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= 030481
(176 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 = 62.0 bits (149), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 31/89 (34%), Positives = 50/89 (56%), Gaps = 7/89 (7%)
Query: 39 SNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQF 98
S+G+ G+ D + TT++VGGL +T+ DLR F Q+GEI ++ + + C F+QF
Sbjct: 2 SSGSSGE------DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQF 55
Query: 99 ANRENAEEALHK-LNGTVIGKQSFRADYG 126
A R+ AE A K N ++ + +G
Sbjct: 56 ATRQAAEVAAEKSFNKLIVNGRRLNVKWG 84
>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 = 57.8 bits (138), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 51/94 (54%), Gaps = 6/94 (6%)
Query: 41 GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCG 94
G+ G Q + S++ +FVG L P +T ED++ F+ +G I+ ++ KG G
Sbjct: 1 GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYG 60
Query: 95 FVQFANRENAEEALHKLNGTVIGKQSFRADYGNQ 128
FV F N+ +AE A+ ++ G +G + R ++ +
Sbjct: 61 FVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATR 94
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 57.8 bits (138), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 44/74 (59%)
Query: 55 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGT 114
N T++ GG+ +TD+ +RQ FS +G+I +++ KG FV+F+ E+A A+ +NGT
Sbjct: 25 NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGT 84
Query: 115 VIGKQSFRADYGNQ 128
I + +G +
Sbjct: 85 TIEGHVVKCYWGKE 98
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 56.6 bits (135), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 51/94 (54%), Gaps = 6/94 (6%)
Query: 41 GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCG 94
G+ G Q + S++ +FVG L P +T ED++ F+ +G+I+ ++ KG G
Sbjct: 1 GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYG 60
Query: 95 FVQFANRENAEEALHKLNGTVIGKQSFRADYGNQ 128
FV F N+ +AE A+ + G +G + R ++ +
Sbjct: 61 FVSFYNKLDAENAIVHMGGQWLGGRQIRTNWATR 94
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 53.5 bits (127), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 43/76 (56%)
Query: 53 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLN 112
+ +FVG L ++T+ED ++ F +YGE + V I +G GF++ +R AE A +L+
Sbjct: 20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELD 79
Query: 113 GTVIGKQSFRADYGNQ 128
GT++ + R +
Sbjct: 80 GTILKSRPLRIRFATH 95
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 32/113 (28%), Positives = 46/113 (40%), Gaps = 38/113 (33%)
Query: 3 EMNGVYCSSRPMRIGAATPRKXXXXXXXXXXXXXXASNGAPGQGPQSEGDSSNTTIFVGG 62
E++G SRP+RI AT +GA + V
Sbjct: 77 ELDGTILKSRPLRIRFAT-------------------HGA--------------ALTVKN 103
Query: 63 LDPNVTDEDLRQPFSQYGEIASVKIPV-----GKGCGFVQFANRENAEEALHK 110
L P V++E L Q FSQ+G + + V G GFV+FA + A +AL +
Sbjct: 104 LSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALER 156
>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 = 52.0 bits (123), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/62 (41%), Positives = 37/62 (59%), Gaps = 6/62 (9%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANRENAEEALHKL 111
++V GL +T ++L Q FSQYG I + +I V +G GF++F R AEEA+ L
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 112 NG 113
NG
Sbjct: 151 NG 152
Score = 45.4 bits (106), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 41/79 (51%), Gaps = 6/79 (7%)
Query: 54 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEA 107
S T + V L N+T E+ R F GEI S K+ K G GFV + + ++AE+A
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 108 LHKLNGTVIGKQSFRADYG 126
++ LNG + ++ + Y
Sbjct: 61 INTLNGLRLQTKTIKVSYA 79
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 51.2 bits (121), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 42/73 (57%), Gaps = 6/73 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEALHKL 111
+FVGGL + ++ L Q FS+YG+I+ V + +G GFV F N ++A++A+ +
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 112 NGTVIGKQSFRAD 124
NG + + R D
Sbjct: 75 NGKSVDGRQIRVD 87
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 49.7 bits (117), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 41/74 (55%)
Query: 53 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLN 112
+ + +FVG L P++T+E++R+ F +YG+ V I KG GF++ R AE A +L+
Sbjct: 20 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELD 79
Query: 113 GTVIGKQSFRADYG 126
+ + R +
Sbjct: 80 NMPLRGKQLRVRFA 93
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 49.7 bits (117), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 31/92 (33%), Positives = 47/92 (51%), Gaps = 10/92 (10%)
Query: 44 GQGPQSEGDSSN----TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGC 93
G+G + G+ +N + V GL T+ DLR+ FS+YG IA V I +G
Sbjct: 31 GRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGF 90
Query: 94 GFVQFANRENAEEALHKLNGTVIGKQSFRADY 125
FV F N ++A+EA + NG + + R D+
Sbjct: 91 AFVYFENVDDAKEAKERANGMELDGRRIRVDF 122
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 38/65 (58%), Gaps = 6/65 (9%)
Query: 55 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANRENAEEAL 108
+ ++V GL ++ +++ Q FSQYG I + +I V +G GF++F R AEEA+
Sbjct: 1 DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
Query: 109 HKLNG 113
LNG
Sbjct: 61 KGLNG 65
>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 = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 36/63 (57%), Gaps = 4/63 (6%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV----GKGCGFVQFANRENAEEALHKLNG 113
IF+ LD ++ ++ L FS +G I S K+ KG GFV F +E AE A+ K+NG
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 160
Query: 114 TVI 116
++
Sbjct: 161 MLL 163
Score = 36.6 bits (83), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 38/80 (47%), Gaps = 10/80 (12%)
Query: 57 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEALHK 110
+++VG L P+VT+ L + FS G I S+++ G +V F +AE AL
Sbjct: 12 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 71
Query: 111 LNGTVIGKQSFRADYGNQWS 130
+N VI + R WS
Sbjct: 72 MNFDVIKGKPVRI----MWS 87
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 38/65 (58%), Gaps = 6/65 (9%)
Query: 55 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANRENAEEAL 108
+ ++V GL ++ +++ Q FSQYG I + +I V +G GF++F R AEEA+
Sbjct: 90 DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 149
Query: 109 HKLNG 113
LNG
Sbjct: 150 KGLNG 154
Score = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 41/79 (51%), Gaps = 6/79 (7%)
Query: 54 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEA 107
S T + V L N+T ++ + F G+I S K+ K G GFV +++ +A++A
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 108 LHKLNGTVIGKQSFRADYG 126
++ LNG + ++ + Y
Sbjct: 63 INTLNGLKLQTKTIKVSYA 81
>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 = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 36/63 (57%), Gaps = 4/63 (6%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV----GKGCGFVQFANRENAEEALHKLNG 113
IF+ LD ++ ++ L FS +G I S K+ KG GFV F +E AE A+ K+NG
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 165
Query: 114 TVI 116
++
Sbjct: 166 MLL 168
Score = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 38/81 (46%), Gaps = 10/81 (12%)
Query: 56 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEALH 109
+++VG L P+VT+ L + FS G I S+++ G +V F +AE AL
Sbjct: 16 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 75
Query: 110 KLNGTVIGKQSFRADYGNQWS 130
+N VI + R WS
Sbjct: 76 TMNFDVIKGKPVRI----MWS 92
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 40/77 (51%), Gaps = 6/77 (7%)
Query: 55 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEAL 108
N + V GL T+ DLR+ FS+YG IA V I +G FV F N ++A+EA
Sbjct: 15 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74
Query: 109 HKLNGTVIGKQSFRADY 125
+ NG + + R D+
Sbjct: 75 ERANGMELDGRRIRVDF 91
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 40/66 (60%), Gaps = 4/66 (6%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV----GKGCGFVQFANRENAEEALHKLNG 113
++V LD + DE LR+ FS +G I S K+ + KG GFV F++ E A +A+ ++NG
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNG 77
Query: 114 TVIGKQ 119
++ +
Sbjct: 78 RIVATK 83
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 40/77 (51%), Gaps = 6/77 (7%)
Query: 55 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEAL 108
N + V GL T+ DLR+ FS+YG IA V I +G FV F N ++A+EA
Sbjct: 12 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 71
Query: 109 HKLNGTVIGKQSFRADY 125
+ NG + + R D+
Sbjct: 72 ERANGMELDGRRIRVDF 88
>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 = 48.9 bits (115), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 36/63 (57%), Gaps = 4/63 (6%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV----GKGCGFVQFANRENAEEALHKLNG 113
IF+ LD ++ ++ L FS +G I S K+ KG GFV F +E AE A+ K+NG
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 67
Query: 114 TVI 116
++
Sbjct: 68 MLL 70
>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 = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 41/74 (55%)
Query: 53 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLN 112
+ + +FVG L P++T+E++R+ F +YG+ V I KG GF++ R AE A +L+
Sbjct: 13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELD 72
Query: 113 GTVIGKQSFRADYG 126
+ + R +
Sbjct: 73 NMPLRGKQLRVRFA 86
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 36/63 (57%), Gaps = 4/63 (6%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV----GKGCGFVQFANRENAEEALHKLNG 113
IF+ LD ++ ++ L FS +G I S K+ KG GFV F +E AE A+ K+NG
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 73
Query: 114 TVI 116
++
Sbjct: 74 MLL 76
>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
pdb|1HD1|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
Length = 75
Score = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 39/69 (56%), Gaps = 10/69 (14%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEAL--- 108
+F+GGL + T +DL+ FS++GE+ + + +G GFV F E+ ++ +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 109 -HKLNGTVI 116
HKLNG VI
Sbjct: 62 EHKLNGKVI 70
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 40/75 (53%), Gaps = 7/75 (9%)
Query: 56 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-------GKGCGFVQFANRENAEEAL 108
T + +G L NVT + + + FS YG+I + +PV KG +V+F N + AE+AL
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
Query: 109 HKLNGTVIGKQSFRA 123
++G I Q A
Sbjct: 65 KHMDGGQIDGQEITA 79
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 47.8 bits (112), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 29/77 (37%), Positives = 39/77 (50%), Gaps = 4/77 (5%)
Query: 44 GQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG----KGCGFVQFA 99
G +E S + V + D DLRQ F Q+G+I V+I KG GFV F
Sbjct: 18 GSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFE 77
Query: 100 NRENAEEALHKLNGTVI 116
N +A+ A KL+GTV+
Sbjct: 78 NSADADRAREKLHGTVV 94
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 47.4 bits (111), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 25/52 (48%), Positives = 32/52 (61%), Gaps = 4/52 (7%)
Query: 69 DEDLRQPFSQYGEIASVKIPV----GKGCGFVQFANRENAEEALHKLNGTVI 116
D DLRQ F Q+G+I V+I KG GFV F N +A+ A KL+GTV+
Sbjct: 29 DPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVV 80
>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 = 47.0 bits (110), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 6/77 (7%)
Query: 56 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEALH 109
T + V L N+T ++LR FS GE+ S K+ K G GFV + ++AE A++
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 64
Query: 110 KLNGTVIGKQSFRADYG 126
LNG + ++ + Y
Sbjct: 65 TLNGLRLQSKTIKVSYA 81
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 46.6 bits (109), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 39/62 (62%), Gaps = 6/62 (9%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKL 111
++VG L N+T++ LR F +G I S+++ + KG GF+ F++ E A++AL +L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 112 NG 113
NG
Sbjct: 89 NG 90
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 46.6 bits (109), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 6/77 (7%)
Query: 56 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEALH 109
T + V L N+T ++LR FS GE+ S K+ K G GFV + ++AE A++
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 110 KLNGTVIGKQSFRADYG 126
LNG + ++ + Y
Sbjct: 63 TLNGLRLQSKTIKVSYA 79
Score = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 6/62 (9%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKL 111
+++ GL +T +D+ FS++G I + ++ V +G F++F R AEEA+
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 112 NG 113
NG
Sbjct: 151 NG 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 = 46.6 bits (109), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 6/77 (7%)
Query: 56 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEALH 109
T + V L N+T ++LR FS GE+ S K+ K G GFV + ++AE A++
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 110 KLNGTVIGKQSFRADYG 126
LNG + ++ + Y
Sbjct: 63 TLNGLRLQSKTIKVSYA 79
Score = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 6/62 (9%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKL 111
+++ GL +T +D+ FS++G I + ++ V +G F++F R AEEA+
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 112 NG 113
NG
Sbjct: 151 NG 152
>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 = 7e-06, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 5/69 (7%)
Query: 46 GPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP-----VGKGCGFVQFAN 100
GP G T+FVGG+D + + ++R F++YG + VKI V KG GFV F N
Sbjct: 1 GPLGSGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYN 60
Query: 101 RENAEEALH 109
+ ++ +
Sbjct: 61 DVDVQKIVE 69
>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 = 46.6 bits (109), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 43/74 (58%), Gaps = 5/74 (6%)
Query: 57 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK---GCGF--VQFANRENAEEALHKL 111
T++VG L T+E + + FS+ G+I + + + K CGF V++ +R +AE A+ +
Sbjct: 20 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMRYI 79
Query: 112 NGTVIGKQSFRADY 125
NGT + + R D+
Sbjct: 80 NGTRLDDRIIRTDW 93
>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 = 45.8 bits (107), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 43/75 (57%), Gaps = 6/75 (8%)
Query: 57 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK----GCGF--VQFANRENAEEALHK 110
T++VG L T+E + + FS+ G+I + + + K CGF V++ +R +AE A+
Sbjct: 41 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100
Query: 111 LNGTVIGKQSFRADY 125
+NGT + + R D+
Sbjct: 101 INGTRLDDRIIRTDW 115
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 45.8 bits (107), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 38/75 (50%), Gaps = 6/75 (8%)
Query: 55 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEAL 108
N + V GL T+ DLR+ FS+YG IA V I +G FV F N ++A+EA
Sbjct: 15 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74
Query: 109 HKLNGTVIGKQSFRA 123
+ NG + + R
Sbjct: 75 ERANGMELDGRRIRV 89
>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 = 45.8 bits (107), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 6/77 (7%)
Query: 56 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEALH 109
T + V L N T ++LR FS GE+ S K+ K G GFV + ++AE A++
Sbjct: 20 TNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 79
Query: 110 KLNGTVIGKQSFRADYG 126
LNG + ++ + Y
Sbjct: 80 TLNGLRLQSKTIKVSYA 96
>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Rna, Uuguucuu
Length = 102
Score = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 5/64 (7%)
Query: 50 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP-----VGKGCGFVQFANRENA 104
EG T+FVGG+D + + ++R F++YG + VKI V KG GFV F N +
Sbjct: 4 EGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDV 63
Query: 105 EEAL 108
++ +
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 = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 5/65 (7%)
Query: 50 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP-----VGKGCGFVQFANRENA 104
EG T+FVGG+D + + ++R F++YG + VKI V KG GFV F N +
Sbjct: 4 EGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDV 63
Query: 105 EEALH 109
++ +
Sbjct: 64 QKIVE 68
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 44.7 bits (104), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 39/75 (52%), Gaps = 6/75 (8%)
Query: 52 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAE 105
D++ T IFVGGL + TD LR+ F +G+I + +G GFV A+R AE
Sbjct: 14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAE 73
Query: 106 EALHKLNGTVIGKQS 120
A N + G+++
Sbjct: 74 RACKDPNPIIDGRKA 88
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 44.7 bits (104), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 39/66 (59%), Gaps = 5/66 (7%)
Query: 54 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEAL 108
S+ +FVG L+ +++D+R+ F +G I I G KGC FV++++ A+ A+
Sbjct: 14 SHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAI 73
Query: 109 HKLNGT 114
+ L+G+
Sbjct: 74 NALHGS 79
>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 = 44.7 bits (104), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 42/81 (51%), Gaps = 9/81 (11%)
Query: 56 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALH 109
T++ V L + + LR+ F +YG + V IP +G FV+F ++ +AE+A+
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 110 KLNGTVIGKQSFR---ADYGN 127
++G V+ + R A YG
Sbjct: 108 AMDGAVLDGRELRVQMARYGR 128
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 44.3 bits (103), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 24/62 (38%), Positives = 37/62 (59%), Gaps = 5/62 (8%)
Query: 58 IFVGGLDPNVTDED---LRQPFSQYGEIASVKIPVG--KGCGFVQFANRENAEEALHKLN 112
+FVG L+ ++ED L QPF E ++ P G KGC FV+F++ A+ A+H L+
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77
Query: 113 GT 114
G+
Sbjct: 78 GS 79
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 44.3 bits (103), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 40/79 (50%), Gaps = 6/79 (7%)
Query: 52 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAE 105
D S ++FVG + T+E L+ FS+ G + S ++ KG GF ++ ++E A
Sbjct: 5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETAL 64
Query: 106 EALHKLNGTVIGKQSFRAD 124
A+ LNG ++ R D
Sbjct: 65 SAMRNLNGREFSGRALRVD 83
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 44.3 bits (103), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 44/81 (54%), Gaps = 6/81 (7%)
Query: 51 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENA 104
G S ++ ++VG L N+T++ LR F +G+I ++ + KG GF+ F++ E A
Sbjct: 1 GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60
Query: 105 EEALHKLNGTVIGKQSFRADY 125
AL +LNG + + R +
Sbjct: 61 RRALEQLNGFELAGRPMRVGH 81
>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
pdb|1U1K|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt 7da
Ggg); A Human Telomeric Repeat Containing
7-Deaza-Adenine
pdb|1U1L|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt Prn
Ggg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1M|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 7gu
Gg); A Human Telomeric Repeat Containing 7-Deaza-Guanine
pdb|1U1N|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta (Prn)
Gg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1O|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggttag(Di)g); A Human Telomeric Repeat Containing
Inosine
pdb|1U1P|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 2pr
Gg); A Human Telomeric Repeat Containing 2-Aminopurine
pdb|1U1Q|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggtta(Di)gg); A Human Telomeric Repeat Containing
Inosine
pdb|1U1R|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(2pr)
G); A Human Telomeric Repeat Containing 2-Aminopurine
Length = 196
Score = 43.9 bits (102), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 10/69 (14%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEAL--- 108
+F+GGL TDE LR F Q+G + + +G GFV +A E + A+
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 109 -HKLNGTVI 116
HK++G V+
Sbjct: 76 PHKVDGRVV 84
Score = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 10/66 (15%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG------FVQFANRENAEEAL--- 108
IFVGG+ + + LR F QYG+I ++I +G G FV F + ++ ++ +
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 166
Query: 109 -HKLNG 113
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 = 43.9 bits (102), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 10/69 (14%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEAL--- 108
+F+GGL TDE LR F Q+G + + +G GFV +A E + A+
Sbjct: 15 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 74
Query: 109 -HKLNGTVI 116
HK++G V+
Sbjct: 75 PHKVDGRVV 83
Score = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 10/66 (15%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG------FVQFANRENAEEAL--- 108
IFVGG+ + + LR F QYG+I ++I +G G FV F + ++ ++ +
Sbjct: 106 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 165
Query: 109 -HKLNG 113
H +NG
Sbjct: 166 YHTVNG 171
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 43.5 bits (101), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 10/69 (14%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEAL--- 108
+F+GGL TDE LR F Q+G + + +G GFV +A E + A+
Sbjct: 17 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 76
Query: 109 -HKLNGTVI 116
HK++G V+
Sbjct: 77 PHKVDGRVV 85
Score = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 10/66 (15%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG------FVQFANRENAEEAL--- 108
IFVGG+ + + LR F QYG+I ++I +G G FV F + ++ ++ +
Sbjct: 108 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 167
Query: 109 -HKLNG 113
H +NG
Sbjct: 168 YHTVNG 173
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 43.5 bits (101), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 25/70 (35%), Positives = 38/70 (54%), Gaps = 3/70 (4%)
Query: 53 SSNTTIFVGGLDPN-VTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKL 111
S N+ +F+G L+ V D+ FS+YG +A V KG FVQ++N +A A+
Sbjct: 25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGC--SVHKGYAFVQYSNERHARAAVLGE 82
Query: 112 NGTVIGKQSF 121
NG V+ Q+
Sbjct: 83 NGRVLAGQTL 92
>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|C Chain C, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|B Chain B, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|D Chain D, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
Length = 88
Score = 43.5 bits (101), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 8/72 (11%)
Query: 53 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI--------PVGKGCGFVQFANRENA 104
S +FVG + +++DLR+ F QYG + + + P KGC FV F R+ A
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 105 EEALHKLNGTVI 116
EA + L+ +
Sbjct: 61 LEAQNALHNMKV 72
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 43.5 bits (101), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 6/74 (8%)
Query: 56 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALH 109
T++ V L + + LR+ F +YG + V IP +G FV+F ++ +AE+A+
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 110 KLNGTVIGKQSFRA 123
++G V+ + R
Sbjct: 131 AMDGAVLDGRELRV 144
>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 = 43.5 bits (101), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 10/69 (14%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEAL--- 108
+F+GGL TDE LR F Q+G + + +G GFV +A E + A+
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68
Query: 109 -HKLNGTVI 116
HK++G V+
Sbjct: 69 PHKVDGRVV 77
Score = 40.4 bits (93), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 10/66 (15%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG------FVQFANRENAEEAL--- 108
IFVGG+ + + LR F QYG+I ++I +G G FV F + ++ ++ +
Sbjct: 100 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 159
Query: 109 -HKLNG 113
H +NG
Sbjct: 160 YHTVNG 165
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 43.5 bits (101), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 5/60 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLN 112
+F+G + T+ D+R FS +G+I +I G +GC FV F R A+ A+ ++
Sbjct: 98 LFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 157
Score = 42.7 bits (99), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 8/72 (11%)
Query: 53 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI--------PVGKGCGFVQFANRENA 104
S +FVG + +++DLR+ F QYG + + + P KGC FV F R+ A
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 105 EEALHKLNGTVI 116
EA + L+ +
Sbjct: 61 LEAQNALHNMKV 72
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 43.5 bits (101), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 10/69 (14%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEAL--- 108
+F+GGL TDE LR F Q+G + + +G GFV +A E + A+
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 109 -HKLNGTVI 116
HK++G V+
Sbjct: 76 PHKVDGRVV 84
Score = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 10/66 (15%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG------FVQFANRENAEEAL--- 108
IFVGG+ + + LR F QYG+I ++I +G G FV F + ++ ++ +
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 166
Query: 109 -HKLNG 113
H +NG
Sbjct: 167 YHTVNG 172
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 43.1 bits (100), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 10/69 (14%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEAL--- 108
+F+GGL TDE LR F Q+G + + +G GFV +A E + A+
Sbjct: 14 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 73
Query: 109 -HKLNGTVI 116
HK++G V+
Sbjct: 74 PHKVDGRVV 82
Score = 40.0 bits (92), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 10/66 (15%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG------FVQFANRENAEEAL--- 108
IFVGG+ + + LR F QYG+I ++I +G G FV F + ++ ++ +
Sbjct: 105 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 164
Query: 109 -HKLNG 113
H +NG
Sbjct: 165 YHTVNG 170
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 43.1 bits (100), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 8/73 (10%)
Query: 52 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI--------PVGKGCGFVQFANREN 103
D +FVG + +++DLR+ F QYG + + + P KGC FV F R+
Sbjct: 12 DLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKA 71
Query: 104 AEEALHKLNGTVI 116
A EA + L+ +
Sbjct: 72 ALEAQNALHNMKV 84
Score = 43.1 bits (100), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 5/60 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLN 112
+F+G + T+ D+R FS +G+I +I G +GC FV F R A+ A+ ++
Sbjct: 110 LFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 169
>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
pdb|3NNA|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 43.1 bits (100), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 30/56 (53%), Gaps = 5/56 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEAL 108
+F+G + T+ D+R FS +G+I +I G +GC FV F R A+ A+
Sbjct: 98 LFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAI 153
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 34/66 (51%), Gaps = 8/66 (12%)
Query: 59 FVGGLDPNVTDEDLRQPFSQYGEIASVKI--------PVGKGCGFVQFANRENAEEALHK 110
FVG + +++DLR+ F QYG + + + P KGC FV F R+ A EA +
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 111 LNGTVI 116
L+ +
Sbjct: 67 LHNXKV 72
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 43.1 bits (100), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 32/60 (53%), Gaps = 5/60 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLN 112
+FVG L TDED+R+ F +G I + G KGC FV+F A+ A++ L+
Sbjct: 15 LFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTLH 74
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 28/69 (40%), Positives = 34/69 (49%), Gaps = 10/69 (14%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEAL--- 108
+FVGGLD + T E LR FSQYGE+ I K G GFV+F + L
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASR 78
Query: 109 -HKLNGTVI 116
H L+G I
Sbjct: 79 PHTLDGRNI 87
>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
pdb|3S7R|B Chain B, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
Length = 87
Score = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 37/68 (54%), Gaps = 10/68 (14%)
Query: 59 FVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEAL---- 108
FVGGL + + +DL+ F+++GE+ I +G GF+ F + + E+ L
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQKE 74
Query: 109 HKLNGTVI 116
H+L+G VI
Sbjct: 75 HRLDGRVI 82
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 42.4 bits (98), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
Query: 48 QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEA 107
+ EG+ SNT +FV +V + +L + F +G + VKI G FV+F E+A +A
Sbjct: 24 RQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--NGFAFVEFEEAESAAKA 81
Query: 108 LHKLNGTVIGKQSFRADY 125
+ +++G Q Y
Sbjct: 82 IEEVHGKSFANQPLEVVY 99
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 42.4 bits (98), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 2/65 (3%)
Query: 49 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEAL 108
S G + +FV L VT+E L + FSQ+G++ VK K F+ F R+ A +A+
Sbjct: 5 SSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--KDYAFIHFDERDGAVKAM 62
Query: 109 HKLNG 113
++NG
Sbjct: 63 EEMNG 67
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 44/80 (55%), Gaps = 10/80 (12%)
Query: 39 SNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP-------VGK 91
S+G+ GQ P+ + + + I V + ++R+ FS +GE+ +V++P +
Sbjct: 2 SSGSSGQVPKKQ---TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHR 58
Query: 92 GCGFVQFANRENAEEALHKL 111
G GFV F +++A++A + L
Sbjct: 59 GFGFVDFITKQDAKKAFNAL 78
>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 = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 39/74 (52%), Gaps = 6/74 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGF------VQFANRENAEEALHKL 111
+FV G+ T+ED+ F++YGEI ++ + + + G+ V++ + A+ A+ L
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 112 NGTVIGKQSFRADY 125
NG + Q D+
Sbjct: 86 NGQDLMGQPISVDW 99
>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 = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 39/68 (57%), Gaps = 9/68 (13%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEAL--- 108
+F+GGL+ + T+++LR+ F +YG + +KI +G GF+ F + +E +
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65
Query: 109 HKLNGTVI 116
H L+G VI
Sbjct: 66 HILDGKVI 73
Score = 34.3 bits (77), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 7/58 (12%)
Query: 47 PQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQF 98
P+ E D + IFVGG+ P+V ++ + FSQ+G I ++ + K G GFV +
Sbjct: 80 PRDEQDKTGK-IFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTY 136
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 38/74 (51%), Gaps = 10/74 (13%)
Query: 53 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI---PVGK---GCGFVQFANRENAEE 106
SS +F+GGL T E LR+ F Q+GE+ + P+ K G GFV F ++ ++
Sbjct: 23 SSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDK 82
Query: 107 AL----HKLNGTVI 116
L H+L+ I
Sbjct: 83 VLAQSRHELDSKTI 96
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 42/82 (51%), Gaps = 6/82 (7%)
Query: 51 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENA 104
G ++ ++VGGL V D+ L F +G+I ++IP+ +G FV+F E+A
Sbjct: 1 GSTTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60
Query: 105 EEALHKLNGTVIGKQSFRADYG 126
A+ +N + + ++ R +
Sbjct: 61 AAAIDNMNESELFGRTIRVNLA 82
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 5/77 (6%)
Query: 57 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK-----GCGFVQFANRENAEEALHKL 111
++VG LD +T++ L+Q F G IA++KI + K FV++ +A AL L
Sbjct: 2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTL 61
Query: 112 NGTVIGKQSFRADYGNQ 128
NG I + ++ Q
Sbjct: 62 NGKQIENNIVKINWAFQ 78
>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 = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 39/74 (52%), Gaps = 6/74 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGF------VQFANRENAEEALHKL 111
+FV G+ T+ED+ F++YGEI ++ + + + G+ V++ + A+ A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 112 NGTVIGKQSFRADY 125
NG + Q D+
Sbjct: 70 NGQDLMGQPISVDW 83
>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 = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 39/74 (52%), Gaps = 6/74 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGF------VQFANRENAEEALHKL 111
+FV G+ T+ED+ F++YGEI ++ + + + G+ V++ + A+ A+ L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 112 NGTVIGKQSFRADY 125
NG + Q D+
Sbjct: 72 NGQDLMGQPISVDW 85
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 39/74 (52%), Gaps = 6/74 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGF------VQFANRENAEEALHKL 111
+FV G+ T+ED+ F++YGEI ++ + + + G+ V++ + A+ A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 112 NGTVIGKQSFRADY 125
NG + Q D+
Sbjct: 70 NGQDLMGQPISVDW 83
>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 = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 39/74 (52%), Gaps = 6/74 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGF------VQFANRENAEEALHKL 111
+FV G+ T+ED+ F++YGEI ++ + + + G+ V++ + A+ A+ L
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 112 NGTVIGKQSFRADY 125
NG + Q D+
Sbjct: 85 NGQDLMGQPISVDW 98
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 49 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEAL 108
S G S +F+G L T++++R F QYG++ I K GFV ++ AE+A+
Sbjct: 2 SSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--KNYGFVHIEDKTAAEDAI 59
Query: 109 HKLN 112
L+
Sbjct: 60 RNLH 63
>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 = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 39/74 (52%), Gaps = 6/74 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGF------VQFANRENAEEALHKL 111
+FV G+ T+ED+ F++YGEI ++ + + + G+ V++ + A+ A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 112 NGTVIGKQSFRADY 125
NG + Q D+
Sbjct: 70 NGQDLMGQPISVDW 83
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 33/67 (49%), Gaps = 6/67 (8%)
Query: 55 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEAL 108
+T ++V L +TD+ L F +YG I I K G FV++ RE A+EA+
Sbjct: 89 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 148
Query: 109 HKLNGTV 115
LN +
Sbjct: 149 SALNNVI 155
Score = 37.0 bits (84), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 36/80 (45%), Gaps = 6/80 (7%)
Query: 53 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANRENAEE 106
+SNT + V L ++TD +L F G I + +I G FV F + +++
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 107 ALHKLNGTVIGKQSFRADYG 126
A+ LNG + + + Y
Sbjct: 61 AIKVLNGITVRNKRLKVSYA 80
>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 = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 9/62 (14%)
Query: 55 NTTIFVGGLD---------PNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAE 105
N T++VGG+D P + +R FS+ G+I ++ K CGFV+F + NAE
Sbjct: 136 NKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAE 195
Query: 106 EA 107
A
Sbjct: 196 FA 197
>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 = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 9/62 (14%)
Query: 55 NTTIFVGGLD---------PNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAE 105
N T++VGG+D P + +R FS+ G+I ++ K CGFV+F + NAE
Sbjct: 134 NKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAE 193
Query: 106 EA 107
A
Sbjct: 194 FA 195
>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 = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 33/67 (49%), Gaps = 6/67 (8%)
Query: 55 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEAL 108
+T ++V L +TD+ L F +YG I I K G FV++ RE A+EA+
Sbjct: 100 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 159
Query: 109 HKLNGTV 115
LN +
Sbjct: 160 SALNNVI 166
Score = 35.8 bits (81), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 35/80 (43%), Gaps = 6/80 (7%)
Query: 53 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANRENAEE 106
+SNT + V L + TD +L F G I + +I G FV F + +++
Sbjct: 12 ASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQR 71
Query: 107 ALHKLNGTVIGKQSFRADYG 126
A+ LNG + + + Y
Sbjct: 72 AIKVLNGITVRNKRLKVSYA 91
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 41/81 (50%), Gaps = 6/81 (7%)
Query: 53 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEE 106
++ ++VGGL V D+ L F +G+I ++IP+ +G FV+F E+A
Sbjct: 10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 69
Query: 107 ALHKLNGTVIGKQSFRADYGN 127
A+ +N + + ++ R +
Sbjct: 70 AIDNMNESELFGRTIRVNLAK 90
>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second
Rna-Binding Domain Of Sex-Lethal Determined By
Multidimensional Heteronuclear Magnetic Resonance
Spectroscopy
Length = 97
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 33/67 (49%), Gaps = 6/67 (8%)
Query: 55 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEAL 108
+T ++V L +TD+ L F +YG I I K G FV++ RE A+EA+
Sbjct: 13 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 72
Query: 109 HKLNGTV 115
LN +
Sbjct: 73 SALNNVI 79
>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 = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 34/59 (57%), Gaps = 6/59 (10%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHK 110
IFVGGL P+ +E +R+ F +GE+ S+++P+ +G F+ F E ++ + K
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 62
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 34/59 (57%), Gaps = 6/59 (10%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHK 110
IFVGGL P+ +E +R+ F +GE+ S+++P+ +G F+ F E ++ + K
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 39/75 (52%), Gaps = 9/75 (12%)
Query: 51 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK---------GCGFVQFANR 101
G S ++ +F+ L+ + T+E L+ FS+ G I S I K G GFV++
Sbjct: 1 GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60
Query: 102 ENAEEALHKLNGTVI 116
E A++AL +L G +
Sbjct: 61 EQAQKALKQLQGHTV 75
>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 = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 2/70 (2%)
Query: 47 PQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEE 106
P+ T++V G D +T LR FS +G I + + + C FV + E+A++
Sbjct: 31 PERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQ 88
Query: 107 ALHKLNGTVI 116
A+ +LNGT +
Sbjct: 89 AVAELNGTQV 98
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 41/80 (51%), Gaps = 6/80 (7%)
Query: 53 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEE 106
++ ++VGGL V D+ L F +G+I ++IP+ +G FV+F E+A
Sbjct: 61 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 120
Query: 107 ALHKLNGTVIGKQSFRADYG 126
A+ +N + + ++ R +
Sbjct: 121 AIDNMNESELFGRTIRVNLA 140
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 41/79 (51%), Gaps = 6/79 (7%)
Query: 54 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEA 107
S T + V L N+T ++ + F G+I S K+ K G GFV +++ +A++A
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 108 LHKLNGTVIGKQSFRADYG 126
++ LNG + ++ + Y
Sbjct: 63 INTLNGLKLQTKTIKVSYA 81
>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 = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 6/79 (7%)
Query: 54 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEA 107
S ++VGGL V D+ L F +G+I ++IP+ +G FV+F E+A A
Sbjct: 1 SKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 60
Query: 108 LHKLNGTVIGKQSFRADYG 126
+ +N + + ++ R +
Sbjct: 61 IDNMNESELFGRTIRVNLA 79
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 41/76 (53%), Gaps = 7/76 (9%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 111
I+VG L + T E +++ FSQ+G++ +VK+ KG GFV+ E+ EA+ KL
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVE-MQEESVSEAIAKL 62
Query: 112 NGTVIGKQSFRADYGN 127
+ T ++ R N
Sbjct: 63 DNTDFMGRTIRVTEAN 78
>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 = 40.8 bits (94), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 41/81 (50%), Gaps = 6/81 (7%)
Query: 53 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEE 106
++ ++VGGL V D+ L F +G+I ++IP+ +G FV+F E+A
Sbjct: 5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 64
Query: 107 ALHKLNGTVIGKQSFRADYGN 127
A+ +N + + ++ R +
Sbjct: 65 AIDNMNESELFGRTIRVNLAK 85
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 40.8 bits (94), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 38/64 (59%), Gaps = 7/64 (10%)
Query: 57 TIFVGGLDPNVTDEDLRQPFSQYGE-IASVKIP------VGKGCGFVQFANRENAEEALH 109
++++G L+P + + + + F+ GE + SVKI + G FV+FA+ AE+ LH
Sbjct: 11 SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70
Query: 110 KLNG 113
K+NG
Sbjct: 71 KING 74
>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 = 5e-04, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 2/73 (2%)
Query: 55 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGT 114
T ++VGGL PN + L + F ++G I ++ G ++Q+ + + A+ A K+ G
Sbjct: 17 TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGF 76
Query: 115 VIG--KQSFRADY 125
+G + R D+
Sbjct: 77 PLGGPDRRLRVDF 89
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 36/56 (64%), Gaps = 1/56 (1%)
Query: 51 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-GKGCGFVQFANRENAE 105
G S ++ +FVG ++T+++LR+ FSQYG++ V IP + FV FA+ + A+
Sbjct: 1 GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQ 56
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 40.4 bits (93), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 39/75 (52%), Gaps = 6/75 (8%)
Query: 51 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENA 104
G S ++ +++ GL P TD+DL + YG+I S K + KG GFV F + A
Sbjct: 1 GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60
Query: 105 EEALHKLNGTVIGKQ 119
++A+ L + + Q
Sbjct: 61 QKAVTALKASGVQAQ 75
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 40.0 bits (92), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 6/79 (7%)
Query: 55 NTTIFVGGLDPNVTDEDLRQPFSQYGEIA----SVKIPVGK--GCGFVQFANRENAEEAL 108
N +++ L P VT+ DL F+++ E ++ G+ G F+ F N+E A +AL
Sbjct: 25 NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 84
Query: 109 HKLNGTVIGKQSFRADYGN 127
H +NG + + ++G
Sbjct: 85 HLVNGYKLYGKILVIEFGK 103
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 40.0 bits (92), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 35/69 (50%), Gaps = 10/69 (14%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEA---- 107
IFVGGL N T ED++ F Q+G++ + K G GFV F + + E+
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 108 LHKLNGTVI 116
H++N ++
Sbjct: 62 FHEINNKMV 70
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 40.0 bits (92), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 39/74 (52%), Gaps = 10/74 (13%)
Query: 54 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEA 107
S +T++V L ++T+ DL + FS+YG++ V I KG F+ F ++++A+
Sbjct: 15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNC 74
Query: 108 LHKLNGTVIGKQSF 121
+N KQ F
Sbjct: 75 TRAIN----NKQLF 84
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 40.0 bits (92), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 2/76 (2%)
Query: 41 GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFAN 100
G+ G + T++V G D +T LR FS +G I + + + C FV +
Sbjct: 1 GSSGSSGERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEK 58
Query: 101 RENAEEALHKLNGTVI 116
E+A++A+ +LNGT +
Sbjct: 59 MESADQAVAELNGTQV 74
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 40.0 bits (92), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 37/64 (57%), Gaps = 6/64 (9%)
Query: 55 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEAL 108
+ T++VGGLD V++ L + F Q G + + +P + G GFV+F + E+A+ A+
Sbjct: 15 DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 74
Query: 109 HKLN 112
++
Sbjct: 75 KIMD 78
>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 = 19/61 (31%), Positives = 34/61 (55%), Gaps = 2/61 (3%)
Query: 54 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNG 113
++T + VG + P T+++LR F +YG + ++ + K FV E+A EA+ L+
Sbjct: 9 ASTKLHVGNISPTCTNQELRAKFEEYGPV--IECDIVKDYAFVHMERAEDAVEAIRGLDN 66
Query: 114 T 114
T
Sbjct: 67 T 67
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 39.7 bits (91), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 33/57 (57%), Gaps = 2/57 (3%)
Query: 57 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNG 113
+FV L VT+E L + FS++G++ VK K FV F +R A +A+ ++NG
Sbjct: 17 VLFVRNLATTVTEEILEKSFSEFGKLERVKKL--KDYAFVHFEDRGAAVKAMDEMNG 71
>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 = 9e-04, Method: Compositional matrix adjust.
Identities = 25/66 (37%), Positives = 35/66 (53%), Gaps = 7/66 (10%)
Query: 65 PNVTDE-DLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKLNGTVIG 117
P DE LRQ F +YG I SVKI +G GFV+F + +A++A+ LNG I
Sbjct: 51 PTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNIL 110
Query: 118 KQSFRA 123
+ +
Sbjct: 111 NKRLKV 116
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 37/68 (54%), Gaps = 9/68 (13%)
Query: 52 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANREN-- 103
D +F+G + N+ ++DL+ F ++G+I + + + KGC F+ + RE+
Sbjct: 10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESAL 69
Query: 104 -AEEALHK 110
A+ ALH+
Sbjct: 70 KAQSALHE 77
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 38/72 (52%), Gaps = 4/72 (5%)
Query: 49 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEI--ASVKIPVGK--GCGFVQFANRENA 104
S G S IFV L + T + L+ F++ G + A +K+ GK GCG V+F + E A
Sbjct: 2 SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVA 61
Query: 105 EEALHKLNGTVI 116
E A +NG +
Sbjct: 62 ERACRMMNGMKL 73
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 7/82 (8%)
Query: 51 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASV-KIPV------GKGCGFVQFANREN 103
G S ++ IF+G LDP + ++ L FS +G I KI KG F+ FA+ +
Sbjct: 1 GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60
Query: 104 AEEALHKLNGTVIGKQSFRADY 125
++ A+ +NG + + Y
Sbjct: 61 SDAAIEAMNGQYLCNRPITVSY 82
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 36/69 (52%), Gaps = 10/69 (14%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKI---PVGK---GCGFVQFANRENAEEAL--- 108
+F+GGL T E LR+ F Q+GE+ + P+ K G GFV F ++ ++ L
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62
Query: 109 -HKLNGTVI 116
H+L+ I
Sbjct: 63 RHELDSKTI 71
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 40/76 (52%), Gaps = 3/76 (3%)
Query: 53 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKG---CGFVQFANRENAEEALH 109
+++ I+VG L P++ +D+ F +YG I + + +G FV+F + +AE+A++
Sbjct: 20 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVY 79
Query: 110 KLNGTVIGKQSFRADY 125
+G R ++
Sbjct: 80 GRDGYDYDGYRLRVEF 95
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/70 (35%), Positives = 39/70 (55%), Gaps = 4/70 (5%)
Query: 51 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEI--ASVKIPVGK--GCGFVQFANRENAEE 106
G S ++ IFV L + T + L+ F++ G + A +K+ GK GCG V+F + E AE
Sbjct: 1 GSSGSSGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAER 60
Query: 107 ALHKLNGTVI 116
A +NG +
Sbjct: 61 ACRMMNGMKL 70
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 39/76 (51%)
Query: 41 GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFAN 100
G+ G + SS ++V L + ++E + + F+ A ++ + FV F+N
Sbjct: 1 GSSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSN 60
Query: 101 RENAEEALHKLNGTVI 116
RE+A EA+ LNG V+
Sbjct: 61 REDAVEAMKALNGKVL 76
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 34/67 (50%)
Query: 49 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEAL 108
S G S +++G L P VT +DLRQ F + ++ + G FV + ++ A A+
Sbjct: 2 SSGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAI 61
Query: 109 HKLNGTV 115
L+G V
Sbjct: 62 ETLSGKV 68
>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 = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 9/79 (11%)
Query: 58 IFVGGLDPNVTDEDL-RQPFSQYGEIASVKIPVGKG-------CGFVQFANRENAEEALH 109
I + L + DE+L R+ F +G I + IP G+ C F F N+++AE AL
Sbjct: 213 IXIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFXVFENKDSAERALQ 272
Query: 110 KLNGTVIGKQSFRADYGNQ 128
N +++G + ++
Sbjct: 273 X-NRSLLGNREISVSLADK 290
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 31/51 (60%), Gaps = 1/51 (1%)
Query: 56 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-GKGCGFVQFANRENAE 105
+ +FVG ++T E+L+Q F QYGE+ V IP + FV FA+ + A+
Sbjct: 12 SKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQ 62
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 40/84 (47%), Gaps = 7/84 (8%)
Query: 46 GPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK-----GC-GFVQFA 99
G Q EG +F+ L TD DL F +G + S K+ + K C GFV F
Sbjct: 32 GKQIEG-PEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFD 90
Query: 100 NRENAEEALHKLNGTVIGKQSFRA 123
N ++A+ A+ +NG +G + +
Sbjct: 91 NPDSAQVAIKAMNGFQVGTKRLKV 114
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 37/69 (53%), Gaps = 10/69 (14%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIAS---VKIPVGK---GCGFVQFANRENAEEAL--- 108
+F+GGL T+E LR + Q+G++ ++ P K G GFV F++ + A+
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAAR 89
Query: 109 -HKLNGTVI 116
H ++G V+
Sbjct: 90 PHSIDGRVV 98
>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 = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 6/81 (7%)
Query: 54 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEA 107
S+ +FVG L P +T + F+ +G I+ ++ KG GFV F N+ +AE A
Sbjct: 5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENA 64
Query: 108 LHKLNGTVIGKQSFRADYGNQ 128
+ ++ G +G + R ++ +
Sbjct: 65 IQQMGGQWLGGRQIRTNWATR 85
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 34/60 (56%), Gaps = 3/60 (5%)
Query: 50 EGDSSNTTIFVGGL-DPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEAL 108
G + +F+G L NV+ EDL + FS YG I ++I + GF+QF N ++ +A+
Sbjct: 17 RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHI--MQINIKNAFGFIQFDNPQSVRDAI 74
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 34/65 (52%), Gaps = 6/65 (9%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 111
+FV L ++EDL + FS YG ++ + P+ KG FV F E+A +A ++
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 112 NGTVI 116
+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 = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 34/60 (56%), Gaps = 3/60 (5%)
Query: 50 EGDSSNTTIFVGGL-DPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEAL 108
G + +F+G L NV+ EDL + FS YG I ++I + GF+QF N ++ +A+
Sbjct: 17 RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHI--MQINIKNAFGFIQFDNPQSVRDAI 74
>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
pdb|2QFJ|B Chain B, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
Length = 216
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 39/71 (54%), Gaps = 6/71 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 111
I+V + +++D+D++ F +G+I S + KG GF+++ +++++A+ +
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 112 NGTVIGKQSFR 122
N +G Q R
Sbjct: 188 NLFDLGGQYLR 198
Score = 35.8 bits (81), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 40/73 (54%), Gaps = 6/73 (8%)
Query: 56 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALH 109
+ ++VG + + ++ +RQ F+ +G I S+ + KG FV++ E A+ AL
Sbjct: 29 SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 88
Query: 110 KLNGTVIGKQSFR 122
++N ++G ++ +
Sbjct: 89 QMNSVMLGGRNIK 101
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet
Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 40/84 (47%), Gaps = 7/84 (8%)
Query: 46 GPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK-----GC-GFVQFA 99
G Q EG +F+ L D+DL Q F +G + S K+ + K C GFV +
Sbjct: 17 GSQKEG-PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYD 75
Query: 100 NRENAEEALHKLNGTVIGKQSFRA 123
N +A+ A+ +NG IG + +
Sbjct: 76 NPVSAQAAIQSMNGFQIGMKRLKV 99
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 38/73 (52%), Gaps = 4/73 (5%)
Query: 49 SEGDSSNT-TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEA 107
S G S NT IFVG + T ++LR F + G + ++ V K FV +A+ A
Sbjct: 2 SSGSSGNTWKIFVGNVSAACTSQELRSLFERRGRV--IECDVVKDYAFVHMEKEADAKAA 59
Query: 108 LHKLNGT-VIGKQ 119
+ +LNG V GK+
Sbjct: 60 IAQLNGKEVKGKR 72
>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 = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 39/72 (54%), Gaps = 6/72 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 111
I+V + +++D+D++ F +G+I S + KG GF+++ +++++A+ +
Sbjct: 113 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 172
Query: 112 NGTVIGKQSFRA 123
N +G Q R
Sbjct: 173 NLFDLGGQYLRV 184
Score = 35.4 bits (80), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 39/72 (54%), Gaps = 6/72 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 111
++VG + + ++ +RQ F+ +G I S+ + KG FV++ E A+ AL ++
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 112 NGTVIGKQSFRA 123
N ++G ++ +
Sbjct: 76 NSVMLGGRNIKV 87
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 2/74 (2%)
Query: 52 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKL 111
+ SNT +FV +V + +L + F +G + VKI G FV+F E+A +A+ ++
Sbjct: 1 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI--LNGFAFVEFEEAESAAKAIEEV 58
Query: 112 NGTVIGKQSFRADY 125
+G Q Y
Sbjct: 59 HGKSFANQPLEVVY 72
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 37.4 bits (85), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 33/54 (61%), Gaps = 3/54 (5%)
Query: 56 TTIFVGGL-DPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEAL 108
+ +F+G L NV+ EDL + FS YG I ++I + GF+QF N ++ +A+
Sbjct: 11 SRLFIGNLPLKNVSKEDLFRIFSPYGHI--MQINIKNAFGFIQFDNPQSVRDAI 62
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 37/74 (50%), Gaps = 6/74 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGF------VQFANRENAEEALHKL 111
+FV + ++++++ F YGEI ++ + + + GF V++ + A A L
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 112 NGTVIGKQSFRADY 125
NG I Q+ + D+
Sbjct: 89 NGAEIMGQTIQVDW 102
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 36/80 (45%), Gaps = 6/80 (7%)
Query: 53 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANRENAEE 106
+SNT + V L ++TD +L F G I + +I G FV F + +++
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 107 ALHKLNGTVIGKQSFRADYG 126
A+ LNG + + + Y
Sbjct: 61 AIKVLNGITVRNKRLKVSYA 80
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 34/68 (50%), Gaps = 5/68 (7%)
Query: 52 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEE 106
+ ++ T+FVG L+ V +E L + F Q G + V I K GFV F + E+
Sbjct: 13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSY 72
Query: 107 ALHKLNGT 114
A+ LNG
Sbjct: 73 AIALLNGI 80
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 37.0 bits (84), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 33/55 (60%), Gaps = 3/55 (5%)
Query: 56 TTIFVGGL-DPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALH 109
+ +F+G L NV+ EDL + FS YG I ++I + GF+QF N ++ +A+
Sbjct: 3 SRLFIGNLPLKNVSKEDLFRIFSPYGHI--MQINIKNAFGFIQFDNPQSVRDAIE 55
>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 = 0.007, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 35/74 (47%), Gaps = 7/74 (9%)
Query: 46 GPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFA 99
GP D N TI V L + + DL++ F +G I+ + + KG F+ F
Sbjct: 7 GPNRRADD-NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFH 65
Query: 100 NRENAEEALHKLNG 113
RE+A A+ ++G
Sbjct: 66 RREDAARAIAGVSG 79
>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 = 36.6 bits (83), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 21/88 (23%), Positives = 39/88 (44%), Gaps = 7/88 (7%)
Query: 43 PGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFV 96
P P ++GD+ T +FV ++ + T+ LR+ F YG I + + K G F+
Sbjct: 91 PHNDPNAQGDAFKT-LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFI 149
Query: 97 QFANRENAEEALHKLNGTVIGKQSFRAD 124
++ + + A +G I + D
Sbjct: 150 EYEHERDMHSAYKHADGKKIDGRRVLVD 177
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 36.6 bits (83), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 38/68 (55%), Gaps = 6/68 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 111
IFVGG+ N + +LR+ F ++G + V + +G GF+ F + ++ ++A++
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMH 72
Query: 112 NGTVIGKQ 119
++GK+
Sbjct: 73 FHDIMGKK 80
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 36.6 bits (83), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK-GCGFVQFANRENAEEALHKLNGTVI 116
++VG L +L + FS YG + +V I G FV+F + +AE+A+ L+G VI
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 62
Query: 117 GKQSFRAD 124
R +
Sbjct: 63 CGSRVRVE 70
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 36.6 bits (83), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 9/65 (13%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEAL--- 108
+ V GL T++DL++ FS +GE+ V++ KG GFV+F E + +
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 77
Query: 109 HKLNG 113
H ++G
Sbjct: 78 HMIDG 82
>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 = 36.6 bits (83), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 37/74 (50%), Gaps = 6/74 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGF------VQFANRENAEEALHKL 111
+FV + ++++++ F YGEI ++ + + + GF V++ + A A L
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 112 NGTVIGKQSFRADY 125
NG I Q+ + D+
Sbjct: 135 NGAEIMGQTIQVDW 148
>pdb|1WG4|A Chain A, Solution Structure Of Rrm Domain In Protein Bab31986
Length = 98
Score = 36.6 bits (83), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 54 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNG 113
S+ + V GL P+ + +DL+ + G++ + G G V++ +E+ E AL KL+
Sbjct: 14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQ-KDGMGMVEYLRKEDMEYALRKLDD 72
Query: 114 T 114
T
Sbjct: 73 T 73
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 36.2 bits (82), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 31/58 (53%), Gaps = 6/58 (10%)
Query: 57 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEAL 108
T+F+ L + +E L + Q+G++ V++ + KGC F QF +E A++ L
Sbjct: 17 TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCL 74
>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 2.50 A Resolution
Length = 200
Score = 35.8 bits (81), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 38/71 (53%), Gaps = 6/71 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 111
I+V + +++D+D++ F +G+I S + KG GF+++ +++++A+
Sbjct: 112 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSX 171
Query: 112 NGTVIGKQSFR 122
N +G Q R
Sbjct: 172 NLFDLGGQYLR 182
Score = 32.0 bits (71), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 36/71 (50%), Gaps = 6/71 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVK------IPVGKGCGFVQFANRENAEEALHKL 111
++VG + + ++ +RQ F+ +G I S+ KG FV++ E A+ AL +
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 112 NGTVIGKQSFR 122
N +G ++ +
Sbjct: 75 NSVXLGGRNIK 85
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 35.8 bits (81), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 35/68 (51%), Gaps = 9/68 (13%)
Query: 52 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANREN-- 103
D +FVG + + ++DL+ F ++G I + + + KGC F+ + R++
Sbjct: 12 DHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSAL 71
Query: 104 -AEEALHK 110
A+ ALH+
Sbjct: 72 KAQSALHE 79
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 35.0 bits (79), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 18/78 (23%), Positives = 39/78 (50%), Gaps = 5/78 (6%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASV-----KIPVGKGCGFVQFANRENAEEALHKLN 112
+F+GGL+ ++ L+ F ++G I+ V + +G F+ F N +A+ A +N
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 113 GTVIGKQSFRADYGNQWS 130
G + ++ + + + S
Sbjct: 70 GKSLHGKAIKVEQAKKPS 87
>pdb|1OWX|A Chain A, Solution Structure Of The C-Terminal Rrm Of Human La
(La225- 334)
Length = 121
Score = 35.0 bits (79), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 26/52 (50%), Gaps = 2/52 (3%)
Query: 59 FVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHK 110
F G LD EDL FS +GEI + G G + F +E A+EAL K
Sbjct: 23 FSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILF--KEKAKEALGK 72
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 35.0 bits (79), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 8/73 (10%)
Query: 57 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP-----VGKGCGFVQFANRENAEEALHKL 111
T+ + L + T+E L++ F + +K+P KG F++FA+ E+A+EAL+
Sbjct: 17 TLVLSNLSYSATEETLQEVFEK---ATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSC 73
Query: 112 NGTVIGKQSFRAD 124
N I ++ R +
Sbjct: 74 NKREIEGRAIRLE 86
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 34.7 bits (78), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 6/65 (9%)
Query: 57 TIFVGGLDPNVTDEDLRQPFSQY------GEIASVKIPVGKGCGFVQFANRENAEEALHK 110
++FVG L P+V D L + F + G++ + V KG GFV+F + + AL +
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE 70
Query: 111 LNGTV 115
G V
Sbjct: 71 CQGAV 75
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 34.7 bits (78), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 32/73 (43%)
Query: 56 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTV 115
TT ++G + T+ DL F +G I K KGC F+++ E A + L
Sbjct: 28 TTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFP 87
Query: 116 IGKQSFRADYGNQ 128
++ R +G +
Sbjct: 88 FQGRNLRTGWGKE 100
>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 = 34.3 bits (77), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 21/88 (23%), Positives = 39/88 (44%), Gaps = 7/88 (7%)
Query: 43 PGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFV 96
P P ++GD+ T +FV ++ + T+ LR+ F YG I + + K G F+
Sbjct: 91 PHNDPNAQGDAFKT-LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFI 149
Query: 97 QFANRENAEEALHKLNGTVIGKQSFRAD 124
++ + + A +G I + D
Sbjct: 150 EYEHERDMHSAYKHADGKKIDGRRVLVD 177
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 34.3 bits (77), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 40/84 (47%), Gaps = 5/84 (5%)
Query: 41 GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG----FV 96
G+ G E D T++VG L +VT+ + Q FSQ G S K+ FV
Sbjct: 1 GSSGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFV 60
Query: 97 QFANRENAEEALHKLNG-TVIGKQ 119
+F +A AL +NG ++GK+
Sbjct: 61 EFYEHRDAAAALAAMNGRKILGKE 84
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 33.9 bits (76), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 5/70 (7%)
Query: 50 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK-----GCGFVQFANRENA 104
EG + + V LD V+D D+++ F+++G + + + G V F R +A
Sbjct: 83 EGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADA 142
Query: 105 EEALHKLNGT 114
+A+ + G
Sbjct: 143 LKAMKQYKGV 152
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 33.5 bits (75), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 1/71 (1%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-KGCGFVQFANRENAEEALHKLNGTVI 116
++VG L N +L + F YG + SV + G FV+F + +A +A+ +L+G +
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTL 135
Query: 117 GKQSFRADYGN 127
R + N
Sbjct: 136 CGCRVRVELSN 146
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 33.5 bits (75), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 5/70 (7%)
Query: 50 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK-----GCGFVQFANRENA 104
EG + + V LD V+D D+++ F+++G + + + G V F R +A
Sbjct: 30 EGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADA 89
Query: 105 EEALHKLNGT 114
+A+ + G
Sbjct: 90 LKAMKQYKGV 99
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 33.5 bits (75), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 5/70 (7%)
Query: 50 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK-----GCGFVQFANRENA 104
EG + + V LD V+D D+++ F+++G + + + G V F R +A
Sbjct: 30 EGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADA 89
Query: 105 EEALHKLNGT 114
+A+ + G
Sbjct: 90 LKAMKQYKGV 99
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 33.5 bits (75), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 37/82 (45%), Gaps = 1/82 (1%)
Query: 45 QGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASV-KIPVGKGCGFVQFANREN 103
+G S+ + T+ L VT ++L++ F EI V K KG +++F +
Sbjct: 83 KGKDSKKERDARTLLAKNLPYKVTQDELKEVFEDAAEIRLVSKDGKSKGIAYIEFKTEAD 142
Query: 104 AEEALHKLNGTVIGKQSFRADY 125
AE+ + GT I +S Y
Sbjct: 143 AEKTFEEKQGTEIDGRSISLYY 164
>pdb|3BEG|B Chain B, Crystal Structure Of Sr Protein Kinase 1 Complexed To Its
Substrate AsfSF2
Length = 115
Score = 33.1 bits (74), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 31/61 (50%), Gaps = 1/61 (1%)
Query: 54 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNG 113
S + V GL P+ + +DL+ + G++ + G G V+F +E+ A+ KL+
Sbjct: 15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADV-YRDGTGVVEFVRKEDMTYAVRKLDN 73
Query: 114 T 114
T
Sbjct: 74 T 74
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 33.1 bits (74), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 34/71 (47%), Gaps = 1/71 (1%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-KGCGFVQFANRENAEEALHKLNGTVI 116
++VG L N +L + F YG + SV + G FV+F + +A +A+ L+G +
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRDLDGRTL 135
Query: 117 GKQSFRADYGN 127
R + N
Sbjct: 136 CGCRVRVELSN 146
>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 = 0.088, Method: Compositional matrix adjust.
Identities = 17/75 (22%), Positives = 37/75 (49%), Gaps = 6/75 (8%)
Query: 57 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHK 110
+++G + + T+E + S G + ++K+ KG F++F + E++ A+
Sbjct: 6 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 65
Query: 111 LNGTVIGKQSFRADY 125
LNG +G + + Y
Sbjct: 66 LNGYQLGSRFLKCGY 80
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 33.1 bits (74), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 35/67 (52%), Gaps = 4/67 (5%)
Query: 57 TIFVGGLDPNVTDEDLRQPFS---QYGEIASVKIPVGKGCGFVQFANRENAEEALHKL-N 112
T+FV GL + T+E L++ F + + + KG GFV F + E+A+ A + +
Sbjct: 17 TLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMED 76
Query: 113 GTVIGKQ 119
G + G +
Sbjct: 77 GEIDGNK 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 = 0.094, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 37/80 (46%), Gaps = 12/80 (15%)
Query: 41 GAPGQGP------QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG---- 90
GA +GP + + + +++VG +D T +DL FS G I + I
Sbjct: 16 GAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSG 75
Query: 91 --KGCGFVQFANRENAEEAL 108
KG +++FA R + + A+
Sbjct: 76 HPKGYAYIEFAERNSVDAAV 95
>pdb|2O3D|A Chain A, Structure Of Human Sf2ASF RNA RECOGNITION MOTIF 2 (RRM2)
Length = 113
Score = 32.7 bits (73), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 31/61 (50%), Gaps = 1/61 (1%)
Query: 54 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNG 113
S + V GL P+ + +DL+ + G++ + G G V+F +E+ A+ KL+
Sbjct: 14 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADV-YRDGTGVVEFVRKEDMTYAVRKLDN 72
Query: 114 T 114
T
Sbjct: 73 T 73
>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 = 32.7 bits (73), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 17/75 (22%), Positives = 37/75 (49%), Gaps = 6/75 (8%)
Query: 57 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHK 110
+++G + + T+E + S G + ++K+ KG F++F + E++ A+
Sbjct: 5 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 64
Query: 111 LNGTVIGKQSFRADY 125
LNG +G + + Y
Sbjct: 65 LNGYQLGSRFLKCGY 79
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 32.7 bits (73), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 17/75 (22%), Positives = 37/75 (49%), Gaps = 6/75 (8%)
Query: 57 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHK 110
+++G + + T+E + S G + ++K+ KG F++F + E++ A+
Sbjct: 4 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63
Query: 111 LNGTVIGKQSFRADY 125
LNG +G + + Y
Sbjct: 64 LNGYQLGSRFLKCGY 78
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 32.0 bits (71), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 15/62 (24%), Positives = 31/62 (50%), Gaps = 5/62 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK-----GCGFVQFANRENAEEALHKLN 112
+ V LD V+D D+++ F+++G + + + G V F + +A +A+ + N
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 90
Query: 113 GT 114
G
Sbjct: 91 GV 92
>pdb|1X4C|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 2
Length = 108
Score = 31.6 bits (70), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGT 114
+ V GL P+ + +DL+ + G++ + G G V+F +E+ A+ KL+ T
Sbjct: 18 VVVSGLPPSGSWQDLKDHMREAGDVCYADV-YRDGTGVVEFVRKEDMTYAVRKLDNT 73
>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 = 31.2 bits (69), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 14/70 (20%), Positives = 35/70 (50%), Gaps = 6/70 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANRENAEEALHKL 111
+F+GGL + D+ +++ + +G + + + + KG F ++ + ++A+ L
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176
Query: 112 NGTVIGKQSF 121
NG +G +
Sbjct: 177 NGMQLGDKKL 186
>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 = 0.31, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 8/66 (12%)
Query: 70 EDLRQPFSQYGEIASVKIPV------GKGCG--FVQFANRENAEEALHKLNGTVIGKQSF 121
ED+R S+YG + S++IP GCG FV+F + + ++A+ L G +
Sbjct: 29 EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVV 88
Query: 122 RADYGN 127
Y +
Sbjct: 89 VTKYCD 94
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 31.2 bits (69), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 1/70 (1%)
Query: 57 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP-VGKGCGFVQFANRENAEEALHKLNGTV 115
T+ L N+T+++L++ F EI V KG +++F + +AE+ L + G
Sbjct: 18 TLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAE 77
Query: 116 IGKQSFRADY 125
I +S Y
Sbjct: 78 IDGRSVSLYY 87
>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 = 0.32, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 8/66 (12%)
Query: 70 EDLRQPFSQYGEIASVKIPV------GKGCG--FVQFANRENAEEALHKLNGTVIGKQSF 121
ED+R S+YG + S++IP GCG FV+F + + ++A+ L G +
Sbjct: 29 EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVV 88
Query: 122 RADYGN 127
Y +
Sbjct: 89 VTKYCD 94
>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 = 31.2 bits (69), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 28/74 (37%), Positives = 41/74 (55%), Gaps = 8/74 (10%)
Query: 44 GQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIA--SVKIPV---GK--GCGFV 96
G+G S +++ + + GL T E++ Q FS EI + +PV GK G FV
Sbjct: 31 GRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFV 89
Query: 97 QFANRENAEEALHK 110
QFA++E AE+AL K
Sbjct: 90 QFASQELAEKALGK 103
>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 = 31.2 bits (69), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 14/70 (20%), Positives = 35/70 (50%), Gaps = 6/70 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANRENAEEALHKL 111
+F+GGL + D+ +++ + +G + + + + KG F ++ + ++A+ L
Sbjct: 99 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 158
Query: 112 NGTVIGKQSF 121
NG +G +
Sbjct: 159 NGMQLGDKKL 168
>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 = 30.8 bits (68), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 39/82 (47%), Gaps = 1/82 (1%)
Query: 45 QGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP-VGKGCGFVQFANREN 103
+G S+ + T+ L N+T+++L++ F EI V KG +++F + +
Sbjct: 89 KGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEAD 148
Query: 104 AEEALHKLNGTVIGKQSFRADY 125
AE+ L + G I +S Y
Sbjct: 149 AEKNLEEKQGAEIDGRSVSLYY 170
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 30.8 bits (68), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 14/70 (20%), Positives = 35/70 (50%), Gaps = 6/70 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANRENAEEALHKL 111
+F+GGL + D+ +++ + +G + + + + KG F ++ + ++A+ L
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 112 NGTVIGKQSF 121
NG +G +
Sbjct: 157 NGMQLGDKKL 166
>pdb|2M2B|A Chain A, Nmr Structure Of The Rrm2 Domain Of The Protein Rbm10 From
Homo Sapiens
Length = 131
Score = 30.8 bits (68), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 38/81 (46%), Gaps = 13/81 (16%)
Query: 42 APGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK--------GC 93
A QG + +++N TI + L+P+ T + + + Y ++S + V K G
Sbjct: 10 ALSQGSEPSSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGF 69
Query: 94 GFVQFANRENAE-----EALH 109
F+Q + E A+ +ALH
Sbjct: 70 AFIQLSTIEAAQLLQILQALH 90
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 30.4 bits (67), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 14/70 (20%), Positives = 35/70 (50%), Gaps = 6/70 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANRENAEEALHKL 111
+F+GGL + D+ +++ + +G + + + + KG F ++ + ++A+ L
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 112 NGTVIGKQSF 121
NG +G +
Sbjct: 64 NGMQLGDKKL 73
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 30.4 bits (67), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 24/42 (57%)
Query: 41 GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEI 82
G+ G + DS N+ I+V GL+ +VT +DL F Q G +
Sbjct: 1 GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVV 42
>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 = 0.64, Method: Compositional matrix adjust.
Identities = 15/62 (24%), Positives = 30/62 (48%), Gaps = 5/62 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK-----GCGFVQFANRENAEEALHKLN 112
+ V LD V+D D+++ F+++G + + + G V F + +A +A + N
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYN 91
Query: 113 GT 114
G
Sbjct: 92 GV 93
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 30.0 bits (66), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 17/37 (45%), Positives = 21/37 (56%)
Query: 50 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVK 86
+ +S N TIFV GL NVT E + F Q G I + K
Sbjct: 2 QDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNK 38
>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 = 29.6 bits (65), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 32/69 (46%), Gaps = 6/69 (8%)
Query: 57 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHK 110
+I+VG +D T E+L F G + V I KG +++F+++E+ +L
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLAL 67
Query: 111 LNGTVIGKQ 119
G+Q
Sbjct: 68 DESLFRGRQ 76
>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 = 29.6 bits (65), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 32/69 (46%), Gaps = 6/69 (8%)
Query: 57 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHK 110
+I+VG +D T E+L F G + V I KG +++F+++E+ +L
Sbjct: 7 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLAL 66
Query: 111 LNGTVIGKQ 119
G+Q
Sbjct: 67 DESLFRGRQ 75
>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 = 0.98, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 31/66 (46%), Gaps = 8/66 (12%)
Query: 70 EDLRQPFSQYGEIASVKIPV------GKGCG--FVQFANRENAEEALHKLNGTVIGKQSF 121
ED+R S+YG + S++IP GCG FV+F + + ++A L G +
Sbjct: 31 EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAXQGLTGRKFANRVV 90
Query: 122 RADYGN 127
Y +
Sbjct: 91 VTKYCD 96
>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 = 29.6 bits (65), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 31/66 (46%), Gaps = 8/66 (12%)
Query: 70 EDLRQPFSQYGEIASVKIPV------GKGCG--FVQFANRENAEEALHKLNGTVIGKQSF 121
ED+R S+YG + S++IP GCG FV+F + + ++A L G +
Sbjct: 30 EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAXQGLTGRKFANRVV 89
Query: 122 RADYGN 127
Y +
Sbjct: 90 VTKYCD 95
>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 = 28.9 bits (63), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 24/42 (57%), Gaps = 3/42 (7%)
Query: 75 PFSQYGEIASVKIPVGKG-CGFVQFANRENAEEALHKLNGTV 115
PF G+IA V+IPVG+G CG N+ E +H +G +
Sbjct: 79 PFQ--GKIACVRIPVGRGVCGTAVARNQVQRIEDVHVFDGHI 118
>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 = 28.9 bits (63), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 16/32 (50%), Positives = 18/32 (56%)
Query: 55 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVK 86
N TIFV GL NVT E + F Q G I + K
Sbjct: 13 NNTIFVQGLGENVTIESVADYFKQIGIIKTNK 44
>pdb|1WHX|A Chain A, Solution Structure Of The Second Rna Binding Domain From
Hypothetical Protein Bab23448
Length = 111
Score = 28.1 bits (61), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 24/57 (42%)
Query: 55 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKL 111
T I L ++++ FS++G + V +P G V+F A +A L
Sbjct: 10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHL 66
>pdb|2E5J|A Chain A, Solution Structure Of Rna Binding Domain In
Methenyltetrahydrofolate Synthetase Domain Containing
Length = 97
Score = 26.9 bits (58), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 17/80 (21%), Positives = 33/80 (41%), Gaps = 1/80 (1%)
Query: 50 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-KGCGFVQFANRENAEEAL 108
EG ++VG L + DL++ + G + G + F+ + + A++A+
Sbjct: 14 EGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAV 73
Query: 109 HKLNGTVIGKQSFRADYGNQ 128
L G +G + R Q
Sbjct: 74 SCLQGLRLGTDTLRVALARQ 93
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation Initiation
Factor 4b
Length = 100
Score = 26.6 bits (57), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 40/79 (50%), Gaps = 9/79 (11%)
Query: 57 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-------KGCGFVQFANRENAEEALH 109
T F+G L +VT+E +++ F I++V++P KG G+ +F + ++ +
Sbjct: 21 TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFED-LDSLLSAL 78
Query: 110 KLNGTVIGKQSFRADYGNQ 128
LN +G + R D +Q
Sbjct: 79 SLNEESLGNRRIRVDVADQ 97
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of Eukaryotic
Initiation Factor 4b
Length = 104
Score = 26.6 bits (57), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 9/79 (11%)
Query: 57 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-------KGCGFVQFANRENAEEALH 109
T F+G L +VT+E +++ F I++V++P KG G+ +F + ++ A
Sbjct: 17 TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA-L 74
Query: 110 KLNGTVIGKQSFRADYGNQ 128
LN +G + R D +Q
Sbjct: 75 SLNEESLGNKRIRVDVADQ 93
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
0.312 0.131 0.393
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,517,318
Number of Sequences: 62578
Number of extensions: 151862
Number of successful extensions: 440
Number of sequences better than 100.0: 186
Number of HSP's better than 100.0 without gapping: 128
Number of HSP's successfully gapped in prelim test: 58
Number of HSP's that attempted gapping in prelim test: 223
Number of HSP's gapped (non-prelim): 213
length of query: 176
length of database: 14,973,337
effective HSP length: 92
effective length of query: 84
effective length of database: 9,216,161
effective search space: 774157524
effective search space used: 774157524
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 48 (23.1 bits)