BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= psy2871
(178 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi)
G); A Human Telomeric Repeat Containing 6-Methyl-8-(2-
Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi)
Length = 195
Score = 206 bits (523), Expect = 7e-54, Method: Compositional matrix adjust.
Identities = 96/158 (60%), Positives = 125/158 (79%), Gaps = 1/158 (0%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
EPE LRK+FIGGL + TTDESL++ FEQWG + D VVM+DP TKRSRGFGF+TY+ + V
Sbjct: 8 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 67
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGLK-DQEEDDLREYFSQF 130
D AM+ RPH +DGRVVE KRAV R++ +P A+ TVKK+FVGG+K D EE LR+YF Q+
Sbjct: 68 DAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 127
Query: 131 GTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSK 168
G IE + ++T++ +G KRGFAF+ F+D+D VDKIV+ K
Sbjct: 128 GKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 165
Score = 60.8 bits (146), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 25/90 (27%), Positives = 54/90 (60%)
Query: 15 SLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA 74
+++K+F+GG+ T + L+ +FEQ+G+I + +M D + + RGF F+T+ + VD
Sbjct: 102 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 161
Query: 75 MSNRPHNIDGRVVETKRAVPRDEIGKPEAN 104
+ + H ++G E ++A+ + E+ ++
Sbjct: 162 VIQKYHTVNGHNCEVRKALSKQEMASASSS 191
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 101 PEANATVKKMFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
P+ ++K+F+GGL + D+ LR +F Q+GT+ ++ + T RGF F+ + +
Sbjct: 6 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 65
Query: 160 VVDKIVLSKITLLLDRRVE 178
VD + ++ + R VE
Sbjct: 66 EVDAAMNARPHKVDGRVVE 84
>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
pdb|1U1K|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt 7da
Ggg); A Human Telomeric Repeat Containing
7-Deaza-Adenine
pdb|1U1L|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt Prn
Ggg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1M|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 7gu
Gg); A Human Telomeric Repeat Containing 7-Deaza-Guanine
pdb|1U1N|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta (Prn)
Gg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1O|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggttag(Di)g); A Human Telomeric Repeat Containing
Inosine
pdb|1U1P|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 2pr
Gg); A Human Telomeric Repeat Containing 2-Aminopurine
pdb|1U1Q|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggtta(Di)gg); A Human Telomeric Repeat Containing
Inosine
pdb|1U1R|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(2pr)
G); A Human Telomeric Repeat Containing 2-Aminopurine
Length = 196
Score = 206 bits (523), Expect = 7e-54, Method: Compositional matrix adjust.
Identities = 96/158 (60%), Positives = 125/158 (79%), Gaps = 1/158 (0%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
EPE LRK+FIGGL + TTDESL++ FEQWG + D VVM+DP TKRSRGFGF+TY+ + V
Sbjct: 9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 68
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGLK-DQEEDDLREYFSQF 130
D AM+ RPH +DGRVVE KRAV R++ +P A+ TVKK+FVGG+K D EE LR+YF Q+
Sbjct: 69 DAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 128
Query: 131 GTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSK 168
G IE + ++T++ +G KRGFAF+ F+D+D VDKIV+ K
Sbjct: 129 GKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 166
Score = 60.8 bits (146), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 25/90 (27%), Positives = 54/90 (60%)
Query: 15 SLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA 74
+++K+F+GG+ T + L+ +FEQ+G+I + +M D + + RGF F+T+ + VD
Sbjct: 103 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 162
Query: 75 MSNRPHNIDGRVVETKRAVPRDEIGKPEAN 104
+ + H ++G E ++A+ + E+ ++
Sbjct: 163 VIQKYHTVNGHNCEVRKALSKQEMASASSS 192
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 101 PEANATVKKMFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
P+ ++K+F+GGL + D+ LR +F Q+GT+ ++ + T RGF F+ + +
Sbjct: 7 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 66
Query: 160 VVDKIVLSKITLLLDRRVE 178
VD + ++ + R VE
Sbjct: 67 EVDAAMNARPHKVDGRVVE 85
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 205 bits (522), Expect = 1e-53, Method: Compositional matrix adjust.
Identities = 96/158 (60%), Positives = 125/158 (79%), Gaps = 1/158 (0%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
EPE LRK+FIGGL + TTDESL++ FEQWG + D VVM+DP TKRSRGFGF+TY+ + V
Sbjct: 10 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 69
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGLK-DQEEDDLREYFSQF 130
D AM+ RPH +DGRVVE KRAV R++ +P A+ TVKK+FVGG+K D EE LR+YF Q+
Sbjct: 70 DAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 129
Query: 131 GTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSK 168
G IE + ++T++ +G KRGFAF+ F+D+D VDKIV+ K
Sbjct: 130 GKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 167
Score = 60.8 bits (146), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 27/101 (26%), Positives = 57/101 (56%)
Query: 4 RYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFI 63
R D + +++K+F+GG+ T + L+ +FEQ+G+I + +M D + + RGF F+
Sbjct: 93 REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFV 152
Query: 64 TYSEAKMVDDAMSNRPHNIDGRVVETKRAVPRDEIGKPEAN 104
T+ + VD + + H ++G E ++A+ + E+ ++
Sbjct: 153 TFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSS 193
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 101 PEANATVKKMFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
P+ ++K+F+GGL + D+ LR +F Q+GT+ ++ + T RGF F+ + +
Sbjct: 8 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 67
Query: 160 VVDKIVLSKITLLLDRRVE 178
VD + ++ + R VE
Sbjct: 68 EVDAAMNARPHKVDGRVVE 86
>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex
pdb|1PO6|A Chain A, Crystal Structure Of Up1 Complexed With
D(Tagg(6mi)ttaggg): A Human Telomeric Repeat Containing
6-Methyl-8-(2-Deoxy-
Beta-Ribofuranosyl)isoxanthopteridine (6mi)
Length = 183
Score = 205 bits (522), Expect = 1e-53, Method: Compositional matrix adjust.
Identities = 96/158 (60%), Positives = 125/158 (79%), Gaps = 1/158 (0%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
EPE LRK+FIGGL + TTDESL++ FEQWG + D VVM+DP TKRSRGFGF+TY+ + V
Sbjct: 2 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 61
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGLK-DQEEDDLREYFSQF 130
D AM+ RPH +DGRVVE KRAV R++ +P A+ TVKK+FVGG+K D EE LR+YF Q+
Sbjct: 62 DAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 121
Query: 131 GTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSK 168
G IE + ++T++ +G KRGFAF+ F+D+D VDKIV+ K
Sbjct: 122 GKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 159
Score = 60.8 bits (146), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 27/96 (28%), Positives = 55/96 (57%)
Query: 4 RYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFI 63
R D + +++K+F+GG+ T + L+ +FEQ+G+I + +M D + + RGF F+
Sbjct: 85 REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFV 144
Query: 64 TYSEAKMVDDAMSNRPHNIDGRVVETKRAVPRDEIG 99
T+ + VD + + H ++G E ++A+ + E+
Sbjct: 145 TFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMA 180
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 205 bits (521), Expect = 1e-53, Method: Compositional matrix adjust.
Identities = 96/158 (60%), Positives = 125/158 (79%), Gaps = 1/158 (0%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
EPE LRK+FIGGL + TTDESL++ FEQWG + D VVM+DP TKRSRGFGF+TY+ + V
Sbjct: 9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 68
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGLK-DQEEDDLREYFSQF 130
D AM+ RPH +DGRVVE KRAV R++ +P A+ TVKK+FVGG+K D EE LR+YF Q+
Sbjct: 69 DAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 128
Query: 131 GTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSK 168
G IE + ++T++ +G KRGFAF+ F+D+D VDKIV+ K
Sbjct: 129 GKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 166
Score = 58.5 bits (140), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 50/81 (61%)
Query: 15 SLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA 74
+++K+F+GG+ T + L+ +FEQ+G+I + +M D + + RGF F+T+ + VD
Sbjct: 103 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 162
Query: 75 MSNRPHNIDGRVVETKRAVPR 95
+ + H ++G E ++A+ +
Sbjct: 163 VIQKYHTVNGHNCEVRKALSK 183
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 101 PEANATVKKMFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
P+ ++K+F+GGL + D+ LR +F Q+GT+ ++ + T RGF F+ + +
Sbjct: 7 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 66
Query: 160 VVDKIVLSKITLLLDRRVE 178
VD + ++ + R VE
Sbjct: 67 EVDAAMNARPHKVDGRVVE 85
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 205 bits (521), Expect = 1e-53, Method: Compositional matrix adjust.
Identities = 96/158 (60%), Positives = 125/158 (79%), Gaps = 1/158 (0%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
EPE LRK+FIGGL + TTDESL++ FEQWG + D VVM+DP TKRSRGFGF+TY+ + V
Sbjct: 7 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 66
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGLK-DQEEDDLREYFSQF 130
D AM+ RPH +DGRVVE KRAV R++ +P A+ TVKK+FVGG+K D EE LR+YF Q+
Sbjct: 67 DAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 126
Query: 131 GTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSK 168
G IE + ++T++ +G KRGFAF+ F+D+D VDKIV+ K
Sbjct: 127 GKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 164
Score = 58.2 bits (139), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 50/81 (61%)
Query: 15 SLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA 74
+++K+F+GG+ T + L+ +FEQ+G+I + +M D + + RGF F+T+ + VD
Sbjct: 101 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 160
Query: 75 MSNRPHNIDGRVVETKRAVPR 95
+ + H ++G E ++A+ +
Sbjct: 161 VIQKYHTVNGHNCEVRKALSK 181
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 101 PEANATVKKMFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
P+ ++K+F+GGL + D+ LR +F Q+GT+ ++ + T RGF F+ + +
Sbjct: 5 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 64
Query: 160 VVDKIVLSKITLLLDRRVE 178
VD + ++ + R VE
Sbjct: 65 EVDAAMNARPHKVDGRVVE 83
>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex
With Rna
pdb|2KM8|C Chain C, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 167
Score = 132 bits (332), Expect = 1e-31, Method: Compositional matrix adjust.
Identities = 65/162 (40%), Positives = 107/162 (66%), Gaps = 8/162 (4%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
K+FIGGL++ TT+++L+ +F ++G + D+ +MKDP T RSRGFGF+++ + VD+ +
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 78 RPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESV 136
+ H +DG+V++ KRA+PRDE K K+FVGG+ D + E+FSQ+GTI
Sbjct: 65 Q-HILDGKVIDPKRAIPRDEQDK------TGKIFVGGIGPDVRPKEFEEFFSQWGTIIDA 117
Query: 137 NMVTNKETGAKRGFAFIEFNDYDVVDKIVLSKITLLLDRRVE 178
++ +K+TG RGF F+ ++ D VD++ +K DR++E
Sbjct: 118 QLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIE 159
Score = 68.9 bits (167), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 34/84 (40%), Positives = 47/84 (55%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
E + K+F+GG+ + + FF QWG I+D +M D T +SRGFGF+TY A V
Sbjct: 83 EQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAV 142
Query: 72 DDAMSNRPHNIDGRVVETKRAVPR 95
D N+ + R +E KRA PR
Sbjct: 143 DRVCQNKFIDFKDRKIEIKRAEPR 166
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 124 bits (312), Expect = 2e-29, Method: Compositional matrix adjust.
Identities = 55/88 (62%), Positives = 70/88 (79%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
E E RK+FIGGL + TT+ESL+ ++EQWG++ D VVM+DP +KRSRGFGF+T+S V
Sbjct: 23 EKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEV 82
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRDEIG 99
D AM+ RPH+IDGRVVE KRAV R+E G
Sbjct: 83 DAAMAARPHSIDGRVVEPKRAVAREESG 110
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 108 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVL 166
+K+F+GGL + E+ LR Y+ Q+G + ++ + + RGF F+ F+ VD +
Sbjct: 28 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA 87
Query: 167 SKITLLLDRRVE 178
++ + R VE
Sbjct: 88 ARPHSIDGRVVE 99
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 94.4 bits (233), Expect = 4e-20, Method: Compositional matrix adjust.
Identities = 37/82 (45%), Positives = 59/82 (71%)
Query: 14 ESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDD 73
+ + K+F+GGLD+ TT E+L+++F Q+GE+VD V+MKD T +SRGFGF+ + + V
Sbjct: 14 DEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGT 73
Query: 74 AMSNRPHNIDGRVVETKRAVPR 95
+++RPH +DGR ++ K PR
Sbjct: 74 VLASRPHTLDGRNIDPKPCTPR 95
Score = 52.8 bits (125), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 107 VKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
+ K+FVGGL ++ LR YFSQ+G + ++ +K T RGF F++F D + V ++
Sbjct: 16 IGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVL 75
Query: 166 LSKITLLLDRRVE 178
S+ L R ++
Sbjct: 76 ASRPHTLDGRNID 88
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 86.3 bits (212), Expect = 8e-18, Method: Compositional matrix adjust.
Identities = 36/78 (46%), Positives = 56/78 (71%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
K+FIGGL ++TT E L+ +F Q+GE+ + +VM+DP+TKRSRGFGF+T+ + VD ++
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 86
Query: 78 RPHNIDGRVVETKRAVPR 95
H +D + ++ K A PR
Sbjct: 87 SRHELDSKTIDPKVAFPR 104
Score = 51.2 bits (121), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 28/74 (37%), Positives = 41/74 (55%), Gaps = 5/74 (6%)
Query: 93 VPRDEIGKPEANATVKKMFVGGLKDQE-EDDLREYFSQFGTIESVNMVTNKETGAKRGFA 151
VPR ++ KMF+GGL Q ++ LREYF QFG ++ ++ + T RGF
Sbjct: 15 VPRGS----HMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFG 70
Query: 152 FIEFNDYDVVDKIV 165
F+ F D VDK++
Sbjct: 71 FVTFMDQAGVDKVL 84
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 81.6 bits (200), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 34/75 (45%), Positives = 54/75 (72%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
K+FIGGL ++TT E L+ +F Q+GE+ + +VM+DP+TKRSRGFGF+T+ + VD ++
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 78 RPHNIDGRVVETKRA 92
H +D + ++ K A
Sbjct: 62 SRHELDSKTIDPKVA 76
Score = 49.7 bits (117), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 25/58 (43%), Positives = 36/58 (62%), Gaps = 1/58 (1%)
Query: 109 KMFVGGLKDQE-EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
KMF+GGL Q ++ LREYF QFG ++ ++ + T RGF F+ F D VDK++
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 59
>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
pdb|1HD1|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
Length = 75
Score = 80.5 bits (197), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 34/74 (45%), Positives = 53/74 (71%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
+FIGGL + TT + L+ +F ++GE+VD + DPIT RSRGFGF+ + E++ VD M +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 79 PHNIDGRVVETKRA 92
H ++G+V++ KRA
Sbjct: 62 EHKLNGKVIDPKRA 75
Score = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 36/57 (63%), Gaps = 1/57 (1%)
Query: 110 MFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
MF+GGL D + DL++YFS+FG + + + TG RGF F+ F + + VDK++
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM 58
>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
pdb|3S7R|B Chain B, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
Length = 87
Score = 77.0 bits (188), Expect = 6e-15, Method: Compositional matrix adjust.
Identities = 33/79 (41%), Positives = 52/79 (65%)
Query: 14 ESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDD 73
E K F+GGL + T+ + L+ +F ++GE+VD + DP T RSRGFGFI + +A V+
Sbjct: 9 EDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEK 68
Query: 74 AMSNRPHNIDGRVVETKRA 92
+ + H +DGRV++ K+A
Sbjct: 69 VLDQKEHRLDGRVIDPKKA 87
Score = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 30/70 (42%), Positives = 40/70 (57%), Gaps = 2/70 (2%)
Query: 109 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLS 167
K FVGGL D + DL++YF++FG + + + TG RGF FI F D V+K VL
Sbjct: 13 KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEK-VLD 71
Query: 168 KITLLLDRRV 177
+ LD RV
Sbjct: 72 QKEHRLDGRV 81
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 71.2 bits (173), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 32/79 (40%), Positives = 54/79 (68%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
K+F+GG+ + + L+ +F+++G + +VV++ D +R RGFGFIT+ + + VD A++
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
Query: 78 RPHNIDGRVVETKRAVPRD 96
H+I G+ VE KRA PRD
Sbjct: 72 HFHDIMGKKVEVKRAEPRD 90
Score = 52.4 bits (124), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 28/71 (39%), Positives = 41/71 (57%), Gaps = 1/71 (1%)
Query: 109 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLS 167
K+FVGG+ + E +LREYF +FG + V M+ + E RGF FI F D VD+ V
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
Query: 168 KITLLLDRRVE 178
++ ++VE
Sbjct: 72 HFHDIMGKKVE 82
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 67.0 bits (162), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 29/74 (39%), Positives = 47/74 (63%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
+F+GGL TT E ++ +FEQ+G++ D ++M D T R RGFGF+T+ +V+
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 79 PHNIDGRVVETKRA 92
H I+ ++VE K+A
Sbjct: 62 FHEINNKMVECKKA 75
Score = 46.2 bits (108), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 110 MFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSK 168
+FVGGL + +D++ YF QFG ++ ++ +K T RGF F+ F D+V+K+
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 169 ITLLLDRRVE 178
+ ++ VE
Sbjct: 62 FHEINNKMVE 71
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 66.6 bits (161), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 32/76 (42%), Positives = 51/76 (67%), Gaps = 1/76 (1%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA-MS 76
K+F+GGL + T ++SL+ F ++G+I +VVV+KD T+RSRGFGF+T+ DA M+
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 77 NRPHNIDGRVVETKRA 92
++DGR + +A
Sbjct: 74 MNGKSVDGRQIRVDQA 89
Score = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/52 (44%), Positives = 32/52 (61%), Gaps = 1/52 (1%)
Query: 109 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
K+FVGGL D E L + FS++G I V +V ++ET RGF F+ F + D
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENID 65
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 63.9 bits (154), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 30/71 (42%), Positives = 46/71 (64%)
Query: 15 SLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA 74
+ K+F+GGL Y TTD SL+ +FE +G+I + VV+ D T +SRG+GF+T ++ + A
Sbjct: 16 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA 75
Query: 75 MSNRPHNIDGR 85
+ IDGR
Sbjct: 76 CKDPNPIIDGR 86
Score = 48.1 bits (113), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 34/57 (59%), Gaps = 1/57 (1%)
Query: 102 EANATVKKMFVGGLKDQEED-DLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
+ + T K+FVGGL D LR+YF FG IE ++T+++TG RG+ F+ D
Sbjct: 12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMAD 68
>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAF|B Chain B, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAG|A Chain A, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAG|B Chain B, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAH|A Chain A, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAH|B Chain B, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAI|A Chain A, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAI|B Chain B, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAJ|A Chain A, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAJ|B Chain B, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAK|A Chain A, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAK|B Chain B, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAL|A Chain A, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|B Chain B, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|D Chain D, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|I Chain I, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAM|A Chain A, Structure Of U2af65 Variant With Bru5c2 Dna
pdb|3VAM|B Chain B, Structure Of U2af65 Variant With Bru5c2 Dna
Length = 174
Score = 62.4 bits (150), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 39/157 (24%), Positives = 79/157 (50%), Gaps = 12/157 (7%)
Query: 15 SLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVV-VMKDPI----TKRSRGFGFITYSEAK 69
S R++++G + + T+E++ FF + + +P+ + + F F+ +
Sbjct: 5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 64
Query: 70 MVDDAMSNRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGLKDQEEDD-LREYFS 128
AM+ G+ ++ +R P D P A+ K+F+GGL + DD ++E +
Sbjct: 65 ETTQAMAFDGIIFQGQSLKIRR--PHDYQPLPGAH----KLFIGGLPNYLNDDQVKELLT 118
Query: 129 QFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
FG +++ N+V + TG +G+AF E+ D +V D+ +
Sbjct: 119 SFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 155
Score = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 31/60 (51%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
K+FIGGL D+ ++ +G + ++KD T S+G+ F Y + + D A++
Sbjct: 97 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 156
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 62.0 bits (149), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 39/157 (24%), Positives = 79/157 (50%), Gaps = 12/157 (7%)
Query: 15 SLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVV-VMKDPI----TKRSRGFGFITYSEAK 69
S R++++G + + T+E++ FF + + +P+ + + F F+ +
Sbjct: 3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62
Query: 70 MVDDAMSNRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGLKDQEEDD-LREYFS 128
AM+ G+ ++ +R P D P A+ K+F+GGL + DD ++E +
Sbjct: 63 ETTQAMAFDGIIFQGQSLKIRR--PHDYQPLPGAH----KLFIGGLPNYLNDDQVKELLT 116
Query: 129 QFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
FG +++ N+V + TG +G+AF E+ D +V D+ +
Sbjct: 117 SFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 153
Score = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 31/60 (51%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
K+FIGGL D+ ++ +G + ++KD T S+G+ F Y + + D A++
Sbjct: 95 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 154
>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos
Rna
pdb|1G2E|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The Tumor
Necrosis Factor Alpha Rna
Length = 167
Score = 60.5 bits (145), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 39/136 (28%), Positives = 74/136 (54%), Gaps = 10/136 (7%)
Query: 24 LDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNRPHNID 83
L T E ++ F GEI +++D IT +S G+GF+ Y + K + A+ + ++
Sbjct: 10 LPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI----NTLN 65
Query: 84 GRVVETKRAVPRDEIGKPEANATVK--KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVT 140
G ++TK + +P ++A+++ ++V GL K + +L + FSQ+G I + ++
Sbjct: 66 GLRLQTKTI--KVSYARP-SSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILV 122
Query: 141 NKETGAKRGFAFIEFN 156
++ TG RG FI F+
Sbjct: 123 DQVTGVSRGVGFIRFD 138
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 32/57 (56%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+++ GL T + L+ F Q+G I+ ++ D +T SRG GFI + + ++A+
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 147
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 60.1 bits (144), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 38/146 (26%), Positives = 78/146 (53%), Gaps = 10/146 (6%)
Query: 14 ESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDD 73
+S + + L T + ++ F G+I +++D IT +S G+GF+ YS+ D
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 74 AMSNRPHNIDGRVVETKRAVPRDEIGKPEANATVK--KMFVGGL-KDQEEDDLREYFSQF 130
A+ + ++G ++TK + +P ++A+++ ++V GL K + ++ + FSQ+
Sbjct: 62 AI----NTLNGLKLQTKTI--KVSYARP-SSASIRDANLYVSGLPKTMSQKEMEQLFSQY 114
Query: 131 GTIESVNMVTNKETGAKRGFAFIEFN 156
G I + ++ ++ TG RG FI F+
Sbjct: 115 GRIITSRILLDQATGVSRGVGFIRFD 140
Score = 37.0 bits (84), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 28/50 (56%)
Query: 116 KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
++ +D+ + F G IES +V +K TG G+ F+ ++D + DK +
Sbjct: 14 QNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI 63
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 59.7 bits (143), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 37/140 (26%), Positives = 72/140 (51%), Gaps = 8/140 (5%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN- 77
+ + L T + L++ F GE+ +++D + S G+GF+ Y AK + A++
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 78 RPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESV 136
+ + ++ A P E+ K +AN +++ GL + + D+ + FS+FG I +
Sbjct: 65 NGLRLQSKTIKVSYARPSSEVIK-DAN-----LYISGLPRTMTQKDVEDMFSRFGRIINS 118
Query: 137 NMVTNKETGAKRGFAFIEFN 156
++ ++ TG RG AFI F+
Sbjct: 119 RVLVDQTTGLSRGVAFIRFD 138
>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
pdb|4ED5|B Chain B, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
Length = 177
Score = 59.7 bits (143), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 38/151 (25%), Positives = 76/151 (50%), Gaps = 8/151 (5%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN- 77
+ + L T + L++ F GE+ +++D + S G+GF+ Y AK + A++
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 78 RPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESV 136
+ + ++ A P E+ K +AN +++ GL + + D+ + FS+FG I +
Sbjct: 65 NGLRLQSKTIKVSYARPSSEVIK-DAN-----LYISGLPRTMTQKDVEDMFSRFGRIINS 118
Query: 137 NMVTNKETGAKRGFAFIEFNDYDVVDKIVLS 167
++ ++ TG RG AFI F+ ++ + S
Sbjct: 119 RVLVDQTTGLSRGVAFIRFDKRSEAEEAITS 149
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 57.4 bits (137), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 42/143 (29%), Positives = 75/143 (52%), Gaps = 9/143 (6%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITK--RSRGFGFITYSEAKMVDDAM 75
K+F+G + +++ L+ FEQ+G + ++ V++D +S+G F+T+ K +A
Sbjct: 17 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA- 75
Query: 76 SNRPHNIDGRVVETKRAVPRDEIGKPEANATV--KKMFVGGL-KDQEEDDLREYFSQFGT 132
N HN+ +V+ + + E N V +K+F+G + K E+D+R FS FG
Sbjct: 76 QNALHNM--KVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQ 133
Query: 133 IESVNMVTNKETGAKRGFAFIEF 155
IE ++ + G RG AF+ F
Sbjct: 134 IEECRILRGPD-GLSRGCAFVTF 155
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 33/59 (55%), Gaps = 1/59 (1%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
RK+FIG + + T+ ++ F +G+I + +++ P SRG F+T++ M A+
Sbjct: 108 RKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAI 165
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 57.4 bits (137), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 42/143 (29%), Positives = 75/143 (52%), Gaps = 9/143 (6%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITK--RSRGFGFITYSEAKMVDDAM 75
K+F+G + +++ L+ FEQ+G + ++ V++D +S+G F+T+ K +A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA- 63
Query: 76 SNRPHNIDGRVVETKRAVPRDEIGKPEANATV--KKMFVGGL-KDQEEDDLREYFSQFGT 132
N HN+ +V+ + + E N V +K+F+G + K E+D+R FS FG
Sbjct: 64 QNALHNM--KVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQ 121
Query: 133 IESVNMVTNKETGAKRGFAFIEF 155
IE ++ + G RG AF+ F
Sbjct: 122 IEECRILRGPD-GLSRGCAFVTF 143
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 33/59 (55%), Gaps = 1/59 (1%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
RK+FIG + + T+ ++ F +G+I + +++ P SRG F+T++ M A+
Sbjct: 96 RKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAI 153
>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D (Auf1) With Telomere Dna
pdb|1X0F|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D(Auf1) With Telomeric Dna
Length = 79
Score = 57.4 bits (137), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 29/63 (46%), Positives = 41/63 (65%), Gaps = 1/63 (1%)
Query: 107 VKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
VKK+FVGGL D E+ +REYF FG +ES+ + + +T +RGF FI F + + V KI+
Sbjct: 1 VKKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 60
Query: 166 LSK 168
K
Sbjct: 61 EKK 63
Score = 53.1 bits (126), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 44/78 (56%)
Query: 16 LRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
++K+F+GGL T +E ++ +F +GE+ + + D T + RGF FIT+ E + V M
Sbjct: 1 VKKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 60
Query: 76 SNRPHNIDGRVVETKRAV 93
+ HN+ E K A+
Sbjct: 61 EKKYHNVGLSKCEIKVAM 78
>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
pdb|3NNA|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 56.6 bits (135), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 42/143 (29%), Positives = 73/143 (51%), Gaps = 9/143 (6%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITK--RSRGFGFITYSEAKMVDDAM 75
K F+G + +++ L+ FEQ+G + ++ V++D +S+G F+T+ K +A
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 76 SNRPHNIDGRVVETKRAVPRDEIGKPEANATV--KKMFVGGL-KDQEEDDLREYFSQFGT 132
N HN +V+ + + E N V +K+F+G + K E+D+R FS FG
Sbjct: 65 -NALHNX--KVLPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQ 121
Query: 133 IESVNMVTNKETGAKRGFAFIEF 155
IE ++ + G RG AF+ F
Sbjct: 122 IEECRILRGPD-GLSRGCAFVTF 143
Score = 36.2 bits (82), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
RK+FIG + + T+ ++ F +G+I + +++ P SRG F+T++ A+
Sbjct: 96 RKLFIGXISKKCTENDIRVXFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAXAQTAI 153
>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of
Fbp-Interacting Repressor (Fir)
pdb|2KXH|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fir In
The Complex With Fbp Nbox Peptide
Length = 199
Score = 56.2 bits (134), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 38/148 (25%), Positives = 76/148 (51%), Gaps = 9/148 (6%)
Query: 16 LRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAKMVD 72
+ +V++G + Y +++++ F +G I + + D +T + +GF F+ Y A++
Sbjct: 13 MCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLAL 72
Query: 73 DAMSN---RPHNID-GRVVETKRAVPRDEIGKPEANATVKKMFVGGL-KDQEEDDLREYF 127
+ M++ NI GR +A P + EA A +++V + +D +DD++ F
Sbjct: 73 EQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARA-FNRIYVASVHQDLSDDDIKSVF 131
Query: 128 SQFGTIESVNMVTNKETGAKRGFAFIEF 155
FG I+S + + TG +G+ FIE+
Sbjct: 132 EAFGKIKSCTLARDPTTGKHKGYGFIEY 159
Score = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/88 (25%), Positives = 49/88 (55%), Gaps = 1/88 (1%)
Query: 7 DSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS 66
D E + ++++ + +D+ +++ FE +G+I + +DP T + +G+GFI Y
Sbjct: 101 DQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYE 160
Query: 67 EAKMVDDAMSN-RPHNIDGRVVETKRAV 93
+A+ DA+S+ ++ G+ + +AV
Sbjct: 161 KAQSSQDAVSSMNLFDLGGQYLRVGKAV 188
>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
pdb|2QFJ|B Chain B, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
Length = 216
Score = 55.8 bits (133), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 38/148 (25%), Positives = 76/148 (51%), Gaps = 9/148 (6%)
Query: 16 LRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAKMVD 72
+ +V++G + Y +++++ F +G I + + D +T + +GF F+ Y A++
Sbjct: 28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLAL 87
Query: 73 DAMSN---RPHNID-GRVVETKRAVPRDEIGKPEANATVKKMFVGGL-KDQEEDDLREYF 127
+ M++ NI GR +A P + EA A +++V + +D +DD++ F
Sbjct: 88 EQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARA-FNRIYVASVHQDLSDDDIKSVF 146
Query: 128 SQFGTIESVNMVTNKETGAKRGFAFIEF 155
FG I+S + + TG +G+ FIE+
Sbjct: 147 EAFGKIKSATLARDPTTGKHKGYGFIEY 174
Score = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/88 (25%), Positives = 49/88 (55%), Gaps = 1/88 (1%)
Query: 7 DSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS 66
D E + ++++ + +D+ +++ FE +G+I + +DP T + +G+GFI Y
Sbjct: 116 DQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYE 175
Query: 67 EAKMVDDAMSN-RPHNIDGRVVETKRAV 93
+A+ DA+S+ ++ G+ + +AV
Sbjct: 176 KAQSSQDAVSSMNLFDLGGQYLRVGKAV 203
>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 2.50 A Resolution
Length = 200
Score = 55.5 bits (132), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 37/146 (25%), Positives = 70/146 (47%), Gaps = 9/146 (6%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
+V++G + Y +++++ F +G I + D +T + +GF F+ Y + A+
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 78 R------PHNID-GRVVETKRAVPRDEIGKPEANATVKKMFVGGL-KDQEEDDLREYFSQ 129
NI GR +A P + EA A +++V + +D +DD++ F
Sbjct: 74 XNSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARA-FNRIYVASVHQDLSDDDIKSVFEA 132
Query: 130 FGTIESVNMVTNKETGAKRGFAFIEF 155
FG I+S + + TG +G+ FIE+
Sbjct: 133 FGKIKSCTLARDPTTGKHKGYGFIEY 158
Score = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/88 (25%), Positives = 49/88 (55%), Gaps = 1/88 (1%)
Query: 7 DSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS 66
D E + ++++ + +D+ +++ FE +G+I + +DP T + +G+GFI Y
Sbjct: 100 DQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYE 159
Query: 67 EAKMVDDAMSNRP-HNIDGRVVETKRAV 93
+A+ DA+S+ ++ G+ + +AV
Sbjct: 160 KAQSSQDAVSSXNLFDLGGQYLRVGKAV 187
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 55.1 bits (131), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 28/68 (41%), Positives = 43/68 (63%), Gaps = 1/68 (1%)
Query: 23 GLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNRPHNI 82
GL ++TT++ L+ +F +GE++ V V KD T S+GFGF+ ++E + MS R H I
Sbjct: 22 GLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR-HMI 80
Query: 83 DGRVVETK 90
DGR + K
Sbjct: 81 DGRWCDCK 88
Score = 43.5 bits (101), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 29/46 (63%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
E DL+EYFS FG + V + + +TG +GF F+ F +Y+ K++
Sbjct: 29 EQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVM 74
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 55.1 bits (131), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 39/171 (22%), Positives = 80/171 (46%), Gaps = 24/171 (14%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVV-VMKDPI----TKRSRGFGFITYSEAKMV 71
R++++G + + T+E++ FF + + +P+ + + F F+ +
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRD-----------EIGKPEANATV-----KKMFVGGL 115
AM+ G+ ++ +R P D + P +TV K+F+GGL
Sbjct: 65 TQAMAFDGIIFQGQSLKIRR--PHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGL 122
Query: 116 KDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
+ DD ++E + FG +++ N+V + TG +G+AF E+ D +V D+ +
Sbjct: 123 PNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 173
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/92 (27%), Positives = 46/92 (50%), Gaps = 5/92 (5%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
P+S K+FIGGL D+ ++ +G + ++KD T S+G+ F Y + + D
Sbjct: 111 PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTD 170
Query: 73 DAMSNRPHNIDG-RVVETKRAVPRDEIGKPEA 103
A++ ++G ++ + K V R +G A
Sbjct: 171 QAIA----GLNGMQLGDKKLLVQRASVGAKNA 198
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 53.5 bits (127), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 41/57 (71%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+++G L + T++ L+ FE +G+I ++V+MKD T RS+G+GFIT+S+++ A+
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 36/64 (56%), Gaps = 1/64 (1%)
Query: 103 ANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVV 161
++ ++VG L + ED LR F FG I+++ ++ + +TG +G+ FI F+D +
Sbjct: 1 GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60
Query: 162 DKIV 165
+ +
Sbjct: 61 RRAL 64
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 52.4 bits (124), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 26/60 (43%), Positives = 38/60 (63%), Gaps = 1/60 (1%)
Query: 110 MFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSK 168
+FVGGL D E+ +REYF FG +ES+ + + +T +RGF FI F + + V KI+ K
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Score = 50.1 bits (118), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 40/74 (54%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
+F+GGL T +E ++ +F +GE+ + + D T + RGF FIT+ E + V M +
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Query: 79 PHNIDGRVVETKRA 92
HN+ E K A
Sbjct: 62 YHNVGLSKCEIKVA 75
>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm
pdb|2LEB|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uccagu-3'
pdb|2LEC|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uggagu-3'
Length = 135
Score = 50.8 bits (120), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 46/77 (59%), Gaps = 4/77 (5%)
Query: 14 ESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDD 73
E + + + L YRT+ ++L+ FE++G + DV + +D TK SRGF F+ + + + +D
Sbjct: 45 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 104
Query: 74 AMSNRPHNIDGRVVETK 90
AM +DG V++ +
Sbjct: 105 AMD----AMDGAVLDGR 117
Score = 33.5 bits (75), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 7/53 (13%)
Query: 121 DDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND-------YDVVDKIVL 166
D LR F ++G + V + ++ T RGFAF+ F+D D +D VL
Sbjct: 62 DTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVL 114
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 50.8 bits (120), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 51/78 (65%), Gaps = 6/78 (7%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY---SEAKMVDDA 74
K+FIGGL+ T ++ L+A F + G I +V+++KD T +SRGF FIT+ ++AK
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAKNAAKD 67
Query: 75 MSNRPHNIDGRVVETKRA 92
M+ + ++ G+ ++ ++A
Sbjct: 68 MNGK--SLHGKAIKVEQA 83
Score = 35.8 bits (81), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 30/50 (60%), Gaps = 2/50 (4%)
Query: 109 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
K+F+GGL ++ E L+ F + G I V ++ ++ T RGFAFI F +
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFEN 57
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 50.4 bits (119), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 46/77 (59%), Gaps = 4/77 (5%)
Query: 14 ESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDD 73
E + + + L YRT+ ++L+ FE++G + DV + +D TK SRGF F+ + + + +D
Sbjct: 68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 127
Query: 74 AMSNRPHNIDGRVVETK 90
AM +DG V++ +
Sbjct: 128 AMD----AMDGAVLDGR 140
Score = 32.3 bits (72), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 22/37 (59%)
Query: 121 DDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
D LR F ++G + V + ++ T RGFAF+ F+D
Sbjct: 85 DTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHD 121
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 50.1 bits (118), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 38/58 (65%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
++++G L + T++ L+ FE +G I + +M D T RS+G+GFIT+S+++ A+
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKAL 85
Score = 46.2 bits (108), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 38/65 (58%), Gaps = 1/65 (1%)
Query: 102 EANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDV 160
+ +A +++VG L + ED LR F FG IES+ ++ + ETG +G+ FI F+D +
Sbjct: 21 KGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSEC 80
Query: 161 VDKIV 165
K +
Sbjct: 81 AKKAL 85
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 50.1 bits (118), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 38/58 (65%), Gaps = 1/58 (1%)
Query: 109 KMFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
K+F+GGL + DD ++E + FG +++ N+V + TG +G+AF E+ D +V D+ +
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 60
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 43/88 (48%), Gaps = 5/88 (5%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
K+FIGGL D+ ++ +G + ++KD T S+G+ F Y + + D A++
Sbjct: 2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 61
Query: 77 NRPHNIDG-RVVETKRAVPRDEIGKPEA 103
++G ++ + K V R +G A
Sbjct: 62 ----GLNGMQLGDKKLLVQRASVGAKNA 85
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 49.7 bits (117), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 34/145 (23%), Positives = 70/145 (48%), Gaps = 7/145 (4%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R +++G LD T++ L+ +F+ G I ++ +M D ++ + F+ Y ++ + A+
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQ 59
Query: 77 N-RPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGLKDQEEDD-LREYFSQFGTIE 134
I+ +V+ A + + +FVG L +D+ LR F F +
Sbjct: 60 TLNGKQIENNIVKINWAFQSQQSSSDD----TFNLFVGDLNVNVDDETLRNAFKDFPSYL 115
Query: 135 SVNMVTNKETGAKRGFAFIEFNDYD 159
S +++ + +TG+ RG+ F+ F D
Sbjct: 116 SGHVMWDMQTGSSRGYGFVSFTSQD 140
Score = 39.7 bits (91), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 23/87 (26%), Positives = 45/87 (51%), Gaps = 1/87 (1%)
Query: 8 SKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSE 67
S+ + + +F+G L+ DE+L+ F+ + + VM D T SRG+GF++++
Sbjct: 79 SQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTS 138
Query: 68 AKMVDDAM-SNRPHNIDGRVVETKRAV 93
+AM S + +++GR + A
Sbjct: 139 QDDAQNAMDSMQGQDLNGRPLRINWAA 165
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 49.7 bits (117), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 49/85 (57%), Gaps = 4/85 (4%)
Query: 16 LRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+R +++G L Y T E ++ F Q+G++ +V ++ D TK+ +GFGF+ E + V +A+
Sbjct: 1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAI 59
Query: 76 SNRPHNID--GRVVETKRAVPRDEI 98
+ + N D GR + A P+ +
Sbjct: 60 A-KLDNTDFMGRTIRVTEANPKKSL 83
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 35/59 (59%), Gaps = 1/59 (1%)
Query: 107 VKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKI 164
++ ++VG L + ++E FSQFG + +V ++ ++ET +GF F+E + V + I
Sbjct: 1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAI 59
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 39/71 (54%), Gaps = 4/71 (5%)
Query: 15 SLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA 74
SLR VF+G + Y T+E L+ F + G +V ++ D T + +G+GF Y + + A
Sbjct: 7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSA 66
Query: 75 MSNRPHNIDGR 85
M N++GR
Sbjct: 67 M----RNLNGR 73
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 37/62 (59%), Gaps = 1/62 (1%)
Query: 101 PEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
P + +++ +FVG + + E+ L++ FS+ G + S +V ++ETG +G+ F E+ D +
Sbjct: 2 PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61
Query: 160 VV 161
Sbjct: 62 TA 63
>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
pdb|4F02|D Chain D, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
Length = 213
Score = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 42/165 (25%), Positives = 78/165 (47%), Gaps = 9/165 (5%)
Query: 16 LRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+ +++G L T+ L F G I+ + V +D IT+RS G+ ++ + + + A+
Sbjct: 15 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL 74
Query: 76 SNRPHN-IDGRVVETKRAVPRDEIGKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTI 133
+ I G+ V + + K + V +F+ L K + L + FS FG I
Sbjct: 75 DTMNFDVIKGKPVRIMWSQRDPSLRK----SGVGNIFIKNLDKSIDNKALYDTFSAFGNI 130
Query: 134 ESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSKITLLL-DRRV 177
S +V + E G+K G+ F+ F + ++ + +LL DR+V
Sbjct: 131 LSCKVVCD-ENGSK-GYGFVHFETQEAAERAIEKMNGMLLNDRKV 173
>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|B Chain B, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|C Chain C, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|D Chain D, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|E Chain E, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|F Chain F, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|G Chain G, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|H Chain H, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
Length = 190
Score = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 42/165 (25%), Positives = 78/165 (47%), Gaps = 9/165 (5%)
Query: 16 LRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+ +++G L T+ L F G I+ + V +D IT+RS G+ ++ + + + A+
Sbjct: 10 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL 69
Query: 76 SNRPHN-IDGRVVETKRAVPRDEIGKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTI 133
+ I G+ V + + K + V +F+ L K + L + FS FG I
Sbjct: 70 DTMNFDVIKGKPVRIMWSQRDPSLRK----SGVGNIFIKNLDKSIDNKALYDTFSAFGNI 125
Query: 134 ESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSKITLLL-DRRV 177
S +V + E G+K G+ F+ F + ++ + +LL DR+V
Sbjct: 126 LSCKVVCD-ENGSK-GYGFVHFETQEAAERAIEKMNGMLLNDRKV 168
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 47.4 bits (111), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 33/51 (64%)
Query: 24 LDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA 74
L YRT+ +SL+ FE++G + DV + ++P TK RGF F+ + + + DA
Sbjct: 21 LTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDA 71
Score = 35.0 bits (79), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 21/37 (56%)
Query: 121 DDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
D LR F ++G + V + T A RGFAF+ F+D
Sbjct: 28 DSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHD 64
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain
Of Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain
Of Xenopus Laevis Epabp2
Length = 124
Score = 47.0 bits (110), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 35/60 (58%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R V++G +DY +T + L+A F G I + ++ D + +G+ +I ++E VD A++
Sbjct: 37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVA 96
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 108 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVL 166
+ ++VG + DL +FS G+I + ++ +K +G +G+A+IEF + + VD V
Sbjct: 37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVA 96
Query: 167 SKITLLLDRRVE 178
T+ R ++
Sbjct: 97 MDETVFRGRTIK 108
>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Rna, Uuguucuu
Length = 102
Score = 47.0 bits (110), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 46/73 (63%), Gaps = 4/73 (5%)
Query: 101 PEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF-NDY 158
PE +FVGG+ +E ++R +F+++G+++ V ++T++ TG +G+ F+ F ND
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDV 61
Query: 159 DVVDKIVLSKITL 171
D V KIV S+I
Sbjct: 62 D-VQKIVESQINF 73
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 33/47 (70%), Gaps = 1/47 (2%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY 65
VF+GG+D R + +++FF ++G + +V ++ D T S+G+GF+++
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 57
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 46.6 bits (109), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 46/73 (63%), Gaps = 4/73 (5%)
Query: 101 PEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF-NDY 158
PE +FVGG+ +E ++R +F+++G+++ V ++T++ TG +G+ F+ F ND
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDV 61
Query: 159 DVVDKIVLSKITL 171
D V KIV S+I
Sbjct: 62 D-VQKIVESQINF 73
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 33/47 (70%), Gaps = 1/47 (2%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY 65
VF+GG+D R + +++FF ++G + +V ++ D T S+G+GF+++
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 57
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 38/138 (27%), Positives = 65/138 (47%), Gaps = 17/138 (12%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
++F+G L T+E + FE++GE +V + +D RGFGFI + + A +
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKA- 76
Query: 78 RPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGLKDQEEDDLREYFSQFGTIESVN 137
+DG +++++ R A TVK + + L + FSQFG +E
Sbjct: 77 ---ELDGTILKSRPL--RIRFATHGAALTVKNL----SPVVSNELLEQAFSQFGPVEKAV 127
Query: 138 MVTNKETGAKRGFAFIEF 155
+V + + G G F+EF
Sbjct: 128 VVVD-DRGRATGKGFVEF 144
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 44/78 (56%), Gaps = 5/78 (6%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY---SEAKMVDDAM 75
V++ L + T+ L F ++G++V V +MKD T++S+G FI + A+ A+
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 76 SNRPHNIDGRVVETKRAV 93
+N+ + GRV++ A+
Sbjct: 79 NNK--QLFGRVIKASIAI 94
Score = 32.3 bits (72), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 24/40 (60%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
+DL FS++G + V ++ +K+T +G AFI F D D
Sbjct: 30 NNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKD 69
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 36/130 (27%), Positives = 58/130 (44%), Gaps = 8/130 (6%)
Query: 29 TDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNRPHNIDGRVVE 88
TD L A F G I +M+D T S G+ F+ ++ A+ ++G V
Sbjct: 16 TDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI----KVLNGITVR 71
Query: 89 TKRAVPRDEIGKPEANATV-KKMFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGA 146
KR + +P + ++V L DD L F ++G+I N++ +K TG
Sbjct: 72 NKRL--KVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGR 129
Query: 147 KRGFAFIEFN 156
RG AF+ +N
Sbjct: 130 PRGVAFVRYN 139
Score = 27.7 bits (60), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 11/40 (27%), Positives = 22/40 (55%)
Query: 116 KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
+D + +L F G I + ++ + +TG G+AF++F
Sbjct: 13 QDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDF 52
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 44.3 bits (103), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 39/78 (50%), Gaps = 6/78 (7%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
KVF+G T E LQ FF Q+GE+VDV I K R F F+T+++ K V ++
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYGEVVDVF-----IPKPFRAFAFVTFADDK-VAQSLCG 66
Query: 78 RPHNIDGRVVETKRAVPR 95
I G V A P+
Sbjct: 67 EDLIIKGISVHISNAEPK 84
Score = 28.1 bits (61), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 31/58 (53%), Gaps = 6/58 (10%)
Query: 109 KMFVG-GLKDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
K+FVG +D ++L+++F Q+G E V++ K R FAF+ F D V +
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYG--EVVDVFIPKPF---RAFAFVTFADDKVAQSLC 65
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of
Hypothetical Polyadenylate-Binding Protein (Pabpn1)
From Homo Sapiens At 1.95 A Resolution
Length = 89
Score = 44.3 bits (103), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 34/60 (56%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R +++G +DY T E L+A F G + V ++ D + +GF +I +S+ + V +++
Sbjct: 7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 66
Score = 37.0 bits (84), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 105 ATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 163
A + ++VG + ++L +F G++ V ++ +K +G +GFA+IEF+D + V
Sbjct: 4 ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRT 63
Query: 164 IVLSKITLLLDRRVE 178
+ +L R+++
Sbjct: 64 SLALDESLFRGRQIK 78
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 44.3 bits (103), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 34/60 (56%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R +++G +DY T E L+A F G + V ++ D + +GF +I +S+ + V +++
Sbjct: 6 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 65
Score = 36.6 bits (83), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 105 ATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 163
A + ++VG + ++L +F G++ V ++ +K +G +GFA+IEF+D + V
Sbjct: 3 ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRT 62
Query: 164 IVLSKITLLLDRRVE 178
+ +L R+++
Sbjct: 63 SLALDESLFRGRQIK 77
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 43.5 bits (101), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 44/64 (68%), Gaps = 4/64 (6%)
Query: 110 MFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF-NDYDVVDKIVLS 167
+FVGG+ +E ++R +F+++G+++ V ++T++ TG +G+ F+ F ND D V KIV S
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVD-VQKIVES 70
Query: 168 KITL 171
+I
Sbjct: 71 QINF 74
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 33/47 (70%), Gaps = 1/47 (2%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY 65
VF+GG+D R + +++FF ++G + +V ++ D T S+G+GF+++
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 58
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 43.5 bits (101), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 35/63 (55%), Gaps = 5/63 (7%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+P VF GL TT+ L+ F ++G I DV ++ D ++RSRGF F+ + V
Sbjct: 44 DPNCCLGVF--GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN---V 98
Query: 72 DDA 74
DDA
Sbjct: 99 DDA 101
Score = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 28/40 (70%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
E DLRE FS++G I V++V ++++ RGFAF+ F + D
Sbjct: 60 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 99
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 43.5 bits (101), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 36/63 (57%), Gaps = 5/63 (7%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+P VF GL TT+ L+ F ++G I DV ++ D ++RSRGF F+ + + V
Sbjct: 13 DPNCCLGVF--GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF---ENV 67
Query: 72 DDA 74
DDA
Sbjct: 68 DDA 70
Score = 40.0 bits (92), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 28/40 (70%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
E DLRE FS++G I V++V ++++ RGFAF+ F + D
Sbjct: 29 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 68
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 43.5 bits (101), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 35/63 (55%), Gaps = 5/63 (7%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+P VF GL TT+ L+ F ++G I DV ++ D ++RSRGF F+ + V
Sbjct: 13 DPNCCLGVF--GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN---V 67
Query: 72 DDA 74
DDA
Sbjct: 68 DDA 70
Score = 40.0 bits (92), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 28/40 (70%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
E DLRE FS++G I V++V ++++ RGFAF+ F + D
Sbjct: 29 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 68
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 43.1 bits (100), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 35/63 (55%), Gaps = 5/63 (7%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+P VF GL TT+ L+ F ++G I DV ++ D ++RSRGF F+ + V
Sbjct: 10 DPNCCLGVF--GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN---V 64
Query: 72 DDA 74
DDA
Sbjct: 65 DDA 67
Score = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 28/40 (70%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
E DLRE FS++G I V++V ++++ RGFAF+ F + D
Sbjct: 26 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 65
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 34/59 (57%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
K+FIG + ++ L+ FE++G+I ++ V+KD T +G F+TY E + A S
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQS 73
Score = 35.0 bits (79), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 32/50 (64%), Gaps = 1/50 (2%)
Query: 109 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
K+F+G + ++ +E DL+ F +FG I + ++ ++ TG +G AF+ + +
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCE 64
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 42.4 bits (98), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 32/53 (60%), Gaps = 2/53 (3%)
Query: 104 NATVKKMFVGGLKDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFN 156
NAT++ + +D E DL+E F FG+I + + +K TG +GFAFI F+
Sbjct: 15 NATIRVTNLS--EDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFH 65
Score = 34.3 bits (77), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 24/41 (58%), Gaps = 2/41 (4%)
Query: 25 DYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY 65
D R TD LQ F +G I + + KD T +S+GF FI++
Sbjct: 26 DTRETD--LQELFRPFGSISRIYLAKDKTTGQSKGFAFISF 64
>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|6 Chain 6, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|7 Chain 7, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|8 Chain 8, Crystal Structure Of Human Spliceosomal U1 Snrnp
Length = 216
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 30/49 (61%), Gaps = 1/49 (2%)
Query: 108 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
K +FV + D E LR F +G I+ ++MV +K +G RG+AFIE+
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEY 151
Score = 36.6 bits (83), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 18/80 (22%), Positives = 42/80 (52%), Gaps = 4/80 (5%)
Query: 14 ESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDD 73
++ + +F+ ++Y TT+ L+ FE +G I + ++ + + RG+ FI Y + +
Sbjct: 100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHS 159
Query: 74 AMSNRPHNIDGRVVETKRAV 93
A + DG+ ++ +R +
Sbjct: 160 AYK----HADGKKIDGRRVL 175
>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In
Cytotoxic Granule-Associated Rna Binding Protein 1
pdb|2RNE|A Chain A, Solution Structure Of The Second Rna Recognition Motif
(Rrm) Of Tia-1
Length = 115
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 1/76 (1%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
VF+G L T E ++A F +G I D V+KD T +S+G+GF+++ ++A+
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 79 PHN-IDGRVVETKRAV 93
+ GR + T A
Sbjct: 78 GGQWLGGRQIRTNWAT 93
Score = 35.4 bits (80), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 2/70 (2%)
Query: 110 MFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIE-FNDYDVVDKIVLS 167
+FVG L + +D++ F+ FG I +V + TG +G+ F+ FN +D + I
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 168 KITLLLDRRV 177
L R++
Sbjct: 78 GGQWLGGRQI 87
>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|B Chain B, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|C Chain C, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
Length = 184
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 36/131 (27%), Positives = 59/131 (45%), Gaps = 10/131 (7%)
Query: 29 TDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNRPHNIDGRVVE 88
TD L A F G I + +D T S G+ F+ ++ A+ ++G V
Sbjct: 27 TDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAI----KVLNGITVR 82
Query: 89 TKRAVPRDEIGKPEANATVK--KMFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETG 145
KR + +P ++K ++V L DD L F ++G+I N++ +K TG
Sbjct: 83 NKRL--KVSYARP-GGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTG 139
Query: 146 AKRGFAFIEFN 156
RG AF+ +N
Sbjct: 140 RPRGVAFVRYN 150
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 40/67 (59%), Gaps = 4/67 (5%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EA 68
+P S RK+F+G L+ + +++ ++ FE +G I + +++ P S+G F+ YS EA
Sbjct: 11 QPPSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGP-DGNSKGCAFVKYSSHAEA 69
Query: 69 KMVDDAM 75
+ +A+
Sbjct: 70 QAAINAL 76
Score = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 32/52 (61%), Gaps = 2/52 (3%)
Query: 108 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 158
+K+FVG L K Q EDD+R F FG IE ++ + G +G AF++++ +
Sbjct: 16 RKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPD-GNSKGCAFVKYSSH 66
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 41/79 (51%), Gaps = 1/79 (1%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R +++GGL D+ L A F +G+I D+ + D T++ RGF F+ + A+ A+
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
Query: 77 NRPHN-IDGRVVETKRAVP 94
N + + GR + A P
Sbjct: 73 NMNESELFGRTIRVNLAKP 91
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 32/53 (60%), Gaps = 2/53 (3%)
Query: 105 ATVKK-MFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
AT K+ ++VGGL ++ +D L F FG I + + + ET RGFAF+EF
Sbjct: 9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 61
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 47/95 (49%), Gaps = 5/95 (5%)
Query: 3 PRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGF 62
PR +++ + + +R D L+ F Q+G+I+DV ++ + + S+GFGF
Sbjct: 16 PRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGF 73
Query: 63 ITYSEAKMVDDAMSNRPHN--IDGRVVETKRAVPR 95
+T+ + D A + H ++GR +E A R
Sbjct: 74 VTFENSADADRA-REKLHGTVVEGRKIEVNNATAR 107
Score = 35.0 bits (79), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 3/72 (4%)
Query: 93 VPRDEIGKPEANATVKKMFVGGLKDQEED-DLREYFSQFGTIESVNMVTNKETGAKRGFA 151
VPR E + K++ V + + D DLR+ F QFG I V ++ N E G+K GF
Sbjct: 15 VPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERGSK-GFG 72
Query: 152 FIEFNDYDVVDK 163
F+ F + D+
Sbjct: 73 FVTFENSADADR 84
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 31/47 (65%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY 65
VF+G L T E +++ F +G+I D V+KD T +S+G+GF+++
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSF 64
Score = 36.6 bits (83), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 35/70 (50%), Gaps = 2/70 (2%)
Query: 110 MFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF-NDYDVVDKIVLS 167
+FVG L + +D++ F+ FG I +V + TG +G+ F+ F N D + IV
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 168 KITLLLDRRV 177
L R++
Sbjct: 78 GGQWLGGRQI 87
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 4/76 (5%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKR---SRGFGFITYSEAKMVDDAM 75
+FI L++ TT+E+L+ F + G I + K S GFGF+ Y + + A+
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 76 SN-RPHNIDGRVVETK 90
+ H +DG +E +
Sbjct: 68 KQLQGHTVDGHKLEVR 83
>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition
In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 84
Score = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 34/61 (55%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R V++G + Y T+E + G ++++ +M DP T RS+G+ FI + + + A+
Sbjct: 5 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 64
Query: 77 N 77
N
Sbjct: 65 N 65
Score = 37.0 bits (84), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 33/55 (60%), Gaps = 1/55 (1%)
Query: 104 NATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
N + +++G + DQ E+ + + S G + ++ M+ + +TG +G+AFIEF D
Sbjct: 1 NPPSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRD 55
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 35/63 (55%)
Query: 15 SLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA 74
S R +++GGL D+ L A F +G+I D+ + D T++ RGF F+ + A+ A
Sbjct: 1 SKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 60
Query: 75 MSN 77
+ N
Sbjct: 61 IDN 63
Score = 37.4 bits (85), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 110 MFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
++VGGL ++ +D L F FG I + + + ET RGFAF+EF
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 51
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 34/57 (59%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
V++GGLD + ++ L F Q G +V+ + KD +T + +G+GF+ + + D A+
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 74
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 30/49 (61%), Gaps = 1/49 (2%)
Query: 108 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
K +FV + D E LR F +G I+ ++MV +K +G RG+AFIE+
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEY 151
Score = 35.8 bits (81), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 18/80 (22%), Positives = 42/80 (52%), Gaps = 4/80 (5%)
Query: 14 ESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDD 73
++ + +F+ ++Y TT+ L+ FE +G I + ++ + + RG+ FI Y + +
Sbjct: 100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHS 159
Query: 74 AMSNRPHNIDGRVVETKRAV 93
A + DG+ ++ +R +
Sbjct: 160 AYK----HADGKKIDGRRVL 175
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 40.4 bits (93), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 34/61 (55%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R V++G + Y T+E + G ++++ +M DP T RS+G+ FI + + + A+
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 77 N 77
N
Sbjct: 63 N 63
Score = 35.8 bits (81), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 26/41 (63%)
Query: 117 DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
DQ E+ + + S G + ++ M+ + +TG +G+AFIEF D
Sbjct: 13 DQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRD 53
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 40.4 bits (93), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 38/71 (53%), Gaps = 4/71 (5%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
++F+ L Y +++E L+ F +G + ++ D +TK+ +GF F+T+ M +
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTF----MFPEHAVK 65
Query: 78 RPHNIDGRVVE 88
+DG+V +
Sbjct: 66 AYAEVDGQVFQ 76
Score = 30.8 bits (68), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 109 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
++FV L E+DL + FS +G + ++ + T +GFAF+ F
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTF 57
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 40.4 bits (93), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 35/65 (53%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
EP+ LR + + + + L+ FE++G I V ++ D T++SRG+GF+ +
Sbjct: 38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSA 97
Query: 72 DDAMS 76
A++
Sbjct: 98 QQAIA 102
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/37 (43%), Positives = 26/37 (70%)
Query: 119 EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
+E LR+ F ++G IESV +V ++ET RG+ F++F
Sbjct: 55 DEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKF 91
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 40.0 bits (92), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 34/61 (55%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R +++GGL D+ L A F +G+I D+ + D T++ RGF F+ + A+ A+
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
Query: 77 N 77
N
Sbjct: 124 N 124
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 32/53 (60%), Gaps = 2/53 (3%)
Query: 105 ATVKK-MFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
AT K+ ++VGGL ++ +D L F FG I + + + ET RGFAF+EF
Sbjct: 60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 112
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 40.0 bits (92), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 34/61 (55%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R V++G + Y T+E + G ++++ +M DP T RS+G+ FI + + + A+
Sbjct: 4 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 63
Query: 77 N 77
N
Sbjct: 64 N 64
Score = 35.4 bits (80), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 26/41 (63%)
Query: 117 DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
DQ E+ + + S G + ++ M+ + +TG +G+AFIEF D
Sbjct: 14 DQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRD 54
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 40.0 bits (92), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 34/61 (55%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R +++GGL D+ L A F +G+I D+ + D T++ RGF F+ + A+ A+
Sbjct: 6 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65
Query: 77 N 77
N
Sbjct: 66 N 66
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 31/53 (58%), Gaps = 1/53 (1%)
Query: 104 NATVKKMFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
+ T + ++VGGL ++ +D L F FG I + + + ET RGFAF+EF
Sbjct: 2 STTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 54
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 40.0 bits (92), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 36/63 (57%), Gaps = 8/63 (12%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
K+FIG L T++ +++ FEQ+G++++ ++K+ +GF+ + +DA+ N
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFVHIEDKTAAEDAIRN 61
Query: 78 RPH 80
H
Sbjct: 62 LHH 64
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 40.0 bits (92), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 34/61 (55%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R +++GGL D+ L A F +G+I D+ + D T++ RGF F+ + A+ A+
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
Query: 77 N 77
N
Sbjct: 68 N 68
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 32/53 (60%), Gaps = 2/53 (3%)
Query: 105 ATVKK-MFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
AT K+ ++VGGL ++ +D L F FG I + + + ET RGFAF+EF
Sbjct: 4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 56
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 39.7 bits (91), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 30/49 (61%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS 66
K+F+G + ++ L+ FE++G I ++ V+KD +T +G F+TY
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYC 65
Score = 35.8 bits (81), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 35/66 (53%), Gaps = 1/66 (1%)
Query: 99 GKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
G P + K+FVG + + +E DL+ F +FG I + ++ ++ TG +G AF+ +
Sbjct: 7 GVPMKDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCA 66
Query: 158 YDVVDK 163
D K
Sbjct: 67 RDSALK 72
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 45/81 (55%), Gaps = 5/81 (6%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
+++ + + +R D L+ F Q+G+I+DV ++ + + S+GFGF+T+ + D A
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSADADRARE 73
Query: 77 NRPHN--IDGRVVETKRAVPR 95
+ H ++GR +E A R
Sbjct: 74 -KLHGTVVEGRKIEVNNATAR 93
Score = 32.3 bits (72), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 33/59 (55%), Gaps = 3/59 (5%)
Query: 106 TVKKMFVGGLKDQEED-DLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 163
T K++ V + + D DLR+ F QFG I V ++ N E G+K GF F+ F + D+
Sbjct: 14 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERGSK-GFGFVTFENSADADR 70
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 38/153 (24%), Positives = 71/153 (46%), Gaps = 27/153 (17%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFI---TYSEAKMVDDA 74
++F+G L T+E ++ FE++G+ +V + KD +GFGFI T + A++
Sbjct: 24 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 77
Query: 75 MSNRPHNIDGRVVETKRAVPRDEIGKPEANATVKKM--FVGGLKDQEEDDLREYFSQFGT 132
+ N P + G+ + + A A+ TV+ + +V + L E FS FG
Sbjct: 78 LDNMP--LRGKQLRVRFAC-------HSASLTVRNLPQYVSN------ELLEEAFSVFGQ 122
Query: 133 IESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
+E ++ + + G G +EF+ K +
Sbjct: 123 VERAVVIVD-DRGRPSGKGIVEFSGKPAARKAL 154
>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
pdb|3MD1|B Chain B, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
Length = 83
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM-S 76
+F+G L+ DE+L+ F+ + + VM D T SRG+GF++++ +AM S
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 77 NRPHNIDGRVVETKRAV 93
+ +++GR + A
Sbjct: 63 MQGQDLNGRPLRINWAA 79
Score = 32.3 bits (72), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 109 KMFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
+FVG L +D+ LR F F + S +++ + +TG+ RG+ F+ F D
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQD 54
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 7/58 (12%)
Query: 99 GKPEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
G + T+ ++VGGL D E DLR +F QFG I ++ +V ++ AFI+F
Sbjct: 4 GSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQC------AFIQF 55
Score = 26.9 bits (58), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 24/39 (61%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMK 50
E +++ +++GGL T+ L+ F Q+GEI + V++
Sbjct: 8 EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ 46
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 33/52 (63%), Gaps = 2/52 (3%)
Query: 108 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 158
+K+FVG L K Q ++D+R+ F FGTI+ ++ + G +G AF++F +
Sbjct: 13 RKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPD-GTSKGCAFVKFQTH 63
Score = 37.0 bits (84), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 37/64 (57%), Gaps = 4/64 (6%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFI---TYSEAKMVDD 73
RK+F+G L + TDE ++ FE +G I + V++ P S+G F+ T++EA+ +
Sbjct: 13 RKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGP-DGTSKGCAFVKFQTHAEAQAAIN 71
Query: 74 AMSN 77
+ +
Sbjct: 72 TLHS 75
>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|X Chain X, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|Y Chain Y, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2V|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
pdb|1N52|B Chain B, Cap Binding Complex
pdb|1N54|B Chain B, Cap Binding Complex M7gpppg Free
pdb|3FEX|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex.
pdb|3FEY|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex
Length = 156
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 42/83 (50%), Gaps = 5/83 (6%)
Query: 12 EPESLRK----VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSE 67
E E L K +++G L + TT+E + F + G+I +++ D + K + GF F+ Y
Sbjct: 31 EQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYS 90
Query: 68 AKMVDDAMSN-RPHNIDGRVVET 89
++AM +D R++ T
Sbjct: 91 RADAENAMRYINGTRLDDRIIRT 113
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/50 (42%), Positives = 34/50 (68%), Gaps = 4/50 (8%)
Query: 108 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFN 156
K +FV GL +D E+ L+E F G++ +VT++ETG+ +GF F++FN
Sbjct: 16 KTLFVKGLSEDTTEETLKESFD--GSVR-ARIVTDRETGSSKGFGFVDFN 62
Score = 35.4 bits (80), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 43/82 (52%), Gaps = 8/82 (9%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAKMVDD 73
+ +F+ GL TT+E+L+ F+ V ++ D T S+GFGF+ ++ +AK +
Sbjct: 16 KTLFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKE 72
Query: 74 AMSNRPHNIDGRVVETKRAVPR 95
AM + IDG V A P+
Sbjct: 73 AMED--GEIDGNKVTLDWAKPK 92
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 6/72 (8%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
+++ LD DE L+ F +G I VM + RS+GFGF+ +S + A++
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVT-- 73
Query: 79 PHNIDGRVVETK 90
++GR+V TK
Sbjct: 74 --EMNGRIVATK 83
Score = 33.9 bits (76), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 33/60 (55%), Gaps = 3/60 (5%)
Query: 107 VKKMFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
V ++V L D +D+ LR+ FS FGTI S ++ E G +GF F+ F+ + K V
Sbjct: 15 VVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMM--EGGRSKGFGFVCFSSPEEATKAV 72
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 27/88 (30%), Positives = 44/88 (50%), Gaps = 7/88 (7%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFG---FITYSEAKMVDD 73
+ VFI L + + +E+L +Q+G++ V V+ P T+ S+G F+T A+
Sbjct: 16 KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 75
Query: 74 AMSNRPHN----IDGRVVETKRAVPRDE 97
A S +DGR ++ AV RDE
Sbjct: 76 AASLEAEGGGLKLDGRQLKVDLAVTRDE 103
Score = 34.3 bits (77), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 108 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVL 166
K +F+ L D EE+ L E QFG ++ V +V + +T +G AF +F + K +
Sbjct: 16 KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 75
Query: 167 S 167
+
Sbjct: 76 A 76
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 37.4 bits (85), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 40/77 (51%), Gaps = 4/77 (5%)
Query: 14 ESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDD 73
+S + + L T + ++ F G+I +++D IT +S G+GF+ YS+ D
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 74 AMSNRPHNIDGRVVETK 90
A+ + ++G ++TK
Sbjct: 62 AI----NTLNGLKLQTK 74
Score = 37.0 bits (84), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 28/50 (56%)
Query: 116 KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
++ +D+ + F G IES +V +K TG G+ F+ ++D + DK +
Sbjct: 14 QNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI 63
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 36.6 bits (83), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 30/58 (51%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
++I GL TTD+ L + +G+IV + D T + +G+GF+ + A++
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65
Score = 30.0 bits (66), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 110 MFVGGLKDQEED-DLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
+++ GL+ D DL + +G I S + +K T +G+ F++F+ K V
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 64
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 36.6 bits (83), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 34/69 (49%)
Query: 7 DSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS 66
D+ E R VF L R L+ FF G++ DV ++ D ++RS+G ++ +
Sbjct: 16 DNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFC 75
Query: 67 EAKMVDDAM 75
E + V A+
Sbjct: 76 EIQSVPLAI 84
Score = 31.6 bits (70), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 11/40 (27%), Positives = 24/40 (60%)
Query: 122 DLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVV 161
DL ++FS G + V +++++ + +G A++EF + V
Sbjct: 41 DLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSV 80
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 36.6 bits (83), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 32/52 (61%), Gaps = 2/52 (3%)
Query: 108 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 158
+K+FVG L K Q E+D+ F FG I+ ++ + G+ +G AF++F+ +
Sbjct: 16 RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPD-GSSKGCAFVKFSSH 66
Score = 32.3 bits (72), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 30/50 (60%), Gaps = 1/50 (2%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS 66
RK+F+G L+ + ++E + F+ +G I + V++ P S+G F+ +S
Sbjct: 16 RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFS 64
>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX
pdb|1P27|D Chain D, Crystal Structure Of The Human Y14MAGOH COMPLEX
Length = 106
Score = 36.2 bits (82), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 40/64 (62%), Gaps = 2/64 (3%)
Query: 96 DEIGKPEANATVKKMFVGGLKDQE-EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIE 154
DE G P+ + +FV G+ ++ E+D+ + F+++G I+++++ ++ TG +G+ +E
Sbjct: 13 DEPG-PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVE 71
Query: 155 FNDY 158
+ Y
Sbjct: 72 YETY 75
Score = 28.9 bits (63), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 28/57 (49%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+F+ G+ T+E + F ++GEI ++ + D T +G+ + Y K AM
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 82
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 36.2 bits (82), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 13/50 (26%), Positives = 34/50 (68%), Gaps = 1/50 (2%)
Query: 110 MFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 158
+FV + ++ +ED+++E F +G I+++++ ++ TG +G+A +E+ +
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETH 78
>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 90
Score = 36.2 bits (82), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 13/50 (26%), Positives = 34/50 (68%), Gaps = 1/50 (2%)
Query: 110 MFVGGLKDQE-EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 158
+FV G+ ++ E+D+ + F+++G I+++++ ++ TG +G+ +E+ Y
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 59
Score = 28.9 bits (63), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 28/57 (49%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+F+ G+ T+E + F ++GEI ++ + D T +G+ + Y K AM
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 36.2 bits (82), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 40/64 (62%), Gaps = 2/64 (3%)
Query: 96 DEIGKPEANATVKKMFVGGLKDQE-EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIE 154
DE G P+ + +FV G+ ++ E+D+ + F+++G I+++++ ++ TG +G+ +E
Sbjct: 12 DEPG-PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVE 70
Query: 155 FNDY 158
+ Y
Sbjct: 71 YETY 74
Score = 28.9 bits (63), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 28/57 (49%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+F+ G+ T+E + F ++GEI ++ + D T +G+ + Y K AM
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 81
>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1HL6|C Chain C, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1RK8|A Chain A, Structure Of The Cytosolic Protein Pym Bound To The Mago-
Y14 Core Of The Exon Junction Complex
pdb|2X1G|A Chain A, Crystal Structure Of Importin13 - Mago-Y14 Complex
pdb|2X1G|C Chain C, Crystal Structure Of Importin13 - Mago-Y14 Complex
Length = 165
Score = 36.2 bits (82), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 13/50 (26%), Positives = 34/50 (68%), Gaps = 1/50 (2%)
Query: 110 MFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 158
+FV + ++ +ED+++E F +G I+++++ ++ TG +G+A +E+ +
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETH 124
Score = 26.6 bits (57), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 31/73 (42%), Gaps = 5/73 (6%)
Query: 4 RYDDSKCTEPESLRKV-----FIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSR 58
R +D EP R V F+ + ++ +Q F +GEI ++ + D T S+
Sbjct: 55 RNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSK 114
Query: 59 GFGFITYSEAKMV 71
G+ + Y K
Sbjct: 115 GYALVEYETHKQA 127
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 36.2 bits (82), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 13/50 (26%), Positives = 34/50 (68%), Gaps = 1/50 (2%)
Query: 110 MFVGGLKDQE-EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 158
+FV G+ ++ E+D+ + F+++G I+++++ ++ TG +G+ +E+ Y
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 61
Score = 28.5 bits (62), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 28/57 (49%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+F+ G+ T+E + F ++GEI ++ + D T +G+ + Y K AM
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 68
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 35.8 bits (81), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 14/59 (23%), Positives = 37/59 (62%), Gaps = 1/59 (1%)
Query: 101 PEANATVKKMFVGGLKDQE-EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 158
P+ + +FV G+ ++ E+D+ + F+++G I+++++ ++ TG +G+ +E+ Y
Sbjct: 1 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 59
Score = 28.5 bits (62), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 28/57 (49%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+F+ G+ T+E + F ++GEI ++ + D T +G+ + Y K AM
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
pdb|2J0Q|G Chain G, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
Length = 109
Score = 35.8 bits (81), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 14/59 (23%), Positives = 37/59 (62%), Gaps = 1/59 (1%)
Query: 101 PEANATVKKMFVGGLKDQE-EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 158
P+ + +FV G+ ++ E+D+ + F+++G I+++++ ++ TG +G+ +E+ Y
Sbjct: 1 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 59
Score = 28.5 bits (62), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 28/57 (49%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+F+ G+ T+E + F ++GEI ++ + D T +G+ + Y K AM
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 35.8 bits (81), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 34/70 (48%), Gaps = 9/70 (12%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVV-VMKDPITKRSRGFGFITYSEAKMVDDA--- 74
+FIG LD ++ L F +G I+ +M+DP T S+G+ FI ++ D A
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 75 -----MSNRP 79
+ NRP
Sbjct: 68 MNGQYLCNRP 77
Score = 35.8 bits (81), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 35/59 (59%), Gaps = 4/59 (6%)
Query: 110 MFVGGLKDQEEDD--LREYFSQFGTI-ESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
+F+G L D E D+ L + FS FG I ++ ++ + +TG +G+AFI F +D D +
Sbjct: 8 IFIGNL-DPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAI 65
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 35.8 bits (81), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 110 MFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFN 156
++V GL K + ++ + FSQ+G I + ++ ++ TG RG FI F+
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFD 51
Score = 35.4 bits (80), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 31/57 (54%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+++ GL + + ++ F Q+G I+ ++ D T SRG GFI + + ++A+
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition
Motif Of Nono
pdb|2RS8|A Chain A, Solution Structure Of The N-Terminal Rna Recognition
Motif Of Nono
Length = 99
Score = 35.4 bits (80), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 36/65 (55%), Gaps = 9/65 (13%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFI---TYSEAKMVDDA 74
++F+G L T+E ++ FE++G+ +V + KD +GFGFI T + A++
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 70
Query: 75 MSNRP 79
+ N P
Sbjct: 71 LDNMP 75
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 35.0 bits (79), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 6/77 (7%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
VF+G T++ L+ FF Q+G+++DV I K R F F+T+++ ++ ++
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVF-----IPKPFRAFAFVTFADDQIA-QSLCGE 61
Query: 79 PHNIDGRVVETKRAVPR 95
I G V A P+
Sbjct: 62 DLIIKGISVHISNAEPK 78
Score = 32.0 bits (71), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 29/57 (50%), Gaps = 6/57 (10%)
Query: 110 MFVG-GLKDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
+FVG D ED+LRE+FSQ+G + V + R FAF+ F D + +
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLC 59
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 35.0 bits (79), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 120 EDDLREYFSQFGT-IESVNMVTNKETGAKRGFAFIEFN 156
EDD+R G V ++ NK +G RGFAF+EF+
Sbjct: 15 EDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFS 52
Score = 28.1 bits (61), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 45 DVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNRPH--NIDGRVVETKRAVPRDEIGK 100
+V +M++ + +SRGF F+ +S + M H NI G+ V + P+ +I +
Sbjct: 31 EVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSDPKPKINE 88
>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|C Chain C, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|B Chain B, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|D Chain D, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
Length = 88
Score = 35.0 bits (79), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 28/50 (56%), Gaps = 3/50 (6%)
Query: 109 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGA--KRGFAFIEF 155
KMFVG + + E DLRE F Q+G + +N++ ++ +G F+ F
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTF 54
Score = 34.7 bits (78), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 38/67 (56%), Gaps = 3/67 (4%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKD--PITKRSRGFGFITYSEAKMVDDAM 75
K+F+G + +++ L+ FEQ+G + ++ V++D +S+G F+T+ K +A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA- 63
Query: 76 SNRPHNI 82
N HN+
Sbjct: 64 QNALHNM 70
>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|B Chain B, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|C Chain C, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|D Chain D, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
Length = 84
Score = 35.0 bits (79), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 23/40 (57%)
Query: 116 KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
++ +D+LR FS G +ES ++ +K G G+ F+ +
Sbjct: 14 QNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNY 53
Score = 34.7 bits (78), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 28/53 (52%)
Query: 24 LDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
L T + L++ F GE+ +++D + S G+GF+ Y AK + A++
Sbjct: 12 LPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 64
>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1)
From Homo Sapiens At 1.90 A Resolution
pdb|4FXV|B Chain B, Crystal Structure Of An Elav-Like Protein 1 (Elavl1)
From Homo Sapiens At 1.90 A Resolution
pdb|4FXV|C Chain C, Crystal Structure Of An Elav-Like Protein 1 (Elavl1)
From Homo Sapiens At 1.90 A Resolution
pdb|4FXV|D Chain D, Crystal Structure Of An Elav-Like Protein 1 (Elavl1)
From Homo Sapiens At 1.90 A Resolution
Length = 99
Score = 34.7 bits (78), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 15/58 (25%), Positives = 30/58 (51%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
+ + L T + L++ F GE+ +++D + S G+GF+ Y AK + A++
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 79
Score = 34.3 bits (77), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 23/40 (57%)
Query: 116 KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
++ +D+LR FS G +ES ++ +K G G+ F+ +
Sbjct: 29 QNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNY 68
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 34.3 bits (77), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 39/83 (46%), Gaps = 4/83 (4%)
Query: 99 GKPEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKE-TGAKRGFAFIEFN 156
G+ T K+ V + Q + ++RE FS FG +++V + TGA RGF F++F
Sbjct: 7 GQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFI 66
Query: 157 DYDVVDKI--VLSKITLLLDRRV 177
K L T L RR+
Sbjct: 67 TKQDAKKAFNALCHSTHLYGRRL 89
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 34.3 bits (77), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 42/83 (50%), Gaps = 6/83 (7%)
Query: 12 EPESLRK----VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSE 67
E E L K +++G L + TT+E + F + G+I +++ D + K + GF F+ Y
Sbjct: 10 EQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKM-KTACGFCFVEYYS 68
Query: 68 AKMVDDAMSN-RPHNIDGRVVET 89
++AM +D R++ T
Sbjct: 69 RADAENAMRYINGTRLDDRIIRT 91
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 33.9 bits (76), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 3/44 (6%)
Query: 32 SLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
SL A F Q+G+I+D+V +K T + RG F+ + E +A+
Sbjct: 26 SLYAIFSQFGQILDIVALK---TLKMRGQAFVIFKEIGSASNAL 66
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 33.5 bits (75), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 109 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVL 166
K+F+ GL +++L E GT++ + +VTN+ G +G A++E+ + + V+
Sbjct: 19 KLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVM 76
>pdb|1A9N|B Chain B, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
pdb|1A9N|D Chain D, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
Length = 96
Score = 33.5 bits (75), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 25/44 (56%), Gaps = 3/44 (6%)
Query: 32 SLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
SL A F Q+G +VD+V +K T + RG F+ + E +A+
Sbjct: 26 SLYALFSQFGHVVDIVALK---TMKMRGQAFVIFKELGSSTNAL 66
>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second
Rna-Binding Domain Of Sex-Lethal Determined By
Multidimensional Heteronuclear Magnetic Resonance
Spectroscopy
Length = 97
Score = 33.5 bits (75), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 23/37 (62%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFN 156
+D L F ++G+I N++ +K TG RG AF+ +N
Sbjct: 27 DDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYN 63
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 32.3 bits (72), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 9/82 (10%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITK--RSRGFGFITYSEAKMVDDA 74
+ + + L Y T+E+LQ FE+ +K P + +S+G+ FI ++ + +A
Sbjct: 16 KTLVLSNLSYSATEETLQEVFEK------ATFIKVPQNQNGKSKGYAFIEFASFEDAKEA 69
Query: 75 M-SNRPHNIDGRVVETKRAVPR 95
+ S I+GR + + PR
Sbjct: 70 LNSCNKREIEGRAIRLELQGPR 91
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 32.3 bits (72), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 25/92 (27%), Positives = 45/92 (48%), Gaps = 13/92 (14%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS-- 76
VF+ LDY+ + L+ F G +V +++D K SRG G +T+ ++ A+S
Sbjct: 18 VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGK-SRGIGTVTFEQSIEAVQAISMF 76
Query: 77 ------NRPHNIDGRVVETKRAVPRDEIGKPE 102
+RP ++ +RA+P+ + PE
Sbjct: 77 NGQLLFDRPMHVK----MDERALPKGDFFPPE 104
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 32.3 bits (72), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 109 KMFVGGL-KDQEEDDLREYFSQFGTIESVNM-VTNKETGAKRGFAFIEFNDYDVVDKIV 165
K+ +G L ++ +D + E FS +G I+ ++M V +G+A++EF + D +K +
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
>pdb|4H7X|A Chain A, Crystal Structure Of The Tetratricopeptide Repeat (Tpr)
Motif Of Human Dual Specificity Protein Kinase Mps1
pdb|4H7X|B Chain B, Crystal Structure Of The Tetratricopeptide Repeat (Tpr)
Motif Of Human Dual Specificity Protein Kinase Mps1
pdb|4H7Y|A Chain A, Crystal Structure Of The Tetratricopeptide Repeat (Tpr)
Motif Of Human Dual Specificity Protein Kinase Mps1
pdb|4H7Y|B Chain B, Crystal Structure Of The Tetratricopeptide Repeat (Tpr)
Motif Of Human Dual Specificity Protein Kinase Mps1
pdb|4H7Y|C Chain C, Crystal Structure Of The Tetratricopeptide Repeat (Tpr)
Motif Of Human Dual Specificity Protein Kinase Mps1
pdb|4H7Y|D Chain D, Crystal Structure Of The Tetratricopeptide Repeat (Tpr)
Motif Of Human Dual Specificity Protein Kinase Mps1
Length = 161
Score = 32.0 bits (71), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 3/57 (5%)
Query: 71 VDDAMSNRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGLKDQEEDDLREYF 127
+ DA+ N+ + GR + A+P D+ G+ E+ A ++ F QE DD R+YF
Sbjct: 30 LSDALLNK---LIGRYSQAIEALPPDKYGQNESFARIQVRFAELKAIQEPDDARDYF 83
>pdb|2GHP|A Chain A, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|B Chain B, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|C Chain C, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|D Chain D, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|E Chain E, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|F Chain F, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|G Chain G, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|H Chain H, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
Length = 292
Score = 32.0 bits (71), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 1/60 (1%)
Query: 119 EEDDLREYFSQFGTIESVNM-VTNKETGAKRGFAFIEFNDYDVVDKIVLSKITLLLDRRV 177
+E+ LRE F FG+IE +N+ KE AF F + D ++ + +LL +R +
Sbjct: 224 DENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFXVFENKDSAERALQXNRSLLGNREI 283
>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 32.0 bits (71), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 27/45 (60%), Gaps = 3/45 (6%)
Query: 31 ESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+SL A F Q+G+I+D++V + + + RG F+ + E +A+
Sbjct: 28 KSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNAL 69
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 31.6 bits (70), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 28/46 (60%)
Query: 132 TIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSKITLLLDRRV 177
+I SV +V +K+T +GF ++EF++ D + + + LL DR +
Sbjct: 40 SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSL 85
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 31.6 bits (70), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 27/45 (60%), Gaps = 3/45 (6%)
Query: 31 ESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+SL A F Q+G+I+D++V + + + RG F+ + E +A+
Sbjct: 28 KSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNAL 69
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein
U1a117, Nmr, 43 Structures
Length = 116
Score = 31.6 bits (70), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 27/45 (60%), Gaps = 3/45 (6%)
Query: 31 ESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+SL A F Q+G+I+D++V + + + RG F+ + E +A+
Sbjct: 27 KSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNAL 68
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 30.8 bits (68), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 30/60 (50%), Gaps = 9/60 (15%)
Query: 99 GKPEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
G PE A VK +FV L E+ L + FS+FG +E V + + +AF+ F D
Sbjct: 7 GDPEVMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKD--------YAFVHFED 58
>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2
pdb|3BS9|B Chain B, X-Ray Structure Of Human Tia-1 Rrm2
Length = 87
Score = 30.8 bits (68), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
VF+G L T ++ A F +G I D V+KD T +S+G+GF+++ ++A+
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 79 PHN-IDGRVVETKRAV 93
+ GR + T A
Sbjct: 69 GGQWLGGRQIRTNWAT 84
Score = 27.3 bits (59), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 1/49 (2%)
Query: 130 FGTIESVNMVTNKETGAKRGFAFIE-FNDYDVVDKIVLSKITLLLDRRV 177
FG I +V + TG +G+ F+ FN +D + I L R++
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 78
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Rna-Binding Protein 14
Length = 90
Score = 30.4 bits (67), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 22/34 (64%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKD 51
K+F+G + T + L++ FE+ G +++ V+KD
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVVKD 44
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 30.4 bits (67), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 9/63 (14%)
Query: 104 NATVKKMFVGGLKDQEE-DDLREYFSQFGTIES--------VNMVTNKETGAKRGFAFIE 154
N+ +FV GL + + + +YF Q G I++ +N+ T++ETG +G A +
Sbjct: 4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVS 63
Query: 155 FND 157
F+D
Sbjct: 64 FDD 66
>pdb|1JI8|A Chain A, Solution Structure Of Pyrobaculum Aerophilum DsrcGAMMA
Subunit Of Dissimilatory Sulfite Reductase
Length = 111
Score = 30.0 bits (66), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 14/23 (60%), Positives = 16/23 (69%), Gaps = 1/23 (4%)
Query: 123 LREYFSQFGTIESVNMVTNKETG 145
LREY+ FGT + MVT KETG
Sbjct: 59 LREYWETFGTCPPIKMVT-KETG 80
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 30.0 bits (66), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 8/49 (16%)
Query: 117 DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
D +E +L E F FG ++ V ++ GFAF+EF + + K +
Sbjct: 42 DVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAKAI 82
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 30.0 bits (66), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 9/57 (15%)
Query: 110 MFVGGLKDQEE-DDLREYFSQFGTIES--------VNMVTNKETGAKRGFAFIEFND 157
+FV GL + + + +YF Q G I++ +N+ T++ETG +G A + F+D
Sbjct: 16 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDD 72
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 30.0 bits (66), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 36/148 (24%), Positives = 65/148 (43%), Gaps = 12/148 (8%)
Query: 8 SKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSE 67
S+ T P +L FIG L+ + L+ + D+ V+ D T +R FG++ +
Sbjct: 8 SESTTPFNL---FIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFES 63
Query: 68 AKMVDDAMSNRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGLKDQEEDDLREYF 127
A+ ++ A+ + G ++ ++ RD A + K + ED+L+E F
Sbjct: 64 AEDLEKALELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNIT---EDELKEVF 120
Query: 128 SQFGTIESVNMVTNKETGAKRGFAFIEF 155
I V+ + G +G A+IEF
Sbjct: 121 EDALEIRLVS-----QDGKSKGIAYIEF 143
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of
Eukaryotic Initiation Factor 4b
Length = 104
Score = 30.0 bits (66), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPIT-KRSRGFGFITY 65
F+G L Y T+ES++ FF I V + ++P +R +GFG+ +
Sbjct: 18 AFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEF 64
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 30.0 bits (66), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 10/34 (29%), Positives = 23/34 (67%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKD 51
K+ +G + T++ L+A FE++G +++ ++KD
Sbjct: 12 KLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD 45
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation
Initiation Factor 4b
Length = 100
Score = 30.0 bits (66), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPIT-KRSRGFGFITY 65
F+G L Y T+ES++ FF I V + ++P +R +GFG+ +
Sbjct: 22 AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEF 68
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug
Triplet Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 30.0 bits (66), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 23/47 (48%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY 65
+FI L D+ L F +G +V V D T S+ FGF++Y
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSY 74
Score = 26.6 bits (57), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 10/38 (26%), Positives = 21/38 (55%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
+ DL + F FG + S + +K+T + F F+ +++
Sbjct: 39 DQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDN 76
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 29.6 bits (65), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 4/75 (5%)
Query: 105 ATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 163
+ V +F+ L K + L + FS FG I S +V + E G+K G+ F+ F + ++
Sbjct: 9 SGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENGSK-GYGFVHFETQEAAER 66
Query: 164 IVLSKITLLL-DRRV 177
+ +LL DR+V
Sbjct: 67 AIEKMNGMLLNDRKV 81
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 29.3 bits (64), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 37/72 (51%), Gaps = 7/72 (9%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM-SN 77
V+ GG+ TD+ ++ F +G+I+++ V + +G+ F+ +S + A+ S
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSV 81
Query: 78 RPHNIDGRVVET 89
I+G VV+
Sbjct: 82 NGTTIEGHVVKC 93
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 29.3 bits (64), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 6/50 (12%)
Query: 109 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
K++VG L + +L FS +G + +V + N GFAF+EF D
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPP-----GFAFVEFED 46
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 29.3 bits (64), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 9/56 (16%)
Query: 105 ATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
A VK +FV L + E+ L + FSQFG +E V + + +AFI F++ D
Sbjct: 9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERD 56
>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
At Ph 6.0
pdb|4F26|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
A Ph 9.0
Length = 115
Score = 28.9 bits (63), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 3/56 (5%)
Query: 123 LREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSKITLLL-DRRV 177
L + FS FG I S +V + E G+K G+ F+ F + ++ + +LL DR+V
Sbjct: 22 LYDTFSAFGNILSCKVVCD-ENGSK-GYGFVHFETQEAAERAIEKMNGMLLNDRKV 75
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 28.9 bits (63), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 8/49 (16%)
Query: 117 DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
D +E +L E F FG ++ V ++ GFAF+EF + + K +
Sbjct: 15 DVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAKAI 55
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 28.9 bits (63), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 110 MFVGGLKDQEED-DLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
+F+ L + D DL F FG + S + +K+T + F F+ F++ D
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPD 93
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 28.9 bits (63), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 7/58 (12%)
Query: 109 KMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND-YDVVDKI 164
K++VG L + + +L F +G + SV + N GFAF+EF D D D +
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPP-----GFAFVEFEDPRDAADAV 127
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 28.5 bits (62), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 6/50 (12%)
Query: 109 KMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
K++VG L + + +L F +G + SV + N GFAF+EF D
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPP-----GFAFVEFED 119
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 28.5 bits (62), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 31/143 (21%), Positives = 61/143 (42%), Gaps = 17/143 (11%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
RK+ I GL T++ + + +K + +G F+T + + A+
Sbjct: 23 RKILIRGLPGDVTNQEVHDLLSDY-------ELKYCFVDKYKGTAFVTLLNGEQAEAAI- 74
Query: 77 NRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGLKDQEEDDLREYFSQFGTIESV 136
N H R+ E + +V ++ +A V + + Q E+ +R FG++E
Sbjct: 75 NAFHQ--SRLRERELSV---QLQPTDALLCVANLPPSLTQQQFEELVRP----FGSLERC 125
Query: 137 NMVTNKETGAKRGFAFIEFNDYD 159
+V ++ TG +G+ F E+ D
Sbjct: 126 FLVYSERTGQSKGYGFAEYMKKD 148
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 28.5 bits (62), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 31/143 (21%), Positives = 61/143 (42%), Gaps = 17/143 (11%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
RK+ I GL T++ + + +K + +G F+T + + A+
Sbjct: 23 RKILIRGLPGDVTNQEVHDLLSDY-------ELKYCFVDKYKGTAFVTLLNGEQAEAAI- 74
Query: 77 NRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGLKDQEEDDLREYFSQFGTIESV 136
N H R+ E + +V ++ +A V + + Q E+ +R FG++E
Sbjct: 75 NAFHQ--SRLRERELSV---QLQPTDALLCVANLPPSLTQQQFEELVRP----FGSLERC 125
Query: 137 NMVTNKETGAKRGFAFIEFNDYD 159
+V ++ TG +G+ F E+ D
Sbjct: 126 FLVYSERTGQSKGYGFAEYMKKD 148
>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
pdb|3H2U|D Chain D, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
Length = 283
Score = 28.5 bits (62), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 31/143 (21%), Positives = 61/143 (42%), Gaps = 17/143 (11%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
RK+ I GL T++ + + +K + +G F+T + + A+
Sbjct: 21 RKILIRGLPGDVTNQEVHDLLSDY-------ELKYCFVDKYKGTAFVTLLNGEQAEAAI- 72
Query: 77 NRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGLKDQEEDDLREYFSQFGTIESV 136
N H R+ E + +V ++ +A V + + Q E+ +R FG++E
Sbjct: 73 NAFHQ--SRLRERELSV---QLQPTDALLCVANLPPSLTQQQFEELVRP----FGSLERC 123
Query: 137 NMVTNKETGAKRGFAFIEFNDYD 159
+V ++ TG +G+ F E+ D
Sbjct: 124 FLVYSERTGQSKGYGFAEYMKKD 146
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 28.1 bits (61), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 11/40 (27%), Positives = 22/40 (55%)
Query: 116 KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
+D + +L F G I + ++ + +TG G+AF++F
Sbjct: 13 QDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDF 52
>pdb|2DHA|A Chain A, Solution Structure Of The Second Rna Recognition Motif
In Hypothetical Protein Flj201171
Length = 123
Score = 27.7 bits (60), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 22/53 (41%), Gaps = 10/53 (18%)
Query: 23 GLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
GL + T E + AFF Q PIT G F+TY + + DA
Sbjct: 30 GLPFTATAEEVVAFFGQ----------HCPITGGKEGILFVTYPDGRPTGDAF 72
>pdb|2E5G|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 21
Length = 94
Score = 27.3 bits (59), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 6/60 (10%)
Query: 107 VKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
++ +FV G + + L EYF FG + SV V +K+ G FA +E D + ++
Sbjct: 8 LRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVL 62
>pdb|3NS6|A Chain A, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
pdb|3NS6|B Chain B, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
Length = 100
Score = 26.9 bits (58), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 13/45 (28%), Positives = 23/45 (51%)
Query: 123 LREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLS 167
L FS+ G + ++ ++ TG +GF F+E + KI+ S
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKS 73
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 26.9 bits (58), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 13/45 (28%), Positives = 23/45 (51%)
Query: 123 LREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLS 167
L FS+ G + ++ ++ TG +GF F+E + KI+ S
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKS 73
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.318 0.137 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,169,332
Number of Sequences: 62578
Number of extensions: 201169
Number of successful extensions: 1031
Number of sequences better than 100.0: 158
Number of HSP's better than 100.0 without gapping: 125
Number of HSP's successfully gapped in prelim test: 33
Number of HSP's that attempted gapping in prelim test: 740
Number of HSP's gapped (non-prelim): 276
length of query: 178
length of database: 14,973,337
effective HSP length: 92
effective length of query: 86
effective length of database: 9,216,161
effective search space: 792589846
effective search space used: 792589846
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)