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= 032319
(143 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 68.2 bits (165), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 33/74 (44%), Positives = 50/74 (67%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
+LFV GLS T ++ L++ F+ +GQ+ V+ DR T RS+GFGFV++ +I++A+ A
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 95 MNAKYLDGWVIFVD 108
MN K +DG I VD
Sbjct: 74 MNGKSVDGRQIRVD 87
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 65.9 bits (159), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 36/76 (47%), Positives = 49/76 (64%), Gaps = 3/76 (3%)
Query: 33 SPRLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAR 92
S LFV GLS TT+E LKE+F V ++++TDR TG SKGFGFV + S E+A+ A+
Sbjct: 15 SKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAK 71
Query: 93 EGMNAKYLDGWVIFVD 108
E M +DG + +D
Sbjct: 72 EAMEDGEIDGNKVTLD 87
>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 = 63.2 bits (152), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 31/68 (45%), Positives = 46/68 (67%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
+FV LS T E +K AFAPFG++ ++V+ D ATG+SKG+GFVS+ + +AE A +
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 95 MNAKYLDG 102
M ++L G
Sbjct: 77 MGGQWLGG 84
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 62.4 bits (150), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 31/68 (45%), Positives = 45/68 (66%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
+FV LS T E +K AFAPFG++ ++V+ D ATG+SKG+GFVS+ + +AE A
Sbjct: 17 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 95 MNAKYLDG 102
M ++L G
Sbjct: 77 MGGQWLGG 84
>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 = 58.2 bits (139), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 33/73 (45%), Positives = 46/73 (63%), Gaps = 5/73 (6%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
+LF+ GLS TTDE L+ F +G L V+ D T RS+GFGFV+Y ++EE + A
Sbjct: 14 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 70
Query: 95 MNAK--YLDGWVI 105
MNA+ +DG V+
Sbjct: 71 MNARPHKVDGRVV 83
Score = 46.6 bits (109), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 42/71 (59%)
Query: 20 SQLGSIRYNSTLTSPRLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGF 79
S+ S R + LT ++FV G+ T + L++ F +G++ +++TDR +G+ +GF F
Sbjct: 90 SREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAF 149
Query: 80 VSYTSIEEAER 90
V++ + ++
Sbjct: 150 VTFDDHDSVDK 160
>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 = 58.2 bits (139), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 33/73 (45%), Positives = 46/73 (63%), Gaps = 5/73 (6%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
+LF+ GLS TTDE L+ F +G L V+ D T RS+GFGFV+Y ++EE + A
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 71
Query: 95 MNAK--YLDGWVI 105
MNA+ +DG V+
Sbjct: 72 MNARPHKVDGRVV 84
Score = 46.6 bits (109), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 42/71 (59%)
Query: 20 SQLGSIRYNSTLTSPRLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGF 79
S+ S R + LT ++FV G+ T + L++ F +G++ +++TDR +G+ +GF F
Sbjct: 91 SREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAF 150
Query: 80 VSYTSIEEAER 90
V++ + ++
Sbjct: 151 VTFDDHDSVDK 161
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 58.2 bits (139), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 33/73 (45%), Positives = 46/73 (63%), Gaps = 5/73 (6%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
+LF+ GLS TTDE L+ F +G L V+ D T RS+GFGFV+Y ++EE + A
Sbjct: 16 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 72
Query: 95 MNAK--YLDGWVI 105
MNA+ +DG V+
Sbjct: 73 MNARPHKVDGRVV 85
Score = 46.6 bits (109), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 42/71 (59%)
Query: 20 SQLGSIRYNSTLTSPRLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGF 79
S+ S R + LT ++FV G+ T + L++ F +G++ +++TDR +G+ +GF F
Sbjct: 92 SREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAF 151
Query: 80 VSYTSIEEAER 90
V++ + ++
Sbjct: 152 VTFDDHDSVDK 162
>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 = 58.2 bits (139), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 33/73 (45%), Positives = 46/73 (63%), Gaps = 5/73 (6%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
+LF+ GLS TTDE L+ F +G L V+ D T RS+GFGFV+Y ++EE + A
Sbjct: 8 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 64
Query: 95 MNAK--YLDGWVI 105
MNA+ +DG V+
Sbjct: 65 MNARPHKVDGRVV 77
Score = 47.0 bits (110), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 42/71 (59%)
Query: 20 SQLGSIRYNSTLTSPRLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGF 79
S+ S R + LT ++FV G+ T + L++ F +G++ +++TDR +G+ +GF F
Sbjct: 84 SREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAF 143
Query: 80 VSYTSIEEAER 90
V++ + ++
Sbjct: 144 VTFDDHDSVDK 154
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 58.2 bits (139), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 33/73 (45%), Positives = 46/73 (63%), Gaps = 5/73 (6%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
+LF+ GLS TTDE L+ F +G L V+ D T RS+GFGFV+Y ++EE + A
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 71
Query: 95 MNAK--YLDGWVI 105
MNA+ +DG V+
Sbjct: 72 MNARPHKVDGRVV 84
Score = 47.0 bits (110), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 42/71 (59%)
Query: 20 SQLGSIRYNSTLTSPRLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGF 79
S+ S R + LT ++FV G+ T + L++ F +G++ +++TDR +G+ +GF F
Sbjct: 91 SREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAF 150
Query: 80 VSYTSIEEAER 90
V++ + ++
Sbjct: 151 VTFDDHDSVDK 161
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 58.2 bits (139), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 33/73 (45%), Positives = 46/73 (63%), Gaps = 5/73 (6%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
+LF+ GLS TTDE L+ F +G L V+ D T RS+GFGFV+Y ++EE + A
Sbjct: 13 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 69
Query: 95 MNAK--YLDGWVI 105
MNA+ +DG V+
Sbjct: 70 MNARPHKVDGRVV 82
Score = 47.0 bits (110), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 42/71 (59%)
Query: 20 SQLGSIRYNSTLTSPRLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGF 79
S+ S R + LT ++FV G+ T + L++ F +G++ +++TDR +G+ +GF F
Sbjct: 89 SREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAF 148
Query: 80 VSYTSIEEAER 90
V++ + ++
Sbjct: 149 VTFDDHDSVDK 159
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 58.2 bits (139), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 30/72 (41%), Positives = 46/72 (63%), Gaps = 2/72 (2%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L+V L DE+L++AF+PFG + +KV+ + GRSKGFGFV ++S EEA +A M
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 96 NAKYLDGWVIFV 107
N + + ++V
Sbjct: 76 NGRIVATKPLYV 87
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 55.8 bits (133), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 45/73 (61%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L V GLS TT+ L+E F+ +G + ++ D+ + RS+GF FV + ++++A+ A+E
Sbjct: 49 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 108
Query: 96 NAKYLDGWVIFVD 108
N LDG I VD
Sbjct: 109 NGMELDGRRIRVD 121
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 55.5 bits (132), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 45/73 (61%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L V GLS TT+ L+E F+ +G + ++ D+ + RS+GF FV + ++++A+ A+E
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 96 NAKYLDGWVIFVD 108
N LDG I VD
Sbjct: 78 NGMELDGRRIRVD 90
>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 = 55.5 bits (132), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 49/75 (65%)
Query: 28 NSTLTSPRLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEE 87
++++ L+VSGL + T ++L++ F+ +G+++ S+++ D+ TG S+G GF+ + E
Sbjct: 83 SASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIE 142
Query: 88 AERAREGMNAKYLDG 102
AE A +G+N + G
Sbjct: 143 AEEAIKGLNGQKPSG 157
Score = 45.4 bits (106), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 40/72 (55%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L V+ L + T E+ + F G++ K++ D+ TG+S G+GFV+Y ++AE+A +
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 96 NAKYLDGWVIFV 107
N L I V
Sbjct: 65 NGLRLQTKTIKV 76
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 55.5 bits (132), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 45/73 (61%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L V GLS TT+ L+E F+ +G + ++ D+ + RS+GF FV + ++++A+ A+E
Sbjct: 15 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 74
Query: 96 NAKYLDGWVIFVD 108
N LDG I VD
Sbjct: 75 NGMELDGRRIRVD 87
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 55.1 bits (131), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 30/68 (44%), Positives = 42/68 (61%), Gaps = 1/68 (1%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
++FV GL TTD L++ F FG + + VITDR TG+S+G+GFV+ AERA +
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 95 MNAKYLDG 102
N +DG
Sbjct: 79 PN-PIIDG 85
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 54.7 bits (130), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 27/68 (39%), Positives = 40/68 (58%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
LFV L+ DE L+ AF F + V+ D TG S+G+GFVS+TS ++A+ A +
Sbjct: 89 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 148
Query: 95 MNAKYLDG 102
M + L+G
Sbjct: 149 MQGQDLNG 156
Score = 35.4 bits (80), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L+V L + T++ LK+ F G + K++ D+ ++ + FV Y +A A + +
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTL 61
Query: 96 NAKYLDGWVIFVD 108
N K ++ ++ ++
Sbjct: 62 NGKQIENNIVKIN 74
>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 = 54.7 bits (130), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 27/68 (39%), Positives = 40/68 (58%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
LFV L+ DE L+ AF F + V+ D TG S+G+GFVS+TS ++A+ A +
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 95 MNAKYLDG 102
M + L+G
Sbjct: 63 MQGQDLNG 70
>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 = 54.3 bits (129), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 48/72 (66%), Gaps = 3/72 (4%)
Query: 33 SPRLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSY---TSIEEAE 89
S ++F+ GL+ TT++ L+E F +G + K++ D ATGRS+GFGF+S+ +S++E
Sbjct: 3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVV 62
Query: 90 RAREGMNAKYLD 101
+ + ++ K +D
Sbjct: 63 KTQHILDGKVID 74
Score = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 42/67 (62%), Gaps = 3/67 (4%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
++FV G+ ++ +E F+ +G ++ ++++ D+ TG+S+GFGFV+Y S + +R
Sbjct: 89 KIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRV--- 145
Query: 95 MNAKYLD 101
K++D
Sbjct: 146 CQNKFID 152
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 54.3 bits (129), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 48/70 (68%)
Query: 29 STLTSPRLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEA 88
+++ L+VSGL + + +++++ F+ +G+++ S+++ D+ATG S+G GF+ + EA
Sbjct: 86 ASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEA 145
Query: 89 ERAREGMNAK 98
E A +G+N +
Sbjct: 146 EEAIKGLNGQ 155
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 39/72 (54%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L V+ L + T ++ K F G + K++ D+ TG+S G+GFV+Y+ +A++A +
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 96 NAKYLDGWVIFV 107
N L I V
Sbjct: 67 NGLKLQTKTIKV 78
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 54.3 bits (129), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 43/73 (58%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
LFV+G+ T+E + + FA +G++ + DR TG KG+ V Y + +EA+ A EG+
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 96 NAKYLDGWVIFVD 108
N + L G I VD
Sbjct: 70 NGQDLMGQPISVD 82
>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 = 54.3 bits (129), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 43/73 (58%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
LFV+G+ T+E + + FA +G++ + DR TG KG+ V Y + +EA+ A EG+
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 96 NAKYLDGWVIFVD 108
N + L G I VD
Sbjct: 70 NGQDLMGQPISVD 82
>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 = 54.3 bits (129), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 43/73 (58%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
LFV+G+ T+E + + FA +G++ + DR TG KG+ V Y + +EA+ A EG+
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 96 NAKYLDGWVIFVD 108
N + L G I VD
Sbjct: 72 NGQDLMGQPISVD 84
>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 = 54.3 bits (129), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 43/73 (58%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
LFV+G+ T+E + + FA +G++ + DR TG KG+ V Y + +EA+ A EG+
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 96 NAKYLDGWVIFVD 108
N + L G I VD
Sbjct: 85 NGQDLMGQPISVD 97
>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 = 54.3 bits (129), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 43/73 (58%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
LFV+G+ T+E + + FA +G++ + DR TG KG+ V Y + +EA+ A EG+
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 96 NAKYLDGWVIFVD 108
N + L G I VD
Sbjct: 86 NGQDLMGQPISVD 98
>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 = 54.3 bits (129), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 43/73 (58%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
LFV+G+ T+E + + FA +G++ + DR TG KG+ V Y + +EA+ A EG+
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 96 NAKYLDGWVIFVD 108
N + L G I VD
Sbjct: 70 NGQDLMGQPISVD 82
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 53.9 bits (128), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 45/63 (71%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L+VSGL + + +++++ F+ +G+++ S+++ D+ATG S+G GF+ + EAE A +G+
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 96 NAK 98
N +
Sbjct: 64 NGQ 66
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 53.1 bits (126), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 35/61 (57%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L+V+ L R TD++L F +G +V ++ D+ TGR +G FV Y EEA+ A +
Sbjct: 92 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151
Query: 96 N 96
N
Sbjct: 152 N 152
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 34/61 (55%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L V+ L + TD +L F G + +++ D TG S G+ FV +TS +++RA + +
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 96 N 96
N
Sbjct: 66 N 66
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 52.8 bits (125), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 27/72 (37%), Positives = 44/72 (61%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L V GLS TT+ L+E F+ +G + ++ D+ + RS+GF FV + ++++A+ A+E
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 96 NAKYLDGWVIFV 107
N LDG I V
Sbjct: 78 NGMELDGRRIRV 89
>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|B Chain B, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|C Chain C, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
Length = 184
Score = 52.8 bits (125), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 35/61 (57%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L+V+ L R TD++L F +G +V ++ D+ TGR +G FV Y EEA+ A +
Sbjct: 103 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 162
Query: 96 N 96
N
Sbjct: 163 N 163
Score = 35.8 bits (81), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 5/71 (7%)
Query: 31 LTSPR-----LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSI 85
+ PR L V+ L + TD +L F G + ++ D TG S G+ FV +TS
Sbjct: 7 MNDPRASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSE 66
Query: 86 EEAERAREGMN 96
+++RA + +N
Sbjct: 67 XDSQRAIKVLN 77
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 52.8 bits (125), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 38/62 (61%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L++ GL TTD+ L + P+G++V +K I D+ T + KG+GFV + S A++A +
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
Query: 96 NA 97
A
Sbjct: 68 KA 69
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 52.8 bits (125), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 26/68 (38%), Positives = 43/68 (63%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
RL+V L T++ L+ F PFG++ +++ D TGRSKG+GF++++ E A++A E
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 95 MNAKYLDG 102
+N L G
Sbjct: 88 LNGFELAG 95
>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The
Second Rna-Binding Domain Of Sex-Lethal Determined By
Multidimensional Heteronuclear Magnetic Resonance
Spectroscopy
Length = 97
Score = 52.8 bits (125), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 35/61 (57%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L+V+ L R TD++L F +G +V ++ D+ TGR +G FV Y EEA+ A +
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 96 N 96
N
Sbjct: 76 N 76
>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 = 52.4 bits (124), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 43/77 (55%), Gaps = 2/77 (2%)
Query: 31 LTSPRLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAER 90
L S +F+ L + ++ L + F+ FG ++ KV+ D SKG+GFV + + E AER
Sbjct: 3 LGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAER 60
Query: 91 AREGMNAKYLDGWVIFV 107
A E MN L+ +FV
Sbjct: 61 AIEKMNGMLLNDRKVFV 77
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 52.0 bits (123), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 25/62 (40%), Positives = 36/62 (58%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
LF+ L + TD L F PFG ++ +KV D+ T SK FGFVS+ + + A+ A +
Sbjct: 42 NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101
Query: 95 MN 96
MN
Sbjct: 102 MN 103
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 52.0 bits (123), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 36/68 (52%)
Query: 33 SPRLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAR 92
+ +LF+ GL D+++KE FG L ++ D ATG SKG+ F Y I ++A
Sbjct: 1 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 60
Query: 93 EGMNAKYL 100
G+N L
Sbjct: 61 AGLNGMQL 68
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 52.0 bits (123), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 44/74 (59%), Gaps = 1/74 (1%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
+LF+ GL+R T ++ LK F G + +I DR T +S+GF F+++ + +A+ A +
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKD 67
Query: 95 MNAKYLDGWVIFVD 108
MN K L G I V+
Sbjct: 68 MNGKSLHGKAIKVE 81
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 52.0 bits (123), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 37/74 (50%)
Query: 27 YNSTLTSPRLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIE 86
Y + +LF+ GL D+++KE FG L ++ D ATG SKG+ F Y I
Sbjct: 88 YQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDIN 147
Query: 87 EAERAREGMNAKYL 100
++A G+N L
Sbjct: 148 VTDQAIAGLNGMQL 161
>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 = 52.0 bits (123), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 37/74 (50%)
Query: 27 YNSTLTSPRLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIE 86
Y + +LF+ GL D+++KE FG L ++ D ATG SKG+ F Y I
Sbjct: 90 YQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDIN 149
Query: 87 EAERAREGMNAKYL 100
++A G+N L
Sbjct: 150 VTDQAIAGLNGMQL 163
>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 = 51.6 bits (122), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 35/66 (53%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
+LF+ GL D+++KE FG L ++ D ATG SKG+ F Y I ++A G
Sbjct: 116 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 175
Query: 95 MNAKYL 100
+N L
Sbjct: 176 LNGMQL 181
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 51.6 bits (122), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 40/73 (54%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
+FV + T+E+LK+ F+ G +V +++ DR TG+ KG+GF Y E A A +
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 96 NAKYLDGWVIFVD 108
N + G + VD
Sbjct: 71 NGREFSGRALRVD 83
>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 = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/62 (41%), Positives = 36/62 (58%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
LF+ L + D+ L + F PFG +V +KV D+ T SK FGFVSY + A+ A +
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86
Query: 95 MN 96
MN
Sbjct: 87 MN 88
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 41/72 (56%), Gaps = 2/72 (2%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
+F+ L + ++ L + F+ FG ++ KV+ D SKG+GFV + + E AERA E M
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKM 71
Query: 96 NAKYLDGWVIFV 107
N L+ +FV
Sbjct: 72 NGMLLNDRKVFV 83
>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 = 50.8 bits (120), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 41/72 (56%), Gaps = 2/72 (2%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
+F+ L + ++ L + F+ FG ++ KV+ D SKG+GFV + + E AERA E M
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 158
Query: 96 NAKYLDGWVIFV 107
N L+ +FV
Sbjct: 159 NGMLLNDRKVFV 170
Score = 43.5 bits (101), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 36/67 (53%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L+V L T+ L E F+P G ++ +V D T RS G+ +V++ +AERA + M
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 72
Query: 96 NAKYLDG 102
N + G
Sbjct: 73 NFDVIKG 79
>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 = 3e-07, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 41/72 (56%), Gaps = 2/72 (2%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
+F+ L + ++ L + F+ FG ++ KV+ D SKG+GFV + + E AERA E M
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 163
Query: 96 NAKYLDGWVIFV 107
N L+ +FV
Sbjct: 164 NGMLLNDRKVFV 175
Score = 43.5 bits (101), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 36/67 (53%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L+V L T+ L E F+P G ++ +V D T RS G+ +V++ +AERA + M
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77
Query: 96 NAKYLDG 102
N + G
Sbjct: 78 NFDVIKG 84
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 50.1 bits (118), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 44/71 (61%), Gaps = 1/71 (1%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
+LF+ GLS TT+E L+ + +G+L V+ D A+ RS+GFGFV+++S+ E + A
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM-A 87
Query: 95 MNAKYLDGWVI 105
+DG V+
Sbjct: 88 ARPHSIDGRVV 98
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 49.7 bits (117), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 39/67 (58%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L++SGL R T + +++ F+ FG+++ S+V+ D+ TG S+G F+ + EAE A
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 96 NAKYLDG 102
N G
Sbjct: 151 NGHKPPG 157
Score = 48.5 bits (114), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 42/72 (58%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L V+ L + T ++L+ F+ G++ +K+I D+ G S G+GFV+Y + ++AERA +
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 96 NAKYLDGWVIFV 107
N L I V
Sbjct: 65 NGLRLQSKTIKV 76
>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 = 49.7 bits (117), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 39/67 (58%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L++SGL R T + +++ F+ FG+++ S+V+ D+ TG S+G F+ + EAE A
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 96 NAKYLDG 102
N G
Sbjct: 151 NGHKPPG 157
Score = 48.5 bits (114), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 42/72 (58%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L V+ L + T ++L+ F+ G++ +K+I D+ G S G+GFV+Y + ++AERA +
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 96 NAKYLDGWVIFV 107
N L I V
Sbjct: 65 NGLRLQSKTIKV 76
>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 = 49.7 bits (117), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 28/70 (40%), Positives = 42/70 (60%), Gaps = 1/70 (1%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
+F+ GLS TT + LK+ F+ FG++V + D TGRS+GFGFV + E ++ +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 96 NAKYLDGWVI 105
K L+G VI
Sbjct: 62 EHK-LNGKVI 70
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 49.3 bits (116), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 27/72 (37%), Positives = 42/72 (58%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L+V L T++ L+ F PFG++ ++ D TGRSKG+GF++++ E A RA E +
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 96 NAKYLDGWVIFV 107
N L G + V
Sbjct: 68 NGFELAGRPMRV 79
>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 = 49.3 bits (116), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 29/68 (42%), Positives = 44/68 (64%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
+FV LS T + AFAPFG++ ++V+ D ATG+SKG+GFVS+ + +AE A +
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 95 MNAKYLDG 102
M ++L G
Sbjct: 68 MGGQWLGG 75
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 48.9 bits (115), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 44/76 (57%), Gaps = 4/76 (5%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAER---- 90
++F+ GLS TT E L+E F FG++ V+ D T RS+GFGFV++ ++
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 86
Query: 91 AREGMNAKYLDGWVIF 106
+R +++K +D V F
Sbjct: 87 SRHELDSKTIDPKVAF 102
>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 = 48.9 bits (115), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 42/72 (58%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L V+ L + T ++L+ F+ G++ +K+I D+ G S G+GFV+Y + ++AERA +
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 96 NAKYLDGWVIFV 107
N L I V
Sbjct: 67 NGLRLQSKTIKV 78
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 48.9 bits (115), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 27/69 (39%), Positives = 40/69 (57%), Gaps = 3/69 (4%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERA---R 92
L V GL TT++ LKE F+ FG+++ +V D TG SKGFGFV +T E + R
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 77
Query: 93 EGMNAKYLD 101
++ ++ D
Sbjct: 78 HMIDGRWCD 86
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 48.9 bits (115), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 44/76 (57%), Gaps = 4/76 (5%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAER---- 90
++F+ GLS TT E L+E F FG++ V+ D T RS+GFGFV++ ++
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 91 AREGMNAKYLDGWVIF 106
+R +++K +D V F
Sbjct: 62 SRHELDSKTIDPKVAF 77
>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 = 48.9 bits (115), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 42/72 (58%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L V+ L + T ++L+ F+ G++ +K+I D+ G S G+GFV+Y + ++AERA +
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 96 NAKYLDGWVIFV 107
N L I V
Sbjct: 82 NGLRLQSKTIKV 93
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 38/73 (52%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L+V GL+ D+ L AF PFG + ++ D T + +GF FV + E+A A + M
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 96 NAKYLDGWVIFVD 108
N L G I V+
Sbjct: 126 NESELFGRTIRVN 138
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 41/71 (57%)
Query: 38 VSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGMNA 97
V+ LS T + L+E F PFG + + D+ TG+SKGF F+S+ E+A RA G++
Sbjct: 20 VTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSG 79
Query: 98 KYLDGWVIFVD 108
D ++ V+
Sbjct: 80 FGYDHLILNVE 90
>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 = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 29/81 (35%), Positives = 42/81 (51%), Gaps = 1/81 (1%)
Query: 29 STLTSPR-LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEE 87
S T+ R L+V GL+ D+ L AF PFG + ++ D T + +GF FV + E+
Sbjct: 2 SMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 61
Query: 88 AERAREGMNAKYLDGWVIFVD 108
A A + MN L G I V+
Sbjct: 62 AAAAIDNMNESELFGRTIRVN 82
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 38/73 (52%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L+V GL+ D+ L AF PFG + ++ D T + +GF FV + E+A A + M
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 96 NAKYLDGWVIFVD 108
N L G I V+
Sbjct: 75 NESELFGRTIRVN 87
>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 = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
+ FV GLS T+ + LK+ F FG++V + D TGRS+GFGF+ + E+ +
Sbjct: 13 KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLD- 71
Query: 95 MNAKYLDGWVI 105
LDG VI
Sbjct: 72 QKEHRLDGRVI 82
>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 = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 38/73 (52%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L+V GL+ D+ L AF PFG + ++ D T + +GF FV + E+A A + M
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 96 NAKYLDGWVIFVD 108
N L G I V+
Sbjct: 65 NESELFGRTIRVN 77
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 38/73 (52%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L+V GL+ D+ L AF PFG + ++ D T + +GF FV + E+A A + M
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 96 NAKYLDGWVIFVD 108
N L G I V+
Sbjct: 68 NESELFGRTIRVN 80
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 47.4 bits (111), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 41/73 (56%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
LFV+ + +++++E F +G++ + DR TG SKG+ V Y + ++A A+E +
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 96 NAKYLDGWVIFVD 108
N + G I VD
Sbjct: 89 NGAEIMGQTIQVD 101
>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 = 47.0 bits (110), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 41/73 (56%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
LFV+ + +++++E F +G++ + DR TG SKG+ V Y + ++A A+E +
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 96 NAKYLDGWVIFVD 108
N + G I VD
Sbjct: 135 NGAEIMGQTIQVD 147
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 46.2 bits (108), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 36/58 (62%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERARE 93
+FV GLS TT E +K F FG++ + ++ D+ T R +GFGFV++ S + E+ E
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59
>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 = 46.2 bits (108), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 47/85 (55%), Gaps = 1/85 (1%)
Query: 23 GSIRYNSTLTSPRLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSY 82
G RY+++L +LF+SGL T E+L+E G + +++T+RA G+ KG +V Y
Sbjct: 7 GVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRA-GKPKGLAYVEY 65
Query: 83 TSIEEAERAREGMNAKYLDGWVIFV 107
+ +A +A M+ + +I V
Sbjct: 66 ENESQASQAVMKMDGMTIKENIIKV 90
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 45.8 bits (107), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 45/77 (58%), Gaps = 2/77 (2%)
Query: 32 TSPRLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERA 91
T RL VS + D L++ F FG+++ ++I + SKGFGFV++ + +A+RA
Sbjct: 14 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRA 71
Query: 92 REGMNAKYLDGWVIFVD 108
RE ++ ++G I V+
Sbjct: 72 REKLHGTVVEGRKIEVN 88
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 45.8 bits (107), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 40/66 (60%), Gaps = 1/66 (1%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYS-KVITDRATGRSKGFGFVSYTSIEEAERAREG 94
+F+ L ++ L + F+ FG ++ + K++ D TG SKG+ F+++ S + ++ A E
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 95 MNAKYL 100
MN +YL
Sbjct: 68 MNGQYL 73
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 44/74 (59%), Gaps = 2/74 (2%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
RL VS + D L++ F FG+++ ++I + SKGFGFV++ + +A+RARE
Sbjct: 31 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREK 88
Query: 95 MNAKYLDGWVIFVD 108
++ ++G I V+
Sbjct: 89 LHGTVVEGRKIEVN 102
>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 = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 40/73 (54%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
R++V+ + + +D+ +K F FG++ + + D TG+ KG+GF+ Y + ++ A
Sbjct: 127 RIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 186
Query: 95 MNAKYLDGWVIFV 107
MN L G + V
Sbjct: 187 MNLFDLGGQYLRV 199
Score = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 39/73 (53%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
R++V + ++ +++AFAPFG + + D T + KGF FV Y E A+ A E
Sbjct: 30 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 89
Query: 95 MNAKYLDGWVIFV 107
MN+ L G I V
Sbjct: 90 MNSVMLGGRNIKV 102
>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 = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 39/73 (53%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
R++V + ++ +++AFAPFG + + D T + KGF FV Y E A+ A E
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 95 MNAKYLDGWVIFV 107
MN+ L G I V
Sbjct: 75 MNSVMLGGRNIKV 87
Score = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 35/62 (56%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
R++V+ + + +D+ +K F FG++ + D TG+ KG+GF+ Y + ++ A
Sbjct: 112 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 171
Query: 95 MN 96
MN
Sbjct: 172 MN 173
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 39/73 (53%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
L V+ L + T ++ K F G + K++ D+ TG+S G+GFV+Y+ +A++A
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 95 MNAKYLDGWVIFV 107
+N L I V
Sbjct: 66 LNGLKLQTKTIKV 78
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 20/48 (41%), Positives = 32/48 (66%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSY 82
+LFV GL TT E L+ F+ +G++V ++ D+ T +S+GFGFV +
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF 65
>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 = 43.5 bits (101), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 40/67 (59%), Gaps = 3/67 (4%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
++FV GLS T +EK++E F FG++ ++ D T + +GF F+++ +E E ++
Sbjct: 3 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITF---KEEEPVKKI 59
Query: 95 MNAKYLD 101
M KY +
Sbjct: 60 MEKKYHN 66
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 43.1 bits (100), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 36/72 (50%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L V+ L T ++ +E PFG L ++ TG+SKG+GF Y + A RA+ +
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 96 NAKYLDGWVIFV 107
K L ++V
Sbjct: 158 LGKPLGPRTLYV 169
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 43.1 bits (100), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 36/72 (50%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L V+ L T ++ +E PFG L ++ TG+SKG+GF Y + A RA+ +
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 96 NAKYLDGWVIFV 107
K L ++V
Sbjct: 158 LGKPLGPRTLYV 169
>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 = 43.1 bits (100), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 36/72 (50%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L V+ L T ++ +E PFG L ++ TG+SKG+GF Y + A RA+ +
Sbjct: 96 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Query: 96 NAKYLDGWVIFV 107
K L ++V
Sbjct: 156 LGKPLGPRTLYV 167
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 42.7 bits (99), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 39/73 (53%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
RLFV LS +++E L++ F+ +G L D T + KGF FV++ E A +A
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 95 MNAKYLDGWVIFV 107
++ + G ++ V
Sbjct: 70 VDGQVFQGRMLHV 82
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 42.7 bits (99), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 41/73 (56%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
++V GL ++ L E F G +V + + DR TG+ +G+GFV + S E+A+ A + M
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 96 NAKYLDGWVIFVD 108
+ L G I V+
Sbjct: 78 DMIKLYGKPIRVN 90
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 42.4 bits (98), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 23/55 (41%), Positives = 33/55 (60%), Gaps = 2/55 (3%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYT--SIEEA 88
++V L T E++KE F+ FG++ K+I DR T + KGFGFV S+ EA
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEA 58
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 42.4 bits (98), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 39/66 (59%), Gaps = 3/66 (4%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
+FV GLS T +EK++E F FG++ ++ D T + +GF F+++ +E E ++ M
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITF---KEEEPVKKIM 58
Query: 96 NAKYLD 101
KY +
Sbjct: 59 EKKYHN 64
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 42.4 bits (98), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 44/77 (57%), Gaps = 9/77 (11%)
Query: 32 TSPR---LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEA 88
+SP+ ++ G++ TD+ +++ F+PFGQ++ +V + KG+ FV +++ E A
Sbjct: 21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESA 74
Query: 89 ERAREGMNAKYLDGWVI 105
A +N ++G V+
Sbjct: 75 AHAIVSVNGTTIEGHVV 91
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 34/53 (64%), Gaps = 1/53 (1%)
Query: 45 TTDE-KLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGMN 96
T DE +L++ F +G + K++ DR T +S+G+GFV + S A++A G+N
Sbjct: 53 TVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLN 105
>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 = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 34/62 (54%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
R++V+ + + +D+ +K F FG++ + D TG+ KG+GF+ Y + ++ A
Sbjct: 111 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 170
Query: 95 MN 96
N
Sbjct: 171 XN 172
Score = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 37/73 (50%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
R++V + ++ +++AFAPFG + D T + KGF FV Y E A+ A E
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 95 MNAKYLDGWVIFV 107
N+ L G I V
Sbjct: 74 XNSVXLGGRNIKV 86
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 35/64 (54%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
+LF+ + R ++ LK F FG++ V+ DR TG KG F++Y E A +A+
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74
Query: 95 MNAK 98
++ +
Sbjct: 75 LHEQ 78
>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 = 41.6 bits (96), Expect = 1e-04, Method: Composition-based stats.
Identities = 19/73 (26%), Positives = 39/73 (53%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
LFV+ ++ TT+ KL+ F +G + ++ + +G+ +G+ F+ Y + A +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 96 NAKYLDGWVIFVD 108
+ K +DG + VD
Sbjct: 165 DGKKIDGRRVLVD 177
>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 = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 39/73 (53%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
LFV+ ++ TT+ KL+ F +G + ++ + +G+ +G+ F+ Y + A +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 96 NAKYLDGWVIFVD 108
+ K +DG + VD
Sbjct: 165 DGKKIDGRRVLVD 177
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 37/70 (52%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
++VS L T+ L F+ +G++V ++ D+ T +SKG F+ + + A+ +
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 96 NAKYLDGWVI 105
N K L G VI
Sbjct: 79 NNKQLFGRVI 88
>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 = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 37/72 (51%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L V L+ T+ + L+ F +G++ + DR T S+GF FV + +AE A + M
Sbjct: 50 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109
Query: 96 NAKYLDGWVIFV 107
+ LDG + V
Sbjct: 110 DGAVLDGRELRV 121
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 36/64 (56%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
+LFV + R ++ LK F FG++ V+ DR TG KG F++Y + + A +A+
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSA 76
Query: 95 MNAK 98
++ +
Sbjct: 77 LHEQ 80
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 37/65 (56%), Gaps = 1/65 (1%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L++S L +++L+ PFGQ++ ++++ D ++G S+G GF S E+ E
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHF 86
Query: 96 NAKYL 100
N K++
Sbjct: 87 NGKFI 91
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 35/67 (52%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L V L+ T+ + L+ F +G++ + DR T S+GF FV + +AE A + M
Sbjct: 73 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132
Query: 96 NAKYLDG 102
+ LDG
Sbjct: 133 DGAVLDG 139
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 40.4 bits (93), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 4/73 (5%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L +S LS T+E L+E F + + KV ++ G+SKG+ F+ + S E+A+ A
Sbjct: 18 LVLSNLSYSATEETLQEVFE---KATFIKVPQNQ-NGKSKGYAFIEFASFEDAKEALNSC 73
Query: 96 NAKYLDGWVIFVD 108
N + ++G I ++
Sbjct: 74 NKREIEGRAIRLE 86
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 39.3 bits (90), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 38/73 (52%), Gaps = 2/73 (2%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
++FV L T + LK+ F G ++Y+ + + G+SKG G V + S E AERA
Sbjct: 10 QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRM 67
Query: 95 MNAKYLDGWVIFV 107
MN L G I V
Sbjct: 68 MNGMKLSGREIDV 80
>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|X Chain X, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|Y Chain Y, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2V|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
pdb|1N52|B Chain B, Cap Binding Complex
pdb|1N54|B Chain B, Cap Binding Complex M7gpppg Free
pdb|3FEX|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex.
pdb|3FEY|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex
Length = 156
Score = 39.3 bits (90), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 40/78 (51%), Gaps = 4/78 (5%)
Query: 33 SPRLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVIT--DRATGRSKGFGFVSYTSIEEAER 90
S L+V LS TT+E++ E F+ G + K+I D+ + GF FV Y S +AE
Sbjct: 39 SCTLYVGNLSFYTTEEQIYELFSKSGDI--KKIIMGLDKMKKTACGFCFVEYYSRADAEN 96
Query: 91 AREGMNAKYLDGWVIFVD 108
A +N LD +I D
Sbjct: 97 AMRYINGTRLDDRIIRTD 114
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 39.3 bits (90), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 27/72 (37%), Positives = 37/72 (51%), Gaps = 2/72 (2%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
+FV L T + LK+ F G ++Y+ + + G+SKG G V + S E AERA M
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMM 65
Query: 96 NAKYLDGWVIFV 107
N L G I V
Sbjct: 66 NGMKLSGREIDV 77
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 36/58 (62%), Gaps = 1/58 (1%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERARE 93
+FV G+ + +++ FA +G + K+ITDR TG SKG+GFVS+ + + ++ E
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE 69
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 8/72 (11%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
LFV L+ T+E L++AF+ FG+L K + D + F+ + + A +A E M
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEM 65
Query: 96 NAKYLDGWVIFV 107
N K L+G I +
Sbjct: 66 NGKDLEGENIEI 77
>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 = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 36/58 (62%), Gaps = 1/58 (1%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERARE 93
+FV G+ + +++ FA +G + K+ITDR TG SKG+GFVS+ + + ++ E
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE 68
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 44/77 (57%), Gaps = 3/77 (3%)
Query: 17 ILKSQLGSIRYNSTLTSPRLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKG 76
ILKS+ IR+ + + L V LS + ++E L++AF+ FG + + V+ D GR+ G
Sbjct: 82 ILKSRPLRIRFATHGAA--LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATG 138
Query: 77 FGFVSYTSIEEAERARE 93
GFV + + A +A E
Sbjct: 139 KGFVEFAAKPPARKALE 155
Score = 28.1 bits (61), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 34/71 (47%), Gaps = 11/71 (15%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
RLFV L T+E K F +G+ S+V + R +GFGF+ S AE A+
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGE--PSEVFIN----RDRGFGFIRLESRTLAEIAK-- 75
Query: 95 MNAKYLDGWVI 105
LDG ++
Sbjct: 76 ---AELDGTIL 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 = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 36/58 (62%), Gaps = 1/58 (1%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERARE 93
+FV G+ + +++ FA +G + K+ITDR TG SKG+GFVS+ + + ++ E
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE 68
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 40/72 (55%), Gaps = 1/72 (1%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGR-SKGFGFVSYTSIEEAERARE 93
++ + L+R T + + E F+ +G++ + +R SKG+ +V + + +EAE+A +
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65
Query: 94 GMNAKYLDGWVI 105
M+ +DG I
Sbjct: 66 HMDGGQIDGQEI 77
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 37/75 (49%), Gaps = 3/75 (4%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQL---VYSKVITDRATGRSKGFGFVSYTSIEEAERAR 92
LF+ L+ TT+E LK F+ G + SK S GFGFV Y E+A++A
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 93 EGMNAKYLDGWVIFV 107
+ + +DG + V
Sbjct: 68 KQLQGHTVDGHKLEV 82
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 34/68 (50%), Gaps = 1/68 (1%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYS-KVITDRATGRSKGFGFVSYTSIEEAERAREG 94
L++ L + + AFA G+ V S K+I +R TG G+ FV + + AE+
Sbjct: 12 LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71
Query: 95 MNAKYLDG 102
+N K L G
Sbjct: 72 INGKPLPG 79
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 34/61 (55%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L V+ L + TD +L F G + +++ D TG S G+ FV +TS +++RA + +
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 96 N 96
N
Sbjct: 66 N 66
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In
Trinucleotide Repeat Containing 4 Variant
Length = 102
Score = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERA 91
+LFV L + TDE +++ F PFG + V+ G SKG FV + + EA+ A
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRG-PDGTSKGCAFVKFQTHAEAQAA 69
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 37.0 bits (84), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 35/67 (52%), Gaps = 3/67 (4%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
++FV G+ + +L+E F FG + +I D R +GFGF+++ E+ + +
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITF---EDEQSVDQA 68
Query: 95 MNAKYLD 101
+N + D
Sbjct: 69 VNMHFHD 75
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 36.6 bits (83), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 39/77 (50%), Gaps = 3/77 (3%)
Query: 33 SPRLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSK-GFGFVSYTSIEEAERA 91
S L+V LS TT+E++ E F+ G + K+I ++ GF FV Y S +AE A
Sbjct: 18 SCTLYVGNLSFYTTEEQIYELFSKSGDI--KKIIMGLDKMKTACGFCFVEYYSRADAENA 75
Query: 92 REGMNAKYLDGWVIFVD 108
+N LD +I D
Sbjct: 76 MRYINGTRLDDRIIRTD 92
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 36.2 bits (82), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 25/68 (36%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
+L VS L +D ++E FA FG L + V DR +GRS G V + +A +A +
Sbjct: 30 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQ 88
Query: 95 MNAKYLDG 102
N LDG
Sbjct: 89 YNGVPLDG 96
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 36.2 bits (82), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 33/73 (45%), Gaps = 8/73 (10%)
Query: 26 RYNSTLTSPRLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSI 85
R L++ RLFV + +L E F PFG + K++ GF FV +
Sbjct: 24 RQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEA 75
Query: 86 EEAERAREGMNAK 98
E A +A E ++ K
Sbjct: 76 ESAAKAIEEVHGK 88
>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex
Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A
Resolution
Length = 107
Score = 36.2 bits (82), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 25/68 (36%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
+L VS L +D ++E FA FG L + V DR +GRS G V + +A +A +
Sbjct: 31 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAXKQ 89
Query: 95 MNAKYLDG 102
N LDG
Sbjct: 90 YNGVPLDG 97
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 36.2 bits (82), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 44/77 (57%), Gaps = 2/77 (2%)
Query: 28 NSTLTSPRLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEE 87
N+ + +LF+ +S+ T+ ++ F+ FGQ+ +++ G S+G FV++T+
Sbjct: 90 NNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAFVTFTTRAM 148
Query: 88 AERAREGMN-AKYLDGW 103
A+ A + M+ A+ ++G
Sbjct: 149 AQTAIKAMHQAQTMEGC 165
Score = 33.1 bits (74), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 3/71 (4%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATG--RSKGFGFVSYTSIEEAERAR 92
++FV + R +++ L+E F +G + V+ DR+ +SKG FV++ + + A A+
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 93 EGM-NAKYLDG 102
+ N K L G
Sbjct: 65 NALHNMKVLPG 75
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 36.2 bits (82), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 44/77 (57%), Gaps = 2/77 (2%)
Query: 28 NSTLTSPRLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEE 87
N+ + +LF+ +S+ T+ ++ F+ FGQ+ +++ G S+G FV++T+
Sbjct: 102 NNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAFVTFTTRAM 160
Query: 88 AERAREGMN-AKYLDGW 103
A+ A + M+ A+ ++G
Sbjct: 161 AQTAIKAMHQAQTMEGC 177
Score = 34.3 bits (77), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 43/86 (50%), Gaps = 11/86 (12%)
Query: 28 NSTLTSP--------RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATG--RSKGF 77
N TL P ++FV + R +++ L+E F +G + V+ DR+ +SKG
Sbjct: 2 NGTLDHPDQPDLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGC 61
Query: 78 GFVSYTSIEEAERAREGM-NAKYLDG 102
FV++ + + A A+ + N K L G
Sbjct: 62 CFVTFYTRKAALEAQNALHNMKVLPG 87
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 36.2 bits (82), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 31/55 (56%)
Query: 46 TDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGMNAKYL 100
T+E++ + + G ++ K++ D TGRSKG+ F+ + +E + A +N L
Sbjct: 15 TEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQL 69
>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 = 36.2 bits (82), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 31/55 (56%)
Query: 46 TDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGMNAKYL 100
T+E++ + + G ++ K++ D TGRSKG+ F+ + +E + A +N L
Sbjct: 16 TEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQL 70
>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 = 36.2 bits (82), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 31/55 (56%)
Query: 46 TDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGMNAKYL 100
T+E++ + + G ++ K++ D TGRSKG+ F+ + +E + A +N L
Sbjct: 17 TEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQL 71
>pdb|3P5T|L Chain L, Cfim25-Cfim68 Complex
pdb|3P5T|M Chain M, Cfim25-Cfim68 Complex
pdb|3P5T|N Chain N, Cfim25-Cfim68 Complex
pdb|3P5T|O Chain O, Cfim25-Cfim68 Complex
pdb|3P5T|P Chain P, Cfim25-Cfim68 Complex
pdb|3P5T|Q Chain Q, Cfim25-Cfim68 Complex
pdb|3P6Y|C Chain C, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|D Chain D, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|G Chain G, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|H Chain H, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|K Chain K, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|L Chain L, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|O Chain O, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|P Chain P, Cf Im25-Cf Im68-Uguaa Complex
Length = 90
Score = 35.8 bits (81), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 35/69 (50%), Gaps = 2/69 (2%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFG--QLVYSKVITDRATGRSKGFGFVSYTSIEEAERARE 93
L++ L+ TTDE L EA G ++ K +RA G+SKGF V S +++ +
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63
Query: 94 GMNAKYLDG 102
+ + L G
Sbjct: 64 LLPKRELHG 72
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 35.4 bits (80), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 37/80 (46%), Gaps = 8/80 (10%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERA---- 91
+F+ LS + +E L E FG L Y +V+ T SKG F + + E A++
Sbjct: 18 VFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAA 77
Query: 92 ---REGMNAKYLDGWVIFVD 108
EG K LDG + VD
Sbjct: 78 SLEAEGGGLK-LDGRQLKVD 96
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 35.0 bits (79), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 34/68 (50%), Gaps = 1/68 (1%)
Query: 24 SIRYNSTLTSPRLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYT 83
+R S L V L + ++E L+EAF+ FGQ+ + VI D GR G G V ++
Sbjct: 87 QLRVRFACHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVD-DRGRPSGKGIVEFS 145
Query: 84 SIEEAERA 91
A +A
Sbjct: 146 GKPAARKA 153
Score = 26.2 bits (56), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 6/73 (8%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
RLFV L T+E++++ F +G+ + D KGFGF+ + AE A+
Sbjct: 24 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 77
Query: 95 MNAKYLDGWVIFV 107
++ L G + V
Sbjct: 78 LDNMPLRGKQLRV 90
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 35.0 bits (79), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 32/68 (47%), Gaps = 8/68 (11%)
Query: 31 LTSPRLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAER 90
L++ RLFV + +L E F PFG + K++ GF FV + E A +
Sbjct: 2 LSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAK 53
Query: 91 AREGMNAK 98
A E ++ K
Sbjct: 54 AIEEVHGK 61
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 34.7 bits (78), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 42/80 (52%), Gaps = 2/80 (2%)
Query: 22 LGSIRYNSTLTSPRLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVS 81
LGS +Y +P + + + L + L F+ G++V + D ATG++KGF FV
Sbjct: 3 LGSDQYIVVNGAPVIPSAKVPVLK--KALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVE 60
Query: 82 YTSIEEAERAREGMNAKYLD 101
S+ +A++ + + K LD
Sbjct: 61 CGSMNDAKKIIKSFHGKRLD 80
>pdb|3NS6|A Chain A, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
pdb|3NS6|B Chain B, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
Length = 100
Score = 34.7 bits (78), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 42/80 (52%), Gaps = 2/80 (2%)
Query: 22 LGSIRYNSTLTSPRLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVS 81
LGS +Y +P + + + L + L F+ G++V + D ATG++KGF FV
Sbjct: 3 LGSDQYIVVNGAPVIPSAKVPVLK--KALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVE 60
Query: 82 YTSIEEAERAREGMNAKYLD 101
S+ +A++ + + K LD
Sbjct: 61 CGSMNDAKKIIKSFHGKRLD 80
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 34.3 bits (77), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
+LFV L++ ++E + F PFG + V+ G SKG FV ++S EA+ A
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRG-PDGSSKGCAFVKFSSHTEAQAAIHA 75
Query: 95 MN 96
++
Sbjct: 76 LH 77
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 34.3 bits (77), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 35/71 (49%), Gaps = 1/71 (1%)
Query: 32 TSPRLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERA 91
T +L VS L +D ++E FA FG L + V DR +GRS G V + +A +A
Sbjct: 34 TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKA 92
Query: 92 REGMNAKYLDG 102
+ LDG
Sbjct: 93 MKQYKGVPLDG 103
>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 = 33.9 bits (76), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 36/64 (56%), Gaps = 1/64 (1%)
Query: 28 NSTLTSPRLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEE 87
N+ + +LF+ +S+ T+ ++ F+ FGQ+ +++ G S+G FV++T+
Sbjct: 90 NNAVEDRKLFIGXISKKCTENDIRVXFSSFGQIEECRILRG-PDGLSRGCAFVTFTTRAX 148
Query: 88 AERA 91
A+ A
Sbjct: 149 AQTA 152
Score = 31.6 bits (70), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 38/71 (53%), Gaps = 3/71 (4%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATG--RSKGFGFVSYTSIEEAERAR 92
+ FV + R +++ L+E F +G + V+ DR+ +SKG FV++ + + A A+
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 93 EGM-NAKYLDG 102
+ N K L G
Sbjct: 65 NALHNXKVLPG 75
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 33.9 bits (76), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 35/71 (49%), Gaps = 1/71 (1%)
Query: 32 TSPRLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERA 91
T +L VS L +D ++E FA FG L + V DR +GRS G V + +A +A
Sbjct: 34 TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKA 92
Query: 92 REGMNAKYLDG 102
+ LDG
Sbjct: 93 MKQYKGVPLDG 103
>pdb|3Q2S|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2S|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2T|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
pdb|3Q2T|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
Length = 229
Score = 33.5 bits (75), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 35/69 (50%), Gaps = 2/69 (2%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFG--QLVYSKVITDRATGRSKGFGFVSYTSIEEAERARE 93
L++ L+ TTDE L EA G ++ K +RA G+SKGF V S +++ +
Sbjct: 71 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 130
Query: 94 GMNAKYLDG 102
+ + L G
Sbjct: 131 LLPKRELHG 139
>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 = 33.5 bits (75), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 3/71 (4%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATG--RSKGFGFVSYTSIEEAERAR 92
++FV + R +++ L+E F +G + V+ DR+ +SKG FV++ + + A A+
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 93 EGM-NAKYLDG 102
+ N K L G
Sbjct: 65 NALHNMKVLPG 75
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 33.5 bits (75), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERA 91
+LFV L++ +++ ++ F FG + ++ G SKG FV Y+S EA+ A
Sbjct: 17 KLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRG-PDGNSKGCAFVKYSSHAEAQAA 72
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 33.1 bits (74), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 37/76 (48%), Gaps = 1/76 (1%)
Query: 32 TSPRLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERA 91
T +L VS L +D ++E FA FG L + V DR +GRS G V + +A +A
Sbjct: 87 TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKA 145
Query: 92 REGMNAKYLDGWVIFV 107
+ LDG + +
Sbjct: 146 MKQYKGVPLDGRPMDI 161
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 33.1 bits (74), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
+F L+ L++ F+ G++ ++I+DR + RSKG +V + I+ A G+
Sbjct: 28 VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLA-IGL 86
Query: 96 NAKYLDGWVIFV 107
+ L G I V
Sbjct: 87 TGQRLLGVPIIV 98
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 32.3 bits (72), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 34/72 (47%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L V L+ T+ + L+ F +G++ + + T +GF FV + +A+ A M
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75
Query: 96 NAKYLDGWVIFV 107
+ LDG + V
Sbjct: 76 DGAELDGRELRV 87
>pdb|2DIS|A Chain A, Solution Structure Of The Rrm Domain Of Unnamed Protein
Product
Length = 109
Score = 32.3 bits (72), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 2/71 (2%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSK--GFGFVSYTSIEEAERAR 92
RLF+ G+ ++ E++ E A + V ++ A + K GF FV Y S A AR
Sbjct: 10 RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 69
Query: 93 EGMNAKYLDGW 103
+ + W
Sbjct: 70 RKLMPGRIQLW 80
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 32.0 bits (71), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 36/65 (55%), Gaps = 1/65 (1%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
+FV+ L +KLKE F+ G +V + ++ D+ G+S+G G V++ EA +A
Sbjct: 18 VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMF 76
Query: 96 NAKYL 100
N + L
Sbjct: 77 NGQLL 81
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 31.6 bits (70), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 9/75 (12%)
Query: 35 RLFVSGLSRLTTDEKLKEA-FAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERARE 93
R+F+ L+ L + EA F+ +G++V V KGF FV Y + A A
Sbjct: 17 RVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVA 68
Query: 94 GMNAKYLDGWVIFVD 108
G + + + G V+ ++
Sbjct: 69 GEDGRMIAGQVLDIN 83
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 31.6 bits (70), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 32 TSPRLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITD-RATGRSKGFGFVSYTSIEEAER 90
T+ ++ V + +++E F+ FG+L ++ TG +GFGFV + + ++A++
Sbjct: 14 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKK 73
Query: 91 A 91
A
Sbjct: 74 A 74
>pdb|3N9U|C Chain C, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
pdb|3N9U|I Chain I, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
Length = 156
Score = 30.4 bits (67), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 2/69 (2%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFG--QLVYSKVITDRATGRSKGFGFVSYTSIEEAERARE 93
++V S TTD++L + G +V K +RA G+SKG+ V S + E
Sbjct: 58 VYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLE 117
Query: 94 GMNAKYLDG 102
+ K L+G
Sbjct: 118 LLPGKVLNG 126
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 30.0 bits (66), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 8/63 (12%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
LFV L+ T+E L+++F+ FG+L K + D + FV + A +A + M
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD--------YAFVHFEDRGAAVKAMDEM 69
Query: 96 NAK 98
N K
Sbjct: 70 NGK 72
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif In Trna Selenocysteine Associated Protein
Length = 104
Score = 30.0 bits (66), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 30/57 (52%), Gaps = 2/57 (3%)
Query: 36 LFVSGLSRLTTDEKLKEAFAP-FGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERA 91
LFV L+ D L E F + KV+ D+ TG SKG+GFV +T E +RA
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRA 67
>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 = 29.6 bits (65), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 13/55 (23%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 41 LSRLTTDEKLKEAFAPFG-QLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
L + T++ ++ G Q +++ ++++G+S+GF FV ++ +++A R E
Sbjct: 9 LPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEA 63
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 29.3 bits (64), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 35/80 (43%), Gaps = 8/80 (10%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSK--------VITDRATGRSKGFGFVSYTSIEE 87
+FV GL T E + + F G + +K + TDR TG+ KG VS+
Sbjct: 16 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 75
Query: 88 AERAREGMNAKYLDGWVIFV 107
A+ A + + K G I V
Sbjct: 76 AKAAIDWFDGKEFSGNPIKV 95
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 28.9 bits (63), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 35/80 (43%), Gaps = 8/80 (10%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSK--------VITDRATGRSKGFGFVSYTSIEE 87
+FV GL T E + + F G + +K + TDR TG+ KG VS+
Sbjct: 10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 69
Query: 88 AERAREGMNAKYLDGWVIFV 107
A+ A + + K G I V
Sbjct: 70 AKAAIDWFDGKEFSGNPIKV 89
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 28.1 bits (61), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 10/74 (13%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPF--GQLVYSKVITDRATGRSKGFGFVSYTSIEEAERARE 93
L+V L T++E +++ F G + K I D + FV +++ E+A A +
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD--------YAFVHFSNREDAVEAMK 69
Query: 94 GMNAKYLDGWVIFV 107
+N K LDG I V
Sbjct: 70 ALNGKVLDGSPIEV 83
>pdb|3KSM|A Chain A, Crystal Structure Of Abc-Type Sugar Transport System,
Periplasmic Component From Hahella Chejuensis
pdb|3KSM|B Chain B, Crystal Structure Of Abc-Type Sugar Transport System,
Periplasmic Component From Hahella Chejuensis
Length = 276
Score = 27.3 bits (59), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 18/38 (47%)
Query: 54 FAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERA 91
F P ++ R +G SK FGF+ + EE E A
Sbjct: 192 FTPNESTTIGALVAIRQSGXSKQFGFIGFDQTEELEAA 229
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 27.3 bits (59), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 35/80 (43%), Gaps = 8/80 (10%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSK--------VITDRATGRSKGFGFVSYTSIEE 87
++V GL+ T + L + F G + +K + D+ TG+ KG VSY
Sbjct: 18 IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPT 77
Query: 88 AERAREGMNAKYLDGWVIFV 107
A+ A E + K G + V
Sbjct: 78 AKAAVEWFDGKDFQGSKLKV 97
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 27.3 bits (59), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 37/69 (53%), Gaps = 8/69 (11%)
Query: 29 STLTSP-RLFVSGLSRLTTDEKLKEAFAPFGQLVYSK---VITDRATGRSKGFGFVSYTS 84
S T+P LF+ L+ + +LK A + +++K + D TG ++ FG+V + S
Sbjct: 12 SESTTPFNLFIGNLNPNKSVAELKVAISE----LFAKNDLAVVDVRTGTNRKFGYVDFES 67
Query: 85 IEEAERARE 93
E+ E+A E
Sbjct: 68 AEDLEKALE 76
>pdb|2H85|A Chain A, Crystal Structure Of Nsp 15 From Sars
Length = 347
Score = 27.3 bits (59), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 16/37 (43%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 40 GLSRLTTDEKLK-EAFAPFGQLVYSKVITDRATGRSK 75
GL++ + D LK E F P V + ITD TG SK
Sbjct: 255 GLAKRSQDSPLKLEDFIPMDSTVKNYFITDAQTGSSK 291
>pdb|2RHB|A Chain A, Crystal Structure Of Nsp15-H234a Mutant- Hexamer In
Asymmetric Unit
pdb|2RHB|B Chain B, Crystal Structure Of Nsp15-H234a Mutant- Hexamer In
Asymmetric Unit
pdb|2RHB|C Chain C, Crystal Structure Of Nsp15-H234a Mutant- Hexamer In
Asymmetric Unit
pdb|2RHB|D Chain D, Crystal Structure Of Nsp15-H234a Mutant- Hexamer In
Asymmetric Unit
pdb|2RHB|E Chain E, Crystal Structure Of Nsp15-H234a Mutant- Hexamer In
Asymmetric Unit
pdb|2RHB|F Chain F, Crystal Structure Of Nsp15-H234a Mutant- Hexamer In
Asymmetric Unit
Length = 353
Score = 27.3 bits (59), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 16/37 (43%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 40 GLSRLTTDEKLK-EAFAPFGQLVYSKVITDRATGRSK 75
GL++ + D LK E F P V + ITD TG SK
Sbjct: 260 GLAKRSQDSPLKLEDFIPMDSTVKNYFITDAQTGSSK 296
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 27.3 bits (59), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 35/70 (50%), Gaps = 5/70 (7%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L LS T+++LKE F ++ ++++ G+SKG ++ + S +AE+ E
Sbjct: 19 LLAKNLSFNITEDELKEVFEDALEI---RLVS--QDGKSKGIAYIEFKSEADAEKNLEEK 73
Query: 96 NAKYLDGWVI 105
+DG +
Sbjct: 74 QGAEIDGRSV 83
>pdb|2OZK|A Chain A, Structure Of An N-Terminal Truncated Form Of Nendou
(Nsp15) From Sars-Coronavirus
pdb|2OZK|B Chain B, Structure Of An N-Terminal Truncated Form Of Nendou
(Nsp15) From Sars-Coronavirus
pdb|2OZK|C Chain C, Structure Of An N-Terminal Truncated Form Of Nendou
(Nsp15) From Sars-Coronavirus
pdb|2OZK|D Chain D, Structure Of An N-Terminal Truncated Form Of Nendou
(Nsp15) From Sars-Coronavirus
Length = 346
Score = 27.3 bits (59), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 16/37 (43%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 40 GLSRLTTDEKLK-EAFAPFGQLVYSKVITDRATGRSK 75
GL++ + D LK E F P V + ITD TG SK
Sbjct: 253 GLAKRSQDSPLKLEDFIPMDSTVKNYFITDAQTGSSK 289
>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 = 26.9 bits (58), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 35/70 (50%), Gaps = 5/70 (7%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREGM 95
L LS T+++LKE F ++ ++++ G+SKG ++ + S +AE+ E
Sbjct: 102 LLAKNLSFNITEDELKEVFEDALEI---RLVS--QDGKSKGIAYIEFKSEADAEKNLEEK 156
Query: 96 NAKYLDGWVI 105
+DG +
Sbjct: 157 QGAEIDGRSV 166
Score = 26.9 bits (58), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 37/69 (53%), Gaps = 8/69 (11%)
Query: 29 STLTSP-RLFVSGLSRLTTDEKLKEAFAPFGQLVYSK---VITDRATGRSKGFGFVSYTS 84
S T+P LF+ L+ + +LK A + +++K + D TG ++ FG+V + S
Sbjct: 8 SESTTPFNLFIGNLNPNKSVAELKVAISE----LFAKNDLAVVDVRTGTNRKFGYVDFES 63
Query: 85 IEEAERARE 93
E+ E+A E
Sbjct: 64 AEDLEKALE 72
>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 = 26.9 bits (58), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 6/73 (8%)
Query: 35 RLFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
RLFV L T+E++++ F +G+ + D KGFGF+ + AE A+
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 70
Query: 95 MNAKYLDGWVIFV 107
++ L G + V
Sbjct: 71 LDNMPLRGKQLRV 83
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 26.6 bits (57), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 18/75 (24%), Positives = 34/75 (45%), Gaps = 9/75 (12%)
Query: 35 RLFVSGLS-RLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERARE 93
R+F+ L+ L ++ F+ +G++ V KG+ FV Y++ A A
Sbjct: 29 RVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVL 80
Query: 94 GMNAKYLDGWVIFVD 108
G N + L G + ++
Sbjct: 81 GENGRVLAGQTLDIN 95
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 26.6 bits (57), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 32/71 (45%), Gaps = 7/71 (9%)
Query: 36 LFVSGLSRLTTDEKLKEAFAPFGQL-VYSKVITDRATGRSKGFGFVSYTSIEEAERAREG 94
L L T ++LKE F ++ + SK G+SKG ++ + + +AE+ E
Sbjct: 96 LLAKNLPYKVTQDELKEVFEDAAEIRLVSK------DGKSKGIAYIEFKTEADAEKTFEE 149
Query: 95 MNAKYLDGWVI 105
+DG I
Sbjct: 150 KQGTEIDGRSI 160
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 26.2 bits (56), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 3/76 (3%)
Query: 34 PR-LFVSGLSRLTTDEKLKEAFAPFGQLVYSKVITDRATGRSKGFGFVSYTSIEEAERAR 92
PR L+V LSR T+ + + F+ G K+IT+ + + + FV + +A A
Sbjct: 15 PRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAAL 72
Query: 93 EGMNAKYLDGWVIFVD 108
MN + + G + V+
Sbjct: 73 AAMNGRKILGKEVKVN 88
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.318 0.134 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,869,615
Number of Sequences: 62578
Number of extensions: 90811
Number of successful extensions: 377
Number of sequences better than 100.0: 156
Number of HSP's better than 100.0 without gapping: 134
Number of HSP's successfully gapped in prelim test: 22
Number of HSP's that attempted gapping in prelim test: 193
Number of HSP's gapped (non-prelim): 182
length of query: 143
length of database: 14,973,337
effective HSP length: 89
effective length of query: 54
effective length of database: 9,403,895
effective search space: 507810330
effective search space used: 507810330
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 bits)