RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3879
(247 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 = 144 bits (366), Expect = 2e-42
Identities = 52/149 (34%), Positives = 81/149 (54%), Gaps = 5/149 (3%)
Query: 9 EQDEKLLQPYTYISQVPGKQIRTKLAYAFNNWLNIPE-EKLLAIGDIIQMLHNSSLLIDD 67
+ E L + Y+ GK++R L L PE E L + I++LH +SL+ DD
Sbjct: 1 SEVELLREALRYLLLAGGKRLRPLLVLLAARALGGPELEAALRLAAAIELLHTASLVHDD 60
Query: 68 IEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGH---PEATAVYTEQLLEL 124
+ DNS LRRG P H ++G A+ I A +Y++A A E + LG+ P A +++E +LEL
Sbjct: 61 VMDNSDLRRGKPTVHKVFGNATAILAGDYLLARAFELLARLGNPYYPRALELFSEAILEL 120
Query: 125 HRGQGMEIYWRDNYTCPSEEEYRTMTIRK 153
GQ +++ + T +EEEY + K
Sbjct: 121 VEGQLLDLLSEYD-TDVTEEEYLRIIRLK 148
Score = 93.0 bits (232), Expect = 1e-22
Identities = 34/91 (37%), Positives = 53/91 (58%), Gaps = 4/91 (4%)
Query: 158 IDDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGH---PEATAVYTEQL 214
DD+ DNS LRRG P H ++G A+ I A +Y++A A E + LG+ P A +++E +
Sbjct: 58 HDDVMDNSDLRRGKPTVHKVFGNATAILAGDYLLARAFELLARLGNPYYPRALELFSEAI 117
Query: 215 LELHRGQGMEIYWRDNYTCPSEEEYRTMTIR 245
LEL GQ +++ + T +EEEY +
Sbjct: 118 LELVEGQLLDLLSEYD-TDVTEEEYLRIIRL 147
>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 = 109 bits (275), Expect = 3e-29
Identities = 42/126 (33%), Positives = 65/126 (51%), Gaps = 2/126 (1%)
Query: 29 IRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNSSLLIDDIEDNSILRRGIPVAHSI-YGI 87
R L L E L + +++LH +SL+ DDI D+S LRRG P AH +G
Sbjct: 1 SRPLLVLLLARALGGDLEAALRLAAAVELLHAASLVHDDIVDDSDLRRGKPTAHLRRFGN 60
Query: 88 ASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELHRGQGMEIYWRDNYTCPSEEEYR 147
A I A +Y++A A + + LG+P A ++ E L EL GQ +++ + + T + +EY
Sbjct: 61 ALAILAGDYLLARAFQLLARLGYPRALELFAEALRELLEGQALDLEFERD-TYETLDEYL 119
Query: 148 TMTIRK 153
K
Sbjct: 120 EYCRYK 125
Score = 79.7 bits (197), Expect = 5e-18
Identities = 32/89 (35%), Positives = 49/89 (55%), Gaps = 2/89 (2%)
Query: 158 IDDIEDNSILRRGIPVAHSI-YGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLE 216
DDI D+S LRRG P AH +G A I A +Y++A A + + LG+P A ++ E L E
Sbjct: 37 HDDIVDDSDLRRGKPTAHLRRFGNALAILAGDYLLARAFQLLARLGYPRALELFAEALRE 96
Query: 217 LHRGQGMEIYWRDNYTCPSEEEYRTMTIR 245
L GQ +++ + + T + +EY
Sbjct: 97 LLEGQALDLEFERD-TYETLDEYLEYCRY 124
>gnl|CDD|215873 pfam00348, polyprenyl_synt, Polyprenyl synthetase.
Length = 260
Score = 101 bits (254), Expect = 6e-26
Identities = 45/146 (30%), Positives = 66/146 (45%), Gaps = 7/146 (4%)
Query: 14 LLQPYTYISQVPGKQIRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNSSLLIDDIEDNSI 73
LL Y GK+IR L L + E LL + I+M+H +SL+ DD+ DNS
Sbjct: 1 LLAAMLYYLLAGGKRIRPLLVVLAARALGVEPETLLYLACAIEMIHTASLVHDDLMDNSD 60
Query: 74 LRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGH--PEATAVYTEQLLELHRGQGME 131
LRRG P H +G A I A + +++ A + + LGH PE + +L QG
Sbjct: 61 LRRGKPTCHKKFGEAGAILAGDALLSRAFQLLALLGHVRPEPKYILISELANAVGAQGE- 119
Query: 132 IYWRDNYTCP----SEEEYRTMTIRK 153
+ + + EEY + K
Sbjct: 120 VGQLMDLETEGKDITLEEYLRIVSYK 145
Score = 68.9 bits (169), Expect = 7e-14
Identities = 27/90 (30%), Positives = 41/90 (45%), Gaps = 7/90 (7%)
Query: 159 DDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGH--PEATAVYTEQLLE 216
DD+ DNS LRRG P H +G A I A + +++ A + + LGH PE + +L
Sbjct: 53 DDLMDNSDLRRGKPTCHKKFGEAGAILAGDALLSRAFQLLALLGHVRPEPKYILISELAN 112
Query: 217 LHRGQGMEIYWRDNYTCP----SEEEYRTM 242
QG + + + EEY +
Sbjct: 113 AVGAQGE-VGQLMDLETEGKDITLEEYLRI 141
>gnl|CDD|223220 COG0142, IspA, Geranylgeranyl pyrophosphate synthase [Coenzyme
metabolism].
Length = 322
Score = 101 bits (253), Expect = 2e-25
Identities = 46/159 (28%), Positives = 75/159 (47%), Gaps = 8/159 (5%)
Query: 1 MLSKSGDPEQDEKLLQPYTYISQVPGKQIRTKL----AYAFNNWLNIPEEKLLAIGDIIQ 56
+LS+ E LL+ Y+ GK++R L A A L L + I+
Sbjct: 17 LLSELLSGSDPELLLEAMRYLLLAGGKRLRPLLVLLAAEALGIDLETGGNDALDLAAAIE 76
Query: 57 MLHNSSLLIDDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGH--PEAT 114
++H +SL+ DD+ D+ LRRG P H+ +G A+ I A + ++A A E + LG EA
Sbjct: 77 LIHTASLIHDDLMDDDDLRRGKPTVHAKFGEATAILAGDALLAAAFELLSKLGSEALEAI 136
Query: 115 AVYTEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRK 153
E + L GQ +++ + + + EEY + K
Sbjct: 137 KALAEAINGLCGGQALDLAFENKP--VTLEEYLRVIELK 173
Score = 65.5 bits (160), Expect = 2e-12
Identities = 27/86 (31%), Positives = 44/86 (51%), Gaps = 4/86 (4%)
Query: 159 DDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGH--PEATAVYTEQLLE 216
DD+ D+ LRRG P H+ +G A+ I A + ++A A E + LG EA E +
Sbjct: 86 DDLMDDDDLRRGKPTVHAKFGEATAILAGDALLAAAFELLSKLGSEALEAIKALAEAING 145
Query: 217 LHRGQGMEIYWRDNYTCPSEEEYRTM 242
L GQ +++ + + + EEY +
Sbjct: 146 LCGGQALDLAFENKP--VTLEEYLRV 169
>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 = 81.4 bits (201), Expect = 1e-18
Identities = 41/115 (35%), Positives = 63/115 (54%), Gaps = 4/115 (3%)
Query: 43 IPEEKLLAIGDIIQMLHNSSLLIDDIEDNSILRRGIPVAH---SIYGIASTINAANYVVA 99
+ E + + ++ LH +SL+ DDI D+S RRG+P AH +I G+ I A + ++A
Sbjct: 7 LLEPEASRLRAAVEKLHAASLVHDDIVDDSGTRRGLPTAHLAVAIDGLPEAILAGDLLLA 66
Query: 100 IALEKVQSLGHPEATAVYTEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRKF 154
A E++ G PEA + E LL+L GQ +++ WR Y P+ EEY K
Sbjct: 67 DAFEELAREGSPEALEILAEALLDLLEGQLLDLKWRREY-VPTLEEYLEYCRYKT 120
Score = 68.7 bits (168), Expect = 7e-14
Identities = 35/92 (38%), Positives = 50/92 (54%), Gaps = 4/92 (4%)
Query: 158 IDDIEDNSILRRGIPVAH---SIYGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQL 214
DDI D+S RRG+P AH +I G+ I A + ++A A E++ G PEA + E L
Sbjct: 29 HDDIVDDSGTRRGLPTAHLAVAIDGLPEAILAGDLLLADAFEELAREGSPEALEILAEAL 88
Query: 215 LELHRGQGMEIYWRDNYTCPSEEEYRTMTIRS 246
L+L GQ +++ WR Y P+ EEY
Sbjct: 89 LDLLEGQLLDLKWRREY-VPTLEEYLEYCRYK 119
>gnl|CDD|182813 PRK10888, PRK10888, octaprenyl diphosphate synthase; Provisional.
Length = 323
Score = 47.9 bits (114), Expect = 2e-06
Identities = 28/100 (28%), Positives = 52/100 (52%)
Query: 20 YISQVPGKQIRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNSSLLIDDIEDNSILRRGIP 79
YI GK+IR +A + + I +I+ +H ++LL DD+ D S +RRG
Sbjct: 38 YIISGGGKRIRPMIAVLAARAVGYQGNAHVTIAALIEFIHTATLLHDDVVDESDMRRGKA 97
Query: 80 VAHSIYGIASTINAANYVVAIALEKVQSLGHPEATAVYTE 119
A++ +G A+++ +++ A + + SLG + V +E
Sbjct: 98 TANAAFGNAASVLVGDFIYTRAFQMMTSLGSLKVLEVMSE 137
Score = 29.0 bits (65), Expect = 1.9
Identities = 16/54 (29%), Positives = 31/54 (57%)
Query: 159 DDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHPEATAVYTE 212
DD+ D S +RRG A++ +G A+++ +++ A + + SLG + V +E
Sbjct: 84 DDVVDESDMRRGKATANAAFGNAASVLVGDFIYTRAFQMMTSLGSLKVLEVMSE 137
>gnl|CDD|164542 CHL00151, preA, prenyl transferase; Reviewed.
Length = 323
Score = 47.1 bits (112), Expect = 3e-06
Identities = 26/85 (30%), Positives = 46/85 (54%), Gaps = 7/85 (8%)
Query: 20 YISQVPGKQIRTKL----AYAFNNWLNI-PEEKLLAIGDIIQMLHNSSLLIDDIEDNSIL 74
++ GK+IR + A A + I ++ LA +I +++H +SL+ DD+ D +
Sbjct: 39 HLFSAGGKRIRPAIVLLVAKATGGNMEIKTSQQRLA--EITEIIHTASLVHDDVIDECSI 96
Query: 75 RRGIPVAHSIYGIASTINAANYVVA 99
RRGIP H I+G + A +++ A
Sbjct: 97 RRGIPTVHKIFGTKIAVLAGDFLFA 121
Score = 33.6 bits (77), Expect = 0.074
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 159 DDIEDNSILRRGIPVAHSIYGIASTINAANYVVA 192
DD+ D +RRGIP H I+G + A +++ A
Sbjct: 88 DDVIDECSIRRGIPTVHKIFGTKIAVLAGDFLFA 121
>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 = 47.0 bits (112), Expect = 3e-06
Identities = 32/116 (27%), Positives = 62/116 (53%), Gaps = 8/116 (6%)
Query: 26 GKQIR---TKLAYAFNNWLNIPEEKLLAIGDIIQMLHNSSLLIDDIEDNSILRRGIPVAH 82
GK+IR LA F ++ + + + ++++H +SL+ DD+ D++ LRRG P
Sbjct: 43 GKRIRPVFVLLAGKFGDY---DLDAIKHVAVALELIHMASLVHDDVIDDADLRRGRPTIK 99
Query: 83 SIYGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELHRGQGMEIYWRDNY 138
S +G + +Y+ A +LE + + P A + + ++E+ RG+ +I +D Y
Sbjct: 100 SKWGNRIAMYTGDYLFAKSLETMTEIKDPRAHQILSHTIVEVCRGEIEQI--KDKY 153
Score = 38.9 bits (91), Expect = 0.001
Identities = 22/73 (30%), Positives = 40/73 (54%), Gaps = 2/73 (2%)
Query: 159 DDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELH 218
DD+ D++ LRRG P S +G + +Y+ A +LE + + P A + + ++E+
Sbjct: 83 DDVIDDADLRRGRPTIKSKWGNRIAMYTGDYLFAKSLETMTEIKDPRAHQILSHTIVEVC 142
Query: 219 RGQGMEIYWRDNY 231
RG+ +I +D Y
Sbjct: 143 RGEIEQI--KDKY 153
>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 = 46.3 bits (110), Expect = 5e-06
Identities = 22/78 (28%), Positives = 44/78 (56%)
Query: 51 IGDIIQMLHNSSLLIDDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGH 110
+ +I +M+H +SL+ DD+ D S RRGI HS++G + A +++ A A + +L +
Sbjct: 72 LAEITEMIHTASLVHDDVIDESDTRRGIETVHSLFGTRVAVLAGDFLFAQASWYLANLEN 131
Query: 111 PEATAVYTEQLLELHRGQ 128
E + ++ + + G+
Sbjct: 132 LEVVKLISKVITDFAEGE 149
Score = 32.4 bits (74), Expect = 0.19
Identities = 17/63 (26%), Positives = 33/63 (52%)
Query: 159 DDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELH 218
DD+ D S RRGI HS++G + A +++ A A + +L + E + ++ + +
Sbjct: 87 DDVIDESDTRRGIETVHSLFGTRVAVLAGDFLFAQASWYLANLENLEVVKLISKVITDFA 146
Query: 219 RGQ 221
G+
Sbjct: 147 EGE 149
>gnl|CDD|182567 PRK10581, PRK10581, geranyltranstransferase; Provisional.
Length = 299
Score = 45.5 bits (108), Expect = 9e-06
Identities = 28/96 (29%), Positives = 49/96 (51%), Gaps = 2/96 (2%)
Query: 8 PEQDEKLLQPYTYISQVPGKQIRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNSSLLIDD 67
P Q+ +++ Y + + GK++R L YA + L A ++ +H SL+ DD
Sbjct: 26 PFQNTPVVEAMQYGALLGGKRLRPFLVYATGQMFGVSTNTLDAPAAAVECIHAYSLIHDD 85
Query: 68 IE--DNSILRRGIPVAHSIYGIASTINAANYVVAIA 101
+ D+ LRRG+P H +G A+ I A + + +A
Sbjct: 86 LPAMDDDDLRRGLPTCHVKFGEANAILAGDALQTLA 121
>gnl|CDD|178478 PLN02890, PLN02890, geranyl diphosphate synthase.
Length = 422
Score = 44.1 bits (104), Expect = 3e-05
Identities = 26/99 (26%), Positives = 53/99 (53%), Gaps = 7/99 (7%)
Query: 51 IGDIIQMLHNSSLLIDDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGH 110
I +I +M+H +SLL DD+ D++ RRG+ + + G ++ A +++++ A + +L +
Sbjct: 166 IAEITEMIHVASLLHDDVLDDADTRRGVGSLNVVMGNKLSVLAGDFLLSRACVALAALKN 225
Query: 111 PEATAVYTEQLLELHRGQGMEIYWRDNYTCPSEEEYRTM 149
E ++ + L G+ M+I S E+ R+M
Sbjct: 226 TEVVSLLATAVEHLVTGETMQI-------TSSREQRRSM 257
Score = 29.9 bits (67), Expect = 1.4
Identities = 19/84 (22%), Positives = 42/84 (50%), Gaps = 7/84 (8%)
Query: 159 DDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELH 218
DD+ D++ RRG+ + + G ++ A +++++ A + +L + E ++ + L
Sbjct: 181 DDVLDDADTRRGVGSLNVVMGNKLSVLAGDFLLSRACVALAALKNTEVVSLLATAVEHLV 240
Query: 219 RGQGMEIYWRDNYTCPSEEEYRTM 242
G+ M+I S E+ R+M
Sbjct: 241 TGETMQI-------TSSREQRRSM 257
>gnl|CDD|215462 PLN02857, PLN02857, octaprenyl-diphosphate synthase.
Length = 416
Score = 42.9 bits (101), Expect = 8e-05
Identities = 20/56 (35%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 44 PEEKLLAIGDIIQMLHNSSLLIDDIEDNSILRRGIPVAHSIYGIASTINAANYVVA 99
E + LA +I +M+H +SL+ DD+ D S +RRG H +YG + A +++ A
Sbjct: 161 TEHRRLA--EITEMIHTASLIHDDVLDESDMRRGKETVHQLYGTRVAVLAGDFMFA 214
Score = 27.5 bits (61), Expect = 7.1
Identities = 12/34 (35%), Positives = 19/34 (55%)
Query: 159 DDIEDNSILRRGIPVAHSIYGIASTINAANYVVA 192
DD+ D S +RRG H +YG + A +++ A
Sbjct: 181 DDVLDESDMRRGKETVHQLYGTRVAVLAGDFMFA 214
>gnl|CDD|223036 PHA03295, PHA03295, envelope glycoprotein H; Provisional.
Length = 714
Score = 30.8 bits (70), Expect = 0.74
Identities = 11/51 (21%), Positives = 20/51 (39%), Gaps = 3/51 (5%)
Query: 18 YTYISQVPGKQIRTKLAYAF---NNWLNIPEEKLLAIGDIIQMLHNSSLLI 65
+ I++ +LAY N + IP+ L I + +H + L
Sbjct: 380 LSTITRDLSIPSLARLAYLLRAQNQQVLIPKWALEQILNFTLSIHKTHLFS 430
>gnl|CDD|203911 pfam08328, ASL_C, Adenylosuccinate lyase C-terminal. This domain
is found at the C-terminus of adenylosuccinate
lyase(ASL; PurB in E. coli). It has been identified in
bacteria, eukaryotes and archaea and is found together
with the lyase domain pfam00206. ASL catalyzes the
cleavage of succinylaminoimidazole carboxamide ribotide
to aminoimidazole carboxamide ribotide and fumarate and
the cleavage of adenylosuccinate to adenylate and
fumarate.
Length = 115
Score = 27.1 bits (61), Expect = 3.9
Identities = 24/86 (27%), Positives = 39/86 (45%), Gaps = 29/86 (33%)
Query: 67 DIEDNSILRR-GIPVAHSIYGIAST--------INA--------ANY-VVAIALEKVQSL 108
D+ D+++LR G+ HS+ S +N AN+ V+A E +Q++
Sbjct: 6 DLTDSTVLRNLGVAFGHSLIAYDSLLKGLGKLEVNEARLAADLDANWEVLA---EPIQTV 62
Query: 109 ----GHPEATAVYTEQLLELHRGQGM 130
G P Y E+L EL RG+ +
Sbjct: 63 MRRYGIPNP---Y-EKLKELTRGKRI 84
Score = 27.1 bits (61), Expect = 3.9
Identities = 24/86 (27%), Positives = 39/86 (45%), Gaps = 29/86 (33%)
Query: 160 DIEDNSILRR-GIPVAHSIYGIAST--------INA--------ANY-VVAIALEKVQSL 201
D+ D+++LR G+ HS+ S +N AN+ V+A E +Q++
Sbjct: 6 DLTDSTVLRNLGVAFGHSLIAYDSLLKGLGKLEVNEARLAADLDANWEVLA---EPIQTV 62
Query: 202 ----GHPEATAVYTEQLLELHRGQGM 223
G P Y E+L EL RG+ +
Sbjct: 63 MRRYGIPNP---Y-EKLKELTRGKRI 84
>gnl|CDD|183886 PRK13192, PRK13192, bifunctional urease subunit gamma/beta;
Reviewed.
Length = 208
Score = 27.6 bits (62), Expect = 4.7
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 108 LGHPEATAVYTEQLLELHR 126
L +PEA A+ +++LE R
Sbjct: 30 LNYPEAVALIADEVLEAAR 48
Score = 27.6 bits (62), Expect = 4.7
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 201 LGHPEATAVYTEQLLELHR 219
L +PEA A+ +++LE R
Sbjct: 30 LNYPEAVALIADEVLEAAR 48
>gnl|CDD|217065 pfam02489, Herpes_glycop_H, Herpesvirus glycoprotein H.
Herpesvirus glycoprotein H (gH) is a virion associated
envelope glycoprotein. Complex formation between gH and
gL has been demonstrated in both virions and infected
cells.
Length = 655
Score = 28.1 bits (63), Expect = 5.0
Identities = 11/34 (32%), Positives = 17/34 (50%)
Query: 32 KLAYAFNNWLNIPEEKLLAIGDIIQMLHNSSLLI 65
+ YA +N LN+ E+ L I II ++ L
Sbjct: 332 RSLYASDNVLNVTEKILSGILRIILAIYTKYLYS 365
>gnl|CDD|238229 cd00390, Urease_gamma, Urease gamma-subunit; Urease is a
nickel-dependent metalloenzyme that catalyzes the
hydrolysis of urea to form ammonia and carbon dioxide.
Nickel-dependent ureases are found in bacteria, archaea,
fungi and plants. Their primary role is to allow the use
of external and internally-generated urea as a nitrogen
source. The enzyme consists of three subunits, alpha,
beta and gamma, which can exist as separate proteins or
can be fused on a single protein chain. The
alpha-beta-gamma heterotrimer forms multimers, mainly
trimers. The large alpha subunit is the catalytic domain
containing an active site with a bi-nickel center
complexed by a carbamylated lysine. The beta and gamma
subunits play a role in subunit association to form the
higher order trimers.
Length = 96
Score = 26.4 bits (59), Expect = 5.8
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 108 LGHPEATAVYTEQLLELHR 126
L +PEA A+ +++LE R
Sbjct: 27 LNYPEAVALIADEILEGAR 45
Score = 26.4 bits (59), Expect = 5.8
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 201 LGHPEATAVYTEQLLELHR 219
L +PEA A+ +++LE R
Sbjct: 27 LNYPEAVALIADEILEGAR 45
>gnl|CDD|215220 PLN02393, PLN02393, leucoanthocyanidin dioxygenase like protein.
Length = 362
Score = 27.7 bits (62), Expect = 6.6
Identities = 13/42 (30%), Positives = 22/42 (52%), Gaps = 8/42 (19%)
Query: 23 QVPGKQIRTKLAYAFNNWLN---IPEEKLLAIGDIIQMLHNS 61
V G Q+R + W+ +P+ ++ IGD IQ+L N+
Sbjct: 249 NVAGLQVRRD-----DAWITVKPVPDAFIVNIGDQIQVLSNA 285
>gnl|CDD|224242 COG1323, COG1323, Predicted nucleotidyltransferase [General
function prediction only].
Length = 358
Score = 27.3 bits (61), Expect = 7.7
Identities = 13/44 (29%), Positives = 20/44 (45%), Gaps = 2/44 (4%)
Query: 50 AIGDIIQMLHNSSLLIDDIEDNSILRRGIPVAHSIYGIASTINA 93
AI + S +D + N+IL G+ +IY I +I A
Sbjct: 141 AISYANKGYRGSVEKLDLDKPNNIL--GLEYVKAIYVIGYSIAA 182
>gnl|CDD|236045 PRK07534, PRK07534, methionine synthase I; Validated.
Length = 336
Score = 27.4 bits (61), Expect = 7.9
Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 3/46 (6%)
Query: 102 LEKVQSLGHPEATAVYTEQLLELHRGQGMEIYWRDNYTCPSEEEYR 147
+E + +L H A + EQ L G G ++ W + T + EE R
Sbjct: 118 MEPMGALTHALAVEAFHEQAEGLKAG-GADVLWVE--TISAPEEIR 160
Score = 27.4 bits (61), Expect = 7.9
Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 3/46 (6%)
Query: 195 LEKVQSLGHPEATAVYTEQLLELHRGQGMEIYWRDNYTCPSEEEYR 240
+E + +L H A + EQ L G G ++ W + T + EE R
Sbjct: 118 MEPMGALTHALAVEAFHEQAEGLKAG-GADVLWVE--TISAPEEIR 160
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
0.317 0.134 0.386
Gapped
Lambda K H
0.267 0.0846 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,016,996
Number of extensions: 1256443
Number of successful extensions: 1082
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1069
Number of HSP's successfully gapped: 51
Length of query: 247
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 153
Effective length of database: 6,768,326
Effective search space: 1035553878
Effective search space used: 1035553878
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 58 (25.9 bits)