RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 016097
(395 letters)
>gnl|CDD|178478 PLN02890, PLN02890, geranyl diphosphate synthase.
Length = 422
Score = 634 bits (1637), Expect = 0.0
Identities = 293/345 (84%), Positives = 324/345 (93%)
Query: 51 SQEQLDPFSLVADELSILAKRLRSMVVAEVPKLASAAEYFFKMGVEGKRFRPTVLLLMAT 110
+EQLDPFSLVADELS+LA +LRSMVVAEVPKLASAAEYFFK+GVEGKRFRPTVLLLMAT
Sbjct: 78 VEEQLDPFSLVADELSLLANKLRSMVVAEVPKLASAAEYFFKVGVEGKRFRPTVLLLMAT 137
Query: 111 ALNVRVPEPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDVLDDADTRRGIGSLN 170
ALNV +PE GV D +A+ELRTRQQ IAEITEMIHVASLLHDDVLDDADTRRG+GSLN
Sbjct: 138 ALNVPLPESTEGGVLDIVASELRTRQQNIAEITEMIHVASLLHDDVLDDADTRRGVGSLN 197
Query: 171 FVMGNKLAVLAGDFLLSRACVALASLKNTEVVTLLATVVEHLVTGETMQMTTSSDQRCSM 230
VMGNKL+VLAGDFLLSRACVALA+LKNTEVV+LLAT VEHLVTGETMQ+T+S +QR SM
Sbjct: 198 VVMGNKLSVLAGDFLLSRACVALAALKNTEVVSLLATAVEHLVTGETMQITSSREQRRSM 257
Query: 231 DYYMQKTYYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTS 290
DYYMQKTYYKTASLISNSCKA+A+LAGQTAEVA+LAF+YG+NLGLA+QLIDDVLDFTGTS
Sbjct: 258 DYYMQKTYYKTASLISNSCKAVAILAGQTAEVAVLAFEYGRNLGLAFQLIDDVLDFTGTS 317
Query: 291 ASLGKGSLSDIRHGIITAPILFAMEEFPQLRTVVEQGFEDSSNVDIALEYLGKSRGIQKT 350
ASLGKGSLSDIRHG+ITAPILFAMEEFPQLR VV++GF++ +NVDIALEYLGKSRGIQ+T
Sbjct: 318 ASLGKGSLSDIRHGVITAPILFAMEEFPQLREVVDRGFDNPANVDIALEYLGKSRGIQRT 377
Query: 351 RELAVKHANLAAAAIDSLPENNDEDVTKSRRALLDLTHRVITRNK 395
RELA +HANLAAAAI+SLPE +DEDV SRRAL+DLT RVITRNK
Sbjct: 378 RELAREHANLAAAAIESLPETDDEDVLTSRRALIDLTERVITRNK 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 = 299 bits (767), Expect = e-100
Identities = 145/336 (43%), Positives = 217/336 (64%), Gaps = 22/336 (6%)
Query: 58 FSLVADELSILAKRLRSMVVAEVPKLASAAEYFFKMGVEGKRFRPTVLLLMATALNVRVP 117
F+ V D+L +L L+S+V A P L +AAE+ F G GKR RP ++LL++ A
Sbjct: 7 FAPVEDDLYLLTDNLKSLVGARHPILYAAAEHLFSAG--GKRLRPAIVLLVSRAT----- 59
Query: 118 EPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDVLDDADTRRGIGSLNFVMGNKL 177
A EL R + +AEITEMIH ASL+HDDV+D++DTRRGI +++ + G ++
Sbjct: 60 ---------AEQQELTPRHRRLAEITEMIHTASLVHDDVIDESDTRRGIETVHSLFGTRV 110
Query: 178 AVLAGDFLLSRACVALASLKNTEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQKT 237
AVLAGDFL ++A LA+L+N EVV L++ V+ GE Q D S++ Y++K+
Sbjct: 111 AVLAGDFLFAQASWYLANLENLEVVKLISKVITDFAEGEIKQGLNQFDSDLSLEDYLEKS 170
Query: 238 YYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKGS 297
+YKTASL++ S KA A+L+ ++VA ++YGK+LGLA+Q++DD+LDFTG++ LGK +
Sbjct: 171 FYKTASLVAASSKAAAVLSDVPSQVANDLYEYGKHLGLAFQVVDDILDFTGSTEQLGKPA 230
Query: 298 LSDIRHGIITAPILFAMEEFPQLRTVVEQGFEDSSNVDIALEYLGKSRGIQKTRELAVKH 357
SD+ G +TAP+LFA+EE P+L ++E+ F +++ AL + KS GI+K RELA +
Sbjct: 231 GSDLMKGNLTAPVLFALEEEPKLSELIEREFSQKGDLEQALSLVRKSGGIKKARELAKEQ 290
Query: 358 ANLAAAAIDSLPENNDEDVTKSRRALLDLTHRVITR 393
A LA ++ LP + R AL +L H V++R
Sbjct: 291 AQLALQSLSFLPP------SPPREALKELVHFVLSR 320
>gnl|CDD|215462 PLN02857, PLN02857, octaprenyl-diphosphate synthase.
Length = 416
Score = 271 bits (695), Expect = 8e-88
Identities = 136/336 (40%), Positives = 211/336 (62%), Gaps = 19/336 (5%)
Query: 58 FSLVADELSILAKRLRSMVVAEVPKLASAAEYFFKMGVEGKRFRPTVLLLMATALNVRVP 117
F VAD+L L L+S+V AE P L SAAE F G GKR RP ++ L++ A
Sbjct: 98 FEPVADDLQQLNDNLQSIVGAENPVLMSAAEQIFGAG--GKRMRPALVFLVSRAT----- 150
Query: 118 EPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDVLDDADTRRGIGSLNFVMGNKL 177
E A EL T + +AEITEMIH ASL+HDDVLD++D RRG +++ + G ++
Sbjct: 151 ------AELAGLKELTTEHRRLAEITEMIHTASLIHDDVLDESDMRRGKETVHQLYGTRV 204
Query: 178 AVLAGDFLLSRACVALASLKNTEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQKT 237
AVLAGDF+ +++ LA+L N EV+ L++ V++ +GE Q ++ D ++D Y+ K+
Sbjct: 205 AVLAGDFMFAQSSWYLANLDNLEVIKLISQVIKDFASGEIKQASSLFDCDVTLDEYLLKS 264
Query: 238 YYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKGS 297
YYKTASLI+ S K+ A+ +G + V ++YGKNLGLA+Q++DD+LDFT ++ LGK +
Sbjct: 265 YYKTASLIAASTKSAAIFSGVDSSVKEQMYEYGKNLGLAFQVVDDILDFTQSTEQLGKPA 324
Query: 298 LSDIRHGIITAPILFAMEEFPQLRTVVEQGFEDSSNVDIALEYLGKSRGIQKTRELAVKH 357
SD+ G +TAP++FA+E+ P+LR ++E F + +++ A+E + + GI++ +ELA +
Sbjct: 325 GSDLAKGNLTAPVIFALEKEPELREIIESEFCEEGSLEEAIELVNEGGGIERAQELAKEK 384
Query: 358 ANLAAAAIDSLPENNDEDVTKSRRALLDLTHRVITR 393
A+LA ++ LP R +L D+ + R
Sbjct: 385 ADLAIQNLECLPR------GAFRSSLEDMVDYNLER 414
>gnl|CDD|164542 CHL00151, preA, prenyl transferase; Reviewed.
Length = 323
Score = 266 bits (682), Expect = 4e-87
Identities = 129/338 (38%), Positives = 209/338 (61%), Gaps = 22/338 (6%)
Query: 58 FSLVADELSILAKRLRSMVVAEVPKLASAAEYFFKMGVEGKRFRPTVLLLMATALNVRVP 117
+ + +EL IL L+ ++ + P L +AA++ F G GKR RP ++LL+A A
Sbjct: 8 LTPIEEELLILEDNLKKLIGSGHPILYAAAKHLFSAG--GKRIRPAIVLLVAKATGG--- 62
Query: 118 EPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDVLDDADTRRGIGSLNFVMGNKL 177
E++T QQ +AEITE+IH ASL+HDDV+D+ RRGI +++ + G K+
Sbjct: 63 -----------NMEIKTSQQRLAEITEIIHTASLVHDDVIDECSIRRGIPTVHKIFGTKI 111
Query: 178 AVLAGDFLLSRACVALASLKNTEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQKT 237
AVLAGDFL +++ LA+L N EVV L++ V+ GE Q D S+ Y++K+
Sbjct: 112 AVLAGDFLFAQSSWYLANLNNLEVVKLISKVITDFAEGEIRQGLVQFDTTLSILNYIEKS 171
Query: 238 YYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKGS 297
+YKTASLI+ SCKA ALL+ + + YGK+LGLA+Q+IDDVLD T ++ SLGK
Sbjct: 172 FYKTASLIAASCKAAALLSDADEKDHNDFYLYGKHLGLAFQIIDDVLDITSSTESLGKPI 231
Query: 298 LSDIRHGIITAPILFAMEEFPQLRTVVEQGFEDSSNVDIALEYLGKSRGIQKTRELAVKH 357
SD+++G +TAP+LFA+ + +L ++E+ F ++ ++ AL+ + ++ GI+K ++LA++H
Sbjct: 232 GSDLKNGNLTAPVLFALTQNSKLAKLIEREFCETKDISQALQIIKETNGIEKAKDLALEH 291
Query: 358 ANLAAAAIDSLPENNDEDVTKSRRALLDLTHRVITRNK 395
A + LP ++ +D +L+++ + +I R
Sbjct: 292 MQAAIQCLKFLPPSSAKD------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 = 240 bits (615), Expect = 1e-77
Identities = 102/319 (31%), Positives = 149/319 (46%), Gaps = 63/319 (19%)
Query: 78 AEVPKLASAAEYFFKMGVEGKRFRPTVLLLMATALNVRVPEPLHDGVEDALATELRTRQQ 137
+EV L A Y G GKR RP ++LL A AL E
Sbjct: 1 SEVELLREALRYLLLAG--GKRLRPLLVLLAARALGGPELE----------------AAL 42
Query: 138 CIAEITEMIHVASLLHDDVLDDADTRRGIGSLNFVMGNKLAVLAGDFLLSRACVALASLK 197
+A E++H ASL+HDDV+D++D RRG +++ V GN A+LAGD+LL+RA LA L
Sbjct: 43 RLAAAIELLHTASLVHDDVMDNSDLRRGKPTVHKVFGNATAILAGDYLLARAFELLARLG 102
Query: 198 N---TEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIAL 254
N + L + + LV G+ + + + D + + Y++ KTA+L + + AL
Sbjct: 103 NPYYPRALELFSEAILELVEGQLLDLLSEYDTDVTEEEYLRIIRLKTAALFAAAPLLGAL 162
Query: 255 LAGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFAM 314
LAG E A +G+NLGLA+Q+ DD+LD G +LGK SD+R G T P+L A+
Sbjct: 163 LAGADEEEAEALKRFGRNLGLAFQIQDDILDLFGDPETLGKPVGSDLREGKCTLPVLLAL 222
Query: 315 EEFPQLRTVVEQGFEDSSNVDIALEYLGKSRGIQKTRELAVKHANLAAAAIDSLPENNDE 374
RELA ++ A A+ +LPE+
Sbjct: 223 ------------------------------------RELAREYEEKALEALKALPESP-- 244
Query: 375 DVTKSRRALLDLTHRVITR 393
+R AL L ++ R
Sbjct: 245 ----AREALRALADFILER 259
>gnl|CDD|223220 COG0142, IspA, Geranylgeranyl pyrophosphate synthase [Coenzyme
metabolism].
Length = 322
Score = 236 bits (603), Expect = 3e-75
Identities = 112/343 (32%), Positives = 178/343 (51%), Gaps = 25/343 (7%)
Query: 56 DPFSLVADELSILAKRLRSMV-VAEVPKLASAAEYFFKMGVEGKRFRPTVLLLMATALNV 114
D +L+ L+ + + L ++ ++ L A Y G GKR RP ++LL A AL +
Sbjct: 2 DLLALLLKRLARIEELLSELLSGSDPELLLEAMRYLLLAG--GKRLRPLLVLLAAEALGI 59
Query: 115 RVPEPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDVLDDADTRRGIGSLNFVMG 174
L G DAL +A E+IH ASL+HDD++DD D RRG +++ G
Sbjct: 60 ----DLETGGNDALD---------LAAAIELIHTASLIHDDLMDDDDLRRGKPTVHAKFG 106
Query: 175 NKLAVLAGDFLLSRACVALASLKN--TEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDY 232
A+LAGD LL+ A L+ L + E + LA + L G+ + + + +++
Sbjct: 107 EATAILAGDALLAAAFELLSKLGSEALEAIKALAEAINGLCGGQALDLAFENKP-VTLEE 165
Query: 233 YMQKTYYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSAS 292
Y++ KTA+L + + A+LAG E+ DYG+NLGLA+Q+ DD+LD TG
Sbjct: 166 YLRVIELKTAALFAAAAVLGAILAGADEELLEALEDYGRNLGLAFQIQDDILDITGDEEE 225
Query: 293 LGKGSLSDIRHGIITAPILFAMEEFPQLRTVVEQGFEDSSNVDIALEYLGKSRGIQKTRE 352
LGK SD++ G T P+L A+E+ + + ++ E V+ ALE L KS I+ +
Sbjct: 226 LGKPVGSDLKEGKPTLPVLLALEKANEDQKLLRILLEGGGEVEEALELLRKSGAIEYAKN 285
Query: 353 LAVKHANLAAAAIDSLPENNDEDVTKSRRALLDLTHRVITRNK 395
LA + A A++ LP++ +++ ALL+L +I R
Sbjct: 286 LAKTYVEKAKEALEKLPDS------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 = 4e-52
Identities = 94/295 (31%), Positives = 137/295 (46%), Gaps = 60/295 (20%)
Query: 100 FRPTVLLLMATALNVRVPEPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDVLDD 159
RP ++LL+A AL + +A E++H ASL+HDD++DD
Sbjct: 1 SRPLLVLLLARALGGDLE-----------------AALRLAAAVELLHAASLVHDDIVDD 43
Query: 160 ADTRRGIGSLN-FVMGNKLAVLAGDFLLSRACVALASLKNTEVVTLLATVVEHLVTGETM 218
+D RRG + + GN LA+LAGD+LL+RA LA L + L A + L+ G+ +
Sbjct: 44 SDLRRGKPTAHLRRFGNALAILAGDYLLARAFQLLARLGYPRALELFAEALRELLEGQAL 103
Query: 219 QMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLGLAYQ 278
+ D ++D Y++ YKTA L+ C A L+G E A DYG+ LGLA+Q
Sbjct: 104 DLEFERDTYETLDEYLEYCRYKTAGLVGLLCLLGAGLSGADDEQAEALKDYGRALGLAFQ 163
Query: 279 LIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFAMEEFPQLRTVVEQGFEDSSNVDIAL 338
L DD+LD G + LGK SD+R G IT P++ A E
Sbjct: 164 LTDDLLDVFGDAEELGK-VGSDLREGRITLPVILARER---------------------- 200
Query: 339 EYLGKSRGIQKTRELAVKHANLAAAAIDSLPENNDEDVTKSRRALLDLTHRVITR 393
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 = 3e-48
Identities = 77/225 (34%), Positives = 119/225 (52%), Gaps = 23/225 (10%)
Query: 97 GKRFRPTVLLLMATALNVRVPEPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDV 156
GKR RP LL++ A + V + A EMIH ASL+HDD+
Sbjct: 13 GKRIRP--LLVVLAARALGVEPETLLYL---------------ACAIEMIHTASLVHDDL 55
Query: 157 LDDADTRRGIGSLNFVMGNKLAVLAGDFLLSRACVALASLK--NTEVVTLLATVVEHLVT 214
+D++D RRG + + G A+LAGD LLSRA LA L E +L + + + V
Sbjct: 56 MDNSDLRRGKPTCHKKFGEAGAILAGDALLSRAFQLLALLGHVRPEPKYILISELANAVG 115
Query: 215 GETM--QMT--TSSDQRCSMDYYMQKTYYKTASLISNSCKAIALLAGQTAEVAILAFDYG 270
+ Q+ + + +++ Y++ YKTA+L S + A++AG E +D+G
Sbjct: 116 AQGEVGQLMDLETEGKDITLEEYLRIVSYKTAALFYASVQLGAIVAGADEEDEKDLYDFG 175
Query: 271 KNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFAME 315
++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 = 164 bits (416), Expect = 1e-47
Identities = 96/342 (28%), Positives = 178/342 (52%), Gaps = 29/342 (8%)
Query: 56 DPFSLVADELSILAKRLRSMVVAEVPKLASAAEYFFKMGVEGKRFRPTVLLLMATALNVR 115
D +S + ++ + K L V AE P L+ A+ + + G GKR RP +LL +
Sbjct: 4 DIYSFLQKDIDSIEKELEKAVQAEHPVLSEASLHLLEAG--GKRIRPVFVLLAGKFGDYD 61
Query: 116 VPEPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDVLDDADTRRGIGSLNFVMGN 175
+ H +A E+IH+ASL+HDDV+DDAD RRG ++ GN
Sbjct: 62 LDAIKH-----------------VAVALELIHMASLVHDDVIDDADLRRGRPTIKSKWGN 104
Query: 176 KLAVLAGDFLLSRACVALASLKNTEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQ 235
++A+ GD+L +++ + +K+ +L+ + + GE Q+ + ++ Y++
Sbjct: 105 RIAMYTGDYLFAKSLETMTEIKDPRAHQILSHTIVEVCRGEIEQIKDKYNFDQNLRTYLR 164
Query: 236 KTYYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGK 295
+ KTA LI+ SC+ A+ +G + + +G +G++YQ+ DD+LDF GT LGK
Sbjct: 165 RIKRKTALLIAASCQLGAIASGANEAIVKKLYWFGYYVGMSYQITDDILDFVGTEEELGK 224
Query: 296 GSLSDIRHGIITAPILFAMEEFPQLRTVVEQGFEDSSNVDIA--LEYLGKSRGIQKTREL 353
+ D+ G +T P+L+AME+ P L+ +EQ E+++ ++ +E + KS I+ +
Sbjct: 225 PAGGDLLQGNVTLPVLYAMED-PFLKKRIEQVLEETTAEEMEPLIEEVKKSDAIEYAYAV 283
Query: 354 AVKHANLAAAAIDSLPENNDEDVTKSRRALLDLTHRVITRNK 395
+ ++ A +D LP+ ++++ L ++ + I + K
Sbjct: 284 SDRYLKKALELLDGLPDG------RAKKPLQEIA-KYIGKRK 318
>gnl|CDD|182813 PRK10888, PRK10888, octaprenyl diphosphate synthase; Provisional.
Length = 323
Score = 159 bits (404), Expect = 8e-46
Identities = 103/302 (34%), Positives = 156/302 (51%), Gaps = 29/302 (9%)
Query: 97 GKRFRPTVLLLMATALNVRVPEPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDV 156
GKR RP + +L A A+ + G IA + E IH A+LLHDDV
Sbjct: 44 GKRIRPMIAVLAARAVG-------YQG----------NAHVTIAALIEFIHTATLLHDDV 86
Query: 157 LDDADTRRGIGSLNFVMGNKLAVLAGDFLLSRACVALASLKNTEVVTLLATVVEHLVTGE 216
+D++D RRG + N GN +VL GDF+ +RA + SL + +V+ +++ V + GE
Sbjct: 87 VDESDMRRGKATANAAFGNAASVLVGDFIYTRAFQMMTSLGSLKVLEVMSEAVNVIAEGE 146
Query: 217 TMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLGLA 276
+Q+ +D + + YM+ Y KTA L + + +LAG T E DYG+ LG A
Sbjct: 147 VLQLMNVNDPDITEENYMRVIYSKTARLFEAAAQCSGILAGCTPEQEKGLQDYGRYLGTA 206
Query: 277 YQLIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFAM-----EEFPQLRTVVEQGFEDS 331
+QLIDD+LD++ +LGK D+ G T P+L AM E+ +RT +EQG
Sbjct: 207 FQLIDDLLDYSADGETLGKNVGDDLNEGKPTLPLLHAMHHGTPEQAAMIRTAIEQG-NGR 265
Query: 332 SNVDIALEYLGKSRGIQKTRELAVKHANLAAAAIDSLPENNDEDVTKSRRALLDLTHRVI 391
++ LE + ++ TR+ A + A+ A AA+ LP+ T R AL+ L H +
Sbjct: 266 HLLEPVLEAMNACGSLEWTRQRAEEEADKAIAALQVLPD------TPWREALIGLAHIAV 319
Query: 392 TR 393
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 = 141 bits (356), Expect = 1e-39
Identities = 72/256 (28%), Positives = 119/256 (46%), Gaps = 31/256 (12%)
Query: 139 IAEITEMIHVASLLHDDVLDDADTRRGIGSLN---FVMGNKLAVLAGDFLLSRACVALAS 195
+ E +H ASL+HDD++DD+ TRRG+ + + + G A+LAGD LL+ A LA
Sbjct: 15 LRAAVEKLHAASLVHDDIVDDSGTRRGLPTAHLAVAIDGLPEAILAGDLLLADAFEELAR 74
Query: 196 LKNTEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIALL 255
+ E + +LA + L+ G+ + + + +++ Y++ YKTA L+ C A L
Sbjct: 75 EGSPEALEILAEALLDLLEGQLLDLKWRREYVPTLEEYLEYCRYKTAGLVGALCLLGAGL 134
Query: 256 AGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFAME 315
+G AE+ G+ LGLA+QL +D+LD+ G + G T P+L+A+E
Sbjct: 135 SGGEAELLEALRKLGRALGLAFQLTNDLLDYEGDAERGE---------GKCTLPVLYALE 185
Query: 316 EFPQLRTVVEQGFEDSSNVDIALEYLGKSRGIQKTRELAVKHANLAAAAIDSLPENNDED 375
L + KS +++ E K A A ++ L + +
Sbjct: 186 YGVPAE---------------DLLLVEKSGSLEEALEELAKLAEEALKELNELILSLPD- 229
Query: 376 VTKSRRALLDLTHRVI 391
RALL L +
Sbjct: 230 ---VPRALLALALNLY 242
>gnl|CDD|182567 PRK10581, PRK10581, geranyltranstransferase; Provisional.
Length = 299
Score = 79.8 bits (197), Expect = 1e-16
Identities = 60/190 (31%), Positives = 99/190 (52%), Gaps = 14/190 (7%)
Query: 140 AEITEMIHVASLLHDDV--LDDADTRRGIGSLNFVMGNKLAVLAGDFLLSRACVALASLK 197
A E IH SL+HDD+ +DD D RRG+ + + G A+LAGD L + A L+
Sbjct: 70 AAAVECIHAYSLIHDDLPAMDDDDLRRGLPTCHVKFGEANAILAGDALQTLAFSILSDAP 129
Query: 198 NTEV--------VTLLATV--VEHLVTGETMQMTTSSDQRCSMDYYMQKTYYKTASLISN 247
EV ++ LA+ + + G+ + + + ++ +D + +KT +LI
Sbjct: 130 MPEVSDRDRISMISELASASGIAGMCGGQALDLE-AEGKQVPLDALERIHRHKTGALIRA 188
Query: 248 SCKAIALLAGQTAEVAILAFD-YGKNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRHGII 306
+ + AL AG A+ D Y +++GLA+Q+ DD+LD G +A+LGK +D + G
Sbjct: 189 AVRLGALSAGDKGRRALPVLDRYAESIGLAFQVQDDILDVVGDTATLGKRQGADQQLGKS 248
Query: 307 TAPILFAMEE 316
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 = 30.6 bits (69), Expect = 0.69
Identities = 17/77 (22%), Positives = 28/77 (36%), Gaps = 13/77 (16%)
Query: 215 GETMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLG 274
GE ++M S D C+ Y+Q ++ ++ L Y N G
Sbjct: 44 GEGLRMLVSRDLDCTHTLYIQFSFKFITKGTPERSHSVLL-------------QYSINGG 90
Query: 275 LAYQLIDDVLDFTGTSA 291
+ + LID+ T T
Sbjct: 91 ITWHLIDEFYFPTTTDV 107
>gnl|CDD|225744 COG3203, OmpC, Outer membrane protein (porin) [Cell envelope
biogenesis, outer membrane].
Length = 354
Score = 30.8 bits (70), Expect = 1.3
Identities = 12/40 (30%), Positives = 17/40 (42%), Gaps = 2/40 (5%)
Query: 267 FDYGKNLGLAYQLID--DVLDFTGTSASLGKGSLSDIRHG 304
DYG+N G+ Y + D L G A+L + R
Sbjct: 111 LDYGRNYGVLYDVAGWTDPLPEFGGDATLVDDNFMTGRAD 150
>gnl|CDD|204097 pfam08926, DUF1908, Domain of unknown function (DUF1908). This
domain is found in a set of hypothetical/structural
eukaryotic proteins.
Length = 282
Score = 30.2 bits (68), Expect = 1.5
Identities = 23/61 (37%), Positives = 30/61 (49%), Gaps = 13/61 (21%)
Query: 20 GRRW----LPSHPLLSGASHSAAAAAADSSVKDTDSQEQLD--PFSLVADELSILAKRLR 73
GRRW LPS SG + ++ SS + SQE+L PF D+L L+K R
Sbjct: 31 GRRWSVASLPS----SGYGTNPPSSTVSSS---SSSQERLHQLPFQPTQDDLHFLSKHFR 83
Query: 74 S 74
S
Sbjct: 84 S 84
>gnl|CDD|224804 COG1892, COG1892, Phosphoenolpyruvate carboxylase [Carbohydrate
transport and metabolism; Energy production and
conversion].
Length = 488
Score = 28.9 bits (65), Expect = 5.4
Identities = 21/81 (25%), Positives = 29/81 (35%), Gaps = 24/81 (29%)
Query: 80 VPKLASAAEYFFKMGVEGKRFRPTVLLLMATALNVRVPEPLHDGVEDALATELRTRQQCI 139
V KL S FF+ + G+ L RVP P VE+A + +
Sbjct: 62 VKKLLSRYPEFFRDHILGEDVF----------LTPRVPNPT---VENAER-------KLL 101
Query: 140 AEITEMI----HVASLLHDDV 156
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 = 28.5 bits (64), Expect = 6.9
Identities = 19/87 (21%), Positives = 30/87 (34%), Gaps = 20/87 (22%)
Query: 310 ILFAMEEFPQLRTVVEQGF-EDSSNVDI--ALEYLGKSRGI------------QKTRELA 354
IL E P+L+ +V G E + + D L K RG + EL
Sbjct: 41 ILEEAVELPELKEIVLGGIGEPTVHPDFIDMLTEA-KERGFAVGLSTNGYLLEEMAEELV 99
Query: 355 VKHANLAAAAIDSLPENNDEDVTKSRR 381
+ +ID+LP + +
Sbjct: 100 GLGVDKIYVSIDALP----DKPYRIIG 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 = 7.7
Identities = 15/50 (30%), Positives = 28/50 (56%), Gaps = 3/50 (6%)
Query: 142 ITEMIHVASLLHDDVLDDAD---TRRGIGSLNFVMGNKLAVLAGDFLLSR 188
+++M+H+AS + ++ A R + + N ++G L V GDF +SR
Sbjct: 122 LSQMLHIASQIASGMVYLASQHFVHRDLATRNCLVGANLLVKIGDFGMSR 171
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
0.318 0.132 0.361
Gapped
Lambda K H
0.267 0.0612 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,883,861
Number of extensions: 1954596
Number of successful extensions: 1851
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1822
Number of HSP's successfully gapped: 33
Length of query: 395
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 296
Effective length of database: 6,546,556
Effective search space: 1937780576
Effective search space used: 1937780576
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 (27.1 bits)