RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9101
(255 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 = 126 bits (320), Expect = 2e-35
Identities = 37/112 (33%), Positives = 56/112 (50%), Gaps = 4/112 (3%)
Query: 133 VSLKTSMGQSLDLSTANDLSKFTMDRYEAIVKYKTAFYSFQLPVALAMHMAGMQDVEVHR 192
L+ GQ LDL + D T + Y I++ KTA P+ A+ D E
Sbjct: 116 AILELVEGQLLDLLSEYDTD-VTEEEYLRIIRLKTAALFAAAPLLGALLAGA--DEEEAE 172
Query: 193 QARTLLLEMGHFFQVQDDYLDCFGTPDVTGK-IGTDIEDGKCSWLAVVALQR 243
+ +G FQ+QDD LD FG P+ GK +G+D+ +GKC+ ++AL+
Sbjct: 173 ALKRFGRNLGLAFQIQDDILDLFGDPETLGKPVGSDLREGKCTLPVLLALRE 224
Score = 36.0 bits (84), Expect = 0.011
Identities = 13/52 (25%), Positives = 25/52 (48%), Gaps = 7/52 (13%)
Query: 83 IVQVLQYNV-PSGKKNRGLALVVAYKMLAQPSELTPENLHLAQILGWCVEIV 133
+ + L+Y + GK+ R L +++A + L P L A L +E++
Sbjct: 6 LREALRYLLLAGGKRLRPLLVLLAARALGGP------ELEAALRLAAAIELL 51
>gnl|CDD|215873 pfam00348, polyprenyl_synt, Polyprenyl synthetase.
Length = 260
Score = 115 bits (291), Expect = 3e-31
Identities = 44/120 (36%), Positives = 62/120 (51%), Gaps = 5/120 (4%)
Query: 133 VSLKTSMGQSLDLSTANDLSKFTMDRYEAIVKYKTAFYSFQLPVALAMHMAGMQDVEVHR 192
V + +GQ +DL T T++ Y IV YKTA F V L +AG D E +
Sbjct: 114 VGAQGEVGQLMDLETE--GKDITLEEYLRIVSYKTAAL-FYASVQLGAIVAG-ADEEDEK 169
Query: 193 QARTLLLEMGHFFQVQDDYLDCFGTPDVTGKI-GTDIEDGKCSWLAVVALQRATPAQRKL 251
++G FQ+QDD LD G + GK GTD+++GK + ++AL+ A QRKL
Sbjct: 170 DLYDFGRDLGLAFQIQDDILDLTGDTEELGKPVGTDLQEGKSTLPVLLALEGAREEQRKL 229
Score = 36.5 bits (85), Expect = 0.008
Identities = 12/49 (24%), Positives = 21/49 (42%), Gaps = 7/49 (14%)
Query: 85 QVLQYNVPSGKKNRGLALVVAYKMLAQPSELTPENLHLAQILGWCVEIV 133
+L Y + GK+ R L +V+A + L E L +E++
Sbjct: 4 AMLYYLLAGGKRIRPLLVVLAARALGVEPE-------TLLYLACAIEMI 45
>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 = 107 bits (268), Expect = 4e-28
Identities = 34/110 (30%), Positives = 52/110 (47%), Gaps = 3/110 (2%)
Query: 135 LKTSMGQSLDLSTANDLSKFTMDRYEAIVKYKTAFYSFQLPVALAMHMAGMQDVEVHRQA 194
+ GQ+LDL D T+D Y +YKTA L + A D E
Sbjct: 95 RELLEGQALDLEFERDTY-ETLDEYLEYCRYKTAGLVGLLCLLGAGLSGA--DDEQAEAL 151
Query: 195 RTLLLEMGHFFQVQDDYLDCFGTPDVTGKIGTDIEDGKCSWLAVVALQRA 244
+ +G FQ+ DD LD FG + GK+G+D+ +G+ + ++A +RA
Sbjct: 152 KDYGRALGLAFQLTDDLLDVFGDAEELGKVGSDLREGRITLPVILARERA 201
>gnl|CDD|223220 COG0142, IspA, Geranylgeranyl pyrophosphate synthase [Coenzyme
metabolism].
Length = 322
Score = 94.7 bits (236), Expect = 7e-23
Identities = 39/150 (26%), Positives = 67/150 (44%), Gaps = 12/150 (8%)
Query: 105 AYKMLAQPSELTPENLHLAQILGWCVEIVSLKTSMGQSLDLSTANDLSKFTMDRYEAIVK 164
A+++L++ E A GQ+LDL+ N T++ Y +++
Sbjct: 121 AFELLSKLGSEALE-AIKALAE------AINGLCGGQALDLAFENK--PVTLEEYLRVIE 171
Query: 165 YKTAFYSFQLPVALAMHMAGMQDVEVHRQARTLLLEMGHFFQVQDDYLDCFGTPDVTGK- 223
KTA V A+ D E+ +G FQ+QDD LD G + GK
Sbjct: 172 LKTAALFAAAAVLGAILAGA--DEELLEALEDYGRNLGLAFQIQDDILDITGDEEELGKP 229
Query: 224 IGTDIEDGKCSWLAVVALQRATPAQRKLME 253
+G+D+++GK + ++AL++A Q+ L
Sbjct: 230 VGSDLKEGKPTLPVLLALEKANEDQKLLRI 259
>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 = 76.0 bits (187), Expect = 2e-16
Identities = 37/152 (24%), Positives = 58/152 (38%), Gaps = 13/152 (8%)
Query: 100 LALVVAYKMLAQPSELTPENLHLAQILGWCVEIVSLKTSMGQSLDLSTANDLSKFTMDRY 159
A++ +LA E + + L GQ LDL + T++ Y
Sbjct: 56 EAILAGDLLLADAFEELAREGSPEALEILAEAL--LDLLEGQLLDLKWRRE-YVPTLEEY 112
Query: 160 EAIVKYKTAFYSFQLPVALAMHMAGMQDVEVHRQARTLLLEMGHFFQVQDDYLDCFGTPD 219
+YKTA L + A G + E+ R L +G FQ+ +D LD G +
Sbjct: 113 LEYCRYKTAGLVGALCLLGAGLSGG--EAELLEALRKLGRALGLAFQLTNDLLDYEGDAE 170
Query: 220 VTGKIGTDIEDGKCSWLAVVALQRATPAQRKL 251
+GKC+ + AL+ PA+ L
Sbjct: 171 RG--------EGKCTLPVLYALEYGVPAEDLL 194
>gnl|CDD|182567 PRK10581, PRK10581, geranyltranstransferase; Provisional.
Length = 299
Score = 39.0 bits (91), Expect = 0.001
Identities = 37/122 (30%), Positives = 58/122 (47%), Gaps = 18/122 (14%)
Query: 140 GQSLDLSTANDLSKFTMDRYEAIVKYKTAFYSFQLPVAL---AMHMAGMQDVEVHRQART 196
GQ+LDL + +D E I ++KT AL A+ + + + R+A
Sbjct: 157 GQALDLEAEG--KQVPLDALERIHRHKTG--------ALIRAAVRLGALSAGDKGRRALP 206
Query: 197 LL----LEMGHFFQVQDDYLDCFGTPDVTGK-IGTDIEDGKCSWLAVVALQRATPAQRKL 251
+L +G FQVQDD LD G GK G D + GK ++ A++ L++A R L
Sbjct: 207 VLDRYAESIGLAFQVQDDILDVVGDTATLGKRQGADQQLGKSTYPALLGLEQARKKARDL 266
Query: 252 ME 253
++
Sbjct: 267 ID 268
>gnl|CDD|178478 PLN02890, PLN02890, geranyl diphosphate synthase.
Length = 422
Score = 31.4 bits (71), Expect = 0.40
Identities = 34/108 (31%), Positives = 52/108 (48%), Gaps = 10/108 (9%)
Query: 131 EIVSLKTSM------GQSLDLSTANDLSKFTMDRYEAIVKYKTAFYSFQLPVALAMHMAG 184
E+VSL + G+++ ++++ + + +MD Y YKTA A+A+ +AG
Sbjct: 227 EVVSLLATAVEHLVTGETMQITSSRE-QRRSMDYYMQKTYYKTASLISNSCKAVAI-LAG 284
Query: 185 MQDVEVHRQARTLLLEMGHFFQVQDDYLDCFGTPDVTGKIG-TDIEDG 231
Q EV A +G FQ+ DD LD GT GK +DI G
Sbjct: 285 -QTAEVAVLAFEYGRNLGLAFQLIDDVLDFTGTSASLGKGSLSDIRHG 331
>gnl|CDD|182813 PRK10888, PRK10888, octaprenyl diphosphate synthase; Provisional.
Length = 323
Score = 29.8 bits (67), Expect = 1.1
Identities = 31/116 (26%), Positives = 49/116 (42%), Gaps = 8/116 (6%)
Query: 140 GQSLDLSTANDLSKFTMDRYEAIVKYKTA--FYSFQLPVALAMHMAGMQDVEVHRQARTL 197
G+ L L ND T + Y ++ KTA F + + Q+ + R L
Sbjct: 145 GEVLQLMNVND-PDITEENYMRVIYSKTARLFEAAAQCSGILAGCTPEQEKGLQDYGRYL 203
Query: 198 LLEMGHFFQVQDDYLDCFGTPDVTGK-IGTDIEDGKCSWLAVVALQRATPAQRKLM 252
G FQ+ DD LD + GK +G D+ +GK + + A+ TP Q ++
Sbjct: 204 ----GTAFQLIDDLLDYSADGETLGKNVGDDLNEGKPTLPLLHAMHHGTPEQAAMI 255
>gnl|CDD|164542 CHL00151, preA, prenyl transferase; Reviewed.
Length = 323
Score = 29.8 bits (67), Expect = 1.4
Identities = 23/82 (28%), Positives = 35/82 (42%), Gaps = 7/82 (8%)
Query: 154 FTMDRYEAIVKYKTAFYSFQLPVALAMHMAGMQDVEVHRQARTLLL--EMGHFFQVQDDY 211
++ Y YKTA L A A + D + L +G FQ+ DD
Sbjct: 162 LSILNYIEKSFYKTA----SLIAASCKAAALLSDADEKDHNDFYLYGKHLGLAFQIIDDV 217
Query: 212 LDCFGTPDVTGK-IGTDIEDGK 232
LD + + GK IG+D+++G
Sbjct: 218 LDITSSTESLGKPIGSDLKNGN 239
>gnl|CDD|193472 pfam12999, PRKCSH-like, Glucosidase II beta subunit-like. The
sequences found in this family are similar to a region
found in the beta-subunit of glucosidase II, which is
also known as protein kinase C substrate 80K-H (PRKCSH).
The enzyme catalyzes the sequential removal of two
alpha-1,3-linked glucose residues in the second step of
N-linked oligosaccharide processing. The beta subunit is
required for the solubility and stability of the
heterodimeric enzyme, and is involved in retaining the
enzyme within the endoplasmic reticulum.
Length = 176
Score = 29.0 bits (65), Expect = 1.7
Identities = 14/31 (45%), Positives = 18/31 (58%), Gaps = 4/31 (12%)
Query: 203 HFFQVQDDYLDCFGTPDVTGKIGTD-IEDGK 232
F QV DDY DC PD + + GT+ +GK
Sbjct: 49 SFDQVNDDYCDC---PDGSDEPGTNACSNGK 76
>gnl|CDD|180933 PRK07329, PRK07329, hypothetical protein; Provisional.
Length = 246
Score = 28.8 bits (65), Expect = 2.1
Identities = 8/33 (24%), Positives = 15/33 (45%)
Query: 47 TDAGRHSDIPDVTKWYAKVLQYNKAISNNVYLG 79
D+PD K+ A++ + N+ N + G
Sbjct: 40 PYDTGQDDVPDYAKYSAEIAELNEKYGNRIKKG 72
>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 = 28.6 bits (64), Expect = 3.7
Identities = 28/103 (27%), Positives = 44/103 (42%), Gaps = 4/103 (3%)
Query: 152 SKFTMDRYEAIVKYKTAFYSFQLPVALAMHMAGMQDVEVHRQARTLLLEMGHFFQVQDDY 211
S +++ Y YKTA S + A + +V +G FQV DD
Sbjct: 159 SDLSLEDYLEKSFYKTA--SLVAASSKAAAVLSDVPSQVANDLYEYGKHLGLAFQVVDDI 216
Query: 212 LDCFGTPDVTGK-IGTDIEDGKCSWLAVVALQRATPAQRKLME 253
LD G+ + GK G+D+ G + + AL+ P +L+E
Sbjct: 217 LDFTGSTEQLGKPAGSDLMKGNLTAPVLFALEE-EPKLSELIE 258
>gnl|CDD|188996 cd06457, M3A_MIP, Peptidase M3 mitochondrial intermediate peptidase
(MIP). Peptidase M3 mitochondrial intermediate
peptidase (MIP; EC 3.4.24.59) belongs to the widespread
subfamily M3A, that show similarity to the Thimet
oligopeptidase (TOP). It is one of three peptidases
responsible for the proteolytic processing of both,
nuclear and mitochondrial encoded precursor polypeptides
targeted to the various subcompartments of the
mitochondria. It cleaves intermediate-size proteins
initially processed by mitochondrial processing
peptidase (MPP) to yield a processing intermediate with
a typical N-terminal octapeptide that is sequentially
cleaved by MIP to mature-size protein. MIP cleaves
precursor proteins of respiratory components, including
subunits of the electron transport chain and
tri-carboxylic acid cycle enzymes, and components of the
mitochondrial genetic machinery, including ribosomal
proteins, translation factors, and proteins required for
mitochondrial DNA metabolism. It has been suggested that
the human MIP (HMIP polypeptide; gene symbol MIPEP) may
be one of the loci predicted to influence the clinical
manifestations of Friedreich's ataxia (FRDA), an
autosomal recessive neurodegenerative disease caused by
lack of human frataxin. These proteins are enriched in
cysteine residues, two of which are highly conserved,
suggesting their importance to stability as well as in
formation of metal binding sites, thus playing a role in
MIP activity.
Length = 606
Score = 28.3 bits (64), Expect = 4.4
Identities = 14/38 (36%), Positives = 17/38 (44%), Gaps = 5/38 (13%)
Query: 171 SFQLP-VALAMHMAGMQDVEV----HRQARTLLLEMGH 203
S+QLP VAL + H + TL EMGH
Sbjct: 369 SYQLPVVALVCNFPPPSGSSPTLLSHGEVETLFHEMGH 406
>gnl|CDD|235972 PRK07225, PRK07225, DNA-directed RNA polymerase subunit B';
Validated.
Length = 605
Score = 28.4 bits (64), Expect = 4.8
Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 16/54 (29%)
Query: 112 PSELTPENLHL----AQILGWCVEIV-------SLKTSMG-----QSLDLSTAN 149
+LT E+ HL + ILG ++ S + +MG QSL L AN
Sbjct: 115 EEDLTEEHTHLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLGLPAAN 168
>gnl|CDD|236394 PRK09169, PRK09169, hypothetical protein; Validated.
Length = 2316
Score = 27.8 bits (62), Expect = 7.8
Identities = 9/44 (20%), Positives = 17/44 (38%)
Query: 178 LAMHMAGMQDVEVHRQARTLLLEMGHFFQVQDDYLDCFGTPDVT 221
L + + D E AR L E+ ++ + L+ D+
Sbjct: 805 LILKLEDQDDEEDLALARARLRELAAHLDLRPERLEQADARDIA 848
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 0.133 0.387
Gapped
Lambda K H
0.267 0.0648 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,705,743
Number of extensions: 1187578
Number of successful extensions: 937
Number of sequences better than 10.0: 1
Number of HSP's gapped: 924
Number of HSP's successfully gapped: 25
Length of query: 255
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 160
Effective length of database: 6,723,972
Effective search space: 1075835520
Effective search space used: 1075835520
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 (26.3 bits)