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= 038933
(347 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 3e-31, Method: Compositional matrix adjust.
Identities = 68/181 (37%), Positives = 106/181 (58%), Gaps = 19/181 (10%)
Query: 8 KLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQH 67
K+F+GG++ +T E+ LREYF +YGTV + I++ TG RGFGF+ F K S ++ ++
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 68 KHHVILGKEVEVKKAIPKGHKLEESNGHSGNCVGDDDTEINTKKIFVGGLPLDIXXXXXX 127
H++ GK ++ K+AIP+ D + T KIFVGG+ D+
Sbjct: 65 -QHILDGKVIDPKRAIPR------------------DEQDKTGKIFVGGIGPDVRPKEFE 105
Query: 128 XXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQTRFHKLKYKMVEVKRSHP 187
GT+ DA ++ DK+TG+ RGFGF+T+DS DA + V Q +F K + +E+KR+ P
Sbjct: 106 EFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAEP 165
Query: 188 K 188
+
Sbjct: 166 R 166
Score = 60.8 bits (146), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 32/83 (38%), Positives = 49/83 (59%), Gaps = 1/83 (1%)
Query: 111 KIFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQT 170
K+F+GGL D GTVTD ++ D TGR RGFGF++F+ + + V++T
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 171 RFHKLKYKMVEVKRSHPKDRIDK 193
+ H L K+++ KR+ P+D DK
Sbjct: 65 Q-HILDGKVIDPKRAIPRDEQDK 86
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 110 bits (275), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 59/190 (31%), Positives = 101/190 (53%), Gaps = 12/190 (6%)
Query: 2 EPVSLRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMA 61
EP LRKLF+GG+S ET +E+LR +F Q+GT+ + +++R T RGFGFV + +
Sbjct: 10 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 69
Query: 62 EDALQHKHHVILGKEVEVKKAIPKGHKLEESNGHSGNCVGDDDTEINTKKIFVGGLPLDI 121
+ A+ + H + G+ VE K+A+ + E + G + KKIFVGG+ D
Sbjct: 70 DAAMNARPHKVDGRVVEPKRAVSR-----EDSQRPG-------AHLTVKKIFVGGIKEDT 117
Query: 122 XXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQTRFHKLKYKMVE 181
G + ++ D+ +G+ RGF F+TFD D+ + ++ ++H + E
Sbjct: 118 EEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCE 177
Query: 182 VKRSHPKDRI 191
V+++ K +
Sbjct: 178 VRKALSKQEM 187
Score = 68.6 bits (166), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 34/95 (35%), Positives = 52/95 (54%)
Query: 4 VSLRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAED 63
++++K+FVGG+ +T E LR+YF QYG +E I+ R +G RGF FV F +
Sbjct: 103 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK 162
Query: 64 ALQHKHHVILGKEVEVKKAIPKGHKLEESNGHSGN 98
+ K+H + G EV+KA+ K S+ G
Sbjct: 163 IVIQKYHTVNGHNCEVRKALSKQEMASASSSQRGR 197
>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 = 110 bits (275), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 59/190 (31%), Positives = 101/190 (53%), Gaps = 12/190 (6%)
Query: 2 EPVSLRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMA 61
EP LRKLF+GG+S ET +E+LR +F Q+GT+ + +++R T RGFGFV + +
Sbjct: 9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 68
Query: 62 EDALQHKHHVILGKEVEVKKAIPKGHKLEESNGHSGNCVGDDDTEINTKKIFVGGLPLDI 121
+ A+ + H + G+ VE K+A+ + E + G + KKIFVGG+ D
Sbjct: 69 DAAMNARPHKVDGRVVEPKRAVSR-----EDSQRPG-------AHLTVKKIFVGGIKEDT 116
Query: 122 XXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQTRFHKLKYKMVE 181
G + ++ D+ +G+ RGF F+TFD D+ + ++ ++H + E
Sbjct: 117 EEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCE 176
Query: 182 VKRSHPKDRI 191
V+++ K +
Sbjct: 177 VRKALSKQEM 186
Score = 68.6 bits (166), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 34/95 (35%), Positives = 52/95 (54%)
Query: 4 VSLRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAED 63
++++K+FVGG+ +T E LR+YF QYG +E I+ R +G RGF FV F +
Sbjct: 102 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK 161
Query: 64 ALQHKHHVILGKEVEVKKAIPKGHKLEESNGHSGN 98
+ K+H + G EV+KA+ K S+ G
Sbjct: 162 IVIQKYHTVNGHNCEVRKALSKQEMASASSSQRGR 196
>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 = 110 bits (275), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 59/190 (31%), Positives = 101/190 (53%), Gaps = 12/190 (6%)
Query: 2 EPVSLRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMA 61
EP LRKLF+GG+S ET +E+LR +F Q+GT+ + +++R T RGFGFV + +
Sbjct: 8 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 67
Query: 62 EDALQHKHHVILGKEVEVKKAIPKGHKLEESNGHSGNCVGDDDTEINTKKIFVGGLPLDI 121
+ A+ + H + G+ VE K+A+ + E + G + KKIFVGG+ D
Sbjct: 68 DAAMNARPHKVDGRVVEPKRAVSR-----EDSQRPG-------AHLTVKKIFVGGIKEDT 115
Query: 122 XXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQTRFHKLKYKMVE 181
G + ++ D+ +G+ RGF F+TFD D+ + ++ ++H + E
Sbjct: 116 EEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCE 175
Query: 182 VKRSHPKDRI 191
V+++ K +
Sbjct: 176 VRKALSKQEM 185
Score = 68.6 bits (166), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 34/95 (35%), Positives = 52/95 (54%)
Query: 4 VSLRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAED 63
++++K+FVGG+ +T E LR+YF QYG +E I+ R +G RGF FV F +
Sbjct: 101 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK 160
Query: 64 ALQHKHHVILGKEVEVKKAIPKGHKLEESNGHSGN 98
+ K+H + G EV+KA+ K S+ G
Sbjct: 161 IVIQKYHTVNGHNCEVRKALSKQEMASASSSQRGR 195
>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 = 110 bits (275), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 59/190 (31%), Positives = 101/190 (53%), Gaps = 12/190 (6%)
Query: 2 EPVSLRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMA 61
EP LRKLF+GG+S ET +E+LR +F Q+GT+ + +++R T RGFGFV + +
Sbjct: 2 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 61
Query: 62 EDALQHKHHVILGKEVEVKKAIPKGHKLEESNGHSGNCVGDDDTEINTKKIFVGGLPLDI 121
+ A+ + H + G+ VE K+A+ + E + G + KKIFVGG+ D
Sbjct: 62 DAAMNARPHKVDGRVVEPKRAVSR-----EDSQRPG-------AHLTVKKIFVGGIKEDT 109
Query: 122 XXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQTRFHKLKYKMVE 181
G + ++ D+ +G+ RGF F+TFD D+ + ++ ++H + E
Sbjct: 110 EEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCE 169
Query: 182 VKRSHPKDRI 191
V+++ K +
Sbjct: 170 VRKALSKQEM 179
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 110 bits (274), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 59/187 (31%), Positives = 100/187 (53%), Gaps = 12/187 (6%)
Query: 2 EPVSLRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMA 61
EP LRKLF+GG+S ET +E+LR +F Q+GT+ + +++R T RGFGFV + +
Sbjct: 9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 68
Query: 62 EDALQHKHHVILGKEVEVKKAIPKGHKLEESNGHSGNCVGDDDTEINTKKIFVGGLPLDI 121
+ A+ + H + G+ VE K+A+ + E + G + KKIFVGG+ D
Sbjct: 69 DAAMNARPHKVDGRVVEPKRAVSR-----EDSQRPG-------AHLTVKKIFVGGIKEDT 116
Query: 122 XXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQTRFHKLKYKMVE 181
G + ++ D+ +G+ RGF F+TFD D+ + ++ ++H + E
Sbjct: 117 EEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCE 176
Query: 182 VKRSHPK 188
V+++ K
Sbjct: 177 VRKALSK 183
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 110 bits (274), Expect = 2e-24, Method: Compositional matrix adjust.
Identities = 59/187 (31%), Positives = 100/187 (53%), Gaps = 12/187 (6%)
Query: 2 EPVSLRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMA 61
EP LRKLF+GG+S ET +E+LR +F Q+GT+ + +++R T RGFGFV + +
Sbjct: 7 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 66
Query: 62 EDALQHKHHVILGKEVEVKKAIPKGHKLEESNGHSGNCVGDDDTEINTKKIFVGGLPLDI 121
+ A+ + H + G+ VE K+A+ + E + G + KKIFVGG+ D
Sbjct: 67 DAAMNARPHKVDGRVVEPKRAVSR-----EDSQRPG-------AHLTVKKIFVGGIKEDT 114
Query: 122 XXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQTRFHKLKYKMVE 181
G + ++ D+ +G+ RGF F+TFD D+ + ++ ++H + E
Sbjct: 115 EEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCE 174
Query: 182 VKRSHPK 188
V+++ K
Sbjct: 175 VRKALSK 181
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 73.9 bits (180), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 33/84 (39%), Positives = 54/84 (64%)
Query: 2 EPVSLRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMA 61
E RKLF+GG+S ET EE+LR Y+ Q+G + + +++R + RGFGFV F+ ++
Sbjct: 23 EKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEV 82
Query: 62 EDALQHKHHVILGKEVEVKKAIPK 85
+ A+ + H I G+ VE K+A+ +
Sbjct: 83 DAAMAARPHSIDGRVVEPKRAVAR 106
Score = 51.6 bits (122), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 41/80 (51%)
Query: 110 KKIFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQ 169
+K+F+GGL + G +TD V+ D + R RGFGF+TF S + +
Sbjct: 28 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA 87
Query: 170 TRFHKLKYKMVEVKRSHPKD 189
R H + ++VE KR+ ++
Sbjct: 88 ARPHSIDGRVVEPKRAVARE 107
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 73.6 bits (179), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 36/90 (40%), Positives = 52/90 (57%), Gaps = 2/90 (2%)
Query: 8 KLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQH 67
KLFVGG+ T +ETLR YFSQYG V + +I++ + T RGFGFV F + L
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 68 KHHVILGKEVEVKKAIPKGHKLEESNGHSG 97
+ H + G+ ++ K P+G ++ S SG
Sbjct: 78 RPHTLDGRNIDPKPCTPRG--MQPSGPSSG 105
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 36/78 (46%)
Query: 111 KIFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQT 170
K+FVGGL G V D ++ DK T + RGFGF+ F + VL +
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 171 RFHKLKYKMVEVKRSHPK 188
R H L + ++ K P+
Sbjct: 78 RPHTLDGRNIDPKPCTPR 95
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 71.2 bits (173), Expect = 8e-13, Method: Composition-based stats.
Identities = 33/78 (42%), Positives = 48/78 (61%)
Query: 8 KLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQH 67
K+F+GG+S +T +E LREYF Q+G V+E L++R LT RGFGFV F + + L
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 86
Query: 68 KHHVILGKEVEVKKAIPK 85
H + K ++ K A P+
Sbjct: 87 SRHELDSKTIDPKVAFPR 104
Score = 44.7 bits (104), Expect = 7e-05, Method: Composition-based stats.
Identities = 25/78 (32%), Positives = 37/78 (47%)
Query: 111 KIFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQT 170
K+F+GGL G V + V+ D T R RGFGF+TF + + VL
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 86
Query: 171 RFHKLKYKMVEVKRSHPK 188
H+L K ++ K + P+
Sbjct: 87 SRHELDSKTIDPKVAFPR 104
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 70.1 bits (170), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 34/79 (43%), Positives = 45/79 (56%)
Query: 111 KIFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQT 170
KIFVGG+P + G VT+ +I D E RPRGFGFITF+ E + + +
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
Query: 171 RFHKLKYKMVEVKRSHPKD 189
FH + K VEVKR+ P+D
Sbjct: 72 HFHDIMGKKVEVKRAEPRD 90
Score = 65.9 bits (159), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 33/81 (40%), Positives = 46/81 (56%)
Query: 8 KLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQH 67
K+FVGG+ E LREYF ++G V E ++I RGFGF+ F + A+
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
Query: 68 KHHVILGKEVEVKKAIPKGHK 88
H I+GK+VEVK+A P+ K
Sbjct: 72 HFHDIMGKKVEVKRAEPRDSK 92
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 70.1 bits (170), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 32/76 (42%), Positives = 51/76 (67%), Gaps = 1/76 (1%)
Query: 8 KLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQH 67
KLFVGG+S +TNE++L + FS+YG + E ++++ R T RGFGFV F I A+DA+
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 68 KH-HVILGKEVEVKKA 82
+ + G+++ V +A
Sbjct: 74 MNGKSVDGRQIRVDQA 89
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 33/58 (56%)
Query: 111 KIFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVL 168
K+FVGGL D G +++ V+ D+ET R RGFGF+TF++ D A + +
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 71
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 68.6 bits (166), Expect = 5e-12, Method: Composition-based stats.
Identities = 32/75 (42%), Positives = 46/75 (61%)
Query: 8 KLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQH 67
K+F+GG+S +T +E LREYF Q+G V+E L++R LT RGFGFV F + + L
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 68 KHHVILGKEVEVKKA 82
H + K ++ K A
Sbjct: 62 SRHELDSKTIDPKVA 76
Score = 42.7 bits (99), Expect = 3e-04, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 34/73 (46%)
Query: 111 KIFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQT 170
K+F+GGL G V + V+ D T R RGFGF+TF + + VL
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 171 RFHKLKYKMVEVK 183
H+L K ++ K
Sbjct: 62 SRHELDSKTIDPK 74
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 65.1 bits (157), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 32/74 (43%), Positives = 43/74 (58%)
Query: 112 IFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQTR 171
IFVGGL ++ G V DA ++ DK T R RGFGF+TF+SED V +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 172 FHKLKYKMVEVKRS 185
FH++ KMVE K++
Sbjct: 62 FHEINNKMVECKKA 75
Score = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 29/74 (39%), Positives = 42/74 (56%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQHK 68
+FVGG+S T E ++ YF Q+G V++ +++ + T RGFGFV F + E +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 69 HHVILGKEVEVKKA 82
H I K VE KKA
Sbjct: 62 FHEINNKMVECKKA 75
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 63.5 bits (153), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 41/163 (25%), Positives = 70/163 (42%), Gaps = 19/163 (11%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQHK 68
L V + + ++ LR FS G VE +IR ++ GH G+GFV + AE A+
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 69 HHVIL-GKEVEVKKAIPKGHKLEESNGHSGNCVGDDDTEINTKKIFVGGLPLDIXXXXXX 127
+ + L K ++V A P ++++N +++ GLP +
Sbjct: 65 NGLRLQSKTIKVSYARPSSEVIKDAN------------------LYISGLPRTMTQKDVE 106
Query: 128 XXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQT 170
G + ++ V+ D+ TG RG FI FD A + +
Sbjct: 107 DMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITS 149
>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 = 63.5 bits (153), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 41/163 (25%), Positives = 70/163 (42%), Gaps = 19/163 (11%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQHK 68
L V + + ++ LR FS G VE +IR ++ GH G+GFV + AE A+
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 69 HHVIL-GKEVEVKKAIPKGHKLEESNGHSGNCVGDDDTEINTKKIFVGGLPLDIXXXXXX 127
+ + L K ++V A P ++++N +++ GLP +
Sbjct: 65 NGLRLQSKTIKVSYARPSSEVIKDAN------------------LYISGLPRTMTQKDVE 106
Query: 128 XXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQT 170
G + ++ V+ D+ TG RG FI FD A + +
Sbjct: 107 DMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITS 149
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 62.4 bits (150), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 46/78 (58%)
Query: 5 SLRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDA 64
+ K+FVGG+ T + +LR+YF +G +EE ++I R TG RG+GFV + AE A
Sbjct: 16 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA 75
Query: 65 LQHKHHVILGKEVEVKKA 82
+ + +I G++ V A
Sbjct: 76 CKDPNPIIDGRKANVNLA 93
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/54 (40%), Positives = 29/54 (53%)
Query: 111 KIFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAA 164
KIFVGGLP G + +A VI D++TG+ RG+GF+T AA
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAA 72
>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 = 60.5 bits (145), Expect = 1e-09, Method: Composition-based stats.
Identities = 29/75 (38%), Positives = 47/75 (62%)
Query: 8 KLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQH 67
K FVGG+S +T+++ L++YF+++G V + I TG RGFGF++F + E L
Sbjct: 13 KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQ 72
Query: 68 KHHVILGKEVEVKKA 82
K H + G+ ++ KKA
Sbjct: 73 KEHRLDGRVIDPKKA 87
Score = 49.7 bits (117), Expect = 3e-06, Method: Composition-based stats.
Identities = 27/80 (33%), Positives = 38/80 (47%)
Query: 106 EINTKKIFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAAN 165
E + K FVGGL D G V D + D TGR RGFGFI F +
Sbjct: 8 EEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVE 67
Query: 166 NVLQTRFHKLKYKMVEVKRS 185
VL + H+L ++++ K++
Sbjct: 68 KVLDQKEHRLDGRVIDPKKA 87
>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 = 60.5 bits (145), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 47/74 (63%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQHK 68
+F+GG+S +T ++ L++YFS++G V + + +TG RGFGFV+F + + + K
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 69 HHVILGKEVEVKKA 82
H + GK ++ K+A
Sbjct: 62 EHKLNGKVIDPKRA 75
Score = 51.2 bits (121), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 38/74 (51%)
Query: 112 IFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQTR 171
+F+GGL D G V D + D TGR RGFGF+ F ++ + V+ +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 172 FHKLKYKMVEVKRS 185
HKL K+++ KR+
Sbjct: 62 EHKLNGKVIDPKRA 75
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 58.9 bits (141), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 30/76 (39%), Positives = 50/76 (65%), Gaps = 2/76 (2%)
Query: 8 KLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQH 67
KLF+GG++RETNE+ L+ F ++G + E L+I+ R T RGF F+ F + A++A +
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKD 67
Query: 68 KHHVIL-GKEVEVKKA 82
+ L GK ++V++A
Sbjct: 68 MNGKSLHGKAIKVEQA 83
Score = 35.4 bits (80), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 5/78 (6%)
Query: 111 KIFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITF----DSEDAANN 166
K+F+GGL + G +++ +I D+ T + RGF FITF D+++AA +
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKD 67
Query: 167 VLQTRFHKLKYKMVEVKR 184
+ H K+ + K+
Sbjct: 68 MNGKSLHGKAIKVEQAKK 85
>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 = 57.4 bits (137), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 39/162 (24%), Positives = 67/162 (41%), Gaps = 19/162 (11%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQHK 68
L V + + +E R F G +E ++R ++TG G+GFV + AE A+
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 69 HHVILG-KEVEVKKAIPKGHKLEESNGHSGNCVGDDDTEINTKKIFVGGLPLDIXXXXXX 127
+ + L K ++V A P + ++N ++V GLP +
Sbjct: 65 NGLRLQTKTIKVSYARPSSASIRDAN------------------LYVSGLPKTMTQKELE 106
Query: 128 XXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQ 169
G + + ++ D+ TG RG GFI FD A ++
Sbjct: 107 QLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 148
Score = 31.6 bits (70), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 20/88 (22%), Positives = 38/88 (43%), Gaps = 1/88 (1%)
Query: 112 IFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITF-DSEDAANNVLQT 170
+ V LP ++ G + ++ DK TG+ G+GF+ + D +DA +
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 171 RFHKLKYKMVEVKRSHPKDRIDKFMNCY 198
+L+ K ++V + P + N Y
Sbjct: 65 NGLRLQTKTIKVSYARPSSASIRDANLY 92
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 56.2 bits (134), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 36/162 (22%), Positives = 69/162 (42%), Gaps = 19/162 (11%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQHK 68
L V + + ++ + F G +E ++R ++TG G+GFV ++ + A+ A+
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 69 HHVILG-KEVEVKKAIPKGHKLEESNGHSGNCVGDDDTEINTKKIFVGGLPLDIXXXXXX 127
+ + L K ++V A P + ++N ++V GLP +
Sbjct: 67 NGLKLQTKTIKVSYARPSSASIRDAN------------------LYVSGLPKTMSQKEME 108
Query: 128 XXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQ 169
G + + ++ D+ TG RG GFI FD A ++
Sbjct: 109 QLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 150
Score = 31.6 bits (70), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 21/88 (23%), Positives = 37/88 (42%), Gaps = 1/88 (1%)
Query: 112 IFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITF-DSEDAANNVLQT 170
+ V LP ++ G + ++ DK TG+ G+GF+ + D DA +
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 171 RFHKLKYKMVEVKRSHPKDRIDKFMNCY 198
KL+ K ++V + P + N Y
Sbjct: 67 NGLKLQTKTIKVSYARPSSASIRDANLY 94
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 36/161 (22%), Positives = 68/161 (42%), Gaps = 19/161 (11%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQHK 68
L V + ++ + L F G + I+R TG+ G+ FV FT ++ A++
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 69 HHV-ILGKEVEVKKAIPKGHKLEESNGHSGNCVGDDDTEINTKKIFVGGLPLDIXXXXXX 127
+ + + K ++V A P G ++++N ++V LP I
Sbjct: 66 NGITVRNKRLKVSYARPGGESIKDTN------------------LYVTNLPRTITDDQLD 107
Query: 128 XXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVL 168
G++ ++ DK TGRPRG F+ ++ + A +
Sbjct: 108 TIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 148
Score = 45.1 bits (105), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 37/64 (57%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQHK 68
L+V + R ++ L F +YG++ + I+R +LTG RG FV + K A++A+
Sbjct: 92 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151
Query: 69 HHVI 72
++VI
Sbjct: 152 NNVI 155
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 52.8 bits (125), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 27/67 (40%), Positives = 39/67 (58%), Gaps = 1/67 (1%)
Query: 4 VSLRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAED 63
V RKLF+G +S++ E +R FS +G +EE I+R G RG FV FT +MA+
Sbjct: 105 VEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQT 163
Query: 64 ALQHKHH 70
A++ H
Sbjct: 164 AIKAMHQ 170
Score = 52.4 bits (124), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 42/168 (25%), Positives = 70/168 (41%), Gaps = 22/168 (13%)
Query: 8 KLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTG--HGRGFGFVIFTKISMAEDAL 65
K+FVG V R +E+ LRE F QYG V E ++R R +G FV F A +A
Sbjct: 17 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 76
Query: 66 QHKHHVILGKEVEVKKAIPKGH---KLEESNGHSGNCVGDDDTEINTKKIFVGGLPLDIX 122
H++ K +P H +++ ++ N V D +K+F+G +
Sbjct: 77 NALHNM---------KVLPGMHHPIQMKPADSEKNNAVED-------RKLFIGMISKKCT 120
Query: 123 XXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQT 170
G + + ++ + G RG F+TF + A ++
Sbjct: 121 ENDIRVMFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRAMAQTAIKA 167
>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 = 52.8 bits (125), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 45/78 (57%)
Query: 6 LRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDAL 65
++K+FVGG+S +T EE +REYF +G VE + T RGF F+ F + + +
Sbjct: 1 VKKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 60
Query: 66 QHKHHVILGKEVEVKKAI 83
+ K+H + + E+K A+
Sbjct: 61 EKKYHNVGLSKCEIKVAM 78
Score = 45.4 bits (106), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 35/75 (46%)
Query: 109 TKKIFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVL 168
KKIFVGGL D G V + D +T + RGF FITF E+ ++
Sbjct: 1 VKKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 60
Query: 169 QTRFHKLKYKMVEVK 183
+ ++H + E+K
Sbjct: 61 EKKYHNVGLSKCEIK 75
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 52.8 bits (125), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 27/67 (40%), Positives = 39/67 (58%), Gaps = 1/67 (1%)
Query: 4 VSLRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAED 63
V RKLF+G +S++ E +R FS +G +EE I+R G RG FV FT +MA+
Sbjct: 93 VEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQT 151
Query: 64 ALQHKHH 70
A++ H
Sbjct: 152 AIKAMHQ 158
Score = 52.4 bits (124), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 42/168 (25%), Positives = 70/168 (41%), Gaps = 22/168 (13%)
Query: 8 KLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTG--HGRGFGFVIFTKISMAEDAL 65
K+FVG V R +E+ LRE F QYG V E ++R R +G FV F A +A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 66 QHKHHVILGKEVEVKKAIPKGH---KLEESNGHSGNCVGDDDTEINTKKIFVGGLPLDIX 122
H++ K +P H +++ ++ N V D +K+F+G +
Sbjct: 65 NALHNM---------KVLPGMHHPIQMKPADSEKNNAVED-------RKLFIGMISKKCT 108
Query: 123 XXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQT 170
G + + ++ + G RG F+TF + A ++
Sbjct: 109 ENDIRVMFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRAMAQTAIKA 155
>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 = 52.0 bits (123), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 36/161 (22%), Positives = 67/161 (41%), Gaps = 19/161 (11%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQHK 68
L V + ++ + L F G + I R TG+ G+ FV FT ++ A++
Sbjct: 17 LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 69 HHV-ILGKEVEVKKAIPKGHKLEESNGHSGNCVGDDDTEINTKKIFVGGLPLDIXXXXXX 127
+ + + K ++V A P G ++++N ++V LP I
Sbjct: 77 NGITVRNKRLKVSYARPGGESIKDTN------------------LYVTNLPRTITDDQLD 118
Query: 128 XXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVL 168
G++ ++ DK TGRPRG F+ ++ + A +
Sbjct: 119 TIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 159
Score = 45.4 bits (106), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 39/71 (54%)
Query: 2 EPVSLRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMA 61
E + L+V + R ++ L F +YG++ + I+R +LTG RG FV + K A
Sbjct: 96 ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 155
Query: 62 EDALQHKHHVI 72
++A+ ++VI
Sbjct: 156 QEAISALNNVI 166
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 52.0 bits (123), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 41/164 (25%), Positives = 73/164 (44%), Gaps = 16/164 (9%)
Query: 7 RKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQ 66
R L+VG + + E+ L++YF G + I+ + + FV + + A ALQ
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQ 59
Query: 67 HKHHVILGKEVEVKKAIPKGHKLEESNGHSGNCVGDDDTEINTKKIFVGGLPLDIXXXXX 126
+ GK++E I K + +S S + +T +FVG L +++
Sbjct: 60 ----TLNGKQIE--NNIVKINWAFQSQQSSSD---------DTFNLFVGDLNVNVDDETL 104
Query: 127 XXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQT 170
+ V+ D +TG RG+GF++F S+D A N + +
Sbjct: 105 RNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 148
>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 = 51.6 bits (122), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 39/169 (23%), Positives = 79/169 (46%), Gaps = 16/169 (9%)
Query: 6 LRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDAL 65
+ +++VG + E E+T+R+ F+ +G ++ + +T +GF FV + A+ AL
Sbjct: 28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLAL 87
Query: 66 QHKHHVIL-GKEVEVKKAIPKGHKLEESNGHSGNCVGDDDTEINT--KKIFVGGLPLDIX 122
+ + V+L G+ ++V + SN + D E +I+V + D+
Sbjct: 88 EQMNSVMLGGRNIKVGR---------PSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLS 138
Query: 123 XXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFD----SEDAANNV 167
G + A + D TG+ +G+GFI ++ S+DA +++
Sbjct: 139 DDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/83 (22%), Positives = 45/83 (54%), Gaps = 1/83 (1%)
Query: 2 EPVSLRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMA 61
E + +++V V ++ +++ ++ F +G ++ + R TG +G+GF+ + K +
Sbjct: 121 EARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSS 180
Query: 62 EDALQHKHHVILGKE-VEVKKAI 83
+DA+ + LG + + V KA+
Sbjct: 181 QDAVSSMNLFDLGGQYLRVGKAV 203
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 51.2 bits (121), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 30/89 (33%), Positives = 48/89 (53%), Gaps = 3/89 (3%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQHK 68
L V G+ +T E+ L+EYFS +G V + + TGH +GFGFV FT+ + +
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 77
Query: 69 HHVILGKEVEVKKAIPKGHKLEESNGHSG 97
H+I G+ + K +P + ++S SG
Sbjct: 78 -HMIDGRWCDCK--LPNSKQSQDSGPSSG 103
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 32/85 (37%), Gaps = 1/85 (1%)
Query: 108 NTKKIFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNV 167
T + V GLP G V V D +TG +GFGF+ F + V
Sbjct: 14 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKV 73
Query: 168 LQTRFHKLKYKMVEVKRSHPKDRID 192
+ R H + + + K + K D
Sbjct: 74 MSQR-HMIDGRWCDCKLPNSKQSQD 97
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 30/83 (36%), Positives = 43/83 (51%), Gaps = 1/83 (1%)
Query: 1 MEPVSLRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISM 60
M+ + L V ++ T+ +TLR F +YG V + I R R T RGF FV F
Sbjct: 65 MDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRD 124
Query: 61 AEDALQHKHHVIL-GKEVEVKKA 82
AEDA+ +L G+E+ V+ A
Sbjct: 125 AEDAMDAMDGAVLDGRELRVQMA 147
>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 = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/68 (38%), Positives = 38/68 (55%), Gaps = 1/68 (1%)
Query: 4 VSLRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAED 63
V RKLF+G +S++ E +R FS +G +EE I+R G RG FV FT + A+
Sbjct: 93 VEDRKLFIGXISKKCTENDIRVXFSSFGQIEECRILRG-PDGLSRGCAFVTFTTRAXAQT 151
Query: 64 ALQHKHHV 71
A++ H
Sbjct: 152 AIKAXHQA 159
Score = 48.9 bits (115), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 43/168 (25%), Positives = 68/168 (40%), Gaps = 22/168 (13%)
Query: 8 KLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTG--HGRGFGFVIFTKISMAEDAL 65
K FVG V R +E+ LRE F QYG V E ++R R +G FV F A +A
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 66 QHKHHVILGKEVEVKKAIPKGH---KLEESNGHSGNCVGDDDTEINTKKIFVGGLPLDIX 122
H+ K +P H + + ++ N V D +K+F+G +
Sbjct: 65 NALHN---------XKVLPGXHHPIQXKPADSEKNNAVED-------RKLFIGXISKKCT 108
Query: 123 XXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQT 170
G + + ++ + G RG F+TF + A ++
Sbjct: 109 ENDIRVXFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRAXAQTAIKA 155
>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 = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 29/75 (38%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQHK 68
L V ++ T+ +TLR F +YG V + I R R T RGF FV F AEDA+
Sbjct: 50 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109
Query: 69 HHVIL-GKEVEVKKA 82
+L G+E+ V+ A
Sbjct: 110 DGAVLDGRELRVQMA 124
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 49.7 bits (117), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 35/101 (34%), Positives = 49/101 (48%), Gaps = 2/101 (1%)
Query: 2 EPVSLRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMA 61
EP LR L V + +E LR+ F +YG +E I+ R T RG+GFV F S A
Sbjct: 38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSA 97
Query: 62 EDALQHKHHV-ILGKEVEVKKAIPKGHKLEESNGHSGNCVG 101
+ A+ + IL K ++V A GH+ G G+ G
Sbjct: 98 QQAIAGLNGFNILNKRLKVALAA-SGHQRPGIAGAVGDGNG 137
Score = 35.8 bits (81), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 14/59 (23%), Positives = 27/59 (45%)
Query: 110 KKIFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVL 168
+ + V +P + G + ++CD+ET + RG+GF+ F S +A +
Sbjct: 43 RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAI 101
>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 = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 38/167 (22%), Positives = 77/167 (46%), Gaps = 16/167 (9%)
Query: 8 KLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQH 67
+++VG + E E+T+R+ F+ +G ++ + +T +GF FV + A+ AL+
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 68 KHHVIL-GKEVEVKKAIPKGHKLEESNGHSGNCVGDDDTEINT--KKIFVGGLPLDIXXX 124
+ V+L G+ ++V + SN + D E +I+V + D+
Sbjct: 75 MNSVMLGGRNIKVGRP---------SNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDD 125
Query: 125 XXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFD----SEDAANNV 167
G + + D TG+ +G+GFI ++ S+DA +++
Sbjct: 126 DIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 172
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/83 (22%), Positives = 45/83 (54%), Gaps = 1/83 (1%)
Query: 2 EPVSLRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMA 61
E + +++V V ++ +++ ++ F +G ++ + R TG +G+GF+ + K +
Sbjct: 106 EARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSS 165
Query: 62 EDALQHKHHVILGKE-VEVKKAI 83
+DA+ + LG + + V KA+
Sbjct: 166 QDAVSSMNLFDLGGQYLRVGKAV 188
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 41/74 (55%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQHK 68
+FVGG+S +T EE +REYF +G VE + T RGF F+ F + + ++ K
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Query: 69 HHVILGKEVEVKKA 82
+H + + E+K A
Sbjct: 62 YHNVGLSKCEIKVA 75
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 33/72 (45%)
Query: 112 IFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQTR 171
IFVGGL D G V + D +T + RGF FITF E+ +++ +
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Query: 172 FHKLKYKMVEVK 183
+H + E+K
Sbjct: 62 YHNVGLSKCEIK 73
>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 = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 44/165 (26%), Positives = 73/165 (44%), Gaps = 19/165 (11%)
Query: 6 LRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDAL 65
+ L+VG + + E L E FS G + + R +T G+ +V F + + AE AL
Sbjct: 15 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL 74
Query: 66 QHKHH-VILGKEVEVKKAIPKGHKLEESNGHSGNCVGDDDTEINTKKIFVGGLPLDIXXX 124
+ VI GK V + + + + S SG VG+ IF+ L I
Sbjct: 75 DTMNFDVIKGKPVRIMWS-----QRDPSLRKSG--VGN---------IFIKNLDKSIDNK 118
Query: 125 XXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQ 169
G + V+CD E G +G+GF+ F++++AA ++
Sbjct: 119 ALYDTFSAFGNILSCKVVCD-ENGS-KGYGFVHFETQEAAERAIE 161
Score = 28.5 bits (62), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 36/74 (48%), Gaps = 7/74 (9%)
Query: 5 SLRK-----LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKIS 59
SLRK +F+ + + + + L + FS +G + ++ +G+GFV F
Sbjct: 97 SLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQE 154
Query: 60 MAEDALQHKHHVIL 73
AE A++ + ++L
Sbjct: 155 AAERAIEKMNGMLL 168
>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 = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 44/162 (27%), Positives = 72/162 (44%), Gaps = 19/162 (11%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQHK 68
L+VG + + E L E FS G + + R +T G+ +V F + + AE AL
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 72
Query: 69 HH-VILGKEVEVKKAIPKGHKLEESNGHSGNCVGDDDTEINTKKIFVGGLPLDIXXXXXX 127
+ VI GK V + + + + S SG VG+ IF+ L I
Sbjct: 73 NFDVIKGKPVRIMWS-----QRDPSLRKSG--VGN---------IFIKNLDKSIDNKALY 116
Query: 128 XXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQ 169
G + V+CD E G +G+GF+ F++++AA ++
Sbjct: 117 DTFSAFGNILSCKVVCD-ENG-SKGYGFVHFETQEAAERAIE 156
Score = 28.1 bits (61), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 36/74 (48%), Gaps = 7/74 (9%)
Query: 5 SLRK-----LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKIS 59
SLRK +F+ + + + + L + FS +G + ++ +G+GFV F
Sbjct: 92 SLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQE 149
Query: 60 MAEDALQHKHHVIL 73
AE A++ + ++L
Sbjct: 150 AAERAIEKMNGMLL 163
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 48.5 bits (114), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 26/68 (38%), Positives = 38/68 (55%), Gaps = 8/68 (11%)
Query: 6 LRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDAL 65
+ KLF+G + RE E+ +R F QYG V E II++ +GFV + AEDA+
Sbjct: 8 MVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFVHIEDKTAAEDAI 59
Query: 66 QHKHHVIL 73
++ HH L
Sbjct: 60 RNLHHYKL 67
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 48.1 bits (113), Expect = 7e-06, Method: Composition-based stats.
Identities = 25/80 (31%), Positives = 43/80 (53%)
Query: 6 LRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDAL 65
+R ++VG + E ++E FSQ+G V +I R T +GFGFV + S++E
Sbjct: 1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIA 60
Query: 66 QHKHHVILGKEVEVKKAIPK 85
+ + +G+ + V +A PK
Sbjct: 61 KLDNTDFMGRTIRVTEANPK 80
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 19/83 (22%), Positives = 36/83 (43%)
Query: 110 KKIFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQ 169
+ I+VG L G V + +I D+ET +P+GFGF+ E + + +
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAK 61
Query: 170 TRFHKLKYKMVEVKRSHPKDRID 192
+ + V ++PK ++
Sbjct: 62 LDNTDFMGRTIRVTEANPKKSLE 84
>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 = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 35/166 (21%), Positives = 73/166 (43%), Gaps = 12/166 (7%)
Query: 8 KLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQH 67
+++VG + E E+T+R+ F+ +G ++ +T +GF FV + A+ AL+
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 68 KHHVIL-GKEVEVKKAIPKGHKLEESNGHSGNCVGDDDTEINT--KKIFVGGLPLDIXXX 124
+ V L G+ ++V + SN + D E +I+V + D+
Sbjct: 74 XNSVXLGGRNIKVGRP---------SNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDD 124
Query: 125 XXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQT 170
G + + D TG+ +G+GFI ++ ++ + + +
Sbjct: 125 DIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 170
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/83 (22%), Positives = 45/83 (54%), Gaps = 1/83 (1%)
Query: 2 EPVSLRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMA 61
E + +++V V ++ +++ ++ F +G ++ + R TG +G+GF+ + K +
Sbjct: 105 EARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSS 164
Query: 62 EDALQHKHHVILGKE-VEVKKAI 83
+DA+ + LG + + V KA+
Sbjct: 165 QDAVSSXNLFDLGGQYLRVGKAV 187
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 43/78 (55%), Gaps = 1/78 (1%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQHK 68
L V G+S T E LRE FS+YG + + I+ + + RGF FV F + A++A +
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 69 HHVIL-GKEVEVKKAIPK 85
+ + L G+ + V +I K
Sbjct: 78 NGMELDGRRIRVDFSITK 95
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 43/78 (55%), Gaps = 1/78 (1%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQHK 68
L V G+S T E LRE FS+YG + + I+ + + RGF FV F + A++A +
Sbjct: 15 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 74
Query: 69 HHVIL-GKEVEVKKAIPK 85
+ + L G+ + V +I K
Sbjct: 75 NGMELDGRRIRVDFSITK 92
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 41/68 (60%), Gaps = 1/68 (1%)
Query: 2 EPVSLRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMA 61
+P S RKLFVG ++++ +E+ +R F +G +EE I+R G+ +G FV ++ + A
Sbjct: 11 QPPSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGP-DGNSKGCAFVKYSSHAEA 69
Query: 62 EDALQHKH 69
+ A+ H
Sbjct: 70 QAAINALH 77
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 34/83 (40%), Positives = 45/83 (54%), Gaps = 10/83 (12%)
Query: 7 RKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQ 66
+ LFV G+S +T EETL+E F G+V I+ R TG +GFGFV F + EDA
Sbjct: 16 KTLFVKGLSEDTTEETLKESFD--GSV-RARIVTDRETGSSKGFGFVDF---NSEEDAKA 69
Query: 67 HKHHV----ILGKEVEVKKAIPK 85
K + I G +V + A PK
Sbjct: 70 AKEAMEDGEIDGNKVTLDWAKPK 92
Score = 36.2 bits (82), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 31/56 (55%), Gaps = 3/56 (5%)
Query: 109 TKKIFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAA 164
+K +FV GL D G+V A ++ D+ETG +GFGF+ F+SE+ A
Sbjct: 15 SKTLFVKGLSEDTTEETLKESFD--GSVR-ARIVTDRETGSSKGFGFVDFNSEEDA 67
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 30/85 (35%), Positives = 46/85 (54%), Gaps = 5/85 (5%)
Query: 3 PVSLRK----LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKI 58
P+S R ++VGG+ + +E L E F Q G V T + + R+TG +G+GFV F
Sbjct: 8 PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSE 67
Query: 59 SMAEDALQHKHHVIL-GKEVEVKKA 82
A+ A++ + L GK + V KA
Sbjct: 68 EDADYAIKIMDMIKLYGKPIRVNKA 92
Score = 32.0 bits (71), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 1/75 (1%)
Query: 112 IFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQTR 171
++VGGL + G V + + D+ TG+ +G+GF+ F SE+ A+ ++
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 172 -FHKLKYKMVEVKRS 185
KL K + V ++
Sbjct: 78 DMIKLYGKPIRVNKA 92
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 43/78 (55%), Gaps = 1/78 (1%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQHK 68
L V G+S T E LRE FS+YG + + I+ + + RGF FV F + A++A +
Sbjct: 49 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 108
Query: 69 HHVIL-GKEVEVKKAIPK 85
+ + L G+ + V +I K
Sbjct: 109 NGMELDGRRIRVDFSITK 126
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 43/162 (26%), Positives = 66/162 (40%), Gaps = 32/162 (19%)
Query: 8 KLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDA-LQ 66
+LFVG + + EE +R+ F +YG E I + +GFGF+ ++AE A ++
Sbjct: 24 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 77
Query: 67 HKHHVILGKEVEVKKAIPKGHKLEESNGHSGNCVGDDDTEINTKKIFVGGLPLDIXXXXX 126
+ + GK++ V+ A HS + V LP +
Sbjct: 78 LDNMPLRGKQLRVRFAC-----------HSASLT-------------VRNLPQYVSNELL 113
Query: 127 XXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVL 168
G V A VI D + GRP G G + F + AA L
Sbjct: 114 EEAFSVFGQVERAVVIVD-DRGRPSGKGIVEFSGKPAARKAL 154
>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 = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 36/66 (54%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQHK 68
+FVG +S E E ++ F+ +G + + +++ TG +G+GFV F AE+A+Q
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 69 HHVILG 74
LG
Sbjct: 78 GGQWLG 83
Score = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 94 GHSGNCVGDDDTEINTKKIFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGF 153
G SG+ DT N +FVG L +I G ++DA V+ D TG+ +G+
Sbjct: 1 GSSGSSGQKKDTS-NHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGY 59
Query: 154 GFITFDSEDAANNVLQ 169
GF++F ++ A N +Q
Sbjct: 60 GFVSFFNKWDAENAIQ 75
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 40/72 (55%), Gaps = 1/72 (1%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQHK 68
L V G+S T E LRE FS+YG + + I+ + + RGF FV F + A++A +
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 69 HHVIL-GKEVEV 79
+ + L G+ + V
Sbjct: 78 NGMELDGRRIRV 89
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 45.4 bits (106), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 36/66 (54%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQHK 68
+FVG +S E E ++ F+ +G + + +++ TG +G+GFV F AE+A+ H
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 69 HHVILG 74
LG
Sbjct: 78 GGQWLG 83
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 94 GHSGNCVGDDDTEINTKKIFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGF 153
G SG+ DT N +FVG L +I G ++DA V+ D TG+ +G+
Sbjct: 1 GSSGSSGQKKDTS-NHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGY 59
Query: 154 GFITFDSEDAANNVL 168
GF++F ++ A N +
Sbjct: 60 GFVSFYNKLDAENAI 74
>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 = 44.7 bits (104), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 21/47 (44%), Positives = 32/47 (68%), Gaps = 1/47 (2%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIF 55
+FVGG+ +E +R +F++YG+V+E II R TG +G+GFV F
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 57
Score = 34.7 bits (78), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 36/70 (51%), Gaps = 3/70 (4%)
Query: 112 IFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVL--Q 169
+FVGG+ + + G+V + +I D+ TG +G+GF++F ++ ++ Q
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 170 TRFHKLKYKM 179
FH K K+
Sbjct: 71 INFHGKKLKL 80
>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 = 44.7 bits (104), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 21/47 (44%), Positives = 32/47 (68%), Gaps = 1/47 (2%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIF 55
+FVGG+ +E +R +F++YG+V+E II R TG +G+GFV F
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 57
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 3/76 (3%)
Query: 106 EINTKKIFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAAN 165
+I +FVGG+ + + G+V + +I D+ TG +G+GF++F ++
Sbjct: 6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQ 64
Query: 166 NVL--QTRFHKLKYKM 179
++ Q FH K K+
Sbjct: 65 KIVESQINFHGKKLKL 80
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 44.7 bits (104), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 21/47 (44%), Positives = 32/47 (68%), Gaps = 1/47 (2%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIF 55
+FVGG+ +E +R +F++YG+V+E II R TG +G+GFV F
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 58
Score = 34.3 bits (77), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 36/70 (51%), Gaps = 3/70 (4%)
Query: 112 IFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVL--Q 169
+FVGG+ + + G+V + +I D+ TG +G+GF++F ++ ++ Q
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 71
Query: 170 TRFHKLKYKM 179
FH K K+
Sbjct: 72 INFHGKKLKL 81
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 44/84 (52%), Gaps = 4/84 (4%)
Query: 8 KLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQ- 66
KLFVG + R +E+ L+ F ++G + E +++ RLTG +G F+ + A A
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSA 76
Query: 67 -HKHHVILG--KEVEVKKAIPKGH 87
H+ + G + ++VK A +G
Sbjct: 77 LHEQKTLPGMNRPIQVKPAASEGR 100
Score = 32.0 bits (71), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 40/85 (47%), Gaps = 5/85 (5%)
Query: 92 SNGHSGNCVGDDDTEINTKKIFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPR 151
S+G SG + D D K+FVG +P + G + + V+ D+ TG +
Sbjct: 2 SSGSSGVPMKDHDA----IKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHK 57
Query: 152 GFGFITFDSEDAANNVLQTRFHKLK 176
G F+T+ + D+A Q+ H+ K
Sbjct: 58 GCAFLTYCARDSALKA-QSALHEQK 81
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 27/87 (31%), Positives = 45/87 (51%), Gaps = 1/87 (1%)
Query: 5 SLRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDA 64
SLR +FVG + E EE L++ FS+ G V ++ R TG +G+GF + A A
Sbjct: 7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSA 66
Query: 65 LQHKH-HVILGKEVEVKKAIPKGHKLE 90
+++ + G+ + V A + +K E
Sbjct: 67 MRNLNGREFSGRALRVDNAASEKNKEE 93
Score = 38.5 bits (88), Expect = 0.006, Method: Composition-based stats.
Identities = 15/55 (27%), Positives = 28/55 (50%)
Query: 110 KKIFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAA 164
+ +FVG +P + G V ++ D+ETG+P+G+GF + ++ A
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETA 63
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 40/77 (51%), Gaps = 6/77 (7%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQHK 68
+FVG + + E+ LRE+FSQYG V + I + R F FV F +A+ +L +
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFADDQIAQ-SLCGE 61
Query: 69 HHVILGKEVEVKKAIPK 85
+I G V + A PK
Sbjct: 62 DLIIKGISVHISNAEPK 78
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 43.9 bits (102), Expect = 1e-04, Method: Composition-based stats.
Identities = 20/58 (34%), Positives = 36/58 (62%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQ 66
L+V G+ + +++ + + FSQYG + + I+ + TG RG GF+ F K AE+A++
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 61
Score = 33.9 bits (76), Expect = 0.15, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 26/58 (44%)
Query: 112 IFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQ 169
++V GLP + G + + ++ D+ TG RG GFI FD A ++
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 61
>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 = 43.9 bits (102), Expect = 1e-04, Method: Composition-based stats.
Identities = 22/71 (30%), Positives = 39/71 (54%)
Query: 2 EPVSLRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMA 61
E + L+V + R ++ L F +YG++ + I+R +LTG RG FV + K A
Sbjct: 9 ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 68
Query: 62 EDALQHKHHVI 72
++A+ ++VI
Sbjct: 69 QEAISALNNVI 79
Score = 33.9 bits (76), Expect = 0.12, Method: Composition-based stats.
Identities = 16/62 (25%), Positives = 27/62 (43%)
Query: 107 INTKKIFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANN 166
I ++V LP I G++ ++ DK TGRPRG F+ ++ + A
Sbjct: 11 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQE 70
Query: 167 VL 168
+
Sbjct: 71 AI 72
>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 = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 47/81 (58%), Gaps = 1/81 (1%)
Query: 3 PVSLRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAE 62
P S KLF+GG+ N++ ++E + +G ++ +++ TG +G+ F + I++ +
Sbjct: 111 PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTD 170
Query: 63 DALQHKHHVILG-KEVEVKKA 82
A+ + + LG K++ V++A
Sbjct: 171 QAIAGLNGMQLGDKKLLVQRA 191
Score = 32.3 bits (72), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 31/160 (19%), Positives = 65/160 (40%), Gaps = 15/160 (9%)
Query: 7 RKLFVGGVSRETNEETLREYFS---QYGTVEETL--IIRSRLTGHGRGFGFVIFTKISMA 61
R+L+VG + EE + ++F+ + G + + + + + F F+ F +
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 62 EDALQHKHHVILGKEVEVKKAIPKGHKLEESNGHSGN----CVGDDDTEI--NTKKIFVG 115
A+ + G+ +++++ H + G S N G T + + K+F+G
Sbjct: 65 TQAMAFDGIIFQGQSLKIRRP----HDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIG 120
Query: 116 GLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGF 155
GLP + G + ++ D TG +G+ F
Sbjct: 121 GLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAF 160
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 42/79 (53%), Gaps = 4/79 (5%)
Query: 8 KLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQ- 66
KLF+G + R +E+ L+ F ++G + E +++ R TG +G F+ + + A A
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74
Query: 67 -HKHHVILG--KEVEVKKA 82
H+ + G + ++VK A
Sbjct: 75 LHEQKTLPGMNRPIQVKPA 93
>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 = 42.0 bits (97), Expect = 5e-04, Method: Composition-based stats.
Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQHK 68
L V + + ++ LR FS G VE +IR ++ GH G+GFV + AE A+
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 69 HHVIL-GKEVEVKKAIP 84
+ + L K ++V A P
Sbjct: 82 NGLRLQSKTIKVSYARP 98
>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 = 42.0 bits (97), Expect = 5e-04, Method: Composition-based stats.
Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQHK 68
L V + + ++ LR FS G VE +IR ++ GH G+GFV + AE A+
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 69 HHVIL-GKEVEVKKAIP 84
+ + L K ++V A P
Sbjct: 67 NGLRLQSKTIKVSYARP 83
>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 = 42.0 bits (97), Expect = 6e-04, Method: Composition-based stats.
Identities = 25/66 (37%), Positives = 34/66 (51%), Gaps = 2/66 (3%)
Query: 8 KLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTG--HGRGFGFVIFTKISMAEDAL 65
K+FVG V R +E+ LRE F QYG V E ++R R +G FV F A +A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 66 QHKHHV 71
H++
Sbjct: 65 NALHNM 70
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 27/82 (32%), Positives = 42/82 (51%), Gaps = 6/82 (7%)
Query: 8 KLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQH 67
K+FVG + + E L+++F QYG V + I + R F FV F +A+ +L
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF-----RAFAFVTFADDKVAQ-SLCG 66
Query: 68 KHHVILGKEVEVKKAIPKGHKL 89
+ +I G V + A PK +KL
Sbjct: 67 EDLIIKGISVHISNAEPKHNKL 88
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 27/94 (28%), Positives = 46/94 (48%), Gaps = 7/94 (7%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQHK 68
L+VG + E+ LR F +G ++ ++++ TG +G+GF+ F+ A AL+
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 69 HHVIL-GKEVEVKKAIPKGHKLEESNGHSGNCVG 101
+ L G+ + V GH E +G SG G
Sbjct: 68 NGFELAGRPMRV------GHVTERLDGGSGPSSG 95
Score = 37.4 bits (85), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 20/84 (23%), Positives = 40/84 (47%), Gaps = 1/84 (1%)
Query: 109 TKKIFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVL 168
+ ++VG L +I G + + ++ D +TGR +G+GFITF + A L
Sbjct: 5 SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
Query: 169 QTRFHKLKYKMVEVKRSHPKDRID 192
+ + + + ++ H +R+D
Sbjct: 65 E-QLNGFELAGRPMRVGHVTERLD 87
>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 = 41.2 bits (95), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 8 KLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQH 67
KLF+GG+ N++ ++E + +G ++ +++ TG +G+ F + I++ + A+
Sbjct: 98 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 157
Query: 68 KHHVILG-KEVEVKKA 82
+ + LG K++ V++A
Sbjct: 158 LNGMQLGDKKLLVQRA 173
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 29/161 (18%), Positives = 60/161 (37%), Gaps = 33/161 (20%)
Query: 5 SLRKLFVGGVSRETNEETLREYFS---QYGTVEETL--IIRSRLTGHGRGFGFVIFTKIS 59
S R+L+VG + EE + ++F+ + G + + + + + F F+ F +
Sbjct: 5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 64
Query: 60 MAEDALQHKHHVILGKEVEVKK-----AIPKGHKLEESNGHSGNCVGDDDTEINTKKIFV 114
A+ + G+ +++++ +P HKL F+
Sbjct: 65 ETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKL-----------------------FI 101
Query: 115 GGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGF 155
GGLP + G + ++ D TG +G+ F
Sbjct: 102 GGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAF 142
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In
Trinucleotide Repeat Containing 4 Variant
Length = 102
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 7 RKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQ 66
RKLFVG + ++ +E +R+ F +GT++E ++R G +G FV F + A+ A+
Sbjct: 13 RKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGP-DGTSKGCAFVKFQTHAEAQAAIN 71
Query: 67 HKH 69
H
Sbjct: 72 TLH 74
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 8 KLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQH 67
KLF+GG+ N++ ++E + +G ++ +++ TG +G+ F + I++ + A+
Sbjct: 96 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 155
Query: 68 KHHVILG-KEVEVKKA 82
+ + LG K++ V++A
Sbjct: 156 LNGMQLGDKKLLVQRA 171
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 29/161 (18%), Positives = 60/161 (37%), Gaps = 33/161 (20%)
Query: 5 SLRKLFVGGVSRETNEETLREYFS---QYGTVEETL--IIRSRLTGHGRGFGFVIFTKIS 59
S R+L+VG + EE + ++F+ + G + + + + + F F+ F +
Sbjct: 3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62
Query: 60 MAEDALQHKHHVILGKEVEVKK-----AIPKGHKLEESNGHSGNCVGDDDTEINTKKIFV 114
A+ + G+ +++++ +P HKL F+
Sbjct: 63 ETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKL-----------------------FI 99
Query: 115 GGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGF 155
GGLP + G + ++ D TG +G+ F
Sbjct: 100 GGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAF 140
>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 = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/82 (23%), Positives = 42/82 (51%), Gaps = 3/82 (3%)
Query: 4 VSLRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAED 63
+ R ++VG V + + L +FS G++ I+ + +GH +G+ ++ F + + +
Sbjct: 34 IDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDA 93
Query: 64 ALQHKHHVILGKEVEVKKAIPK 85
A+ V G+ ++V +PK
Sbjct: 94 AVAMDETVFRGRTIKV---LPK 112
Score = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 21/90 (23%), Positives = 43/90 (47%), Gaps = 3/90 (3%)
Query: 101 GDDDTEINTKKIFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITF-- 158
++ EI+ + ++VG + G++ ++CDK +G P+G+ +I F
Sbjct: 28 AEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAE 87
Query: 159 -DSEDAANNVLQTRFHKLKYKMVEVKRSHP 187
+S DAA + +T F K++ + + P
Sbjct: 88 RNSVDAAVAMDETVFRGRTIKVLPKRTNMP 117
>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 = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 32/63 (50%)
Query: 5 SLRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDA 64
+ + LFV V+ +T E LR F YG ++ ++ S+ +G RG+ F+ + A
Sbjct: 101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSA 160
Query: 65 LQH 67
+H
Sbjct: 161 YKH 163
Score = 29.3 bits (64), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 13/52 (25%), Positives = 23/52 (44%)
Query: 110 KKIFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSE 161
K +FV + D G + ++ K +G+PRG+ FI ++ E
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHE 154
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 7 RKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQ 66
RKLFVG ++++ +EE + F +G ++E ++R G +G FV F+ + A+ A+
Sbjct: 16 RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIH 74
Query: 67 HKH 69
H
Sbjct: 75 ALH 77
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 38/82 (46%), Gaps = 1/82 (1%)
Query: 111 KIFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQT 170
+++VG L +I G + ++ D ETGR +G+GFITF + A L+
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALE- 86
Query: 171 RFHKLKYKMVEVKRSHPKDRID 192
+ + + +K H +R D
Sbjct: 87 QLNGFELAGRPMKVGHVTERTD 108
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 32/60 (53%)
Query: 8 KLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQH 67
+L+VG + E+ LR F +G +E ++ TG +G+GF+ F+ A+ AL+
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
>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 = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 32/57 (56%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDAL 65
LFVG ++ ++ETLR F + + ++ TG RG+GFV FT A++A+
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60
Score = 37.7 bits (86), Expect = 0.009, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 31/62 (50%)
Query: 109 TKKIFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVL 168
T +FVG L +++ + V+ D +TG RG+GF++F S+D A N +
Sbjct: 1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60
Query: 169 QT 170
+
Sbjct: 61 DS 62
>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 = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 40/79 (50%), Gaps = 4/79 (5%)
Query: 5 SLRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDA 64
+ + LFV V+ +T E LR F YG ++ ++ S+ +G RG+ F+ + A
Sbjct: 101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSA 160
Query: 65 LQHKHHVILGKEVEVKKAI 83
+H GK+++ ++ +
Sbjct: 161 YKHAD----GKKIDGRRVL 175
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 19/76 (25%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 8 KLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQH 67
KLF+GG+ N++ ++E + +G ++ +++ TG +G+ F + I++ + A+
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 68 KHHVILG-KEVEVKKA 82
+ + LG K++ V++A
Sbjct: 63 LNGMQLGDKKLLVQRA 78
>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 = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 3/79 (3%)
Query: 7 RKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQ 66
R ++VG V E L +F G+V I+ + +GH +GF ++ F+ +L
Sbjct: 7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 66
Query: 67 HKHHVILGKEVEVKKAIPK 85
+ G++++V IPK
Sbjct: 67 LDESLFRGRQIKV---IPK 82
Score = 37.7 bits (86), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 19/85 (22%), Positives = 39/85 (45%), Gaps = 3/85 (3%)
Query: 106 EINTKKIFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAAN 165
E + + I+VG + G+V ++CDK +G P+GF +I F +++
Sbjct: 3 EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62
Query: 166 NVL---QTRFHKLKYKMVEVKRSHP 187
L ++ F + K++ + + P
Sbjct: 63 TSLALDESLFRGRQIKVIPKRTNRP 87
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 29/95 (30%), Positives = 47/95 (49%), Gaps = 9/95 (9%)
Query: 7 RKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQ 66
R L+VGG++ E +++ L F +G + + I T RGF FV F +AEDA
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF---ELAEDAAA 69
Query: 67 HKHHV----ILGKEVEVKKAIPKGHKLEESNGHSG 97
++ + G+ + V A P +++ES SG
Sbjct: 70 AIDNMNESELFGRTIRVNLAKP--MRIKESGPSSG 102
Score = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 40/81 (49%), Gaps = 2/81 (2%)
Query: 109 TKKI-FVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFD-SEDAANN 166
TK++ +VGGL ++ G +TD + D ET + RGF F+ F+ +EDAA
Sbjct: 11 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 70
Query: 167 VLQTRFHKLKYKMVEVKRSHP 187
+ +L + + V + P
Sbjct: 71 IDNMNESELFGRTIRVNLAKP 91
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 41/76 (53%), Gaps = 4/76 (5%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGH---GRGFGFVIFTKISMAEDAL 65
LF+ ++ T EETL+ FS+ G ++ I + + GFGFV + K A+ AL
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 66 -QHKHHVILGKEVEVK 80
Q + H + G ++EV+
Sbjct: 68 KQLQGHTVDGHKLEVR 83
>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 = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 3/79 (3%)
Query: 7 RKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQ 66
R ++VG V E L +F G+V I+ + +GH +GF ++ F+ +L
Sbjct: 6 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 65
Query: 67 HKHHVILGKEVEVKKAIPK 85
+ G++++V IPK
Sbjct: 66 LDESLFRGRQIKV---IPK 81
Score = 37.4 bits (85), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 19/85 (22%), Positives = 39/85 (45%), Gaps = 3/85 (3%)
Query: 106 EINTKKIFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAAN 165
E + + I+VG + G+V ++CDK +G P+GF +I F +++
Sbjct: 2 EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 61
Query: 166 NVL---QTRFHKLKYKMVEVKRSHP 187
L ++ F + K++ + + P
Sbjct: 62 TSLALDESLFRGRQIKVIPKRTNRP 86
>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 = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 32/58 (55%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQ 66
LFV GV E EE + + F++YG ++ + R TG+ +G+ V + A+ A++
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 67
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 38.5 bits (88), Expect = 0.005, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 32/58 (55%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQ 66
LFV GV E EE + + F++YG ++ + R TG+ +G+ V + A+ A++
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 67
>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 = 38.5 bits (88), Expect = 0.005, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 32/58 (55%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQ 66
LFV GV E EE + + F++YG ++ + R TG+ +G+ V + A+ A++
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 67
>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 = 38.5 bits (88), Expect = 0.006, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 32/58 (55%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQ 66
LFV GV E EE + + F++YG ++ + R TG+ +G+ V + A+ A++
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 69
>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 = 38.1 bits (87), Expect = 0.007, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 32/58 (55%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQ 66
LFV GV E EE + + F++YG ++ + R TG+ +G+ V + A+ A++
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 83
>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 = 37.7 bits (86), Expect = 0.010, Method: Composition-based stats.
Identities = 22/60 (36%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 5 SLRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDA 64
S R L+VGG++ E +++ L F +G + + I T RGF FV F +AEDA
Sbjct: 1 SKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF---ELAEDA 57
Score = 36.2 bits (82), Expect = 0.028, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 112 IFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFD-SEDAA 164
++VGGL ++ G +TD + D ET + RGF F+ F+ +EDAA
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 58
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 37.4 bits (85), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 40/162 (24%), Positives = 58/162 (35%), Gaps = 30/162 (18%)
Query: 8 KLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQH 67
+LFVG + + EE + F +YG E I R RGFGF+ ++AE A
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIA--- 74
Query: 68 KHHVILGKEVEVKKAIPKGHKLEESNGHSGNCVGDDDTEINTKKIFVGGLPLDIXXXXXX 127
+ E+ I K L G + V L +
Sbjct: 75 --------KAELDGTILKSRPLRIRFATHGAALT------------VKNLSPVVSNELLE 114
Query: 128 XXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQ 169
G V A V+ D + GR G GF+ F ++ A L+
Sbjct: 115 QAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALE 155
>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 = 37.4 bits (85), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 32/58 (55%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQ 66
LFV GV E EE + + F++YG ++ + R TG+ +G+ V + A+ A++
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 82
>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 = 37.4 bits (85), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 24/96 (25%), Positives = 47/96 (48%), Gaps = 4/96 (4%)
Query: 92 SNGHSGNCVGDDDTEINTKKIFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPR 151
S+G SG V T + K+F+ GLP GTV D ++ ++ G+P+
Sbjct: 2 SSGSSG--VFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPK 58
Query: 152 GFGFITFDSE-DAANNVLQTRFHKLKYKMVEVKRSH 186
G ++ +++E A+ V++ +K +++V S+
Sbjct: 59 GLAYVEYENESQASQAVMKMDGMTIKENIIKVAISN 94
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 2/76 (2%)
Query: 8 KLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQH 67
KLF+ G+ +E L E +GTV++ ++ +R G +G +V + S A A+
Sbjct: 19 KLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMK 77
Query: 68 KHHVILGKEVEVKKAI 83
+ + KE +K AI
Sbjct: 78 MDGMTI-KENIIKVAI 92
>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 = 37.4 bits (85), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 41/76 (53%), Gaps = 7/76 (9%)
Query: 8 KLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDA-LQ 66
+LFVG + + EE +R+ F +YG E I + +GFGF+ ++AE A ++
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 70
Query: 67 HKHHVILGKEVEVKKA 82
+ + GK++ V+ A
Sbjct: 71 LDNMPLRGKQLRVRFA 86
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 37.4 bits (85), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 31/58 (53%), Gaps = 3/58 (5%)
Query: 7 RKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDA 64
R L+VGG++ E +++ L F +G + + I T RGF FV F +AEDA
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF---ELAEDA 118
Score = 37.0 bits (84), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 2/58 (3%)
Query: 109 TKKI-FVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFD-SEDAA 164
TK++ +VGGL ++ G +TD + D ET + RGF F+ F+ +EDAA
Sbjct: 62 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 119
>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 = 37.0 bits (84), Expect = 0.018, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 31/58 (53%), Gaps = 3/58 (5%)
Query: 7 RKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDA 64
R L+VGG++ E +++ L F +G + + I T RGF FV F +AEDA
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF---ELAEDA 62
Score = 36.6 bits (83), Expect = 0.023, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 2/58 (3%)
Query: 109 TKKI-FVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFD-SEDAA 164
TK++ +VGGL ++ G +TD + D ET + RGF F+ F+ +EDAA
Sbjct: 6 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 63
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 36.6 bits (83), Expect = 0.020, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 31/58 (53%), Gaps = 3/58 (5%)
Query: 7 RKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDA 64
R L+VGG++ E +++ L F +G + + I T RGF FV F +AEDA
Sbjct: 6 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF---ELAEDA 60
Score = 36.2 bits (82), Expect = 0.026, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 2/58 (3%)
Query: 109 TKKI-FVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFD-SEDAA 164
TK++ +VGGL ++ G +TD + D ET + RGF F+ F+ +EDAA
Sbjct: 4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 61
>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 = 36.6 bits (83), Expect = 0.021, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 32/58 (55%)
Query: 112 IFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQ 169
+FVG L +I G ++DA V+ D TG+ +G+GF++F ++ A N +Q
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 66
Score = 34.7 bits (78), Expect = 0.078, Method: Composition-based stats.
Identities = 18/59 (30%), Positives = 32/59 (54%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQH 67
+FVG +S E + F+ +G + + +++ TG +G+GFV F AE+A+Q
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 36.2 bits (82), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 39/69 (56%), Gaps = 6/69 (8%)
Query: 8 KLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHG--RGFGFVIFTKISMAE--- 62
K+ V + + N+ +RE FS +G ++ T+ + ++TG G RGFGFV F A+
Sbjct: 17 KILVRNIPFQANQREIRELFSTFGELK-TVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 75
Query: 63 DALQHKHHV 71
+AL H H+
Sbjct: 76 NALCHSTHL 84
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 36.2 bits (82), Expect = 0.026, Method: Composition-based stats.
Identities = 17/59 (28%), Positives = 35/59 (59%), Gaps = 1/59 (1%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEET-LIIRSRLTGHGRGFGFVIFTKISMAEDALQ 66
+F+G + E +E+ L + FS +G + +T I+R TG+ +G+ F+ F ++ A++
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66
Score = 31.6 bits (70), Expect = 0.60, Method: Composition-based stats.
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 1/59 (1%)
Query: 112 IFVGGLPLDIXXXXXXXXXXXXGTVTDAPVIC-DKETGRPRGFGFITFDSEDAANNVLQ 169
IF+G L +I G + P I D +TG +G+ FI F S DA++ ++
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 36.2 bits (82), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 26/48 (54%)
Query: 8 KLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIF 55
+LFV +S ++EE L + FS YG + E LT +GF FV F
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTF 57
>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 = 35.8 bits (81), Expect = 0.035, Method: Composition-based stats.
Identities = 20/69 (28%), Positives = 36/69 (52%), Gaps = 3/69 (4%)
Query: 20 EETLREYFSQYGT-VEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQHKHHV--ILGKE 76
E+ +R +G E ++R++ +G RGF FV F+ + A ++ H ILG++
Sbjct: 15 EDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQK 74
Query: 77 VEVKKAIPK 85
V + + PK
Sbjct: 75 VSMHYSDPK 83
Score = 29.6 bits (65), Expect = 2.9, Method: Composition-based stats.
Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 2/52 (3%)
Query: 144 DKETGRPRGFGFITFDSEDAANNVLQTRFHKLKY--KMVEVKRSHPKDRIDK 193
+K +G+ RGF F+ F A ++ H L + V + S PK +I++
Sbjct: 37 NKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSDPKPKINE 88
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 35.8 bits (81), Expect = 0.039, Method: Composition-based stats.
Identities = 16/55 (29%), Positives = 29/55 (52%)
Query: 11 VGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDAL 65
V +S +T E L+E F +G++ + + + TG +GF F+ F + A A+
Sbjct: 20 VTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 74
Score = 27.7 bits (60), Expect = 9.3, Method: Composition-based stats.
Identities = 25/78 (32%), Positives = 35/78 (44%), Gaps = 7/78 (8%)
Query: 92 SNGHSG-NCVGDDDTEINTKKIFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRP 150
S+G SG N DD+ I V L D G+++ + DK TG+
Sbjct: 2 SSGSSGPNRRADDNATIR-----VTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQS 56
Query: 151 RGFGFITFD-SEDAANNV 167
+GF FI+F EDAA +
Sbjct: 57 KGFAFISFHRREDAARAI 74
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 35.8 bits (81), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 41/80 (51%), Gaps = 3/80 (3%)
Query: 7 RKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQ 66
++L V + + LR+ F Q+G + + II + +GFGFV F + A+ A +
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRARE 73
Query: 67 HKH-HVILGKEVEVKKAIPK 85
H V+ G+++EV A +
Sbjct: 74 KLHGTVVEGRKIEVNNATAR 93
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 35.4 bits (80), Expect = 0.042, Method: Composition-based stats.
Identities = 23/83 (27%), Positives = 40/83 (48%), Gaps = 5/83 (6%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIF---TKISMAEDAL 65
LFV + E E+ ++E F YG ++ + R TG +G+ V + + A++AL
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 66 QHKHHVILGKEVEVKKAIPKGHK 88
I+G+ ++V KG K
Sbjct: 89 NGAE--IMGQTIQVDWCFVKGPK 109
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 35.4 bits (80), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 41/80 (51%), Gaps = 3/80 (3%)
Query: 7 RKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQ 66
++L V + + LR+ F Q+G + + II + +GFGFV F + A+ A +
Sbjct: 30 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRARE 87
Query: 67 HKH-HVILGKEVEVKKAIPK 85
H V+ G+++EV A +
Sbjct: 88 KLHGTVVEGRKIEVNNATAR 107
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 35.0 bits (79), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 6/74 (8%)
Query: 112 IFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAAN------ 165
+F+ LP + G V A V DK+T + FGF++FD+ D+A
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 166 NVLQTRFHKLKYKM 179
N Q +LK ++
Sbjct: 103 NGFQVGTKRLKVQL 116
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 35.0 bits (79), Expect = 0.067, Method: Composition-based stats.
Identities = 21/56 (37%), Positives = 29/56 (51%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDA 64
L V ++ T+ ++LR F +YG V + I R T RGF FV F A+DA
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDA 71
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 34.7 bits (78), Expect = 0.079, Method: Composition-based stats.
Identities = 25/68 (36%), Positives = 35/68 (51%), Gaps = 5/68 (7%)
Query: 9 LFVGGVSRETNEETLREYFSQYG-TVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQH 67
L++G + +E + F+ G TV IIR+RLTG G+ FV F ++ AE L
Sbjct: 12 LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCL-- 69
Query: 68 KHHVILGK 75
H I GK
Sbjct: 70 --HKINGK 75
>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 = 34.7 bits (78), Expect = 0.082, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 8/77 (10%)
Query: 109 TKKIFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITF-DSEDAANNV 167
++ +++G +P D G V + ++ D +TGR +G+ FI F D E +A+ V
Sbjct: 4 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 63
Query: 168 -------LQTRFHKLKY 177
L +RF K Y
Sbjct: 64 RNLNGYQLGSRFLKCGY 80
Score = 28.1 bits (61), Expect = 8.4, Method: Composition-based stats.
Identities = 15/68 (22%), Positives = 33/68 (48%)
Query: 7 RKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQ 66
R +++G + + EE + + S G V ++ TG +G+ F+ F + + A++
Sbjct: 5 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 64
Query: 67 HKHHVILG 74
+ + LG
Sbjct: 65 NLNGYQLG 72
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 34.7 bits (78), Expect = 0.082, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 8/77 (10%)
Query: 109 TKKIFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITF-DSEDAANNV 167
++ +++G +P D G V + ++ D +TGR +G+ FI F D E +A+ V
Sbjct: 2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61
Query: 168 -------LQTRFHKLKY 177
L +RF K Y
Sbjct: 62 RNLNGYQLGSRFLKCGY 78
Score = 28.1 bits (61), Expect = 8.3, Method: Composition-based stats.
Identities = 15/68 (22%), Positives = 33/68 (48%)
Query: 7 RKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQ 66
R +++G + + EE + + S G V ++ TG +G+ F+ F + + A++
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 67 HKHHVILG 74
+ + LG
Sbjct: 63 NLNGYQLG 70
>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 = 34.3 bits (77), Expect = 0.094, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 8/77 (10%)
Query: 109 TKKIFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITF-DSEDAANNV 167
++ +++G +P D G V + ++ D +TGR +G+ FI F D E +A+ V
Sbjct: 3 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 62
Query: 168 -------LQTRFHKLKY 177
L +RF K Y
Sbjct: 63 RNLNGYQLGSRFLKCGY 79
Score = 27.7 bits (60), Expect = 9.0, Method: Composition-based stats.
Identities = 15/68 (22%), Positives = 33/68 (48%)
Query: 7 RKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQ 66
R +++G + + EE + + S G V ++ TG +G+ F+ F + + A++
Sbjct: 4 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 63
Query: 67 HKHHVILG 74
+ + LG
Sbjct: 64 NLNGYQLG 71
>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 = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 40/83 (48%), Gaps = 5/83 (6%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIF---TKISMAEDAL 65
LFV + E E+ ++E F YG ++ + R TG +G+ V + + A++AL
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 66 QHKHHVILGKEVEVKKAIPKGHK 88
I+G+ ++V KG K
Sbjct: 135 NGAE--IMGQTIQVDWCFVKGPK 155
>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 = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 26/97 (26%), Positives = 49/97 (50%), Gaps = 3/97 (3%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQHK 68
L+VG +S T EE + E FS+ G +++ ++ ++ GF FV + + AE+A+++
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 69 HHVILGKEVEVKKAIPKGHK--LEESNGHSGNCVGDD 103
+ L + ++ G K + G SG V D+
Sbjct: 102 NGTRLDDRI-IRTDWDAGFKEGRQYGRGRSGGQVRDE 137
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 33.9 bits (76), Expect = 0.13, Method: Composition-based stats.
Identities = 20/81 (24%), Positives = 40/81 (49%), Gaps = 1/81 (1%)
Query: 5 SLRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDA 64
S L V + + ++ + F G +E ++R ++TG G+GFV ++ + A+ A
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 65 LQHKHHVIL-GKEVEVKKAIP 84
+ + + L K ++V A P
Sbjct: 63 INTLNGLKLQTKTIKVSYARP 83
Score = 30.4 bits (67), Expect = 1.4, Method: Composition-based stats.
Identities = 18/77 (23%), Positives = 35/77 (45%), Gaps = 1/77 (1%)
Query: 112 IFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQT- 170
+ V LP ++ G + ++ DK TG+ G+GF+ + + A+ + T
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 171 RFHKLKYKMVEVKRSHP 187
KL+ K ++V + P
Sbjct: 67 NGLKLQTKTIKVSYARP 83
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 33.9 bits (76), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 31/94 (32%), Positives = 50/94 (53%), Gaps = 6/94 (6%)
Query: 9 LFVGGVSRETNEETLREYFSQ-YGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQH 67
LFVG ++ + ++ L E+F + Y + ++ + TG +G+GFV FT + AL
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTE 70
Query: 68 -KHHVILG-KEVEVKKAIPKGHKLE--ESNGHSG 97
+ V LG K V + AIPK +++ ES SG
Sbjct: 71 CQGAVGLGSKPVRLSVAIPKASRVKPVESGPSSG 104
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 33.1 bits (74), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 33/65 (50%), Gaps = 2/65 (3%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQHK 68
L+V + ++E LR+ FS +GT+ ++ G +GFGFV F+ A A+
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 69 HHVIL 73
+ I+
Sbjct: 76 NGRIV 80
Score = 33.1 bits (74), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 33/75 (44%), Gaps = 3/75 (4%)
Query: 94 GHSGNCVGDDDTEINTKKIFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGF 153
G SG+ GD T ++V L I GT+T A V+ E GR +GF
Sbjct: 1 GSSGSS-GDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMM--EGGRSKGF 57
Query: 154 GFITFDSEDAANNVL 168
GF+ F S + A +
Sbjct: 58 GFVCFSSPEEATKAV 72
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 32.7 bits (73), Expect = 0.28, Method: Composition-based stats.
Identities = 15/55 (27%), Positives = 25/55 (45%)
Query: 112 IFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANN 166
++V LP + G V ++ DK+T + +G FI F +D+A N
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQN 73
Score = 28.9 bits (63), Expect = 4.0, Method: Composition-based stats.
Identities = 19/69 (27%), Positives = 36/69 (52%), Gaps = 6/69 (8%)
Query: 18 TNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAED---ALQHKHHVILG 74
TN + R FS+YG V + I++ + T +G F++F A++ A+ +K + G
Sbjct: 29 TNNDLYR-IFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQ--LFG 85
Query: 75 KEVEVKKAI 83
+ ++ AI
Sbjct: 86 RVIKASIAI 94
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 32.7 bits (73), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 35/170 (20%), Positives = 63/170 (37%), Gaps = 22/170 (12%)
Query: 2 EPVSLRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMA 61
EP + LFVG ++ + L+ S + ++ R+ G R FG+V F
Sbjct: 3 EPTTAFNLFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRI-GMTRKFGYVDFESAEDL 61
Query: 62 EDALQHKHHVILGKEVEVKKAIPKGHKLEESNGHSGNCVGDDDTEINTKKIFVGGLPLDI 121
E AL+ + G E++++K PKG D E + + + LP +
Sbjct: 62 EKALELTGLKVFGNEIKLEK--PKGK--------------DSKKERDARTLLAKNLPYKV 105
Query: 122 XXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQTR 171
A + + G+ +G +I F +E A + +
Sbjct: 106 TQDELKEVFEDA-----AEIRLVSKDGKSKGIAYIEFKTEADAEKTFEEK 150
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 32.3 bits (72), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 3/79 (3%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQHK 68
LF+G ++ + L+ S+ + ++ R TG R FG+V F E AL+
Sbjct: 20 LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAEDLEKALELT 78
Query: 69 HHVILGKEVEVKKAIPKGH 87
+ G E++++K PKG
Sbjct: 79 GLKVFGNEIKLEK--PKGR 95
>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 = 32.0 bits (71), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 37/163 (22%), Positives = 66/163 (40%), Gaps = 29/163 (17%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQHK 68
LF+G ++ + L+ S+ + ++ R TG R FG+V F E AL+
Sbjct: 16 LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAEDLEKALELT 74
Query: 69 HHVILGKEVEVKKAIPKGH---KLEESNGHSGNCVGDDDTEINTKKIFVGGLPLDIXXXX 125
+ G E++++K PKG K+ + + + TE K++F L + +
Sbjct: 75 GLKVFGNEIKLEK--PKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-- 130
Query: 126 XXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSE-DAANNV 167
+ G+ +G +I F SE DA N+
Sbjct: 131 --------------------QDGKSKGIAYIEFKSEADAEKNL 153
>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 = 31.6 bits (70), Expect = 0.67, Method: Composition-based stats.
Identities = 18/59 (30%), Positives = 35/59 (59%), Gaps = 1/59 (1%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQH 67
L+VG +S T EE + E FS+ G +++ ++ ++ GF FV + + AE+A+++
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKT-ACGFCFVEYYSRADAENAMRY 78
>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 = 31.6 bits (70), Expect = 0.71, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 3/77 (3%)
Query: 112 IFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQTR 171
+F+ LP + G V A V DK+T + FGF+++D+ +A +Q+
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 172 --FH-KLKYKMVEVKRS 185
F +K V++KRS
Sbjct: 88 NGFQIGMKRLKVQLKRS 104
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 31.6 bits (70), Expect = 0.75, Method: Composition-based stats.
Identities = 13/35 (37%), Positives = 19/35 (54%)
Query: 134 GTVTDAPVICDKETGRPRGFGFITFDSEDAANNVL 168
G + I DK T + +G+GF+ FDS AA +
Sbjct: 30 GKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 64
Score = 30.8 bits (68), Expect = 1.1, Method: Composition-based stats.
Identities = 17/57 (29%), Positives = 29/57 (50%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDAL 65
L++ G+ T ++ L + YG + T I + T +G+GFV F S A+ A+
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 64
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 31.2 bits (69), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 16/69 (23%), Positives = 31/69 (44%), Gaps = 4/69 (5%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQHK 68
L V + ++ E +G++E ++ S TG +G+GF + M +D+
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEY----MKKDSAARA 153
Query: 69 HHVILGKEV 77
+LGK +
Sbjct: 154 KSDLLGKPL 162
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 31.2 bits (69), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 16/69 (23%), Positives = 31/69 (44%), Gaps = 4/69 (5%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQHK 68
L V + ++ E +G++E ++ S TG +G+GF + M +D+
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEY----MKKDSAARA 153
Query: 69 HHVILGKEV 77
+LGK +
Sbjct: 154 KSDLLGKPL 162
>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 = 31.2 bits (69), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 16/69 (23%), Positives = 31/69 (44%), Gaps = 4/69 (5%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQHK 68
L V + ++ E +G++E ++ S TG +G+GF + M +D+
Sbjct: 96 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEY----MKKDSAARA 151
Query: 69 HHVILGKEV 77
+LGK +
Sbjct: 152 KSDLLGKPL 160
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 28/58 (48%), Gaps = 2/58 (3%)
Query: 112 IFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQ 169
IF+ L I G + V+CD E G +G+GF+ F++++AA ++
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENG-SKGYGFVHFETQEAAERAIE 69
Score = 27.7 bits (60), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 36/74 (48%), Gaps = 7/74 (9%)
Query: 5 SLRK-----LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKIS 59
SLRK +F+ + + + + L + FS +G + ++ +G+GFV F
Sbjct: 5 SLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQE 62
Query: 60 MAEDALQHKHHVIL 73
AE A++ + ++L
Sbjct: 63 AAERAIEKMNGMLL 76
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 30.8 bits (68), Expect = 1.3, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 28/61 (45%), Gaps = 2/61 (3%)
Query: 110 KKIFVGGLPLDIXXXXXXXXXXXXGT-VTDAPVICD-KETGRPRGFGFITFDSEDAANNV 167
+K+FVGGLP DI G V D P + K P+G+ F+ F E + +
Sbjct: 9 RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQAL 68
Query: 168 L 168
+
Sbjct: 69 I 69
>pdb|2E5G|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 21
Length = 94
Score = 30.8 bits (68), Expect = 1.3, Method: Composition-based stats.
Identities = 19/75 (25%), Positives = 30/75 (40%), Gaps = 5/75 (6%)
Query: 6 LRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDAL 65
LR +FV G R + L EYF +G V ++ + + F V + E L
Sbjct: 8 LRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGV-----FAIVEMGDVGAREAVL 62
Query: 66 QHKHHVILGKEVEVK 80
H + G + V+
Sbjct: 63 SQSQHSLGGHRLRVR 77
>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 = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 28/58 (48%), Gaps = 2/58 (3%)
Query: 112 IFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVLQ 169
IF+ L I G + V+CD E G +G+GF+ F++++AA ++
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENG-SKGYGFVHFETQEAAERAIE 63
Score = 27.7 bits (60), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 15/71 (21%), Positives = 34/71 (47%), Gaps = 2/71 (2%)
Query: 3 PVSLRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAE 62
P+ +F+ + + + + L + FS +G + ++ +G+GFV F AE
Sbjct: 2 PLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAE 59
Query: 63 DALQHKHHVIL 73
A++ + ++L
Sbjct: 60 RAIEKMNGMLL 70
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 30.4 bits (67), Expect = 1.7, Method: Composition-based stats.
Identities = 20/83 (24%), Positives = 39/83 (46%), Gaps = 1/83 (1%)
Query: 9 LFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQHK 68
L V + ++ + L F G + I+R TG+ G+ FV FT ++ A++
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 69 HHV-ILGKEVEVKKAIPKGHKLE 90
+ + + K ++V A P G ++
Sbjct: 66 NGITVRNKRLKVSYARPGGESIK 88
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 28/90 (31%), Positives = 40/90 (44%), Gaps = 4/90 (4%)
Query: 7 RKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTK-ISMAEDAL 65
R L+VG +SR+ E + + FSQ G + +I + + FV F + A
Sbjct: 16 RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSND--PYCFVEFYEHRDAAAALA 73
Query: 66 QHKHHVILGKEVEVKKA-IPKGHKLEESNG 94
ILGKEV+V A P K S+G
Sbjct: 74 AMNGRKILGKEVKVNWATTPSSQKSGPSSG 103
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor
9g8
Length = 101
Score = 29.6 bits (65), Expect = 2.3, Method: Composition-based stats.
Identities = 24/74 (32%), Positives = 33/74 (44%), Gaps = 6/74 (8%)
Query: 8 KLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQH 67
K++VG + + L FS YG + I R+ GF FV F AEDA++
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRG 56
Query: 68 -KHHVILGKEVEVK 80
VI G V V+
Sbjct: 57 LDGKVICGSRVRVE 70
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
28
Length = 111
Score = 29.6 bits (65), Expect = 2.5, Method: Composition-based stats.
Identities = 15/59 (25%), Positives = 28/59 (47%)
Query: 7 RKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDAL 65
+ +F+ +S ++ EE L E Q+G ++ ++ T H +G F F A+ L
Sbjct: 16 KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCL 74
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 29.3 bits (64), Expect = 3.1, Method: Composition-based stats.
Identities = 19/81 (23%), Positives = 37/81 (45%), Gaps = 8/81 (9%)
Query: 2 EPVSLRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMA 61
E ++ L+VGG+ E LR +F Q+G + +++ + F+ F A
Sbjct: 8 EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQC------AFIQFATRQAA 61
Query: 62 EDALQHKHH--VILGKEVEVK 80
E A + + ++ G+ + VK
Sbjct: 62 EVAAEKSFNKLIVNGRRLNVK 82
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 28.9 bits (63), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 14/59 (23%), Positives = 25/59 (42%), Gaps = 1/59 (1%)
Query: 110 KKIFVGGLPLDIXXXXXXXXXXXXGTVTDAPVICDKETGRPRGFGFITFDSEDAANNVL 168
+ +FVG L + G +T IC G+P+ FGF+ F ++ + +
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKV-TICKDREGKPKSFGFVCFKHPESVSYAI 74
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 28.5 bits (62), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 26/60 (43%), Gaps = 5/60 (8%)
Query: 8 KLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQH 67
K++VG + N+ L F YG + + R + GF FV F A DA++
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVAR-----NPPGFAFVEFEDPRDAADAVRE 129
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 28.1 bits (61), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 26/59 (44%), Gaps = 5/59 (8%)
Query: 8 KLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDALQ 66
K++VG + N+ L F YG + + R + GF FV F A DA++
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVAR-----NPPGFAFVEFEDPRDAADAVR 128
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 28.1 bits (61), Expect = 6.9, Method: Composition-based stats.
Identities = 22/87 (25%), Positives = 41/87 (47%), Gaps = 9/87 (10%)
Query: 6 LRKLFVGGVSRETNEETLREYFSQYGTVEETLIIRSRLTGHGRGFGFVIFTKISMAEDAL 65
++ LFV ++ EE L + FSQ+G +E ++ + F+ F + A A+
Sbjct: 11 VKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAM 62
Query: 66 QHKHHVIL-GKEVEVKKAIPKGHKLEE 91
+ + L G+ +E+ A P K +E
Sbjct: 63 EEMNGKDLEGENIEIVFAKPPDQKRKE 89
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 28.1 bits (61), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 27/106 (25%), Positives = 44/106 (41%), Gaps = 13/106 (12%)
Query: 94 GHSGNCVGDDDTEINTKKIFVGGLPLDIXXXXXXXXXXXXGTV-----TDAPVI---CDK 145
G SG+ GD D + + I+V GL + G V T P+I DK
Sbjct: 1 GSSGSS-GDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDK 59
Query: 146 ETGRPRGFGFITFDSEDAANNVLQ----TRFHKLKYKMVEVKRSHP 187
ETG+P+G ++++ A ++ F K K+ ++ P
Sbjct: 60 ETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPP 105
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
0.317 0.135 0.401
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,742,954
Number of Sequences: 62578
Number of extensions: 374083
Number of successful extensions: 1094
Number of sequences better than 100.0: 146
Number of HSP's better than 100.0 without gapping: 112
Number of HSP's successfully gapped in prelim test: 34
Number of HSP's that attempted gapping in prelim test: 842
Number of HSP's gapped (non-prelim): 250
length of query: 347
length of database: 14,973,337
effective HSP length: 100
effective length of query: 247
effective length of database: 8,715,537
effective search space: 2152737639
effective search space used: 2152737639
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)