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= 016658
(385 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 = 52.0 bits (123), Expect = 6e-07, Method: Composition-based stats.
Identities = 24/67 (35%), Positives = 40/67 (59%)
Query: 106 NDSLVLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEK 165
+D L++ LS + NE L ++FS +G++ +V +V DR RG G+V F+ DA+
Sbjct: 10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 69
Query: 166 AQLYMDG 172
A + M+G
Sbjct: 70 AMMAMNG 76
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 50.4 bits (119), Expect = 2e-06, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 40/62 (64%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
LY+ L + +++ + ++FS +G ++ +++D+A + RG G++RF R +AE+A +
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 171 DG 172
+G
Sbjct: 64 NG 65
>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 = 3e-06, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 38/62 (61%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
LYI L R + + + ++FS FG +++ +++D+ L RG ++RF R++AE+A
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 171 DG 172
+G
Sbjct: 151 NG 152
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 36/64 (56%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
L ++ L +N+ + LR +FS+ GEV +L+ D+ G G+V + T DAE+A +
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 171 DGFH 174
+G
Sbjct: 65 NGLR 68
>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 = 3e-06, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 38/62 (61%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
LYI L R + + + ++FS FG +++ +++D+ L RG ++RF R++AE+A
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 171 DG 172
+G
Sbjct: 151 NG 152
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 36/64 (56%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
L ++ L +N+ + LR +FS+ GEV +L+ D+ G G+V + T DAE+A +
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 171 DGFH 174
+G
Sbjct: 65 NGLR 68
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 49.3 bits (116), Expect = 4e-06, Method: Composition-based stats.
Identities = 24/63 (38%), Positives = 42/63 (66%), Gaps = 1/63 (1%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRA-VNLPRGSGYVRFKTRADAEKAQLY 169
++I L+RNV + H+ EIFS +G++ +++ ++R +L +G YV F+ +AEKA +
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 170 MDG 172
MDG
Sbjct: 67 MDG 69
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 48.9 bits (115), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 40/62 (64%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
LY+ L + +++ + ++FS +G ++ +++D+A + RG G++RF R +AE+A +
Sbjct: 93 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 152
Query: 171 DG 172
+G
Sbjct: 153 NG 154
Score = 34.7 bits (78), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 16/64 (25%), Positives = 33/64 (51%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
L ++ L +N+ + + +F + G++ +LV D+ G G+V + DA+KA +
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 171 DGFH 174
+G
Sbjct: 67 NGLK 70
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 48.1 bits (113), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 35/64 (54%)
Query: 109 LVLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQL 168
+ L +D+L+ + LR +F +G V DV + + PRG +VRF R DA+ A+
Sbjct: 14 ITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEA 73
Query: 169 YMDG 172
MDG
Sbjct: 74 AMDG 77
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 48.1 bits (113), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 40/64 (62%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
L ++ + V+E LR++F +G + V++V DR RG G+V+F++ + A++A +
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 171 DGFH 174
+GF+
Sbjct: 105 NGFN 108
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 47.8 bits (112), Expect = 1e-05, Method: Composition-based stats.
Identities = 23/63 (36%), Positives = 35/63 (55%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
LY+ SL N+ E LR IF FG + ++L+MD +G G++ F A+KA +
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 171 DGF 173
+GF
Sbjct: 89 NGF 91
>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 = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 38/62 (61%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
LY+ L + + + L ++FS +G ++ +++D+ + RG G++RF R +AE+A +
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 171 DG 172
+G
Sbjct: 151 NG 152
Score = 37.7 bits (86), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 33/64 (51%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
L ++ L +N+ + R +F + GE+ +LV D+ G G+V + DAEKA +
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 171 DGFH 174
+G
Sbjct: 65 NGLR 68
>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 = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/62 (38%), Positives = 33/62 (53%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
L +D+L+ + LR +F +G V DV + DR RG +VRF + DAE A M
Sbjct: 50 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109
Query: 171 DG 172
DG
Sbjct: 110 DG 111
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 39/64 (60%), Gaps = 2/64 (3%)
Query: 106 NDSLVLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLP--RGSGYVRFKTRADA 163
+D++ +++ + R +E LRE+F +G V ++ ++ DR+ N P +G +V F TR A
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 164 EKAQ 167
+AQ
Sbjct: 61 LEAQ 64
Score = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 32/56 (57%), Gaps = 1/56 (1%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
L+I +S+ E +R +FS+FG++ + ++ L RG +V F TRA A+ A
Sbjct: 98 LFIGMISKKCTENDIRVMFSSFGQIEECR-ILRGPDGLSRGCAFVTFTTRAMAQTA 152
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/62 (38%), Positives = 33/62 (53%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
L +D+L+ + LR +F +G V DV + DR RG +VRF + DAE A M
Sbjct: 73 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132
Query: 171 DG 172
DG
Sbjct: 133 DG 134
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 45.4 bits (106), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 2/63 (3%)
Query: 107 DSLVLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLP--RGSGYVRFKTRADAE 164
D++ +++ + R +E LRE+F +G V ++ ++ DR+ N P +G +V F TR A
Sbjct: 14 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 73
Query: 165 KAQ 167
+AQ
Sbjct: 74 EAQ 76
Score = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 32/56 (57%), Gaps = 1/56 (1%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
L+I +S+ E +R +FS+FG++ + ++ L RG +V F TRA A+ A
Sbjct: 110 LFIGMISKKCTENDIRVMFSSFGQIEECR-ILRGPDGLSRGCAFVTFTTRAMAQTA 164
>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 = 45.4 bits (106), Expect = 5e-05, Method: Composition-based stats.
Identities = 18/56 (32%), Positives = 32/56 (57%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
LY+ +L R + + L IF +G +V ++ D+ PRG +VR+ R +A++A
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 71
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 44.7 bits (104), Expect = 8e-05, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 39/63 (61%)
Query: 105 ENDSLVLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAE 164
++D++ L+I + RN++E L+ +F FG++ ++ ++ DR + +G ++ + R A
Sbjct: 10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESAL 69
Query: 165 KAQ 167
KAQ
Sbjct: 70 KAQ 72
>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 = 44.7 bits (104), Expect = 8e-05, Method: Composition-based stats.
Identities = 21/64 (32%), Positives = 39/64 (60%), Gaps = 2/64 (3%)
Query: 106 NDSLVLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSG--YVRFKTRADA 163
+D++ +++ + R +E LRE+F +G V ++ ++ DR+ N P+ G +V F TR A
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 164 EKAQ 167
+AQ
Sbjct: 61 LEAQ 64
>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 = 44.7 bits (104), Expect = 1e-04, Method: Composition-based stats.
Identities = 21/63 (33%), Positives = 36/63 (57%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
L ++ L +N+ + LR +FS+ GEV +L+ D+ G G+V + T DAE+A +
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 171 DGF 173
+G
Sbjct: 67 NGL 69
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 32/56 (57%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
LY+ +L R + + L IF +G +V ++ D+ PRG +VR+ R +A++A
Sbjct: 92 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 147
>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 = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 32/56 (57%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
LY+ +L R + + L IF +G +V ++ D+ PRG +VR+ R +A++A
Sbjct: 103 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 158
>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 = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 21/63 (33%), Positives = 35/63 (55%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
L ++ L +N + LR +FS+ GEV +L+ D+ G G+V + T DAE+A +
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 171 DGF 173
+G
Sbjct: 82 NGL 84
>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 = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 38/64 (59%), Gaps = 2/64 (3%)
Query: 106 NDSLVLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLP--RGSGYVRFKTRADA 163
+D++ ++ + R +E LRE+F +G V ++ ++ DR+ N P +G +V F TR A
Sbjct: 1 SDAIKXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 164 EKAQ 167
+AQ
Sbjct: 61 LEAQ 64
Score = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
L+I +S+ E +R FS+FG++ + ++ L RG +V F TRA A+ A
Sbjct: 98 LFIGXISKKCTENDIRVXFSSFGQIEECRILRG-PDGLSRGCAFVTFTTRAXAQTA 152
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 43.9 bits (102), Expect = 2e-04, Method: Composition-based stats.
Identities = 19/48 (39%), Positives = 29/48 (60%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFK 158
L++ L + + LR FS +GEVVD ++ D+ N RG G+V+FK
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFK 66
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 43.5 bits (101), Expect = 2e-04, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 34/62 (54%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
+++ LS + ++ F+ FG++ D +V D A +G G+V F + DAE A ++M
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 171 DG 172
G
Sbjct: 78 GG 79
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 43.1 bits (100), Expect = 3e-04, Method: Composition-based stats.
Identities = 17/54 (31%), Positives = 33/54 (61%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAE 164
+Y+ +L + ++E+FS FG+V +V+L+ DR P+G G+V + + +E
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSE 57
>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 = 42.7 bits (99), Expect = 3e-04, Method: Composition-based stats.
Identities = 21/55 (38%), Positives = 30/55 (54%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEK 165
++I LS + + L++ FS FGEVVD L +D RG G+V FK +K
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDK 56
>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 = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 36/65 (55%)
Query: 108 SLVLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQ 167
S LY+ +LS E + E+FS G++ + + +D+ G +V + +RADAE A
Sbjct: 39 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAM 98
Query: 168 LYMDG 172
Y++G
Sbjct: 99 RYING 103
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 42.4 bits (98), Expect = 4e-04, Method: Composition-based stats.
Identities = 21/57 (36%), Positives = 32/57 (56%)
Query: 116 LSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYMDG 172
LS E LRE+FS +G + DV +V D+ RG +V F+ DA++A+ +G
Sbjct: 23 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 42.4 bits (98), Expect = 4e-04, Method: Composition-based stats.
Identities = 21/57 (36%), Positives = 32/57 (56%)
Query: 116 LSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYMDG 172
LS E LRE+FS +G + DV +V D+ RG +V F+ DA++A+ +G
Sbjct: 23 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 42.4 bits (98), Expect = 4e-04, Method: Composition-based stats.
Identities = 19/68 (27%), Positives = 35/68 (51%)
Query: 106 NDSLVLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEK 165
+D+ + + +LS + E L+E+F FG + + L D+ +G ++ F R DA +
Sbjct: 13 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAAR 72
Query: 166 AQLYMDGF 173
A + GF
Sbjct: 73 AIAGVSGF 80
>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 = 42.4 bits (98), Expect = 4e-04, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 33/61 (54%)
Query: 105 ENDSLVLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAE 164
E D+ ++ LS + ++ L++ F+ FGEVVD + D RG G++ FK A E
Sbjct: 8 EEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVE 67
Query: 165 K 165
K
Sbjct: 68 K 68
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 42.4 bits (98), Expect = 4e-04, Method: Composition-based stats.
Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
L+I L+R NE L+ +F G + +V L+ DR RG ++ F+ ADA+ A M
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSK-SRGFAFITFENPADAKNAAKDM 68
Query: 171 DG 172
+G
Sbjct: 69 NG 70
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 42.0 bits (97), Expect = 5e-04, Method: Composition-based stats.
Identities = 21/57 (36%), Positives = 32/57 (56%)
Query: 116 LSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYMDG 172
LS E LRE+FS +G + DV +V D+ RG +V F+ DA++A+ +G
Sbjct: 20 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 76
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 42.0 bits (97), Expect = 6e-04, Method: Composition-based stats.
Identities = 21/63 (33%), Positives = 34/63 (53%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
LY+ SL N+ E LR IF FG++ ++ L+ D +G G++ F A +A +
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 171 DGF 173
+GF
Sbjct: 68 NGF 70
>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 = 42.0 bits (97), Expect = 6e-04, Method: Composition-based stats.
Identities = 20/55 (36%), Positives = 29/55 (52%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEK 165
+++ LS + E +RE F FGEV +EL MD N RG ++ FK +K
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKK 58
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 42.0 bits (97), Expect = 6e-04, Method: Composition-based stats.
Identities = 20/55 (36%), Positives = 29/55 (52%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEK 165
+++ LS + E +RE F FGEV +EL MD N RG ++ FK +K
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKK 56
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 41.6 bits (96), Expect = 7e-04, Method: Composition-based stats.
Identities = 17/63 (26%), Positives = 37/63 (58%)
Query: 105 ENDSLVLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAE 164
++D++ L++ + R ++E L+ +F FG + ++ ++ DR L +G ++ + R A
Sbjct: 12 DHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSAL 71
Query: 165 KAQ 167
KAQ
Sbjct: 72 KAQ 74
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 41.6 bits (96), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 35/65 (53%)
Query: 108 SLVLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQ 167
+ L + LS E LRE+FS +G + DV +V D+ RG +V F+ DA++A+
Sbjct: 46 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 105
Query: 168 LYMDG 172
+G
Sbjct: 106 ERANG 110
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 29/56 (51%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
+++ + N E LRE F FG V +V ++ D PRG G++ F+ ++A
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQA 68
>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
At Ph 6.0
pdb|4F26|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
A Ph 9.0
Length = 115
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 20/62 (32%), Positives = 38/62 (61%), Gaps = 2/62 (3%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
++I +L ++++ L + FS FG ++ ++V D N +G G+V F+T+ AE+A M
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 65
Query: 171 DG 172
+G
Sbjct: 66 NG 67
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 20/62 (32%), Positives = 38/62 (61%), Gaps = 2/62 (3%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
++I +L ++++ L + FS FG ++ ++V D N +G G+V F+T+ AE+A M
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 71
Query: 171 DG 172
+G
Sbjct: 72 NG 73
>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 = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 38/62 (61%), Gaps = 2/62 (3%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
++I +L ++++ L + FS FG ++ ++V D N +G G+V F+T+ AE+A M
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 158
Query: 171 DG 172
+G
Sbjct: 159 NG 160
Score = 35.4 bits (80), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 28/56 (50%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
LY+ L +V E L E FS G ++ + + D G YV F+ ADAE+A
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERA 68
>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 = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 38/62 (61%), Gaps = 2/62 (3%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
++I +L ++++ L + FS FG ++ ++V D N +G G+V F+T+ AE+A M
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 163
Query: 171 DG 172
+G
Sbjct: 164 NG 165
Score = 35.8 bits (81), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 28/56 (50%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
LY+ L +V E L E FS G ++ + + D G YV F+ ADAE+A
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERA 73
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 39/62 (62%), Gaps = 2/62 (3%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
L++ ++ + LR++F FG+++DVE++ + + +G G+V F+ ADA++A+ +
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTFENSADADRAREKL 75
Query: 171 DG 172
G
Sbjct: 76 HG 77
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 30/56 (53%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
+++ L + + LR+ F FG++ + ++ DR RG G+V RA AE+A
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA 75
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 22/71 (30%), Positives = 43/71 (60%), Gaps = 4/71 (5%)
Query: 104 TENDSLV--LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRA 161
TEN S L++ ++ + LR++F FG+++DVE++ + + +G G+V F+ A
Sbjct: 23 TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTFENSA 80
Query: 162 DAEKAQLYMDG 172
DA++A+ + G
Sbjct: 81 DADRAREKLHG 91
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 36/69 (52%)
Query: 104 TENDSLVLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADA 163
+ +D+ L++ L+ NV++ LR F +F + ++ D RG G+V F ++ DA
Sbjct: 83 SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDA 142
Query: 164 EKAQLYMDG 172
+ A M G
Sbjct: 143 QNAMDSMQG 151
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 32/62 (51%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
+++ ++ E L++IFS G VV LV DR P+G G+ ++ + A A +
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 171 DG 172
+G
Sbjct: 71 NG 72
>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 = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
L+I L + + L EI G V D+ LV +RA P+G YV ++ + A +A + M
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRA-GKPKGLAYVEYENESQASQAVMKM 78
Query: 171 DG 172
DG
Sbjct: 79 DG 80
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 16/63 (25%), Positives = 34/63 (53%)
Query: 110 VLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLY 169
+L++ S+ E ++E F ++GE+ ++ L +DR +G V ++T A A+
Sbjct: 28 ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87
Query: 170 MDG 172
++G
Sbjct: 88 LNG 90
>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 = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 21/65 (32%), Positives = 37/65 (56%), Gaps = 1/65 (1%)
Query: 108 SLVLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQ 167
S LY+ +LS E + E+FS G++ + + +D+ + G +V + +RADAE A
Sbjct: 18 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDK-MKTACGFCFVEYYSRADAENAM 76
Query: 168 LYMDG 172
Y++G
Sbjct: 77 RYING 81
>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 40/68 (58%), Gaps = 7/68 (10%)
Query: 110 VLYIDSLSRNVNEGHLRE----IFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEK 165
+YI++L+ + + L++ IFS FG+++D+ ++ R++ + RG +V FK + A
Sbjct: 11 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDI--LVSRSLKM-RGQAFVIFKEVSSATN 67
Query: 166 AQLYMDGF 173
A M GF
Sbjct: 68 ALRSMQGF 75
>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 = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 31/62 (50%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
+++ LS + ++ F+ FG + D +V D A +G G+V F + DAE A M
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 171 DG 172
G
Sbjct: 78 GG 79
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 32/66 (48%)
Query: 106 NDSLVLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEK 165
N +Y+ L V+E L E+F G VV+ + DR +G G+V F + DA+
Sbjct: 13 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 72
Query: 166 AQLYMD 171
A MD
Sbjct: 73 AIKIMD 78
>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1HL6|C Chain C, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1RK8|A Chain A, Structure Of The Cytosolic Protein Pym Bound To The Mago-
Y14 Core Of The Exon Junction Complex
pdb|2X1G|A Chain A, Crystal Structure Of Importin13 - Mago-Y14 Complex
pdb|2X1G|C Chain C, Crystal Structure Of Importin13 - Mago-Y14 Complex
Length = 165
Score = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 16/66 (24%), Positives = 35/66 (53%)
Query: 107 DSLVLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
+ +L++ S+ E ++E F ++GE+ ++ L +DR +G V ++T A A
Sbjct: 71 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 130
Query: 167 QLYMDG 172
+ ++G
Sbjct: 131 KEALNG 136
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet
Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 38.5 bits (88), Expect = 0.006, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 33/64 (51%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
L+I L + + L ++F FG VV ++ +D+ NL + G+V + A+ A M
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 171 DGFH 174
+GF
Sbjct: 88 NGFQ 91
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 38.5 bits (88), Expect = 0.007, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 29/55 (52%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEK 165
+++ LS N ++ F FG+V D L+ D+ N RG G+V F++ EK
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEK 56
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 38.1 bits (87), Expect = 0.008, Method: Composition-based stats.
Identities = 21/67 (31%), Positives = 40/67 (59%), Gaps = 7/67 (10%)
Query: 111 LYIDSLSRNVNEGHLRE----IFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
+YI++L+ + + L++ IFS FG+++D+ ++ R++ + RG +V FK + A A
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDI--LVSRSLKM-RGQAFVIFKEVSSATNA 68
Query: 167 QLYMDGF 173
M GF
Sbjct: 69 LRSMQGF 75
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 38.1 bits (87), Expect = 0.008, Method: Composition-based stats.
Identities = 21/67 (31%), Positives = 40/67 (59%), Gaps = 7/67 (10%)
Query: 111 LYIDSLSRNVNEGHLRE----IFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
+YI++L+ + + L++ IFS FG+++D+ ++ R++ + RG +V FK + A A
Sbjct: 11 IYINNLNEKIKKDELKKSLYAIFSQFGQILDI--LVSRSLKM-RGQAFVIFKEVSSATNA 67
Query: 167 QLYMDGF 173
M GF
Sbjct: 68 LRSMQGF 74
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 38.1 bits (87), Expect = 0.008, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 30/57 (52%)
Query: 110 VLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
VLY+ L+ V++ L F FG++ D+++ +D RG +V F+ DA A
Sbjct: 14 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 70
>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 = 38.1 bits (87), Expect = 0.009, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 30/57 (52%)
Query: 110 VLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
VLY+ L+ V++ L F FG++ D+++ +D RG +V F+ DA A
Sbjct: 9 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 65
>pdb|1U6B|A Chain A, Crystal Structure Of A Self-Splicing Group I Intron With
Both Exons
pdb|1ZZN|A Chain A, Crystal Structure Of A Group I IntronTWO EXON COMPLEX THAT
Includes All Catalytic Metal Ion Ligands.
pdb|3G8S|A Chain A, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|B Chain B, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|C Chain C, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|D Chain D, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8T|A Chain A, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|B Chain B, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|C Chain C, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|D Chain D, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G96|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G9C|A Chain A, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|B Chain B, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|C Chain C, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|D Chain D, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3IRW|P Chain P, Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3MUM|P Chain P, Crystal Structure Of The G20a Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUR|P Chain P, Crystal Structure Of The C92u Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUT|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Gmp
pdb|3MUV|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Amp
pdb|3MXH|P Chain P, Native Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3P49|B Chain B, Crystal Structure Of A Glycine Riboswitch From
Fusobacterium Nucleatum
pdb|3R1H|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1H|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1L|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3R1L|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3UCU|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Pgpg
pdb|3UCZ|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Gpg
pdb|3UD3|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Pgpa
pdb|3UD4|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Gpa
Length = 98
Score = 38.1 bits (87), Expect = 0.009, Method: Composition-based stats.
Identities = 21/67 (31%), Positives = 40/67 (59%), Gaps = 7/67 (10%)
Query: 111 LYIDSLSRNVNEGHLRE----IFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
+YI++L+ + + L++ IFS FG+++D+ ++ R++ + RG +V FK + A A
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDI--LVSRSLKM-RGQAFVIFKEVSSATNA 68
Query: 167 QLYMDGF 173
M GF
Sbjct: 69 LRSMQGF 75
>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures
pdb|1DZ5|A Chain A, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
pdb|1DZ5|B Chain B, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
Length = 101
Score = 38.1 bits (87), Expect = 0.009, Method: Composition-based stats.
Identities = 21/67 (31%), Positives = 40/67 (59%), Gaps = 7/67 (10%)
Query: 111 LYIDSLSRNVNEGHLRE----IFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
+YI++L+ + + L++ IFS FG+++D+ ++ R++ + RG +V FK + A A
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDI--LVSRSLKM-RGQAFVIFKEVSSATNA 67
Query: 167 QLYMDGF 173
M GF
Sbjct: 68 LRSMQGF 74
>pdb|3L3C|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
Length = 90
Score = 38.1 bits (87), Expect = 0.009, Method: Composition-based stats.
Identities = 21/67 (31%), Positives = 40/67 (59%), Gaps = 7/67 (10%)
Query: 111 LYIDSLSRNVNEGHLRE----IFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
+YI++L+ + + L++ IFS FG+++D+ ++ R++ + RG +V FK + A A
Sbjct: 6 IYINNLNEKIKKDELKKSLHAIFSRFGQILDI--LVSRSLKM-RGQAFVIFKEVSSATNA 62
Query: 167 QLYMDGF 173
M GF
Sbjct: 63 LRSMQGF 69
>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|B Chain B, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|C Chain C, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|D Chain D, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
Length = 96
Score = 38.1 bits (87), Expect = 0.009, Method: Composition-based stats.
Identities = 21/67 (31%), Positives = 40/67 (59%), Gaps = 7/67 (10%)
Query: 111 LYIDSLSRNVNEGHLRE----IFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
+YI++L+ + + L++ IFS FG+++D+ ++ R++ + RG +V FK + A A
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDI--LVSRSLKM-RGQAFVIFKEVSSATNA 67
Query: 167 QLYMDGF 173
M GF
Sbjct: 68 LRSMQGF 74
>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
pdb|3IWN|D Chain D, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
Length = 91
Score = 38.1 bits (87), Expect = 0.009, Method: Composition-based stats.
Identities = 21/67 (31%), Positives = 40/67 (59%), Gaps = 7/67 (10%)
Query: 111 LYIDSLSRNVNEGHLRE----IFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
+YI++L+ + + L++ IFS FG+++D+ ++ R++ + RG +V FK + A A
Sbjct: 7 IYINNLNEKIKKDELKKSLHAIFSRFGQILDI--LVSRSLKM-RGQAFVIFKEVSSATNA 63
Query: 167 QLYMDGF 173
M GF
Sbjct: 64 LRSMQGF 70
>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO3|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO4|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3IIN|A Chain A, Plasticity Of The Kink Turn Structural Motif
Length = 95
Score = 38.1 bits (87), Expect = 0.009, Method: Composition-based stats.
Identities = 21/67 (31%), Positives = 40/67 (59%), Gaps = 7/67 (10%)
Query: 111 LYIDSLSRNVNEGHLRE----IFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
+YI++L+ + + L++ IFS FG+++D+ ++ R++ + RG +V FK + A A
Sbjct: 9 IYINNLNEKIKKDELKKSLHAIFSRFGQILDI--LVSRSLKM-RGQAFVIFKEVSSATNA 65
Query: 167 QLYMDGF 173
M GF
Sbjct: 66 LRSMQGF 72
>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|B Chain B, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|C Chain C, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|D Chain D, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
Length = 94
Score = 38.1 bits (87), Expect = 0.009, Method: Composition-based stats.
Identities = 21/67 (31%), Positives = 40/67 (59%), Gaps = 7/67 (10%)
Query: 111 LYIDSLSRNVNEGHLRE----IFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
+YI++L+ + + L++ IFS FG+++D+ ++ R++ + RG +V FK + A A
Sbjct: 8 IYINNLNEKIKKDELKKSLHAIFSRFGQILDI--LVSRSLKM-RGQAFVIFKEVSSATNA 64
Query: 167 QLYMDGF 173
M GF
Sbjct: 65 LRSMQGF 71
>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|B Chain B, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|C Chain C, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1NU4|A Chain A, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|1NU4|B Chain B, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|3HHN|B Chain B, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
pdb|3HHN|D Chain D, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
Length = 97
Score = 38.1 bits (87), Expect = 0.009, Method: Composition-based stats.
Identities = 21/67 (31%), Positives = 40/67 (59%), Gaps = 7/67 (10%)
Query: 111 LYIDSLSRNVNEGHLRE----IFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
+YI++L+ + + L++ IFS FG+++D+ ++ R++ + RG +V FK + A A
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDI--LVSRSLKM-RGQAFVIFKEVSSATNA 67
Query: 167 QLYMDGF 173
M GF
Sbjct: 68 LRSMQGF 74
>pdb|1M5K|C Chain C, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5K|F Chain F, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5O|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5O|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1SJ3|P Chain P, Hepatitis Delta Virus Gemonic Ribozyme Precursor, With
Mg2+ Bound
pdb|1SJ4|P Chain P, Crystal Structure Of A C75u Mutant Hepatitis Delta Virus
Ribozyme Precursor, In Cu2+ Solution
pdb|1SJF|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Cobalt
Hexammine Solution
pdb|1VBX|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Edta Solution
pdb|1VBY|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, And Mn2+ Bound
pdb|1VBZ|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Ba2+ Solution
pdb|1VC0|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Imidazole And
Sr2+ Solution
pdb|1VC5|A Chain A, Crystal Structure Of The Wild Type Hepatitis Delta Virus
Gemonic Ribozyme Precursor, In Edta Solution
pdb|1VC6|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Product With C75u Mutaion, Cleaved In Imidazole
And Mg2+ Solutions
pdb|1VC7|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Sr2+ Solution
pdb|2OIH|A Chain A, Hepatitis Delta Virus Gemonic Ribozyme Precursor With C75u
Mutation And Bound To Monovalent Cation Tl+
pdb|2OJ3|A Chain A, Hepatitis Delta Virus Ribozyme Precursor Structure, With
C75u Mutation, Bound To Tl+ And Cobalt Hexammine
(Co(Nh3) 63+)
Length = 100
Score = 38.1 bits (87), Expect = 0.009, Method: Composition-based stats.
Identities = 21/67 (31%), Positives = 40/67 (59%), Gaps = 7/67 (10%)
Query: 111 LYIDSLSRNVNEGHLRE----IFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
+YI++L+ + + L++ IFS FG+++D+ ++ R++ + RG +V FK + A A
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDI--LVSRSLKM-RGQAFVIFKEVSSATNA 68
Query: 167 QLYMDGF 173
M GF
Sbjct: 69 LRSMQGF 75
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 38.1 bits (87), Expect = 0.009, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 30/57 (52%)
Query: 110 VLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
VLY+ L+ V++ L F FG++ D+++ +D RG +V F+ DA A
Sbjct: 7 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 63
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 37.7 bits (86), Expect = 0.010, Method: Composition-based stats.
Identities = 23/56 (41%), Positives = 31/56 (55%), Gaps = 5/56 (8%)
Query: 116 LSRNV----NEGHLREIFSNFGEVVDVELVMD-RAVNLPRGSGYVRFKTRADAEKA 166
L RN+ N+ +RE+FS FGE+ V L RG G+V F T+ DA+KA
Sbjct: 19 LVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKA 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 = 37.7 bits (86), Expect = 0.010, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 32/62 (51%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
L++ L+ NV++ LR F +F + ++ D RG G+V F ++ DA+ A M
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 171 DG 172
G
Sbjct: 64 QG 65
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 37.7 bits (86), Expect = 0.012, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 30/57 (52%)
Query: 110 VLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
VLY+ L+ V++ L F FG++ D+++ +D RG +V F+ DA A
Sbjct: 4 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 60
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 37.4 bits (85), Expect = 0.013, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 36/62 (58%), Gaps = 2/62 (3%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
LY+ +L +++ LR+ FS FG + +++M+ + +G G+V F + +A KA M
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRS--KGFGFVCFSSPEEATKAVTEM 75
Query: 171 DG 172
+G
Sbjct: 76 NG 77
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 37.0 bits (84), Expect = 0.021, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 28/55 (50%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEK 165
++I LS + LRE F FGEV + ++ D RG G+V F +A +K
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDK 57
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 36.6 bits (83), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 30/57 (52%)
Query: 110 VLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
VLY+ L+ V++ L F FG++ D+++ +D RG +V F+ DA A
Sbjct: 65 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 121
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 36.2 bits (82), Expect = 0.029, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 28/55 (50%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEK 165
++I LS + LRE F FGEV + ++ D RG G+V F +A +K
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDK 82
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 36.2 bits (82), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 34/62 (54%), Gaps = 6/62 (9%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
L++ +L ++ E + +F +GE +V +N RG G++R ++R AE A+ +
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEV------FINRDRGFGFIRLESRTLAEIAKAEL 78
Query: 171 DG 172
DG
Sbjct: 79 DG 80
Score = 28.5 bits (62), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 29/60 (48%), Gaps = 7/60 (11%)
Query: 110 VLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMD---RAVNLPRGSGYVRFKTRADAEKA 166
L + +LS V+ L + FS FG V +V+D RA G G+V F + A KA
Sbjct: 98 ALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRAT----GKGFVEFAAKPPARKA 153
>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 = 36.2 bits (82), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 26/47 (55%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRF 157
+++ + + E HLR+ F +G++ +E++ DR RG +V F
Sbjct: 100 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 146
>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 = 36.2 bits (82), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADA 163
+++ + +V E FS +G ++D +L++D+ RG G+V + + ADA
Sbjct: 90 IFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDS-ADA 141
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 35.8 bits (81), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 26/47 (55%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRF 157
+++ + + E HLR+ F +G++ +E++ DR RG +V F
Sbjct: 105 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 151
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 35.8 bits (81), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 26/47 (55%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRF 157
+++ + + E HLR+ F +G++ +E++ DR RG +V F
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 35.8 bits (81), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 26/47 (55%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRF 157
+++ + + E HLR+ F +G++ +E++ DR RG +V F
Sbjct: 108 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 154
>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 = 35.8 bits (81), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 26/47 (55%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRF 157
+++ + + E HLR+ F +G++ +E++ DR RG +V F
Sbjct: 106 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 152
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 35.8 bits (81), Expect = 0.038, Method: Composition-based stats.
Identities = 16/63 (25%), Positives = 33/63 (52%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
L ++ L +N+ + + +F + G++ +LV D+ G G+V + DA+KA +
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 171 DGF 173
+G
Sbjct: 67 NGL 69
>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 = 35.8 bits (81), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 26/47 (55%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRF 157
+++ + + E HLR+ F +G++ +E++ DR RG +V F
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 35.4 bits (80), Expect = 0.050, Method: Composition-based stats.
Identities = 16/56 (28%), Positives = 31/56 (55%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
LYI L + L ++ +G++V + ++D+ N +G G+V F + + A+KA
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA 63
>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
pdb|2RS8|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
Length = 99
Score = 35.4 bits (80), Expect = 0.056, Method: Composition-based stats.
Identities = 17/61 (27%), Positives = 36/61 (59%), Gaps = 6/61 (9%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
L++ +L ++ E +R++F +G+ +V + D+ G G++R +TR AE A++ +
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLETRTLAEIAKVEL 71
Query: 171 D 171
D
Sbjct: 72 D 72
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 34.7 bits (78), Expect = 0.082, Method: Composition-based stats.
Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 3/64 (4%)
Query: 108 SLVLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQ 167
S L++ LS + E L+E +F V +V DR +G G+V F + DA+ A+
Sbjct: 15 SKTLFVKGLSEDTTEETLKE---SFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAK 71
Query: 168 LYMD 171
M+
Sbjct: 72 EAME 75
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 34.7 bits (78), Expect = 0.092, Method: Composition-based stats.
Identities = 18/47 (38%), Positives = 25/47 (53%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRF 157
L + L E L+E FS FGEV+ V++ D +G G+VRF
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF 64
>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|6 Chain 6, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|7 Chain 7, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|8 Chain 8, Crystal Structure Of Human Spliceosomal U1 Snrnp
Length = 216
Score = 34.7 bits (78), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 14/63 (22%), Positives = 29/63 (46%)
Query: 110 VLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLY 169
L++ ++ + E LR F +G + + +V + PRG ++ ++ D A +
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 170 MDG 172
DG
Sbjct: 164 ADG 166
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 34.3 bits (77), Expect = 0.11, Method: Composition-based stats.
Identities = 18/68 (26%), Positives = 33/68 (48%), Gaps = 1/68 (1%)
Query: 105 ENDSLVLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAE 164
E D LYI +L +++E L + FG+V+ ++ D + RG G+ R ++ E
Sbjct: 22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSS-GTSRGVGFARMESTEKCE 80
Query: 165 KAQLYMDG 172
+ +G
Sbjct: 81 AVIGHFNG 88
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 34.3 bits (77), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 36/62 (58%), Gaps = 6/62 (9%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
L++ +L ++ E +R++F +G+ +V + D+ G G++R +TR AE A++ +
Sbjct: 25 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLETRTLAEIAKVEL 78
Query: 171 DG 172
D
Sbjct: 79 DN 80
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 34.3 bits (77), Expect = 0.12, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 31/55 (56%), Gaps = 5/55 (9%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEK 165
L +LS N+ E L+E+F + +++ LV + +G Y+ FK+ ADAEK
Sbjct: 19 LLAKNLSFNITEDELKEVFE---DALEIRLVSQDGKS--KGIAYIEFKSEADAEK 68
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 34.3 bits (77), Expect = 0.12, Method: Composition-based stats.
Identities = 18/64 (28%), Positives = 31/64 (48%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
L+I L + + L F FG V+ ++ +D+ +L + G+V F A+ A M
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 171 DGFH 174
+GF
Sbjct: 103 NGFQ 106
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 33.9 bits (76), Expect = 0.14, Method: Composition-based stats.
Identities = 20/67 (29%), Positives = 38/67 (56%), Gaps = 7/67 (10%)
Query: 111 LYIDSLSRNVNEGHLRE----IFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
+YI++L+ + + L++ IFS FG+++D+ ++ R++ RG +V FK + A A
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDI--LVSRSLKX-RGQAFVIFKEVSSATNA 67
Query: 167 QLYMDGF 173
GF
Sbjct: 68 LRSXQGF 74
>pdb|3CUL|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUL|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3EGZ|A Chain A, Crystal Structure Of An In Vitro Evolved Tetracycline
Aptamer And Artificial Riboswitch
Length = 98
Score = 33.9 bits (76), Expect = 0.14, Method: Composition-based stats.
Identities = 20/67 (29%), Positives = 38/67 (56%), Gaps = 7/67 (10%)
Query: 111 LYIDSLSRNVNEGHLRE----IFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
+YI++L+ + + L++ IFS FG+++D+ ++ R++ RG +V FK + A A
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDI--LVSRSLKX-RGQAFVIFKEVSSATNA 68
Query: 167 QLYMDGF 173
GF
Sbjct: 69 LRSXQGF 75
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 33.9 bits (76), Expect = 0.14, Method: Composition-based stats.
Identities = 20/67 (29%), Positives = 38/67 (56%), Gaps = 7/67 (10%)
Query: 111 LYIDSLSRNVNEGHLRE----IFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
+YI++L+ + + L++ IFS FG+++D+ ++ R++ RG +V FK + A A
Sbjct: 9 IYINNLNEKIKKDELKKSLHAIFSRFGQILDI--LVSRSLKX-RGQAFVIFKEVSSATNA 65
Query: 167 QLYMDGF 173
GF
Sbjct: 66 LRSXQGF 72
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 33.9 bits (76), Expect = 0.16, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 32/62 (51%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
L++ +LS +E L ++FS +G + ++ +D P+G +V F A KA +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 171 DG 172
DG
Sbjct: 71 DG 72
>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 = 33.5 bits (75), Expect = 0.19, Method: Composition-based stats.
Identities = 14/63 (22%), Positives = 33/63 (52%)
Query: 110 VLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLY 169
+L++ + E + + F+ +GE+ ++ L +DR +G V ++T +A+ A
Sbjct: 9 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 68
Query: 170 MDG 172
++G
Sbjct: 69 LNG 71
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 33.5 bits (75), Expect = 0.21, Method: Composition-based stats.
Identities = 14/63 (22%), Positives = 33/63 (52%)
Query: 110 VLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLY 169
+L++ + E + + F+ +GE+ ++ L +DR +G V ++T +A+ A
Sbjct: 9 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 68
Query: 170 MDG 172
++G
Sbjct: 69 LNG 71
>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 90
Score = 33.5 bits (75), Expect = 0.22, Method: Composition-based stats.
Identities = 14/63 (22%), Positives = 33/63 (52%)
Query: 110 VLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLY 169
+L++ + E + + F+ +GE+ ++ L +DR +G V ++T +A+ A
Sbjct: 9 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 68
Query: 170 MDG 172
++G
Sbjct: 69 LNG 71
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 33.5 bits (75), Expect = 0.22, Method: Composition-based stats.
Identities = 14/63 (22%), Positives = 33/63 (52%)
Query: 110 VLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLY 169
+L++ + E + + F+ +GE+ ++ L +DR +G V ++T +A+ A
Sbjct: 11 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 70
Query: 170 MDG 172
++G
Sbjct: 71 LNG 73
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 33.1 bits (74), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 5/62 (8%)
Query: 105 ENDSLVLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAE 164
E D+ L +L V + L+E+F + E+ LV + +G Y+ FKT ADAE
Sbjct: 90 ERDARTLLAKNLPYKVTQDELKEVFEDAAEI---RLVSKDGKS--KGIAYIEFKTEADAE 144
Query: 165 KA 166
K
Sbjct: 145 KT 146
>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 = 33.1 bits (74), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 5/56 (8%)
Query: 110 VLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEK 165
L +LS N+ E L+E+F + +++ LV + +G Y+ FK+ ADAEK
Sbjct: 101 TLLAKNLSFNITEDELKEVFED---ALEIRLVSQDGKS--KGIAYIEFKSEADAEK 151
>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 = 33.1 bits (74), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 14/63 (22%), Positives = 29/63 (46%)
Query: 110 VLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLY 169
L++ ++ + E LR F +G + + +V + PRG ++ ++ D A +
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 170 MDG 172
DG
Sbjct: 164 ADG 166
>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 = 33.1 bits (74), Expect = 0.26, Method: Composition-based stats.
Identities = 14/67 (20%), Positives = 35/67 (52%)
Query: 108 SLVLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQ 167
S V+Y+ S+ + E + ++ SN G V++++++ D +G ++ F+ + A
Sbjct: 4 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 63
Query: 168 LYMDGFH 174
++G+
Sbjct: 64 RNLNGYQ 70
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 33.1 bits (74), Expect = 0.26, Method: Composition-based stats.
Identities = 14/67 (20%), Positives = 35/67 (52%)
Query: 108 SLVLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQ 167
S V+Y+ S+ + E + ++ SN G V++++++ D +G ++ F+ + A
Sbjct: 3 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 62
Query: 168 LYMDGFH 174
++G+
Sbjct: 63 RNLNGYQ 69
>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 = 33.1 bits (74), Expect = 0.26, Method: Composition-based stats.
Identities = 14/63 (22%), Positives = 33/63 (52%)
Query: 110 VLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLY 169
+L++ + E + + F+ +GE+ ++ L +DR +G V ++T +A+ A
Sbjct: 24 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 83
Query: 170 MDG 172
++G
Sbjct: 84 LNG 86
>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX
pdb|1P27|D Chain D, Crystal Structure Of The Human Y14MAGOH COMPLEX
Length = 106
Score = 33.1 bits (74), Expect = 0.27, Method: Composition-based stats.
Identities = 14/63 (22%), Positives = 33/63 (52%)
Query: 110 VLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLY 169
+L++ + E + + F+ +GE+ ++ L +DR +G V ++T +A+ A
Sbjct: 25 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 84
Query: 170 MDG 172
++G
Sbjct: 85 LNG 87
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 33.1 bits (74), Expect = 0.29, Method: Composition-based stats.
Identities = 14/67 (20%), Positives = 35/67 (52%)
Query: 108 SLVLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQ 167
S V+Y+ S+ + E + ++ SN G V++++++ D +G ++ F+ + A
Sbjct: 2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61
Query: 168 LYMDGFH 174
++G+
Sbjct: 62 RNLNGYQ 68
>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 = 32.7 bits (73), Expect = 0.30, Method: Composition-based stats.
Identities = 16/41 (39%), Positives = 21/41 (51%)
Query: 132 FGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYMDG 172
FG + D +V D A +G G+V F + DAE A M G
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGG 70
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 32.7 bits (73), Expect = 0.35, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGE-VVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLY 169
L++ L ++E + F+ GE V+ V+++ +R +P G +V F A AEK
Sbjct: 12 LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71
Query: 170 MDG 172
++G
Sbjct: 72 ING 74
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 32.7 bits (73), Expect = 0.36, Method: Composition-based stats.
Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 7/67 (10%)
Query: 110 VLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLP--RGSGYVRFKTRADAEKAQ 167
+LYI +L + + +IF +G + + R N P RG+ YV ++ DA+ A
Sbjct: 10 ILYIRNLPYKITAEEMYDIFGKYGPIRQI-----RVGNTPETRGTAYVVYEDIFDAKNAV 64
Query: 168 LYMDGFH 174
++ GF+
Sbjct: 65 DHLSGFN 71
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 32.3 bits (72), Expect = 0.42, Method: Composition-based stats.
Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 7/67 (10%)
Query: 110 VLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLP--RGSGYVRFKTRADAEKAQ 167
+LYI +L + + +IF +G + + R N P RG+ YV ++ DA+ A
Sbjct: 20 ILYIRNLPYKITAEEMYDIFGKYGPIRQI-----RVGNTPETRGTAYVVYEDIFDAKNAC 74
Query: 168 LYMDGFH 174
++ GF+
Sbjct: 75 DHLSGFN 81
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 32.3 bits (72), Expect = 0.42, Method: Composition-based stats.
Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 7/67 (10%)
Query: 110 VLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLP--RGSGYVRFKTRADAEKAQ 167
+LYI +L + + +IF +G + + R N P RG+ YV ++ DA+ A
Sbjct: 14 ILYIRNLPYKITAEEMYDIFGKYGPIRQI-----RVGNTPETRGTAYVVYEDIFDAKNAC 68
Query: 168 LYMDGFH 174
++ GF+
Sbjct: 69 DHLSGFN 75
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 32.3 bits (72), Expect = 0.42, Method: Composition-based stats.
Identities = 14/54 (25%), Positives = 29/54 (53%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAE 164
+Y+ +L ++ L IFS +G+VV V ++ D+ +G ++ F + A+
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQ 72
>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 = 32.3 bits (72), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 12/63 (19%), Positives = 33/63 (52%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
+Y+ S+ +++++ ++ +F FG++ L D +G G++ ++ ++ A M
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 171 DGF 173
+ F
Sbjct: 188 NLF 190
Score = 29.3 bits (64), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 14/61 (22%), Positives = 31/61 (50%), Gaps = 3/61 (4%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
+Y+ S+ + E +R+ F+ FG + +++ D +G +V ++ E AQL +
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEV---PEAAQLAL 87
Query: 171 D 171
+
Sbjct: 88 E 88
>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 = 32.3 bits (72), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 12/63 (19%), Positives = 33/63 (52%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
+Y+ S+ +++++ ++ +F FG++ L D +G G++ ++ ++ A M
Sbjct: 113 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 172
Query: 171 DGF 173
+ F
Sbjct: 173 NLF 175
Score = 29.3 bits (64), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 14/61 (22%), Positives = 31/61 (50%), Gaps = 3/61 (4%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
+Y+ S+ + E +R+ F+ FG + +++ D +G +V ++ E AQL +
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEV---PEAAQLAL 72
Query: 171 D 171
+
Sbjct: 73 E 73
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 32.3 bits (72), Expect = 0.51, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 26/53 (49%)
Query: 105 ENDSLVLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRF 157
E D+ ++ L+ + L + FS G+V DV ++ DR +G YV F
Sbjct: 22 ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEF 74
>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 = 32.0 bits (71), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 14/62 (22%), Positives = 31/62 (50%), Gaps = 6/62 (9%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
+Y+ S+ +++++ ++ +F FG++ L D +G G++ + EKAQ
Sbjct: 112 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEY------EKAQSSQ 165
Query: 171 DG 172
D
Sbjct: 166 DA 167
Score = 28.5 bits (62), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 14/61 (22%), Positives = 30/61 (49%), Gaps = 3/61 (4%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
+Y+ S+ + E +R+ F+ FG + ++ D +G +V ++ E AQL +
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEV---PEAAQLAL 71
Query: 171 D 171
+
Sbjct: 72 E 72
>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 = 32.0 bits (71), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 25/47 (53%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRF 157
L+I L +N+ ++E+ ++FG + LV D A L +G + +
Sbjct: 99 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEY 145
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 32.0 bits (71), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 25/47 (53%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRF 157
L+I L +N+ ++E+ ++FG + LV D A L +G + +
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEY 143
>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 = 32.0 bits (71), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 25/47 (53%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRF 157
L+I L +N+ ++E+ ++FG + LV D A L +G + +
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEY 163
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 31.6 bits (70), Expect = 0.70, Method: Composition-based stats.
Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 8/63 (12%)
Query: 110 VLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLY 169
VL++ +L+ V E L + FS FG++ V+ + D A +V F+ R A KA
Sbjct: 17 VLFVRNLATTVTEEILEKSFSEFGKLERVKKLKDYA--------FVHFEDRGAAVKAMDE 68
Query: 170 MDG 172
M+G
Sbjct: 69 MNG 71
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 31.2 bits (69), Expect = 1.0, Method: Composition-based stats.
Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 8/63 (12%)
Query: 110 VLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLY 169
VL++ +L+ V E L + FS FG++ V+ + D A ++ F R A KA
Sbjct: 13 VLFVRNLANTVTEEILEKAFSQFGKLERVKKLKDYA--------FIHFDERDGAVKAMEE 64
Query: 170 MDG 172
M+G
Sbjct: 65 MNG 67
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 31.2 bits (69), Expect = 1.0, Method: Composition-based stats.
Identities = 13/47 (27%), Positives = 25/47 (53%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRF 157
L+I L +N+ ++E+ ++FG + LV D A L +G + +
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEY 50
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 30.8 bits (68), Expect = 1.2, Method: Composition-based stats.
Identities = 18/56 (32%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
L + +L V++ ++E+F+ FG + + DR+ G+ V F+ RADA KA
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRS-GRSLGTADVHFERRADALKA 92
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 30.8 bits (68), Expect = 1.2, Method: Composition-based stats.
Identities = 18/56 (32%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
L + +L V++ ++E+F+ FG + + DR+ G+ V F+ RADA KA
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRS-GRSLGTADVHFERRADALKA 92
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 30.4 bits (67), Expect = 1.6, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 6/56 (10%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
LY+ L + E LR F FGE+ + +V + +++F TR AE A
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQC------AFIQFATRQAAEVA 64
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 30.4 bits (67), Expect = 1.7, Method: Composition-based stats.
Identities = 14/56 (25%), Positives = 29/56 (51%), Gaps = 8/56 (14%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
L+I +L R E +R +F +G+V++ +++ + G+V + + AE A
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDA 58
>pdb|1A9N|B Chain B, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
pdb|1A9N|D Chain D, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
Length = 96
Score = 30.4 bits (67), Expect = 1.7, Method: Composition-based stats.
Identities = 19/67 (28%), Positives = 35/67 (52%), Gaps = 7/67 (10%)
Query: 111 LYIDSLSRNVNEGHLRE----IFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
+YI++++ + + L+ +FS FG VVD+ V + + + RG +V FK + A
Sbjct: 9 IYINNMNDKIKKEELKRSLYALFSQFGHVVDI--VALKTMKM-RGQAFVIFKELGSSTNA 65
Query: 167 QLYMDGF 173
+ GF
Sbjct: 66 LRQLQGF 72
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 30.4 bits (67), Expect = 1.7, Method: Composition-based stats.
Identities = 14/62 (22%), Positives = 33/62 (53%), Gaps = 6/62 (9%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
+Y ++ + + +R+ FS FG+++++ + ++ G +VRF T A A + +
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFSTHESAAHAIVSV 81
Query: 171 DG 172
+G
Sbjct: 82 NG 83
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 30.4 bits (67), Expect = 1.8, Method: Composition-based stats.
Identities = 18/49 (36%), Positives = 26/49 (53%), Gaps = 3/49 (6%)
Query: 125 LREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYMDGF 173
L IFS FG+++D+ V + + + RG +V FK A A M GF
Sbjct: 27 LYAIFSQFGQILDI--VALKTLKM-RGQAFVIFKEIGSASNALRTMQGF 72
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 30.0 bits (66), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 30/64 (46%), Gaps = 5/64 (7%)
Query: 109 LVLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQL 168
+ +Y+ +L +G L FS +G + V + + P G +V F+ DAE A
Sbjct: 1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVR 55
Query: 169 YMDG 172
+DG
Sbjct: 56 GLDG 59
>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 = 30.0 bits (66), Expect = 2.1, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
L + +L V++ ++E+F+ FG + + DR+ G+ V F+ +ADA KA
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRS-GRSLGTADVHFERKADALKAXKQY 90
Query: 171 DG 172
+G
Sbjct: 91 NG 92
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
L + +L V++ ++E+F+ FG + + DR+ G+ V F+ +ADA KA
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRS-GRSLGTADVHFERKADALKAMKQY 89
Query: 171 DG 172
+G
Sbjct: 90 NG 91
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 30.0 bits (66), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
L + +L V++ ++E+F+ FG + + DR+ G+ V F+ RADA KA
Sbjct: 91 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRS-GRSLGTADVHFERRADALKA 145
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 30.0 bits (66), Expect = 2.5, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 2/62 (3%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKAQLYM 170
LY+ +LSR+V E + ++FS G +++ + N P +V F DA A M
Sbjct: 18 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAALAAM 75
Query: 171 DG 172
+G
Sbjct: 76 NG 77
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 29.3 bits (64), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 29/57 (50%)
Query: 110 VLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEKA 166
++I +LS + E L E+ FG++ V +V+ +G + +F T+ A+K
Sbjct: 17 TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKC 73
>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
pdb|2F9J|B Chain B, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
Length = 125
Score = 29.3 bits (64), Expect = 3.8, Method: Composition-based stats.
Identities = 18/67 (26%), Positives = 33/67 (49%), Gaps = 7/67 (10%)
Query: 110 VLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLP--RGSGYVRFKTRADAEKAQ 167
+L I +L + + +IF +G + + R N P RG+ YV ++ DA+ A
Sbjct: 20 ILMIRNLPYKITAEEMYDIFGKYGPIRQI-----RVGNTPETRGTAYVVYEDIFDAKNAC 74
Query: 168 LYMDGFH 174
++ GF+
Sbjct: 75 DHLSGFN 81
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 28.1 bits (61), Expect = 8.5, Method: Composition-based stats.
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 3/65 (4%)
Query: 111 LYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDR---AVNLPRGSGYVRFKTRADAEKAQ 167
L+I +L+ + E L+ +FS G + + + V L G G+V +K A+KA
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 168 LYMDG 172
+ G
Sbjct: 68 KQLQG 72
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 28.1 bits (61), Expect = 8.8, Method: Composition-based stats.
Identities = 17/68 (25%), Positives = 34/68 (50%), Gaps = 3/68 (4%)
Query: 106 NDSLVLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAEK 165
N+ +Y+ +L ++ + ++F +G + D++L +R P +V F+ DAE
Sbjct: 20 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL-KNRRGGPP--FAFVEFEDPRDAED 76
Query: 166 AQLYMDGF 173
A DG+
Sbjct: 77 AVYGRDGY 84
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
Length = 124
Score = 28.1 bits (61), Expect = 9.3, Method: Composition-based stats.
Identities = 14/62 (22%), Positives = 27/62 (43%)
Query: 105 ENDSLVLYIDSLSRNVNEGHLREIFSNFGEVVDVELVMDRAVNLPRGSGYVRFKTRADAE 164
E D +Y+ ++ L FS+ G + + ++ D+ P+G Y+ F R +
Sbjct: 33 EIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVD 92
Query: 165 KA 166
A
Sbjct: 93 AA 94
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
0.322 0.142 0.423
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,617,084
Number of Sequences: 62578
Number of extensions: 273079
Number of successful extensions: 730
Number of sequences better than 100.0: 145
Number of HSP's better than 100.0 without gapping: 97
Number of HSP's successfully gapped in prelim test: 48
Number of HSP's that attempted gapping in prelim test: 594
Number of HSP's gapped (non-prelim): 160
length of query: 385
length of database: 14,973,337
effective HSP length: 101
effective length of query: 284
effective length of database: 8,652,959
effective search space: 2457440356
effective search space used: 2457440356
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)