RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17022
(287 letters)
>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 = 130 bits (329), Expect = 2e-36
Identities = 51/183 (27%), Positives = 83/183 (45%), Gaps = 41/183 (22%)
Query: 1 MAGDFILAVACQMISRLRDNDVTLTLSQIMTDLVQGEFMQLGSKETENERFAHYLTKTYR 60
+AGD++LA A ++++RL N ++ ++
Sbjct: 85 LAGDYLLARAFELLARL-GNPYYPRALELFSE---------------------------- 115
Query: 61 KTASLIANCVKAIMTDLVQGEFMQLGSKETENERFAHYLTKTYRKTASLIANCVKASAML 120
+ +LV+G+ + L S+ + YL KTA+L A A+L
Sbjct: 116 ------------AILELVEGQLLDLLSEYDTDVTEEEYLRIIRLKTAALFAAAPLLGALL 163
Query: 121 GGADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACE 180
GAD++ +E +GRNLG+AFQ+ DD+LD + +GKP +DL+ G T PVL A
Sbjct: 164 AGADEEEAEALKRFGRNLGLAFQIQDDILDLFGDPETLGKPVGSDLREGKCTLPVLLALR 223
Query: 181 KSA 183
+ A
Sbjct: 224 ELA 226
Score = 90.3 bits (225), Expect = 2e-21
Identities = 34/77 (44%), Positives = 47/77 (61%), Gaps = 3/77 (3%)
Query: 172 TAPVLF--ACEKSAMLGGADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAA 229
TA LF A A+L GAD++ +E +GRNLG+AFQ+ DD+LD + +GKP +
Sbjct: 149 TA-ALFAAAPLLGALLAGADEEEAEALKRFGRNLGLAFQIQDDILDLFGDPETLGKPVGS 207
Query: 230 DLKLGLATAPVLFACEK 246
DL+ G T PVL A +
Sbjct: 208 DLREGKCTLPVLLALRE 224
>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 = 123 bits (310), Expect = 3e-33
Identities = 49/117 (41%), Positives = 80/117 (68%), Gaps = 1/117 (0%)
Query: 172 TAPVLFA-CEKSAMLGGADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAAD 230
TA ++ A + +A+L +++ +EYG++LG+AFQ+VDD+LDF S++ +GKP +D
Sbjct: 174 TASLVAASSKAAAVLSDVPSQVANDLYEYGKHLGLAFQVVDDILDFTGSTEQLGKPAGSD 233
Query: 231 LKLGLATAPVLFACEKFPELNPMIMRRFQEPGDVEKAFEFVHKSQGLEQTKFLARKH 287
L G TAPVLFA E+ P+L+ +I R F + GD+E+A V KS G+++ + LA++
Sbjct: 234 LMKGNLTAPVLFALEEEPKLSELIEREFSQKGDLEQALSLVRKSGGIKKARELAKEQ 290
Score = 119 bits (301), Expect = 7e-32
Identities = 55/140 (39%), Positives = 82/140 (58%), Gaps = 4/140 (2%)
Query: 73 IMTDLVQGEFMQLGSKETENERFAHYLTKTYRKTASLIANCVKASAMLGGADDKLSEVAF 132
++TD +GE Q ++ + YL K++ KTASL+A KA+A+L +++ +
Sbjct: 141 VITDFAEGEIKQGLNQFDSDLSLEDYLEKSFYKTASLVAASSKAAAVLSDVPSQVANDLY 200
Query: 133 EYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACEKSAMLGGADDKL 192
EYG++LG+AFQ+VDD+LDF S++ +GKP +DL G TAPVLFA E+ L +L
Sbjct: 201 EYGKHLGLAFQVVDDILDFTGSTEQLGKPAGSDLMKGNLTAPVLFALEEEPKL----SEL 256
Query: 193 SEVAFEYGRNLGIAFQLVDD 212
E F +L A LV
Sbjct: 257 IEREFSQKGDLEQALSLVRK 276
>gnl|CDD|178478 PLN02890, PLN02890, geranyl diphosphate synthase.
Length = 422
Score = 120 bits (303), Expect = 2e-31
Identities = 51/110 (46%), Positives = 84/110 (76%)
Query: 178 ACEKSAMLGGADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLAT 237
+C+ A+L G +++ +AFEYGRNLG+AFQL+DD+LDF +S ++GK + +D++ G+ T
Sbjct: 275 SCKAVAILAGQTAEVAVLAFEYGRNLGLAFQLIDDVLDFTGTSASLGKGSLSDIRHGVIT 334
Query: 238 APVLFACEKFPELNPMIMRRFQEPGDVEKAFEFVHKSQGLEQTKFLARKH 287
AP+LFA E+FP+L ++ R F P +V+ A E++ KS+G+++T+ LAR+H
Sbjct: 335 APILFAMEEFPQLREVVDRGFDNPANVDIALEYLGKSRGIQRTRELAREH 384
Score = 116 bits (292), Expect = 6e-30
Identities = 74/212 (34%), Positives = 112/212 (52%), Gaps = 51/212 (24%)
Query: 1 MAGDFILAVACQMISRLRDNDVTLTLSQIMTDLVQGEFMQLGSKETENERFAHYLTKTYR 60
+AGDF+L+ AC ++ L++ +V
Sbjct: 207 LAGDFLLSRACVALAALKNTEVV------------------------------------- 229
Query: 61 KTASLIANCVKAIMTDLVQGEFMQLGSKETENERFAHYLTKTYRKTASLIANCVKASAML 120
SL+A V+ LV GE MQ+ S + +Y+ KTY KTASLI+N KA A+L
Sbjct: 230 ---SLLATAVE----HLVTGETMQITSSREQRRSMDYYMQKTYYKTASLISNSCKAVAIL 282
Query: 121 GGADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACE 180
G +++ +AFEYGRNLG+AFQL+DD+LDF +S ++GK + +D++ G+ TAP+LFA E
Sbjct: 283 AGQTAEVAVLAFEYGRNLGLAFQLIDDVLDFTGTSASLGKGSLSDIRHGVITAPILFAME 342
Query: 181 KSAMLGGADDKLS------EVAFEY-GRNLGI 205
+ L D+ ++A EY G++ GI
Sbjct: 343 EFPQLREVVDRGFDNPANVDIALEYLGKSRGI 374
>gnl|CDD|164542 CHL00151, preA, prenyl transferase; Reviewed.
Length = 323
Score = 116 bits (292), Expect = 1e-30
Identities = 66/212 (31%), Positives = 109/212 (51%), Gaps = 48/212 (22%)
Query: 1 MAGDFILAVACQMISRLRDNDVTLTLSQIMTDLVQGEFMQLGSKETENERFAHYLTKTYR 60
+AGDF+ A + ++ L + +V +S+++TD +GE Q L + +
Sbjct: 114 LAGDFLFAQSSWYLANLNNLEVVKLISKVITDFAEGEIRQ-------------GLVQ-FD 159
Query: 61 KTASLIANCVKAIMTDLVQGEFMQLGSKETENERFAHYLTKTYRKTASLIANCVKASAML 120
T S++ Y+ K++ KTASLIA KA+A+L
Sbjct: 160 TTLSILN------------------------------YIEKSFYKTASLIAASCKAAALL 189
Query: 121 GGADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACE 180
AD+K + YG++LG+AFQ++DD+LD SS++++GKP +DLK G TAPVLFA
Sbjct: 190 SDADEKDHNDFYLYGKHLGLAFQIIDDVLDITSSTESLGKPIGSDLKNGNLTAPVLFALT 249
Query: 181 KSAMLGGADDKLSEVAFEYGRNLGIAFQLVDD 212
+++ L KL E F +++ A Q++ +
Sbjct: 250 QNSKL----AKLIEREFCETKDISQALQIIKE 277
Score = 116 bits (292), Expect = 1e-30
Identities = 46/110 (41%), Positives = 75/110 (68%)
Query: 178 ACEKSAMLGGADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLAT 237
+C+ +A+L AD+K + YG++LG+AFQ++DD+LD SS++++GKP +DLK G T
Sbjct: 182 SCKAAALLSDADEKDHNDFYLYGKHLGLAFQIIDDVLDITSSTESLGKPIGSDLKNGNLT 241
Query: 238 APVLFACEKFPELNPMIMRRFQEPGDVEKAFEFVHKSQGLEQTKFLARKH 287
APVLFA + +L +I R F E D+ +A + + ++ G+E+ K LA +H
Sbjct: 242 APVLFALTQNSKLAKLIEREFCETKDISQALQIIKETNGIEKAKDLALEH 291
>gnl|CDD|215462 PLN02857, PLN02857, octaprenyl-diphosphate synthase.
Length = 416
Score = 113 bits (283), Expect = 1e-28
Identities = 52/116 (44%), Positives = 78/116 (67%), Gaps = 1/116 (0%)
Query: 172 TAPVLFA-CEKSAMLGGADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAAD 230
TA ++ A + +A+ G D + E +EYG+NLG+AFQ+VDD+LDF S++ +GKP +D
Sbjct: 268 TASLIAASTKSAAIFSGVDSSVKEQMYEYGKNLGLAFQVVDDILDFTQSTEQLGKPAGSD 327
Query: 231 LKLGLATAPVLFACEKFPELNPMIMRRFQEPGDVEKAFEFVHKSQGLEQTKFLARK 286
L G TAPV+FA EK PEL +I F E G +E+A E V++ G+E+ + LA++
Sbjct: 328 LAKGNLTAPVIFALEKEPELREIIESEFCEEGSLEEAIELVNEGGGIERAQELAKE 383
Score = 106 bits (265), Expect = 4e-26
Identities = 52/113 (46%), Positives = 70/113 (61%)
Query: 73 IMTDLVQGEFMQLGSKETENERFAHYLTKTYRKTASLIANCVKASAMLGGADDKLSEVAF 132
++ D GE Q S + YL K+Y KTASLIA K++A+ G D + E +
Sbjct: 235 VIKDFASGEIKQASSLFDCDVTLDEYLLKSYYKTASLIAASTKSAAIFSGVDSSVKEQMY 294
Query: 133 EYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACEKSAML 185
EYG+NLG+AFQ+VDD+LDF S++ +GKP +DL G TAPV+FA EK L
Sbjct: 295 EYGKNLGLAFQVVDDILDFTQSTEQLGKPAGSDLAKGNLTAPVIFALEKEPEL 347
>gnl|CDD|223220 COG0142, IspA, Geranylgeranyl pyrophosphate synthase [Coenzyme
metabolism].
Length = 322
Score = 109 bits (274), Expect = 5e-28
Identities = 45/107 (42%), Positives = 60/107 (56%), Gaps = 1/107 (0%)
Query: 76 DLVQGEFMQLGSKETENERFAHYLTKTYRKTASLIANCVKASAMLGGADDKLSEVAFEYG 135
L G+ + L E + YL KTA+L A A+L GAD++L E +YG
Sbjct: 145 GLCGGQALDLAF-ENKPVTLEEYLRVIELKTAALFAAAAVLGAILAGADEELLEALEDYG 203
Query: 136 RNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACEKS 182
RNLG+AFQ+ DD+LD + +GKP +DLK G T PVL A EK+
Sbjct: 204 RNLGLAFQIQDDILDITGDEEELGKPVGSDLKEGKPTLPVLLALEKA 250
Score = 101 bits (253), Expect = 5e-25
Identities = 47/111 (42%), Positives = 66/111 (59%)
Query: 177 FACEKSAMLGGADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLA 236
A A+L GAD++L E +YGRNLG+AFQ+ DD+LD + +GKP +DLK G
Sbjct: 180 AAAVLGAILAGADEELLEALEDYGRNLGLAFQIQDDILDITGDEEELGKPVGSDLKEGKP 239
Query: 237 TAPVLFACEKFPELNPMIMRRFQEPGDVEKAFEFVHKSQGLEQTKFLARKH 287
T PVL A EK E ++ + G+VE+A E + KS +E K LA+ +
Sbjct: 240 TLPVLLALEKANEDQKLLRILLEGGGEVEEALELLRKSGAIEYAKNLAKTY 290
>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 = 101 bits (254), Expect = 8e-26
Identities = 41/108 (37%), Positives = 59/108 (54%), Gaps = 1/108 (0%)
Query: 73 IMTDLVQGEFMQLGSKETENERFAHYLTKTYRKTASLIANCVKASAMLGGADDKLSEVAF 132
+ +L++G+ + L + E YL KTA L+ A L GADD+ +E
Sbjct: 93 ALRELLEGQALDLEFERDTYETLDEYLEYCRYKTAGLVGLLCLLGAGLSGADDEQAEALK 152
Query: 133 EYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACE 180
+YGR LG+AFQL DDLLD ++ +GK +DL+ G T PV+ A E
Sbjct: 153 DYGRALGLAFQLTDDLLDVFGDAEELGK-VGSDLREGRITLPVILARE 199
Score = 69.3 bits (170), Expect = 6e-14
Identities = 32/70 (45%), Positives = 43/70 (61%), Gaps = 1/70 (1%)
Query: 178 ACEKSAMLGGADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLAT 237
C A L GADD+ +E +YGR LG+AFQL DDLLD ++ +GK +DL+ G T
Sbjct: 133 LCLLGAGLSGADDEQAEALKDYGRALGLAFQLTDDLLDVFGDAEELGK-VGSDLREGRIT 191
Query: 238 APVLFACEKF 247
PV+ A E+
Sbjct: 192 LPVILARERA 201
>gnl|CDD|215873 pfam00348, polyprenyl_synt, Polyprenyl synthetase.
Length = 260
Score = 90.4 bits (225), Expect = 2e-21
Identities = 42/107 (39%), Positives = 63/107 (58%), Gaps = 2/107 (1%)
Query: 78 VQGEFMQLGSKETENERF--AHYLTKTYRKTASLIANCVKASAMLGGADDKLSEVAFEYG 135
QGE QL ETE + YL KTA+L V+ A++ GAD++ + +++G
Sbjct: 116 AQGEVGQLMDLETEGKDITLEEYLRIVSYKTAALFYASVQLGAIVAGADEEDEKDLYDFG 175
Query: 136 RNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACEKS 182
R+LG+AFQ+ DD+LD ++ +GKP DL+ G +T PVL A E +
Sbjct: 176 RDLGLAFQIQDDILDLTGDTEELGKPVGTDLQEGKSTLPVLLALEGA 222
Score = 73.5 bits (181), Expect = 3e-15
Identities = 37/106 (34%), Positives = 60/106 (56%), Gaps = 6/106 (5%)
Query: 178 ACEKSAMLGGADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLAT 237
+ + A++ GAD++ + +++GR+LG+AFQ+ DD+LD ++ +GKP DL+ G +T
Sbjct: 153 SVQLGAIVAGADEEDEKDLYDFGRDLGLAFQIQDDILDLTGDTEELGKPVGTDLQEGKST 212
Query: 238 APVLFACEKFPELNPMIMRRFQEPGDVEKAFEFVHKSQGLEQTKFL 283
PVL A E E ++R E E A +QG+ TK L
Sbjct: 213 LPVLLALEGAREEQRKLLREAYEQKLSEAA------AQGVALTKAL 252
>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 = 84.8 bits (210), Expect = 6e-19
Identities = 46/179 (25%), Positives = 81/179 (45%), Gaps = 46/179 (25%)
Query: 3 GDFILAVACQMISRLRDNDVTLTLSQIMTDLVQGEFMQLGSKETENERFAHYLTKTYRKT 62
GD++ A + + ++ ++D LS + ++ +GE Q+ K ++ YL + RKT
Sbjct: 111 GDYLFAKSLETMTEIKDPRAHQILSHTIVEVCRGEIEQIKDKYNFDQNLRTYLRRIKRKT 170
Query: 63 ASLIA-NCVKAIMTDLVQGEFMQLGSKETENERFAHYLTKTYRKTASLIANCVKASAMLG 121
A LIA +C QLG A+
Sbjct: 171 ALLIAASC--------------QLG-------------------------------AIAS 185
Query: 122 GADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACE 180
GA++ + + + +G +G+++Q+ DD+LDF+ + + +GKP DL G T PVL+A E
Sbjct: 186 GANEAIVKKLYWFGYYVGMSYQITDDILDFVGTEEELGKPAGGDLLQGNVTLPVLYAME 244
Score = 66.3 bits (162), Expect = 2e-12
Identities = 32/108 (29%), Positives = 60/108 (55%), Gaps = 11/108 (10%)
Query: 178 ACEKSAMLGGADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLAT 237
+C+ A+ GA++ + + + +G +G+++Q+ DD+LDF+ + + +GKP DL G T
Sbjct: 177 SCQLGAIASGANEAIVKKLYWFGYYVGMSYQITDDILDFVGTEEELGKPAGGDLLQGNVT 236
Query: 238 APVLFACEKFPELNPMIMRRFQEPG------DVEKAFEFVHKSQGLEQ 279
PVL+A E +P + +R ++ ++E E V KS +E
Sbjct: 237 LPVLYAME-----DPFLKKRIEQVLEETTAEEMEPLIEEVKKSDAIEY 279
>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 = 78.3 bits (193), Expect = 4e-17
Identities = 42/181 (23%), Positives = 70/181 (38%), Gaps = 11/181 (6%)
Query: 51 FAHYLTKTYRKTASLIANCVKAIMTDLVQGEFMQLGSKETENERFAHYLTKTYRKTASLI 110
A + R+ + + + DL++G+ + L + YL KTA L+
Sbjct: 65 LADAFEELAREGSPEALEILAEALLDLLEGQLLDLKWRREYVPTLEEYLEYCRYKTAGLV 124
Query: 111 ANCVKASAMLGGADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGL 170
A L G + +L E + GR LG+AFQL +DLLD+ ++ G
Sbjct: 125 GALCLLGAGLSGGEAELLEALRKLGRALGLAFQLTNDLLDYEGDAERGE---------GK 175
Query: 171 ATAPVLFACEKSAMLGGADDKLSEVAFEYGRNL--GIAFQLVDDLLDFISSSDAMGKPTA 228
T PVL+A E + E +A + + +L + I S + +
Sbjct: 176 CTLPVLYALEYGVPAEDLLLVEKSGSLEEALEELAKLAEEALKELNELILSLPDVPRALL 235
Query: 229 A 229
A
Sbjct: 236 A 236
>gnl|CDD|182813 PRK10888, PRK10888, octaprenyl diphosphate synthase; Provisional.
Length = 323
Score = 76.4 bits (188), Expect = 5e-16
Identities = 54/178 (30%), Positives = 86/178 (48%), Gaps = 19/178 (10%)
Query: 32 DLVQGEFMQLGSKETENERFAH---------YLTKTYRKTASLIANCVKAIMTDLV---- 78
D+V M+ G K T N F + T+ ++ SL + V +M++ V
Sbjct: 85 DVVDESDMRRG-KATANAAFGNAASVLVGDFIYTRAFQMMTSLGSLKVLEVMSEAVNVIA 143
Query: 79 QGEFMQLGSKETENERFAHYLTKTYRKTASLIANCVKASAMLGGADDKLSEVAFEYGRNL 138
+GE +QL + + +Y+ Y KTA L + S +L G + + +YGR L
Sbjct: 144 EGEVLQLMNVNDPDITEENYMRVIYSKTARLFEAAAQCSGILAGCTPEQEKGLQDYGRYL 203
Query: 139 GIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFAC-----EKSAMLGGADDK 191
G AFQL+DDLLD+ + + +GK DL G T P+L A E++AM+ A ++
Sbjct: 204 GTAFQLIDDLLDYSADGETLGKNVGDDLNEGKPTLPLLHAMHHGTPEQAAMIRTAIEQ 261
Score = 60.2 bits (146), Expect = 2e-10
Identities = 27/66 (40%), Positives = 38/66 (57%)
Query: 178 ACEKSAMLGGADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLAT 237
A + S +L G + + +YGR LG AFQL+DDLLD+ + + +GK DL G T
Sbjct: 178 AAQCSGILAGCTPEQEKGLQDYGRYLGTAFQLIDDLLDYSADGETLGKNVGDDLNEGKPT 237
Query: 238 APVLFA 243
P+L A
Sbjct: 238 LPLLHA 243
>gnl|CDD|182567 PRK10581, PRK10581, geranyltranstransferase; Provisional.
Length = 299
Score = 48.2 bits (115), Expect = 2e-06
Identities = 26/79 (32%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 105 KTASLIANCVKASAMLGGADDKLSEVAFE-YGRNLGIAFQLVDDLLDFISSSDAMGKPTA 163
KT +LI V+ A+ G + + + Y ++G+AFQ+ DD+LD + + +GK
Sbjct: 181 KTGALIRAAVRLGALSAGDKGRRALPVLDRYAESIGLAFQVQDDILDVVGDTATLGKRQG 240
Query: 164 ADLKLGLATAPVLFACEKS 182
AD +LG +T P L E++
Sbjct: 241 ADQQLGKSTYPALLGLEQA 259
Score = 42.5 bits (100), Expect = 1e-04
Identities = 19/48 (39%), Positives = 30/48 (62%)
Query: 199 YGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACEK 246
Y ++G+AFQ+ DD+LD + + +GK AD +LG +T P L E+
Sbjct: 211 YAESIGLAFQVQDDILDVVGDTATLGKRQGADQQLGKSTYPALLGLEQ 258
>gnl|CDD|234402 TIGR03928, T7_EssCb_Firm, type VII secretion protein EssC, C-terminal
domain. This model describes the C-terminal domain, or
longer subunit, of the Firmicutes type VII secretion
protein EssC. This protein (homologous to EccC in
Actinobacteria) and the WXG100 target proteins are the
only homologous parts of type VII secretion between
Firmicutes and Actinobacteria [Protein fate, Protein and
peptide secretion and trafficking].
Length = 1296
Score = 34.2 bits (79), Expect = 0.082
Identities = 22/152 (14%), Positives = 51/152 (33%), Gaps = 10/152 (6%)
Query: 13 MISRLRDNDVTLTLSQIMTDLVQGEFMQLGSKETENERFAHY----LTKTYRKTASLIAN 68
+I D+ T L ++ L + E ++G ++ + Y TY + +
Sbjct: 1100 LIVGESDDGKTNVLKSLLKTLAKQEKEKIGLIDSIDRGLLAYRDLKEVATYIEEKEDLKE 1159
Query: 69 CVKAIMTDLVQGEFMQLGSKETENERFAHYLTKTYRKTASLIANCVKASAMLGGADDKLS 128
+ + ++ E + + E A ++ +I + +
Sbjct: 1160 ILAELKEEIELREAAYKEALQNETGEPA------FKPILLIIDDLEDFIQRTDLEIQDIL 1213
Query: 129 EVAFEYGRNLGIAFQLVDDLLDFISSSDAMGK 160
+ + G+ LGI F + + S D + K
Sbjct: 1214 ALIMKNGKKLGIHFIVAGTHSELSKSYDGVPK 1245
>gnl|CDD|214396 CHL00206, ycf2, Ycf2; Provisional.
Length = 2281
Score = 29.9 bits (67), Expect = 1.9
Identities = 15/44 (34%), Positives = 20/44 (45%), Gaps = 1/44 (2%)
Query: 245 EKFPELNPMIMRRFQEPGDV-EKAFEFVHKSQGLEQTKFLARKH 287
E+F E+ + EP V K F F S GL+Q +FL
Sbjct: 612 ERFQEMADLFTLSITEPDLVYHKGFAFSIDSYGLDQKQFLNEVF 655
>gnl|CDD|197778 smart00535, RIBOc, Ribonuclease III family.
Length = 129
Score = 28.0 bits (63), Expect = 3.1
Identities = 13/68 (19%), Positives = 28/68 (41%), Gaps = 13/68 (19%)
Query: 25 TLSQIMTDLVQGEFMQLGSKETENERFAHYLTKTYRKTASLIANCVKAIMTDLVQGEFMQ 84
TL+++ L GEF++LG E R ++A+ +A++ + ++
Sbjct: 62 TLARLAKKLGLGEFIRLGRGE---------AISGGRDKPKILADVFEALIGAI----YLD 108
Query: 85 LGSKETEN 92
G +
Sbjct: 109 SGLEAARE 116
>gnl|CDD|222241 pfam13583, Reprolysin_4, Metallo-peptidase family M12B
Reprolysin-like. This zinc-binding metallo-peptidase
has the characteristic binding motif HExxGHxxGxxH of
Reprolysin-like peptidases of family M12B.
Length = 195
Score = 28.1 bits (63), Expect = 3.6
Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 3/46 (6%)
Query: 102 TYRKTASLIANCVKASAMLGGADDKLSEVAFEYGRNLGIAFQLVDD 147
Y + + K A + +L+EV YGRN+GI+ L+ D
Sbjct: 12 DYSYYSIFGGSVDKVKAFINNVVARLNEV---YGRNVGISLTLIGD 54
Score = 27.4 bits (61), Expect = 6.5
Identities = 15/46 (32%), Positives = 23/46 (50%), Gaps = 8/46 (17%)
Query: 175 VLFACEKSAMLGGADDKLSE-----VAFE---YGRNLGIAFQLVDD 212
V+ ++ GG+ DK+ VA YGRN+GI+ L+ D
Sbjct: 9 VVADYSYYSIFGGSVDKVKAFINNVVARLNEVYGRNVGISLTLIGD 54
>gnl|CDD|143652 cd07828, nitrobindin, nitrobindin heme-binding domain. Nitrobindin
is a heme-containing lipocalin that may reversibly bind
nitric oxide. This heme-binding domain forms a beta
barrel structure, and in a small family of proteins from
tetrapods, it is found C-terminal to a THAP zinc finger
domain (a sequence-specific DNA binding domain). Members
of this group are putatively related to fatty
acid-binding proteins (FABPs).
Length = 148
Score = 27.6 bits (62), Expect = 4.3
Identities = 6/29 (20%), Positives = 11/29 (37%)
Query: 33 LVQGEFMQLGSKETENERFAHYLTKTYRK 61
LV G T + H+L+ ++
Sbjct: 120 LVDGTLSYTVDMATVGQPLTHHLSARLKR 148
Score = 27.6 bits (62), Expect = 4.3
Identities = 6/29 (20%), Positives = 11/29 (37%)
Query: 77 LVQGEFMQLGSKETENERFAHYLTKTYRK 105
LV G T + H+L+ ++
Sbjct: 120 LVDGTLSYTVDMATVGQPLTHHLSARLKR 148
>gnl|CDD|202669 pfam03495, Binary_toxB, Clostridial binary toxin B/anthrax toxin
PA. The N-terminal region of this family contains a
calcium-binding motif that may be an EF-hand.
Length = 406
Score = 28.2 bits (63), Expect = 5.8
Identities = 10/48 (20%), Positives = 17/48 (35%)
Query: 19 DNDVTLTLSQIMTDLVQGEFMQLGSKETENERFAHYLTKTYRKTASLI 66
DN L L + G+ + ++ L + TAS+I
Sbjct: 255 DNGKPLMLETDQVYGNYATYNSNGNIVVDGNNWSPILPQIKSTTASII 302
>gnl|CDD|237090 PRK12402, PRK12402, replication factor C small subunit 2; Reviewed.
Length = 337
Score = 28.0 bits (63), Expect = 6.3
Identities = 13/32 (40%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 38 FMQLGSKE-TENERFAHYLTKTYRKTASLIAN 68
F G K E+ RFAH+L R +S I N
Sbjct: 77 FFDQGKKYLVEDPRFAHFLGTDKRIRSSKIDN 108
Score = 28.0 bits (63), Expect = 6.3
Identities = 13/32 (40%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 82 FMQLGSKE-TENERFAHYLTKTYRKTASLIAN 112
F G K E+ RFAH+L R +S I N
Sbjct: 77 FFDQGKKYLVEDPRFAHFLGTDKRIRSSKIDN 108
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 0.134 0.377
Gapped
Lambda K H
0.267 0.0777 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,226,159
Number of extensions: 1347222
Number of successful extensions: 1191
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1180
Number of HSP's successfully gapped: 52
Length of query: 287
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 191
Effective length of database: 6,679,618
Effective search space: 1275807038
Effective search space used: 1275807038
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: 58 (26.0 bits)