHKIFGTK-IAVLAGDFLFAQSSWYLANLNNL 133
Query: 127 EVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIALLAGQT 186
EVV L++ V+ GE Q D S+ Y++K++YKTASLI+ SCKA ALL+
Sbjct: 134 EVVKLISKVITDFAEGEIRQGLVQFDTTLSILNYIEKSFYKTASLIAASCKAAALLSDAD 193
Query: 187 AEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFAMEEFPQ 246
+ + YGK+LGLA+Q+IDDVLD T ++ SLGK SD+++G +TAP+LFA+ + +
Sbjct: 194 EKDHNDFYLYGKHLGLAFQIIDDVLDITSSTESLGKPIGSDLKNGNLTAPVLFALTQNSK 253
Query: 247 LRTVVEQGFEDSSNVDIALEYLGKSRGIQKTRELAVKHANLAAAAIDSLPENNDEDVTKS 306
L ++E+ F ++ ++ AL+ + ++ GI+K ++LA++H A + LP ++ +D
Sbjct: 254 LAKLIEREFCETKDISQALQIIKETNGIEKAKDLALEHMQAAIQCLKFLPPSSAKD---- 309
Query: 307 RRALLDLTHRVITRNK 322
+L+++ + +I R
Sbjct: 310 --SLIEIANFIINRLN 323
>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 = 236 bits (604), Expect = 4e-77
Identities = 102/320 (31%), Positives = 149/320 (46%), Gaps = 64/320 (20%)
Query: 4 AEVPKLASAAEYFFKMGVEGKRFRPTVLLLMATALNVRVPEPLHDGVEDALATELRTRQQ 63
+EV L A Y G GKR RP ++LL A AL E
Sbjct: 1 SEVELLREALRYLLLAG--GKRLRPLLVLLAARALGGPELE----------------AAL 42
Query: 64 CIAEITEMIHVASLLHDDVLDDADTRRGIGSLNFVMGNKVLAVLAGDFLLSRACVALASL 123
+A E++H ASL+HDDV+D++D RRG +++ V GN A+LAGD+LL+RA LA L
Sbjct: 43 RLAAAIELLHTASLVHDDVMDNSDLRRGKPTVHKVFGNAT-AILAGDYLLARAFELLARL 101
Query: 124 KN---TEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIA 180
N + L + + LV G+ + + + D + + Y++ KTA+L + + A
Sbjct: 102 GNPYYPRALELFSEAILELVEGQLLDLLSEYDTDVTEEEYLRIIRLKTAALFAAAPLLGA 161
Query: 181 LLAGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFA 240
LLAG E A +G+NLGLA+Q+ DD+LD G +LGK SD+R G T P+L A
Sbjct: 162 LLAGADEEEAEALKRFGRNLGLAFQIQDDILDLFGDPETLGKPVGSDLREGKCTLPVLLA 221
Query: 241 MEEFPQLRTVVEQGFEDSSNVDIALEYLGKSRGIQKTRELAVKHANLAAAAIDSLPENND 300
+ RELA ++ A A+ +LPE+
Sbjct: 222 L------------------------------------RELAREYEEKALEALKALPESP- 244
Query: 301 EDVTKSRRALLDLTHRVITR 320
+R AL L ++ R
Sbjct: 245 -----AREALRALADFILER 259
>gnl|CDD|223220 COG0142, IspA, Geranylgeranyl pyrophosphate synthase [Coenzyme
metabolism].
Length = 322
Score = 228 bits (583), Expect = 4e-73
Identities = 108/320 (33%), Positives = 166/320 (51%), Gaps = 25/320 (7%)
Query: 5 EVPKLASAAEYFFKMGVEGKRFRPTVLLLMATALNVRVPEPLHDGVEDALATELRTRQQC 64
+ L A Y G GKR RP ++LL A AL + L G DAL
Sbjct: 26 DPELLLEAMRYLLLAG--GKRLRPLLVLLAAEALGI----DLETGGNDALD--------- 70
Query: 65 IAEITEMIHVASLLHDDVLDDADTRRGIGSLNFVMGNKVLAVLAGDFLLSRACVALASLK 124
+A E+IH ASL+HDD++DD D RRG +++ G A+LAGD LL+ A L+ L
Sbjct: 71 LAAAIELIHTASLIHDDLMDDDDLRRGKPTVHAKFGEAT-AILAGDALLAAAFELLSKLG 129
Query: 125 N--TEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIALL 182
+ E + LA + L G+ + + + +++ Y++ KTA+L + + A+L
Sbjct: 130 SEALEAIKALAEAINGLCGGQALDLAFENKP-VTLEEYLRVIELKTAALFAAAAVLGAIL 188
Query: 183 AGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFAME 242
AG E+ DYG+NLGLA+Q+ DD+LD TG LGK SD++ G T P+L A+E
Sbjct: 189 AGADEELLEALEDYGRNLGLAFQIQDDILDITGDEEELGKPVGSDLKEGKPTLPVLLALE 248
Query: 243 EFPQLRTVVEQGFEDSSNVDIALEYLGKSRGIQKTRELAVKHANLAAAAIDSLPENNDED 302
+ + + ++ E V+ ALE L KS I+ + LA + A A++ LP++
Sbjct: 249 KANEDQKLLRILLEGGGEVEEALELLRKSGAIEYAKNLAKTYVEKAKEALEKLPDS---- 304
Query: 303 VTKSRRALLDLTHRVITRNK 322
+++ ALL+L +I R
Sbjct: 305 --EAKEALLELADFIIKRKY 322
>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 = 171 bits (436), Expect = 3e-52
Identities = 92/295 (31%), Positives = 135/295 (45%), Gaps = 59/295 (20%)
Query: 26 FRPTVLLLMATALNVRVPEPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDVLDD 85
RP ++LL+A AL + +A E++H ASL+HDD++DD
Sbjct: 1 SRPLLVLLLARALGGDLE-----------------AALRLAAAVELLHAASLVHDDIVDD 43
Query: 86 ADTRRGIGSLNFVMGNKVLAVLAGDFLLSRACVALASLKNTEVVTLLATVVEHLVTGETM 145
+D RRG + + LA+LAGD+LL+RA LA L + L A + L+ G+ +
Sbjct: 44 SDLRRGKPTAHLRRFGNALAILAGDYLLARAFQLLARLGYPRALELFAEALRELLEGQAL 103
Query: 146 QMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLGLAYQ 205
+ D ++D Y++ YKTA L+ C A L+G E A DYG+ LGLA+Q
Sbjct: 104 DLEFERDTYETLDEYLEYCRYKTAGLVGLLCLLGAGLSGADDEQAEALKDYGRALGLAFQ 163
Query: 206 LIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFAMEEFPQLRTVVEQGFEDSSNVDIAL 265
L DD+LD G + LGK SD+R G IT P++ A E
Sbjct: 164 LTDDLLDVFGDAEELGK-VGSDLREGRITLPVILARER---------------------- 200
Query: 266 EYLGKSRGIQKTRELAVKHANLAAAAIDSLPENNDEDVTKSRRALLDLTHRVITR 320
A ++A A AA+++LP + RRAL+ L + R
Sbjct: 201 ---------------AAEYAEEAYAALEALPPSLPRA----RRALIALADFLYRR 236
>gnl|CDD|215873 pfam00348, polyprenyl_synt, Polyprenyl synthetase.
Length = 260
Score = 160 bits (407), Expect = 1e-47
Identities = 77/226 (34%), Positives = 119/226 (52%), Gaps = 24/226 (10%)
Query: 23 GKRFRPTVLLLMATALNVRVPEPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDV 82
GKR RP LL++ A + V + A EMIH ASL+HDD+
Sbjct: 13 GKRIRP--LLVVLAARALGVEPETLLYL---------------ACAIEMIHTASLVHDDL 55
Query: 83 LDDADTRRGIGSLNFVMGNKVLAVLAGDFLLSRACVALASLK--NTEVVTLLATVVEHLV 140
+D++D RRG + + G A+LAGD LLSRA LA L E +L + + + V
Sbjct: 56 MDNSDLRRGKPTCHKKFGE-AGAILAGDALLSRAFQLLALLGHVRPEPKYILISELANAV 114
Query: 141 TGETM--QMT--TSSDQRCSMDYYMQKTYYKTASLISNSCKAIALLAGQTAEVAILAFDY 196
+ Q+ + + +++ Y++ YKTA+L S + A++AG E +D+
Sbjct: 115 GAQGEVGQLMDLETEGKDITLEEYLRIVSYKTAALFYASVQLGAIVAGADEEDEKDLYDF 174
Query: 197 GKNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFAME 242
G++LGLA+Q+ DD+LD TG + LGK +D++ G T P+L A+E
Sbjct: 175 GRDLGLAFQIQDDILDLTGDTEELGKPVGTDLQEGKSTLPVLLALE 220
>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 = 156 bits (397), Expect = 1e-45
Identities = 92/323 (28%), Positives = 169/323 (52%), Gaps = 30/323 (9%)
Query: 2 VVAEVPKLASAAEYFFKMGVEGKRFRPTVLLLMATALNVRVPEPLHDGVEDALATELRTR 61
V AE P L+ A+ + + G GKR RP +LL + + H
Sbjct: 24 VQAEHPVLSEASLHLLEAG--GKRIRPVFVLLAGKFGDYDLDAIKH-------------- 67
Query: 62 QQCIAEITEMIHVASLLHDDVLDDADTRRGIGSLNFVMGNKVLAVLAGDFLLSRACVALA 121
+A E+IH+ASL+HDDV+DDAD RRG ++ GN++ A+ GD+L +++ +
Sbjct: 68 ---VAVALELIHMASLVHDDVIDDADLRRGRPTIKSKWGNRI-AMYTGDYLFAKSLETMT 123
Query: 122 SLKNTEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIAL 181
+K+ +L+ + + GE Q+ + ++ Y+++ KTA LI+ SC+ A+
Sbjct: 124 EIKDPRAHQILSHTIVEVCRGEIEQIKDKYNFDQNLRTYLRRIKRKTALLIAASCQLGAI 183
Query: 182 LAGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFAM 241
+G + + +G +G++YQ+ DD+LDF GT LGK + D+ G +T P+L+AM
Sbjct: 184 ASGANEAIVKKLYWFGYYVGMSYQITDDILDFVGTEEELGKPAGGDLLQGNVTLPVLYAM 243
Query: 242 EEFPQLRTVVEQGFEDSSNVDIA--LEYLGKSRGIQKTRELAVKHANLAAAAIDSLPENN 299
E+ P L+ +EQ E+++ ++ +E + KS I+ ++ ++ A +D LP+
Sbjct: 244 ED-PFLKKRIEQVLEETTAEEMEPLIEEVKKSDAIEYAYAVSDRYLKKALELLDGLPDG- 301
Query: 300 DEDVTKSRRALLDLTHRVITRNK 322
++++ L ++ + I + K
Sbjct: 302 -----RAKKPLQEIA-KYIGKRK 318
>gnl|CDD|182813 PRK10888, PRK10888, octaprenyl diphosphate synthase; Provisional.
Length = 323
Score = 155 bits (392), Expect = 8e-45
Identities = 103/303 (33%), Positives = 156/303 (51%), Gaps = 30/303 (9%)
Query: 23 GKRFRPTVLLLMATALNVRVPEPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDV 82
GKR RP + +L A A+ + G IA + E IH A+LLHDDV
Sbjct: 44 GKRIRPMIAVLAARAVG-------YQG----------NAHVTIAALIEFIHTATLLHDDV 86
Query: 83 LDDADTRRGIGSLNFVMGNKVLAVLAGDFLLSRACVALASLKNTEVVTLLATVVEHLVTG 142
+D++D RRG + N GN +VL GDF+ +RA + SL + +V+ +++ V + G
Sbjct: 87 VDESDMRRGKATANAAFGNAA-SVLVGDFIYTRAFQMMTSLGSLKVLEVMSEAVNVIAEG 145
Query: 143 ETMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLGL 202
E +Q+ +D + + YM+ Y KTA L + + +LAG T E DYG+ LG
Sbjct: 146 EVLQLMNVNDPDITEENYMRVIYSKTARLFEAAAQCSGILAGCTPEQEKGLQDYGRYLGT 205
Query: 203 AYQLIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFAM-----EEFPQLRTVVEQGFED 257
A+QLIDD+LD++ +LGK D+ G T P+L AM E+ +RT +EQG
Sbjct: 206 AFQLIDDLLDYSADGETLGKNVGDDLNEGKPTLPLLHAMHHGTPEQAAMIRTAIEQG-NG 264
Query: 258 SSNVDIALEYLGKSRGIQKTRELAVKHANLAAAAIDSLPENNDEDVTKSRRALLDLTHRV 317
++ LE + ++ TR+ A + A+ A AA+ LP+ T R AL+ L H
Sbjct: 265 RHLLEPVLEAMNACGSLEWTRQRAEEEADKAIAALQVLPD------TPWREALIGLAHIA 318
Query: 318 ITR 320
+ R
Sbjct: 319 VQR 321
>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 = 138 bits (349), Expect = 2e-39
Identities = 71/256 (27%), Positives = 118/256 (46%), Gaps = 30/256 (11%)
Query: 65 IAEITEMIHVASLLHDDVLDDADTRRGIGSLN--FVMGNKVLAVLAGDFLLSRACVALAS 122
+ E +H ASL+HDD++DD+ TRRG+ + + + A+LAGD LL+ A LA
Sbjct: 15 LRAAVEKLHAASLVHDDIVDDSGTRRGLPTAHLAVAIDGLPEAILAGDLLLADAFEELAR 74
Query: 123 LKNTEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIALL 182
+ E + +LA + L+ G+ + + + +++ Y++ YKTA L+ C A L
Sbjct: 75 EGSPEALEILAEALLDLLEGQLLDLKWRREYVPTLEEYLEYCRYKTAGLVGALCLLGAGL 134
Query: 183 AGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFAME 242
+G AE+ G+ LGLA+QL +D+LD+ G + G T P+L+A+E
Sbjct: 135 SGGEAELLEALRKLGRALGLAFQLTNDLLDYEGDAERGE---------GKCTLPVLYALE 185
Query: 243 EFPQLRTVVEQGFEDSSNVDIALEYLGKSRGIQKTRELAVKHANLAAAAIDSLPENNDED 302
L + KS +++ E K A A ++ L + +
Sbjct: 186 YGVPAE---------------DLLLVEKSGSLEEALEELAKLAEEALKELNELILSLPD- 229
Query: 303 VTKSRRALLDLTHRVI 318
RALL L +
Sbjct: 230 ---VPRALLALALNLY 242
>gnl|CDD|182567 PRK10581, PRK10581, geranyltranstransferase; Provisional.
Length = 299
Score = 76.3 bits (188), Expect = 8e-16
Identities = 60/191 (31%), Positives = 100/191 (52%), Gaps = 15/191 (7%)
Query: 66 AEITEMIHVASLLHDDV--LDDADTRRGIGSLNFVMGNKVLAVLAGDFLLSRACVALASL 123
A E IH SL+HDD+ +DD D RRG+ + + G + A+LAGD L + A L+
Sbjct: 70 AAAVECIHAYSLIHDDLPAMDDDDLRRGLPTCHVKFG-EANAILAGDALQTLAFSILSDA 128
Query: 124 KNTEV--------VTLLATV--VEHLVTGETMQMTTSSDQRCSMDYYMQKTYYKTASLIS 173
EV ++ LA+ + + G+ + + + ++ +D + +KT +LI
Sbjct: 129 PMPEVSDRDRISMISELASASGIAGMCGGQALDLE-AEGKQVPLDALERIHRHKTGALIR 187
Query: 174 NSCKAIALLAGQTAEVAILAFD-YGKNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRHGI 232
+ + AL AG A+ D Y +++GLA+Q+ DD+LD G +A+LGK +D + G
Sbjct: 188 AAVRLGALSAGDKGRRALPVLDRYAESIGLAFQVQDDILDVVGDTATLGKRQGADQQLGK 247
Query: 233 ITAPILFAMEE 243
T P L +E+
Sbjct: 248 STYPALLGLEQ 258
>gnl|CDD|197356 cd10048, Reelin_repeat_4_subrepeat_2, C-terminal subrepeat of
tandem repeat unit 4 of reelin and related proteins.
Reelin is an extracellular glycoprotein involved in
neuronal development, specifically in the brain cortex.
It contains 8 tandemly repeated units, each of which is
composed of two highly similar subrepeats and a central
EGF domain. This model characterizes the C-terminal
subrepeat, which directly contacts the N-terminal
subrepeat and the EGF domain in a compact arrangement.
Consecutive reelin repeat units are packed together to
form an overall rod-like molecular structure. Reelin
repeats 5 and 6 are reported to interact with neuronal
receptors, the apolipoprotein E receptor 2 (ApoER2) and
the very-low-density lipoprotein receptor (VLDLR),
triggering a signaling cascade upon binding and
subsequent tyrosine phosphorylation of the cytoplasmic
disabled-1 (Dab1).
Length = 150
Score = 31.0 bits (70), Expect = 0.43
Identities = 17/77 (22%), Positives = 28/77 (36%), Gaps = 13/77 (16%)
Query: 142 GETMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLG 201
GE ++M S D C+ Y+Q ++ ++ L Y N G
Sbjct: 44 GEGLRMLVSRDLDCTHTLYIQFSFKFITKGTPERSHSVLL-------------QYSINGG 90
Query: 202 LAYQLIDDVLDFTGTSA 218
+ + LID+ T T
Sbjct: 91 ITWHLIDEFYFPTTTDV 107
>gnl|CDD|225744 COG3203, OmpC, Outer membrane protein (porin) [Cell envelope
biogenesis, outer membrane].
Length = 354
Score = 30.4 bits (69), Expect = 1.2
Identities = 12/40 (30%), Positives = 17/40 (42%), Gaps = 2/40 (5%)
Query: 194 FDYGKNLGLAYQLID--DVLDFTGTSASLGKGSLSDIRHG 231
DYG+N G+ Y + D L G A+L + R
Sbjct: 111 LDYGRNYGVLYDVAGWTDPLPEFGGDATLVDDNFMTGRAD 150
>gnl|CDD|224804 COG1892, COG1892, Phosphoenolpyruvate carboxylase [Carbohydrate
transport and metabolism; Energy production and
conversion].
Length = 488
Score = 28.9 bits (65), Expect = 4.1
Identities = 21/81 (25%), Positives = 29/81 (35%), Gaps = 24/81 (29%)
Query: 6 VPKLASAAEYFFKMGVEGKRFRPTVLLLMATALNVRVPEPLHDGVEDALATELRTRQQCI 65
V KL S FF+ + G+ L RVP P VE+A + +
Sbjct: 62 VKKLLSRYPEFFRDHILGEDVF----------LTPRVPNPT---VENAER-------KLL 101
Query: 66 AEITEMI----HVASLLHDDV 82
E E I A + + DV
Sbjct: 102 LETLESIARSYDYARVFYGDV 122
>gnl|CDD|234539 TIGR04317, W_rSAM_matur, tungsten cofactor oxidoreducase radical
SAM maturase. Members of this family are radical SAM
enzymes involved in the maturation of tungsten
(W)-containing cofactors in the enzymes aldehyde
ferredoxin oxidoreductase, formaldehyde ferredoxin
oxidoreductase, and others, and tend to be encoded by an
adjacent gene.
Length = 349
Score = 28.1 bits (63), Expect = 6.5
Identities = 19/82 (23%), Positives = 30/82 (36%), Gaps = 16/82 (19%)
Query: 237 ILFAMEEFPQLRTVVEQGF-EDSSNVDI--ALEYLGKSRGI------------QKTRELA 281
IL E P+L+ +V G E + + D L K RG + EL
Sbjct: 41 ILEEAVELPELKEIVLGGIGEPTVHPDFIDMLTEA-KERGFAVGLSTNGYLLEEMAEELV 99
Query: 282 VKHANLAAAAIDSLPENNDEDV 303
+ +ID+LP+ +
Sbjct: 100 GLGVDKIYVSIDALPDKPYRII 121
>gnl|CDD|148527 pfam06956, RtcR, Regulator of RNA terminal phosphate cyclase.
RtcR is a sigma54-dependent enhancer binding protein
that activates transcription of the rtcBA operon. The
product of the rtcA gene is an RNA 3'-terminal
phosphate cyclase. This domain is found at the N
terminus of the RtcR sequence. RtcR, and other
sigma54-dependent activators, contain pfam00158 in the
central region of the protein sequence.
Length = 183
Score = 27.3 bits (61), Expect = 9.3
Identities = 20/59 (33%), Positives = 28/59 (47%), Gaps = 6/59 (10%)
Query: 25 RFRPTVLLLMATALNVRVPEPLHDGVEDALATELRTRQQCIAEI---TEMIHVASLLHD 80
++RPTV L L V E LHD + +LA +R IA++ TE+ L D
Sbjct: 25 KWRPTVSLCQQPDLPVDRLELLHDARDRSLAERVRAD---IAQVSPETEVRLHPMELDD 80
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 0.133 0.364
Gapped
Lambda K H
0.267 0.0732 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,182,067
Number of extensions: 1576674
Number of successful extensions: 1369
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1334
Number of HSP's successfully gapped: 30
Length of query: 322
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 225
Effective length of database: 6,635,264
Effective search space: 1492934400
Effective search space used: 1492934400
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: 59 (26.5 bits)