RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 014640
(421 letters)
>gnl|CDD|178478 PLN02890, PLN02890, geranyl diphosphate synthase.
Length = 422
Score = 692 bits (1786), Expect = 0.0
Identities = 324/427 (75%), Positives = 366/427 (85%), Gaps = 11/427 (2%)
Query: 1 MLIYRGLSRISRISKKTSFGRRWLPSHPLLSGASHSAA------AAAADSSVKVLGCREA 54
ML+ R ++RIS + G S AS AA + S+ KV+GCR
Sbjct: 1 MLLSRRVARIS-----ATSGGGRGAYGCSQSLASSRAALLGRHGHPLSQSTSKVVGCRGT 55
Query: 55 YSWSLPALHGIRHQIHHQSSSVIEEQLDPFSLVADELSILAKRLRSMVVAEVPKLASAAE 114
YS S LHG ++Q+ HQSSS++EEQLDPFSLVADELS+LA +LRSMVVAEVPKLASAAE
Sbjct: 56 YSVSSRWLHGFQYQVRHQSSSLVEEQLDPFSLVADELSLLANKLRSMVVAEVPKLASAAE 115
Query: 115 YFFKMGVEGKRFRPTVLLLMATALNVRVPEPLHDGVEDALATELRTRQQCIAEITEMIHV 174
YFFK+GVEGKRFRPTVLLLMATALNV +PE GV D +A+ELRTRQQ IAEITEMIHV
Sbjct: 116 YFFKVGVEGKRFRPTVLLLMATALNVPLPESTEGGVLDIVASELRTRQQNIAEITEMIHV 175
Query: 175 ASLLHDDVLDDADTRRGIGSLNFVMGNKLAVLAGDFLLSRACVALASLKNTEVVTLLATV 234
ASLLHDDVLDDADTRRG+GSLN VMGNKL+VLAGDFLLSRACVALA+LKNTEVV+LLAT
Sbjct: 176 ASLLHDDVLDDADTRRGVGSLNVVMGNKLSVLAGDFLLSRACVALAALKNTEVVSLLATA 235
Query: 235 VEHLVTGETMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIALLAGQTAEVAILAFD 294
VEHLVTGETMQ+T+S +QR SMDYYMQKTYYKTASLISNSCKA+A+LAGQTAEVA+LAF+
Sbjct: 236 VEHLVTGETMQITSSREQRRSMDYYMQKTYYKTASLISNSCKAVAILAGQTAEVAVLAFE 295
Query: 295 YGKNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFAMEEFPQLRTVVEQGF 354
YG+NLGLA+QLIDDVLDFTGTSASLGKGSLSDIRHG+ITAPILFAMEEFPQLR VV++GF
Sbjct: 296 YGRNLGLAFQLIDDVLDFTGTSASLGKGSLSDIRHGVITAPILFAMEEFPQLREVVDRGF 355
Query: 355 EDSSNVDIALEYLGKSRGIQKTRELAVKHANLAAAAIDSLPENNDEDVTKSRRALLDLTH 414
++ +NVDIALEYLGKSRGIQ+TRELA +HANLAAAAI+SLPE +DEDV SRRAL+DLT
Sbjct: 356 DNPANVDIALEYLGKSRGIQRTRELAREHANLAAAAIESLPETDDEDVLTSRRALIDLTE 415
Query: 415 RVITRNK 421
RVITRNK
Sbjct: 416 RVITRNK 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 = 300 bits (770), Expect = e-100
Identities = 145/336 (43%), Positives = 217/336 (64%), Gaps = 22/336 (6%)
Query: 84 FSLVADELSILAKRLRSMVVAEVPKLASAAEYFFKMGVEGKRFRPTVLLLMATALNVRVP 143
F+ V D+L +L L+S+V A P L +AAE+ F G GKR RP ++LL++ A
Sbjct: 7 FAPVEDDLYLLTDNLKSLVGARHPILYAAAEHLFSAG--GKRLRPAIVLLVSRAT----- 59
Query: 144 EPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDVLDDADTRRGIGSLNFVMGNKL 203
A EL R + +AEITEMIH ASL+HDDV+D++DTRRGI +++ + G ++
Sbjct: 60 ---------AEQQELTPRHRRLAEITEMIHTASLVHDDVIDESDTRRGIETVHSLFGTRV 110
Query: 204 AVLAGDFLLSRACVALASLKNTEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQKT 263
AVLAGDFL ++A LA+L+N EVV L++ V+ GE Q D S++ Y++K+
Sbjct: 111 AVLAGDFLFAQASWYLANLENLEVVKLISKVITDFAEGEIKQGLNQFDSDLSLEDYLEKS 170
Query: 264 YYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKGS 323
+YKTASL++ S KA A+L+ ++VA ++YGK+LGLA+Q++DD+LDFTG++ LGK +
Sbjct: 171 FYKTASLVAASSKAAAVLSDVPSQVANDLYEYGKHLGLAFQVVDDILDFTGSTEQLGKPA 230
Query: 324 LSDIRHGIITAPILFAMEEFPQLRTVVEQGFEDSSNVDIALEYLGKSRGIQKTRELAVKH 383
SD+ G +TAP+LFA+EE P+L ++E+ F +++ AL + KS GI+K RELA +
Sbjct: 231 GSDLMKGNLTAPVLFALEEEPKLSELIEREFSQKGDLEQALSLVRKSGGIKKARELAKEQ 290
Query: 384 ANLAAAAIDSLPENNDEDVTKSRRALLDLTHRVITR 419
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 = 273 bits (700), Expect = 3e-88
Identities = 136/336 (40%), Positives = 211/336 (62%), Gaps = 19/336 (5%)
Query: 84 FSLVADELSILAKRLRSMVVAEVPKLASAAEYFFKMGVEGKRFRPTVLLLMATALNVRVP 143
F VAD+L L L+S+V AE P L SAAE F G GKR RP ++ L++ A
Sbjct: 98 FEPVADDLQQLNDNLQSIVGAENPVLMSAAEQIFGAG--GKRMRPALVFLVSRAT----- 150
Query: 144 EPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDVLDDADTRRGIGSLNFVMGNKL 203
E A EL T + +AEITEMIH ASL+HDDVLD++D RRG +++ + G ++
Sbjct: 151 ------AELAGLKELTTEHRRLAEITEMIHTASLIHDDVLDESDMRRGKETVHQLYGTRV 204
Query: 204 AVLAGDFLLSRACVALASLKNTEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQKT 263
AVLAGDF+ +++ LA+L N EV+ L++ V++ +GE Q ++ D ++D Y+ K+
Sbjct: 205 AVLAGDFMFAQSSWYLANLDNLEVIKLISQVIKDFASGEIKQASSLFDCDVTLDEYLLKS 264
Query: 264 YYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKGS 323
YYKTASLI+ S K+ A+ +G + V ++YGKNLGLA+Q++DD+LDFT ++ LGK +
Sbjct: 265 YYKTASLIAASTKSAAIFSGVDSSVKEQMYEYGKNLGLAFQVVDDILDFTQSTEQLGKPA 324
Query: 324 LSDIRHGIITAPILFAMEEFPQLRTVVEQGFEDSSNVDIALEYLGKSRGIQKTRELAVKH 383
SD+ G +TAP++FA+E+ P+LR ++E F + +++ A+E + + GI++ +ELA +
Sbjct: 325 GSDLAKGNLTAPVIFALEKEPELREIIESEFCEEGSLEEAIELVNEGGGIERAQELAKEK 384
Query: 384 ANLAAAAIDSLPENNDEDVTKSRRALLDLTHRVITR 419
A+LA ++ LP R +L D+ + R
Sbjct: 385 ADLAIQNLECLPR------GAFRSSLEDMVDYNLER 414
>gnl|CDD|164542 CHL00151, preA, prenyl transferase; Reviewed.
Length = 323
Score = 267 bits (685), Expect = 3e-87
Identities = 129/338 (38%), Positives = 209/338 (61%), Gaps = 22/338 (6%)
Query: 84 FSLVADELSILAKRLRSMVVAEVPKLASAAEYFFKMGVEGKRFRPTVLLLMATALNVRVP 143
+ + +EL IL L+ ++ + P L +AA++ F G GKR RP ++LL+A A
Sbjct: 8 LTPIEEELLILEDNLKKLIGSGHPILYAAAKHLFSAG--GKRIRPAIVLLVAKATGG--- 62
Query: 144 EPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDVLDDADTRRGIGSLNFVMGNKL 203
E++T QQ +AEITE+IH ASL+HDDV+D+ RRGI +++ + G K+
Sbjct: 63 -----------NMEIKTSQQRLAEITEIIHTASLVHDDVIDECSIRRGIPTVHKIFGTKI 111
Query: 204 AVLAGDFLLSRACVALASLKNTEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQKT 263
AVLAGDFL +++ LA+L N EVV L++ V+ GE Q D S+ Y++K+
Sbjct: 112 AVLAGDFLFAQSSWYLANLNNLEVVKLISKVITDFAEGEIRQGLVQFDTTLSILNYIEKS 171
Query: 264 YYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKGS 323
+YKTASLI+ SCKA ALL+ + + YGK+LGLA+Q+IDDVLD T ++ SLGK
Sbjct: 172 FYKTASLIAASCKAAALLSDADEKDHNDFYLYGKHLGLAFQIIDDVLDITSSTESLGKPI 231
Query: 324 LSDIRHGIITAPILFAMEEFPQLRTVVEQGFEDSSNVDIALEYLGKSRGIQKTRELAVKH 383
SD+++G +TAP+LFA+ + +L ++E+ F ++ ++ AL+ + ++ GI+K ++LA++H
Sbjct: 232 GSDLKNGNLTAPVLFALTQNSKLAKLIEREFCETKDISQALQIIKETNGIEKAKDLALEH 291
Query: 384 ANLAAAAIDSLPENNDEDVTKSRRALLDLTHRVITRNK 421
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 = 241 bits (618), Expect = 7e-78
Identities = 102/319 (31%), Positives = 149/319 (46%), Gaps = 63/319 (19%)
Query: 104 AEVPKLASAAEYFFKMGVEGKRFRPTVLLLMATALNVRVPEPLHDGVEDALATELRTRQQ 163
+EV L A Y G GKR RP ++LL A AL E
Sbjct: 1 SEVELLREALRYLLLAG--GKRLRPLLVLLAARALGGPELE----------------AAL 42
Query: 164 CIAEITEMIHVASLLHDDVLDDADTRRGIGSLNFVMGNKLAVLAGDFLLSRACVALASLK 223
+A E++H ASL+HDDV+D++D RRG +++ V GN A+LAGD+LL+RA LA L
Sbjct: 43 RLAAAIELLHTASLVHDDVMDNSDLRRGKPTVHKVFGNATAILAGDYLLARAFELLARLG 102
Query: 224 N---TEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIAL 280
N + L + + LV G+ + + + D + + Y++ KTA+L + + AL
Sbjct: 103 NPYYPRALELFSEAILELVEGQLLDLLSEYDTDVTEEEYLRIIRLKTAALFAAAPLLGAL 162
Query: 281 LAGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFAM 340
LAG E A +G+NLGLA+Q+ DD+LD G +LGK SD+R G T P+L A+
Sbjct: 163 LAGADEEEAEALKRFGRNLGLAFQIQDDILDLFGDPETLGKPVGSDLREGKCTLPVLLAL 222
Query: 341 EEFPQLRTVVEQGFEDSSNVDIALEYLGKSRGIQKTRELAVKHANLAAAAIDSLPENNDE 400
RELA ++ A A+ +LPE+
Sbjct: 223 ------------------------------------RELAREYEEKALEALKALPESP-- 244
Query: 401 DVTKSRRALLDLTHRVITR 419
+R AL L ++ R
Sbjct: 245 ----AREALRALADFILER 259
>gnl|CDD|223220 COG0142, IspA, Geranylgeranyl pyrophosphate synthase [Coenzyme
metabolism].
Length = 322
Score = 237 bits (607), Expect = 2e-75
Identities = 112/343 (32%), Positives = 178/343 (51%), Gaps = 25/343 (7%)
Query: 82 DPFSLVADELSILAKRLRSMV-VAEVPKLASAAEYFFKMGVEGKRFRPTVLLLMATALNV 140
D +L+ L+ + + L ++ ++ L A Y G GKR RP ++LL A AL +
Sbjct: 2 DLLALLLKRLARIEELLSELLSGSDPELLLEAMRYLLLAG--GKRLRPLLVLLAAEALGI 59
Query: 141 RVPEPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDVLDDADTRRGIGSLNFVMG 200
L G DAL +A E+IH ASL+HDD++DD D RRG +++ G
Sbjct: 60 ----DLETGGNDALD---------LAAAIELIHTASLIHDDLMDDDDLRRGKPTVHAKFG 106
Query: 201 NKLAVLAGDFLLSRACVALASLKN--TEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDY 258
A+LAGD LL+ A L+ L + E + LA + L G+ + + + +++
Sbjct: 107 EATAILAGDALLAAAFELLSKLGSEALEAIKALAEAINGLCGGQALDLAFENKP-VTLEE 165
Query: 259 YMQKTYYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSAS 318
Y++ KTA+L + + A+LAG E+ DYG+NLGLA+Q+ DD+LD TG
Sbjct: 166 YLRVIELKTAALFAAAAVLGAILAGADEELLEALEDYGRNLGLAFQIQDDILDITGDEEE 225
Query: 319 LGKGSLSDIRHGIITAPILFAMEEFPQLRTVVEQGFEDSSNVDIALEYLGKSRGIQKTRE 378
LGK SD++ G T P+L A+E+ + + ++ E V+ ALE L KS I+ +
Sbjct: 226 LGKPVGSDLKEGKPTLPVLLALEKANEDQKLLRILLEGGGEVEEALELLRKSGAIEYAKN 285
Query: 379 LAVKHANLAAAAIDSLPENNDEDVTKSRRALLDLTHRVITRNK 421
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 = 174 bits (444), Expect = 2e-52
Identities = 94/295 (31%), Positives = 137/295 (46%), Gaps = 60/295 (20%)
Query: 126 FRPTVLLLMATALNVRVPEPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDVLDD 185
RP ++LL+A AL + +A E++H ASL+HDD++DD
Sbjct: 1 SRPLLVLLLARALGGDLE-----------------AALRLAAAVELLHAASLVHDDIVDD 43
Query: 186 ADTRRGIGSLN-FVMGNKLAVLAGDFLLSRACVALASLKNTEVVTLLATVVEHLVTGETM 244
+D RRG + + GN LA+LAGD+LL+RA LA L + L A + L+ G+ +
Sbjct: 44 SDLRRGKPTAHLRRFGNALAILAGDYLLARAFQLLARLGYPRALELFAEALRELLEGQAL 103
Query: 245 QMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLGLAYQ 304
+ D ++D Y++ YKTA L+ C A L+G E A DYG+ LGLA+Q
Sbjct: 104 DLEFERDTYETLDEYLEYCRYKTAGLVGLLCLLGAGLSGADDEQAEALKDYGRALGLAFQ 163
Query: 305 LIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFAMEEFPQLRTVVEQGFEDSSNVDIAL 364
L DD+LD G + LGK SD+R G IT P++ A E
Sbjct: 164 LTDDLLDVFGDAEELGK-VGSDLREGRITLPVILARER---------------------- 200
Query: 365 EYLGKSRGIQKTRELAVKHANLAAAAIDSLPENNDEDVTKSRRALLDLTHRVITR 419
A ++A A AA+++LP + RRAL+ L + R
Sbjct: 201 ---------------AAEYAEEAYAALEALPPSLPRA----RRALIALADFLYRR 236
>gnl|CDD|215873 pfam00348, polyprenyl_synt, Polyprenyl synthetase.
Length = 260
Score = 165 bits (420), Expect = 2e-48
Identities = 77/225 (34%), Positives = 119/225 (52%), Gaps = 23/225 (10%)
Query: 123 GKRFRPTVLLLMATALNVRVPEPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDV 182
GKR RP LL++ A + V + A EMIH ASL+HDD+
Sbjct: 13 GKRIRP--LLVVLAARALGVEPETLLYL---------------ACAIEMIHTASLVHDDL 55
Query: 183 LDDADTRRGIGSLNFVMGNKLAVLAGDFLLSRACVALASLK--NTEVVTLLATVVEHLVT 240
+D++D RRG + + G A+LAGD LLSRA LA L E +L + + + V
Sbjct: 56 MDNSDLRRGKPTCHKKFGEAGAILAGDALLSRAFQLLALLGHVRPEPKYILISELANAVG 115
Query: 241 GETM--QMT--TSSDQRCSMDYYMQKTYYKTASLISNSCKAIALLAGQTAEVAILAFDYG 296
+ Q+ + + +++ Y++ YKTA+L S + A++AG E +D+G
Sbjct: 116 AQGEVGQLMDLETEGKDITLEEYLRIVSYKTAALFYASVQLGAIVAGADEEDEKDLYDFG 175
Query: 297 KNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFAME 341
++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 = 165 bits (419), Expect = 1e-47
Identities = 96/342 (28%), Positives = 178/342 (52%), Gaps = 29/342 (8%)
Query: 82 DPFSLVADELSILAKRLRSMVVAEVPKLASAAEYFFKMGVEGKRFRPTVLLLMATALNVR 141
D +S + ++ + K L V AE P L+ A+ + + G GKR RP +LL +
Sbjct: 4 DIYSFLQKDIDSIEKELEKAVQAEHPVLSEASLHLLEAG--GKRIRPVFVLLAGKFGDYD 61
Query: 142 VPEPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDVLDDADTRRGIGSLNFVMGN 201
+ H +A E+IH+ASL+HDDV+DDAD RRG ++ GN
Sbjct: 62 LDAIKH-----------------VAVALELIHMASLVHDDVIDDADLRRGRPTIKSKWGN 104
Query: 202 KLAVLAGDFLLSRACVALASLKNTEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQ 261
++A+ GD+L +++ + +K+ +L+ + + GE Q+ + ++ Y++
Sbjct: 105 RIAMYTGDYLFAKSLETMTEIKDPRAHQILSHTIVEVCRGEIEQIKDKYNFDQNLRTYLR 164
Query: 262 KTYYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGK 321
+ KTA LI+ SC+ A+ +G + + +G +G++YQ+ DD+LDF GT LGK
Sbjct: 165 RIKRKTALLIAASCQLGAIASGANEAIVKKLYWFGYYVGMSYQITDDILDFVGTEEELGK 224
Query: 322 GSLSDIRHGIITAPILFAMEEFPQLRTVVEQGFEDSSNVDIA--LEYLGKSRGIQKTREL 379
+ D+ G +T P+L+AME+ P L+ +EQ E+++ ++ +E + KS I+ +
Sbjct: 225 PAGGDLLQGNVTLPVLYAMED-PFLKKRIEQVLEETTAEEMEPLIEEVKKSDAIEYAYAV 283
Query: 380 AVKHANLAAAAIDSLPENNDEDVTKSRRALLDLTHRVITRNK 421
+ ++ A +D LP+ ++++ L ++ + I + K
Sbjct: 284 SDRYLKKALELLDGLPDG------RAKKPLQEIA-KYIGKRK 318
>gnl|CDD|182813 PRK10888, PRK10888, octaprenyl diphosphate synthase; Provisional.
Length = 323
Score = 161 bits (408), Expect = 5e-46
Identities = 103/302 (34%), Positives = 156/302 (51%), Gaps = 29/302 (9%)
Query: 123 GKRFRPTVLLLMATALNVRVPEPLHDGVEDALATELRTRQQCIAEITEMIHVASLLHDDV 182
GKR RP + +L A A+ + G IA + E IH A+LLHDDV
Sbjct: 44 GKRIRPMIAVLAARAVG-------YQG----------NAHVTIAALIEFIHTATLLHDDV 86
Query: 183 LDDADTRRGIGSLNFVMGNKLAVLAGDFLLSRACVALASLKNTEVVTLLATVVEHLVTGE 242
+D++D RRG + N GN +VL GDF+ +RA + SL + +V+ +++ V + GE
Sbjct: 87 VDESDMRRGKATANAAFGNAASVLVGDFIYTRAFQMMTSLGSLKVLEVMSEAVNVIAEGE 146
Query: 243 TMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLGLA 302
+Q+ +D + + YM+ Y KTA L + + +LAG T E DYG+ LG A
Sbjct: 147 VLQLMNVNDPDITEENYMRVIYSKTARLFEAAAQCSGILAGCTPEQEKGLQDYGRYLGTA 206
Query: 303 YQLIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFAM-----EEFPQLRTVVEQGFEDS 357
+QLIDD+LD++ +LGK D+ G T P+L AM E+ +RT +EQG
Sbjct: 207 FQLIDDLLDYSADGETLGKNVGDDLNEGKPTLPLLHAMHHGTPEQAAMIRTAIEQG-NGR 265
Query: 358 SNVDIALEYLGKSRGIQKTRELAVKHANLAAAAIDSLPENNDEDVTKSRRALLDLTHRVI 417
++ LE + ++ TR+ A + A+ A AA+ LP+ T R AL+ L H +
Sbjct: 266 HLLEPVLEAMNACGSLEWTRQRAEEEADKAIAALQVLPD------TPWREALIGLAHIAV 319
Query: 418 TR 419
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 (357), Expect = 1e-39
Identities = 72/256 (28%), Positives = 119/256 (46%), Gaps = 31/256 (12%)
Query: 165 IAEITEMIHVASLLHDDVLDDADTRRGIGSLN---FVMGNKLAVLAGDFLLSRACVALAS 221
+ E +H ASL+HDD++DD+ TRRG+ + + + G A+LAGD LL+ A LA
Sbjct: 15 LRAAVEKLHAASLVHDDIVDDSGTRRGLPTAHLAVAIDGLPEAILAGDLLLADAFEELAR 74
Query: 222 LKNTEVVTLLATVVEHLVTGETMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIALL 281
+ E + +LA + L+ G+ + + + +++ Y++ YKTA L+ C A L
Sbjct: 75 EGSPEALEILAEALLDLLEGQLLDLKWRREYVPTLEEYLEYCRYKTAGLVGALCLLGAGL 134
Query: 282 AGQTAEVAILAFDYGKNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRHGIITAPILFAME 341
+G AE+ G+ LGLA+QL +D+LD+ G + G T P+L+A+E
Sbjct: 135 SGGEAELLEALRKLGRALGLAFQLTNDLLDYEGDAERGE---------GKCTLPVLYALE 185
Query: 342 EFPQLRTVVEQGFEDSSNVDIALEYLGKSRGIQKTRELAVKHANLAAAAIDSLPENNDED 401
L + KS +++ E K A A ++ L + +
Sbjct: 186 YGVPAE---------------DLLLVEKSGSLEEALEELAKLAEEALKELNELILSLPD- 229
Query: 402 VTKSRRALLDLTHRVI 417
RALL L +
Sbjct: 230 ---VPRALLALALNLY 242
>gnl|CDD|182567 PRK10581, PRK10581, geranyltranstransferase; Provisional.
Length = 299
Score = 80.2 bits (198), Expect = 7e-17
Identities = 60/190 (31%), Positives = 99/190 (52%), Gaps = 14/190 (7%)
Query: 166 AEITEMIHVASLLHDDV--LDDADTRRGIGSLNFVMGNKLAVLAGDFLLSRACVALASLK 223
A E IH SL+HDD+ +DD D RRG+ + + G A+LAGD L + A L+
Sbjct: 70 AAAVECIHAYSLIHDDLPAMDDDDLRRGLPTCHVKFGEANAILAGDALQTLAFSILSDAP 129
Query: 224 NTEV--------VTLLATV--VEHLVTGETMQMTTSSDQRCSMDYYMQKTYYKTASLISN 273
EV ++ LA+ + + G+ + + + ++ +D + +KT +LI
Sbjct: 130 MPEVSDRDRISMISELASASGIAGMCGGQALDLE-AEGKQVPLDALERIHRHKTGALIRA 188
Query: 274 SCKAIALLAGQTAEVAILAFD-YGKNLGLAYQLIDDVLDFTGTSASLGKGSLSDIRHGII 332
+ + AL AG A+ D Y +++GLA+Q+ DD+LD G +A+LGK +D + G
Sbjct: 189 AVRLGALSAGDKGRRALPVLDRYAESIGLAFQVQDDILDVVGDTATLGKRQGADQQLGKS 248
Query: 333 TAPILFAMEE 342
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 = 0.70
Identities = 17/77 (22%), Positives = 28/77 (36%), Gaps = 13/77 (16%)
Query: 241 GETMQMTTSSDQRCSMDYYMQKTYYKTASLISNSCKAIALLAGQTAEVAILAFDYGKNLG 300
GE ++M S D C+ Y+Q ++ ++ L Y N G
Sbjct: 44 GEGLRMLVSRDLDCTHTLYIQFSFKFITKGTPERSHSVLL-------------QYSINGG 90
Query: 301 LAYQLIDDVLDFTGTSA 317
+ + 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 = 0.95
Identities = 12/40 (30%), Positives = 17/40 (42%), Gaps = 2/40 (5%)
Query: 293 FDYGKNLGLAYQLID--DVLDFTGTSASLGKGSLSDIRHG 330
DYG+N G+ Y + D L G A+L + R
Sbjct: 111 LDYGRNYGVLYDVAGWTDPLPEFGGDATLVDDNFMTGRAD 150
>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 = 30.8 bits (70), Expect = 1.4
Identities = 19/73 (26%), Positives = 30/73 (41%), Gaps = 11/73 (15%)
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 EEQLDPFSLVADE 90
++ D L+ E
Sbjct: 113 DDGADLIFLLHTE 125
>gnl|CDD|224804 COG1892, COG1892, Phosphoenolpyruvate carboxylase [Carbohydrate
transport and metabolism; Energy production and
conversion].
Length = 488
Score = 28.9 bits (65), Expect = 5.2
Identities = 21/81 (25%), Positives = 29/81 (35%), Gaps = 24/81 (29%)
Query: 106 VPKLASAAEYFFKMGVEGKRFRPTVLLLMATALNVRVPEPLHDGVEDALATELRTRQQCI 165
V KL S FF+ + G+ L RVP P VE+A + +
Sbjct: 62 VKKLLSRYPEFFRDHILGEDVF----------LTPRVPNPT---VENAER-------KLL 101
Query: 166 AEITEMI----HVASLLHDDV 182
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 = 19/87 (21%), Positives = 30/87 (34%), Gaps = 20/87 (22%)
Query: 336 ILFAMEEFPQLRTVVEQGF-EDSSNVDI--ALEYLGKSRGI------------QKTRELA 380
IL E P+L+ +V G E + + D L K RG + EL
Sbjct: 41 ILEEAVELPELKEIVLGGIGEPTVHPDFIDMLTEA-KERGFAVGLSTNGYLLEEMAEELV 99
Query: 381 VKHANLAAAAIDSLPENNDEDVTKSRR 407
+ +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 = 8.9
Identities = 15/50 (30%), Positives = 28/50 (56%), Gaps = 3/50 (6%)
Query: 168 ITEMIHVASLLHDDVLDDAD---TRRGIGSLNFVMGNKLAVLAGDFLLSR 214
+++M+H+AS + ++ A R + + N ++G L V GDF +SR
Sbjct: 122 LSQMLHIASQIASGMVYLASQHFVHRDLATRNCLVGANLLVKIGDFGMSR 171
>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 = 27.3 bits (61), Expect = 9.2
Identities = 15/78 (19%), Positives = 32/78 (41%), Gaps = 12/78 (15%)
Query: 47 KVLGCREAYSWS----LPALHGI-RHQIHHQSS-----SVIEEQLDPFSLVADELSILAK 96
V R +S++ P + + RH+ + + E P + + + K
Sbjct: 62 TVTELRPGHSFTWTGPAPGISAVHRHEFEAKPDGGVRVTTSESLSGPLAFLFGLF--VGK 119
Query: 97 RLRSMVVAEVPKLASAAE 114
+LR+++ + L +AAE
Sbjct: 120 KLRALLPEWLEGLKAAAE 137
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 0.368
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: 21,327,150
Number of extensions: 2103547
Number of successful extensions: 1952
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1923
Number of HSP's successfully gapped: 34
Length of query: 421
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 322
Effective length of database: 6,546,556
Effective search space: 2107991032
Effective search space used: 2107991032
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)