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= psy16454
(304 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 217 bits (553), Expect = 6e-57, Method: Compositional matrix adjust.
Identities = 98/180 (54%), Positives = 134/180 (74%)
Query: 3 KEPEHLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHM 62
KEPE LRKLFIGGL + T+ E+L+SHFE WG + D VVM+DP TK+SRGFGF+TY++
Sbjct: 8 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 67
Query: 63 VDDAQAARPHTIDSKVVEPKRAVPRTEINRPEAGATVKKLFVGSLRDDITEEDLKEYFGQ 122
VD A ARPH +D +VVEPKRAV R + RP A TVKK+FVG +++D E L++YF Q
Sbjct: 68 VDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQ 127
Query: 123 FGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKGTHLVKGKKVDVKKALSKEEMA 182
+G++ + ++T++ +GKKRGF FV ++D+D VDK ++ H V G +V+KALSK+EMA
Sbjct: 128 YGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMA 187
Score = 64.7 bits (156), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 32/91 (35%), Positives = 54/91 (59%)
Query: 93 PEAGATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYD 152
P+ ++KLF+G L + T+E L+ +F Q+G +T ++ + T + RGFGFV Y +
Sbjct: 7 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 66
Query: 153 PVDKACLKGTHLVKGKKVDVKKALSKEEMAK 183
VD A H V G+ V+ K+A+S+E+ +
Sbjct: 67 EVDAAMNARPHKVDGRVVEPKRAVSREDSQR 97
>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 = 217 bits (553), Expect = 6e-57, Method: Compositional matrix adjust.
Identities = 98/180 (54%), Positives = 134/180 (74%)
Query: 3 KEPEHLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHM 62
KEPE LRKLFIGGL + T+ E+L+SHFE WG + D VVM+DP TK+SRGFGF+TY++
Sbjct: 7 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 66
Query: 63 VDDAQAARPHTIDSKVVEPKRAVPRTEINRPEAGATVKKLFVGSLRDDITEEDLKEYFGQ 122
VD A ARPH +D +VVEPKRAV R + RP A TVKK+FVG +++D E L++YF Q
Sbjct: 67 VDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQ 126
Query: 123 FGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKGTHLVKGKKVDVKKALSKEEMA 182
+G++ + ++T++ +GKKRGF FV ++D+D VDK ++ H V G +V+KALSK+EMA
Sbjct: 127 YGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMA 186
Score = 64.3 bits (155), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 32/91 (35%), Positives = 54/91 (59%)
Query: 93 PEAGATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYD 152
P+ ++KLF+G L + T+E L+ +F Q+G +T ++ + T + RGFGFV Y +
Sbjct: 6 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 65
Query: 153 PVDKACLKGTHLVKGKKVDVKKALSKEEMAK 183
VD A H V G+ V+ K+A+S+E+ +
Sbjct: 66 EVDAAMNARPHKVDGRVVEPKRAVSREDSQR 96
>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 = 217 bits (552), Expect = 8e-57, Method: Compositional matrix adjust.
Identities = 98/180 (54%), Positives = 134/180 (74%)
Query: 3 KEPEHLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHM 62
KEPE LRKLFIGGL + T+ E+L+SHFE WG + D VVM+DP TK+SRGFGF+TY++
Sbjct: 1 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60
Query: 63 VDDAQAARPHTIDSKVVEPKRAVPRTEINRPEAGATVKKLFVGSLRDDITEEDLKEYFGQ 122
VD A ARPH +D +VVEPKRAV R + RP A TVKK+FVG +++D E L++YF Q
Sbjct: 61 VDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQ 120
Query: 123 FGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKGTHLVKGKKVDVKKALSKEEMA 182
+G++ + ++T++ +GKKRGF FV ++D+D VDK ++ H V G +V+KALSK+EMA
Sbjct: 121 YGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMA 180
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 216 bits (551), Expect = 9e-57, Method: Compositional matrix adjust.
Identities = 98/180 (54%), Positives = 134/180 (74%)
Query: 3 KEPEHLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHM 62
KEPE LRKLFIGGL + T+ E+L+SHFE WG + D VVM+DP TK+SRGFGF+TY++
Sbjct: 9 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 68
Query: 63 VDDAQAARPHTIDSKVVEPKRAVPRTEINRPEAGATVKKLFVGSLRDDITEEDLKEYFGQ 122
VD A ARPH +D +VVEPKRAV R + RP A TVKK+FVG +++D E L++YF Q
Sbjct: 69 VDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQ 128
Query: 123 FGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKGTHLVKGKKVDVKKALSKEEMA 182
+G++ + ++T++ +GKKRGF FV ++D+D VDK ++ H V G +V+KALSK+EMA
Sbjct: 129 YGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMA 188
Score = 64.3 bits (155), Expect = 9e-11, Method: Compositional matrix adjust.
Identities = 32/91 (35%), Positives = 54/91 (59%)
Query: 93 PEAGATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYD 152
P+ ++KLF+G L + T+E L+ +F Q+G +T ++ + T + RGFGFV Y +
Sbjct: 8 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 67
Query: 153 PVDKACLKGTHLVKGKKVDVKKALSKEEMAK 183
VD A H V G+ V+ K+A+S+E+ +
Sbjct: 68 EVDAAMNARPHKVDGRVVEPKRAVSREDSQR 98
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 211 bits (536), Expect = 6e-55, Method: Compositional matrix adjust.
Identities = 95/177 (53%), Positives = 131/177 (74%)
Query: 3 KEPEHLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHM 62
KEPE LRKLFIGGL + T+ E+L+SHFE WG + D VVM+DP TK+SRGFGF+TY++
Sbjct: 8 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 67
Query: 63 VDDAQAARPHTIDSKVVEPKRAVPRTEINRPEAGATVKKLFVGSLRDDITEEDLKEYFGQ 122
VD A ARPH +D +VVEPKRAV R + RP A TVKK+FVG +++D E L++YF Q
Sbjct: 68 VDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQ 127
Query: 123 FGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKGTHLVKGKKVDVKKALSKE 179
+G++ + ++T++ +GKKRGF FV ++D+D VDK ++ H V G +V+KALSK+
Sbjct: 128 YGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQ 184
Score = 64.3 bits (155), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 32/91 (35%), Positives = 54/91 (59%)
Query: 93 PEAGATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYD 152
P+ ++KLF+G L + T+E L+ +F Q+G +T ++ + T + RGFGFV Y +
Sbjct: 7 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 66
Query: 153 PVDKACLKGTHLVKGKKVDVKKALSKEEMAK 183
VD A H V G+ V+ K+A+S+E+ +
Sbjct: 67 EVDAAMNARPHKVDGRVVEPKRAVSREDSQR 97
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 210 bits (535), Expect = 7e-55, Method: Compositional matrix adjust.
Identities = 95/177 (53%), Positives = 131/177 (74%)
Query: 3 KEPEHLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHM 62
KEPE LRKLFIGGL + T+ E+L+SHFE WG + D VVM+DP TK+SRGFGF+TY++
Sbjct: 6 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 65
Query: 63 VDDAQAARPHTIDSKVVEPKRAVPRTEINRPEAGATVKKLFVGSLRDDITEEDLKEYFGQ 122
VD A ARPH +D +VVEPKRAV R + RP A TVKK+FVG +++D E L++YF Q
Sbjct: 66 VDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQ 125
Query: 123 FGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKGTHLVKGKKVDVKKALSKE 179
+G++ + ++T++ +GKKRGF FV ++D+D VDK ++ H V G +V+KALSK+
Sbjct: 126 YGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQ 182
Score = 64.3 bits (155), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 32/91 (35%), Positives = 54/91 (59%)
Query: 93 PEAGATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYD 152
P+ ++KLF+G L + T+E L+ +F Q+G +T ++ + T + RGFGFV Y +
Sbjct: 5 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 64
Query: 153 PVDKACLKGTHLVKGKKVDVKKALSKEEMAK 183
VD A H V G+ V+ K+A+S+E+ +
Sbjct: 65 EVDAAMNARPHKVDGRVVEPKRAVSREDSQR 95
>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 = 135 bits (341), Expect = 2e-32, Method: Compositional matrix adjust.
Identities = 64/166 (38%), Positives = 106/166 (63%), Gaps = 7/166 (4%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
K+FIGGL++ T+ + L+ +F +G V D+ +MKDP T +SRGFGF+++ VD+
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 70 RPHTIDSKVVEPKRAVPRTEINRPEAGATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSV 129
+ H +D KV++PKRA+PR E ++ K+FVG + D+ ++ +E+F Q+G +
Sbjct: 65 Q-HILDGKVIDPKRAIPRDEQDK------TGKIFVGGIGPDVRPKEFEEFFSQWGTIIDA 117
Query: 130 ALVTEKETGKKRGFGFVEYNDYDPVDKACLKGTHLVKGKKVDVKKA 175
L+ +K+TG+ RGFGFV Y+ D VD+ C K +K+++K+A
Sbjct: 118 QLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRA 163
Score = 71.2 bits (173), Expect = 7e-13, Method: Compositional matrix adjust.
Identities = 33/83 (39%), Positives = 56/83 (67%), Gaps = 1/83 (1%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
K+F+G L D TE++L+EYFG++G VT + ++ + TG+ RGFGF+ + VD+ +K
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV-VK 63
Query: 161 GTHLVKGKKVDVKKALSKEEMAK 183
H++ GK +D K+A+ ++E K
Sbjct: 64 TQHILDGKVIDPKRAIPRDEQDK 86
Score = 60.1 bits (144), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 30/84 (35%), Positives = 44/84 (52%)
Query: 4 EPEHLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMV 63
E + K+F+GG+ + + F WG ++D +M D T +SRGFGF+TY SA V
Sbjct: 83 EQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAV 142
Query: 64 DDAQAARPHTIDSKVVEPKRAVPR 87
D + + +E KRA PR
Sbjct: 143 DRVCQNKFIDFKDRKIEIKRAEPR 166
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 120 bits (301), Expect = 1e-27, Method: Compositional matrix adjust.
Identities = 52/87 (59%), Positives = 68/87 (78%)
Query: 3 KEPEHLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHM 62
+E E RKLFIGGL + T+ E+L++++E WG + D VVM+DP +K+SRGFGF+T+SS
Sbjct: 22 REKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAE 81
Query: 63 VDDAQAARPHTIDSKVVEPKRAVPRTE 89
VD A AARPH+ID +VVEPKRAV R E
Sbjct: 82 VDAAMAARPHSIDGRVVEPKRAVAREE 108
Score = 64.3 bits (155), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 29/81 (35%), Positives = 51/81 (62%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACL 159
+KLF+G L + TEE L+ Y+ Q+G++T ++ + + + RGFGFV ++ VD A
Sbjct: 28 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA 87
Query: 160 KGTHLVKGKKVDVKKALSKEE 180
H + G+ V+ K+A+++EE
Sbjct: 88 ARPHSIDGRVVEPKRAVAREE 108
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 94.7 bits (234), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 41/92 (44%), Positives = 63/92 (68%), Gaps = 1/92 (1%)
Query: 6 EHLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDD 65
+ + KLF+GGLD+ T+ ETL+S+F +G+VVD V+MKD T +SRGFGF+ + + V
Sbjct: 14 DEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGT 73
Query: 66 AQAARPHTIDSKVVEPKRAVPR-TEINRPEAG 96
A+RPHT+D + ++PK PR + + P +G
Sbjct: 74 VLASRPHTLDGRNIDPKPCTPRGMQPSGPSSG 105
Score = 63.2 bits (152), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 29/80 (36%), Positives = 44/80 (55%)
Query: 99 VKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC 158
+ KLFVG L T+E L+ YF Q+GEV ++ +K T + RGFGFV++ D + V
Sbjct: 16 IGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVL 75
Query: 159 LKGTHLVKGKKVDVKKALSK 178
H + G+ +D K +
Sbjct: 76 ASRPHTLDGRNIDPKPCTPR 95
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 83.6 bits (205), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 37/78 (47%), Positives = 54/78 (69%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
K+FIGGL ++T+ E L+ +F +G+V + +VM+DP TK+SRGFGF+T+ VD A
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 86
Query: 70 RPHTIDSKVVEPKRAVPR 87
H +DSK ++PK A PR
Sbjct: 87 SRHELDSKTIDPKVAFPR 104
Score = 67.0 bits (162), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 37/99 (37%), Positives = 52/99 (52%), Gaps = 4/99 (4%)
Query: 85 VPRTEINRPEAGATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFG 144
VPR G++ K+F+G L T+E L+EYFGQFGEV ++ + T + RGFG
Sbjct: 15 VPRGS----HMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFG 70
Query: 145 FVEYNDYDPVDKACLKGTHLVKGKKVDVKKALSKEEMAK 183
FV + D VDK + H + K +D K A + K
Sbjct: 71 FVTFMDQAGVDKVLAQSRHELDSKTIDPKVAFPRRAQPK 109
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 79.0 bits (193), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 35/75 (46%), Positives = 52/75 (69%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
K+FIGGL ++T+ E L+ +F +G+V + +VM+DP TK+SRGFGF+T+ VD A
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 70 RPHTIDSKVVEPKRA 84
H +DSK ++PK A
Sbjct: 62 SRHELDSKTIDPKVA 76
Score = 63.5 bits (153), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 32/76 (42%), Positives = 44/76 (57%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
K+F+G L T+E L+EYFGQFGEV ++ + T + RGFGFV + D VDK +
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 161 GTHLVKGKKVDVKKAL 176
H + K +D K A
Sbjct: 62 SRHELDSKTIDPKVAF 77
>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 = 75.1 bits (183), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 34/83 (40%), Positives = 51/83 (61%)
Query: 2 TKEPEHLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAH 61
+K E K F+GGL + TS + LK +F +G+VVD + DP T +SRGFGFI + A
Sbjct: 5 SKNEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAA 64
Query: 62 MVDDAQAARPHTIDSKVVEPKRA 84
V+ + H +D +V++PK+A
Sbjct: 65 SVEKVLDQKEHRLDGRVIDPKKA 87
Score = 62.4 bits (150), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 33/86 (38%), Positives = 49/86 (56%)
Query: 90 INRPEAGATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYN 149
IN + K FVG L D +++DLK+YF +FGEV + + TG+ RGFGF+ +
Sbjct: 2 INASKNEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFK 61
Query: 150 DYDPVDKACLKGTHLVKGKKVDVKKA 175
D V+K + H + G+ +D KKA
Sbjct: 62 DAASVEKVLDQKEHRLDGRVIDPKKA 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 = 72.0 bits (175), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 31/74 (41%), Positives = 48/74 (64%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAAR 70
+FIGGL + T+ + LK +F +G+VVD + DP T +SRGFGF+ + + VD +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 71 PHTIDSKVVEPKRA 84
H ++ KV++PKRA
Sbjct: 62 EHKLNGKVIDPKRA 75
Score = 64.7 bits (156), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 32/74 (43%), Positives = 47/74 (63%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKG 161
+F+G L D T++DLK+YF +FGEV L + TG+ RGFGFV + + + VDK +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 162 THLVKGKKVDVKKA 175
H + GK +D K+A
Sbjct: 62 EHKLNGKVIDPKRA 75
>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 = 70.9 bits (172), Expect = 9e-13, Method: Compositional matrix adjust.
Identities = 36/79 (45%), Positives = 50/79 (63%)
Query: 99 VKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC 158
VKK+FVG L D EE ++EYFG FGEV S+ L + +T K+RGF F+ + + +PV K
Sbjct: 1 VKKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 60
Query: 159 LKGTHLVKGKKVDVKKALS 177
K H V K ++K A+S
Sbjct: 61 EKKYHNVGLSKCEIKVAMS 79
Score = 47.8 bits (112), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 40/78 (51%)
Query: 8 LRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQ 67
++K+F+GGL T E ++ +F +G+V + + D +T K RGF FIT+ V
Sbjct: 1 VKKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 60
Query: 68 AARPHTIDSKVVEPKRAV 85
+ H + E K A+
Sbjct: 61 EKKYHNVGLSKCEIKVAM 78
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 66.2 bits (160), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 32/76 (42%), Positives = 48/76 (63%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACL 159
K+FVG + + E +L+EYF +FG VT V ++ + E + RGFGF+ + D VD+A
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN 70
Query: 160 KGTHLVKGKKVDVKKA 175
H + GKKV+VK+A
Sbjct: 71 MHFHDIMGKKVEVKRA 86
Score = 63.2 bits (152), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 31/78 (39%), Positives = 46/78 (58%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
K+F+GG+ + L+ +F+ +G V +VV++ D + ++ RGFGFIT+ VD A
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
Query: 70 RPHTIDSKVVEPKRAVPR 87
H I K VE KRA PR
Sbjct: 72 HFHDIMGKKVEVKRAEPR 89
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 65.9 bits (159), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 30/74 (40%), Positives = 47/74 (63%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAAR 70
+F+GGL T+ E +K +FE +G V D ++M D T + RGFGF+T+ S +V+
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 71 PHTIDSKVVEPKRA 84
H I++K+VE K+A
Sbjct: 62 FHEINNKMVECKKA 75
Score = 64.3 bits (155), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 33/74 (44%), Positives = 44/74 (59%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKG 161
+FVG L + T ED+K YF QFG+V L+ +K T + RGFGFV + D V+K C
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 162 THLVKGKKVDVKKA 175
H + K V+ KKA
Sbjct: 62 FHEINNKMVECKKA 75
>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 = 64.7 bits (156), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 45/177 (25%), Positives = 84/177 (47%), Gaps = 15/177 (8%)
Query: 8 LRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY----SSAHMV 63
+ ++++G + Y +T++ F +G + + + D T K +GF F+ Y ++ +
Sbjct: 28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLAL 87
Query: 64 DDAQAARPHTIDSKVVEPK---RAVPRTEINRPEAGATVKKLFVGSLRDDITEEDLKEYF 120
+ + + KV P +A P + EA A +++V S+ D++++D+K F
Sbjct: 88 EQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARA-FNRIYVASVHQDLSDDDIKSVF 146
Query: 121 GQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC-------LKGTHLVKGKKV 170
FG++ S L + TGK +G+GF+EY A L G +L GK V
Sbjct: 147 EAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAV 203
Score = 44.7 bits (104), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 35/66 (53%)
Query: 1 ITKEPEHLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSA 60
+ +E ++++ + S + +KS FEA+G + + +DP T K +G+GFI Y A
Sbjct: 118 LAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKA 177
Query: 61 HMVDDA 66
DA
Sbjct: 178 QSSQDA 183
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/92 (25%), Positives = 48/92 (52%), Gaps = 7/92 (7%)
Query: 91 NRPEAGATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYN- 149
R A A + +++VGS+ ++ E+ +++ F FG + S+ + + T K +GF FVEY
Sbjct: 20 QRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEV 79
Query: 150 ------DYDPVDKACLKGTHLVKGKKVDVKKA 175
+ ++ L G ++ G+ ++ +A
Sbjct: 80 PEAAQLALEQMNSVMLGGRNIKVGRPSNIGQA 111
>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 = 64.7 bits (156), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 45/177 (25%), Positives = 84/177 (47%), Gaps = 15/177 (8%)
Query: 8 LRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY----SSAHMV 63
+ ++++G + Y +T++ F +G + + + D T K +GF F+ Y ++ +
Sbjct: 13 MCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLAL 72
Query: 64 DDAQAARPHTIDSKVVEPK---RAVPRTEINRPEAGATVKKLFVGSLRDDITEEDLKEYF 120
+ + + KV P +A P + EA A +++V S+ D++++D+K F
Sbjct: 73 EQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARA-FNRIYVASVHQDLSDDDIKSVF 131
Query: 121 GQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC-------LKGTHLVKGKKV 170
FG++ S L + TGK +G+GF+EY A L G +L GK V
Sbjct: 132 EAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAV 188
Score = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 35/66 (53%)
Query: 1 ITKEPEHLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSA 60
+ +E ++++ + S + +KS FEA+G + + +DP T K +G+GFI Y A
Sbjct: 103 LAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKA 162
Query: 61 HMVDDA 66
DA
Sbjct: 163 QSSQDA 168
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/92 (25%), Positives = 48/92 (52%), Gaps = 7/92 (7%)
Query: 91 NRPEAGATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYN- 149
R A A + +++VGS+ ++ E+ +++ F FG + S+ + + T K +GF FVEY
Sbjct: 5 QRQRALAIMCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEV 64
Query: 150 ------DYDPVDKACLKGTHLVKGKKVDVKKA 175
+ ++ L G ++ G+ ++ +A
Sbjct: 65 PEAAQLALEQMNSVMLGGRNIKVGRPSNIGQA 96
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 63.9 bits (154), Expect = 9e-11, Method: Compositional matrix adjust.
Identities = 43/170 (25%), Positives = 80/170 (47%), Gaps = 9/170 (5%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA-Q 67
R L++G LD + + LK +F+ G + ++ +M D + K+ + F+ Y +H + A Q
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQ 59
Query: 68 AARPHTIDSKVVEPKRAVPRTEINRPEAGATVKKLFVGSLRDDITEEDLKEYFGQFGEVT 127
I++ +V+ A + + LFVG L ++ +E L+ F F
Sbjct: 60 TLNGKQIENNIVKINWAFQSQQ----SSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYL 115
Query: 128 SVALVTEKETGKKRGFGFVEYNDYDPVDKA--CLKGTHLVKGKKVDVKKA 175
S ++ + +TG RG+GFV + D A ++G L G+ + + A
Sbjct: 116 SGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDL-NGRPLRINWA 164
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 63.9 bits (154), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 35/96 (36%), Positives = 55/96 (57%), Gaps = 9/96 (9%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
K+F+GGL Y T+ +L+ +FE +GD+ + VV+ D QT KSRG+GF+T M D A A
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVT-----MADRAAAE 73
Query: 70 RPHTIDSKVVEPKRAVPRTEINRPEAGATVKKLFVG 105
R + +++ ++A +N GA + L G
Sbjct: 74 RACKDPNPIIDGRKA----NVNLAYLGAKPRSLQTG 105
Score = 62.4 bits (150), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 30/89 (33%), Positives = 50/89 (56%)
Query: 98 TVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
T K+FVG L T+ L++YF FG++ ++T+++TGK RG+GFV D ++A
Sbjct: 16 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA 75
Query: 158 CLKGTHLVKGKKVDVKKALSKEEMAKLKT 186
C ++ G+K +V A + L+T
Sbjct: 76 CKDPNPIIDGRKANVNLAYLGAKPRSLQT 104
>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 = 63.5 bits (153), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 45/175 (25%), Positives = 82/175 (46%), Gaps = 15/175 (8%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY----SSAHMVDD 65
++++G + Y +T++ F +G + + D T K +GF F+ Y ++ ++
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 66 AQAARPHTIDSKVVEPK---RAVPRTEINRPEAGATVKKLFVGSLRDDITEEDLKEYFGQ 122
+ + KV P +A P + EA A +++V S+ D++++D+K F
Sbjct: 74 XNSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARA-FNRIYVASVHQDLSDDDIKSVFEA 132
Query: 123 FGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC-------LKGTHLVKGKKV 170
FG++ S L + TGK +G+GF+EY A L G +L GK V
Sbjct: 133 FGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVGKAV 187
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 35/66 (53%)
Query: 1 ITKEPEHLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSA 60
+ +E ++++ + S + +KS FEA+G + + +DP T K +G+GFI Y A
Sbjct: 102 LAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKA 161
Query: 61 HMVDDA 66
DA
Sbjct: 162 QSSQDA 167
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 33/58 (56%)
Query: 91 NRPEAGATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
R A A +++VGS+ ++ E+ +++ F FG + S+ + T K +GF FVEY
Sbjct: 4 QRQRALAIXCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEY 61
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 63.5 bits (153), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 32/74 (43%), Positives = 45/74 (60%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKG 161
+FVG L D EE ++EYFG FGEV S+ L + +T K+RGF F+ + + +PV K K
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Query: 162 THLVKGKKVDVKKA 175
H V K ++K A
Sbjct: 62 YHNVGLSKCEIKVA 75
Score = 45.1 bits (105), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 36/74 (48%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAAR 70
+F+GGL T E ++ +F +G+V + + D +T K RGF FIT+ V +
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Query: 71 PHTIDSKVVEPKRA 84
H + E K A
Sbjct: 62 YHNVGLSKCEIKVA 75
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 61.2 bits (147), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 33/93 (35%), Positives = 59/93 (63%), Gaps = 10/93 (10%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQ-- 67
KLF+GGL + T+ ++L+ F +G + +VVV+KD +T++SRGFGF+T+ + +DDA+
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFEN---IDDAKDA 70
Query: 68 --AARPHTIDSKVVEPKRAVPRTEINR--PEAG 96
A ++D + + +A ++ NR P +G
Sbjct: 71 MMAMNGKSVDGRQIRVDQA-GKSSDNRSGPSSG 102
Score = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 45/74 (60%), Gaps = 4/74 (5%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
KLFVG L D E+ L++ F ++G+++ V +V ++ET + RGFGFV + + D A +
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 161 GTHLVKGKKVDVKK 174
+ GK VD ++
Sbjct: 74 ----MNGKSVDGRQ 83
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 58.5 bits (140), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 34/142 (23%), Positives = 75/142 (52%), Gaps = 9/142 (6%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
L + L + + KS F + GD+ +++D T +S G+GF+ YS + D A
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA--- 62
Query: 70 RPHTIDSKVVEPKRAVPRTEINRPEAGATVK--KLFVGSLRDDITEEDLKEYFGQFGEVT 127
+T++ ++ K + RP + A+++ L+V L ++++++++ F Q+G +
Sbjct: 63 -INTLNGLKLQTKTI--KVSYARPSS-ASIRDANLYVSGLPKTMSQKEMEQLFSQYGRII 118
Query: 128 SVALVTEKETGKKRGFGFVEYN 149
+ ++ ++ TG RG GF+ ++
Sbjct: 119 TSRILLDQATGVSRGVGFIRFD 140
Score = 51.6 bits (122), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 26/66 (39%), Positives = 38/66 (57%), Gaps = 2/66 (3%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC-- 158
L V L ++T+++ K FG G++ S LV +K TG+ G+GFV Y+D + DKA
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 159 LKGTHL 164
L G L
Sbjct: 66 LNGLKL 71
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 58.5 bits (140), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 37/99 (37%), Positives = 54/99 (54%), Gaps = 6/99 (6%)
Query: 93 PEAGATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYD 152
P +++ +FVG++ + TEE LK+ F + G V S LV ++ETGK +G+GF EY D +
Sbjct: 2 PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61
Query: 153 PVDKAC--LKGTHLVKGKKVDVKKALS---KEEMAKLKT 186
A L G G+ + V A S KEE+ L T
Sbjct: 62 TALSAMRNLNGREF-SGRALRVDNAASEKNKEELKSLGT 99
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 28/50 (56%)
Query: 8 LRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
LR +F+G + Y + E LK F G VV ++ D +T K +G+GF Y
Sbjct: 8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEY 57
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 57.0 bits (136), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 41/142 (28%), Positives = 69/142 (48%), Gaps = 9/142 (6%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
L + L + L + F A G + +M+D +T S G+ F+ ++S D+Q A
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEM---DSQRA 61
Query: 70 RPHTIDSKVVEPKRAVPRTEINRPEAGATVK--KLFVGSLRDDITEEDLKEYFGQFGEVT 127
++ V KR + RP G ++K L+V +L IT++ L FG++G +
Sbjct: 62 -IKVLNGITVRNKRL--KVSYARP-GGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIV 117
Query: 128 SVALVTEKETGKKRGFGFVEYN 149
++ +K TG+ RG FV YN
Sbjct: 118 QKNILRDKLTGRPRGVAFVRYN 139
Score = 32.3 bits (72), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 27/52 (51%)
Query: 97 ATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
A+ L V L D+T+ +L F G + + ++ + +TG G+ FV++
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDF 52
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 55.8 bits (133), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 47/159 (29%), Positives = 74/159 (46%), Gaps = 21/159 (13%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
+LF+G L + E K FE +G+ +V + +D RGFGFI S + + A+A
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKA- 76
Query: 70 RPHTIDSKVVEPKRAVPRTEINRPEAGATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSV 129
+D +++ + R A TVK +L ++ E L++ F QFG V
Sbjct: 77 ---ELDGTILKSRPL--RIRFATHGAALTVK-----NLSPVVSNELLEQAFSQFGPVEKA 126
Query: 130 ALVTEKETGKKRGFGFVEYNDYDPVDKA---CLKGTHLV 165
+V + + G+ G GFVE+ P KA C G L+
Sbjct: 127 VVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFLL 164
Score = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 29/77 (37%), Positives = 44/77 (57%), Gaps = 9/77 (11%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFV--EYNDYDPVDKAC 158
+LFVG+L DITEED K F ++GE + V + + RGFGF+ E + KA
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFI------NRDRGFGFIRLESRTLAEIAKAE 77
Query: 159 LKGTHLVKGKKVDVKKA 175
L GT ++K + + ++ A
Sbjct: 78 LDGT-ILKSRPLRIRFA 93
>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 = 55.5 bits (132), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 33/150 (22%), Positives = 72/150 (48%), Gaps = 7/150 (4%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA-QA 68
L + L + + L+S F + G+V +++D S G+GF+ Y +A + A
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 69 ARPHTIDSKVVEPKRAVPRTEINRPEAGATVKKLFVGSLRDDITEEDLKEYFGQFGEVTS 128
+ SK ++ A P +E+ + L++ L +T++D+++ F +FG + +
Sbjct: 64 LNGLRLQSKTIKVSYARPSSEVIKD------ANLYISGLPRTMTQKDVEDMFSRFGRIIN 117
Query: 129 VALVTEKETGKKRGFGFVEYNDYDPVDKAC 158
++ ++ TG RG F+ ++ ++A
Sbjct: 118 SRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 41/85 (48%), Gaps = 3/85 (3%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC-- 158
L V L ++T+++L+ F GEV S L+ +K G G+GFV Y ++A
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 159 LKGTHLVKGKKVDVKKALSKEEMAK 183
L G L + K + V A E+ K
Sbjct: 64 LNGLRL-QSKTIKVSYARPSSEVIK 87
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 55.5 bits (132), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 47/180 (26%), Positives = 81/180 (45%), Gaps = 26/180 (14%)
Query: 9 RKLFIGGLDYRTSSETLKSHF----------EAWGDVVDVVVMKDPQTKKSRGFGFITYS 58
R+L++G + + + E + F +A G+ V V Q + + F F+ +
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAV-----QINQDKNFAFLEFR 59
Query: 59 SAHMVDDAQAARPHTIDSKVVEPKRA-VPRTEINRPEAGATVKKLFVGSLRDDITEEDLK 117
S A A D + + + + R +P GA KLF+G L + + ++ +K
Sbjct: 60 SVDETTQAMA-----FDGIIFQGQSLKIRRPHDYQPLPGA--HKLFIGGLPNYLNDDQVK 112
Query: 118 EYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC--LKGTHLVKGKKVDVKKA 175
E FG + + LV + TG +G+ F EY D + D+A L G L KK+ V++A
Sbjct: 113 ELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL-GDKKLLVQRA 171
Score = 29.6 bits (65), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 17/83 (20%), Positives = 41/83 (49%), Gaps = 5/83 (6%)
Query: 97 ATVKKLFVGSLRDDITEEDLKEYFG---QFGEVTSVA--LVTEKETGKKRGFGFVEYNDY 151
+ ++L+VG++ ITEE + ++F + G +T V + + + F F+E+
Sbjct: 2 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 61
Query: 152 DPVDKACLKGTHLVKGKKVDVKK 174
D +A + +G+ + +++
Sbjct: 62 DETTQAMAFDGIIFQGQSLKIRR 84
>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 = 55.5 bits (132), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 47/180 (26%), Positives = 81/180 (45%), Gaps = 26/180 (14%)
Query: 9 RKLFIGGLDYRTSSETLKSHF----------EAWGDVVDVVVMKDPQTKKSRGFGFITYS 58
R+L++G + + + E + F +A G+ V V Q + + F F+ +
Sbjct: 7 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAV-----QINQDKNFAFLEFR 61
Query: 59 SAHMVDDAQAARPHTIDSKVVEPKRA-VPRTEINRPEAGATVKKLFVGSLRDDITEEDLK 117
S A A D + + + + R +P GA KLF+G L + + ++ +K
Sbjct: 62 SVDETTQAMA-----FDGIIFQGQSLKIRRPHDYQPLPGA--HKLFIGGLPNYLNDDQVK 114
Query: 118 EYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC--LKGTHLVKGKKVDVKKA 175
E FG + + LV + TG +G+ F EY D + D+A L G L KK+ V++A
Sbjct: 115 ELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL-GDKKLLVQRA 173
Score = 29.6 bits (65), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 17/83 (20%), Positives = 41/83 (49%), Gaps = 5/83 (6%)
Query: 97 ATVKKLFVGSLRDDITEEDLKEYFG---QFGEVTSVA--LVTEKETGKKRGFGFVEYNDY 151
+ ++L+VG++ ITEE + ++F + G +T V + + + F F+E+
Sbjct: 4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 63
Query: 152 DPVDKACLKGTHLVKGKKVDVKK 174
D +A + +G+ + +++
Sbjct: 64 DETTQAMAFDGIIFQGQSLKIRR 86
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 55.1 bits (131), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 36/98 (36%), Positives = 50/98 (51%), Gaps = 12/98 (12%)
Query: 82 KRAVPRTEINRPEAGATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKR 141
KRAV +T L V L TE+DLKEYF FGEV V + + +TG +
Sbjct: 9 KRAVQKTS-----------DLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSK 57
Query: 142 GFGFVEYNDYDPVDKACLKGTHLVKGKKVDVKKALSKE 179
GFGFV + +Y+ K + H++ G+ D K SK+
Sbjct: 58 GFGFVRFTEYETQVKV-MSQRHMIDGRWCDCKLPNSKQ 94
Score = 45.1 bits (105), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAAR 70
L + GL ++T+ + LK +F +G+V+ V V KD +T S+GFGF+ ++ + R
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 77
Query: 71 PHTIDSKVVEPK 82
H ID + + K
Sbjct: 78 -HMIDGRWCDCK 88
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 55.1 bits (131), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 33/150 (22%), Positives = 72/150 (48%), Gaps = 7/150 (4%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA-QA 68
L + L + + L+S F + G+V +++D S G+GF+ Y +A + A
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 69 ARPHTIDSKVVEPKRAVPRTEINRPEAGATVKKLFVGSLRDDITEEDLKEYFGQFGEVTS 128
+ SK ++ A P +E+ + L++ L +T++D+++ F +FG + +
Sbjct: 64 LNGLRLQSKTIKVSYARPSSEVIKD------ANLYISGLPRTMTQKDVEDMFSRFGRIIN 117
Query: 129 VALVTEKETGKKRGFGFVEYNDYDPVDKAC 158
++ ++ TG RG F+ ++ ++A
Sbjct: 118 SRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 41/85 (48%), Gaps = 3/85 (3%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC-- 158
L V L ++T+++L+ F GEV S L+ +K G G+GFV Y ++A
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 159 LKGTHLVKGKKVDVKKALSKEEMAK 183
L G L + K + V A E+ K
Sbjct: 64 LNGLRL-QSKTIKVSYARPSSEVIK 87
>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 = 54.7 bits (130), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 35/142 (24%), Positives = 75/142 (52%), Gaps = 9/142 (6%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
L + L + E +S F + G++ +++D T +S G+GF+ Y DA+ A
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPK---DAEKA 60
Query: 70 RPHTIDSKVVEPKRAVPRTEINRPEAGATVK--KLFVGSLRDDITEEDLKEYFGQFGEVT 127
+T++ ++ K + RP + A+++ L+V L +T+++L++ F Q+G +
Sbjct: 61 -INTLNGLRLQTKTI--KVSYARPSS-ASIRDANLYVSGLPKTMTQKELEQLFSQYGRII 116
Query: 128 SVALVTEKETGKKRGFGFVEYN 149
+ ++ ++ TG RG GF+ ++
Sbjct: 117 TSRILVDQVTGVSRGVGFIRFD 138
Score = 48.9 bits (115), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 26/66 (39%), Positives = 36/66 (54%), Gaps = 2/66 (3%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC-- 158
L V L ++T+E+ + FG GE+ S LV +K TG+ G+GFV Y D +KA
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 159 LKGTHL 164
L G L
Sbjct: 64 LNGLRL 69
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 54.3 bits (129), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 42/67 (62%)
Query: 91 NRPEAGATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYND 150
N + A +L+VGSL +ITE+ L+ F FG + S+ L+ + ETG+ +G+GF+ ++D
Sbjct: 18 NLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSD 77
Query: 151 YDPVDKA 157
+ KA
Sbjct: 78 SECAKKA 84
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 35/57 (61%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA 66
+L++G L + + + L+ FE +G + + +M D +T +S+G+GFIT+S + A
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKA 84
>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 = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 40/142 (28%), Positives = 68/142 (47%), Gaps = 9/142 (6%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
L + L + L + F A G + + +D +T S G+ F+ ++S D+Q A
Sbjct: 16 NLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEX---DSQRA 72
Query: 70 RPHTIDSKVVEPKRAVPRTEINRPEAGATVK--KLFVGSLRDDITEEDLKEYFGQFGEVT 127
++ V KR + RP G ++K L+V +L IT++ L FG++G +
Sbjct: 73 -IKVLNGITVRNKRL--KVSYARP-GGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIV 128
Query: 128 SVALVTEKETGKKRGFGFVEYN 149
++ +K TG+ RG FV YN
Sbjct: 129 QKNILRDKLTGRPRGVAFVRYN 150
Score = 31.6 bits (70), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 2/59 (3%)
Query: 90 INRPEAGATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
+N P A T L V L D T+ +L F G + + + + +TG G+ FV++
Sbjct: 7 MNDPRASNT--NLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDF 63
>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 = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 43/83 (51%), Gaps = 1/83 (1%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVE-YNDYDPVDKACLK 160
+FVG L +IT ED+K F FG ++ +V + TGK +G+GFV +N +D +
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 161 GTHLVKGKKVDVKKALSKEEMAK 183
G + G+++ A K K
Sbjct: 78 GGQWLGGRQIRTNWATRKPPAPK 100
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 31/47 (65%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
+F+G L ++E +K+ F +G + D V+KD T KS+G+GF+++
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSF 64
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 42/78 (53%), Gaps = 1/78 (1%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVE-YNDYDPVDKACLK 160
+FVG L +IT ED+K F FG+++ +V + TGK +G+GFV YN D +
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 161 GTHLVKGKKVDVKKALSK 178
G + G+++ A K
Sbjct: 78 GGQWLGGRQIRTNWATRK 95
Score = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 31/47 (65%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
+F+G L ++E +KS F +G + D V+KD T KS+G+GF+++
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSF 64
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 52.4 bits (124), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 26/54 (48%), Positives = 38/54 (70%), Gaps = 1/54 (1%)
Query: 4 EPEHLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
E +H KLFIGGL+ T+ + LK+ F G + +V+++KD +T KSRGF FIT+
Sbjct: 3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITF 55
Score = 44.7 bits (104), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 42/76 (55%), Gaps = 2/76 (2%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY-NDYDPVDKACL 159
KLF+G L + E+ LK FG+ G ++ V L+ ++ T K RGF F+ + N D + A
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKD 67
Query: 160 KGTHLVKGKKVDVKKA 175
+ GK + V++A
Sbjct: 68 MNGKSLHGKAIKVEQA 83
>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 = 52.0 bits (123), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 50/197 (25%), Positives = 83/197 (42%), Gaps = 40/197 (20%)
Query: 9 RKLFIGGLDYRTSSETLKSHF----------EAWGDVVDVVVMKDPQTKKSRGFGFITYS 58
R+L++G + + + E + F +A G+ V V Q + + F F+ +
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAV-----QINQDKNFAFLEFR 59
Query: 59 SAHMVDDAQAA-------------RPHTIDSKVVEPKRAVPRTEINRPEAGATV-----K 100
S A A RPH D + + P + P +TV
Sbjct: 60 SVDETTQAMAFDGIIFQGQSLKIRRPH--DYQPLPGMSENPSVYV--PGVVSTVVPDSAH 115
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC-- 158
KLF+G L + + ++ +KE FG + + LV + TG +G+ F EY D + D+A
Sbjct: 116 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 175
Query: 159 LKGTHLVKGKKVDVKKA 175
L G L KK+ V++A
Sbjct: 176 LNGMQL-GDKKLLVQRA 191
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 34/68 (50%)
Query: 2 TKEPEHLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAH 61
T P+ KLFIGGL + + +K ++G + ++KD T S+G+ F Y +
Sbjct: 108 TVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDIN 167
Query: 62 MVDDAQAA 69
+ D A A
Sbjct: 168 VTDQAIAG 175
Score = 33.1 bits (74), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 19/84 (22%), Positives = 42/84 (50%), Gaps = 5/84 (5%)
Query: 96 GATVKKLFVGSLRDDITEEDLKEYFG---QFGEVTSVA--LVTEKETGKKRGFGFVEYND 150
GA ++L+VG++ ITEE + ++F + G +T V + + + F F+E+
Sbjct: 1 GAMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRS 60
Query: 151 YDPVDKACLKGTHLVKGKKVDVKK 174
D +A + +G+ + +++
Sbjct: 61 VDETTQAMAFDGIIFQGQSLKIRR 84
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 26/62 (41%), Positives = 41/62 (66%), Gaps = 1/62 (1%)
Query: 99 VKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC 158
++ ++VG+L T E +KE F QFG+V +V L+ ++ET K +GFGFVE + + V +A
Sbjct: 1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAI 59
Query: 159 LK 160
K
Sbjct: 60 AK 61
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 32/48 (66%)
Query: 8 LRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFI 55
+R +++G L Y +SE +K F +G V +V ++ D +TKK +GFGF+
Sbjct: 1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFV 48
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 38/143 (26%), Positives = 69/143 (48%), Gaps = 8/143 (5%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKD--PQTKKSRGFGFITYSSAHMVDDAQ 67
K+F+G + S + L+ FE +G V ++ V++D +S+G F+T+ + +AQ
Sbjct: 17 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 76
Query: 68 AARPHTIDSKVVEPKRAVPRTEINRPEAGATV--KKLFVGSLRDDITEEDLKEYFGQFGE 125
A H + KV+ + + E V +KLF+G + TE D++ F FG+
Sbjct: 77 NAL-HNM--KVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQ 133
Query: 126 VTSVALVTEKETGKKRGFGFVEY 148
+ ++ + G RG FV +
Sbjct: 134 IEECRILRGPD-GLSRGCAFVTF 155
Score = 36.6 bits (83), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA 66
RKLFIG + + + ++ F ++G + + +++ P SRG F+T+++ M A
Sbjct: 108 RKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRAMAQTA 164
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 38/143 (26%), Positives = 69/143 (48%), Gaps = 8/143 (5%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKD--PQTKKSRGFGFITYSSAHMVDDAQ 67
K+F+G + S + L+ FE +G V ++ V++D +S+G F+T+ + +AQ
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 68 AARPHTIDSKVVEPKRAVPRTEINRPEAGATV--KKLFVGSLRDDITEEDLKEYFGQFGE 125
A H + KV+ + + E V +KLF+G + TE D++ F FG+
Sbjct: 65 NAL-HNM--KVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQ 121
Query: 126 VTSVALVTEKETGKKRGFGFVEY 148
+ ++ + G RG FV +
Sbjct: 122 IEECRILRGPD-GLSRGCAFVTF 143
Score = 37.0 bits (84), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA 66
RKLFIG + + + ++ F ++G + + +++ P SRG F+T+++ M A
Sbjct: 96 RKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRAMAQTA 152
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 24/59 (40%), Positives = 35/59 (59%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
L + L YRTS ++L+ FE +G V DV + ++P TK RGF F+ + DA+AA
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 49.7 bits (117), Expect = 2e-06, Method: Composition-based stats.
Identities = 23/56 (41%), Positives = 35/56 (62%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
L V L ++T+++ K FG G++ S LV +K TG+ G+GFV Y+D + DKA
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Score = 33.5 bits (75), Expect = 0.13, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 29/56 (51%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA 66
L + L + + KS F + GD+ +++D T +S G+GF+ YS + D A
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 49.7 bits (117), Expect = 2e-06, Method: Composition-based stats.
Identities = 22/60 (36%), Positives = 39/60 (65%), Gaps = 6/60 (10%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAAR 70
L++G L + + + L+ FE +G + ++V+MKD T +S+G+GFIT+S D++ AR
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFS------DSECAR 61
Score = 48.9 bits (115), Expect = 3e-06, Method: Composition-based stats.
Identities = 20/56 (35%), Positives = 39/56 (69%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
L+VGSL +ITE+ L+ F FG++ ++ L+ + +TG+ +G+GF+ ++D + +A
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRA 63
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/64 (40%), Positives = 37/64 (57%)
Query: 6 EHLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDD 65
E + L + L YRTS +TL+ FE +G V DV + +D TK+SRGF F+ + +D
Sbjct: 68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 127
Query: 66 AQAA 69
A A
Sbjct: 128 AMDA 131
Score = 32.0 bits (71), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 7/56 (12%)
Query: 116 LKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYND-------YDPVDKACLKGTHL 164
L+ F ++G V V + ++ T + RGF FV ++D D +D A L G L
Sbjct: 87 LRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGREL 142
>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 = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 26/64 (40%), Positives = 37/64 (57%)
Query: 6 EHLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDD 65
E + L + L YRTS +TL+ FE +G V DV + +D TK+SRGF F+ + +D
Sbjct: 45 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 104
Query: 66 AQAA 69
A A
Sbjct: 105 AMDA 108
Score = 32.7 bits (73), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 7/73 (9%)
Query: 99 VKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYND-------Y 151
+ L V +L + + L+ F ++G V V + ++ T + RGF FV ++D
Sbjct: 47 MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAM 106
Query: 152 DPVDKACLKGTHL 164
D +D A L G L
Sbjct: 107 DAMDGAVLDGREL 119
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 33/96 (34%), Positives = 54/96 (56%), Gaps = 5/96 (5%)
Query: 85 VPRTEINRPEAGATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFG 144
VPR E + K+L V ++ + DL++ FGQFG++ V ++ E G K GFG
Sbjct: 15 VPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIF-NERGSK-GFG 72
Query: 145 FVEYNDYDPVDKAC--LKGTHLVKGKKVDVKKALSK 178
FV + + D+A L GT +V+G+K++V A ++
Sbjct: 73 FVTFENSADADRAREKLHGT-VVEGRKIEVNNATAR 107
Score = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 16/66 (24%), Positives = 36/66 (54%), Gaps = 2/66 (3%)
Query: 2 TKEPEHLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAH 61
T+ ++L + + +R L+ F +G ++DV ++ + + S+GFGF+T+ ++
Sbjct: 23 TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSA 80
Query: 62 MVDDAQ 67
D A+
Sbjct: 81 DADRAR 86
>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 = 48.5 bits (114), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 28/87 (32%), Positives = 42/87 (48%), Gaps = 5/87 (5%)
Query: 91 NRPEA-GATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYN 149
N P A G K LFV + D TE L+ F +G + + +V K +GK RG+ F+EY
Sbjct: 93 NDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYE 152
Query: 150 DYDPVDKACLKGTHLVKGKKVDVKKAL 176
++ GKK+D ++ L
Sbjct: 153 H----ERDMHSAYKHADGKKIDGRRVL 175
Score = 36.2 bits (82), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 28/50 (56%)
Query: 8 LRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
+ LF+ ++Y T+ L+ FE +G + + ++ ++ K RG+ FI Y
Sbjct: 102 FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEY 151
>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 = 48.5 bits (114), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 37/143 (25%), Positives = 67/143 (46%), Gaps = 8/143 (5%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKD--PQTKKSRGFGFITYSSAHMVDDAQ 67
K F+G + S + L+ FE +G V ++ V++D +S+G F+T+ + +AQ
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 68 AARPHTIDSKVVEPKRAVPRTEINRPEAGATV--KKLFVGSLRDDITEEDLKEYFGQFGE 125
A + KV+ + + E V +KLF+G + TE D++ F FG+
Sbjct: 65 NA---LHNXKVLPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQ 121
Query: 126 VTSVALVTEKETGKKRGFGFVEY 148
+ ++ + G RG FV +
Sbjct: 122 IEECRILRGPD-GLSRGCAFVTF 143
Score = 35.0 bits (79), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSS 59
RKLFIG + + + ++ F ++G + + +++ P SRG F+T+++
Sbjct: 96 RKLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDG-LSRGCAFVTFTT 145
>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 = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 41/174 (23%), Positives = 80/174 (45%), Gaps = 6/174 (3%)
Query: 8 LRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQ 67
+ L++G L + L F G ++ + V +D T++S G+ ++ + D +
Sbjct: 10 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQP--ADAER 67
Query: 68 AARPHTIDSKVVEPKRAVPRTEINRPEAGATVKKLFVGSLRDDITEEDLKEYFGQFGEVT 127
A D +P R + ++ + + V +F+ +L I + L + F FG +
Sbjct: 68 ALDTMNFDVIKGKPVR-IMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNIL 126
Query: 128 SVALVTEKETGKKRGFGFVEYNDYDPVDKACLK-GTHLVKGKKVDVKKALSKEE 180
S +V + E G K G+GFV + + ++A K L+ +KV V + S++E
Sbjct: 127 SCKVVCD-ENGSK-GYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKE 178
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 30/83 (36%), Positives = 50/83 (60%), Gaps = 5/83 (6%)
Query: 98 TVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
T K+L V ++ + DL++ FGQFG++ V ++ E G K GFGFV + + D+A
Sbjct: 14 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIF-NERGSK-GFGFVTFENSADADRA 71
Query: 158 C--LKGTHLVKGKKVDVKKALSK 178
L GT +V+G+K++V A ++
Sbjct: 72 REKLHGT-VVEGRKIEVNNATAR 93
Score = 35.0 bits (79), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 22/90 (24%), Positives = 46/90 (51%), Gaps = 4/90 (4%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
++L + + +R L+ F +G ++DV ++ + + S+GFGF+T+ ++ D A+
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSADADRARE 73
Query: 69 ARPHT-IDSKVVEPKRAVPRTEINR-PEAG 96
T ++ + +E A R N P +G
Sbjct: 74 KLHGTVVEGRKIEVNNATARVMTNSGPSSG 103
>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 = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 47/183 (25%), Positives = 84/183 (45%), Gaps = 9/183 (4%)
Query: 8 LRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQ 67
+ L++G L + L F G ++ + V +D T++S G+ ++ + DA+
Sbjct: 15 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPA---DAE 71
Query: 68 AARPHTIDSKVVEPKRAVPRTEINRPEA-GATVKKLFVGSLRDDITEEDLKEYFGQFGEV 126
A T++ V++ K P + V +F+ +L I + L + F FG +
Sbjct: 72 RAL-DTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNI 130
Query: 127 TSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK-GTHLVKGKKVDVKKALS-KEEMAKL 184
S +V + E G K G+GFV + + ++A K L+ +KV V + S KE A+L
Sbjct: 131 LSCKVVCD-ENGSK-GYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAEL 188
Query: 185 KTR 187
R
Sbjct: 189 GAR 191
Score = 35.8 bits (81), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 22/88 (25%), Positives = 39/88 (44%), Gaps = 1/88 (1%)
Query: 86 PRTEINRPEAGATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGF 145
P +N + L+VG L D+TE L E F G + S+ + + T + G+ +
Sbjct: 2 PLGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAY 61
Query: 146 VEYNDYDPVDKAC-LKGTHLVKGKKVDV 172
V + ++A ++KGK V +
Sbjct: 62 VNFQQPADAERALDTMNFDVIKGKPVRI 89
>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 = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 28/87 (32%), Positives = 42/87 (48%), Gaps = 5/87 (5%)
Query: 91 NRPEA-GATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYN 149
N P A G K LFV + D TE L+ F +G + + +V K +GK RG+ F+EY
Sbjct: 93 NDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYE 152
Query: 150 DYDPVDKACLKGTHLVKGKKVDVKKAL 176
++ GKK+D ++ L
Sbjct: 153 H----ERDMHSAYKHADGKKIDGRRVL 175
Score = 35.0 bits (79), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 28/50 (56%)
Query: 8 LRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
+ LF+ ++Y T+ L+ FE +G + + ++ ++ K RG+ FI Y
Sbjct: 102 FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEY 151
>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 = 46.6 bits (109), Expect = 2e-05, Method: Composition-based stats.
Identities = 24/59 (40%), Positives = 36/59 (61%), Gaps = 3/59 (5%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
LF+G L+ ETL++ F+ + + VM D QT SRG+GF++++S DDAQ A
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQ---DDAQNA 59
Score = 40.0 bits (92), Expect = 0.001, Method: Composition-based stats.
Identities = 19/56 (33%), Positives = 29/56 (51%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
LFVG L ++ +E L+ F F S ++ + +TG RG+GFV + D A
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNA 59
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 46.2 bits (108), Expect = 2e-05, Method: Composition-based stats.
Identities = 27/77 (35%), Positives = 43/77 (55%), Gaps = 3/77 (3%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC-- 158
KLF+G L + + ++ +KE FG + + LV + TG +G+ F EY D + D+A
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 159 LKGTHLVKGKKVDVKKA 175
L G L KK+ V++A
Sbjct: 63 LNGMQL-GDKKLLVQRA 78
Score = 35.4 bits (80), Expect = 0.041, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 31/60 (51%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
KLFIGGL + + +K ++G + ++KD T S+G+ F Y ++ D A A
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 26/50 (52%), Positives = 33/50 (66%), Gaps = 3/50 (6%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYN 149
K LFV L +D TEE LKE F G V +VT++ETG +GFGFV++N
Sbjct: 16 KTLFVKGLSEDTTEETLKESFD--GSVR-ARIVTDRETGSSKGFGFVDFN 62
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 39/70 (55%), Gaps = 6/70 (8%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
+ LF+ GL T+ ETLK F+ V ++ D +T S+GFGF+ ++S DA+A
Sbjct: 16 KTLFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFGFVDFNSEE---DAKA 69
Query: 69 ARPHTIDSKV 78
A+ D ++
Sbjct: 70 AKEAMEDGEI 79
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 28/98 (28%), Positives = 54/98 (55%), Gaps = 5/98 (5%)
Query: 85 VPRTEINRPEAGATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFG 144
+P T++N PE ++ L V + + E L++ F ++G + SV +V ++ET + RG+G
Sbjct: 30 IPPTQMN-PEP-DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYG 87
Query: 145 FVEYNDYDPVDKAC--LKGTHLVKGKKVDVKKALSKEE 180
FV++ +A L G +++ K++ V A S +
Sbjct: 88 FVKFQSGSSAQQAIAGLNGFNILN-KRLKVALAASGHQ 124
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 35/69 (50%)
Query: 1 ITKEPEHLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSA 60
+ EP+ LR L + + L+ FE +G + V ++ D +T++SRG+GF+ + S
Sbjct: 35 MNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSG 94
Query: 61 HMVDDAQAA 69
A A
Sbjct: 95 SSAQQAIAG 103
>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 = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 28/91 (30%), Positives = 50/91 (54%), Gaps = 4/91 (4%)
Query: 93 PEAGATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVE-YNDY 151
PE +FVG + + E +++ +F ++G V V ++T++ TG +G+GFV YND
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDV 61
Query: 152 DPVDKACLKGTHLVKGKKVDVKKALSKEEMA 182
D V K + GKK+ + A+ K+ ++
Sbjct: 62 D-VQKIVESQINF-HGKKLKLGPAIRKQNLS 90
Score = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 31/47 (65%), Gaps = 1/47 (2%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
+F+GG+D R ++S F +G V +V ++ D +T S+G+GF+++
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSF 57
>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 = 45.1 bits (105), Expect = 6e-05, Method: Composition-based stats.
Identities = 19/56 (33%), Positives = 33/56 (58%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
LFV + ++ TEED+ + F ++GE+ ++ L ++ TG +G+ VEY Y A
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 65
>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 = 45.1 bits (105), Expect = 6e-05, Method: Composition-based stats.
Identities = 19/56 (33%), Positives = 33/56 (58%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
LFV + ++ TEED+ + F ++GE+ ++ L ++ TG +G+ VEY Y A
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 67
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 45.1 bits (105), Expect = 6e-05, Method: Composition-based stats.
Identities = 19/56 (33%), Positives = 33/56 (58%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
LFV + ++ TEED+ + F ++GE+ ++ L ++ TG +G+ VEY Y A
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 65
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 44.7 bits (104), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 42/67 (62%), Gaps = 4/67 (5%)
Query: 3 KEPEHLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHM 62
++P RKLF+G L+ + S + ++ FEA+G++ + +++ P S+G F+ YSS H
Sbjct: 10 RQPPSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPD-GNSKGCAFVKYSS-HA 67
Query: 63 VDDAQAA 69
+AQAA
Sbjct: 68 --EAQAA 72
Score = 36.2 bits (82), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 3/70 (4%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA-- 157
+KLFVG L +E+D++ F FG + ++ + G +G FV+Y+ + A
Sbjct: 16 RKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPD-GNSKGCAFVKYSSHAEAQAAIN 74
Query: 158 CLKGTHLVKG 167
L G+ + G
Sbjct: 75 ALHGSQTMPG 84
>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 = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 40/70 (57%), Gaps = 3/70 (4%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
R L++GGL + L + F +GD+ D+ + D +T+K RGF F+ + + +DA A
Sbjct: 3 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE---LAEDAAA 59
Query: 69 ARPHTIDSKV 78
A + +S++
Sbjct: 60 AIDNMNESEL 69
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 31/49 (63%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
+ L+VG L +++ ++ L F FG++T + + + ET K RGF FVE+
Sbjct: 3 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 51
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 40/70 (57%), Gaps = 3/70 (4%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
R L++GGL + L + F +GD+ D+ + D +T+K RGF F+ + + +DA A
Sbjct: 6 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF---ELAEDAAA 62
Query: 69 ARPHTIDSKV 78
A + +S++
Sbjct: 63 AIDNMNESEL 72
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 35/54 (64%), Gaps = 1/54 (1%)
Query: 96 GATVKK-LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
G+T K+ L+VG L +++ ++ L F FG++T + + + ET K RGF FVE+
Sbjct: 1 GSTTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 54
>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 = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 40/70 (57%), Gaps = 3/70 (4%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
R L++GGL + L + F +GD+ D+ + D +T+K RGF F+ + + +DA A
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF---ELAEDAAA 64
Query: 69 ARPHTIDSKV 78
A + +S++
Sbjct: 65 AIDNMNESEL 74
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 34/53 (64%), Gaps = 1/53 (1%)
Query: 97 ATVKK-LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
AT K+ L+VG L +++ ++ L F FG++T + + + ET K RGF FVE+
Sbjct: 4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 56
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 43.9 bits (102), Expect = 1e-04, Method: Composition-based stats.
Identities = 24/78 (30%), Positives = 44/78 (56%), Gaps = 8/78 (10%)
Query: 98 TVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
T+ L+VG L D ITE DL+ +F QFGE+ ++ +V ++ F+++ + A
Sbjct: 11 TITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQC------AFIQFATRQAAEVA 64
Query: 158 CLKGTH--LVKGKKVDVK 173
K + +V G++++VK
Sbjct: 65 AEKSFNKLIVNGRRLNVK 82
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 40/70 (57%), Gaps = 3/70 (4%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
R L++GGL + L + F +GD+ D+ + D +T+K RGF F+ + + +DA A
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE---LAEDAAA 120
Query: 69 ARPHTIDSKV 78
A + +S++
Sbjct: 121 AIDNMNESEL 130
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 34/53 (64%), Gaps = 1/53 (1%)
Query: 97 ATVKK-LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
AT K+ L+VG L +++ ++ L F FG++T + + + ET K RGF FVE+
Sbjct: 60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 112
>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 = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 43/76 (56%)
Query: 97 ATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDK 156
A + ++VG++ T E+L+ +F G V V ++ +K +G +GF ++E++D + V
Sbjct: 3 ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRT 62
Query: 157 ACLKGTHLVKGKKVDV 172
+ L +G+++ V
Sbjct: 63 SLALDESLFRGRQIKV 78
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 42/87 (48%), Gaps = 8/87 (9%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
R +++G +DY ++E L++HF G V V ++ D + +GF +I +S V + A
Sbjct: 6 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 65
Query: 69 ARPHTIDSKVVE--PKRAVPRTEINRP 93
+ ++ PKR NRP
Sbjct: 66 LDESLFRGRQIKVIPKRT------NRP 86
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 43/76 (56%)
Query: 97 ATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDK 156
A + ++VG++ T E+L+ +F G V V ++ +K +G +GF ++E++D + V
Sbjct: 4 ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRT 63
Query: 157 ACLKGTHLVKGKKVDV 172
+ L +G+++ V
Sbjct: 64 SLALDESLFRGRQIKV 79
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 42/87 (48%), Gaps = 8/87 (9%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
R +++G +DY ++E L++HF G V V ++ D + +GF +I +S V + A
Sbjct: 7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 66
Query: 69 ARPHTIDSKVVE--PKRAVPRTEINRP 93
+ ++ PKR NRP
Sbjct: 67 LDESLFRGRQIKVIPKRT------NRP 87
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 43.5 bits (101), Expect = 1e-04, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 3/60 (5%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAAR 70
L + GL T+ L+ F +G + DV ++ D Q+++SRGF F+ + + VDDA+ A+
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN---VDDAKEAK 74
Score = 41.6 bits (96), Expect = 5e-04, Method: Composition-based stats.
Identities = 16/46 (34%), Positives = 30/46 (65%)
Query: 112 TEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
TE DL+E F ++G + V++V ++++ + RGF FV + + D +A
Sbjct: 28 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 73
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 40/70 (57%), Gaps = 3/70 (4%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
R L++GGL + L + F +GD+ D+ + D +T+K RGF F+ + + +DA A
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF---ELAEDAAA 69
Query: 69 ARPHTIDSKV 78
A + +S++
Sbjct: 70 AIDNMNESEL 79
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 34/53 (64%), Gaps = 1/53 (1%)
Query: 97 ATVKK-LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
AT K+ L+VG L +++ ++ L F FG++T + + + ET K RGF FVE+
Sbjct: 9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 61
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 41/73 (56%), Gaps = 3/73 (4%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC--L 159
LFV + ++ TEED+ + F ++GE+ ++ L ++ TG +G+ VEY Y A L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 160 KGTHLVKGKKVDV 172
G L+ G+ + V
Sbjct: 70 NGQDLM-GQPISV 81
>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 = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 42/79 (53%), Gaps = 3/79 (3%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC--L 159
LFV + ++ TEED+ + F ++GE+ ++ L ++ TG +G+ VEY Y A L
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 160 KGTHLVKGKKVDVKKALSK 178
G L+ G+ + V +
Sbjct: 86 NGQDLM-GQPISVDWCFVR 103
>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 = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 37/60 (61%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
R +++G +DY ++++ L++HF + G + + ++ D + +G+ +I ++ + VD A A
Sbjct: 37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVA 96
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 16/73 (21%), Positives = 41/73 (56%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACL 159
+ ++VG++ T +DL+ +F G + + ++ +K +G +G+ ++E+ + + VD A
Sbjct: 37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVA 96
Query: 160 KGTHLVKGKKVDV 172
+ +G+ + V
Sbjct: 97 MDETVFRGRTIKV 109
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 43.1 bits (100), Expect = 2e-04, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 3/60 (5%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAAR 70
L + GL T+ L+ F +G + DV ++ D Q+++SRGF F+ + + VDDA+ A+
Sbjct: 15 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN---VDDAKEAK 71
Score = 42.7 bits (99), Expect = 2e-04, Method: Composition-based stats.
Identities = 19/68 (27%), Positives = 42/68 (61%), Gaps = 1/68 (1%)
Query: 112 TEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKGTHL-VKGKKV 170
TE DL+E F ++G + V++V ++++ + RGF FV + + D +A + + + G+++
Sbjct: 25 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 84
Query: 171 DVKKALSK 178
V +++K
Sbjct: 85 RVDFSITK 92
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 43.1 bits (100), Expect = 2e-04, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 3/60 (5%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAAR 70
L + GL T+ L+ F +G + DV ++ D Q+++SRGF F+ + + VDDA+ A+
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN---VDDAKEAK 74
Score = 42.7 bits (99), Expect = 2e-04, Method: Composition-based stats.
Identities = 19/68 (27%), Positives = 42/68 (61%), Gaps = 1/68 (1%)
Query: 112 TEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKGTHL-VKGKKV 170
TE DL+E F ++G + V++V ++++ + RGF FV + + D +A + + + G+++
Sbjct: 28 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 87
Query: 171 DVKKALSK 178
V +++K
Sbjct: 88 RVDFSITK 95
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 3/60 (5%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAAR 70
L + GL T+ L+ F +G + DV ++ D Q+++SRGF F+ + + VDDA+ A+
Sbjct: 49 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN---VDDAKEAK 105
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 42/68 (61%), Gaps = 1/68 (1%)
Query: 112 TEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKGTHL-VKGKKV 170
TE DL+E F ++G + V++V ++++ + RGF FV + + D +A + + + G+++
Sbjct: 59 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 118
Query: 171 DVKKALSK 178
V +++K
Sbjct: 119 RVDFSITK 126
>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 = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 41/73 (56%), Gaps = 3/73 (4%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC--L 159
LFV + ++ TEED+ + F ++GE+ ++ L ++ TG +G+ VEY Y A L
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 160 KGTHLVKGKKVDV 172
G L+ G+ + V
Sbjct: 85 NGQDLM-GQPISV 96
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 28/88 (31%), Positives = 48/88 (54%), Gaps = 4/88 (4%)
Query: 93 PEAGATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVE-YNDY 151
PE +FVG + + E +++ +F ++G V V ++T++ TG +G+GFV YND
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDV 61
Query: 152 DPVDKACLKGTHLVKGKKVDVKKALSKE 179
D V K + GKK+ + A+ K+
Sbjct: 62 D-VQKIVESQINF-HGKKLKLGPAIRKQ 87
Score = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 31/47 (65%), Gaps = 1/47 (2%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
+F+GG+D R ++S F +G V +V ++ D +T S+G+GF+++
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSF 57
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 34/57 (59%), Gaps = 3/57 (5%)
Query: 92 RPEAGATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
R + AT++ V +L +D E DL+E F FG ++ + L +K TG+ +GF F+ +
Sbjct: 11 RADDNATIR---VTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISF 64
Score = 30.0 bits (66), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 25/45 (55%), Gaps = 3/45 (6%)
Query: 25 LKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
L+ F +G + + + KD T +S+GF FI++ H +DA A
Sbjct: 32 LQELFRPFGSISRIYLAKDKTTGQSKGFAFISF---HRREDAARA 73
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 44/76 (57%), Gaps = 3/76 (3%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKG 161
++VG L + ++E L E F Q G V + + ++ TG+ +G+GFVE+ + D A +K
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA-IKI 76
Query: 162 THLVK--GKKVDVKKA 175
++K GK + V KA
Sbjct: 77 MDMIKLYGKPIRVNKA 92
Score = 34.7 bits (78), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 30/56 (53%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA 66
+++GGLD + S L F G VV+ + KD T + +G+GF+ + S D A
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA 73
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 29/83 (34%), Positives = 45/83 (54%), Gaps = 3/83 (3%)
Query: 99 VKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC 158
V L+V +L D I +E L++ F FG +TS ++ E G+ +GFGFV ++ + KA
Sbjct: 15 VVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG--GRSKGFGFVCFSSPEEATKAV 72
Query: 159 LK-GTHLVKGKKVDVKKALSKEE 180
+ +V K + V A KEE
Sbjct: 73 TEMNGRIVATKPLYVALAQRKEE 95
Score = 32.0 bits (71), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 26/50 (52%), Gaps = 2/50 (4%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSS 59
L++ LD E L+ F +G + VM + +S+GFGF+ +SS
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMM--EGGRSKGFGFVCFSS 64
>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 = 41.6 bits (96), Expect = 6e-04, Method: Composition-based stats.
Identities = 23/68 (33%), Positives = 38/68 (55%), Gaps = 3/68 (4%)
Query: 92 RPEAGATVK--KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYN 149
RP G ++K L+V +L IT++ L FG++G + ++ +K TG+ RG FV YN
Sbjct: 5 RP-GGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYN 63
Query: 150 DYDPVDKA 157
+ +A
Sbjct: 64 KREEAQEA 71
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 32/57 (56%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
KLFVG + + E+DLK F +FG + + ++ ++ TG +G F+ Y D KA
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKA 73
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 32/60 (53%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
KLF+G + + LK FE +G + ++ V+KD T +G F+TY + AQ+A
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSA 76
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 35/57 (61%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
KLF+G + ++ E+DLK F +FG++ + ++ ++ TG +G F+ Y + + KA
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKA 71
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 31/60 (51%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
KLFIG + + LK FE +G + ++ V+KD T +G F+TY AQ+A
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 41.2 bits (95), Expect = 7e-04, Method: Composition-based stats.
Identities = 26/78 (33%), Positives = 41/78 (52%), Gaps = 6/78 (7%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
K+FVG +D+T E+L+++F Q+GEV V + R F FV + D D V ++
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYGEVVDVFI-----PKPFRAFAFVTFAD-DKVAQSLCG 66
Query: 161 GTHLVKGKKVDVKKALSK 178
++KG V + A K
Sbjct: 67 EDLIIKGISVHISNAEPK 84
Score = 30.8 bits (68), Expect = 0.88, Method: Composition-based stats.
Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 5/49 (10%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYS 58
K+F+G ++E L+ F +G+VVDV + K R F F+T++
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYGEVVDVFI-----PKPFRAFAFVTFA 56
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 40.8 bits (94), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 42/79 (53%), Gaps = 3/79 (3%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDP--VDKACL 159
LFV S+ ++ E++++E F +GE+ ++ L ++ TG +G+ VEY + K L
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 160 KGTHLVKGKKVDVKKALSK 178
G ++ G+ + V K
Sbjct: 89 NGAEIM-GQTIQVDWCFVK 106
>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 = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 31/47 (65%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
LFV S+ ++ E++++E F +GE+ ++ L ++ TG +G+ VEY
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEY 121
>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 = 40.0 bits (92), Expect = 0.001, Method: Composition-based stats.
Identities = 18/47 (38%), Positives = 27/47 (57%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
L V L ++T+++L+ F GEV S L+ +K G G+GFV Y
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNY 53
Score = 29.6 bits (65), Expect = 2.3, Method: Composition-based stats.
Identities = 17/59 (28%), Positives = 30/59 (50%), Gaps = 3/59 (5%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
L + L + + L+S F + G+V +++D S G+GF+ Y +A DA+ A
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTA---KDAERA 62
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 39/77 (50%), Gaps = 6/77 (7%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGK---KRGFGFVEYNDYDPVDKAC 158
LF+ +L TEE LK F + G + S + +K GFGFVEY + KA
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 159 --LKGTHLVKGKKVDVK 173
L+G H V G K++V+
Sbjct: 68 KQLQG-HTVDGHKLEVR 83
Score = 36.2 bits (82), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 33/74 (44%), Gaps = 4/74 (5%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKK---SRGFGFITYSSAHMVDDA- 66
LFI L++ T+ ETLK F G + + K S GFGF+ Y A
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 67 QAARPHTIDSKVVE 80
+ + HT+D +E
Sbjct: 68 KQLQGHTVDGHKLE 81
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 29/48 (60%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
+LF+ L Y +S E L+ F A+G + ++ D TKK +GF F+T+
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTF 57
Score = 34.3 bits (77), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 7/71 (9%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY-------NDYDP 153
+LFV +L +EEDL++ F +G ++ + + T K +GF FV + Y
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 154 VDKACLKGTHL 164
VD +G L
Sbjct: 70 VDGQVFQGRML 80
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 39.7 bits (91), Expect = 0.002, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 1/60 (1%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDV-VVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
+FIG LD + L F A+G ++ +M+DP T S+G+ FI ++S D A A
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Score = 37.4 bits (85), Expect = 0.012, Method: Composition-based stats.
Identities = 21/81 (25%), Positives = 42/81 (51%), Gaps = 4/81 (4%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSV-ALVTEKETGKKRGFGFVEYNDYDPVDKA--C 158
+F+G+L +I E+ L + F FG + ++ + +TG +G+ F+ + +D D A
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 159 LKGTHLVKGKKVDVKKALSKE 179
+ G +L + + V A K+
Sbjct: 68 MNGQYLCN-RPITVSYAFKKD 87
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 39.7 bits (91), Expect = 0.002, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 6/77 (7%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKG 161
+FVG D+TE++L+E+F Q+G+V V + R F FV + D D + ++
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFI-----PKPFRAFAFVTFAD-DQIAQSLCGE 61
Query: 162 THLVKGKKVDVKKALSK 178
++KG V + A K
Sbjct: 62 DLIIKGISVHISNAEPK 78
Score = 29.3 bits (64), Expect = 3.2, Method: Composition-based stats.
Identities = 14/48 (29%), Positives = 25/48 (52%), Gaps = 5/48 (10%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYS 58
+F+G + + L+ F +GDV+DV + K R F F+T++
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFI-----PKPFRAFAFVTFA 50
>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 = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 18/47 (38%), Positives = 26/47 (55%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
L V L + T+++L+ F GEV S L+ +K G G+GFV Y
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNY 68
Score = 29.6 bits (65), Expect = 2.2, Method: Composition-based stats.
Identities = 17/59 (28%), Positives = 30/59 (50%), Gaps = 3/59 (5%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
L + L + + L+S F + G+V +++D S G+GF+ Y +A DA+ A
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTA---KDAERA 77
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 4/64 (6%)
Query: 89 EINRPEAGATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
+I PE LF+ L + T+ DL F FG V S + +K+T + FGFV +
Sbjct: 34 QIEGPEGC----NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSF 89
Query: 149 NDYD 152
++ D
Sbjct: 90 DNPD 93
Score = 35.0 bits (79), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 30/60 (50%), Gaps = 3/60 (5%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
LFI L + L S F +G+V+ V D QT S+ FGF+++ + D AQ A
Sbjct: 42 NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNP---DSAQVA 98
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 29/56 (51%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
L V +L +T++ +E FG + LV + TG+ +G+GF EY D +A
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA 153
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 29/56 (51%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
L V +L +T++ +E FG + LV + TG+ +G+GF EY D +A
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA 153
>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 = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 29/56 (51%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
L V +L +T++ +E FG + LV + TG+ +G+GF EY D +A
Sbjct: 96 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA 151
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 38.5 bits (88), Expect = 0.005, Method: Composition-based stats.
Identities = 27/75 (36%), Positives = 41/75 (54%), Gaps = 4/75 (5%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC- 158
+ +FVG+L + EE L E F Q G +T V + ++E GK + FGFV + + V A
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIA 75
Query: 159 -LKGTHLVKGKKVDV 172
L G L G+ ++V
Sbjct: 76 LLNGIRLY-GRPINV 89
>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 = 38.1 bits (87), Expect = 0.006, Method: Composition-based stats.
Identities = 14/51 (27%), Positives = 32/51 (62%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYD 152
+++GS+ D TEE + + G V ++ ++ + +TG+ +G+ F+E+ D +
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLE 57
Score = 36.6 bits (83), Expect = 0.017, Method: Composition-based stats.
Identities = 15/49 (30%), Positives = 29/49 (59%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
R +++G + Y + E + G V+++ +M DPQT +S+G+ FI +
Sbjct: 5 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEF 53
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 38.1 bits (87), Expect = 0.006, Method: Composition-based stats.
Identities = 14/51 (27%), Positives = 32/51 (62%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYD 152
+++GS+ D TEE + + G V ++ ++ + +TG+ +G+ F+E+ D +
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLE 55
Score = 36.6 bits (83), Expect = 0.017, Method: Composition-based stats.
Identities = 15/49 (30%), Positives = 29/49 (59%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
R +++G + Y + E + G V+++ +M DPQT +S+G+ FI +
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEF 51
>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 = 38.1 bits (87), Expect = 0.006, Method: Composition-based stats.
Identities = 14/51 (27%), Positives = 32/51 (62%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYD 152
+++GS+ D TEE + + G V ++ ++ + +TG+ +G+ F+E+ D +
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLE 56
Score = 36.6 bits (83), Expect = 0.017, Method: Composition-based stats.
Identities = 15/49 (30%), Positives = 29/49 (59%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
R +++G + Y + E + G V+++ +M DPQT +S+G+ FI +
Sbjct: 4 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEF 52
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 36/145 (24%), Positives = 68/145 (46%), Gaps = 10/145 (6%)
Query: 4 EPEHLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMV 63
EP LF+G L++ S+ LK+ D+ V+ D + +R FG++ + SA +
Sbjct: 3 EPTTAFNLFVGNLNFNKSAPELKTGISDVFAKNDLAVV-DVRIGMTRKFGYVDFESAEDL 61
Query: 64 DDAQAARPHTIDSKVVEPKRAVPRTEINRPEAGATVKKLFVGSLRDDITEEDLKEYFGQF 123
+ A + E K P+ + ++ E A + L +L +T+++LKE F
Sbjct: 62 EKALELTGLKVFGN--EIKLEKPKGKDSKKERDA--RTLLAKNLPYKVTQDELKEVFEDA 117
Query: 124 GEVTSVALVTEKETGKKRGFGFVEY 148
E+ V+ + GK +G ++E+
Sbjct: 118 AEIRLVS-----KDGKSKGIAYIEF 137
>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 = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 28/50 (56%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYND 150
LF+ L + ++DL + F FG V S + +K+T + FGFV Y++
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDN 76
Score = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 26/55 (47%)
Query: 3 KEPEHLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
KE LFI L + L F +G+VV V D QT S+ FGF++Y
Sbjct: 20 KEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSY 74
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 37.7 bits (86), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 45/76 (59%), Gaps = 7/76 (9%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
+LFVG+L DITEE++++ F ++G+ V + K +GFGF+ + A ++
Sbjct: 24 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFI------HKDKGFGFIRLETRTLAEIAKVE 77
Query: 161 GTHL-VKGKKVDVKKA 175
++ ++GK++ V+ A
Sbjct: 78 LDNMPLRGKQLRVRFA 93
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 37.7 bits (86), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 31/47 (65%), Gaps = 1/47 (2%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
+F+GG+D R ++S F +G V +V ++ D +T S+G+GF+++
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSF 58
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 37.4 bits (85), Expect = 0.011, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 27/47 (57%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
+++ L + ++ L F +G VV V +MKD T+KS+G FI +
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILF 65
Score = 36.2 bits (82), Expect = 0.021, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 30/51 (58%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYD 152
++V +L +T DL F ++G+V V ++ +K+T K +G F+ + D D
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKD 69
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 37.0 bits (84), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 4/71 (5%)
Query: 98 TVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKE-TGKKRGFGFVEY---NDYDP 153
T K+ V ++ + +++E F FGE+ +V L + TG RGFGFV++ D
Sbjct: 14 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKK 73
Query: 154 VDKACLKGTHL 164
A THL
Sbjct: 74 AFNALCHSTHL 84
>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 = 37.0 bits (84), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 39/151 (25%), Positives = 62/151 (41%), Gaps = 36/151 (23%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA---- 66
LFIG L+ S LK D+ V+ D +T +R FG++ + SA ++ A
Sbjct: 16 LFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDLEKALELT 74
Query: 67 ---------QAARPHTIDSKVVEPKRAVPRTEINRPEAGATVKKLFVGSLRDDITEEDLK 117
+ +P DSK V R L +L +ITE++LK
Sbjct: 75 GLKVFGNEIKLEKPKGRDSKKVRAART-----------------LLAKNLSFNITEDELK 117
Query: 118 EYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
E F E+ V+ + GK +G ++E+
Sbjct: 118 EVFEDALEIRLVS-----QDGKSKGIAYIEF 143
>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 = 36.6 bits (83), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 45/76 (59%), Gaps = 7/76 (9%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
+LFVG+L DITEE++++ F ++G+ V + K +GFGF+ + A ++
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFI------HKDKGFGFIRLETRTLAEIAKVE 70
Query: 161 GTHL-VKGKKVDVKKA 175
++ ++GK++ V+ A
Sbjct: 71 LDNMPLRGKQLRVRFA 86
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 36.2 bits (82), Expect = 0.021, Method: Composition-based stats.
Identities = 12/48 (25%), Positives = 31/48 (64%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYN 149
L+V L ++++++++ F Q+G + + ++ ++ TG RG GF+ ++
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFD 51
Score = 31.2 bits (69), Expect = 0.74, Method: Composition-based stats.
Identities = 14/47 (29%), Positives = 25/47 (53%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
L++ GL S + ++ F +G ++ ++ D T SRG GFI +
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRF 50
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 36.2 bits (82), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 32/68 (47%), Gaps = 8/68 (11%)
Query: 91 NRPEAGATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYND 150
+R E + +LFV D+ E +L E FG FG + V ++ GF FVE+ +
Sbjct: 23 HRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEE 74
Query: 151 YDPVDKAC 158
+ KA
Sbjct: 75 AESAAKAI 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 = 36.2 bits (82), Expect = 0.025, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 1/60 (1%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
KLF+ L T+E+L+E G V + LVT + GK +G +VEY + +A +K
Sbjct: 19 KLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMK 77
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 35.8 bits (81), Expect = 0.029, Method: Composition-based stats.
Identities = 16/56 (28%), Positives = 32/56 (57%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
L++ L+ T++DL + +G++ S + +K T K +G+GFV+++ KA
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA 63
Score = 32.3 bits (72), Expect = 0.35, Method: Composition-based stats.
Identities = 17/59 (28%), Positives = 28/59 (47%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
L+I GL T+ + L + +G +V + D T K +G+GF+ + S A A
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA 66
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 35.8 bits (81), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 38/88 (43%), Gaps = 6/88 (6%)
Query: 83 RAVPRTEINRPEAGATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRG 142
R +P P G K L++ +L +TE DL F +F E + TG+ RG
Sbjct: 11 RKIPMFSSYNP--GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRG 68
Query: 143 FGFVEYNDYDPVDKACLKGTHLVKGKKV 170
F+ + P + + HLV G K+
Sbjct: 69 QAFITF----PNKEIAWQALHLVNGYKL 92
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 35.4 bits (80), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 35/67 (52%), Gaps = 1/67 (1%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC- 158
+ +F L I DL+++F G+V V +++++ + + +G +VE+ + V A
Sbjct: 26 RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG 85
Query: 159 LKGTHLV 165
L G L+
Sbjct: 86 LTGQRLL 92
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 34.7 bits (78), Expect = 0.064, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 5/75 (6%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC-- 158
++FV +L D T + LK+ F + G V + + E GK +G G V++ + ++AC
Sbjct: 10 QIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVKFESPEVAERACRM 67
Query: 159 LKGTHLVKGKKVDVK 173
+ G L G+++DV+
Sbjct: 68 MNGMKL-SGREIDVR 81
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 34.7 bits (78), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 35/61 (57%), Gaps = 4/61 (6%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
RKLF+G L+ + S E + F+ +G + + V++ P S+G F+ +SS +AQA
Sbjct: 16 RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPD-GSSKGCAFVKFSSH---TEAQA 71
Query: 69 A 69
A
Sbjct: 72 A 72
Score = 32.7 bits (73), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 3/70 (4%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA-- 157
+KLFVG L +EED+ F FG V V G +G FV+++ + A
Sbjct: 16 RKLFVGMLNKQQSEEDVLRLFQPFG-VIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIH 74
Query: 158 CLKGTHLVKG 167
L G+ + G
Sbjct: 75 ALHGSQTMPG 84
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 34.3 bits (77), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 9/76 (11%)
Query: 93 PEAGATVKKLFVGSLRDDITEEDLKEYFGQFGEV--------TSVALVTEKETGKKRGFG 144
P+ + ++V L D +T +DL ++F Q G V + + +KETGK +G
Sbjct: 9 PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDA 68
Query: 145 FVEYNDYDPVDKACLK 160
V Y D P KA ++
Sbjct: 69 TVSYED-PPTAKAAVE 83
>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 = 34.3 bits (77), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 5/83 (6%)
Query: 2 TKEPEHLRK----LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
+E E L K L++G L + T+ E + F GD+ +++ D K + GF F+ Y
Sbjct: 29 NEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEY 88
Query: 58 SSAHMVDDAQAARPHT-IDSKVV 79
S ++A T +D +++
Sbjct: 89 YSRADAENAMRYINGTRLDDRII 111
Score = 31.2 bits (69), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 26/47 (55%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
L+VG+L TEE + E F + G++ + + +K GF FVEY
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEY 88
>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 = 34.3 bits (77), Expect = 0.100, Method: Composition-based stats.
Identities = 23/78 (29%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVE-YNDYDPVDKACLK 160
+FVG L +IT + F FG ++ +V + TGK +G+GFV +N +D +
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 161 GTHLVKGKKVDVKKALSK 178
G + G+++ A K
Sbjct: 69 GGQWLGGRQIRTNWATRK 86
Score = 31.2 bits (69), Expect = 0.76, Method: Composition-based stats.
Identities = 15/47 (31%), Positives = 29/47 (61%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
+F+G L ++ + + F +G + D V+KD T KS+G+GF+++
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSF 55
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of Eukaryotic
Initiation Factor 4b
Length = 104
Score = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 30/47 (63%), Gaps = 2/47 (4%)
Query: 103 FVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKK-RGFGFVEY 148
F+G+L D+TEE +KE+F +++V L E ++ +GFG+ E+
Sbjct: 19 FLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEF 64
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In
Trinucleotide Repeat Containing 4 Variant
Length = 102
Score = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 35/61 (57%), Gaps = 4/61 (6%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
RKLF+G L + + E ++ FE +G + + V++ P S+G F+ + + H +AQA
Sbjct: 13 RKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPD-GTSKGCAFVKFQT-HA--EAQA 68
Query: 69 A 69
A
Sbjct: 69 A 69
Score = 31.6 bits (70), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDY 151
+KLFVG L T+ED+++ F FG + ++ + G +G FV++ +
Sbjct: 13 RKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPD-GTSKGCAFVKFQTH 63
>pdb|2M2B|A Chain A, Nmr Structure Of The Rrm2 Domain Of The Protein Rbm10 From
Homo Sapiens
Length = 131
Score = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 20/48 (41%), Positives = 28/48 (58%), Gaps = 4/48 (8%)
Query: 37 DVVVMKDPQTKKSRGFGFI---TYSSAHMVDDAQAARPH-TIDSKVVE 80
+V V+KD QT+ +RGF FI T +A ++ QA P TID K +
Sbjct: 54 NVRVIKDKQTQLNRGFAFIQLSTIEAAQLLQILQALHPPLTIDGKTIN 101
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 34/62 (54%), Gaps = 8/62 (12%)
Query: 97 ATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDK 156
A VK LFV +L + +TEE L++ F QFG++ V K + + F+ +++ D K
Sbjct: 9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVK--------KLKDYAFIHFDERDGAVK 60
Query: 157 AC 158
A
Sbjct: 61 AM 62
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 33.5 bits (75), Expect = 0.13, Method: Composition-based stats.
Identities = 23/74 (31%), Positives = 41/74 (55%), Gaps = 5/74 (6%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC--L 159
+FV +L D T + LK+ F + G V + + E GK +G G V++ + ++AC +
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVKFESPEVAERACRMM 65
Query: 160 KGTHLVKGKKVDVK 173
G L G+++DV+
Sbjct: 66 NGMKL-SGREIDVR 78
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 33.5 bits (75), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 29/52 (55%), Gaps = 2/52 (3%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDY 151
+ L+VG+L D+TE + + F Q G S ++TE + + FVE+ ++
Sbjct: 16 RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEH 65
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 33.5 bits (75), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 33/66 (50%), Gaps = 8/66 (12%)
Query: 93 PEAGATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYD 152
PE A VK LFV +L +TEE L++ F +FG++ V K + + FV + D
Sbjct: 9 PEVMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVK--------KLKDYAFVHFEDRG 60
Query: 153 PVDKAC 158
KA
Sbjct: 61 AAVKAM 66
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 33.5 bits (75), Expect = 0.15, Method: Composition-based stats.
Identities = 24/83 (28%), Positives = 43/83 (51%), Gaps = 8/83 (9%)
Query: 99 VKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA- 157
+ KL++G+L +T +DL++ FG L + K G+ FV+Y D + +A
Sbjct: 8 MNKLYIGNLSPAVTADDLRQLFG------DRKLPLAGQVLLKSGYAFVDYPDQNWAIRAI 61
Query: 158 -CLKGTHLVKGKKVDVKKALSKE 179
L G + GK ++V ++SK+
Sbjct: 62 ETLSGKVELHGKIMEVDYSVSKK 84
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 33.1 bits (74), Expect = 0.19, Method: Composition-based stats.
Identities = 21/80 (26%), Positives = 40/80 (50%), Gaps = 9/80 (11%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
KLF+G+L + TE++++ F Q+G+V ++ + +GFV D + A ++
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDA-IR 60
Query: 161 GTHLVKGKKVDVKKALSKEE 180
H K V++ SK +
Sbjct: 61 NLHHYKLHGVNINVEASKNK 80
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 33.1 bits (74), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 36/66 (54%), Gaps = 9/66 (13%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTS--------VALVTEKETGKKRGFGFVEYNDYDP 153
+FV L +++T E + +YF Q G + + + L T++ETGK +G V ++D P
Sbjct: 10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDD-PP 68
Query: 154 VDKACL 159
KA +
Sbjct: 69 SAKAAI 74
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 33.1 bits (74), Expect = 0.20, Method: Composition-based stats.
Identities = 21/66 (31%), Positives = 36/66 (54%), Gaps = 9/66 (13%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTS--------VALVTEKETGKKRGFGFVEYNDYDP 153
+FV L +++T E + +YF Q G + + + L T++ETGK +G V ++D P
Sbjct: 16 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDD-PP 74
Query: 154 VDKACL 159
KA +
Sbjct: 75 SAKAAI 80
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 33.1 bits (74), Expect = 0.21, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 8/57 (14%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
+LFV D+ E +L E FG FG + V ++ GF FVE+ + + KA
Sbjct: 6 RLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAKA 54
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 32.7 bits (73), Expect = 0.25, Method: Composition-based stats.
Identities = 25/83 (30%), Positives = 43/83 (51%), Gaps = 3/83 (3%)
Query: 99 VKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC 158
V +F+ +L I + L + F FG + S +V + E G K G+GFV + + ++A
Sbjct: 11 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENGSK-GYGFVHFETQEAAERAI 68
Query: 159 LK-GTHLVKGKKVDVKKALSKEE 180
K L+ +KV V + S++E
Sbjct: 69 EKMNGMLLNDRKVFVGRFKSRKE 91
Score = 28.1 bits (61), Expect = 6.5, Method: Composition-based stats.
Identities = 15/56 (26%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA 66
+FI LD ++ L F A+G+++ V+ D S+G+GF+ + + + A
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERA 67
>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 = 32.3 bits (72), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 45/89 (50%), Gaps = 4/89 (4%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
+F+ +L I + L + F FG + S +V + E G K G+GFV + + ++A K
Sbjct: 7 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENGSK-GYGFVHFETQEAAERAIEK 64
Query: 161 -GTHLVKGKKVDVKKALS-KEEMAKLKTR 187
L+ +KV V + S KE A+L R
Sbjct: 65 MNGMLLNDRKVFVGRFKSRKEREAELGAR 93
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 29/57 (50%), Gaps = 2/57 (3%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA 66
+FI LD ++ L F A+G+++ V+ D S+G+GF+ + + + A
Sbjct: 7 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERA 61
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 32.3 bits (72), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 33/68 (48%), Gaps = 6/68 (8%)
Query: 5 PEHLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVD 64
PE R L+I L Y+ ++E + F +G + + V P+T RG ++ Y +
Sbjct: 15 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYED---IF 68
Query: 65 DAQAARPH 72
DA+ A H
Sbjct: 69 DAKNACDH 76
Score = 32.3 bits (72), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 3/57 (5%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC 158
L++ +L IT E++ + FG++G + + + ET RG +V Y D AC
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIFDAKNAC 74
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 32.3 bits (72), Expect = 0.36, Method: Composition-based stats.
Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 3/57 (5%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC 158
L++ +L IT E++ + FG++G + + + ET RG +V Y D AC
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIFDAKNAC 68
Score = 31.2 bits (69), Expect = 0.76, Method: Composition-based stats.
Identities = 20/68 (29%), Positives = 33/68 (48%), Gaps = 6/68 (8%)
Query: 5 PEHLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVD 64
PE R L+I L Y+ ++E + F +G + + V P+T RG ++ Y +
Sbjct: 9 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYED---IF 62
Query: 65 DAQAARPH 72
DA+ A H
Sbjct: 63 DAKNACDH 70
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 32.3 bits (72), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 26/49 (53%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYND 150
LFVG L D+ + L E+F + V +TG +G+GFV++ D
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTD 60
>pdb|2E5G|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 21
Length = 94
Score = 32.0 bits (71), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 35/81 (43%), Gaps = 5/81 (6%)
Query: 99 VKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC 158
++ +FV + L EYF FG V SV V +K+ G F VE D +
Sbjct: 8 LRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVL 62
Query: 159 LKGTHLVKGKKVDVKKALSKE 179
+ H + G ++ V+ KE
Sbjct: 63 SQSQHSLGGHRLRVRPREQKE 83
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation Initiation
Factor 4b
Length = 100
Score = 32.0 bits (71), Expect = 0.44, Method: Composition-based stats.
Identities = 17/47 (36%), Positives = 30/47 (63%), Gaps = 2/47 (4%)
Query: 103 FVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKK-RGFGFVEY 148
F+G+L D+TEE +KE+F +++V L E ++ +GFG+ E+
Sbjct: 23 FLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEF 68
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 32.0 bits (71), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 33/68 (48%), Gaps = 6/68 (8%)
Query: 5 PEHLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVD 64
PE R L+I L Y+ ++E + F +G + + V P+T RG ++ Y +
Sbjct: 5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYED---IF 58
Query: 65 DAQAARPH 72
DA+ A H
Sbjct: 59 DAKNAVDH 66
Score = 29.6 bits (65), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 3/49 (6%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYND 150
L++ +L IT E++ + FG++G + + + ET RG +V Y D
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYED 56
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 32.0 bits (71), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 42/78 (53%), Gaps = 1/78 (1%)
Query: 103 FVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKGT 162
+VG+L + + D+ F + SV LV +K+T K +GF +VE+++ D + +A
Sbjct: 19 YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDG 77
Query: 163 HLVKGKKVDVKKALSKEE 180
L+ + + V A +++
Sbjct: 78 ALLGDRSLRVDIAEGRKQ 95
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Rna-Binding Protein 14
Length = 90
Score = 31.6 bits (70), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 14/75 (18%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA- 68
K+F+G + +S+ L+S FE G V++ V+KD Y+ HM +A A
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVVKD-------------YAFVHMEKEADAK 57
Query: 69 ARPHTIDSKVVEPKR 83
A ++ K V+ KR
Sbjct: 58 AAIAQLNGKEVKGKR 72
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 31.2 bits (69), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 4/73 (5%)
Query: 104 VGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKGTH 163
+ S + + ++ L F + G+V ++ ++ TGK +GF FVE + K +K H
Sbjct: 17 IPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKK-IIKSFH 75
Query: 164 LVKGKKVDVKKAL 176
GK++D+K L
Sbjct: 76 ---GKRLDLKHRL 85
>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 31.2 bits (69), Expect = 0.71, Method: Composition-based stats.
Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 9/52 (17%)
Query: 35 VVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAAR-------PHTIDSKVV 79
V ++ ++KD QT+++RGF F+ SSA +D +Q + P ID K +
Sbjct: 38 VNNIRLIKDKQTQQNRGFAFVQLSSA--MDASQLLQILQSLHPPLKIDGKTI 87
>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
pdb|2F9J|B Chain B, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
Length = 125
Score = 31.2 bits (69), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 3/57 (5%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC 158
L + +L IT E++ + FG++G + + + ET RG +V Y D AC
Sbjct: 21 LMIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIFDAKNAC 74
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 31.2 bits (69), Expect = 0.77, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 30/58 (51%), Gaps = 4/58 (6%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
K L + +L TEE L+E F E + V + + GK +G+ F+E+ ++ +A
Sbjct: 16 KTLVLSNLSYSATEETLQEVF----EKATFIKVPQNQNGKSKGYAFIEFASFEDAKEA 69
>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 = 30.8 bits (68), Expect = 0.93, Method: Composition-based stats.
Identities = 15/50 (30%), Positives = 29/50 (58%), Gaps = 2/50 (4%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETG--KKRGFGFVEY 148
K+FVG + +E+DL+E F Q+G V + ++ ++ + +G FV +
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTF 54
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 30.8 bits (68), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 7/57 (12%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
K++VG+L ++ + +L+ FG +G + SV + GF FVE+ DP D A
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPP-----GFAFVEFE--DPRDAA 124
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 30.8 bits (68), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 7/57 (12%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
K++VG+L ++ + +L+ FG +G + SV + GF FVE+ DP D A
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPP-----GFAFVEFE--DPRDAA 124
>pdb|3NS6|A Chain A, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
pdb|3NS6|B Chain B, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
Length = 100
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 4/73 (5%)
Query: 104 VGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKGTH 163
+ S + + ++ L F + G+V ++ ++ TGK +GF FVE + K +K H
Sbjct: 17 IPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDA-KKIIKSFH 75
Query: 164 LVKGKKVDVKKAL 176
GK++D+K L
Sbjct: 76 ---GKRLDLKHRL 85
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 30.4 bits (67), Expect = 1.2, Method: Composition-based stats.
Identities = 14/52 (26%), Positives = 27/52 (51%)
Query: 97 ATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
A+ L V L D+T+ +L F G + + ++ + +TG G+ FV++
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDF 52
>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 = 30.4 bits (67), Expect = 1.3, Method: Composition-based stats.
Identities = 14/39 (35%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 112 TEEDLKEYFGQFG-EVTSVALVTEKETGKKRGFGFVEYN 149
TE+D++ G + V L+ K +G+ RGF FVE++
Sbjct: 14 TEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFS 52
>pdb|2GAO|A Chain A, Crystal Structure Of Human Sar1a In Complex With Gdp
pdb|2GAO|B Chain B, Crystal Structure Of Human Sar1a In Complex With Gdp
Length = 208
Score = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 34/68 (50%), Gaps = 5/68 (7%)
Query: 76 SKVVEPKRAVPRTEINRPEAGATVKKLFVGS---LRDDITEEDLKEYFGQFGEVTSVALV 132
S++VE K V + E + V L +G+ D I+EE L+E FG +G+ T V
Sbjct: 116 SRLVESK--VELNALMTDETISNVPILILGNKIDRTDAISEEKLREIFGLYGQTTGKGNV 173
Query: 133 TEKETGKK 140
T KE +
Sbjct: 174 TLKELNAR 181
>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 = 29.6 bits (65), Expect = 1.9, Method: Composition-based stats.
Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 5/68 (7%)
Query: 3 KEPEHLRK----LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYS 58
+E E L K L++G L + T+ E + F GD+ +++ D + K + GF F+ Y
Sbjct: 9 EEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLD-KMKTACGFCFVEYY 67
Query: 59 SAHMVDDA 66
S ++A
Sbjct: 68 SRADAENA 75
Score = 28.9 bits (63), Expect = 4.1, Method: Composition-based stats.
Identities = 17/47 (36%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
L+VG+L TEE + E F + G++ + + +K GF FVEY
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDK-MKTACGFCFVEY 66
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
28
Length = 111
Score = 29.6 bits (65), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 28/61 (45%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
+ +FI L + + E L + +GD+ V V+ P T+ S+G F + + A
Sbjct: 16 KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 75
Query: 69 A 69
A
Sbjct: 76 A 76
>pdb|2HZC|A Chain A, Crystal Structure Of The N-terminal Rrm Of The U2af Large
Subunit
Length = 87
Score = 29.6 bits (65), Expect = 2.5, Method: Composition-based stats.
Identities = 17/83 (20%), Positives = 41/83 (49%), Gaps = 5/83 (6%)
Query: 97 ATVKKLFVGSLRDDITEEDLKEYFG---QFGEVTSVA--LVTEKETGKKRGFGFVEYNDY 151
+ ++L+VG++ ITEE + ++F + G +T V + + + F F+E+
Sbjct: 4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 63
Query: 152 DPVDKACLKGTHLVKGKKVDVKK 174
D +A + +G+ + +++
Sbjct: 64 DETTQAMAFDGIIFQGQSLKIRR 86
>pdb|2DIS|A Chain A, Solution Structure Of The Rrm Domain Of Unnamed Protein
Product
Length = 109
Score = 29.3 bits (64), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 2/52 (3%)
Query: 10 KLFIGGL-DYRTSSETLKSHFEAWGDVVDVVVMKDPQTK-KSRGFGFITYSS 59
+LFIGG+ + E L+ + V+DV+V K K+RGF F+ Y S
Sbjct: 10 RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYES 61
>pdb|1U2F|A Chain A, Solution Structure Of The First Rna-Binding Domain Of
Hu2af65
Length = 90
Score = 28.9 bits (63), Expect = 3.6, Method: Composition-based stats.
Identities = 17/80 (21%), Positives = 40/80 (50%), Gaps = 5/80 (6%)
Query: 100 KKLFVGSLRDDITEEDLKEYFG---QFGEVTSVA--LVTEKETGKKRGFGFVEYNDYDPV 154
++L+VG++ ITEE + ++F + G +T V + + + F F+E+ D
Sbjct: 2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 61
Query: 155 DKACLKGTHLVKGKKVDVKK 174
+A + +G+ + +++
Sbjct: 62 TQAMAFDGIIFQGQSLKIRR 81
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 28.5 bits (62), Expect = 5.4, Method: Composition-based stats.
Identities = 16/60 (26%), Positives = 27/60 (45%), Gaps = 6/60 (10%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
+L+VG L + + L F +FG + ++ V K F +++Y D AC K
Sbjct: 19 RLWVGGLGPNTSLAALAREFDRFGSIRTIDHV------KGDSFAYIQYESLDAAQAACAK 72
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 27.3 bits (59), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
LF+G+L + + +LK + +A+V + TG R FG+V++ + ++KA
Sbjct: 19 NLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDLEKA 74
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
0.315 0.133 0.380
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,590,242
Number of Sequences: 62578
Number of extensions: 228684
Number of successful extensions: 1144
Number of sequences better than 100.0: 167
Number of HSP's better than 100.0 without gapping: 129
Number of HSP's successfully gapped in prelim test: 38
Number of HSP's that attempted gapping in prelim test: 841
Number of HSP's gapped (non-prelim): 299
length of query: 304
length of database: 14,973,337
effective HSP length: 98
effective length of query: 206
effective length of database: 8,840,693
effective search space: 1821182758
effective search space used: 1821182758
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)
S2: 51 (24.3 bits)