RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11203
(438 letters)
>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 = 134 bits (338), Expect = 7e-36
Identities = 100/363 (27%), Positives = 167/363 (46%), Gaps = 60/363 (16%)
Query: 81 TSFLSLRWLLSDEIANVALHLRKLVGSNHPLLKTAKSLLYN--GRNNMQAWGLIVLLISK 138
S SL + D++ + +L+ LVG+ HP+L A L++ G+ A IVLL+S+
Sbjct: 1 ASATSLFAPVEDDLYLLTDNLKSLVGARHPILYAAAEHLFSAGGKRLRPA---IVLLVSR 57
Query: 139 AAGHLNVDEMEEDKAAGVLHSQRALAEVTEMIRTSHLVHKGIVNITPGLYSEPVVLNDMT 198
A E +E R LAE+TEMI T+ LVH +++ + V +
Sbjct: 58 ATA-----EQQELTP-----RHRRLAEITEMIHTASLVHDDVIDESDTRRGIETVHSL-- 105
Query: 199 FGNKIALLSGDYLLSNSCSELAALRNQHLVELMSGAVRDLTESEFLGRRDLQNNPLPPQF 258
FG ++A+L+GD+L + + LA L N +V+L+S + D E E
Sbjct: 106 FGTRVAVLAGDFLFAQASWYLANLENLEVVKLISKVITDFAEGE---------------- 149
Query: 259 LTTKTSPDDSNQIMESLDELPMTPALADWTTRNVLSAGSLLGKSCKGTLKLAGQDAELQE 318
I + L++ +L D+ ++ SL+ S K L+ +++
Sbjct: 150 ------------IKQGLNQFDSDLSLEDYLEKSFYKTASLVAASSKAAAVLSDVPSQVAN 197
Query: 319 QGYQFGKHLALAWQACLDLEPFTSNYA-----PGTIF---NLTSAPVMFHLEQEKS-DEL 369
Y++GKHL LA+Q D+ FT + G+ NLT APV+F LE+E EL
Sbjct: 198 DLYEYGKHLGLAFQVVDDILDFTGSTEQLGKPAGSDLMKGNLT-APVLFALEEEPKLSEL 256
Query: 370 LNEINKGTESVTNIDYKKVYNIVSKGPGMRLTKQLQKQHSQQAMKVLQVFKESDARTALS 429
+ E D ++ ++V K G++ ++L K+ +Q A++ L S R AL
Sbjct: 257 IER-----EFSQKGDLEQALSLVRKSGGIKKARELAKEQAQLALQSLSFLPPSPPREALK 311
Query: 430 NII 432
++
Sbjct: 312 ELV 314
>gnl|CDD|164542 CHL00151, preA, prenyl transferase; Reviewed.
Length = 323
Score = 122 bits (307), Expect = 2e-31
Identities = 105/360 (29%), Positives = 162/360 (45%), Gaps = 64/360 (17%)
Query: 85 SLRWLLSDEIANVALHLRKLVGSNHPLL-KTAKSLLYNGRNNMQAWGLIVLLISKAAGHL 143
+L + +E+ + +L+KL+GS HP+L AK L G ++ IVLL++KA G
Sbjct: 6 NLLTPIEEELLILEDNLKKLIGSGHPILYAAAKHLFSAGGKRIRP--AIVLLVAKATG-- 61
Query: 144 NVDEMEEDKAAGVLHSQRALAEVTEMIRTSHLVHKGIVNITPGLYSEPVVLNDMTFGNKI 203
+ SQ+ LAE+TE+I T+ LVH +++ P V FG KI
Sbjct: 62 --------GNMEIKTSQQRLAEITEIIHTASLVHDDVIDECSIRRGIPTVHKI--FGTKI 111
Query: 204 ALLSGDYLLSNSCSELAALRNQHLVELMSGAVRDLTESEFLGRRDLQNNPLPPQFLTTKT 263
A+L+GD+L + S LA L N +V+L+S + D E E R+ L QF TT +
Sbjct: 112 AVLAGDFLFAQSSWYLANLNNLEVVKLISKVITDFAEGEI--RQGLV------QFDTTLS 163
Query: 264 SPDDSNQIMESLDELPMTPALADWTTRNVLSAGSLLGKSCKGTLKLAGQDAELQEQGYQF 323
+ ++ ++ SL+ SCK L+ D + Y +
Sbjct: 164 --------------------ILNYIEKSFYKTASLIAASCKAAALLSDADEKDHNDFYLY 203
Query: 324 GKHLALAWQACLDL-----------EPFTSNYAPGTIFNLTSAPVMFHLEQE-KSDELLN 371
GKHL LA+Q D+ +P S+ G NLT APV+F L Q K +L+
Sbjct: 204 GKHLGLAFQIIDDVLDITSSTESLGKPIGSDLKNG---NLT-APVLFALTQNSKLAKLIE 259
Query: 372 EINKGTESVTNIDYKKVYNIVSKGPGMRLTKQLQKQHSQQAMKVLQVFKESDARTALSNI 431
E D + I+ + G+ K L +H Q A++ L+ S A+ +L I
Sbjct: 260 R-----EFCETKDISQALQIIKETNGIEKAKDLALEHMQAAIQCLKFLPPSSAKDSLIEI 314
>gnl|CDD|215462 PLN02857, PLN02857, octaprenyl-diphosphate synthase.
Length = 416
Score = 109 bits (273), Expect = 3e-26
Identities = 92/366 (25%), Positives = 174/366 (47%), Gaps = 61/366 (16%)
Query: 80 PTSFLSLRWLLSDEIANVALHLRKLVGSNHPLLKTAKSLLYN-GRNNMQAWGLIVLLISK 138
P S L ++D++ + +L+ +VG+ +P+L +A ++ G M+ +V L+S+
Sbjct: 91 PISLSELFEPVADDLQQLNDNLQSIVGAENPVLMSAAEQIFGAGGKRMRP--ALVFLVSR 148
Query: 139 AAGHL-NVDEMEEDKAAGVLHSQRALAEVTEMIRTSHLVHKGIVNITPGLYSEPVVLNDM 197
A L + E+ + R LAE+TEMI T+ L+H +++ + + V
Sbjct: 149 ATAELAGLKELTTE--------HRRLAEITEMIHTASLIHDDVLDESDMRRGKETV--HQ 198
Query: 198 TFGNKIALLSGDYLLSNSCSELAALRNQHLVELMSGAVRDLTESEFLGRRDLQNNPLPPQ 257
+G ++A+L+GD++ + S LA L N +++L+S ++D E
Sbjct: 199 LYGTRVAVLAGDFMFAQSSWYLANLDNLEVIKLISQVIKDFASGEI-------------- 244
Query: 258 FLTTKTSPDDSNQIMESLDELPMTPALADWTTRNVLSAGSLLGKSCKGTLKLAGQDAELQ 317
+ SL + +T L ++ ++ SL+ S K +G D+ ++
Sbjct: 245 ------------KQASSLFDCDVT--LDEYLLKSYYKTASLIAASTKSAAIFSGVDSSVK 290
Query: 318 EQGYQFGKHLALAWQACLDLEPFT-----------SNYAPGTIFNLTSAPVMFHLEQEKS 366
EQ Y++GK+L LA+Q D+ FT S+ A G NLT APV+F LE+E
Sbjct: 291 EQMYEYGKNLGLAFQVVDDILDFTQSTEQLGKPAGSDLAKG---NLT-APVIFALEKEP- 345
Query: 367 DELLNEINKGTESVTNIDYKKVYNIVSKGPGMRLTKQLQKQHSQQAMKVLQVFKESDART 426
EL I +E ++ +V++G G+ ++L K+ + A++ L+ R+
Sbjct: 346 -ELREIIE--SEFCEEGSLEEAIELVNEGGGIERAQELAKEKADLAIQNLECLPRGAFRS 402
Query: 427 ALSNII 432
+L +++
Sbjct: 403 SLEDMV 408
>gnl|CDD|178478 PLN02890, PLN02890, geranyl diphosphate synthase.
Length = 422
Score = 108 bits (272), Expect = 6e-26
Identities = 111/451 (24%), Positives = 201/451 (44%), Gaps = 81/451 (17%)
Query: 2 ASKLLRSTSKSLLARQSLPPCILAHQSALCRSSSSAVSTTTESSSAAKFTPTHTVPSSNT 61
S+ L S+ +LL R P + CR + S S ++ H S
Sbjct: 23 CSQSLASSRAALLGRHGHPLSQSTSKVVGCRGTYSVSSRWLHG---FQYQVRHQSSSLVE 79
Query: 62 NRPDWNRAVSEAEKIVGYPTSFLSLRWLLSDEIANVALHLRKLVGSNHPLLKTAKSLLYN 121
+ D P S L++DE++ +A LR +V + P L +A +
Sbjct: 80 EQLD--------------PFS------LVADELSLLANKLRSMVVAEVPKLASAAEYFFK 119
Query: 122 GRNNMQAWGLIVLLISKAAGHLNVDEMEEDKAAGVLHS-----QRALAEVTEMIRTSHLV 176
+ + VLL+ A ++ + E E ++ S Q+ +AE+TEMI + L+
Sbjct: 120 VGVEGKRFRPTVLLLMATALNVPLPESTEGGVLDIVASELRTRQQNIAEITEMIHVASLL 179
Query: 177 HKGIVN---ITPGLYSEPVVLNDMTFGNKIALLSGDYLLSNSCSELAALRNQHLVELMSG 233
H +++ G+ S VV+ GNK+++L+GD+LLS +C LAAL+N +V L++
Sbjct: 180 HDDVLDDADTRRGVGSLNVVM-----GNKLSVLAGDFLLSRACVALAALKNTEVVSLLAT 234
Query: 234 AVRDLTESEFLGRRDLQNNPLPPQFLTTKTSPDDSNQIMESLDELPMTPALADWTTRNVL 293
AV L E + TS + + M+ + +
Sbjct: 235 AVEHLVTGETM----------------QITSSREQRRSMDY------------YMQKTYY 266
Query: 294 SAGSLLGKSCKGTLKLAGQDAELQEQGYQFGKHLALAWQACLDLEPFTSNYAP---GTIF 350
SL+ SCK LAGQ AE+ +++G++L LA+Q D+ FT A G++
Sbjct: 267 KTASLISNSCKAVAILAGQTAEVAVLAFEYGRNLGLAFQLIDDVLDFTGTSASLGKGSLS 326
Query: 351 NL----TSAPVMFHLEQEKSDELLNEINKGTESVTNIDYKKVYNIVSKGPGMRLTKQLQK 406
++ +AP++F +E+ +L +++G ++ N+D Y + K G++ T++L +
Sbjct: 327 DIRHGVITAPILFAMEE--FPQLREVVDRGFDNPANVDIALEY--LGKSRGIQRTRELAR 382
Query: 407 QHSQQAMKVLQVFKESD------ARTALSNI 431
+H+ A ++ E+D +R AL ++
Sbjct: 383 EHANLAAAAIESLPETDDEDVLTSRRALIDL 413
>gnl|CDD|223220 COG0142, IspA, Geranylgeranyl pyrophosphate synthase [Coenzyme
metabolism].
Length = 322
Score = 59.7 bits (145), Expect = 7e-10
Identities = 80/362 (22%), Positives = 145/362 (40%), Gaps = 71/362 (19%)
Query: 89 LLSDEIANVALHLRKLVGSNHP--LLKTAKSLLYNG----RNNMQAWGLIVLLISKAAGH 142
LL +A + L +L+ + P LL+ + LL G R L+VLL ++A
Sbjct: 6 LLLKRLARIEELLSELLSGSDPELLLEAMRYLLLAGGKRLR------PLLVLLAAEA--- 56
Query: 143 LNVDEMEEDKAAGVLHSQRALAEVTEMIRTSHLVHKGIV---NITPGLYSEPVVLNDMTF 199
L +D A LA E+I T+ L+H ++ ++ G + F
Sbjct: 57 LGIDLETGGNDA------LDLAAAIELIHTASLIHDDLMDDDDLRRGKPTVHAK-----F 105
Query: 200 GNKIALLSGDYLLSNSCSELAALRNQHL--VELMSGAVRDLTESEFLGRRDLQNNPLPPQ 257
G A+L+GD LL+ + L+ L ++ L ++ ++ A+ L + L DL
Sbjct: 106 GEATAILAGDALLAAAFELLSKLGSEALEAIKALAEAINGLCGGQAL---DL-------A 155
Query: 258 FLTTKTSPDDSNQIMESLDELPMTPALADWTTRNVLSAGSLLGKSCKGTLKLAGQDAELQ 317
F + ++ +++E T +L + LAG D EL
Sbjct: 156 FENKPVTLEEYLRVIELK-----T--------------AALFAAAAVLGAILAGADEELL 196
Query: 318 EQGYQFGKHLALAWQA---CLDLEPFTSNY--APGTIFNL--TSAPVMFHLEQEKSDELL 370
E +G++L LA+Q LD+ G+ + PV+ LE+ D+ L
Sbjct: 197 EALEDYGRNLGLAFQIQDDILDITGDEEELGKPVGSDLKEGKPTLPVLLALEKANEDQKL 256
Query: 371 NEINKGTESVTNIDYKKVYNIVSKGPGMRLTKQLQKQHSQQAMKVLQVFKESDARTALSN 430
I + ++ ++ K + K L K + ++A + L+ +S+A+ AL
Sbjct: 257 LRILLEGG----GEVEEALELLRKSGAIEYAKNLAKTYVEKAKEALEKLPDSEAKEALLE 312
Query: 431 II 432
+
Sbjct: 313 LA 314
>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 = 54.9 bits (133), Expect = 2e-08
Identities = 54/216 (25%), Positives = 85/216 (39%), Gaps = 65/216 (30%)
Query: 130 GLIVLLISKAAGHLNVDEMEEDKAAGVLHSQRALAEVTEMIRTSHLVHKGIVNITPGLYS 189
L+VLL ++A G L + LA E++ T+ LVH +++
Sbjct: 23 PLLVLLAARALG------------GPELEAALRLAAAIELLHTASLVHDDVMD------- 63
Query: 190 EPVVLNDMT----------FGNKIALLSGDYLLSNSCSELAALRNQH---LVELMSGAVR 236
N FGN A+L+GDYLL+ + LA L N + +EL S A+
Sbjct: 64 -----NSDLRRGKPTVHKVFGNATAILAGDYLLARAFELLARLGNPYYPRALELFSEAIL 118
Query: 237 DLTESEFLGRRDLQNNPLPPQFLTTKTSPDDSNQIMESLDELPMTPALADWTTRNVLSAG 296
+L E + L DL + T + ++ +I+ L
Sbjct: 119 ELVEGQLL---DLLSEY------DTDVTEEEYLRIIR-------------------LKTA 150
Query: 297 SLLGKSCKGTLKLAGQDAELQEQGYQFGKHLALAWQ 332
+L + LAG D E E +FG++L LA+Q
Sbjct: 151 ALFAAAPLLGALLAGADEEEAEALKRFGRNLGLAFQ 186
>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 = 53.6 bits (129), Expect = 8e-08
Identities = 72/360 (20%), Positives = 144/360 (40%), Gaps = 66/360 (18%)
Query: 90 LSDEIANVALHLRKLVGSNHPLLKTAKSLLYNGRNNMQAWG-----LIVLLISKAAGHLN 144
L +I ++ L K V + HP+L A L ++A G + VLL K G +
Sbjct: 9 LQKDIDSIEKELEKAVQAEHPVLSEASLHL------LEAGGKRIRPVFVLLAGKF-GDYD 61
Query: 145 VDEMEEDKAAGVLHSQRALAEVTEMIRTSHLVHKGIVNITPGLYSEPVVLNDMTFGNKIA 204
+D ++ H AL E+I + LVH +++ P + + +GN+IA
Sbjct: 62 LDAIK--------HVAVAL----ELIHMASLVHDDVIDDADLRRGRPTIKS--KWGNRIA 107
Query: 205 LLSGDYLLSNSCSELAALRNQHLVELMSGAVRDLTESEFLGRRDLQNNPLPPQFLTTKTS 264
+ +GDYL + S + +++ +++S + ++ E +D K +
Sbjct: 108 MYTGDYLFAKSLETMTEIKDPRAHQILSHTIVEVCRGEIEQIKD-------------KYN 154
Query: 265 PDDSNQIMESLDELPMTPALADWTTRNVLSAGSLLGKSCKGTLKLAGQDAELQEQGYQFG 324
D + L + R L+ SC+ +G + + ++ Y FG
Sbjct: 155 FDQN---------------LRTYLRRIKRKTALLIAASCQLGAIASGANEAIVKKLYWFG 199
Query: 325 KHLALAWQACLDLEPFTSNY------APGTIF--NLTSAPVMFHLEQEKSDELLNEINKG 376
++ +++Q D+ F A G + N+T PV++ +E L I +
Sbjct: 200 YYVGMSYQITDDILDFVGTEEELGKPAGGDLLQGNVT-LPVLYAMEDPF---LKKRIEQV 255
Query: 377 TESVTNIDYKKVYNIVSKGPGMRLTKQLQKQHSQQAMKVLQVFKESDARTALSNIIVAMG 436
E T + + + V K + + ++ ++A+++L + A+ L I +G
Sbjct: 256 LEETTAEEMEPLIEEVKKSDAIEYAYAVSDRYLKKALELLDGLPDGRAKKPLQEIAKYIG 315
>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 = 50.8 bits (122), Expect = 3e-07
Identities = 53/206 (25%), Positives = 85/206 (41%), Gaps = 48/206 (23%)
Query: 130 GLIVLLISKAAGHLNVDEMEEDKAAGVLHSQRALAEVTEMIRTSHLVHKGIV---NITPG 186
L+VLL+++A G G L + LA E++ + LVH IV ++ G
Sbjct: 3 PLLVLLLARALG-------------GDLEAALRLAAAVELLHAASLVHDDIVDDSDLRRG 49
Query: 187 LYSEPVVLNDMTFGNKIALLSGDYLLSNSCSELAALRNQHLVELMSGAVRDLTESEFLGR 246
+ + FGN +A+L+GDYLL+ + LA L +EL + A+R+L E + L
Sbjct: 50 KPT----AHLRRFGNALAILAGDYLLARAFQLLARLGYPRALELFAEALRELLEGQAL-- 103
Query: 247 RDLQNNPLPPQFLTTKTSPDDSNQIMESLDELPMTPALADWTTRNVLSAGSLLGKSCKGT 306
DL+ + + D+ + L+G C
Sbjct: 104 -DLEFERDTYE------TLDEYLEYCR----------------YKT---AGLVGLLCLLG 137
Query: 307 LKLAGQDAELQEQGYQFGKHLALAWQ 332
L+G D E E +G+ L LA+Q
Sbjct: 138 AGLSGADDEQAEALKDYGRALGLAFQ 163
>gnl|CDD|215873 pfam00348, polyprenyl_synt, Polyprenyl synthetase.
Length = 260
Score = 44.6 bits (106), Expect = 4e-05
Identities = 49/210 (23%), Positives = 76/210 (36%), Gaps = 51/210 (24%)
Query: 130 GLIVLLISKAAGHLNVDEMEEDKAAGVLHSQRALAEVTEMIRTSHLVHKGIV---NITPG 186
L+V+L ++A G E E + LA EMI T+ LVH ++ ++ G
Sbjct: 18 PLLVVLAARALG----VEPE---------TLLYLACAIEMIHTASLVHDDLMDNSDLRRG 64
Query: 187 LYSEPVVLNDMTFGNKIALLSGDYLLSNSCSELAALRN----QHLVELMSGAVRDLTESE 242
P FG A+L+GD LLS + LA L + + + A + E
Sbjct: 65 K---PTCHKK--FGEAGAILAGDALLSRAFQLLALLGHVRPEPKYILISELANAVGAQGE 119
Query: 243 FLGRRDLQNNPLPPQFLTTKTSPDDSNQIMESLDELPMTPALADWTTRNVLSAGSLLGKS 302
DL+ +L+E +L S
Sbjct: 120 VGQLMDLETEGKD-----------------ITLEEYLRI---------VSYKTAALFYAS 153
Query: 303 CKGTLKLAGQDAELQEQGYQFGKHLALAWQ 332
+ +AG D E ++ Y FG+ L LA+Q
Sbjct: 154 VQLGAIVAGADEEDEKDLYDFGRDLGLAFQ 183
>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 = 43.3 bits (102), Expect = 1e-04
Identities = 34/135 (25%), Positives = 57/135 (42%), Gaps = 30/135 (22%)
Query: 199 FGNKIALLSGDYLLSNSCSELAALRNQHLVELMSGAVRDLTESEFLGRRDLQNNPLPPQF 258
G A+L+GD LL+++ ELA + +E+++ A+ DL E + L DL+
Sbjct: 52 DGLPEAILAGDLLLADAFEELAREGSPEALEILAEALLDLLEGQLL---DLKW------- 101
Query: 259 LTTKTSPDDSNQIMESLDELPMTPALADWTTRNV-LSAGSLLGKSCKGTLKLAGQDAELQ 317
+ + +L+E L+G C L+G +AEL
Sbjct: 102 ---------RREYVPTLEEY----------LEYCRYKTAGLVGALCLLGAGLSGGEAELL 142
Query: 318 EQGYQFGKHLALAWQ 332
E + G+ L LA+Q
Sbjct: 143 EALRKLGRALGLAFQ 157
>gnl|CDD|182813 PRK10888, PRK10888, octaprenyl diphosphate synthase; Provisional.
Length = 323
Score = 36.4 bits (84), Expect = 0.024
Identities = 63/297 (21%), Positives = 125/297 (42%), Gaps = 61/297 (20%)
Query: 153 AAGVLHSQR----ALAEVTEMIRTSHLVHKGIVNITPGLYSEPVVLNDMTFGNKIALLSG 208
AA + Q +A + E I T+ L+H +V+ + + + FGN ++L G
Sbjct: 55 AARAVGYQGNAHVTIAALIEFIHTATLLHDDVVDESDMRRGKATA--NAAFGNAASVLVG 112
Query: 209 DYLLSNSCSELAALRNQHLVELMSGAVRDLTESEFLGRRDLQNNPLPPQFLTTKTSPDDS 268
D++ + + + +L + ++E+MS AV + E E L ++ N+P + ++
Sbjct: 113 DFIYTRAFQMMTSLGSLKVLEVMSEAVNVIAEGEVLQLMNV-NDP--------DITEENY 163
Query: 269 NQIMESLDELPMTPALADWTTRNVLSAGSLLGKSCKGTLKLAGQDAELQEQGYQ-FGKHL 327
+++ S T R L + + + LAG E QE+G Q +G++L
Sbjct: 164 MRVIYSK------------TAR-------LFEAAAQCSGILAGCTPE-QEKGLQDYGRYL 203
Query: 328 ALAWQACLDLEPFTSNYAPGTIFNLTSAPVMFHLEQEKSDELLNEINKGTESVTNIDYKK 387
A+Q DL ++++ G + E + + LL+ ++ GT +
Sbjct: 204 GTAFQLIDDLLDYSAD---GETLGKNVGDDLN--EGKPTLPLLHAMHHGTPEQAAM---- 254
Query: 388 VYNIVSKGPGMRL----------------TKQLQKQHSQQAMKVLQVFKESDARTAL 428
+ + +G G L T+Q ++ + +A+ LQV ++ R AL
Sbjct: 255 IRTAIEQGNGRHLLEPVLEAMNACGSLEWTRQRAEEEADKAIAALQVLPDTPWREAL 311
>gnl|CDD|112505 pfam03693, RHH_2, Uncharacterized protein family (UPF0156). This
family of proteins are about 80 amino acids in length
and their function is unknown. The proteins contain a
conserved GRY motif. This family appears to be related
to ribbon-helix-helix DNA-binding proteins.
Length = 81
Score = 28.3 bits (63), Expect = 2.3
Identities = 12/47 (25%), Positives = 17/47 (36%)
Query: 207 SGDYLLSNSCSELAALRNQHLVELMSGAVRDLTESEFLGRRDLQNNP 253
S LL ++LAALR + SG F+ R +
Sbjct: 35 SALRLLEEQETKLAALRAALIEGEESGESEPFDFDAFIEERSRAHAR 81
>gnl|CDD|206563 pfam14395, COOH-NH2_lig, Phage phiEco32-like COOH.NH2 ligase-type
2. A family of COOH-NH2 ligases/GCS superfamily found
in the neighborhood of YheC/D-like ATP-grasp and the
CotE family of proteins in the firmicutes. Contextual
analysis suggests that it might be involved in cell wall
modification and spore coat biosynthesis.
Length = 261
Score = 29.6 bits (67), Expect = 2.8
Identities = 12/25 (48%), Positives = 16/25 (64%)
Query: 88 WLLSDEIANVALHLRKLVGSNHPLL 112
WL+S +A ALHL KLV ++ L
Sbjct: 162 WLVSPAVARAALHLAKLVARHYREL 186
>gnl|CDD|181913 PRK09501, potD, spermidine/putrescine ABC transporter periplasmic
substrate-binding protein; Reviewed.
Length = 348
Score = 29.5 bits (66), Expect = 3.4
Identities = 17/34 (50%), Positives = 22/34 (64%), Gaps = 3/34 (8%)
Query: 63 RPDWNRAVSEAEKIVGYPTSFLSLRWLLSDEIAN 96
RPD + V+E +GYPT L+ R LLS E+AN
Sbjct: 280 RPDVAKQVAET---IGYPTPNLAARKLLSPEVAN 310
>gnl|CDD|203210 pfam05218, DUF713, Protein of unknown function (DUF713). This
family contains several proteins of unknown function
from C.elegans. The GO annotation suggests that this
protein is involved in nematode development and has a
positive regulation on growth rate.
Length = 182
Score = 28.9 bits (65), Expect = 3.6
Identities = 17/70 (24%), Positives = 31/70 (44%), Gaps = 6/70 (8%)
Query: 360 HLEQEKSDELLNEINKGTESVTNI------DYKKVYNIVSKGPGMRLTKQLQKQHSQQAM 413
E+E+S E+ EI+ E V + ++++ + K LQK S+QA
Sbjct: 63 KSEEEESTEIQEEISIFAEKVFSAQYTLEEAFEQLQELTEIFDDKLFIKVLQKSISEQAT 122
Query: 414 KVLQVFKESD 423
K+L++
Sbjct: 123 KLLEILNSLG 132
>gnl|CDD|176073 cd08691, C2_NEDL1-like, C2 domain present in NEDL1 (NEDD4-like
ubiquitin protein ligase-1). NEDL1 (AKA HECW1(HECT,
C2 and WW domain containing E3 ubiquitin protein ligase
1)) is a newly identified HECT-type E3 ubiquitin
protein ligase highly expressed in favorable
neuroblastomas. In vertebrates it is found primarily in
neuronal tissues, including the spinal cord. NEDL1 is
thought to normally function in the quality control of
cellular proteins by eliminating misfolded proteins.
This is thought to be accomplished via a mechanism
analogous to that of ER-associated degradation by
forming tight complexes and aggregating misfolded
proteins that have escaped ubiquitin-mediated
degradation. NEDL1, is composed of a C2 domain, two WW
domains, and a ubiquitin ligase Hect domain. C2 domains
fold into an 8-standed beta-sandwich that can adopt 2
structural arrangements: Type I and Type II,
distinguished by a circular permutation involving their
N- and C-terminal beta strands. Many C2 domains are
Ca2+-dependent membrane-targeting modules that bind a
wide variety of substances including bind
phospholipids, inositol polyphosphates, and
intracellular proteins. Most C2 domain proteins are
either signal transduction enzymes that contain a
single C2 domain, such as protein kinase C, or membrane
trafficking proteins which contain at least two C2
domains, such as synaptotagmin 1. However, there are a
few exceptions to this including RIM isoforms and some
splice variants of piccolo/aczonin and intersectin
which only have a single C2 domain. C2 domains with a
calcium binding region have negatively charged
residues, primarily aspartates, that serve as ligands
for calcium ions.
Length = 137
Score = 28.1 bits (63), Expect = 4.9
Identities = 12/33 (36%), Positives = 14/33 (42%), Gaps = 3/33 (9%)
Query: 54 HTVPSSNTNRPDWNRAVSEAEKIVGYPTSFLSL 86
T NT P W+R E VG PT L +
Sbjct: 48 RTSIVENTINPVWHR---EQFVFVGLPTDVLEI 77
>gnl|CDD|226489 COG3981, COG3981, Predicted acetyltransferase [General function
prediction only].
Length = 174
Score = 28.1 bits (63), Expect = 6.4
Identities = 12/33 (36%), Positives = 18/33 (54%), Gaps = 4/33 (12%)
Query: 69 AVSEAEKIVGYPTSFLSLRWLLSDEIANVALHL 101
AV E +IVG F++LR L+D + H+
Sbjct: 73 AVDEDGQIVG----FINLRHQLNDFLLEEGGHI 101
>gnl|CDD|216989 pfam02354, Latrophilin, Latrophilin Cytoplasmic C-terminal region.
This family consists of the cytoplasmic C-terminal
region in latrophilin. Latrophilin is a synaptic Ca2+
independent alpha- latrotoxin (LTX) receptor and is a
novel member of the secretin family of G-protein coupled
receptors that are involved in secretion. Latrophilin
mRNA is present only in neuronal tissue. Lactrophillin
interacts with G-alpha O.
Length = 366
Score = 28.5 bits (63), Expect = 7.0
Identities = 16/57 (28%), Positives = 23/57 (40%)
Query: 199 FGNKIALLSGDYLLSNSCSELAALRNQHLVELMSGAVRDLTESEFLGRRDLQNNPLP 255
F N +L SGDY LS+ + N + + +L + GR QN L
Sbjct: 139 FNNSYSLRSGDYPLSDGVQIIDRGYNLNDTAFEKMIISELVHNNLRGRSSEQNRNLM 195
>gnl|CDD|223031 PHA03273, PHA03273, envelope glycoprotein C; Provisional.
Length = 486
Score = 28.4 bits (63), Expect = 8.9
Identities = 17/69 (24%), Positives = 25/69 (36%), Gaps = 6/69 (8%)
Query: 23 ILAHQSALCRSSSSAVS-TTTESSSAAKFTPTHTVPSSNTN-----RPDWNRAVSEAEKI 76
IL + S SSS S +T + TPTHT + + N +E+
Sbjct: 21 ILTYASGASTSSSIENSDNSTAEMQSTPATPTHTTSNLTSPFGTGTDNSTNANGTESTTQ 80
Query: 77 VGYPTSFLS 85
P S +
Sbjct: 81 ASQPHSHET 89
>gnl|CDD|218287 pfam04841, Vps16_N, Vps16, N-terminal region. This protein forms
part of the Class C vacuolar protein sorting (Vps)
complex. Vps16 is essential for vacuolar protein
sorting, which is essential for viability in plants, but
not yeast. The Class C Vps complex is required for
SNARE-mediated membrane fusion at the lysosome-like
yeast vacuole. It is thought to play essential roles in
membrane docking and fusion at the Golgi-to-endosome and
endosome-to-vacuole stages of transport. The role of
VPS16 in this complex is not known.
Length = 408
Score = 28.2 bits (63), Expect = 9.7
Identities = 15/63 (23%), Positives = 27/63 (42%), Gaps = 11/63 (17%)
Query: 361 LEQEKSDELLNEINKGTESVTNIDYKKVYNIVSKGPGMRLTK--QLQKQHSQQAMKVLQV 418
+ E L+ + +E NI + I S PG L + Q + HS +A + L+
Sbjct: 309 ITTSSH-EFLSRVPAASE---NI-----FAIGSTEPGAMLVEAFQEMEDHSPKADEYLKE 359
Query: 419 FKE 421
++
Sbjct: 360 IQD 362
>gnl|CDD|180865 PRK07178, PRK07178, pyruvate carboxylase subunit A; Validated.
Length = 472
Score = 28.1 bits (63), Expect = 9.7
Identities = 12/26 (46%), Positives = 16/26 (61%), Gaps = 1/26 (3%)
Query: 55 TVPSSNTNRPDWNRAVSEAEKIVGYP 80
P S N D + A++EAE+I GYP
Sbjct: 129 VTPGSEGNLADLDEALAEAERI-GYP 153
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
0.314 0.128 0.361
Gapped
Lambda K H
0.267 0.0707 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 21,378,237
Number of extensions: 2021907
Number of successful extensions: 1313
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1286
Number of HSP's successfully gapped: 33
Length of query: 438
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 338
Effective length of database: 6,502,202
Effective search space: 2197744276
Effective search space used: 2197744276
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 60 (26.9 bits)