RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 037716
(354 letters)
>gnl|CDD|215873 pfam00348, polyprenyl_synt, Polyprenyl synthetase.
Length = 260
Score = 265 bits (679), Expect = 5e-88
Identities = 111/256 (43%), Positives = 162/256 (63%), Gaps = 5/256 (1%)
Query: 91 IHKAMRYSLLAGGKRVRPLLCIASCELVGGDESWAMPAACALEMIHTMSLIHDDLPFLDN 150
+ AM Y LLAGGKR+RPLL + + +G + + ACA+EMIHT SL+HDDL +DN
Sbjct: 1 LLAAMLYYLLAGGKRIRPLLVVLAARALGVEPETLLYLACAIEMIHTASLVHDDL--MDN 58
Query: 151 DERRRSKPASHEVFGESTAILAGDALLSLALEHVAVNIAGVSPDRVVRAIAEMCSAMGVE 210
+ RR KP H+ FGE+ AILAGDALLS A + +A + V P+ I+E+ +A+G +
Sbjct: 59 SDLRRGKPTCHKKFGEAGAILAGDALLSRAFQLLA-LLGHVRPEPKYILISELANAVGAQ 117
Query: 211 GLVAGEFVDIASEGKDVSLKELEYIHVHKTAKLLEAAVVCGAVIGGGNAIEVERVRNYAR 270
G V G+ +D+ +EGKD++L+E I +KTA L A+V GA++ G + + + + ++ R
Sbjct: 118 GEV-GQLMDLETEGKDITLEEYLRIVSYKTAALFYASVQLGAIVAGADEEDEKDLYDFGR 176
Query: 271 CIGLLFQVVDDILDVTKSSEELGKTAGKDLASGKATYPKLMGIENAKSFAGELLGQAIE- 329
+GL FQ+ DDILD+T +EELGK G DL GK+T P L+ +E A+ +LL +A E
Sbjct: 177 DLGLAFQIQDDILDLTGDTEELGKPVGTDLQEGKSTLPVLLALEGAREEQRKLLREAYEQ 236
Query: 330 ELAYFEASKAAPLYFL 345
+L+ A A L
Sbjct: 237 KLSEAAAQGVALTKAL 252
>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 = 264 bits (678), Expect = 9e-88
Identities = 107/265 (40%), Positives = 150/265 (56%), Gaps = 14/265 (5%)
Query: 91 IHKAMRYSLLAGGKRVRPLLCIASCELVGGDESW-AMPAACALEMIHTMSLIHDDLPFLD 149
+ +A+RY LLAGGKR+RPLL + + +GG E A+ A A+E++HT SL+HDD+ +D
Sbjct: 6 LREALRYLLLAGGKRLRPLLVLLAARALGGPELEAALRLAAAIELLHTASLVHDDV--MD 63
Query: 150 NDERRRSKPASHEVFGESTAILAGDALLSLALEHVAVNIAGVSPDRVVRAIAEMCSAMGV 209
N + RR KP H+VFG +TAILAGD LL+ A E +A + R + +E
Sbjct: 64 NSDLRRGKPTVHKVFGNATAILAGDYLLARAFELLA-RLGNPYYPRALELFSEAI----- 117
Query: 210 EGLVAGEFVDIASEGK-DVSLKELEYIHVHKTAKLLEAAVVCGAVIGGGNAIEVERVRNY 268
LV G+ +D+ SE DV+ +E I KTA L AA + GA++ G + E E ++ +
Sbjct: 118 LELVEGQLLDLLSEYDTDVTEEEYLRIIRLKTAALFAAAPLLGALLAGADEEEAEALKRF 177
Query: 269 ARCIGLLFQVVDDILDVTKSSEELGKTAGKDLASGKATYPKLMGIENAKSFAGELLGQAI 328
R +GL FQ+ DDILD+ E LGK G DL GK T P L+ + A E +A+
Sbjct: 178 GRNLGLAFQIQDDILDLFGDPETLGKPVGSDLREGKCTLPVLLALRE---LAREYEEKAL 234
Query: 329 EELAYFEASKA-APLYFLANYIASR 352
E L S A L LA++I R
Sbjct: 235 EALKALPESPAREALRALADFILER 259
>gnl|CDD|223220 COG0142, IspA, Geranylgeranyl pyrophosphate synthase [Coenzyme
metabolism].
Length = 322
Score = 264 bits (677), Expect = 6e-87
Identities = 119/330 (36%), Positives = 173/330 (52%), Gaps = 47/330 (14%)
Query: 63 PFEEYMIRKAEQVNKALDEAVVLQPPVKIHKAMRYSLLAGGKRVRPLLCIASCELVGGDE 122
++++ ++ + L E + P + +AMRY LLAGGKR+RPLL + + E +G D
Sbjct: 2 DLLALLLKRLARIEELLSELLSGSDPELLLEAMRYLLLAGGKRLRPLLVLLAAEALGIDL 61
Query: 123 SW----AMPAACALEMIHTMSLIHDDLPFLDNDERRRSKPASHEVFGESTAILAGDALLS 178
A+ A A+E+IHT SLIHDDL +D+D+ RR KP H FGE+TAILAGDALL+
Sbjct: 62 ETGGNDALDLAAAIELIHTASLIHDDL--MDDDDLRRGKPTVHAKFGEATAILAGDALLA 119
Query: 179 LALEHVAVNIAGVSPDRVVRAIAEMCSAMGVEGLVAGEFVDIASEGKDVSLKELEYIHVH 238
A E ++ + + ++A+AE + GL G+ +D+A E K V+L+E +
Sbjct: 120 AAFELLS-KLGSEAL-EAIKALAE-----AINGLCGGQALDLAFENKPVTLEEYLRVIEL 172
Query: 239 KTAKLLEAAVVCGAVIGGGNAIEVERVRNYARCIGLLFQVVDDILDVTKSSEELGKTAGK 298
KTA L AA V GA++ G + +E + +Y R +GL FQ+ DDILD+T EELGK G
Sbjct: 173 KTAALFAAAAVLGAILAGADEELLEALEDYGRNLGLAFQIQDDILDITGDEEELGKPVGS 232
Query: 299 DLASGKATYPKLMGIENAK---------------------------------SFAGELLG 325
DL GK T P L+ +E A + A +
Sbjct: 233 DLKEGKPTLPVLLALEKANEDQKLLRILLEGGGEVEEALELLRKSGAIEYAKNLAKTYVE 292
Query: 326 QAIEELAYFEASKAA-PLYFLANYIASRQN 354
+A E L S+A L LA++I R+
Sbjct: 293 KAKEALEKLPDSEAKEALLELADFIIKRKY 322
>gnl|CDD|182567 PRK10581, PRK10581, geranyltranstransferase; Provisional.
Length = 299
Score = 217 bits (554), Expect = 8e-69
Identities = 123/304 (40%), Positives = 167/304 (54%), Gaps = 20/304 (6%)
Query: 64 FEEYMIRKAEQVNKALDEAVVLQP--PVKIHKAMRYSLLAGGKRVRPLLCIASCELVG-G 120
F + + +Q N+AL + P + +AM+Y L GGKR+RP L A+ ++ G
Sbjct: 3 FPQQLQACVQQANQALSRFIAPLPFQNTPVVEAMQYGALLGGKRLRPFLVYATGQMFGVS 62
Query: 121 DESWAMPAACALEMIHTMSLIHDDLPFLDNDERRRSKPASHEVFGESTAILAGDALLSLA 180
+ PAA A+E IH SLIHDDLP +D+D+ RR P H FGE+ AILAGDAL +LA
Sbjct: 63 TNTLDAPAA-AVECIHAYSLIHDDLPAMDDDDLRRGLPTCHVKFGEANAILAGDALQTLA 121
Query: 181 LEHVA-VNIAGVSPDRVVRAIAEMCSAMGVEGLVAGEFVDIASEGKDVSLKELEYIHVHK 239
++ + VS + I+E+ SA G+ G+ G+ +D+ +EGK V L LE IH HK
Sbjct: 122 FSILSDAPMPEVSDRDRISMISELASASGIAGMCGGQALDLEAEGKQVPLDALERIHRHK 181
Query: 240 TAKLLEAAVVCGAVIGGGNAIEVERVRN-------YARCIGLLFQVVDDILDVTKSSEEL 292
T L+ AAV GA+ G ++ R YA IGL FQV DDILDV + L
Sbjct: 182 TGALIRAAVRLGALSAG------DKGRRALPVLDRYAESIGLAFQVQDDILDVVGDTATL 235
Query: 293 GKTAGKDLASGKATYPKLMGIENAKSFAGELLGQAIEELAYFEASKA--APLYFLANYIA 350
GK G D GK+TYP L+G+E A+ A +L+ A + L A + L LANYI
Sbjct: 236 GKRQGADQQLGKSTYPALLGLEQARKKARDLIDDARQSLDQLAAQSLDTSALEALANYII 295
Query: 351 SRQN 354
R
Sbjct: 296 QRDK 299
>gnl|CDD|164542 CHL00151, preA, prenyl transferase; Reviewed.
Length = 323
Score = 189 bits (482), Expect = 1e-57
Identities = 93/322 (28%), Positives = 146/322 (45%), Gaps = 54/322 (16%)
Query: 73 EQVNKALDEAVVLQPPVKIHKAMRYSLLAGGKRVRPLLCIASCELVGGDESWAMP---AA 129
+ L + + P+ ++ A ++ AGGKR+RP + + + GG+ A
Sbjct: 16 LILEDNLKKLIGSGHPI-LYAAAKHLFSAGGKRIRPAIVLLVAKATGGNMEIKTSQQRLA 74
Query: 130 CALEMIHTMSLIHDDLPFLDNDERRRSKPASHEVFGESTAILAGDALLSLALEHVAVNIA 189
E+IHT SL+HDD+ +D RR P H++FG A+LAGD L + + ++A N+
Sbjct: 75 EITEIIHTASLVHDDV--IDECSIRRGIPTVHKIFGTKIAVLAGDFLFAQSSWYLA-NLN 131
Query: 190 GVSP-DRVVRAIAEMCSAMGVEGLVAGEFVDIASEGKDVSLKELEYIH--VHKTAKLLEA 246
+ + + I + +GLV +F D +L L YI +KTA L+ A
Sbjct: 132 NLEVVKLISKVITDFAEGEIRQGLV--QF--------DTTLSILNYIEKSFYKTASLIAA 181
Query: 247 AVVCGAVIGGGNAIEVERVRNYARCIGLLFQVVDDILDVTKSSEELGKTAGKDLASGKAT 306
+ A++ + + Y + +GL FQ++DD+LD+T S+E LGK G DL +G T
Sbjct: 182 SCKAAALLSDADEKDHNDFYLYGKHLGLAFQIIDDVLDITSSTESLGKPIGSDLKNGNLT 241
Query: 307 YPKLM---------------------------------GIENAKSFAGELLGQAIEELAY 333
P L GIE AK A E + AI+ L +
Sbjct: 242 APVLFALTQNSKLAKLIEREFCETKDISQALQIIKETNGIEKAKDLALEHMQAAIQCLKF 301
Query: 334 FEASKA-APLYFLANYIASRQN 354
S A L +AN+I +R N
Sbjct: 302 LPPSSAKDSLIEIANFIINRLN 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 = 182 bits (463), Expect = 7e-56
Identities = 85/249 (34%), Positives = 128/249 (51%), Gaps = 15/249 (6%)
Query: 106 VRPLLCIASCELVGGDESWAMPAACALEMIHTMSLIHDDLPFLDNDERRRSKPASHEV-F 164
RPLL + +GGD A+ A A+E++H SL+HDD+ +D+ + RR KP +H F
Sbjct: 1 SRPLLVLLLARALGGDLEAALRLAAAVELLHAASLVHDDI--VDDSDLRRGKPTAHLRRF 58
Query: 165 GESTAILAGDALLSLALEHVAVNIAGVSPDRVVRAIAEMCSAMGVEGLVAGEFVDIASEG 224
G + AILAGD LL+ A + +A R + AE L+ G+ +D+ E
Sbjct: 59 GNALAILAGDYLLARAFQLLARL----GYPRALELFAEAL-----RELLEGQALDLEFER 109
Query: 225 -KDVSLKELEYIHVHKTAKLLEAAVVCGAVIGGGNAIEVERVRNYARCIGLLFQVVDDIL 283
+L E +KTA L+ + GA + G + + E +++Y R +GL FQ+ DD+L
Sbjct: 110 DTYETLDEYLEYCRYKTAGLVGLLCLLGAGLSGADDEQAEALKDYGRALGLAFQLTDDLL 169
Query: 284 DVTKSSEELGKTAGKDLASGKATYPKLMGIENAKSFAGELLGQAIEELAYFEASKAAPLY 343
DV +EELGK G DL G+ T P ++ E A +A E A+E L L
Sbjct: 170 DVFGDAEELGK-VGSDLREGRITLPVILARERAAEYAEEAY-AALEALPPSLPRARRALI 227
Query: 344 FLANYIASR 352
LA+++ R
Sbjct: 228 ALADFLYRR 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 = 122 bits (307), Expect = 7e-33
Identities = 67/234 (28%), Positives = 99/234 (42%), Gaps = 32/234 (13%)
Query: 107 RPLLCIASCELVGGDESWAMPAACALEMIHTMSLIHDDLPFLDNDERRRSKPASHEV--- 163
RPL + E A A+E +H SL+HDD+ +D+ RR P +H
Sbjct: 2 RPLAVLLEPE--------ASRLRAAVEKLHAASLVHDDI--VDDSGTRRGLPTAHLAVAI 51
Query: 164 FGESTAILAGDALLSLALEHVAVNIAGVSPDRVVRAIAEMCSAMGVEGLVAGEFVDIASE 223
G AILAGD LL+ A E +A + + +AE L+ G+ +D+
Sbjct: 52 DGLPEAILAGDLLLADAFEELAREGS----PEALEILAEAL-----LDLLEGQLLDLKWR 102
Query: 224 G-KDVSLKELEYIHVHKTAKLLEAAVVCGAVIGGGNAIEVERVRNYARCIGLLFQVVDDI 282
+L+E +KTA L+ A + GA + GG A +E +R R +GL FQ+ +D+
Sbjct: 103 REYVPTLEEYLEYCRYKTAGLVGALCLLGAGLSGGEAELLEALRKLGRALGLAFQLTNDL 162
Query: 283 LDVTKSSEELGKTAGKDLASGKATYPKLMGIENAKSFAGELLGQAIEELAYFEA 336
LD +E GK T P L +E LL + L
Sbjct: 163 LDYEGDAERGE---------GKCTLPVLYALEYGVPAEDLLLVEKSGSLEEALE 207
>gnl|CDD|215462 PLN02857, PLN02857, octaprenyl-diphosphate synthase.
Length = 416
Score = 121 bits (304), Expect = 5e-31
Identities = 90/250 (36%), Positives = 135/250 (54%), Gaps = 19/250 (7%)
Query: 73 EQVNKALDEAVVLQPPVKIHKAMRYSLLAGGKRVRPLLCI----ASCELVGGDESWAMPA 128
+Q+N L V + PV + A + AGGKR+RP L A+ EL G E
Sbjct: 106 QQLNDNLQSIVGAENPVLMSAAEQI-FGAGGKRMRPALVFLVSRATAELAGLKELTTEHR 164
Query: 129 ACA--LEMIHTMSLIHDDLPFLDNDERRRSKPASHEVFGESTAILAGDALLSLALEHVAV 186
A EMIHT SLIHDD+ LD + RR K H+++G A+LAGD + + + ++A
Sbjct: 165 RLAEITEMIHTASLIHDDV--LDESDMRRGKETVHQLYGTRVAVLAGDFMFAQSSWYLA- 221
Query: 187 NIAGVSPDRVVRAIAEMCSAMGVEGLVAGEFVDIASE-GKDVSLKELEYIHVHKTAKLLE 245
N+ + V++ I+++ ++ +GE +S DV+L E +KTA L+
Sbjct: 222 NLDNL---EVIKLISQV-----IKDFASGEIKQASSLFDCDVTLDEYLLKSYYKTASLIA 273
Query: 246 AAVVCGAVIGGGNAIEVERVRNYARCIGLLFQVVDDILDVTKSSEELGKTAGKDLASGKA 305
A+ A+ G ++ E++ Y + +GL FQVVDDILD T+S+E+LGK AG DLA G
Sbjct: 274 ASTKSAAIFSGVDSSVKEQMYEYGKNLGLAFQVVDDILDFTQSTEQLGKPAGSDLAKGNL 333
Query: 306 TYPKLMGIEN 315
T P + +E
Sbjct: 334 TAPVIFALEK 343
>gnl|CDD|182813 PRK10888, PRK10888, octaprenyl diphosphate synthase; Provisional.
Length = 323
Score = 114 bits (288), Expect = 3e-29
Identities = 70/236 (29%), Positives = 122/236 (51%), Gaps = 14/236 (5%)
Query: 97 YSLLAGGKRVRPLLCIASCELVGGDESWAMPAACALEMIHTMSLIHDDLPFLDNDERRRS 156
Y + GGKR+RP++ + + VG + + A +E IHT +L+HDD+ +D + RR
Sbjct: 38 YIISGGGKRIRPMIAVLAARAVGYQGNAHVTIAALIEFIHTATLLHDDV--VDESDMRRG 95
Query: 157 KPASHEVFGESTAILAGDALLSLALEHVAVNIAGVSPDRVVRAIAEMCSAMGVEGLVAGE 216
K ++ FG + ++L GD + + A + + + ++ + M A+ V + GE
Sbjct: 96 KATANAAFGNAASVLVGDFIYTRAFQMM-------TSLGSLKVLEVMSEAVNV--IAEGE 146
Query: 217 FVDIASEGKDVSLKELEYIHV--HKTAKLLEAAVVCGAVIGGGNAIEVERVRNYARCIGL 274
+ + + D + E Y+ V KTA+L EAA C ++ G + + +++Y R +G
Sbjct: 147 VLQLMN-VNDPDITEENYMRVIYSKTARLFEAAAQCSGILAGCTPEQEKGLQDYGRYLGT 205
Query: 275 LFQVVDDILDVTKSSEELGKTAGKDLASGKATYPKLMGIENAKSFAGELLGQAIEE 330
FQ++DD+LD + E LGK G DL GK T P L + + ++ AIE+
Sbjct: 206 AFQLIDDLLDYSADGETLGKNVGDDLNEGKPTLPLLHAMHHGTPEQAAMIRTAIEQ 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 = 114 bits (287), Expect = 3e-29
Identities = 80/246 (32%), Positives = 126/246 (51%), Gaps = 17/246 (6%)
Query: 73 EQVNKALDEAVVLQPPVKIHKAMRYSLLAGGKRVRPLLCIASCELVGGDESWAMPAACAL 132
+ + K L++AV + PV + +A + L AGGKR+RP+ + + + D A AL
Sbjct: 14 DSIEKELEKAVQAEHPV-LSEASLHLLEAGGKRIRPVFVLLAGKFGDYDLDAIKHVAVAL 72
Query: 133 EMIHTMSLIHDDLPFLDNDERRRSKPASHEVFGESTAILAGDALLSLALEHVAVNIAGVS 192
E+IH SL+HDD+ +D+ + RR +P +G A+ GD L + +LE + I
Sbjct: 73 ELIHMASLVHDDV--IDDADLRRGRPTIKSKWGNRIAMYTGDYLFAKSLETMT-EIKDPR 129
Query: 193 PDRVV-RAIAEMCSAMGVEGLVAGEFVDIASEGK-DVSLKE-LEYIHVHKTAKLLEAAVV 249
+++ I E+C GE I + D +L+ L I KTA L+ A+
Sbjct: 130 AHQILSHTIVEVCR---------GEIEQIKDKYNFDQNLRTYLRRIK-RKTALLIAASCQ 179
Query: 250 CGAVIGGGNAIEVERVRNYARCIGLLFQVVDDILDVTKSSEELGKTAGKDLASGKATYPK 309
GA+ G N V+++ + +G+ +Q+ DDILD + EELGK AG DL G T P
Sbjct: 180 LGAIASGANEAIVKKLYWFGYYVGMSYQITDDILDFVGTEEELGKPAGGDLLQGNVTLPV 239
Query: 310 LMGIEN 315
L +E+
Sbjct: 240 LYAMED 245
>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 = 114 bits (286), Expect = 5e-29
Identities = 77/220 (35%), Positives = 108/220 (49%), Gaps = 17/220 (7%)
Query: 101 AGGKRVRP---LLCIASCELVGGDESWAMPAACALEMIHTMSLIHDDLPFLDNDERRRSK 157
AGGKR+RP LL + A EMIHT SL+HDD+ +D + RR
Sbjct: 42 AGGKRLRPAIVLLVSRATAEQQELTPRHRRLAEITEMIHTASLVHDDV--IDESDTRRGI 99
Query: 158 PASHEVFGESTAILAGDALLSLALEHVAVNIAGVSPDRVVRAIAEMCSAMGVEGLVAGEF 217
H +FG A+LAGD L + A ++A N+ + VV+ I+++ + GE
Sbjct: 100 ETVHSLFGTRVAVLAGDFLFAQASWYLA-NLENL---EVVKLISKVITDFA-----EGEI 150
Query: 218 VDIASEGKDVSLKELEYIH--VHKTAKLLEAAVVCGAVIGGGNAIEVERVRNYARCIGLL 275
D L +Y+ +KTA L+ A+ AV+ + + Y + +GL
Sbjct: 151 KQ-GLNQFDSDLSLEDYLEKSFYKTASLVAASSKAAAVLSDVPSQVANDLYEYGKHLGLA 209
Query: 276 FQVVDDILDVTKSSEELGKTAGKDLASGKATYPKLMGIEN 315
FQVVDDILD T S+E+LGK AG DL G T P L +E
Sbjct: 210 FQVVDDILDFTGSTEQLGKPAGSDLMKGNLTAPVLFALEE 249
>gnl|CDD|178478 PLN02890, PLN02890, geranyl diphosphate synthase.
Length = 422
Score = 86.9 bits (215), Expect = 6e-19
Identities = 65/185 (35%), Positives = 94/185 (50%), Gaps = 16/185 (8%)
Query: 133 EMIHTMSLIHDDLPFLDNDERRRSKPASHEVFGESTAILAGDALLSLALEHVAVNIAGVS 192
EMIH SL+HDD+ LD+ + RR + + V G ++LAGD LLS A V +A +
Sbjct: 171 EMIHVASLLHDDV--LDDADTRRGVGSLNVVMGNKLSVLAGDFLLSRA----CVALAALK 224
Query: 193 PDRVVRAIAEMCSAMGVEGLVAGEFVDIASEGKDVSLKELEYI---HVHKTAKLLEAAVV 249
VV +A VE LV GE + I S + + ++Y +KTA L+ +
Sbjct: 225 NTEVVSLLA-----TAVEHLVTGETMQITSSRE--QRRSMDYYMQKTYYKTASLISNSCK 277
Query: 250 CGAVIGGGNAIEVERVRNYARCIGLLFQVVDDILDVTKSSEELGKTAGKDLASGKATYPK 309
A++ G A Y R +GL FQ++DD+LD T +S LGK + D+ G T P
Sbjct: 278 AVAILAGQTAEVAVLAFEYGRNLGLAFQLIDDVLDFTGTSASLGKGSLSDIRHGVITAPI 337
Query: 310 LMGIE 314
L +E
Sbjct: 338 LFAME 342
>gnl|CDD|239459 cd03343, cpn60, cpn60 chaperonin family. Chaperonins are involved
in productive folding of proteins. They share a common
general morphology, a double toroid of 2 stacked rings.
Archaeal cpn60 (thermosome), together with TF55 from
thermophilic bacteria and the eukaryotic cytosol
chaperonin (CTT), belong to the type II group of
chaperonins. Cpn60 consists of two stacked octameric
rings, which are composed of one or two different
subunits. Their common function is to sequester
nonnative proteins inside their central cavity and
promote folding by using energy derived from ATP
hydrolysis.
Length = 517
Score = 29.9 bits (68), Expect = 2.0
Identities = 21/81 (25%), Positives = 37/81 (45%), Gaps = 27/81 (33%)
Query: 251 GAVIGGGNAIEVE---RVRNYARCIGLLFQV------------------------VDDIL 283
G V+ GG A+E+E R+R YAR +G Q+ +D ++
Sbjct: 397 GKVVAGGGAVEIELAKRLREYARSVGGREQLAVEAFADALEEIPRTLAENAGLDPIDTLV 456
Query: 284 DVTKSSEELGKTAGKDLASGK 304
++ + E+ K AG D+ +G+
Sbjct: 457 ELRAAHEKGNKNAGLDVYTGE 477
>gnl|CDD|234401 TIGR03925, T7SS_EccC_b, type VII secretion protein EccCb. This
model represents the C-terminal domain or EccCb subunit
of the type VII secretion protein EccC as found in the
Actinobacteria. Type VII secretion is defined more
broadly as including secretion systems for ESAT-6-like
proteins in the Firmicutes as well as in the
Actinobacteria, but this family does not show close
homologs in the Firmicutes [Protein fate, Protein and
peptide secretion and trafficking].
Length = 566
Score = 29.9 bits (68), Expect = 2.4
Identities = 16/40 (40%), Positives = 22/40 (55%), Gaps = 3/40 (7%)
Query: 171 LAGDALLSLA-LEHVAVNIAG-VSPDRVVRAIAEMCSAMG 208
G L SLA L HV +AG + P+RV R +AE+ +
Sbjct: 119 FGGGTLASLADLPHVG-GVAGRLDPERVRRTVAEVEGLLR 157
>gnl|CDD|215487 PLN02900, PLN02900, alanyl-tRNA synthetase.
Length = 936
Score = 30.0 bits (68), Expect = 2.4
Identities = 24/84 (28%), Positives = 33/84 (39%), Gaps = 18/84 (21%)
Query: 152 ERRRSKPASHEVFGESTAILAGDALLSLALEHVAVN------IAGVSPDRVVRAIAEMCS 205
R RS+ A+H G LA +A L + VA + VV+AI
Sbjct: 453 ARERSR-AAHLKAGGGAIELAAEATSWLQKQGVAATDDFLKYDWLSDHEAVVKAI----- 506
Query: 206 AMGVEGLVAGEFVDIASEGKDVSL 229
L G FV+ SEG +V +
Sbjct: 507 ------LTGGGFVESVSEGDEVGI 524
>gnl|CDD|233823 TIGR02339, thermosome_arch, thermosome, various subunits, archaeal.
Thermosome is the name given to the archaeal rather
than eukaryotic form of the group II chaperonin
(counterpart to the group I chaperonin, GroEL/GroES, in
bacterial), a torroidal, ATP-dependent molecular
chaperone that assists in the folding or refolding of
nascent or denatured proteins. Various homologous
subunits, one to five per archaeal genome, may be
designated alpha, beta, etc., but phylogenetic analysis
does not show distinct alpha subunit and beta subunit
lineages traceable to ancient paralogs [Protein fate,
Protein folding and stabilization].
Length = 519
Score = 29.7 bits (67), Expect = 2.8
Identities = 14/26 (53%), Positives = 19/26 (73%), Gaps = 3/26 (11%)
Query: 251 GAVIGGGNAIEVE---RVRNYARCIG 273
G V+ GG A+E+E R+R+YAR IG
Sbjct: 400 GKVVAGGGAVEIEIALRLRSYARKIG 425
>gnl|CDD|201390 pfam00682, HMGL-like, HMGL-like. This family contains a diverse
set of enzymes. These include various aldolases and a
region of pyruvate carboxylase.
Length = 236
Score = 28.8 bits (65), Expect = 3.3
Identities = 18/69 (26%), Positives = 23/69 (33%), Gaps = 10/69 (14%)
Query: 196 VVRAIAEMCSAMGVEGLVAG---------EFV-DIASEGKDVSLKELEYIHVHKTAKLLE 245
AIA GV+ + G E V IA K ++ L H +E
Sbjct: 14 EKLAIARALDEAGVDEIEVGFPFMSPTDFESVRAIAEVLKKAKIQALLRPVEHDIDAAVE 73
Query: 246 AAVVCGAVI 254
AA GA
Sbjct: 74 AAKGAGADR 82
>gnl|CDD|179896 PRK04940, PRK04940, hypothetical protein; Provisional.
Length = 180
Score = 28.4 bits (64), Expect = 4.5
Identities = 11/31 (35%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 264 RVRNYARCIGLLFQVVDDILDVTKSSEELGK 294
R +N RC+ +L D++LD +++EEL
Sbjct: 120 REKNRDRCLVIL-SRNDEVLDSQRTAEELHP 149
>gnl|CDD|204301 pfam09735, Nckap1, Membrane-associated apoptosis protein.
Expression of this protein was found to be markedly
reduced in patients with Alzheimer's disease. It is
involved in the regulation of actin polymerisation in
the brain as part of a WAVE2 signalling complex.
Length = 1118
Score = 28.5 bits (64), Expect = 6.7
Identities = 17/64 (26%), Positives = 23/64 (35%), Gaps = 15/64 (23%)
Query: 170 ILAGDALLSLALEHV---------------AVNIAGVSPDRVVRAIAEMCSAMGVEGLVA 214
IL+ L AL V ++ V+ +V+ I EM SA GV V
Sbjct: 908 ILSFRDLAQEALRAVLESHVPFLMSSIEDLKEHVPEVTDKKVILRIFEMASAAGVPCDVD 967
Query: 215 GEFV 218
V
Sbjct: 968 PALV 971
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
0.319 0.134 0.383
Gapped
Lambda K H
0.267 0.0672 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,354,918
Number of extensions: 1824473
Number of successful extensions: 1792
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1754
Number of HSP's successfully gapped: 37
Length of query: 354
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 256
Effective length of database: 6,590,910
Effective search space: 1687272960
Effective search space used: 1687272960
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: 59 (26.6 bits)