RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 038404
(287 letters)
>gnl|CDD|215873 pfam00348, polyprenyl_synt, Polyprenyl synthetase.
Length = 260
Score = 280 bits (718), Expect = 5e-95
Identities = 117/260 (45%), Positives = 164/260 (63%), Gaps = 4/260 (1%)
Query: 24 IHEAMRYSLLAGGKRVRPVLCIASCELVGGDESSAMPVACALEMIHTMSLVHDDLPCMDN 83
+ AM Y LLAGGKR+RP+L + + +G + + + +ACA+EMIHT SLVHDDL MDN
Sbjct: 1 LLAAMLYYLLAGGKRIRPLLVVLAARALGVEPETLLYLACAIEMIHTASLVHDDL--MDN 58
Query: 84 DDFRRGKPTNHKVFGEDTAILAGDALLSLAFEHVAAKSTEISPDRVVRAIAELGSAVGSE 143
D RRGKPT HK FGE AILAGDALLS AF+ +A + P+ I+EL +AVG++
Sbjct: 59 SDLRRGKPTCHKKFGEAGAILAGDALLSRAFQLLALLG-HVRPEPKYILISELANAVGAQ 117
Query: 144 GLVAGEIMDIDSEGKDVSLNELENIHLHKTAKLLEAAVVCGVIIGGGNMIEVERVRKYAR 203
G V G++MD+++EGKD++L E I +KTA L A+V G I+ G + + + + + R
Sbjct: 118 GEV-GQLMDLETEGKDITLEEYLRIVSYKTAALFYASVQLGAIVAGADEEDEKDLYDFGR 176
Query: 204 CIGLLFQVVDDILDVTKSSKELGKTAGKDLVSDKATYPKLMGIENARKFACDLLAQATEE 263
+GL FQ+ DDILD+T ++ELGK G DL K+T P L+ +E AR+ LL +A E+
Sbjct: 177 DLGLAFQIQDDILDLTGDTEELGKPVGTDLQEGKSTLPVLLALEGAREEQRKLLREAYEQ 236
Query: 264 LAYFEVARAAPLYHLAYYIA 283
A+ L +A
Sbjct: 237 KLSEAAAQGVALTKALEALA 256
>gnl|CDD|223220 COG0142, IspA, Geranylgeranyl pyrophosphate synthase [Coenzyme
metabolism].
Length = 322
Score = 266 bits (682), Expect = 1e-88
Identities = 111/257 (43%), Positives = 149/257 (57%), Gaps = 13/257 (5%)
Query: 6 KRVNKALDETVQLRHPAKIHEAMRYSLLAGGKRVRPVLCIASCELVGGDESS----AMPV 61
R+ + L E + P + EAMRY LLAGGKR+RP+L + + E +G D + A+ +
Sbjct: 12 ARIEELLSELLSGSDPELLLEAMRYLLLAGGKRLRPLLVLLAAEALGIDLETGGNDALDL 71
Query: 62 ACALEMIHTMSLVHDDLPCMDNDDFRRGKPTNHKVFGEDTAILAGDALLSLAFEHVAAKS 121
A A+E+IHT SL+HDDL MD+DD RRGKPT H FGE TAILAGDALL+ AFE ++
Sbjct: 72 AAAIELIHTASLIHDDL--MDDDDLRRGKPTVHAKFGEATAILAGDALLAAAFELLS--K 127
Query: 122 TEISPDRVVRAIAELGSAVGSEGLVAGEIMDIDSEGKDVSLNELENIHLHKTAKLLEAAV 181
++A+AE GL G+ +D+ E K V+L E + KTA L AA
Sbjct: 128 LGSEALEAIKALAE-----AINGLCGGQALDLAFENKPVTLEEYLRVIELKTAALFAAAA 182
Query: 182 VCGVIIGGGNMIEVERVRKYARCIGLLFQVVDDILDVTKSSKELGKTAGKDLVSDKATYP 241
V G I+ G + +E + Y R +GL FQ+ DDILD+T +ELGK G DL K T P
Sbjct: 183 VLGAILAGADEELLEALEDYGRNLGLAFQIQDDILDITGDEEELGKPVGSDLKEGKPTLP 242
Query: 242 KLMGIENARKFACDLLA 258
L+ +E A + L
Sbjct: 243 VLLALEKANEDQKLLRI 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 = 262 bits (672), Expect = 5e-88
Identities = 110/269 (40%), Positives = 153/269 (56%), Gaps = 14/269 (5%)
Query: 20 HPAKIHEAMRYSLLAGGKRVRPVLCIASCELVGGDES-SAMPVACALEMIHTMSLVHDDL 78
+ EA+RY LLAGGKR+RP+L + + +GG E +A+ +A A+E++HT SLVHDD+
Sbjct: 2 EVELLREALRYLLLAGGKRLRPLLVLLAARALGGPELEAALRLAAAIELLHTASLVHDDV 61
Query: 79 PCMDNDDFRRGKPTNHKVFGEDTAILAGDALLSLAFEHVAAKSTEISPDRVVRAIAELGS 138
MDN D RRGKPT HKVFG TAILAGD LL+ AFE +A + RA+
Sbjct: 62 --MDNSDLRRGKPTVHKVFGNATAILAGDYLLARAFELLA----RLGNPYYPRALELF-- 113
Query: 139 AVGSEGLVAGEIMDIDSEGK-DVSLNELENIHLHKTAKLLEAAVVCGVIIGGGNMIEVER 197
+ LV G+++D+ SE DV+ E I KTA L AA + G ++ G + E E
Sbjct: 114 SEAILELVEGQLLDLLSEYDTDVTEEEYLRIIRLKTAALFAAAPLLGALLAGADEEEAEA 173
Query: 198 VRKYARCIGLLFQVVDDILDVTKSSKELGKTAGKDLVSDKATYPKLMGIENARKFACDLL 257
++++ R +GL FQ+ DDILD+ + LGK G DL K T P L+ + R+ A +
Sbjct: 174 LKRFGRNLGLAFQIQDDILDLFGDPETLGKPVGSDLREGKCTLPVLLAL---RELAREYE 230
Query: 258 AQATEELAYFEVARA-APLYHLAYYIASR 285
+A E L + A L LA +I R
Sbjct: 231 EKALEALKALPESPAREALRALADFILER 259
>gnl|CDD|182567 PRK10581, PRK10581, geranyltranstransferase; Provisional.
Length = 299
Score = 216 bits (552), Expect = 2e-69
Identities = 121/270 (44%), Positives = 156/270 (57%), Gaps = 16/270 (5%)
Query: 26 EAMRYSLLAGGKRVRPVLCIASCELVGGDESSAMPVACALEMIHTMSLVHDDLPCMDNDD 85
EAM+Y L GGKR+RP L A+ ++ G ++ A A+E IH SL+HDDLP MD+DD
Sbjct: 34 EAMQYGALLGGKRLRPFLVYATGQMFGVSTNTLDAPAAAVECIHAYSLIHDDLPAMDDDD 93
Query: 86 FRRGKPTNHKVFGEDTAILAGDALLSLAFEHVA-AKSTEISPDRVVRAIAELGSAVGSEG 144
RRG PT H FGE AILAGDAL +LAF ++ A E+S + I+EL SA G G
Sbjct: 94 LRRGLPTCHVKFGEANAILAGDALQTLAFSILSDAPMPEVSDRDRISMISELASASGIAG 153
Query: 145 LVAGEIMDIDSEGKDVSLNELENIHLHKTAKLLEAAVVCGVIIGGGNMIEVERVR----- 199
+ G+ +D+++EGK V L+ LE IH HKT L+ AAV G + G ++ R
Sbjct: 154 MCGGQALDLEAEGKQVPLDALERIHRHKTGALIRAAVRLGALSAG------DKGRRALPV 207
Query: 200 --KYARCIGLLFQVVDDILDVTKSSKELGKTAGKDLVSDKATYPKLMGIENARKFACDLL 257
+YA IGL FQV DDILDV + LGK G D K+TYP L+G+E ARK A DL+
Sbjct: 208 LDRYAESIGLAFQVQDDILDVVGDTATLGKRQGADQQLGKSTYPALLGLEQARKKARDLI 267
Query: 258 AQATEELAYFEVARA--APLYHLAYYIASR 285
A + L + L LA YI R
Sbjct: 268 DDARQSLDQLAAQSLDTSALEALANYIIQR 297
>gnl|CDD|164542 CHL00151, preA, prenyl transferase; Reviewed.
Length = 323
Score = 198 bits (504), Expect = 6e-62
Identities = 84/319 (26%), Positives = 138/319 (43%), Gaps = 54/319 (16%)
Query: 8 VNKALDETVQLRHPAKIHEAMRYSLLAGGKRVRPVLCIASCELVGGDESSAMP---VACA 64
+ L + + HP ++ A ++ AGGKR+RP + + + GG+ +A
Sbjct: 18 LEDNLKKLIGSGHPI-LYAAAKHLFSAGGKRIRPAIVLLVAKATGGNMEIKTSQQRLAEI 76
Query: 65 LEMIHTMSLVHDDLPCMDNDDFRRGKPTNHKVFGEDTAILAGDALLSLAFEHVAAKSTEI 124
E+IHT SLVHDD+ +D RRG PT HK+FG A+LAGD L + + ++A +
Sbjct: 77 TEIIHTASLVHDDV--IDECSIRRGIPTVHKIFGTKIAVLAGDFLFAQSSWYLANLNNLE 134
Query: 125 SPDRVVRAIAELGSAVGSEGLVAGEIMDIDSEGKDVSLNELENIH--LHKTAKLLEAAVV 182
+ + I + +GLV D +L+ L I +KTA L+ A+
Sbjct: 135 VVKLISKVITDFAEGEIRQGLVQ----------FDTTLSILNYIEKSFYKTASLIAASCK 184
Query: 183 CGVIIGGGNMIEVERVRKYARCIGLLFQVVDDILDVTKSSKELGKTAGKDLVSDKATYPK 242
++ + + Y + +GL FQ++DD+LD+T S++ LGK G DL + T P
Sbjct: 185 AAALLSDADEKDHNDFYLYGKHLGLAFQIIDDVLDITSSTESLGKPIGSDLKNGNLTAPV 244
Query: 243 LMGIENARKFACDLLA----------------------QATEELAYFEVARA-------- 272
L + K A L+ + ++LA + A
Sbjct: 245 LFALTQNSKLA-KLIEREFCETKDISQALQIIKETNGIEKAKDLALEHMQAAIQCLKFLP 303
Query: 273 -----APLYHLAYYIASRQ 286
L +A +I +R
Sbjct: 304 PSSAKDSLIEIANFIINRL 322
>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 = 185 bits (471), Expect = 5e-58
Identities = 85/249 (34%), Positives = 131/249 (52%), Gaps = 15/249 (6%)
Query: 39 VRPVLCIASCELVGGDESSAMPVACALEMIHTMSLVHDDLPCMDNDDFRRGKPTNHKV-F 97
RP+L + +GGD +A+ +A A+E++H SLVHDD+ +D+ D RRGKPT H F
Sbjct: 1 SRPLLVLLLARALGGDLEAALRLAAAVELLHAASLVHDDI--VDDSDLRRGKPTAHLRRF 58
Query: 98 GEDTAILAGDALLSLAFEHVAAKSTEISPDRVVRAIAELGSAVGSEGLVAGEIMDIDSEG 157
G AILAGD LL+ AF+ +A + R + AE L+ G+ +D++ E
Sbjct: 59 GNALAILAGDYLLARAFQLLA----RLGYPRALELFAE-----ALRELLEGQALDLEFER 109
Query: 158 -KDVSLNELENIHLHKTAKLLEAAVVCGVIIGGGNMIEVERVRKYARCIGLLFQVVDDIL 216
+L+E +KTA L+ + G + G + + E ++ Y R +GL FQ+ DD+L
Sbjct: 110 DTYETLDEYLEYCRYKTAGLVGLLCLLGAGLSGADDEQAEALKDYGRALGLAFQLTDDLL 169
Query: 217 DVTKSSKELGKTAGKDLVSDKATYPKLMGIENARKFACDLLAQATEELAYFEVARAAPLY 276
DV ++ELGK G DL + T P ++ E A ++A + A AR A +
Sbjct: 170 DVFGDAEELGK-VGSDLREGRITLPVILARERAAEYAEEAYAALEALPPSLPRARRALIA 228
Query: 277 HLAYYIASR 285
LA ++ R
Sbjct: 229 -LADFLYRR 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 = 134 bits (339), Expect = 2e-37
Identities = 91/258 (35%), Positives = 131/258 (50%), Gaps = 17/258 (6%)
Query: 8 VNKALDETVQLRHPAKIHEAMRYSLLAGGKRVRPVLCIASCELVGGDESSAMPVACALEM 67
+ K L++ VQ HP + EA + L AGGKR+RPV + + + D + VA ALE+
Sbjct: 16 IEKELEKAVQAEHPV-LSEASLHLLEAGGKRIRPVFVLLAGKFGDYDLDAIKHVAVALEL 74
Query: 68 IHTMSLVHDDLPCMDNDDFRRGKPTNHKVFGEDTAILAGDALLSLAFEHVAAKSTEISPD 127
IH SLVHDD+ +D+ D RRG+PT +G A+ GD L + + E + TEI
Sbjct: 75 IHMASLVHDDV--IDDADLRRGRPTIKSKWGNRIAMYTGDYLFAKSLETM----TEIKDP 128
Query: 128 RVVRAIAELGSAVGSEGLVAGEIMDI-DSEGKDVSL-NELENIHLHKTAKLLEAAVVCGV 185
R + ++ V GEI I D D +L L I KTA L+ A+ G
Sbjct: 129 RAHQILSHTIVEV-----CRGEIEQIKDKYNFDQNLRTYLRRIK-RKTALLIAASCQLGA 182
Query: 186 IIGGGNMIEVERVRKYARCIGLLFQVVDDILDVTKSSKELGKTAGKDLVSDKATYPKLMG 245
I G N V+++ + +G+ +Q+ DDILD + +ELGK AG DL+ T P L
Sbjct: 183 IASGANEAIVKKLYWFGYYVGMSYQITDDILDFVGTEEELGKPAGGDLLQGNVTLPVLYA 242
Query: 246 IENARKFACDLLAQATEE 263
+E+ F + Q EE
Sbjct: 243 MED--PFLKKRIEQVLEE 258
>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 = 125 bits (316), Expect = 7e-35
Identities = 67/231 (29%), Positives = 100/231 (43%), Gaps = 32/231 (13%)
Query: 40 RPVLCIASCELVGGDESSAMPVACALEMIHTMSLVHDDLPCMDNDDFRRGKPTNHKV--- 96
RP+ + E A + A+E +H SLVHDD+ +D+ RRG PT H
Sbjct: 2 RPLAVLLEPE--------ASRLRAAVEKLHAASLVHDDI--VDDSGTRRGLPTAHLAVAI 51
Query: 97 FGEDTAILAGDALLSLAFEHVAAKSTEISPDRVVRAIAELGSAVGSEGLVAGEIMDIDSE 156
G AILAGD LL+ AFE +A + +AE L+ G+++D+
Sbjct: 52 DGLPEAILAGDLLLADAFEELA----REGSPEALEILAE-----ALLDLLEGQLLDLKWR 102
Query: 157 G-KDVSLNELENIHLHKTAKLLEAAVVCGVIIGGGNMIEVERVRKYARCIGLLFQVVDDI 215
+L E +KTA L+ A + G + GG +E +RK R +GL FQ+ +D+
Sbjct: 103 REYVPTLEEYLEYCRYKTAGLVGALCLLGAGLSGGEAELLEALRKLGRALGLAFQLTNDL 162
Query: 216 LDVTKSSKELGKTAGKDLVSDKATYPKLMGIENARKFACDLLAQATEELAY 266
LD ++ K T P L +E LL + + L
Sbjct: 163 LDYEGDAERGE---------GKCTLPVLYALEYGVPAEDLLLVEKSGSLEE 204
>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 = 117 bits (294), Expect = 7e-31
Identities = 84/245 (34%), Positives = 124/245 (50%), Gaps = 14/245 (5%)
Query: 7 RVNKALDETVQLRHPAKIHEAMRYSLLAGGKRVRP--VLCIASCELVGGD-ESSAMPVAC 63
+ L V RHP ++ A + AGGKR+RP VL ++ + +A
Sbjct: 16 LLTDNLKSLVGARHPI-LYAAAEHLFSAGGKRLRPAIVLLVSRATAEQQELTPRHRRLAE 74
Query: 64 ALEMIHTMSLVHDDLPCMDNDDFRRGKPTNHKVFGEDTAILAGDALLSLAFEHVAAKSTE 123
EMIHT SLVHDD+ +D D RRG T H +FG A+LAGD L + A ++A
Sbjct: 75 ITEMIHTASLVHDDV--IDESDTRRGIETVHSLFGTRVAVLAGDFLFAQASWYLA----N 128
Query: 124 ISPDRVVRAIAELGSAVGSEGLVAGEIMDIDSEGKDVSLNELENIHLHKTAKLLEAAVVC 183
+ VV+ I+++ + EG + + DS D+SL + +KTA L+ A+
Sbjct: 129 LENLEVVKLISKVITDFA-EGEIKQGLNQFDS---DLSLEDYLEKSFYKTASLVAASSKA 184
Query: 184 GVIIGGGNMIEVERVRKYARCIGLLFQVVDDILDVTKSSKELGKTAGKDLVSDKATYPKL 243
++ + +Y + +GL FQVVDDILD T S+++LGK AG DL+ T P L
Sbjct: 185 AAVLSDVPSQVANDLYEYGKHLGLAFQVVDDILDFTGSTEQLGKPAGSDLMKGNLTAPVL 244
Query: 244 MGIEN 248
+E
Sbjct: 245 FALEE 249
>gnl|CDD|215462 PLN02857, PLN02857, octaprenyl-diphosphate synthase.
Length = 416
Score = 117 bits (294), Expect = 3e-30
Identities = 82/222 (36%), Positives = 121/222 (54%), Gaps = 18/222 (8%)
Query: 34 AGGKRVRPVLCI----ASCELVGGDE--SSAMPVACALEMIHTMSLVHDDLPCMDNDDFR 87
AGGKR+RP L A+ EL G E + +A EMIHT SL+HDD+ +D D R
Sbjct: 133 AGGKRMRPALVFLVSRATAELAGLKELTTEHRRLAEITEMIHTASLIHDDV--LDESDMR 190
Query: 88 RGKPTNHKVFGEDTAILAGDALLSLAFEHVAAKSTEISPDRVVRAIAELGSAVGSEGLVA 147
RGK T H+++G A+LAGD + + + ++A + V++ I+++ S
Sbjct: 191 RGKETVHQLYGTRVAVLAGDFMFAQSSWYLA----NLDNLEVIKLISQVIKDFAS----- 241
Query: 148 GEIMDIDSE-GKDVSLNELENIHLHKTAKLLEAAVVCGVIIGGGNMIEVERVRKYARCIG 206
GEI S DV+L+E +KTA L+ A+ I G + E++ +Y + +G
Sbjct: 242 GEIKQASSLFDCDVTLDEYLLKSYYKTASLIAASTKSAAIFSGVDSSVKEQMYEYGKNLG 301
Query: 207 LLFQVVDDILDVTKSSKELGKTAGKDLVSDKATYPKLMGIEN 248
L FQVVDDILD T+S+++LGK AG DL T P + +E
Sbjct: 302 LAFQVVDDILDFTQSTEQLGKPAGSDLAKGNLTAPVIFALEK 343
>gnl|CDD|182813 PRK10888, PRK10888, octaprenyl diphosphate synthase; Provisional.
Length = 323
Score = 115 bits (289), Expect = 4e-30
Identities = 73/240 (30%), Positives = 128/240 (53%), Gaps = 10/240 (4%)
Query: 24 IHEAMRYSLLAGGKRVRPVLCIASCELVGGDESSAMPVACALEMIHTMSLVHDDLPCMDN 83
I++ Y + GGKR+RP++ + + VG ++ + +A +E IHT +L+HDD+ +D
Sbjct: 32 INQLGYYIISGGGKRIRPMIAVLAARAVGYQGNAHVTIAALIEFIHTATLLHDDV--VDE 89
Query: 84 DDFRRGKPTNHKVFGEDTAILAGDALLSLAFEHVAAKSTEISPDRVVRAIAELGSAVGSE 143
D RRGK T + FG ++L GD + + AF+ + T + +V+ ++E V +E
Sbjct: 90 SDMRRGKATANAAFGNAASVLVGDFIYTRAFQMM----TSLGSLKVLEVMSE-AVNVIAE 144
Query: 144 GLVAGEIMDIDSEGKDVSLNELENIHLHKTAKLLEAAVVCGVIIGGGNMIEVERVRKYAR 203
G V ++M+++ D++ + KTA+L EAA C I+ G + + ++ Y R
Sbjct: 145 GEVL-QLMNVND--PDITEENYMRVIYSKTARLFEAAAQCSGILAGCTPEQEKGLQDYGR 201
Query: 204 CIGLLFQVVDDILDVTKSSKELGKTAGKDLVSDKATYPKLMGIENARKFACDLLAQATEE 263
+G FQ++DD+LD + + LGK G DL K T P L + + ++ A E+
Sbjct: 202 YLGTAFQLIDDLLDYSADGETLGKNVGDDLNEGKPTLPLLHAMHHGTPEQAAMIRTAIEQ 261
>gnl|CDD|178478 PLN02890, PLN02890, geranyl diphosphate synthase.
Length = 422
Score = 85.7 bits (212), Expect = 6e-19
Identities = 71/186 (38%), Positives = 101/186 (54%), Gaps = 18/186 (9%)
Query: 66 EMIHTMSLVHDDLPCMDNDDFRRGKPTNHKVFGEDTAILAGDALLSLAFEHVAA-KSTEI 124
EMIH SL+HDD+ +D+ D RRG + + V G ++LAGD LLS A +AA K+TE+
Sbjct: 171 EMIHVASLLHDDV--LDDADTRRGVGSLNVVMGNKLSVLAGDFLLSRACVALAALKNTEV 228
Query: 125 SPDRVVRAIAELGSAVGSEGLVAGEIMDIDSEGKD-VSLNELENIHLHKTAKLLEAAVVC 183
++ L +AV E LV GE M I S + S++ +KTA L+ + C
Sbjct: 229 --------VSLLATAV--EHLVTGETMQITSSREQRRSMDYYMQKTYYKTASLISNS--C 276
Query: 184 -GVIIGGGNMIEVERVR-KYARCIGLLFQVVDDILDVTKSSKELGKTAGKDLVSDKATYP 241
V I G EV + +Y R +GL FQ++DD+LD T +S LGK + D+ T P
Sbjct: 277 KAVAILAGQTAEVAVLAFEYGRNLGLAFQLIDDVLDFTGTSASLGKGSLSDIRHGVITAP 336
Query: 242 KLMGIE 247
L +E
Sbjct: 337 ILFAME 342
>gnl|CDD|215410 PLN02766, PLN02766, coniferyl-aldehyde dehydrogenase.
Length = 501
Score = 30.2 bits (68), Expect = 1.4
Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 5/76 (6%)
Query: 210 QVVDDILDVTKSSKELGKTAGKDLVSDKATYPKLMGIENAR---KFACDLLAQATEELAY 266
+V+ I + K +L A ++ D +P++ G E R KFA DL+ + EELA
Sbjct: 47 EVIARIAEGDKEDVDLAVKAAREAF-DHGPWPRMSGFERGRIMMKFA-DLIEEHIEELAA 104
Query: 267 FEVARAAPLYHLAYYI 282
+ A L+ L +
Sbjct: 105 LDTIDAGKLFALGKAV 120
>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function
unknown].
Length = 652
Score = 28.9 bits (65), Expect = 3.3
Identities = 17/44 (38%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 98 GEDTAILAGDALLSLAFEHVAAKST-EISPDRVVRAIAELGSAV 140
G D I G A+L L E + +S I VV I+ELG V
Sbjct: 248 GIDPGITTGIAVLDLDGEVLDLESRRGIDRSEVVEFISELGKPV 291
>gnl|CDD|168293 PRK05910, PRK05910, type III secretion system protein; Validated.
Length = 584
Score = 29.0 bits (65), Expect = 3.4
Identities = 37/144 (25%), Positives = 57/144 (39%), Gaps = 24/144 (16%)
Query: 96 VFGEDTAILAGDALLSLAF--EHVAAKSTEISPDRVVRAIAELGSAVGSEGLVAGEIMDI 153
VF E+ + ++ L F + V + E+S ++ ++ L SE V + +
Sbjct: 351 VFPEEIVVRHVESSPRLIFSGQEVYLR--ELSCPAILPSLRNLAPEAISERFVKRLVEEF 408
Query: 154 DSEG---------KDVSLNEL---------ENIHLHKTAKLLEAAVVCGVIIGGGNMIEV 195
K +S N L E + LH K+LEA V G G + V
Sbjct: 409 QEVAGISIEEIIPKKISENSLVFLLRALVRERVSLHLFPKILEAIAVYGS-QGKSSEELV 467
Query: 196 ERVRKY-ARCIGLLFQVVDDILDV 218
E+VRKY + IG D L+V
Sbjct: 468 EKVRKYLGKQIGRSLWNRQDTLEV 491
>gnl|CDD|130587 TIGR01524, ATPase-IIIB_Mg, magnesium-translocating P-type ATPase.
This model describes the magnesium translocating P-type
ATPase found in a limited number of bacterial species
and best described in Salmonella typhimurium, which
contains two isoforms. These transporters are active in
low external Mg2+ concentrations and pump the ion into
the cytoplasm. The magnesium ATPases have been
classified as type IIIB by a phylogenetic analysis
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 867
Score = 29.1 bits (65), Expect = 3.7
Identities = 26/112 (23%), Positives = 43/112 (38%), Gaps = 23/112 (20%)
Query: 89 GKPTNHKVFGEDTAILAGDALLSLAFE-HVAAKSTEISPDRVVRAIAELGSAVGSEG--- 144
G N + G D L+ + L + H+ A+ T + R++ + + G VG G
Sbjct: 553 GIDANDFLLGADIEELSDEELARELRKYHIFARLTPMQKSRIIGLLKKAGHTVGFLGDGI 612
Query: 145 -----LVAGEI-------MDIDSEGKDVSLNELENIHLHKTAKLLEAAVVCG 184
L ++ DI E D+ I L K+ +LE V+ G
Sbjct: 613 NDAPALRKADVGISVDTAADIAKEASDI-------ILLEKSLMVLEEGVIEG 657
>gnl|CDD|233322 TIGR01227, hutG, formimidoylglutamase. Formiminoglutamase, the
fourth enzyme of histidine degradation, is similar to
arginases and agmatinases. It is often encoded near
other enzymes of the histidine degredation pathway:
histidine ammonia-lyase, urocanate hydratase, and
imidazolonepropionase [Energy metabolism, Amino acids
and amines].
Length = 307
Score = 28.6 bits (64), Expect = 4.0
Identities = 23/71 (32%), Positives = 34/71 (47%), Gaps = 11/71 (15%)
Query: 126 PDRVVRAIAELGSAVGSEGLVAGEIMDIDSEGKDVSLNELENIHLHKTAKLLEAAVVCG- 184
P + +A+A LG SE L ++ DI G D LE+ H+ A+ A +
Sbjct: 61 PSAIRQALAHLGDWHVSELLY--DLGDIVIHGDD-----LEDTQ-HEIAQTAAALLADHR 112
Query: 185 --VIIGGGNMI 193
VI+GGG+ I
Sbjct: 113 VPVILGGGHSI 123
>gnl|CDD|143460 cd07142, ALDH_F2BC, Arabidosis aldehyde dehydrogenase family 2 B4,
B7, C4-like. Included in this CD is the Arabidosis
aldehyde dehydrogenase family 2 members B4 and B7
(EC=1.2.1.3), which are mitochondrial homotetramers
that oxidize acetaldehyde and glycolaldehyde, but not
L-lactaldehyde. Also in this group, is the Arabidosis
cytosolic, homotetramer ALDH2C4 (EC=1.2.1.3), an enzyme
involved in the oxidation of sinapalehyde and
coniferaldehyde.
Length = 476
Score = 28.6 bits (64), Expect = 4.4
Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 4/50 (8%)
Query: 236 DKATYPKLMGIENAR---KFACDLLAQATEELAYFEVARAAPLYHLAYYI 282
D+ +P++ G E +R +FA DLL + +ELA E Y A Y
Sbjct: 55 DEGPWPRMTGYERSRILLRFA-DLLEKHADELAALETWDNGKPYEQARYA 103
>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 = 28.4 bits (64), Expect = 5.0
Identities = 13/39 (33%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 104 LAGDALLSLA-FEHVAAKSTEISPDRVVRAIAELGSAVG 141
G L SLA HV + + P+RV R +AE+ +
Sbjct: 119 FGGGTLASLADLPHVGGVAGRLDPERVRRTVAEVEGLLR 157
>gnl|CDD|240345 PTZ00287, PTZ00287, 6-phosphofructokinase; Provisional.
Length = 1419
Score = 28.5 bits (63), Expect = 5.6
Identities = 14/29 (48%), Positives = 18/29 (62%)
Query: 208 LFQVVDDILDVTKSSKELGKTAGKDLVSD 236
L++VV DI DV + ELGK G L+ D
Sbjct: 1046 LWRVVQDIADVVCARAELGKNYGTVLIPD 1074
>gnl|CDD|182528 PRK10535, PRK10535, macrolide transporter ATP-binding /permease
protein; Provisional.
Length = 648
Score = 27.8 bits (62), Expect = 9.3
Identities = 17/41 (41%), Positives = 22/41 (53%), Gaps = 9/41 (21%)
Query: 78 LPCMDNDDFRRGKPTN--HKVFGEDTAILAGDALLSLAFEH 116
L C+D KPT+ ++V G+D A L DAL L EH
Sbjct: 54 LGCLD-------KPTSGTYRVAGQDVATLDADALAQLRREH 87
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 0.380
Gapped
Lambda K H
0.267 0.0796 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,567,752
Number of extensions: 1419859
Number of successful extensions: 1354
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1318
Number of HSP's successfully gapped: 31
Length of query: 287
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 191
Effective length of database: 6,679,618
Effective search space: 1275807038
Effective search space used: 1275807038
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 58 (26.0 bits)