RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 018980
(348 letters)
>gnl|CDD|178478 PLN02890, PLN02890, geranyl diphosphate synthase.
Length = 422
Score = 527 bits (1360), Expect = 0.0
Identities = 255/353 (72%), Positives = 287/353 (81%), Gaps = 17/353 (4%)
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 EMIHVASLLHDDVLDDADTRRGIGSLNFVMGNKLAVLAGDFLLSRACVALASLKNTEVVT 234
EMIHVASLLHDDVLDDADTRRG+GSLN VMGNKL+VLAGDFLLSRACVALA+LKNTEVV+
Sbjct: 171 EMIHVASLLHDDVLDDADTRRGVGSLNVVMGNKLSVLAGDFLLSRACVALAALKNTEVVS 230
Query: 235 LLATVVEHLVTGETMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIALLAGQTAEVA 294
LLAT VEHLVTGETMQ+T+S +QR SMDYYMQKTYYKTASLISNSCKA+A+LAGQTAEVA
Sbjct: 231 LLATAVEHLVTGETMQITSSREQRRSMDYYMQKTYYKTASLISNSCKAVAILAGQTAEVA 290
Query: 295 ILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRH-VIYLSLLFIASE 346
+LAF+YG+NLGLA+QLIDDVLDFTGTSASLGKGSLSDIRH VI +LF E
Sbjct: 291 VLAFEYGRNLGLAFQLIDDVLDFTGTSASLGKGSLSDIRHGVITAPILFAMEE 343
>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 = 225 bits (576), Expect = 7e-72
Identities = 109/245 (44%), Positives = 162/245 (66%), Gaps = 16/245 (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 EPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDVLDDADTRRGIGSLNFVMGNKL 208
A EL R + +AEITEMIH ASL+HDDV+D++DTRRGI +++ + G ++
Sbjct: 60 ---------AEQQELTPRHRRLAEITEMIHTASLVHDDVIDESDTRRGIETVHSLFGTRV 110
Query: 209 AVLAGDFLLSRACVALASLKNTEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQKT 268
AVLAGDFL ++A LA+L+N EVV L++ V+ GE Q D S++ Y++K+
Sbjct: 111 AVLAGDFLFAQASWYLANLENLEVVKLISKVITDFAEGEIKQGLNQFDSDLSLEDYLEKS 170
Query: 269 YYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKGS 328
+YKTASL++ S KA A+L+ ++VA ++YGK+LGLA+Q++DD+LDFTG++ LGK +
Sbjct: 171 FYKTASLVAASSKAAAVLSDVPSQVANDLYEYGKHLGLAFQVVDDILDFTGSTEQLGKPA 230
Query: 329 LSDIR 333
SD+
Sbjct: 231 GSDLM 235
>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 = 212 bits (543), Expect = 1e-67
Identities = 83/229 (36%), Positives = 120/229 (52%), Gaps = 21/229 (9%)
Query: 109 AEVPKLASAAEYFFKMGVEGKRFRPTVLLLMATALNVRVPEPLHDGVEDALATELRTRQQ 168
+EV L A Y G GKR RP ++LL A AL E
Sbjct: 1 SEVELLREALRYLLLAG--GKRLRPLLVLLAARALGGPELE----------------AAL 42
Query: 169 CIAEITEMIHVASLLHDDVLDDADTRRGIGSLNFVMGNKLAVLAGDFLLSRACVALASLK 228
+A E++H ASL+HDDV+D++D RRG +++ V GN A+LAGD+LL+RA LA L
Sbjct: 43 RLAAAIELLHTASLVHDDVMDNSDLRRGKPTVHKVFGNATAILAGDYLLARAFELLARLG 102
Query: 229 N---TEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIAL 285
N + L + + LV G+ + + + D + + Y++ KTA+L + + AL
Sbjct: 103 NPYYPRALELFSEAILELVEGQLLDLLSEYDTDVTEEEYLRIIRLKTAALFAAAPLLGAL 162
Query: 286 LAGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRH 334
LAG E A +G+NLGLA+Q+ DD+LD G +LGK SD+R
Sbjct: 163 LAGADEEEAEALKRFGRNLGLAFQIQDDILDLFGDPETLGKPVGSDLRE 211
>gnl|CDD|215462 PLN02857, PLN02857, octaprenyl-diphosphate synthase.
Length = 416
Score = 213 bits (545), Expect = 5e-66
Identities = 108/244 (44%), Positives = 158/244 (64%), Gaps = 13/244 (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 EPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDVLDDADTRRGIGSLNFVMGNKL 208
E A EL T + +AEITEMIH ASL+HDDVLD++D RRG +++ + G ++
Sbjct: 151 ------AELAGLKELTTEHRRLAEITEMIHTASLIHDDVLDESDMRRGKETVHQLYGTRV 204
Query: 209 AVLAGDFLLSRACVALASLKNTEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQKT 268
AVLAGDF+ +++ LA+L N EV+ L++ V++ +GE Q ++ D ++D Y+ K+
Sbjct: 205 AVLAGDFMFAQSSWYLANLDNLEVIKLISQVIKDFASGEIKQASSLFDCDVTLDEYLLKS 264
Query: 269 YYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKGS 328
YYKTASLI+ S K+ A+ +G + V ++YGKNLGLA+Q++DD+LDFT ++ LGK +
Sbjct: 265 YYKTASLIAASTKSAAIFSGVDSSVKEQMYEYGKNLGLAFQVVDDILDFTQSTEQLGKPA 324
Query: 329 LSDI 332
SD+
Sbjct: 325 GSDL 328
>gnl|CDD|164542 CHL00151, preA, prenyl transferase; Reviewed.
Length = 323
Score = 209 bits (534), Expect = 2e-65
Identities = 104/245 (42%), Positives = 152/245 (62%), Gaps = 16/245 (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 EPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDVLDDADTRRGIGSLNFVMGNKL 208
E++T QQ +AEITE+IH ASL+HDDV+D+ RRGI +++ + G K+
Sbjct: 63 -----------NMEIKTSQQRLAEITEIIHTASLVHDDVIDECSIRRGIPTVHKIFGTKI 111
Query: 209 AVLAGDFLLSRACVALASLKNTEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQKT 268
AVLAGDFL +++ LA+L N EVV L++ V+ GE Q D S+ Y++K+
Sbjct: 112 AVLAGDFLFAQSSWYLANLNNLEVVKLISKVITDFAEGEIRQGLVQFDTTLSILNYIEKS 171
Query: 269 YYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKGS 328
+YKTASLI+ SCKA ALL+ + + YGK+LGLA+Q+IDDVLD T ++ SLGK
Sbjct: 172 FYKTASLIAASCKAAALLSDADEKDHNDFYLYGKHLGLAFQIIDDVLDITSSTESLGKPI 231
Query: 329 LSDIR 333
SD++
Sbjct: 232 GSDLK 236
>gnl|CDD|223220 COG0142, IspA, Geranylgeranyl pyrophosphate synthase [Coenzyme
metabolism].
Length = 322
Score = 189 bits (481), Expect = 1e-57
Identities = 85/251 (33%), Positives = 131/251 (52%), Gaps = 19/251 (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 NKLAVLAGDFLLSRACVALASLKN--TEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDY 263
A+LAGD LL+ A L+ L + E + LA + L G+ + + + +++
Sbjct: 107 EATAILAGDALLAAAFELLSKLGSEALEAIKALAEAINGLCGGQALDLAFENKP-VTLEE 165
Query: 264 YMQKTYYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSAS 323
Y++ KTA+L + + A+LAG E+ DYG+NLGLA+Q+ DD+LD TG
Sbjct: 166 YLRVIELKTAALFAAAAVLGAILAGADEELLEALEDYGRNLGLAFQIQDDILDITGDEEE 225
Query: 324 LGKGSLSDIRH 334
LGK SD++
Sbjct: 226 LGKPVGSDLKE 236
>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 = 155 bits (394), Expect = 9e-46
Identities = 77/214 (35%), Positives = 112/214 (52%), Gaps = 20/214 (9%)
Query: 131 FRPTVLLLMATALNVRVPEPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDVLDD 190
RP ++LL+A AL + +A E++H ASL+HDD++DD
Sbjct: 1 SRPLLVLLLARALGGDLE-----------------AALRLAAAVELLHAASLVHDDIVDD 43
Query: 191 ADTRRGIGSLN-FVMGNKLAVLAGDFLLSRACVALASLKNTEVVTLLATVVEHLVTGETM 249
+D RRG + + GN LA+LAGD+LL+RA LA L + L A + L+ G+ +
Sbjct: 44 SDLRRGKPTAHLRRFGNALAILAGDYLLARAFQLLARLGYPRALELFAEALRELLEGQAL 103
Query: 250 QMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLGLAYQ 309
+ D ++D Y++ YKTA L+ C A L+G E A DYG+ LGLA+Q
Sbjct: 104 DLEFERDTYETLDEYLEYCRYKTAGLVGLLCLLGAGLSGADDEQAEALKDYGRALGLAFQ 163
Query: 310 LIDDVLDFTGTSASLGKGSLSDIRH-VIYLSLLF 342
L DD+LD G + LGK SD+R I L ++
Sbjct: 164 LTDDLLDVFGDAEELGK-VGSDLREGRITLPVIL 196
>gnl|CDD|215873 pfam00348, polyprenyl_synt, Polyprenyl synthetase.
Length = 260
Score = 154 bits (390), Expect = 7e-45
Identities = 71/212 (33%), Positives = 111/212 (52%), Gaps = 23/212 (10%)
Query: 128 GKRFRPTVLLLMATALNVRVPEPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDV 187
GKR RP LL++ A + V + A EMIH ASL+HDD+
Sbjct: 13 GKRIRP--LLVVLAARALGVEPETLLYL---------------ACAIEMIHTASLVHDDL 55
Query: 188 LDDADTRRGIGSLNFVMGNKLAVLAGDFLLSRACVALASLK--NTEVVTLLATVVEHLVT 245
+D++D RRG + + G A+LAGD LLSRA LA L E +L + + + V
Sbjct: 56 MDNSDLRRGKPTCHKKFGEAGAILAGDALLSRAFQLLALLGHVRPEPKYILISELANAVG 115
Query: 246 GETM--QMT--TSSDQRCSMDYYMQKTYYKTASLISNSCKAIALLAGQTAEVAILAFDYG 301
+ Q+ + + +++ Y++ YKTA+L S + A++AG E +D+G
Sbjct: 116 AQGEVGQLMDLETEGKDITLEEYLRIVSYKTAALFYASVQLGAIVAGADEEDEKDLYDFG 175
Query: 302 KNLGLAYQLIDDVLDFTGTSASLGKGSLSDIR 333
++LGLA+Q+ DD+LD TG + LGK +D++
Sbjct: 176 RDLGLAFQIQDDILDLTGDTEELGKPVGTDLQ 207
>gnl|CDD|182813 PRK10888, PRK10888, octaprenyl diphosphate synthase; Provisional.
Length = 323
Score = 135 bits (341), Expect = 5e-37
Identities = 73/205 (35%), Positives = 110/205 (53%), Gaps = 17/205 (8%)
Query: 128 GKRFRPTVLLLMATALNVRVPEPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDV 187
GKR RP + +L A A+ + G IA + E IH A+LLHDDV
Sbjct: 44 GKRIRPMIAVLAARAVG-------YQG----------NAHVTIAALIEFIHTATLLHDDV 86
Query: 188 LDDADTRRGIGSLNFVMGNKLAVLAGDFLLSRACVALASLKNTEVVTLLATVVEHLVTGE 247
+D++D RRG + N GN +VL GDF+ +RA + SL + +V+ +++ V + GE
Sbjct: 87 VDESDMRRGKATANAAFGNAASVLVGDFIYTRAFQMMTSLGSLKVLEVMSEAVNVIAEGE 146
Query: 248 TMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLGLA 307
+Q+ +D + + YM+ Y KTA L + + +LAG T E DYG+ LG A
Sbjct: 147 VLQLMNVNDPDITEENYMRVIYSKTARLFEAAAQCSGILAGCTPEQEKGLQDYGRYLGTA 206
Query: 308 YQLIDDVLDFTGTSASLGKGSLSDI 332
+QLIDD+LD++ +LGK D+
Sbjct: 207 FQLIDDLLDYSADGETLGKNVGDDL 231
>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 = 134 bits (338), Expect = 1e-36
Identities = 73/247 (29%), Positives = 127/247 (51%), Gaps = 19/247 (7%)
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 KLAVLAGDFLLSRACVALASLKNTEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQ 266
++A+ GD+L +++ + +K+ +L+ + + GE Q+ + ++ Y++
Sbjct: 105 RIAMYTGDYLFAKSLETMTEIKDPRAHQILSHTIVEVCRGEIEQIKDKYNFDQNLRTYLR 164
Query: 267 KTYYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGK 326
+ KTA LI+ SC+ A+ +G + + +G +G++YQ+ DD+LDF GT LGK
Sbjct: 165 RIKRKTALLIAASCQLGAIASGANEAIVKKLYWFGYYVGMSYQITDDILDFVGTEEELGK 224
Query: 327 GSLSDIR 333
+ D+
Sbjct: 225 PAGGDLL 231
>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 = 122 bits (308), Expect = 4e-33
Identities = 53/158 (33%), Positives = 88/158 (55%), Gaps = 3/158 (1%)
Query: 170 IAEITEMIHVASLLHDDVLDDADTRRGIGSLN---FVMGNKLAVLAGDFLLSRACVALAS 226
+ E +H ASL+HDD++DD+ TRRG+ + + + G A+LAGD LL+ A LA
Sbjct: 15 LRAAVEKLHAASLVHDDIVDDSGTRRGLPTAHLAVAIDGLPEAILAGDLLLADAFEELAR 74
Query: 227 LKNTEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIALL 286
+ E + +LA + L+ G+ + + + +++ Y++ YKTA L+ C A L
Sbjct: 75 EGSPEALEILAEALLDLLEGQLLDLKWRREYVPTLEEYLEYCRYKTAGLVGALCLLGAGL 134
Query: 287 AGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASL 324
+G AE+ G+ LGLA+QL +D+LD+ G +
Sbjct: 135 SGGEAELLEALRKLGRALGLAFQLTNDLLDYEGDAERG 172
>gnl|CDD|182567 PRK10581, PRK10581, geranyltranstransferase; Provisional.
Length = 299
Score = 72.9 bits (179), Expect = 2e-14
Identities = 55/177 (31%), Positives = 92/177 (51%), Gaps = 14/177 (7%)
Query: 171 AEITEMIHVASLLHDDV--LDDADTRRGIGSLNFVMGNKLAVLAGDFLLSRACVALASLK 228
A E IH SL+HDD+ +DD D RRG+ + + G A+LAGD L + A L+
Sbjct: 70 AAAVECIHAYSLIHDDLPAMDDDDLRRGLPTCHVKFGEANAILAGDALQTLAFSILSDAP 129
Query: 229 NTEV--------VTLLATV--VEHLVTGETMQMTTSSDQRCSMDYYMQKTYYKTASLISN 278
EV ++ LA+ + + G+ + + + ++ +D + +KT +LI
Sbjct: 130 MPEVSDRDRISMISELASASGIAGMCGGQALDLE-AEGKQVPLDALERIHRHKTGALIRA 188
Query: 279 SCKAIALLAGQTAEVAILAFD-YGKNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRH 334
+ + AL AG A+ D Y +++GLA+Q+ DD+LD G +A+LGK +D +
Sbjct: 189 AVRLGALSAGDKGRRALPVLDRYAESIGLAFQVQDDILDVVGDTATLGKRQGADQQL 245
>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 = 34.6 bits (80), Expect = 0.021
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 = 33.1 bits (76), Expect = 0.22
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 = 0.62
Identities = 17/77 (22%), Positives = 28/77 (36%), Gaps = 13/77 (16%)
Query: 246 GETMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLG 305
GE ++M S D C+ Y+Q ++ ++ L Y N G
Sbjct: 44 GEGLRMLVSRDLDCTHTLYIQFSFKFITKGTPERSHSVLL-------------QYSINGG 90
Query: 306 LAYQLIDDVLDFTGTSA 322
+ + 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 = 1.1
Identities = 12/39 (30%), Positives = 17/39 (43%), Gaps = 2/39 (5%)
Query: 298 FDYGKNLGLAYQLID--DVLDFTGTSASLGKGSLSDIRH 334
DYG+N G+ Y + D L G A+L + R
Sbjct: 111 LDYGRNYGVLYDVAGWTDPLPEFGGDATLVDDNFMTGRA 149
>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 = 1.4
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|224804 COG1892, COG1892, Phosphoenolpyruvate carboxylase [Carbohydrate
transport and metabolism; Energy production and
conversion].
Length = 488
Score = 29.3 bits (66), Expect = 3.3
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|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 = 4.0
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|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 = 7.2
Identities = 15/50 (30%), Positives = 28/50 (56%), Gaps = 3/50 (6%)
Query: 173 ITEMIHVASLLHDDVLDDAD---TRRGIGSLNFVMGNKLAVLAGDFLLSR 219
+++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
0.320 0.132 0.371
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: 17,413,843
Number of extensions: 1678480
Number of successful extensions: 1537
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1513
Number of HSP's successfully gapped: 31
Length of query: 348
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 250
Effective length of database: 6,590,910
Effective search space: 1647727500
Effective search space used: 1647727500
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 (21.9 bits)
S2: 59 (26.5 bits)