RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 024239
(270 letters)
>gnl|CDD|215873 pfam00348, polyprenyl_synt, Polyprenyl synthetase.
Length = 260
Score = 271 bits (695), Expect = 8e-92
Identities = 116/263 (44%), Positives = 165/263 (62%), Gaps = 8/263 (3%)
Query: 7 IHEAMRYSLLAGGKRIRPVLCIASCELVGGDESLVMPMACALEMTHTMSLIHDDLPALDN 66
+ AM Y LLAGGKRIRP+L + + +G + ++ +ACA+EM HT SL+HDDL +DN
Sbjct: 1 LLAAMLYYLLAGGKRIRPLLVVLAARALGVEPETLLYLACAIEMIHTASLVHDDL--MDN 58
Query: 67 DDLRRGKPTNHKVFGEPTAILAGDALLALAFEHVAAKTVGVSTDRVVRAITELGSALGAE 126
DLRRGKPT HK FGE AILAGDALL+ AF+ +A V + I+EL +A+GA+
Sbjct: 59 SDLRRGKPTCHKKFGEAGAILAGDALLSRAFQLLALLG-HVRPEPKYILISELANAVGAQ 117
Query: 127 GLLKGQVTDLDSEGKDVSLSELEYIHVHKTAKLLEASVVCGVIIGGGNVIEIERVRNYAR 186
G + GQ+ DL++EGKD++L E I +KTA L ASV G I+ G + + + + ++ R
Sbjct: 118 GEV-GQLMDLETEGKDITLEEYLRIVSYKTAALFYASVQLGAIVAGADEEDEKDLYDFGR 176
Query: 187 CIGLLFQVVDDILDVTKSSTVLGKTAGKDLVSDKATYPKLMGIENAKKFAEELFSQAT-K 245
+GL FQ+ DDILD+T + LGK G DL K+T P L+ +E A++ +L +A +
Sbjct: 177 DLGLAFQIQDDILDLTGDTEELGKPVGTDLQEGKSTLPVLLALEGAREEQRKLLREAYEQ 236
Query: 246 ELAYFEVSKAAP---LYHLAKYI 265
+L+ A L LA+YI
Sbjct: 237 KLSEAAAQGVALTKALEALAEYI 259
>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 = 257 bits (658), Expect = 5e-86
Identities = 109/270 (40%), Positives = 149/270 (55%), Gaps = 14/270 (5%)
Query: 2 QHPEKIHEAMRYSLLAGGKRIRPVLCIASCELVGGDES-LVMPMACALEMTHTMSLIHDD 60
E + EA+RY LLAGGKR+RP+L + + +GG E + +A A+E+ HT SL+HDD
Sbjct: 1 SEVELLREALRYLLLAGGKRLRPLLVLLAARALGGPELEAALRLAAAIELLHTASLVHDD 60
Query: 61 LPALDNDDLRRGKPTNHKVFGEPTAILAGDALLALAFEHVAAKTVGVSTDRVVRAITELG 120
+ +DN DLRRGKPT HKVFG TAILAGD LLA AFE +A + R + +E
Sbjct: 61 V--MDNSDLRRGKPTVHKVFGNATAILAGDYLLARAFELLA-RLGNPYYPRALELFSE-- 115
Query: 121 SALGAEGLLKGQVTDLDSEGK-DVSLSELEYIHVHKTAKLLEASVVCGVIIGGGNVIEIE 179
L++GQ+ DL SE DV+ E I KTA L A+ + G ++ G + E E
Sbjct: 116 ---AILELVEGQLLDLLSEYDTDVTEEEYLRIIRLKTAALFAAAPLLGALLAGADEEEAE 172
Query: 180 RVRNYARCIGLLFQVVDDILDVTKSSTVLGKTAGKDLVSDKATYPKLMGIENAKKFAEEL 239
++ + R +GL FQ+ DDILD+ LGK G DL K T P L+ + + A E
Sbjct: 173 ALKRFGRNLGLAFQIQDDILDLFGDPETLGKPVGSDLREGKCTLPVLLALR---ELAREY 229
Query: 240 FSQATKELAYF-EVSKAAPLYHLAKYIVSR 268
+A + L E L LA +I+ R
Sbjct: 230 EEKALEALKALPESPAREALRALADFILER 259
>gnl|CDD|223220 COG0142, IspA, Geranylgeranyl pyrophosphate synthase [Coenzyme
metabolism].
Length = 322
Score = 254 bits (652), Expect = 3e-84
Identities = 118/305 (38%), Positives = 156/305 (51%), Gaps = 47/305 (15%)
Query: 4 PEKIHEAMRYSLLAGGKRIRPVLCIASCELVGGDESL----VMPMACALEMTHTMSLIHD 59
PE + EAMRY LLAGGKR+RP+L + + E +G D + +A A+E+ HT SLIHD
Sbjct: 27 PELLLEAMRYLLLAGGKRLRPLLVLLAAEALGIDLETGGNDALDLAAAIELIHTASLIHD 86
Query: 60 DLPALDNDDLRRGKPTNHKVFGEPTAILAGDALLALAFEHVAAKTVGVSTDRVVRAITEL 119
DL +D+DDLRRGKPT H FGE TAILAGDALLA AFE ++ +G ++A+ E
Sbjct: 87 DL--MDDDDLRRGKPTVHAKFGEATAILAGDALLAAAFELLS--KLGSEALEAIKALAE- 141
Query: 120 GSALGAEGLLKGQVTDLDSEGKDVSLSELEYIHVHKTAKLLEASVVCGVIIGGGNVIEIE 179
GL GQ DL E K V+L E + KTA L A+ V G I+ G + +E
Sbjct: 142 ----AINGLCGGQALDLAFENKPVTLEEYLRVIELKTAALFAAAAVLGAILAGADEELLE 197
Query: 180 RVRNYARCIGLLFQVVDDILDVTKSSTVLGKTAGKDLVSDKATYPKLMGIENAK------ 233
+ +Y R +GL FQ+ DDILD+T LGK G DL K T P L+ +E A
Sbjct: 198 ALEDYGRNLGLAFQIQDDILDITGDEEELGKPVGSDLKEGKPTLPVLLALEKANEDQKLL 257
Query: 234 ---------------------------KFAEELFSQATKELAYFEVSKAA-PLYHLAKYI 265
A+ +A + L S+A L LA +I
Sbjct: 258 RILLEGGGEVEEALELLRKSGAIEYAKNLAKTYVEKAKEALEKLPDSEAKEALLELADFI 317
Query: 266 VSRQN 270
+ R+
Sbjct: 318 IKRKY 322
>gnl|CDD|182567 PRK10581, PRK10581, geranyltranstransferase; Provisional.
Length = 299
Score = 223 bits (569), Expect = 3e-72
Identities = 123/273 (45%), Positives = 153/273 (56%), Gaps = 18/273 (6%)
Query: 9 EAMRYSLLAGGKRIRPVLCIASCELVG-GDESLVMPMACALEMTHTMSLIHDDLPALDND 67
EAM+Y L GGKR+RP L A+ ++ G +L P A A+E H SLIHDDLPA+D+D
Sbjct: 34 EAMQYGALLGGKRLRPFLVYATGQMFGVSTNTLDAP-AAAVECIHAYSLIHDDLPAMDDD 92
Query: 68 DLRRGKPTNHKVFGEPTAILAGDALLALAFEHVA-AKTVGVSTDRVVRAITELGSALGAE 126
DLRRG PT H FGE AILAGDAL LAF ++ A VS + I+EL SA G
Sbjct: 93 DLRRGLPTCHVKFGEANAILAGDALQTLAFSILSDAPMPEVSDRDRISMISELASASGIA 152
Query: 127 GLLKGQVTDLDSEGKDVSLSELEYIHVHKTAKLLEASVVCGVIIGGGNVIEIERVRN--- 183
G+ GQ DL++EGK V L LE IH HKT L+ A+V G + G ++ R
Sbjct: 153 GMCGGQALDLEAEGKQVPLDALERIHRHKTGALIRAAVRLGALSAG------DKGRRALP 206
Query: 184 ----YARCIGLLFQVVDDILDVTKSSTVLGKTAGKDLVSDKATYPKLMGIENAKKFAEEL 239
YA IGL FQV DDILDV + LGK G D K+TYP L+G+E A+K A +L
Sbjct: 207 VLDRYAESIGLAFQVQDDILDVVGDTATLGKRQGADQQLGKSTYPALLGLEQARKKARDL 266
Query: 240 FSQATKELAYFEVSKA--APLYHLAKYIVSRQN 270
A + L + L LA YI+ R
Sbjct: 267 IDDARQSLDQLAAQSLDTSALEALANYIIQRDK 299
>gnl|CDD|164542 CHL00151, preA, prenyl transferase; Reviewed.
Length = 323
Score = 205 bits (523), Expect = 5e-65
Identities = 89/303 (29%), Positives = 139/303 (45%), Gaps = 51/303 (16%)
Query: 7 IHEAMRYSLLAGGKRIRPVLCIASCELVGGDESLVMP---MACALEMTHTMSLIHDDLPA 63
++ A ++ AGGKRIRP + + + GG+ + +A E+ HT SL+HDD+
Sbjct: 33 LYAAAKHLFSAGGKRIRPAIVLLVAKATGGNMEIKTSQQRLAEITEIIHTASLVHDDV-- 90
Query: 64 LDNDDLRRGKPTNHKVFGEPTAILAGDALLALAFEHVAAKTVGVSTDRVVRAITELGSAL 123
+D +RRG PT HK+FG A+LAGD L A + ++A + + IT+
Sbjct: 91 IDECSIRRGIPTVHKIFGTKIAVLAGDFLFAQSSWYLANLNNLEVVKLISKVITDF---- 146
Query: 124 GAEGLLKGQVTDLDSEGKDVSLSELEYIH--VHKTAKLLEASVVCGVIIGGGNVIEIERV 181
AEG ++ + D +LS L YI +KTA L+ AS ++ + +
Sbjct: 147 -AEGEIRQGLVQFD-----TTLSILNYIEKSFYKTASLIAASCKAAALLSDADEKDHNDF 200
Query: 182 RNYARCIGLLFQVVDDILDVTKSSTVLGKTAGKDLVSDKATYPKLMGIENAKKFAEEL-- 239
Y + +GL FQ++DD+LD+T S+ LGK G DL + T P L + K A+ +
Sbjct: 201 YLYGKHLGLAFQIIDDVLDITSSTESLGKPIGSDLKNGNLTAPVLFALTQNSKLAKLIER 260
Query: 240 -------FSQA------------TKELAYFEVSKA-------------APLYHLAKYIVS 267
SQA K+LA + A L +A +I++
Sbjct: 261 EFCETKDISQALQIIKETNGIEKAKDLALEHMQAAIQCLKFLPPSSAKDSLIEIANFIIN 320
Query: 268 RQN 270
R N
Sbjct: 321 RLN 323
>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 = 181 bits (461), Expect = 1e-56
Identities = 85/249 (34%), Positives = 128/249 (51%), Gaps = 15/249 (6%)
Query: 22 IRPVLCIASCELVGGDESLVMPMACALEMTHTMSLIHDDLPALDNDDLRRGKPTNHKV-F 80
RP+L + +GGD + +A A+E+ H SL+HDD+ +D+ DLRRGKPT H F
Sbjct: 1 SRPLLVLLLARALGGDLEAALRLAAAVELLHAASLVHDDI--VDDSDLRRGKPTAHLRRF 58
Query: 81 GEPTAILAGDALLALAFEHVAAKTVGVSTDRVVRAITELGSALGAEGLLKGQVTDLDSEG 140
G AILAGD LLA AF+ +A + R + E LL+GQ DL+ E
Sbjct: 59 GNALAILAGDYLLARAFQLLAR----LGYPRALELFAE-----ALRELLEGQALDLEFER 109
Query: 141 -KDVSLSELEYIHVHKTAKLLEASVVCGVIIGGGNVIEIERVRNYARCIGLLFQVVDDIL 199
+L E +KTA L+ + G + G + + E +++Y R +GL FQ+ DD+L
Sbjct: 110 DTYETLDEYLEYCRYKTAGLVGLLCLLGAGLSGADDEQAEALKDYGRALGLAFQLTDDLL 169
Query: 200 DVTKSSTVLGKTAGKDLVSDKATYPKLMGIENAKKFAEELFSQATKELAYFEVSKAAPLY 259
DV + LGK G DL + T P ++ E A ++AEE ++ ++ A +
Sbjct: 170 DVFGDAEELGK-VGSDLREGRITLPVILARERAAEYAEEAYAALEALPPSLPRARRALIA 228
Query: 260 HLAKYIVSR 268
LA ++ R
Sbjct: 229 -LADFLYRR 236
>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 = 127 bits (322), Expect = 6e-36
Identities = 67/232 (28%), Positives = 100/232 (43%), Gaps = 32/232 (13%)
Query: 22 IRPVLCIASCELVGGDESLVMPMACALEMTHTMSLIHDDLPALDNDDLRRGKPTNHKV-- 79
RP+ + E + A+E H SL+HDD+ +D+ RRG PT H
Sbjct: 1 FRPLAVLLEPEAS--------RLRAAVEKLHAASLVHDDI--VDDSGTRRGLPTAHLAVA 50
Query: 80 -FGEPTAILAGDALLALAFEHVAAKTVGVSTDRVVRAITELGSALGAEGLLKGQVTDLDS 138
G P AILAGD LLA AFE +A + + + + A+ +L L+GQ+ DL
Sbjct: 51 IDGLPEAILAGDLLLADAFEELAREGSPEALEILAEALLDL---------LEGQLLDLKW 101
Query: 139 EG-KDVSLSELEYIHVHKTAKLLEASVVCGVIIGGGNVIEIERVRNYARCIGLLFQVVDD 197
+L E +KTA L+ A + G + GG +E +R R +GL FQ+ +D
Sbjct: 102 RREYVPTLEEYLEYCRYKTAGLVGALCLLGAGLSGGEAELLEALRKLGRALGLAFQLTND 161
Query: 198 ILDVTKSSTVLGKTAGKDLVSDKATYPKLMGIENAKKFAEELFSQATKELAY 249
+LD + K T P L +E + L + + L
Sbjct: 162 LLDYEGDAERGE---------GKCTLPVLYALEYGVPAEDLLLVEKSGSLEE 204
>gnl|CDD|215462 PLN02857, PLN02857, octaprenyl-diphosphate synthase.
Length = 416
Score = 123 bits (310), Expect = 1e-32
Identities = 87/236 (36%), Positives = 124/236 (52%), Gaps = 16/236 (6%)
Query: 17 AGGKRIRPVLCI----ASCELVGGDESLVMP--MACALEMTHTMSLIHDDLPALDNDDLR 70
AGGKR+RP L A+ EL G E +A EM HT SLIHDD+ LD D+R
Sbjct: 133 AGGKRMRPALVFLVSRATAELAGLKELTTEHRRLAEITEMIHTASLIHDDV--LDESDMR 190
Query: 71 RGKPTNHKVFGEPTAILAGDALLALAFEHVAAKTVGVSTDRVVRAITELGSALGAEGLLK 130
RGK T H+++G A+LAGD + A + ++A + V++ I+++ A G +K
Sbjct: 191 RGKETVHQLYGTRVAVLAGDFMFAQSSWYLA----NLDNLEVIKLISQVIKDF-ASGEIK 245
Query: 131 GQVTDLDSEGKDVSLSELEYIHVHKTAKLLEASVVCGVIIGGGNVIEIERVRNYARCIGL 190
+ D DV+L E +KTA L+ AS I G + E++ Y + +GL
Sbjct: 246 QASSLFDC---DVTLDEYLLKSYYKTASLIAASTKSAAIFSGVDSSVKEQMYEYGKNLGL 302
Query: 191 LFQVVDDILDVTKSSTVLGKTAGKDLVSDKATYPKLMGIENAKKFAEELFSQATKE 246
FQVVDDILD T+S+ LGK AG DL T P + +E + E + S+ +E
Sbjct: 303 AFQVVDDILDFTQSTEQLGKPAGSDLAKGNLTAPVIFALEKEPELREIIESEFCEE 358
>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 = 119 bits (301), Expect = 5e-32
Identities = 88/237 (37%), Positives = 120/237 (50%), Gaps = 24/237 (10%)
Query: 17 AGGKRIRP--VLCIASC-----ELVGGDESLVMPMACALEMTHTMSLIHDDLPALDNDDL 69
AGGKR+RP VL ++ EL L A EM HT SL+HDD+ +D D
Sbjct: 42 AGGKRLRPAIVLLVSRATAEQQELTPRHRRL----AEITEMIHTASLVHDDV--IDESDT 95
Query: 70 RRGKPTNHKVFGEPTAILAGDALLALAFEHVAAKTVGVSTDRVVRAITELGSALGAEGLL 129
RRG T H +FG A+LAGD L A A ++A + VV+ I+++ + AEG +
Sbjct: 96 RRGIETVHSLFGTRVAVLAGDFLFAQASWYLA----NLENLEVVKLISKVITDF-AEGEI 150
Query: 130 KGQVTDLDSEGKDVSLSELEYIHVHKTAKLLEASVVCGVIIGGGNVIEIERVRNYARCIG 189
K + DS D+SL + +KTA L+ AS ++ + Y + +G
Sbjct: 151 KQGLNQFDS---DLSLEDYLEKSFYKTASLVAASSKAAAVLSDVPSQVANDLYEYGKHLG 207
Query: 190 LLFQVVDDILDVTKSSTVLGKTAGKDLVSDKATYPKLMGIENAKKFAEEL---FSQA 243
L FQVVDDILD T S+ LGK AG DL+ T P L +E K +E + FSQ
Sbjct: 208 LAFQVVDDILDFTGSTEQLGKPAGSDLMKGNLTAPVLFALEEEPKLSELIEREFSQK 264
>gnl|CDD|182813 PRK10888, PRK10888, octaprenyl diphosphate synthase; Provisional.
Length = 323
Score = 110 bits (276), Expect = 2e-28
Identities = 73/242 (30%), Positives = 126/242 (52%), Gaps = 14/242 (5%)
Query: 7 IHEAMRYSLLAGGKRIRPVLCIASCELVGGDESLVMPMACALEMTHTMSLIHDDLPALDN 66
I++ Y + GGKRIRP++ + + VG + + +A +E HT +L+HDD+ +D
Sbjct: 32 INQLGYYIISGGGKRIRPMIAVLAARAVGYQGNAHVTIAALIEFIHTATLLHDDV--VDE 89
Query: 67 DDLRRGKPTNHKVFGEPTAILAGDALLALAFEHVAAKTVGVSTDRVVRAITELGSALGAE 126
D+RRGK T + FG ++L GD + AF+ + + + + +V+ ++E + + AE
Sbjct: 90 SDMRRGKATANAAFGNAASVLVGDFIYTRAFQMMTS----LGSLKVLEVMSEAVNVI-AE 144
Query: 127 GLLKGQVTDLDSEGKDVSLSELEYIHV--HKTAKLLEASVVCGVIIGGGNVIEIERVRNY 184
G +V L D ++E Y+ V KTA+L EA+ C I+ G + + +++Y
Sbjct: 145 G----EVLQL-MNVNDPDITEENYMRVIYSKTARLFEAAAQCSGILAGCTPEQEKGLQDY 199
Query: 185 ARCIGLLFQVVDDILDVTKSSTVLGKTAGKDLVSDKATYPKLMGIENAKKFAEELFSQAT 244
R +G FQ++DD+LD + LGK G DL K T P L + + + A
Sbjct: 200 GRYLGTAFQLIDDLLDYSADGETLGKNVGDDLNEGKPTLPLLHAMHHGTPEQAAMIRTAI 259
Query: 245 KE 246
++
Sbjct: 260 EQ 261
>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 = 107 bits (270), Expect = 2e-27
Identities = 78/242 (32%), Positives = 121/242 (50%), Gaps = 16/242 (6%)
Query: 9 EAMRYSLLAGGKRIRPVLCIASCELVGGDESLVMPMACALEMTHTMSLIHDDLPALDNDD 68
EA + L AGGKRIRPV + + + D + +A ALE+ H SL+HDD+ +D+ D
Sbjct: 33 EASLHLLEAGGKRIRPVFVLLAGKFGDYDLDAIKHVAVALELIHMASLVHDDV--IDDAD 90
Query: 69 LRRGKPTNHKVFGEPTAILAGDALLALAFEHVAAKTVGVSTDRVVRAITELGSALGAEGL 128
LRRG+PT +G A+ GD L A + E + + R + ++ +
Sbjct: 91 LRRGRPTIKSKWGNRIAMYTGDYLFAKSLETMTE----IKDPRAHQILSHT-----IVEV 141
Query: 129 LKGQVTDL-DSEGKDVSLSE-LEYIHVHKTAKLLEASVVCGVIIGGGNVIEIERVRNYAR 186
+G++ + D D +L L I KTA L+ AS G I G N ++++ +
Sbjct: 142 CRGEIEQIKDKYNFDQNLRTYLRRIK-RKTALLIAASCQLGAIASGANEAIVKKLYWFGY 200
Query: 187 CIGLLFQVVDDILDVTKSSTVLGKTAGKDLVSDKATYPKLMGIEN--AKKFAEELFSQAT 244
+G+ +Q+ DDILD + LGK AG DL+ T P L +E+ KK E++ + T
Sbjct: 201 YVGMSYQITDDILDFVGTEEELGKPAGGDLLQGNVTLPVLYAMEDPFLKKRIEQVLEETT 260
Query: 245 KE 246
E
Sbjct: 261 AE 262
>gnl|CDD|178478 PLN02890, PLN02890, geranyl diphosphate synthase.
Length = 422
Score = 70.7 bits (173), Expect = 7e-14
Identities = 60/185 (32%), Positives = 88/185 (47%), Gaps = 16/185 (8%)
Query: 49 EMTHTMSLIHDDLPALDNDDLRRGKPTNHKVFGEPTAILAGDALLALAFEHVAAKTVGVS 108
EM H SL+HDD+ LD+ D RRG + + V G ++LAGD LL+ A +AA +
Sbjct: 171 EMIHVASLLHDDV--LDDADTRRGVGSLNVVMGNKLSVLAGDFLLSRACVALAA----LK 224
Query: 109 TDRVVRAITELGSALGAEGLLKGQVTDLDSEGKDVSLSELEYI---HVHKTAKLLEASVV 165
VV + A E L+ G+ + S + ++Y +KTA L+ S
Sbjct: 225 NTEVVSLL-----ATAVEHLVTGETMQITSSRE--QRRSMDYYMQKTYYKTASLISNSCK 277
Query: 166 CGVIIGGGNVIEIERVRNYARCIGLLFQVVDDILDVTKSSTVLGKTAGKDLVSDKATYPK 225
I+ G Y R +GL FQ++DD+LD T +S LGK + D+ T P
Sbjct: 278 AVAILAGQTAEVAVLAFEYGRNLGLAFQLIDDVLDFTGTSASLGKGSLSDIRHGVITAPI 337
Query: 226 LMGIE 230
L +E
Sbjct: 338 LFAME 342
>gnl|CDD|217845 pfam04016, DUF364, Domain of unknown function (DUF364). This
domain of unknown function has a PLP-dependent
transferase-like fold. Its genomic context suggests that
it may have a role in anaerobic vitamin B12
biosynthesis. This domain is often found at the
C-terminus of proteins containing DUF4213, pfam13938.
Length = 147
Score = 30.2 bits (69), Expect = 0.54
Identities = 17/69 (24%), Positives = 28/69 (40%), Gaps = 5/69 (7%)
Query: 54 MSLIHDDLPALDNDDLRRGKPTNHKVFGEPTAILAGDALLALAFEHVAAKTVGVSTDRVV 113
+L++ L L L + V P+A L +AL + + A D+++
Sbjct: 71 TTLVNGTLERL----LALARKAAEVVLVGPSAPLLPEALFGYGVDVL-AGVRVTDPDKLL 125
Query: 114 RAITELGSA 122
RAI E G
Sbjct: 126 RAIAEGGGT 134
>gnl|CDD|119324 cd06582, TM_PBP1_LivH_like, Transmembrane subunit (TM) of
Escherichia coli LivH and related proteins. LivH is one
of two TMs of the E. coli LIV-1/LS transporter, a
Periplasmic Binding Protein (PBP)-dependent ATP-Binding
Cassette (ABC) transporter involved in the uptake of
branched-chain amino acids (AAs). These types of
transporters generally bind type 1 PBPs. PBP-dependent
ABC transporters consist of a PBP, two TMs, and two
cytoplasmic ABCs, and are mainly involved in importing
solutes from the environment. The solute is captured by
the PBP, which delivers it to a gated translocation
pathway formed by the two TMs. The two ABCs bind and
hydrolyze ATP and drive the transport reaction. E. coli
LivH forms a heterodimer with another TM, LivM, to
generate the transmembrane pore. LivM is not included in
this subgroup. The LIV-1/LS transporter is comprised of
two TMs (LivM and LivH), two ABCs (LivG and LivF), and
one of two alternative PBPs, LivJ (LIV-BP) or LivK
(LS-BP). In addition to transporting branched-chain AAs
including leucine, isoleucine and valine, the E. coli
LIV-1/LS transporter is involved in the uptake of the
aromatic AA, phenylalanine.
Length = 272
Score = 29.3 bits (67), Expect = 1.6
Identities = 13/37 (35%), Positives = 20/37 (54%)
Query: 89 GDALLALAFEHVAAKTVGVSTDRVVRAITELGSALGA 125
G A+ A+A AA+ +G++ RV LG+AL
Sbjct: 154 GRAIRAVAQNPEAARLLGINVRRVFALTFALGAALAG 190
>gnl|CDD|163175 TIGR03178, allantoinase, allantoinase. This enzyme carries out the
first step in the degradation of allantoin, a
ring-opening hydrolysis. The seed members of this model
are all in the vicinity of other genes involved in the
processes of xanthine/urate/allantoin catabolism.
Although not included in the seed, many eukaryotic
homologs of this family are included above the trusted
cutoff. Below the noise cutoff are related
hydantoinases.
Length = 443
Score = 29.3 bits (66), Expect = 2.5
Identities = 12/52 (23%), Positives = 21/52 (40%), Gaps = 1/52 (1%)
Query: 59 DDLPALDNDDLRRGKPTNHKVFGEPTAILAGDALLALAFEHVAAKTVGVSTD 110
D+ P +D+ L +G + G+ + A + + A A GV D
Sbjct: 153 DEFPHVDDWQLYKGMRELAR-LGQLLLVHAENPAITSALGEEAPPQGGVGAD 203
>gnl|CDD|183880 PRK13184, pknD, serine/threonine-protein kinase; Reviewed.
Length = 932
Score = 28.2 bits (63), Expect = 5.4
Identities = 11/34 (32%), Positives = 17/34 (50%)
Query: 237 EELFSQATKELAYFEVSKAAPLYHLAKYIVSRQN 270
F+QA E +Y APL +L K +V ++
Sbjct: 532 PRDFTQALSEFSYLHGGVGAPLEYLGKALVYQRL 565
>gnl|CDD|218580 pfam05409, Peptidase_C30, Coronavirus endopeptidase C30.
Corresponds to Merops family C30. These peptidases are
involved in viral polyprotein processing in replication.
Length = 293
Score = 27.4 bits (61), Expect = 7.9
Identities = 17/46 (36%), Positives = 23/46 (50%), Gaps = 6/46 (13%)
Query: 84 TAILAGDALLALAFEHVAAKTVGVSTDRVVRAITELGSALGAEGLL 129
T I DA LA AKT GV ++++ AI L S G + +L
Sbjct: 212 TPISTTDAFSILA-----AKT-GVDVEKLLAAIQVLNSGFGGKQIL 251
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
0.318 0.135 0.379
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: 13,725,639
Number of extensions: 1337097
Number of successful extensions: 1321
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1284
Number of HSP's successfully gapped: 31
Length of query: 270
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 175
Effective length of database: 6,723,972
Effective search space: 1176695100
Effective search space used: 1176695100
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 (21.7 bits)
S2: 58 (26.3 bits)