RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 038854
(353 letters)
>gnl|CDD|215873 pfam00348, polyprenyl_synt, Polyprenyl synthetase.
Length = 260
Score = 267 bits (685), Expect = 5e-89
Identities = 116/256 (45%), Positives = 153/256 (59%), Gaps = 11/256 (4%)
Query: 96 IHESMRYSLLAGGKRVRPVLCLAACDLVGGHESMAMPAACSIEMIHTMSLIHDDLPCMDN 155
+ +M Y LLAGGKR+RP+L + A +G + AC+IEMIHT SL+HDDL MDN
Sbjct: 1 LLAAMLYYLLAGGKRIRPLLVVLAARALGVEPETLLYLACAIEMIHTASLVHDDL--MDN 58
Query: 156 DPLRRGKPTNHTIYGEDVAVLAGDALLAYAFEHIAVCTKGVSPARIVRAIAELAKYIGAD 215
LRRGKPT H +GE A+LAGDALL+ AF+ +A+ V P I+ELA +GA
Sbjct: 59 SDLRRGKPTCHKKFGEAGAILAGDALLSRAFQLLAL-LGHVRPEPKYILISELANAVGAQ 117
Query: 216 GLVAGQ------AEKDLGIEHLEFIHEHKTAALLEAAVVLGAILGGGTDNEVEKLRTFAR 269
G V GQ KD+ +E I +KTAAL A+V LGAI+ G + + + L F R
Sbjct: 118 GEV-GQLMDLETEGKDITLEEYLRIVSYKTAALFYASVQLGAIVAGADEEDEKDLYDFGR 176
Query: 270 CIGLLFQVVDDILDLTKSSKELGKTAGKDLVADKLTYPKLLGIEESKKLADKLNKDAQQQ 329
+GL FQ+ DDILDLT ++ELGK G DL K T P LL +E +++ KL ++A +Q
Sbjct: 177 DLGLAFQIQDDILDLTGDTEELGKPVGTDLQEGKSTLPVLLALEGAREEQRKLLREAYEQ 236
Query: 330 -LSEFDQEKAVPLIAL 344
LSE + AL
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 = 267 bits (684), Expect = 1e-88
Identities = 112/265 (42%), Positives = 146/265 (55%), Gaps = 20/265 (7%)
Query: 96 IHESMRYSLLAGGKRVRPVLCLAACDLVGGHESM-AMPAACSIEMIHTMSLIHDDLPCMD 154
+ E++RY LLAGGKR+RP+L L A +GG E A+ A +IE++HT SL+HDD+ MD
Sbjct: 6 LREALRYLLLAGGKRLRPLLVLLAARALGGPELEAALRLAAAIELLHTASLVHDDV--MD 63
Query: 155 NDPLRRGKPTNHTIYGEDVAVLAGDALLAYAFEHIAVCTKGVSPARIVRAIAELAKYIGA 214
N LRRGKPT H ++G A+LAGD LLA AFE +A P R + +E
Sbjct: 64 NSDLRRGKPTVHKVFGNATAILAGDYLLARAFELLARLGNPYYP-RALELFSEAIL---- 118
Query: 215 DGLVAGQA-------EKDLGIEHLEFIHEHKTAALLEAAVVLGAILGGGTDNEVEKLRTF 267
LV GQ + D+ E I KTAAL AA +LGA+L G + E E L+ F
Sbjct: 119 -ELVEGQLLDLLSEYDTDVTEEEYLRIIRLKTAALFAAAPLLGALLAGADEEEAEALKRF 177
Query: 268 ARCIGLLFQVVDDILDLTKSSKELGKTAGKDLVADKLTYPKLLGIEESKKLADKLNKDAQ 327
R +GL FQ+ DDILDL + LGK G DL K T P LL + E LA + + A
Sbjct: 178 GRNLGLAFQIQDDILDLFGDPETLGKPVGSDLREGKCTLPVLLALRE---LAREYEEKAL 234
Query: 328 QQLSEF-DQEKAVPLIALANYIAYR 351
+ L + L ALA++I R
Sbjct: 235 EALKALPESPAREALRALADFILER 259
>gnl|CDD|223220 COG0142, IspA, Geranylgeranyl pyrophosphate synthase [Coenzyme
metabolism].
Length = 322
Score = 265 bits (680), Expect = 2e-87
Identities = 122/296 (41%), Positives = 170/296 (57%), Gaps = 22/296 (7%)
Query: 68 DFKSYMIQKASTVNQALDAAVSLKDPVKIHESMRYSLLAGGKRVRPVLCLAACDLVGGHE 127
D + ++++ + + + L +S DP + E+MRY LLAGGKR+RP+L L A + +G
Sbjct: 2 DLLALLLKRLARIEELLSELLSGSDPELLLEAMRYLLLAGGKRLRPLLVLLAAEALGIDL 61
Query: 128 SM----AMPAACSIEMIHTMSLIHDDLPCMDNDPLRRGKPTNHTIYGEDVAVLAGDALLA 183
A+ A +IE+IHT SLIHDDL MD+D LRRGKPT H +GE A+LAGDALLA
Sbjct: 62 ETGGNDALDLAAAIELIHTASLIHDDL--MDDDDLRRGKPTVHAKFGEATAILAGDALLA 119
Query: 184 YAFEHIAVCTKGVSPARIVRAIAELAKYIGADGLVAGQA------EKDLGIEHLEFIHEH 237
AFE ++ G ++A+AE +GL GQA K + +E + E
Sbjct: 120 AAFELLS--KLGSEALEAIKALAE-----AINGLCGGQALDLAFENKPVTLEEYLRVIEL 172
Query: 238 KTAALLEAAVVLGAILGGGTDNEVEKLRTFARCIGLLFQVVDDILDLTKSSKELGKTAGK 297
KTAAL AA VLGAIL G + +E L + R +GL FQ+ DDILD+T +ELGK G
Sbjct: 173 KTAALFAAAAVLGAILAGADEELLEALEDYGRNLGLAFQIQDDILDITGDEEELGKPVGS 232
Query: 298 DLVADKLTYPKLLGIEESKKLADKLNKDAQQQLSEFDQEKAVPLIALANYIAYRQN 353
DL K T P LL +E++ + KL + + E E+A+ L+ + I Y +N
Sbjct: 233 DLKEGKPTLPVLLALEKANE-DQKLLRILLEGGGEV--EEALELLRKSGAIEYAKN 285
>gnl|CDD|164542 CHL00151, preA, prenyl transferase; Reviewed.
Length = 323
Score = 217 bits (554), Expect = 2e-68
Identities = 92/313 (29%), Positives = 143/313 (45%), Gaps = 46/313 (14%)
Query: 80 VNQALDAAVSLKDPVKIHESMRYSLLAGGKRVRPVLCLAACDLVGGHESMAMP---AACS 136
+ L + P+ ++ + ++ AGGKR+RP + L GG+ + A
Sbjct: 18 LEDNLKKLIGSGHPI-LYAAAKHLFSAGGKRIRPAIVLLVAKATGGNMEIKTSQQRLAEI 76
Query: 137 IEMIHTMSLIHDDLPCMDNDPLRRGKPTNHTIYGEDVAVLAGDALLAYAFEHIAVCTKGV 196
E+IHT SL+HDD+ +D +RRG PT H I+G +AVLAGD L A + ++A
Sbjct: 77 TEIIHTASLVHDDV--IDECSIRRGIPTVHKIFGTKIAVLAGDFLFAQSSWYLANLNNLE 134
Query: 197 SPARIVRAIAELAKYIGADGLVAGQAEKDLGIEHLEFIHE--HKTAALLEAAVVLGAILG 254
I + I + A+ GLV + D + L +I + +KTA+L+ A+ A+L
Sbjct: 135 VVKLISKVITDFAEGEIRQGLV----QFDTTLSILNYIEKSFYKTASLIAASCKAAALLS 190
Query: 255 GGTDNEVEKLRTFARCIGLLFQVVDDILDLTKSSKELGKTAGKDLVADKLTYPKLLGIEE 314
+ + + + +GL FQ++DD+LD+T S++ LGK G DL LT P L + +
Sbjct: 191 DADEKDHNDFYLYGKHLGLAFQIIDDVLDITSSTESLGKPIGSDLKNGNLTAPVLFALTQ 250
Query: 315 SKKLADKL------NKDAQQQLS----------------EFDQ------------EKAVP 340
+ KLA + KD Q L E Q
Sbjct: 251 NSKLAKLIEREFCETKDISQALQIIKETNGIEKAKDLALEHMQAAIQCLKFLPPSSAKDS 310
Query: 341 LIALANYIAYRQN 353
LI +AN+I R N
Sbjct: 311 LIEIANFIINRLN 323
>gnl|CDD|182567 PRK10581, PRK10581, geranyltranstransferase; Provisional.
Length = 299
Score = 195 bits (498), Expect = 2e-60
Identities = 117/267 (43%), Positives = 148/267 (55%), Gaps = 12/267 (4%)
Query: 98 ESMRYSLLAGGKRVRPVLCLAACDLVG-GHESMAMPAACSIEMIHTMSLIHDDLPCMDND 156
E+M+Y L GGKR+RP L A + G ++ PAA ++E IH SLIHDDLP MD+D
Sbjct: 34 EAMQYGALLGGKRLRPFLVYATGQMFGVSTNTLDAPAA-AVECIHAYSLIHDDLPAMDDD 92
Query: 157 PLRRGKPTNHTIYGEDVAVLAGDALLAYAFEHIA-VCTKGVSPARIVRAIAELAKYIGAD 215
LRRG PT H +GE A+LAGDAL AF ++ VS + I+ELA G
Sbjct: 93 DLRRGLPTCHVKFGEANAILAGDALQTLAFSILSDAPMPEVSDRDRISMISELASASGIA 152
Query: 216 GLVAGQA------EKDLGIEHLEFIHEHKTAALLEAAVVLGAILGGGTDNEV-EKLRTFA 268
G+ GQA K + ++ LE IH HKT AL+ AAV LGA+ G L +A
Sbjct: 153 GMCGGQALDLEAEGKQVPLDALERIHRHKTGALIRAAVRLGALSAGDKGRRALPVLDRYA 212
Query: 269 RCIGLLFQVVDDILDLTKSSKELGKTAGKDLVADKLTYPKLLGIEESKKLADKLNKDAQQ 328
IGL FQV DDILD+ + LGK G D K TYP LLG+E+++K A L DA+Q
Sbjct: 213 ESIGLAFQVQDDILDVVGDTATLGKRQGADQQLGKSTYPALLGLEQARKKARDLIDDARQ 272
Query: 329 QLSEFDQEKA--VPLIALANYIAYRQN 353
L + + L ALANYI R
Sbjct: 273 SLDQLAAQSLDTSALEALANYIIQRDK 299
>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 = 189 bits (483), Expect = 6e-59
Identities = 82/249 (32%), Positives = 128/249 (51%), Gaps = 21/249 (8%)
Query: 111 VRPVLCLAACDLVGGHESMAMPAACSIEMIHTMSLIHDDLPCMDNDPLRRGKPTNHTI-Y 169
RP+L L +GG A+ A ++E++H SL+HDD+ +D+ LRRGKPT H +
Sbjct: 1 SRPLLVLLLARALGGDLEAALRLAAAVELLHAASLVHDDI--VDDSDLRRGKPTAHLRRF 58
Query: 170 GEDVAVLAGDALLAYAFEHIAVCTKGVSPARIVRAIAELAKYIGADGLVAGQA------- 222
G +A+LAGD LLA AF+ +A R + AE L+ GQA
Sbjct: 59 GNALAILAGDYLLARAFQLLARLGY----PRALELFAE-----ALRELLEGQALDLEFER 109
Query: 223 EKDLGIEHLEFIHEHKTAALLEAAVVLGAILGGGTDNEVEKLRTFARCIGLLFQVVDDIL 282
+ ++ +KTA L+ +LGA L G D + E L+ + R +GL FQ+ DD+L
Sbjct: 110 DTYETLDEYLEYCRYKTAGLVGLLCLLGAGLSGADDEQAEALKDYGRALGLAFQLTDDLL 169
Query: 283 DLTKSSKELGKTAGKDLVADKLTYPKLLGIEESKKLADKLNKDAQQQLSEFDQEKAVPLI 342
D+ ++ELGK G DL ++T P +L E + + A++ + + + LI
Sbjct: 170 DVFGDAEELGK-VGSDLREGRITLPVILARERAAEYAEEAYAALEALPPSLPRARR-ALI 227
Query: 343 ALANYIAYR 351
ALA+++ R
Sbjct: 228 ALADFLYRR 236
>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 = 130 bits (330), Expect = 2e-35
Identities = 90/267 (33%), Positives = 140/267 (52%), Gaps = 14/267 (5%)
Query: 79 TVNQALDAAVSLKDPVKIHESMRYSLLAGGKRVRPVLCLAACDLVGGHESMAMP-AACSI 137
++ + L+ AV + PV + E+ + L AGGKR+RPV L A G ++ A+ A ++
Sbjct: 15 SIEKELEKAVQAEHPV-LSEASLHLLEAGGKRIRPVFVLLAGKF-GDYDLDAIKHVAVAL 72
Query: 138 EMIHTMSLIHDDLPCMDNDPLRRGKPTNHTIYGEDVAVLAGDALLAYAFEHIAVCTKGVS 197
E+IH SL+HDD+ +D+ LRRG+PT + +G +A+ GD L A + E + +
Sbjct: 73 ELIHMASLVHDDV--IDDADLRRGRPTIKSKWGNRIAMYTGDYLFAKSLETMTEIKDPRA 130
Query: 198 PARIVRAIAELAKYIGADGLVAGQAEKDLGIE-HLEFIHEHKTAALLEAAVVLGAILGGG 256
+ I E+ G + + D + +L I + KTA L+ A+ LGAI G
Sbjct: 131 HQILSHTIVEVC--RGEIEQIKDKYNFDQNLRTYLRRI-KRKTALLIAASCQLGAIASGA 187
Query: 257 TDNEVEKLRTFARCIGLLFQVVDDILDLTKSSKELGKTAGKDLVADKLTYPKLLGIEESK 316
+ V+KL F +G+ +Q+ DDILD + +ELGK AG DL+ +T P L +E+
Sbjct: 188 NEAIVKKLYWFGYYVGMSYQITDDILDFVGTEEELGKPAGGDLLQGNVTLPVLYAMED-- 245
Query: 317 KLADKLNKDAQQQLSEFDQEKAVPLIA 343
L K +Q L E E+ PLI
Sbjct: 246 ---PFLKKRIEQVLEETTAEEMEPLIE 269
>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 (320), Expect = 9e-35
Identities = 75/262 (28%), Positives = 113/262 (43%), Gaps = 45/262 (17%)
Query: 112 RPVLCLAACDLVGGHESMAMPAACSIEMIHTMSLIHDDLPCMDNDPLRRGKPTNH---TI 168
RP+ L + A ++E +H SL+HDD+ +D+ RRG PT H I
Sbjct: 2 RPLAVLLEPE--------ASRLRAAVEKLHAASLVHDDI--VDDSGTRRGLPTAHLAVAI 51
Query: 169 YGEDVAVLAGDALLAYAFEHIAVCTKGVSPARIVRAIAELAKYIGADGLVAGQAEKDLGI 228
G A+LAGD LLA AFE +A + + A+ +L + D + + E +
Sbjct: 52 DGLPEAILAGDLLLADAFEELAREGSPEALEILAEALLDLLEGQLLD--LKWRREYVPTL 109
Query: 229 EHLEFIHEHKTAALLEAAVVLGAILGGGTDNEVEKLRTFARCIGLLFQVVDDILDLTKSS 288
E +KTA L+ A +LGA L GG +E LR R +GL FQ+ +D+LD +
Sbjct: 110 EEYLEYCRYKTAGLVGALCLLGAGLSGGEAELLEALRKLGRALGLAFQLTNDLLDYEGDA 169
Query: 289 KELGKTAGKDLVADKLTYPKLL------------------GIEESKKLADKLNKDAQQQL 330
+ K T P L +EE+ + KL ++A ++L
Sbjct: 170 ERG---------EGKCTLPVLYALEYGVPAEDLLLVEKSGSLEEALEELAKLAEEALKEL 220
Query: 331 -SEFDQEKAVP--LIALANYIA 349
VP L+ALA +
Sbjct: 221 NELILSLPDVPRALLALALNLY 242
>gnl|CDD|215462 PLN02857, PLN02857, octaprenyl-diphosphate synthase.
Length = 416
Score = 130 bits (328), Expect = 2e-34
Identities = 108/360 (30%), Positives = 164/360 (45%), Gaps = 53/360 (14%)
Query: 1 MSCVNLAAWTQT--CSIFNQASSRR----SNKTQPFRTLKTLPVSLASQRPRRPVSISAV 54
MSC N+ T C + ASSRR + T ++ S R V
Sbjct: 3 MSCRNIDLGTSLVACGCSSNASSRRRVVRNGATPVCKSCSRSYASSLVTSRRDIGRCRVV 62
Query: 55 QTLEENPA-------PSPTFDFKSYMIQKAS-------------TVNQALDAAVSLKDPV 94
E P+ D K+ + S +N L + V ++PV
Sbjct: 63 SPSPETSLVNGIGQGPTVALDLKAESKEPISLSELFEPVADDLQQLNDNLQSIVGAENPV 122
Query: 95 KIHESMRYSLLAGGKRVRPVLCL----AACDLVG------GHESMAMPAACSIEMIHTMS 144
+ + + AGGKR+RP L A +L G H +A EMIHT S
Sbjct: 123 LMSAAEQI-FGAGGKRMRPALVFLVSRATAELAGLKELTTEHRRLAE----ITEMIHTAS 177
Query: 145 LIHDDLPCMDNDPLRRGKPTNHTIYGEDVAVLAGDALLAYAFEHIAVCTKGVSPARIVRA 204
LIHDD+ +D +RRGK T H +YG VAVLAGD + A + ++A + +++
Sbjct: 178 LIHDDV--LDESDMRRGKETVHQLYGTRVAVLAGDFMFAQSSWYLA----NLDNLEVIKL 231
Query: 205 IAELAKYIGADGLVAGQAEK----DLGIEHLEFIHEHKTAALLEAAVVLGAILGGGTDNE 260
I+++ K A G + QA D+ ++ +KTA+L+ A+ AI G +
Sbjct: 232 ISQVIKDF-ASGEIK-QASSLFDCDVTLDEYLLKSYYKTASLIAASTKSAAIFSGVDSSV 289
Query: 261 VEKLRTFARCIGLLFQVVDDILDLTKSSKELGKTAGKDLVADKLTYPKLLGIEESKKLAD 320
E++ + + +GL FQVVDDILD T+S+++LGK AG DL LT P + +E+ +L +
Sbjct: 290 KEQMYEYGKNLGLAFQVVDDILDFTQSTEQLGKPAGSDLAKGNLTAPVIFALEKEPELRE 349
>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 = 124 bits (314), Expect = 5e-33
Identities = 84/246 (34%), Positives = 131/246 (53%), Gaps = 22/246 (8%)
Query: 106 AGGKRVRPVLCL-------AACDLVGGHESMAMPAACSIEMIHTMSLIHDDLPCMDNDPL 158
AGGKR+RP + L +L H +A EMIHT SL+HDD+ +D
Sbjct: 42 AGGKRLRPAIVLLVSRATAEQQELTPRHRRLAE----ITEMIHTASLVHDDV--IDESDT 95
Query: 159 RRGKPTNHTIYGEDVAVLAGDALLAYAFEHIAVCTKGVSPARIVRAIAELAKYIGADGLV 218
RRG T H+++G VAVLAGD L A A ++A + +V+ I+++ +
Sbjct: 96 RRGIETVHSLFGTRVAVLAGDFLFAQASWYLA----NLENLEVVKLISKVITDFAEGEIK 151
Query: 219 AGQAEKDLGIEHLEFIHE--HKTAALLEAAVVLGAILGGGTDNEVEKLRTFARCIGLLFQ 276
G + D + +++ + +KTA+L+ A+ A+L L + + +GL FQ
Sbjct: 152 QGLNQFDSDLSLEDYLEKSFYKTASLVAASSKAAAVLSDVPSQVANDLYEYGKHLGLAFQ 211
Query: 277 VVDDILDLTKSSKELGKTAGKDLVADKLTYPKLLGIEESKKLADKLNKDAQQQLSEFDQE 336
VVDDILD T S+++LGK AG DL+ LT P L +EE KL++ + ++ Q + D E
Sbjct: 212 VVDDILDFTGSTEQLGKPAGSDLMKGNLTAPVLFALEEEPKLSELIEREFSQ---KGDLE 268
Query: 337 KAVPLI 342
+A+ L+
Sbjct: 269 QALSLV 274
>gnl|CDD|182813 PRK10888, PRK10888, octaprenyl diphosphate synthase; Provisional.
Length = 323
Score = 106 bits (265), Expect = 4e-26
Identities = 72/221 (32%), Positives = 113/221 (51%), Gaps = 10/221 (4%)
Query: 92 DPVKIHESMRYSLLAGGKRVRPVLCLAACDLVGGHESMAMPAACSIEMIHTMSLIHDDLP 151
D I++ Y + GGKR+RP++ + A VG + + A IE IHT +L+HDD+
Sbjct: 28 DVQLINQLGYYIISGGGKRIRPMIAVLAARAVGYQGNAHVTIAALIEFIHTATLLHDDV- 86
Query: 152 CMDNDPLRRGKPTNHTIYGEDVAVLAGDALLAYAFEHIAVCTKGVSPARIVRAIAELAKY 211
+D +RRGK T + +G +VL GD + AF+ + + +++ ++E
Sbjct: 87 -VDESDMRRGKATANAAFGNAASVLVGDFIYTRAFQMMT----SLGSLKVLEVMSEAVNV 141
Query: 212 IGADGLV---AGQAEKDLGIEHLEFIHEHKTAALLEAAVVLGAILGGGTDNEVEKLRTFA 268
I A+G V + D+ E+ + KTA L EAA IL G T + + L+ +
Sbjct: 142 I-AEGEVLQLMNVNDPDITEENYMRVIYSKTARLFEAAAQCSGILAGCTPEQEKGLQDYG 200
Query: 269 RCIGLLFQVVDDILDLTKSSKELGKTAGKDLVADKLTYPKL 309
R +G FQ++DD+LD + + LGK G DL K T P L
Sbjct: 201 RYLGTAFQLIDDLLDYSADGETLGKNVGDDLNEGKPTLPLL 241
>gnl|CDD|178478 PLN02890, PLN02890, geranyl diphosphate synthase.
Length = 422
Score = 78.4 bits (193), Expect = 4e-16
Identities = 60/184 (32%), Positives = 96/184 (52%), Gaps = 10/184 (5%)
Query: 138 EMIHTMSLIHDDLPCMDNDPLRRGKPTNHTIYGEDVAVLAGDALLAYAFEHIAVCTKGVS 197
EMIH SL+HDD+ +D+ RRG + + + G ++VLAGD LL+ A V +
Sbjct: 171 EMIHVASLLHDDV--LDDADTRRGVGSLNVVMGNKLSVLAGDFLLSRA----CVALAALK 224
Query: 198 PARIVRAIAELAKYI--GADGLVAGQAEKDLGIEHLEFIHEHKTAALLEAAVVLGAILGG 255
+V +A +++ G + E+ +++ +KTA+L+ + AIL G
Sbjct: 225 NTEVVSLLATAVEHLVTGETMQITSSREQRRSMDYYMQKTYYKTASLISNSCKAVAILAG 284
Query: 256 GTDNEVEKLR-TFARCIGLLFQVVDDILDLTKSSKELGKTAGKDLVADKLTYPKLLGIEE 314
T EV L + R +GL FQ++DD+LD T +S LGK + D+ +T P L +EE
Sbjct: 285 QT-AEVAVLAFEYGRNLGLAFQLIDDVLDFTGTSASLGKGSLSDIRHGVITAPILFAMEE 343
Query: 315 SKKL 318
+L
Sbjct: 344 FPQL 347
>gnl|CDD|236797 PRK10927, PRK10927, essential cell division protein FtsN;
Provisional.
Length = 319
Score = 35.0 bits (80), Expect = 0.044
Identities = 18/78 (23%), Positives = 33/78 (42%), Gaps = 4/78 (5%)
Query: 9 WTQTCSIFNQASSRRSNKTQPFRTLKTLPVSLASQRPRRPVSISAVQTLEENPAPSPTFD 68
+ + Q+ + + Q RT + PV ++ + + Q L + PA + T
Sbjct: 162 LAEQQRLAQQSRTTEQSWQQQTRTSQAAPVQAQPRQSKPASTQQPYQDLLQTPAHT-TAQ 220
Query: 69 FKSYMIQKASTVNQALDA 86
K Q+A+ V +A DA
Sbjct: 221 SKP---QQAAPVTRAADA 235
>gnl|CDD|163651 cd07408, MPP_SA0022_N, Staphylococcus aureus SA0022 and related
proteins, N-terminal metallophosphatase domain. SA0022
is an uncharacterized Staphylococcus aureus UshA-like
protein with two putative domains, an N-terminal
metallophosphatase domain and a C-terminal nucleotidase
domain. SA0022 also contains a putative C-terminal cell
wall anchor domain. The N-terminal metallophosphatase
domain belongs to a large superfamily of distantly
related metallophosphatases (MPPs) that includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). MPPs are functionally
diverse, but all share a conserved domain with an active
site consisting of two metal ions (usually manganese,
iron, or zinc) coordinated with octahedral geometry by a
cage of histidine, aspartate, and asparagine residues.
The conserved domain is a double beta-sheet sandwich
with a di-metal active site made up of residues located
at the C-terminal side of the sheets. This domain is
thought to allow for productive metal coordination.
Length = 257
Score = 30.7 bits (70), Expect = 0.87
Identities = 8/29 (27%), Positives = 14/29 (48%)
Query: 203 RAIAELAKYIGADGLVAGQAEKDLGIEHL 231
I ++ +G D + G E D G++ L
Sbjct: 60 ETIIKIMNAVGYDAVTPGNHEFDYGLDRL 88
>gnl|CDD|203296 pfam05637, Glyco_transf_34, galactosyl transferase GMA12/MNN10
family. This family contains a number of
glycosyltransferase enzymes that contain a DXD motif.
This family includes a number of C. elegans homologues
where the DXD is replaced by DXH. Some members of this
family are included in glycosyltransferase family 34.
Length = 239
Score = 30.0 bits (68), Expect = 1.6
Identities = 13/32 (40%), Positives = 15/32 (46%)
Query: 145 LIHDDLPCMDNDPLRRGKPTNHTIYGEDVAVL 176
L + DPLRR K TN GEDV +
Sbjct: 106 LTLALIKNSPFDPLRRYKRTNLVDDGEDVMFI 137
>gnl|CDD|224600 COG1686, DacC, D-alanyl-D-alanine carboxypeptidase [Cell envelope
biogenesis, outer membrane].
Length = 389
Score = 30.0 bits (68), Expect = 1.7
Identities = 11/29 (37%), Positives = 15/29 (51%)
Query: 245 AAVVLGAILGGGTDNEVEKLRTFARCIGL 273
AAV L L G D V K+ A+ +G+
Sbjct: 130 AAVALAEHLAGSEDAFVAKMNAKAKELGM 158
>gnl|CDD|165317 PHA03018, PHA03018, hypothetical protein; Provisional.
Length = 174
Score = 29.3 bits (65), Expect = 2.2
Identities = 18/80 (22%), Positives = 34/80 (42%), Gaps = 6/80 (7%)
Query: 271 IGLLFQVVD-DILDLTKSSKELGKTA-----GKDLVADKLTYPKLLGIEESKKLADKLNK 324
+F+ +D DI D S ++G K ++ +K+ P E+ K+ +
Sbjct: 29 FNKIFEDIDLDISDYNFDSDDIGLLIININDKKKMLVEKIHIPDKYLDEDKIKIDKLFDN 88
Query: 325 DAQQQLSEFDQEKAVPLIAL 344
D + LSE ++ K I +
Sbjct: 89 DKIKSLSEDEKLKDNIFIEI 108
>gnl|CDD|237582 PRK14011, PRK14011, prefoldin subunit alpha; Provisional.
Length = 144
Score = 29.0 bits (65), Expect = 2.2
Identities = 28/88 (31%), Positives = 38/88 (43%), Gaps = 22/88 (25%)
Query: 251 AILGGGTDNEVEKLRTFARCIGLLFQVVDDILDLTKSSKELGKTAGKDLVADKLTYPKLL 310
AILG G+D +EK V + I D KS +EL KT K K
Sbjct: 72 AILGVGSDIYLEK------------DVSEVIEDFKKSVEELDKT--KKEGNKK------- 110
Query: 311 GIEESKKLADKLNKDAQQQLSEFDQEKA 338
IEE K KL K+ +++ +Q +A
Sbjct: 111 -IEELNKEITKLRKELEKRAQAIEQRQA 137
>gnl|CDD|234232 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. [Cellular
processes, Chemotaxis and motility].
Length = 283
Score = 28.8 bits (65), Expect = 3.6
Identities = 13/40 (32%), Positives = 24/40 (60%), Gaps = 3/40 (7%)
Query: 261 VEKLRTFARCIGLLFQVVDDILDLTKSSKELGKTAGKDLV 300
VE+L+T+A +G+ +V D +L ++ L + KDL+
Sbjct: 241 VEQLKTYAEILGVPVKVARDPKEL---AEALDRLRDKDLI 277
>gnl|CDD|225191 COG2309, AmpS, Leucyl aminopeptidase (aminopeptidase T) [Amino acid
transport and metabolism].
Length = 385
Score = 28.8 bits (65), Expect = 4.3
Identities = 19/72 (26%), Positives = 27/72 (37%), Gaps = 12/72 (16%)
Query: 202 VRAIAELAKYIGADGLVAGQAEKDLGI----------EHLEFIHEHKTAALLEAAVVLGA 251
VR I + A GA V D + E E I E + AA+ EA A
Sbjct: 36 VRLIVKEAYEAGA-RPVK-VCLGDPEVARAVYTLAPDEEFEEIPEWEAAAMEEADANGAA 93
Query: 252 ILGGGTDNEVEK 263
L T+ +++
Sbjct: 94 RLPINTEGLLDE 105
>gnl|CDD|240073 cd04722, TIM_phosphate_binding, TIM barrel proteins share a
structurally conserved phosphate binding motif and in
general share an eight beta/alpha closed barrel
structure. Specific for this family is the conserved
phosphate binding site at the edges of strands 7 and 8.
The phosphate comes either from the substrate, as in the
case of inosine monophosphate dehydrogenase (IMPDH), or
from ribulose-5-phosphate 3-epimerase (RPE) or from
cofactors, like FMN.
Length = 200
Score = 28.3 bits (63), Expect = 4.5
Identities = 23/105 (21%), Positives = 32/105 (30%), Gaps = 1/105 (0%)
Query: 168 IYGEDVAVLAGDALLAYAFEHIAVCTKGVSPARIVRAIAELAKYIGADGLVAGQAEKDLG 227
D + + + V A V A A+ GADG+ A L
Sbjct: 40 EAETDDKEVLKEVAAETDL-PLGVQLAINDAAAAVDIAAAAARAAGADGVEIHGAVGYLA 98
Query: 228 IEHLEFIHEHKTAALLEAAVVLGAILGGGTDNEVEKLRTFARCIG 272
E LE I E + A VV + G E+ +G
Sbjct: 99 REDLELIRELREAVPDVKVVVKLSPTGELAAAAAEEAGVDEVGLG 143
>gnl|CDD|224414 COG1497, COG1497, Predicted transcriptional regulator
[Transcription].
Length = 260
Score = 28.5 bits (64), Expect = 5.1
Identities = 35/127 (27%), Positives = 50/127 (39%), Gaps = 20/127 (15%)
Query: 170 GEDVAVLAGDALLAYAFEHIAVCT-----KGVSPARIVRAIAELAK---YIGADGLVAGQ 221
GEDV + ++ + + +G S + + EL+ I A G A
Sbjct: 141 GEDVGITEIGGMIDVEKGEVTIVKVPGVAEGGSRKVDLDRLKELSASEDIIAAMGTEALV 200
Query: 222 AEKDLGIE-HLEFIHEHKTAALLEAAV----VLGAILGGGTDNEVEKLRTFARCIGLLFQ 276
A + LGIE +EF A +EAAV VL I T + L GL ++
Sbjct: 201 ALRKLGIEPDIEFGTLE---AAIEAAVRGLSVLVVI----TRRMLRYLLRKLEEEGLEYE 253
Query: 277 VVDDILD 283
V D I D
Sbjct: 254 VKDLIKD 260
>gnl|CDD|215319 PLN02585, PLN02585, magnesium protoporphyrin IX methyltransferase.
Length = 315
Score = 28.3 bits (63), Expect = 5.8
Identities = 17/100 (17%), Positives = 31/100 (31%), Gaps = 13/100 (13%)
Query: 12 TCSIFNQASSRRSNKTQPFRTLKTLPVSLASQRPRRPVSISAVQTLEENPAPSPTFDFKS 71
+ + + ++ P S A+ +++A + S TF
Sbjct: 6 SALSASSSVAQFLPPFPNATLFAVPPRSRAA-------TVAAASVADLAGVDSTTF---- 54
Query: 72 YMIQKASTVNQALDAAVSLKDPVKIHESMRYSLLAGGKRV 111
AL AA+SL DP + + + K V
Sbjct: 55 --AVGGGGAVAALAAALSLTDPERRRQLQAEEVGGDDKEV 92
>gnl|CDD|218792 pfam05880, Fiji_64_capsid, Fijivirus 64 kDa capsid protein. This
family consists of several Fijivirus 64 kDa capsid
proteins.
Length = 559
Score = 28.3 bits (63), Expect = 7.0
Identities = 13/31 (41%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 294 TAGKDLVADKLTYPKLLGIEESKKLADKLNK 324
GKDL Y KL G+E++ LA L K
Sbjct: 423 KRGKDLAVKYFDYIKL-GVEKASHLAGVLMK 452
>gnl|CDD|227731 COG5444, COG5444, Uncharacterized conserved protein [Function
unknown].
Length = 565
Score = 28.2 bits (63), Expect = 7.2
Identities = 16/64 (25%), Positives = 22/64 (34%), Gaps = 20/64 (31%)
Query: 278 VDDILDLTKSSKELGKTAGKDLVADKLTYPKLLGIEESKKLADKLNKDAQQQLSEFDQEK 337
V ILDL K E D++ A K KD ++L + DQE
Sbjct: 130 VSHILDLGKLDTED--------FKDEVD------------SARKHAKDTLEKLYKLDQEG 169
Query: 338 AVPL 341
+
Sbjct: 170 MTLM 173
>gnl|CDD|240345 PTZ00287, PTZ00287, 6-phosphofructokinase; Provisional.
Length = 1419
Score = 28.1 bits (62), Expect = 8.5
Identities = 14/31 (45%), Positives = 19/31 (61%)
Query: 274 LFQVVDDILDLTKSSKELGKTAGKDLVADKL 304
L++VV DI D+ + ELGK G L+ D L
Sbjct: 1046 LWRVVQDIADVVCARAELGKNYGTVLIPDAL 1076
>gnl|CDD|224373 COG1456, CdhE, CO dehydrogenase/acetyl-CoA synthase gamma subunit
(corrinoid Fe-S protein) [Energy production and
conversion].
Length = 467
Score = 27.8 bits (62), Expect = 9.9
Identities = 19/67 (28%), Positives = 36/67 (53%), Gaps = 6/67 (8%)
Query: 278 VDDILDLTKSSKELGKTAGKDLVADKLTYPKLLGIEESKKLADKLNKDAQQQLSEFDQEK 337
+DD+ +L + + G KD+V D TYP G++++ + + A + FD++
Sbjct: 216 LDDLKNLAVTYAQAGI---KDIVLDPGTYPGGEGLKDTFDNFVMIRRAA---IEGFDKDF 269
Query: 338 AVPLIAL 344
A P++AL
Sbjct: 270 AYPIMAL 276
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 0.133 0.378
Gapped
Lambda K H
0.267 0.0676 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,873,964
Number of extensions: 1757271
Number of successful extensions: 2088
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2049
Number of HSP's successfully gapped: 48
Length of query: 353
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 255
Effective length of database: 6,590,910
Effective search space: 1680682050
Effective search space used: 1680682050
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: 59 (26.6 bits)