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= 028313
(210 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 = 76.3 bits (186), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 40/77 (51%), Positives = 50/77 (64%)
Query: 38 TSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKY 97
TSL V NL + P+ LR F ++GR+ D+Y+PRD YT E RGF FV++ D DA DA
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 98 HMDGYLLLGRELTVVFA 114
MDG +L GREL V A
Sbjct: 131 AMDGAVLDGRELRVQMA 147
>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 = 75.1 bits (183), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 41/81 (50%), Positives = 51/81 (62%)
Query: 38 TSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKY 97
TSL V NL + P+ LR F ++GR+ D+Y+PRD YT E RGF FV++ D DA DA
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 98 HMDGYLLLGRELTVVFAEENR 118
MDG +L 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 = 38/84 (45%), Positives = 52/84 (61%)
Query: 39 SLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYH 98
+L V NL + P+ LR F ++GR+ D+Y+PR+ +T PRGF FV++ D DA DA+
Sbjct: 15 TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74
Query: 99 MDGYLLLGRELTVVFAEENRKKPS 122
MDG L GREL V A R+ S
Sbjct: 75 MDGAELDGRELRVQVARYGRRDLS 98
>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 = 59.7 bits (143), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 32/91 (35%), Positives = 47/91 (51%), Gaps = 5/91 (5%)
Query: 38 TSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKY 97
T+L+V L + E+ R FG G ++ L RD TG+ G+GFV YIDP DA A
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 98 HMDGYLLLGRELTVVFAEENRKKPSEMRARE 128
++G L + + V +A +PS R+
Sbjct: 63 TLNGLRLQTKTIKVSYA-----RPSSASIRD 88
Score = 32.7 bits (73), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 2/78 (2%)
Query: 39 SLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYH 98
+L V L ++L F Q+GR+ + D TG RG GF+++ +A +A
Sbjct: 90 NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 149
Query: 99 MDGYLLLGRE--LTVVFA 114
++G G +TV FA
Sbjct: 150 LNGQKPSGATEPITVKFA 167
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 58.5 bits (140), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 45/83 (54%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
+ V +L + ED++ F FG++ D + +D TG+ +G+GFV + + DA +A HM
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 100 DGYLLLGRELTVVFAEENRKKPS 122
G 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 = 57.8 bits (138), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 28/83 (33%), Positives = 46/83 (55%), Gaps = 2/83 (2%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
+ V +L + ED++ F FGR+ D + +D TG+ +G+GFV + + DA +A M
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 100 DGYLLLGRELTVVFAEENRKKPS 122
G L GR++ +A RK P+
Sbjct: 78 GGQWLGGRQIRTNWA--TRKPPA 98
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 57.0 bits (136), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 40/73 (54%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
L VRNL + EDL F +G L +++ P D T +P+GF FV ++ P A A +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 100 DGYLLLGRELTVV 112
DG + GR L V+
Sbjct: 71 DGQVFQGRMLHVL 83
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 54.3 bits (129), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 30/94 (31%), Positives = 47/94 (50%), Gaps = 5/94 (5%)
Query: 35 DLPTSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAAD 94
D T+L+V L + ++ + FG G ++ L RD TG+ G+GFV Y DP DA
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 95 AKYHMDGYLLLGRELTVVFAEENRKKPSEMRARE 128
A ++G L + + V +A +PS R+
Sbjct: 62 AINTLNGLKLQTKTIKVSYA-----RPSSASIRD 90
Score = 33.5 bits (75), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 2/80 (2%)
Query: 39 SLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYH 98
+L V L +++ F Q+GR+ + D TG RG GF+++ +A +A
Sbjct: 92 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 151
Query: 99 MDGYLLLGRE--LTVVFAEE 116
++G LG +TV FA
Sbjct: 152 LNGQKPLGAAEPITVKFANN 171
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 53.9 bits (128), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 30/93 (32%), Positives = 46/93 (49%), Gaps = 5/93 (5%)
Query: 35 DLPTSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAAD 94
D T+L+V L + ++ + FG G ++ L RD TG+ G+GFV Y DP DA
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 95 AKYHMDGYLLLGRELTVVFAEENRKKPSEMRAR 127
A ++G L + + V +A +PS R
Sbjct: 62 AINTLNGLKLQTKTIKVSYA-----RPSSASIR 89
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 53.1 bits (126), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 30/88 (34%), Positives = 47/88 (53%), Gaps = 5/88 (5%)
Query: 35 DLPTSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAAD 94
D P L + L + + L+ FG+ G + ++ L +D T + RGF F+ + +PADA +
Sbjct: 5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKN 63
Query: 95 AKYHMDGYLLLGRELTVVFAEENRKKPS 122
A M+G L G+ + V E KKPS
Sbjct: 64 AAKDMNGKSLHGKAIKV----EQAKKPS 87
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 52.8 bits (125), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 29/86 (33%), Positives = 45/86 (52%), Gaps = 3/86 (3%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
L V L D + L F ++G++ ++ + +D T RGFGFV + + DA DA M
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 100 DGYLLLGRELTVVFA---EENRKKPS 122
+G + GR++ V A +NR PS
Sbjct: 75 NGKSVDGRQIRVDQAGKSSDNRSGPS 100
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 51.6 bits (122), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 28/80 (35%), Positives = 42/80 (52%)
Query: 32 RGRDLPTSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPAD 91
+G P L V +L + + LRG F FGR++ I L D TG +G+GF+ + D
Sbjct: 21 KGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSEC 80
Query: 92 AADAKYHMDGYLLLGRELTV 111
A A ++G+ L GR + V
Sbjct: 81 AKKALEQLNGFELAGRPMKV 100
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 28/84 (33%), Positives = 44/84 (52%), Gaps = 2/84 (2%)
Query: 28 HYGGRGRDLPTSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYI 87
H + P L V N+ R DLR FGQFG++ D+ + + +GFGFV +
Sbjct: 20 HMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEII--FNERGSKGFGFVTFE 77
Query: 88 DPADAADAKYHMDGYLLLGRELTV 111
+ ADA A+ + G ++ GR++ V
Sbjct: 78 NSADADRAREKLHGTVVEGRKIEV 101
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 31/83 (37%), Positives = 42/83 (50%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
L V L + + L F FG + DI +P DY T + RGF FV++ DAA A +M
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 100 DGYLLLGRELTVVFAEENRKKPS 122
+ L GR + V A+ R K S
Sbjct: 75 NESELFGRTIRVNLAKPMRIKES 97
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 48.1 bits (113), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 25/68 (36%), Positives = 36/68 (52%)
Query: 35 DLPTSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAAD 94
D ++ V NL D R DL+ F FG + IYL +D TG+ +GF F+ + DAA
Sbjct: 13 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAAR 72
Query: 95 AKYHMDGY 102
A + G+
Sbjct: 73 AIAGVSGF 80
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 48.1 bits (113), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 41/76 (53%), Gaps = 5/76 (6%)
Query: 36 LPTSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADA 95
L + V NL ++ +L FG +G L+ +++ R+ P GF FV++ DP DAADA
Sbjct: 72 LDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADA 126
Query: 96 KYHMDGYLLLGRELTV 111
+DG L G + V
Sbjct: 127 VRELDGRTLCGCRVRV 142
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 47.8 bits (112), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 29/85 (34%), Positives = 42/85 (49%), Gaps = 2/85 (2%)
Query: 34 RDLPTSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYY-TGEPRGFGFVQYIDPADA 92
+ + +LVRN+ ++R F FG LK + LP+ TG RGFGFV +I DA
Sbjct: 12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 71
Query: 93 ADAKYHM-DGYLLLGRELTVVFAEE 116
A + L GR L + +A+
Sbjct: 72 KKAFNALCHSTHLYGRRLVLEWADS 96
>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 = 47.8 bits (112), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 38/77 (49%)
Query: 38 TSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKY 97
T+L+V L + ++LR F G ++ L RD G G+GFV Y+ DA A
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 98 HMDGYLLLGRELTVVFA 114
++G L + + V +A
Sbjct: 63 TLNGLRLQSKTIKVSYA 79
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 47.8 bits (112), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 43/84 (51%)
Query: 33 GRDLPTSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADA 92
G + L V +L + + LRG F FG++ +I L +D TG +G+GF+ + D A
Sbjct: 1 GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60
Query: 93 ADAKYHMDGYLLLGRELTVVFAEE 116
A ++G+ L GR + V E
Sbjct: 61 RRALEQLNGFELAGRPMRVGHVTE 84
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 47.4 bits (111), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 38/77 (49%)
Query: 38 TSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKY 97
T+L+V L + ++LR F G ++ L RD G G+GFV Y+ DA A
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 98 HMDGYLLLGRELTVVFA 114
++G L + + V +A
Sbjct: 63 TLNGLRLQSKTIKVSYA 79
>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|B Chain B, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|C Chain C, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|D Chain D, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
Length = 84
Score = 47.4 bits (111), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 38/77 (49%)
Query: 38 TSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKY 97
T+L+V L + ++LR F G ++ L RD G G+GFV Y+ DA A
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 64
Query: 98 HMDGYLLLGRELTVVFA 114
++G L + + V +A
Sbjct: 65 TLNGLRLQSKTIKVSYA 81
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 47.4 bits (111), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 41/76 (53%), Gaps = 5/76 (6%)
Query: 36 LPTSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADA 95
L + V NL ++ +L FG +G L+ +++ R+ P GF FV++ DP DAADA
Sbjct: 72 LDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADA 126
Query: 96 KYHMDGYLLLGRELTV 111
+DG L G + V
Sbjct: 127 VRDLDGRTLCGCRVRV 142
>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 = 47.0 bits (110), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 38/77 (49%)
Query: 38 TSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKY 97
T+L+V L + ++LR F G ++ L RD G G+GFV Y+ DA A
Sbjct: 20 TNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 79
Query: 98 HMDGYLLLGRELTVVFA 114
++G L + + V +A
Sbjct: 80 TLNGLRLQSKTIKVSYA 96
>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 = 47.0 bits (110), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 40/72 (55%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
+ V ++ D +D++ F FG++K L RD TG+ +G+GF++Y + DA M
Sbjct: 113 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 172
Query: 100 DGYLLLGRELTV 111
+ + L G+ L V
Sbjct: 173 NLFDLGGQYLRV 184
Score = 40.4 bits (93), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 36/70 (51%)
Query: 42 VRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHMDG 101
V ++ ++ + +R F FG +K I + D T + +GF FV+Y P A A M+
Sbjct: 18 VGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNS 77
Query: 102 YLLLGRELTV 111
+L GR + V
Sbjct: 78 VMLGGRNIKV 87
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 47.0 bits (110), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 42/75 (56%), Gaps = 2/75 (2%)
Query: 37 PTSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAK 96
P L V N+ R DLR FGQFG++ D+ + + +GFGFV + + ADA A+
Sbjct: 15 PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEII--FNERGSKGFGFVTFENSADADRAR 72
Query: 97 YHMDGYLLLGRELTV 111
+ G ++ GR++ V
Sbjct: 73 EKLHGTVVEGRKIEV 87
>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 = 46.6 bits (109), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 40/72 (55%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
+ V ++ D +D++ F FG++K L RD TG+ +G+GF++Y + DA M
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 100 DGYLLLGRELTV 111
+ + L G+ L V
Sbjct: 188 NLFDLGGQYLRV 199
Score = 40.0 bits (92), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 36/70 (51%)
Query: 42 VRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHMDG 101
V ++ ++ + +R F FG +K I + D T + +GF FV+Y P A A M+
Sbjct: 33 VGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNS 92
Query: 102 YLLLGRELTV 111
+L GR + V
Sbjct: 93 VMLGGRNIKV 102
>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 = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 43/79 (54%), Gaps = 3/79 (3%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
L++RNL + E++ FG++G ++ I R T E RG +V Y D DA +A H+
Sbjct: 21 LMIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYEDIFDAKNACDHL 77
Query: 100 DGYLLLGRELTVVFAEENR 118
G+ + R L V++ NR
Sbjct: 78 SGFNVCNRYLVVLYYNANR 96
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 46.2 bits (108), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 45/85 (52%), Gaps = 3/85 (3%)
Query: 39 SLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYH 98
++ V NL + E ++ F QFG++ ++ L D T +P+GFGFV+ + ++A
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVE-MQEESVSEAIAK 61
Query: 99 MDGYLLLGRELTVVFAEENRKKPSE 123
+D +GR T+ E N KK E
Sbjct: 62 LDNTDFMGR--TIRVTEANPKKSLE 84
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 41/82 (50%)
Query: 39 SLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYH 98
S+ V N+ ++ E L+ F + G + L D TG+P+G+GF +Y D A A +
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 99 MDGYLLLGRELTVVFAEENRKK 120
++G GR L V A + K
Sbjct: 70 LNGREFSGRALRVDNAASEKNK 91
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/61 (40%), Positives = 33/61 (54%)
Query: 54 LRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHMDGYLLLGRELTVVF 113
L F FG + DI +P DY T + RGF FV++ DAA A +M+ L GR + V
Sbjct: 80 LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 139
Query: 114 A 114
A
Sbjct: 140 A 140
>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 = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 28/76 (36%), Positives = 39/76 (51%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
L V L + + L F FG + DI +P DY T + RGF FV++ DAA A +M
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 100 DGYLLLGRELTVVFAE 115
+ L GR + V A+
Sbjct: 70 NESELFGRTIRVNLAK 85
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 28/76 (36%), Positives = 39/76 (51%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
L V L + + L F FG + DI +P DY T + RGF FV++ DAA A +M
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 100 DGYLLLGRELTVVFAE 115
+ L GR + V A+
Sbjct: 68 NESELFGRTIRVNLAK 83
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/93 (27%), Positives = 40/93 (43%), Gaps = 3/93 (3%)
Query: 33 GRDLPTSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGE---PRGFGFVQYIDP 89
G + L ++NL E L+G F + G +K + + GFGFV+Y P
Sbjct: 1 GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60
Query: 90 ADAADAKYHMDGYLLLGRELTVVFAEENRKKPS 122
A A + G+ + G +L V +E K S
Sbjct: 61 EQAQKALKQLQGHTVDGHKLEVRISERATKPAS 93
>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 = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 28/75 (37%), Positives = 38/75 (50%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
L V L + + L F FG + DI +P DY T + RGF FV++ DAA A +M
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 100 DGYLLLGRELTVVFA 114
+ L GR + V A
Sbjct: 65 NESELFGRTIRVNLA 79
>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 = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 32/54 (59%)
Query: 61 FGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHMDGYLLLGRELTVVFA 114
FGR+ D + +D TG+ +G+GFV + + DA +A M G L GR++ +A
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA 83
>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 = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 42/79 (53%), Gaps = 3/79 (3%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
L +RNL + E++ FG++G ++ I R T E RG +V Y D DA +A H+
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYEDIFDAKNACDHL 77
Query: 100 DGYLLLGRELTVVFAEENR 118
G+ + R L V++ NR
Sbjct: 78 SGFNVCNRYLVVLYYNANR 96
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 44.7 bits (104), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 42/79 (53%), Gaps = 3/79 (3%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
L +RNL + E++ FG++G ++ I R T E RG +V Y D DA +A H+
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYEDIFDAKNAVDHL 67
Query: 100 DGYLLLGRELTVVFAEENR 118
G+ + R L V++ NR
Sbjct: 68 SGFNVSNRYLVVLYYNANR 86
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 44.3 bits (103), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 32/83 (38%), Positives = 43/83 (51%), Gaps = 3/83 (3%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
+ V NL D R +D+ F ++G ++DI L ++ G P F FV++ DP DA DA Y
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDL-KNRRGGPP--FAFVEFEDPRDAEDAVYGR 81
Query: 100 DGYLLLGRELTVVFAEENRKKPS 122
DGY G L V F R S
Sbjct: 82 DGYDYDGYRLRVEFPRSGRGTGS 104
>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 = 44.3 bits (103), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 25/61 (40%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 34 RDLPTSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAA 93
+D + V + D RP++ F Q+G + D L D TG+ RGFGFV Y D ADA
Sbjct: 84 QDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTY-DSADAV 142
Query: 94 D 94
D
Sbjct: 143 D 143
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 38/68 (55%), Gaps = 3/68 (4%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPA---DAADAK 96
+ + L D ++LR FG++G + D+ + +D TG RGFGF+ + P+ + +
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65
Query: 97 YHMDGYLL 104
+ +DG ++
Sbjct: 66 HILDGKVI 73
>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 = 44.3 bits (103), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 39/72 (54%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
+ V ++ D +D++ F FG++K L RD TG+ +G+GF++Y + DA
Sbjct: 112 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSX 171
Query: 100 DGYLLLGRELTV 111
+ + L G+ L V
Sbjct: 172 NLFDLGGQYLRV 183
Score = 35.4 bits (80), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 36/80 (45%)
Query: 32 RGRDLPTSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPAD 91
R + + V ++ ++ + +R F FG +K I D T + +GF FV+Y P
Sbjct: 7 RALAIXCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEA 66
Query: 92 AADAKYHMDGYLLLGRELTV 111
A A + L GR + V
Sbjct: 67 AQLALEQXNSVXLGGRNIKV 86
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 43.9 bits (102), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 43/85 (50%), Gaps = 1/85 (1%)
Query: 38 TSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKY 97
+ V + H+C +LR F +FG + ++ + D PRGFGF+ + D + D
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFED-EQSVDQAV 69
Query: 98 HMDGYLLLGRELTVVFAEENRKKPS 122
+M + ++G+++ V AE K S
Sbjct: 70 NMHFHDIMGKKVEVKRAEPRDSKSS 94
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 43.5 bits (101), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 37/77 (48%), Gaps = 8/77 (10%)
Query: 28 HYGGRGRDLPTSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYI 87
H G G + + L E LR FGQFG +K+ + RD T RGFGFV ++
Sbjct: 20 HMGSSG----CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFM 75
Query: 88 DPADA----ADAKYHMD 100
D A A +++ +D
Sbjct: 76 DQAGVDKVLAQSRHELD 92
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 43.5 bits (101), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 34/65 (52%), Gaps = 4/65 (6%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADA----ADA 95
+ + L E LR FGQFG +K+ + RD T RGFGFV ++D A A +
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62
Query: 96 KYHMD 100
++ +D
Sbjct: 63 RHELD 67
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 30/100 (30%), Positives = 44/100 (44%), Gaps = 13/100 (13%)
Query: 30 GGRGRDLPTSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDP 89
G G L VRNL + E L F QFG+L+ + +DY F+ + +
Sbjct: 4 GSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKDY--------AFIHFDER 55
Query: 90 ADAADAKYHMDGYLLLGRELTVVFAEENRKKPSEMRARER 129
A A M+G L G + +VFA KP + + +ER
Sbjct: 56 DGAVKAMEEMNGKDLEGENIEIVFA-----KPPDQKRKER 90
>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 = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 41/75 (54%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
L V ++ + + ++++ F +G +K+I+L D TG +G+ V+Y A AK +
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 100 DGYLLLGRELTVVFA 114
+G ++G+ + V +
Sbjct: 135 NGAEIMGQTIQVDWC 149
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 40/72 (55%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
L V ++ + + ++++ F +G +K+I+L D TG +G+ V+Y A AK +
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 100 DGYLLLGRELTV 111
+G ++G+ + V
Sbjct: 89 NGAEIMGQTIQV 100
>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 = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 28/84 (33%), Positives = 43/84 (51%), Gaps = 2/84 (2%)
Query: 38 TSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKY 97
T+L V NL + L FG++G + + RD TG PRG FV+Y +A +A
Sbjct: 14 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 73
Query: 98 HMDGYLLLG--RELTVVFAEENRK 119
++ + G + L+V AEE+ K
Sbjct: 74 ALNNVIPEGGSQPLSVRLAEEHGK 97
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 30/92 (32%), Positives = 42/92 (45%), Gaps = 1/92 (1%)
Query: 28 HYGGRGRDLPTSLL-VRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQY 86
H G R P L V L DLR F ++G + D+ + D + RGF FV +
Sbjct: 36 HVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF 95
Query: 87 IDPADAADAKYHMDGYLLLGRELTVVFAEENR 118
+ DA +AK +G L GR + V F+ R
Sbjct: 96 ENVDDAKEAKERANGMELDGRRIRVDFSITKR 127
>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 = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 37/78 (47%)
Query: 39 SLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYH 98
+L V +L + E LR F F ++ D TG RG+GFV + DA +A
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 99 MDGYLLLGRELTVVFAEE 116
M G L GR L + +A +
Sbjct: 63 MQGQDLNGRPLRINWAAK 80
>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 = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/69 (39%), Positives = 38/69 (55%), Gaps = 4/69 (5%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQY--IDPADAA-DAK 96
L + L + E LR F Q+G L D + RD T RGFGFV Y ++ DAA +A+
Sbjct: 15 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 74
Query: 97 YH-MDGYLL 104
H +DG ++
Sbjct: 75 PHKVDGRVV 83
Score = 36.6 bits (83), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 5/64 (7%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAAD----A 95
+ V ++ D LR F Q+G+++ I + D +G+ RGF FV + D D+ D
Sbjct: 106 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF-DDHDSVDKIVIQ 164
Query: 96 KYHM 99
KYH
Sbjct: 165 KYHT 168
>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 = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/69 (39%), Positives = 38/69 (55%), Gaps = 4/69 (5%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQY--IDPADAA-DAK 96
L + L + E LR F Q+G L D + RD T RGFGFV Y ++ DAA +A+
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 97 YH-MDGYLL 104
H +DG ++
Sbjct: 76 PHKVDGRVV 84
Score = 36.6 bits (83), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 5/63 (7%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAAD----A 95
+ V ++ D LR F Q+G+++ I + D +G+ RGF FV + D D+ D
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF-DDHDSVDKIVIQ 165
Query: 96 KYH 98
KYH
Sbjct: 166 KYH 168
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/69 (39%), Positives = 38/69 (55%), Gaps = 4/69 (5%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQY--IDPADAA-DAK 96
L + L + E LR F Q+G L D + RD T RGFGFV Y ++ DAA +A+
Sbjct: 17 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 76
Query: 97 YH-MDGYLL 104
H +DG ++
Sbjct: 77 PHKVDGRVV 85
Score = 36.6 bits (83), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 5/64 (7%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAAD----A 95
+ V ++ D LR F Q+G+++ I + D +G+ RGF FV + D D+ D
Sbjct: 108 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF-DDHDSVDKIVIQ 166
Query: 96 KYHM 99
KYH
Sbjct: 167 KYHT 170
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 38/75 (50%), Gaps = 6/75 (8%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
L V NL D ED + F ++G ++++ RD RGFGF++ A AK +
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAEL 78
Query: 100 DGYLLLGRELTVVFA 114
DG +L R L + FA
Sbjct: 79 DGTILKSRPLRIRFA 93
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 37/78 (47%)
Query: 39 SLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYH 98
+L V +L + E LR F F ++ D TG RG+GFV + DA +A
Sbjct: 89 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 148
Query: 99 MDGYLLLGRELTVVFAEE 116
M G L GR L + +A +
Sbjct: 149 MQGQDLNGRPLRINWAAK 166
>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 = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 28/84 (33%), Positives = 43/84 (51%), Gaps = 2/84 (2%)
Query: 38 TSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKY 97
T+L V NL + L FG++G + + RD TG PRG FV+Y +A +A
Sbjct: 101 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 160
Query: 98 HMDGYLLLG--RELTVVFAEENRK 119
++ + G + L+V AEE+ K
Sbjct: 161 ALNNVIPEGGSQPLSVRLAEEHGK 184
>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex
pdb|1PO6|A Chain A, Crystal Structure Of Up1 Complexed With
D(Tagg(6mi)ttaggg): A Human Telomeric Repeat Containing
6-Methyl-8-(2-Deoxy-
Beta-Ribofuranosyl)isoxanthopteridine (6mi)
Length = 183
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/69 (39%), Positives = 38/69 (55%), Gaps = 4/69 (5%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQY--IDPADAA-DAK 96
L + L + E LR F Q+G L D + RD T RGFGFV Y ++ DAA +A+
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68
Query: 97 YH-MDGYLL 104
H +DG ++
Sbjct: 69 PHKVDGRVV 77
Score = 36.6 bits (83), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 5/63 (7%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAAD----A 95
+ V ++ D LR F Q+G+++ I + D +G+ RGF FV + D D+ D
Sbjct: 100 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF-DDHDSVDKIVIQ 158
Query: 96 KYH 98
KYH
Sbjct: 159 KYH 161
>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 = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 37/73 (50%)
Query: 39 SLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYH 98
+L V + +D LR F +G +K I++ +G+PRG+ F++Y D A H
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 99 MDGYLLLGRELTV 111
DG + GR + V
Sbjct: 164 ADGKKIDGRRVLV 176
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/69 (39%), Positives = 38/69 (55%), Gaps = 4/69 (5%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQY--IDPADAA-DAK 96
L + L + E LR F Q+G L D + RD T RGFGFV Y ++ DAA +A+
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 97 YH-MDGYLL 104
H +DG ++
Sbjct: 76 PHKVDGRVV 84
Score = 36.6 bits (83), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 5/64 (7%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAAD----A 95
+ V ++ D LR F Q+G+++ I + D +G+ RGF FV + D D+ D
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF-DDHDSVDKIVIQ 165
Query: 96 KYHM 99
KYH
Sbjct: 166 KYHT 169
>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 = 21/72 (29%), Positives = 39/72 (54%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
L V + + ED+ F ++G +K+I+L D TG +G+ V+Y +A A +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 100 DGYLLLGRELTV 111
+G L+G+ ++V
Sbjct: 70 NGQDLMGQPISV 81
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/69 (39%), Positives = 38/69 (55%), Gaps = 4/69 (5%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQY--IDPADAA-DAK 96
L + L + E LR F Q+G L D + RD T RGFGFV Y ++ DAA +A+
Sbjct: 14 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 73
Query: 97 YH-MDGYLL 104
H +DG ++
Sbjct: 74 PHKVDGRVV 82
Score = 36.2 bits (82), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 5/64 (7%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAAD----A 95
+ V ++ D LR F Q+G+++ I + D +G+ RGF FV + D D+ D
Sbjct: 105 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF-DDHDSVDKIVIQ 163
Query: 96 KYHM 99
KYH
Sbjct: 164 KYHT 167
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 39/72 (54%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
L V + + ED+ F ++G +K+I+L D TG +G+ V+Y +A A +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 100 DGYLLLGRELTV 111
+G L+G+ ++V
Sbjct: 70 NGQDLMGQPISV 81
>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 = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 40/75 (53%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
L V + + ED+ F ++G +K+I+L D TG +G+ V+Y +A A +
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 100 DGYLLLGRELTVVFA 114
+G L+G+ ++V +
Sbjct: 85 NGQDLMGQPISVDWC 99
>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 90
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 39/72 (54%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
L V + + ED+ F ++G +K+I+L D TG +G+ V+Y +A A +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 100 DGYLLLGRELTV 111
+G L+G+ ++V
Sbjct: 70 NGQDLMGQPISV 81
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 41/89 (46%), Gaps = 5/89 (5%)
Query: 38 TSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKY 97
+L V+NL E LR F FG + + + G +GFGFV + P +A A
Sbjct: 16 VNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVT 73
Query: 98 HMDGYLLLGRELTVVFA---EENRKKPSE 123
M+G ++ + L V A EE + PS
Sbjct: 74 EMNGRIVATKPLYVALAQRKEERQSGPSS 102
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 39/72 (54%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
L V + + ED+ F ++G +K+I+L D TG +G+ V+Y +A A +
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 100 DGYLLLGRELTV 111
+G L+G+ ++V
Sbjct: 72 NGQDLMGQPISV 83
>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 = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 40/75 (53%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
L V + + ED+ F ++G +K+I+L D TG +G+ V+Y +A A +
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 100 DGYLLLGRELTVVFA 114
+G L+G+ ++V +
Sbjct: 86 NGQDLMGQPISVDWC 100
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 40/74 (54%), Gaps = 3/74 (4%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
L +RNL + E++ FG++G ++ I R T E RG +V Y D DA +A H+
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYEDIFDAKNACDHL 71
Query: 100 DGYLLLGRELTVVF 113
G+ + R L V++
Sbjct: 72 SGFNVCNRYLVVLY 85
>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 = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 39 SLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYH 98
S+ V N+ + +DL F G + I + D ++G P+G+ ++++ + ++ DA
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAE-RNSVDAAVA 96
Query: 99 MDGYLLLGRELTVV 112
MD + GR + V+
Sbjct: 97 MDETVFRGRTIKVL 110
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 27/50 (54%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDP 89
L V L E LR F Q+G + D + +D T + RGFGFV++ DP
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDP 68
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 40.8 bits (94), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 35/66 (53%)
Query: 53 DLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHMDGYLLLGRELTVV 112
DLR F ++G + D+ + D + RGF FV + + DA +AK +G L GR + V
Sbjct: 31 DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD 90
Query: 113 FAEENR 118
F+ R
Sbjct: 91 FSITKR 96
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 40.8 bits (94), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 35/66 (53%)
Query: 53 DLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHMDGYLLLGRELTVV 112
DLR F ++G + D+ + D + RGF FV + + DA +AK +G L GR + V
Sbjct: 28 DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD 87
Query: 113 FAEENR 118
F+ R
Sbjct: 88 FSITKR 93
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 40.4 bits (93), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 44/87 (50%)
Query: 35 DLPTSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAAD 94
D+ +L+V + LR F ++G ++ + + D T + RG+GFV++ + A
Sbjct: 40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQ 99
Query: 95 AKYHMDGYLLLGRELTVVFAEENRKKP 121
A ++G+ +L + L V A ++P
Sbjct: 100 AIAGLNGFNILNKRLKVALAASGHQRP 126
>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 = 40.4 bits (93), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 37/73 (50%)
Query: 39 SLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYH 98
+L V + +D LR F +G +K I++ +G+PRG+ F++Y D A H
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 99 MDGYLLLGRELTV 111
DG + GR + V
Sbjct: 164 ADGKKIDGRRVLV 176
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 40.4 bits (93), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 6/77 (7%)
Query: 38 TSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKY 97
+ L V NL D E++R F ++G+ ++++ +D +GFGF++ A AK
Sbjct: 23 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKV 76
Query: 98 HMDGYLLLGRELTVVFA 114
+D L G++L V FA
Sbjct: 77 ELDNMPLRGKQLRVRFA 93
>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
pdb|3S7R|B Chain B, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
Length = 87
Score = 40.4 bits (93), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 34/68 (50%), Gaps = 4/68 (5%)
Query: 41 LVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAA---DAKY 97
V L D +DL+ F +FG + D + D TG RGFGF+ + D A D K
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQKE 74
Query: 98 H-MDGYLL 104
H +DG ++
Sbjct: 75 HRLDGRVI 82
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 40.4 bits (93), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 27/88 (30%), Positives = 41/88 (46%), Gaps = 4/88 (4%)
Query: 28 HYGGRGRDLPT-SLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQY 86
G R P+ +L V+ L D E L+ F R + + D TG +GFGFV +
Sbjct: 5 SSGPNARSQPSKTLFVKGLSEDTTEETLKESFDGSVRAR---IVTDRETGSSKGFGFVDF 61
Query: 87 IDPADAADAKYHMDGYLLLGRELTVVFA 114
DA AK M+ + G ++T+ +A
Sbjct: 62 NSEEDAKAAKEAMEDGEIDGNKVTLDWA 89
>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 = 8e-04, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 40/75 (53%), Gaps = 6/75 (8%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
L V NL D E++R F ++G+ ++++ +D +GFGF++ A AK +
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVEL 71
Query: 100 DGYLLLGRELTVVFA 114
D L G++L V FA
Sbjct: 72 DNMPLRGKQLRVRFA 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 = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 40/80 (50%), Gaps = 1/80 (1%)
Query: 39 SLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYH 98
S+ V N+ + E+L F G + + + D ++G P+GF ++++ D ++
Sbjct: 7 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDK-ESVRTSLA 65
Query: 99 MDGYLLLGRELTVVFAEENR 118
+D L GR++ V+ NR
Sbjct: 66 LDESLFRGRQIKVIPKRTNR 85
>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 = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 40/80 (50%), Gaps = 1/80 (1%)
Query: 39 SLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYH 98
S+ V N+ + E+L F G + + + D ++G P+GF ++++ D ++
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDK-ESVRTSLA 66
Query: 99 MDGYLLLGRELTVVFAEENR 118
+D L GR++ V+ NR
Sbjct: 67 LDESLFRGRQIKVIPKRTNR 86
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 5/70 (7%)
Query: 42 VRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHMDG 101
V NL +L F +G L+ +++ R+ P GF FV++ DP DA DA +DG
Sbjct: 5 VGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDG 59
Query: 102 YLLLGRELTV 111
++ G + V
Sbjct: 60 KVICGSRVRV 69
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 36/65 (55%)
Query: 58 FGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHMDGYLLLGRELTVVFAEEN 117
F Q G + + ++P+D TG+ +G+GFV+++ DA A MD L G+ + V A +
Sbjct: 36 FLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAH 95
Query: 118 RKKPS 122
K S
Sbjct: 96 NKNLS 100
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 33/66 (50%)
Query: 38 TSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKY 97
T+L V NL + L FG++G + + RD TG PRG FV+Y +A +A
Sbjct: 90 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 149
Query: 98 HMDGYL 103
++ +
Sbjct: 150 ALNNVI 155
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 29/93 (31%), Positives = 45/93 (48%), Gaps = 9/93 (9%)
Query: 35 DLPTSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAAD 94
+LP SL + E+L PFG R +Y R TG+ +G+GF +Y+ AA
Sbjct: 102 NLPPSLTQQQF------EELVRPFGSLERCFLVYSER---TGQSKGYGFAEYMKKDSAAR 152
Query: 95 AKYHMDGYLLLGRELTVVFAEENRKKPSEMRAR 127
AK + G L R L V + + + P+ + +R
Sbjct: 153 AKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSR 185
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 29/93 (31%), Positives = 45/93 (48%), Gaps = 9/93 (9%)
Query: 35 DLPTSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAAD 94
+LP SL + E+L PFG R +Y R TG+ +G+GF +Y+ AA
Sbjct: 102 NLPPSLTQQQF------EELVRPFGSLERCFLVYSER---TGQSKGYGFAEYMKKDSAAR 152
Query: 95 AKYHMDGYLLLGRELTVVFAEENRKKPSEMRAR 127
AK + G L R L V + + + P+ + +R
Sbjct: 153 AKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSR 185
>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 = 0.002, Method: Compositional matrix adjust.
Identities = 29/93 (31%), Positives = 45/93 (48%), Gaps = 9/93 (9%)
Query: 35 DLPTSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAAD 94
+LP SL + E+L PFG R +Y R TG+ +G+GF +Y+ AA
Sbjct: 100 NLPPSLTQQQF------EELVRPFGSLERCFLVYSER---TGQSKGYGFAEYMKKDSAAR 150
Query: 95 AKYHMDGYLLLGRELTVVFAEENRKKPSEMRAR 127
AK + G L R L V + + + P+ + +R
Sbjct: 151 AKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSR 183
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 36/69 (52%), Gaps = 4/69 (5%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPA--DAADAK- 96
L + L + E LR + Q+G+L D + RD + RGFGFV + A DAA A
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAAR 89
Query: 97 -YHMDGYLL 104
+ +DG ++
Sbjct: 90 PHSIDGRVV 98
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
Query: 37 PTSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRD-YYTGEPRGFGFVQYIDPADAADA 95
PT + + L + + + F +G++K I +P + + +G+ +V++ +P +A A
Sbjct: 4 PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKA 63
Query: 96 KYHMDGYLLLGRELTVV 112
HMDG + G+E+T
Sbjct: 64 LKHMDGGQIDGQEITAT 80
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 32/59 (54%)
Query: 53 DLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHMDGYLLLGRELTV 111
DLR F ++G + D+ + D + RGF FV + + DA +AK +G L GR + V
Sbjct: 31 DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 89
>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 = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 1/65 (1%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
L + L C E+L G +KD+ L + G+P+G +V+Y + + A+ A M
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKM 78
Query: 100 DGYLL 104
DG +
Sbjct: 79 DGMTI 83
>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 = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 25/47 (53%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQY 86
+ + L D +DL+ F +FG + D L D TG RGFGFV +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLF 48
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 37/82 (45%), Gaps = 2/82 (2%)
Query: 30 GGRGRDLPTSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDP 89
G G + VRNL D + L+ F + G + +Y G+ +G G V++ P
Sbjct: 1 GSSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHV--LYADIKMENGKSKGCGVVKFESP 58
Query: 90 ADAADAKYHMDGYLLLGRELTV 111
A A M+G L GRE+ V
Sbjct: 59 EVAERACRMMNGMKLSGREIDV 80
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 36/73 (49%), Gaps = 1/73 (1%)
Query: 39 SLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYH 98
++ V NL R E L F Q G L + + +D G+P+ FGFV + P + A
Sbjct: 18 TVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYAIAL 76
Query: 99 MDGYLLLGRELTV 111
++G L GR + V
Sbjct: 77 LNGIRLYGRPINV 89
>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 = 37.0 bits (84), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 31/65 (47%), Gaps = 3/65 (4%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDP---ADAADAK 96
+ V L D E +R FG FG ++ I LP D T + RGF F+ + + + K
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 63
Query: 97 YHMDG 101
YH G
Sbjct: 64 YHNVG 68
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 36.6 bits (83), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 31/65 (47%), Gaps = 3/65 (4%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDP---ADAADAK 96
+ V L D E +R FG FG ++ I LP D T + RGF F+ + + + K
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Query: 97 YHMDG 101
YH G
Sbjct: 62 YHNVG 66
>pdb|2KRB|A Chain A, Solution Structure Of Eif3b-Rrm Bound To Eif3j Peptide
Length = 81
Score = 36.6 bits (83), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 29/47 (61%), Gaps = 2/47 (4%)
Query: 58 FGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHMDGYLL 104
F +FG++ + + P + G+ +G+ F++Y PA A DA + DGY L
Sbjct: 28 FSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAVDAVKNADGYKL 72
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 36.6 bits (83), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 37/79 (46%), Gaps = 2/79 (2%)
Query: 33 GRDLPTSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADA 92
G + + VRNL D + L+ F + G + +Y G+ +G G V++ P A
Sbjct: 1 GSSGSSGIFVRNLPFDFTWKMLKDKFNECGHV--LYADIKMENGKSKGCGVVKFESPEVA 58
Query: 93 ADAKYHMDGYLLLGRELTV 111
A M+G L GRE+ V
Sbjct: 59 ERACRMMNGMKLSGREIDV 77
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 36.6 bits (83), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 25/47 (53%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQY 86
+ V L + ED++ F QFG++ D L D T RGFGFV +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF 48
>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 = 0.011, Method: Compositional matrix adjust.
Identities = 32/94 (34%), Positives = 41/94 (43%), Gaps = 15/94 (15%)
Query: 38 TSLLVRNLRHDCRPEDLRGPFGQFGRLK----------DIYLPRDYYTGEPRGFGFVQYI 87
+++ V+ L +DL F Q G +K IYL D TG+P+G V Y
Sbjct: 16 SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYL--DKETGKPKGDATVSYE 73
Query: 88 DPADAADAKYHMDGYLLLGRELTVVFAEENRKKP 121
DP A A DG G +L V A RKKP
Sbjct: 74 DPPTAKAAVEWFDGKDFQGSKLKVSLA---RKKP 104
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 36.6 bits (83), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 24/94 (25%), Positives = 43/94 (45%), Gaps = 12/94 (12%)
Query: 34 RDLPTSLLVRNLRH-DCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADA 92
R + + + + NL + D+ F ++G++ + + GF FVQY++ +A
Sbjct: 12 RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK--------GFAFVQYVNERNA 63
Query: 93 ADAKYHMDGYLLLGRELTVVFAEE---NRKKPSE 123
A DG ++ G+ L + A E NR PS
Sbjct: 64 RAAVAGEDGRMIAGQVLDINLAAEPKVNRSGPSS 97
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 36.2 bits (82), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 38/82 (46%), Gaps = 8/82 (9%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
+ V N+ C ++LR F + GR+ + + +DY FV ADA A +
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKDY--------AFVHMEKEADAKAAIAQL 63
Query: 100 DGYLLLGRELTVVFAEENRKKP 121
+G + G+ + V + + +KK
Sbjct: 64 NGKEVKGKRINVELSTKGQKKS 85
>pdb|2NLW|A Chain A, Solution Structure Of The Rrm Domain Of Human Eukaryotic
Initiation Factor 3b
Length = 105
Score = 36.2 bits (82), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 29/47 (61%), Gaps = 2/47 (4%)
Query: 58 FGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHMDGYLL 104
F +FG++ + + P + G+ +G+ F++Y PA A DA + DGY L
Sbjct: 42 FSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAVDAVKNADGYKL 86
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 36.2 bits (82), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 29/57 (50%)
Query: 32 RGRDLPTSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYID 88
R + L+V L +DL+ F FG + + + +D TG +GFGFV++ +
Sbjct: 10 RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTE 66
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 35.4 bits (80), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 39/88 (44%), Gaps = 8/88 (9%)
Query: 28 HYGGRGRDLPTSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYI 87
H+ G T L VR D + +L FG FG +K++ + GF FV++
Sbjct: 22 HHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFE 73
Query: 88 DPADAADAKYHMDGYLLLGRELTVVFAE 115
+ AA A + G + L VV+++
Sbjct: 74 EAESAAKAIEEVHGKSFANQPLEVVYSK 101
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 35.4 bits (80), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 17/77 (22%), Positives = 36/77 (46%)
Query: 38 TSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKY 97
+++ V NL DL F ++G++ + + +D T + +G F+ ++D A +
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
Query: 98 HMDGYLLLGRELTVVFA 114
++ L GR + A
Sbjct: 77 AINNKQLFGRVIKASIA 93
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 35.0 bits (79), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
Query: 37 PTSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAK 96
P +L V NL D + F Q G K + ++ + +P + FV++ + DAA A
Sbjct: 15 PRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAAL 72
Query: 97 YHMDGYLLLGRELTVVFA 114
M+G +LG+E+ V +A
Sbjct: 73 AAMNGRKILGKEVKVNWA 90
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 34.7 bits (78), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 31 GRGRDLPTSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPA 90
G G+ +P ++ V + ++R F ++G +K++ + D TG +G+GFV + +
Sbjct: 4 GSGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDV 62
Query: 91 DA 92
D
Sbjct: 63 DV 64
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 34.7 bits (78), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 38/83 (45%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
L ++NL DL F +F K + TG RG F+ + + A A + +
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87
Query: 100 DGYLLLGRELTVVFAEENRKKPS 122
+GY L G+ L + F + +++ S
Sbjct: 88 NGYKLYGKILVIEFGKNKKQRSS 110
>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 = 34.7 bits (78), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFG-RLKDIYLPRDYYTGEPRGFGFVQYIDPADAA---DA 95
+++R L +D+RG G + +++ L R+ +G+ RGF FV++ DA +A
Sbjct: 4 VMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEA 63
Query: 96 KYHMDGYLLLGRELTVVFAE 115
H +LG+++++ +++
Sbjct: 64 NQH--SLNILGQKVSMHYSD 81
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 34.7 bits (78), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 35/77 (45%), Gaps = 8/77 (10%)
Query: 38 TSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKY 97
T L VR D + +L FG FG +K++ + GF FV++ + AA A
Sbjct: 5 TRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAKAIE 56
Query: 98 HMDGYLLLGRELTVVFA 114
+ G + L VV++
Sbjct: 57 EVHGKSFANQPLEVVYS 73
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 34.3 bits (77), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 20/91 (21%), Positives = 45/91 (49%), Gaps = 7/91 (7%)
Query: 39 SLLVRNLRHDCRPEDLR----GPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAAD 94
++ + NL + ++L+ F QFG++ DI + R + RG FV + + + A +
Sbjct: 10 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSL---KMRGQAFVIFKEVSSATN 66
Query: 95 AKYHMDGYLLLGRELTVVFAEENRKKPSEMR 125
A M G+ + + + +A+ + ++M+
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMK 97
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 34.3 bits (77), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 38/79 (48%), Gaps = 2/79 (2%)
Query: 38 TSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKY 97
+L V L +++ F Q+GR+ + D TG RG GF+++ +A +A
Sbjct: 2 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 61
Query: 98 HMDGYLLLGRE--LTVVFA 114
++G LG +TV FA
Sbjct: 62 GLNGQKPLGAAEPITVKFA 80
>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 = 33.5 bits (75), Expect = 0.093, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 34/74 (45%)
Query: 38 TSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKY 97
+L + +L + +DL F FG + + D T + FGFV Y +P A A
Sbjct: 26 ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 85
Query: 98 HMDGYLLLGRELTV 111
M+G+ + + L V
Sbjct: 86 SMNGFQIGMKRLKV 99
>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 = 33.5 bits (75), Expect = 0.095, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 31/68 (45%)
Query: 37 PTSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAK 96
+L V NL E + F + G +K I + D GF FV+Y ADA +A
Sbjct: 39 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAM 98
Query: 97 YHMDGYLL 104
+++G L
Sbjct: 99 RYINGTRL 106
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 33.1 bits (74), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 19/83 (22%), Positives = 41/83 (49%), Gaps = 7/83 (8%)
Query: 39 SLLVRNLRHDCRPEDLR----GPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAAD 94
++ + NL + ++L+ F QFG++ DI + R + RG FV + + + A +
Sbjct: 11 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSL---KMRGQAFVIFKEVSSATN 67
Query: 95 AKYHMDGYLLLGRELTVVFAEEN 117
A M G+ + + + +A+ +
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKTD 90
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 33.1 bits (74), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 32/60 (53%), Gaps = 1/60 (1%)
Query: 33 GRDLPTSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADA 92
G+ +P ++ V + ++R F ++G +K++ + D TG +G+GFV + + D
Sbjct: 5 GKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDV 63
>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 33.1 bits (74), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 20/91 (21%), Positives = 44/91 (48%), Gaps = 7/91 (7%)
Query: 39 SLLVRNLRHDCRPEDLR----GPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAAD 94
++ + NL + ++L+ F QFG++ DI + R RG FV + + + A +
Sbjct: 11 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKM---RGQAFVIFKEVSSATN 67
Query: 95 AKYHMDGYLLLGRELTVVFAEENRKKPSEMR 125
A M G+ + + + +A+ + ++M+
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMK 98
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 32.7 bits (73), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 27/55 (49%)
Query: 38 TSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADA 92
T + V L + LR F FG +++ + D TG+ RG+GFV D A A
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAA 72
>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Rna, Uuguucuu
Length = 102
Score = 32.3 bits (72), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 32/60 (53%), Gaps = 1/60 (1%)
Query: 33 GRDLPTSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADA 92
G+ +P ++ V + ++R F ++G +K++ + D TG +G+GFV + + D
Sbjct: 5 GKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDV 63
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 32.3 bits (72), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 35/82 (42%), Gaps = 1/82 (1%)
Query: 30 GGRGRDLPTSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDP 89
GG G + LLV NL D++ F +FG LK + D +G G V +
Sbjct: 28 GGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERR 86
Query: 90 ADAADAKYHMDGYLLLGRELTV 111
ADA A G L GR + +
Sbjct: 87 ADALKAMKQYKGVPLDGRPMDI 108
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 32.3 bits (72), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 38/83 (45%), Gaps = 8/83 (9%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
L VRNL E L F +FG+L+ + +DY FV + D A A M
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKDY--------AFVHFEDRGAAVKAMDEM 69
Query: 100 DGYLLLGRELTVVFAEENRKKPS 122
+G + G E+ +V A+ KK S
Sbjct: 70 NGKEIEGEEIEIVLAKPPDKKRS 92
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 32.3 bits (72), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 35/82 (42%), Gaps = 1/82 (1%)
Query: 30 GGRGRDLPTSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDP 89
GG G + LLV NL D++ F +FG LK + D +G G V +
Sbjct: 28 GGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERR 86
Query: 90 ADAADAKYHMDGYLLLGRELTV 111
ADA A G L GR + +
Sbjct: 87 ADALKAMKQYKGVPLDGRPMDI 108
>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 = 0.24, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 35/82 (42%), Gaps = 1/82 (1%)
Query: 30 GGRGRDLPTSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDP 89
GG G + LLV NL D++ F +FG LK + D +G G V +
Sbjct: 81 GGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERR 139
Query: 90 ADAADAKYHMDGYLLLGRELTV 111
ADA A G L GR + +
Sbjct: 140 ADALKAMKQYKGVPLDGRPMDI 161
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 31.6 bits (70), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 33/73 (45%)
Query: 39 SLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYH 98
+L + +L + DL F FG + + D T + FGFV + +P A A
Sbjct: 42 NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101
Query: 99 MDGYLLLGRELTV 111
M+G+ + + L V
Sbjct: 102 MNGFQVGTKRLKV 114
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 31.6 bits (70), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 26/51 (50%), Gaps = 5/51 (9%)
Query: 38 TSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYID 88
+ + V D E+L+ F Q+G + D+++P+ + R F FV + D
Sbjct: 12 SKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF-----RAFAFVTFAD 57
>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 = 31.6 bits (70), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 22/91 (24%), Positives = 42/91 (46%), Gaps = 2/91 (2%)
Query: 39 SLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYH 98
++ ++NL + L F FG + + D +G+GFV + A A
Sbjct: 7 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEK 64
Query: 99 MDGYLLLGRELTVVFAEENRKKPSEMRARER 129
M+G LL R++ V + +++ +E+ AR +
Sbjct: 65 MNGMLLNDRKVFVGRFKSRKEREAELGARAK 95
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 31.2 bits (69), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 31/75 (41%), Gaps = 9/75 (12%)
Query: 47 HDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHMDGYLLLG 106
D P LRG F FG + D+ + PR FV Y A A ++G +
Sbjct: 23 EDMTPTLLRGAFSPFGNIIDLSM------DPPRNCAFVTYEKMESADQAVAELNGTQVES 76
Query: 107 RELTVVFAEENRKKP 121
+L V A RK+P
Sbjct: 77 VQLKVNIA---RKQP 88
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 31.2 bits (69), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 26/52 (50%)
Query: 60 QFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHMDGYLLLGRELTV 111
FG LK L +D TG +G+ F +Y+D A ++G L ++L V
Sbjct: 24 SFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLV 75
>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAF|B Chain B, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAG|A Chain A, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAG|B Chain B, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAH|A Chain A, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAH|B Chain B, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAI|A Chain A, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAI|B Chain B, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAJ|A Chain A, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAJ|B Chain B, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAK|A Chain A, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAK|B Chain B, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAL|A Chain A, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|B Chain B, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|D Chain D, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|I Chain I, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAM|A Chain A, Structure Of U2af65 Variant With Bru5c2 Dna
pdb|3VAM|B Chain B, Structure Of U2af65 Variant With Bru5c2 Dna
Length = 174
Score = 31.2 bits (69), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 33/72 (45%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
L + L + + ++ FG LK L +D TG +G+ F +Y+D A +
Sbjct: 99 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 158
Query: 100 DGYLLLGRELTV 111
+G L ++L V
Sbjct: 159 NGMQLGDKKLLV 170
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 31.2 bits (69), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 33/72 (45%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
L + L + + ++ FG LK L +D TG +G+ F +Y+D A +
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 100 DGYLLLGRELTV 111
+G L ++L V
Sbjct: 157 NGMQLGDKKLLV 168
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 31.2 bits (69), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 33/72 (45%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
L + L + + ++ FG LK L +D TG +G+ F +Y+D A +
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176
Query: 100 DGYLLLGRELTV 111
+G L ++L V
Sbjct: 177 NGMQLGDKKLLV 188
>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 = 31.2 bits (69), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 31/75 (41%), Gaps = 9/75 (12%)
Query: 47 HDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHMDGYLLLG 106
D P LRG F FG + D+ + PR FV Y A A ++G +
Sbjct: 47 EDMTPTLLRGAFSPFGNIIDLSM------DPPRNCAFVTYEKMESADQAVAELNGTQVES 100
Query: 107 RELTVVFAEENRKKP 121
+L V A RK+P
Sbjct: 101 VQLKVNIA---RKQP 112
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 30.8 bits (68), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 31/57 (54%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAK 96
L + + + +DL+ F +FG++ ++ + +D +TG +G F+ Y + A A+
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQ 72
>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 = 0.53, Method: Compositional matrix adjust.
Identities = 22/91 (24%), Positives = 42/91 (46%), Gaps = 2/91 (2%)
Query: 39 SLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYH 98
++ ++NL + L F FG + + D +G+GFV + A A
Sbjct: 100 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEK 157
Query: 99 MDGYLLLGRELTVVFAEENRKKPSEMRARER 129
M+G LL R++ V + +++ +E+ AR +
Sbjct: 158 MNGMLLNDRKVFVGRFKSRKEREAELGARAK 188
>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 = 0.55, Method: Compositional matrix adjust.
Identities = 22/91 (24%), Positives = 42/91 (46%), Gaps = 2/91 (2%)
Query: 39 SLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYH 98
++ ++NL + L F FG + + D +G+GFV + A A
Sbjct: 105 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEK 162
Query: 99 MDGYLLLGRELTVVFAEENRKKPSEMRARER 129
M+G LL R++ V + +++ +E+ AR +
Sbjct: 163 MNGMLLNDRKVFVGRFKSRKEREAELGARAK 193
>pdb|2DIT|A Chain A, Solution Structure Of The Rrm_1 Domain Of Hiv Tat Specific
Factor 1 Variant
Length = 112
Score = 30.8 bits (68), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 52 EDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHMDGYLLLGRELTV 111
EDLR +FG+++ + L + P G V + DP +A +DG GR++T
Sbjct: 41 EDLRVECSKFGQIRKLLL----FDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITA 96
>pdb|3ZZY|A Chain A, Crystal Structure Of A Raver1 Pri3 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
pdb|3ZZY|B Chain B, Crystal Structure Of A Raver1 Pri3 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
pdb|3ZZZ|A Chain A, Crystal Structure Of A Raver1 Pri4 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
pdb|3ZZZ|B Chain B, Crystal Structure Of A Raver1 Pri4 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
Length = 130
Score = 30.8 bits (68), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 4/62 (6%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
++V NL + + L F +FG + I +T + +QY DP A AK +
Sbjct: 31 IIVENLFYPVTLDVLHQIFSKFGTVLKIIT----FTKNNQFQALLQYADPVSAQHAKLSL 86
Query: 100 DG 101
DG
Sbjct: 87 DG 88
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 30.4 bits (67), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 3/82 (3%)
Query: 39 SLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYH 98
++ L RP DL F G+++D+ + D + +G +V++ + +
Sbjct: 27 TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCE-IQSVPLAIG 85
Query: 99 MDGYLLLGRELTVVF--AEENR 118
+ G LLG + V AE+NR
Sbjct: 86 LTGQRLLGVPIIVQASQAEKNR 107
>pdb|1SJR|A Chain A, Nmr Structure Of Rrm2 From Human Polypyrimidine Tract
Binding Protein Isoform 1 (Ptb1)
Length = 164
Score = 30.4 bits (67), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 4/62 (6%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
++V NL + + L F +FG + I +T + +QY DP A AK +
Sbjct: 49 IIVENLFYPVTLDVLHQIFSKFGTVLKII----TFTKNNQFQALLQYADPVSAQHAKLSL 104
Query: 100 DG 101
DG
Sbjct: 105 DG 106
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 30.4 bits (67), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 34/84 (40%), Gaps = 8/84 (9%)
Query: 39 SLLVRNLRHDCRPEDLRGPFGQFGRLKD--------IYLPRDYYTGEPRGFGFVQYIDPA 90
++ V+ L + E + F Q G +K I L D TG+ +G V + DP
Sbjct: 9 TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 68
Query: 91 DAADAKYHMDGYLLLGRELTVVFA 114
A A DG G + V FA
Sbjct: 69 SAKAAIDWFDGKEFSGNPIKVSFA 92
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 30.4 bits (67), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 34/84 (40%), Gaps = 8/84 (9%)
Query: 39 SLLVRNLRHDCRPEDLRGPFGQFGRLKD--------IYLPRDYYTGEPRGFGFVQYIDPA 90
++ V+ L + E + F Q G +K I L D TG+ +G V + DP
Sbjct: 15 TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 74
Query: 91 DAADAKYHMDGYLLLGRELTVVFA 114
A A DG G + V FA
Sbjct: 75 SAKAAIDWFDGKEFSGNPIKVSFA 98
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 30.4 bits (67), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 27/56 (48%), Gaps = 5/56 (8%)
Query: 33 GRDLPTSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYID 88
G + + V D ++LR F Q+G + D+++P+ + R F FV + D
Sbjct: 1 GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFAD 51
>pdb|2E5J|A Chain A, Solution Structure Of Rna Binding Domain In
Methenyltetrahydrofolate Synthetase Domain Containing
Length = 97
Score = 30.4 bits (67), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 33/88 (37%), Gaps = 5/88 (5%)
Query: 33 GRDLPTSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADA 92
G L + V NL D R DL+ + G +P PR F+ Y D A A
Sbjct: 15 GAPLAADVYVGNLPRDARVSDLKRALRELG-----SVPLRLTWQGPRRRAFLHYPDSAAA 69
Query: 93 ADAKYHMDGYLLLGRELTVVFAEENRKK 120
A + G L L V A + R K
Sbjct: 70 QQAVSCLQGLRLGTDTLRVALARQQRDK 97
>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 = 30.4 bits (67), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 3/65 (4%)
Query: 53 DLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHMDGYLLLGRELTVV 112
DL G LK ++ P+ TG +G+ F+++ D +A A +++GY L R L
Sbjct: 23 DLCSNVGPVINLKMMFDPQ---TGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCG 79
Query: 113 FAEEN 117
++ +
Sbjct: 80 YSSNS 84
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 30.4 bits (67), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 32/72 (44%), Gaps = 1/72 (1%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
LLV NL D++ F +FG LK + D +G G V + ADA A
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQY 89
Query: 100 DGYLLLGRELTV 111
+G L GR + +
Sbjct: 90 NGVPLDGRPMNI 101
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 30.0 bits (66), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 21/87 (24%), Positives = 36/87 (41%), Gaps = 9/87 (10%)
Query: 32 RGRDLPTSLLVRNL-RHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPA 90
RG + + L + NL + EDL F +G + I + FGF+Q+ +P
Sbjct: 17 RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQFDNPQ 68
Query: 91 DAADAKYHMDGYLLLGRELTVVFAEEN 117
DA + G++L + + N
Sbjct: 69 SVRDAIEXESQEMNFGKKLILEVSSSN 95
>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 = 30.0 bits (66), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 30/65 (46%), Gaps = 1/65 (1%)
Query: 37 PTSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAK 96
+L V NL E + F + G +K I + D GF FV+Y ADA +A
Sbjct: 18 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDK-MKTACGFCFVEYYSRADAENAM 76
Query: 97 YHMDG 101
+++G
Sbjct: 77 RYING 81
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 30.0 bits (66), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 3/65 (4%)
Query: 53 DLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHMDGYLLLGRELTVV 112
DL G LK ++ P+ TG +G+ F+++ D +A A +++GY L R L
Sbjct: 21 DLCSNVGPVINLKMMFDPQ---TGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCG 77
Query: 113 FAEEN 117
++ +
Sbjct: 78 YSSNS 82
>pdb|2ADB|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd2 Complexed With Cucucu Rna
Length = 148
Score = 30.0 bits (66), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 4/62 (6%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
++V NL + + L F +FG + I +T + +QY DP A AK +
Sbjct: 36 IIVENLFYPVTLDVLHQIFSKFGTVLKIIT----FTKNNQFQALLQYADPVSAQHAKLSL 91
Query: 100 DG 101
DG
Sbjct: 92 DG 93
>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 = 30.0 bits (66), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 3/65 (4%)
Query: 53 DLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHMDGYLLLGRELTVV 112
DL G LK ++ P+ TG +G+ F+++ D +A A +++GY L R L
Sbjct: 22 DLCSNVGPVINLKMMFDPQ---TGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCG 78
Query: 113 FAEEN 117
++ +
Sbjct: 79 YSSNS 83
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 34/82 (41%), Gaps = 6/82 (7%)
Query: 39 SLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPA------DA 92
++ +RNL D E L QFG LK + + T +G F Q++ A
Sbjct: 17 TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 76
Query: 93 ADAKYHMDGYLLLGRELTVVFA 114
A + G L GR+L V A
Sbjct: 77 ASLEAEGGGLKLDGRQLKVDLA 98
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 21/87 (24%), Positives = 36/87 (41%), Gaps = 9/87 (10%)
Query: 32 RGRDLPTSLLVRNL-RHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPA 90
RG + + L + NL + EDL F +G + I + FGF+Q+ +P
Sbjct: 17 RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQFDNPQ 68
Query: 91 DAADAKYHMDGYLLLGRELTVVFAEEN 117
DA + G++L + + N
Sbjct: 69 SVRDAIECESQEMNFGKKLILEVSSSN 95
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 29.6 bits (65), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 27/52 (51%), Gaps = 3/52 (5%)
Query: 75 TGEPRGFGFVQYIDPADAADAKYHMDGYLLLGRE---LTVVFAEENRKKPSE 123
TG +G+GFV++ D + A G + LG + L+V + +R KP E
Sbjct: 47 TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIPKASRVKPVE 98
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 29.3 bits (64), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 33/77 (42%), Gaps = 8/77 (10%)
Query: 38 TSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKY 97
T L V N+ C ++LR F ++G + + + +DY FV DA +A
Sbjct: 11 TKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKDY--------AFVHMERAEDAVEAIR 62
Query: 98 HMDGYLLLGRELTVVFA 114
+D G+ + V +
Sbjct: 63 GLDNTEFQGKRMHVQLS 79
>pdb|3E35|A Chain A, Actinobacteria-Specific Protein Of Unknown Function,
Sco1997
Length = 325
Score = 29.3 bits (64), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 2/60 (3%)
Query: 70 PRDYYTGEPRGFGFVQYIDPADAAD--AKYHMDGYLLLGRELTVVFAEENRKKPSEMRAR 127
P+D YT EP+G V ++A YH DGY+ G + + P ++ AR
Sbjct: 4 PQDLYTWEPKGLAVVDXALAQESAGLVXLYHFDGYIDAGETGDQIVDQVLDSLPHQVVAR 63
>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 = 29.3 bits (64), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 31/72 (43%), Gaps = 1/72 (1%)
Query: 40 LLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKYHM 99
LLV NL D++ F +FG LK + D +G G V + ADA A
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAXKQY 90
Query: 100 DGYLLLGRELTV 111
+G L GR +
Sbjct: 91 NGVPLDGRPXNI 102
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 29.3 bits (64), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 2/49 (4%)
Query: 52 EDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYI--DPADAADAKYH 98
+DL+ F +FGR+ ++ + +D TG +G F+ Y D A A + H
Sbjct: 30 QDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSALH 78
>pdb|1WHX|A Chain A, Solution Structure Of The Second Rna Binding Domain From
Hypothetical Protein Bab23448
Length = 111
Score = 29.3 bits (64), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 29/62 (46%), Gaps = 6/62 (9%)
Query: 38 TSLLVRNLRHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKY 97
T +L +NL +++ F +FG L + LP T V++++P +A A
Sbjct: 11 TVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGIT------AIVEFLEPLEARKAFR 64
Query: 98 HM 99
H+
Sbjct: 65 HL 66
>pdb|1YWG|O Chain O, The Structure Of Glyceraldehyde-3-Phosphate Dehydrogenase
From Plasmodium Falciparum
pdb|1YWG|P Chain P, The Structure Of Glyceraldehyde-3-Phosphate Dehydrogenase
From Plasmodium Falciparum
pdb|1YWG|Q Chain Q, The Structure Of Glyceraldehyde-3-Phosphate Dehydrogenase
From Plasmodium Falciparum
pdb|1YWG|R Chain R, The Structure Of Glyceraldehyde-3-Phosphate Dehydrogenase
From Plasmodium Falciparum
Length = 337
Score = 27.3 bits (59), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 18/27 (66%), Gaps = 3/27 (11%)
Query: 98 HMDGYLLLGRELTVVFAEENRKKPSEM 124
H DG+LL+G + VFAE K PS++
Sbjct: 62 HADGFLLIGEKKVSVFAE---KDPSQI 85
>pdb|2B4R|O Chain O, Crystal Structure Of Glyceraldehyde-3-Phosphate
Dehydrogenase From Plasmodium Falciparum At 2.25
Angstrom Resolution Reveals Intriguing Extra Electron
Density In The Active Site
pdb|2B4R|P Chain P, Crystal Structure Of Glyceraldehyde-3-Phosphate
Dehydrogenase From Plasmodium Falciparum At 2.25
Angstrom Resolution Reveals Intriguing Extra Electron
Density In The Active Site
pdb|2B4R|Q Chain Q, Crystal Structure Of Glyceraldehyde-3-Phosphate
Dehydrogenase From Plasmodium Falciparum At 2.25
Angstrom Resolution Reveals Intriguing Extra Electron
Density In The Active Site
pdb|2B4R|R Chain R, Crystal Structure Of Glyceraldehyde-3-Phosphate
Dehydrogenase From Plasmodium Falciparum At 2.25
Angstrom Resolution Reveals Intriguing Extra Electron
Density In The Active Site
pdb|2B4T|O Chain O, Crystal Structure Of Glyceraldehyde-3-Phosphate
Dehydrogenase From Plasmodium Falciparum At 2.25
Angstrom Resolution Reveals Intriguing Extra Electron
Density In The Active Site
pdb|2B4T|P Chain P, Crystal Structure Of Glyceraldehyde-3-Phosphate
Dehydrogenase From Plasmodium Falciparum At 2.25
Angstrom Resolution Reveals Intriguing Extra Electron
Density In The Active Site
pdb|2B4T|Q Chain Q, Crystal Structure Of Glyceraldehyde-3-Phosphate
Dehydrogenase From Plasmodium Falciparum At 2.25
Angstrom Resolution Reveals Intriguing Extra Electron
Density In The Active Site
pdb|2B4T|R Chain R, Crystal Structure Of Glyceraldehyde-3-Phosphate
Dehydrogenase From Plasmodium Falciparum At 2.25
Angstrom Resolution Reveals Intriguing Extra Electron
Density In The Active Site
Length = 345
Score = 27.3 bits (59), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 18/27 (66%), Gaps = 3/27 (11%)
Query: 98 HMDGYLLLGRELTVVFAEENRKKPSEM 124
H DG+LL+G + VFAE K PS++
Sbjct: 70 HADGFLLIGEKKVSVFAE---KDPSQI 93
>pdb|3LVP|A Chain A, Crystal Structure Of Bisphosphorylated Igf1-R Kinase
Domain (2p) In Complex With A Bis-Azaindole Inhibitor
pdb|3LVP|B Chain B, Crystal Structure Of Bisphosphorylated Igf1-R Kinase
Domain (2p) In Complex With A Bis-Azaindole Inhibitor
pdb|3LVP|C Chain C, Crystal Structure Of Bisphosphorylated Igf1-R Kinase
Domain (2p) In Complex With A Bis-Azaindole Inhibitor
pdb|3LVP|D Chain D, Crystal Structure Of Bisphosphorylated Igf1-R Kinase
Domain (2p) In Complex With A Bis-Azaindole Inhibitor
Length = 336
Score = 27.3 bits (59), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 1/52 (1%)
Query: 46 RHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKY 97
R+ ED G FG +DIY DYY +G V+++ P D +
Sbjct: 189 RNCMVAEDFTVKIGDFGMTRDIY-ETDYYRKGGKGLLPVRWMSPESLKDGVF 239
>pdb|3QQU|A Chain A, Cocrystal Structure Of Unphosphorylated Igf With
Pyrimidine 8
pdb|3QQU|B Chain B, Cocrystal Structure Of Unphosphorylated Igf With
Pyrimidine 8
pdb|3QQU|C Chain C, Cocrystal Structure Of Unphosphorylated Igf With
Pyrimidine 8
pdb|3QQU|D Chain D, Cocrystal Structure Of Unphosphorylated Igf With
Pyrimidine 8
Length = 301
Score = 26.9 bits (58), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 1/52 (1%)
Query: 46 RHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKY 97
R+ ED G FG +DIY DYY +G V+++ P D +
Sbjct: 154 RNCMVAEDFTVKIGDFGMTRDIY-ETDYYRKGGKGLLPVRWMSPESLKDGVF 204
>pdb|2OJ9|A Chain A, Structure Of Igf-1r Kinase Domain Complexed With A
Benzimidazole Inhibitor
pdb|3NW5|A Chain A, Crystal Structure Of Insulin-Like Growth Factor 1 Receptor
(Igf-1r-Wt) Complex With A Carbon-Linked Proline
Isostere Inhibitor (11b)
pdb|3NW6|A Chain A, Crystal Structure Of Insulin-Like Growth Factor 1 Receptor
(Igf-1r-Wt) Complex With A Carbon-Linked Proline
Isostere Inhibitor (11a)
pdb|3NW7|A Chain A, Crystal Structure Of Insulin-Like Growth Factor 1 Receptor
(Igf-1r-Wt) Complex With A Carbon-Linked Proline
Isostere Inhibitor (34)
Length = 307
Score = 26.9 bits (58), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 1/52 (1%)
Query: 46 RHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKY 97
R+ ED G FG +DIY DYY +G V+++ P D +
Sbjct: 160 RNCMVAEDFTVKIGDFGMTRDIY-ETDYYRKGGKGLLPVRWMSPESLKDGVF 210
>pdb|3O23|A Chain A, Human Unphosphorylated Igf1-R Kinase Domain In Complex
With An Hydantoin Inhibitor
Length = 305
Score = 26.9 bits (58), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 1/52 (1%)
Query: 46 RHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKY 97
R+ ED G FG +DIY DYY +G V+++ P D +
Sbjct: 158 RNCMVAEDFTVKIGDFGMTRDIY-ETDYYRKGGKGLLPVRWMSPESLKDGVF 208
>pdb|3I81|A Chain A, Crystal Structure Of Insulin-Like Growth Factor 1 Receptor
(Igf-1r-Wt) Complex With Bms-754807
[1-(4-((5-Cyclopropyl-
1h-Pyrazol-3-Yl)amino)pyrrolo[2,1-F][1,2,
4]triazin-2-Yl)-N-
(6-Fluoro-3-Pyridinyl)-2-Methyl-L-Prolinamide]
Length = 315
Score = 26.9 bits (58), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 1/52 (1%)
Query: 46 RHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKY 97
R+ ED G FG +DIY DYY +G V+++ P D +
Sbjct: 160 RNCMVAEDFTVKIGDFGMTRDIY-ETDYYRKGGKGLLPVRWMSPESLKDGVF 210
>pdb|3LW0|A Chain A, Igf-1rk In Complex With Ligand Msc1609119a-1
pdb|3LW0|B Chain B, Igf-1rk In Complex With Ligand Msc1609119a-1
pdb|3LW0|C Chain C, Igf-1rk In Complex With Ligand Msc1609119a-1
pdb|3LW0|D Chain D, Igf-1rk In Complex With Ligand Msc1609119a-1
Length = 304
Score = 26.9 bits (58), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 1/52 (1%)
Query: 46 RHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKY 97
R+ ED G FG +DIY DYY +G V+++ P D +
Sbjct: 157 RNCMVAEDFTVKIGDFGMTRDIY-ETDYYRKGGKGLLPVRWMSPESLKDGVF 207
>pdb|1JQH|A Chain A, Igf-1 Receptor Kinase Domain
pdb|1JQH|B Chain B, Igf-1 Receptor Kinase Domain
pdb|1JQH|C Chain C, Igf-1 Receptor Kinase Domain
Length = 308
Score = 26.9 bits (58), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 1/52 (1%)
Query: 46 RHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKY 97
R+ ED G FG +DIY DYY +G V+++ P D +
Sbjct: 161 RNCMVAEDFTVKIGDFGMTRDIY-ETDYYRKGGKGLLPVRWMSPESLKDGVF 211
>pdb|3D94|A Chain A, Crystal Structure Of The Insulin-Like Growth Factor-1
Receptor Kinase In Complex With Pqip
Length = 301
Score = 26.9 bits (58), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 1/52 (1%)
Query: 46 RHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKY 97
R+ ED G FG +DIY DYY +G V+++ P D +
Sbjct: 154 RNCXVAEDFTVKIGDFGMTRDIY-ETDYYRKGGKGLLPVRWMSPESLKDGVF 204
>pdb|1M7N|A Chain A, Crystal Structure Of Unactivated Apo Insulin-Like Growth
Factor-1 Receptor Kinase Domain
pdb|1M7N|B Chain B, Crystal Structure Of Unactivated Apo Insulin-Like Growth
Factor-1 Receptor Kinase Domain
Length = 322
Score = 26.9 bits (58), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 1/52 (1%)
Query: 46 RHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKY 97
R+ ED G FG +DIY DYY +G V+++ P D +
Sbjct: 167 RNCMVAEDFTVKIGDFGMTRDIY-ETDYYRKGGKGLLPVRWMSPESLKDGVF 217
>pdb|1P4O|A Chain A, Structure Of Apo Unactivated Igf-1r Kinase Domain At 1.5a
Resolution.
pdb|1P4O|B Chain B, Structure Of Apo Unactivated Igf-1r Kinase Domain At 1.5a
Resolution
Length = 322
Score = 26.9 bits (58), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 1/52 (1%)
Query: 46 RHDCRPEDLRGPFGQFGRLKDIYLPRDYYTGEPRGFGFVQYIDPADAADAKY 97
R+ ED G FG +DIY DYY +G V+++ P D +
Sbjct: 167 RNCMVAEDFTVKIGDFGMTRDIY-ETDYYRKGGKGLLPVRWMSPESLKDGVF 217
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
0.324 0.146 0.456
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,526,903
Number of Sequences: 62578
Number of extensions: 150944
Number of successful extensions: 418
Number of sequences better than 100.0: 169
Number of HSP's better than 100.0 without gapping: 118
Number of HSP's successfully gapped in prelim test: 51
Number of HSP's that attempted gapping in prelim test: 278
Number of HSP's gapped (non-prelim): 184
length of query: 210
length of database: 14,973,337
effective HSP length: 95
effective length of query: 115
effective length of database: 9,028,427
effective search space: 1038269105
effective search space used: 1038269105
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 49 (23.5 bits)