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= 031682
(155 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 52.8 bits (125), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 38/61 (62%), Gaps = 6/61 (9%)
Query: 39 SNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQF 98
S+G+ G+ D + TT++VGGL +T+ DLR F Q+GEI ++ + + C F+QF
Sbjct: 2 SSGSSGE------DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQF 55
Query: 99 A 99
A
Sbjct: 56 A 56
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 46.6 bits (109), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 53 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQF-ANSLGQIMAINGV 111
+ + +FVG L P++T+E++R+ F +YG+ V I KG GF++ +L +I +
Sbjct: 20 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELD 79
Query: 112 GHTMEGKFMMV 122
+ GK + V
Sbjct: 80 NMPLRGKQLRV 90
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 45.8 bits (107), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 34/95 (35%), Positives = 48/95 (50%), Gaps = 20/95 (21%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFA--NSLGQIMAIN 109
+FVGGLD + T E LR FSQYGE+ I K G GFV+F N +G ++A
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASR 78
Query: 110 GVGHTMEGKFMMVMGMLFRHQMTQACTLQQLRPMG 144
HT++G R+ + CT + ++P G
Sbjct: 79 --PHTLDG----------RNIDPKPCTPRGMQPSG 101
>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
pdb|2RS8|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
Length = 99
Score = 45.8 bits (107), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 53 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQF-ANSLGQIMAINGV 111
+ + +FVG L P++T+E++R+ F +YG+ V I KG GF++ +L +I +
Sbjct: 13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELD 72
Query: 112 GHTMEGKFMMV 122
+ GK + V
Sbjct: 73 NMPLRGKQLRV 83
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 45.8 bits (107), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/62 (38%), Positives = 34/62 (54%), Gaps = 5/62 (8%)
Query: 46 GPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP-----VGKGCGFVQFAN 100
GP G T+FVGG+D + + ++R F++YG + VKI V KG GFV F N
Sbjct: 1 GPLGSGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYN 60
Query: 101 SL 102
+
Sbjct: 61 DV 62
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 45.8 bits (107), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 6/74 (8%)
Query: 41 GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCG 94
G+ G Q + S++ +FVG L P +T ED++ F+ +G+I+ ++ KG G
Sbjct: 1 GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYG 60
Query: 95 FVQFANSLGQIMAI 108
FV F N L AI
Sbjct: 61 FVSFYNKLDAENAI 74
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 39/67 (58%), Gaps = 1/67 (1%)
Query: 55 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANSLGQIMAINGV-GH 113
N T++ GG+ +TD+ +RQ FS +G+I +++ KG FV+F+ AI V G
Sbjct: 25 NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGT 84
Query: 114 TMEGKFM 120
T+EG +
Sbjct: 85 TIEGHVV 91
>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 = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 33/58 (56%), Gaps = 5/58 (8%)
Query: 50 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP-----VGKGCGFVQFANSL 102
EG T+FVGG+D + + ++R F++YG + VKI V KG GFV F N +
Sbjct: 4 EGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDV 61
>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 = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 33/58 (56%), Gaps = 5/58 (8%)
Query: 50 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP-----VGKGCGFVQFANSL 102
EG T+FVGG+D + + ++R F++YG + VKI V KG GFV F N +
Sbjct: 4 EGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDV 61
>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 = 43.9 bits (102), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 6/78 (7%)
Query: 41 GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCG 94
G+ G Q + S++ +FVG L P +T ED++ F+ +G I+ ++ KG G
Sbjct: 1 GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYG 60
Query: 95 FVQFANSLGQIMAINGVG 112
FV F N AI +G
Sbjct: 61 FVSFFNKWDAENAIQQMG 78
>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi)
G); A Human Telomeric Repeat Containing 6-Methyl-8-(2-
Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi)
Length = 195
Score = 43.1 bits (100), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 27/90 (30%), Positives = 41/90 (45%), Gaps = 6/90 (6%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG------FVQFANSLGQIMAINGV 111
IFVGG+ + + LR F QYG+I ++I +G G FV F + +
Sbjct: 106 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 165
Query: 112 GHTMEGKFMMVMGMLFRHQMTQACTLQQLR 141
HT+ G V L + +M A + Q+ R
Sbjct: 166 YHTVNGHNCEVRKALSKQEMASASSSQRGR 195
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 6/69 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANSLGQIMAINGV 111
+F+GGL TDE LR F Q+G + + +G GFV +A A+N
Sbjct: 15 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 74
Query: 112 GHTMEGKFM 120
H ++G+ +
Sbjct: 75 PHKVDGRVV 83
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 43.1 bits (100), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 27/90 (30%), Positives = 41/90 (45%), Gaps = 6/90 (6%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG------FVQFANSLGQIMAINGV 111
IFVGG+ + + LR F QYG+I ++I +G G FV F + +
Sbjct: 108 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 167
Query: 112 GHTMEGKFMMVMGMLFRHQMTQACTLQQLR 141
HT+ G V L + +M A + Q+ R
Sbjct: 168 YHTVNGHNCEVRKALSKQEMASASSSQRGR 197
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 6/69 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANSLGQIMAINGV 111
+F+GGL TDE LR F Q+G + + +G GFV +A A+N
Sbjct: 17 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 76
Query: 112 GHTMEGKFM 120
H ++G+ +
Sbjct: 77 PHKVDGRVV 85
>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
pdb|1U1K|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt 7da
Ggg); A Human Telomeric Repeat Containing
7-Deaza-Adenine
pdb|1U1L|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt Prn
Ggg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1M|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 7gu
Gg); A Human Telomeric Repeat Containing 7-Deaza-Guanine
pdb|1U1N|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta (Prn)
Gg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1O|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggttag(Di)g); A Human Telomeric Repeat Containing
Inosine
pdb|1U1P|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 2pr
Gg); A Human Telomeric Repeat Containing 2-Aminopurine
pdb|1U1Q|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggtta(Di)gg); A Human Telomeric Repeat Containing
Inosine
pdb|1U1R|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(2pr)
G); A Human Telomeric Repeat Containing 2-Aminopurine
Length = 196
Score = 43.1 bits (100), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 27/90 (30%), Positives = 41/90 (45%), Gaps = 6/90 (6%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG------FVQFANSLGQIMAINGV 111
IFVGG+ + + LR F QYG+I ++I +G G FV F + +
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 166
Query: 112 GHTMEGKFMMVMGMLFRHQMTQACTLQQLR 141
HT+ G V L + +M A + Q+ R
Sbjct: 167 YHTVNGHNCEVRKALSKQEMASASSSQRGR 196
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 6/69 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANSLGQIMAINGV 111
+F+GGL TDE LR F Q+G + + +G GFV +A A+N
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 112 GHTMEGKFM 120
H ++G+ +
Sbjct: 76 PHKVDGRVV 84
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 32/49 (65%), Gaps = 1/49 (2%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQF-ANSLGQI 105
+FVG L ++T+ED ++ F +YGE + V I +G GF++ + +L +I
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEI 73
Score = 33.5 bits (75), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 29/102 (28%), Positives = 40/102 (39%), Gaps = 38/102 (37%)
Query: 3 EMNGVYCSSRPMRIGAATPRKXXXXXXXXXXXXXXASNGAPGQGPQSEGDSSNTTIFVGG 62
E++G SRP+RI AT +GA + V
Sbjct: 77 ELDGTILKSRPLRIRFAT-------------------HGA--------------ALTVKN 103
Query: 63 LDPNVTDEDLRQPFSQYGEIASVKIPV-----GKGCGFVQFA 99
L P V++E L Q FSQ+G + + V G GFV+FA
Sbjct: 104 LSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFA 145
>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 = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 34/63 (53%), Gaps = 6/63 (9%)
Query: 55 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANSLGQIMAI 108
+ ++V GL +T ++L Q FSQYG I + +I V +G GF++F + AI
Sbjct: 88 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 147
Query: 109 NGV 111
G+
Sbjct: 148 KGL 150
Score = 32.0 bits (71), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 28/62 (45%), Gaps = 6/62 (9%)
Query: 54 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANSLGQIMA 107
S T + V L N+T E+ R F GEI S K+ K G GFV + + A
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 108 IN 109
IN
Sbjct: 61 IN 62
>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 = 40.0 bits (92), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 37/84 (44%), Gaps = 6/84 (7%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG------FVQFANSLGQIMAINGV 111
IFVGG+ + + LR F QYG+I ++I +G G FV F + +
Sbjct: 100 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 159
Query: 112 GHTMEGKFMMVMGMLFRHQMTQAC 135
HT+ G V L + +M A
Sbjct: 160 YHTVNGHNCEVRKALSKQEMASAS 183
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 6/69 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANSLGQIMAINGV 111
+F+GGL TDE LR F Q+G + + +G GFV +A A+N
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68
Query: 112 GHTMEGKFM 120
H ++G+ +
Sbjct: 69 PHKVDGRVV 77
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 40.0 bits (92), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 38/70 (54%), Gaps = 3/70 (4%)
Query: 54 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANSLGQIMAINGVGH 113
++T + VG + P T+++LR F +YG + ++ + K FV + + AI G+ +
Sbjct: 9 ASTKLHVGNISPTCTNQELRAKFEEYGPV--IECDIVKDYAFVHMERAEDAVEAIRGLDN 66
Query: 114 T-MEGKFMMV 122
T +GK M V
Sbjct: 67 TEFQGKRMHV 76
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 39.7 bits (91), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 34/72 (47%), Gaps = 9/72 (12%)
Query: 53 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI--------PVGKGCGFVQFANSLGQ 104
S +FVG + +++DLR+ F QYG + + + P KGC FV F
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 105 IMAINGVGHTME 116
+ A N + H M+
Sbjct: 61 LEAQNAL-HNMK 71
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 33/71 (46%), Gaps = 7/71 (9%)
Query: 54 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANSLGQIMAI 108
+ +F+G + T+ D+R FS +G+I +I G +GC FV F AI
Sbjct: 94 EDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAI 153
Query: 109 NGV--GHTMEG 117
+ TMEG
Sbjct: 154 KAMHQAQTMEG 164
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 39.7 bits (91), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 43/79 (54%), Gaps = 11/79 (13%)
Query: 53 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFAN---SLG 103
S +FVGGL + ++ L Q FS+YG+I+ V + +G GFV F N +
Sbjct: 10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 69
Query: 104 QIMAINGVGHTMEGKFMMV 122
+MA+N G +++G+ + V
Sbjct: 70 AMMAMN--GKSVDGRQIRV 86
>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|C Chain C, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|B Chain B, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|D Chain D, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
Length = 88
Score = 39.7 bits (91), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 34/72 (47%), Gaps = 9/72 (12%)
Query: 53 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI--------PVGKGCGFVQFANSLGQ 104
S +FVG + +++DLR+ F QYG + + + P KGC FV F
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 105 IMAINGVGHTME 116
+ A N + H M+
Sbjct: 61 LEAQNAL-HNMK 71
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 39.3 bits (90), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 34/73 (46%), Gaps = 9/73 (12%)
Query: 52 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI--------PVGKGCGFVQFANSLG 103
D +FVG + +++DLR+ F QYG + + + P KGC FV F
Sbjct: 12 DLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKA 71
Query: 104 QIMAINGVGHTME 116
+ A N + H M+
Sbjct: 72 ALEAQNAL-HNMK 83
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 33/71 (46%), Gaps = 7/71 (9%)
Query: 54 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANSLGQIMAI 108
+ +F+G + T+ D+R FS +G+I +I G +GC FV F AI
Sbjct: 106 EDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAI 165
Query: 109 NGV--GHTMEG 117
+ TMEG
Sbjct: 166 KAMHQAQTMEG 176
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 39.3 bits (90), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 36/72 (50%), Gaps = 6/72 (8%)
Query: 53 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIAS---VKIPVGK---GCGFVQFANSLGQIM 106
SS +F+GGL T E LR+ F Q+GE+ ++ P+ K G GFV F + G
Sbjct: 23 SSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDK 82
Query: 107 AINGVGHTMEGK 118
+ H ++ K
Sbjct: 83 VLAQSRHELDSK 94
>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 = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 6/67 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANSLGQIMAINGV 111
+F+GGL + T +DL+ FS++GE+ + + +G GFV F S ++
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 112 GHTMEGK 118
H + GK
Sbjct: 62 EHKLNGK 68
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 6/69 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANSLGQIMAINGV 111
+F+GGL TDE LR F Q+G + + +G GFV +A A+N
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 112 GHTMEGKFM 120
H ++G+ +
Sbjct: 76 PHKVDGRVV 84
Score = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 31/66 (46%), Gaps = 6/66 (9%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG------FVQFANSLGQIMAINGV 111
IFVGG+ + + LR F QYG+I ++I +G G FV F + +
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 166
Query: 112 GHTMEG 117
HT+ G
Sbjct: 167 YHTVNG 172
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 39/68 (57%), Gaps = 7/68 (10%)
Query: 51 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-GKGCGFVQFANS------LG 103
G S ++ +FVG ++T+++LR+ FSQYG++ V IP + FV FA+ G
Sbjct: 1 GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG 60
Query: 104 QIMAINGV 111
+ + I G+
Sbjct: 61 EDLIIKGI 68
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 6/69 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANSLGQIMAINGV 111
+F+GGL TDE LR F Q+G + + +G GFV +A A+N
Sbjct: 14 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 73
Query: 112 GHTMEGKFM 120
H ++G+ +
Sbjct: 74 PHKVDGRVV 82
Score = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 31/66 (46%), Gaps = 6/66 (9%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG------FVQFANSLGQIMAINGV 111
IFVGG+ + + LR F QYG+I ++I +G G FV F + +
Sbjct: 105 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 164
Query: 112 GHTMEG 117
HT+ G
Sbjct: 165 YHTVNG 170
>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 = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 29/50 (58%), Gaps = 6/50 (12%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANS 101
IFVGGL P+ +E +R+ F +GE+ S+++P+ +G F+ F
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEE 53
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 29/50 (58%), Gaps = 6/50 (12%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANS 101
IFVGGL P+ +E +R+ F +GE+ S+++P+ +G F+ F
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEE 51
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 29/60 (48%), Gaps = 5/60 (8%)
Query: 55 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANSLGQIMAIN 109
+ +FVG L TDED+R+ F +G I + G KGC FV+F AIN
Sbjct: 12 DRKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAIN 71
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 10/83 (12%)
Query: 39 SNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP-------VGK 91
S+G+ GQ P+ + + + I V + ++R+ FS +GE+ +V++P +
Sbjct: 2 SSGSSGQVPKKQ---TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHR 58
Query: 92 GCGFVQFANSLGQIMAINGVGHT 114
G GFV F A N + H+
Sbjct: 59 GFGFVDFITKQDAKKAFNALCHS 81
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 5/63 (7%)
Query: 54 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANSLGQIMAI 108
S+ +FVG L+ +++D+R+ F +G I I G KGC FV++++ AI
Sbjct: 14 SHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAI 73
Query: 109 NGV 111
N +
Sbjct: 74 NAL 76
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 6/63 (9%)
Query: 55 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANSLGQIMAI 108
+ ++V GL ++ +++ Q FSQYG I + +I V +G GF++F + AI
Sbjct: 1 DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
Query: 109 NGV 111
G+
Sbjct: 61 KGL 63
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 39/71 (54%), Gaps = 9/71 (12%)
Query: 56 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-GKGCGFVQFANSLGQIMAINGVGHT 114
+ +FVG ++T E+L+Q F QYGE+ V IP + FV FA+ + V +
Sbjct: 12 SKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFAD--------DKVAQS 63
Query: 115 MEGKFMMVMGM 125
+ G+ +++ G+
Sbjct: 64 LCGEDLIIKGI 74
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 6/63 (9%)
Query: 55 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANSLGQIMAI 108
+ ++V GL ++ +++ Q FSQYG I + +I V +G GF++F + AI
Sbjct: 90 DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 149
Query: 109 NGV 111
G+
Sbjct: 150 KGL 152
Score = 28.5 bits (62), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 7/76 (9%)
Query: 54 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANSLGQIMA 107
S T + V L N+T ++ + F G+I S K+ K G GFV +++ A
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 108 INGV-GHTMEGKFMMV 122
IN + G ++ K + V
Sbjct: 63 INTLNGLKLQTKTIKV 78
>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
pdb|3NNA|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 8/61 (13%)
Query: 59 FVGGLDPNVTDEDLRQPFSQYGEIASVKI--------PVGKGCGFVQFANSLGQIMAING 110
FVG + +++DLR+ F QYG + + + P KGC FV F + A N
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 111 V 111
+
Sbjct: 67 L 67
Score = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 31/71 (43%), Gaps = 7/71 (9%)
Query: 54 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANSLGQIMAI 108
+ +F+G + T+ D+R FS +G+I +I G +GC FV F AI
Sbjct: 94 EDRKLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAI 153
Query: 109 NGV--GHTMEG 117
T EG
Sbjct: 154 KAXHQAQTXEG 164
>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 = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 42/71 (59%), Gaps = 11/71 (15%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKI---PV---GKGCGFVQFA--NSLGQIMAIN 109
+F+GGL+ + T+++LR+ F +YG + +KI P +G GF+ F +S+ +++
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65
Query: 110 GVGHTMEGKFM 120
H ++GK +
Sbjct: 66 ---HILDGKVI 73
Score = 35.0 bits (79), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 7/61 (11%)
Query: 47 PQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFAN 100
P+ E D + IFVGG+ P+V ++ + FSQ+G I ++ + K G GFV + +
Sbjct: 80 PRDEQDKTGK-IFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDS 138
Query: 101 S 101
+
Sbjct: 139 A 139
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 6/67 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIAS---VKIPVGK---GCGFVQFANSLGQIMAINGV 111
+F+GGL T E LR+ F Q+GE+ ++ P+ K G GFV F + G +
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62
Query: 112 GHTMEGK 118
H ++ K
Sbjct: 63 RHELDSK 69
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 37.0 bits (84), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 28/52 (53%), Gaps = 7/52 (13%)
Query: 56 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-------GKGCGFVQFAN 100
T + +G L NVT + + + FS YG+I + +PV KG +V+F N
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFEN 56
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 36.6 bits (83), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 37/69 (53%), Gaps = 6/69 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIAS---VKIPVGK---GCGFVQFANSLGQIMAINGV 111
+F+GGL T+E LR + Q+G++ ++ P K G GFV F++ A+
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAAR 89
Query: 112 GHTMEGKFM 120
H+++G+ +
Sbjct: 90 PHSIDGRVV 98
>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 = 36.6 bits (83), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 26/40 (65%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQ 97
+FV G+ T+ED+ F++YGEI ++ + + + G+++
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK 49
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 36.6 bits (83), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 28/57 (49%), Gaps = 4/57 (7%)
Query: 49 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG----KGCGFVQFANS 101
+E S + V + D DLRQ F Q+G+I V+I KG GFV F NS
Sbjct: 23 TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENS 79
>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
pdb|3S7R|B Chain B, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
Length = 87
Score = 36.6 bits (83), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 35/68 (51%), Gaps = 6/68 (8%)
Query: 59 FVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANSLGQIMAINGVG 112
FVGGL + + +DL+ F+++GE+ I +G GF+ F ++ ++
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQKE 74
Query: 113 HTMEGKFM 120
H ++G+ +
Sbjct: 75 HRLDGRVI 82
>pdb|3TP2|A Chain A, Crystal Structure Of The Splicing Factor Cwc2 From Yeast
pdb|3TP2|B Chain B, Crystal Structure Of The Splicing Factor Cwc2 From Yeast
Length = 229
Score = 36.6 bits (83), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 9/55 (16%)
Query: 53 SSNTTIFVGGLD---------PNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQF 98
N T++VGG+D P + +R FS+ G+I ++ K CGFV+F
Sbjct: 134 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKF 188
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 36.6 bits (83), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 26/40 (65%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQ 97
+FV G+ T+ED+ F++YGEI ++ + + + G+++
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK 49
>pdb|3U1L|A Chain A, Structure Of The Mrna Splicing Complex Component Cwc2
pdb|3U1M|A Chain A, Structure Of The Mrna Splicing Complex Component Cwc2
Length = 240
Score = 36.2 bits (82), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 9/55 (16%)
Query: 53 SSNTTIFVGGLD---------PNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQF 98
N T++VGG+D P + +R FS+ G+I ++ K CGFV+F
Sbjct: 132 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKF 186
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 36.2 bits (82), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 26/50 (52%), Gaps = 6/50 (12%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANS 101
IFVGGL N T ED++ F Q+G++ + K G GFV F +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESE 51
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 36.2 bits (82), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 35/70 (50%), Gaps = 6/70 (8%)
Query: 51 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANSLGQ 104
G ++ ++VGGL V D+ L F +G+I ++IP+ +G FV+F +
Sbjct: 1 GSTTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60
Query: 105 IMAINGVGHT 114
AI+ + +
Sbjct: 61 AAAIDNMNES 70
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 36.2 bits (82), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 36/76 (47%), Gaps = 2/76 (2%)
Query: 49 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANSLGQIMAI 108
S G S +++G L P VT +DLRQ F + ++ + G FV + + I AI
Sbjct: 2 SSGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAI 61
Query: 109 NGVGHTME--GKFMMV 122
+ +E GK M V
Sbjct: 62 ETLSGKVELHGKIMEV 77
>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 = 36.2 bits (82), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 29/52 (55%), Gaps = 2/52 (3%)
Query: 46 GPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQ 97
GPQ +FV G+ T+ED+ F++YGEI ++ + + + G+++
Sbjct: 2 GPQR--SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK 51
>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 = 36.2 bits (82), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 26/40 (65%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQ 97
+FV G+ T+ED+ F++YGEI ++ + + + G+++
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK 64
>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 = 36.2 bits (82), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 26/40 (65%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQ 97
+FV G+ T+ED+ F++YGEI ++ + + + G+++
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK 49
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 35.8 bits (81), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 39/84 (46%), Gaps = 7/84 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANSLGQIMAINGV 111
+FV L ++EDL + FS YG ++ + P+ KG FV F + A V
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 112 -GHTMEGKFMMVMGMLFRHQMTQA 134
G +G+ + V+ + + +Q+
Sbjct: 71 DGQVFQGRMLHVLPSTIKKEASQS 94
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 35.8 bits (81), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 29/51 (56%), Gaps = 3/51 (5%)
Query: 51 GDSSNTTIFVGGLD-PNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFAN 100
G + +F+G L NV+ EDL + FS YG I ++I + GF+QF N
Sbjct: 18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHI--MQINIKNAFGFIQFDN 66
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 35.8 bits (81), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 38/71 (53%), Gaps = 7/71 (9%)
Query: 55 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANSLGQIMAI 108
+ + V GL T++DL++ FS +GE+ V++ KG GFV+F Q+ +
Sbjct: 15 TSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVM 74
Query: 109 NGVGHTMEGKF 119
+ H ++G++
Sbjct: 75 SQR-HMIDGRW 84
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 35.8 bits (81), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 29/51 (56%), Gaps = 3/51 (5%)
Query: 51 GDSSNTTIFVGGLD-PNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFAN 100
G + +F+G L NV+ EDL + FS YG I ++I + GF+QF N
Sbjct: 18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHI--MQINIKNAFGFIQFDN 66
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 35.8 bits (81), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 49 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANSLGQIMAI 108
S G S +F+G L T++++R F QYG++ ++ + K GFV + AI
Sbjct: 2 SSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKV--LECDIIKNYGFVHIEDKTAAEDAI 59
Query: 109 NGVGH 113
+ H
Sbjct: 60 RNLHH 64
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 35.8 bits (81), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 6/54 (11%)
Query: 51 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQF 98
G S ++ +++ GL P TD+DL + YG+I S K + KG GFV F
Sbjct: 1 GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDF 54
>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 = 35.8 bits (81), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 26/40 (65%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQ 97
+FV G+ T+ED+ F++YGEI ++ + + + G+++
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK 65
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 35.4 bits (80), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 29/55 (52%), Gaps = 6/55 (10%)
Query: 52 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFAN 100
D++ T IFVGGL + TD LR+ F +G+I + +G GFV A+
Sbjct: 14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMAD 68
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 35.4 bits (80), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 2/64 (3%)
Query: 48 QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANSLGQIMA 107
+ EG+ SNT +FV +V + +L + F +G + VKI G FV+F + A
Sbjct: 24 RQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI--LNGFAFVEFEEAESAAKA 81
Query: 108 INGV 111
I V
Sbjct: 82 IEEV 85
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 35.4 bits (80), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 34/68 (50%), Gaps = 6/68 (8%)
Query: 53 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANSLGQIM 106
++ ++VGGL V D+ L F +G+I ++IP+ +G FV+F +
Sbjct: 61 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 120
Query: 107 AINGVGHT 114
AI+ + +
Sbjct: 121 AIDNMNES 128
>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 = 35.4 bits (80), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 33/67 (49%), Gaps = 6/67 (8%)
Query: 54 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANSLGQIMA 107
S ++VGGL V D+ L F +G+I ++IP+ +G FV+F + A
Sbjct: 1 SKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 60
Query: 108 INGVGHT 114
I+ + +
Sbjct: 61 IDNMNES 67
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 35.0 bits (79), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 24/59 (40%), Positives = 31/59 (52%), Gaps = 5/59 (8%)
Query: 69 DEDLRQPFSQYGEIASVKIPV----GKGCGFVQFANSLGQIMAINGV-GHTMEGKFMMV 122
D DLRQ F Q+G+I V+I KG GFV F NS A + G +EG+ + V
Sbjct: 29 DPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV 87
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 35.0 bits (79), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 33/67 (49%), Gaps = 10/67 (14%)
Query: 44 GQGPQSEGDSSNTT----IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGC 93
G+G + G+ +N + V GL T+ DLR+ FS+YG IA V I +G
Sbjct: 31 GRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGF 90
Query: 94 GFVQFAN 100
FV F N
Sbjct: 91 AFVYFEN 97
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 35.0 bits (79), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 30/50 (60%), Gaps = 6/50 (12%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANS 101
++VG L N+T++ LR F +G I S+++ + KG GF+ F++S
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDS 78
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 35.0 bits (79), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 34/68 (50%), Gaps = 6/68 (8%)
Query: 53 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANSLGQIM 106
++ ++VGGL V D+ L F +G+I ++IP+ +G FV+F +
Sbjct: 5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 64
Query: 107 AINGVGHT 114
AI+ + +
Sbjct: 65 AIDNMNES 72
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 35.0 bits (79), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 3/76 (3%)
Query: 49 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANSLGQIMAI 108
S G + +FV L VT+E L + FSQ+G++ VK K F+ F G + A+
Sbjct: 5 SSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--KDYAFIHFDERDGAVKAM 62
Query: 109 NGV-GHTMEGKFMMVM 123
+ G +EG+ + ++
Sbjct: 63 EEMNGKDLEGENIEIV 78
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 34.7 bits (78), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 19/46 (41%), Positives = 28/46 (60%), Gaps = 3/46 (6%)
Query: 56 TTIFVGGLD-PNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFAN 100
+ +F+G L NV+ EDL + FS YG I ++I + GF+QF N
Sbjct: 3 SRLFIGNLPLKNVSKEDLFRIFSPYGHI--MQINIKNAFGFIQFDN 46
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 34.7 bits (78), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 19/46 (41%), Positives = 28/46 (60%), Gaps = 3/46 (6%)
Query: 56 TTIFVGGLD-PNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFAN 100
+ +F+G L NV+ EDL + FS YG I ++I + GF+QF N
Sbjct: 11 SRLFIGNLPLKNVSKEDLFRIFSPYGHI--MQINIKNAFGFIQFDN 54
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 34.7 bits (78), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 34/68 (50%), Gaps = 6/68 (8%)
Query: 53 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANSLGQIM 106
++ ++VGGL V D+ L F +G+I ++IP+ +G FV+F +
Sbjct: 10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 69
Query: 107 AINGVGHT 114
AI+ + +
Sbjct: 70 AIDNMNES 77
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 34.3 bits (77), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 6/53 (11%)
Query: 54 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFAN 100
S +T++V L ++T+ DL + FS+YG++ V I KG F+ F +
Sbjct: 15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLD 67
>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 = 34.3 bits (77), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 36/74 (48%), Gaps = 7/74 (9%)
Query: 56 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANSLGQIMAIN 109
T + V L N+T ++LR FS GE+ S K+ K G GFV + + AIN
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 64
Query: 110 GV-GHTMEGKFMMV 122
+ G ++ K + V
Sbjct: 65 TLNGLRLQSKTIKV 78
>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 = 34.3 bits (77), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 21/87 (24%), Positives = 42/87 (48%), Gaps = 8/87 (9%)
Query: 43 PGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFV 96
P P ++GD+ T +FV ++ + T+ LR+ F YG I + + K G F+
Sbjct: 91 PHNDPNAQGDAFKT-LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFI 149
Query: 97 QFANSLGQIMAI-NGVGHTMEGKFMMV 122
++ + A + G ++G+ ++V
Sbjct: 150 EYEHERDMHSAYKHADGKKIDGRRVLV 176
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 34.3 bits (77), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 36/74 (48%), Gaps = 7/74 (9%)
Query: 56 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANSLGQIMAIN 109
T + V L N+T ++LR FS GE+ S K+ K G GFV + + AIN
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 110 GV-GHTMEGKFMMV 122
+ G ++ K + V
Sbjct: 63 TLNGLRLQSKTIKV 76
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 34.3 bits (77), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 26/52 (50%), Gaps = 6/52 (11%)
Query: 55 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFAN 100
N + V GL T+ DLR+ FS+YG IA V I +G FV F N
Sbjct: 15 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 66
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 33.9 bits (76), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 6/60 (10%)
Query: 55 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANSLGQIMAI 108
+ T++VGGLD V++ L + F Q G + + +P + G GFV+F + AI
Sbjct: 15 DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 74
>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 = 33.9 bits (76), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 36/74 (48%), Gaps = 7/74 (9%)
Query: 56 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANSLGQIMAIN 109
T + V L N+T ++LR FS GE+ S K+ K G GFV + + AIN
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 110 GV-GHTMEGKFMMV 122
+ G ++ K + V
Sbjct: 63 TLNGLRLQSKTIKV 76
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 33.9 bits (76), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 26/52 (50%), Gaps = 6/52 (11%)
Query: 55 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFAN 100
N + V GL T+ DLR+ FS+YG IA V I +G FV F N
Sbjct: 12 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 63
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 33.9 bits (76), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 26/43 (60%)
Query: 57 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFA 99
++VG LD +T++ L+Q F G IA++KI + K V +A
Sbjct: 2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYA 44
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 33.9 bits (76), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 26/52 (50%), Gaps = 6/52 (11%)
Query: 55 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFAN 100
N + V GL T+ DLR+ FS+YG IA V I +G FV F N
Sbjct: 15 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 66
>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|B Chain B, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|C Chain C, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|D Chain D, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
Length = 99
Score = 33.5 bits (75), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 35/74 (47%), Gaps = 7/74 (9%)
Query: 56 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANSLGQIMAIN 109
T + V L N T ++LR FS GE+ S K+ K G GFV + + AIN
Sbjct: 20 TNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 79
Query: 110 GV-GHTMEGKFMMV 122
+ G ++ K + V
Sbjct: 80 TLNGLRLQSKTIKV 93
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 33.5 bits (75), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 28/46 (60%), Gaps = 6/46 (13%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQ 97
I+VG L + T E +++ FSQ+G++ +VK+ KG GFV+
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVE 49
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 33.5 bits (75), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 6/71 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANSLGQIMAINGV 111
IFVGG+ N + +LR+ F ++G + V + +G GF+ F + A+N
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMH 72
Query: 112 GHTMEGKFMMV 122
H + GK + V
Sbjct: 73 FHDIMGKKVEV 83
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 33.1 bits (74), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 33/57 (57%), Gaps = 6/57 (10%)
Query: 51 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANS 101
G S ++ ++VG L N+T++ LR F +G+I ++ + KG GF+ F++S
Sbjct: 1 GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDS 57
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 32.7 bits (73), Expect = 0.076, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 10/82 (12%)
Query: 51 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK---------GCGFVQFANS 101
G S ++ +F+ L+ + T+E L+ FS+ G I S I K G GFV++
Sbjct: 1 GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60
Query: 102 LGQIMAINGV-GHTMEGKFMMV 122
A+ + GHT++G + V
Sbjct: 61 EQAQKALKQLQGHTVDGHKLEV 82
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 32.7 bits (73), Expect = 0.093, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 4/74 (5%)
Query: 53 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKG---CGFVQFANSLGQIMAIN 109
+++ I+VG L P++ +D+ F +YG I + + +G FV+F + A+
Sbjct: 20 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVY 79
Query: 110 GV-GHTMEGKFMMV 122
G G+ +G + V
Sbjct: 80 GRDGYDYDGYRLRV 93
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 32.3 bits (72), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 7/78 (8%)
Query: 52 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANSLGQI 105
D S ++FVG + T+E L+ FS+ G + S ++ KG GF ++ + +
Sbjct: 5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETAL 64
Query: 106 MAINGV-GHTMEGKFMMV 122
A+ + G G+ + V
Sbjct: 65 SAMRNLNGREFSGRALRV 82
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 32.3 bits (72), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 36/72 (50%), Gaps = 14/72 (19%)
Query: 51 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV---------GKGCGFVQFAN- 100
G S ++ IF+G LDP + ++ L FS +G I ++ P KG F+ FA+
Sbjct: 1 GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVI--LQTPKIMRDPDTGNSKGYAFINFASF 58
Query: 101 --SLGQIMAING 110
S I A+NG
Sbjct: 59 DASDAAIEAMNG 70
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 32.0 bits (71), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 22/54 (40%), Positives = 27/54 (50%), Gaps = 7/54 (12%)
Query: 65 PNVTDE-DLRQPFSQYGEIASVKIPV------GKGCGFVQFANSLGQIMAINGV 111
P DE LRQ F +YG I SVKI +G GFV+F + AI G+
Sbjct: 51 PTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 32.0 bits (71), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 6/59 (10%)
Query: 57 TIFVGGLDPNVTDEDLRQPFSQY------GEIASVKIPVGKGCGFVQFANSLGQIMAIN 109
++FVG L P+V D L + F + G++ + V KG GFV+F + L Q A+
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALT 69
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 32.0 bits (71), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 5/62 (8%)
Query: 55 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANSLGQIMAIN 109
+ +FVG L+ ++ED+ + F +G I + G KGC FV+F++ AI+
Sbjct: 15 DRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIH 74
Query: 110 GV 111
+
Sbjct: 75 AL 76
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 31.6 bits (70), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 24/43 (55%)
Query: 56 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQF 98
T ++VGGL PN + L + F ++G I ++ G ++Q+
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQY 60
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 31.6 bits (70), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 2/53 (3%)
Query: 57 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANSLGQIMAIN 109
+FV L VT+E L + FS++G++ VK K FV F + + A++
Sbjct: 17 VLFVRNLATTVTEEILEKSFSEFGKLERVKKL--KDYAFVHFEDRGAAVKAMD 67
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 31.2 bits (69), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 14/62 (22%), Positives = 30/62 (48%), Gaps = 6/62 (9%)
Query: 52 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANSLGQI 105
D +F+G + N+ ++DL+ F ++G+I + + + KGC F+ + +
Sbjct: 10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESAL 69
Query: 106 MA 107
A
Sbjct: 70 KA 71
>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 = 30.8 bits (68), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 21/87 (24%), Positives = 42/87 (48%), Gaps = 8/87 (9%)
Query: 43 PGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFV 96
P P ++GD+ T +FV ++ + T+ LR+ F YG I + + K G F+
Sbjct: 91 PHNDPNAQGDAFKT-LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFI 149
Query: 97 QFANSLGQIMAI-NGVGHTMEGKFMMV 122
++ + A + G ++G+ ++V
Sbjct: 150 EYEHERDMHSAYKHADGKKIDGRRVLV 176
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 30.4 bits (67), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 30/72 (41%), Gaps = 7/72 (9%)
Query: 46 GPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFA 99
GP D N TI V L + + DL++ F +G I+ + + KG F+ F
Sbjct: 7 GPNRRADD-NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFH 65
Query: 100 NSLGQIMAINGV 111
AI GV
Sbjct: 66 RREDAARAIAGV 77
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
28
Length = 111
Score = 30.0 bits (66), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 25/48 (52%), Gaps = 6/48 (12%)
Query: 57 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQF 98
T+F+ L + +E L + Q+G++ V++ + KGC F QF
Sbjct: 17 TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQF 64
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 30.0 bits (66), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 28/58 (48%), Gaps = 2/58 (3%)
Query: 54 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANSLGQIMAINGV 111
SNT +FV +V + +L + F +G + VKI G FV+F + AI V
Sbjct: 3 SNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI--LNGFAFVEFEEAESAAKAIEEV 58
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 30.0 bits (66), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 29/66 (43%), Gaps = 14/66 (21%)
Query: 41 GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFAN 100
G+ G + DS N+ I+V GL+ +VT +DL F Q CG V+
Sbjct: 1 GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQ--------------CGVVKMNK 46
Query: 101 SLGQIM 106
GQ M
Sbjct: 47 RTGQPM 52
>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 = 30.0 bits (66), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 12/50 (24%), Positives = 27/50 (54%), Gaps = 6/50 (12%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANS 101
I+V + +++D+D++ F +G+I S + KG GF+++ +
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKA 177
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 30.0 bits (66), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 35/75 (46%), Gaps = 7/75 (9%)
Query: 55 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANSLGQIMAI 108
N +++ L P VT+ DL F+++ E I +G F+ F N A+
Sbjct: 25 NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 84
Query: 109 NGV-GHTMEGKFMMV 122
+ V G+ + GK +++
Sbjct: 85 HLVNGYKLYGKILVI 99
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 30.0 bits (66), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 38/78 (48%), Gaps = 8/78 (10%)
Query: 49 SEGDSSNT-TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQF---ANSLGQ 104
S G S NT IFVG + T ++LR F + G + ++ V K FV A++
Sbjct: 2 SSGSSGNTWKIFVGNVSAACTSQELRSLFERRGRV--IECDVVKDYAFVHMEKEADAKAA 59
Query: 105 IMAINGVGHTMEGKFMMV 122
I +N G ++GK + V
Sbjct: 60 IAQLN--GKEVKGKRINV 75
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 30.0 bits (66), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 18/79 (22%), Positives = 39/79 (49%), Gaps = 12/79 (15%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGF------VQFA---NSLGQIMAI 108
+FV + ++++++ F YGEI ++ + + + GF V++ +L A+
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 109 NG---VGHTMEGKFMMVMG 124
NG +G T++ + V G
Sbjct: 89 NGAEIMGQTIQVDWCFVKG 107
>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 = 30.0 bits (66), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 39/83 (46%), Gaps = 14/83 (16%)
Query: 41 GAPGQGP------QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG---- 90
GA +GP + + + +++VG +D T +DL FS G I + I
Sbjct: 16 GAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSG 75
Query: 91 --KGCGFVQFA--NSLGQIMAIN 109
KG +++FA NS+ +A++
Sbjct: 76 HPKGYAYIEFAERNSVDAAVAMD 98
>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 = 29.6 bits (65), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 18/79 (22%), Positives = 39/79 (49%), Gaps = 12/79 (15%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGF------VQFA---NSLGQIMAI 108
+FV + ++++++ F YGEI ++ + + + GF V++ +L A+
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 109 NG---VGHTMEGKFMMVMG 124
NG +G T++ + V G
Sbjct: 135 NGAEIMGQTIQVDWCFVKG 153
>pdb|1OWX|A Chain A, Solution Structure Of The C-Terminal Rrm Of Human La
(La225- 334)
Length = 121
Score = 29.6 bits (65), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 18/40 (45%)
Query: 59 FVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQF 98
F G LD EDL FS +GEI + G G + F
Sbjct: 23 FSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILF 62
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 29.3 bits (64), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 17/38 (44%), Positives = 21/38 (55%)
Query: 49 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVK 86
+ +S N TIFV GL NVT E + F Q G I + K
Sbjct: 1 EQDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNK 38
>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 = 29.3 bits (64), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 12/50 (24%), Positives = 27/50 (54%), Gaps = 6/50 (12%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANS 101
I+V + +++D+D++ F +G+I S + KG GF+++ +
Sbjct: 113 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKA 162
>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 = 29.3 bits (64), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 8/62 (12%)
Query: 57 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK---GCG--FVQF---ANSLGQIMAI 108
T++VG L T+E + + FS+ G+I + + + K CG FV++ A++ + I
Sbjct: 20 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMRYI 79
Query: 109 NG 110
NG
Sbjct: 80 NG 81
>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 = 29.3 bits (64), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 21/32 (65%)
Query: 56 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI 87
+++VG L P+VT+ L + FS G I S+++
Sbjct: 11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRV 42
>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 = 28.9 bits (63), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 21/32 (65%)
Query: 56 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI 87
+++VG L P+VT+ L + FS G I S+++
Sbjct: 16 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRV 47
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 28.9 bits (63), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 34/71 (47%), Gaps = 6/71 (8%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASV-----KIPVGKGCGFVQFANSLGQIMAINGV- 111
+F+GGL+ ++ L+ F ++G I+ V + +G F+ F N A +
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 112 GHTMEGKFMMV 122
G ++ GK + V
Sbjct: 70 GKSLHGKAIKV 80
>pdb|2GHP|A Chain A, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|B Chain B, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|C Chain C, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|D Chain D, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|E Chain E, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|F Chain F, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|G Chain G, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|H Chain H, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
Length = 292
Score = 28.9 bits (63), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 23/51 (45%), Gaps = 8/51 (15%)
Query: 58 IFVGGLDPNVTDEDL-RQPFSQYGEIASVKIPVGKG-------CGFVQFAN 100
I + L + DE+L R+ F +G I + IP G+ C F F N
Sbjct: 213 IXIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFXVFEN 263
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 28.9 bits (63), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 22/43 (51%)
Query: 56 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQF 98
TT ++G + T+ DL F +G I K KGC F+++
Sbjct: 28 TTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKY 70
>pdb|2M2B|A Chain A, Nmr Structure Of The Rrm2 Domain Of The Protein Rbm10 From
Homo Sapiens
Length = 131
Score = 28.9 bits (63), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 22/93 (23%), Positives = 43/93 (46%), Gaps = 12/93 (12%)
Query: 42 APGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV--------GKGC 93
A QG + +++N TI + L+P+ T + + + Y ++S + V +G
Sbjct: 10 ALSQGSEPSSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGF 69
Query: 94 GFVQFAN-SLGQIMAINGVGH---TMEGKFMMV 122
F+Q + Q++ I H T++GK + V
Sbjct: 70 AFIQLSTIEAAQLLQILQALHPPLTIDGKTINV 102
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 28.5 bits (62), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 7/76 (9%)
Query: 54 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANSLGQIMA 107
S T + V L N+T ++ + F G+I S K+ K G GFV +++ A
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 108 INGV-GHTMEGKFMMV 122
IN + G ++ K + V
Sbjct: 63 INTLNGLKLQTKTIKV 78
>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 = 28.5 bits (62), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 34/64 (53%), Gaps = 9/64 (14%)
Query: 57 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK----GCG--FVQF---ANSLGQIMA 107
T++VG L T+E + + FS+ G+I + + + K CG FV++ A++ +
Sbjct: 41 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100
Query: 108 INGV 111
ING
Sbjct: 101 INGT 104
>pdb|3R27|A Chain A, Crystal Structure Of The First Rrm Domain Of Heterogeneous
Nuclear Ribonucleoprotein L (Hnrnp L)
pdb|3R27|B Chain B, Crystal Structure Of The First Rrm Domain Of Heterogeneous
Nuclear Ribonucleoprotein L (Hnrnp L)
Length = 100
Score = 28.5 bits (62), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 28/56 (50%)
Query: 54 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANSLGQIMAIN 109
++ + + GL V + DL + ++G I+ V + K V+F + LG A+N
Sbjct: 20 ASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVN 75
>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 = 28.5 bits (62), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 12/50 (24%), Positives = 27/50 (54%), Gaps = 6/50 (12%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANS 101
I+V + +++D+D++ F +G+I S + KG GF+++ +
Sbjct: 112 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKA 161
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 28.5 bits (62), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 13/53 (24%), Positives = 26/53 (49%), Gaps = 6/53 (11%)
Query: 52 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQF 98
D +FVG + + ++DL+ F ++G I + + + KGC F+ +
Sbjct: 12 DHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTY 64
>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 = 28.5 bits (62), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 30/69 (43%), Gaps = 7/69 (10%)
Query: 46 GPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGC------GFVQFA 99
G Q EG +F+ L D+DL Q F +G + S K+ + K GFV +
Sbjct: 17 GSQKEG-PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYD 75
Query: 100 NSLGQIMAI 108
N + AI
Sbjct: 76 NPVSAQAAI 84
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 28.5 bits (62), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 24/47 (51%)
Query: 41 GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI 87
G+ G E D T++VG L +VT+ + Q FSQ G S K+
Sbjct: 1 GSSGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKM 47
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 28.1 bits (61), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 16/33 (48%), Positives = 18/33 (54%)
Query: 54 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVK 86
N TIFV GL NVT E + F Q G I + K
Sbjct: 12 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNK 44
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 28.1 bits (61), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 30/72 (41%), Gaps = 7/72 (9%)
Query: 46 GPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGC------GFVQFA 99
G Q EG +F+ L TD DL F +G + S K+ + K GFV F
Sbjct: 32 GKQIEG-PEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFD 90
Query: 100 NSLGQIMAINGV 111
N +AI +
Sbjct: 91 NPDSAQVAIKAM 102
>pdb|3QDK|A Chain A, Structural Insight On Mechanism And Diverse Substrate
Selection Strategy Of Ribulokinase
pdb|3QDK|B Chain B, Structural Insight On Mechanism And Diverse Substrate
Selection Strategy Of Ribulokinase
pdb|3QDK|C Chain C, Structural Insight On Mechanism And Diverse Substrate
Selection Strategy Of Ribulokinase
pdb|3QDK|D Chain D, Structural Insight On Mechanism And Diverse Substrate
Selection Strategy Of Ribulokinase
Length = 572
Score = 27.7 bits (60), Expect = 2.8, Method: Composition-based stats.
Identities = 27/92 (29%), Positives = 37/92 (40%), Gaps = 10/92 (10%)
Query: 48 QSEGDSSNTTIFVGGLDP---NVTDEDLRQPFSQYGEIASVKIP-----VGKGCGFVQFA 99
+ EG SN F LDP ++T LR GE A +P +G G
Sbjct: 213 KREGYPSNE--FFKALDPRLEHLTTTKLRGDIVPLGERAGGLLPEMAEKMGLNPGIAVAV 270
Query: 100 NSLGQIMAINGVGHTMEGKFMMVMGMLFRHQM 131
++ A+ VG T GK +M MG H +
Sbjct: 271 GNVDAHAAVPAVGVTTPGKLVMAMGTSICHML 302
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 27.3 bits (59), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 13/50 (26%)
Query: 57 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV--------GKGCGFVQF 98
T+FV GL + T+E L++ F SV+ + KG GFV F
Sbjct: 17 TLFVKGLSEDTTEETLKESFD-----GSVRARIVTDRETGSSKGFGFVDF 61
>pdb|1O0P|A Chain A, Solution Structure Of The Third Rna Recognition Motif
(Rrm) Of U2af65 In Complex With An N-Terminal Sf1
Peptide
Length = 104
Score = 27.3 bits (59), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 8/50 (16%)
Query: 70 EDLRQPFSQYGEIASVKIPVG------KGCG--FVQFANSLGQIMAINGV 111
ED+R S+YG + S++IP GCG FV+F + A+ G+
Sbjct: 29 EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGL 78
>pdb|1OPI|A Chain A, Solution Structure Of The Third Rna Recognition Motif
(Rrm) Of U2af65 In Complex With An N-Terminal Sf1
Peptide
pdb|2M0G|B Chain B, Structure, Phosphorylation And U2af65 Binding Of The
Nterminal Domain Of Splicing Factor 1 During 3 Splice
Site Recognition
Length = 104
Score = 27.3 bits (59), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 8/50 (16%)
Query: 70 EDLRQPFSQYGEIASVKIPVG------KGCG--FVQFANSLGQIMAINGV 111
ED+R S+YG + S++IP GCG FV+F + A+ G+
Sbjct: 29 EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGL 78
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 26.9 bits (58), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 39/81 (48%), Gaps = 10/81 (12%)
Query: 50 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV---GKGCG-----FVQFANS 101
EG + + V LD V+D D+++ F+++G + + G+ G F + A++
Sbjct: 83 EGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADA 142
Query: 102 LGQIMAINGVGHTMEGKFMMV 122
L + GV ++G+ M +
Sbjct: 143 LKAMKQYKGV--PLDGRPMDI 161
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 26.9 bits (58), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 34/77 (44%), Gaps = 7/77 (9%)
Query: 53 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANSLGQIM 106
+SNT + V L ++TD +L F G I + +I G FV F + +
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 107 AINGV-GHTMEGKFMMV 122
AI + G T+ K + V
Sbjct: 61 AIKVLNGITVRNKRLKV 77
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 26.9 bits (58), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 8/70 (11%)
Query: 50 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK-----GCGFVQF---ANS 101
EG + + V LD V+D D+++ F+++G + + + G V F A++
Sbjct: 30 EGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADA 89
Query: 102 LGQIMAINGV 111
L + GV
Sbjct: 90 LKAMKQYKGV 99
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 26.9 bits (58), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 9/71 (12%)
Query: 50 EGDSSNT--TIFVGGLDPNVTDEDLRQPFSQY---GEIASVKIPVG--KGCGFVQF--AN 100
EG S T +F+G L+PN + +L+ S+ ++A V + G + G+V F A
Sbjct: 6 EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAE 65
Query: 101 SLGQIMAINGV 111
L + + + G+
Sbjct: 66 DLEKALELTGL 76
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 26.6 bits (57), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 8/70 (11%)
Query: 50 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK-----GCGFVQF---ANS 101
EG + + V LD V+D D+++ F+++G + + + G V F A++
Sbjct: 30 EGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADA 89
Query: 102 LGQIMAINGV 111
L + GV
Sbjct: 90 LKAMKQYKGV 99
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 26.6 bits (57), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 34/77 (44%), Gaps = 7/77 (9%)
Query: 53 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANSLGQIM 106
+SNT + V L ++TD +L F G I + +I G FV F + +
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 107 AINGV-GHTMEGKFMMV 122
AI + G T+ K + V
Sbjct: 61 AIKVLNGITVRNKRLKV 77
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 26.2 bits (56), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 9/71 (12%)
Query: 50 EGDSSNT--TIFVGGLDPNVTDEDLRQPFSQY---GEIASVKIPVG--KGCGFVQF--AN 100
EG S T +F+G L+PN + +L+ S+ ++A V + G + G+V F A
Sbjct: 10 EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAE 69
Query: 101 SLGQIMAINGV 111
L + + + G+
Sbjct: 70 DLEKALELTGL 80
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 26.2 bits (56), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 8/26 (30%), Positives = 18/26 (69%)
Query: 58 IFVGGLDPNVTDEDLRQPFSQYGEIA 83
+FVGGL P++ ++++ F ++G +
Sbjct: 11 VFVGGLPPDIDEDEITASFRRFGPLV 36
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
0.319 0.133 0.398
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,056,499
Number of Sequences: 62578
Number of extensions: 139758
Number of successful extensions: 410
Number of sequences better than 100.0: 143
Number of HSP's better than 100.0 without gapping: 108
Number of HSP's successfully gapped in prelim test: 35
Number of HSP's that attempted gapping in prelim test: 275
Number of HSP's gapped (non-prelim): 163
length of query: 155
length of database: 14,973,337
effective HSP length: 91
effective length of query: 64
effective length of database: 9,278,739
effective search space: 593839296
effective search space used: 593839296
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)