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= 029152
(198 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 67.0 bits (162), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 33/90 (36%), Positives = 53/90 (58%), Gaps = 7/90 (7%)
Query: 48 SNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQF 107
S+G+ G+ D + TT++VGGL +T+ DLR F Q+GEI ++ + + C F+QF
Sbjct: 2 SSGSSGE------DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQF 55
Query: 108 ANRENAEEALHK-LNGTVIGKQSVRLSWGR 136
A R+ AE A K N ++ + + + WGR
Sbjct: 56 ATRQAAEVAAEKSFNKLIVNGRRLNVKWGR 85
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 62.0 bits (149), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 45/73 (61%)
Query: 64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGT 123
N T++ GG+ +TD+ +RQ FS +G+I +++ KG FV+F+ E+A A+ +NGT
Sbjct: 25 NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGT 84
Query: 124 VIGKQSVRLSWGR 136
I V+ WG+
Sbjct: 85 TIEGHVVKCYWGK 97
>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 = 59.7 bits (143), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 53/96 (55%), Gaps = 7/96 (7%)
Query: 50 GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCG 103
G+ G Q + S++ +FVG L P +T ED++ F+ +G I+ ++ KG G
Sbjct: 1 GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYG 60
Query: 104 FVQFANRENAEEALHKLNGTVIGKQSVRLSWG-RNP 138
FV F N+ +AE A+ ++ G +G + +R +W R P
Sbjct: 61 FVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKP 96
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 58.2 bits (139), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 53/96 (55%), Gaps = 7/96 (7%)
Query: 50 GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCG 103
G+ G Q + S++ +FVG L P +T ED++ F+ +G+I+ ++ KG G
Sbjct: 1 GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYG 60
Query: 104 FVQFANRENAEEALHKLNGTVIGKQSVRLSWG-RNP 138
FV F N+ +AE A+ + G +G + +R +W R P
Sbjct: 61 FVSFYNKLDAENAIVHMGGQWLGGRQIRTNWATRKP 96
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 53.9 bits (128), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 46/73 (63%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIG 126
+FVG L ++T+ED ++ F +YGE + V I +G GF++ +R AE A +L+GT++
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTILK 84
Query: 127 KQSVRLSWGRNPA 139
+ +R+ + + A
Sbjct: 85 SRPLRIRFATHGA 97
Score = 36.2 bits (82), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 5/63 (7%)
Query: 62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-----GKGCGFVQFANRENAEEA 116
+ + V L P V++E L Q FSQ+G + + V G GFV+FA + A +A
Sbjct: 94 THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKA 153
Query: 117 LHK 119
L +
Sbjct: 154 LER 156
>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 = 51.6 bits (122), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 30/86 (34%), Positives = 47/86 (54%), Gaps = 6/86 (6%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV----GKGCGFVQFANRENAEEALHKLNG 122
IF+ LD ++ ++ L FS +G I S K+ KG GFV F +E AE A+ K+NG
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 160
Query: 123 TVIGKQSVRLSWGRNPANKQFRADYG 148
++ + V + GR + K+ A+ G
Sbjct: 161 MLLNDRKVFV--GRFKSRKEREAELG 184
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 45/85 (52%), Gaps = 7/85 (8%)
Query: 65 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEALH 118
+++VG L P+VT+ L + FS G I S+++ G +V F +AE AL
Sbjct: 11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 70
Query: 119 KLNGTVIGKQSVRLSWG-RNPANKQ 142
+N VI + VR+ W R+P+ ++
Sbjct: 71 TMNFDVIKGKPVRIMWSQRDPSLRK 95
>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 = 51.2 bits (121), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 39/71 (54%), Gaps = 6/71 (8%)
Query: 58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANRE 111
S + ++V GL +T ++L Q FSQYG I + +I V +G GF++F R
Sbjct: 82 SSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRI 141
Query: 112 NAEEALHKLNG 122
AEEA+ LNG
Sbjct: 142 EAEEAIKGLNG 152
Score = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 29/88 (32%), Positives = 49/88 (55%), Gaps = 7/88 (7%)
Query: 63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEA 116
S T + V L N+T E+ R F GEI S K+ K G GFV + + ++AE+A
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 117 LHKLNGTVIGKQSVRLSWGRNPANKQFR 144
++ LNG + +++++S+ R P++ R
Sbjct: 61 INTLNGLRLQTKTIKVSYAR-PSSASIR 87
>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 = 51.2 bits (121), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 33/98 (33%), Positives = 51/98 (52%), Gaps = 11/98 (11%)
Query: 55 GPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV----GKGCGFVQFANR 110
GP G+ IF+ LD ++ ++ L FS +G I S K+ KG GFV F +
Sbjct: 1 GPLGSGN-----IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQ 55
Query: 111 ENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYG 148
E AE A+ K+NG ++ + V + GR + K+ A+ G
Sbjct: 56 EAAERAIEKMNGMLLNDRKVFV--GRFKSRKEREAELG 91
>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 = 51.2 bits (121), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 30/86 (34%), Positives = 47/86 (54%), Gaps = 6/86 (6%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV----GKGCGFVQFANRENAEEALHKLNG 122
IF+ LD ++ ++ L FS +G I S K+ KG GFV F +E AE A+ K+NG
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 165
Query: 123 TVIGKQSVRLSWGRNPANKQFRADYG 148
++ + V + GR + K+ A+ G
Sbjct: 166 MLLNDRKVFV--GRFKSRKEREAELG 189
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 45/85 (52%), Gaps = 7/85 (8%)
Query: 65 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEALH 118
+++VG L P+VT+ L + FS G I S+++ G +V F +AE AL
Sbjct: 16 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 75
Query: 119 KLNGTVIGKQSVRLSWG-RNPANKQ 142
+N VI + VR+ W R+P+ ++
Sbjct: 76 TMNFDVIKGKPVRIMWSQRDPSLRK 100
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 50.4 bits (119), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 46/80 (57%), Gaps = 4/80 (5%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV----GKGCGFVQFANRENAEEALHKLNG 122
++V LD + DE LR+ FS +G I S K+ + KG GFV F++ E A +A+ ++NG
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNG 77
Query: 123 TVIGKQSVRLSWGRNPANKQ 142
++ + + ++ + +Q
Sbjct: 78 RIVATKPLYVALAQRKEERQ 97
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 50.4 bits (119), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 48/82 (58%), Gaps = 7/82 (8%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKL 120
+FVGGL + ++ L Q FS+YG+I+ V + +G GFV F N ++A++A+ +
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 121 NGTVIGKQSVRLSW-GRNPANK 141
NG + + +R+ G++ N+
Sbjct: 75 NGKSVDGRQIRVDQAGKSSDNR 96
>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 = 50.1 bits (118), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 44/78 (56%), Gaps = 6/78 (7%)
Query: 65 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEALH 118
T + V L N+T ++LR FS GE+ S K+ K G GFV + ++AE A++
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 64
Query: 119 KLNGTVIGKQSVRLSWGR 136
LNG + +++++S+ R
Sbjct: 65 TLNGLRLQSKTIKVSYAR 82
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 50.1 bits (118), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 44/78 (56%), Gaps = 6/78 (7%)
Query: 65 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEALH 118
T + V L N+T ++LR FS GE+ S K+ K G GFV + ++AE A++
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 119 KLNGTVIGKQSVRLSWGR 136
LNG + +++++S+ R
Sbjct: 63 TLNGLRLQSKTIKVSYAR 80
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 35/65 (53%), Gaps = 6/65 (9%)
Query: 64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEAL 117
+ +++ GL +T +D+ FS++G I + ++ V +G F++F R AEEA+
Sbjct: 88 DANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147
Query: 118 HKLNG 122
NG
Sbjct: 148 TSFNG 152
>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 = 50.1 bits (118), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 44/78 (56%), Gaps = 6/78 (7%)
Query: 65 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEALH 118
T + V L N+T ++LR FS GE+ S K+ K G GFV + ++AE A++
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 119 KLNGTVIGKQSVRLSWGR 136
LNG + +++++S+ R
Sbjct: 63 TLNGLRLQSKTIKVSYAR 80
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 35/65 (53%), Gaps = 6/65 (9%)
Query: 64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEAL 117
+ +++ GL +T +D+ FS++G I + ++ V +G F++F R AEEA+
Sbjct: 88 DANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147
Query: 118 HKLNG 122
NG
Sbjct: 148 TSFNG 152
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 50.1 bits (118), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 47/83 (56%)
Query: 62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLN 121
+ + +FVG L P++T+E++R+ F +YG+ V I KG GF++ R AE A +L+
Sbjct: 20 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELD 79
Query: 122 GTVIGKQSVRLSWGRNPANKQFR 144
+ + +R+ + + A+ R
Sbjct: 80 NMPLRGKQLRVRFACHSASLTVR 102
>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 = 49.7 bits (117), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 43/78 (55%), Gaps = 6/78 (7%)
Query: 65 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEALH 118
T + V L N T ++LR FS GE+ S K+ K G GFV + ++AE A++
Sbjct: 20 TNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 79
Query: 119 KLNGTVIGKQSVRLSWGR 136
LNG + +++++S+ R
Sbjct: 80 TLNGLRLQSKTIKVSYAR 97
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 29/84 (34%), Positives = 46/84 (54%), Gaps = 6/84 (7%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV----GKGCGFVQFANRENAEEALHKLNG 122
IF+ LD ++ ++ L FS +G I S K+ KG GFV F +E AE A+ K+NG
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 73
Query: 123 TVIGKQSVRLSWGRNPANKQFRAD 146
++ + V + GR + K+ A+
Sbjct: 74 MLLNDRKVFV--GRFKSRKEREAE 95
>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 = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 46/79 (58%)
Query: 62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLN 121
+ + +FVG L P++T+E++R+ F +YG+ V I KG GF++ R AE A +L+
Sbjct: 13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELD 72
Query: 122 GTVIGKQSVRLSWGRNPAN 140
+ + +R+ + + A+
Sbjct: 73 NMPLRGKQLRVRFACHSAS 91
>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 = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 29/98 (29%), Positives = 50/98 (51%), Gaps = 16/98 (16%)
Query: 66 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK----GCGF--VQFANRENAEEALHK 119
T++VG L T+E + + FS+ G+I + + + K CGF V++ +R +AE A+
Sbjct: 41 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100
Query: 120 LNGTVIGKQSVRLSW----------GRNPANKQFRADY 147
+NGT + + +R W GR + Q R +Y
Sbjct: 101 INGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVRDEY 138
>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 = 2e-06, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 46/84 (54%), Gaps = 8/84 (9%)
Query: 64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANRENAEEAL 117
+ ++V GL ++ +++ Q FSQYG I + +I V +G GF++F R AEEA+
Sbjct: 90 DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 149
Query: 118 HKLNGT--VIGKQSVRLSWGRNPA 139
LNG + + + + + NP+
Sbjct: 150 KGLNGQKPLGAAEPITVKFANNPS 173
Score = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 49/88 (55%), Gaps = 7/88 (7%)
Query: 63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEA 116
S T + V L N+T ++ + F G+I S K+ K G GFV +++ +A++A
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 117 LHKLNGTVIGKQSVRLSWGRNPANKQFR 144
++ LNG + +++++S+ R P++ R
Sbjct: 63 INTLNGLKLQTKTIKVSYAR-PSSASIR 89
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 46/84 (54%), Gaps = 8/84 (9%)
Query: 64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANRENAEEAL 117
+ ++V GL ++ +++ Q FSQYG I + +I V +G GF++F R AEEA+
Sbjct: 1 DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
Query: 118 HKLNGT--VIGKQSVRLSWGRNPA 139
LNG + + + + + NP+
Sbjct: 61 KGLNGQKPLGAAEPITVKFANNPS 84
>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 = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 43/74 (58%), Gaps = 5/74 (6%)
Query: 66 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK---GCGF--VQFANRENAEEALHKL 120
T++VG L T+E + + FS+ G+I + + + K CGF V++ +R +AE A+ +
Sbjct: 20 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMRYI 79
Query: 121 NGTVIGKQSVRLSW 134
NGT + + +R W
Sbjct: 80 NGTRLDDRIIRTDW 93
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 48.1 bits (113), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 40/73 (54%), Gaps = 7/73 (9%)
Query: 65 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-------GKGCGFVQFANRENAEEAL 117
T + +G L NVT + + + FS YG+I + +PV KG +V+F N + AE+AL
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
Query: 118 HKLNGTVIGKQSV 130
++G I Q +
Sbjct: 65 KHMDGGQIDGQEI 77
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 47.8 bits (112), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 46/85 (54%), Gaps = 2/85 (2%)
Query: 57 QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEA 116
+ EG+ SNT +FV +V + +L + F +G + VKI G FV+F E+A +A
Sbjct: 24 RQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI--LNGFAFVEFEEAESAAKA 81
Query: 117 LHKLNGTVIGKQSVRLSWGRNPANK 141
+ +++G Q + + + + PA +
Sbjct: 82 IEEVHGKSFANQPLEVVYSKLPAKR 106
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 47.4 bits (111), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 40/75 (53%), Gaps = 5/75 (6%)
Query: 66 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK-----GCGFVQFANRENAEEALHKL 120
++VG LD +T++ L+Q F G IA++KI + K FV++ +A AL L
Sbjct: 2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTL 61
Query: 121 NGTVIGKQSVRLSWG 135
NG I V+++W
Sbjct: 62 NGKQIENNIVKINWA 76
Score = 47.4 bits (111), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 27/87 (31%), Positives = 47/87 (54%), Gaps = 8/87 (9%)
Query: 57 QSEGDSSNTT--IFVGGLDPNVTDEDLRQPFSQYGEIAS------VKIPVGKGCGFVQFA 108
QS+ SS+ T +FVG L+ NV DE LR F + S ++ +G GFV F
Sbjct: 78 QSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFT 137
Query: 109 NRENAEEALHKLNGTVIGKQSVRLSWG 135
++++A+ A+ + G + + +R++W
Sbjct: 138 SQDDAQNAMDSMQGQDLNGRPLRINWA 164
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 47.4 bits (111), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 28/76 (36%), Positives = 41/76 (53%), Gaps = 6/76 (7%)
Query: 64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEAL 117
N + V GL T+ DLR+ FS+YG IA V I +G FV F N ++A+EA
Sbjct: 15 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74
Query: 118 HKLNGTVIGKQSVRLS 133
+ NG + + +R+S
Sbjct: 75 ERANGMELDGRRIRVS 90
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 47.4 bits (111), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 29/85 (34%), Positives = 43/85 (50%), Gaps = 4/85 (4%)
Query: 53 GQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV----GKGCGFVQFA 108
G +E S + V + D DLRQ F Q+G+I V+I KG GFV F
Sbjct: 18 GSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFE 77
Query: 109 NRENAEEALHKLNGTVIGKQSVRLS 133
N +A+ A KL+GTV+ + + ++
Sbjct: 78 NSADADRAREKLHGTVVEGRKIEVN 102
>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 = 47.4 bits (111), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 39/69 (56%), Gaps = 10/69 (14%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEAL--- 117
+F+GGL + T +DL+ FS++GE+ + + +G GFV F E+ ++ +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 118 -HKLNGTVI 125
HKLNG VI
Sbjct: 62 EHKLNGKVI 70
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 47.0 bits (110), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 41/77 (53%), Gaps = 6/77 (7%)
Query: 64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEAL 117
N + V GL T+ DLR+ FS+YG IA V I +G FV F N ++A+EA
Sbjct: 12 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 71
Query: 118 HKLNGTVIGKQSVRLSW 134
+ NG + + +R+ +
Sbjct: 72 ERANGMELDGRRIRVDF 88
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 47.0 bits (110), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 29/91 (31%), Positives = 44/91 (48%), Gaps = 6/91 (6%)
Query: 50 GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCG 103
G+ G N + V GL T+ DLR+ FS+YG IA V I +G
Sbjct: 1 GSSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 60
Query: 104 FVQFANRENAEEALHKLNGTVIGKQSVRLSW 134
FV F N ++A+EA + NG + + +R+ +
Sbjct: 61 FVYFENVDDAKEAKERANGMELDGRRIRVDF 91
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 47.0 bits (110), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 25/60 (41%), Positives = 36/60 (60%), Gaps = 4/60 (6%)
Query: 78 DEDLRQPFSQYGEIASVKIPV----GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLS 133
D DLRQ F Q+G+I V+I KG GFV F N +A+ A KL+GTV+ + + ++
Sbjct: 29 DPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN 88
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 47.0 bits (110), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 41/77 (53%), Gaps = 6/77 (7%)
Query: 64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEAL 117
N + V GL T+ DLR+ FS+YG IA V I +G FV F N ++A+EA
Sbjct: 46 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 105
Query: 118 HKLNGTVIGKQSVRLSW 134
+ NG + + +R+ +
Sbjct: 106 ERANGMELDGRRIRVDF 122
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 5/69 (7%)
Query: 55 GPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP-----VGKGCGFVQFAN 109
GP G T+FVGG+D + + ++R F++YG + VKI V KG GFV F N
Sbjct: 1 GPLGSGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYN 60
Query: 110 RENAEEALH 118
+ ++ +
Sbjct: 61 DVDVQKIVE 69
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 46.2 bits (108), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 42/70 (60%), Gaps = 6/70 (8%)
Query: 59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANREN 112
+G + ++VG L N+T++ LR F +G I S+++ + KG GF+ F++ E
Sbjct: 21 KGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSEC 80
Query: 113 AEEALHKLNG 122
A++AL +LNG
Sbjct: 81 AKKALEQLNG 90
>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 = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 45/87 (51%), Gaps = 9/87 (10%)
Query: 56 PQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFAN 109
P EG T++ V L + + LR+ F +YG + V IP +G FV+F +
Sbjct: 42 PDVEG---MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHD 98
Query: 110 RENAEEALHKLNGTVIGKQSVRLSWGR 136
+ +AE+A+ ++G V+ + +R+ R
Sbjct: 99 KRDAEDAMDAMDGAVLDGRELRVQMAR 125
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 45/83 (54%), Gaps = 6/83 (7%)
Query: 60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENA 113
G ++ ++VGGL V D+ L F +G+I ++IP+ +G FV+F E+A
Sbjct: 1 GSTTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60
Query: 114 EEALHKLNGTVIGKQSVRLSWGR 136
A+ +N + + +++R++ +
Sbjct: 61 AAAIDNMNESELFGRTIRVNLAK 83
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 49/88 (55%), Gaps = 7/88 (7%)
Query: 63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEA 116
S T + V L N+T ++ + F G+I S K+ K G GFV +++ +A++A
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 117 LHKLNGTVIGKQSVRLSWGRNPANKQFR 144
++ LNG + +++++S+ R P++ R
Sbjct: 63 INTLNGLKLQTKTIKVSYAR-PSSASIR 89
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 31/90 (34%), Positives = 47/90 (52%), Gaps = 8/90 (8%)
Query: 61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAE 114
D++ T IFVGGL + TD LR+ F +G+I + +G GFV A+R AE
Sbjct: 14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAE 73
Query: 115 EALHKLNGTVIGKQS-VRLSW-GRNPANKQ 142
A N + G+++ V L++ G P + Q
Sbjct: 74 RACKDPNPIIDGRKANVNLAYLGAKPRSLQ 103
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 42/78 (53%), Gaps = 6/78 (7%)
Query: 65 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANRENAEEALH 118
T++ V L + + LR+ F +YG + V IP +G FV+F ++ +AE+A+
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 119 KLNGTVIGKQSVRLSWGR 136
++G V+ + +R+ R
Sbjct: 131 AMDGAVLDGRELRVQMAR 148
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 29/94 (30%), Positives = 49/94 (52%), Gaps = 13/94 (13%)
Query: 60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENA 113
G S ++ ++VG L N+T++ LR F +G+I ++ + KG GF+ F++ E A
Sbjct: 1 GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60
Query: 114 EEALHKLNG-------TVIGKQSVRLSWGRNPAN 140
AL +LNG +G + RL G P++
Sbjct: 61 RRALEQLNGFELAGRPMRVGHVTERLDGGSGPSS 94
>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 = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/95 (25%), Positives = 45/95 (47%), Gaps = 6/95 (6%)
Query: 46 YASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGF- 104
Y S G P + +FV G+ T+ED+ F++YGEI ++ + + + G+
Sbjct: 5 YDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYL 64
Query: 105 -----VQFANRENAEEALHKLNGTVIGKQSVRLSW 134
V++ + A+ A+ LNG + Q + + W
Sbjct: 65 KGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 99
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 46/85 (54%), Gaps = 2/85 (2%)
Query: 58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEAL 117
S G + +FV L VT+E L + FSQ+G++ VK K F+ F R+ A +A+
Sbjct: 5 SSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--KDYAFIHFDERDGAVKAM 62
Query: 118 HKLNGTVIGKQSVRLSWGRNPANKQ 142
++NG + +++ + + + P K+
Sbjct: 63 EEMNGKDLEGENIEIVFAKPPDQKR 87
>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 = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 44/95 (46%), Gaps = 6/95 (6%)
Query: 46 YASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------ 99
Y S G P + +FV G+ T+ED+ F++YGEI ++ + +
Sbjct: 4 YDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYL 63
Query: 100 KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW 134
KG V++ + A+ A+ LNG + Q + + W
Sbjct: 64 KGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 98
>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 = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 40/75 (53%), Gaps = 6/75 (8%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIAS------VKIPVGKGCGFVQFANRENAEEALHKL 120
+FVG L+ NV DE LR F + S ++ +G GFV F ++++A+ A+ +
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 121 NGTVIGKQSVRLSWG 135
G + + +R++W
Sbjct: 64 QGQDLNGRPLRINWA 78
>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Rna, Uuguucuu
Length = 102
Score = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 5/64 (7%)
Query: 59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP-----VGKGCGFVQFANRENA 113
EG T+FVGG+D + + ++R F++YG + VKI V KG GFV F N +
Sbjct: 4 EGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDV 63
Query: 114 EEAL 117
++ +
Sbjct: 64 QKIV 67
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 44.7 bits (104), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 5/65 (7%)
Query: 59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP-----VGKGCGFVQFANRENA 113
EG T+FVGG+D + + ++R F++YG + VKI V KG GFV F N +
Sbjct: 4 EGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDV 63
Query: 114 EEALH 118
++ +
Sbjct: 64 QKIVE 68
>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 = 44.3 bits (103), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 6/74 (8%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 120
+FV G+ T+ED+ F++YGEI ++ + + KG V++ + A+ A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 121 NGTVIGKQSVRLSW 134
NG + Q + + W
Sbjct: 70 NGQDLMGQPISVDW 83
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 44.3 bits (103), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 6/74 (8%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 120
+FV G+ T+ED+ F++YGEI ++ + + KG V++ + A+ A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 121 NGTVIGKQSVRLSW 134
NG + Q + + W
Sbjct: 70 NGQDLMGQPISVDW 83
>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 = 44.3 bits (103), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 6/74 (8%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 120
+FV G+ T+ED+ F++YGEI ++ + + KG V++ + A+ A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 121 NGTVIGKQSVRLSW 134
NG + Q + + W
Sbjct: 70 NGQDLMGQPISVDW 83
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 44.3 bits (103), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 42/78 (53%), Gaps = 3/78 (3%)
Query: 62 SSNTTIFVGGLDPN-VTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKL 120
S N+ +F+G L+ V D+ FS+YG +A V KG FVQ++N +A A+
Sbjct: 25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCS--VHKGYAFVQYSNERHARAAVLGE 82
Query: 121 NGTVIGKQSVRLSWGRNP 138
NG V+ Q++ ++ P
Sbjct: 83 NGRVLAGQTLDINMAGEP 100
>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 = 43.9 bits (102), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 6/74 (8%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 120
+FV G+ T+ED+ F++YGEI ++ + + KG V++ + A+ A+ L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 121 NGTVIGKQSVRLSW 134
NG + Q + + W
Sbjct: 72 NGQDLMGQPISVDW 85
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 43.9 bits (102), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 45/88 (51%), Gaps = 6/88 (6%)
Query: 61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAE 114
D S ++FVG + T+E L+ FS+ G + S ++ KG GF ++ ++E A
Sbjct: 5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETAL 64
Query: 115 EALHKLNGTVIGKQSVRLSWGRNPANKQ 142
A+ LNG +++R+ + NK+
Sbjct: 65 SAMRNLNGREFSGRALRVDNAASEKNKE 92
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 43.9 bits (102), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 44/81 (54%), Gaps = 6/81 (7%)
Query: 62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEE 115
++ ++VGGL V D+ L F +G+I ++IP+ +G FV+F E+A
Sbjct: 5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 64
Query: 116 ALHKLNGTVIGKQSVRLSWGR 136
A+ +N + + +++R++ +
Sbjct: 65 AIDNMNESELFGRTIRVNLAK 85
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 43.5 bits (101), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 24/62 (38%), Positives = 37/62 (59%), Gaps = 5/62 (8%)
Query: 67 IFVGGLDPNVTDED---LRQPFSQYGEIASVKIPVG--KGCGFVQFANRENAEEALHKLN 121
+FVG L+ ++ED L QPF E ++ P G KGC FV+F++ A+ A+H L+
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77
Query: 122 GT 123
G+
Sbjct: 78 GS 79
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 43.5 bits (101), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 42/79 (53%), Gaps = 6/79 (7%)
Query: 63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEA 116
S ++VGGL V D+ L F +G+I ++IP+ +G FV+F E+A A
Sbjct: 1 SKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 60
Query: 117 LHKLNGTVIGKQSVRLSWG 135
+ +N + + +++R++
Sbjct: 61 IDNMNESELFGRTIRVNLA 79
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 43.5 bits (101), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 44/81 (54%), Gaps = 6/81 (7%)
Query: 62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEE 115
++ ++VGGL V D+ L F +G+I ++IP+ +G FV+F E+A
Sbjct: 10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 69
Query: 116 ALHKLNGTVIGKQSVRLSWGR 136
A+ +N + + +++R++ +
Sbjct: 70 AIDNMNESELFGRTIRVNLAK 90
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 43.1 bits (100), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 43/80 (53%), Gaps = 6/80 (7%)
Query: 62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEE 115
++ ++VGGL V D+ L F +G+I ++IP+ +G FV+F E+A
Sbjct: 61 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 120
Query: 116 ALHKLNGTVIGKQSVRLSWG 135
A+ +N + + +++R++
Sbjct: 121 AIDNMNESELFGRTIRVNLA 140
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 30/83 (36%), Positives = 46/83 (55%), Gaps = 6/83 (7%)
Query: 66 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVI 125
T++V G D +T LR FS +G I + + + C FV + E+A++A+ +LNGT +
Sbjct: 17 TLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQV 74
Query: 126 GKQSVRLSWGRNPANKQFRADYG 148
+SV+L N A KQ D G
Sbjct: 75 --ESVQLKV--NIARKQPMLDSG 93
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 2/81 (2%)
Query: 56 PQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEE 115
P+ T++V G D +T LR FS +G I + + + C FV + E+A++
Sbjct: 31 PERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQ 88
Query: 116 ALHKLNGTVIGKQSVRLSWGR 136
A+ +LNGT + ++++ R
Sbjct: 89 AVAELNGTQVESVQLKVNIAR 109
>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 = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 10/69 (14%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEAL--- 117
+F+GGL TDE LR F Q+G + + +G GFV +A E + A+
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 118 -HKLNGTVI 125
HK++G V+
Sbjct: 76 PHKVDGRVV 84
Score = 40.0 bits (92), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 10/66 (15%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG------FVQFANRENAEEAL--- 117
IFVGG+ + + LR F QYG+I ++I +G G FV F + ++ ++ +
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 166
Query: 118 -HKLNG 122
H +NG
Sbjct: 167 YHTVNG 172
>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 = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 10/69 (14%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEAL--- 117
+F+GGL TDE LR F Q+G + + +G GFV +A E + A+
Sbjct: 15 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 74
Query: 118 -HKLNGTVI 125
HK++G V+
Sbjct: 75 PHKVDGRVV 83
Score = 40.0 bits (92), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 10/66 (15%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG------FVQFANRENAEEAL--- 117
IFVGG+ + + LR F QYG+I ++I +G G FV F + ++ ++ +
Sbjct: 106 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 165
Query: 118 -HKLNG 122
H +NG
Sbjct: 166 YHTVNG 171
>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 = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 10/69 (14%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEAL--- 117
+F+GGL TDE LR F Q+G + + +G GFV +A E + A+
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68
Query: 118 -HKLNGTVI 125
HK++G V+
Sbjct: 69 PHKVDGRVV 77
Score = 40.0 bits (92), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 10/66 (15%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG------FVQFANRENAEEAL--- 117
IFVGG+ + + LR F QYG+I ++I +G G FV F + ++ ++ +
Sbjct: 100 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 159
Query: 118 -HKLNG 122
H +NG
Sbjct: 160 YHTVNG 165
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 10/69 (14%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEAL--- 117
+F+GGL TDE LR F Q+G + + +G GFV +A E + A+
Sbjct: 17 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 76
Query: 118 -HKLNGTVI 125
HK++G V+
Sbjct: 77 PHKVDGRVV 85
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 10/66 (15%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG------FVQFANRENAEEAL--- 117
IFVGG+ + + LR F QYG+I ++I +G G FV F + ++ ++ +
Sbjct: 108 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 167
Query: 118 -HKLNG 122
H +NG
Sbjct: 168 YHTVNG 173
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 10/69 (14%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEAL--- 117
+F+GGL TDE LR F Q+G + + +G GFV +A E + A+
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 118 -HKLNGTVI 125
HK++G V+
Sbjct: 76 PHKVDGRVV 84
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 10/66 (15%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG------FVQFANRENAEEAL--- 117
IFVGG+ + + LR F QYG+I ++I +G G FV F + ++ ++ +
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 166
Query: 118 -HKLNG 122
H +NG
Sbjct: 167 YHTVNG 172
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 39/66 (59%), Gaps = 5/66 (7%)
Query: 63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEAL 117
S+ +FVG L+ +++D+R+ F +G I I G KGC FV++++ A+ A+
Sbjct: 14 SHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAI 73
Query: 118 HKLNGT 123
+ L+G+
Sbjct: 74 NALHGS 79
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 10/69 (14%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEAL--- 117
+F+GGL TDE LR F Q+G + + +G GFV +A E + A+
Sbjct: 14 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 73
Query: 118 -HKLNGTVI 125
HK++G V+
Sbjct: 74 PHKVDGRVV 82
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 10/66 (15%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG------FVQFANRENAEEAL--- 117
IFVGG+ + + LR F QYG+I ++I +G G FV F + ++ ++ +
Sbjct: 105 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 164
Query: 118 -HKLNG 122
H +NG
Sbjct: 165 YHTVNG 170
>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|C Chain C, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|B Chain B, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|D Chain D, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
Length = 88
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 8/72 (11%)
Query: 62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI--------PVGKGCGFVQFANRENA 113
S +FVG + +++DLR+ F QYG + + + P KGC FV F R+ A
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 114 EEALHKLNGTVI 125
EA + L+ +
Sbjct: 61 LEAQNALHNMKV 72
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 5/60 (8%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLN 121
+F+G + T+ D+R FS +G+I +I G +GC FV F R A+ A+ ++
Sbjct: 98 LFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 157
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 8/72 (11%)
Query: 62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI--------PVGKGCGFVQFANRENA 113
S +FVG + +++DLR+ F QYG + + + P KGC FV F R+ A
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 114 EEALHKLNGTVI 125
EA + L+ +
Sbjct: 61 LEAQNALHNMKV 72
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/103 (25%), Positives = 53/103 (51%), Gaps = 11/103 (10%)
Query: 48 SNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP-------VGK 100
S+G+ GQ P+ + + + I V + ++R+ FS +GE+ +V++P +
Sbjct: 2 SSGSSGQVPKKQ---TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHR 58
Query: 101 GCGFVQFANRENAEEALHKL-NGTVIGKQSVRLSWGRNPANKQ 142
G GFV F +++A++A + L + T + + + L W + Q
Sbjct: 59 GFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQ 101
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 5/62 (8%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLN 121
+FVG L TDED+R+ F +G I + G KGC FV+F A+ A++ L+
Sbjct: 15 LFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTLH 74
Query: 122 GT 123
+
Sbjct: 75 SS 76
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 45/78 (57%), Gaps = 8/78 (10%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 120
I+VG L + T E +++ FSQ+G++ +VK+ KG GFV+ E+ EA+ KL
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEM-QEESVSEAIAKL 62
Query: 121 NGTVIGKQSVRLSWGRNP 138
+ T +++R++ NP
Sbjct: 63 DNTDFMGRTIRVTEA-NP 79
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 31/85 (36%), Positives = 46/85 (54%), Gaps = 11/85 (12%)
Query: 60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK---------GCGFVQFANR 110
G S ++ +F+ L+ + T+E L+ FS+ G I S I K G GFV++
Sbjct: 1 GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60
Query: 111 ENAEEALHKLNG-TVIG-KQSVRLS 133
E A++AL +L G TV G K VR+S
Sbjct: 61 EQAQKALKQLQGHTVDGHKLEVRIS 85
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 5/60 (8%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLN 121
+F+G + T+ D+R FS +G+I +I G +GC FV F R A+ A+ ++
Sbjct: 110 LFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 169
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 8/73 (10%)
Query: 61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI--------PVGKGCGFVQFANREN 112
D +FVG + +++DLR+ F QYG + + + P KGC FV F R+
Sbjct: 12 DLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKA 71
Query: 113 AEEALHKLNGTVI 125
A EA + L+ +
Sbjct: 72 ALEAQNALHNMKV 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 = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 30/56 (53%), Gaps = 5/56 (8%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEAL 117
+F+G + T+ D+R FS +G+I +I G +GC FV F R A+ A+
Sbjct: 98 LFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAI 153
Score = 40.0 bits (92), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 8/62 (12%)
Query: 68 FVGGLDPNVTDEDLRQPFSQYGEIASVKI--------PVGKGCGFVQFANRENAEEALHK 119
FVG + +++DLR+ F QYG + + + P KGC FV F R+ A EA +
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 120 LN 121
L+
Sbjct: 67 LH 68
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 42/82 (51%), Gaps = 7/82 (8%)
Query: 60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-------GKGCGFVQFANREN 112
G S ++ IF+G LDP + ++ L FS +G I + KG F+ FA+ +
Sbjct: 1 GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60
Query: 113 AEEALHKLNGTVIGKQSVRLSW 134
++ A+ +NG + + + +S+
Sbjct: 61 SDAAIEAMNGQYLCNRPITVSY 82
>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 = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 34/59 (57%), Gaps = 6/59 (10%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHK 119
IFVGGL P+ +E +R+ F +GE+ S+++P+ +G F+ F E ++ + K
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 62
>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 = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 40/68 (58%), Gaps = 9/68 (13%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKI---PV---GKGCGFVQFANRENAEEAL--- 117
+F+GGL+ + T+++LR+ F +YG + +KI P +G GF+ F + +E +
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65
Query: 118 HKLNGTVI 125
H L+G VI
Sbjct: 66 HILDGKVI 73
Score = 34.7 bits (78), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 7/65 (10%)
Query: 56 PQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFAN 109
P+ E D + IFVGG+ P+V ++ + FSQ+G I ++ + K G GFV + +
Sbjct: 80 PRDEQDKTGK-IFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDS 138
Query: 110 RENAE 114
+ +
Sbjct: 139 ADAVD 143
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 29/97 (29%), Positives = 47/97 (48%), Gaps = 4/97 (4%)
Query: 50 GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG----FV 105
G+ G E D T++VG L +VT+ + Q FSQ G S K+ FV
Sbjct: 1 GSSGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFV 60
Query: 106 QFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQ 142
+F +A AL +NG I + V+++W P++++
Sbjct: 61 EFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQK 97
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 28/86 (32%), Positives = 44/86 (51%), Gaps = 4/86 (4%)
Query: 58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEI--ASVKIPVGK--GCGFVQFANRENA 113
S G S IFV L + T + L+ F++ G + A +K+ GK GCG V+F + E A
Sbjct: 2 SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVA 61
Query: 114 EEALHKLNGTVIGKQSVRLSWGRNPA 139
E A +NG + + + + RN +
Sbjct: 62 ERACRMMNGMKLSGREIDVRIDRNAS 87
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 34/59 (57%), Gaps = 6/59 (10%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHK 119
IFVGGL P+ +E +R+ F +GE+ S+++P+ +G F+ F E ++ + K
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 41/80 (51%), Gaps = 6/80 (7%)
Query: 60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENA 113
G S ++ +++ GL P TD+DL + YG+I S K + KG GFV F + A
Sbjct: 1 GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60
Query: 114 EEALHKLNGTVIGKQSVRLS 133
++A+ L + + Q + S
Sbjct: 61 QKAVTALKASGVQAQMAKQS 80
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 33/67 (49%), Gaps = 6/67 (8%)
Query: 64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEAL 117
+T ++V L +TD+ L F +YG I I K G FV++ RE A+EA+
Sbjct: 89 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 148
Query: 118 HKLNGTV 124
LN +
Sbjct: 149 SALNNVI 155
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 40/81 (49%), Gaps = 6/81 (7%)
Query: 62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANRENAEE 115
+SNT + V L ++TD +L F G I + +I G FV F + +++
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 116 ALHKLNGTVIGKQSVRLSWGR 136
A+ LNG + + +++S+ R
Sbjct: 61 AIKVLNGITVRNKRLKVSYAR 81
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 43/80 (53%), Gaps = 6/80 (7%)
Query: 64 NTTIFVGGLDPNVTDEDLRQPFSQY----GEIASVKIPVGK--GCGFVQFANRENAEEAL 117
N +++ L P VT+ DL F+++ G ++ G+ G F+ F N+E A +AL
Sbjct: 25 NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 84
Query: 118 HKLNGTVIGKQSVRLSWGRN 137
H +NG + + + + +G+N
Sbjct: 85 HLVNGYKLYGKILVIEFGKN 104
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 45/84 (53%), Gaps = 4/84 (4%)
Query: 60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEI--ASVKIPVGK--GCGFVQFANRENAEE 115
G S ++ IFV L + T + L+ F++ G + A +K+ GK GCG V+F + E AE
Sbjct: 1 GSSGSSGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAER 60
Query: 116 ALHKLNGTVIGKQSVRLSWGRNPA 139
A +NG + + + + RN +
Sbjct: 61 ACRMMNGMKLSGREIDVRIDRNAS 84
>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 = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 37/68 (54%), Gaps = 10/68 (14%)
Query: 68 FVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEAL---- 117
FVGGL + + +DL+ F+++GE+ I +G GF+ F + + E+ L
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQKE 74
Query: 118 HKLNGTVI 125
H+L+G VI
Sbjct: 75 HRLDGRVI 82
>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 = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 42/78 (53%), Gaps = 6/78 (7%)
Query: 63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEA 116
S+ +FVG L P +T + F+ +G I+ ++ KG GFV F N+ +AE A
Sbjct: 5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENA 64
Query: 117 LHKLNGTVIGKQSVRLSW 134
+ ++ G +G + +R +W
Sbjct: 65 IQQMGGQWLGGRQIRTNW 82
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 27/66 (40%), Positives = 33/66 (50%), Gaps = 10/66 (15%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEAL--- 117
+FVGGLD + T E LR FSQYGE+ I K G GFV+F + L
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASR 78
Query: 118 -HKLNG 122
H L+G
Sbjct: 79 PHTLDG 84
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 40.8 bits (94), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEAL 117
S G S +F+G L T++++R F QYG++ I K GFV ++ AE+A+
Sbjct: 2 SSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--KNYGFVHIEDKTAAEDAI 59
Query: 118 HKLN 121
L+
Sbjct: 60 RNLH 63
>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 = 40.8 bits (94), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 33/67 (49%), Gaps = 6/67 (8%)
Query: 64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEAL 117
+T ++V L +TD+ L F +YG I I K G FV++ RE A+EA+
Sbjct: 100 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 159
Query: 118 HKLNGTV 124
LN +
Sbjct: 160 SALNNVI 166
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 6/81 (7%)
Query: 62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANRENAEE 115
+SNT + V L + TD +L F G I + +I G FV F + +++
Sbjct: 12 ASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQR 71
Query: 116 ALHKLNGTVIGKQSVRLSWGR 136
A+ LNG + + +++S+ R
Sbjct: 72 AIKVLNGITVRNKRLKVSYAR 92
>pdb|3U1L|A Chain A, Structure Of The Mrna Splicing Complex Component Cwc2
pdb|3U1M|A Chain A, Structure Of The Mrna Splicing Complex Component Cwc2
Length = 240
Score = 40.8 bits (94), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 9/71 (12%)
Query: 64 NTTIFVGGLD---------PNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAE 114
N T++VGG+D P + +R FS+ G+I ++ K CGFV+F + NAE
Sbjct: 134 NKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAE 193
Query: 115 EALHKLNGTVI 125
A ++ +
Sbjct: 194 FAKEAMSNQTL 204
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 40.8 bits (94), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 10/74 (13%)
Query: 62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIAS---VKIPVGK---GCGFVQFANRENAEE 115
SS +F+GGL T E LR+ F Q+GE+ ++ P+ K G GFV F ++ ++
Sbjct: 23 SSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDK 82
Query: 116 AL----HKLNGTVI 125
L H+L+ I
Sbjct: 83 VLAQSRHELDSKTI 96
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 40.8 bits (94), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 43/76 (56%), Gaps = 6/76 (7%)
Query: 64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEAL 117
+ T++VGGLD V++ L + F Q G + + +P + G GFV+F + E+A+ A+
Sbjct: 15 DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 74
Query: 118 HKLNGTVIGKQSVRLS 133
++ + + +R++
Sbjct: 75 KIMDMIKLYGKPIRVN 90
>pdb|3TP2|A Chain A, Crystal Structure Of The Splicing Factor Cwc2 From Yeast
pdb|3TP2|B Chain B, Crystal Structure Of The Splicing Factor Cwc2 From Yeast
Length = 229
Score = 40.8 bits (94), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 9/71 (12%)
Query: 64 NTTIFVGGLD---------PNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAE 114
N T++VGG+D P + +R FS+ G+I ++ K CGFV+F + NAE
Sbjct: 136 NKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAE 195
Query: 115 EALHKLNGTVI 125
A ++ +
Sbjct: 196 FAKEAMSNQTL 206
>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 = 40.4 bits (93), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 33/67 (49%), Gaps = 6/67 (8%)
Query: 64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEAL 117
+T ++V L +TD+ L F +YG I I K G FV++ RE A+EA+
Sbjct: 13 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 72
Query: 118 HKLNGTV 124
LN +
Sbjct: 73 SALNNVI 79
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 40.4 bits (93), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 28/91 (30%), Positives = 48/91 (52%), Gaps = 16/91 (17%)
Query: 66 TIFVGGLDPNVTDEDLRQPFSQYGE-IASVKIP------VGKGCGFVQFANRENAEEALH 118
++++G L+P + + + + F+ GE + SVKI + G FV+FA+ AE+ LH
Sbjct: 11 SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70
Query: 119 KLNGTVIGKQSVRLSWGRNPANKQFRADYGN 149
K+NG + G PA K+F+ +Y
Sbjct: 71 KINGKPLP--------GATPA-KRFKLNYAT 92
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 40.4 bits (93), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 36/69 (52%)
Query: 64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGT 123
T ++VGGL PN + L + F ++G I ++ G ++Q+ + + A+ A K+ G
Sbjct: 17 TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGF 76
Query: 124 VIGKQSVRL 132
+G RL
Sbjct: 77 PLGGPDRRL 85
>pdb|2GHP|A Chain A, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|B Chain B, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|C Chain C, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|D Chain D, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|E Chain E, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|F Chain F, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|G Chain G, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|H Chain H, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
Length = 292
Score = 40.4 bits (93), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 9/77 (11%)
Query: 67 IFVGGLDPNVTDEDL-RQPFSQYGEIASVKIPVGKG-------CGFVQFANRENAEEALH 118
I + L + DE+L R+ F +G I + IP G+ C F F N+++AE AL
Sbjct: 213 IXIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFXVFENKDSAERALQ 272
Query: 119 KLNGTVIGKQSVRLSWG 135
N +++G + + +S
Sbjct: 273 X-NRSLLGNREISVSLA 288
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 40.4 bits (93), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 35/69 (50%), Gaps = 10/69 (14%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEA---- 116
IFVGGL N T ED++ F Q+G++ + K G GFV F + + E+
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 117 LHKLNGTVI 125
H++N ++
Sbjct: 62 FHEINNKMV 70
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 40.0 bits (92), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 40/76 (52%), Gaps = 4/76 (5%)
Query: 63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNG 122
++T + VG + P T+++LR F +YG + ++ + K FV E+A EA+ L+
Sbjct: 9 ASTKLHVGNISPTCTNQELRAKFEEYGPV--IECDIVKDYAFVHMERAEDAVEAIRGLDN 66
Query: 123 TVI--GKQSVRLSWGR 136
T + V+LS R
Sbjct: 67 TEFQGKRMHVQLSTSR 82
>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 = 40.0 bits (92), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 43/89 (48%), Gaps = 7/89 (7%)
Query: 55 GPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGC------GFVQFA 108
G Q EG +F+ L D+DL Q F +G + S K+ + K GFV +
Sbjct: 17 GSQKEG-PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYD 75
Query: 109 NRENAEEALHKLNGTVIGKQSVRLSWGRN 137
N +A+ A+ +NG IG + +++ R+
Sbjct: 76 NPVSAQAAIQSMNGFQIGMKRLKVQLKRS 104
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 40.0 bits (92), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 40/81 (49%), Gaps = 6/81 (7%)
Query: 62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANRENAEE 115
+SNT + V L ++TD +L F G I + +I G FV F + +++
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 116 ALHKLNGTVIGKQSVRLSWGR 136
A+ LNG + + +++S+ R
Sbjct: 61 AIKVLNGITVRNKRLKVSYAR 81
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 36/56 (64%), Gaps = 1/56 (1%)
Query: 60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-GKGCGFVQFANRENAE 114
G S ++ +FVG ++T+++LR+ FSQYG++ V IP + FV FA+ + A+
Sbjct: 1 GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQ 56
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 38/69 (55%), Gaps = 7/69 (10%)
Query: 74 PNVTDE-DLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKLNGTVIG 126
P DE LRQ F +YG I SVKI +G GFV+F + +A++A+ LNG I
Sbjct: 51 PTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNIL 110
Query: 127 KQSVRLSWG 135
+ ++++
Sbjct: 111 NKRLKVALA 119
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 36/65 (55%), Gaps = 6/65 (9%)
Query: 63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANRENAEEA 116
S +T++V L ++T+ DL + FS+YG++ V I KG F+ F ++++A+
Sbjct: 15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNC 74
Query: 117 LHKLN 121
+N
Sbjct: 75 TRAIN 79
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 42/88 (47%), Gaps = 7/88 (7%)
Query: 55 GPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGC------GFVQFA 108
G Q EG +F+ L TD DL F +G + S K+ + K GFV F
Sbjct: 32 GKQIEG-PEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFD 90
Query: 109 NRENAEEALHKLNGTVIGKQSVRLSWGR 136
N ++A+ A+ +NG +G + +++ +
Sbjct: 91 NPDSAQVAIKAMNGFQVGTKRLKVQLKK 118
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/78 (23%), Positives = 41/78 (52%), Gaps = 5/78 (6%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASV-----KIPVGKGCGFVQFANRENAEEALHKLN 121
+F+GGL+ ++ L+ F ++G I+ V + +G F+ F N +A+ A +N
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 122 GTVIGKQSVRLSWGRNPA 139
G + +++++ + P+
Sbjct: 70 GKSLHGKAIKVEQAKKPS 87
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 2/76 (2%)
Query: 61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKL 120
+ SNT +FV +V + +L + F +G + VKI G FV+F E+A +A+ ++
Sbjct: 1 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI--LNGFAFVEFEEAESAAKAIEEV 58
Query: 121 NGTVIGKQSVRLSWGR 136
+G Q + + + +
Sbjct: 59 HGKSFANQPLEVVYSK 74
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGF------VQFANRENAEEALHKL 120
+FV + ++++++ F YGEI ++ + + + GF V++ + A A L
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 121 NGTVIGKQSVRLSW 134
NG I Q++++ W
Sbjct: 89 NGAEIMGQTIQVDW 102
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/93 (25%), Positives = 46/93 (49%), Gaps = 1/93 (1%)
Query: 50 GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFAN 109
G+ G + SS ++V L + ++E + + F+ A ++ + FV F+N
Sbjct: 1 GSSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSN 60
Query: 110 RENAEEALHKLNGTVIGKQSVRLSWGRNPANKQ 142
RE+A EA+ LNG V+ + ++ + P +K
Sbjct: 61 REDAVEAMKALNGKVLDGSPIEVTLAK-PVDKD 92
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 43/79 (54%), Gaps = 3/79 (3%)
Query: 62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKG---CGFVQFANRENAEEALH 118
+++ I+VG L P++ +D+ F +YG I + + +G FV+F + +AE+A++
Sbjct: 20 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVY 79
Query: 119 KLNGTVIGKQSVRLSWGRN 137
+G +R+ + R+
Sbjct: 80 GRDGYDYDGYRLRVEFPRS 98
>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 = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGF------VQFANRENAEEALHKL 120
+FV + ++++++ F YGEI ++ + + + GF V++ + A A L
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 121 NGTVIGKQSVRLSW 134
NG I Q++++ W
Sbjct: 135 NGAEIMGQTIQVDW 148
>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
pdb|2QFJ|B Chain B, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
Length = 216
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/78 (23%), Positives = 42/78 (53%), Gaps = 6/78 (7%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 120
I+V + +++D+D++ F +G+I S + KG GF+++ +++++A+ +
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 121 NGTVIGKQSVRLSWGRNP 138
N +G Q +R+ P
Sbjct: 188 NLFDLGGQYLRVGKAVTP 205
Score = 37.0 bits (84), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 43/82 (52%), Gaps = 6/82 (7%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 120
++VG + + ++ +RQ F+ +G I S+ + KG FV++ E A+ AL ++
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 121 NGTVIGKQSVRLSWGRNPANKQ 142
N ++G +++++ N Q
Sbjct: 91 NSVMLGGRNIKVGRPSNIGQAQ 112
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 43/83 (51%), Gaps = 7/83 (8%)
Query: 66 TIFVGGLDPNVTDEDLRQPFSQY------GEIASVKIPVGKGCGFVQFANRENAEEALHK 119
++FVG L P+V D L + F + G++ + V KG GFV+F + + AL +
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE 70
Query: 120 LNGTV-IGKQSVRLSWGRNPANK 141
G V +G + VRLS A++
Sbjct: 71 CQGAVGLGSKPVRLSVAIPKASR 93
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 34/67 (50%)
Query: 58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEAL 117
S G S +++G L P VT +DLRQ F + ++ + G FV + ++ A A+
Sbjct: 2 SSGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAI 61
Query: 118 HKLNGTV 124
L+G V
Sbjct: 62 ETLSGKV 68
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 2/73 (2%)
Query: 50 GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFAN 109
G+ G E + +FV L VT+E L + FS++G++ VK K FV F +
Sbjct: 1 GSSGSSGDPEVMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVKKL--KDYAFVHFED 58
Query: 110 RENAEEALHKLNG 122
R A +A+ ++NG
Sbjct: 59 RGAAVKAMDEMNG 71
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 36/67 (53%), Gaps = 1/67 (1%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK-GCGFVQFANRENAEEALHKLNGTVI 125
++VG L +L + FS YG + +V I G FV+F + +AE+A+ L+G VI
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 62
Query: 126 GKQSVRL 132
VR+
Sbjct: 63 CGSRVRV 69
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 36/69 (52%), Gaps = 10/69 (14%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKI---PVGK---GCGFVQFANRENAEEAL--- 117
+F+GGL T E LR+ F Q+GE+ + P+ K G GFV F ++ ++ L
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62
Query: 118 -HKLNGTVI 125
H+L+ I
Sbjct: 63 RHELDSKTI 71
>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 = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/78 (23%), Positives = 42/78 (53%), Gaps = 6/78 (7%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 120
I+V + +++D+D++ F +G+I S + KG GF+++ +++++A+ +
Sbjct: 113 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 172
Query: 121 NGTVIGKQSVRLSWGRNP 138
N +G Q +R+ P
Sbjct: 173 NLFDLGGQYLRVGKAVTP 190
Score = 37.4 bits (85), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 43/82 (52%), Gaps = 6/82 (7%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 120
++VG + + ++ +RQ F+ +G I S+ + KG FV++ E A+ AL ++
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 121 NGTVIGKQSVRLSWGRNPANKQ 142
N ++G +++++ N Q
Sbjct: 76 NSVMLGGRNIKVGRPSNIGQAQ 97
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 35/74 (47%), Gaps = 3/74 (4%)
Query: 66 TIFVGGLDPNVTDEDLRQPFS---QYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNG 122
T+FV GL + T+E L++ F + + + KG GFV F + E+A+ A +
Sbjct: 17 TLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMED 76
Query: 123 TVIGKQSVRLSWGR 136
I V L W +
Sbjct: 77 GEIDGNKVTLDWAK 90
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 34/59 (57%), Gaps = 3/59 (5%)
Query: 60 GDSSNTTIFVGGLD-PNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEAL 117
G + +F+G L NV+ EDL + FS YG I ++I + GF+QF N ++ +A+
Sbjct: 18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHI--MQINIKNAFGFIQFDNPQSVRDAI 74
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 37/69 (53%), Gaps = 10/69 (14%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIAS---VKIPVGK---GCGFVQFANRENAEEAL--- 117
+F+GGL T+E LR + Q+G++ ++ P K G GFV F++ + A+
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAAR 89
Query: 118 -HKLNGTVI 125
H ++G V+
Sbjct: 90 PHSIDGRVV 98
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 33/72 (45%)
Query: 65 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTV 124
TT ++G + T+ DL F +G I K KGC F+++ E A + L
Sbjct: 28 TTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFP 87
Query: 125 IGKQSVRLSWGR 136
+++R WG+
Sbjct: 88 FQGRNLRTGWGK 99
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 34/65 (52%), Gaps = 6/65 (9%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 120
+FV L ++EDL + FS YG ++ + P+ KG FV F E+A +A ++
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 121 NGTVI 125
+G V
Sbjct: 71 DGQVF 75
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 34/59 (57%), Gaps = 3/59 (5%)
Query: 60 GDSSNTTIFVGGLD-PNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEAL 117
G + +F+G L NV+ EDL + FS YG I ++I + GF+QF N ++ +A+
Sbjct: 18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHI--MQINIKNAFGFIQFDNPQSVRDAI 74
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 31/51 (60%), Gaps = 1/51 (1%)
Query: 65 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-GKGCGFVQFANRENAE 114
+ +FVG ++T E+L+Q F QYGE+ V IP + FV FA+ + A+
Sbjct: 12 SKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQ 62
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 37/68 (54%), Gaps = 9/68 (13%)
Query: 61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANREN-- 112
D +F+G + N+ ++DL+ F ++G+I + + + KGC F+ + RE+
Sbjct: 10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESAL 69
Query: 113 -AEEALHK 119
A+ ALH+
Sbjct: 70 KAQSALHE 77
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 37.4 bits (85), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 34/66 (51%), Gaps = 3/66 (4%)
Query: 58 SEGDSSNT-TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEA 116
S G S NT IFVG + T ++LR F + G + ++ V K FV +A+ A
Sbjct: 2 SSGSSGNTWKIFVGNVSAACTSQELRSLFERRGRV--IECDVVKDYAFVHMEKEADAKAA 59
Query: 117 LHKLNG 122
+ +LNG
Sbjct: 60 IAQLNG 65
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 37.0 bits (84), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 40/86 (46%), Gaps = 1/86 (1%)
Query: 54 QGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASV-KIPVGKGCGFVQFANREN 112
+G S+ + T+ L VT ++L++ F EI V K KG +++F +
Sbjct: 83 KGKDSKKERDARTLLAKNLPYKVTQDELKEVFEDAAEIRLVSKDGKSKGIAYIEFKTEAD 142
Query: 113 AEEALHKLNGTVIGKQSVRLSWGRNP 138
AE+ + GT I +S+ L + P
Sbjct: 143 AEKTFEEKQGTEIDGRSISLYYTGEP 168
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 37.0 bits (84), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 33/55 (60%), Gaps = 3/55 (5%)
Query: 65 TTIFVGGLD-PNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALH 118
+ +F+G L NV+ EDL + FS YG I ++I + GF+QF N ++ +A+
Sbjct: 3 SRLFIGNLPLKNVSKEDLFRIFSPYGHI--MQINIKNAFGFIQFDNPQSVRDAIE 55
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 37.0 bits (84), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 33/54 (61%), Gaps = 3/54 (5%)
Query: 65 TTIFVGGLD-PNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEAL 117
+ +F+G L NV+ EDL + FS YG I ++I + GF+QF N ++ +A+
Sbjct: 11 SRLFIGNLPLKNVSKEDLFRIFSPYGHI--MQINIKNAFGFIQFDNPQSVRDAI 62
>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 = 36.6 bits (83), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 18/78 (23%), Positives = 41/78 (52%), Gaps = 6/78 (7%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 120
I+V + +++D+D++ F +G+I S + KG GF+++ +++++A+
Sbjct: 112 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSX 171
Query: 121 NGTVIGKQSVRLSWGRNP 138
N +G Q +R+ P
Sbjct: 172 NLFDLGGQYLRVGKAVTP 189
Score = 33.5 bits (75), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 40/82 (48%), Gaps = 6/82 (7%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVK------IPVGKGCGFVQFANRENAEEALHKL 120
++VG + + ++ +RQ F+ +G I S+ KG FV++ E A+ AL +
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 121 NGTVIGKQSVRLSWGRNPANKQ 142
N +G +++++ N Q
Sbjct: 75 NSVXLGGRNIKVGRPSNIGQAQ 96
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 36.6 bits (83), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 24/93 (25%), Positives = 40/93 (43%), Gaps = 7/93 (7%)
Query: 54 QGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQF 107
GP D N TI V L + + DL++ F +G I+ + + KG F+ F
Sbjct: 6 SGPNRRADD-NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISF 64
Query: 108 ANRENAEEALHKLNGTVIGKQSVRLSWGRNPAN 140
RE+A A+ ++G + + W + N
Sbjct: 65 HRREDAARAIAGVSGFGYDHLILNVEWAKPSTN 97
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 36.6 bits (83), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 8/72 (11%)
Query: 66 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP-----VGKGCGFVQFANRENAEEALHKL 120
T+ + L + T+E L++ F + +K+P KG F++FA+ E+A+EAL+
Sbjct: 17 TLVLSNLSYSATEETLQEVFEK---ATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSC 73
Query: 121 NGTVIGKQSVRL 132
N I +++RL
Sbjct: 74 NKREIEGRAIRL 85
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 36.2 bits (82), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 5/78 (6%)
Query: 61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEE 115
+ ++ T+FVG L+ V +E L + F Q G + V I K GFV F + E+
Sbjct: 13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSY 72
Query: 116 ALHKLNGTVIGKQSVRLS 133
A+ LNG + + + +S
Sbjct: 73 AIALLNGIRLYGRPINVS 90
>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 = 35.8 bits (81), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 22/91 (24%), Positives = 41/91 (45%), Gaps = 7/91 (7%)
Query: 52 PGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFV 105
P P ++GD+ T +FV ++ + T+ LR+ F YG I + + K G F+
Sbjct: 91 PHNDPNAQGDAFKT-LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFI 149
Query: 106 QFANRENAEEALHKLNGTVIGKQSVRLSWGR 136
++ + + A +G I + V + R
Sbjct: 150 EYEHERDMHSAYKHADGKKIDGRRVLVDVER 180
>pdb|1WG4|A Chain A, Solution Structure Of Rrm Domain In Protein Bab31986
Length = 98
Score = 35.8 bits (81), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNG 122
S+ + V GL P+ + +DL+ + G++ + G G V++ +E+ E AL KL+
Sbjct: 14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQ-KDGMGMVEYLRKEDMEYALRKLDD 72
Query: 123 T 123
T
Sbjct: 73 T 73
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 35.8 bits (81), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 38/82 (46%), Gaps = 9/82 (10%)
Query: 50 GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCG 103
G+ G + + V GL T++DL++ FS +GE+ V++ KG G
Sbjct: 1 GSSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFG 60
Query: 104 FVQFANRENAEEAL---HKLNG 122
FV+F E + + H ++G
Sbjct: 61 FVRFTEYETQVKVMSQRHMIDG 82
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 35.8 bits (81), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 38/68 (55%), Gaps = 6/68 (8%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 120
IFVGG+ N + +LR+ F ++G + V + +G GF+ F + ++ ++A++
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMH 72
Query: 121 NGTVIGKQ 128
++GK+
Sbjct: 73 FHDIMGKK 80
>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 = 35.4 bits (80), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 16/72 (22%), Positives = 38/72 (52%), Gaps = 5/72 (6%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLN 121
+F+ GL + T E+L + +G + +++ KG +V++ N A +A+ K++
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMD 79
Query: 122 GTVIGKQSVRLS 133
G I + ++++
Sbjct: 80 GMTIKENIIKVA 91
>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 = 35.4 bits (80), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 27/94 (28%), Positives = 48/94 (51%), Gaps = 8/94 (8%)
Query: 59 EGDSSNT--TIFVGGLDPNVTDEDLRQPFSQY---GEIASVKIPVG--KGCGFVQFANRE 111
EG S T +F+G L+PN + +L+ S+ ++A V + G + G+V F + E
Sbjct: 6 EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAE 65
Query: 112 NAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRA 145
+ E+AL L G + ++L + +K+ RA
Sbjct: 66 DLEKALE-LTGLKVFGNEIKLEKPKGRDSKKVRA 98
Score = 33.9 bits (76), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 42/82 (51%), Gaps = 1/82 (1%)
Query: 54 QGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASV-KIPVGKGCGFVQFANREN 112
+G S+ + T+ L N+T+++L++ F EI V + KG +++F + +
Sbjct: 89 KGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEAD 148
Query: 113 AEEALHKLNGTVIGKQSVRLSW 134
AE+ L + G I +SV L +
Sbjct: 149 AEKNLEEKQGAEIDGRSVSLYY 170
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 34.7 bits (78), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 66 TIFVGGLDPNVTDEDLRQPFSQYGEIASV-KIPVGKGCGFVQFANRENAEEALHKLNGTV 124
T+ L N+T+++L++ F EI V + KG +++F + +AE+ L + G
Sbjct: 18 TLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAE 77
Query: 125 IGKQSVRLSW 134
I +SV L +
Sbjct: 78 IDGRSVSLYY 87
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 34.7 bits (78), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 31/58 (53%), Gaps = 6/58 (10%)
Query: 66 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEAL 117
T+F+ L + +E L + Q+G++ V++ + KGC F QF +E A++ L
Sbjct: 17 TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCL 74
>pdb|1OWX|A Chain A, Solution Structure Of The C-Terminal Rrm Of Human La
(La225- 334)
Length = 121
Score = 34.3 bits (77), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 26/52 (50%), Gaps = 2/52 (3%)
Query: 68 FVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHK 119
F G LD EDL FS +GEI + G G + F +E A+EAL K
Sbjct: 23 FSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILF--KEKAKEALGK 72
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 33.9 bits (76), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 35/67 (52%), Gaps = 1/67 (1%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-KGCGFVQFANRENAEEALHKLNGTVI 125
++VG L N +L + F YG + SV + G FV+F + +A +A+ +L+G +
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTL 135
Query: 126 GKQSVRL 132
VR+
Sbjct: 136 CGCRVRV 142
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 33.5 bits (75), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 15/85 (17%)
Query: 44 GGYASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI------P 97
G S+G P + D +FVG + + ++DL+ F ++G I + +
Sbjct: 1 GSSGSSGVPMK------DHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTG 54
Query: 98 VGKGCGFVQFANREN---AEEALHK 119
+ KGC F+ + R++ A+ ALH+
Sbjct: 55 LHKGCAFLTYCARDSALKAQSALHE 79
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 33.5 bits (75), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 1/67 (1%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-KGCGFVQFANRENAEEALHKLNGTVI 125
++VG L N +L + F YG + SV + G FV+F + +A +A+ L+G +
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRDLDGRTL 135
Query: 126 GKQSVRL 132
VR+
Sbjct: 136 CGCRVRV 142
>pdb|2O3D|A Chain A, Structure Of Human Sf2ASF RNA RECOGNITION MOTIF 2 (RRM2)
Length = 113
Score = 33.1 bits (74), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 3/69 (4%)
Query: 55 GPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAE 114
GP S S + V GL P+ + +DL+ + G++ + G G V+F +E+
Sbjct: 8 GPPSR--RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADV-YRDGTGVVEFVRKEDMT 64
Query: 115 EALHKLNGT 123
A+ KL+ T
Sbjct: 65 YAVRKLDNT 73
>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 = 0.11, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 5/70 (7%)
Query: 59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK-----GCGFVQFANRENA 113
EG + + V LD V+D D+++ F+++G + + + G V F R +A
Sbjct: 83 EGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADA 142
Query: 114 EEALHKLNGT 123
+A+ + G
Sbjct: 143 LKAMKQYKGV 152
>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 = 0.11, Method: Compositional matrix adjust.
Identities = 17/78 (21%), Positives = 39/78 (50%), Gaps = 6/78 (7%)
Query: 66 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHK 119
+++G + + T+E + S G + ++K+ KG F++F + E++ A+
Sbjct: 6 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 65
Query: 120 LNGTVIGKQSVRLSWGRN 137
LNG +G + ++ + N
Sbjct: 66 LNGYQLGSRFLKCGYSSN 83
>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 = 33.1 bits (74), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 38/73 (52%), Gaps = 7/73 (9%)
Query: 66 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHK 119
+++VG +D T +DL FS G I + I KG +++FA R + + A+
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-A 96
Query: 120 LNGTVIGKQSVRL 132
++ TV +++++
Sbjct: 97 MDETVFRGRTIKV 109
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 32.7 bits (73), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 5/70 (7%)
Query: 59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK-----GCGFVQFANRENA 113
EG + + V LD V+D D+++ F+++G + + + G V F R +A
Sbjct: 30 EGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADA 89
Query: 114 EEALHKLNGT 123
+A+ + G
Sbjct: 90 LKAMKQYKGV 99
>pdb|3BEG|B Chain B, Crystal Structure Of Sr Protein Kinase 1 Complexed To Its
Substrate AsfSF2
Length = 115
Score = 32.7 bits (73), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 3/69 (4%)
Query: 55 GPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAE 114
GP S S + V GL P+ + +DL+ + G++ + G G V+F +E+
Sbjct: 9 GPPSR--RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADV-YRDGTGVVEFVRKEDMT 65
Query: 115 EALHKLNGT 123
A+ KL+ T
Sbjct: 66 YAVRKLDNT 74
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 32.7 bits (73), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 5/70 (7%)
Query: 59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK-----GCGFVQFANRENA 113
EG + + V LD V+D D+++ F+++G + + + G V F R +A
Sbjct: 30 EGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADA 89
Query: 114 EEALHKLNGT 123
+A+ + G
Sbjct: 90 LKAMKQYKGV 99
>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 = 32.3 bits (72), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 17/78 (21%), Positives = 39/78 (50%), Gaps = 6/78 (7%)
Query: 66 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHK 119
+++G + + T+E + S G + ++K+ KG F++F + E++ A+
Sbjct: 5 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 64
Query: 120 LNGTVIGKQSVRLSWGRN 137
LNG +G + ++ + N
Sbjct: 65 LNGYQLGSRFLKCGYSSN 82
>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 = 32.3 bits (72), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 21/85 (24%), Positives = 39/85 (45%), Gaps = 7/85 (8%)
Query: 52 PGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFV 105
P P ++GD+ T +FV ++ + T+ LR+ F YG I + + K G F+
Sbjct: 91 PHNDPNAQGDAFKT-LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFI 149
Query: 106 QFANRENAEEALHKLNGTVIGKQSV 130
++ + + A +G I + V
Sbjct: 150 EYEHERDMHSAYKHADGKKIDGRRV 174
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 32.3 bits (72), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 17/78 (21%), Positives = 39/78 (50%), Gaps = 6/78 (7%)
Query: 66 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHK 119
+++G + + T+E + S G + ++K+ KG F++F + E++ A+
Sbjct: 4 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63
Query: 120 LNGTVIGKQSVRLSWGRN 137
LNG +G + ++ + N
Sbjct: 64 LNGYQLGSRFLKCGYSSN 81
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 32.0 bits (71), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 7/77 (9%)
Query: 59 EGDSSNT--TIFVGGLDPNVTDEDLRQPFSQY---GEIASVKIPVG--KGCGFVQFANRE 111
EG S T +F+G L+PN + +L+ S+ ++A V + G + G+V F + E
Sbjct: 10 EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAE 69
Query: 112 NAEEALHKLNGTVIGKQ 128
+ E+AL V G +
Sbjct: 70 DLEKALELTGLKVFGNE 86
>pdb|1X4C|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 2
Length = 108
Score = 32.0 bits (71), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGT 123
+ V GL P+ + +DL+ + G++ + G G V+F +E+ A+ KL+ T
Sbjct: 18 VVVSGLPPSGSWQDLKDHMREAGDVCYADV-YRDGTGVVEFVRKEDMTYAVRKLDNT 73
>pdb|2M2B|A Chain A, Nmr Structure Of The Rrm2 Domain Of The Protein Rbm10 From
Homo Sapiens
Length = 131
Score = 31.6 bits (70), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 41/87 (47%), Gaps = 13/87 (14%)
Query: 45 GYASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK---- 100
G ++ A QG + +++N TI + L+P+ T + + + Y ++S + V K
Sbjct: 4 GVLASQALSQGSEPSSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQT 63
Query: 101 ----GCGFVQFANRENAE-----EALH 118
G F+Q + E A+ +ALH
Sbjct: 64 QLNRGFAFIQLSTIEAAQLLQILQALH 90
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 31.6 bits (70), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 15/62 (24%), Positives = 31/62 (50%), Gaps = 5/62 (8%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK-----GCGFVQFANRENAEEALHKLN 121
+ V LD V+D D+++ F+++G + + + G V F + +A +A+ + N
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 90
Query: 122 GT 123
G
Sbjct: 91 GV 92
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 31.2 bits (69), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 38/78 (48%), Gaps = 6/78 (7%)
Query: 63 SNTTIFVGGLDPNVTD---EDLRQPFSQYGE---IASVKIPVGKGCGFVQFANRENAEEA 116
++ + V L P++T E+L +PF + S + KG GF ++ +++A A
Sbjct: 94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA 153
Query: 117 LHKLNGTVIGKQSVRLSW 134
L G +G +++ + W
Sbjct: 154 KSDLLGKPLGPRTLYVHW 171
>pdb|1O0P|A Chain A, Solution Structure Of The Third Rna Recognition Motif
(Rrm) Of U2af65 In Complex With An N-Terminal Sf1
Peptide
Length = 104
Score = 31.2 bits (69), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 29/52 (55%), Gaps = 8/52 (15%)
Query: 79 EDLRQPFSQYGEIASVKIP------VGKGCG--FVQFANRENAEEALHKLNG 122
ED+R S+YG + S++IP GCG FV+F + + ++A+ L G
Sbjct: 29 EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG 80
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 31.2 bits (69), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 38/78 (48%), Gaps = 6/78 (7%)
Query: 63 SNTTIFVGGLDPNVTD---EDLRQPFSQYGE---IASVKIPVGKGCGFVQFANRENAEEA 116
++ + V L P++T E+L +PF + S + KG GF ++ +++A A
Sbjct: 94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA 153
Query: 117 LHKLNGTVIGKQSVRLSW 134
L G +G +++ + W
Sbjct: 154 KSDLLGKPLGPRTLYVHW 171
>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
pdb|3H2U|D Chain D, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
Length = 283
Score = 31.2 bits (69), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 38/78 (48%), Gaps = 6/78 (7%)
Query: 63 SNTTIFVGGLDPNVTD---EDLRQPFSQYGE---IASVKIPVGKGCGFVQFANRENAEEA 116
++ + V L P++T E+L +PF + S + KG GF ++ +++A A
Sbjct: 92 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA 151
Query: 117 LHKLNGTVIGKQSVRLSW 134
L G +G +++ + W
Sbjct: 152 KSDLLGKPLGPRTLYVHW 169
>pdb|1OPI|A Chain A, Solution Structure Of The Third Rna Recognition Motif
(Rrm) Of U2af65 In Complex With An N-Terminal Sf1
Peptide
pdb|2M0G|B Chain B, Structure, Phosphorylation And U2af65 Binding Of The
Nterminal Domain Of Splicing Factor 1 During 3 Splice
Site Recognition
Length = 104
Score = 31.2 bits (69), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 29/52 (55%), Gaps = 8/52 (15%)
Query: 79 EDLRQPFSQYGEIASVKIP------VGKGCG--FVQFANRENAEEALHKLNG 122
ED+R S+YG + S++IP GCG FV+F + + ++A+ L G
Sbjct: 29 EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG 80
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 30.8 bits (68), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 14/70 (20%), Positives = 36/70 (51%), Gaps = 6/70 (8%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANRENAEEALHKL 120
+F+GGL + D+ +++ + +G + + + + KG F ++ + ++A+ L
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 121 NGTVIGKQSV 130
NG +G + +
Sbjct: 157 NGMQLGDKKL 166
>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 = 30.8 bits (68), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 14/70 (20%), Positives = 36/70 (51%), Gaps = 6/70 (8%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANRENAEEALHKL 120
+F+GGL + D+ +++ + +G + + + + KG F ++ + ++A+ L
Sbjct: 99 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 158
Query: 121 NGTVIGKQSV 130
NG +G + +
Sbjct: 159 NGMQLGDKKL 168
>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 = 30.4 bits (67), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 14/70 (20%), Positives = 36/70 (51%), Gaps = 6/70 (8%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANRENAEEALHKL 120
+F+GGL + D+ +++ + +G + + + + KG F ++ + ++A+ L
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176
Query: 121 NGTVIGKQSV 130
NG +G + +
Sbjct: 177 NGMQLGDKKL 186
>pdb|2HGM|A Chain A, Nmr Structure Of The Second Qrrm Domain Of Human Hnrnp F
pdb|2KG0|A Chain A, Structure Of The Second Qrrm Domain Of Hnrnp F In Complex
With A Agggau G-Tract Rna
Length = 126
Score = 30.4 bits (67), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 28/74 (37%), Positives = 41/74 (55%), Gaps = 8/74 (10%)
Query: 53 GQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIA--SVKIPV---GK--GCGFV 105
G+G S +++ + + GL T E++ Q FS EI + +PV GK G FV
Sbjct: 31 GRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFV 89
Query: 106 QFANRENAEEALHK 119
QFA++E AE+AL K
Sbjct: 90 QFASQELAEKALGK 103
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 30.4 bits (67), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 14/70 (20%), Positives = 36/70 (51%), Gaps = 6/70 (8%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANRENAEEALHKL 120
+F+GGL + D+ +++ + +G + + + + KG F ++ + ++A+ L
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 121 NGTVIGKQSV 130
NG +G + +
Sbjct: 64 NGMQLGDKKL 73
>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 = 0.97, Method: Compositional matrix adjust.
Identities = 15/62 (24%), Positives = 30/62 (48%), Gaps = 5/62 (8%)
Query: 67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK-----GCGFVQFANRENAEEALHKLN 121
+ V LD V+D D+++ F+++G + + + G V F + +A +A + N
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYN 91
Query: 122 GT 123
G
Sbjct: 92 GV 93
>pdb|1WHX|A Chain A, Solution Structure Of The Second Rna Binding Domain From
Hypothetical Protein Bab23448
Length = 111
Score = 29.6 bits (65), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 16/72 (22%), Positives = 28/72 (38%)
Query: 64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGT 123
T I L ++++ FS++G + V +P G V+F A +A L +
Sbjct: 10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYS 69
Query: 124 VIGKQSVRLSWG 135
+ L W
Sbjct: 70 KFHHVPLYLEWA 81
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 29.6 bits (65), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 17/37 (45%), Positives = 21/37 (56%)
Query: 59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVK 95
+ +S N TIFV GL NVT E + F Q G I + K
Sbjct: 2 QDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNK 38
>pdb|2E5J|A Chain A, Solution Structure Of Rna Binding Domain In
Methenyltetrahydrofolate Synthetase Domain Containing
Length = 97
Score = 29.6 bits (65), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/84 (21%), Positives = 38/84 (45%), Gaps = 1/84 (1%)
Query: 59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-KGCGFVQFANRENAEEAL 117
EG ++VG L + DL++ + G + G + F+ + + A++A+
Sbjct: 14 EGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAV 73
Query: 118 HKLNGTVIGKQSVRLSWGRNPANK 141
L G +G ++R++ R +K
Sbjct: 74 SCLQGLRLGTDTLRVALARQQRDK 97
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 24/42 (57%)
Query: 50 GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEI 91
G+ G + DS N+ I+V GL+ +VT +DL F Q G +
Sbjct: 1 GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVV 42
>pdb|4FXW|A Chain A, Structure Of Phosphorylated Sf1 Complex With U2af65-uhm
Domain
pdb|4FXW|C Chain C, Structure Of Phosphorylated Sf1 Complex With U2af65-uhm
Domain
Length = 106
Score = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 28/52 (53%), Gaps = 8/52 (15%)
Query: 79 EDLRQPFSQYGEIASVKIP------VGKGCG--FVQFANRENAEEALHKLNG 122
ED+R S+YG + S++IP GCG FV+F + + ++A L G
Sbjct: 31 EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAXQGLTG 82
>pdb|3V4M|A Chain A, Crystal Structure Of A Rna Binding Domain Of A U2 Small
Nuclear Ribonucleoprotein Auxiliary Factor 2 (U2af) From
Mus Musculus At 1.80 A Resolution
pdb|3V4M|B Chain B, Crystal Structure Of A Rna Binding Domain Of A U2 Small
Nuclear Ribonucleoprotein Auxiliary Factor 2 (U2af) From
Mus Musculus At 1.80 A Resolution
Length = 105
Score = 29.3 bits (64), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 28/52 (53%), Gaps = 8/52 (15%)
Query: 79 EDLRQPFSQYGEIASVKIP------VGKGCG--FVQFANRENAEEALHKLNG 122
ED+R S+YG + S++IP GCG FV+F + + ++A L G
Sbjct: 30 EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAXQGLTG 81
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of Hypothetical
Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens
At 1.95 A Resolution
Length = 89
Score = 29.3 bits (64), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 29/58 (50%), Gaps = 6/58 (10%)
Query: 66 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEAL 117
+I+VG +D T E+L F G + V I KG +++F+++E+ +L
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 65
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 29.3 bits (64), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 29/58 (50%), Gaps = 6/58 (10%)
Query: 66 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEAL 117
+I+VG +D T E+L F G + V I KG +++F+++E+ +L
Sbjct: 7 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 64
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 28.9 bits (63), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 34/74 (45%), Gaps = 7/74 (9%)
Query: 57 QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI-----PVGKGCGFVQFANRE 111
Q E D +N +++ L ++ +++L +G++ S +I +G GF + + E
Sbjct: 20 QQEQDPTN--LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTE 77
Query: 112 NAEEALHKLNGTVI 125
E + NG I
Sbjct: 78 KCEAVIGHFNGKFI 91
>pdb|1VHM|A Chain A, Crystal Structure Of An Hypothetical Protein
pdb|1VHM|B Chain B, Crystal Structure Of An Hypothetical Protein
Length = 195
Score = 28.5 bits (62), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 24/42 (57%), Gaps = 3/42 (7%)
Query: 84 PFSQYGEIASVKIPVGKG-CGFVQFANRENAEEALHKLNGTV 124
PF G+IA V+IPVG+G CG N+ E +H +G +
Sbjct: 79 PFQ--GKIACVRIPVGRGVCGTAVARNQVQRIEDVHVFDGHI 118
>pdb|3F7M|A Chain A, Crystal Structure Of Apo Cuticle-Degrading Protease
(Ver112) From Verticillium Psalliotae
Length = 279
Score = 28.1 bits (61), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 25/99 (25%), Positives = 38/99 (38%), Gaps = 15/99 (15%)
Query: 2 EKRRHCCERKGEREERTLLYKLCFHRNSSYCQFNIVFLLVLIGGY---ASNGAPGQGPQS 58
+ R+C R Y ++ ++ Q + VF+ V G A+N +P P
Sbjct: 119 RQSRNCPRRTVASMSLGGGYSAALNQAAARLQSSGVFVAVAAGNDNRDAANTSPASEP-- 176
Query: 59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP 97
T VG D N D+R FS YG + + P
Sbjct: 177 ------TVCTVGATDSN----DVRSTFSNYGRVVDIFAP 205
>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 = 28.1 bits (61), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 16/32 (50%), Positives = 18/32 (56%)
Query: 64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVK 95
N TIFV GL NVT E + F Q G I + K
Sbjct: 13 NNTIFVQGLGENVTIESVADYFKQIGIIKTNK 44
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 26.9 bits (58), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 18/75 (24%), Positives = 37/75 (49%), Gaps = 3/75 (4%)
Query: 65 TTIFVGGLDPNVTDEDLRQPFSQYGEIAS--VKIPVGKGCGFVQFANRENAEEALHKLNG 122
T+ + + P+V++EDL+ FS G + + +Q + E A +AL L+
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHN 180
Query: 123 TVIGK-QSVRLSWGR 136
+G+ +R+S+ +
Sbjct: 181 HDLGENHHLRVSFSK 195
>pdb|2ADC|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd34 Complexed With Cucucu Rna
pdb|2EVZ|A Chain A, Structure Of Rna Binding Domains 3 And 4 Of Polypyrimidine
Tract Binding Protein
Length = 229
Score = 26.9 bits (58), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 18/77 (23%), Positives = 39/77 (50%), Gaps = 3/77 (3%)
Query: 64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIAS--VKIPVGKGCGFVQFANRENAEEALHKLN 121
+ T+ + + P+V++EDL+ FS G + + +Q + E A +AL L+
Sbjct: 151 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLH 210
Query: 122 GTVIGK-QSVRLSWGRN 137
+G+ +R+S+ ++
Sbjct: 211 NHDLGENHHLRVSFSKS 227
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.317 0.135 0.419
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,646,551
Number of Sequences: 62578
Number of extensions: 211187
Number of successful extensions: 547
Number of sequences better than 100.0: 193
Number of HSP's better than 100.0 without gapping: 134
Number of HSP's successfully gapped in prelim test: 59
Number of HSP's that attempted gapping in prelim test: 314
Number of HSP's gapped (non-prelim): 220
length of query: 198
length of database: 14,973,337
effective HSP length: 94
effective length of query: 104
effective length of database: 9,091,005
effective search space: 945464520
effective search space used: 945464520
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)