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= psy7847
(170 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 71.2 bits (173), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 52/166 (31%), Positives = 78/166 (46%), Gaps = 29/166 (17%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L+ GDL DVT+ +L FS L +V RD T ++ G+ +V+F+ P D RA M
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 72
Query: 85 NDDF-----------------------RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVR 121
N D +F +L + ++ L TFS + + L KVV
Sbjct: 73 NFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC 132
Query: 122 DKRTNKTKGFGFVSFKDPQDFIRANKEMNEF----PHLFVGDLKTR 163
D+ N +KG+GFV F+ + RA ++MN +FVG K+R
Sbjct: 133 DE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR 176
>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 = 71.2 bits (173), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 52/166 (31%), Positives = 78/166 (46%), Gaps = 29/166 (17%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L+ GDL DVT+ +L FS L +V RD T ++ G+ +V+F+ P D RA M
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77
Query: 85 NDDF-----------------------RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVR 121
N D +F +L + ++ L TFS + + L KVV
Sbjct: 78 NFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC 137
Query: 122 DKRTNKTKGFGFVSFKDPQDFIRANKEMNEF----PHLFVGDLKTR 163
D+ N +KG+GFV F+ + RA ++MN +FVG K+R
Sbjct: 138 DE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR 181
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 64.3 bits (155), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 43/148 (29%), Positives = 64/148 (43%), Gaps = 24/148 (16%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L+ G+L +T+++L + F K++ DK NK + FV + D A + +
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTL 61
Query: 85 N-----------------------DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVR 121
N D F LF GDL +V DE L F +PS+L V+
Sbjct: 62 NGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW 121
Query: 122 DKRTNKTKGFGFVSFKDPQDFIRANKEM 149
D +T ++G+GFVSF D A M
Sbjct: 122 DMQTGSSRGYGFVSFTSQDDAQNAMDSM 149
Score = 54.3 bits (129), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 28/76 (36%), Positives = 41/76 (53%), Gaps = 2/76 (2%)
Query: 11 SWIKKTCEDEND--FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGF 68
+W ++ + +D F LF GDL +V DE L F +PS+L V+ D +T ++G+GF
Sbjct: 74 NWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGF 133
Query: 69 VSFKDPQDFIRANKEM 84
VSF D A M
Sbjct: 134 VSFTSQDDAQNAMDSM 149
>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 = 63.9 bits (154), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 41/145 (28%), Positives = 72/145 (49%), Gaps = 21/145 (14%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK- 82
++F G L D T++ L F KY + K+++D T +++GFGF+SF+ P K
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 83 ------------------EMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKR 124
E + ++F G +G DV + FS++ + + A+++ DK
Sbjct: 65 QHILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKD 124
Query: 125 TNKTKGFGFVSF--KDPQDFIRANK 147
T +++GFGFV++ D D + NK
Sbjct: 125 TGQSRGFGFVTYDSADAVDRVCQNK 149
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 39/67 (58%), Gaps = 2/67 (2%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF--KDPQ 75
E + ++F G +G DV + FS++ + + A+++ DK T +++GFGFV++ D
Sbjct: 83 EQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAV 142
Query: 76 DFIRANK 82
D + NK
Sbjct: 143 DRVCQNK 149
>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
pdb|3MD1|B Chain B, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
Length = 83
Score = 53.5 bits (127), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 26/62 (41%), Positives = 34/62 (54%)
Query: 23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 82
F LF GDL +V DE L F +PS+L V+ D +T ++G+GFVSF D A
Sbjct: 2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 83 EM 84
M
Sbjct: 62 SM 63
Score = 53.5 bits (127), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 26/62 (41%), Positives = 34/62 (54%)
Query: 88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 147
F LF GDL +V DE L F +PS+L V+ D +T ++G+GFVSF D A
Sbjct: 2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 148 EM 149
M
Sbjct: 62 SM 63
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 53.1 bits (126), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 38/147 (25%), Positives = 60/147 (40%), Gaps = 21/147 (14%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L L D+TD L F +++RD +T + G+ FV F D RA K +
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 85 ND---------------------DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDK 123
N D L+ +L +TD+ L F KY S ++ ++RDK
Sbjct: 66 NGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDK 125
Query: 124 RTNKTKGFGFVSFKDPQDFIRANKEMN 150
T + +G FV + ++ A +N
Sbjct: 126 LTGRPRGVAFVRYNKREEAQEAISALN 152
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 38/76 (50%)
Query: 11 SWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVS 70
S+ + E D L+ +L +TD+ L F KY S ++ ++RDK T + +G FV
Sbjct: 78 SYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVR 137
Query: 71 FKDPQDFIRANKEMND 86
+ ++ A +N+
Sbjct: 138 YNKREEAQEAISALNN 153
>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos
Rna
pdb|1G2E|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The Tumor
Necrosis Factor Alpha Rna
Length = 167
Score = 51.6 bits (122), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 37/147 (25%), Positives = 64/147 (43%), Gaps = 21/147 (14%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L L ++T E F K+VRDK T ++ G+GFV++ DP+D +A +
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 85 ND---------------------DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDK 123
N D L+ L +T + L + FS+Y + ++++ D+
Sbjct: 65 NGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQ 124
Query: 124 RTNKTKGFGFVSFKDPQDFIRANKEMN 150
T ++G GF+ F + A K +N
Sbjct: 125 VTGVSRGVGFIRFDKRIEAEEAIKGLN 151
Score = 33.9 bits (76), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 18/75 (24%), Positives = 37/75 (49%)
Query: 11 SWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVS 70
S+ + + D L+ L +T + L + FS+Y + ++++ D+ T ++G GF+
Sbjct: 77 SYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIR 136
Query: 71 FKDPQDFIRANKEMN 85
F + A K +N
Sbjct: 137 FDKRIEAEEAIKGLN 151
>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 = 50.4 bits (119), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 39/69 (56%)
Query: 20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 79
N F +F GDL ++T E + F+ + A+VV+D T K+KG+GFVSF + D
Sbjct: 13 SNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAEN 72
Query: 80 ANKEMNDDF 88
A ++M +
Sbjct: 73 AIQQMGGQW 81
Score = 50.1 bits (118), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 25/68 (36%), Positives = 41/68 (60%)
Query: 82 KEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
K+ ++ F +F GDL ++T E + F+ + A+VV+D T K+KG+GFVSF + D
Sbjct: 10 KDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWD 69
Query: 142 FIRANKEM 149
A ++M
Sbjct: 70 AENAIQQM 77
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 50.4 bits (119), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 25/66 (37%), Positives = 40/66 (60%)
Query: 85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 144
+D+ +LF G L D ++ L + FSKY + VV+D+ T +++GFGFV+F++ D
Sbjct: 10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 69
Query: 145 ANKEMN 150
A MN
Sbjct: 70 AMMAMN 75
Score = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/62 (38%), Positives = 37/62 (59%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
+LF G L D ++ L + FSKY + VV+D+ T +++GFGFV+F++ D A
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 84 MN 85
MN
Sbjct: 74 MN 75
>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 = 50.1 bits (118), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 38/147 (25%), Positives = 58/147 (39%), Gaps = 21/147 (14%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L L D TD L F ++ RD +T + G+ FV F D RA K +
Sbjct: 17 LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 85 ND---------------------DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDK 123
N D L+ +L +TD+ L F KY S ++ ++RDK
Sbjct: 77 NGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDK 136
Query: 124 RTNKTKGFGFVSFKDPQDFIRANKEMN 150
T + +G FV + ++ A +N
Sbjct: 137 LTGRPRGVAFVRYNKREEAQEAISALN 163
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 38/76 (50%)
Query: 11 SWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVS 70
S+ + E D L+ +L +TD+ L F KY S ++ ++RDK T + +G FV
Sbjct: 89 SYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVR 148
Query: 71 FKDPQDFIRANKEMND 86
+ ++ A +N+
Sbjct: 149 YNKREEAQEAISALNN 164
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 49.7 bits (117), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 38/147 (25%), Positives = 63/147 (42%), Gaps = 26/147 (17%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
E E +LF G L + TDE L F ++ + V+RD T +++GFGFV++ ++
Sbjct: 10 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 69
Query: 78 -----IRANK------------EMNDDFR---------LFCGDLGNDVTDELLIRTFSKY 111
R +K D R +F G + D + L F +Y
Sbjct: 70 DAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 129
Query: 112 PSFLKAKVVRDKRTNKTKGFGFVSFKD 138
+++ D+ + K +GF FV+F D
Sbjct: 130 GKIEVIEIMTDRGSGKKRGFAFVTFDD 156
Score = 43.5 bits (101), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
+LF G L + TDE L F ++ + V+RD T +++GFGFV++ ++ A
Sbjct: 16 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 72
Query: 149 MNEFPH 154
MN PH
Sbjct: 73 MNARPH 78
>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 = 49.7 bits (117), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 38/147 (25%), Positives = 63/147 (42%), Gaps = 26/147 (17%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
E E +LF G L + TDE L F ++ + V+RD T +++GFGFV++ ++
Sbjct: 8 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 67
Query: 78 -----IRANK------------EMNDDFR---------LFCGDLGNDVTDELLIRTFSKY 111
R +K D R +F G + D + L F +Y
Sbjct: 68 DAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 127
Query: 112 PSFLKAKVVRDKRTNKTKGFGFVSFKD 138
+++ D+ + K +GF FV+F D
Sbjct: 128 GKIEVIEIMTDRGSGKKRGFAFVTFDD 154
Score = 43.5 bits (101), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
+LF G L + TDE L F ++ + V+RD T +++GFGFV++ ++ A
Sbjct: 14 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 70
Query: 149 MNEFPH 154
MN PH
Sbjct: 71 MNARPH 76
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 49.7 bits (117), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 38/147 (25%), Positives = 63/147 (42%), Gaps = 26/147 (17%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
E E +LF G L + TDE L F ++ + V+RD T +++GFGFV++ ++
Sbjct: 9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 68
Query: 78 -----IRANK------------EMNDDFR---------LFCGDLGNDVTDELLIRTFSKY 111
R +K D R +F G + D + L F +Y
Sbjct: 69 DAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 128
Query: 112 PSFLKAKVVRDKRTNKTKGFGFVSFKD 138
+++ D+ + K +GF FV+F D
Sbjct: 129 GKIEVIEIMTDRGSGKKRGFAFVTFDD 155
Score = 43.1 bits (100), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
+LF G L + TDE L F ++ + V+RD T +++GFGFV++ ++ A
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 71
Query: 149 MNEFPH 154
MN PH
Sbjct: 72 MNARPH 77
>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 = 49.3 bits (116), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 38/147 (25%), Positives = 63/147 (42%), Gaps = 26/147 (17%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
E E +LF G L + TDE L F ++ + V+RD T +++GFGFV++ ++
Sbjct: 9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 68
Query: 78 -----IRANK------------EMNDDFR---------LFCGDLGNDVTDELLIRTFSKY 111
R +K D R +F G + D + L F +Y
Sbjct: 69 DAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 128
Query: 112 PSFLKAKVVRDKRTNKTKGFGFVSFKD 138
+++ D+ + K +GF FV+F D
Sbjct: 129 GKIEVIEIMTDRGSGKKRGFAFVTFDD 155
Score = 43.5 bits (101), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
+LF G L + TDE L F ++ + V+RD T +++GFGFV++ ++ A
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 71
Query: 149 MNEFPH 154
MN PH
Sbjct: 72 MNARPH 77
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 49.3 bits (116), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 38/147 (25%), Positives = 63/147 (42%), Gaps = 26/147 (17%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
E E +LF G L + TDE L F ++ + V+RD T +++GFGFV++ ++
Sbjct: 7 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 66
Query: 78 -----IRANK------------EMNDDFR---------LFCGDLGNDVTDELLIRTFSKY 111
R +K D R +F G + D + L F +Y
Sbjct: 67 DAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 126
Query: 112 PSFLKAKVVRDKRTNKTKGFGFVSFKD 138
+++ D+ + K +GF FV+F D
Sbjct: 127 GKIEVIEIMTDRGSGKKRGFAFVTFDD 153
Score = 43.1 bits (100), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
+LF G L + TDE L F ++ + V+RD T +++GFGFV++ ++ A
Sbjct: 13 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 69
Query: 149 MNEFPH 154
MN PH
Sbjct: 70 MNARPH 75
>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 = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 38/147 (25%), Positives = 63/147 (42%), Gaps = 26/147 (17%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
E E +LF G L + TDE L F ++ + V+RD T +++GFGFV++ ++
Sbjct: 2 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 61
Query: 78 -----IRANK------------EMNDDFR---------LFCGDLGNDVTDELLIRTFSKY 111
R +K D R +F G + D + L F +Y
Sbjct: 62 DAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 121
Query: 112 PSFLKAKVVRDKRTNKTKGFGFVSFKD 138
+++ D+ + K +GF FV+F D
Sbjct: 122 GKIEVIEIMTDRGSGKKRGFAFVTFDD 148
Score = 43.5 bits (101), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
+LF G L + TDE L F ++ + V+RD T +++GFGFV++ ++ A
Sbjct: 8 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 64
Query: 149 MNEFPH 154
MN PH
Sbjct: 65 MNARPH 70
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 37/69 (53%)
Query: 20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 79
N F +F GDL ++T E + F+ + A+VV+D T K+KG+GFVSF + D
Sbjct: 13 SNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAEN 72
Query: 80 ANKEMNDDF 88
A M +
Sbjct: 73 AIVHMGGQW 81
Score = 48.9 bits (115), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 39/69 (56%)
Query: 82 KEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
K+ ++ F +F GDL ++T E + F+ + A+VV+D T K+KG+GFVSF + D
Sbjct: 10 KDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLD 69
Query: 142 FIRANKEMN 150
A M
Sbjct: 70 AENAIVHMG 78
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/105 (25%), Positives = 51/105 (48%), Gaps = 21/105 (20%)
Query: 53 KVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND---------------------DFRLF 91
K+VRDK T ++ G+GFV++ DP D +A +N D L+
Sbjct: 35 KLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYARPSSASIRDANLY 94
Query: 92 CGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 136
L ++ + + + FS+Y + ++++ D+ T ++G GF+ F
Sbjct: 95 VSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRF 139
Score = 35.8 bits (81), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 32/67 (47%)
Query: 84 MNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 143
M+ L L ++T + F K+VRDK T ++ G+GFV++ DP D
Sbjct: 1 MDSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDAD 60
Query: 144 RANKEMN 150
+A +N
Sbjct: 61 KAINTLN 67
Score = 32.3 bits (72), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 13/61 (21%), Positives = 32/61 (52%)
Query: 11 SWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVS 70
S+ + + D L+ L ++ + + + FS+Y + ++++ D+ T ++G GF+
Sbjct: 79 SYARPSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIR 138
Query: 71 F 71
F
Sbjct: 139 F 139
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/51 (45%), Positives = 32/51 (62%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 74
+LF G L T E L FS+Y + +++DK TN+++GFGFV FKDP
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDP 68
Score = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/51 (45%), Positives = 32/51 (62%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
+LF G L T E L FS+Y + +++DK TN+++GFGFV FKDP
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDP 68
>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 = 47.8 bits (112), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 33/161 (20%), Positives = 63/161 (39%), Gaps = 32/161 (19%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
R++ G + ++ ++ + + F+ + + D T K KGF FV ++ P+ A ++
Sbjct: 30 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 89
Query: 84 MNDDF--------------------------------RLFCGDLGNDVTDELLIRTFSKY 111
MN R++ + D++D+ + F +
Sbjct: 90 MNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAF 149
Query: 112 PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEF 152
A + RD T K KG+GF+ ++ Q A MN F
Sbjct: 150 GKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLF 190
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 1/74 (1%)
Query: 13 IKKTCEDENDF-RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 71
I + E+ F R++ + D++D+ + F + A + RD T K KG+GF+ +
Sbjct: 115 IDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEY 174
Query: 72 KDPQDFIRANKEMN 85
+ Q A MN
Sbjct: 175 EKAQSSQDAVSSMN 188
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 47.4 bits (111), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 42/69 (60%), Gaps = 1/69 (1%)
Query: 17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
E ++ +LF G L + +++L F K+ + +++D RT+K++GF F++F++P D
Sbjct: 2 VEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPAD 60
Query: 77 FIRANKEMN 85
A K+MN
Sbjct: 61 AKNAAKDMN 69
Score = 46.6 bits (109), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 41/68 (60%), Gaps = 1/68 (1%)
Query: 83 EMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 142
E + +LF G L + +++L F K+ + +++D RT+K++GF F++F++P D
Sbjct: 3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADA 61
Query: 143 IRANKEMN 150
A K+MN
Sbjct: 62 KNAAKDMN 69
>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of
Fbp-Interacting Repressor (Fir)
pdb|2KXH|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fir In
The Complex With Fbp Nbox Peptide
Length = 199
Score = 45.8 bits (107), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 32/161 (19%), Positives = 62/161 (38%), Gaps = 32/161 (19%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
R++ G + ++ ++ + + F+ + + D T K KGF FV ++ P+ A ++
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 84 MNDDF--------------------------------RLFCGDLGNDVTDELLIRTFSKY 111
MN R++ + D++D+ + F +
Sbjct: 75 MNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAF 134
Query: 112 PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEF 152
+ RD T K KG+GF+ ++ Q A MN F
Sbjct: 135 GKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLF 175
Score = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 35/80 (43%), Gaps = 1/80 (1%)
Query: 7 GPISSWIKKTCEDENDF-RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKG 65
G I + E+ F R++ + D++D+ + F + + RD T K KG
Sbjct: 94 GQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKG 153
Query: 66 FGFVSFKDPQDFIRANKEMN 85
+GF+ ++ Q A MN
Sbjct: 154 YGFIEYEKAQSSQDAVSSMN 173
>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 = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 40/73 (54%)
Query: 80 ANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
+ KE + LF L + D+ L++ F + + + AKV DK+TN +K FGFVS+ +P
Sbjct: 18 SQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNP 77
Query: 140 QDFIRANKEMNEF 152
A + MN F
Sbjct: 78 VSAQAAIQSMNGF 90
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 36/68 (52%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
E LF L + D+ L++ F + + + AKV DK+TN +K FGFVS+ +P
Sbjct: 21 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSA 80
Query: 78 IRANKEMN 85
A + MN
Sbjct: 81 QAAIQSMN 88
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif In Trna Selenocysteine Associated Protein
Length = 104
Score = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 30/70 (42%), Positives = 37/70 (52%), Gaps = 2/70 (2%)
Query: 22 DFRLFCGDLGNDVTDELLIRTFSK-YPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 80
++ LF GDL DV D +L F K YPS KVV D +T +KG+GFV F D + RA
Sbjct: 9 EYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFVKFTDELEQKRA 67
Query: 81 NKEMNDDFRL 90
E L
Sbjct: 68 LTECQGAVGL 77
Score = 44.3 bits (103), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 29/72 (40%), Positives = 38/72 (52%), Gaps = 2/72 (2%)
Query: 80 ANKEMNDDFRLFCGDLGNDVTDELLIRTFSK-YPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
++ ++ LF GDL DV D +L F K YPS KVV D +T +KG+GFV F D
Sbjct: 2 SSGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFVKFTD 60
Query: 139 PQDFIRANKEMN 150
+ RA E
Sbjct: 61 ELEQKRALTECQ 72
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 44.7 bits (104), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 28/70 (40%), Positives = 37/70 (52%)
Query: 83 EMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 142
E + LF L + TD L TF + + + AKV DK+T+ +K FGFVSF +P
Sbjct: 36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSA 95
Query: 143 IRANKEMNEF 152
A K MN F
Sbjct: 96 QVAIKAMNGF 105
Score = 44.3 bits (103), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 28/71 (39%), Positives = 36/71 (50%)
Query: 15 KTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 74
K E LF L + TD L TF + + + AKV DK+T+ +K FGFVSF +P
Sbjct: 33 KQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNP 92
Query: 75 QDFIRANKEMN 85
A K MN
Sbjct: 93 DSAQVAIKAMN 103
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 43.1 bits (100), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
LF L D T+E L +F ++A++V D+ T +KGFGFV F +D A + M
Sbjct: 18 LFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAM 74
Query: 85 ND 86
D
Sbjct: 75 ED 76
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
LF L D T+E L +F ++A++V D+ T +KGFGFV F +D A + M
Sbjct: 18 LFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAM 74
Query: 150 NE 151
+
Sbjct: 75 ED 76
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 43.1 bits (100), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 36/61 (59%), Gaps = 2/61 (3%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L+ +L + + DE L + FS + + AKV+ + ++KGFGFV F P++ +A EM
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG--GRSKGFGFVCFSSPEEATKAVTEM 75
Query: 85 N 85
N
Sbjct: 76 N 76
Score = 43.1 bits (100), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 36/61 (59%), Gaps = 2/61 (3%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
L+ +L + + DE L + FS + + AKV+ + ++KGFGFV F P++ +A EM
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG--GRSKGFGFVCFSSPEEATKAVTEM 75
Query: 150 N 150
N
Sbjct: 76 N 76
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 43.1 bits (100), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 39/128 (30%), Positives = 56/128 (43%), Gaps = 22/128 (17%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
RLF G+L D+T+E R F +Y + + RD +GFGF+ + A E
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAE 77
Query: 84 MNDDF---------------RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKT 128
++ L +L V++ELL + FS++ KA VV D R T
Sbjct: 78 LDGTILKSRPLRIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRAT 137
Query: 129 KGFGFVSF 136
G GFV F
Sbjct: 138 -GKGFVEF 144
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 30/133 (22%), Positives = 57/133 (42%), Gaps = 21/133 (15%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD-------- 76
L L ++T + L FS AK++RDK + G+GFV++ +D
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 77 -------------FIRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDK 123
+ R + E+ D L+ L +T + + FS++ + ++V+ D+
Sbjct: 65 NGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQ 124
Query: 124 RTNKTKGFGFVSF 136
T ++G F+ F
Sbjct: 125 TTGLSRGVAFIRF 137
Score = 33.9 bits (76), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 30/61 (49%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
L L ++T + L FS AK++RDK + G+GFV++ +D RA +
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 150 N 150
N
Sbjct: 65 N 65
>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 = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 30/133 (22%), Positives = 57/133 (42%), Gaps = 21/133 (15%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD-------- 76
L L ++T + L FS AK++RDK + G+GFV++ +D
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 77 -------------FIRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDK 123
+ R + E+ D L+ L +T + + FS++ + ++V+ D+
Sbjct: 65 NGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQ 124
Query: 124 RTNKTKGFGFVSF 136
T ++G F+ F
Sbjct: 125 TTGLSRGVAFIRF 137
Score = 33.9 bits (76), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 30/61 (49%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
L L ++T + L FS AK++RDK + G+GFV++ +D RA +
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 150 N 150
N
Sbjct: 65 N 65
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 42.4 bits (98), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 38/65 (58%)
Query: 88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 147
RL+ G L ++T+++L F + +++ D T ++KG+GF++F D + +A +
Sbjct: 27 MRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALE 86
Query: 148 EMNEF 152
++N F
Sbjct: 87 QLNGF 91
Score = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 37/63 (58%)
Query: 23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 82
RL+ G L ++T+++L F + +++ D T ++KG+GF++F D + +A +
Sbjct: 27 MRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALE 86
Query: 83 EMN 85
++N
Sbjct: 87 QLN 89
>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 = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 38/76 (50%)
Query: 11 SWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVS 70
S+ + E D L+ +L +TD+ L F KY S ++ ++RDK T + +G FV
Sbjct: 2 SYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVR 61
Query: 71 FKDPQDFIRANKEMND 86
+ ++ A +N+
Sbjct: 62 YNKREEAQEAISALNN 77
Score = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 36/74 (48%)
Query: 77 FIRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 136
+ R E D L+ +L +TD+ L F KY S ++ ++RDK T + +G FV +
Sbjct: 3 YARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRY 62
Query: 137 KDPQDFIRANKEMN 150
++ A +N
Sbjct: 63 NKREEAQEAISALN 76
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 35/72 (48%), Gaps = 7/72 (9%)
Query: 22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 81
D +++ G+LGN+ L R F Y V R+ GF FV F+DP+D A
Sbjct: 73 DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAV 127
Query: 82 KEMNDDFRLFCG 93
+E+ D R CG
Sbjct: 128 REL--DGRTLCG 137
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 5/64 (7%)
Query: 87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 146
D +++ G+LGN+ L R F Y V R+ GF FV F+DP+D A
Sbjct: 73 DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAV 127
Query: 147 KEMN 150
+E++
Sbjct: 128 RELD 131
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 43/78 (55%), Gaps = 6/78 (7%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
+F +L + ++ L TFS + + L KVV D+ N +KG+GFV F+ + RA ++M
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 71
Query: 150 NEF----PHLFVGDLKTR 163
N +FVG K+R
Sbjct: 72 NGMLLNDRKVFVGRFKSR 89
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 42/73 (57%), Gaps = 6/73 (8%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
+F +L + ++ L TFS + + L KVV D+ N +KG+GFV F+ + RA ++M
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 71
Query: 85 N----DDFRLFCG 93
N +D ++F G
Sbjct: 72 NGMLLNDRKVFVG 84
>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
At Ph 6.0
pdb|4F26|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
A Ph 9.0
Length = 115
Score = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 43/78 (55%), Gaps = 6/78 (7%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
+F +L + ++ L TFS + + L KVV D+ N +KG+GFV F+ + RA ++M
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 65
Query: 150 NEF----PHLFVGDLKTR 163
N +FVG K+R
Sbjct: 66 NGMLLNDRKVFVGRFKSR 83
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 42/73 (57%), Gaps = 6/73 (8%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
+F +L + ++ L TFS + + L KVV D+ N +KG+GFV F+ + RA ++M
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 65
Query: 85 N----DDFRLFCG 93
N +D ++F G
Sbjct: 66 NGMLLNDRKVFVG 78
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 37/74 (50%), Gaps = 2/74 (2%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
++E D +F G+L V +E+L F + K + +D R K K FGFV FK P+
Sbjct: 12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKD-REGKPKSFGFVCFKHPESV 70
Query: 78 IRANKEMNDDFRLF 91
A +N RL+
Sbjct: 71 SYAIALLN-GIRLY 83
Score = 37.4 bits (85), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 31/64 (48%), Gaps = 1/64 (1%)
Query: 87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 146
D +F G+L V +E+L F + K + +D R K K FGFV FK P+ A
Sbjct: 16 DRTVFVGNLEARVREEILYELFLQAGPLTKVTICKD-REGKPKSFGFVCFKHPESVSYAI 74
Query: 147 KEMN 150
+N
Sbjct: 75 ALLN 78
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 34/62 (54%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
++F G L TD L + F + +A V+ D++T K++G+GFV+ D RA K+
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 84 MN 85
N
Sbjct: 79 PN 80
Score = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 34/62 (54%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
++F G L TD L + F + +A V+ D++T K++G+GFV+ D RA K+
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 149 MN 150
N
Sbjct: 79 PN 80
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 38/69 (55%), Gaps = 2/69 (2%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
+F G++ + T+E L FS+ + ++V D+ T K KG+GF ++D + + A + +
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 85 NDDFRLFCG 93
N R F G
Sbjct: 71 NG--REFSG 77
Score = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 35/61 (57%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
+F G++ + T+E L FS+ + ++V D+ T K KG+GF ++D + + A + +
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 150 N 150
N
Sbjct: 71 N 71
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 40.0 bits (92), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 35/72 (48%), Gaps = 7/72 (9%)
Query: 22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 81
D +++ G+LGN+ L R F Y V R+ GF FV F+DP+D A
Sbjct: 73 DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAV 127
Query: 82 KEMNDDFRLFCG 93
+++ D R CG
Sbjct: 128 RDL--DGRTLCG 137
Score = 36.2 bits (82), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 5/64 (7%)
Query: 87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 146
D +++ G+LGN+ L R F Y V R+ GF FV F+DP+D A
Sbjct: 73 DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAV 127
Query: 147 KEMN 150
++++
Sbjct: 128 RDLD 131
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 39.7 bits (91), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 37/63 (58%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
L+ G L ++T+++L F + +++D T ++KG+GF++F D + RA +++
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 150 NEF 152
N F
Sbjct: 68 NGF 70
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 36/61 (59%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L+ G L ++T+++L F + +++D T ++KG+GF++F D + RA +++
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 85 N 85
N
Sbjct: 68 N 68
>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2
pdb|3BS9|B Chain B, X-Ray Structure Of Human Tia-1 Rrm2
Length = 87
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 38/68 (55%)
Query: 21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 80
+ F +F GDL ++T + F+ + A+VV+D T K+KG+GFVSF + D A
Sbjct: 5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENA 64
Query: 81 NKEMNDDF 88
++M +
Sbjct: 65 IQQMGGQW 72
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 37/67 (55%)
Query: 84 MNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 143
+ F +F GDL ++T + F+ + A+VV+D T K+KG+GFVSF + D
Sbjct: 3 LGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAE 62
Query: 144 RANKEMN 150
A ++M
Sbjct: 63 NAIQQMG 69
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 28/56 (50%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 80
L+ L TD+ L++ Y + K + DK TNK KG+GFV F P +A
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA 63
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 28/56 (50%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
L+ L TD+ L++ Y + K + DK TNK KG+GFV F P +A
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA 63
>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 = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 30/161 (18%), Positives = 59/161 (36%), Gaps = 32/161 (19%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
R++ G + ++ ++ + + F+ + D T K KGF FV ++ P+ A ++
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 84 MNDDF--------------------------------RLFCGDLGNDVTDELLIRTFSKY 111
N R++ + D++D+ + F +
Sbjct: 74 XNSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAF 133
Query: 112 PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEF 152
+ RD T K KG+GF+ ++ Q A N F
Sbjct: 134 GKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLF 174
Score = 34.7 bits (78), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 1/70 (1%)
Query: 7 GPISSWIKKTCEDENDF-RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKG 65
G I + E+ F R++ + D++D+ + F + + RD T K KG
Sbjct: 93 GQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKG 152
Query: 66 FGFVSFKDPQ 75
+GF+ ++ Q
Sbjct: 153 YGFIEYEKAQ 162
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 37/72 (51%), Gaps = 2/72 (2%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
RLF +L ++E L + FS Y + D T K KGF FV+F P+ ++A E
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 84 MNDDFRLFCGDL 95
+ D ++F G +
Sbjct: 70 V--DGQVFQGRM 79
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 32/62 (51%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
RLF +L ++E L + FS Y + D T K KGF FV+F P+ ++A E
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 149 MN 150
++
Sbjct: 70 VD 71
>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 = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 30/62 (48%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
L+ G L +V D++L F + ++ D T K +GF FV F+ +D A M
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 150 NE 151
NE
Sbjct: 65 NE 66
Score = 37.4 bits (85), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 30/62 (48%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L+ G L +V D++L F + ++ D T K +GF FV F+ +D A M
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 85 ND 86
N+
Sbjct: 65 NE 66
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 30/62 (48%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
L+ G L +V D++L F + ++ D T K +GF FV F+ +D A M
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 150 NE 151
NE
Sbjct: 70 NE 71
Score = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 30/62 (48%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L+ G L +V D++L F + ++ D T K +GF FV F+ +D A M
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 85 ND 86
N+
Sbjct: 70 NE 71
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 30/62 (48%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
L+ G L +V D++L F + ++ D T K +GF FV F+ +D A M
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 150 NE 151
NE
Sbjct: 68 NE 69
Score = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 30/62 (48%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L+ G L +V D++L F + ++ D T K +GF FV F+ +D A M
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 85 ND 86
N+
Sbjct: 68 NE 69
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 30/62 (48%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
L+ G L +V D++L F + ++ D T K +GF FV F+ +D A M
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 150 NE 151
NE
Sbjct: 75 NE 76
Score = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 30/62 (48%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L+ G L +V D++L F + ++ D T K +GF FV F+ +D A M
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 85 ND 86
N+
Sbjct: 75 NE 76
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 30/62 (48%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
L+ G L +V D++L F + ++ D T K +GF FV F+ +D A M
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 150 NE 151
NE
Sbjct: 126 NE 127
Score = 37.0 bits (84), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 30/62 (48%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L+ G L +V D++L F + ++ D T K +GF FV F+ +D A M
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 85 ND 86
N+
Sbjct: 126 NE 127
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 31/60 (51%)
Query: 79 RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
R + + ++F G L T E L F ++ + V+RD T +++GFGFV+F D
Sbjct: 17 RGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMD 76
Score = 37.4 bits (85), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 28/50 (56%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 73
++F G L T E L F ++ + V+RD T +++GFGFV+F D
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMD 76
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 37/65 (56%), Gaps = 5/65 (7%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD---PQDFIRA- 80
++ +L +T+ L R FSKY +K +++DK T K+KG F+ F D Q+ RA
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 81 -NKEM 84
NK++
Sbjct: 79 NNKQL 83
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 37/65 (56%), Gaps = 5/65 (7%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD---PQDFIRA- 145
++ +L +T+ L R FSKY +K +++DK T K+KG F+ F D Q+ RA
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 146 -NKEM 149
NK++
Sbjct: 79 NNKQL 83
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 37/80 (46%), Gaps = 4/80 (5%)
Query: 82 KEMNDDFR-LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
K + FR LF G L + T+E L + ++ V+RD + +++GFGFV+F
Sbjct: 21 KREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTF---S 77
Query: 141 DFIRANKEMNEFPHLFVGDL 160
+ M PH G +
Sbjct: 78 SMAEVDAAMAARPHSIDGRV 97
Score = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 32/58 (55%)
Query: 14 KKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 71
+K E E +LF G L + T+E L + ++ V+RD + +++GFGFV+F
Sbjct: 19 RKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTF 76
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 36/128 (28%), Positives = 56/128 (43%), Gaps = 22/128 (17%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
RLF G+L D+T+E + + F KY + + +D KGFGF+ + A E
Sbjct: 24 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 77
Query: 84 MND--------DFRLFCG-------DLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKT 128
+++ R C +L V++ELL FS + +A V+ D R +
Sbjct: 78 LDNMPLRGKQLRVRFACHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDDR-GRP 136
Query: 129 KGFGFVSF 136
G G V F
Sbjct: 137 SGKGIVEF 144
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 41/88 (46%), Gaps = 18/88 (20%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
LF +L N VT+E+L + FS++ +R K K + F+ F + ++A +EM
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKL--------ERVKKLKDYAFIHFDERDGAVKAMEEM 65
Query: 85 NDDFRLFCGDLGNDVTDELLIRTFSKYP 112
N G D+ E + F+K P
Sbjct: 66 N----------GKDLEGENIEIVFAKPP 83
Score = 35.8 bits (81), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 8/61 (13%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
LF +L N VT+E+L + FS++ +R K K + F+ F + ++A +EM
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKL--------ERVKKLKDYAFIHFDERDGAVKAMEEM 65
Query: 150 N 150
N
Sbjct: 66 N 66
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 27/49 (55%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 73
++ G+L T E + FS++ K++ D+ T K KGFGFV ++
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE 52
Score = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 27/49 (55%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
++ G+L T E + FS++ K++ D+ T K KGFGFV ++
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE 52
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 28/50 (56%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 73
++F G L T E L F ++ + V+RD T +++GFGFV+F D
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMD 51
Score = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 28/50 (56%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
++F G L T E L F ++ + V+RD T +++GFGFV+F D
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMD 51
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 37.0 bits (84), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 2/79 (2%)
Query: 81 NKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
N+ +D+ + +L D + L F + S + + +DK T ++KGF F+SF +
Sbjct: 9 NRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRE 68
Query: 141 DFIRANKEMNEFP--HLFV 157
D RA ++ F HL +
Sbjct: 69 DAARAIAGVSGFGYDHLIL 87
Score = 33.1 bits (74), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 2/71 (2%)
Query: 10 SSWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFV 69
SS + +D R+ +L D + L F + S + + +DK T ++KGF F+
Sbjct: 5 SSGPNRRADDNATIRVT--NLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFI 62
Query: 70 SFKDPQDFIRA 80
SF +D RA
Sbjct: 63 SFHRREDAARA 73
>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 = 36.6 bits (83), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 32/62 (51%)
Query: 78 IRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFK 137
I A+K D + F G L D + + L F+K+ + + D T +++GFGF+ FK
Sbjct: 2 INASKNEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFK 61
Query: 138 DP 139
D
Sbjct: 62 DA 63
Score = 33.5 bits (75), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 32/62 (51%)
Query: 13 IKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFK 72
I + +E+ + F G L D + + L F+K+ + + D T +++GFGF+ FK
Sbjct: 2 INASKNEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFK 61
Query: 73 DP 74
D
Sbjct: 62 DA 63
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 36.6 bits (83), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 36/65 (55%), Gaps = 1/65 (1%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKA-KVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
+F G+L ++ ++LL TFS + L+ K++RD T +KG+ F++F A +
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 84 MNDDF 88
MN +
Sbjct: 68 MNGQY 72
Score = 36.2 bits (82), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 31/49 (63%), Gaps = 1/49 (2%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKA-KVVRDKRTNKTKGFGFVSFK 137
+F G+L ++ ++LL TFS + L+ K++RD T +KG+ F++F
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFA 56
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 36.2 bits (82), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 32/67 (47%)
Query: 84 MNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 143
M+ L L ++T + F K+VRDK T ++ G+GFV++ DP D
Sbjct: 1 MDSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDAD 60
Query: 144 RANKEMN 150
+A +N
Sbjct: 61 KAINTLN 67
Score = 35.4 bits (80), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 23/33 (69%)
Query: 53 KVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
K+VRDK T ++ G+GFV++ DP D +A +N
Sbjct: 35 KLVRDKITGQSLGYGFVNYSDPNDADKAINTLN 67
>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|6 Chain 6, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|7 Chain 7, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|8 Chain 8, Crystal Structure Of Human Spliceosomal U1 Snrnp
Length = 216
Score = 35.8 bits (81), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 29/61 (47%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
LF + D T+ L R F Y + +V KR+ K +G+ F+ ++ +D A K
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 85 N 85
+
Sbjct: 165 D 165
Score = 35.8 bits (81), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 29/61 (47%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
LF + D T+ L R F Y + +V KR+ K +G+ F+ ++ +D A K
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 150 N 150
+
Sbjct: 165 D 165
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 35.0 bits (79), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 8/61 (13%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
LF +L VT+E+L ++FS++ +R K K + FV F+D ++A EM
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKL--------ERVKKLKDYAFVHFEDRGAAVKAMDEM 69
Query: 85 N 85
N
Sbjct: 70 N 70
Score = 35.0 bits (79), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 8/61 (13%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
LF +L VT+E+L ++FS++ +R K K + FV F+D ++A EM
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKL--------ERVKKLKDYAFVHFEDRGAAVKAMDEM 69
Query: 150 N 150
N
Sbjct: 70 N 70
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 35.0 bits (79), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 35/70 (50%), Gaps = 6/70 (8%)
Query: 81 NKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
N+ + ++CG + + +TD+L+ +TFS + ++ +V + KG+ FV F +
Sbjct: 19 NQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHE 72
Query: 141 DFIRANKEMN 150
A +N
Sbjct: 73 SAAHAIVSVN 82
Score = 33.9 bits (76), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 32/61 (52%), Gaps = 6/61 (9%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
++CG + + +TD+L+ +TFS + ++ +V + KG+ FV F + A +
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSV 81
Query: 85 N 85
N
Sbjct: 82 N 82
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 35.0 bits (79), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 15/63 (23%), Positives = 34/63 (53%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
++ G + D T+E ++ S + K++ D +T ++KG+ F+ F+D + A + +
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 150 NEF 152
N +
Sbjct: 65 NGY 67
Score = 34.3 bits (77), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 33/61 (54%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
++ G + D T+E ++ S + K++ D +T ++KG+ F+ F+D + A + +
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 85 N 85
N
Sbjct: 65 N 65
>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 = 34.7 bits (78), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 15/63 (23%), Positives = 34/63 (53%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
++ G + D T+E ++ S + K++ D +T ++KG+ F+ F+D + A + +
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 150 NEF 152
N +
Sbjct: 67 NGY 69
Score = 34.3 bits (77), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 33/61 (54%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
++ G + D T+E ++ S + K++ D +T ++KG+ F+ F+D + A + +
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 85 N 85
N
Sbjct: 67 N 67
>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 = 34.7 bits (78), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 15/63 (23%), Positives = 34/63 (53%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
++ G + D T+E ++ S + K++ D +T ++KG+ F+ F+D + A + +
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 150 NEF 152
N +
Sbjct: 66 NGY 68
Score = 33.9 bits (76), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 33/61 (54%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
++ G + D T+E ++ S + K++ D +T ++KG+ F+ F+D + A + +
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 85 N 85
N
Sbjct: 66 N 66
>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 = 34.7 bits (78), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 29/61 (47%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
LF + D T+ L R F Y + +V KR+ K +G+ F+ ++ +D A K
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 85 N 85
+
Sbjct: 165 D 165
Score = 34.7 bits (78), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 29/61 (47%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
LF + D T+ L R F Y + +V KR+ K +G+ F+ ++ +D A K
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 150 N 150
+
Sbjct: 165 D 165
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor
9g8
Length = 101
Score = 34.3 bits (77), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 33/72 (45%), Gaps = 7/72 (9%)
Query: 23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 82
+++ G+LG L R FS Y + R+ GF FV F+DP+D A +
Sbjct: 1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVR 55
Query: 83 EMNDDFRLFCGD 94
+ D ++ CG
Sbjct: 56 GL--DGKVICGS 65
Score = 32.0 bits (71), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 25/54 (46%), Gaps = 5/54 (9%)
Query: 88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
+++ G+LG L R FS Y + R+ GF FV F+DP+D
Sbjct: 1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRD 49
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 34.3 bits (77), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 100 TDELLIRT-FSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEF 152
DE+ +R F +Y K+V D+ T +++G+GFV F+ +A +N F
Sbjct: 54 VDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGF 107
Score = 32.3 bits (72), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 35 TDELLIRT-FSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
DE+ +R F +Y K+V D+ T +++G+GFV F+ +A +N
Sbjct: 54 VDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLN 105
>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 = 33.9 bits (76), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 35/69 (50%), Gaps = 3/69 (4%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
+F G L D T + L FSK+ + + D T +++GFGFV FK+ + +K M
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESE---SVDKVM 58
Query: 150 NEFPHLFVG 158
++ H G
Sbjct: 59 DQKEHKLNG 67
Score = 32.7 bits (73), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 28/51 (54%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 75
+F G L D T + L FSK+ + + D T +++GFGFV FK+ +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESE 52
>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 = 33.9 bits (76), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 30/61 (49%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L L ++T + L FS AK++RDK + G+GFV++ +D RA +
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 85 N 85
N
Sbjct: 67 N 67
Score = 33.9 bits (76), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 30/61 (49%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
L L ++T + L FS AK++RDK + G+GFV++ +D RA +
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 150 N 150
N
Sbjct: 67 N 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 = 33.5 bits (75), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 24/54 (44%), Positives = 34/54 (62%), Gaps = 5/54 (9%)
Query: 25 LFCGDLGNDV-TDELLIRTF-SKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
+F G G DV DE IR+F ++Y S + K++ D RT +KG+GFVSF + D
Sbjct: 12 VFVG--GIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVD 62
Score = 33.5 bits (75), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 24/54 (44%), Positives = 34/54 (62%), Gaps = 5/54 (9%)
Query: 90 LFCGDLGNDV-TDELLIRTF-SKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
+F G G DV DE IR+F ++Y S + K++ D RT +KG+GFVSF + D
Sbjct: 12 VFVG--GIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVD 62
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 33.5 bits (75), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
+F G L + T E + F ++ A ++ DK TN+ +GFGFV+F + +D + E+
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF-ESEDIVEKVCEI 60
Query: 85 N 85
+
Sbjct: 61 H 61
Score = 33.5 bits (75), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
+F G L + T E + F ++ A ++ DK TN+ +GFGFV+F + +D + E+
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF-ESEDIVEKVCEI 60
Query: 150 N 150
+
Sbjct: 61 H 61
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 33.5 bits (75), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 24/54 (44%), Positives = 34/54 (62%), Gaps = 5/54 (9%)
Query: 25 LFCGDLGNDV-TDELLIRTF-SKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
+F G G DV DE IR+F ++Y S + K++ D RT +KG+GFVSF + D
Sbjct: 13 VFVG--GIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVD 63
Score = 33.5 bits (75), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 24/54 (44%), Positives = 34/54 (62%), Gaps = 5/54 (9%)
Query: 90 LFCGDLGNDV-TDELLIRTF-SKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
+F G G DV DE IR+F ++Y S + K++ D RT +KG+GFVSF + D
Sbjct: 13 VFVG--GIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVD 63
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 33.5 bits (75), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 2/72 (2%)
Query: 79 RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
RAN + N +F L T+ L FSKY +V D+++ +++GF FV F++
Sbjct: 6 RANPDPNCCLGVF--GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 63
Query: 139 PQDFIRANKEMN 150
D A + N
Sbjct: 64 VDDAKEAKERAN 75
Score = 33.1 bits (74), Expect = 0.076, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 27/52 (51%)
Query: 34 VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
T+ L FSKY +V D+++ +++GF FV F++ D A + N
Sbjct: 24 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERAN 75
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 33.5 bits (75), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 2/72 (2%)
Query: 79 RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
RAN + N +F L T+ L FSKY +V D+++ +++GF FV F++
Sbjct: 9 RANPDPNCCLGVF--GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 66
Query: 139 PQDFIRANKEMN 150
D A + N
Sbjct: 67 VDDAKEAKERAN 78
Score = 33.1 bits (74), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 27/52 (51%)
Query: 34 VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
T+ L FSKY +V D+++ +++GF FV F++ D A + N
Sbjct: 27 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERAN 78
>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Rna, Uuguucuu
Length = 102
Score = 33.1 bits (74), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 24/54 (44%), Positives = 34/54 (62%), Gaps = 5/54 (9%)
Query: 25 LFCGDLGNDV-TDELLIRTF-SKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
+F G G DV DE IR+F ++Y S + K++ D RT +KG+GFVSF + D
Sbjct: 12 VFVG--GIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVD 62
Score = 33.1 bits (74), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 24/54 (44%), Positives = 34/54 (62%), Gaps = 5/54 (9%)
Query: 90 LFCGDLGNDV-TDELLIRTF-SKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
+F G G DV DE IR+F ++Y S + K++ D RT +KG+GFVSF + D
Sbjct: 12 VFVG--GIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVD 62
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 33.1 bits (74), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 27/52 (51%)
Query: 34 VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
T+ L FSKY +V D+++ +++GF FV F++ D A + N
Sbjct: 27 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERAN 78
Score = 33.1 bits (74), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 27/52 (51%)
Query: 99 VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
T+ L FSKY +V D+++ +++GF FV F++ D A + N
Sbjct: 27 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERAN 78
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 33.1 bits (74), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 2/72 (2%)
Query: 79 RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
RAN + N +F L T+ L FSKY +V D+++ +++GF FV F++
Sbjct: 40 RANPDPNCCLGVF--GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 97
Query: 139 PQDFIRANKEMN 150
D A + N
Sbjct: 98 VDDAKEAKERAN 109
Score = 33.1 bits (74), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 27/52 (51%)
Query: 34 VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
T+ L FSKY +V D+++ +++GF FV F++ D A + N
Sbjct: 58 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERAN 109
>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 = 33.1 bits (74), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 29/61 (47%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L L + T + L FS AK++RDK + G+GFV++ +D RA +
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 85 N 85
N
Sbjct: 82 N 82
Score = 33.1 bits (74), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 29/61 (47%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
L L + T + L FS AK++RDK + G+GFV++ +D RA +
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 150 N 150
N
Sbjct: 82 N 82
>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain
Of Hnrnp D (Auf1) With Telomere Dna
pdb|1X0F|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain
Of Hnrnp D(Auf1) With Telomeric Dna
Length = 79
Score = 32.7 bits (73), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 28/52 (53%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 75
++F G L D +E + F + ++ D +TNK +GF F++FK+ +
Sbjct: 3 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEE 54
Score = 32.7 bits (73), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 28/52 (53%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
++F G L D +E + F + ++ D +TNK +GF F++FK+ +
Sbjct: 3 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEE 54
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 32.7 bits (73), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 30/57 (52%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 80
++F G + ++ + L F K+ + ++ D + +GFGF++F+D Q +A
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQA 68
Score = 32.7 bits (73), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 30/57 (52%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
++F G + ++ + L F K+ + ++ D + +GFGF++F+D Q +A
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQA 68
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 32.3 bits (72), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 2/71 (2%)
Query: 10 SSWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFV 69
SS +K+ + +D + L T++ L FS + L +V +D +T +KGFGFV
Sbjct: 5 SSGVKRAVQKTSDLIVL--GLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFV 62
Query: 70 SFKDPQDFIRA 80
F + + ++
Sbjct: 63 RFTEYETQVKV 73
Score = 30.8 bits (68), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 26/47 (55%)
Query: 99 VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
T++ L FS + L +V +D +T +KGFGFV F + + ++
Sbjct: 27 TTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKV 73
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 32.3 bits (72), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 27/61 (44%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L L D+TD L F +++RD +T + G+ FV F D RA K +
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 85 N 85
N
Sbjct: 66 N 66
Score = 32.3 bits (72), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 27/61 (44%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
L L D+TD L F +++RD +T + G+ FV F D RA K +
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 150 N 150
N
Sbjct: 66 N 66
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 32.3 bits (72), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 27/51 (52%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 75
+F G L D +E + F + ++ D +TNK +GF F++FK+ +
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEE 52
Score = 32.3 bits (72), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 27/51 (52%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
+F G L D +E + F + ++ D +TNK +GF F++FK+ +
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEE 52
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 32.0 bits (71), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 25/49 (51%)
Query: 37 ELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
+ L R F KY + RD+ T +++GF FV F D +D A M+
Sbjct: 85 DTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMD 133
Score = 32.0 bits (71), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 25/49 (51%)
Query: 102 ELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
+ L R F KY + RD+ T +++GF FV F D +D A M+
Sbjct: 85 DTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMD 133
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 32.0 bits (71), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 5/70 (7%)
Query: 84 MNDDFR---LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
M DD + L+ G+L DVT+ L+++ FS+ K++ + +N + FV F + +
Sbjct: 9 MEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHR 66
Query: 141 DFIRANKEMN 150
D A MN
Sbjct: 67 DAAAALAAMN 76
Score = 32.0 bits (71), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 3/69 (4%)
Query: 18 EDENDFR-LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
ED+ R L+ G+L DVT+ L+++ FS+ K++ + +N + FV F + +D
Sbjct: 10 EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRD 67
Query: 77 FIRANKEMN 85
A MN
Sbjct: 68 AAAALAAMN 76
>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 = 32.0 bits (71), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 26/52 (50%)
Query: 34 VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
+ + L R F KY + RD+ T +++GF FV F D +D A M+
Sbjct: 59 TSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMD 110
Score = 32.0 bits (71), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 26/52 (50%)
Query: 99 VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
+ + L R F KY + RD+ T +++GF FV F D +D A M+
Sbjct: 59 TSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMD 110
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 31.6 bits (70), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 32/67 (47%), Gaps = 13/67 (19%)
Query: 24 RLFCGDLG-NDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA-- 80
RLF G+L +V+ E L R FS Y ++ N FGF+ F +PQ A
Sbjct: 24 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQ--------INIKNAFGFIQFDNPQSVRDAIE 75
Query: 81 --NKEMN 85
++EMN
Sbjct: 76 XESQEMN 82
Score = 31.6 bits (70), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 32/67 (47%), Gaps = 13/67 (19%)
Query: 89 RLFCGDLG-NDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA-- 145
RLF G+L +V+ E L R FS Y ++ N FGF+ F +PQ A
Sbjct: 24 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQ--------INIKNAFGFIQFDNPQSVRDAIE 75
Query: 146 --NKEMN 150
++EMN
Sbjct: 76 XESQEMN 82
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 31.6 bits (70), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 34/160 (21%), Positives = 65/160 (40%), Gaps = 28/160 (17%)
Query: 19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN--KTKGFGFVSF----- 71
D + ++F G + +++ L F +Y + + V+RD+ N ++KG FV+F
Sbjct: 12 DLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKA 71
Query: 72 -----------------KDPQDFIRANKEMN---DDFRLFCGDLGNDVTDELLIRTFSKY 111
P A+ E N +D +LF G + T+ + FS +
Sbjct: 72 ALEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSF 131
Query: 112 PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNE 151
+ +++R ++G FV+F A K M++
Sbjct: 132 GQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQ 170
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 31.2 bits (69), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 32/67 (47%), Gaps = 13/67 (19%)
Query: 24 RLFCGDLG-NDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA-- 80
RLF G+L +V+ E L R FS Y ++ N FGF+ F +PQ A
Sbjct: 24 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQ--------INIKNAFGFIQFDNPQSVRDAIE 75
Query: 81 --NKEMN 85
++EMN
Sbjct: 76 CESQEMN 82
Score = 31.2 bits (69), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 32/67 (47%), Gaps = 13/67 (19%)
Query: 89 RLFCGDLG-NDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA-- 145
RLF G+L +V+ E L R FS Y ++ N FGF+ F +PQ A
Sbjct: 24 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQ--------INIKNAFGFIQFDNPQSVRDAIE 75
Query: 146 --NKEMN 150
++EMN
Sbjct: 76 CESQEMN 82
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 31.2 bits (69), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 32/67 (47%), Gaps = 13/67 (19%)
Query: 24 RLFCGDLG-NDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA-- 80
RLF G+L +V+ E L R FS Y ++ N FGF+ F +PQ A
Sbjct: 4 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQ--------INIKNAFGFIQFDNPQSVRDAIE 55
Query: 81 --NKEMN 85
++EMN
Sbjct: 56 CESQEMN 62
Score = 31.2 bits (69), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 32/67 (47%), Gaps = 13/67 (19%)
Query: 89 RLFCGDLG-NDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA-- 145
RLF G+L +V+ E L R FS Y ++ N FGF+ F +PQ A
Sbjct: 4 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQ--------INIKNAFGFIQFDNPQSVRDAIE 55
Query: 146 --NKEMN 150
++EMN
Sbjct: 56 CESQEMN 62
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 31.2 bits (69), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 32/67 (47%), Gaps = 13/67 (19%)
Query: 24 RLFCGDLG-NDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA-- 80
RLF G+L +V+ E L R FS Y ++ N FGF+ F +PQ A
Sbjct: 12 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQ--------INIKNAFGFIQFDNPQSVRDAIE 63
Query: 81 --NKEMN 85
++EMN
Sbjct: 64 CESQEMN 70
Score = 31.2 bits (69), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 32/67 (47%), Gaps = 13/67 (19%)
Query: 89 RLFCGDLG-NDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA-- 145
RLF G+L +V+ E L R FS Y ++ N FGF+ F +PQ A
Sbjct: 12 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQ--------INIKNAFGFIQFDNPQSVRDAIE 63
Query: 146 --NKEMN 150
++EMN
Sbjct: 64 CESQEMN 70
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 31.2 bits (69), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 12/50 (24%), Positives = 28/50 (56%)
Query: 22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 71
D L+ L ++ + + + FS+Y + ++++ D+ T ++G GF+ F
Sbjct: 1 DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRF 50
Score = 31.2 bits (69), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 12/50 (24%), Positives = 28/50 (56%)
Query: 87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 136
D L+ L ++ + + + FS+Y + ++++ D+ T ++G GF+ F
Sbjct: 1 DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRF 50
>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 = 31.2 bits (69), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 6/65 (9%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
RLF G+L D+T+E + + F KY + + +D KGFGF+ + A E
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 70
Query: 149 MNEFP 153
++ P
Sbjct: 71 LDNMP 75
Score = 30.4 bits (67), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 27/49 (55%), Gaps = 6/49 (12%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFK 72
RLF G+L D+T+E + + F KY + + +D KGFGF+ +
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLE 59
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 30.8 bits (68), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 32/68 (47%), Gaps = 7/68 (10%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNK-----TKGFGFVSFKDPQDFIR 79
LF +L T+E L FSK + + K+ NK + GFGFV +K P+ +
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTI--SKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 80 ANKEMNDD 87
A K++
Sbjct: 66 ALKQLQGH 73
Score = 30.8 bits (68), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 32/66 (48%), Gaps = 7/66 (10%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNK-----TKGFGFVSFKDPQDFIR 144
LF +L T+E L FSK + + K+ NK + GFGFV +K P+ +
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTI--SKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 145 ANKEMN 150
A K++
Sbjct: 66 ALKQLQ 71
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 30.8 bits (68), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 33/156 (21%), Positives = 63/156 (40%), Gaps = 28/156 (17%)
Query: 23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN--KTKGFGFVSF--------- 71
++F G + +++ L F +Y + + V+RD+ N ++KG FV+F
Sbjct: 4 IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Query: 72 -------------KDPQDFIRANKEMN---DDFRLFCGDLGNDVTDELLIRTFSKYPSFL 115
P A+ E N +D +LF G + T+ + FS +
Sbjct: 64 QNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIE 123
Query: 116 KAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNE 151
+ +++R ++G FV+F A K M++
Sbjct: 124 ECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQ 158
Score = 29.6 bits (65), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 35/68 (51%), Gaps = 2/68 (2%)
Query: 85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN--KTKGFGFVSFKDPQDF 142
+D ++F G + +++ L F +Y + + V+RD+ N ++KG FV+F +
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 143 IRANKEMN 150
+ A ++
Sbjct: 61 LEAQNALH 68
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14
Complex
Length = 110
Score = 30.8 bits (68), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 18/85 (21%), Positives = 34/85 (40%), Gaps = 14/85 (16%)
Query: 4 LRPGP---ISSWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRT 60
L PGP + WI LF + + ++ + F Y + D+RT
Sbjct: 16 LEPGPQRSVEGWI-----------LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRT 64
Query: 61 NKTKGFGFVSFKDPQDFIRANKEMN 85
+KG+ V ++ + + A + +N
Sbjct: 65 GFSKGYALVEYETHKQALAAKEALN 89
>pdb|2KPK|A Chain A, Magi-1 Pdz1
pdb|2KPL|A Chain A, Magi-1 Pdz1 E6CT
Length = 129
Score = 30.8 bits (68), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 2/62 (3%)
Query: 108 FSKYPSFLKAKVVRDKRTNKTKGFGF--VSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS 165
F++ PS LK K + K ++GFGF V +P +F++ + + P G ++T
Sbjct: 8 FTRNPSELKGKFIHTKLRKSSRGFGFTVVGGDEPDEFLQIKSLVLDGPAALDGKMETGDV 67
Query: 166 IT 167
I
Sbjct: 68 IV 69
Score = 28.9 bits (63), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 7/70 (10%)
Query: 43 FSKYPSFLKAKVVRDKRTNKTKGFGF--VSFKDPQDFIRANKEMND-----DFRLFCGDL 95
F++ PS LK K + K ++GFGF V +P +F++ + D D ++ GD+
Sbjct: 8 FTRNPSELKGKFIHTKLRKSSRGFGFTVVGGDEPDEFLQIKSLVLDGPAALDGKMETGDV 67
Query: 96 GNDVTDELLI 105
V D ++
Sbjct: 68 IVSVNDTCVL 77
>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 = 30.4 bits (67), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 18/85 (21%), Positives = 34/85 (40%), Gaps = 14/85 (16%)
Query: 4 LRPGP---ISSWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRT 60
L PGP + WI LF + + ++ + F Y + D+RT
Sbjct: 62 LEPGPQRSVEGWI-----------LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRT 110
Query: 61 NKTKGFGFVSFKDPQDFIRANKEMN 85
+KG+ V ++ + + A + +N
Sbjct: 111 GFSKGYALVEYETHKQALAAKEALN 135
Score = 26.2 bits (56), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 12/61 (19%), Positives = 27/61 (44%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
LF + + ++ + F Y + D+RT +KG+ V ++ + + A + +
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 150 N 150
N
Sbjct: 135 N 135
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 30.4 bits (67), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 31/68 (45%), Gaps = 5/68 (7%)
Query: 6 PGPISSWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKG 65
PG +S+ + + +LF G L N + D+ + + + +V+D T +KG
Sbjct: 103 PGVVSTVVPDSAH-----KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKG 157
Query: 66 FGFVSFKD 73
+ F + D
Sbjct: 158 YAFCEYVD 165
Score = 27.7 bits (60), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 13/50 (26%), Positives = 24/50 (48%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
+LF G L N + D+ + + + +V+D T +KG+ F + D
Sbjct: 116 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVD 165
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 29.6 bits (65), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 21/47 (44%)
Query: 39 LIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
L R F KY + R+ T +GF FV F D +D A M+
Sbjct: 30 LRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMD 76
Score = 29.6 bits (65), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 21/47 (44%)
Query: 104 LIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
L R F KY + R+ T +GF FV F D +D A M+
Sbjct: 30 LRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMD 76
>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 = 29.6 bits (65), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 30/54 (55%), Gaps = 2/54 (3%)
Query: 85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN--KTKGFGFVSF 136
+D ++F G + +++ L F +Y + + V+RD+ N ++KG FV+F
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTF 54
Score = 28.1 bits (61), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 15/66 (22%), Positives = 34/66 (51%), Gaps = 2/66 (3%)
Query: 23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN--KTKGFGFVSFKDPQDFIRA 80
++F G + +++ L F +Y + + V+RD+ N ++KG FV+F + + A
Sbjct: 4 IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Query: 81 NKEMND 86
+++
Sbjct: 64 QNALHN 69
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 29.6 bits (65), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 20/86 (23%), Positives = 36/86 (41%), Gaps = 14/86 (16%)
Query: 3 GLRPGP---ISSWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKR 59
G PGP + WI LF + + T+E + F++Y + D+R
Sbjct: 11 GDEPGPQRSVEGWI-----------LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRR 59
Query: 60 TNKTKGFGFVSFKDPQDFIRANKEMN 85
T KG+ V ++ ++ A + +N
Sbjct: 60 TGYLKGYTLVEYETYKEAQAAMEGLN 85
>pdb|3NVQ|A Chain A, Molecular Mechanism Of Guidance Cue Recognition
pdb|3NVQ|E Chain E, Molecular Mechanism Of Guidance Cue Recognition
Length = 590
Score = 29.3 bits (64), Expect = 1.1, Method: Composition-based stats.
Identities = 25/87 (28%), Positives = 40/87 (45%), Gaps = 6/87 (6%)
Query: 42 TFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDDFRLFCGDLGNDVTD 101
T + P F+KA +V + K + F +P A ++ +L GD G + +
Sbjct: 173 TVMQNPQFIKATIVHQDQAYDDKIYYFFREDNPDKNPEAPLNVSRVAQLCRGDQGGESS- 231
Query: 102 ELLIRTFSKYPSFLKAKVV-RDKRTNK 127
+ SK+ +FLKA +V D TNK
Sbjct: 232 ----LSVSKWNTFLKAMLVCSDAATNK 254
>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 = 28.9 bits (63), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 27/144 (18%), Positives = 53/144 (36%), Gaps = 33/144 (22%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSF-----LKAKVVRDKRTNKTKGFGFVSFKD----- 73
RL+ G++ +T+E ++ F+ V + N+ K F F+ F+
Sbjct: 8 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67
Query: 74 -------------------PQDFIRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSF 114
P D+ + + +LF G L N + D+ + + +
Sbjct: 68 QAMAFDGIIFQGQSLKIRRPHDY----QPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPL 123
Query: 115 LKAKVVRDKRTNKTKGFGFVSFKD 138
+V+D T +KG+ F + D
Sbjct: 124 KAFNLVKDSATGLSKGYAFCEYVD 147
>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 = 28.9 bits (63), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 20/86 (23%), Positives = 36/86 (41%), Gaps = 14/86 (16%)
Query: 3 GLRPGP---ISSWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKR 59
G PGP + WI LF + + T+E + F++Y + D+R
Sbjct: 12 GDEPGPQRSVEGWI-----------LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRR 60
Query: 60 TNKTKGFGFVSFKDPQDFIRANKEMN 85
T KG+ V ++ ++ A + +N
Sbjct: 61 TGYLKGYTLVEYETYKEAQAAMEGLN 86
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 28.9 bits (63), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 4/55 (7%)
Query: 113 SFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT 167
S ++VRDK T+K KGF +V F D + + KE + +GD R I
Sbjct: 40 SIRSVRLVRDKDTDKFKGFCYVEF----DEVDSLKEALTYDGALLGDRSLRVDIA 90
>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 = 28.9 bits (63), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 27/141 (19%), Positives = 57/141 (40%), Gaps = 28/141 (19%)
Query: 23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN--KTKGFGFVSFKDPQDFIRA 80
+ F G + +++ L F +Y + + V+RD+ N ++KG FV+F + + A
Sbjct: 4 IKXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Query: 81 NKEMN-------------------------DDFRLFCGDLGNDVTDELLIRTFSKYPSFL 115
++ +D +LF G + T+ + FS +
Sbjct: 64 QNALHNXKVLPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQIE 123
Query: 116 KAKVVRDKRTNKTKGFGFVSF 136
+ +++R ++G FV+F
Sbjct: 124 ECRILRGP-DGLSRGCAFVTF 143
Score = 28.1 bits (61), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 34/68 (50%), Gaps = 2/68 (2%)
Query: 85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN--KTKGFGFVSFKDPQDF 142
+D + F G + +++ L F +Y + + V+RD+ N ++KG FV+F +
Sbjct: 1 SDAIKXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 143 IRANKEMN 150
+ A ++
Sbjct: 61 LEAQNALH 68
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1
In Complex With Ugcaugu
Length = 109
Score = 28.9 bits (63), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 35/62 (56%), Gaps = 2/62 (3%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
RL ++ D L + F ++ L +++ ++R +KGFGFV+F++ D RA ++
Sbjct: 31 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREK 88
Query: 84 MN 85
++
Sbjct: 89 LH 90
Score = 28.9 bits (63), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 35/62 (56%), Gaps = 2/62 (3%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
RL ++ D L + F ++ L +++ ++R +KGFGFV+F++ D RA ++
Sbjct: 31 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREK 88
Query: 149 MN 150
++
Sbjct: 89 LH 90
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 28.9 bits (63), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 26/140 (18%), Positives = 53/140 (37%), Gaps = 25/140 (17%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSF-----LKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
RL+ G++ +T+E ++ F+ V + N+ K F F+ F+ +
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 79 RA--------------------NKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAK 118
+A + + +LF G L N + D+ + + +
Sbjct: 66 QAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFN 125
Query: 119 VVRDKRTNKTKGFGFVSFKD 138
+V+D T +KG+ F + D
Sbjct: 126 LVKDSATGLSKGYAFCEYVD 145
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 28.9 bits (63), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 35/62 (56%), Gaps = 2/62 (3%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
RL ++ D L + F ++ L +++ ++R +KGFGFV+F++ D RA ++
Sbjct: 17 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREK 74
Query: 84 MN 85
++
Sbjct: 75 LH 76
Score = 28.9 bits (63), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 35/62 (56%), Gaps = 2/62 (3%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
RL ++ D L + F ++ L +++ ++R +KGFGFV+F++ D RA ++
Sbjct: 17 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREK 74
Query: 149 MN 150
++
Sbjct: 75 LH 76
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 28.5 bits (62), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 9/60 (15%)
Query: 85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKG---FGFVSFKDPQD 141
N+D R++ G+L D+ + + F KY +RD +G F FV F+DP+D
Sbjct: 20 NNDCRIYVGNLPPDIRTKDIEDVFYKY------GAIRDIDLKNRRGGPPFAFVEFEDPRD 73
Score = 28.5 bits (62), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 9/59 (15%)
Query: 21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKG---FGFVSFKDPQD 76
ND R++ G+L D+ + + F KY +RD +G F FV F+DP+D
Sbjct: 21 NDCRIYVGNLPPDIRTKDIEDVFYKY------GAIRDIDLKNRRGGPPFAFVEFEDPRD 73
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 28.5 bits (62), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 16/71 (22%), Positives = 30/71 (42%), Gaps = 1/71 (1%)
Query: 8 PISSWIKKTCEDENDFR-LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGF 66
P+ + +E D R +FC L + L FS +++ D+ + ++KG
Sbjct: 10 PVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGI 69
Query: 67 GFVSFKDPQDF 77
+V F + Q
Sbjct: 70 AYVEFCEIQSV 80
Score = 26.6 bits (57), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 16/72 (22%), Positives = 31/72 (43%), Gaps = 2/72 (2%)
Query: 71 FKDPQDFIRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKG 130
++P D + + E D +FC L + L FS +++ D+ + ++KG
Sbjct: 11 VREPVDNL--SPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKG 68
Query: 131 FGFVSFKDPQDF 142
+V F + Q
Sbjct: 69 IAYVEFCEIQSV 80
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 28.1 bits (61), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 10/29 (34%), Positives = 19/29 (65%)
Query: 51 KAKVVRDKRTNKTKGFGFVSFKDPQDFIR 79
+ +++R+K + +++GF FV F QD R
Sbjct: 31 EVRLMRNKSSGQSRGFAFVEFSHLQDATR 59
Score = 28.1 bits (61), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 10/29 (34%), Positives = 19/29 (65%)
Query: 116 KAKVVRDKRTNKTKGFGFVSFKDPQDFIR 144
+ +++R+K + +++GF FV F QD R
Sbjct: 31 EVRLMRNKSSGQSRGFAFVEFSHLQDATR 59
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 28.1 bits (61), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 25 LFCGDLGNDVTDELLIRTFSKY-PSFLKAKVVRDKRTNKTKGFGFVSFKD 73
L+ GDL + + + R F+ + + K++R++ T G+ FV F D
Sbjct: 12 LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFAD 61
Score = 28.1 bits (61), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 90 LFCGDLGNDVTDELLIRTFSKY-PSFLKAKVVRDKRTNKTKGFGFVSFKD 138
L+ GDL + + + R F+ + + K++R++ T G+ FV F D
Sbjct: 12 LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFAD 61
>pdb|3IJP|A Chain A, Crystal Structure Of Dihydrodipicolinate Reductase From
Bartonella Henselae At 2.0a Resolution
pdb|3IJP|B Chain B, Crystal Structure Of Dihydrodipicolinate Reductase From
Bartonella Henselae At 2.0a Resolution
Length = 288
Score = 28.1 bits (61), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 29/70 (41%), Gaps = 1/70 (1%)
Query: 49 FLKAKVVRDKRTNKTKGFGFVSFKDPQ-DFIRANKEMNDDFRLFCGDLGNDVTDELLIRT 107
FL ++ D + + G + F PQ + AN G G T+E I
Sbjct: 73 FLGVRITDDPESAFSNTEGILDFSQPQASVLYANYAAQKSLIHIIGTTGFSKTEEAQIAD 132
Query: 108 FSKYPSFLKA 117
F+KY + +K+
Sbjct: 133 FAKYTTIVKS 142
>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 = 28.1 bits (61), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 2/69 (2%)
Query: 84 MNDDFR-LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 142
M D R ++ G++ T E L F S + ++ DK + KGF ++ F D +
Sbjct: 1 MEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKES- 59
Query: 143 IRANKEMNE 151
+R + ++E
Sbjct: 60 VRTSLALDE 68
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 27.7 bits (60), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 30/66 (45%), Gaps = 4/66 (6%)
Query: 85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 144
+D +LF G LG TDE + + F + + + V+R +KG FV F Q
Sbjct: 10 GEDRKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGP-DGTSKGCAFVKF---QTHAE 65
Query: 145 ANKEMN 150
A +N
Sbjct: 66 AQAAIN 71
Score = 26.9 bits (58), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 29/65 (44%), Gaps = 4/65 (6%)
Query: 21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 80
D +LF G LG TDE + + F + + + V+R +KG FV F Q A
Sbjct: 11 EDRKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGP-DGTSKGCAFVKF---QTHAEA 66
Query: 81 NKEMN 85
+N
Sbjct: 67 QAAIN 71
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 27.7 bits (60), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 30/60 (50%), Gaps = 11/60 (18%)
Query: 23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD---PQDFIR 79
+LF G+L + T++ + F +Y L+ ++++ +GFV +D +D IR
Sbjct: 9 VKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFVHIEDKTAAEDAIR 60
Score = 27.7 bits (60), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 30/60 (50%), Gaps = 11/60 (18%)
Query: 88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD---PQDFIR 144
+LF G+L + T++ + F +Y L+ ++++ +GFV +D +D IR
Sbjct: 9 VKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFVHIEDKTAAEDAIR 60
>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 = 27.3 bits (59), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 16/66 (24%), Positives = 31/66 (46%), Gaps = 1/66 (1%)
Query: 86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
D ++ G++ T E L F S + ++ DK + KGF ++ F D + +R
Sbjct: 5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKES-VRT 63
Query: 146 NKEMNE 151
+ ++E
Sbjct: 64 SLALDE 69
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 26.9 bits (58), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 13/50 (26%), Positives = 24/50 (48%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 73
+LF G L N + D+ + + + +V+D T +KG+ F + D
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVD 52
Score = 26.9 bits (58), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 13/50 (26%), Positives = 24/50 (48%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
+LF G L N + D+ + + + +V+D T +KG+ F + D
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVD 52
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 26.9 bits (58), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 24/48 (50%), Gaps = 3/48 (6%)
Query: 37 ELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
E L+R F S + +V +RT ++KG+GF + RA ++
Sbjct: 113 EELVRPFG---SLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Score = 26.9 bits (58), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 24/48 (50%), Gaps = 3/48 (6%)
Query: 102 ELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
E L+R F S + +V +RT ++KG+GF + RA ++
Sbjct: 113 EELVRPFG---SLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
pdb|3H2U|D Chain D, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
Length = 283
Score = 26.9 bits (58), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 24/48 (50%), Gaps = 3/48 (6%)
Query: 37 ELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
E L+R F S + +V +RT ++KG+GF + RA ++
Sbjct: 111 EELVRPFG---SLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Score = 26.9 bits (58), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 24/48 (50%), Gaps = 3/48 (6%)
Query: 102 ELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
E L+R F S + +V +RT ++KG+GF + RA ++
Sbjct: 111 EELVRPFG---SLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 26.9 bits (58), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 24/48 (50%), Gaps = 3/48 (6%)
Query: 37 ELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
E L+R F S + +V +RT ++KG+GF + RA ++
Sbjct: 113 EELVRPFG---SLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Score = 26.9 bits (58), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 24/48 (50%), Gaps = 3/48 (6%)
Query: 102 ELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
E L+R F S + +V +RT ++KG+GF + RA ++
Sbjct: 113 EELVRPFG---SLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
>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 = 26.6 bits (57), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 31/73 (42%), Gaps = 6/73 (8%)
Query: 13 IKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFK 72
+KK+C L+ G+L T+E + FSK K + DK GF FV +
Sbjct: 36 LKKSCT------LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYY 89
Query: 73 DPQDFIRANKEMN 85
D A + +N
Sbjct: 90 SRADAENAMRYIN 102
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
0.323 0.141 0.426
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,192,329
Number of Sequences: 62578
Number of extensions: 209777
Number of successful extensions: 811
Number of sequences better than 100.0: 133
Number of HSP's better than 100.0 without gapping: 102
Number of HSP's successfully gapped in prelim test: 31
Number of HSP's that attempted gapping in prelim test: 527
Number of HSP's gapped (non-prelim): 279
length of query: 170
length of database: 14,973,337
effective HSP length: 92
effective length of query: 78
effective length of database: 9,216,161
effective search space: 718860558
effective search space used: 718860558
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 bits)