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= 025401
(253 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 78.2 bits (191), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 39/81 (48%), Positives = 52/81 (64%)
Query: 42 TSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKR 101
TSL V NL + P+ +RR FE++G + D+Y+PRD Y+ E RGF F++F + DA +A
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 102 HMDGQVLLGRELTVVFAEENR 122
MDG VL GREL V A R
Sbjct: 131 AMDGAVLDGRELRVQMARYGR 151
>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 = 77.8 bits (190), Expect = 6e-15, Method: Compositional matrix adjust.
Identities = 39/81 (48%), Positives = 52/81 (64%)
Query: 42 TSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKR 101
TSL V NL + P+ +RR FE++G + D+Y+PRD Y+ E RGF F++F + DA +A
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 102 HMDGQVLLGRELTVVFAEENR 122
MDG VL GREL V A R
Sbjct: 108 AMDGAVLDGRELRVQMARYGR 128
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 69.3 bits (168), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 36/88 (40%), Positives = 54/88 (61%)
Query: 39 DLPTSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAE 98
D +L V NL + P+ +RR FE++G + D+Y+PR+ ++ PRGF F++F + DA +
Sbjct: 11 DGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQD 70
Query: 99 AKRHMDGQVLLGRELTVVFAEENRKKPS 126
A+ MDG L GREL V A R+ S
Sbjct: 71 AEAAMDGAELDGRELRVQVARYGRRDLS 98
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 62.8 bits (151), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 44/73 (60%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
L VRNL + ED+ + F +G + +++ P D + +P+GF F+ F+ P+ A +A +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 104 DGQVLLGRELTVV 116
DGQV GR L V+
Sbjct: 71 DGQVFQGRMLHVL 83
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 58.2 bits (139), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 29/83 (34%), Positives = 43/83 (51%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
+ V +L + EDI+ F FG I D + +D +G+ +G+GF+ F DA A HM
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 104 DGQVLLGRELTVVFAEENRKKPS 126
GQ L GR++ +A PS
Sbjct: 78 GGQWLGGRQIRTNWATRKPPAPS 100
>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 = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 29/83 (34%), Positives = 45/83 (54%), Gaps = 2/83 (2%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
+ V +L + EDI+ F FG I D + +D +G+ +G+GF+ F DA A + M
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 104 DGQVLLGRELTVVFAEENRKKPS 126
GQ L GR++ +A RK P+
Sbjct: 78 GGQWLGGRQIRTNWA--TRKPPA 98
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 53.5 bits (127), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 28/86 (32%), Positives = 46/86 (53%), Gaps = 3/86 (3%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
L V L D + + + F ++G I ++ + +D + RGFGF+ F DDA +A M
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 104 DGQVLLGRELTVVFA---EENRKKPS 126
+G+ + GR++ V A +NR PS
Sbjct: 75 NGKSVDGRQIRVDQAGKSSDNRSGPS 100
>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 = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 41/73 (56%)
Query: 43 SLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRH 102
+L V + +D +RR FE +G IK I++ SG+PRG+ FI++ D A +H
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 103 MDGQVLLGRELTV 115
DG+ + GR + V
Sbjct: 164 ADGKKIDGRRVLV 176
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 36/63 (57%)
Query: 43 SLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRH 102
++ V NL D R D++ F FG+I IYL +D +G+ +GF FI F +DAA A
Sbjct: 17 TIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAG 76
Query: 103 MDG 105
+ G
Sbjct: 77 VSG 79
>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 = 52.4 bits (124), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 41/73 (56%)
Query: 43 SLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRH 102
+L V + +D +RR FE +G IK I++ SG+PRG+ FI++ D A +H
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 103 MDGQVLLGRELTV 115
DG+ + GR + V
Sbjct: 164 ADGKKIDGRRVLV 176
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 51.2 bits (121), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 30/88 (34%), Positives = 45/88 (51%), Gaps = 5/88 (5%)
Query: 39 DLPTSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAE 98
D P L + L + + ++ F + G I ++ L +D S + RGF FI F P DA
Sbjct: 5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTS-KSRGFAFITFENPADAKN 63
Query: 99 AKRHMDGQVLLGRELTVVFAEENRKKPS 126
A + M+G+ L G+ + V E KKPS
Sbjct: 64 AAKDMNGKSLHGKAIKV----EQAKKPS 87
>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 = 50.4 bits (119), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 42/77 (54%)
Query: 42 TSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKR 101
T+L+V L + E+ R F G I+ L RD +G+ G+GF+ +++P DA +A
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 102 HMDGQVLLGRELTVVFA 118
++G L + + V +A
Sbjct: 63 TLNGLRLQTKTIKVSYA 79
Score = 37.4 bits (85), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 34/64 (53%)
Query: 43 SLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRH 102
+L V L +++ + F Q+G I + D +G RG GFI+F + +A EA +
Sbjct: 90 NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 149
Query: 103 MDGQ 106
++GQ
Sbjct: 150 LNGQ 153
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 50.4 bits (119), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 30/83 (36%), Positives = 43/83 (51%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
L V L + + + F FG I DI +P DY + + RGF F++F +DAA A +M
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 104 DGQVLLGRELTVVFAEENRKKPS 126
+ L GR + V A+ R K S
Sbjct: 75 NESELFGRTIRVNLAKPMRIKES 97
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 43/76 (56%), Gaps = 5/76 (6%)
Query: 40 LPTSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEA 99
L + V NL ++ ++ R F +G ++ +++ R+ P GF F++F +P DAA+A
Sbjct: 72 LDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADA 126
Query: 100 KRHMDGQVLLGRELTV 115
R +DG+ L G + V
Sbjct: 127 VRELDGRTLCGCRVRV 142
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 43/76 (56%), Gaps = 5/76 (6%)
Query: 40 LPTSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEA 99
L + V NL ++ ++ R F +G ++ +++ R+ P GF F++F +P DAA+A
Sbjct: 72 LDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADA 126
Query: 100 KRHMDGQVLLGRELTV 115
R +DG+ L G + V
Sbjct: 127 VRDLDGRTLCGCRVRV 142
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 48.9 bits (115), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 41/78 (52%), Gaps = 2/78 (2%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYY-SGEPRGFGFIQFVEPDDAAEAKRH 102
+LVRN+ +IR F FG +K + LP+ +G RGFGF+ F+ DA +A
Sbjct: 18 ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNA 77
Query: 103 MDGQV-LLGRELTVVFAE 119
+ L GR L + +A+
Sbjct: 78 LCHSTHLYGRRLVLEWAD 95
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 48.5 bits (114), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 26/66 (39%), Positives = 35/66 (53%)
Query: 57 DIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHMDGQVLLGRELTVV 116
D+R F ++G I D+ + D S RGF F+ F DDA EAK +G L GR + V
Sbjct: 31 DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD 90
Query: 117 FAEENR 122
F+ R
Sbjct: 91 FSITKR 96
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 48.5 bits (114), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 28/88 (31%), Positives = 45/88 (51%), Gaps = 5/88 (5%)
Query: 42 TSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKR 101
+L V+NL E +R+ F FG I + + G +GFGF+ F P++A +A
Sbjct: 16 VNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVT 73
Query: 102 HMDGQVLLGRELTVVFA---EENRKKPS 126
M+G+++ + L V A EE + PS
Sbjct: 74 EMNGRIVATKPLYVALAQRKEERQSGPS 101
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 48.5 bits (114), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 29/75 (38%), Positives = 40/75 (53%), Gaps = 6/75 (8%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
L V NL D ED +R FE++G ++++ RD RGFGFI+ A AK +
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAEL 78
Query: 104 DGQVLLGRELTVVFA 118
DG +L R L + FA
Sbjct: 79 DGTILKSRPLRIRFA 93
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 48.1 bits (113), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 39/76 (51%), Gaps = 8/76 (10%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
L VRNL + E + + F QFG ++ + +DY FI F E D A +A M
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKDY--------AFIHFDERDGAVKAMEEM 65
Query: 104 DGQVLLGRELTVVFAE 119
+G+ L G + +VFA+
Sbjct: 66 NGKDLEGENIEIVFAK 81
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 48.1 bits (113), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 43/80 (53%)
Query: 39 DLPTSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAE 98
D T+L+V L + ++ + F G I+ L RD +G+ G+GF+ + +P+DA +
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 99 AKRHMDGQVLLGRELTVVFA 118
A ++G L + + V +A
Sbjct: 62 AINTLNGLKLQTKTIKVSYA 81
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 48.1 bits (113), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 40/78 (51%)
Query: 43 SLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRH 102
+L V +L + E +R F+ F + ++ D +G RG+GF+ F DDA A
Sbjct: 89 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 148
Query: 103 MDGQVLLGRELTVVFAEE 120
M GQ L GR L + +A +
Sbjct: 149 MQGQDLNGRPLRINWAAK 166
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 48.1 bits (113), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 26/66 (39%), Positives = 35/66 (53%)
Query: 57 DIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHMDGQVLLGRELTVV 116
D+R F ++G I D+ + D S RGF F+ F DDA EAK +G L GR + V
Sbjct: 28 DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD 87
Query: 117 FAEENR 122
F+ R
Sbjct: 88 FSITKR 93
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 47.8 bits (112), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 26/66 (39%), Positives = 35/66 (53%)
Query: 57 DIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHMDGQVLLGRELTVV 116
D+R F ++G I D+ + D S RGF F+ F DDA EAK +G L GR + V
Sbjct: 62 DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD 121
Query: 117 FAEENR 122
F+ R
Sbjct: 122 FSITKR 127
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 47.4 bits (111), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 43/80 (53%)
Query: 39 DLPTSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAE 98
D T+L+V L + ++ + F G I+ L RD +G+ G+GF+ + +P+DA +
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 99 AKRHMDGQVLLGRELTVVFA 118
A ++G L + + V +A
Sbjct: 62 AINTLNGLKLQTKTIKVSYA 81
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 41/78 (52%), Gaps = 2/78 (2%)
Query: 43 SLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRH 102
+L V L +++ + F Q+G I + D +G RG GFI+F + +A EA +
Sbjct: 92 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 151
Query: 103 MDGQVLLGRE--LTVVFA 118
++GQ LG +TV FA
Sbjct: 152 LNGQKPLGAAEPITVKFA 169
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 47.4 bits (111), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 39/75 (52%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
L V L + + + F FG I DI +P DY + + RGF F++F +DAA A +M
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 104 DGQVLLGRELTVVFA 118
+ L GR + V A
Sbjct: 126 NESELFGRTIRVNLA 140
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 47.0 bits (110), Expect = 9e-06, Method: Composition-based stats.
Identities = 27/76 (35%), Positives = 40/76 (52%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
L V L + + + F FG I DI +P DY + + RGF F++F +DAA A +M
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 104 DGQVLLGRELTVVFAE 119
+ L GR + V A+
Sbjct: 68 NESELFGRTIRVNLAK 83
>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 = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 40/76 (52%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
L V L + + + F FG I DI +P DY + + RGF F++F +DAA A +M
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 104 DGQVLLGRELTVVFAE 119
+ L GR + V A+
Sbjct: 70 NESELFGRTIRVNLAK 85
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 45/82 (54%), Gaps = 3/82 (3%)
Query: 43 SLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRH 102
++ V NL + E ++ F QFG + ++ L D + +P+GFGF++ ++ + +EA
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVE-MQEESVSEAIAK 61
Query: 103 MDGQVLLGRELTVVFAEENRKK 124
+D +GR + V E N KK
Sbjct: 62 LDNTDFMGRTIRV--TEANPKK 81
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 40/75 (53%)
Query: 41 PTSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAK 100
P L V +L + + +R FE FG I+ I L D +G +G+GFI F + + A +A
Sbjct: 26 PMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKAL 85
Query: 101 RHMDGQVLLGRELTV 115
++G L GR + V
Sbjct: 86 EQLNGFELAGRPMKV 100
>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 = 46.6 bits (109), Expect = 1e-05, Method: Composition-based stats.
Identities = 27/75 (36%), Positives = 39/75 (52%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
L V L + + + F FG I DI +P DY + + RGF F++F +DAA A +M
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 104 DGQVLLGRELTVVFA 118
+ L GR + V A
Sbjct: 65 NESELFGRTIRVNLA 79
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 41 PTSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRD-YYSGEPRGFGFIQFVEPDDAAEA 99
PT + + L + + I F +G IK I +P + + +G+ +++F PD+A +A
Sbjct: 4 PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKA 63
Query: 100 KRHMDGQVLLGRELT 114
+HMDG + G+E+T
Sbjct: 64 LKHMDGGQIDGQEIT 78
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/59 (40%), Positives = 32/59 (54%)
Query: 57 DIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHMDGQVLLGRELTV 115
D+R F ++G I D+ + D S RGF F+ F DDA EAK +G L GR + V
Sbjct: 31 DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 89
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
Length = 124
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 1/74 (1%)
Query: 43 SLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRH 102
S+ V N+ + +D+ F G+I I + D +SG P+G+ +I+F E ++ +A
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAE-RNSVDAAVA 96
Query: 103 MDGQVLLGRELTVV 116
MD V GR + V+
Sbjct: 97 MDETVFRGRTIKVL 110
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 44/83 (53%), Gaps = 1/83 (1%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
+ V + H+C ++R F++FG + ++ + D PRGFGFI F E + + + +M
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITF-EDEQSVDQAVNM 71
Query: 104 DGQVLLGRELTVVFAEENRKKPS 126
++G+++ V AE K S
Sbjct: 72 HFHDIMGKKVEVKRAEPRDSKSS 94
>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 = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 43/77 (55%), Gaps = 6/77 (7%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
+ V ++ D +DI+ FE FG IK L RD +G+ +G+GFI++ + + +A M
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 104 D-----GQVL-LGRELT 114
+ GQ L +G+ +T
Sbjct: 188 NLFDLGGQYLRVGKAVT 204
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 39/72 (54%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
+ V ++ ++ + IR+ F FG IK I + D + + +GF F+++ P+ A A M
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 104 DGQVLLGRELTV 115
+ +L GR + V
Sbjct: 91 NSVMLGGRNIKV 102
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 41/79 (51%)
Query: 42 TSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKR 101
+ L V +L + + +R FE FG I +I L +D +G +G+GFI F + + A A
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 102 HMDGQVLLGRELTVVFAEE 120
++G L GR + V E
Sbjct: 66 QLNGFELAGRPMRVGHVTE 84
>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
pdb|3MD1|B Chain B, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
Length = 83
Score = 45.4 bits (106), Expect = 3e-05, Method: Composition-based stats.
Identities = 26/76 (34%), Positives = 39/76 (51%)
Query: 43 SLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRH 102
+L V +L + E +R F+ F + ++ D +G RG+GF+ F DDA A
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 103 MDGQVLLGRELTVVFA 118
M GQ L GR L + +A
Sbjct: 63 MQGQDLNGRPLRINWA 78
>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of
Fbp-Interacting Repressor (Fir)
pdb|2KXH|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fir In
The Complex With Fbp Nbox Peptide
Length = 199
Score = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 43/77 (55%), Gaps = 6/77 (7%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
+ V ++ D +DI+ FE FG IK L RD +G+ +G+GFI++ + + +A M
Sbjct: 113 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 172
Query: 104 D-----GQVL-LGRELT 114
+ GQ L +G+ +T
Sbjct: 173 NLFDLGGQYLRVGKAVT 189
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 38/70 (54%)
Query: 46 VRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHMDG 105
V ++ ++ + IR+ F FG IK I + D + + +GF F+++ P+ A A M+
Sbjct: 18 VGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNS 77
Query: 106 QVLLGRELTV 115
+L GR + V
Sbjct: 78 VMLGGRNIKV 87
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 44/82 (53%)
Query: 43 SLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRH 102
S+ V N+ ++ E ++ F + G + L D +G+P+G+GF ++ + + A A R+
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 103 MDGQVLLGRELTVVFAEENRKK 124
++G+ GR L V A + K
Sbjct: 70 LNGREFSGRALRVDNAASEKNK 91
>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX
pdb|1P27|D Chain D, Crystal Structure Of The Human Y14MAGOH COMPLEX
Length = 106
Score = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 40/72 (55%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
L V + + EDI F ++G IK+I+L D +G +G+ +++ +A A +
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 104 DGQVLLGRELTV 115
+GQ L+G+ ++V
Sbjct: 86 NGQDLMGQPISV 97
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 3/85 (3%)
Query: 42 TSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGE---PRGFGFIQFVEPDDAAE 98
+ L ++NL E ++ F + GAIK + + GFGF+++ +P+ A +
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 99 AKRHMDGQVLLGRELTVVFAEENRK 123
A + + G + G +L V +E K
Sbjct: 66 ALKQLQGHTVDGHKLEVRISERATK 90
>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 = 44.7 bits (104), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 40/72 (55%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
L V + + EDI F ++G IK+I+L D +G +G+ +++ +A A +
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 104 DGQVLLGRELTV 115
+GQ L+G+ ++V
Sbjct: 85 NGQDLMGQPISV 96
>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 = 44.7 bits (104), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 40/72 (55%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
L V + + EDI F ++G IK+I+L D +G +G+ +++ +A A +
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 104 DGQVLLGRELTV 115
+GQ L+G+ ++V
Sbjct: 72 NGQDLMGQPISV 83
>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 90
Score = 44.7 bits (104), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 40/72 (55%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
L V + + EDI F ++G IK+I+L D +G +G+ +++ +A A +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 104 DGQVLLGRELTV 115
+GQ L+G+ ++V
Sbjct: 70 NGQDLMGQPISV 81
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 44.7 bits (104), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 37/69 (53%), Gaps = 4/69 (5%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQF---VEPDDAAEAK 100
L + L + E +R +EQ+G + D + RD S RGFGF+ F E D A A+
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAAR 89
Query: 101 RH-MDGQVL 108
H +DG+V+
Sbjct: 90 PHSIDGRVV 98
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 44.7 bits (104), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 40/72 (55%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
L V + + EDI F ++G IK+I+L D +G +G+ +++ +A A +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 104 DGQVLLGRELTV 115
+GQ L+G+ ++V
Sbjct: 70 NGQDLMGQPISV 81
>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 = 44.7 bits (104), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 39/68 (57%), Gaps = 3/68 (4%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEP---DDAAEAK 100
+ + L D +++R F ++G + D+ + +D +G RGFGF+ F +P D+ + +
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65
Query: 101 RHMDGQVL 108
+DG+V+
Sbjct: 66 HILDGKVI 73
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 4/61 (6%)
Query: 39 DLPTSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAE 98
D + V + D RP++ F Q+G I D L D +G+ RGFGF+ + D+A+
Sbjct: 85 DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTY----DSAD 140
Query: 99 A 99
A
Sbjct: 141 A 141
>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
pdb|2J0Q|G Chain G, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
Length = 109
Score = 44.7 bits (104), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 40/72 (55%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
L V + + EDI F ++G IK+I+L D +G +G+ +++ +A A +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 104 DGQVLLGRELTV 115
+GQ L+G+ ++V
Sbjct: 70 NGQDLMGQPISV 81
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 44.3 bits (103), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 5/70 (7%)
Query: 46 VRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHMDG 105
V NL ++ R F +G ++ +++ R+ P GF F++F +P DA +A R +DG
Sbjct: 5 VGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDG 59
Query: 106 QVLLGRELTV 115
+V+ G + V
Sbjct: 60 KVICGSRVRV 69
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 44.3 bits (103), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 41 PTSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAK 100
P L V N+ R D+R+ F QFG I D+ + + +GFGF+ F DA A+
Sbjct: 15 PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEII--FNERGSKGFGFVTFENSADADRAR 72
Query: 101 RHMDGQVLLGRELTV 115
+ G V+ GR++ V
Sbjct: 73 EKLHGTVVEGRKIEV 87
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 43.9 bits (102), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 41 PTSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAK 100
P L V N+ R D+R+ F QFG I D+ + + +GFGF+ F DA A+
Sbjct: 29 PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEII--FNERGSKGFGFVTFENSADADRAR 86
Query: 101 RHMDGQVLLGRELTV 115
+ G V+ GR++ V
Sbjct: 87 EKLHGTVVEGRKIEV 101
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 41/75 (54%), Gaps = 6/75 (8%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
L V NL D E++R+ FE++G ++++ +D +GFGFI+ A AK +
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVEL 71
Query: 104 DGQVLLGRELTVVFA 118
D L G++L V FA
Sbjct: 72 DNMPLRGKQLRVRFA 86
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 41/75 (54%), Gaps = 6/75 (8%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
L V NL D E++R+ FE++G ++++ +D +GFGFI+ A AK +
Sbjct: 25 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVEL 78
Query: 104 DGQVLLGRELTVVFA 118
D L G++L V FA
Sbjct: 79 DNMPLRGKQLRVRFA 93
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 45/87 (51%)
Query: 39 DLPTSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAE 98
D+ +L+V + +R+ FE++G I+ + + D + + RG+GF++F A +
Sbjct: 40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQ 99
Query: 99 AKRHMDGQVLLGRELTVVFAEENRKKP 125
A ++G +L + L V A ++P
Sbjct: 100 AIAGLNGFNILNKRLKVALAASGHQRP 126
>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 = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 6/77 (7%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRH- 102
+ V ++ D +DI+ FE FG IK L RD +G+ +G+GFI++ + + +A
Sbjct: 112 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSX 171
Query: 103 ----MDGQVL-LGRELT 114
+ GQ L +G+ +T
Sbjct: 172 NLFDLGGQYLRVGKAVT 188
Score = 36.6 bits (83), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 36/72 (50%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
+ V ++ ++ + IR+ F FG IK I D + + +GF F+++ P+ A A
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 104 DGQVLLGRELTV 115
+ L GR + V
Sbjct: 75 NSVXLGGRNIKV 86
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 31/54 (57%)
Query: 65 FGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHMDGQVLLGRELTVVFA 118
FG I D + +D +G+ +G+GF+ F DA A + M GQ L GR++ +A
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA 83
>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
pdb|1U1K|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt 7da
Ggg); A Human Telomeric Repeat Containing
7-Deaza-Adenine
pdb|1U1L|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt Prn
Ggg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1M|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 7gu
Gg); A Human Telomeric Repeat Containing 7-Deaza-Guanine
pdb|1U1N|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta (Prn)
Gg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1O|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggttag(Di)g); A Human Telomeric Repeat Containing
Inosine
pdb|1U1P|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 2pr
Gg); A Human Telomeric Repeat Containing 2-Aminopurine
pdb|1U1Q|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggtta(Di)gg); A Human Telomeric Repeat Containing
Inosine
pdb|1U1R|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(2pr)
G); A Human Telomeric Repeat Containing 2-Aminopurine
Length = 196
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 4/69 (5%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFV---EPDDAAEAK 100
L + L + E +R FEQ+G + D + RD + RGFGF+ + E D A A+
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 101 RH-MDGQVL 108
H +DG+V+
Sbjct: 76 PHKVDGRVV 84
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 28/53 (52%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDA 96
+ V ++ D +R FEQ+G I+ I + D SG+ RGF F+ F + D
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 159
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 42/78 (53%), Gaps = 2/78 (2%)
Query: 41 PTSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAK 100
P +L V NL D I + F Q G K + ++ S +P + F++F E DAA A
Sbjct: 15 PRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAAL 72
Query: 101 RHMDGQVLLGRELTVVFA 118
M+G+ +LG+E+ V +A
Sbjct: 73 AAMNGRKILGKEVKVNWA 90
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 4/69 (5%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFV---EPDDAAEAK 100
L + L + E +R FEQ+G + D + RD + RGFGF+ + E D A A+
Sbjct: 17 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 76
Query: 101 RH-MDGQVL 108
H +DG+V+
Sbjct: 77 PHKVDGRVV 85
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 28/53 (52%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDA 96
+ V ++ D +R FEQ+G I+ I + D SG+ RGF F+ F + D
Sbjct: 108 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 160
>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi)
G); A Human Telomeric Repeat Containing 6-Methyl-8-(2-
Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi)
Length = 195
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 4/69 (5%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFV---EPDDAAEAK 100
L + L + E +R FEQ+G + D + RD + RGFGF+ + E D A A+
Sbjct: 15 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 74
Query: 101 RH-MDGQVL 108
H +DG+V+
Sbjct: 75 PHKVDGRVV 83
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 28/53 (52%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDA 96
+ V ++ D +R FEQ+G I+ I + D SG+ RGF F+ F + D
Sbjct: 106 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 158
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 42/77 (54%), Gaps = 3/77 (3%)
Query: 43 SLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRH 102
+L V+ L D E ++ F+ G+++ + D +G +GFGF+ F +DA AK
Sbjct: 17 TLFVKGLSEDTTEETLKESFD--GSVR-ARIVTDRETGSSKGFGFVDFNSEEDAKAAKEA 73
Query: 103 MDGQVLLGRELTVVFAE 119
M+ + G ++T+ +A+
Sbjct: 74 MEDGEIDGNKVTLDWAK 90
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 38/65 (58%)
Query: 62 FEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHMDGQVLLGRELTVVFAEEN 121
F Q G + + ++P+D +G+ +G+GF++F+ +DA A + MD L G+ + V A +
Sbjct: 36 FLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAH 95
Query: 122 RKKPS 126
K S
Sbjct: 96 NKNLS 100
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 4/69 (5%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFV---EPDDAAEAK 100
L + L + E +R FEQ+G + D + RD + RGFGF+ + E D A A+
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 101 RH-MDGQVL 108
H +DG+V+
Sbjct: 76 PHKVDGRVV 84
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 28/53 (52%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDA 96
+ V ++ D +R FEQ+G I+ I + D SG+ RGF F+ F + D
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 159
>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex
pdb|1PO6|A Chain A, Crystal Structure Of Up1 Complexed With
D(Tagg(6mi)ttaggg): A Human Telomeric Repeat Containing
6-Methyl-8-(2-Deoxy-
Beta-Ribofuranosyl)isoxanthopteridine (6mi)
Length = 183
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 4/69 (5%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFV---EPDDAAEAK 100
L + L + E +R FEQ+G + D + RD + RGFGF+ + E D A A+
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68
Query: 101 RH-MDGQVL 108
H +DG+V+
Sbjct: 69 PHKVDGRVV 77
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 28/53 (52%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDA 96
+ V ++ D +R FEQ+G I+ I + D SG+ RGF F+ F + D
Sbjct: 100 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 152
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 4/69 (5%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFV---EPDDAAEAK 100
L + L + E +R FEQ+G + D + RD + RGFGF+ + E D A A+
Sbjct: 14 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 73
Query: 101 RH-MDGQVL 108
H +DG+V+
Sbjct: 74 PHKVDGRVV 82
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 28/53 (52%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDA 96
+ V ++ D +R FEQ+G I+ I + D SG+ RGF F+ F + D
Sbjct: 105 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 157
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 34/62 (54%), Gaps = 2/62 (3%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAE--AKR 101
L+V L +D++ F FG + + + +D +G +GFGF++F E + + ++R
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 77
Query: 102 HM 103
HM
Sbjct: 78 HM 79
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 31/83 (37%), Positives = 42/83 (50%), Gaps = 3/83 (3%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
+ V NL D R +DI F ++GAI+DI L ++ G P F F++F +P DA +A
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDL-KNRRGGPP--FAFVEFEDPRDAEDAVYGR 81
Query: 104 DGQVLLGRELTVVFAEENRKKPS 126
DG G L V F R S
Sbjct: 82 DGYDYDGYRLRVEFPRSGRGTGS 104
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 39/74 (52%), Gaps = 2/74 (2%)
Query: 42 TSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKR 101
+ + VRNL D + ++ F + G + +Y +G+ +G G ++F P+ A A R
Sbjct: 6 SGIFVRNLPFDFTWKMLKDKFNECGHV--LYADIKMENGKSKGCGVVKFESPEVAERACR 63
Query: 102 HMDGQVLLGRELTV 115
M+G L GRE+ V
Sbjct: 64 MMNGMKLSGREIDV 77
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 2/75 (2%)
Query: 41 PTSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAK 100
+ VRNL D + ++ F + G + +Y +G+ +G G ++F P+ A A
Sbjct: 8 ACQIFVRNLPFDFTWKMLKDKFNECGHV--LYADIKMENGKSKGCGVVKFESPEVAERAC 65
Query: 101 RHMDGQVLLGRELTV 115
R M+G L GRE+ V
Sbjct: 66 RMMNGMKLSGREIDV 80
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of Hypothetical
Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens
At 1.95 A Resolution
Length = 89
Score = 40.4 bits (93), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 41/80 (51%), Gaps = 1/80 (1%)
Query: 43 SLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRH 102
S+ V N+ + E++ F G++ + + D +SG P+GF +I+F + ++
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDK-ESVRTSLA 66
Query: 103 MDGQVLLGRELTVVFAEENR 122
+D + GR++ V+ NR
Sbjct: 67 LDESLFRGRQIKVIPKRTNR 86
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 41/80 (51%), Gaps = 1/80 (1%)
Query: 43 SLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRH 102
S+ V N+ + E++ F G++ + + D +SG P+GF +I+F + ++
Sbjct: 7 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDK-ESVRTSLA 65
Query: 103 MDGQVLLGRELTVVFAEENR 122
+D + GR++ V+ NR
Sbjct: 66 LDESLFRGRQIKVIPKRTNR 85
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 37/78 (47%), Gaps = 10/78 (12%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQF--GAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKR 101
L VRNL E I + F GA++ + RDY F+ F +DA EA +
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDY--------AFVHFSNREDAVEAMK 69
Query: 102 HMDGQVLLGRELTVVFAE 119
++G+VL G + V A+
Sbjct: 70 ALNGKVLDGSPIEVTLAK 87
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 28/51 (54%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPD 94
L V L E +R F Q+G + D + +D + + RGFGF++F +P+
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPN 69
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 40.0 bits (92), Expect = 0.001, Method: Composition-based stats.
Identities = 19/43 (44%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 56 EDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAE 98
ED++ FEQFG + D L D + RGFGF+ F E +D E
Sbjct: 14 EDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF-ESEDIVE 55
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 40/86 (46%), Gaps = 1/86 (1%)
Query: 42 TSLLVRNLRHDCRPEDIRRPFEQFGAIKDI-YLPRDYYSGEPRGFGFIQFVEPDDAAEAK 100
+ + + NL + + + F FG I + RD +G +G+ FI F D + A
Sbjct: 6 SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAI 65
Query: 101 RHMDGQVLLGRELTVVFAEENRKKPS 126
M+GQ L R +TV +A + K S
Sbjct: 66 EAMNGQYLCNRPITVSYAFKKDSKGS 91
>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
pdb|3S7R|B Chain B, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
Length = 87
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 45 LVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHMD 104
V L D +D++ F +FG + D + D +G RGFGFI F DAA ++ +D
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILF---KDAASVEKVLD 71
>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 = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 45/84 (53%), Gaps = 2/84 (2%)
Query: 42 TSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKR 101
T+L V NL + + F ++G+I + RD +G PRG F+++ + ++A EA
Sbjct: 14 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 73
Query: 102 HMDGQVLLG--RELTVVFAEENRK 123
++ + G + L+V AEE+ K
Sbjct: 74 ALNNVIPEGGSQPLSVRLAEEHGK 97
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 1/73 (1%)
Query: 43 SLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRH 102
++ V NL R E + F Q G + + + +D G+P+ FGF+ F P+ + A
Sbjct: 18 TVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYAIAL 76
Query: 103 MDGQVLLGRELTV 115
++G L GR + V
Sbjct: 77 LNGIRLYGRPINV 89
>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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 45/84 (53%), Gaps = 2/84 (2%)
Query: 42 TSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKR 101
T+L V NL + + F ++G+I + RD +G PRG F+++ + ++A EA
Sbjct: 101 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 160
Query: 102 HMDGQVLLG--RELTVVFAEENRK 123
++ + G + L+V AEE+ K
Sbjct: 161 ALNNVIPEGGSQPLSVRLAEEHGK 184
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 41/79 (51%), Gaps = 2/79 (2%)
Query: 42 TSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKR 101
+L V L +++ + F Q+G I + D +G RG GFI+F + +A EA +
Sbjct: 2 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 61
Query: 102 HMDGQVLLGRE--LTVVFA 118
++GQ LG +TV FA
Sbjct: 62 GLNGQKPLGAAEPITVKFA 80
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/65 (24%), Positives = 33/65 (50%), Gaps = 1/65 (1%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
L + L C E++ + G +KD+ L + +G+P+G ++++ A++A M
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKM 78
Query: 104 DGQVL 108
DG +
Sbjct: 79 DGMTI 83
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 42/73 (57%), Gaps = 3/73 (4%)
Query: 56 EDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHMDGQVLLGRELTV 115
E++ RPF G+++ +L +G+ +G+GF ++++ D AA AK + G+ L R L V
Sbjct: 113 EELVRPF---GSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 169
Query: 116 VFAEENRKKPSDM 128
+ + + P+ +
Sbjct: 170 HWTDAGQLTPALL 182
>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
pdb|3H2U|D Chain D, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
Length = 283
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 42/73 (57%), Gaps = 3/73 (4%)
Query: 56 EDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHMDGQVLLGRELTV 115
E++ RPF G+++ +L +G+ +G+GF ++++ D AA AK + G+ L R L V
Sbjct: 111 EELVRPF---GSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 167
Query: 116 VFAEENRKKPSDM 128
+ + + P+ +
Sbjct: 168 HWTDAGQLTPALL 180
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 42/73 (57%), Gaps = 3/73 (4%)
Query: 56 EDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHMDGQVLLGRELTV 115
E++ RPF G+++ +L +G+ +G+GF ++++ D AA AK + G+ L R L V
Sbjct: 113 EELVRPF---GSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 169
Query: 116 VFAEENRKKPSDM 128
+ + + P+ +
Sbjct: 170 HWTDAGQLTPALL 182
>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
pdb|1HD1|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
Length = 75
Score = 38.9 bits (89), Expect = 0.003, Method: Composition-based stats.
Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 4/69 (5%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEP---DDAAEAK 100
+ + L D +D++ F +FG + D L D +G RGFGF+ F E D + K
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 101 RH-MDGQVL 108
H ++G+V+
Sbjct: 62 EHKLNGKVI 70
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDA----AEA 99
+ + L E +R F QFG +K+ + RD + RGFGF+ F++ A++
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 87
Query: 100 KRHMDGQVL 108
+ +D + +
Sbjct: 88 RHELDSKTI 96
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 8/74 (10%)
Query: 42 TSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKR 101
T L V N+ C +++R FE++G + + + +DY F+ +DA EA R
Sbjct: 11 TKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKDY--------AFVHMERAEDAVEAIR 62
Query: 102 HMDGQVLLGRELTV 115
+D G+ + V
Sbjct: 63 GLDNTEFQGKRMHV 76
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 37.0 bits (84), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 41/71 (57%), Gaps = 9/71 (12%)
Query: 43 SLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEA--- 99
+L++ NL + E ++ FE+ IK +P++ +G+ +G+ FI+F +DA EA
Sbjct: 17 TLVLSNLSYSATEETLQEVFEKATFIK---VPQNQ-NGKSKGYAFIEFASFEDAKEALNS 72
Query: 100 --KRHMDGQVL 108
KR ++G+ +
Sbjct: 73 CNKREIEGRAI 83
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 37.0 bits (84), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGA-IKDIYLPRDYYSGEPRGFGFIQFVEPDDAA---EA 99
+++R L +DIR + G +++ L R+ SG+ RGF F++F DA EA
Sbjct: 4 VMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEA 63
Query: 100 KRHMDGQVLLGRELTVVFAE 119
+H +LG+++++ +++
Sbjct: 64 NQHSLN--ILGQKVSMHYSD 81
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 37.0 bits (84), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 35/66 (53%)
Query: 42 TSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKR 101
T+L V NL + + F ++G+I + RD +G PRG F+++ + ++A EA
Sbjct: 90 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 149
Query: 102 HMDGQV 107
++ +
Sbjct: 150 ALNNVI 155
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 36.6 bits (83), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 25/92 (27%), Positives = 43/92 (46%), Gaps = 11/92 (11%)
Query: 42 TSLLVRNLRHDCRPEDIRRPFEQFGAIKD--------IYLPRDYYSGEPRGFGFIQFVEP 93
+++ V+ L +D+ F+Q G +K I++ D +G+P+G + + +P
Sbjct: 16 SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 75
Query: 94 DDAAEAKRHMDGQVLLGRELTVVFAEENRKKP 125
A A DG+ G +L V A RKKP
Sbjct: 76 PTAKAAVEWFDGKDFQGSKLKVSLA---RKKP 104
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 36.2 bits (82), Expect = 0.020, Method: Composition-based stats.
Identities = 17/57 (29%), Positives = 31/57 (54%), Gaps = 4/57 (7%)
Query: 56 EDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDA----AEAKRHMDGQVL 108
E +R F QFG +K+ + RD + RGFGF+ F++ A+++ +D + +
Sbjct: 15 EGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTI 71
>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain
Of Hnrnp D (Auf1) With Telomere Dna
pdb|1X0F|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain
Of Hnrnp D(Auf1) With Telomeric Dna
Length = 79
Score = 35.8 bits (81), Expect = 0.022, Method: Composition-based stats.
Identities = 20/51 (39%), Positives = 26/51 (50%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPD 94
+ V L D E IR F FG ++ I LP D + + RGF FI F E +
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEE 54
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 35.8 bits (81), Expect = 0.025, Method: Composition-based stats.
Identities = 20/51 (39%), Positives = 26/51 (50%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPD 94
+ V L D E IR F FG ++ I LP D + + RGF FI F E +
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEE 52
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 35.4 bits (80), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 18/82 (21%), Positives = 39/82 (47%), Gaps = 8/82 (9%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
+ V N+ C +++R FE+ G + + + +DY F+ + DA A +
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKDY--------AFVHMEKEADAKAAIAQL 63
Query: 104 DGQVLLGRELTVVFAEENRKKP 125
+G+ + G+ + V + + +KK
Sbjct: 64 NGKEVKGKRINVELSTKGQKKS 85
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 35.4 bits (80), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 16/66 (24%), Positives = 36/66 (54%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
L + + + +D++ FE+FG I ++ + +D ++G +G F+ + E + A +A+ +
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSAL 75
Query: 104 DGQVLL 109
Q L
Sbjct: 76 HEQKTL 81
>pdb|1WHX|A Chain A, Solution Structure Of The Second Rna Binding Domain From
Hypothetical Protein Bab23448
Length = 111
Score = 35.0 bits (79), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 6/62 (9%)
Query: 42 TSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKR 101
T +L +NL +I+ F +FG++ + LP + ++F+EP +A +A R
Sbjct: 11 TVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGIT------AIVEFLEPLEARKAFR 64
Query: 102 HM 103
H+
Sbjct: 65 HL 66
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 35.0 bits (79), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 8/78 (10%)
Query: 42 TSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKR 101
T L VR D + ++ F FG +K++ + GF F++F E + AA+A
Sbjct: 32 TRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAKAIE 83
Query: 102 HMDGQVLLGRELTVVFAE 119
+ G+ + L VV+++
Sbjct: 84 EVHGKSFANQPLEVVYSK 101
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 35.0 bits (79), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 27/86 (31%), Positives = 43/86 (50%), Gaps = 2/86 (2%)
Query: 41 PTSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAK 100
P + V NL + DI F+ +I+ + L RD + + +GF +++F E D EA
Sbjct: 15 PYTAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL 73
Query: 101 RHMDGQVLLGRELTVVFAEENRKKPS 126
+ DG +L R L V AE ++ S
Sbjct: 74 TY-DGALLGDRSLRVDIAEGRKQDKS 98
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 34.7 bits (78), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 42 TSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKR 101
T + V L + +R+ FE FG I++ + D +G+ RG+GF+ D A A+R
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMA---DRAAAER 74
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 34.3 bits (77), Expect = 0.073, Method: Composition-based stats.
Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 8/78 (10%)
Query: 42 TSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKR 101
T L VR D + ++ F FG +K++ + GF F++F E + AA+A
Sbjct: 5 TRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAKAIE 56
Query: 102 HMDGQVLLGRELTVVFAE 119
+ G+ + L VV+++
Sbjct: 57 EVHGKSFANQPLEVVYSK 74
>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 = 0.079, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 5/78 (6%)
Query: 40 LPTSLLVRNLRHDCRPEDIRRPFEQFGAI--KDIYLPRDYYSGEPRGFGFIQFVEPDDAA 97
L +++ V NL + + ++ F G + DI +D G+ RG G + F + +A
Sbjct: 14 LGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD---GKSRGIGTVTFEQSIEAV 70
Query: 98 EAKRHMDGQVLLGRELTV 115
+A +GQ+L R + V
Sbjct: 71 QAISMFNGQLLFDRPMHV 88
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 33.9 bits (76), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 33/72 (45%), Gaps = 1/72 (1%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
LLV NL DI+ F +FG +K + D SG G + F DA +A +
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQY 89
Query: 104 DGQVLLGRELTV 115
+G L GR + +
Sbjct: 90 NGVPLDGRPMNI 101
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 33.9 bits (76), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 37/82 (45%), Gaps = 3/82 (3%)
Query: 43 SLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRH 102
++ L RP D+ F G ++D+ + D S +G +++F E A
Sbjct: 27 TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-G 85
Query: 103 MDGQVLLGRELTVVF--AEENR 122
+ GQ LLG + V AE+NR
Sbjct: 86 LTGQRLLGVPIIVQASQAEKNR 107
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 33.9 bits (76), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 40/83 (48%), Gaps = 4/83 (4%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
L V L +D+RR FE FG I++ + R G +G F+++ +A A +
Sbjct: 18 LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRG-PDGNSKGCAFVKYSSHAEAQAAINAL 76
Query: 104 DG-QVLLG--RELTVVFAEENRK 123
G Q + G L V FA+ +++
Sbjct: 77 HGSQTMPGASSSLVVKFADTDKE 99
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 33.5 bits (75), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 11/77 (14%)
Query: 53 CRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHMDGQVLLGRE 112
+ D+ F ++G I + + GF F+Q+V +A A DG+++ G+
Sbjct: 28 VKKSDVEAIFSKYGKIVGCSVHK--------GFAFVQYVNERNARAAVAGEDGRMIAGQV 79
Query: 113 LTVVFAEE---NRKKPS 126
L + A E NR PS
Sbjct: 80 LDINLAAEPKVNRSGPS 96
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 9/83 (10%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
L + NL + ++IR FEQ+G + + + ++Y GF+ + A +A R++
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDIIKNY--------GFVHIEDKTAAEDAIRNL 62
Query: 104 DGQVLLGRELTVVFAEENRKKPS 126
L G + V A +N+ K S
Sbjct: 63 HHYKLHGVNINVE-ASKNKSKAS 84
>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 = 33.1 bits (74), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 31/68 (45%), Gaps = 1/68 (1%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
LLV NL DI+ F +FG +K + D SG G + F DA +A +
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAXKQY 90
Query: 104 DGQVLLGR 111
+G L GR
Sbjct: 91 NGVPLDGR 98
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 32.7 bits (73), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 56 EDIRRPFEQFGAIKDIYLPRDYYSGEP--RGFGFIQFVEPDDAAEAKRHMDGQVLL 109
+D+R FEQ+GA+ +I + RD P +G F+ F A EA+ + +L
Sbjct: 18 KDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVL 73
>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 = 32.7 bits (73), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 56 EDIRRPFEQFGAIKDIYLPRDYYSGEP--RGFGFIQFVEPDDAAEAKRHMDGQVLL 109
+D+R FEQ+GA+ +I + RD P +G F+ F A EA+ + +L
Sbjct: 18 KDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVL 73
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 32.7 bits (73), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 33/66 (50%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
L V + +D++ FE+FG I ++ + +D +G +G F+ + D A +A+ +
Sbjct: 18 LFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSAL 77
Query: 104 DGQVLL 109
Q L
Sbjct: 78 HEQKTL 83
>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 = 32.7 bits (73), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 56 EDIRRPFEQFGAIKDIYLPRDYYSGEP--RGFGFIQFVEPDDAAEAKRHMDGQVLL 109
+D+R FEQ+GA+ +I + RD P +G F+ F A EA+ + +L
Sbjct: 18 KDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNXKVL 73
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 32.7 bits (73), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 56 EDIRRPFEQFGAIKDIYLPRDYYSGEP--RGFGFIQFVEPDDAAEAKRHMDGQVLL 109
+D+R FEQ+GA+ +I + RD P +G F+ F A EA+ + +L
Sbjct: 30 KDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVL 85
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 32.7 bits (73), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 29/64 (45%)
Query: 42 TSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKR 101
+L + +L + D+ F FG + + D + + FGF+ F PD A A +
Sbjct: 41 CNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIK 100
Query: 102 HMDG 105
M+G
Sbjct: 101 AMNG 104
>pdb|2NLW|A Chain A, Solution Structure Of The Rrm Domain Of Human Eukaryotic
Initiation Factor 3b
Length = 105
Score = 32.3 bits (72), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 29/51 (56%), Gaps = 2/51 (3%)
Query: 58 IRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHMDGQVL 108
I + F +FG I + + P + G+ +G+ F+++ P A +A ++ DG L
Sbjct: 38 IHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAVDAVKNADGYKL 86
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 32.3 bits (72), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 16/72 (22%), Positives = 35/72 (48%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
L + L + + ++ FG +K L +D +G +G+ F ++V+ + +A +
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176
Query: 104 DGQVLLGRELTV 115
+G L ++L V
Sbjct: 177 NGMQLGDKKLLV 188
>pdb|2DIT|A Chain A, Solution Structure Of The Rrm_1 Domain Of Hiv Tat Specific
Factor 1 Variant
Length = 112
Score = 32.0 bits (71), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 31/59 (52%), Gaps = 4/59 (6%)
Query: 56 EDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHMDGQVLLGRELT 114
ED+R +FG I+ + L + P G + F +P++A + +DG+ GR++T
Sbjct: 41 EDLRVECSKFGQIRKLLL----FDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQIT 95
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 32.0 bits (71), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 16/72 (22%), Positives = 35/72 (48%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
L + L + + ++ FG +K L +D +G +G+ F ++V+ + +A +
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 104 DGQVLLGRELTV 115
+G L ++L V
Sbjct: 64 NGMQLGDKKLLV 75
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 32.0 bits (71), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 32/74 (43%), Gaps = 1/74 (1%)
Query: 42 TSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKR 101
LLV NL DI+ F +FG +K + D SG G + F DA +A +
Sbjct: 89 AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADALKAMK 147
Query: 102 HMDGQVLLGRELTV 115
G L GR + +
Sbjct: 148 QYKGVPLDGRPMDI 161
>pdb|2KRB|A Chain A, Solution Structure Of Eif3b-Rrm Bound To Eif3j Peptide
Length = 81
Score = 32.0 bits (71), Expect = 0.37, Method: Composition-based stats.
Identities = 15/51 (29%), Positives = 29/51 (56%), Gaps = 2/51 (3%)
Query: 58 IRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHMDGQVL 108
I + F +FG I + + P + G+ +G+ F+++ P A +A ++ DG L
Sbjct: 24 IHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAVDAVKNADGYKL 72
>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAF|B Chain B, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAG|A Chain A, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAG|B Chain B, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAH|A Chain A, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAH|B Chain B, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAI|A Chain A, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAI|B Chain B, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAJ|A Chain A, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAJ|B Chain B, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAK|A Chain A, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAK|B Chain B, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAL|A Chain A, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|B Chain B, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|D Chain D, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|I Chain I, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAM|A Chain A, Structure Of U2af65 Variant With Bru5c2 Dna
pdb|3VAM|B Chain B, Structure Of U2af65 Variant With Bru5c2 Dna
Length = 174
Score = 32.0 bits (71), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 16/72 (22%), Positives = 35/72 (48%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
L + L + + ++ FG +K L +D +G +G+ F ++V+ + +A +
Sbjct: 99 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 158
Query: 104 DGQVLLGRELTV 115
+G L ++L V
Sbjct: 159 NGMQLGDKKLLV 170
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 31.6 bits (70), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 16/72 (22%), Positives = 35/72 (48%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
L + L + + ++ FG +K L +D +G +G+ F ++V+ + +A +
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 104 DGQVLLGRELTV 115
+G L ++L V
Sbjct: 157 NGMQLGDKKLLV 168
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 31.6 bits (70), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 33/74 (44%), Gaps = 14/74 (18%)
Query: 42 TSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKR 101
+ + V D +++R F Q+G + D+++P+ + R F F+ F + A
Sbjct: 6 SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFADDQIA----- 55
Query: 102 HMDGQVLLGRELTV 115
Q L G +L +
Sbjct: 56 ----QSLCGEDLII 65
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 31.6 bits (70), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 30/64 (46%)
Query: 43 SLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRH 102
+L + L +D+ F +FG I + + D +G RG FI+F + +A EA
Sbjct: 90 NLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITS 149
Query: 103 MDGQ 106
+G
Sbjct: 150 FNGH 153
>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 = 31.6 bits (70), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 30/64 (46%)
Query: 43 SLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRH 102
+L + L +D+ F +FG I + + D +G RG FI+F + +A EA
Sbjct: 90 NLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITS 149
Query: 103 MDGQ 106
+G
Sbjct: 150 FNGH 153
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 31.2 bits (69), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 8/76 (10%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
L VRNL E + + F +FG ++ + +DY F+ F + A +A M
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKDY--------AFVHFEDRGAAVKAMDEM 69
Query: 104 DGQVLLGRELTVVFAE 119
+G+ + G E+ +V A+
Sbjct: 70 NGKEIEGEEIEIVLAK 85
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 31.2 bits (69), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 32/72 (44%), Gaps = 1/72 (1%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
LLV NL DI+ F +FG +K + D SG G + F DA +A +
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADALKAMKQY 96
Query: 104 DGQVLLGRELTV 115
G L GR + +
Sbjct: 97 KGVPLDGRPMDI 108
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 31.2 bits (69), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 34/74 (45%), Gaps = 14/74 (18%)
Query: 42 TSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKR 101
+ + V D E++++ F Q+G + D+++P+ + R F F+ F DD
Sbjct: 12 SKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF-----RAFAFVTF--ADDKV---- 60
Query: 102 HMDGQVLLGRELTV 115
Q L G +L +
Sbjct: 61 ---AQSLCGEDLII 71
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 30.8 bits (68), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 32/72 (44%), Gaps = 1/72 (1%)
Query: 44 LLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHM 103
LLV NL DI+ F +FG +K + D SG G + F DA +A +
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADALKAMKQY 96
Query: 104 DGQVLLGRELTV 115
G L GR + +
Sbjct: 97 KGVPLDGRPMDI 108
>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 = 30.8 bits (68), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 35/71 (49%)
Query: 51 HDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHMDGQVLLG 110
+D E I G + ++ + D +G +G+ FI+F + + +A A R+++G L
Sbjct: 14 YDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGS 73
Query: 111 RELTVVFAEEN 121
R L ++ +
Sbjct: 74 RFLKCGYSSNS 84
>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 = 30.8 bits (68), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 2/73 (2%)
Query: 43 SLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRH 102
++ ++NL + + F FG I + D +G+GF+ F + A A
Sbjct: 105 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEK 162
Query: 103 MDGQVLLGRELTV 115
M+G +L R++ V
Sbjct: 163 MNGMLLNDRKVFV 175
>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 = 30.8 bits (68), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 2/73 (2%)
Query: 43 SLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRH 102
++ ++NL + + F FG I + D +G+GF+ F + A A
Sbjct: 100 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEK 157
Query: 103 MDGQVLLGRELTV 115
M+G +L R++ V
Sbjct: 158 MNGMLLNDRKVFV 170
>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 = 30.8 bits (68), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 35/71 (49%)
Query: 51 HDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHMDGQVLLG 110
+D E I G + ++ + D +G +G+ FI+F + + +A A R+++G L
Sbjct: 13 YDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGS 72
Query: 111 RELTVVFAEEN 121
R L ++ +
Sbjct: 73 RFLKCGYSSNS 83
>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 = 30.4 bits (67), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 2/73 (2%)
Query: 43 SLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRH 102
++ ++NL + + F FG I + D +G+GF+ F + A A
Sbjct: 7 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEK 64
Query: 103 MDGQVLLGRELTV 115
M+G +L R++ V
Sbjct: 65 MNGMLLNDRKVFV 77
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 30.4 bits (67), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 30/68 (44%), Gaps = 1/68 (1%)
Query: 41 PTSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAK 100
PT+L + NL +++ + FG + + RD SG RG GF + +
Sbjct: 25 PTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVI 83
Query: 101 RHMDGQVL 108
H +G+ +
Sbjct: 84 GHFNGKFI 91
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 30.4 bits (67), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 32/63 (50%)
Query: 51 HDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRHMDGQVLLG 110
+D E I G + ++ + D +G +G+ FI+F + + +A A R+++G L
Sbjct: 12 YDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGS 71
Query: 111 REL 113
R L
Sbjct: 72 RFL 74
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 2/73 (2%)
Query: 43 SLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRH 102
++ ++NL + + F FG I + D +G+GF+ F + A A
Sbjct: 13 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEK 70
Query: 103 MDGQVLLGRELTV 115
M+G +L R++ V
Sbjct: 71 MNGMLLNDRKVFV 83
>pdb|3V4M|A Chain A, Crystal Structure Of A Rna Binding Domain Of A U2 Small
Nuclear Ribonucleoprotein Auxiliary Factor 2 (U2af) From
Mus Musculus At 1.80 A Resolution
pdb|3V4M|B Chain B, Crystal Structure Of A Rna Binding Domain Of A U2 Small
Nuclear Ribonucleoprotein Auxiliary Factor 2 (U2af) From
Mus Musculus At 1.80 A Resolution
Length = 105
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 2/66 (3%)
Query: 56 EDIRRPFEQFGAIKDIYLPRDYYSGEPRGFG--FIQFVEPDDAAEAKRHMDGQVLLGREL 113
ED+R ++G +K I +PR E G G F++F D +A + + G+ R +
Sbjct: 30 EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAXQGLTGRKFANRVV 89
Query: 114 TVVFAE 119
+ +
Sbjct: 90 VTKYCD 95
>pdb|1OPI|A Chain A, Solution Structure Of The Third Rna Recognition Motif
(Rrm) Of U2af65 In Complex With An N-Terminal Sf1
Peptide
pdb|2M0G|B Chain B, Structure, Phosphorylation And U2af65 Binding Of The
Nterminal Domain Of Splicing Factor 1 During 3 Splice
Site Recognition
Length = 104
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 2/66 (3%)
Query: 56 EDIRRPFEQFGAIKDIYLPRDYYSGEPRGFG--FIQFVEPDDAAEAKRHMDGQVLLGREL 113
ED+R ++G +K I +PR E G G F++F D +A + + G+ R +
Sbjct: 29 EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVV 88
Query: 114 TVVFAE 119
+ +
Sbjct: 89 VTKYCD 94
>pdb|4FXW|A Chain A, Structure Of Phosphorylated Sf1 Complex With U2af65-uhm
Domain
pdb|4FXW|C Chain C, Structure Of Phosphorylated Sf1 Complex With U2af65-uhm
Domain
Length = 106
Score = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 2/66 (3%)
Query: 56 EDIRRPFEQFGAIKDIYLPRDYYSGEPRGFG--FIQFVEPDDAAEAKRHMDGQVLLGREL 113
ED+R ++G +K I +PR E G G F++F D +A + + G+ R +
Sbjct: 31 EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAXQGLTGRKFANRVV 90
Query: 114 TVVFAE 119
+ +
Sbjct: 91 VTKYCD 96
>pdb|1O0P|A Chain A, Solution Structure Of The Third Rna Recognition Motif
(Rrm) Of U2af65 In Complex With An N-Terminal Sf1
Peptide
Length = 104
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 2/66 (3%)
Query: 56 EDIRRPFEQFGAIKDIYLPRDYYSGEPRGFG--FIQFVEPDDAAEAKRHMDGQVLLGREL 113
ED+R ++G +K I +PR E G G F++F D +A + + G+ R +
Sbjct: 29 EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVV 88
Query: 114 TVVFAE 119
+ +
Sbjct: 89 VTKYCD 94
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 14/62 (22%), Positives = 29/62 (46%)
Query: 42 TSLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKR 101
+ L +R L+ +D+ + + +G I D + + +G+GF+ F P A +A
Sbjct: 6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65
Query: 102 HM 103
+
Sbjct: 66 AL 67
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 29.6 bits (65), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 18/78 (23%), Positives = 38/78 (48%), Gaps = 5/78 (6%)
Query: 43 SLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRH 102
+LL +NL + ++++ FE I+ + +D G+ +G +I+F DA +
Sbjct: 95 TLLAKNLPYKVTQDELKEVFEDAAEIR--LVSKD---GKSKGIAYIEFKTEADAEKTFEE 149
Query: 103 MDGQVLLGRELTVVFAEE 120
G + GR +++ + E
Sbjct: 150 KQGTEIDGRSISLYYTGE 167
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 36/82 (43%), Gaps = 6/82 (7%)
Query: 43 SLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPD------DA 96
++ +RNL D E + +QFG +K + + + +G F QF+ + A
Sbjct: 17 TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 76
Query: 97 AEAKRHMDGQVLLGRELTVVFA 118
A + G L GR+L V A
Sbjct: 77 ASLEAEGGGLKLDGRQLKVDLA 98
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 29.3 bits (64), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 18/78 (23%), Positives = 39/78 (50%), Gaps = 5/78 (6%)
Query: 43 SLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRH 102
+LL +NL + ++++ FE A++ + +D G+ +G +I+F DA +
Sbjct: 18 TLLAKNLSFNITEDELKEVFED--ALEIRLVSQD---GKSKGIAYIEFKSEADAEKNLEE 72
Query: 103 MDGQVLLGRELTVVFAEE 120
G + GR +++ + E
Sbjct: 73 KQGAEIDGRSVSLYYTGE 90
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 35/83 (42%), Gaps = 9/83 (10%)
Query: 40 LPTSLLVRNL-RHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAE 98
+ + L + NL + ED+ R F +G I I + FGFIQF P +
Sbjct: 21 MKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQFDNPQSVRD 72
Query: 99 AKRHMDGQVLLGRELTVVFAEEN 121
A ++ G++L + + N
Sbjct: 73 AIEXESQEMNFGKKLILEVSSSN 95
>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 = 28.9 bits (63), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 18/78 (23%), Positives = 39/78 (50%), Gaps = 5/78 (6%)
Query: 43 SLLVRNLRHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRH 102
+LL +NL + ++++ FE A++ + +D G+ +G +I+F DA +
Sbjct: 101 TLLAKNLSFNITEDELKEVFED--ALEIRLVSQD---GKSKGIAYIEFKSEADAEKNLEE 155
Query: 103 MDGQVLLGRELTVVFAEE 120
G + GR +++ + E
Sbjct: 156 KQGAEIDGRSVSLYYTGE 173
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 28.9 bits (63), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 34/81 (41%), Gaps = 9/81 (11%)
Query: 44 LLVRNL-RHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAEAKRH 102
L + NL + ED+ R F +G I I + FGFIQF P +A
Sbjct: 13 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQFDNPQSVRDAIEC 64
Query: 103 MDGQVLLGRELTVVFAEENRK 123
++ G++L + + N +
Sbjct: 65 ESQEMNFGKKLILEVSSSNAR 85
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 28.5 bits (62), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 35/83 (42%), Gaps = 9/83 (10%)
Query: 40 LPTSLLVRNL-RHDCRPEDIRRPFEQFGAIKDIYLPRDYYSGEPRGFGFIQFVEPDDAAE 98
+ + L + NL + ED+ R F +G I I + FGFIQF P +
Sbjct: 21 MKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQFDNPQSVRD 72
Query: 99 AKRHMDGQVLLGRELTVVFAEEN 121
A ++ G++L + + N
Sbjct: 73 AIECESQEMNFGKKLILEVSSSN 95
>pdb|1REQ|B Chain B, Methylmalonyl-Coa Mutase
pdb|1REQ|D Chain D, Methylmalonyl-Coa Mutase
pdb|2REQ|B Chain B, Methylmalonyl-Coa Mutase, Non-Productive Coa Complex, In
Open Conformation Representing Substrate-Free State
pdb|2REQ|D Chain D, Methylmalonyl-Coa Mutase, Non-Productive Coa Complex, In
Open Conformation Representing Substrate-Free State
pdb|3REQ|B Chain B, Methylmalonyl-Coa Mutase, Substrate-Free State (Poor
Quality Structure)
pdb|6REQ|B Chain B, Methylmalonyl-Coa Mutase, 3-Carboxypropyl-Coa Inhibitor
Complex
pdb|6REQ|D Chain D, Methylmalonyl-Coa Mutase, 3-Carboxypropyl-Coa Inhibitor
Complex
pdb|7REQ|B Chain B, Methylmalonyl-Coa Mutase, 2-Carboxypropyl-Coa Inhibitor
Complex
pdb|7REQ|D Chain D, Methylmalonyl-Coa Mutase, 2-Carboxypropyl-Coa Inhibitor
Complex
pdb|4REQ|B Chain B, Methylmalonyl-Coa Mutase Substrate Complex
pdb|4REQ|D Chain D, Methylmalonyl-Coa Mutase Substrate Complex
pdb|5REQ|B Chain B, Methylmalonyl-Coa Mutase, Y89f Mutant, Substrate Complex
pdb|5REQ|D Chain D, Methylmalonyl-Coa Mutase, Y89f Mutant, Substrate Complex
pdb|1E1C|B Chain B, Methylmalonyl-Coa Mutase H244a Mutant
pdb|1E1C|D Chain D, Methylmalonyl-Coa Mutase H244a Mutant
Length = 637
Score = 28.1 bits (61), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 23/38 (60%), Gaps = 7/38 (18%)
Query: 77 YYSGEPRGFGFIQFVEPDDAAEAKRHMDGQVLLGRELT 114
Y SG + FG DDAAEA++ +DG++ +G ++
Sbjct: 593 YLSGAFKEFG-------DDAAEAEKLIDGRLFMGMDVV 623
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 27.7 bits (60), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 3/50 (6%)
Query: 79 SGEPRGFGFIQFVEPDDAAEAKRHMDGQVLLGRE---LTVVFAEENRKKP 125
+G +G+GF++F + + A G V LG + L+V + +R KP
Sbjct: 47 TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIPKASRVKP 96
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
0.318 0.138 0.422
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,183,887
Number of Sequences: 62578
Number of extensions: 125548
Number of successful extensions: 397
Number of sequences better than 100.0: 153
Number of HSP's better than 100.0 without gapping: 116
Number of HSP's successfully gapped in prelim test: 37
Number of HSP's that attempted gapping in prelim test: 252
Number of HSP's gapped (non-prelim): 172
length of query: 253
length of database: 14,973,337
effective HSP length: 97
effective length of query: 156
effective length of database: 8,903,271
effective search space: 1388910276
effective search space used: 1388910276
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)