RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 020765
(321 letters)
>gnl|CDD|178478 PLN02890, PLN02890, geranyl diphosphate synthase.
Length = 422
Score = 598 bits (1544), Expect = 0.0
Identities = 274/321 (85%), Positives = 302/321 (94%)
Query: 1 MVVAEVPKLASAAEYFFKMGVEGKRFRPTVLLLMATALNVRVPEPLHDGVEDALATELRT 60
MVVAEVPKLASAAEYFFK+GVEGKRFRPTVLLLMATALNV +PE GV D +A+ELRT
Sbjct: 102 MVVAEVPKLASAAEYFFKVGVEGKRFRPTVLLLMATALNVPLPESTEGGVLDIVASELRT 161
Query: 61 RQQCIAEITEMIHVASLLHDDVLDDADTRRGIGSLNFVMGNKLAVLAGDFLLSRACVALA 120
RQQ IAEITEMIHVASLLHDDVLDDADTRRG+GSLN VMGNKL+VLAGDFLLSRACVALA
Sbjct: 162 RQQNIAEITEMIHVASLLHDDVLDDADTRRGVGSLNVVMGNKLSVLAGDFLLSRACVALA 221
Query: 121 SLKNTEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIAL 180
+LKNTEVV+LLAT VEHLVTGETMQ+T+S +QR SMDYYMQKTYYKTASLISNSCKA+A+
Sbjct: 222 ALKNTEVVSLLATAVEHLVTGETMQITSSREQRRSMDYYMQKTYYKTASLISNSCKAVAI 281
Query: 181 LAGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFAM 240
LAGQTAEVA+LAF+YG+NLGLA+QLIDDVLDFTGTSASLGKGSLSDIRHG+ITAPILFAM
Sbjct: 282 LAGQTAEVAVLAFEYGRNLGLAFQLIDDVLDFTGTSASLGKGSLSDIRHGVITAPILFAM 341
Query: 241 EEFPQLRTVVEQGFEDSSNVDIALEYLGKSRGIQKTRELAVKHANLAAAAIDSLPENNDE 300
EEFPQLR VV++GF++ +NVDIALEYLGKSRGIQ+TRELA +HANLAAAAI+SLPE +DE
Sbjct: 342 EEFPQLREVVDRGFDNPANVDIALEYLGKSRGIQRTRELAREHANLAAAAIESLPETDDE 401
Query: 301 DVTKSRRALLDLTHRVITRNK 321
DV SRRAL+DLT RVITRNK
Sbjct: 402 DVLTSRRALIDLTERVITRNK 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 = 286 bits (734), Expect = 6e-96
Identities = 138/319 (43%), Positives = 206/319 (64%), Gaps = 22/319 (6%)
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 RQQCIAEITEMIHVASLLHDDVLDDADTRRGIGSLNFVMGNKLAVLAGDFLLSRACVALA 120
R + +AEITEMIH ASL+HDDV+D++DTRRGI +++ + G ++AVLAGDFL ++A LA
Sbjct: 68 RHRRLAEITEMIHTASLVHDDVIDESDTRRGIETVHSLFGTRVAVLAGDFLFAQASWYLA 127
Query: 121 SLKNTEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIAL 180
+L+N EVV L++ V+ GE Q D S++ Y++K++YKTASL++ S KA A+
Sbjct: 128 NLENLEVVKLISKVITDFAEGEIKQGLNQFDSDLSLEDYLEKSFYKTASLVAASSKAAAV 187
Query: 181 LAGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFAM 240
L+ ++VA ++YGK+LGLA+Q++DD+LDFTG++ LGK + SD+ G +TAP+LFA+
Sbjct: 188 LSDVPSQVANDLYEYGKHLGLAFQVVDDILDFTGSTEQLGKPAGSDLMKGNLTAPVLFAL 247
Query: 241 EEFPQLRTVVEQGFEDSSNVDIALEYLGKSRGIQKTRELAVKHANLAAAAIDSLPENNDE 300
EE P+L ++E+ F +++ AL + KS GI+K RELA + A LA ++ LP
Sbjct: 248 EEEPKLSELIEREFSQKGDLEQALSLVRKSGGIKKARELAKEQAQLALQSLSFLPP---- 303
Query: 301 DVTKSRRALLDLTHRVITR 319
+ R AL +L H V++R
Sbjct: 304 --SPPREALKELVHFVLSR 320
>gnl|CDD|164542 CHL00151, preA, prenyl transferase; Reviewed.
Length = 323
Score = 258 bits (661), Expect = 6e-85
Identities = 124/315 (39%), Positives = 197/315 (62%), Gaps = 22/315 (6%)
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 EITEMIHVASLLHDDVLDDADTRRGIGSLNFVMGNKLAVLAGDFLLSRACVALASLKNTE 126
EITE+IH ASL+HDDV+D+ RRGI +++ + G K+AVLAGDFL +++ LA+L N E
Sbjct: 75 EITEIIHTASLVHDDVIDECSIRRGIPTVHKIFGTKIAVLAGDFLFAQSSWYLANLNNLE 134
Query: 127 VVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIALLAGQTA 186
VV L++ V+ GE Q D S+ Y++K++YKTASLI+ SCKA ALL+
Sbjct: 135 VVKLISKVITDFAEGEIRQGLVQFDTTLSILNYIEKSFYKTASLIAASCKAAALLSDADE 194
Query: 187 EVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFAMEEFPQL 246
+ + YGK+LGLA+Q+IDDVLD T ++ SLGK SD+++G +TAP+LFA+ + +L
Sbjct: 195 KDHNDFYLYGKHLGLAFQIIDDVLDITSSTESLGKPIGSDLKNGNLTAPVLFALTQNSKL 254
Query: 247 RTVVEQGFEDSSNVDIALEYLGKSRGIQKTRELAVKHANLAAAAIDSLPENNDEDVTKSR 306
++E+ F ++ ++ AL+ + ++ GI+K ++LA++H A + LP ++ +D
Sbjct: 255 AKLIEREFCETKDISQALQIIKETNGIEKAKDLALEHMQAAIQCLKFLPPSSAKD----- 309
Query: 307 RALLDLTHRVITRNK 321
+L+++ + +I R
Sbjct: 310 -SLIEIANFIINRLN 323
>gnl|CDD|215462 PLN02857, PLN02857, octaprenyl-diphosphate synthase.
Length = 416
Score = 260 bits (666), Expect = 2e-84
Identities = 128/319 (40%), Positives = 201/319 (63%), Gaps = 19/319 (5%)
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 RQQCIAEITEMIHVASLLHDDVLDDADTRRGIGSLNFVMGNKLAVLAGDFLLSRACVALA 120
+ +AEITEMIH ASL+HDDVLD++D RRG +++ + G ++AVLAGDF+ +++ LA
Sbjct: 162 EHRRLAEITEMIHTASLIHDDVLDESDMRRGKETVHQLYGTRVAVLAGDFMFAQSSWYLA 221
Query: 121 SLKNTEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIAL 180
+L N EV+ L++ V++ +GE Q ++ D ++D Y+ K+YYKTASLI+ S K+ A+
Sbjct: 222 NLDNLEVIKLISQVIKDFASGEIKQASSLFDCDVTLDEYLLKSYYKTASLIAASTKSAAI 281
Query: 181 LAGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFAM 240
+G + V ++YGKNLGLA+Q++DD+LDFT ++ LGK + SD+ G +TAP++FA+
Sbjct: 282 FSGVDSSVKEQMYEYGKNLGLAFQVVDDILDFTQSTEQLGKPAGSDLAKGNLTAPVIFAL 341
Query: 241 EEFPQLRTVVEQGFEDSSNVDIALEYLGKSRGIQKTRELAVKHANLAAAAIDSLPENNDE 300
E+ P+LR ++E F + +++ A+E + + GI++ +ELA + A+LA ++ LP
Sbjct: 342 EKEPELREIIESEFCEEGSLEEAIELVNEGGGIERAQELAKEKADLAIQNLECLPR---- 397
Query: 301 DVTKSRRALLDLTHRVITR 319
R +L D+ + R
Sbjct: 398 --GAFRSSLEDMVDYNLER 414
>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 = 240 bits (614), Expect = 1e-78
Identities = 102/319 (31%), Positives = 149/319 (46%), Gaps = 63/319 (19%)
Query: 4 AEVPKLASAAEYFFKMGVEGKRFRPTVLLLMATALNVRVPEPLHDGVEDALATELRTRQQ 63
+EV L A Y G GKR RP ++LL A AL E
Sbjct: 1 SEVELLREALRYLLLAG--GKRLRPLLVLLAARALGGPELE----------------AAL 42
Query: 64 CIAEITEMIHVASLLHDDVLDDADTRRGIGSLNFVMGNKLAVLAGDFLLSRACVALASLK 123
+A E++H ASL+HDDV+D++D RRG +++ V GN A+LAGD+LL+RA LA L
Sbjct: 43 RLAAAIELLHTASLVHDDVMDNSDLRRGKPTVHKVFGNATAILAGDYLLARAFELLARLG 102
Query: 124 N---TEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIAL 180
N + L + + LV G+ + + + D + + Y++ KTA+L + + AL
Sbjct: 103 NPYYPRALELFSEAILELVEGQLLDLLSEYDTDVTEEEYLRIIRLKTAALFAAAPLLGAL 162
Query: 181 LAGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFAM 240
LAG E A +G+NLGLA+Q+ DD+LD G +LGK SD+R G T P+L A+
Sbjct: 163 LAGADEEEAEALKRFGRNLGLAFQIQDDILDLFGDPETLGKPVGSDLREGKCTLPVLLAL 222
Query: 241 EEFPQLRTVVEQGFEDSSNVDIALEYLGKSRGIQKTRELAVKHANLAAAAIDSLPENNDE 300
RELA ++ A A+ +LPE+
Sbjct: 223 ------------------------------------RELAREYEEKALEALKALPESP-- 244
Query: 301 DVTKSRRALLDLTHRVITR 319
+R AL L ++ R
Sbjct: 245 ----AREALRALADFILER 259
>gnl|CDD|223220 COG0142, IspA, Geranylgeranyl pyrophosphate synthase [Coenzyme
metabolism].
Length = 322
Score = 231 bits (591), Expect = 2e-74
Identities = 108/319 (33%), Positives = 166/319 (52%), Gaps = 24/319 (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 IAEITEMIHVASLLHDDVLDDADTRRGIGSLNFVMGNKLAVLAGDFLLSRACVALASLKN 124
+A E+IH ASL+HDD++DD D RRG +++ G A+LAGD LL+ A L+ L +
Sbjct: 71 LAAAIELIHTASLIHDDLMDDDDLRRGKPTVHAKFGEATAILAGDALLAAAFELLSKLGS 130
Query: 125 --TEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIALLA 182
E + LA + L G+ + + + +++ Y++ KTA+L + + A+LA
Sbjct: 131 EALEAIKALAEAINGLCGGQALDLAFENKP-VTLEEYLRVIELKTAALFAAAAVLGAILA 189
Query: 183 GQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFAMEE 242
G E+ DYG+NLGLA+Q+ DD+LD TG LGK SD++ G T P+L A+E+
Sbjct: 190 GADEELLEALEDYGRNLGLAFQIQDDILDITGDEEELGKPVGSDLKEGKPTLPVLLALEK 249
Query: 243 FPQLRTVVEQGFEDSSNVDIALEYLGKSRGIQKTRELAVKHANLAAAAIDSLPENNDEDV 302
+ + ++ E V+ ALE L KS I+ + LA + A A++ LP++
Sbjct: 250 ANEDQKLLRILLEGGGEVEEALELLRKSGAIEYAKNLAKTYVEKAKEALEKLPDS----- 304
Query: 303 TKSRRALLDLTHRVITRNK 321
+++ 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 = 173 bits (440), Expect = 8e-53
Identities = 94/295 (31%), Positives = 137/295 (46%), Gaps = 60/295 (20%)
Query: 26 FRPTVLLLMATALNVRVPEPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDVLDD 85
RP ++LL+A AL + +A E++H ASL+HDD++DD
Sbjct: 1 SRPLLVLLLARALGGDLE-----------------AALRLAAAVELLHAASLVHDDIVDD 43
Query: 86 ADTRRGIGSLN-FVMGNKLAVLAGDFLLSRACVALASLKNTEVVTLLATVVEHLVTGETM 144
+D RRG + + GN LA+LAGD+LL+RA LA L + L A + L+ G+ +
Sbjct: 44 SDLRRGKPTAHLRRFGNALAILAGDYLLARAFQLLARLGYPRALELFAEALRELLEGQAL 103
Query: 145 QMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLGLAYQ 204
+ D ++D Y++ YKTA L+ C A L+G E A DYG+ LGLA+Q
Sbjct: 104 DLEFERDTYETLDEYLEYCRYKTAGLVGLLCLLGAGLSGADDEQAEALKDYGRALGLAFQ 163
Query: 205 LIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFAMEEFPQLRTVVEQGFEDSSNVDIAL 264
L DD+LD G + LGK SD+R G IT P++ A E
Sbjct: 164 LTDDLLDVFGDAEELGK-VGSDLREGRITLPVILARER---------------------- 200
Query: 265 EYLGKSRGIQKTRELAVKHANLAAAAIDSLPENNDEDVTKSRRALLDLTHRVITR 319
A ++A A AA+++LP + RRAL+ L + R
Sbjct: 201 ---------------AAEYAEEAYAALEALPPSLPRA----RRALIALADFLYRR 236
>gnl|CDD|215873 pfam00348, polyprenyl_synt, Polyprenyl synthetase.
Length = 260
Score = 164 bits (417), Expect = 4e-49
Identities = 77/225 (34%), Positives = 119/225 (52%), Gaps = 23/225 (10%)
Query: 23 GKRFRPTVLLLMATALNVRVPEPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDV 82
GKR RP LL++ A + V + A EMIH ASL+HDD+
Sbjct: 13 GKRIRP--LLVVLAARALGVEPETLLYL---------------ACAIEMIHTASLVHDDL 55
Query: 83 LDDADTRRGIGSLNFVMGNKLAVLAGDFLLSRACVALASLK--NTEVVTLLATVVEHLVT 140
+D++D RRG + + G A+LAGD LLSRA LA L E +L + + + V
Sbjct: 56 MDNSDLRRGKPTCHKKFGEAGAILAGDALLSRAFQLLALLGHVRPEPKYILISELANAVG 115
Query: 141 GETM--QMT--TSSDQRCSMDYYMQKTYYKTASLISNSCKAIALLAGQTAEVAILAFDYG 196
+ Q+ + + +++ Y++ YKTA+L S + A++AG E +D+G
Sbjct: 116 AQGEVGQLMDLETEGKDITLEEYLRIVSYKTAALFYASVQLGAIVAGADEEDEKDLYDFG 175
Query: 197 KNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFAME 241
++LGLA+Q+ DD+LD TG + LGK +D++ G T P+L A+E
Sbjct: 176 RDLGLAFQIQDDILDLTGDTEELGKPVGTDLQEGKSTLPVLLALE 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 = 160 bits (406), Expect = 7e-47
Identities = 92/322 (28%), Positives = 169/322 (52%), Gaps = 29/322 (9%)
Query: 2 VVAEVPKLASAAEYFFKMGVEGKRFRPTVLLLMATALNVRVPEPLHDGVEDALATELRTR 61
V AE P L+ A+ + + G GKR RP +LL + + H
Sbjct: 24 VQAEHPVLSEASLHLLEAG--GKRIRPVFVLLAGKFGDYDLDAIKH-------------- 67
Query: 62 QQCIAEITEMIHVASLLHDDVLDDADTRRGIGSLNFVMGNKLAVLAGDFLLSRACVALAS 121
+A E+IH+ASL+HDDV+DDAD RRG ++ GN++A+ GD+L +++ +
Sbjct: 68 ---VAVALELIHMASLVHDDVIDDADLRRGRPTIKSKWGNRIAMYTGDYLFAKSLETMTE 124
Query: 122 LKNTEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIALL 181
+K+ +L+ + + GE Q+ + ++ Y+++ KTA LI+ SC+ A+
Sbjct: 125 IKDPRAHQILSHTIVEVCRGEIEQIKDKYNFDQNLRTYLRRIKRKTALLIAASCQLGAIA 184
Query: 182 AGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFAME 241
+G + + +G +G++YQ+ DD+LDF GT LGK + D+ G +T P+L+AME
Sbjct: 185 SGANEAIVKKLYWFGYYVGMSYQITDDILDFVGTEEELGKPAGGDLLQGNVTLPVLYAME 244
Query: 242 EFPQLRTVVEQGFEDSSNVDIA--LEYLGKSRGIQKTRELAVKHANLAAAAIDSLPENND 299
+ P L+ +EQ E+++ ++ +E + KS I+ ++ ++ A +D LP+
Sbjct: 245 D-PFLKKRIEQVLEETTAEEMEPLIEEVKKSDAIEYAYAVSDRYLKKALELLDGLPDG-- 301
Query: 300 EDVTKSRRALLDLTHRVITRNK 321
++++ L ++ + I + K
Sbjct: 302 ----RAKKPLQEIA-KYIGKRK 318
>gnl|CDD|182813 PRK10888, PRK10888, octaprenyl diphosphate synthase; Provisional.
Length = 323
Score = 159 bits (403), Expect = 2e-46
Identities = 103/302 (34%), Positives = 156/302 (51%), Gaps = 29/302 (9%)
Query: 23 GKRFRPTVLLLMATALNVRVPEPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDV 82
GKR RP + +L A A+ + G IA + E IH A+LLHDDV
Sbjct: 44 GKRIRPMIAVLAARAVG-------YQG----------NAHVTIAALIEFIHTATLLHDDV 86
Query: 83 LDDADTRRGIGSLNFVMGNKLAVLAGDFLLSRACVALASLKNTEVVTLLATVVEHLVTGE 142
+D++D RRG + N GN +VL GDF+ +RA + SL + +V+ +++ V + GE
Sbjct: 87 VDESDMRRGKATANAAFGNAASVLVGDFIYTRAFQMMTSLGSLKVLEVMSEAVNVIAEGE 146
Query: 143 TMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLGLA 202
+Q+ +D + + YM+ Y KTA L + + +LAG T E DYG+ LG A
Sbjct: 147 VLQLMNVNDPDITEENYMRVIYSKTARLFEAAAQCSGILAGCTPEQEKGLQDYGRYLGTA 206
Query: 203 YQLIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFAM-----EEFPQLRTVVEQGFEDS 257
+QLIDD+LD++ +LGK D+ G T P+L AM E+ +RT +EQG
Sbjct: 207 FQLIDDLLDYSADGETLGKNVGDDLNEGKPTLPLLHAMHHGTPEQAAMIRTAIEQG-NGR 265
Query: 258 SNVDIALEYLGKSRGIQKTRELAVKHANLAAAAIDSLPENNDEDVTKSRRALLDLTHRVI 317
++ LE + ++ TR+ A + A+ A AA+ LP+ T R AL+ L H +
Sbjct: 266 HLLEPVLEAMNACGSLEWTRQRAEEEADKAIAALQVLPD------TPWREALIGLAHIAV 319
Query: 318 TR 319
R
Sbjct: 320 QR 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 = 140 bits (354), Expect = 5e-40
Identities = 72/256 (28%), Positives = 119/256 (46%), Gaps = 31/256 (12%)
Query: 65 IAEITEMIHVASLLHDDVLDDADTRRGIGSLN---FVMGNKLAVLAGDFLLSRACVALAS 121
+ E +H ASL+HDD++DD+ TRRG+ + + + G A+LAGD LL+ A LA
Sbjct: 15 LRAAVEKLHAASLVHDDIVDDSGTRRGLPTAHLAVAIDGLPEAILAGDLLLADAFEELAR 74
Query: 122 LKNTEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIALL 181
+ E + +LA + L+ G+ + + + +++ Y++ YKTA L+ C A L
Sbjct: 75 EGSPEALEILAEALLDLLEGQLLDLKWRREYVPTLEEYLEYCRYKTAGLVGALCLLGAGL 134
Query: 182 AGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFAME 241
+G AE+ G+ LGLA+QL +D+LD+ G + G T P+L+A+E
Sbjct: 135 SGGEAELLEALRKLGRALGLAFQLTNDLLDYEGDAERGE---------GKCTLPVLYALE 185
Query: 242 EFPQLRTVVEQGFEDSSNVDIALEYLGKSRGIQKTRELAVKHANLAAAAIDSLPENNDED 301
L + KS +++ E K A A ++ L + +
Sbjct: 186 YGVPAE---------------DLLLVEKSGSLEEALEELAKLAEEALKELNELILSLPD- 229
Query: 302 VTKSRRALLDLTHRVI 317
RALL L +
Sbjct: 230 ---VPRALLALALNLY 242
>gnl|CDD|182567 PRK10581, PRK10581, geranyltranstransferase; Provisional.
Length = 299
Score = 80.2 bits (198), Expect = 3e-17
Identities = 60/190 (31%), Positives = 99/190 (52%), Gaps = 14/190 (7%)
Query: 66 AEITEMIHVASLLHDDV--LDDADTRRGIGSLNFVMGNKLAVLAGDFLLSRACVALASLK 123
A E IH SL+HDD+ +DD D RRG+ + + G A+LAGD L + A L+
Sbjct: 70 AAAVECIHAYSLIHDDLPAMDDDDLRRGLPTCHVKFGEANAILAGDALQTLAFSILSDAP 129
Query: 124 NTEV--------VTLLATV--VEHLVTGETMQMTTSSDQRCSMDYYMQKTYYKTASLISN 173
EV ++ LA+ + + G+ + + + ++ +D + +KT +LI
Sbjct: 130 MPEVSDRDRISMISELASASGIAGMCGGQALDLE-AEGKQVPLDALERIHRHKTGALIRA 188
Query: 174 SCKAIALLAGQTAEVAILAFD-YGKNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRHGII 232
+ + AL AG A+ D Y +++GLA+Q+ DD+LD G +A+LGK +D + G
Sbjct: 189 AVRLGALSAGDKGRRALPVLDRYAESIGLAFQVQDDILDVVGDTATLGKRQGADQQLGKS 248
Query: 233 TAPILFAMEE 242
T P L +E+
Sbjct: 249 TYPALLGLEQ 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 = 0.44
Identities = 17/77 (22%), Positives = 28/77 (36%), Gaps = 13/77 (16%)
Query: 141 GETMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLG 200
GE ++M S D C+ Y+Q ++ ++ L Y N G
Sbjct: 44 GEGLRMLVSRDLDCTHTLYIQFSFKFITKGTPERSHSVLL-------------QYSINGG 90
Query: 201 LAYQLIDDVLDFTGTSA 217
+ + 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: 193 FDYGKNLGLAYQLID--DVLDFTGTSASLGKGSLSDIRHG 230
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 = 4.0
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|173650 cd05094, PTKc_TrkC, Catalytic domain of the Protein Tyrosine
Kinase, Tropomyosin Related Kinase C. Protein Tyrosine
Kinase (PTK) family; Tropomyosin Related Kinase C
(TrkC); catalytic (c) domain. The PTKc family is part of
a larger superfamily that includes the catalytic domains
of other kinases such as protein serine/threonine
kinases, RIO kinases, and phosphoinositide 3-kinase
(PI3K). PTKs catalyze the transfer of the
gamma-phosphoryl group from ATP to tyrosine (tyr)
residues in protein substrates. TrkC is a member of the
Trk subfamily of proteins, which are receptor tyr
kinases (RTKs) containing an extracellular region with
arrays of leucine-rich motifs flanked by two
cysteine-rich clusters followed by two
immunoglobulin-like domains, a transmembrane segment,
and an intracellular catalytic domain. Binding of TrkC
to its ligand, neurotrophin 3 (NT3), results in receptor
oligomerization and activation of the catalytic domain.
TrkC is broadly expressed in the nervous system and in
some non-neural tissues including the developing heart.
NT3/TrkC signaling plays an important role in the
innervation of the cardiac conducting system and the
development of smooth muscle cells. Mice deficient with
NT3 and TrkC have multiple heart defects. NT3/TrkC
signaling is also critical for the development and
maintenance of enteric neurons that are important for
the control of gut peristalsis.
Length = 291
Score = 28.0 bits (62), Expect = 5.7
Identities = 15/50 (30%), Positives = 28/50 (56%), Gaps = 3/50 (6%)
Query: 68 ITEMIHVASLLHDDVLDDAD---TRRGIGSLNFVMGNKLAVLAGDFLLSR 114
+++M+H+AS + ++ A R + + N ++G L V GDF +SR
Sbjct: 122 LSQMLHIASQIASGMVYLASQHFVHRDLATRNCLVGANLLVKIGDFGMSR 171
>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 = 6.4
Identities = 19/82 (23%), Positives = 30/82 (36%), Gaps = 16/82 (19%)
Query: 236 ILFAMEEFPQLRTVVEQGF-EDSSNVDI--ALEYLGKSRGI------------QKTRELA 280
IL E P+L+ +V G E + + D L K RG + EL
Sbjct: 41 ILEEAVELPELKEIVLGGIGEPTVHPDFIDMLTEA-KERGFAVGLSTNGYLLEEMAEELV 99
Query: 281 VKHANLAAAAIDSLPENNDEDV 302
+ +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 = 9.4
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 0.0703 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,126,244
Number of extensions: 1569895
Number of successful extensions: 1358
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1330
Number of HSP's successfully gapped: 33
Length of query: 321
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 224
Effective length of database: 6,635,264
Effective search space: 1486299136
Effective search space used: 1486299136
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 (26.6 bits)