RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 019903
(334 letters)
>gnl|CDD|223220 COG0142, IspA, Geranylgeranyl pyrophosphate synthase [Coenzyme
metabolism].
Length = 322
Score = 204 bits (520), Expect = 1e-63
Identities = 101/338 (29%), Positives = 150/338 (44%), Gaps = 67/338 (19%)
Query: 41 DLKTYWTTLITEIDQNLEKAITVKYPEQIYESMRYSVLAKGTKRAPPVMCVAACELFGVN 100
DL + I++ L + ++ PE + E+MRY +LA G KR P++ + A E G++
Sbjct: 2 DLLALLLKRLARIEELLSELLSGSDPELLLEAMRYLLLAGG-KRLRPLLVLLAAEALGID 60
Query: 101 RIA----AFPTACALEMVHAASLIHDDLPCMDDDPSRRGQPSNHTVYGVDIAILAGDALF 156
A A A+E++H ASLIHDDL MDDD RRG+P+ H +G AILAGDAL
Sbjct: 61 LETGGNDALDLAAAIELIHTASLIHDDL--MDDDDLRRGKPTVHAKFGEATAILAGDALL 118
Query: 157 PLGFQHIVSHTPPHLVPEPRVLRVIAEIARAVGSTGMAAGQFLDLEGEPNLV-----EFV 211
F+ + ++ +AE G+ GQ LDL E V V
Sbjct: 119 AAAFELLSKLG----SEALEAIKALAE-----AINGLCGGQALDLAFENKPVTLEEYLRV 169
Query: 212 QEKKFGEMSECSAVCGGFLAGADDDEIQSLRRYGRAVGVLYQVVDDILEAKAQTPRDEEK 271
E K + +AV G LAGAD++ +++L YGR +G+ +Q+ DDIL+ DEE+
Sbjct: 170 IELKTAALFAAAAVLGAILAGADEELLEALEDYGRNLGLAFQIQDDILDITG----DEEE 225
Query: 272 KKKK-------GK-SYVAFYGVEKAME--------------------------------- 290
K GK + +EKA E
Sbjct: 226 LGKPVGSDLKEGKPTLPVLLALEKANEDQKLLRILLEGGGEVEEALELLRKSGAIEYAKN 285
Query: 291 VAEELRAKAKEELDRFKKYGDNVLPLYSFIDYAADREF 328
+A+ KAKE L++ + L D+ R++
Sbjct: 286 LAKTYVEKAKEALEKLPD-SEAKEALLELADFIIKRKY 322
>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 = 195 bits (497), Expect = 6e-61
Identities = 85/276 (30%), Positives = 132/276 (47%), Gaps = 34/276 (12%)
Query: 66 PEQIYESMRYSVLAKGTKRAPPVMCVAACELFGVNRI-AAFPTACALEMVHAASLIHDDL 124
E + E++RY +LA G KR P++ + A G + AA A A+E++H ASL+HDD+
Sbjct: 3 VELLREALRYLLLAGG-KRLRPLLVLLAARALGGPELEAALRLAAAIELLHTASLVHDDV 61
Query: 125 PCMDDDPSRRGQPSNHTVYGVDIAILAGDALFPLGFQHIVSHTPPHLVPEPRVLRVIAEI 184
MD+ RRG+P+ H V+G AILAGD L F+ + P+ PR L + +E
Sbjct: 62 --MDNSDLRRGKPTVHKVFGNATAILAGDYLLARAFELLARLGNPYY---PRALELFSE- 115
Query: 185 ARAVGSTGMAAGQFLDLEGEPNL------VEFVQEKKFGEMSECSAVCGGFLAGADDDEI 238
+ GQ LDL E + + K + + + G LAGAD++E
Sbjct: 116 ----AILELVEGQLLDLLSEYDTDVTEEEYLRIIRLKTAALFAAAPLLGALLAGADEEEA 171
Query: 239 QSLRRYGRAVGVLYQVVDDILEAKAQTPRDEEKKKK-------KGK-SYVAFYGVEKAME 290
++L+R+GR +G+ +Q+ DDIL+ D E K +GK + + E
Sbjct: 172 EALKRFGRNLGLAFQIQDDILDLFG----DPETLGKPVGSDLREGKCTLPVLLALR---E 224
Query: 291 VAEELRAKAKEELDRFKKYGDNVLPLYSFIDYAADR 326
+A E KA E L + L + D+ +R
Sbjct: 225 LAREYEEKALEALKALPE-SPAREALRALADFILER 259
>gnl|CDD|215873 pfam00348, polyprenyl_synt, Polyprenyl synthetase.
Length = 260
Score = 167 bits (424), Expect = 5e-50
Identities = 86/270 (31%), Positives = 131/270 (48%), Gaps = 26/270 (9%)
Query: 69 IYESMRYSVLAKGTKRAPPVMCVAACELFGVNRIAAFPTACALEMVHAASLIHDDLPCMD 128
+ +M Y +LA G KR P++ V A GV ACA+EM+H ASL+HDDL MD
Sbjct: 1 LLAAMLYYLLAGG-KRIRPLLVVLAARALGVEPETLLYLACAIEMIHTASLVHDDL--MD 57
Query: 129 DDPSRRGQPSNHTVYGVDIAILAGDALFPLGFQHIVSHTPPHLVPEPRVLRVIAEIARAV 188
+ RRG+P+ H +G AILAGDAL FQ + H+ PEP+ + + E+A AV
Sbjct: 58 NSDLRRGKPTCHKKFGEAGAILAGDALLSRAFQLLAL--LGHVRPEPKYILIS-ELANAV 114
Query: 189 GSTGMAAGQFLDLEGEPNLV-----EFVQEKKFGEMSECSAVCGGFLAGADDDEIQSLRR 243
G+ G GQ +DLE E + + K + S G +AGAD+++ + L
Sbjct: 115 GAQGE-VGQLMDLETEGKDITLEEYLRIVSYKTAALFYASVQLGAIVAGADEEDEKDLYD 173
Query: 244 YGRAVGVLYQVVDDILEAKAQTPRDEEKKKKKG--------KSYVAFYGVEKAMEVAEEL 295
+GR +G+ +Q+ DDIL+ D E+ K + +E A E +L
Sbjct: 174 FGRDLGLAFQIQDDILDLTG----DTEELGKPVGTDLQEGKSTLPVLLALEGAREEQRKL 229
Query: 296 RAKAKEELDRFKKYGDNVLPLYSFIDYAAD 325
+A E+ + + L ++ A+
Sbjct: 230 LREAYEQKL--SEAAAQGVALTKALEALAE 257
>gnl|CDD|182567 PRK10581, PRK10581, geranyltranstransferase; Provisional.
Length = 299
Score = 158 bits (402), Expect = 2e-46
Identities = 97/267 (36%), Positives = 137/267 (51%), Gaps = 12/267 (4%)
Query: 71 ESMRYSVLAKGTKRAPPVMCVAACELFGVNRIAAFPTACALEMVHAASLIHDDLPCMDDD 130
E+M+Y L G KR P + A ++FGV+ A A+E +HA SLIHDDLP MDDD
Sbjct: 34 EAMQYGALLGG-KRLRPFLVYATGQMFGVSTNTLDAPAAAVECIHAYSLIHDDLPAMDDD 92
Query: 131 PSRRGQPSNHTVYGVDIAILAGDALFPLGFQHIVSHTPPHLVPEPRVLRVIAEIARAVGS 190
RRG P+ H +G AILAGDAL L F I+S P V + + +I+E+A A G
Sbjct: 93 DLRRGLPTCHVKFGEANAILAGDALQTLAFS-ILSDAPMPEVSDRDRISMISELASASGI 151
Query: 191 TGMAAGQFLDLEGEPNLV-----EFVQEKKFGEMSECSAVCGGFLAG-ADDDEIQSLRRY 244
GM GQ LDLE E V E + K G + + G AG + L RY
Sbjct: 152 AGMCGGQALDLEAEGKQVPLDALERIHRHKTGALIRAAVRLGALSAGDKGRRALPVLDRY 211
Query: 245 GRAVGVLYQVVDDILEA---KAQTPRDEEKKKKKGKS-YVAFYGVEKAMEVAEELRAKAK 300
++G+ +QV DDIL+ A + + ++ GKS Y A G+E+A + A +L A+
Sbjct: 212 AESIGLAFQVQDDILDVVGDTATLGKRQGADQQLGKSTYPALLGLEQARKKARDLIDDAR 271
Query: 301 EELDRFKKYGDNVLPLYSFIDYAADRE 327
+ LD+ + L + +Y R+
Sbjct: 272 QSLDQLAAQSLDTSALEALANYIIQRD 298
>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 = 139 bits (352), Expect = 1e-39
Identities = 74/230 (32%), Positives = 110/230 (47%), Gaps = 27/230 (11%)
Query: 87 PVMCVAACELFGVNRIAAFPTACALEMVHAASLIHDDLPCMDDDPSRRGQPSNHTV-YGV 145
P++ + G + AA A A+E++HAASL+HDD+ +DD RRG+P+ H +G
Sbjct: 3 PLLVLLLARALGGDLEAALRLAAAVELLHAASLVHDDI--VDDSDLRRGKPTAHLRRFGN 60
Query: 146 DIAILAGDALFPLGFQHIVSHTPPHLVPEPRVLRVIAEIARAVGSTGMAAGQFLDLEGEP 205
+AILAGD L FQ + PR L + AE R + GQ LDLE E
Sbjct: 61 ALAILAGDYLLARAFQLLARL------GYPRALELFAEALRE-----LLEGQALDLEFER 109
Query: 206 NLVE------FVQEKKFGEMSECSAVCGGFLAGADDDEIQSLRRYGRAVGVLYQVVDDIL 259
+ E K + + G L+GADD++ ++L+ YGRA+G+ +Q+ DD+L
Sbjct: 110 DTYETLDEYLEYCRYKTAGLVGLLCLLGAGLSGADDEQAEALKDYGRALGLAFQLTDDLL 169
Query: 260 EAKAQTPRDEEKKKKKG---KSYVAFYGVEKAMEVAEELRAKAKEELDRF 306
+ D E+ K G + V A E A E +A L+
Sbjct: 170 DVFG----DAEELGKVGSDLREGRITLPVILARERAAEYAEEAYAALEAL 215
>gnl|CDD|164542 CHL00151, preA, prenyl transferase; Reviewed.
Length = 323
Score = 132 bits (335), Expect = 3e-36
Identities = 70/282 (24%), Positives = 128/282 (45%), Gaps = 30/282 (10%)
Query: 37 STQFDLKTYWTTLITEIDQNLEKAITVKYPEQIYESMRYSVLAKGTKRAPPVMCVAACEL 96
+T +L T + ++ NL+K I +P +Y + ++ A G KR P + + +
Sbjct: 2 ATNSNLLTPIEEELLILEDNLKKLIGSGHP-ILYAAAKHLFSAGG-KRIRPAIVLLVAKA 59
Query: 97 FGVNRIAAFPT---ACALEMVHAASLIHDDLPCMDDDPSRRGQPSNHTVYGVDIAILAGD 153
G N A E++H ASL+HDD+ +D+ RRG P+ H ++G IA+LAGD
Sbjct: 60 TGGNMEIKTSQQRLAEITEIIHTASLVHDDV--IDECSIRRGIPTVHKIFGTKIAVLAGD 117
Query: 154 ALFPLGFQHIVSHTPPHLVPEPRVLRVIAEIARAVGSTGMAAGQF-LDLEGEPNLVEFVQ 212
LF ++ + +L + +VI + A G+ QF L ++ ++
Sbjct: 118 FLFAQSSWYLANLN--NLEVVKLISKVITDFAEGEIRQGLV--QFDTTLS----ILNYI- 168
Query: 213 EKKF---GEMSECSAVCGGFLAGADDDEIQSLRRYGRAVGVLYQVVDDILEAKAQTPRDE 269
EK F + S L+ AD+ + YG+ +G+ +Q++DD+L+ + T E
Sbjct: 169 EKSFYKTASLIAASCKAAALLSDADEKDHNDFYLYGKHLGLAFQIIDDVLDITSST---E 225
Query: 270 EKKK------KKGK-SYVAFYGVEKAMEVAEELRAKAKEELD 304
K K G + + + + ++A+ + + E D
Sbjct: 226 SLGKPIGSDLKNGNLTAPVLFALTQNSKLAKLIEREFCETKD 267
>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 = 101 bits (254), Expect = 2e-25
Identities = 59/227 (25%), Positives = 104/227 (45%), Gaps = 47/227 (20%)
Query: 108 ACALEMVHAASLIHDDLPCMDDDPSRRGQPSNH---TVYGVDIAILAGDALFPLGFQHIV 164
A+E +HAASL+HDD+ +DD +RRG P+ H + G+ AILAGD L F+ +
Sbjct: 16 RAAVEKLHAASLVHDDI--VDDSGTRRGLPTAHLAVAIDGLPEAILAGDLLLADAFEELA 73
Query: 165 SHTPPHLVPEPRVLRVIAEIARAVGSTGMAAGQFLDLEGEPNLVEFVQE------KKFGE 218
P L ++AE + GQ LDL+ V ++E K
Sbjct: 74 REGSP------EALEILAEALLD-----LLEGQLLDLKWRREYVPTLEEYLEYCRYKTAG 122
Query: 219 MSECSAVCGGFLAGADDDEIQSLRRYGRAVGVLYQVVDDILEAKAQTPRDEEKKKKKGKS 278
+ + G L+G + + +++LR+ GRA+G+ +Q+ +D+L+ + + ++ +GK
Sbjct: 123 LVGALCLLGAGLSGGEAELLEALRKLGRALGLAFQLTNDLLDYE------GDAERGEGKC 176
Query: 279 Y-------------------VAFYGVEKAMEVAEELRAKAKEELDRF 306
+E+A+E +L +A +EL+
Sbjct: 177 TLPVLYALEYGVPAEDLLLVEKSGSLEEALEELAKLAEEALKELNEL 223
>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 = 81.3 bits (201), Expect = 2e-17
Identities = 63/216 (29%), Positives = 107/216 (49%), Gaps = 19/216 (8%)
Query: 50 ITEIDQNLEKAITVKYPEQIYESMRYSVLAKGTKRAPPVMCVAACEL--FGVNRIAAFPT 107
I I++ LEKA+ ++P + +L G KR PV + A + + ++ I
Sbjct: 13 IDSIEKELEKAVQAEHP--VLSEASLHLLEAGGKRIRPVFVLLAGKFGDYDLDAIKH--V 68
Query: 108 ACALEMVHAASLIHDDLPCMDDDPSRRGQPSNHTVYGVDIAILAGDALFPLGFQHIVSHT 167
A ALE++H ASL+HDD+ +DD RRG+P+ + +G IA+ GD LF + +
Sbjct: 69 AVALELIHMASLVHDDV--IDDADLRRGRPTIKSKWGNRIAMYTGDYLFAKSLETMTE-- 124
Query: 168 PPHLVPEPRVLRVIAEIARAVGSTGMAAGQFLD-LEGEPNLVEFVQEKKFGEMSECSAVC 226
+ +PR ++++ V G Q D + NL +++ K +A C
Sbjct: 125 ----IKDPRAHQILSHTIVEV-CRGEIE-QIKDKYNFDQNLRTYLRRIKRKTALLIAASC 178
Query: 227 --GGFLAGADDDEIQSLRRYGRAVGVLYQVVDDILE 260
G +GA++ ++ L +G VG+ YQ+ DDIL+
Sbjct: 179 QLGAIASGANEAIVKKLYWFGYYVGMSYQITDDILD 214
>gnl|CDD|182813 PRK10888, PRK10888, octaprenyl diphosphate synthase; Provisional.
Length = 323
Score = 79.5 bits (196), Expect = 7e-17
Identities = 57/195 (29%), Positives = 99/195 (50%), Gaps = 19/195 (9%)
Query: 75 YSVLAKGTKRAPPVMCVAACELFGVNRIAAFPTACALEMVHAASLIHDDLPCMDDDPSRR 134
Y +++ G KR P++ V A G A A +E +H A+L+HDD+ +D+ RR
Sbjct: 37 YYIISGGGKRIRPMIAVLAARAVGYQGNAHVTIAALIEFIHTATLLHDDV--VDESDMRR 94
Query: 135 GQPSNHTVYGVDIAILAGDALFPLGFQHIVSHTPPHLVPEPRVLRVIAEIARAVGSTGMA 194
G+ + + +G ++L GD ++ FQ + S + +VL V++E + A
Sbjct: 95 GKATANAAFGNAASVLVGDFIYTRAFQMMTS------LGSLKVLEVMSEAVNVI-----A 143
Query: 195 AGQFLDLEG--EPNLVE----FVQEKKFGEMSECSAVCGGFLAGADDDEIQSLRRYGRAV 248
G+ L L +P++ E V K + E +A C G LAG ++ + L+ YGR +
Sbjct: 144 EGEVLQLMNVNDPDITEENYMRVIYSKTARLFEAAAQCSGILAGCTPEQEKGLQDYGRYL 203
Query: 249 GVLYQVVDDILEAKA 263
G +Q++DD+L+ A
Sbjct: 204 GTAFQLIDDLLDYSA 218
>gnl|CDD|215462 PLN02857, PLN02857, octaprenyl-diphosphate synthase.
Length = 416
Score = 74.1 bits (182), Expect = 9e-15
Identities = 60/224 (26%), Positives = 106/224 (47%), Gaps = 35/224 (15%)
Query: 53 IDQNLEKAITVKYP------EQIYESMRYSVLAKGTKRAPPVMCV----AACELFGVNRI 102
++ NL+ + + P EQI+ G KR P + A EL G+ +
Sbjct: 108 LNDNLQSIVGAENPVLMSAAEQIF--------GAGGKRMRPALVFLVSRATAELAGLKEL 159
Query: 103 AAFPTACA--LEMVHAASLIHDDLPCMDDDPSRRGQPSNHTVYGVDIAILAGDALFPLGF 160
A EM+H ASLIHDD+ +D+ RRG+ + H +YG +A+LAGD +F
Sbjct: 160 TTEHRRLAEITEMIHTASLIHDDV--LDESDMRRGKETVHQLYGTRVAVLAGDFMFAQSS 217
Query: 161 QHIVSHTPPHLVPEPRVLRVIAEIAR--AVGSTGMAAGQFLDLEGEPNLVEFVQEKKFGE 218
++ + + V+++I+++ + A G A+ F + + L E++ + +
Sbjct: 218 WYLAN------LDNLEVIKLISQVIKDFASGEIKQASSLF---DCDVTLDEYLLKSYYKT 268
Query: 219 MSECSAVCGG--FLAGADDDEIQSLRRYGRAVGVLYQVVDDILE 260
S +A +G D + + YG+ +G+ +QVVDDIL+
Sbjct: 269 ASLIAASTKSAAIFSGVDSSVKEQMYEYGKNLGLAFQVVDDILD 312
>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 = 68.6 bits (168), Expect = 4e-13
Identities = 45/156 (28%), Positives = 80/156 (51%), Gaps = 21/156 (13%)
Query: 112 EMVHAASLIHDDLPCMDDDPSRRGQPSNHTVYGVDIAILAGDALFPLGFQHIVSHTPPHL 171
EM+H ASL+HDD+ +D+ +RRG + H+++G +A+LAGD LF ++ +
Sbjct: 77 EMIHTASLVHDDV--IDESDTRRGIETVHSLFGTRVAVLAGDFLFAQASWYLAN------ 128
Query: 172 VPEPRVLRVIAEIAR--AVGSTGMAAGQF---LDLEGEPNLVEFVQEKKFGEMSECSAVC 226
+ V+++I+++ A G QF L LE +++++ + S +A
Sbjct: 129 LENLEVVKLISKVITDFAEGEIKQGLNQFDSDLSLE------DYLEKSFYKTASLVAASS 182
Query: 227 --GGFLAGADDDEIQSLRRYGRAVGVLYQVVDDILE 260
L+ L YG+ +G+ +QVVDDIL+
Sbjct: 183 KAAAVLSDVPSQVANDLYEYGKHLGLAFQVVDDILD 218
>gnl|CDD|178478 PLN02890, PLN02890, geranyl diphosphate synthase.
Length = 422
Score = 51.9 bits (124), Expect = 2e-07
Identities = 47/162 (29%), Positives = 71/162 (43%), Gaps = 33/162 (20%)
Query: 112 EMVHAASLIHDDLPCMDDDPSRRGQPSNHTVYGVDIAILAGD--------ALFPLGFQHI 163
EM+H ASL+HDD+ +DD +RRG S + V G +++LAGD AL L +
Sbjct: 171 EMIHVASLLHDDV--LDDADTRRGVGSLNVVMGNKLSVLAGDFLLSRACVALAALKNTEV 228
Query: 164 VS---HTPPHLVPEPRVLRVIAEIARAVGSTGMAAGQFLDLEGEPNLVEFVQEKKFGEMS 220
VS HLV TG E ++ ++Q+ + S
Sbjct: 229 VSLLATAVEHLV------------------TGETMQITSSREQRRSMDYYMQKTYYKTAS 270
Query: 221 ECSAVCG--GFLAGADDDEIQSLRRYGRAVGVLYQVVDDILE 260
S C LAG + YGR +G+ +Q++DD+L+
Sbjct: 271 LISNSCKAVAILAGQTAEVAVLAFEYGRNLGLAFQLIDDVLD 312
>gnl|CDD|218148 pfam04557, tRNA_synt_1c_R2, Glutaminyl-tRNA synthetase,
non-specific RNA binding region part 2. This is a
region found N terminal to the catalytic domain of
glutaminyl-tRNA synthetase (EC 6.1.1.18) in eukaryotes
but not in Escherichia coli. This region is thought to
bind RNA in a non-specific manner, enhancing
interactions between the tRNA and enzyme, but is not
essential for enzyme function.
Length = 83
Score = 30.4 bits (69), Expect = 0.26
Identities = 16/55 (29%), Positives = 19/55 (34%), Gaps = 7/55 (12%)
Query: 265 TPRDEEKKKKKGKSYVAFYGVEKAMEVAEEL-----RAKAKEEL--DRFKKYGDN 312
T D KKKKK K A A A E ++F K G+N
Sbjct: 18 TEADLVKKKKKKKKKKAEDTAATAKAKKATAEDVSEGAMFMEGFLGEKFHKPGEN 72
>gnl|CDD|240576 cd12932, RRP7_like, RRP7 domain ribosomal RNA-processing protein 7
(Rrp7p), ribosomal RNA-processing protein 7 homolog A
(Rrp7A), and similar proteins. This CD corresponds to
the RRP7 domain of Rrp7p and Rrp7A. Rrp7p is encoded by
YCL031C gene from Saccharomyces cerevisiae. It is an
essential yeast protein involved in pre-rRNA processing
and ribosome assembly, and is speculated to be required
for correct assembly of rpS27 into the pre-ribosomal
particle. Rrp7A, also termed gastric cancer antigen
Zg14, is the Rrp7p homolog mainly found in Metazoans.
The cellular function of Rrp7A remains unclear
currently. Both Rrp7p and Rrp7A harbor an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal RRP7 domain.
Length = 118
Score = 29.9 bits (68), Expect = 0.77
Identities = 20/51 (39%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 258 ILEAKAQTPRDEEKKKKKGKSYVAFYGV---EKAMEVAEELRAKAKEELDR 305
EA +++EKKKKK K FY EK E ELR K +E+ R
Sbjct: 67 REEAVEAKAKEKEKKKKKKKELEDFYRFQIREKKKEELAELRKKFEEDKKR 117
>gnl|CDD|179302 PRK01558, PRK01558, V-type ATP synthase subunit E; Provisional.
Length = 198
Score = 30.5 bits (69), Expect = 0.93
Identities = 11/25 (44%), Positives = 20/25 (80%)
Query: 285 VEKAMEVAEELRAKAKEELDRFKKY 309
+ KA E A+EL+AKA++E + +K++
Sbjct: 39 IAKAEEEAKELKAKAEKEANDYKRH 63
>gnl|CDD|233251 TIGR01054, rgy, reverse gyrase. This model describes reverse
gyrase, found in both archaeal and bacterial
thermophiles. This enzyme, a fusion of a type I
topoisomerase domain and a helicase domain, introduces
positive supercoiling to increase the melting
temperature of DNA double strands. Generally, these
gyrases are encoded as a single polypeptide. An
exception was found in Methanopyrus kandleri, where
enzyme is split within the topoisomerase domain,
yielding a heterodimer of gene products designated RgyB
and RgyA [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1171
Score = 30.9 bits (70), Expect = 1.1
Identities = 25/87 (28%), Positives = 35/87 (40%), Gaps = 21/87 (24%)
Query: 237 EIQSLRRYGRAVGVLYQVVDDILEAKAQTPRDEEKKKKKGKS---YVA-FYGVEKAMEVA 292
E+ R V +Y +D+ E E KK G YV+ YG EKA E+A
Sbjct: 293 EVGGGSDTLRNVVDVYVEDEDLKETLL------EIVKKLGTGGIVYVSIDYGKEKAEEIA 346
Query: 293 EELR-----------AKAKEELDRFKK 308
E L K KE+ ++F +
Sbjct: 347 EFLENHGVKAVAYHATKPKEDYEKFAE 373
>gnl|CDD|224035 COG1110, COG1110, Reverse gyrase [DNA replication, recombination,
and repair].
Length = 1187
Score = 30.8 bits (70), Expect = 1.3
Identities = 22/77 (28%), Positives = 33/77 (42%), Gaps = 13/77 (16%)
Query: 245 GRAVGVLYQVVD--DILEAKAQTPRDEEKKKKKGKSYVA-FYGVEKAMEVAEELR----- 296
G L +VD E+ + +K G +V YG EKA E+AE LR
Sbjct: 305 GSGGEGLRNIVDIYVESESLEKVVELVKKLGDGGLIFVPIDYGREKAEELAEYLRSHGIN 364
Query: 297 -----AKAKEELDRFKK 308
A+ +E L+ F++
Sbjct: 365 AELIHAEKEEALEDFEE 381
>gnl|CDD|188151 TIGR01517, ATPase-IIB_Ca, plasma-membrane calcium-translocating
P-type ATPase. This model describes the P-type ATPase
responsible for translocating calcium ions across the
plasma membrane of eukaryotes , out of the cell. In some
organisms, this type of pump may also be found in
vacuolar membranes. In humans and mice, at least, there
are multiple isoforms of the PMCA pump with overlapping
but not redundant functions. Accordingly, there are no
human diseases linked to PMCA defects, although
alterations of PMCA function do elicit physiological
effects. The calcium P-type ATPases have been
characterized as Type IIB based on a phylogenetic
analysis which distinguishes this group from the Type
IIA SERCA calcium pump. A separate analysis divides Type
IIA into sub-types (SERCA and PMR1) which are modelled
by TIGR01116 and TIGR01522. This model is well separated
from those.
Length = 944
Score = 30.5 bits (69), Expect = 1.4
Identities = 15/75 (20%), Positives = 23/75 (30%), Gaps = 5/75 (6%)
Query: 246 RAVGVLYQVVDDILEAKAQTPRDEEKKKKKGKSYVAFYGVEK-----AMEVAEELRAKAK 300
R + D + + K+ Y G E ++ E +R +
Sbjct: 6 RRTSIRDNFTDGFDVGVSILTDLTDIFKRAMPLYEKLGGAEGIATKLKTDLNEGVRLSSS 65
Query: 301 EELDRFKKYGDNVLP 315
R K YG N LP
Sbjct: 66 TLERREKVYGKNELP 80
>gnl|CDD|235908 PRK07008, PRK07008, long-chain-fatty-acid--CoA ligase; Validated.
Length = 539
Score = 30.4 bits (69), Expect = 1.5
Identities = 24/94 (25%), Positives = 36/94 (38%), Gaps = 19/94 (20%)
Query: 71 ESMRYSVLAK---GTKRAPPVMCVAACELFGVNRIAA--------FPTACALEMVHAASL 119
+R+S L + G PP M + +GV I A T C L+
Sbjct: 288 AGLRFSTLRRTVIGGSACPPAMIRTFEDEYGVEVIHAWGMTEMSPLGTLCKLK------W 341
Query: 120 IHDDLPCMDDDPSRRGQPSNHTVYGVDIAILAGD 153
H LP D+ + + +YGVD+ I+ D
Sbjct: 342 KHSQLP--LDEQRKLLEKQGRVIYGVDMKIVGDD 373
>gnl|CDD|240578 cd12951, RRP7_Rrp7A, RRP7 domain ribosomal RNA-processing protein 7
homolog A (Rrp7A) and similar proteins. The family
corresponds to the RRP7 domain of Rrp7A, also termed
gastric cancer antigen Zg14, and similar proteins which
are yeast ribosomal RNA-processing protein 7 (Rrp7p)
homologs mainly found in Metazoans. The cellular
function of Rrp7A remains unclear currently. Rrp7A
harbors an N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal RRP7
domain.
Length = 129
Score = 28.8 bits (65), Expect = 2.1
Identities = 18/49 (36%), Positives = 23/49 (46%), Gaps = 3/49 (6%)
Query: 260 EAKAQTPRDEEKKKKKGKSYVAFYGV---EKAMEVAEELRAKAKEELDR 305
E+ A ++EKKKKK K FY E ELR K +E+ R
Sbjct: 68 ESVAAKAAEKEKKKKKKKELKNFYRFQIRESKRNELAELRKKFEEDKKR 116
>gnl|CDD|224536 COG1621, SacC, Beta-fructosidases (levanase/invertase)
[Carbohydrate transport and metabolism].
Length = 486
Score = 29.3 bits (66), Expect = 3.4
Identities = 9/51 (17%), Positives = 18/51 (35%), Gaps = 3/51 (5%)
Query: 13 CVCLPRKFPVRCSSL---PVSAASQLRSTQFDLKTYWTTLITEIDQNLEKA 60
+ LPR+ + L PV LR + + ++++ A
Sbjct: 318 AMTLPRELTLEDGKLYQTPVRELESLRKPEEAAHNTTLSGNSKLELPSGDA 368
>gnl|CDD|111813 pfam02965, Met_synt_B12, Vitamin B12 dependent methionine synthase,
activation domain.
Length = 126
Score = 28.0 bits (63), Expect = 3.5
Identities = 14/51 (27%), Positives = 20/51 (39%), Gaps = 4/51 (7%)
Query: 273 KKKGKSYVAFY----GVEKAMEVAEELRAKAKEELDRFKKYGDNVLPLYSF 319
KG Y A G A +AE L + ++E +K G + YS
Sbjct: 23 FAKGDDYKAIIVDALGSALAEALAEYLHKRLRKEWGYGEKEGLKITIRYSP 73
>gnl|CDD|223322 COG0244, RplJ, Ribosomal protein L10 [Translation, ribosomal
structure and biogenesis].
Length = 175
Score = 28.4 bits (64), Expect = 3.8
Identities = 19/74 (25%), Positives = 33/74 (44%), Gaps = 3/74 (4%)
Query: 236 DEIQSLRRYGRAVGVLYQVVDDILEAKA--QTPRDEEKKKKKGKSYVAFYGVEKAMEVAE 293
++ LR+ R G +VV + L +A + + KG + +AF E + A+
Sbjct: 36 AQLTELRKKLREAGAKLKVVKNTLLRRALEEAGLEGLDDLLKGPTAIAF-SNEDPVAAAK 94
Query: 294 ELRAKAKEELDRFK 307
L+ AKE D+
Sbjct: 95 LLKDFAKEAGDKAP 108
>gnl|CDD|225354 COG2759, MIS1, Formyltetrahydrofolate synthetase [Nucleotide
transport and metabolism].
Length = 554
Score = 29.2 bits (66), Expect = 3.9
Identities = 15/37 (40%), Positives = 20/37 (54%), Gaps = 6/37 (16%)
Query: 294 ELRAKAKEELDRFKKYGDNVLPL------YSFIDYAA 324
E KAKE+L F+K G + LP+ YSF D +
Sbjct: 460 EFSPKAKEQLKTFEKQGFDNLPICMAKTQYSFSDDPS 496
>gnl|CDD|221857 pfam12923, RRP7, Ribosomal RNA-processing protein 7 (RRP7). RRP7
is an essential protein in yeast that is involved in
pre-rRNA processing and ribosome assembly. It is
speculated to be required for correct assembly of rpS27
into the pre-ribosomal particle.
Length = 131
Score = 28.0 bits (63), Expect = 4.3
Identities = 19/52 (36%), Positives = 27/52 (51%), Gaps = 3/52 (5%)
Query: 260 EAKAQTPRDEEKKKKKGKSYVAFY---GVEKAMEVAEELRAKAKEELDRFKK 308
+A + + +EKKKKK K FY EK E ELR K +E+ R ++
Sbjct: 70 KAAEERRKLKEKKKKKKKELENFYRFQIREKKKEELAELRKKFEEDKKRIEQ 121
>gnl|CDD|223358 COG0281, SfcA, Malic enzyme [Energy production and conversion].
Length = 432
Score = 28.7 bits (65), Expect = 4.4
Identities = 10/31 (32%), Positives = 15/31 (48%)
Query: 166 HTPPHLVPEPRVLRVIAEIARAVGSTGMAAG 196
+++P P RVI+ +A AV M G
Sbjct: 373 VLEEYIIPPPFDPRVISRVAVAVAKAAMEEG 403
>gnl|CDD|224581 COG1667, COG1667, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 254
Score = 28.3 bits (63), Expect = 5.4
Identities = 21/101 (20%), Positives = 43/101 (42%), Gaps = 11/101 (10%)
Query: 230 LAGADDDEIQSLRRYGRAVGVLYQVVDDILEA--------KAQTPRDEEKKKKKGKSYVA 281
L ++ +E+ L +YG V + ++ + EA + + P EE KK G
Sbjct: 130 LKSSEREEL--LEKYGIRVPEIEEIERILDEAVGSDYFSEEIEEPSREELLKKLGIKEPD 187
Query: 282 FYGVEKAMEVAEELRAKAKEELDR-FKKYGDNVLPLYSFID 321
VE ++V + + +EE +R + + V + ++
Sbjct: 188 ENWVETILKVFRGVDEELEEEKERILSEIVNKVKSMEGVVE 228
>gnl|CDD|239452 cd03336, TCP1_beta, TCP-1 (CTT or eukaryotic type II) chaperonin
family, beta subunit. Chaperonins are involved in
productive folding of proteins. They share a common
general morphology, a double toroid of 2 stacked rings.
In contrast to bacterial group I chaperonins (GroEL),
each ring of the eukaryotic cytosolic chaperonin (CTT)
consists of eight different, but homologous subunits.
Their common function is to sequester nonnative proteins
inside their central cavity and promote folding by using
energy derived from ATP hydrolysis. The best studied in
vivo substrates of CTT are actin and tubulin.
Length = 517
Score = 28.4 bits (64), Expect = 5.5
Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 1/51 (1%)
Query: 263 AQTPRDEEKKKKKGKSYVAFYGVEKAMEVAEELRAKAKEELDRFKKYGDNV 313
A TP D +K K G + V K E+ E + K K ++++ K+G N
Sbjct: 230 ANTPMDTDKIKIFG-AKVRVDSTAKVAEIEEAEKEKMKNKVEKILKHGINC 279
>gnl|CDD|235176 PRK03932, asnC, asparaginyl-tRNA synthetase; Validated.
Length = 450
Score = 28.5 bits (65), Expect = 5.9
Identities = 9/43 (20%), Positives = 18/43 (41%), Gaps = 8/43 (18%)
Query: 280 VAFYGVEKAMEVAEEL--------RAKAKEELDRFKKYGDNVL 314
+AF +E M++AEE+ ++L+ + D
Sbjct: 238 MAFADLEDNMDLAEEMLKYVVKYVLENCPDDLEFLNRRVDKGD 280
>gnl|CDD|181382 PRK08317, PRK08317, hypothetical protein; Provisional.
Length = 241
Score = 28.0 bits (63), Expect = 7.0
Identities = 11/46 (23%), Positives = 18/46 (39%), Gaps = 4/46 (8%)
Query: 182 AEIARAVGSTGMAAGQFLDLEGEPNLVEFVQEKKFGEMSECSAVCG 227
E+AR VG G G ++ ++ +E+ G V G
Sbjct: 35 RELARRVGPEGRVVG----IDRSEAMLALAKERAAGLGPNVEFVRG 76
>gnl|CDD|211733 TIGR02341, chap_CCT_beta, T-complex protein 1, beta subunit.
Members of this family, all eukaryotic, are part of the
group II chaperonin complex called CCT (chaperonin
containing TCP-1) or TRiC. The archaeal equivalent group
II chaperonin is often called the thermosome. Both are
somewhat related to the group I chaperonin of bacterial,
GroEL/GroES. This family consists exclusively of the CCT
beta chain (part of a paralogous family) from animals,
plants, fungi, and other eukaryotes.
Length = 518
Score = 28.3 bits (63), Expect = 7.3
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 1/51 (1%)
Query: 263 AQTPRDEEKKKKKGKSYVAFYGVEKAMEVAEELRAKAKEELDRFKKYGDNV 313
A T D +K K G S V K E+ + R K KE++++ K+G N
Sbjct: 230 ANTTMDTDKVKIFG-SRVRVDSTAKLAELEKAEREKMKEKVEKILKHGINC 279
>gnl|CDD|153066 cd03596, CLECT_tetranectin_like, C-type lectin-like domain (CTLD)
of the type found in the tetranectin (TN), cartilage
derived C-type lectin (CLECSF1), and stem cell growth
factor (SCGF). CLECT_tetranectin_like: C-type
lectin-like domain (CTLD) of the type found in the
tetranectin (TN), cartilage derived C-type lectin
(CLECSF1), and stem cell growth factor (SCGF). CTLD
refers to a domain homologous to the
carbohydrate-recognition domains (CRDs) of the C-type
lectins. TN binds to plasminogen and stimulates
activation of plasminogen, playing a key role in the
regulation of proteolytic processes. The TN CTLD binds
two calcium ions. Its calcium free form binds to
various kringle-like protein ligands. Two residues
involved in the coordination of calcium are critical for
the binding of TN to the fourth kringle (K4) domain of
plasminogen (Plg K4). TN binds the kringle 1-4 form of
angiostatin (AST K1-4). AST K1-4 is a fragment of Plg,
commonly found in cancer tissues. TN inhibits the
binding of Plg and AST K1-4 to the extracellular matrix
(EMC) of endothelial cells and counteracts the
antiproliferative effects of AST K1-4 on these cells.
TN also binds the tenth kringle domain of apolipoprotein
(a). In addition, TN binds fibrin and complex
polysaccharides in a Ca2+ dependent manner. The binding
site for complex sulfated polysaccharides is N-terminal
to the CTLD. TN is homotrimeric; N-terminal to the CTLD
is an alpha helical domain responsible for trimerization
of monomeric units. TN may modulate angiogenesis
through interactions with angiostatin and coagulation
through interaction with fibrin. TN may play a role in
myogenesis and in bone development. Mice having a
deletion in the TN gene exhibit a kyphotic spine
abnormality. TN is a useful prognostic marker of
certain cancer types. CLECSF1 is expressed in cartilage
tissue, which is primarily intracellular matrix (ECM),
and is a candidate for organizing ECM. SCGF is strongly
expressed in bone marrow and is a cytokine for primitive
hematopoietic progenitor cells.
Length = 129
Score = 27.0 bits (60), Expect = 7.4
Identities = 17/40 (42%), Positives = 21/40 (52%), Gaps = 3/40 (7%)
Query: 210 FVQEKKFGEMSE-CSAVCGGFLA-GADDDEIQSLRRYGRA 247
+ K + E SE C A GG LA D DE +LR Y +A
Sbjct: 15 SEETKHYHEASEDCIAR-GGTLATPRDSDENDALRDYVKA 53
>gnl|CDD|227238 COG4901, COG4901, Ribosomal protein S25 [Translation, ribosomal
structure and biogenesis].
Length = 107
Score = 26.8 bits (59), Expect = 7.9
Identities = 14/46 (30%), Positives = 23/46 (50%), Gaps = 7/46 (15%)
Query: 262 KAQTPRDEEKKKKKGKSYVAFYGVEKAMEVAEELRAKAKEELDRFK 307
A+ + KKKKK + +A+ V EEL K ++E+ R +
Sbjct: 20 TAKDKKKWSKKKKKEE-------ARRAVTVDEELLDKIRKEVPRER 58
>gnl|CDD|235600 PRK05771, PRK05771, V-type ATP synthase subunit I; Validated.
Length = 646
Score = 28.0 bits (63), Expect = 8.3
Identities = 16/64 (25%), Positives = 23/64 (35%), Gaps = 4/64 (6%)
Query: 237 EIQSLRRYGRAVGVLYQVVDDILEAKAQTPRD---EEKKKKKGKSYVAFYG-VEKAMEVA 292
++ L + + V +D LE E KG YV E + EV
Sbjct: 135 DLSLLLGFKYVSVFVGTVPEDKLEELKLESDVENVEYISTDKGYVYVVVVVLKELSDEVE 194
Query: 293 EELR 296
EEL+
Sbjct: 195 EELK 198
>gnl|CDD|240324 PTZ00234, PTZ00234, variable surface protein Vir12; Provisional.
Length = 433
Score = 28.1 bits (62), Expect = 8.4
Identities = 16/50 (32%), Positives = 29/50 (58%), Gaps = 5/50 (10%)
Query: 268 DEEKKKKKGKSYVAFYGVEKAMEVAEELRAKAKEELDRFKKYGDNVLPLY 317
DE KK+K SY+ + ++ ++ ++ KE+ D++ KY DN+ LY
Sbjct: 143 DEWKKRKL--SYIYM---KNYNDIKSKVFSQKKEKCDKYTKYLDNINKLY 187
>gnl|CDD|236278 PRK08506, PRK08506, replicative DNA helicase; Provisional.
Length = 472
Score = 28.1 bits (63), Expect = 8.4
Identities = 13/43 (30%), Positives = 24/43 (55%), Gaps = 1/43 (2%)
Query: 256 DDILEAKAQTPRDEEKKKKKGKSYVAFYGVEKAMEVAEELRAK 298
DD+ + + + + E+K KK+GK + K++E AE + K
Sbjct: 387 DDVYKEREEKEK-EKKAKKEGKEERRIHFQNKSIEEAEIIIGK 428
>gnl|CDD|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in
RNA-binding protein 5 (RBM5) and similar proteins. This
subfamily includes the RRM1 and RRM2 of RNA-binding
protein 5 (RBM5 or LUCA15 or H37) and RNA-binding
protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding
protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs
share high sequence homology and may play an important
role in regulating apoptosis. RBM5 is a known modulator
of apoptosis. It may also act as a tumor suppressor or
an RNA splicing factor. RBM6 has been predicted to be a
nuclear factor based on its nuclear localization signal.
Both, RBM6 and RBM5, specifically bind poly(G) RNA.
RBM10 is a paralog of RBM5. It may play an important
role in mRNA generation, processing and degradation in
several cell types. The rat homolog of human RBM10 is
protein S1-1, a hypothetical RNA binding protein with
poly(G) and poly(U) binding capabilities. All family
members contain two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc fingers,
and a G-patch/D111 domain. .
Length = 84
Score = 26.0 bits (58), Expect = 8.6
Identities = 14/52 (26%), Positives = 22/52 (42%), Gaps = 5/52 (9%)
Query: 267 RDEEKKKKKGKSYVAFYGVEKAMEVAEELRAKAKEELDRFKKYGDNVLPLYS 318
RD+ +G ++V F +E A + + L LD F G V Y+
Sbjct: 38 RDKLTGTSRGFAFVEFPSLEDATQWMDALN-----NLDPFVIDGRVVRVSYA 84
>gnl|CDD|236498 PRK09401, PRK09401, reverse gyrase; Reviewed.
Length = 1176
Score = 28.0 bits (63), Expect = 8.9
Identities = 20/86 (23%), Positives = 35/86 (40%), Gaps = 20/86 (23%)
Query: 237 EIQSLRRYGRAVGVLYQVVDDILEAKAQTPRDEEKKKKKGKSYVAF----YGVEKAMEVA 292
E+ S Y R + Y V +D +E + E K+ G + F G E A E+A
Sbjct: 295 EVGSPVFYLRNIVDSYIVDEDSVE------KLVELVKRLGDGGLIFVPSDKGKEYAEELA 348
Query: 293 EELR----------AKAKEELDRFKK 308
E L + + + ++F++
Sbjct: 349 EYLEDLGINAELAISGFERKFEKFEE 374
>gnl|CDD|206130 pfam13960, DUF4218, Domain of unknown function (DUF4218).
Length = 129
Score = 26.8 bits (60), Expect = 9.2
Identities = 10/23 (43%), Positives = 12/23 (52%)
Query: 156 FPLGFQHIVSHTPPHLVPEPRVL 178
FP F I+ H HLV E R+
Sbjct: 41 FPPSFFDIMVHLIVHLVREARLG 63
>gnl|CDD|236976 PRK11773, uvrD, DNA-dependent helicase II; Provisional.
Length = 721
Score = 27.9 bits (63), Expect = 9.2
Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 3/51 (5%)
Query: 168 PPHLVPEPRVLRVIAEIARAVGSTGMAAGQFLDLEGEPNLVEFVQEKKFGE 218
P V E +R+ A ++R V M + L + V+ KFGE
Sbjct: 637 PEECVEE---VRLRATVSRPVSHQRMGTPAVEANDSGFKLGQRVRHPKFGE 684
>gnl|CDD|216402 pfam01268, FTHFS, Formate--tetrahydrofolate ligase.
Length = 557
Score = 27.8 bits (63), Expect = 9.4
Identities = 12/39 (30%), Positives = 18/39 (46%), Gaps = 8/39 (20%)
Query: 122 DDLP-CM-------DDDPSRRGQPSNHTVYGVDIAILAG 152
LP CM DDP +G P+ T+ ++ + AG
Sbjct: 481 GHLPVCMAKTQYSLSDDPKLKGAPTGFTLPVREVRLSAG 519
>gnl|CDD|187734 cd09765, Csx14_I-U, CRISPR/Cas system-associated protein Csx14.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Protein containing C-terminal alpha-helical domain
resembling Cas8a2, also known as GSU0052.
Length = 272
Score = 27.6 bits (61), Expect = 9.4
Identities = 12/40 (30%), Positives = 16/40 (40%)
Query: 66 PEQIYESMRYSVLAKGTKRAPPVMCVAACELFGVNRIAAF 105
P ++ ++RY A P V AA L I AF
Sbjct: 224 PLRLQANLRYRYGAWFGPLVPTVAARAALGLSNPGFIRAF 263
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
0.320 0.136 0.399
Gapped
Lambda K H
0.267 0.0788 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,577,155
Number of extensions: 1744697
Number of successful extensions: 2420
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2379
Number of HSP's successfully gapped: 64
Length of query: 334
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 237
Effective length of database: 6,635,264
Effective search space: 1572557568
Effective search space used: 1572557568
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 (26.4 bits)