RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780940|ref|YP_003065353.1| ribonuclease III [Candidatus
Liberibacter asiaticus str. psy62]
(227 letters)
>3n3w_A Ribonuclease III; nuclease domain, ribonuclase III, IDP90862,
csgid, structura genomics; 2.21A {Campylobacter jejuni
subsp}
Length = 248
Score = 198 bits (504), Expect = 1e-51
Identities = 73/220 (33%), Positives = 121/220 (55%), Gaps = 4/220 (1%)
Query: 7 STLEKRIGYAFANRSLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFDSA 66
LE+ + Y F +++LL ALTH S + ERLEFLGD +L L++ LF+ F
Sbjct: 29 EKLEQSLTYEFKDKNLLIHALTHKS--FKKSYNNERLEFLGDAVLDLVVGEYLFHKFAKD 86
Query: 67 KEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAAL 126
EG+LS +LV+ ++ +++A L+L FI +S + SI +D +E++I A+
Sbjct: 87 AEGDLSKLRAALVNEKSFAKIANSLNLGDFILMSVAEENNGGKEKPSILSDALEAIIGAI 146
Query: 127 YLDGGIEVAGTFVDKYWKQR--ALKSGKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPD 184
+L+ G E A T + ++ + + +D KT+LQE K G TP+Y+ GPD
Sbjct: 147 HLEAGFEFAKTIALRLIEKNFPQIDAKILIKDYKTKLQEITQGKIGQTPQYETVRAFGPD 206
Query: 185 HDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREG 224
H +F + + + G A+ + SK+ A+Q+AA L++ G
Sbjct: 207 HLKQFEIALMLDGKELARAIAGSKKEAQQMAAKIALEKLG 246
>1o0w_A Ribonuclease III, RNAse III; TM1102, structural genomics, JCSG,
PSI, protein structure initiative, joint center for
structural genomics; 2.00A {Thermotoga maritima} SCOP:
a.149.1.1 d.50.1.1
Length = 252
Score = 186 bits (473), Expect = 4e-48
Identities = 71/223 (31%), Positives = 110/223 (49%), Gaps = 9/223 (4%)
Query: 9 LEKRIGYAFANRSLLEKALTHSSISHSY-------QESYERLEFLGDRILGLLISTLLFN 61
+K G F N LL +AL HSS ++ ES E+LEFLGD +L L + +L+
Sbjct: 24 FQKETGINFKNEELLFRALCHSSYANEQNQAGRKDVESNEKLEFLGDAVLELFVCEILYK 83
Query: 62 HFDSAKEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVES 121
+ A+ G+L+ ++ S E + V+R+++L F+ + K SI AD E+
Sbjct: 84 KYPEAEVGDLARVKSAAASEEVLAMVSRKMNLGKFLFLGKGEEKTGGRDRDSILADAFEA 143
Query: 122 LIAALYLDGGIEVAGTFVDKYWKQRALKSGKFR--RDAKTELQEWAHAKFGVTPEYKVTF 179
L+AA+YLD G E ++ ++ K K D KT LQE ++ V PEY +
Sbjct: 144 LLAAIYLDQGYEKIKELFEQEFEFYIEKIMKGEMLFDYKTALQEIVQSEHKVPPEYILVR 203
Query: 180 RSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKR 222
D D F V V ++G A G +K+ AE+ AA ++
Sbjct: 204 TEKNDGDRIFVVEVRVNGKTIATGKGRTKKEAEKEAARIAYEK 246
>3c4b_A Endoribonuclease dicer; RNAse, dsRNA binding protein, ATP-binding,
endonuclease, helicase, hydrolase, nucleotide-binding,
phosphoprotein; HET: MSE; 1.68A {Mus musculus} PDB:
3c4t_A 2eb1_A
Length = 265
Score = 140 bits (353), Expect = 2e-34
Identities = 59/250 (23%), Positives = 103/250 (41%), Gaps = 37/250 (14%)
Query: 6 YSTLEKRIGYAFANRSLLEKALTHSSISHSY-QESYERLEFLGDRILGLLISTLLFNHFD 64
+ T EK+I Y F N++ L +A TH+S ++ + Y+RLEFLGD IL LI+ L+
Sbjct: 15 FETFEKKINYRFKNKAYLLQAFTHASYHYNTITDCYQRLEFLGDAILDYLITKHLYEDPR 74
Query: 65 SAKEGELSVRFNSLVSAETCSQVARELDLASFIRVSS-DLRKDVCSFM------------ 111
G L+ ++LV+ + +A + D + + S +L + F+
Sbjct: 75 QHSPGVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELFHVIDDFVKFQLEKNEMQGM 134
Query: 112 -------------------TSIQADVVESLIAALYLDGGIEVAGTFVDKYWKQRALKSGK 152
D+ ESL A+Y+D G+ + + Y + L
Sbjct: 135 DSELRRSEEDEEKEEDIEVPKAMGDIFESLAGAIYMDSGMSLEVVWQVYYPMMQPLIEKF 194
Query: 153 FRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAE 212
++ ++E + PE + +D + V VE+ G +G+ S R A+
Sbjct: 195 SANVPRSPVRELLEME----PETAKFSPAERTYDGKVRVTVEVVGKGKFKGVGRSYRIAK 250
Query: 213 QVAAAEVLKR 222
AA L+
Sbjct: 251 SAAARRALRS 260
>2nug_A Ribonuclease III, RNAse III; dsRNA, RNA interference,
endonucleolytic cleavage, hydrolase/RNA complex; 1.70A
{Aquifex aeolicus} SCOP: a.149.1.1 d.50.1.1 PDB: 1yyw_A
2nue_A 2nuf_A 1yyk_A 1yz9_A 1yyo_A 2ez6_A 1rc7_A 1i4s_A
1jfz_A 1rc5_A
Length = 221
Score = 138 bits (349), Expect = 6e-34
Identities = 82/219 (37%), Positives = 118/219 (53%), Gaps = 14/219 (6%)
Query: 9 LEKRIGYAFANRSLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFDSAKE 68
LEK++GY F ++SLLEKALTH S +S +E YE LEFLGD ++ I LL + + +E
Sbjct: 7 LEKKLGYTFKDKSLLEKALTHVS--YSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKRE 64
Query: 69 GELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAALYL 128
G LS L+S E + +A++L+L FIR+ + I DV E+L AA+Y+
Sbjct: 65 GFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINET------IIGDVFEALWAAVYI 118
Query: 129 DGGIEVAGTFVDKYWK-----QRALKSGKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGP 183
D G + T Y A+K G+ ++D KT LQE ++ PEY++ GP
Sbjct: 119 DSGRDANFTRELFYKLFKEDILSAIKEGRVKKDYKTILQEITQKRWKERPEYRLISVEGP 178
Query: 184 DHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKR 222
H +F V +I G SK+ AEQ AA E++K
Sbjct: 179 HHKKKFIVEAKIKEYR-TLGEGKSKKEAEQRAAEELIKL 216
>3o2r_A Ribonuclease III; structural genomics, center for structural
genomics of infec diseases, csgid, nuclease domain,
ribonuclase III; HET: MLZ; 1.25A {Campylobacter jejuni
subsp} PDB: 3o2r_B*
Length = 170
Score = 136 bits (343), Expect = 5e-33
Identities = 47/140 (33%), Positives = 78/140 (55%), Gaps = 2/140 (1%)
Query: 7 STLEKRIGYAFANRSLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFDSA 66
LE+ + Y F +++LL ALTH S + ERLEFLGD +L L++ LF+ F
Sbjct: 29 EKLEQSLTYEFKDKNLLIHALTHKS--FKKSYNNERLEFLGDAVLDLVVGEYLFHKFAKD 86
Query: 67 KEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAAL 126
EG+LS +LV+ ++ +++A L+L FI +S + SI +D +E++I A+
Sbjct: 87 AEGDLSKLRAALVNEKSFAKIANSLNLGDFILMSVAEENNGGKEKPSILSDALEAIIGAI 146
Query: 127 YLDGGIEVAGTFVDKYWKQR 146
+L+ G E A T + ++
Sbjct: 147 HLEAGFEFAKTIALRLIEKN 166
>2a11_A Ribonuclease III, RNAse III; nuclease domain, structural genomics,
PSI, protein structure initiative; 2.10A {Mycobacterium
tuberculosis}
Length = 242
Score = 132 bits (332), Expect = 7e-32
Identities = 72/223 (32%), Positives = 103/223 (46%), Gaps = 9/223 (4%)
Query: 7 STLEKRIGYAFANRSLLEKALTHSSISHSYQ--ESYERLEFLGDRILGLLISTLLFNHFD 64
L +G + LL ALTH S ++ + ERLEFLGD +LGL I+ LF+
Sbjct: 8 QPLLDALGVDLPDE-LLSLALTHRSYAYENGGLPTNERLEFLGDAVLGLTITDALFHRHP 66
Query: 65 SAKEGELSVRFNSLVSAETCSQVARELDLAS---FIRVSSDLRKDVCSFMTSIQADVVES 121
EG+L+ S+V+ + + VAR L + + + +SI AD +ES
Sbjct: 67 DRSEGDLAKLRASVVNTQALADVARRLCAEGLGVHVLLGRGEANTGGADKSSILADGMES 126
Query: 122 LIAALYLDGGIEVAGTFVDKYWKQRALKSGKF--RRDAKTELQEWAHAKFGVTPEYKVTF 179
L+ A+YL G+E A + + + + D KT LQE A+ P Y VT
Sbjct: 127 LLGAIYLQHGMEKAREVILRLFGPLLDAAPTLGAGLDWKTSLQELTAARGLGAPSYLVT- 185
Query: 180 RSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKR 222
+GPDHD FT VV + G+ SK+ AEQ K
Sbjct: 186 STGPDHDKEFTAVVVVMDSEYGSGVGRSKKEAEQKXXXXXWKA 228
>2gsl_A Hypothetical protein; alpha-helical protein, structural genomics,
PSI, protein structure initiative; 2.60A {Fusobacterium
nucleatum subsp}
Length = 137
Score = 90.4 bits (224), Expect = 3e-19
Identities = 23/118 (19%), Positives = 40/118 (33%), Gaps = 12/118 (10%)
Query: 37 QESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAETCSQVARELDLASF 96
S L FLGD I L I L+ + V+A+ S + +++
Sbjct: 12 DYSGLELAFLGDAIWELEIRKYYLQFG--YNIPTLNKYVKAKVNAKYQSLIYKKIINDLD 69
Query: 97 I----------RVSSDLRKDVCSFMTSIQADVVESLIAALYLDGGIEVAGTFVDKYWK 144
+ C+ M +A +E++I A+YL E ++ K
Sbjct: 70 EEFKVIGKRAKNSNIKTFPRSCTVMEYKEATALEAIIGAMYLLKKEEEIKKIINIVIK 127
>2khx_A Ribonuclease 3; drosha, RNA binding domain, hydrolase, gene
regulation, nuclear protein; NMR {Homo sapiens}
Length = 85
Score = 84.2 bits (208), Expect = 2e-17
Identities = 22/72 (30%), Positives = 30/72 (41%), Gaps = 5/72 (6%)
Query: 156 DAKTELQEWAH-----AKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRA 210
D K++LQ+ K P YK GP H +TV V G G S +
Sbjct: 2 DPKSQLQQCCLTLRTEGKEPDIPLYKTLQTVGPSHARTYTVAVYFKGERIGCGKGPSIQQ 61
Query: 211 AEQVAAAEVLKR 222
AE AA + L++
Sbjct: 62 AEMGAAMDALEK 73
>1u61_A Hypothetical protein; structural genomics, PSI, protein structure
initiative, midwest center for structural genomics,
MCSG, unknown function; 2.15A {Bacillus cereus} SCOP:
a.149.1.1
Length = 138
Score = 84.3 bits (208), Expect = 2e-17
Identities = 23/121 (19%), Positives = 37/121 (30%), Gaps = 13/121 (10%)
Query: 37 QESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAETCSQVARELDLASF 96
Q + L ++GD + I L + +L S VSA+ ++V L +F
Sbjct: 9 QLNSLALAYMGDAVYEQYIRYHLLQKGK-VRPNQLHRLGTSFVSAKAQAKVVYHLLETAF 67
Query: 97 IRVS------------SDLRKDVCSFMTSIQADVVESLIAALYLDGGIEVAGTFVDKYWK 144
+ S T + E+LI +L E V K
Sbjct: 68 LTEEEEAVLRRGRNANSGTVPKNTDVQTYRHSTAFEALIGYHHLLNNRERLDEIVYKAIA 127
Query: 145 Q 145
Sbjct: 128 V 128
>3adj_A F21M12.9 protein; HYL1, miRNA processing, RNA binding protein, gene
regulation; 3.00A {Arabidopsis thaliana} PDB: 2l2m_A
Length = 76
Score = 76.9 bits (189), Expect = 4e-15
Identities = 18/65 (27%), Positives = 24/65 (36%)
Query: 158 KTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAA 217
K LQE+A P Y+ +FT VEI G+ +K+ AE A
Sbjct: 7 KNLLQEYAQKMNYAIPLYQCQKVETLGRVTQFTCTVEIGGIKYTGAATRTKKDAEISAGR 66
Query: 218 EVLKR 222
L
Sbjct: 67 TALLA 71
>3adl_A RISC-loading complex subunit tarbp2; TRBP2, miRNA processing, gene
regulation-RNA complex; 2.20A {Homo sapiens}
Length = 88
Score = 75.3 bits (185), Expect = 1e-14
Identities = 24/68 (35%), Positives = 31/68 (45%), Gaps = 1/68 (1%)
Query: 155 RDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQV 214
LQE K PEY VT SGP H FT+ + G SK+ A++
Sbjct: 15 SHEVGALQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRVERFI-EIGSGTSKKLAKRN 73
Query: 215 AAAEVLKR 222
AAA++L R
Sbjct: 74 AAAKMLLR 81
>1qu6_A Protein kinase PKR; dsRNA-binding domain, solution structure,
transferase; NMR {Homo sapiens} SCOP: d.50.1.1 d.50.1.1
Length = 179
Score = 72.9 bits (178), Expect = 5e-14
Identities = 23/68 (33%), Positives = 31/68 (45%), Gaps = 1/68 (1%)
Query: 154 RRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQ 213
EL + K GV +Y+ SGP HD RFT V I G +G SK+ A+
Sbjct: 12 AGFFMEELNTYRQ-KQGVVLKYQELPNSGPPHDRRFTFQVIIDGREFPEGEGRSKKEAKN 70
Query: 214 VAAAEVLK 221
AA ++
Sbjct: 71 AAAKLAVE 78
Score = 53.3 bits (127), Expect = 4e-08
Identities = 16/103 (15%), Positives = 33/103 (32%), Gaps = 2/103 (1%)
Query: 120 ESLIAALYLDGGIEVAGTFVDKYWKQRALKSGKFRRDAKTELQEWAHAKFGVTPEYKVTF 179
++ A L ++ + G + + A K +T Y+
Sbjct: 69 KNAAAKLAVEILNKEKKAVSPLLLTTTNSSEGLSMGNYIGLINRIAQ-KKRLTVNYEQC- 126
Query: 180 RSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKR 222
SG F ++ + G +K+ A+Q+AA +
Sbjct: 127 ASGVHGPEGFHYKCKMGQKEYSIGTGSTKQEAKQLAAKLAYLQ 169
>1di2_A XLRBPA, double stranded RNA binding protein A; protein-RNA complex,
protein-RNA interactions, RNA-bining protein; 1.90A
{Xenopus laevis} SCOP: d.50.1.1
Length = 69
Score = 69.9 bits (171), Expect = 4e-13
Identities = 23/65 (35%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 158 KTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAA 217
LQE A K PEY V SGP H FT+ + G SK+ A++VAA
Sbjct: 3 VGSLQELAVQKGWRLPEYTVAQESGPPHKREFTITCRVETFV-ETGSGTSKQVAKRVAAE 61
Query: 218 EVLKR 222
++L +
Sbjct: 62 KLLTK 66
>2l2n_A Hyponastic leave 1; DSRBD, miRNA, RNA binding protein, plant
protein; NMR {Arabidopsis thaliana}
Length = 103
Score = 69.2 bits (169), Expect = 8e-13
Identities = 21/68 (30%), Positives = 32/68 (47%), Gaps = 2/68 (2%)
Query: 156 DAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDC-SKRAAEQV 214
K+ LQE+A TP Y++ + GP H F V + G+ +++AAEQ
Sbjct: 18 VFKSRLQEYAQKYKLPTPVYEIV-KEGPSHKSLFQSTVILDGVRYNSLPGFFNRKAAEQS 76
Query: 215 AAAEVLKR 222
AA L+
Sbjct: 77 AAEVALRE 84
>3adg_A F21M12.9 protein; HYL1, miRNA processing mechanism, RNA binding
protein, gene regulation; 1.70A {Arabidopsis thaliana}
PDB: 3adi_A
Length = 73
Score = 69.0 bits (169), Expect = 8e-13
Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 2/66 (3%)
Query: 158 KTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLA-PAQGMDCSKRAAEQVAA 216
K+ LQE+A TP Y++ + GP H F V + G+ + +++AAEQ AA
Sbjct: 6 KSRLQEYAQKYKLPTPVYEIV-KEGPSHKSLFQSTVILDGVRYNSLPGFFNRKAAEQSAA 64
Query: 217 AEVLKR 222
L+
Sbjct: 65 EVALRE 70
>2l33_A Interleukin enhancer-binding factor 3; structural genomics,
northeast structural genomics consortiu PSI-biology,
protein structure initiative, DRBM; NMR {Homo sapiens}
Length = 91
Score = 68.3 bits (167), Expect = 1e-12
Identities = 22/74 (29%), Positives = 34/74 (45%), Gaps = 9/74 (12%)
Query: 149 KSGKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSK 208
K GK + EL E +Y++ +G HD RF + VE+ G QG +K
Sbjct: 14 KHGK---NPVMELNEKRRG-----LKYELISETGGSHDKRFVMEVEVDGQ-KFQGAGSNK 64
Query: 209 RAAEQVAAAEVLKR 222
+ A+ AA L++
Sbjct: 65 KVAKAYAALAALEK 78
>2yt4_A Protein DGCR8; DSRBD, RNA binding domain, RNA binding protein;
2.60A {Homo sapiens}
Length = 232
Score = 68.2 bits (166), Expect = 2e-12
Identities = 17/68 (25%), Positives = 23/68 (33%), Gaps = 2/68 (2%)
Query: 154 RRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQ 213
+ L E+ V P Y P F V I G+ G SK+ A+
Sbjct: 21 GKSEVCILHEYMQRVLKVRPVYNFFECENPSEP--FGASVTIDGVTYGSGTASSKKLAKN 78
Query: 214 VAAAEVLK 221
AA L+
Sbjct: 79 KAARATLE 86
Score = 48.9 bits (116), Expect = 8e-07
Identities = 12/62 (19%), Positives = 26/62 (41%), Gaps = 2/62 (3%)
Query: 161 LQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVL 220
L E G+ + + F P + + V+ +G +KR +Q+A+ ++L
Sbjct: 136 LHECLKRNHGM-GDTSIKFEVVPGKNQKSEYVMACGKHT-VRGWCKNKRVGKQLASQKIL 193
Query: 221 KR 222
+
Sbjct: 194 QL 195
>1t4o_A Ribonuclease III; RNT1P, DSRBD, RNA-binding, hydrolase; 2.50A
{Saccharomyces cerevisiae} SCOP: d.50.1.1 PDB: 1t4l_B
Length = 117
Score = 67.8 bits (165), Expect = 2e-12
Identities = 12/78 (15%), Positives = 24/78 (30%), Gaps = 1/78 (1%)
Query: 148 LKSGKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCS 207
+K+ K +AK +L + Y + G G+ +
Sbjct: 1 MKTDKLDMNAKRQLYSLI-GYASLRLHYVTVKKPTAVDPNSIVECRVGDGTVLGTGVGRN 59
Query: 208 KRAAEQVAAAEVLKREGI 225
+ A AA L+ + +
Sbjct: 60 IKIAGIRAAENALRDKKM 77
>1ekz_A DSRBDIII, maternal effect protein (staufen); structure,
protein/RNA, protein DSRBD, RNA hairpin; NMR {Drosophila
melanogaster} SCOP: d.50.1.1 PDB: 1stu_A
Length = 76
Score = 66.8 bits (163), Expect = 3e-12
Identities = 14/68 (20%), Positives = 29/68 (42%), Gaps = 2/68 (2%)
Query: 155 RDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQV 214
+ +++ E + +T +KV GP H F + G +G K+ +++
Sbjct: 7 KSPISQVHEIGIKR-NMTVHFKVLREEGPAHMKNFITACIV-GSIVTEGEGNGKKVSKKR 64
Query: 215 AAAEVLKR 222
AA ++L
Sbjct: 65 AAEKMLVE 72
>2b7t_A Double-stranded RNA-specific editase 1; RNA editing, RNA-binding
protein, hydrolase; NMR {Rattus norvegicus} SCOP:
d.50.1.1
Length = 73
Score = 66.9 bits (163), Expect = 4e-12
Identities = 19/67 (28%), Positives = 33/67 (49%), Gaps = 3/67 (4%)
Query: 155 RDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQV 214
K L + K G +Y + ++GP H P F + VE++G +G +K+ A+
Sbjct: 4 VLPKNALMQLNEIKPG--LQYMLLSQTGPVHAPLFVMSVEVNGQ-VFEGSGPTKKKAKLH 60
Query: 215 AAAEVLK 221
AA + L+
Sbjct: 61 AAEKALR 67
>1x49_A Interferon-induced, double-stranded RNA- activated protein kinase;
structure genomics, DSRM domain, structural genomics,
NPPSFA; NMR {Mus musculus} SCOP: d.50.1.1
Length = 97
Score = 65.5 bits (159), Expect = 9e-12
Identities = 20/67 (29%), Positives = 26/67 (38%), Gaps = 1/67 (1%)
Query: 156 DAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVA 215
+L ++ GV YK SGP HD RFT V I + SK+ A A
Sbjct: 15 FYMDKLNKYRQ-MHGVAITYKELSTSGPPHDRRFTFQVLIDEKEFPEAKGRSKQEARNAA 73
Query: 216 AAEVLKR 222
A +
Sbjct: 74 AKLAVDI 80
>2dmy_A Spermatid perinuclear RNA-binding protein; DSRM domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.50.1.1
Length = 97
Score = 64.6 bits (157), Expect = 2e-11
Identities = 21/70 (30%), Positives = 33/70 (47%), Gaps = 3/70 (4%)
Query: 156 DAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVA 215
D L + G +YK+ +SGP H P FT+ V++ G + SK+ A+
Sbjct: 17 DLMNALMRLNQIRPG--LQYKLLSQSGPVHAPVFTMSVDVDGT-TYEASGPSKKTAKLHV 73
Query: 216 AAEVLKREGI 225
A +VL+ G
Sbjct: 74 AVKVLQAMGY 83
>2b7v_A Double-stranded RNA-specific editase 1; RNA editing, RNA-binding
protein, hydrolase; NMR {Rattus norvegicus} SCOP:
d.50.1.1
Length = 71
Score = 62.1 bits (151), Expect = 1e-10
Identities = 15/68 (22%), Positives = 24/68 (35%), Gaps = 6/68 (8%)
Query: 155 RDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQV 214
++ L E +Y SG H F + V + G +G +K+ A+
Sbjct: 4 KNPVMILNELRPG-----LKYDFLSESGESHAKSFVMSVVVDGQ-FFEGSGRNKKLAKAR 57
Query: 215 AAAEVLKR 222
AA L
Sbjct: 58 AAQSALAT 65
>1t4n_A Ribonuclease III; DSRBD, RNA-binding, hydrolase; NMR {Saccharomyces
cerevisiae} SCOP: d.50.1.1
Length = 94
Score = 61.2 bits (148), Expect = 2e-10
Identities = 10/71 (14%), Positives = 20/71 (28%), Gaps = 1/71 (1%)
Query: 155 RDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQV 214
+AK +L + Y + G G+ + + A
Sbjct: 6 MNAKRQLYSLI-GYASLRLHYVTVKKPTAVDPNSIVECRVGDGTVLGTGVGRNIKIAGIR 64
Query: 215 AAAEVLKREGI 225
AA L+ + +
Sbjct: 65 AAENALRDKKM 75
>2l3j_A Double-stranded RNA-specific editase 1; editing, dsRNA recognition,
DSRBM, hydrolase-RNA complex; NMR {Rattus norvegicus}
Length = 236
Score = 59.9 bits (144), Expect = 5e-10
Identities = 19/66 (28%), Positives = 33/66 (50%), Gaps = 3/66 (4%)
Query: 156 DAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVA 215
K L + K G +Y + ++GP H P F + VE++G +G +K+ A+ A
Sbjct: 5 LPKNALMQLNEIKPG--LQYMLLSQTGPVHAPLFVMSVEVNGQV-FEGSGPTKKKAKLHA 61
Query: 216 AAEVLK 221
A + L+
Sbjct: 62 AEKALR 67
Score = 59.1 bits (142), Expect = 8e-10
Identities = 16/103 (15%), Positives = 27/103 (26%), Gaps = 6/103 (5%)
Query: 120 ESLIAALYLDGGIEVAGTFVDKYWKQRALKSGKFRRDAKTELQEWAHAKFGVTPEYKVTF 179
+ V + ++ L E +Y
Sbjct: 126 SFSSSGDVSLSASPVPASLTQPPLPIPPPFPPPSGKNPVMILNELRPG-----LKYDFLS 180
Query: 180 RSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKR 222
SG H F + V + G +G +K+ A+ AA L
Sbjct: 181 ESGESHAKSFVMSVVVDGQ-FFEGSGRNKKLAKARAAQSALAT 222
>1x48_A Interferon-induced, double-stranded RNA- activated protein kinase;
structure genomics, DSRM domain, structural genomics,
NPPSFA; NMR {Mus musculus} SCOP: d.50.1.1
Length = 88
Score = 56.6 bits (136), Expect = 5e-09
Identities = 12/67 (17%), Positives = 24/67 (35%), Gaps = 2/67 (2%)
Query: 156 DAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVA 215
+ +A K ++ + RF +I G +K+ A+Q+A
Sbjct: 7 GYIGLVNSFAQ-KKKLSV-NYEQCEPNSELPQRFICKCKIGQTMYGTGSGVTKQEAKQLA 64
Query: 216 AAEVLKR 222
A E ++
Sbjct: 65 AKEAYQK 71
>1whn_A Hypothetical protein riken cDNA 2310016K04; double-stranded RNA
binding domain, DSRBD, DSRM, riken structural
genomics/proteomics initiative, RSGI; NMR {Mus musculus}
SCOP: d.50.1.1
Length = 128
Score = 56.3 bits (135), Expect = 5e-09
Identities = 22/97 (22%), Positives = 38/97 (39%), Gaps = 4/97 (4%)
Query: 130 GGIEVAGTFVDKYWKQRALKSGKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRF 189
G +G+ + K + ++ + K L EW + P Y+ D F
Sbjct: 1 GSSGSSGSGIIKMAIRFDRRAYPPQITPKMCLLEWCRREKLPQPVYETVQ---RTIDRMF 57
Query: 190 TVVVEISGLAPAQGMDC-SKRAAEQVAAAEVLKREGI 225
VV ++ + SK+ AEQ AA L+ +G+
Sbjct: 58 CSVVTVAEQKYQSTLWDKSKKLAEQTAAIVCLRSQGL 94
>2dix_A Interferon-inducible double stranded RNA- dependent protein kinase
activator A; structure genomics, DSRM domain,
hypothetical protein PRKRA; NMR {Homo sapiens} SCOP:
d.50.1.1
Length = 84
Score = 56.3 bits (135), Expect = 5e-09
Identities = 18/73 (24%), Positives = 25/73 (34%), Gaps = 2/73 (2%)
Query: 150 SGKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKR 209
SG + L E+ K P Y+ H P FT V + G SK+
Sbjct: 3 SGSSGKTPIQVLHEYGM-KTKNIPVYECERSDVQIHVPTFTFRVTVGD-ITCTGEGTSKK 60
Query: 210 AAEQVAAAEVLKR 222
A+ AA +
Sbjct: 61 LAKHRAAEAAINI 73
>1x47_A DGCR8 protein; structural genomics, DSRM domain, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens} SCOP: d.50.1.1
Length = 98
Score = 54.4 bits (130), Expect = 2e-08
Identities = 17/69 (24%), Positives = 23/69 (33%), Gaps = 2/69 (2%)
Query: 154 RRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQ 213
+ L E+ V P Y P F V I G+ G SK+ A+
Sbjct: 15 GKSEVCILHEYMQRVLKVRPVYNFFECENPSEP--FGASVTIDGVTYGSGTASSKKLAKN 72
Query: 214 VAAAEVLKR 222
AA L+
Sbjct: 73 KAARATLEI 81
>2cpn_A TAR RNA-binding protein 2; double-stranded RNA binding domain,
DSRBD, DSRM., structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: d.50.1.1
Length = 89
Score = 54.1 bits (129), Expect = 2e-08
Identities = 24/67 (35%), Positives = 32/67 (47%), Gaps = 1/67 (1%)
Query: 156 DAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVA 215
+ LQE K PEY VT SGP H FT+ + G SK+ A++ A
Sbjct: 17 NPVGALQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRVER-FIEIGSGTSKKLAKRNA 75
Query: 216 AAEVLKR 222
AA++L R
Sbjct: 76 AAKMLLR 82
>1uil_A Double-stranded RNA-binding motif; structural genomics, DSRM, riken
structural genomics/proteomics initiative, RSGI RNA
binding protein; NMR {Mus musculus} SCOP: d.50.1.1
Length = 113
Score = 53.6 bits (128), Expect = 4e-08
Identities = 19/73 (26%), Positives = 33/73 (45%), Gaps = 7/73 (9%)
Query: 155 RDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAP-----AQGMDCSKR 209
+AK L ++ K + EYK T + GPDH+ F + I A+ +K+
Sbjct: 26 ENAKARLNQYFQ-KEKIQGEYKYT-QVGPDHNRSFIAEMTIYIKQLGRRIFAREHGSNKK 83
Query: 210 AAEQVAAAEVLKR 222
A Q A ++++
Sbjct: 84 LAAQSCALSLVRQ 96
>1whq_A RNA helicase A; double-stranded RNA binding domain, DSRBD, DSRM,
riken structural genomics/proteomics initiative, RSGI,
structural genomics; NMR {Mus musculus} SCOP: d.50.1.1
Length = 99
Score = 52.9 bits (126), Expect = 6e-08
Identities = 14/76 (18%), Positives = 22/76 (28%), Gaps = 4/76 (5%)
Query: 155 RDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQV 214
K L W + +TP Y++ + V G +K+ A+
Sbjct: 6 SGIKNFLYAWCGKR-KMTPAYEIRAVGNKNRQKFMCEVRVEGFNYAGMGNSTNKKDAQSN 64
Query: 215 AAA---EVLKREGIWT 227
AA L R
Sbjct: 65 AARDFVNYLVRINEVK 80
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 52.6 bits (126), Expect = 6e-08
Identities = 34/190 (17%), Positives = 58/190 (30%), Gaps = 53/190 (27%)
Query: 16 AFANRSLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFDSAKEG---ELS 72
A++ R L L+H S+ H LL+ T F +E L
Sbjct: 3 AYSTRPL---TLSHGSLEHV-----------------LLVPTASFFIASQLQEQFNKILP 42
Query: 73 VRFNSLVSAETCSQVARELDLASFIR-VSSDLRKDVCSFMTSI--------------QAD 117
+ + + A EL + F+ VSS + + D
Sbjct: 43 EPTEGFAADDEPTTPA-EL-VGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGND 100
Query: 118 VVESLIAAL--YLDGGIEVAGTFVDKYWKQRALKSGKFRRDAKTELQEWA---HAK---- 168
+ +L A L D + + Y R + F + + + L +A+
Sbjct: 101 -IHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAI 159
Query: 169 F---GVTPEY 175
F G T +Y
Sbjct: 160 FGGQGNTDDY 169
Score = 33.4 bits (76), Expect = 0.039
Identities = 25/130 (19%), Positives = 43/130 (33%), Gaps = 51/130 (39%)
Query: 15 YAFANRSLLE-KA---LTHSSISHSYQESYER-LEFLGDRILGLLISTLLFNHFDSAKEG 69
Y N +L + KA L S I S ER L+F N F
Sbjct: 387 YGL-NLTLRKAKAPSGLDQSRIPFS-----ERKLKF--------------SNRF------ 420
Query: 70 EL--SVRFNS--LVSAETCSQVARELDLASFIRVSSDLR---------KDVCSFMTSIQA 116
L + F+S LV A + ++L + + D++ D + +
Sbjct: 421 -LPVASPFHSHLLVPAS--DLINKDLVKNNVSFNAKDIQIPVYDTFDGSD----LRVLSG 473
Query: 117 DVVESLIAAL 126
+ E ++ +
Sbjct: 474 SISERIVDCI 483
>1uhz_A Staufen (RNA binding protein) homolog 2; DSRM, staufen homolog 2,
structural genomics, riken structural
genomics/proteomics initiative, RSGI; NMR {Mus musculus}
SCOP: d.50.1.1
Length = 89
Score = 52.6 bits (125), Expect = 7e-08
Identities = 14/70 (20%), Positives = 28/70 (40%), Gaps = 1/70 (1%)
Query: 155 RDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQV 214
+ L + A+ P+Y + G F + V++ G +K+ A++
Sbjct: 6 SGPISRLAQIQQARKEKEPDYILLSERGMPRRREFVMQVKVGNEVA-TGTGPNKKIAKKN 64
Query: 215 AAAEVLKREG 224
AA +L + G
Sbjct: 65 AAEAMLLQLG 74
>2qvw_A GLP_546_48378_50642; dicer, RNAI,pseudo-merohedral twin, hydrolase;
3.00A {Giardia intestinalis} PDB: 2ffl_A
Length = 756
Score = 40.8 bits (95), Expect = 2e-04
Identities = 24/93 (25%), Positives = 44/93 (47%), Gaps = 5/93 (5%)
Query: 35 SYQESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAETCSQVARELDLA 94
S+ + ++RLE LGD +LG +++ L F A G L LV E + + + L L
Sbjct: 329 SHTDVFQRLELLGDAVLGFIVTARLLCLFPDASVGTLVELKMELVRNEALNYLVQTLGLP 388
Query: 95 SFIRVSSDLRKDVCSFMTSIQADVVESLIAALY 127
S++L + AD+ E ++ +++
Sbjct: 389 QLAEFSNNLVAK-----SKTWADMYEEIVGSIF 416
Score = 33.1 bits (75), Expect = 0.047
Identities = 30/124 (24%), Positives = 51/124 (41%), Gaps = 16/124 (12%)
Query: 22 LLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSA 81
LL+ ALT Y++LE LGD L ++ L + EG L+ S +
Sbjct: 637 LLQIALT--------PHVYQKLELLGDAFLKCSLALHLHALHPTLTEGALTRMRQSAETN 688
Query: 82 ETCSQVARELD---LASFIRVSSDLRKDVCSFMTSIQADVVESLIAALYLDGGIEVAGTF 138
++ + I ++ D + + D E+++AA+ L G E AG F
Sbjct: 689 SVLGRLTKRFPSVVSEVIIESHPKIQPD-----SKVYGDTFEAILAAILLACGEEAAGAF 743
Query: 139 VDKY 142
V ++
Sbjct: 744 VREH 747
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 32.2 bits (72), Expect = 0.11
Identities = 12/62 (19%), Positives = 25/62 (40%), Gaps = 17/62 (27%)
Query: 132 IEVAGTFVDKYWKQRALKSGKFRRDAKTELQEWAHAKFGVTPEYKV-------TFRSGPD 184
++ A +++ W+++A K +L+EW + + K+ F PD
Sbjct: 101 LDAASKVMEQEWREKA----------KKDLEEWNQRQSEQVEKNKINNRIADKAFYQQPD 150
Query: 185 HD 186
D
Sbjct: 151 AD 152
>1wdd_A Ribulose bisphosphate carboxylase large chain; rubisco,
photosynthesis, alpha/beta barrel, N- methylmethionine,
post-translational modification; HET: KCX CAP; 1.35A
{Oryza sativa} SCOP: c.1.14.1 d.58.9.1 PDB: 1rlc_L*
4rub_A* 3rub_L 1ej7_L 1aa1_L* 1aus_L 1rbo_L* 1rco_L*
1rcx_L* 1rxo_L* 1gk8_A* 1ir2_A* 1uzd_A* 1uzh_A* 2v69_A*
1uwa_A* 2v63_A* 2v67_A* 8ruc_A* 1upm_B* ...
Length = 477
Score = 29.4 bits (66), Expect = 0.74
Identities = 16/59 (27%), Positives = 31/59 (52%), Gaps = 3/59 (5%)
Query: 158 KTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAA 216
+TE + K GV +YK+T+ + P+++ + T ++ + P G+ + A VAA
Sbjct: 4 QTETKASVGFKAGVK-DYKLTYYT-PEYETKDTDILAAFRVTPQPGVP-PEEAGAAVAA 59
>3evf_A RNA-directed RNA polymerase NS5; NS5 methyltransferase, RNA CAP
binding, ATP-binding, capsid protein, cleavage on PAIR
of basic residues; HET: GTA SAH; 1.45A {Yellow fever
virus 17D} PDB: 3evb_A* 3evc_A* 3evd_A* 3eve_A* 3eva_A*
Length = 277
Score = 26.4 bits (58), Expect = 5.4
Identities = 9/49 (18%), Positives = 18/49 (36%), Gaps = 1/49 (2%)
Query: 129 DGGIEVAGTFVDKYWKQRALKSGKFRRDAKTELQEWAHAKFGVTPEYKV 177
+EV ++ + + +G +L W H + V E +V
Sbjct: 31 TDIVEVDRDTARRHLAEGKVDTGVAVSRGTAKL-RWFHERGYVKLEGRV 78
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.319 0.132 0.377
Gapped
Lambda K H
0.267 0.0545 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,874,019
Number of extensions: 82240
Number of successful extensions: 241
Number of sequences better than 10.0: 1
Number of HSP's gapped: 195
Number of HSP's successfully gapped: 46
Length of query: 227
Length of database: 5,693,230
Length adjustment: 89
Effective length of query: 138
Effective length of database: 3,535,514
Effective search space: 487900932
Effective search space used: 487900932
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: 55 (25.4 bits)