RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 037594
(295 letters)
>gnl|CDD|173833 cd00685, Trans_IPPS_HT, Trans-Isoprenyl Diphosphate Synthases,
head-to-tail. These trans-Isoprenyl Diphosphate
Synthases (Trans_IPPS) catalyze head-to-tail (HT) (1'-4)
condensation reactions. This CD includes all-trans
(E)-isoprenyl diphosphate synthases which synthesize
various chain length (C10, C15, C20, C25, C30, C35, C40,
C45, and C50) linear isoprenyl diphosphates from
precursors, isopentenyl diphosphate (IPP) and
dimethylallyl diphosphate (DMAPP). They catalyze the
successive 1'-4 condensation of the 5-carbon IPP to
allylic substrates geranyl-, farnesyl-, or
geranylgeranyl-diphosphate. Isoprenoid chain elongation
reactions proceed via electrophilic alkylations in which
a new carbon-carbon single bond is generated through
interaction between a highly reactive electron-deficient
allylic carbocation and an electron-rich carbon-carbon
double bond. The catalytic site consists of a large
central cavity formed by mostly antiparallel alpha
helices with two aspartate-rich regions (DDXX(XX)D)
located on opposite walls. These residues mediate
binding of prenyl phosphates via bridging Mg2+ ions,
inducing proposed conformational changes that close the
active site to solvent, protecting and stabilizing
reactive carbocation intermediates. Farnesyl diphosphate
synthases produce the precursors of steroids,
cholesterol, sesquiterpenes, farnsylated proteins, heme,
and vitamin K12; and geranylgeranyl diphosphate and
longer chain synthases produce the precursors of
carotenoids, retinoids, diterpenes, geranylgeranylated
chlorophylls, ubiquinone, and archaeal ether linked
lipids. Isoprenyl diphosphate synthases are widely
distributed among archaea, bacteria, and eukareya.
Length = 259
Score = 206 bits (527), Expect = 5e-66
Identities = 93/262 (35%), Positives = 143/262 (54%), Gaps = 15/262 (5%)
Query: 39 HPAILHEAMRYSL-PGGKRLMSTLCIASCEMIGGSQS-VAMSMACAIELLVTMAVIQDDL 96
+L EA+RY L GGKRL L + + +GG + A+ +A AIELL T +++ DD+
Sbjct: 2 EVELLREALRYLLLAGGKRLRPLLVLLAARALGGPELEAALRLAAAIELLHTASLVHDDV 61
Query: 97 PCLDNDDLRRGKPSNHKVFGEATAILACQALHCLAMQHIAIIKAKNINSAV-----GSEG 151
+DN DLRRGKP+ HKVFG ATAILA L A + +A + A+
Sbjct: 62 --MDNSDLRRGKPTVHKVFGNATAILAGDYLLARAFELLARLGNPYYPRALELFSEAILE 119
Query: 152 IAAGQIMDINSEGK-EVSLSELNFIHRHKTGKFIEASIVSGVIIGGGNEEEIERMRNFGK 210
+ GQ++D+ SE +V+ E I R KT A+ + G ++ G +EEE E ++ FG+
Sbjct: 120 LVEGQLLDLLSEYDTDVTEEEYLRIIRLKTAALFAAAPLLGALLAGADEEEAEALKRFGR 179
Query: 211 YVGMAYQLWNDIVDVIGSPEMREK-TGRDMMRDKATYPKLVGIDGSKKHAKELIAEAKQE 269
+G+A+Q+ +DI+D+ G PE K G D+ K T P L+ + ++ A+E +A +
Sbjct: 180 NLGLAFQIQDDILDLFGDPETLGKPVGSDLREGKCTLPVLLAL---RELAREYEEKALEA 236
Query: 270 LAYFDPTRA-APLDHLVNFIVS 290
L + A L L +FI+
Sbjct: 237 LKALPESPAREALRALADFILE 258
>gnl|CDD|223220 COG0142, IspA, Geranylgeranyl pyrophosphate synthase [Coenzyme
metabolism].
Length = 322
Score = 205 bits (523), Expect = 1e-64
Identities = 100/311 (32%), Positives = 153/311 (49%), Gaps = 48/311 (15%)
Query: 25 KQINEALDEAVPLPHPAILHEAMRYSLP-GGKRLMSTLCIASCEMIGGS----QSVAMSM 79
+I E L E + P +L EAMRY L GGKRL L + + E +G + A+ +
Sbjct: 12 ARIEELLSELLSGSDPELLLEAMRYLLLAGGKRLRPLLVLLAAEALGIDLETGGNDALDL 71
Query: 80 ACAIELLVTMAVIQDDLPCLDNDDLRRGKPSNHKVFGEATAILACQALHCLAMQHIA--- 136
A AIEL+ T ++I DDL +D+DDLRRGKP+ H FGEATAILA AL A + ++
Sbjct: 72 AAAIELIHTASLIHDDL--MDDDDLRRGKPTVHAKFGEATAILAGDALLAAAFELLSKLG 129
Query: 137 --IIKAKNINSAVGSEGIAAGQIMDINSEGKEVSLSELNFIHRHKTGKFIEASIVSGVII 194
++A + G+ GQ +D+ E K V+L E + KT A+ V G I+
Sbjct: 130 SEALEAIKALAEA-INGLCGGQALDLAFENKPVTLEEYLRVIELKTAALFAAAAVLGAIL 188
Query: 195 GGGNEEEIERMRNFGKYVGMAYQLWNDIVDVIGSPE-MREKTGRDMMRDKATYPKLVG-- 251
G +EE +E + ++G+ +G+A+Q+ +DI+D+ G E + + G D+ K T P L+
Sbjct: 189 AGADEELLEALEDYGRNLGLAFQIQDDILDITGDEEELGKPVGSDLKEGKPTLPVLLALE 248
Query: 252 -------------------------------IDGSKKHAKELIAEAKQELAYFDPTRAA- 279
I+ +K AK + +AK+ L + A
Sbjct: 249 KANEDQKLLRILLEGGGEVEEALELLRKSGAIEYAKNLAKTYVEKAKEALEKLPDSEAKE 308
Query: 280 PLDHLVNFIVS 290
L L +FI+
Sbjct: 309 ALLELADFIIK 319
>gnl|CDD|215873 pfam00348, polyprenyl_synt, Polyprenyl synthetase.
Length = 260
Score = 193 bits (493), Expect = 9e-61
Identities = 89/236 (37%), Positives = 143/236 (60%), Gaps = 15/236 (6%)
Query: 43 LHEAMRYSL-PGGKRLMSTLCIASCEMIGGSQSVAMSMACAIELLVTMAVIQDDLPCLDN 101
L AM Y L GGKR+ L + + +G + +ACAIE++ T +++ DDL +DN
Sbjct: 1 LLAAMLYYLLAGGKRIRPLLVVLAARALGVEPETLLYLACAIEMIHTASLVHDDL--MDN 58
Query: 102 DDLRRGKPSNHKVFGEATAILACQALHCLAMQHIAII-------KAKNINS---AVGSEG 151
DLRRGKP+ HK FGEA AILA AL A Q +A++ K I+ AVG++G
Sbjct: 59 SDLRRGKPTCHKKFGEAGAILAGDALLSRAFQLLALLGHVRPEPKYILISELANAVGAQG 118
Query: 152 IAAGQIMDINSEGKEVSLSELNFIHRHKTGKFIEASIVSGVIIGGGNEEEIERMRNFGKY 211
GQ+MD+ +EGK+++L E I +KT AS+ G I+ G +EE+ + + +FG+
Sbjct: 119 -EVGQLMDLETEGKDITLEEYLRIVSYKTAALFYASVQLGAIVAGADEEDEKDLYDFGRD 177
Query: 212 VGMAYQLWNDIVDVIGSPE-MREKTGRDMMRDKATYPKLVGIDGSKKHAKELIAEA 266
+G+A+Q+ +DI+D+ G E + + G D+ K+T P L+ ++G+++ ++L+ EA
Sbjct: 178 LGLAFQIQDDILDLTGDTEELGKPVGTDLQEGKSTLPVLLALEGAREEQRKLLREA 233
>gnl|CDD|182567 PRK10581, PRK10581, geranyltranstransferase; Provisional.
Length = 299
Score = 177 bits (451), Expect = 3e-54
Identities = 104/284 (36%), Positives = 161/284 (56%), Gaps = 19/284 (6%)
Query: 25 KQINEALDEAV-PLPHPAI-LHEAMRY-SLPGGKRLMSTLCIASCEMIGGSQSVAMSMAC 81
+Q N+AL + PLP + EAM+Y +L GGKRL L A+ +M G S + + A
Sbjct: 12 QQANQALSRFIAPLPFQNTPVVEAMQYGALLGGKRLRPFLVYATGQMFGVSTNTLDAPAA 71
Query: 82 AIELLVTMAVIQDDLPCLDNDDLRRGKPSNHKVFGEATAILACQALHCLA--------MQ 133
A+E + ++I DDLP +D+DDLRRG P+ H FGEA AILA AL LA M
Sbjct: 72 AVECIHAYSLIHDDLPAMDDDDLRRGLPTCHVKFGEANAILAGDALQTLAFSILSDAPMP 131
Query: 134 HIA----IIKAKNINSAVGSEGIAAGQIMDINSEGKEVSLSELNFIHRHKTGKFIEASIV 189
++ I + SA G G+ GQ +D+ +EGK+V L L IHRHKTG I A++
Sbjct: 132 EVSDRDRISMISELASASGIAGMCGGQALDLEAEGKQVPLDALERIHRHKTGALIRAAVR 191
Query: 190 SGVIIGGGN-EEEIERMRNFGKYVGMAYQLWNDIVDVIG-SPEMREKTGRDMMRDKATYP 247
G + G + + + + +G+A+Q+ +DI+DV+G + + ++ G D K+TYP
Sbjct: 192 LGALSAGDKGRRALPVLDRYAESIGLAFQVQDDILDVVGDTATLGKRQGADQQLGKSTYP 251
Query: 248 KLVGIDGSKKHAKELIAEAKQELAYFD--PTRAAPLDHLVNFIV 289
L+G++ ++K A++LI +A+Q L + L+ L N+I+
Sbjct: 252 ALLGLEQARKKARDLIDDARQSLDQLAAQSLDTSALEALANYII 295
>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 = 150 bits (382), Expect = 2e-44
Identities = 67/236 (28%), Positives = 115/236 (48%), Gaps = 7/236 (2%)
Query: 59 STLCIASCEMIGGSQSVAMSMACAIELLVTMAVIQDDLPCLDNDDLRRGKPSNHKV-FGE 117
L + +GG A+ +A A+ELL +++ DD+ +D+ DLRRGKP+ H FG
Sbjct: 3 PLLVLLLARALGGDLEAALRLAAAVELLHAASLVHDDI--VDDSDLRRGKPTAHLRRFGN 60
Query: 118 ATAILACQALHCLAMQHIAIIKAKNINS--AVGSEGIAAGQIMDINSEG-KEVSLSELNF 174
A AILA L A Q +A + A + GQ +D+ E +L E
Sbjct: 61 ALAILAGDYLLARAFQLLARLGYPRALELFAEALRELLEGQALDLEFERDTYETLDEYLE 120
Query: 175 IHRHKTGKFIEASIVSGVIIGGGNEEEIERMRNFGKYVGMAYQLWNDIVDVIGSPEMREK 234
R+KT + + G + G ++E+ E ++++G+ +G+A+QL +D++DV G E K
Sbjct: 121 YCRYKTAGLVGLLCLLGAGLSGADDEQAEALKDYGRALGLAFQLTDDLLDVFGDAEELGK 180
Query: 235 TGRDMMRDKATYPKLVGIDGSKKHAKELIAEAKQELAYFDPTRAAPLDHLVNFIVS 290
G D+ + T P ++ + + ++A+E A + P L L +F+
Sbjct: 181 VGSDLREGRITLPVILARERAAEYAEEAYAALEALPPS-LPRARRALIALADFLYR 235
>gnl|CDD|164542 CHL00151, preA, prenyl transferase; Reviewed.
Length = 323
Score = 134 bits (338), Expect = 3e-37
Identities = 68/266 (25%), Positives = 127/266 (47%), Gaps = 24/266 (9%)
Query: 26 QINEALDEAVPLPHPAILHEAMRYSL-PGGKRLMSTLCIASCEMIGGSQSVAMS---MAC 81
+ + L + + HP IL+ A ++ GGKR+ + + + GG+ + S +A
Sbjct: 17 ILEDNLKKLIGSGHP-ILYAAAKHLFSAGGKRIRPAIVLLVAKATGGNMEIKTSQQRLAE 75
Query: 82 AIELLVTMAVIQDDLPCLDNDDLRRGKPSNHKVFGEATAILACQALHCLAMQHIAIIKAK 141
E++ T +++ DD+ +D +RRG P+ HK+FG A+LA L + ++A
Sbjct: 76 ITEIIHTASLVHDDV--IDECSIRRGIPTVHKIFGTKIAVLAGDFLFAQSSWYLA----- 128
Query: 142 NINSAVGSEGI-------AAGQIMDINSEGKEVSLSELNFIHR--HKTGKFIEASIVSGV 192
N+N+ + I A G+I + +LS LN+I + +KT I AS +
Sbjct: 129 NLNNLEVVKLISKVITDFAEGEIRQ-GLVQFDTTLSILNYIEKSFYKTASLIAASCKAAA 187
Query: 193 IIGGGNEEEIERMRNFGKYVGMAYQLWNDIVDVIGSPE-MREKTGRDMMRDKATYPKLVG 251
++ +E++ +GK++G+A+Q+ +D++D+ S E + + G D+ T P L
Sbjct: 188 LLSDADEKDHNDFYLYGKHLGLAFQIIDDVLDITSSTESLGKPIGSDLKNGNLTAPVLFA 247
Query: 252 IDGSKKHAKELIAEAKQELAYFDPTR 277
+ + K A +LI E
Sbjct: 248 LTQNSKLA-KLIEREFCETKDISQAL 272
>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 = 102 bits (256), Expect = 5e-26
Identities = 50/210 (23%), Positives = 89/210 (42%), Gaps = 22/210 (10%)
Query: 80 ACAIELLVTMAVIQDDLPCLDNDDLRRGKPSNHKV---FGEATAILACQALHCLAMQHIA 136
A+E L +++ DD+ +D+ RRG P+ H G AILA L A + +A
Sbjct: 16 RAAVEKLHAASLVHDDI--VDDSGTRRGLPTAHLAVAIDGLPEAILAGDLLLADAFEELA 73
Query: 137 IIKAKNINS--AVGSEGIAAGQIMDI-NSEGKEVSLSELNFIHRHKTGKFIEASIVSGVI 193
+ A + GQ++D+ +L E R+KT + A + G
Sbjct: 74 REGSPEALEILAEALLDLLEGQLLDLKWRREYVPTLEEYLEYCRYKTAGLVGALCLLGAG 133
Query: 194 IGGGNEEEIERMRNFGKYVGMAYQLWNDIVDVIGSPEMREKTGR-----DMMRDKATYPK 248
+ GG E +E +R G+ +G+A+QL ND++D G + G+ + +
Sbjct: 134 LSGGEAELLEALRKLGRALGLAFQLTNDLLDYEG--DAERGEGKCTLPVLYALEYGVPAE 191
Query: 249 LV-------GIDGSKKHAKELIAEAKQELA 271
+ ++ + + +L EA +EL
Sbjct: 192 DLLLVEKSGSLEEALEELAKLAEEALKELN 221
>gnl|CDD|182813 PRK10888, PRK10888, octaprenyl diphosphate synthase; Provisional.
Length = 323
Score = 74.1 bits (182), Expect = 4e-15
Identities = 59/226 (26%), Positives = 112/226 (49%), Gaps = 16/226 (7%)
Query: 53 GGKRLMSTLCIASCEMIGGSQSVAMSMACAIELLVTMAVIQDDLPCLDNDDLRRGKPSNH 112
GGKR+ + + + +G + +++A IE + T ++ DD+ +D D+RRGK + +
Sbjct: 43 GGKRIRPMIAVLAARAVGYQGNAHVTIAALIEFIHTATLLHDDV--VDESDMRRGKATAN 100
Query: 113 KVFGEATAILACQALHCLAMQHIAIIKAKNINSAVGSEG---IAAG---QIMDINSEGKE 166
FG A ++L ++ A Q + + + + V SE IA G Q+M++N +
Sbjct: 101 AAFGNAASVLVGDFIYTRAFQMMTSLGSLKV-LEVMSEAVNVIAEGEVLQLMNVN----D 155
Query: 167 VSLSELNFIH--RHKTGKFIEASIVSGVIIGGGNEEEIERMRNFGKYVGMAYQLWNDIVD 224
++E N++ KT + EA+ I+ G E+ + ++++G+Y+G A+QL +D++D
Sbjct: 156 PDITEENYMRVIYSKTARLFEAAAQCSGILAGCTPEQEKGLQDYGRYLGTAFQLIDDLLD 215
Query: 225 VIGSPEMREK-TGRDMMRDKATYPKLVGIDGSKKHAKELIAEAKQE 269
E K G D+ K T P L + +I A ++
Sbjct: 216 YSADGETLGKNVGDDLNEGKPTLPLLHAMHHGTPEQAAMIRTAIEQ 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 = 73.6 bits (181), Expect = 5e-15
Identities = 78/264 (29%), Positives = 125/264 (47%), Gaps = 30/264 (11%)
Query: 27 INEALDEAVPLPHPAILHEAMRYSL-PGGKRLMSTLCIASCEMIGGSQSVAMSMACAIEL 85
I + L++AV HP +L EA + L GGKR+ + + + +A A+EL
Sbjct: 16 IEKELEKAVQAEHP-VLSEASLHLLEAGGKRIRPVFVLLAGKFGDYDLDAIKHVAVALEL 74
Query: 86 LVTMAVIQDDLPCLDNDDLRRGKPSNHKVFGEATAI-----LACQALHCLAMQHIAIIKA 140
+ +++ DD+ +D+ DLRRG+P+ +G A+ L ++L M I +A
Sbjct: 75 IHMASLVHDDV--IDDADLRRGRPTIKSKWGNRIAMYTGDYLFAKSLET--MTEIKDPRA 130
Query: 141 KNINSAVGSEGIAAGQIMDINSEGK-EVSLSE-LNFIHRHKTGKFIEASIVSGVIIGGGN 198
I S E + G+I I + + +L L I R KT I AS G I G N
Sbjct: 131 HQILSHTIVE-VCRGEIEQIKDKYNFDQNLRTYLRRIKR-KTALLIAASCQLGAIASGAN 188
Query: 199 EEEIERMRNFGKYVGMAYQLWNDIVDVIGSPEMREK-TGRDMMRDKATYPKL-------- 249
E ++++ FG YVGM+YQ+ +DI+D +G+ E K G D+++ T P L
Sbjct: 189 EAIVKKLYWFGYYVGMSYQITDDILDFVGTEEELGKPAGGDLLQGNVTLPVLYAMEDPFL 248
Query: 250 ------VGIDGSKKHAKELIAEAK 267
V + + + + LI E K
Sbjct: 249 KKRIEQVLEETTAEEMEPLIEEVK 272
>gnl|CDD|215462 PLN02857, PLN02857, octaprenyl-diphosphate synthase.
Length = 416
Score = 72.6 bits (178), Expect = 2e-14
Identities = 71/254 (27%), Positives = 122/254 (48%), Gaps = 23/254 (9%)
Query: 25 KQINEALDEAVPLPHPAILHEAMRYSLPGGKRLMSTLCI----ASCEMIGGSQSVA--MS 78
+Q+N+ L V +P ++ A + GGKR+ L A+ E+ G +
Sbjct: 106 QQLNDNLQSIVGAENPVLMSAAEQIFGAGGKRMRPALVFLVSRATAELAGLKELTTEHRR 165
Query: 79 MACAIELLVTMAVIQDDLPCLDNDDLRRGKPSNHKVFGEATAILA-----CQALHCLA-M 132
+A E++ T ++I DD+ LD D+RRGK + H+++G A+LA Q+ LA +
Sbjct: 166 LAEITEMIHTASLIHDDV--LDESDMRRGKETVHQLYGTRVAVLAGDFMFAQSSWYLANL 223
Query: 133 QHIAIIK--AKNINSAVGSEGIAAGQIMDINSEGKEVSLSELNFIHRHKTGKFIEASIVS 190
++ +IK ++ I E A + D +V+L E +KT I AS S
Sbjct: 224 DNLEVIKLISQVIKDFASGEIKQASSLFDC-----DVTLDEYLLKSYYKTASLIAASTKS 278
Query: 191 GVIIGGGNEEEIERMRNFGKYVGMAYQLWNDIVDVIGSPEMREK-TGRDMMRDKATYPKL 249
I G + E+M +GK +G+A+Q+ +DI+D S E K G D+ + T P +
Sbjct: 279 AAIFSGVDSSVKEQMYEYGKNLGLAFQVVDDILDFTQSTEQLGKPAGSDLAKGNLTAPVI 338
Query: 250 VGIDGSKKHAKELI 263
++ + +E+I
Sbjct: 339 FALEKEPE-LREII 351
>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 = 59.4 bits (144), Expect = 4e-10
Identities = 46/171 (26%), Positives = 84/171 (49%), Gaps = 6/171 (3%)
Query: 83 IELLVTMAVIQDDLPCLDNDDLRRGKPSNHKVFGEATAILACQALHCLAMQHIAIIKAKN 142
E++ T +++ DD+ +D D RRG + H +FG A+LA L A ++A ++
Sbjct: 76 TEMIHTASLVHDDV--IDESDTRRGIETVHSLFGTRVAVLAGDFLFAQASWYLANLENLE 133
Query: 143 INSAVGS--EGIAAGQIMD-INSEGKEVSLSELNFIHRHKTGKFIEASIVSGVIIGGGNE 199
+ + A G+I +N ++SL + +KT + AS + ++
Sbjct: 134 VVKLISKVITDFAEGEIKQGLNQFDSDLSLEDYLEKSFYKTASLVAASSKAAAVLSDVPS 193
Query: 200 EEIERMRNFGKYVGMAYQLWNDIVDVIGSPEMREK-TGRDMMRDKATYPKL 249
+ + +GK++G+A+Q+ +DI+D GS E K G D+M+ T P L
Sbjct: 194 QVANDLYEYGKHLGLAFQVVDDILDFTGSTEQLGKPAGSDLMKGNLTAPVL 244
>gnl|CDD|178478 PLN02890, PLN02890, geranyl diphosphate synthase.
Length = 422
Score = 46.8 bits (111), Expect = 6e-06
Identities = 43/155 (27%), Positives = 76/155 (49%), Gaps = 7/155 (4%)
Query: 78 SMACAIELLVTMAVIQDDLPCLDNDDLRRGKPSNHKVFGEATAILACQALHCLAMQHIAI 137
++A E++ +++ DD+ LD+ D RRG S + V G ++LA L A +A
Sbjct: 165 NIAEITEMIHVASLLHDDV--LDDADTRRGVGSLNVVMGNKLSVLAGDFLLSRACVALAA 222
Query: 138 IKAKNINS--AVGSEGIAAGQIMDINSEGKEVSLSELNFIHR--HKTGKFIEASIVSGVI 193
+K + S A E + G+ M I S +E S ++ + +KT I S + I
Sbjct: 223 LKNTEVVSLLATAVEHLVTGETMQITSS-REQRRSMDYYMQKTYYKTASLISNSCKAVAI 281
Query: 194 IGGGNEEEIERMRNFGKYVGMAYQLWNDIVDVIGS 228
+ G E +G+ +G+A+QL +D++D G+
Sbjct: 282 LAGQTAEVAVLAFEYGRNLGLAFQLIDDVLDFTGT 316
>gnl|CDD|240712 cd12266, RRM_like_XS, RNA recognition motif-like XS domain found in
plants. This XS (named after rice gene X and SGS3)
domain is a single-stranded RNA-binding domain (RBD) and
possesses a unique version of a RNA recognition motif
(RRM) fold. It is conserved in a family of plant
proteins including gene X and SGS3. Although its
function is still unknown, the plant SGS3 proteins are
thought to be involved in post-transcriptional gene
silencing (PTGS) pathways. In addition, they contain a
conserved aspartate residue that may be functionally
important. .
Length = 107
Score = 31.2 bits (71), Expect = 0.19
Identities = 14/46 (30%), Positives = 18/46 (39%), Gaps = 4/46 (8%)
Query: 253 DGSKKHAKELIAEAKQELAYFDPTRAAPL----DHLVNFIVSFGNN 294
D +K E + L F+PTR PL H IV F +
Sbjct: 17 DDERKMEGMGNKELLERLRKFNPTRVKPLYGYQGHTGFAIVEFAKD 62
>gnl|CDD|224156 COG1235, PhnP, Metal-dependent hydrolases of the beta-lactamase
superfamily I [General function prediction only].
Length = 269
Score = 32.4 bits (74), Expect = 0.23
Identities = 30/160 (18%), Positives = 46/160 (28%), Gaps = 15/160 (9%)
Query: 14 FQVNEYKALKAKQINEALDEAVPLPHPAILHEAMRYSLPGGKRLMSTLCIASCEMIGGSQ 73
+ + I P+PH AI G K T E G
Sbjct: 112 LFRHPFPPFSLPAIGGLEVTPFPVPHDAIEPVGFVIIRTGRKLHGGTDIGYGLEWRIGD- 170
Query: 74 SVAMSM-ACAIE--LLVTMAVIQD-DLPCLDNDDLRRGKPSNHKVFGEATAILACQALHC 129
VA V + L D G SNH EA ++
Sbjct: 171 -VAYLTDTELFPSNHDVELLDNGLYPLDIKDRILPDPGHLSNHLSAEEALELIEKLKPKR 229
Query: 130 LAMQHI---------AIIKAKNINSAVGSEGIAAGQIMDI 160
L + H+ ++A+ + A G GI G+++ +
Sbjct: 230 LVLTHLSHKNDDEELPELEAEEVEPAYGGMGIDVGEVLLV 269
>gnl|CDD|218769 pfam05833, FbpA, Fibronectin-binding protein A N-terminus (FbpA).
This family consists of the N-terminal region of the
prokaryotic fibronectin-binding protein. Fibronectin
binding is considered to be an important virulence
factor in streptococcal infections. Fibronectin is a
dimeric glycoprotein that is present in a soluble form
in plasma and extracellular fluids; it is also present
in a fibrillar form on cell surfaces. Both the soluble
and cellular forms of fibronectin may be incorporated
into the extracellular tissue matrix. While fibronectin
has critical roles in eukaryotic cellular processes,
such as adhesion, migration and differentiation, it is
also a substrate for the attachment of bacteria. The
binding of pathogenic Streptococcus pyogenes and
Staphylococcus aureus to epithelial cells via
fibronectin facilitates their internalisation and
systemic spread within the host.
Length = 447
Score = 31.4 bits (72), Expect = 0.57
Identities = 6/20 (30%), Positives = 12/20 (60%)
Query: 255 SKKHAKELIAEAKQELAYFD 274
+ + +E I E K+E+ Y +
Sbjct: 387 AVEAVEEQIEETKEEIEYLE 406
>gnl|CDD|129242 TIGR00136, gidA, glucose-inhibited division protein A. GidA, the
longer of two forms of GidA-related proteins, appears to
be present in all complete eubacterial genomes so far,
as well as Saccharomyces cerevisiae. A subset of these
organisms have a closely related protein. GidA is absent
in the Archaea. It appears to act with MnmE, in an
alpha2/beta2 heterotetramer, in the
5-carboxymethylaminomethyl modification of uridine 34 in
certain tRNAs. The shorter, related protein, previously
called gid or gidA(S), is now called TrmFO (see model
TIGR00137) [Protein synthesis, tRNA and rRNA base
modification].
Length = 617
Score = 31.2 bits (71), Expect = 0.68
Identities = 16/68 (23%), Positives = 34/68 (50%), Gaps = 3/68 (4%)
Query: 199 EEEIERMRNFGKYVGMAYQLWNDIVDVIGSPEMREKTGRDMMRDKA-TYPKLVGIDGSKK 257
EEEI+R+++ ++ + ++ ++ + + SP RE +G D++R KL +
Sbjct: 469 EEEIQRLKST--WLTPSKEVKEELKNHLQSPLKREASGEDLLRRPEMNLEKLTKLTPFLP 526
Query: 258 HAKELIAE 265
E + E
Sbjct: 527 ALDEEVLE 534
>gnl|CDD|181762 PRK09291, PRK09291, short chain dehydrogenase; Provisional.
Length = 257
Score = 29.6 bits (67), Expect = 1.6
Identities = 17/64 (26%), Positives = 22/64 (34%), Gaps = 13/64 (20%)
Query: 223 VDVIGSPEMREKTGRDMMRDKA------------TYPKLVGIDGSKKHAKELIAEA-KQE 269
+V G E+ + R M+ G + KHA E IAEA E
Sbjct: 103 TNVFGPLELTQGFVRKMVARGKGKVVFTSSMAGLITGPFTGAYCASKHALEAIAEAMHAE 162
Query: 270 LAYF 273
L F
Sbjct: 163 LKPF 166
>gnl|CDD|139538 PRK13390, PRK13390, acyl-CoA synthetase; Provisional.
Length = 501
Score = 30.0 bits (67), Expect = 1.8
Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 9/58 (15%)
Query: 223 VDVIG--SPEMREKTGRDMMRDKATYPKLVGIDGSKKHAKELIAEAKQELAYFDPTRA 278
V VIG PEM E+ KA + GI GS + A+ELI + +A++ R+
Sbjct: 430 VAVIGVPDPEMGEQV-------KAVIQLVEGIRGSDELARELIDYTRSRIAHYKAPRS 480
>gnl|CDD|212591 cd11692, HRI1_N_like, N-terminal domain of HRI1 and related
proteins. Saccharomyces cerevisiae Hri1p
(Hrr25-interacting protein 1, YLR301w) is a
non-essential gene product named for its interaction
with the yeast protein kinase Hrr25p. It has also been
characterized as an interaction partner for Sec72p, but
does not seem to be required for protein translocation
into the ER. It may be a cytosolic protein. Hri1p
contains a tandem repeat of a structural unit that forms
a beta-barrel with structural similarity to nitrobindin.
This N-terminal repeat is involved in homodimerization
and may contain a ligand binding site.
Length = 134
Score = 28.5 bits (64), Expect = 2.2
Identities = 11/59 (18%), Positives = 19/59 (32%), Gaps = 6/59 (10%)
Query: 170 SELNFIHRHKTGKFIEASIVSGV-----IIGGGNEEEIERMRNFGKYVGMAYQ-LWNDI 222
S +F H + + + + G+ E RM N Y+ LW +
Sbjct: 72 SHQDFTHWIDSRVYNPPEADGDIGTFYPLWDSGDRLETGRMVNPETGRVEEYEELWRPL 130
>gnl|CDD|236830 PRK11049, PRK11049, D-alanine/D-serine/glycine permease;
Provisional.
Length = 469
Score = 29.3 bits (66), Expect = 3.0
Identities = 12/26 (46%), Positives = 15/26 (57%), Gaps = 2/26 (7%)
Query: 39 HPAILHEAMRYSLPGGKRLMSTLCIA 64
P LHE Y +P GK LM +C+A
Sbjct: 400 RPH-LHEKSIYKMPLGK-LMCWVCMA 423
>gnl|CDD|225500 COG2949, SanA, Uncharacterized membrane protein [Function unknown].
Length = 235
Score = 28.1 bits (63), Expect = 4.7
Identities = 9/28 (32%), Positives = 11/28 (39%), Gaps = 5/28 (17%)
Query: 112 HKVFGEATAILACQALHC-----LAMQH 134
KVFG + Q HC +A Q
Sbjct: 145 RKVFGTNDFTIITQRFHCERALFIARQM 172
>gnl|CDD|153415 cd07961, Anticodon_Ia_Ile_ABEc, Anticodon-binding domain of
archaeal, bacterial, and eukaryotic cytoplasmic
isoleucyl tRNA synthetases. This domain is found in
isoleucyl tRNA synthetases (IleRS), which belong to the
class Ia aminoacyl tRNA synthetases. It lies C-terminal
to the catalytic core domain, and recognizes and
specifically binds to the tRNA anticodon. This family
includes bacterial, archaeal, and eukaryotic cytoplasmic
members. IleRS catalyzes the transfer of isoleucine to
the 3'-end of its tRNA.
Length = 183
Score = 27.9 bits (63), Expect = 5.1
Identities = 9/28 (32%), Positives = 13/28 (46%), Gaps = 2/28 (7%)
Query: 262 LIAEAKQELAYFDPTRAAPLDHLVNFIV 289
LI E +E+ +D A L+ FI
Sbjct: 59 LIKEVTEEMEAYDLYTAVR--ALLEFID 84
>gnl|CDD|220807 pfam10552, ORF6C, ORF6C domain. This domain was identified by
Iyer and colleagues.
Length = 114
Score = 26.8 bits (60), Expect = 7.5
Identities = 10/31 (32%), Positives = 14/31 (45%), Gaps = 4/31 (12%)
Query: 2 INSQRNDTLPKFFQVNEYKALKAKQINEALD 32
I Q F V+ YKA+ K +EA +
Sbjct: 72 IYRQLKRE----FGVSSYKAIPRKDFDEAKE 98
>gnl|CDD|235160 PRK03803, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 448
Score = 27.6 bits (62), Expect = 9.1
Identities = 19/49 (38%), Positives = 24/49 (48%), Gaps = 5/49 (10%)
Query: 24 AKQINEALDEAVPLPHPAILHEAMRYSL----PGGKRLMSTLCIASCEM 68
A +I AL AVPL A L EA+ + G L+S C AS +M
Sbjct: 381 ADKIAAALGGAVPLVRVATLAEAVAKAAELAQAGDIVLLSPAC-ASLDM 428
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 0.387
Gapped
Lambda K H
0.267 0.0757 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,254,752
Number of extensions: 1486369
Number of successful extensions: 1423
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1389
Number of HSP's successfully gapped: 31
Length of query: 295
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 199
Effective length of database: 6,679,618
Effective search space: 1329243982
Effective search space used: 1329243982
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 (21.7 bits)
S2: 59 (26.5 bits)