RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 014276
(427 letters)
>gnl|CDD|178478 PLN02890, PLN02890, geranyl diphosphate synthase.
Length = 422
Score = 680 bits (1757), Expect = 0.0
Identities = 324/433 (74%), Positives = 366/433 (84%), Gaps = 17/433 (3%)
Query: 1 MLIYRGLSRISRISKKTSFGRRWLPSHPLLSGASHSAA------AAAADSSVKVLGCREA 54
ML+ R ++RIS + G S AS AA + S+ KV+GCR
Sbjct: 1 MLLSRRVARIS-----ATSGGGRGAYGCSQSLASSRAALLGRHGHPLSQSTSKVVGCRGT 55
Query: 55 YSWSLPALHGIRHQIHHQSSSVIEDTDSQEQLDPFSLVADELSILAKRLRSMVVAEVPKL 114
YS S LHG ++Q+ HQSSS++E EQLDPFSLVADELS+LA +LRSMVVAEVPKL
Sbjct: 56 YSVSSRWLHGFQYQVRHQSSSLVE-----EQLDPFSLVADELSLLANKLRSMVVAEVPKL 110
Query: 115 ASAAEYFFKMGVEGKRFRPTVLLLMATALNVRVPEPLHDGVEDALATELRTRQQCIAEIT 174
ASAAEYFFK+GVEGKRFRPTVLLLMATALNV +PE GV D +A+ELRTRQQ IAEIT
Sbjct: 111 ASAAEYFFKVGVEGKRFRPTVLLLMATALNVPLPESTEGGVLDIVASELRTRQQNIAEIT 170
Query: 175 EMIHVASLLHDDVLDDADTRRGIGSLNFVMGNKVLAVLAGDFLLSRACVALASLKNTEVV 234
EMIHVASLLHDDVLDDADTRRG+GSLN VMGNK L+VLAGDFLLSRACVALA+LKNTEVV
Sbjct: 171 EMIHVASLLHDDVLDDADTRRGVGSLNVVMGNK-LSVLAGDFLLSRACVALAALKNTEVV 229
Query: 235 TLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIALLAGQTAEV 294
+LLAT VEHLVTGETMQ+T+S +QR SMDYYMQKTYYKTASLISNSCKA+A+LAGQTAEV
Sbjct: 230 SLLATAVEHLVTGETMQITSSREQRRSMDYYMQKTYYKTASLISNSCKAVAILAGQTAEV 289
Query: 295 AILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFAMEEFPQLRT 354
A+LAF+YG+NLGLA+QLIDDVLDFTGTSASLGKGSLSDIRHG+ITAPILFAMEEFPQLR
Sbjct: 290 AVLAFEYGRNLGLAFQLIDDVLDFTGTSASLGKGSLSDIRHGVITAPILFAMEEFPQLRE 349
Query: 355 VVEQGFEDSSNVDIALEYLGKSRGIQKTRELAVKHANLAAAAIDSLPENNDEDVTKSRRA 414
VV++GF++ +NVDIALEYLGKSRGIQ+TRELA +HANLAAAAI+SLPE +DEDV SRRA
Sbjct: 350 VVDRGFDNPANVDIALEYLGKSRGIQRTRELAREHANLAAAAIESLPETDDEDVLTSRRA 409
Query: 415 LLDLTHRVITRNK 427
L+DLT RVITRNK
Sbjct: 410 LIDLTERVITRNK 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 = 297 bits (762), Expect = 1e-98
Identities = 146/337 (43%), Positives = 217/337 (64%), Gaps = 23/337 (6%)
Query: 89 FSLVADELSILAKRLRSMVVAEVPKLASAAEYFFKMGVEGKRFRPTVLLLMATALNVRVP 148
F+ V D+L +L L+S+V A P L +AAE+ F G GKR RP ++LL++ A
Sbjct: 7 FAPVEDDLYLLTDNLKSLVGARHPILYAAAEHLFSAG--GKRLRPAIVLLVSRAT----- 59
Query: 149 EPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDVLDDADTRRGIGSLNFVMGNKV 208
A EL R + +AEITEMIH ASL+HDDV+D++DTRRGI +++ + G +V
Sbjct: 60 ---------AEQQELTPRHRRLAEITEMIHTASLVHDDVIDESDTRRGIETVHSLFGTRV 110
Query: 209 LAVLAGDFLLSRACVALASLKNTEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQK 268
AVLAGDFL ++A LA+L+N EVV L++ V+ GE Q D S++ Y++K
Sbjct: 111 -AVLAGDFLFAQASWYLANLENLEVVKLISKVITDFAEGEIKQGLNQFDSDLSLEDYLEK 169
Query: 269 TYYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKG 328
++YKTASL++ S KA A+L+ ++VA ++YGK+LGLA+Q++DD+LDFTG++ LGK
Sbjct: 170 SFYKTASLVAASSKAAAVLSDVPSQVANDLYEYGKHLGLAFQVVDDILDFTGSTEQLGKP 229
Query: 329 SLSDIRHGIITAPILFAMEEFPQLRTVVEQGFEDSSNVDIALEYLGKSRGIQKTRELAVK 388
+ SD+ G +TAP+LFA+EE P+L ++E+ F +++ AL + KS GI+K RELA +
Sbjct: 230 AGSDLMKGNLTAPVLFALEEEPKLSELIEREFSQKGDLEQALSLVRKSGGIKKARELAKE 289
Query: 389 HANLAAAAIDSLPENNDEDVTKSRRALLDLTHRVITR 425
A LA ++ LP + R AL +L H V++R
Sbjct: 290 QAQLALQSLSFLPP------SPPREALKELVHFVLSR 320
>gnl|CDD|215462 PLN02857, PLN02857, octaprenyl-diphosphate synthase.
Length = 416
Score = 270 bits (693), Expect = 5e-87
Identities = 137/337 (40%), Positives = 211/337 (62%), Gaps = 20/337 (5%)
Query: 89 FSLVADELSILAKRLRSMVVAEVPKLASAAEYFFKMGVEGKRFRPTVLLLMATALNVRVP 148
F VAD+L L L+S+V AE P L SAAE F G GKR RP ++ L++ A
Sbjct: 98 FEPVADDLQQLNDNLQSIVGAENPVLMSAAEQIFGAG--GKRMRPALVFLVSRAT----- 150
Query: 149 EPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDVLDDADTRRGIGSLNFVMGNKV 208
E A EL T + +AEITEMIH ASL+HDDVLD++D RRG +++ + G +V
Sbjct: 151 ------AELAGLKELTTEHRRLAEITEMIHTASLIHDDVLDESDMRRGKETVHQLYGTRV 204
Query: 209 LAVLAGDFLLSRACVALASLKNTEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQK 268
AVLAGDF+ +++ LA+L N EV+ L++ V++ +GE Q ++ D ++D Y+ K
Sbjct: 205 -AVLAGDFMFAQSSWYLANLDNLEVIKLISQVIKDFASGEIKQASSLFDCDVTLDEYLLK 263
Query: 269 TYYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKG 328
+YYKTASLI+ S K+ A+ +G + V ++YGKNLGLA+Q++DD+LDFT ++ LGK
Sbjct: 264 SYYKTASLIAASTKSAAIFSGVDSSVKEQMYEYGKNLGLAFQVVDDILDFTQSTEQLGKP 323
Query: 329 SLSDIRHGIITAPILFAMEEFPQLRTVVEQGFEDSSNVDIALEYLGKSRGIQKTRELAVK 388
+ SD+ G +TAP++FA+E+ P+LR ++E F + +++ A+E + + GI++ +ELA +
Sbjct: 324 AGSDLAKGNLTAPVIFALEKEPELREIIESEFCEEGSLEEAIELVNEGGGIERAQELAKE 383
Query: 389 HANLAAAAIDSLPENNDEDVTKSRRALLDLTHRVITR 425
A+LA ++ LP R +L D+ + R
Sbjct: 384 KADLAIQNLECLPR------GAFRSSLEDMVDYNLER 414
>gnl|CDD|164542 CHL00151, preA, prenyl transferase; Reviewed.
Length = 323
Score = 263 bits (673), Expect = 3e-85
Identities = 129/339 (38%), Positives = 209/339 (61%), Gaps = 23/339 (6%)
Query: 89 FSLVADELSILAKRLRSMVVAEVPKLASAAEYFFKMGVEGKRFRPTVLLLMATALNVRVP 148
+ + +EL IL L+ ++ + P L +AA++ F G GKR RP ++LL+A A
Sbjct: 8 LTPIEEELLILEDNLKKLIGSGHPILYAAAKHLFSAG--GKRIRPAIVLLVAKATGG--- 62
Query: 149 EPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDVLDDADTRRGIGSLNFVMGNKV 208
E++T QQ +AEITE+IH ASL+HDDV+D+ RRGI +++ + G K
Sbjct: 63 -----------NMEIKTSQQRLAEITEIIHTASLVHDDVIDECSIRRGIPTVHKIFGTK- 110
Query: 209 LAVLAGDFLLSRACVALASLKNTEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQK 268
+AVLAGDFL +++ LA+L N EVV L++ V+ GE Q D S+ Y++K
Sbjct: 111 IAVLAGDFLFAQSSWYLANLNNLEVVKLISKVITDFAEGEIRQGLVQFDTTLSILNYIEK 170
Query: 269 TYYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKG 328
++YKTASLI+ SCKA ALL+ + + YGK+LGLA+Q+IDDVLD T ++ SLGK
Sbjct: 171 SFYKTASLIAASCKAAALLSDADEKDHNDFYLYGKHLGLAFQIIDDVLDITSSTESLGKP 230
Query: 329 SLSDIRHGIITAPILFAMEEFPQLRTVVEQGFEDSSNVDIALEYLGKSRGIQKTRELAVK 388
SD+++G +TAP+LFA+ + +L ++E+ F ++ ++ AL+ + ++ GI+K ++LA++
Sbjct: 231 IGSDLKNGNLTAPVLFALTQNSKLAKLIEREFCETKDISQALQIIKETNGIEKAKDLALE 290
Query: 389 HANLAAAAIDSLPENNDEDVTKSRRALLDLTHRVITRNK 427
H A + LP ++ +D +L+++ + +I R
Sbjct: 291 HMQAAIQCLKFLPPSSAKD------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 = 238 bits (609), Expect = 2e-76
Identities = 102/320 (31%), Positives = 149/320 (46%), Gaps = 64/320 (20%)
Query: 109 AEVPKLASAAEYFFKMGVEGKRFRPTVLLLMATALNVRVPEPLHDGVEDALATELRTRQQ 168
+EV L A Y G GKR RP ++LL A AL E
Sbjct: 1 SEVELLREALRYLLLAG--GKRLRPLLVLLAARALGGPELE----------------AAL 42
Query: 169 CIAEITEMIHVASLLHDDVLDDADTRRGIGSLNFVMGNKVLAVLAGDFLLSRACVALASL 228
+A E++H ASL+HDDV+D++D RRG +++ V GN A+LAGD+LL+RA LA L
Sbjct: 43 RLAAAIELLHTASLVHDDVMDNSDLRRGKPTVHKVFGNAT-AILAGDYLLARAFELLARL 101
Query: 229 KN---TEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIA 285
N + L + + LV G+ + + + D + + Y++ KTA+L + + A
Sbjct: 102 GNPYYPRALELFSEAILELVEGQLLDLLSEYDTDVTEEEYLRIIRLKTAALFAAAPLLGA 161
Query: 286 LLAGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFA 345
LLAG E A +G+NLGLA+Q+ DD+LD G +LGK SD+R G T P+L A
Sbjct: 162 LLAGADEEEAEALKRFGRNLGLAFQIQDDILDLFGDPETLGKPVGSDLREGKCTLPVLLA 221
Query: 346 MEEFPQLRTVVEQGFEDSSNVDIALEYLGKSRGIQKTRELAVKHANLAAAAIDSLPENND 405
+ RELA ++ A A+ +LPE+
Sbjct: 222 L------------------------------------RELAREYEEKALEALKALPESP- 244
Query: 406 EDVTKSRRALLDLTHRVITR 425
+R AL L ++ R
Sbjct: 245 -----AREALRALADFILER 259
>gnl|CDD|223220 COG0142, IspA, Geranylgeranyl pyrophosphate synthase [Coenzyme
metabolism].
Length = 322
Score = 234 bits (599), Expect = 3e-74
Identities = 112/344 (32%), Positives = 178/344 (51%), Gaps = 26/344 (7%)
Query: 87 DPFSLVADELSILAKRLRSMV-VAEVPKLASAAEYFFKMGVEGKRFRPTVLLLMATALNV 145
D +L+ L+ + + L ++ ++ L A Y G GKR RP ++LL A AL +
Sbjct: 2 DLLALLLKRLARIEELLSELLSGSDPELLLEAMRYLLLAG--GKRLRPLLVLLAAEALGI 59
Query: 146 RVPEPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDVLDDADTRRGIGSLNFVMG 205
L G DAL +A E+IH ASL+HDD++DD D RRG +++ G
Sbjct: 60 ----DLETGGNDALD---------LAAAIELIHTASLIHDDLMDDDDLRRGKPTVHAKFG 106
Query: 206 NKVLAVLAGDFLLSRACVALASLKN--TEVVTLLATVVEHLVTGETMQMTTSSDQRCSMD 263
A+LAGD LL+ A L+ L + E + LA + L G+ + + + +++
Sbjct: 107 EAT-AILAGDALLAAAFELLSKLGSEALEAIKALAEAINGLCGGQALDLAFENKP-VTLE 164
Query: 264 YYMQKTYYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSA 323
Y++ KTA+L + + A+LAG E+ DYG+NLGLA+Q+ DD+LD TG
Sbjct: 165 EYLRVIELKTAALFAAAAVLGAILAGADEELLEALEDYGRNLGLAFQIQDDILDITGDEE 224
Query: 324 SLGKGSLSDIRHGIITAPILFAMEEFPQLRTVVEQGFEDSSNVDIALEYLGKSRGIQKTR 383
LGK SD++ G T P+L A+E+ + + ++ E V+ ALE L KS I+ +
Sbjct: 225 ELGKPVGSDLKEGKPTLPVLLALEKANEDQKLLRILLEGGGEVEEALELLRKSGAIEYAK 284
Query: 384 ELAVKHANLAAAAIDSLPENNDEDVTKSRRALLDLTHRVITRNK 427
LA + A A++ LP++ +++ ALL+L +I R
Sbjct: 285 NLAKTYVEKAKEALEKLPDS------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 (441), Expect = 8e-52
Identities = 92/295 (31%), Positives = 135/295 (45%), Gaps = 59/295 (20%)
Query: 131 FRPTVLLLMATALNVRVPEPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDVLDD 190
RP ++LL+A AL + +A E++H ASL+HDD++DD
Sbjct: 1 SRPLLVLLLARALGGDLE-----------------AALRLAAAVELLHAASLVHDDIVDD 43
Query: 191 ADTRRGIGSLNFVMGNKVLAVLAGDFLLSRACVALASLKNTEVVTLLATVVEHLVTGETM 250
+D RRG + + LA+LAGD+LL+RA LA L + L A + L+ G+ +
Sbjct: 44 SDLRRGKPTAHLRRFGNALAILAGDYLLARAFQLLARLGYPRALELFAEALRELLEGQAL 103
Query: 251 QMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLGLAYQ 310
+ D ++D Y++ YKTA L+ C A L+G E A DYG+ LGLA+Q
Sbjct: 104 DLEFERDTYETLDEYLEYCRYKTAGLVGLLCLLGAGLSGADDEQAEALKDYGRALGLAFQ 163
Query: 311 LIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFAMEEFPQLRTVVEQGFEDSSNVDIAL 370
L DD+LD G + LGK SD+R G IT P++ A E
Sbjct: 164 LTDDLLDVFGDAEELGK-VGSDLREGRITLPVILARER---------------------- 200
Query: 371 EYLGKSRGIQKTRELAVKHANLAAAAIDSLPENNDEDVTKSRRALLDLTHRVITR 425
A ++A A AA+++LP + RRAL+ L + R
Sbjct: 201 ---------------AAEYAEEAYAALEALPPSLPRA----RRALIALADFLYRR 236
>gnl|CDD|215873 pfam00348, polyprenyl_synt, Polyprenyl synthetase.
Length = 260
Score = 161 bits (410), Expect = 7e-47
Identities = 77/226 (34%), Positives = 119/226 (52%), Gaps = 24/226 (10%)
Query: 128 GKRFRPTVLLLMATALNVRVPEPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDV 187
GKR RP LL++ A + V + A EMIH ASL+HDD+
Sbjct: 13 GKRIRP--LLVVLAARALGVEPETLLYL---------------ACAIEMIHTASLVHDDL 55
Query: 188 LDDADTRRGIGSLNFVMGNKVLAVLAGDFLLSRACVALASLK--NTEVVTLLATVVEHLV 245
+D++D RRG + + G A+LAGD LLSRA LA L E +L + + + V
Sbjct: 56 MDNSDLRRGKPTCHKKFGE-AGAILAGDALLSRAFQLLALLGHVRPEPKYILISELANAV 114
Query: 246 TGETM--QMT--TSSDQRCSMDYYMQKTYYKTASLISNSCKAIALLAGQTAEVAILAFDY 301
+ Q+ + + +++ Y++ YKTA+L S + A++AG E +D+
Sbjct: 115 GAQGEVGQLMDLETEGKDITLEEYLRIVSYKTAALFYASVQLGAIVAGADEEDEKDLYDF 174
Query: 302 GKNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFAME 347
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 = 161 bits (410), Expect = 3e-46
Identities = 96/343 (27%), Positives = 178/343 (51%), Gaps = 30/343 (8%)
Query: 87 DPFSLVADELSILAKRLRSMVVAEVPKLASAAEYFFKMGVEGKRFRPTVLLLMATALNVR 146
D +S + ++ + K L V AE P L+ A+ + + G GKR RP +LL +
Sbjct: 4 DIYSFLQKDIDSIEKELEKAVQAEHPVLSEASLHLLEAG--GKRIRPVFVLLAGKFGDYD 61
Query: 147 VPEPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDVLDDADTRRGIGSLNFVMGN 206
+ H +A E+IH+ASL+HDDV+DDAD RRG ++ GN
Sbjct: 62 LDAIKH-----------------VAVALELIHMASLVHDDVIDDADLRRGRPTIKSKWGN 104
Query: 207 KVLAVLAGDFLLSRACVALASLKNTEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYM 266
++ A+ GD+L +++ + +K+ +L+ + + GE Q+ + ++ Y+
Sbjct: 105 RI-AMYTGDYLFAKSLETMTEIKDPRAHQILSHTIVEVCRGEIEQIKDKYNFDQNLRTYL 163
Query: 267 QKTYYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLG 326
++ KTA LI+ SC+ A+ +G + + +G +G++YQ+ DD+LDF GT LG
Sbjct: 164 RRIKRKTALLIAASCQLGAIASGANEAIVKKLYWFGYYVGMSYQITDDILDFVGTEEELG 223
Query: 327 KGSLSDIRHGIITAPILFAMEEFPQLRTVVEQGFEDSSNVDIA--LEYLGKSRGIQKTRE 384
K + D+ G +T P+L+AME+ P L+ +EQ E+++ ++ +E + KS I+
Sbjct: 224 KPAGGDLLQGNVTLPVLYAMED-PFLKKRIEQVLEETTAEEMEPLIEEVKKSDAIEYAYA 282
Query: 385 LAVKHANLAAAAIDSLPENNDEDVTKSRRALLDLTHRVITRNK 427
++ ++ A +D LP+ ++++ L ++ + I + K
Sbjct: 283 VSDRYLKKALELLDGLPDG------RAKKPLQEIA-KYIGKRK 318
>gnl|CDD|182813 PRK10888, PRK10888, octaprenyl diphosphate synthase; Provisional.
Length = 323
Score = 156 bits (396), Expect = 3e-44
Identities = 103/303 (33%), Positives = 156/303 (51%), Gaps = 30/303 (9%)
Query: 128 GKRFRPTVLLLMATALNVRVPEPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDV 187
GKR RP + +L A A+ + G IA + E IH A+LLHDDV
Sbjct: 44 GKRIRPMIAVLAARAVG-------YQG----------NAHVTIAALIEFIHTATLLHDDV 86
Query: 188 LDDADTRRGIGSLNFVMGNKVLAVLAGDFLLSRACVALASLKNTEVVTLLATVVEHLVTG 247
+D++D RRG + N GN +VL GDF+ +RA + SL + +V+ +++ V + G
Sbjct: 87 VDESDMRRGKATANAAFGNAA-SVLVGDFIYTRAFQMMTSLGSLKVLEVMSEAVNVIAEG 145
Query: 248 ETMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLGL 307
E +Q+ +D + + YM+ Y KTA L + + +LAG T E DYG+ LG
Sbjct: 146 EVLQLMNVNDPDITEENYMRVIYSKTARLFEAAAQCSGILAGCTPEQEKGLQDYGRYLGT 205
Query: 308 AYQLIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFAM-----EEFPQLRTVVEQGFED 362
A+QLIDD+LD++ +LGK D+ G T P+L AM E+ +RT +EQG
Sbjct: 206 AFQLIDDLLDYSADGETLGKNVGDDLNEGKPTLPLLHAMHHGTPEQAAMIRTAIEQG-NG 264
Query: 363 SSNVDIALEYLGKSRGIQKTRELAVKHANLAAAAIDSLPENNDEDVTKSRRALLDLTHRV 422
++ LE + ++ TR+ A + A+ A AA+ LP+ T R AL+ L H
Sbjct: 265 RHLLEPVLEAMNACGSLEWTRQRAEEEADKAIAALQVLPD------TPWREALIGLAHIA 318
Query: 423 ITR 425
+ 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 = 140 bits (354), Expect = 5e-39
Identities = 71/256 (27%), Positives = 118/256 (46%), Gaps = 30/256 (11%)
Query: 170 IAEITEMIHVASLLHDDVLDDADTRRGIGSLN--FVMGNKVLAVLAGDFLLSRACVALAS 227
+ E +H ASL+HDD++DD+ TRRG+ + + + A+LAGD LL+ A LA
Sbjct: 15 LRAAVEKLHAASLVHDDIVDDSGTRRGLPTAHLAVAIDGLPEAILAGDLLLADAFEELAR 74
Query: 228 LKNTEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIALL 287
+ E + +LA + L+ G+ + + + +++ Y++ YKTA L+ C A L
Sbjct: 75 EGSPEALEILAEALLDLLEGQLLDLKWRREYVPTLEEYLEYCRYKTAGLVGALCLLGAGL 134
Query: 288 AGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFAME 347
+G AE+ G+ LGLA+QL +D+LD+ G + G T P+L+A+E
Sbjct: 135 SGGEAELLEALRKLGRALGLAFQLTNDLLDYEGDAERGE---------GKCTLPVLYALE 185
Query: 348 EFPQLRTVVEQGFEDSSNVDIALEYLGKSRGIQKTRELAVKHANLAAAAIDSLPENNDED 407
L + KS +++ E K A A ++ L + +
Sbjct: 186 YGVPAE---------------DLLLVEKSGSLEEALEELAKLAEEALKELNELILSLPD- 229
Query: 408 VTKSRRALLDLTHRVI 423
RALL L +
Sbjct: 230 ---VPRALLALALNLY 242
>gnl|CDD|182567 PRK10581, PRK10581, geranyltranstransferase; Provisional.
Length = 299
Score = 76.3 bits (188), Expect = 2e-15
Identities = 60/191 (31%), Positives = 100/191 (52%), Gaps = 15/191 (7%)
Query: 171 AEITEMIHVASLLHDDV--LDDADTRRGIGSLNFVMGNKVLAVLAGDFLLSRACVALASL 228
A E IH SL+HDD+ +DD D RRG+ + + G + A+LAGD L + A L+
Sbjct: 70 AAAVECIHAYSLIHDDLPAMDDDDLRRGLPTCHVKFG-EANAILAGDALQTLAFSILSDA 128
Query: 229 KNTEV--------VTLLATV--VEHLVTGETMQMTTSSDQRCSMDYYMQKTYYKTASLIS 278
EV ++ LA+ + + G+ + + + ++ +D + +KT +LI
Sbjct: 129 PMPEVSDRDRISMISELASASGIAGMCGGQALDLE-AEGKQVPLDALERIHRHKTGALIR 187
Query: 279 NSCKAIALLAGQTAEVAILAFD-YGKNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRHGI 337
+ + AL AG A+ D Y +++GLA+Q+ DD+LD G +A+LGK +D + G
Sbjct: 188 AAVRLGALSAGDKGRRALPVLDRYAESIGLAFQVQDDILDVVGDTATLGKRQGADQQLGK 247
Query: 338 ITAPILFAMEE 348
T P L +E+
Sbjct: 248 STYPALLGLEQ 258
>gnl|CDD|176871 cd08862, SRPBCC_Smu440-like, Ligand-binding SRPBCC domain of
Streptococcus mutans Smu.440 and related proteins. This
family includes the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of
Streptococcus mutans Smu.440 and related proteins. This
domain belongs to the SRPBCC domain superfamily of
proteins that bind hydrophobic ligands. SRPBCC domains
have a deep hydrophobic ligand-binding pocket.
Streptococcus mutans is a dental pathogen, and the
leading cause of dental caries. In this pathogen, the
gene encoding Smu.440 is in the same operon as the gene
encoding SMU.441, a member of the MarR protein family of
transcriptional regulators involved in multiple
antibiotic resistance. It has been suggested that
SMU.440 is involved in polyketide-like antibiotic
resistance.
Length = 138
Score = 34.3 bits (79), Expect = 0.039
Identities = 16/78 (20%), Positives = 34/78 (43%), Gaps = 7/78 (8%)
Query: 47 KVLGCREAYSWS----LPALHGI-RHQIHHQSSSVIEDTDSQEQLDPFSLVADELSILAK 101
V R +S++ P + + RH+ + + T S+ P + + + K
Sbjct: 62 TVTELRPGHSFTWTGPAPGISAVHRHEFEAKPDGGVRVTTSESLSGPLAFLFGLF--VGK 119
Query: 102 RLRSMVVAEVPKLASAAE 119
+LR+++ + L +AAE
Sbjct: 120 KLRALLPEWLEGLKAAAE 137
>gnl|CDD|213572 TIGR00936, ahcY, adenosylhomocysteinase. This enzyme hydrolyzes
adenosylhomocysteine as part of a cycle for the
regeneration of the methyl donor S-adenosylmethionine.
Species that lack this enzyme are likely to have
adenosylhomocysteine nucleosidase (EC 3.2.2.9), an
enzyme which also acts as 5'-methyladenosine
nucleosidase (see TIGR01704) [Energy metabolism, Amino
acids and amines].
Length = 407
Score = 32.8 bits (75), Expect = 0.38
Identities = 25/99 (25%), Positives = 40/99 (40%), Gaps = 20/99 (20%)
Query: 22 RWLPSHPLLSGASHSAAAAAADSSVKVLGCR----EAYSWSLPALHGIRHQIHHQSSSVI 77
W +PL S AAA A + + V R E Y W+ I + H+ + +I
Sbjct: 60 AWTSCNPL-STQDDVAAALAKGAGIPVFAWRGETNEEYYWA------IEQVLDHEPNIII 112
Query: 78 ED---------TDSQEQLDPFSLVADELSILAKRLRSMV 107
+D T+ E L+ ++E + RLR+M
Sbjct: 113 DDGADLIFLLHTERPELLEKIIGGSEETTTGVIRLRAME 151
>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 = 0.74
Identities = 17/77 (22%), Positives = 28/77 (36%), Gaps = 13/77 (16%)
Query: 247 GETMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLG 306
GE ++M S D C+ Y+Q ++ ++ L Y N G
Sbjct: 44 GEGLRMLVSRDLDCTHTLYIQFSFKFITKGTPERSHSVLL-------------QYSINGG 90
Query: 307 LAYQLIDDVLDFTGTSA 323
+ + LID+ T T
Sbjct: 91 ITWHLIDEFYFPTTTDV 107
>gnl|CDD|225744 COG3203, OmpC, Outer membrane protein (porin) [Cell envelope
biogenesis, outer membrane].
Length = 354
Score = 31.2 bits (71), Expect = 1.0
Identities = 12/40 (30%), Positives = 17/40 (42%), Gaps = 2/40 (5%)
Query: 299 FDYGKNLGLAYQLID--DVLDFTGTSASLGKGSLSDIRHG 336
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 = 2.0
Identities = 25/84 (29%), Positives = 40/84 (47%), Gaps = 6/84 (7%)
Query: 28 PLLSGASHSAAAAAADSSVKVLGCREAYS----WSLPALHGIRHQIHHQSSSVIEDTDSQ 83
PL S + SA+A+ + + R + WS+ +L + + SS+V + SQ
Sbjct: 1 PLDSPRNFSASASINFPFARRIASRRGRADGRRWSVASLPSSGYGTNPPSSTVSSSSSSQ 60
Query: 84 EQLD--PFSLVADELSILAKRLRS 105
E+L PF D+L L+K RS
Sbjct: 61 ERLHQLPFQPTQDDLHFLSKHFRS 84
>gnl|CDD|119267 pfam10747, DUF2522, Protein of unknown function (DUF2522). This
family of proteins with unknown function appears to be
restricted to Bacillus.
Length = 142
Score = 28.0 bits (63), Expect = 5.0
Identities = 16/83 (19%), Positives = 29/83 (34%), Gaps = 10/83 (12%)
Query: 58 SLPALHGIRHQIHHQSSSVI--EDTDSQEQLDP-------FSLVADELSILAKRLRSMVV 108
+P LH + ++ Q S+ I E + +L P + + + A S
Sbjct: 51 PIPFLH-LHQRLKQQLSAKIYYERIGNAYRLLPNGKGTAALYVKDRYIELNASGSYSAET 109
Query: 109 AEVPKLASAAEYFFKMGVEGKRF 131
L + F M + KR+
Sbjct: 110 TFFEVLRKVSPCFLAMDFDNKRY 132
>gnl|CDD|224804 COG1892, COG1892, Phosphoenolpyruvate carboxylase [Carbohydrate
transport and metabolism; Energy production and
conversion].
Length = 488
Score = 28.9 bits (65), Expect = 5.1
Identities = 21/81 (25%), Positives = 29/81 (35%), Gaps = 24/81 (29%)
Query: 111 VPKLASAAEYFFKMGVEGKRFRPTVLLLMATALNVRVPEPLHDGVEDALATELRTRQQCI 170
V KL S FF+ + G+ L RVP P VE+A + +
Sbjct: 62 VKKLLSRYPEFFRDHILGEDVF----------LTPRVPNPT---VENAER-------KLL 101
Query: 171 AEITEMI----HVASLLHDDV 187
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 = 7.8
Identities = 19/82 (23%), Positives = 30/82 (36%), Gaps = 16/82 (19%)
Query: 342 ILFAMEEFPQLRTVVEQGF-EDSSNVDI--ALEYLGKSRGI------------QKTRELA 386
IL E P+L+ +V G E + + D L K RG + EL
Sbjct: 41 ILEEAVELPELKEIVLGGIGEPTVHPDFIDMLTEA-KERGFAVGLSTNGYLLEEMAEELV 99
Query: 387 VKHANLAAAAIDSLPENNDEDV 408
+ +ID+LP+ +
Sbjct: 100 GLGVDKIYVSIDALPDKPYRII 121
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.132 0.367
Gapped
Lambda K H
0.267 0.0748 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 21,550,720
Number of extensions: 2120384
Number of successful extensions: 1953
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1915
Number of HSP's successfully gapped: 31
Length of query: 427
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 327
Effective length of database: 6,502,202
Effective search space: 2126220054
Effective search space used: 2126220054
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 (26.9 bits)