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= psy1188
(230 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 103 bits (258), Expect = 5e-23, Method: Compositional matrix adjust.
Identities = 45/90 (50%), Positives = 67/90 (74%)
Query: 89 TETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITAMNE 148
+ M+KVKVL+VRNL TEE L++AF Q+G++ERVK++KDYAF+HF++R A+ AM E
Sbjct: 5 SSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKDYAFIHFDERDGAVKAMEE 64
Query: 149 LNGQTVAGSTLEVSLAKPPSDKKKKEEILR 178
+NG+ + G +E+ AKPP K+K+ + R
Sbjct: 65 MNGKDLEGENIEIVFAKPPDQKRKERKAQR 94
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 99.8 bits (247), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 49/85 (57%), Positives = 68/85 (80%), Gaps = 1/85 (1%)
Query: 88 DTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITAMN 147
D E M+KVKVL+VRNL TEE L+++F ++G++ERVK++KDYAFVHFEDR A+ AM+
Sbjct: 8 DPEVMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKDYAFVHFEDRGAAVKAMD 67
Query: 148 ELNGQTVAGSTLEVSLAKPPSDKKK 172
E+NG+ + G +E+ LAKPP DKK+
Sbjct: 68 EMNGKEIEGEEIEIVLAKPP-DKKR 91
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 93.6 bits (231), Expect = 7e-20, Method: Compositional matrix adjust.
Identities = 44/81 (54%), Positives = 60/81 (74%), Gaps = 2/81 (2%)
Query: 88 DTETMSKVKVLYVRNLTQYCTEEKLKEAFEQY--GRVERVKRIKDYAFVHFEDRQEAITA 145
D +TMS VK+LYVRNL +EE +++ F G VERVK+I+DYAFVHF +R++A+ A
Sbjct: 8 DEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEA 67
Query: 146 MNELNGQTVAGSTLEVSLAKP 166
M LNG+ + GS +EV+LAKP
Sbjct: 68 MKALNGKVLDGSPIEVTLAKP 88
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 60.5 bits (145), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 27/67 (40%), Positives = 42/67 (62%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITAMNELNGQTVAGS 157
++V N++ CT ++L+ FE+ GRV +KDYAFVH E +A A+ +LNG+ V G
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKDYAFVHMEKEADAKAAIAQLNGKEVKGK 71
Query: 158 TLEVSLA 164
+ V L+
Sbjct: 72 RINVELS 78
>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 = 57.0 bits (136), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 38/114 (33%), Positives = 58/114 (50%), Gaps = 19/114 (16%)
Query: 65 TGKHLLSRGCDIIVDWADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVER 124
TG + RG + + P PD E M+ +KV NLT + + L+ FE+YGRV
Sbjct: 25 TGGQQMGRGS---MSYGRP--PPDVEGMTSLKV---DNLTYRTSPDTLRRVFEKYGRVGD 76
Query: 125 V--------KRIKDYAFVHFEDRQEAITAMNELNGQTVAGSTLEVSLA---KPP 167
V K + +AFV F D+++A AM+ ++G + G L V +A +PP
Sbjct: 77 VYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPP 130
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 54.3 bits (129), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 40/67 (59%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITAMNELNGQTVAGS 157
L+V N++ CT ++L+ FE+YG V +KDYAFVH E ++A+ A+ L+ G
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIVKDYAFVHMERAEDAVEAIRGLDNTEFQGK 72
Query: 158 TLEVSLA 164
+ V L+
Sbjct: 73 RMHVQLS 79
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 53.9 bits (128), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 41/71 (57%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITAMNELNGQTVAGS 157
L++ NL + TE++++ FEQYG+V IK+Y FVH ED+ A A+ L+ + G
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAIRNLHHYKLHGV 70
Query: 158 TLEVSLAKPPS 168
+ V +K S
Sbjct: 71 NINVEASKNKS 81
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 52.0 bits (123), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 31/84 (36%), Positives = 46/84 (54%), Gaps = 6/84 (7%)
Query: 88 DTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVK------RIKDYAFVHFEDRQE 141
D T +V LYV+NL +E+L++AF +G + K R K + FV F +E
Sbjct: 8 DRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEE 67
Query: 142 AITAMNELNGQTVAGSTLEVSLAK 165
A A+ E+NG+ VA L V+LA+
Sbjct: 68 ATKAVTEMNGRIVATKPLYVALAQ 91
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 51.2 bits (121), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 32/91 (35%), Positives = 49/91 (53%), Gaps = 14/91 (15%)
Query: 88 DTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERV--------KRIKDYAFVHFEDR 139
D E M+ +KV NLT + + L+ FE+YGRV V K + +AFV F D+
Sbjct: 66 DVEGMTSLKV---DNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDK 122
Query: 140 QEAITAMNELNGQTVAGSTLEVSLA---KPP 167
++A AM+ ++G + G L V +A +PP
Sbjct: 123 RDAEDAMDAMDGAVLDGRELRVQMARYGRPP 153
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 43/75 (57%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITAMNELNGQTVAGS 157
L+VR E +L E F +G ++ VK + +AFV FE+ + A A+ E++G++ A
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKILNGFAFVEFEEAESAAKAIEEVHGKSFANQ 93
Query: 158 TLEVSLAKPPSDKKK 172
LEV +K P+ + +
Sbjct: 94 PLEVVYSKLPAKRYR 108
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 41/79 (51%), Gaps = 8/79 (10%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
L V L Q T+++ K F G +E K ++D Y FV++ D +A A+N L
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 150 NGQTVAGSTLEVSLAKPPS 168
NG + T++VS A+P S
Sbjct: 67 NGLKLQTKTIKVSYARPSS 85
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 43/82 (52%), Gaps = 8/82 (9%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
L+V L+ E+ L++ F +YG++ V +KD + FV FE+ +A AM +
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 150 NGQTVAGSTLEVSLAKPPSDKK 171
NG++V G + V A SD +
Sbjct: 75 NGKSVDGRQIRVDQAGKSSDNR 96
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 30/87 (34%), Positives = 45/87 (51%), Gaps = 11/87 (12%)
Query: 87 PDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERV--------KRIKDYAFVHFED 138
PD + M +KV NLT + + L+ FE+YGRV V K + +AFV F D
Sbjct: 8 PDVDGMITLKV---DNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHD 64
Query: 139 RQEAITAMNELNGQTVAGSTLEVSLAK 165
R++A A ++G + G L V +A+
Sbjct: 65 RRDAQDAEAAMDGAELDGRELRVQVAR 91
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 43/78 (55%), Gaps = 7/78 (8%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEAITAMNELN 150
L++ L + E+ LK F ++G + V IKD +AF+ FE+ +A A ++N
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 151 GQTVAGSTLEVSLAKPPS 168
G+++ G ++V AK PS
Sbjct: 70 GKSLHGKAIKVEQAKKPS 87
>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic
Granule-Associated Rna Binding Protein 1
pdb|2RNE|A Chain A, Solution Structure Of The Second Rna Recognition Motif
(Rrm) Of Tia-1
Length = 115
Score = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 45/87 (51%), Gaps = 10/87 (11%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
++V +L+ T E +K AF +GR+ + +KD Y FV F ++ +A A+ ++
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 150 NGQTVAGSTLEVSLA--KPPSDKKKKE 174
GQ + G + + A KPP+ K E
Sbjct: 78 GGQWLGGRQIRTNWATRKPPAPKSTYE 104
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 48.1 bits (113), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 28/90 (31%), Positives = 49/90 (54%), Gaps = 11/90 (12%)
Query: 95 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAM 146
++ ++V N+ TEE+LK+ F + G V + + D Y F ++D++ A++AM
Sbjct: 8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAM 67
Query: 147 NELNGQTVAGSTLEVSLAKPPSDKKKKEEI 176
LNG+ +G L V A + +K KEE+
Sbjct: 68 RNLNGREFSGRALRVDNA---ASEKNKEEL 94
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 48.1 bits (113), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 41/79 (51%), Gaps = 8/79 (10%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
L V L Q T+++ K F G +E K ++D Y FV++ D +A A+N L
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 150 NGQTVAGSTLEVSLAKPPS 168
NG + T++VS A+P S
Sbjct: 67 NGLKLQTKTIKVSYARPSS 85
Score = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 42/81 (51%), Gaps = 10/81 (12%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYA--------FVHFEDRQEAITAMNEL 149
LYV L + +++++++ F QYGR+ + + D A F+ F+ R EA A+ L
Sbjct: 93 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 152
Query: 150 NGQTVAGST--LEVSLAKPPS 168
NGQ G+ + V A PS
Sbjct: 153 NGQKPLGAAEPITVKFANNPS 173
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 48.1 bits (113), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 28/80 (35%), Positives = 43/80 (53%), Gaps = 8/80 (10%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
L V L Q T+++L+ F G VE K I+D Y FV++ ++A A+N L
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 150 NGQTVAGSTLEVSLAKPPSD 169
NG + T++VS A+P S+
Sbjct: 65 NGLRLQSKTIKVSYARPSSE 84
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 25/91 (27%), Positives = 43/91 (47%), Gaps = 13/91 (14%)
Query: 76 IIVDWADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD----- 130
I V +A P E + K LY+ L + T++ +++ F ++GR+ + + D
Sbjct: 74 IKVSYARPSSE-----VIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGL 128
Query: 131 ---YAFVHFEDRQEAITAMNELNGQTVAGST 158
AF+ F+ R EA A+ NG GS+
Sbjct: 129 SRGVAFIRFDKRSEAEEAITSFNGHKPPGSS 159
>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 = 48.1 bits (113), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 28/80 (35%), Positives = 43/80 (53%), Gaps = 8/80 (10%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
L V L Q T+++L+ F G VE K I+D Y FV++ ++A A+N L
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 150 NGQTVAGSTLEVSLAKPPSD 169
NG + T++VS A+P S+
Sbjct: 65 NGLRLQSKTIKVSYARPSSE 84
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 25/91 (27%), Positives = 43/91 (47%), Gaps = 13/91 (14%)
Query: 76 IIVDWADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD----- 130
I V +A P E + K LY+ L + T++ +++ F ++GR+ + + D
Sbjct: 74 IKVSYARPSSE-----VIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGL 128
Query: 131 ---YAFVHFEDRQEAITAMNELNGQTVAGST 158
AF+ F+ R EA A+ NG GS+
Sbjct: 129 SRGVAFIRFDKRSEAEEAITSFNGHKPPGSS 159
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 47.4 bits (111), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 42/80 (52%), Gaps = 8/80 (10%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVK--------RIKDYAFVHFEDRQEAITAMNEL 149
LYV +L TE+ L+ FE +GR+E ++ R K Y F+ F D + A A+ +L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 150 NGQTVAGSTLEVSLAKPPSD 169
NG +AG ++V +D
Sbjct: 89 NGFELAGRPMKVGHVTERTD 108
>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos
Rna
pdb|1G2E|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The Tumor
Necrosis Factor Alpha Rna
Length = 167
Score = 47.0 bits (110), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 42/79 (53%), Gaps = 8/79 (10%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
L V L Q T+E+ + F G +E K ++D Y FV++ D ++A A+N L
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 150 NGQTVAGSTLEVSLAKPPS 168
NG + T++VS A+P S
Sbjct: 65 NGLRLQTKTIKVSYARPSS 83
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 38/69 (55%), Gaps = 8/69 (11%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
LYV L + T+++L++ F QYGR+ + + D F+ F+ R EA A+ L
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 150 NGQTVAGST 158
NGQ +G+T
Sbjct: 151 NGQKPSGAT 159
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 39/68 (57%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITAMNELNGQTVAGS 157
L+VR E +L E F +G ++ VK + +AFV FE+ + A A+ E++G++ A
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFGPMKEVKILNGFAFVEFEEAESAAKAIEEVHGKSFANQ 66
Query: 158 TLEVSLAK 165
LEV +K
Sbjct: 67 PLEVVYSK 74
>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 = 46.2 bits (108), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 41/77 (53%), Gaps = 8/77 (10%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
L V L Q T+++L+ F G VE K I+D Y FV++ ++A A+N L
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 150 NGQTVAGSTLEVSLAKP 166
NG + T++VS A+P
Sbjct: 67 NGLRLQSKTIKVSYARP 83
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 98 LYVRNL-TQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITAMNELNGQTVAG 156
+++ NL T + ++ F +YGRV K YAFV + + + A A+ NG+ +AG
Sbjct: 30 VFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKGYAFVQYSNERHARAAVLGENGRVLAG 89
Query: 157 STLEVSLAKPP 167
TL++++A P
Sbjct: 90 QTLDINMAGEP 100
>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|B Chain B, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|C Chain C, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|D Chain D, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
Length = 99
Score = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 41/77 (53%), Gaps = 8/77 (10%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
L V L Q T+++L+ F G VE K I+D Y FV++ ++A A+N L
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 150 NGQTVAGSTLEVSLAKP 166
NG + T++VS A+P
Sbjct: 82 NGLRLQSKTIKVSYARP 98
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 34/113 (30%), Positives = 53/113 (46%), Gaps = 19/113 (16%)
Query: 65 TGKHLLSRGCDIIVDWADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVER 124
TG + RG + + A+P +P+ L V L+ Y TE L+E F +YG +
Sbjct: 25 TGGQQMGRGSRHVGNRANP--DPNC-------CLGVFGLSLYTTERDLREVFSKYGPIAD 75
Query: 125 V--------KRIKDYAFVHFEDRQEAITAMNELNGQTVAGSTLEV--SLAKPP 167
V +R + +AFV+FE+ +A A NG + G + V S+ K P
Sbjct: 76 VSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRP 128
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 42/76 (55%), Gaps = 7/76 (9%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEAITAMNE 148
+VLYV NL + TE+ LK+ F+ G + +K + D YAFV + +A A+
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQT 60
Query: 149 LNGQTVAGSTLEVSLA 164
LNG+ + + ++++ A
Sbjct: 61 LNGKQIENNIVKINWA 76
Score = 35.8 bits (81), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 25/96 (26%), Positives = 45/96 (46%), Gaps = 13/96 (13%)
Query: 78 VDWA-DPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQY-----GRVE---RVKRI 128
++WA Q+ +T + L+V +L +E L+ AF+ + G V +
Sbjct: 73 INWAFQSQQSSSDDTFN----LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSS 128
Query: 129 KDYAFVHFEDRQEAITAMNELNGQTVAGSTLEVSLA 164
+ Y FV F + +A AM+ + GQ + G L ++ A
Sbjct: 129 RGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 164
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 41/71 (57%), Gaps = 3/71 (4%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD---YAFVHFEDRQEAITAMNELNGQTV 154
+YV NL + +L+ AF YG + V ++ +AFV FED ++A A+ EL+G+T+
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTL 135
Query: 155 AGSTLEVSLAK 165
G + V L+
Sbjct: 136 CGCRVRVELSN 146
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 44.7 bits (104), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 8/73 (10%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
LYV +L TE+ L+ FE +G+++ + +KD Y F+ F D + A A+ +L
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 150 NGQTVAGSTLEVS 162
NG +AG + V
Sbjct: 68 NGFELAGRPMRVG 80
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 44.7 bits (104), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 8/72 (11%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERV--------KRIKDYAFVHFEDRQEAITAMNEL 149
L+VRNL+ +EE L++ F YG + + K+ K +AFV F + A+ A E+
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 150 NGQTVAGSTLEV 161
+GQ G L V
Sbjct: 71 DGQVFQGRMLHV 82
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 44.7 bits (104), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 42/79 (53%), Gaps = 8/79 (10%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDY--------AFVHFEDRQEAITAMN 147
+VLYV L + ++ L AF +G + ++ DY AFV FE ++A A++
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
Query: 148 ELNGQTVAGSTLEVSLAKP 166
+N + G T+ V+LAKP
Sbjct: 73 NMNESELFGRTIRVNLAKP 91
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 44.7 bits (104), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 30/95 (31%), Positives = 51/95 (53%), Gaps = 14/95 (14%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD---YAFVHFEDRQEAITAMNELNGQTV 154
+YV NL + +L+ AF YG + V ++ +AFV FED ++A A+ L+G+ +
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 62
Query: 155 AGSTLEVSLA----------KPPSDKKKKEEILRN 179
GS + V L+ +PP+ ++K E+L N
Sbjct: 63 CGSRVRVELSTGMPRRSRFDRPPA-RRKLLEVLFN 96
>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 = 44.3 bits (103), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 42/88 (47%), Gaps = 8/88 (9%)
Query: 85 EEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVE--------RVKRIKDYAFVHF 136
+EP + + +L+V + + TEE + + F +YG ++ R +K Y V +
Sbjct: 13 DEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 72
Query: 137 EDRQEAITAMNELNGQTVAGSTLEVSLA 164
E +EA AM LNGQ + G + V
Sbjct: 73 ETYKEAQAAMEGLNGQDLMGQPISVDWC 100
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 44.3 bits (103), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 10/81 (12%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
++V +L+ T E +K AF +G++ + +KD Y FV F ++ +A A+ +
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 150 NGQTVAGSTLEVSLA--KPPS 168
GQ + G + + A KPP+
Sbjct: 78 GGQWLGGRQIRTNWATRKPPA 98
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 43.9 bits (102), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 41/71 (57%), Gaps = 3/71 (4%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD---YAFVHFEDRQEAITAMNELNGQTV 154
+YV NL + +L+ AF YG + V ++ +AFV FED ++A A+ +L+G+T+
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRDLDGRTL 135
Query: 155 AGSTLEVSLAK 165
G + V L+
Sbjct: 136 CGCRVRVELSN 146
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 43.9 bits (102), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 44/82 (53%), Gaps = 6/82 (7%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------YAFVHFEDRQEAITAMNEL 149
+ LYV NL++ TE + + F Q G + K I + Y FV F + ++A A+ +
Sbjct: 16 RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAM 75
Query: 150 NGQTVAGSTLEVSLAKPPSDKK 171
NG+ + G ++V+ A PS +K
Sbjct: 76 NGRKILGKEVKVNWATTPSSQK 97
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/94 (25%), Positives = 46/94 (48%), Gaps = 10/94 (10%)
Query: 80 WADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDY 131
W DP +P+ + K L+V + TE KL+ FE YG ++R+ + + Y
Sbjct: 89 W-DPHNDPNAQG-DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGY 146
Query: 132 AFVHFEDRQEAITAMNELNGQTVAGSTLEVSLAK 165
AF+ +E ++ +A +G+ + G + V + +
Sbjct: 147 AFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 180
>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 = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 42/88 (47%), Gaps = 8/88 (9%)
Query: 85 EEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVE--------RVKRIKDYAFVHF 136
+EP + + +L+V + + TEE + + F +YG ++ R +K Y V +
Sbjct: 12 DEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 71
Query: 137 EDRQEAITAMNELNGQTVAGSTLEVSLA 164
E +EA AM LNGQ + G + V
Sbjct: 72 ETYKEAQAAMEGLNGQDLMGQPISVDWC 99
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 8/76 (10%)
Query: 97 VLYVRNLTQYCTEEKLKEAFEQYGRVE--------RVKRIKDYAFVHFEDRQEAITAMNE 148
+L+V + + TEE + + F +YG ++ R +K Y V +E +EA AM
Sbjct: 11 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 70
Query: 149 LNGQTVAGSTLEVSLA 164
LNGQ + G + V
Sbjct: 71 LNGQDLMGQPISVDWC 86
>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 90
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 8/76 (10%)
Query: 97 VLYVRNLTQYCTEEKLKEAFEQYGRVE--------RVKRIKDYAFVHFEDRQEAITAMNE 148
+L+V + + TEE + + F +YG ++ R +K Y V +E +EA AM
Sbjct: 9 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 68
Query: 149 LNGQTVAGSTLEVSLA 164
LNGQ + G + V
Sbjct: 69 LNGQDLMGQPISVDWC 84
>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 = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/94 (25%), Positives = 46/94 (48%), Gaps = 10/94 (10%)
Query: 80 WADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDY 131
W DP +P+ + K L+V + TE KL+ FE YG ++R+ + + Y
Sbjct: 89 W-DPHNDPNAQG-DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGY 146
Query: 132 AFVHFEDRQEAITAMNELNGQTVAGSTLEVSLAK 165
AF+ +E ++ +A +G+ + G + V + +
Sbjct: 147 AFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 180
>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 = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 29/103 (28%), Positives = 50/103 (48%), Gaps = 10/103 (9%)
Query: 82 DPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVE--------RVKRIKDYAF 133
D + EP + + +L+V ++ + E++++E F YG ++ R K YA
Sbjct: 59 DDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYAL 118
Query: 134 VHFEDRQEAITAMNELNGQTVAGSTLEVS--LAKPPSDKKKKE 174
V +E ++A+ A LNG + G T++V K P KK E
Sbjct: 119 VEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKRVKKSE 161
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/89 (30%), Positives = 43/89 (48%), Gaps = 11/89 (12%)
Query: 84 QEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVH 135
Q P+ + + + V Y+ E +L++ FE+YG +E VK + D Y FV
Sbjct: 34 QMNPEPDVLRNLMVNYIPTTVD---EVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVK 90
Query: 136 FEDRQEAITAMNELNGQTVAGSTLEVSLA 164
F+ A A+ LNG + L+V+LA
Sbjct: 91 FQSGSSAQQAIAGLNGFNILNKRLKVALA 119
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 8/76 (10%)
Query: 97 VLYVRNLTQYCTEEKLKEAFEQYGRVE--------RVKRIKDYAFVHFEDRQEAITAMNE 148
+L+V + + TEE + + F +YG ++ R +K Y V +E +EA AM
Sbjct: 9 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 68
Query: 149 LNGQTVAGSTLEVSLA 164
LNGQ + G + V
Sbjct: 69 LNGQDLMGQPISVDWC 84
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 45/83 (54%), Gaps = 6/83 (7%)
Query: 88 DTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI------KDYAFVHFEDRQE 141
+TE S+ K L+V N+ + L++ F Q+G++ V+ I K + FV FE+ +
Sbjct: 22 NTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSAD 81
Query: 142 AITAMNELNGQTVAGSTLEVSLA 164
A A +L+G V G +EV+ A
Sbjct: 82 ADRAREKLHGTVVEGRKIEVNNA 104
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 37/74 (50%), Gaps = 8/74 (10%)
Query: 97 VLYVRNLTQYCTEEKLKEAFEQYGRVERV--------KRIKDYAFVHFEDRQEAITAMNE 148
L V L+ Y TE L+E F +YG + V +R + +AFV+FE+ +A A
Sbjct: 17 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76
Query: 149 LNGQTVAGSTLEVS 162
NG + G + VS
Sbjct: 77 ANGMELDGRRIRVS 90
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 41/80 (51%), Gaps = 2/80 (2%)
Query: 87 PDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--YAFVHFEDRQEAIT 144
P +T ++ L+V NL TEE++++ FE+YG+ V KD + F+ E R A
Sbjct: 14 PGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEI 73
Query: 145 AMNELNGQTVAGSTLEVSLA 164
A EL+ + G L V A
Sbjct: 74 AKVELDNMPLRGKQLRVRFA 93
Score = 36.6 bits (83), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 28/87 (32%), Positives = 40/87 (45%), Gaps = 7/87 (8%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEAITAMNELN 150
L VRNL QY + E L+EAF +G+VER I D V F + A A++ +
Sbjct: 99 LTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKALDRCS 158
Query: 151 GQTVAGSTLEVSLAKPPSDKKKKEEIL 177
+ +T + P D+ EE L
Sbjct: 159 EGSFLLTTFPRPVTVEPMDQLDDEEGL 185
>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
pdb|2J0Q|G Chain G, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
Length = 109
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 8/76 (10%)
Query: 97 VLYVRNLTQYCTEEKLKEAFEQYGRVE--------RVKRIKDYAFVHFEDRQEAITAMNE 148
+L+V + + TEE + + F +YG ++ R +K Y V +E +EA AM
Sbjct: 9 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 68
Query: 149 LNGQTVAGSTLEVSLA 164
LNGQ + G + V
Sbjct: 69 LNGQDLMGQPISVDWC 84
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/91 (26%), Positives = 45/91 (49%), Gaps = 8/91 (8%)
Query: 82 DPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVE--------RVKRIKDYAF 133
D + EP + + +L+V ++ + E++++E F YG ++ R K YA
Sbjct: 13 DDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYAL 72
Query: 134 VHFEDRQEAITAMNELNGQTVAGSTLEVSLA 164
V +E ++A+ A LNG + G T++V
Sbjct: 73 VEYETHKQALAAKEALNGAEIMGQTIQVDWC 103
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 29/93 (31%), Positives = 50/93 (53%), Gaps = 10/93 (10%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVK-----RIKDYAFVHFEDRQEAITAMNELN 150
++LY+RNL T E++ + F +YG + +++ + A+V +ED +A A++ L+
Sbjct: 9 RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLS 68
Query: 151 GQTVAGSTLEV-----SLAKPPSDKKKKEEILR 178
G V+ L V + A D KKKEE L+
Sbjct: 69 GFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLK 101
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 40/81 (49%), Gaps = 10/81 (12%)
Query: 97 VLYVRNLTQYCTEEKLKEAFEQYGRVERV--------KRIKDYAFVHFEDRQEAITAMNE 148
L V L+ Y TE L+E F +YG + V +R + +AFV+FE+ +A A
Sbjct: 17 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76
Query: 149 LNGQTVAGSTLEV--SLAKPP 167
NG + G + V S+ K P
Sbjct: 77 ANGMELDGRRIRVDFSITKRP 97
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 8/76 (10%)
Query: 97 VLYVRNLTQYCTEEKLKEAFEQYGRVERV--------KRIKDYAFVHFEDRQEAITAMNE 148
L V L+ Y TE L+E F +YG + V +R + +AFV+FE+ +A A
Sbjct: 14 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 73
Query: 149 LNGQTVAGSTLEVSLA 164
NG + G + V +
Sbjct: 74 ANGMELDGRRIRVDFS 89
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 42/81 (51%), Gaps = 10/81 (12%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYA--------FVHFEDRQEAITAMNEL 149
LYV L + +++++++ F QYGR+ + + D A F+ F+ R EA A+ L
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 150 NGQTVAGST--LEVSLAKPPS 168
NGQ G+ + V A PS
Sbjct: 64 NGQKPLGAAEPITVKFANNPS 84
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 40.8 bits (94), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 40/81 (49%), Gaps = 9/81 (11%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
++V + C E +L+E F+++G V V I D + F+ FED Q A+N +
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-M 71
Query: 150 NGQTVAGSTLEVSLAKPPSDK 170
+ + G +EV A+P K
Sbjct: 72 HFHDIMGKKVEVKRAEPRDSK 92
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 40.8 bits (94), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 43/78 (55%), Gaps = 11/78 (14%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAIT-AMNE 148
+YV NL T E++KE F Q+G+V VK I D + FV E ++E+++ A+ +
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFV--EMQEESVSEAIAK 61
Query: 149 LNGQTVAGSTLEVSLAKP 166
L+ G T+ V+ A P
Sbjct: 62 LDNTDFMGRTIRVTEANP 79
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 40.4 bits (93), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 29/93 (31%), Positives = 48/93 (51%), Gaps = 10/93 (10%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVK-----RIKDYAFVHFEDRQEAITAMNELN 150
++LY+RNL T E++ + F +YG + +++ + A+V +ED +A A + L+
Sbjct: 19 RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLS 78
Query: 151 GQTVAGSTLEV-----SLAKPPSDKKKKEEILR 178
G V L V + A D KKKEE L+
Sbjct: 79 GFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLK 111
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 40.4 bits (93), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 41/87 (47%), Gaps = 15/87 (17%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIK-----------DYAFVHFEDRQEAITAM 146
L+++NL TEE LK F + G ++ K + FV ++ ++A A+
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 147 NELNGQTVAGSTLEVSLA----KPPSD 169
+L G TV G LEV ++ KP S
Sbjct: 68 KQLQGHTVDGHKLEVRISERATKPASG 94
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 40.4 bits (93), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 33/105 (31%), Positives = 45/105 (42%), Gaps = 24/105 (22%)
Query: 81 ADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI------------ 128
DP E+ D +YV+ L T + L + F+Q G V+ KR
Sbjct: 7 GDPDEDSDNS------AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE 60
Query: 129 ----KDYAFVHFEDRQEAITAMNELNGQTVAGSTLEVSLA--KPP 167
K A V +ED A A+ +G+ GS L+VSLA KPP
Sbjct: 61 TGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPP 105
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 40.4 bits (93), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 41/78 (52%), Gaps = 8/78 (10%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDY--------AFVHFEDRQEAITAMN 147
+VLYV L + ++ L AF +G + ++ DY AFV FE ++A A++
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
Query: 148 ELNGQTVAGSTLEVSLAK 165
+N + G T+ V+LAK
Sbjct: 68 NMNESELFGRTIRVNLAK 85
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 40.4 bits (93), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 38/78 (48%), Gaps = 9/78 (11%)
Query: 101 RNLTQYC-------TEEKLKEAFEQYGRVERVKRI--KDYAFVHFEDRQEAITAMNELNG 151
+N T YC T++ +++ F +G++ ++ K Y+FV F + A A+ +NG
Sbjct: 24 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNG 83
Query: 152 QTVAGSTLEVSLAKPPSD 169
T+ G ++ K D
Sbjct: 84 TTIEGHVVKCYWGKESPD 101
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 40.4 bits (93), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 4/75 (5%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVE----RVKRIKDYAFVHFEDRQEAITAMNELNG 151
K L + NL+ TEE L+E FE+ ++ + + K YAF+ F ++A A+N N
Sbjct: 16 KTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNK 75
Query: 152 QTVAGSTLEVSLAKP 166
+ + G + + L P
Sbjct: 76 REIEGRAIRLELQGP 90
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 40.4 bits (93), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 37/80 (46%), Gaps = 2/80 (2%)
Query: 87 PDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERV--KRIKDYAFVHFEDRQEAIT 144
P +T ++ L+V NL TEE K FE+YG V R + + F+ E R A
Sbjct: 14 PGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEI 73
Query: 145 AMNELNGQTVAGSTLEVSLA 164
A EL+G + L + A
Sbjct: 74 AKAELDGTILKSRPLRIRFA 93
Score = 28.1 bits (61), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 21/34 (61%)
Query: 97 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD 130
L V+NL+ + E L++AF Q+G VE+ + D
Sbjct: 98 ALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD 131
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 40.4 bits (93), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 41/78 (52%), Gaps = 8/78 (10%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDY--------AFVHFEDRQEAITAMN 147
+VLYV L + ++ L AF +G + ++ DY AFV FE ++A A++
Sbjct: 6 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65
Query: 148 ELNGQTVAGSTLEVSLAK 165
+N + G T+ V+LAK
Sbjct: 66 NMNESELFGRTIRVNLAK 83
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 98 LYVRNLTQYCTEEKLKEA-FEQYGRVERVKRIKDYAFVHFEDRQEAITAMNELNGQTVAG 156
+++ NL ++ EA F +YG++ K +AFV + + + A A+ +G+ +AG
Sbjct: 18 VFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERNARAAVAGEDGRMIAG 77
Query: 157 STLEVSLAKPP 167
L+++LA P
Sbjct: 78 QVLDINLAAEP 88
>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 = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 40/77 (51%), Gaps = 2/77 (2%)
Query: 90 ETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--YAFVHFEDRQEAITAMN 147
+T ++ L+V NL TEE++++ FE+YG+ V KD + F+ E R A A
Sbjct: 10 KTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKV 69
Query: 148 ELNGQTVAGSTLEVSLA 164
EL+ + G L V A
Sbjct: 70 ELDNMPLRGKQLRVRFA 86
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 5/76 (6%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVK-----RIKDYAFVHFEDRQEAITAMNELN 150
K L+V+ L++ TEE LKE+F+ R V K + FV F ++A A +
Sbjct: 16 KTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAME 75
Query: 151 GQTVAGSTLEVSLAKP 166
+ G+ + + AKP
Sbjct: 76 DGEIDGNKVTLDWAKP 91
>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
pdb|4F02|D Chain D, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
Length = 213
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/89 (25%), Positives = 44/89 (49%), Gaps = 9/89 (10%)
Query: 72 RGCDIIVDWADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD- 130
+G + + W+ Q +P S V ++++NL + + L + F +G + K + D
Sbjct: 83 KGKPVRIMWS--QRDPSLRK-SGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE 139
Query: 131 -----YAFVHFEDRQEAITAMNELNGQTV 154
Y FVHFE ++ A A+ ++NG +
Sbjct: 140 NGSKGYGFVHFETQEAAERAIEKMNGMLL 168
Score = 31.6 bits (70), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 9/83 (10%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
LYV +L TE L E F G + ++ +D YA+V+F+ +A A++ +
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77
Query: 150 NGQTVAGSTLEVSLA-KPPSDKK 171
N + G + + + + PS +K
Sbjct: 78 NFDVIKGKPVRIMWSQRDPSLRK 100
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 39/81 (48%), Gaps = 8/81 (9%)
Query: 97 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNE 148
+ V NL++ E L+E F +G + R+ KD +AF+ F R++A A+
Sbjct: 17 TIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAG 76
Query: 149 LNGQTVAGSTLEVSLAKPPSD 169
++G L V AKP ++
Sbjct: 77 VSGFGYDHLILNVEWAKPSTN 97
>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 = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/89 (25%), Positives = 44/89 (49%), Gaps = 9/89 (10%)
Query: 72 RGCDIIVDWADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD- 130
+G + + W+ Q +P S V ++++NL + + L + F +G + K + D
Sbjct: 78 KGKPVRIMWS--QRDPSLRK-SGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE 134
Query: 131 -----YAFVHFEDRQEAITAMNELNGQTV 154
Y FVHFE ++ A A+ ++NG +
Sbjct: 135 NGSKGYGFVHFETQEAAERAIEKMNGMLL 163
Score = 30.8 bits (68), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 9/83 (10%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
LYV +L TE L E F G + ++ +D YA+V+F+ +A A++ +
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 72
Query: 150 NGQTVAGSTLEVSLA-KPPSDKK 171
N + G + + + + PS +K
Sbjct: 73 NFDVIKGKPVRIMWSQRDPSLRK 95
>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 = 0.003, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 8/77 (10%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDY--------AFVHFEDRQEAITAMN 147
+VLYV L + ++ L AF +G + ++ DY AFV FE ++A A++
Sbjct: 3 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 62
Query: 148 ELNGQTVAGSTLEVSLA 164
+N + G T+ V+LA
Sbjct: 63 NMNESELFGRTIRVNLA 79
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 7/73 (9%)
Query: 86 EPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERV-------KRIKDYAFVHFED 138
E + + K LYV NL+ Y TEE++ E F + G ++++ K + FV +
Sbjct: 9 EEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYS 68
Query: 139 RQEAITAMNELNG 151
R +A AM +NG
Sbjct: 69 RADAENAMRYING 81
>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 = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 8/74 (10%)
Query: 86 EPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERV--------KRIKDYAFVHFE 137
E + + K LYV NL+ Y TEE++ E F + G ++++ K + FV +
Sbjct: 30 EEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYY 89
Query: 138 DRQEAITAMNELNG 151
R +A AM +NG
Sbjct: 90 SRADAENAMRYING 103
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 8/75 (10%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
+YV NL T L F +YG+V +V +KD AF+ F D+ A +
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 150 NGQTVAGSTLEVSLA 164
N + + G ++ S+A
Sbjct: 79 NNKQLFGRVIKASIA 93
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 40/75 (53%), Gaps = 6/75 (8%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI------KDYAFVHFEDRQEAITAMNEL 149
K L+V N+ + L++ F Q+G++ V+ I K + FV FE+ +A A +L
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKL 75
Query: 150 NGQTVAGSTLEVSLA 164
+G V G +EV+ A
Sbjct: 76 HGTVVEGRKIEVNNA 90
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 26/102 (25%), Positives = 47/102 (46%), Gaps = 12/102 (11%)
Query: 85 EEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD----------YAFV 134
+ PD + +K ++V + + +E+ L+E FEQYG V + ++D FV
Sbjct: 6 DHPDQPDLDAIK-MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFV 64
Query: 135 HFEDRQEAITAMNELNGQTVAGSTLEVSLAKPPSDKKKKEEI 176
F R+ A+ A N L+ V + + P+D +K +
Sbjct: 65 TFYTRKAALEAQNALHNMKVLPG-MHHPIQMKPADSEKNNAV 105
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 37.7 bits (86), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 8/77 (10%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDY--------AFVHFEDRQEAITAMN 147
+VLYV L + ++ L AF +G + ++ DY AFV FE ++A A++
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
Query: 148 ELNGQTVAGSTLEVSLA 164
+N + G T+ V+LA
Sbjct: 124 NMNESELFGRTIRVNLA 140
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 37.7 bits (86), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 5/72 (6%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERV---KRIKDYAFVHFEDRQEAITAMNELNGQTV 154
++V T TE++L+E F QYG V V K + +AFV F D Q A + E +
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGE--DLII 65
Query: 155 AGSTLEVSLAKP 166
G ++ +S A+P
Sbjct: 66 KGISVHISNAEP 77
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 37.4 bits (85), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 9/79 (11%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVER----VKRI-----KDYAFVHFEDRQEAITAMNE 148
+++ LT+ T++ + E F YG+++ V+R+ K YA+V FE+ EA A+
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 149 LNGQTVAGSTLEVSLAKPP 167
++G + G + + P
Sbjct: 67 MDGGQIDGQEITATAVLAP 85
>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
pdb|2F9J|B Chain B, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
Length = 125
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 28/93 (30%), Positives = 47/93 (50%), Gaps = 10/93 (10%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVK-----RIKDYAFVHFEDRQEAITAMNELN 150
++L +RNL T E++ + F +YG + +++ + A+V +ED +A A + L+
Sbjct: 19 RILMIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLS 78
Query: 151 GQTVAGSTLEV-----SLAKPPSDKKKKEEILR 178
G V L V + A D KKKEE L+
Sbjct: 79 GFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLK 111
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 39/87 (44%), Gaps = 8/87 (9%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDY--------AFVHFEDRQEAITAMNEL 149
L V L Q T+ +L F G + + ++DY AFV F ++ A+ L
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 150 NGQTVAGSTLEVSLAKPPSDKKKKEEI 176
NG TV L+VS A+P + K +
Sbjct: 66 NGITVRNKRLKVSYARPGGESIKDTNL 92
Score = 37.0 bits (84), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 30/97 (30%), Positives = 46/97 (47%), Gaps = 15/97 (15%)
Query: 78 VDWADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------- 130
V +A P E +T LYV NL + T+++L F +YG + + ++D
Sbjct: 77 VSYARPGGESIKDTN-----LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPR 131
Query: 131 -YAFVHFEDRQEAITAMNELNGQTVAGST--LEVSLA 164
AFV + R+EA A++ LN G + L V LA
Sbjct: 132 GVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 35/68 (51%), Gaps = 6/68 (8%)
Query: 93 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------YAFVHFEDRQEAITAM 146
S V ++++NL + + L + F +G + K + D Y FVHFE ++ A A+
Sbjct: 9 SGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAI 68
Query: 147 NELNGQTV 154
++NG +
Sbjct: 69 EKMNGMLL 76
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 36/71 (50%), Gaps = 5/71 (7%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYG-----RVERVKRIKDYAFVHFEDRQEAITAMNELN 150
++LY+RNL T E++ + F +YG RV + A+V +ED +A A + L+
Sbjct: 13 RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLS 72
Query: 151 GQTVAGSTLEV 161
G V L V
Sbjct: 73 GFNVCNRYLVV 83
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 37.0 bits (84), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 38/83 (45%), Gaps = 8/83 (9%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDY--------AFVHFEDRQEAITAMNEL 149
L V L Q T+ +L F G + + ++DY AFV F ++ A+ L
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 150 NGQTVAGSTLEVSLAKPPSDKKK 172
NG TV L+VS A+P + K
Sbjct: 66 NGITVRNKRLKVSYARPGGESIK 88
>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 = 37.0 bits (84), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 30/98 (30%), Positives = 47/98 (47%), Gaps = 15/98 (15%)
Query: 78 VDWADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------- 130
V +A P E +T LYV NL + T+++L F +YG + + ++D
Sbjct: 88 VSYARPGGESIKDTN-----LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPR 142
Query: 131 -YAFVHFEDRQEAITAMNELNGQTVAGST--LEVSLAK 165
AFV + R+EA A++ LN G + L V LA+
Sbjct: 143 GVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLAE 180
Score = 35.8 bits (81), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 38/87 (43%), Gaps = 8/87 (9%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDY--------AFVHFEDRQEAITAMNEL 149
L V L Q T+ +L F G + + +DY AFV F ++ A+ L
Sbjct: 17 LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 150 NGQTVAGSTLEVSLAKPPSDKKKKEEI 176
NG TV L+VS A+P + K +
Sbjct: 77 NGITVRNKRLKVSYARPGGESIKDTNL 103
>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 = 37.0 bits (84), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 40/78 (51%), Gaps = 10/78 (12%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
LYV NL + T+++L F +YG + + ++D AFV + R+EA A++ L
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 150 NGQTVAGST--LEVSLAK 165
N G + L V LA+
Sbjct: 76 NNVIPEGGSQPLSVRLAE 93
>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 = 36.6 bits (83), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 21/85 (24%), Positives = 45/85 (52%), Gaps = 8/85 (9%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------YAFVHFEDRQEAITAMNELNG 151
++++NL + + L + F +G + K + D Y FVHFE ++ A A+ ++NG
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 67
Query: 152 QTVAGSTLEVSLAKPPSDKKKKEEI 176
+ + +V + + S K+++ E+
Sbjct: 68 MLL--NDRKVFVGRFKSRKEREAEL 90
>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 = 36.6 bits (83), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 38/78 (48%), Gaps = 8/78 (10%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
+YV ++ Q +++ +K FE +G+++ +D Y F+ +E Q + A++ +
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 150 NGQTVAGSTLEVSLAKPP 167
N + G L V A P
Sbjct: 188 NLFDLGGQYLRVGKAVTP 205
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 36.6 bits (83), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 8/78 (10%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVE--------RVKRIKDYAFVHFEDRQEAITAMN 147
KVLY++NL+ TE L F ++ + R++ AF+ F +++ A A++
Sbjct: 26 KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 85
Query: 148 ELNGQTVAGSTLEVSLAK 165
+NG + G L + K
Sbjct: 86 LVNGYKLYGKILVIEFGK 103
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 36.6 bits (83), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 43/74 (58%), Gaps = 7/74 (9%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVE-------RVKRIKDYAFVHFEDRQEAITAMNELN 150
L++ L CT+E+L+E + +G V+ R + K A+V +E+ +A A+ +++
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMD 79
Query: 151 GQTVAGSTLEVSLA 164
G T+ + ++V+++
Sbjct: 80 GMTIKENIIKVAIS 93
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 36.2 bits (82), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 9/78 (11%)
Query: 95 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAM 146
VK ++V + + E L++ FEQYG++E ++ + D +AFV F+D +++ +
Sbjct: 105 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKI 163
Query: 147 NELNGQTVAGSTLEVSLA 164
TV G EV A
Sbjct: 164 VIQKYHTVNGHNCEVRKA 181
Score = 31.6 bits (70), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 8/62 (12%)
Query: 94 KVKVLYVRNLTQYCTEEKLKEAFEQYG--------RVERVKRIKDYAFVHFEDRQEAITA 145
+++ L++ L+ T+E L+ FEQ+G R KR + + FV + +E A
Sbjct: 13 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 72
Query: 146 MN 147
MN
Sbjct: 73 MN 74
>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 = 36.2 bits (82), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 9/78 (11%)
Query: 95 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAM 146
VK ++V + + E L++ FEQYG++E ++ + D +AFV F+D +++ +
Sbjct: 103 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKI 161
Query: 147 NELNGQTVAGSTLEVSLA 164
TV G EV A
Sbjct: 162 VIQKYHTVNGHNCEVRKA 179
Score = 31.2 bits (69), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 8/62 (12%)
Query: 94 KVKVLYVRNLTQYCTEEKLKEAFEQYG--------RVERVKRIKDYAFVHFEDRQEAITA 145
+++ L++ L+ T+E L+ FEQ+G R KR + + FV + +E A
Sbjct: 11 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 70
Query: 146 MN 147
MN
Sbjct: 71 MN 72
>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of
Fbp-Interacting Repressor (Fir)
pdb|2KXH|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fir In
The Complex With Fbp Nbox Peptide
Length = 199
Score = 36.2 bits (82), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 38/78 (48%), Gaps = 8/78 (10%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
+YV ++ Q +++ +K FE +G+++ +D Y F+ +E Q + A++ +
Sbjct: 113 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 172
Query: 150 NGQTVAGSTLEVSLAKPP 167
N + G L V A P
Sbjct: 173 NLFDLGGQYLRVGKAVTP 190
>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 = 36.2 bits (82), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 9/78 (11%)
Query: 95 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAM 146
VK ++V + + E L++ FEQYG++E ++ + D +AFV F+D +++ +
Sbjct: 104 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKI 162
Query: 147 NELNGQTVAGSTLEVSLA 164
TV G EV A
Sbjct: 163 VIQKYHTVNGHNCEVRKA 180
Score = 31.2 bits (69), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 8/62 (12%)
Query: 94 KVKVLYVRNLTQYCTEEKLKEAFEQYG--------RVERVKRIKDYAFVHFEDRQEAITA 145
+++ L++ L+ T+E L+ FEQ+G R KR + + FV + +E A
Sbjct: 12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 71
Query: 146 MN 147
MN
Sbjct: 72 MN 73
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 36.2 bits (82), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 9/78 (11%)
Query: 95 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAM 146
VK ++V + + E L++ FEQYG++E ++ + D +AFV F+D +++ +
Sbjct: 104 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKI 162
Query: 147 NELNGQTVAGSTLEVSLA 164
TV G EV A
Sbjct: 163 VIQKYHTVNGHNCEVRKA 180
Score = 30.8 bits (68), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 8/62 (12%)
Query: 94 KVKVLYVRNLTQYCTEEKLKEAFEQYG--------RVERVKRIKDYAFVHFEDRQEAITA 145
+++ L++ L+ T+E L+ FEQ+G R KR + + FV + +E A
Sbjct: 12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 71
Query: 146 MN 147
MN
Sbjct: 72 MN 73
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 36.2 bits (82), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 9/78 (11%)
Query: 95 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAM 146
VK ++V + + E L++ FEQYG++E ++ + D +AFV F+D +++ +
Sbjct: 102 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKI 160
Query: 147 NELNGQTVAGSTLEVSLA 164
TV G EV A
Sbjct: 161 VIQKYHTVNGHNCEVRKA 178
Score = 30.8 bits (68), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 8/62 (12%)
Query: 94 KVKVLYVRNLTQYCTEEKLKEAFEQYG--------RVERVKRIKDYAFVHFEDRQEAITA 145
+++ L++ L+ T+E L+ FEQ+G R KR + + FV + +E A
Sbjct: 10 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 69
Query: 146 MN 147
MN
Sbjct: 70 MN 71
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 35.8 bits (81), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 42/82 (51%), Gaps = 8/82 (9%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRI-------KDYAFVHFEDRQEAITAMNELN 150
L+V L + +E+ ++ FE +G +E + K AFV + EA A+N L+
Sbjct: 18 LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINALH 77
Query: 151 G-QTVAGSTLEVSLAKPPSDKK 171
G QT+ G++ + + +DK+
Sbjct: 78 GSQTMPGASSSLVVKFADTDKE 99
>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 = 35.8 bits (81), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 9/78 (11%)
Query: 95 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAM 146
VK ++V + + E L++ FEQYG++E ++ + D +AFV F+D +++ +
Sbjct: 97 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKI 155
Query: 147 NELNGQTVAGSTLEVSLA 164
TV G EV A
Sbjct: 156 VIQKYHTVNGHNCEVRKA 173
Score = 30.8 bits (68), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 8/62 (12%)
Query: 94 KVKVLYVRNLTQYCTEEKLKEAFEQYG--------RVERVKRIKDYAFVHFEDRQEAITA 145
+++ L++ L+ T+E L+ FEQ+G R KR + + FV + +E A
Sbjct: 5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 64
Query: 146 MN 147
MN
Sbjct: 65 MN 66
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 35.8 bits (81), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 7/73 (9%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRV-------ERVKRIKDYAFVHFEDRQEAITAMNELN 150
L V NL ++ ++E F ++G + +R R A VHFE + +A+ AM + N
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 90
Query: 151 GQTVAGSTLEVSL 163
G + G + + L
Sbjct: 91 GVPLDGRPMNIQL 103
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 35.0 bits (79), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 23/89 (25%), Positives = 41/89 (46%), Gaps = 11/89 (12%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD----------YAFVHFEDRQEAITAMN 147
++V + + +E+ L+E FEQYG V + ++D FV F R+ A+ A N
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 148 ELNGQTVAGSTLEVSLAKPPSDKKKKEEI 176
L+ V + + P+D +K +
Sbjct: 66 ALHNMKVLPG-MHHPIQMKPADSEKNNAV 93
>pdb|2DGX|A Chain A, Solution Structure Of The Rna Recognition Motif In
Kiaa0430 Protein
Length = 96
Score = 35.0 bits (79), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 37/65 (56%), Gaps = 5/65 (7%)
Query: 109 EEKLKEAFEQYGRVERVKRI--KDY---AFVHFEDRQEAITAMNELNGQTVAGSTLEVSL 163
++ L+EAF ++G+V+ V+ DY A V E+ Q+AI A+N L+ + + VSL
Sbjct: 27 QQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSL 86
Query: 164 AKPPS 168
A S
Sbjct: 87 ATGAS 91
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 34.7 bits (78), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 9/76 (11%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRI---------KDYAFVHFEDRQEAITAMNE 148
+++ NL E+ L + F +G + + +I K YAF++F + A+
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 149 LNGQTVAGSTLEVSLA 164
+NGQ + + VS A
Sbjct: 68 MNGQYLCNRPITVSYA 83
>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 = 34.7 bits (78), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 33/67 (49%), Gaps = 10/67 (14%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD----------YAFVHFEDRQEAITAMN 147
++V + + +E+ L+E FEQYG V + ++D FV F R+ A+ A N
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 148 ELNGQTV 154
L+ V
Sbjct: 66 ALHNMKV 72
>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 = 34.7 bits (78), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 37/78 (47%), Gaps = 8/78 (10%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
+YV ++ Q +++ +K FE +G+++ +D Y F+ +E Q + A++
Sbjct: 112 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSX 171
Query: 150 NGQTVAGSTLEVSLAKPP 167
N + G L V A P
Sbjct: 172 NLFDLGGQYLRVGKAVTP 189
>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 = 34.7 bits (78), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 8/75 (10%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQY-----GRVE---RVKRIKDYAFVHFEDRQEAITAMNEL 149
L+V +L +E L+ AF+ + G V + + Y FV F + +A AM+ +
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 150 NGQTVAGSTLEVSLA 164
GQ + G L ++ A
Sbjct: 64 QGQDLNGRPLRINWA 78
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 34.3 bits (77), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 32/74 (43%), Gaps = 3/74 (4%)
Query: 95 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--KDYAFVHFEDRQEA-ITAMNELNG 151
+ LYV L TE L+ F Q+G + + + + AF+ F RQ A + A N
Sbjct: 12 ITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNK 71
Query: 152 QTVAGSTLEVSLAK 165
V G L V +
Sbjct: 72 LIVNGRRLNVKWGR 85
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 33.9 bits (76), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 33/73 (45%), Gaps = 7/73 (9%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEAITAMNELN 150
++V NL +KLKE F G V R ++D V FE EA+ A++ N
Sbjct: 18 VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFN 77
Query: 151 GQTVAGSTLEVSL 163
GQ + + V +
Sbjct: 78 GQLLFDRPMHVKM 90
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 33.5 bits (75), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 3/72 (4%)
Query: 93 SKVKVLYVRNLTQYCTEEKLKEAF--EQYGRVERVKRIKDYAFVHFEDRQEAITAMNELN 150
S + LY+ NL+ T + L++ F + +V YAFV + D+ AI A+ L+
Sbjct: 6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLS 65
Query: 151 GQT-VAGSTLEV 161
G+ + G +EV
Sbjct: 66 GKVELHGKIMEV 77
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 11/60 (18%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFED---RQEAITAM 146
LY+R L T++ L + + YG++ K I K Y FV F+ Q+A+TA+
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
pdb|3NNA|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 33.1 bits (74), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 32/66 (48%), Gaps = 10/66 (15%)
Query: 99 YVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD----------YAFVHFEDRQEAITAMNE 148
+V + + +E+ L+E FEQYG V + ++D FV F R+ A+ A N
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 149 LNGQTV 154
L+ V
Sbjct: 67 LHNXKV 72
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 33.1 bits (74), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 9/70 (12%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGR-VERVKRIKD--------YAFVHFEDRQEAITAMNE 148
L++ +L Y E + AF G V VK I++ Y FV F D A +++
Sbjct: 12 LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71
Query: 149 LNGQTVAGST 158
+NG+ + G+T
Sbjct: 72 INGKPLPGAT 81
>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 = 32.3 bits (72), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 8/77 (10%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVK--------RIKDYAFVHFEDRQEAITAMN 147
+V+Y+ ++ TEE++ + G V +K R K YAF+ F D + + +A+
Sbjct: 5 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 64
Query: 148 ELNGQTVAGSTLEVSLA 164
LNG + L+ +
Sbjct: 65 NLNGYQLGSRFLKCGYS 81
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 32.3 bits (72), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 10/77 (12%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRI-------KDYAFVHFEDRQEAITAMNELN 150
L+V L + T+E +++ FE +G ++ + K AFV F+ EA A+N L+
Sbjct: 15 LFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTLH 74
Query: 151 GQTV---AGSTLEVSLA 164
A S+L V A
Sbjct: 75 SSRTLPGASSSLVVKFA 91
>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 = 32.3 bits (72), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 8/82 (9%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
L++ +L Q ++ L + F +G V K D + FV +++ A A+ +
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 150 NGQTVAGSTLEVSLAKPPSDKK 171
NG + L+V L + +D K
Sbjct: 88 NGFQIGMKRLKVQLKRSKNDSK 109
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 32.0 bits (71), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 4/81 (4%)
Query: 87 PDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKR--IKDYAFVHFEDRQEAIT 144
P+ K LYV + T L+ AF +G + + ++ AFV +E + A
Sbjct: 31 PERRAPRKGNTLYVYG--EDMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQ 88
Query: 145 AMNELNGQTVAGSTLEVSLAK 165
A+ ELNG V L+V++A+
Sbjct: 89 AVAELNGTQVESVQLKVNIAR 109
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 32.0 bits (71), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 40/83 (48%), Gaps = 14/83 (16%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHF---EDRQEAIT 144
K +++RNL+ EE L E +Q+G ++ V+ + K AF F E Q+ +
Sbjct: 16 KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 75
Query: 145 AMN---ELNGQTVAGSTLEVSLA 164
A + E G + G L+V LA
Sbjct: 76 AASLEAEGGGLKLDGRQLKVDLA 98
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 32.0 bits (71), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 8/74 (10%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVK--------RIKDYAFVHFEDRQEAITAMN 147
+V+Y+ ++ TEE++ + G V +K R K YAF+ F D + + +A+
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 148 ELNGQTVAGSTLEV 161
LNG + L+
Sbjct: 63 NLNGYQLGSRFLKC 76
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 32.0 bits (71), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 8/78 (10%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVK--------RIKDYAFVHFEDRQEAITAMN 147
+V+Y+ ++ TEE++ + G V +K R K YAF+ F D + + +A+
Sbjct: 4 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 63
Query: 148 ELNGQTVAGSTLEVSLAK 165
LNG + L+ +
Sbjct: 64 NLNGYQLGSRFLKCGYSS 81
>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAF|B Chain B, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAG|A Chain A, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAG|B Chain B, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAH|A Chain A, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAH|B Chain B, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAI|A Chain A, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAI|B Chain B, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAJ|A Chain A, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAJ|B Chain B, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAK|A Chain A, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAK|B Chain B, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAL|A Chain A, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|B Chain B, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|D Chain D, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|I Chain I, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAM|A Chain A, Structure Of U2af65 Variant With Bru5c2 Dna
pdb|3VAM|B Chain B, Structure Of U2af65 Variant With Bru5c2 Dna
Length = 174
Score = 32.0 bits (71), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 20/85 (23%), Positives = 35/85 (41%), Gaps = 8/85 (9%)
Query: 88 DTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDR 139
D + + L++ L Y ++++KE +G ++ +KD YAF + D
Sbjct: 89 DYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDI 148
Query: 140 QEAITAMNELNGQTVAGSTLEVSLA 164
A+ LNG + L V A
Sbjct: 149 NVTDQAIAGLNGMQLGDKKLLVQRA 173
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 32.0 bits (71), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 12/73 (16%)
Query: 94 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERV--------KRIKDYAFVHFEDRQEAITA 145
+ + L++ L+ TEE L+ +EQ+G++ KR + + FV F E A
Sbjct: 26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAA 85
Query: 146 M----NELNGQTV 154
M + ++G+ V
Sbjct: 86 MAARPHSIDGRVV 98
>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2
pdb|3BS9|B Chain B, X-Ray Structure Of Human Tia-1 Rrm2
Length = 87
Score = 32.0 bits (71), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 14/54 (25%), Positives = 27/54 (50%), Gaps = 8/54 (14%)
Query: 119 YGRVERVKRIKD--------YAFVHFEDRQEAITAMNELNGQTVAGSTLEVSLA 164
+GR+ + +KD Y FV F ++ +A A+ ++ GQ + G + + A
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA 83
>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex
Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A
Resolution
Length = 107
Score = 31.6 bits (70), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 7/73 (9%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRV-------ERVKRIKDYAFVHFEDRQEAITAMNELN 150
L V NL ++ ++E F ++G + +R R A VHFE + +A+ A + N
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYN 91
Query: 151 GQTVAGSTLEVSL 163
G + G + L
Sbjct: 92 GVPLDGRPXNIQL 104
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 31.6 bits (70), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 4/74 (5%)
Query: 94 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKR--IKDYAFVHFEDRQEAITAMNELNG 151
K LYV + T L+ AF +G + + ++ AFV +E + A A+ ELNG
Sbjct: 14 KGNTLYVYG--EDMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNG 71
Query: 152 QTVAGSTLEVSLAK 165
V L+V++A+
Sbjct: 72 TQVESVQLKVNIAR 85
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 31.6 bits (70), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 41/82 (50%), Gaps = 8/82 (9%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRI-------KDYAFVHFEDRQEAITAMNELN 150
L+V L + +EE + F+ +G ++ + K AFV F EA A++ L+
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77
Query: 151 G-QTVAGSTLEVSLAKPPSDKK 171
G QT+ G++ + + +DK+
Sbjct: 78 GSQTMPGASSSLVVKFADTDKE 99
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 31.6 bits (70), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 7/74 (9%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------YAFVHFEDRQEAITAMNELNG 151
+YV NL + +++ F +YG + + +K+ +AFV FED ++A A+ +G
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDID-LKNRRGGPPFAFVEFEDPRDAEDAVYGRDG 83
Query: 152 QTVAGSTLEVSLAK 165
G L V +
Sbjct: 84 YDYDGYRLRVEFPR 97
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 31.6 bits (70), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 8/50 (16%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERV--------KRIKDYAFVHFEDR 139
+++ L+ T+E L+E F Q+G V+ KR + + FV F D+
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 77
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 31.6 bits (70), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 20/85 (23%), Positives = 35/85 (41%), Gaps = 8/85 (9%)
Query: 88 DTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDR 139
D + + L++ L Y ++++KE +G ++ +KD YAF + D
Sbjct: 87 DYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDI 146
Query: 140 QEAITAMNELNGQTVAGSTLEVSLA 164
A+ LNG + L V A
Sbjct: 147 NVTDQAIAGLNGMQLGDKKLLVQRA 171
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 31.6 bits (70), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 32/75 (42%), Gaps = 8/75 (10%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
L++ L Y ++++KE +G ++ +KD YAF + D A+ L
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176
Query: 150 NGQTVAGSTLEVSLA 164
NG + L V A
Sbjct: 177 NGMQLGDKKLLVQRA 191
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 31.2 bits (69), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 31/69 (44%), Gaps = 12/69 (17%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAM--- 146
L+V L T+E L+ F QYG V +KD + FV F+D T +
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASR 78
Query: 147 -NELNGQTV 154
+ L+G+ +
Sbjct: 79 PHTLDGRNI 87
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 31.2 bits (69), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 8/63 (12%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
L+V + + E+ LK FE++GR+ + +KD AF+ + R A+ A + L
Sbjct: 18 LFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSAL 77
Query: 150 NGQ 152
+ Q
Sbjct: 78 HEQ 80
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 30.8 bits (68), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 31/72 (43%), Gaps = 8/72 (11%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
L++ L Y ++++KE +G ++ +KD YAF + D A+ L
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 150 NGQTVAGSTLEV 161
NG + L V
Sbjct: 64 NGMQLGDKKLLV 75
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 30.4 bits (67), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 3/77 (3%)
Query: 88 DTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVK---RIKDYAFVHFEDRQEAIT 144
D++ + + L +NL+ TE++LKE FE + V + K A++ F+ +A
Sbjct: 92 DSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEK 151
Query: 145 AMNELNGQTVAGSTLEV 161
+ E G + G ++ +
Sbjct: 152 NLEEKQGAEIDGRSVSL 168
>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 = 30.4 bits (67), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 33/68 (48%), Gaps = 11/68 (16%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFE---DRQEAITAM 146
+++ L TE+ L+E F +YG V +K +KD + F+ FE E +
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65
Query: 147 NELNGQTV 154
+ L+G+ +
Sbjct: 66 HILDGKVI 73
>pdb|2E44|A Chain A, Solution Structure Of Rna Binding Domain In Insulin-Like
Growth Factor 2 Mrna Binding Protein 3
Length = 96
Score = 30.4 bits (67), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 5/74 (6%)
Query: 94 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-----YAFVHFEDRQEAITAMNE 148
+++ L +RN+ + E L QYG VE +++ V + + +A A+++
Sbjct: 14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDK 73
Query: 149 LNGQTVAGSTLEVS 162
LNG + TL+V+
Sbjct: 74 LNGFQLENFTLKVA 87
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 8/50 (16%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERV--------KRIKDYAFVHFEDR 139
+++ L+ T+E L+E F Q+G V+ KR + + FV F D+
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 52
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 29.6 bits (65), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 34/63 (53%), Gaps = 8/63 (12%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
L++ + + E+ LK FE++G++ + +KD AF+ + +R+ A+ A + L
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSAL 75
Query: 150 NGQ 152
+ Q
Sbjct: 76 HEQ 78
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 29.3 bits (64), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/83 (22%), Positives = 36/83 (43%), Gaps = 3/83 (3%)
Query: 88 DTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVK---RIKDYAFVHFEDRQEAIT 144
D++ + L +NL T+++LKE FE + V + K A++ F+ +A
Sbjct: 86 DSKKERDARTLLAKNLPYKVTQDELKEVFEDAAEIRLVSKDGKSKGIAYIEFKTEADAEK 145
Query: 145 AMNELNGQTVAGSTLEVSLAKPP 167
E G + G ++ + P
Sbjct: 146 TFEEKQGTEIDGRSISLYYTGEP 168
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 28.9 bits (63), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 8/59 (13%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNE 148
L V L TE+ LKE F +G V V+ KD + FV F + + + M++
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ 76
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 28.9 bits (63), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 6/77 (7%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERV------KRIKDYAFVHFEDRQEAITAMNELNG 151
++VRNL T + LK+ F + G V + K V FE + A A +NG
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNG 67
Query: 152 QTVAGSTLEVSLAKPPS 168
++G ++V + + S
Sbjct: 68 MKLSGREIDVRIDRNAS 84
>pdb|2GHP|A Chain A, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|B Chain B, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|C Chain C, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|D Chain D, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|E Chain E, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|F Chain F, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|G Chain G, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|H Chain H, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
Length = 292
Score = 28.9 bits (63), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 28/105 (26%), Positives = 53/105 (50%), Gaps = 15/105 (14%)
Query: 73 GCDIIVDWADPQEEP---DTETMSKVKVLYVRNL-TQYCTEEKLKEAFEQYGRVERVK-- 126
G ++ ++P E+ D+ T+ + + +RNL T+ E L+E+FE +G +E++
Sbjct: 186 GYTLVTKVSNPLEKSKRTDSATLEG-REIXIRNLSTELLDENLLRESFEGFGSIEKINIP 244
Query: 127 -RIKDY------AFVHFEDRQEAITAMNELNGQTVAGSTLEVSLA 164
K++ AF FE++ A A+ + N + + VSLA
Sbjct: 245 AGQKEHSFNNCCAFXVFENKDSAERAL-QXNRSLLGNREISVSLA 288
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 28.9 bits (63), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 34/70 (48%), Gaps = 3/70 (4%)
Query: 95 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVK---RIKDYAFVHFEDRQEAITAMNELNG 151
+ L +NL+ TE++LKE FE + V + K A++ F+ +A + E G
Sbjct: 16 ARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQG 75
Query: 152 QTVAGSTLEV 161
+ G ++ +
Sbjct: 76 AEIDGRSVSL 85
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 6/77 (7%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERV------KRIKDYAFVHFEDRQEAITAMNELNG 151
++VRNL T + LK+ F + G V + K V FE + A A +NG
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNG 70
Query: 152 QTVAGSTLEVSLAKPPS 168
++G ++V + + S
Sbjct: 71 MKLSGREIDVRIDRNAS 87
>pdb|3EGN|A Chain A, C-Terminal Rna Recognition Motif Of The U11U12 65K PROTEIN
Length = 143
Score = 28.5 bits (62), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 24/91 (26%), Positives = 42/91 (46%), Gaps = 13/91 (14%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYG-------------RVERVKRIKDYAFVHFEDRQEAIT 144
+YV+NL ++ E+ LK F +Y R+ + R+K AF+ + + A
Sbjct: 48 IYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAK 107
Query: 145 AMNELNGQTVAGSTLEVSLAKPPSDKKKKEE 175
A+ E NG + G + V A+ K+ +E
Sbjct: 108 ALKEANGYVLFGKPMVVQFARSARPKQDPKE 138
>pdb|1XH9|A Chain A, Crystal Structures Of Protein Kinase B Selective
Inhibitors In Complex With Protein Kinase A And Mutants
Length = 350
Score = 28.5 bits (62), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 25/43 (58%), Gaps = 5/43 (11%)
Query: 43 YTKLLEYGLDKRIAGKLDDIFKTGKHL-----LSRGCDIIVDW 80
Y K+ ++GL KR+ G+ + T ++L LS+G + VDW
Sbjct: 179 YIKVTDFGLAKRVKGRTWXLCGTPEYLAPEIILSKGYNKAVDW 221
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 28.1 bits (61), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 39/87 (44%), Gaps = 9/87 (10%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQY------GRV--ERVKRIKDYAFVHFEDRQEAITAMNEL 149
L+V +LT + L E F + G+V ++ K Y FV F D E A+ E
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTEC 71
Query: 150 NGQTVAGST-LEVSLAKPPSDKKKKEE 175
G GS + +S+A P + + K E
Sbjct: 72 QGAVGLGSKPVRLSVAIPKASRVKPVE 98
>pdb|1X4F|A Chain A, Solution Structure Of The Second Rrm Domain In Matrin 3
Length = 112
Score = 28.1 bits (61), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 8/73 (10%)
Query: 83 PQEEPDTETMSKV---KVLYVRNL--TQYCTEEKLKEAFEQYGRVER--VKRIKDYAFVH 135
P+ +PD + K +V+++ NL + Y LK A E YG+++ + R+K AF+
Sbjct: 10 PEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLA-EPYGKIKNYILMRMKSQAFIE 68
Query: 136 FEDRQEAITAMNE 148
E R++A+ ++
Sbjct: 69 METREDAMAMVDH 81
>pdb|2JDT|A Chain A, Structure Of Pka-Pkb Chimera Complexed With
Isoquinoline-5- Sulfonic Acid (2-(2-(4-Chlorobenzyloxy)
Ethylamino)ethyl) Amide
pdb|2JDV|A Chain A, Structure Of Pka-Pkb Chimera Complexed With A-443654
pdb|2UVX|A Chain A, Structure Of Pka-Pkb Chimera Complexed With 7-Azaindole
pdb|2UW4|A Chain A, Structure Of Pka-Pkb Chimera Complexed With
2-(4-(5-Methyl- 1h-Pyrazol-4-Yl)-Phenyl)-Ethylamine
pdb|2UW7|A Chain A, Structure Of Pka-Pkb Chimera Complexed With 4-(4-Chloro-
Phenyl)-4-(4-(1h-Pyrazol-4-Yl)-Phenyl)-Piperidine
pdb|4AXA|A Chain A, Structure Of Pka-pkb Chimera Complexed With
(1s)-2-amino-1-(
4-chlorophenyl)-1-(4-(1h-pyrazol-4-yl)phenyl)ethan-1-ol
Length = 351
Score = 27.3 bits (59), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 24/43 (55%), Gaps = 5/43 (11%)
Query: 43 YTKLLEYGLDKRIAGKLDDIFKTGKHL-----LSRGCDIIVDW 80
Y K+ ++G KR+ G+ + T ++L LS+G + VDW
Sbjct: 180 YIKVTDFGFAKRVKGRTWXLCGTPEYLAPEIILSKGYNKAVDW 222
>pdb|1Q61|A Chain A, Pka Triple Mutant Model Of Pkb
Length = 350
Score = 27.3 bits (59), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 24/43 (55%), Gaps = 5/43 (11%)
Query: 43 YTKLLEYGLDKRIAGKLDDIFKTGKHL-----LSRGCDIIVDW 80
Y K+ ++G KR+ G+ + T ++L LS+G + VDW
Sbjct: 179 YIKVTDFGFAKRVKGRTWXLCGTPEYLAPEIILSKGYNKAVDW 221
>pdb|3L9M|A Chain A, Crystal Structure Of Pkab3 (Pka Triple Mutant V123a,
L173m, Q181k) With Compound 18
pdb|3L9M|B Chain B, Crystal Structure Of Pkab3 (Pka Triple Mutant V123a,
L173m, Q181k) With Compound 18
pdb|3L9N|A Chain A, Crystal Structure Of Pkab3 (Pka Triple Mutant V123a,
L173m, Q181k) With Compound 27
Length = 351
Score = 27.3 bits (59), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 24/43 (55%), Gaps = 5/43 (11%)
Query: 43 YTKLLEYGLDKRIAGKLDDIFKTGKHL-----LSRGCDIIVDW 80
Y K+ ++G KR+ G+ + T ++L LS+G + VDW
Sbjct: 180 YIKVTDFGFAKRVKGRTWXLCGTPEYLAPEIILSKGYNKAVDW 222
>pdb|1SZM|A Chain A, Dual Binding Mode Of Bisindolylmaleimide 2 To Protein
Kinase A (Pka)
pdb|1SZM|B Chain B, Dual Binding Mode Of Bisindolylmaleimide 2 To Protein
Kinase A (Pka)
Length = 350
Score = 27.3 bits (59), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 24/43 (55%), Gaps = 5/43 (11%)
Query: 43 YTKLLEYGLDKRIAGKLDDIFKTGKHL-----LSRGCDIIVDW 80
Y K+ ++G KR+ G+ + T ++L LS+G + VDW
Sbjct: 179 YIKVTDFGFAKRVKGRTWXLCGTPEYLAPEIILSKGYNKAVDW 221
>pdb|2VO0|A Chain A, Structure Of Pka-Pkb Chimera Complexed With C-(4-(4-
Chlorophenyl)-1-(7h-Pyrrolo(2,
3-D)pyrimidin-4-Yl)piperidin- 4-Yl)methylamine
Length = 351
Score = 27.3 bits (59), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 24/43 (55%), Gaps = 5/43 (11%)
Query: 43 YTKLLEYGLDKRIAGKLDDIFKTGKHL-----LSRGCDIIVDW 80
Y K+ ++G KR+ G+ + T ++L LS+G + VDW
Sbjct: 180 YIKVTDFGFAKRVKGRTWXLCGTPEYLAPEIILSKGYNKAVDW 222
>pdb|2UVY|A Chain A, Structure Of Pka-pkb Chimera Complexed With Methyl-(4-(9h-
Purin-6-yl)-benzyl)-amine
pdb|2UVZ|A Chain A, Structure Of Pka-Pkb Chimera Complexed With
C-Phenyl-C-(4-( 9h-Purin-6-Yl)-Phenyl)-Methylamine
pdb|2UW0|A Chain A, Structure Of Pka-Pkb Chimera Complexed With 6-(4-(4-(4-
Chloro-Phenyl)-Piperidin-4-Yl)-Phenyl)-9h-Purine
pdb|2UW3|A Chain A, Structure Of Pka-Pkb Chimera Complexed With 5-Methyl-4-
Phenyl-1h-Pyrazole
pdb|2UW5|A Chain A, Structure Of Pka-Pkb Chimera Complexed With (R)-2-(4-
Chloro-Phenyl)-2-(4-1h-Pyrazol-4-Yl)-Phenyl)-Ethylamine
pdb|2UW6|A Chain A, Structure Of Pka-Pkb Chimera Complexed With (S)-2-(4-
Chloro-Phenyl)-2-(4-1h-Pyrazol-4-Yl)-Phenyl)-Ethylamine
pdb|2UW8|A Chain A, Structure Of Pka-Pkb Chimera Complexed With 2-(4-Chloro-
Phenyl)-2-Phenyl-Ethylamine
pdb|2VNW|A Chain A, Structure Of Pka-Pkb Chimera Complexed With
(1-(9h-Purin-6- Yl)piperidin-4-Yl)methanamine
pdb|2VNY|A Chain A, Structure Of Pka-Pkb Chimera Complexed With
(1-(9h-Purin-6- Yl)piperidin-4-Yl)amine
pdb|2VO3|A Chain A, Structure Of Pka-Pkb Chimera Complexed With C-(4-(4-
Chlorophenyl)-1-(7h-Pyrrolo(2,
3-D)pyrimidin-4-Yl)piperidin- 4-Yl)methylamine
pdb|2VO6|A Chain A, Structure Of Pka-Pkb Chimera Complexed With 4-(4-
Chlorobenzyl)-1-(7h-Pyrrolo(2,
3-D)pyrimidin-4-Yl)piperidin- 4-Ylamine
Length = 351
Score = 27.3 bits (59), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 24/43 (55%), Gaps = 5/43 (11%)
Query: 43 YTKLLEYGLDKRIAGKLDDIFKTGKHL-----LSRGCDIIVDW 80
Y K+ ++G KR+ G+ + T ++L LS+G + VDW
Sbjct: 180 YIKVTDFGFAKRVKGRTWXLCGTPEYLAPEIILSKGYNKAVDW 222
>pdb|3AMA|A Chain A, Protein Kinase A Sixfold Mutant Model Of Aurora B With
Inhibitor Jnj- 7706621
pdb|3AMB|A Chain A, Protein Kinase A Sixfold Mutant Model Of Aurora B With
Inhibitor Vx- 680
Length = 351
Score = 27.3 bits (59), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 24/43 (55%), Gaps = 5/43 (11%)
Query: 43 YTKLLEYGLDKRIAGKLDDIFKTGKHL-----LSRGCDIIVDW 80
Y K+ ++G KR+ G+ + T ++L LS+G + VDW
Sbjct: 180 YIKVADFGFAKRVKGRTWXLCGTPEYLAPEIILSKGYNKAVDW 222
>pdb|1SMH|A Chain A, Protein Kinase A Variant Complex With Completely Ordered
N- Terminal Helix
pdb|1XHA|A Chain A, Crystal Structures Of Protein Kinase B Selective
Inhibitors In Complex With Protein Kinase A And Mutants
Length = 350
Score = 27.3 bits (59), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 25/43 (58%), Gaps = 5/43 (11%)
Query: 43 YTKLLEYGLDKRIAGKLDDIFKTGKHL-----LSRGCDIIVDW 80
Y ++ ++GL KR+ G+ + T ++L LS+G + VDW
Sbjct: 179 YIQVTDFGLAKRVKGRTWXLCGTPEYLAPEIILSKGYNKAVDW 221
>pdb|2GNJ|A Chain A, Pka Three Fold Mutant Model Of Rho-Kinase With Y-27632
pdb|2GNL|A Chain A, Pka Threefold Mutant Model Of Rho-Kinase With Inhibitor H-
1152p
Length = 350
Score = 27.3 bits (59), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 24/43 (55%), Gaps = 5/43 (11%)
Query: 43 YTKLLEYGLDKRIAGKLDDIFKTGKHL-----LSRGCDIIVDW 80
Y K+ ++G KR+ G+ + T ++L LS+G + VDW
Sbjct: 179 YIKVADFGFAKRVKGRTWXLCGTPEYLAPEIILSKGYNKAVDW 221
>pdb|3AIB|A Chain A, Crystal Structure Of Glucansucrase
pdb|3AIB|B Chain B, Crystal Structure Of Glucansucrase
pdb|3AIB|C Chain C, Crystal Structure Of Glucansucrase
pdb|3AIB|D Chain D, Crystal Structure Of Glucansucrase
pdb|3AIB|G Chain G, Crystal Structure Of Glucansucrase
pdb|3AIB|E Chain E, Crystal Structure Of Glucansucrase
pdb|3AIB|F Chain F, Crystal Structure Of Glucansucrase
pdb|3AIB|H Chain H, Crystal Structure Of Glucansucrase
pdb|3AIC|A Chain A, Crystal Structure Of Glucansucrase From Streptococcus
Mutans
pdb|3AIC|B Chain B, Crystal Structure Of Glucansucrase From Streptococcus
Mutans
pdb|3AIC|C Chain C, Crystal Structure Of Glucansucrase From Streptococcus
Mutans
pdb|3AIC|D Chain D, Crystal Structure Of Glucansucrase From Streptococcus
Mutans
pdb|3AIC|E Chain E, Crystal Structure Of Glucansucrase From Streptococcus
Mutans
pdb|3AIC|F Chain F, Crystal Structure Of Glucansucrase From Streptococcus
Mutans
pdb|3AIC|G Chain G, Crystal Structure Of Glucansucrase From Streptococcus
Mutans
pdb|3AIC|H Chain H, Crystal Structure Of Glucansucrase From Streptococcus
Mutans
pdb|3AIE|A Chain A, Crystal Structure Of Glucansucrase From Streptococcus
Mutans
pdb|3AIE|B Chain B, Crystal Structure Of Glucansucrase From Streptococcus
Mutans
pdb|3AIE|C Chain C, Crystal Structure Of Glucansucrase From Streptococcus
Mutans
pdb|3AIE|D Chain D, Crystal Structure Of Glucansucrase From Streptococcus
Mutans
pdb|3AIE|E Chain E, Crystal Structure Of Glucansucrase From Streptococcus
Mutans
pdb|3AIE|F Chain F, Crystal Structure Of Glucansucrase From Streptococcus
Mutans
pdb|3AIE|G Chain G, Crystal Structure Of Glucansucrase From Streptococcus
Mutans
pdb|3AIE|H Chain H, Crystal Structure Of Glucansucrase From Streptococcus
Mutans
Length = 844
Score = 27.3 bits (59), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 2/43 (4%)
Query: 57 GKLDDIFKTGKHLLSRGCDIIVDWADPQ--EEPDTETMSKVKV 97
G DD+ K K L S+G ++ DW Q P+ E ++ +V
Sbjct: 690 GTADDLVKAIKALHSKGIKVMADWVPDQMYALPEKEVVTATRV 732
>pdb|2GNF|A Chain A, Protein Kinase A Fivefold Mutant Model Of Rho-Kinase With
Y- 27632
Length = 350
Score = 27.3 bits (59), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 24/43 (55%), Gaps = 5/43 (11%)
Query: 43 YTKLLEYGLDKRIAGKLDDIFKTGKHL-----LSRGCDIIVDW 80
Y K+ ++G KR+ G+ + T ++L LS+G + VDW
Sbjct: 179 YIKVADFGFAKRVKGRTWXLCGTPEYLAPEIILSKGYNKAVDW 221
>pdb|2GNG|A Chain A, Protein Kinase A Fivefold Mutant Model Of Rho-Kinase
pdb|2GNH|A Chain A, Pka Five Fold Mutant Model Of Rho-Kinase With H1152p
pdb|2GNI|A Chain A, Pka Fivefold Mutant Model Of Rho-Kinase With Inhibitor
Fasudil (Ha1077)
Length = 350
Score = 27.3 bits (59), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 24/43 (55%), Gaps = 5/43 (11%)
Query: 43 YTKLLEYGLDKRIAGKLDDIFKTGKHL-----LSRGCDIIVDW 80
Y K+ ++G KR+ G+ + T ++L LS+G + VDW
Sbjct: 179 YIKVADFGFAKRVKGRTWXLCGTPEYLAPEIILSKGYNKAVDW 221
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
0.314 0.131 0.368
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,075,689
Number of Sequences: 62578
Number of extensions: 226192
Number of successful extensions: 688
Number of sequences better than 100.0: 163
Number of HSP's better than 100.0 without gapping: 98
Number of HSP's successfully gapped in prelim test: 65
Number of HSP's that attempted gapping in prelim test: 518
Number of HSP's gapped (non-prelim): 180
length of query: 230
length of database: 14,973,337
effective HSP length: 96
effective length of query: 134
effective length of database: 8,965,849
effective search space: 1201423766
effective search space used: 1201423766
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 50 (23.9 bits)