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= 021295
(314 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex
With Rna
pdb|2KM8|C Chain C, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 167
Score = 114 bits (286), Expect = 6e-26, Method: Compositional matrix adjust.
Identities = 59/136 (43%), Positives = 91/136 (66%), Gaps = 5/136 (3%)
Query: 1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVGSKDFKTKKIF 60
MKD TG+ RGFGF+++ PS VD+V++ HI++GK ++ KR IP+ + KT KIF
Sbjct: 36 MKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDGKVIDPKRAIPR----DEQDKTGKIF 91
Query: 61 VGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK 120
VGGI V EF++FF Q+G + + Q+M D T +SRGFGF+T+D+ AV D + +
Sbjct: 92 VGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAV-DRVCQNKF 150
Query: 121 LELAGAQVEVKKAEPK 136
++ ++E+K+AEP+
Sbjct: 151 IDFKDRKIEIKRAEPR 166
Score = 60.1 bits (144), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 28/82 (34%), Positives = 55/82 (67%), Gaps = 2/82 (2%)
Query: 55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDL 114
++ K+F+GG+ ED +++F ++G V + +IM+D +T RSRGFGF++F+ +VD++
Sbjct: 2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61
Query: 115 LAKGNKLELAGAQVEVKKAEPK 136
+ + L+ G ++ K+A P+
Sbjct: 62 VKTQHILD--GKVIDPKRAIPR 81
>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 = 88.6 bits (218), Expect = 4e-18, Method: Compositional matrix adjust.
Identities = 56/155 (36%), Positives = 80/155 (51%), Gaps = 14/155 (9%)
Query: 1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDT-HIINGKQVEIKRTIPKGAVGSKD------ 53
M+D T + RGFGFVTYA VD + H ++G+ VE PK AV +D
Sbjct: 46 MRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVE-----PKRAVSREDSQRPGA 100
Query: 54 -FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVD 112
KKIFVGGI E +D+F Q+G ++ +IM D + + RGF F+TFD +VD
Sbjct: 101 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVD 160
Query: 113 DLLAKGNKLELAGAQVEVKKAEPKKPNLPQPSYRR 147
++ + + G EV+KA K+ S +R
Sbjct: 161 KIVIQKYHT-VNGHNCEVRKALSKQEMASASSSQR 194
Score = 55.5 bits (132), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 29/80 (36%), Positives = 51/80 (63%), Gaps = 3/80 (3%)
Query: 55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDL 114
+ +K+F+GG+ ++ + F Q+G + + +MRD +T RSRGFGF+T+ T + VD
Sbjct: 12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 71
Query: 115 L-AKGNKLELAGAQVEVKKA 133
+ A+ +K++ G VE K+A
Sbjct: 72 MNARPHKVD--GRVVEPKRA 89
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 88.6 bits (218), Expect = 4e-18, Method: Compositional matrix adjust.
Identities = 56/155 (36%), Positives = 80/155 (51%), Gaps = 14/155 (9%)
Query: 1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDT-HIINGKQVEIKRTIPKGAVGSKD------ 53
M+D T + RGFGFVTYA VD + H ++G+ VE PK AV +D
Sbjct: 47 MRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVE-----PKRAVSREDSQRPGA 101
Query: 54 -FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVD 112
KKIFVGGI E +D+F Q+G ++ +IM D + + RGF F+TFD +VD
Sbjct: 102 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVD 161
Query: 113 DLLAKGNKLELAGAQVEVKKAEPKKPNLPQPSYRR 147
++ + + G EV+KA K+ S +R
Sbjct: 162 KIVIQKYHT-VNGHNCEVRKALSKQEMASASSSQR 195
Score = 55.5 bits (132), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 29/80 (36%), Positives = 51/80 (63%), Gaps = 3/80 (3%)
Query: 55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDL 114
+ +K+F+GG+ ++ + F Q+G + + +MRD +T RSRGFGF+T+ T + VD
Sbjct: 13 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 72
Query: 115 L-AKGNKLELAGAQVEVKKA 133
+ A+ +K++ G VE K+A
Sbjct: 73 MNARPHKVD--GRVVEPKRA 90
>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 = 88.6 bits (218), Expect = 5e-18, Method: Compositional matrix adjust.
Identities = 56/155 (36%), Positives = 80/155 (51%), Gaps = 14/155 (9%)
Query: 1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDT-HIINGKQVEIKRTIPKGAVGSKD------ 53
M+D T + RGFGFVTYA VD + H ++G+ VE PK AV +D
Sbjct: 45 MRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVE-----PKRAVSREDSQRPGA 99
Query: 54 -FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVD 112
KKIFVGGI E +D+F Q+G ++ +IM D + + RGF F+TFD +VD
Sbjct: 100 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVD 159
Query: 113 DLLAKGNKLELAGAQVEVKKAEPKKPNLPQPSYRR 147
++ + + G EV+KA K+ S +R
Sbjct: 160 KIVIQKYHT-VNGHNCEVRKALSKQEMASASSSQR 193
Score = 55.1 bits (131), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 29/80 (36%), Positives = 51/80 (63%), Gaps = 3/80 (3%)
Query: 55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDL 114
+ +K+F+GG+ ++ + F Q+G + + +MRD +T RSRGFGF+T+ T + VD
Sbjct: 11 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 70
Query: 115 L-AKGNKLELAGAQVEVKKA 133
+ A+ +K++ G VE K+A
Sbjct: 71 MNARPHKVD--GRVVEPKRA 88
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 87.0 bits (214), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 54/145 (37%), Positives = 77/145 (53%), Gaps = 14/145 (9%)
Query: 1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDT-HIINGKQVEIKRTIPKGAVGSKD------ 53
M+D T + RGFGFVTYA VD + H ++G+ VE PK AV +D
Sbjct: 46 MRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVE-----PKRAVSREDSQRPGA 100
Query: 54 -FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVD 112
KKIFVGGI E +D+F Q+G ++ +IM D + + RGF F+TFD +VD
Sbjct: 101 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVD 160
Query: 113 DLLAKGNKLELAGAQVEVKKAEPKK 137
++ + + G EV+KA K+
Sbjct: 161 KIVIQKYHT-VNGHNCEVRKALSKQ 184
Score = 55.1 bits (131), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 29/80 (36%), Positives = 51/80 (63%), Gaps = 3/80 (3%)
Query: 55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDL 114
+ +K+F+GG+ ++ + F Q+G + + +MRD +T RSRGFGF+T+ T + VD
Sbjct: 12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 71
Query: 115 L-AKGNKLELAGAQVEVKKA 133
+ A+ +K++ G VE K+A
Sbjct: 72 MNARPHKVD--GRVVEPKRA 89
>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 = 87.0 bits (214), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 54/145 (37%), Positives = 77/145 (53%), Gaps = 14/145 (9%)
Query: 1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDT-HIINGKQVEIKRTIPKGAVGSKD------ 53
M+D T + RGFGFVTYA VD + H ++G+ VE PK AV +D
Sbjct: 39 MRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVE-----PKRAVSREDSQRPGA 93
Query: 54 -FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVD 112
KKIFVGGI E +D+F Q+G ++ +IM D + + RGF F+TFD +VD
Sbjct: 94 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVD 153
Query: 113 DLLAKGNKLELAGAQVEVKKAEPKK 137
++ + + G EV+KA K+
Sbjct: 154 KIVIQKYHT-VNGHNCEVRKALSKQ 177
Score = 55.1 bits (131), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 29/80 (36%), Positives = 51/80 (63%), Gaps = 3/80 (3%)
Query: 55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDL 114
+ +K+F+GG+ ++ + F Q+G + + +MRD +T RSRGFGF+T+ T + VD
Sbjct: 5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 64
Query: 115 L-AKGNKLELAGAQVEVKKA 133
+ A+ +K++ G VE K+A
Sbjct: 65 MNARPHKVD--GRVVEPKRA 82
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 87.0 bits (214), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 54/145 (37%), Positives = 77/145 (53%), Gaps = 14/145 (9%)
Query: 1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDT-HIINGKQVEIKRTIPKGAVGSKD------ 53
M+D T + RGFGFVTYA VD + H ++G+ VE PK AV +D
Sbjct: 44 MRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVE-----PKRAVSREDSQRPGA 98
Query: 54 -FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVD 112
KKIFVGGI E +D+F Q+G ++ +IM D + + RGF F+TFD +VD
Sbjct: 99 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVD 158
Query: 113 DLLAKGNKLELAGAQVEVKKAEPKK 137
++ + + G EV+KA K+
Sbjct: 159 KIVIQKYHT-VNGHNCEVRKALSKQ 182
Score = 55.1 bits (131), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 29/80 (36%), Positives = 51/80 (63%), Gaps = 3/80 (3%)
Query: 55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDL 114
+ +K+F+GG+ ++ + F Q+G + + +MRD +T RSRGFGF+T+ T + VD
Sbjct: 10 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 69
Query: 115 L-AKGNKLELAGAQVEVKKA 133
+ A+ +K++ G VE K+A
Sbjct: 70 MNARPHKVD--GRVVEPKRA 87
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 73.6 bits (179), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 39/119 (32%), Positives = 67/119 (56%), Gaps = 8/119 (6%)
Query: 1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRT-IPKGAVGSKDFKTKKI 59
++D+ TGQ G+GFV Y+DP+ DK I + +NG +++ K + S + +
Sbjct: 37 VRDKITGQSLGYGFVNYSDPNDADKAI---NTLNGLKLQTKTIKVSYARPSSASIRDANL 93
Query: 60 FVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFD----TEQAVDDL 114
+V G+P ++++ E + F Q+G + +I+ D +T SRG GFI FD E+A+ L
Sbjct: 94 YVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 152
Score = 52.0 bits (123), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 46/88 (52%), Gaps = 1/88 (1%)
Query: 53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVD 112
D KT + V +P ++ +DEFK F GD++ +++RD T +S G+GF+ + D
Sbjct: 2 DSKTN-LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDAD 60
Query: 113 DLLAKGNKLELAGAQVEVKKAEPKKPNL 140
+ N L+L ++V A P ++
Sbjct: 61 KAINTLNGLKLQTKTIKVSYARPSSASI 88
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 72.8 bits (177), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 39/87 (44%), Positives = 55/87 (63%), Gaps = 1/87 (1%)
Query: 58 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
KIFVGGIP + E E +++F +FG V E ++ D R RGFGFITF+ EQ+VD +
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
Query: 118 GNKLELAGAQVEVKKAEPKKPNLPQPS 144
+ ++ G +VEVK+AEP+ PS
Sbjct: 72 -HFHDIMGKKVEVKRAEPRDSKSSGPS 97
Score = 41.2 bits (95), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 21/50 (42%), Positives = 31/50 (62%), Gaps = 1/50 (2%)
Query: 3 DRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGAVGS 51
D + +PRGFGF+T+ D VD+ + H I GK+VE+KR P+ + S
Sbjct: 45 DAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVKRAEPRDSKSS 94
>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 = 69.3 bits (168), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 38/119 (31%), Positives = 63/119 (52%), Gaps = 8/119 (6%)
Query: 1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRT-IPKGAVGSKDFKTKKI 59
++D+ TGQ G+GFV Y DP +K I + +NG +++ K + S + +
Sbjct: 35 VRDKITGQSLGYGFVNYIDPKDAEKAI---NTLNGLRLQTKTIKVSYARPSSASIRDANL 91
Query: 60 FVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFD----TEQAVDDL 114
+V G+P ++ + E + F Q+G + +I+ D T SRG GFI FD E+A+ L
Sbjct: 92 YVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Score = 48.5 bits (114), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 47/86 (54%), Gaps = 8/86 (9%)
Query: 59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDL 114
+ V +P ++ ++EF+ F G+++ +++RD T +S G+GF+ + D E+A++ L
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 115 LAKGNKLELAGAQVEVKKAEPKKPNL 140
N L L ++V A P ++
Sbjct: 65 ----NGLRLQTKTIKVSYARPSSASI 86
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 67.0 bits (162), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 36/97 (37%), Positives = 61/97 (62%), Gaps = 5/97 (5%)
Query: 44 IPKGA-VGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGF 102
+P+G+ +GS K +F+GG+ ++ +++F QFG+V+E +MRD T RSRGFGF
Sbjct: 15 VPRGSHMGSSGCK---MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGF 71
Query: 103 ITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPN 139
+TF + VD +LA+ ++ EL ++ K A P++
Sbjct: 72 VTFMDQAGVDKVLAQ-SRHELDSKTIDPKVAFPRRAQ 107
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 31/49 (63%), Gaps = 1/49 (2%)
Query: 1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDT-HIINGKQVEIKRTIPKGA 48
M+D T + RGFGFVT+ D + VDKV+ + H ++ K ++ K P+ A
Sbjct: 58 MRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVAFPRRA 106
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 62.4 bits (150), Expect = 3e-10, Method: Composition-based stats.
Identities = 31/76 (40%), Positives = 50/76 (65%), Gaps = 1/76 (1%)
Query: 58 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
K+F+GG+ ++ +++F QFG+V+E +MRD T RSRGFGF+TF + VD +LA+
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 118 GNKLELAGAQVEVKKA 133
++ EL ++ K A
Sbjct: 62 -SRHELDSKTIDPKVA 76
Score = 35.8 bits (81), Expect = 0.034, Method: Composition-based stats.
Identities = 18/42 (42%), Positives = 28/42 (66%), Gaps = 1/42 (2%)
Query: 1 MKDRKTGQPRGFGFVTYADPSVVDKVI-EDTHIINGKQVEIK 41
M+D T + RGFGFVT+ D + VDKV+ + H ++ K ++ K
Sbjct: 33 MRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPK 74
>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 = 60.8 bits (146), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 39/150 (26%), Positives = 74/150 (49%), Gaps = 14/150 (9%)
Query: 3 DRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKR---------TIPKGAVGS 51
D T + +GF FV Y P +E ++ ++ G+ +++ R I + A +
Sbjct: 63 DSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEA 122
Query: 52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAV 111
+ F +I+V + +++D+ K F FG ++ + RD +T + +G+GFI ++ Q+
Sbjct: 123 RAFN--RIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSS 180
Query: 112 DDLLAKGNKLELAGAQVEVKKA-EPKKPNL 140
D ++ N +L G + V KA P P L
Sbjct: 181 QDAVSSMNLFDLGGQYLRVGKAVTPPMPLL 210
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 41/86 (47%), Gaps = 2/86 (2%)
Query: 58 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
+++VG I + ED + F FG ++ + D T + +GF F+ ++ +A L +
Sbjct: 30 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 89
Query: 118 GNKLELAGAQVEVKKAEPKKPNLPQP 143
N + L G ++V + P QP
Sbjct: 90 MNSVMLGGRNIKVGR--PSNIGQAQP 113
>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 = 60.8 bits (146), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 39/150 (26%), Positives = 73/150 (48%), Gaps = 14/150 (9%)
Query: 3 DRKTGQPRGFGFVTYADPSVVDKVIEDTH--IINGKQVEIKR---------TIPKGAVGS 51
D T + +GF FV Y P +E + ++ G+ +++ R I + A +
Sbjct: 48 DSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEA 107
Query: 52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAV 111
+ F +I+V + +++D+ K F FG ++ + RD +T + +G+GFI ++ Q+
Sbjct: 108 RAFN--RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSS 165
Query: 112 DDLLAKGNKLELAGAQVEVKKA-EPKKPNL 140
D ++ N +L G + V KA P P L
Sbjct: 166 QDAVSSMNLFDLGGQYLRVGKAVTPPMPLL 195
Score = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 37/73 (50%)
Query: 58 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
+++VG I + ED + F FG ++ + D T + +GF F+ ++ +A L +
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 118 GNKLELAGAQVEV 130
N + L G ++V
Sbjct: 75 MNSVMLGGRNIKV 87
>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 = 60.5 bits (145), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 39/150 (26%), Positives = 73/150 (48%), Gaps = 14/150 (9%)
Query: 3 DRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKR---------TIPKGAVGS 51
D T + +GF FV Y P +E ++ + G+ +++ R I + A +
Sbjct: 47 DSVTXKHKGFAFVEYEVPEAAQLALEQXNSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEA 106
Query: 52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAV 111
+ F +I+V + +++D+ K F FG ++ + RD +T + +G+GFI ++ Q+
Sbjct: 107 RAFN--RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSS 164
Query: 112 DDLLAKGNKLELAGAQVEVKKA-EPKKPNL 140
D ++ N +L G + V KA P P L
Sbjct: 165 QDAVSSXNLFDLGGQYLRVGKAVTPPXPLL 194
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 36/73 (49%)
Query: 58 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
+++VG I + ED + F FG ++ D T + +GF F+ ++ +A L +
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 118 GNKLELAGAQVEV 130
N + L G ++V
Sbjct: 74 XNSVXLGGRNIKV 86
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 60.5 bits (145), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 30/87 (34%), Positives = 45/87 (51%)
Query: 58 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
K+FVGG+ NE + F ++G + E +++D T RSRGFGF+TF+ D +
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 118 GNKLELAGAQVEVKKAEPKKPNLPQPS 144
N + G Q+ V +A N PS
Sbjct: 74 MNGKSVDGRQIRVDQAGKSSDNRSGPS 100
Score = 32.7 bits (73), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 25/39 (64%), Gaps = 3/39 (7%)
Query: 1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVE 39
+KDR+T + RGFGFVT+ + +D + +NGK V+
Sbjct: 45 VKDRETQRSRGFGFVTFEN---IDDAKDAMMAMNGKSVD 80
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 59.7 bits (143), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 29/88 (32%), Positives = 52/88 (59%), Gaps = 1/88 (1%)
Query: 57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 116
+K+F+GG+ E+ ++++ Q+G + + +MRD ++ RSRGFGF+TF + VD +A
Sbjct: 28 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA 87
Query: 117 KGNKLELAGAQVEVKKAEPKKPNLPQPS 144
+ G VE K+A ++ + PS
Sbjct: 88 -ARPHSIDGRVVEPKRAVAREESGSGPS 114
Score = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 31/52 (59%), Gaps = 1/52 (1%)
Query: 1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDT-HIINGKQVEIKRTIPKGAVGS 51
M+D + + RGFGFVT++ + VD + H I+G+ VE KR + + GS
Sbjct: 60 MRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAREESGS 111
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 58.9 bits (141), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 35/129 (27%), Positives = 64/129 (49%), Gaps = 5/129 (3%)
Query: 1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRT-IPKGAVGSKDFKTKKI 59
M+D KTG G+ FV + + I+ ++NG V KR + G + K +
Sbjct: 36 MRDYKTGYSYGYAFVDFTSEMDSQRAIK---VLNGITVRNKRLKVSYARPGGESIKDTNL 92
Query: 60 FVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDT-EQAVDDLLAKG 118
+V +P ++ +D+ F ++G + + I+RD T R RG F+ ++ E+A + + A
Sbjct: 93 YVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 152
Query: 119 NKLELAGAQ 127
N + G+Q
Sbjct: 153 NVIPEGGSQ 161
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 58.5 bits (140), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 28/79 (35%), Positives = 46/79 (58%), Gaps = 1/79 (1%)
Query: 58 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
K+FVGG+ S ++ + +F Q+G+V + IM+D +T++SRGFGF+ F V +LA
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 118 GNKLELAGAQVEVKKAEPK 136
L G ++ K P+
Sbjct: 78 -RPHTLDGRNIDPKPCTPR 95
Score = 44.7 bits (104), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 20/48 (41%), Positives = 30/48 (62%), Gaps = 1/48 (2%)
Query: 1 MKDRKTGQPRGFGFVTYADPSVVDKVIED-THIINGKQVEIKRTIPKG 47
MKD+ T Q RGFGFV + DP+ V V+ H ++G+ ++ K P+G
Sbjct: 49 MKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRNIDPKPCTPRG 96
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 57.8 bits (138), Expect = 8e-09, Method: Composition-based stats.
Identities = 30/75 (40%), Positives = 47/75 (62%), Gaps = 1/75 (1%)
Query: 59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
IFVGG+ + ++ K +F QFG V + +M D +T+R RGFGF+TF++E V+ + +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEK-VCEI 60
Query: 119 NKLELAGAQVEVKKA 133
+ E+ VE KKA
Sbjct: 61 HFHEINNKMVECKKA 75
Score = 39.7 bits (91), Expect = 0.002, Method: Composition-based stats.
Identities = 21/43 (48%), Positives = 27/43 (62%), Gaps = 1/43 (2%)
Query: 1 MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKR 42
M D+ T + RGFGFVT+ +V+KV E H IN K VE K+
Sbjct: 32 MFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKK 74
>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 = 57.8 bits (138), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 29/120 (24%), Positives = 60/120 (50%), Gaps = 4/120 (3%)
Query: 1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRT-IPKGAVGSKDFKTKKI 59
++D+ G G+GFV Y ++ I + +NG +++ K + S+ K +
Sbjct: 35 IRDKVAGHSLGYGFVNYVTAKDAERAI---NTLNGLRLQSKTIKVSYARPSSEVIKDANL 91
Query: 60 FVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN 119
++ G+P ++ + + +D F +FG + +++ D +T SRG FI FD ++ + N
Sbjct: 92 YISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFN 151
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 8/81 (9%)
Query: 59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDL 114
+ V +P ++ +DE + F G+V+ +++RD S G+GF+ + D E+A++ L
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 115 LAKGNKLELAGAQVEVKKAEP 135
N L L ++V A P
Sbjct: 65 ----NGLRLQSKTIKVSYARP 81
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 57.8 bits (138), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 29/120 (24%), Positives = 60/120 (50%), Gaps = 4/120 (3%)
Query: 1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRT-IPKGAVGSKDFKTKKI 59
++D+ G G+GFV Y ++ I + +NG +++ K + S+ K +
Sbjct: 35 IRDKVAGHSLGYGFVNYVTAKDAERAI---NTLNGLRLQSKTIKVSYARPSSEVIKDANL 91
Query: 60 FVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN 119
++ G+P ++ + + +D F +FG + +++ D +T SRG FI FD ++ + N
Sbjct: 92 YISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFN 151
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 8/81 (9%)
Query: 59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDL 114
+ V +P ++ +DE + F G+V+ +++RD S G+GF+ + D E+A++ L
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 115 LAKGNKLELAGAQVEVKKAEP 135
N L L ++V A P
Sbjct: 65 ----NGLRLQSKTIKVSYARP 81
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 42/73 (57%)
Query: 58 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
+++VG + ++ ED + F FG ++ Q+M D T RS+G+GFITF + L +
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 118 GNKLELAGAQVEV 130
N ELAG ++V
Sbjct: 88 LNGFELAGRPMKV 100
Score = 32.7 bits (73), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 11/28 (39%), Positives = 19/28 (67%)
Query: 1 MKDRKTGQPRGFGFVTYADPSVVDKVIE 28
M D +TG+ +G+GF+T++D K +E
Sbjct: 59 MMDSETGRSKGYGFITFSDSECAKKALE 86
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 53.5 bits (127), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 34/104 (32%), Positives = 53/104 (50%), Gaps = 10/104 (9%)
Query: 47 GAVGSKDFKTKK--IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFIT 104
G+ GS T K ++VGG+ V++ F+ FGD+ + QI D+ T + RGF F+
Sbjct: 1 GSSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 60
Query: 105 F----DTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPNLPQPS 144
F D A+D++ N+ EL G + V A+P + PS
Sbjct: 61 FELAEDAAAAIDNM----NESELFGRTIRVNLAKPMRIKESGPS 100
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 53.5 bits (127), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 35/61 (57%)
Query: 52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAV 111
KD KIFVGG+P + + +F FGD++E ++ D T +SRG+GF+T A
Sbjct: 13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAA 72
Query: 112 D 112
+
Sbjct: 73 E 73
Score = 37.7 bits (86), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 29/41 (70%), Gaps = 1/41 (2%)
Query: 1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDTH-IINGKQVEI 40
+ DR+TG+ RG+GFVT AD + ++ +D + II+G++ +
Sbjct: 50 ITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANV 90
>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 = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 30/76 (39%), Positives = 46/76 (60%), Gaps = 1/76 (1%)
Query: 58 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
K FVGG+ ++ + KD+F +FG+V + I D +T RSRGFGFI F +V+ +L +
Sbjct: 13 KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQ 72
Query: 118 GNKLELAGAQVEVKKA 133
+ L G ++ KKA
Sbjct: 73 -KEHRLDGRVIDPKKA 87
Score = 33.5 bits (75), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 28/42 (66%), Gaps = 1/42 (2%)
Query: 3 DRKTGQPRGFGFVTYADPSVVDKVIED-THIINGKQVEIKRT 43
D TG+ RGFGF+ + D + V+KV++ H ++G+ ++ K+
Sbjct: 46 DPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDGRVIDPKKA 87
>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 = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 48/76 (63%), Gaps = 1/76 (1%)
Query: 56 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL 115
KKIFVGG+ E++ +++F FG+V+ ++ D+ T++ RGF FITF E+ V ++
Sbjct: 1 VKKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 60
Query: 116 AKG-NKLELAGAQVEV 130
K + + L+ +++V
Sbjct: 61 EKKYHNVGLSKCEIKV 76
Score = 29.6 bits (65), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 3 DRKTGQPRGFGFVTYADPSVVDKVIEDT-HIINGKQVEIK 41
D KT + RGF F+T+ + V K++E H + + EIK
Sbjct: 36 DNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIK 75
>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 = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 30/135 (22%), Positives = 66/135 (48%), Gaps = 13/135 (9%)
Query: 5 KTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGAVGSKDFK----TKKI 59
+ Q + F F+ + + + D I G+ ++I+R D++ K+
Sbjct: 48 QINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRR--------PHDYQPLPGAHKL 99
Query: 60 FVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN 119
F+GG+P+ +N+D+ K+ FG ++ +++D +T S+G+ F + D +A N
Sbjct: 100 FIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLN 159
Query: 120 KLELAGAQVEVKKAE 134
++L ++ V++A
Sbjct: 160 GMQLGDKKLLVQRAS 174
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 3/48 (6%)
Query: 1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGA 48
+KD TG +G+ F Y D +V D+ I +NG Q+ K+ + + A
Sbjct: 129 VKDSATGLSKGYAFCEYVDINVTDQAIAG---LNGMQLGDKKLLVQRA 173
Score = 27.7 bits (60), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 40/79 (50%), Gaps = 11/79 (13%)
Query: 56 TKKIFVGGIPSSVNEDEFKDFF---MQFGDVQEH--QIMRDHSTSRSRGFGFITF----D 106
++++VG IP + E+ DFF M+ G + + + ++ + F F+ F +
Sbjct: 6 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 65
Query: 107 TEQAV--DDLLAKGNKLEL 123
T QA+ D ++ +G L++
Sbjct: 66 TTQAMAFDGIIFQGQSLKI 84
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 30/135 (22%), Positives = 66/135 (48%), Gaps = 13/135 (9%)
Query: 5 KTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGAVGSKDFK----TKKI 59
+ Q + F F+ + + + D I G+ ++I+R D++ K+
Sbjct: 46 QINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRR--------PHDYQPLPGAHKL 97
Query: 60 FVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN 119
F+GG+P+ +N+D+ K+ FG ++ +++D +T S+G+ F + D +A N
Sbjct: 98 FIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLN 157
Query: 120 KLELAGAQVEVKKAE 134
++L ++ V++A
Sbjct: 158 GMQLGDKKLLVQRAS 172
Score = 30.8 bits (68), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 3/48 (6%)
Query: 1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGA 48
+KD TG +G+ F Y D +V D+ I +NG Q+ K+ + + A
Sbjct: 127 VKDSATGLSKGYAFCEYVDINVTDQAIAG---LNGMQLGDKKLLVQRA 171
Score = 27.7 bits (60), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 40/79 (50%), Gaps = 11/79 (13%)
Query: 56 TKKIFVGGIPSSVNEDEFKDFF---MQFGDVQEH--QIMRDHSTSRSRGFGFITF----D 106
++++VG IP + E+ DFF M+ G + + + ++ + F F+ F +
Sbjct: 4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63
Query: 107 TEQAV--DDLLAKGNKLEL 123
T QA+ D ++ +G L++
Sbjct: 64 TTQAMAFDGIIFQGQSLKI 82
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 52.8 bits (125), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 46/88 (52%), Gaps = 1/88 (1%)
Query: 53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVD 112
D KT + V +P ++ +DEFK F GD++ +++RD T +S G+GF+ + D
Sbjct: 2 DSKTN-LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDAD 60
Query: 113 DLLAKGNKLELAGAQVEVKKAEPKKPNL 140
+ N L+L ++V A P ++
Sbjct: 61 KAINTLNGLKLQTKTIKVSYARPSSASI 88
Score = 37.7 bits (86), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIK 41
++D+ TGQ G+GFV Y+DP+ DK I + +NG +++ K
Sbjct: 37 VRDKITGQSLGYGFVNYSDPNDADKAI---NTLNGLKLQTK 74
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 52.4 bits (124), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 45/77 (58%)
Query: 58 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
K+F+GG+P+ +N+D+ K+ FG ++ +++D +T S+G+ F + D +A
Sbjct: 116 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 175
Query: 118 GNKLELAGAQVEVKKAE 134
N ++L ++ V++A
Sbjct: 176 LNGMQLGDKKLLVQRAS 192
Score = 33.5 bits (75), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 31/54 (57%), Gaps = 4/54 (7%)
Query: 1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQV-EIKRTIPKGAVGSKD 53
+KD TG +G+ F Y D +V D+ I +NG Q+ + K + + +VG+K+
Sbjct: 147 VKDSATGLSKGYAFCEYVDINVTDQAIAG---LNGMQLGDKKLLVQRASVGAKN 197
Score = 28.1 bits (61), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 40/79 (50%), Gaps = 11/79 (13%)
Query: 56 TKKIFVGGIPSSVNEDEFKDFF---MQFGDVQEH--QIMRDHSTSRSRGFGFITF----D 106
++++VG IP + E+ DFF M+ G + + + ++ + F F+ F +
Sbjct: 4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63
Query: 107 TEQAV--DDLLAKGNKLEL 123
T QA+ D ++ +G L++
Sbjct: 64 TTQAMAFDGIIFQGQSLKI 82
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 52.4 bits (124), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 27/89 (30%), Positives = 43/89 (48%)
Query: 56 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL 115
+ ++VG + ++ ED + F FG + +M+D T RS+G+GFITF + L
Sbjct: 5 SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
Query: 116 AKGNKLELAGAQVEVKKAEPKKPNLPQPS 144
+ N ELAG + V + PS
Sbjct: 65 EQLNGFELAGRPMRVGHVTERLDGGSGPS 93
Score = 32.7 bits (73), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 11/28 (39%), Positives = 19/28 (67%)
Query: 1 MKDRKTGQPRGFGFVTYADPSVVDKVIE 28
MKD TG+ +G+GF+T++D + +E
Sbjct: 38 MKDSDTGRSKGYGFITFSDSECARRALE 65
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 52.4 bits (124), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 46/81 (56%), Gaps = 1/81 (1%)
Query: 57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 116
+ I+VG + S ++ K+ F QFG V +++ D T + +GFGF+ E++V + +A
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIA 60
Query: 117 KGNKLELAGAQVEVKKAEPKK 137
K + + G + V +A PKK
Sbjct: 61 KLDNTDFMGRTIRVTEANPKK 81
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 30/49 (61%), Gaps = 3/49 (6%)
Query: 3 DRKTGQPRGFGFVTYADPSVVDKV--IEDTHIINGKQVEIKRTIPKGAV 49
DR+T +P+GFGFV + SV + + +++T + G+ + + PK ++
Sbjct: 36 DRETKKPKGFGFVEMQEESVSEAIAKLDNTDFM-GRTIRVTEANPKKSL 83
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 51.6 bits (122), Expect = 6e-07, Method: Composition-based stats.
Identities = 21/76 (27%), Positives = 45/76 (59%)
Query: 58 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
K+F+GG+P+ +N+D+ K+ FG ++ +++D +T S+G+ F + D +A
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 118 GNKLELAGAQVEVKKA 133
N ++L ++ V++A
Sbjct: 63 LNGMQLGDKKLLVQRA 78
Score = 32.3 bits (72), Expect = 0.34, Method: Composition-based stats.
Identities = 18/54 (33%), Positives = 31/54 (57%), Gaps = 4/54 (7%)
Query: 1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKR-TIPKGAVGSKD 53
+KD TG +G+ F Y D +V D+ I +NG Q+ K+ + + +VG+K+
Sbjct: 34 VKDSATGLSKGYAFCEYVDINVTDQAIAG---LNGMQLGDKKLLVQRASVGAKN 84
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 50.8 bits (120), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 45/86 (52%)
Query: 59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
++VGG+ V+E + F+Q G V + +D T + +G+GF+ F +E+ D +
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 119 NKLELAGAQVEVKKAEPKKPNLPQPS 144
+ ++L G + V KA NL PS
Sbjct: 78 DMIKLYGKPIRVNKASAHNKNLSGPS 103
Score = 27.7 bits (60), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 23/44 (52%), Gaps = 2/44 (4%)
Query: 2 KDRKTGQPRGFGFVTYADPSVVDKVIEDTHIIN--GKQVEIKRT 43
KDR TGQ +G+GFV + D I+ +I GK + + +
Sbjct: 49 KDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA 92
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 50.8 bits (120), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 31/90 (34%), Positives = 47/90 (52%), Gaps = 3/90 (3%)
Query: 58 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
K+F+GG+ NE K F + G + E +++D TS+SRGF FITF+ +
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKD 67
Query: 118 GNKLELAGAQVEVKKAEPKKPNLPQPSYRR 147
N L G ++V++A KKP+ RR
Sbjct: 68 MNGKSLHGKAIKVEQA--KKPSFQSGGRRR 95
Score = 28.1 bits (61), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 13/45 (28%), Positives = 28/45 (62%), Gaps = 3/45 (6%)
Query: 1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDTH--IINGKQVEIKRT 43
+KDR T + RGF F+T+ +P+ +D + ++GK +++++
Sbjct: 40 IKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA 83
>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 = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 46/75 (61%), Gaps = 1/75 (1%)
Query: 59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
+F+GG+ + + KD+F +FG+V + + D T RSRGFGF+ F ++VD ++ +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ- 60
Query: 119 NKLELAGAQVEVKKA 133
+ +L G ++ K+A
Sbjct: 61 KEHKLNGKVIDPKRA 75
Score = 36.6 bits (83), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 18/39 (46%), Positives = 26/39 (66%), Gaps = 1/39 (2%)
Query: 6 TGQPRGFGFVTYADPSVVDKVIED-THIINGKQVEIKRT 43
TG+ RGFGFV + + VDKV++ H +NGK ++ KR
Sbjct: 37 TGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKRA 75
>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 = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 34/144 (23%), Positives = 72/144 (50%), Gaps = 16/144 (11%)
Query: 1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDTH--IINGKQVEIKRT-----IPKGAVGSKD 53
+D T + G+ +V + P+ ++ ++ + +I GK V I + + K VG+
Sbjct: 48 CRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGN-- 105
Query: 54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDD 113
IF+ + S++ D F FG++ +++ D + S+ G+GF+ F+T++A +
Sbjct: 106 -----IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSK--GYGFVHFETQEAAER 158
Query: 114 LLAKGNKLELAGAQVEVKKAEPKK 137
+ K N + L +V V + + +K
Sbjct: 159 AIEKMNGMLLNDRKVFVGRFKSRK 182
>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 = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 34/144 (23%), Positives = 72/144 (50%), Gaps = 16/144 (11%)
Query: 1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDTH--IINGKQVEIKRT-----IPKGAVGSKD 53
+D T + G+ +V + P+ ++ ++ + +I GK V I + + K VG+
Sbjct: 43 CRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGN-- 100
Query: 54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDD 113
IF+ + S++ D F FG++ +++ D + S+ G+GF+ F+T++A +
Sbjct: 101 -----IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSK--GYGFVHFETQEAAER 153
Query: 114 LLAKGNKLELAGAQVEVKKAEPKK 137
+ K N + L +V V + + +K
Sbjct: 154 AIEKMNGMLLNDRKVFVGRFKSRK 177
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 46/73 (63%), Gaps = 1/73 (1%)
Query: 59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
IFVGG+ E++ +++F FG+V+ ++ D+ T++ RGF FITF E+ V ++ K
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Query: 119 -NKLELAGAQVEV 130
+ + L+ +++V
Sbjct: 62 YHNVGLSKCEIKV 74
Score = 29.3 bits (64), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 3 DRKTGQPRGFGFVTYADPSVVDKVIEDT-HIINGKQVEIK 41
D KT + RGF F+T+ + V K++E H + + EIK
Sbjct: 34 DNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIK 73
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 30/89 (33%), Positives = 43/89 (48%), Gaps = 7/89 (7%)
Query: 56 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL 115
+ +FVG + EDE ++FF Q+GDV + I + R F F+TF +Q L
Sbjct: 5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFADDQIAQSLC 59
Query: 116 AKGNKLELAGAQVEVKKAEPKKPNLPQPS 144
G L + G V + AEPK + PS
Sbjct: 60 --GEDLIIKGISVHISNAEPKHNSNSGPS 86
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 18/37 (48%)
Query: 10 RGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPK 46
R F FVT+AD + + + II G V I PK
Sbjct: 42 RAFAFVTFADDQIAQSLCGEDLIIKGISVHISNAEPK 78
>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 = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 48/87 (55%), Gaps = 1/87 (1%)
Query: 59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
+FVG + + ++ K F FG + + ++++D +T +S+G+GF++F + ++ + +
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 119 NKLELAGAQVEVKKAEPKKPNLPQPSY 145
L G Q+ A +KP P+ +Y
Sbjct: 78 GGQWLGGRQIRTNWAT-RKPPAPKSTY 103
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 30/85 (35%), Positives = 49/85 (57%), Gaps = 6/85 (7%)
Query: 47 GAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF- 105
G +GS +FVGGI ++E E + FF ++G V+E +I+ D T S+G+GF++F
Sbjct: 1 GPLGSGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFY 59
Query: 106 ---DTEQAVDDLLA-KGNKLELAGA 126
D ++ V+ + G KL+L A
Sbjct: 60 NDVDVQKIVESQINFHGKKLKLGPA 84
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 48.5 bits (114), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 44/86 (51%)
Query: 59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
+FVG + + ++ K F FG + + ++++D +T +S+G+GF++F + ++ +
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 119 NKLELAGAQVEVKKAEPKKPNLPQPS 144
L G Q+ A K P PS
Sbjct: 78 GGQWLGGRQIRTNWATRKPPAPSGPS 103
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 48.5 bits (114), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 41/85 (48%)
Query: 53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVD 112
D + +FVG IP E++ KD F + G V +++ D T + +G+GF + ++
Sbjct: 5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETAL 64
Query: 113 DLLAKGNKLELAGAQVEVKKAEPKK 137
+ N E +G + V A +K
Sbjct: 65 SAMRNLNGREFSGRALRVDNAASEK 89
Score = 29.6 bits (65), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 21/35 (60%), Gaps = 3/35 (8%)
Query: 3 DRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQ 37
DR+TG+P+G+GF Y D + + +NG++
Sbjct: 43 DRETGKPKGYGFCEYQDQETALSAMRN---LNGRE 74
>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 = 48.5 bits (114), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 8/81 (9%)
Query: 59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDL 114
+ V +P ++ +DE + F G+V+ +++RD S G+GF+ + D E+A++ L
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 115 LAKGNKLELAGAQVEVKKAEP 135
N L L ++V A P
Sbjct: 67 ----NGLRLQSKTIKVSYARP 83
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 48.1 bits (113), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 35/59 (59%)
Query: 47 GAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF 105
G+ G KD K+F+G IP +++E + K F +FG + E +++D T +G F+T+
Sbjct: 4 GSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTY 62
>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 = 48.1 bits (113), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 8/86 (9%)
Query: 54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQ 109
F+ + V +P + +DE + F G+V+ +++RD S G+GF+ + D E+
Sbjct: 17 FQGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 76
Query: 110 AVDDLLAKGNKLELAGAQVEVKKAEP 135
A++ L N L L ++V A P
Sbjct: 77 AINTL----NGLRLQSKTIKVSYARP 98
>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 = 48.1 bits (113), Expect = 6e-06, Method: Composition-based stats.
Identities = 25/85 (29%), Positives = 43/85 (50%)
Query: 50 GSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQ 109
GS + ++VGG+ V++ F+ FGD+ + QI D+ T + RGF F+ F+ +
Sbjct: 1 GSMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 60
Query: 110 AVDDLLAKGNKLELAGAQVEVKKAE 134
+ N+ EL G + V A+
Sbjct: 61 DAAAAIDNMNESELFGRTIRVNLAK 85
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 47.8 bits (112), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 43/77 (55%)
Query: 57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 116
+ + V IP++V+E + + F ++G ++ +I+ D T +SRG+GF+ F + + +A
Sbjct: 43 RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA 102
Query: 117 KGNKLELAGAQVEVKKA 133
N + +++V A
Sbjct: 103 GLNGFNILNKRLKVALA 119
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 47.4 bits (111), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 4/60 (6%)
Query: 59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFD----TEQAVDDL 114
++V G+P ++++ E + F Q+G + +I+ D +T SRG GFI FD E+A+ L
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 30/92 (32%), Positives = 52/92 (56%), Gaps = 5/92 (5%)
Query: 53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTS--RSRGFGFITFDTEQ- 109
D K+FVG +P + +E + ++ F Q+G V E ++RD S + +S+G F+TF T +
Sbjct: 12 DLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKA 71
Query: 110 AVDDLLAKGNKLELAGAQ--VEVKKAEPKKPN 139
A++ A N L G +++K A+ +K N
Sbjct: 72 ALEAQNALHNMKVLPGMHHPIQMKPADSEKNN 103
Score = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 29/112 (25%), Positives = 54/112 (48%), Gaps = 7/112 (6%)
Query: 1 MKDRKTGQP--RGFGFVT-YADPSVVD--KVIEDTHIINGKQVEIKRTIPKGAVGSKDFK 55
++DR P +G FVT Y + ++ + + ++ G I+ P + + +
Sbjct: 48 LRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMK-PADSEKNNAVE 106
Query: 56 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDT 107
+K+F+G I E++ + F FG ++E +I+R SRG F+TF T
Sbjct: 107 DRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAFVTFTT 157
>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 = 46.6 bits (109), Expect = 2e-05, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 39/75 (52%)
Query: 59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
++VGG+ V++ F+ FGD+ + QI D+ T + RGF F+ F+ + +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 119 NKLELAGAQVEVKKA 133
N+ EL G + V A
Sbjct: 65 NESELFGRTIRVNLA 79
>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 = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 45/73 (61%), Gaps = 6/73 (8%)
Query: 59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDL 114
+FVGGI ++E E + FF ++G V+E +I+ D T S+G+GF++F D ++ V+
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 115 LA-KGNKLELAGA 126
+ G KL+L A
Sbjct: 71 INFHGKKLKLGPA 83
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 45/73 (61%), Gaps = 6/73 (8%)
Query: 59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDL 114
+FVGGI ++E E + FF ++G V+E +I+ D T S+G+GF++F D ++ V+
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 115 LA-KGNKLELAGA 126
+ G KL+L A
Sbjct: 71 INFHGKKLKLGPA 83
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 43/81 (53%), Gaps = 8/81 (9%)
Query: 57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVD 112
+ ++VGG+ V++ F+ FGD+ + QI D+ T + RGF F+ F D A+D
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
Query: 113 DLLAKGNKLELAGAQVEVKKA 133
++ N+ EL G + V A
Sbjct: 124 NM----NESELFGRTIRVNLA 140
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 29/87 (33%), Positives = 51/87 (58%), Gaps = 5/87 (5%)
Query: 58 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTS--RSRGFGFITFDTEQ-AVDDL 114
K+FVG +P + +E + ++ F Q+G V E ++RD S + +S+G F+TF T + A++
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 115 LAKGNKLELAGAQ--VEVKKAEPKKPN 139
A N L G +++K A+ +K N
Sbjct: 65 NALHNMKVLPGMHHPIQMKPADSEKNN 91
Score = 41.2 bits (95), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 29/112 (25%), Positives = 54/112 (48%), Gaps = 7/112 (6%)
Query: 1 MKDRKTGQP--RGFGFVT-YADPSVVD--KVIEDTHIINGKQVEIKRTIPKGAVGSKDFK 55
++DR P +G FVT Y + ++ + + ++ G I+ P + + +
Sbjct: 36 LRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMK-PADSEKNNAVE 94
Query: 56 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDT 107
+K+F+G I E++ + F FG ++E +I+R SRG F+TF T
Sbjct: 95 DRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAFVTFTT 145
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 43/81 (53%), Gaps = 8/81 (9%)
Query: 57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVD 112
+ ++VGG+ V++ F+ FGD+ + QI D+ T + RGF F+ F D A+D
Sbjct: 6 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65
Query: 113 DLLAKGNKLELAGAQVEVKKA 133
++ N+ EL G + V A
Sbjct: 66 NM----NESELFGRTIRVNLA 82
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 30/51 (58%)
Query: 55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF 105
KT + V G+P E + K++F FG+V Q+ +D T S+GFGF+ F
Sbjct: 14 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF 64
Score = 37.4 bits (85), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 24/40 (60%)
Query: 2 KDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIK 41
KD KTG +GFGFV + + KV+ H+I+G+ + K
Sbjct: 49 KDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCK 88
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 31/54 (57%)
Query: 52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF 105
KD K+FVG IP ++E + K F +FG + E +++D T +G F+T+
Sbjct: 11 KDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTY 64
>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 = 44.7 bits (104), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 35/56 (62%), Gaps = 2/56 (3%)
Query: 58 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTS--RSRGFGFITFDTEQAV 111
K FVG +P + +E + ++ F Q+G V E ++RD S + +S+G F+TF T +A
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Score = 41.2 bits (95), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 29/112 (25%), Positives = 54/112 (48%), Gaps = 7/112 (6%)
Query: 1 MKDRKTGQP--RGFGFVT-YADPSVVD--KVIEDTHIINGKQVEIKRTIPKGAVGSKDFK 55
++DR P +G FVT Y + ++ + + ++ G I+ P + + +
Sbjct: 36 LRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNXKVLPGXHHPIQXK-PADSEKNNAVE 94
Query: 56 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDT 107
+K+F+G I E++ + F FG ++E +I+R SRG F+TF T
Sbjct: 95 DRKLFIGXISKKCTENDIRVXFSSFGQIEECRILRG-PDGLSRGCAFVTFTT 145
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 44.3 bits (103), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 41/79 (51%)
Query: 61 VGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK 120
V G+ E + ++ F ++G + + I+ D + RSRGF F+ F+ + + N
Sbjct: 17 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 76
Query: 121 LELAGAQVEVKKAEPKKPN 139
+EL G ++ V + K+P+
Sbjct: 77 MELDGRRIRVDFSITKRPH 95
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 41/79 (51%)
Query: 61 VGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK 120
V G+ E + ++ F ++G + + I+ D + RSRGF F+ F+ + + N
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 121 LELAGAQVEVKKAEPKKPN 139
+EL G ++ V + K+P+
Sbjct: 80 MELDGRRIRVDFSITKRPH 98
>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 = 43.9 bits (102), Expect = 1e-04, Method: Composition-based stats.
Identities = 21/55 (38%), Positives = 36/55 (65%), Gaps = 2/55 (3%)
Query: 58 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTS--RSRGFGFITFDTEQA 110
K+FVG +P + +E + ++ F Q+G V E ++RD S + +S+G F+TF T +A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKA 59
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 42/87 (48%), Gaps = 8/87 (9%)
Query: 58 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
K+F+G +P E E + F Q+G V E I+++ +GF+ + + A +D +
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFVHIEDKTAAEDAIRN 61
Query: 118 GNKLELAGAQVEVKKAEPKKPNLPQPS 144
+ +L G + V+ ++ K PS
Sbjct: 62 LHHYKLHGVNINVEASKNKSKASSGPS 88
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 41/79 (51%)
Query: 61 VGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK 120
V G+ E + ++ F ++G + + I+ D + RSRGF F+ F+ + + N
Sbjct: 51 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 110
Query: 121 LELAGAQVEVKKAEPKKPN 139
+EL G ++ V + K+P+
Sbjct: 111 MELDGRRIRVDFSITKRPH 129
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 29/129 (22%), Positives = 62/129 (48%), Gaps = 8/129 (6%)
Query: 3 DRKTGQPRGFGFVTYADPSVVDKVIEDTHI-INGKQVEIKRTIPKGAVGSKDFKTKKIFV 61
D + G R FG+V + ++K +E T + + G ++++++ PKG K+ + +
Sbjct: 41 DVRIGMTRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEK--PKGKDSKKERDARTLLA 98
Query: 62 GGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKL 121
+P V +DE K+ F +++ + +D +S+G +I F TE + +
Sbjct: 99 KNLPYKVTQDELKEVFEDAAEIR--LVSKD---GKSKGIAYIEFKTEADAEKTFEEKQGT 153
Query: 122 ELAGAQVEV 130
E+ G + +
Sbjct: 154 EIDGRSISL 162
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 30/117 (25%), Positives = 54/117 (46%), Gaps = 10/117 (8%)
Query: 5 KTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVE---IKRTIPKGAVGSKDFKTKKIFV 61
K + + FV Y + ++ +NGKQ+E +K + S T +FV
Sbjct: 36 KNNKNVNYAFVEYHQSHDANIALQ---TLNGKQIENNIVKINWAFQSQQSSSDDTFNLFV 92
Query: 62 GGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDL 114
G + +V+++ ++ F F +M D T SRG+GF++F D + A+D +
Sbjct: 93 GDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 149
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 39/83 (46%), Gaps = 7/83 (8%)
Query: 58 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
K+FVG + +E + FF Q+G+V + I + R F F+TF ++ L
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF-----RAFAFVTFADDKVAQSLC-- 65
Query: 118 GNKLELAGAQVEVKKAEPKKPNL 140
G L + G V + AEPK L
Sbjct: 66 GEDLIIKGISVHISNAEPKHNKL 88
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 18/37 (48%)
Query: 10 RGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPK 46
R F FVT+AD V + + II G V I PK
Sbjct: 48 RAFAFVTFADDKVAQSLCGEDLIIKGISVHISNAEPK 84
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 29/98 (29%), Positives = 47/98 (47%), Gaps = 11/98 (11%)
Query: 50 GSKDFKTK-KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTE 108
G K F + ++FVG +P + E+E + F ++G E I +D +GFGFI +T
Sbjct: 15 GEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETR 68
Query: 109 QAVDDLLAKGNKLELAGAQVEVK----KAEPKKPNLPQ 142
+ + + + L G Q+ V+ A NLPQ
Sbjct: 69 TLAEIAKVELDNMPLRGKQLRVRFACHSASLTVRNLPQ 106
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 25/68 (36%), Positives = 38/68 (55%), Gaps = 11/68 (16%)
Query: 58 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
++FVG +P+ + E++FK F ++G+ E I RD RGFGFI ++ LA+
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRT-----LAE 72
Query: 118 GNKLELAG 125
K EL G
Sbjct: 73 IAKAELDG 80
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 28/87 (32%), Positives = 39/87 (44%), Gaps = 1/87 (1%)
Query: 59 IFVGGIPSSVNEDEFKDFFMQFGDV-QEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
IF+G + ++E D F FG + Q +IMRD T S+G+ FI F + A D +
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 118 GNKLELAGAQVEVKKAEPKKPNLPQPS 144
N L + V A K PS
Sbjct: 68 MNGQYLCNRPITVSYAFKKDSKGSGPS 94
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 41.2 bits (95), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 36/70 (51%)
Query: 61 VGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK 120
V G+ E + ++ F ++G + + I+ D + RSRGF F+ F+ + + N
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 121 LELAGAQVEV 130
+EL G ++ V
Sbjct: 80 MELDGRRIRV 89
>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 = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 6/76 (7%)
Query: 58 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
++FVG +P + E+E + F ++G E I +D +GFGFI +T + +
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 70
Query: 118 GNKLELAGAQVEVKKA 133
+ + L G Q+ V+ A
Sbjct: 71 LDNMPLRGKQLRVRFA 86
>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 = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 44/79 (55%), Gaps = 2/79 (2%)
Query: 59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
IF+ + S++ D F FG++ +++ D + S+ G+GF+ F+T++A + + K
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSK--GYGFVHFETQEAAERAIEKM 65
Query: 119 NKLELAGAQVEVKKAEPKK 137
N + L +V V + + +K
Sbjct: 66 NGMLLNDRKVFVGRFKSRK 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 = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 31/129 (24%), Positives = 62/129 (48%), Gaps = 8/129 (6%)
Query: 3 DRKTGQPRGFGFVTYADPSVVDKVIEDTHI-INGKQVEIKRTIPKGAVGSKDFKTKKIFV 61
D +TG R FG+V + ++K +E T + + G ++++++ PKG K + +
Sbjct: 47 DVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEK--PKGRDSKKVRAARTLLA 104
Query: 62 GGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKL 121
+ ++ EDE K+ F D E +++ +S+G +I F +E + L +
Sbjct: 105 KNLSFNITEDELKEVFE---DALEIRLV--SQDGKSKGIAYIEFKSEADAEKNLEEKQGA 159
Query: 122 ELAGAQVEV 130
E+ G V +
Sbjct: 160 EIDGRSVSL 168
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 40/81 (49%), Gaps = 6/81 (7%)
Query: 57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSR--SRGFGFITFDTEQAV--- 111
+K+FVGG+P ++EDE F +FG + + S S +G+ F+ F E +V
Sbjct: 9 RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQAL 68
Query: 112 -DDLLAKGNKLELAGAQVEVK 131
D L + KL L + +K
Sbjct: 69 IDACLEEDGKLYLCVSSPTIK 89
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 38/74 (51%), Gaps = 1/74 (1%)
Query: 57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 116
+ +FVG + + V E+ + F+Q G + + I +D + + FGF+ F ++V +A
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIA 75
Query: 117 KGNKLELAGAQVEV 130
N + L G + V
Sbjct: 76 LLNGIRLYGRPINV 89
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/90 (26%), Positives = 46/90 (51%), Gaps = 3/90 (3%)
Query: 56 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL 115
+ +F + + + + +DFF G V++ +I+ D ++ RS+G ++ F Q+V L
Sbjct: 25 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVP--L 82
Query: 116 AKG-NKLELAGAQVEVKKAEPKKPNLPQPS 144
A G L G + V+ ++ +K L PS
Sbjct: 83 AIGLTGQRLLGVPIIVQASQAEKNRLSGPS 112
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 44/79 (55%), Gaps = 2/79 (2%)
Query: 59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
IF+ + S++ D F FG++ +++ D + S+ G+GF+ F+T++A + + K
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSK--GYGFVHFETQEAAERAIEKM 71
Query: 119 NKLELAGAQVEVKKAEPKK 137
N + L +V V + + +K
Sbjct: 72 NGMLLNDRKVFVGRFKSRK 90
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 28/84 (33%), Positives = 42/84 (50%), Gaps = 9/84 (10%)
Query: 56 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHS-TSRSRGFGFITFDTEQ----A 110
T KI V IP N+ E ++ F FG+++ ++ + + T RGFGF+ F T+Q A
Sbjct: 15 TSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKA 74
Query: 111 VDDLLAK----GNKLELAGAQVEV 130
+ L G +L L A EV
Sbjct: 75 FNALCHSTHLYGRRLVLEWADSEV 98
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 49/95 (51%), Gaps = 4/95 (4%)
Query: 44 IPKGAVGSKDFKT--KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFG 101
+P+G+ + + K+ K++ V IP + + + F QFG + + +I+ + S+ GFG
Sbjct: 15 VPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSK--GFG 72
Query: 102 FITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPK 136
F+TF+ D K + + G ++EV A +
Sbjct: 73 FVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107
Score = 28.9 bits (63), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 11/39 (28%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 10 RGFGFVTYADPSVVDKVIEDTH--IINGKQVEIKRTIPK 46
+GFGFVT+ + + D+ E H ++ G+++E+ +
Sbjct: 69 KGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107
>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 = 38.9 bits (89), Expect = 0.004, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 40/75 (53%), Gaps = 2/75 (2%)
Query: 64 IPSSVNEDEFKDFFMQFG-DVQEHQIMRDHSTSRSRGFGFITFDTEQ-AVDDLLAKGNKL 121
+P + ED+ + G +E ++MR+ S+ +SRGF F+ F Q A + A + L
Sbjct: 9 LPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSL 68
Query: 122 ELAGAQVEVKKAEPK 136
+ G +V + ++PK
Sbjct: 69 NILGQKVSMHYSDPK 83
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 37/73 (50%)
Query: 59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
+F+ +P + + F+ FG+V ++ D TS S+ FGF++FD + +
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 119 NKLELAGAQVEVK 131
N ++ +++V+
Sbjct: 103 NGFQVGTKRLKVQ 115
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 42/88 (47%), Gaps = 2/88 (2%)
Query: 57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 116
K++ V IP + + + F QFG + + +I+ + S+ GFGF+TF+ D
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSK--GFGFVTFENSADADRARE 73
Query: 117 KGNKLELAGAQVEVKKAEPKKPNLPQPS 144
K + + G ++EV A + PS
Sbjct: 74 KLHGTVVEGRKIEVNNATARVMTNSGPS 101
Score = 28.9 bits (63), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 12/44 (27%), Positives = 24/44 (54%), Gaps = 2/44 (4%)
Query: 10 RGFGFVTYADPSVVDKVIEDTH--IINGKQVEIKRTIPKGAVGS 51
+GFGFVT+ + + D+ E H ++ G+++E+ + S
Sbjct: 55 KGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVMTNS 98
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 43/79 (54%), Gaps = 10/79 (12%)
Query: 56 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTE------- 108
+K +FV G+ E+ K+ F G V+ +I+ D T S+GFGF+ F++E
Sbjct: 15 SKTLFVKGLSEDTTEETLKESFD--GSVR-ARIVTDRETGSSKGFGFVDFNSEEDAKAAK 71
Query: 109 QAVDDLLAKGNKLELAGAQ 127
+A++D GNK+ L A+
Sbjct: 72 EAMEDGEIDGNKVTLDWAK 90
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 26/49 (53%), Gaps = 4/49 (8%)
Query: 1 MKDRKTGQPRGFGFVTY---ADPSVVDKVIEDTHIINGKQVEIKRTIPK 46
+ DR+TG +GFGFV + D + +ED I+G +V + PK
Sbjct: 45 VTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGE-IDGNKVTLDWAKPK 92
>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 = 38.5 bits (88), Expect = 0.005, Method: Composition-based stats.
Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 4/63 (6%)
Query: 56 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAV 111
T +FVG + +V+++ ++ F F +M D T SRG+GF++F D + A+
Sbjct: 1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60
Query: 112 DDL 114
D +
Sbjct: 61 DSM 63
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
+++ +P S++E E ++ FG V +I+RD S+ SRG GF ++ + + ++
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHF 86
Query: 119 N 119
N
Sbjct: 87 N 87
>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 = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 19/86 (22%), Positives = 41/86 (47%)
Query: 59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
+F+ +P + + FM FG+V ++ D T+ S+ FGF+++D + +
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 119 NKLELAGAQVEVKKAEPKKPNLPQPS 144
N ++ +++V+ K + PS
Sbjct: 88 NGFQIGMKRLKVQLKRSKNDSKSGPS 113
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 23/40 (57%), Gaps = 3/40 (7%)
Query: 3 DRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKR 42
D++T + FGFV+Y +P I+ +NG Q+ +KR
Sbjct: 60 DKQTNLSKCFGFVSYDNPVSAQAAIQS---MNGFQIGMKR 96
>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 = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 24/91 (26%), Positives = 43/91 (47%), Gaps = 4/91 (4%)
Query: 59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
+FV I EDE ++ F +G+++ + D T S+G+ + ++T + L AK
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQA--LAAKE 132
Query: 119 --NKLELAGAQVEVKKAEPKKPNLPQPSYRR 147
N E+ G ++V K P + S +R
Sbjct: 133 ALNGAEIMGQTIQVDWCFVKGPKRVKKSEKR 163
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 37.7 bits (86), Expect = 0.008, Method: Composition-based stats.
Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 1/63 (1%)
Query: 59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF-DTEQAVDDLLAK 117
++V +P S+ ++ F ++G V + IM+D T +S+G FI F D + A + A
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 118 GNK 120
NK
Sbjct: 79 NNK 81
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 37.4 bits (85), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 25/94 (26%), Positives = 43/94 (45%), Gaps = 6/94 (6%)
Query: 57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL- 115
K +F+ + E+ + QFGD++ +++ T S+G F F T++A L
Sbjct: 16 KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 75
Query: 116 -----AKGNKLELAGAQVEVKKAEPKKPNLPQPS 144
A+G L+L G Q++V A + PS
Sbjct: 76 AASLEAEGGGLKLDGRQLKVDLAVTRDEAASGPS 109
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 37.4 bits (85), Expect = 0.011, Method: Composition-based stats.
Identities = 25/88 (28%), Positives = 46/88 (52%), Gaps = 9/88 (10%)
Query: 47 GAVGS--KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFIT 104
G+ GS +D ++VGG+ ++ E + ++ F QFG+++ +++ + FI
Sbjct: 1 GSSGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCA------FIQ 54
Query: 105 FDTEQAVDDLLAKG-NKLELAGAQVEVK 131
F T QA + K NKL + G ++ VK
Sbjct: 55 FATRQAAEVAAEKSFNKLIVNGRRLNVK 82
>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 = 37.4 bits (85), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 34/68 (50%)
Query: 71 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 130
D + F ++G V + I RD T SRGF F+ F ++ +D + + L G ++ V
Sbjct: 62 DTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV 121
Query: 131 KKAEPKKP 138
+ A +P
Sbjct: 122 QMARYGRP 129
>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 = 37.0 bits (84), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 39/86 (45%), Gaps = 4/86 (4%)
Query: 56 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL 115
+ I+VG + +E + F G V I+ D + +GF +I F +++V L
Sbjct: 6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 65
Query: 116 AKGNKLELAGAQVEVKKAEPKKPNLP 141
A L G Q++V PK+ N P
Sbjct: 66 ALDESL-FRGRQIKVI---PKRTNRP 87
Score = 29.6 bits (65), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 28/47 (59%), Gaps = 4/47 (8%)
Query: 1 MKDRKTGQPRGFGFVTYAD-PSVVDKVIEDTHIINGKQVEIKRTIPK 46
+ D+ +G P+GF ++ ++D SV + D + G+Q+++ IPK
Sbjct: 39 LCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKV---IPK 82
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 37.0 bits (84), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 36/80 (45%)
Query: 59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
+FV I EDE ++ F +G+++ + D T S+G+ + ++T +
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 119 NKLELAGAQVEVKKAEPKKP 138
N E+ G ++V K P
Sbjct: 89 NGAEIMGQTIQVDWCFVKGP 108
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 36.6 bits (83), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 44/88 (50%), Gaps = 4/88 (4%)
Query: 57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTE---QAVDD 113
+K+FVG + +ED+ + F FG+++E I+R S+G F+ + + QA +
Sbjct: 16 RKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRG-PDGNSKGCAFVKYSSHAEAQAAIN 74
Query: 114 LLAKGNKLELAGAQVEVKKAEPKKPNLP 141
L + A + + VK A+ K + P
Sbjct: 75 ALHGSQTMPGASSSLVVKFADTDKESGP 102
>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 = 36.2 bits (82), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 39/86 (45%), Gaps = 4/86 (4%)
Query: 56 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL 115
+ I+VG + +E + F G V I+ D + +GF +I F +++V L
Sbjct: 5 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 64
Query: 116 AKGNKLELAGAQVEVKKAEPKKPNLP 141
A L G Q++V PK+ N P
Sbjct: 65 ALDESL-FRGRQIKVI---PKRTNRP 86
Score = 29.6 bits (65), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 28/47 (59%), Gaps = 4/47 (8%)
Query: 1 MKDRKTGQPRGFGFVTYAD-PSVVDKVIEDTHIINGKQVEIKRTIPK 46
+ D+ +G P+GF ++ ++D SV + D + G+Q+++ IPK
Sbjct: 38 LCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKV---IPK 81
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 35.8 bits (81), Expect = 0.034, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 27/50 (54%)
Query: 56 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF 105
++ +++G IP E++ D G V ++M D T RS+G+ FI F
Sbjct: 2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEF 51
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 35.8 bits (81), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 37/78 (47%)
Query: 61 VGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK 120
V + + D + F ++G V + I RD T SRGF F+ F ++ +D + +
Sbjct: 75 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 134
Query: 121 LELAGAQVEVKKAEPKKP 138
L G ++ V+ A +P
Sbjct: 135 AVLDGRELRVQMARYGRP 152
>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 = 35.4 bits (80), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 18/78 (23%), Positives = 39/78 (50%)
Query: 59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
+FVG + + F FG + + ++++D +T +S+G+GF++F + ++ + +
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 119 NKLELAGAQVEVKKAEPK 136
L G Q+ A K
Sbjct: 69 GGQWLGGRQIRTNWATRK 86
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 35.4 bits (80), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 25/113 (22%), Positives = 49/113 (43%), Gaps = 14/113 (12%)
Query: 10 RGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTI-PKGAVGSKDFKTKKIFVGGIPSSV 68
+G FVT + + I H ++ E+ + P A+ + V +P S+
Sbjct: 57 KGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDAL---------LCVANLPPSL 107
Query: 69 NEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDLLAK 117
+ +F++ FG ++ ++ T +S+G+GF + +A DLL K
Sbjct: 108 TQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGK 160
>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 = 35.4 bits (80), Expect = 0.044, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 27/50 (54%)
Query: 56 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF 105
++ +++G IP E++ D G V ++M D T RS+G+ FI F
Sbjct: 4 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEF 53
>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 = 35.4 bits (80), Expect = 0.044, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 27/50 (54%)
Query: 56 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF 105
++ +++G IP E++ D G V ++M D T RS+G+ FI F
Sbjct: 3 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEF 52
>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 = 35.4 bits (80), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 25/113 (22%), Positives = 49/113 (43%), Gaps = 14/113 (12%)
Query: 10 RGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTI-PKGAVGSKDFKTKKIFVGGIPSSV 68
+G FVT + + I H ++ E+ + P A+ + V +P S+
Sbjct: 55 KGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDAL---------LCVANLPPSL 105
Query: 69 NEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDLLAK 117
+ +F++ FG ++ ++ T +S+G+GF + +A DLL K
Sbjct: 106 TQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGK 158
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 35.0 bits (79), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 25/113 (22%), Positives = 49/113 (43%), Gaps = 14/113 (12%)
Query: 10 RGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTI-PKGAVGSKDFKTKKIFVGGIPSSV 68
+G FVT + + I H ++ E+ + P A+ + V +P S+
Sbjct: 57 KGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDAL---------LCVANLPPSL 107
Query: 69 NEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDLLAK 117
+ +F++ FG ++ ++ T +S+G+GF + +A DLL K
Sbjct: 108 TQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGK 160
>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 = 34.3 bits (77), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 21/97 (21%), Positives = 41/97 (42%), Gaps = 4/97 (4%)
Query: 45 PKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFIT 104
P A K+ + ++VG + + + F G + I+ D + +G+ +I
Sbjct: 25 PLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIE 84
Query: 105 FDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPNLP 141
F +VD +A + G ++V PK+ N+P
Sbjct: 85 FAERNSVDAAVAMDETV-FRGRTIKVL---PKRTNMP 117
Score = 27.7 bits (60), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 12/46 (26%), Positives = 28/46 (60%), Gaps = 3/46 (6%)
Query: 1 MKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEI--KRT 43
+ D+ +G P+G+ ++ +A+ + VD + D + G+ +++ KRT
Sbjct: 69 LCDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRGRTIKVLPKRT 114
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 34.3 bits (77), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 19/91 (20%), Positives = 43/91 (47%), Gaps = 2/91 (2%)
Query: 54 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDD 113
++ ++V + ++++ + F FG + ++M + RS+GFGF+ F + +
Sbjct: 13 YQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGG--RSKGFGFVCFSSPEEATK 70
Query: 114 LLAKGNKLELAGAQVEVKKAEPKKPNLPQPS 144
+ + N +A + V A+ K+ PS
Sbjct: 71 AVTEMNGRIVATKPLYVALAQRKEERQSGPS 101
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 34.3 bits (77), Expect = 0.099, Method: Compositional matrix adjust.
Identities = 24/90 (26%), Positives = 43/90 (47%), Gaps = 9/90 (10%)
Query: 47 GAVGSKDF-KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF 105
G+ GS K K +FV + ++V E+ + F QFG ++ + ++D + FI F
Sbjct: 1 GSSGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHF 52
Query: 106 DTEQAVDDLLAKGNKLELAGAQVEVKKAEP 135
D + + N +L G +E+ A+P
Sbjct: 53 DERDGAVKAMEEMNGKDLEGENIEIVFAKP 82
>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 = 24/88 (27%), Positives = 43/88 (48%), Gaps = 4/88 (4%)
Query: 57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTE---QAVDD 113
+K+FVG + +++ + F FG + E ++R + S+G F+ F T QA +
Sbjct: 13 RKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGT-SKGCAFVKFQTHAEAQAAIN 71
Query: 114 LLAKGNKLELAGAQVEVKKAEPKKPNLP 141
L L A + + VK A+ +K + P
Sbjct: 72 TLHSSRTLPGASSSLVVKFADTEKESGP 99
>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 = 33.9 bits (76), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 16/80 (20%), Positives = 36/80 (45%)
Query: 59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
+FV G+ E++ D F ++G+++ + D T +G+ + ++T + +
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 119 NKLELAGAQVEVKKAEPKKP 138
N +L G + V + P
Sbjct: 86 NGQDLMGQPISVDWCFVRGP 105
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 33.5 bits (75), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 25/47 (53%)
Query: 59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF 105
I V + E + ++ F FG + + +D +T +S+GF FI+F
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISF 64
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 33.5 bits (75), Expect = 0.16, Method: Composition-based stats.
Identities = 15/72 (20%), Positives = 34/72 (47%)
Query: 59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
+FV G+ E++ D F ++G+++ + D T +G+ + ++T + +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 119 NKLELAGAQVEV 130
N +L G + V
Sbjct: 70 NGQDLMGQPISV 81
>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 = 33.1 bits (74), Expect = 0.18, Method: Composition-based stats.
Identities = 15/72 (20%), Positives = 34/72 (47%)
Query: 59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
+FV G+ E++ D F ++G+++ + D T +G+ + ++T + +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 119 NKLELAGAQVEV 130
N +L G + V
Sbjct: 70 NGQDLMGQPISV 81
>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 = 33.1 bits (74), Expect = 0.21, Method: Composition-based stats.
Identities = 15/72 (20%), Positives = 34/72 (47%)
Query: 59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
+FV G+ E++ D F ++G+++ + D T +G+ + ++T + +
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 119 NKLELAGAQVEV 130
N +L G + V
Sbjct: 72 NGQDLMGQPISV 83
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 32.7 bits (73), Expect = 0.24, Method: Composition-based stats.
Identities = 24/67 (35%), Positives = 34/67 (50%), Gaps = 11/67 (16%)
Query: 1 MKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPKGAVGSKDFKTKKIF 60
+++R TG P G+ FV +AD + +K + H INGK + GA +K FK
Sbjct: 43 IRNRLTGIPAGYCFVEFADLATAEKCL---HKINGKPL-------PGATPAKRFKLNYAT 92
Query: 61 VGGIPSS 67
G PSS
Sbjct: 93 YSG-PSS 98
>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 = 32.3 bits (72), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 15/72 (20%), Positives = 34/72 (47%)
Query: 59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
+FV G+ E++ D F ++G+++ + D T +G+ + ++T + +
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 119 NKLELAGAQVEV 130
N +L G + V
Sbjct: 85 NGQDLMGQPISV 96
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 32.3 bits (72), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 16/76 (21%), Positives = 33/76 (43%), Gaps = 6/76 (7%)
Query: 55 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDL 114
K ++ GGI S + + + F FG + E ++ + +G+ F+ F T ++
Sbjct: 24 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHA 77
Query: 115 LAKGNKLELAGAQVEV 130
+ N + G V+
Sbjct: 78 IVSVNGTTIEGHVVKC 93
>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 = 32.3 bits (72), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 15/72 (20%), Positives = 34/72 (47%)
Query: 59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
+FV G+ E++ D F ++G+++ + D T +G+ + ++T + +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 119 NKLELAGAQVEV 130
N +L G + V
Sbjct: 70 NGQDLMGQPISV 81
>pdb|2DNN|A Chain A, Solution Structure Of Rna Binding Domain In Rna-Binding
Protein 12
Length = 109
Score = 32.3 bits (72), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 3/79 (3%)
Query: 59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
+ V G+P S E++ +DFF V +++DH R+ G G + F + Q + L K
Sbjct: 19 VSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGLVKFLSPQDTFEAL-KR 75
Query: 119 NKLELAGAQVEVKKAEPKK 137
N++ + VEV A ++
Sbjct: 76 NRMLMIQRYVEVSPATERQ 94
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 31.6 bits (70), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 13/48 (27%), Positives = 26/48 (54%)
Query: 58 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF 105
++FV + + +E++ + F +G + E D T + +GF F+TF
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTF 57
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 31.2 bits (69), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 24/101 (23%), Positives = 44/101 (43%), Gaps = 8/101 (7%)
Query: 52 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQ--------IMRDHSTSRSRGFGFI 103
+D I+V G+ SV D+ DFF Q G V+ ++ I D T + +G +
Sbjct: 11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATV 70
Query: 104 TFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPNLPQPS 144
+++ + + + G++++V A K P PS
Sbjct: 71 SYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSGPS 111
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 31.2 bits (69), Expect = 0.87, Method: Composition-based stats.
Identities = 15/70 (21%), Positives = 37/70 (52%), Gaps = 4/70 (5%)
Query: 59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDT----EQAVDDL 114
+++ G+ + + +G + + + D +T++ +G+GF+ FD+ ++AV L
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
Query: 115 LAKGNKLELA 124
A G + ++A
Sbjct: 68 KASGVQAQMA 77
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 30.8 bits (68), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 20/85 (23%), Positives = 40/85 (47%), Gaps = 2/85 (2%)
Query: 60 FVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN 119
+VG +P + + + F ++ +++RD T + +GF ++ FD ++ + L
Sbjct: 19 YVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDG 77
Query: 120 KLELAGAQVEVKKAEPKKPNLPQPS 144
L L + V AE +K + PS
Sbjct: 78 AL-LGDRSLRVDIAEGRKQDKSGPS 101
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 22/94 (23%), Positives = 40/94 (42%), Gaps = 13/94 (13%)
Query: 53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVD 112
+ ++FV P V E E + F FG ++E +I+ GF F+ F+ ++
Sbjct: 28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAA 79
Query: 113 DLLAKGNKLELAGAQVEVKKAEPKKPNLPQPSYR 146
+ + + A +EV ++ LP YR
Sbjct: 80 KAIEEVHGKSFANQPLEVVYSK-----LPAKRYR 108
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 20/91 (21%), Positives = 42/91 (46%), Gaps = 12/91 (13%)
Query: 44 IPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRG---F 100
+ +G G+ D + I+VG +P + + +D F ++G +RD RG F
Sbjct: 13 VIRGPAGNNDCR---IYVGNLPPDIRTKDIEDVFYKYG------AIRDIDLKNRRGGPPF 63
Query: 101 GFITFDTEQAVDDLLAKGNKLELAGAQVEVK 131
F+ F+ + +D + + + G ++ V+
Sbjct: 64 AFVEFEDPRDAEDAVYGRDGYDYDGYRLRVE 94
>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 = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 17/94 (18%), Positives = 41/94 (43%)
Query: 37 QVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSR 96
+ E+K P ++ K +FV + E + + F +G ++ ++ + +
Sbjct: 83 ETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGK 142
Query: 97 SRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 130
RG+ FI ++ E+ + + ++ G +V V
Sbjct: 143 PRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV 176
>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 = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 17/94 (18%), Positives = 41/94 (43%)
Query: 37 QVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSR 96
+ E+K P ++ K +FV + E + + F +G ++ ++ + +
Sbjct: 83 ETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGK 142
Query: 97 SRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 130
RG+ FI ++ E+ + + ++ G +V V
Sbjct: 143 PRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV 176
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 41/88 (46%), Gaps = 4/88 (4%)
Query: 57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTE---QAVDD 113
+K+FVG + +E++ F FG + E ++R S S+G F+ F + QA
Sbjct: 16 RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGS-SKGCAFVKFSSHTEAQAAIH 74
Query: 114 LLAKGNKLELAGAQVEVKKAEPKKPNLP 141
L + A + + VK A+ K + P
Sbjct: 75 ALHGSQTMPGASSSLVVKFADTDKESGP 102
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 29.6 bits (65), Expect = 2.2, Method: Composition-based stats.
Identities = 18/74 (24%), Positives = 37/74 (50%), Gaps = 2/74 (2%)
Query: 58 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 117
+IFV +P KD F + G V I ++ +S+G G + F++ + +
Sbjct: 10 QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENG--KSKGCGVVKFESPEVAERACRM 67
Query: 118 GNKLELAGAQVEVK 131
N ++L+G +++V+
Sbjct: 68 MNGMKLSGREIDVR 81
>pdb|3BEG|B Chain B, Crystal Structure Of Sr Protein Kinase 1 Complexed To Its
Substrate AsfSF2
Length = 115
Score = 29.6 bits (65), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 28/101 (27%), Positives = 43/101 (42%), Gaps = 13/101 (12%)
Query: 45 PKGAVGSKDFKTK-KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFI 103
P+G G +++ ++ V G+P S + + KD + GDV + RD G G +
Sbjct: 4 PRGRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVV 56
Query: 104 TF----DTEQAVDDL-LAKGNKLELAGAQVEVKKAEPKKPN 139
F D AV L K E A + VK P+ P+
Sbjct: 57 EFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPS 97
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of Eukaryotic
Initiation Factor 4b
Length = 104
Score = 29.3 bits (64), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 60 FVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHST-SRSRGFGFITFD 106
F+G +P V E+ K+FF ++ ++ R+ S R +GFG+ F+
Sbjct: 19 FLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEFE 65
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 29.3 bits (64), Expect = 3.1, Method: Composition-based stats.
Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 9/59 (15%)
Query: 58 KIFVGGIP-SSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL 115
++F+G +P +V++++ F +G + + I FGFI FD Q+V D +
Sbjct: 24 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAI 74
>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 = 28.9 bits (63), Expect = 3.4, Method: Composition-based stats.
Identities = 18/81 (22%), Positives = 43/81 (53%), Gaps = 8/81 (9%)
Query: 51 SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTE-- 108
S + K+F+ G+P S ++E ++ G V++ +++ + + + +G ++ ++ E
Sbjct: 12 STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRA-GKPKGLAYVEYENESQ 70
Query: 109 --QAV---DDLLAKGNKLELA 124
QAV D + K N +++A
Sbjct: 71 ASQAVMKMDGMTIKENIIKVA 91
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 28.9 bits (63), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 19/88 (21%), Positives = 40/88 (45%), Gaps = 9/88 (10%)
Query: 58 KIFVGGIPSS-VNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 116
++F+G + ++ V + + + F ++G V S +G+ F+ + E+ +
Sbjct: 29 RVFIGNLNTALVKKSDVETIFSKYGRVA--------GCSVHKGYAFVQYSNERHARAAVL 80
Query: 117 KGNKLELAGAQVEVKKAEPKKPNLPQPS 144
N LAG +++ A KP+ PS
Sbjct: 81 GENGRVLAGQTLDINMAGEPKPDRSGPS 108
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 28.9 bits (63), Expect = 3.6, Method: Composition-based stats.
Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 9/59 (15%)
Query: 58 KIFVGGIP-SSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL 115
++F+G +P +V++++ F +G + + I FGFI FD Q+V D +
Sbjct: 4 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAI 54
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation Initiation
Factor 4b
Length = 100
Score = 28.9 bits (63), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 60 FVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHST-SRSRGFGFITFD 106
F+G +P V E+ K+FF ++ ++ R+ S R +GFG+ F+
Sbjct: 23 FLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEFE 69
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 28.9 bits (63), Expect = 4.0, Method: Composition-based stats.
Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 2/73 (2%)
Query: 59 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 118
IFV +P KD F + G V I ++ +S+G G + F++ + +
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENG--KSKGCGVVKFESPEVAERACRMM 65
Query: 119 NKLELAGAQVEVK 131
N ++L+G +++V+
Sbjct: 66 NGMKLSGREIDVR 78
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 28.5 bits (62), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 18/78 (23%), Positives = 34/78 (43%), Gaps = 8/78 (10%)
Query: 53 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVD 112
+ ++FV P V E E + F FG ++E +I+ GF F+ F+ ++
Sbjct: 1 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAA 52
Query: 113 DLLAKGNKLELAGAQVEV 130
+ + + A +EV
Sbjct: 53 KAIEEVHGKSFANQPLEV 70
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 28.5 bits (62), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 9/59 (15%)
Query: 58 KIFVGGIP-SSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL 115
++F+G +P +V++++ F +G + + I FGFI FD Q+V D +
Sbjct: 12 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAI 62
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 28.1 bits (61), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 9/59 (15%)
Query: 58 KIFVGGIP-SSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL 115
++F+G +P +V++++ F +G + + I FGFI FD Q+V D +
Sbjct: 24 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAI 74
>pdb|1I1I|P Chain P, Neurolysin (Endopeptidase 24.16) Crystal Structure
Length = 681
Score = 28.1 bits (61), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 61 VGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRG 99
V G PS + DE + +F +FG V HQI +R G
Sbjct: 457 VAGRPSLLRHDEVRTYFHEFGHVM-HQICAQTDFARFSG 494
>pdb|2E5G|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 21
Length = 94
Score = 27.7 bits (60), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 19/85 (22%), Positives = 39/85 (45%), Gaps = 6/85 (7%)
Query: 57 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 116
+ +FV G P V+ + ++F+ FG V + +D F + A + +L+
Sbjct: 9 RSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGV-----FAIVEMGDVGAREAVLS 63
Query: 117 KGNKLELAGAQVEVKKAEPKKPNLP 141
+ ++ L G ++ V+ E K+ P
Sbjct: 64 Q-SQHSLGGHRLRVRPREQKEFQSP 87
>pdb|1U2F|A Chain A, Solution Structure Of The First Rna-Binding Domain Of
Hu2af65
Length = 90
Score = 27.7 bits (60), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 40/79 (50%), Gaps = 11/79 (13%)
Query: 56 TKKIFVGGIPSSVNEDEFKDFF---MQFGDVQEH--QIMRDHSTSRSRGFGFITF----D 106
++++VG IP + E+ DFF M+ G + + + ++ + F F+ F +
Sbjct: 1 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 60
Query: 107 TEQAV--DDLLAKGNKLEL 123
T QA+ D ++ +G L++
Sbjct: 61 TTQAMAFDGIIFQGQSLKI 79
>pdb|2O3D|A Chain A, Structure Of Human Sf2ASF RNA RECOGNITION MOTIF 2 (RRM2)
Length = 113
Score = 27.7 bits (60), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 8/62 (12%)
Query: 45 PKGAVGSKDFKTK-KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFI 103
P+G G +++ ++ V G+P S + + KD + GDV + RD G G +
Sbjct: 3 PRGRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVV 55
Query: 104 TF 105
F
Sbjct: 56 EF 57
>pdb|2HZC|A Chain A, Crystal Structure Of The N-terminal Rrm Of The U2af Large
Subunit
Length = 87
Score = 27.7 bits (60), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 40/80 (50%), Gaps = 11/80 (13%)
Query: 55 KTKKIFVGGIPSSVNEDEFKDFF---MQFGDVQEH--QIMRDHSTSRSRGFGFITF---- 105
++++VG IP + E+ DFF M+ G + + + ++ + F F+ F
Sbjct: 5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 64
Query: 106 DTEQAV--DDLLAKGNKLEL 123
+T QA+ D ++ +G L++
Sbjct: 65 ETTQAMAFDGIIFQGQSLKI 84
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
0.316 0.138 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,208,637
Number of Sequences: 62578
Number of extensions: 214354
Number of successful extensions: 741
Number of sequences better than 100.0: 158
Number of HSP's better than 100.0 without gapping: 115
Number of HSP's successfully gapped in prelim test: 43
Number of HSP's that attempted gapping in prelim test: 495
Number of HSP's gapped (non-prelim): 255
length of query: 314
length of database: 14,973,337
effective HSP length: 99
effective length of query: 215
effective length of database: 8,778,115
effective search space: 1887294725
effective search space used: 1887294725
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 51 (24.3 bits)