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= psy13066
(115 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 126 bits (317), Expect = 3e-30, Method: Compositional matrix adjust.
Identities = 57/85 (67%), Positives = 69/85 (81%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
EPE LRK+FIGGL + TTDESL++ FEQWG + D VVM+DP TKRSRGFGF+TY+ + V
Sbjct: 9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 68
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRD 96
D AM+ RPH +DGRVVE KRAV R+
Sbjct: 69 DAAMNARPHKVDGRVVEPKRAVSRE 93
Score = 58.5 bits (140), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 26/92 (28%), Positives = 53/92 (57%)
Query: 4 RYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFI 63
R D + +++K+F+GG+ T + L+ +FEQ+G+I + +M D + + RGF F+
Sbjct: 92 REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFV 151
Query: 64 TYSEAKMVDDAMSNRPHNIDGRVVETKRAVPR 95
T+ + VD + + H ++G E ++A+ +
Sbjct: 152 TFDDHDSVDKIVIQKYHTVNGHNCEVRKALSK 183
>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 = 126 bits (317), Expect = 3e-30, Method: Compositional matrix adjust.
Identities = 57/85 (67%), Positives = 69/85 (81%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
EPE LRK+FIGGL + TTDESL++ FEQWG + D VVM+DP TKRSRGFGF+TY+ + V
Sbjct: 8 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 67
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRD 96
D AM+ RPH +DGRVVE KRAV R+
Sbjct: 68 DAAMNARPHKVDGRVVEPKRAVSRE 92
Score = 58.5 bits (140), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 26/92 (28%), Positives = 53/92 (57%)
Query: 4 RYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFI 63
R D + +++K+F+GG+ T + L+ +FEQ+G+I + +M D + + RGF F+
Sbjct: 91 REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFV 150
Query: 64 TYSEAKMVDDAMSNRPHNIDGRVVETKRAVPR 95
T+ + VD + + H ++G E ++A+ +
Sbjct: 151 TFDDHDSVDKIVIQKYHTVNGHNCEVRKALSK 182
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 126 bits (316), Expect = 3e-30, Method: Compositional matrix adjust.
Identities = 57/85 (67%), Positives = 69/85 (81%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
EPE LRK+FIGGL + TTDESL++ FEQWG + D VVM+DP TKRSRGFGF+TY+ + V
Sbjct: 10 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 69
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRD 96
D AM+ RPH +DGRVVE KRAV R+
Sbjct: 70 DAAMNARPHKVDGRVVEPKRAVSRE 94
Score = 58.5 bits (140), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 26/92 (28%), Positives = 53/92 (57%)
Query: 4 RYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFI 63
R D + +++K+F+GG+ T + L+ +FEQ+G+I + +M D + + RGF F+
Sbjct: 93 REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFV 152
Query: 64 TYSEAKMVDDAMSNRPHNIDGRVVETKRAVPR 95
T+ + VD + + H ++G E ++A+ +
Sbjct: 153 TFDDHDSVDKIVIQKYHTVNGHNCEVRKALSK 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 = 126 bits (316), Expect = 3e-30, Method: Compositional matrix adjust.
Identities = 57/85 (67%), Positives = 69/85 (81%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
EPE LRK+FIGGL + TTDESL++ FEQWG + D VVM+DP TKRSRGFGF+TY+ + V
Sbjct: 2 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 61
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRD 96
D AM+ RPH +DGRVVE KRAV R+
Sbjct: 62 DAAMNARPHKVDGRVVEPKRAVSRE 86
Score = 59.3 bits (142), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 26/92 (28%), Positives = 53/92 (57%)
Query: 4 RYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFI 63
R D + +++K+F+GG+ T + L+ +FEQ+G+I + +M D + + RGF F+
Sbjct: 85 REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFV 144
Query: 64 TYSEAKMVDDAMSNRPHNIDGRVVETKRAVPR 95
T+ + VD + + H ++G E ++A+ +
Sbjct: 145 TFDDHDSVDKIVIQKYHTVNGHNCEVRKALSK 176
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 126 bits (316), Expect = 4e-30, Method: Compositional matrix adjust.
Identities = 57/85 (67%), Positives = 69/85 (81%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
EPE LRK+FIGGL + TTDESL++ FEQWG + D VVM+DP TKRSRGFGF+TY+ + V
Sbjct: 9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 68
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRD 96
D AM+ RPH +DGRVVE KRAV R+
Sbjct: 69 DAAMNARPHKVDGRVVEPKRAVSRE 93
Score = 58.9 bits (141), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 26/92 (28%), Positives = 53/92 (57%)
Query: 4 RYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFI 63
R D + +++K+F+GG+ T + L+ +FEQ+G+I + +M D + + RGF F+
Sbjct: 92 REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFV 151
Query: 64 TYSEAKMVDDAMSNRPHNIDGRVVETKRAVPR 95
T+ + VD + + H ++G E ++A+ +
Sbjct: 152 TFDDHDSVDKIVIQKYHTVNGHNCEVRKALSK 183
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 125 bits (315), Expect = 4e-30, Method: Compositional matrix adjust.
Identities = 57/85 (67%), Positives = 69/85 (81%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
EPE LRK+FIGGL + TTDESL++ FEQWG + D VVM+DP TKRSRGFGF+TY+ + V
Sbjct: 7 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 66
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRD 96
D AM+ RPH +DGRVVE KRAV R+
Sbjct: 67 DAAMNARPHKVDGRVVEPKRAVSRE 91
Score = 58.9 bits (141), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 26/92 (28%), Positives = 53/92 (57%)
Query: 4 RYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFI 63
R D + +++K+F+GG+ T + L+ +FEQ+G+I + +M D + + RGF F+
Sbjct: 90 REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFV 149
Query: 64 TYSEAKMVDDAMSNRPHNIDGRVVETKRAVPR 95
T+ + VD + + H ++G E ++A+ +
Sbjct: 150 TFDDHDSVDKIVIQKYHTVNGHNCEVRKALSK 181
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 120 bits (301), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 54/90 (60%), Positives = 70/90 (77%)
Query: 7 DSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS 66
+ K E E RK+FIGGL + TT+ESL+ ++EQWG++ D VVM+DP +KRSRGFGF+T+S
Sbjct: 18 ERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFS 77
Query: 67 EAKMVDDAMSNRPHNIDGRVVETKRAVPRD 96
VD AM+ RPH+IDGRVVE KRAV R+
Sbjct: 78 SMAEVDAAMAARPHSIDGRVVEPKRAVARE 107
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 93.6 bits (231), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 37/85 (43%), Positives = 61/85 (71%)
Query: 14 ESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDD 73
+ + K+F+GGLD+ TT E+L+++F Q+GE+VD V+MKD T +SRGFGF+ + + V
Sbjct: 14 DEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGT 73
Query: 74 AMSNRPHNIDGRVVETKRAVPRDVR 98
+++RPH +DGR ++ K PR ++
Sbjct: 74 VLASRPHTLDGRNIDPKPCTPRGMQ 98
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 85.9 bits (211), Expect = 6e-18, Method: Compositional matrix adjust.
Identities = 36/78 (46%), Positives = 56/78 (71%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
K+FIGGL ++TT E L+ +F Q+GE+ + +VM+DP+TKRSRGFGF+T+ + VD ++
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 86
Query: 78 RPHNIDGRVVETKRAVPR 95
H +D + ++ K A PR
Sbjct: 87 SRHELDSKTIDPKVAFPR 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 = 84.3 bits (207), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 36/79 (45%), Positives = 61/79 (77%), Gaps = 1/79 (1%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
K+FIGGL++ TT+++L+ +F ++G + D+ +MKDP T RSRGFGF+++ + VD+ +
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 78 RPHNIDGRVVETKRAVPRD 96
+ H +DG+V++ KRA+PRD
Sbjct: 65 Q-HILDGKVIDPKRAIPRD 82
Score = 68.9 bits (167), Expect = 6e-13, Method: Compositional matrix adjust.
Identities = 34/84 (40%), Positives = 47/84 (55%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
E + K+F+GG+ + + FF QWG I+D +M D T +SRGFGF+TY A V
Sbjct: 83 EQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAV 142
Query: 72 DDAMSNRPHNIDGRVVETKRAVPR 95
D N+ + R +E KRA PR
Sbjct: 143 DRVCQNKFIDFKDRKIEIKRAEPR 166
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 81.3 bits (199), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 34/75 (45%), Positives = 54/75 (72%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
K+FIGGL ++TT E L+ +F Q+GE+ + +VM+DP+TKRSRGFGF+T+ + VD ++
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 78 RPHNIDGRVVETKRA 92
H +D + ++ K A
Sbjct: 62 SRHELDSKTIDPKVA 76
>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 = 80.5 bits (197), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 34/74 (45%), Positives = 53/74 (71%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
+FIGGL + TT + L+ +F ++GE+VD + DPIT RSRGFGF+ + E++ VD M +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 79 PHNIDGRVVETKRA 92
H ++G+V++ KRA
Sbjct: 62 EHKLNGKVIDPKRA 75
>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 = 76.6 bits (187), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 33/79 (41%), Positives = 52/79 (65%)
Query: 14 ESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDD 73
E K F+GGL + T+ + L+ +F ++GE+VD + DP T RSRGFGFI + +A V+
Sbjct: 9 EDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEK 68
Query: 74 AMSNRPHNIDGRVVETKRA 92
+ + H +DGRV++ K+A
Sbjct: 69 VLDQKEHRLDGRVIDPKKA 87
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 71.2 bits (173), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 32/81 (39%), Positives = 55/81 (67%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
K+F+GG+ + + L+ +F+++G + +VV++ D +R RGFGFIT+ + + VD A++
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
Query: 78 RPHNIDGRVVETKRAVPRDVR 98
H+I G+ VE KRA PRD +
Sbjct: 72 HFHDIMGKKVEVKRAEPRDSK 92
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 67.0 bits (162), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 29/74 (39%), Positives = 47/74 (63%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
+F+GGL TT E ++ +FEQ+G++ D ++M D T R RGFGF+T+ +V+
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 79 PHNIDGRVVETKRA 92
H I+ ++VE K+A
Sbjct: 62 FHEINNKMVECKKA 75
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 66.6 bits (161), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 32/76 (42%), Positives = 51/76 (67%), Gaps = 1/76 (1%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA-MS 76
K+F+GGL + T ++SL+ F ++G+I +VVV+KD T+RSRGFGF+T+ DA M+
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 77 NRPHNIDGRVVETKRA 92
++DGR + +A
Sbjct: 74 MNGKSVDGRQIRVDQA 89
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 64.7 bits (156), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 35/96 (36%), Positives = 53/96 (55%), Gaps = 4/96 (4%)
Query: 15 SLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA 74
+ K+F+GGL Y TTD SL+ +FE +G+I + VV+ D T +SRG+GF+T ++ + A
Sbjct: 16 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA 75
Query: 75 MSNRPHNIDGRVVETK----RAVPRDVRLYLVFCVS 106
+ IDGR A PR ++ VS
Sbjct: 76 CKDPNPIIDGRKANVNLAYLGAKPRSLQTGFAIGVS 111
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 53.9 bits (128), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 28/68 (41%), Positives = 43/68 (63%), Gaps = 1/68 (1%)
Query: 23 GLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNRPHNI 82
GL ++TT++ L+ +F +GE++ V V KD T S+GFGF+ ++E + MS R H I
Sbjct: 22 GLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR-HMI 80
Query: 83 DGRVVETK 90
DGR + K
Sbjct: 81 DGRWCDCK 88
>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 = 53.1 bits (126), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 44/78 (56%)
Query: 16 LRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
++K+F+GGL T +E ++ +F +GE+ + + D T + RGF FIT+ E + V M
Sbjct: 1 VKKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 60
Query: 76 SNRPHNIDGRVVETKRAV 93
+ HN+ E K A+
Sbjct: 61 EKKYHNVGLSKCEIKVAM 78
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 52.8 bits (125), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 41/57 (71%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+++G L + T++ L+ FE +G+I ++V+MKD T RS+G+GFIT+S+++ A+
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
>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 = 51.2 bits (121), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 46/77 (59%), Gaps = 4/77 (5%)
Query: 14 ESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDD 73
E + + + L YRT+ ++L+ FE++G + DV + +D TK SRGF F+ + + + +D
Sbjct: 45 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 104
Query: 74 AMSNRPHNIDGRVVETK 90
AM +DG V++ +
Sbjct: 105 AMD----AMDGAVLDGR 117
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 50.8 bits (120), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 51/78 (65%), Gaps = 6/78 (7%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY---SEAKMVDDA 74
K+FIGGL+ T ++ L+A F + G I +V+++KD T +SRGF FIT+ ++AK
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAKNAAKD 67
Query: 75 MSNRPHNIDGRVVETKRA 92
M+ + ++ G+ ++ ++A
Sbjct: 68 MNGK--SLHGKAIKVEQA 83
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 50.4 bits (119), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 46/77 (59%), Gaps = 4/77 (5%)
Query: 14 ESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDD 73
E + + + L YRT+ ++L+ FE++G + DV + +D TK SRGF F+ + + + +D
Sbjct: 68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 127
Query: 74 AMSNRPHNIDGRVVETK 90
AM +DG V++ +
Sbjct: 128 AMD----AMDGAVLDGR 140
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 50.1 bits (118), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 40/74 (54%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
+F+GGL T +E ++ +F +GE+ + + D T + RGF FIT+ E + V M +
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Query: 79 PHNIDGRVVETKRA 92
HN+ E K A
Sbjct: 62 YHNVGLSKCEIKVA 75
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 50.1 bits (118), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 48/82 (58%), Gaps = 4/82 (4%)
Query: 16 LRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+R +++G L Y T E ++ F Q+G++ +V ++ D TK+ +GFGF+ E + V +A+
Sbjct: 1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAI 59
Query: 76 SNRPHNID--GRVVETKRAVPR 95
+ + N D GR + A P+
Sbjct: 60 A-KLDNTDFMGRTIRVTEANPK 80
>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 = 49.7 bits (117), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 22/88 (25%), Positives = 49/88 (55%), Gaps = 1/88 (1%)
Query: 7 DSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS 66
D E + ++++ + +D+ +++ FE +G+I + +DP T + +G+GFI Y
Sbjct: 101 DQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYE 160
Query: 67 EAKMVDDAMSN-RPHNIDGRVVETKRAV 93
+A+ DA+S+ ++ G+ + +AV
Sbjct: 161 KAQSSQDAVSSMNLFDLGGQYLRVGKAV 188
Score = 32.3 bits (72), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 12/48 (25%), Positives = 28/48 (58%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY 65
+V++G + Y +++++ F +G I + + D +T + +GF F+ Y
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEY 62
>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 = 49.7 bits (117), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 22/88 (25%), Positives = 49/88 (55%), Gaps = 1/88 (1%)
Query: 7 DSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS 66
D E + ++++ + +D+ +++ FE +G+I + +DP T + +G+GFI Y
Sbjct: 100 DQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYE 159
Query: 67 EAKMVDDAMSNRP-HNIDGRVVETKRAV 93
+A+ DA+S+ ++ G+ + +AV
Sbjct: 160 KAQSSQDAVSSXNLFDLGGQYLRVGKAV 187
Score = 32.0 bits (71), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 12/48 (25%), Positives = 27/48 (56%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY 65
+V++G + Y +++++ F +G I + D +T + +GF F+ Y
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEY 61
>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 = 49.7 bits (117), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 22/88 (25%), Positives = 49/88 (55%), Gaps = 1/88 (1%)
Query: 7 DSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS 66
D E + ++++ + +D+ +++ FE +G+I + +DP T + +G+GFI Y
Sbjct: 116 DQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYE 175
Query: 67 EAKMVDDAMSN-RPHNIDGRVVETKRAV 93
+A+ DA+S+ ++ G+ + +AV
Sbjct: 176 KAQSSQDAVSSMNLFDLGGQYLRVGKAV 203
Score = 32.3 bits (72), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 12/50 (24%), Positives = 29/50 (58%)
Query: 16 LRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY 65
+ +V++G + Y +++++ F +G I + + D +T + +GF F+ Y
Sbjct: 28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEY 77
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 49.3 bits (116), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 38/58 (65%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
++++G L + T++ L+ FE +G I + +M D T RS+G+GFIT+S+++ A+
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKAL 85
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 48.1 bits (113), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 39/71 (54%), Gaps = 4/71 (5%)
Query: 15 SLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA 74
SLR VF+G + Y T+E L+ F + G +V ++ D T + +G+GF Y + + A
Sbjct: 7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSA 66
Query: 75 MSNRPHNIDGR 85
M N++GR
Sbjct: 67 M----RNLNGR 73
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 46.6 bits (109), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 33/51 (64%)
Query: 24 LDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA 74
L YRT+ +SL+ FE++G + DV + ++P TK RGF F+ + + + DA
Sbjct: 21 LTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDA 71
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain
Of Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain
Of Xenopus Laevis Epabp2
Length = 124
Score = 46.2 bits (108), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 35/60 (58%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R V++G +DY +T + L+A F G I + ++ D + +G+ +I ++E VD A++
Sbjct: 37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVA 96
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 30/82 (36%), Positives = 41/82 (50%), Gaps = 6/82 (7%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
KVF+G T E LQ FF Q+GE+VDV I K R F F+T+++ K V ++
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYGEVVDVF-----IPKPFRAFAFVTFADDK-VAQSLCG 66
Query: 78 RPHNIDGRVVETKRAVPRDVRL 99
I G V A P+ +L
Sbjct: 67 EDLIIKGISVHISNAEPKHNKL 88
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 44/78 (56%), Gaps = 5/78 (6%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY---SEAKMVDDAM 75
V++ L + T+ L F ++G++V V +MKD T++S+G FI + A+ A+
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 76 SNRPHNIDGRVVETKRAV 93
+N+ + GRV++ A+
Sbjct: 79 NNK--QLFGRVIKASIAI 94
>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 = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 34/60 (56%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R +++G +DY T E L+A F G + V ++ D + +GF +I +S+ + V +++
Sbjct: 6 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 65
>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 = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 34/60 (56%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R +++G +DY T E L+A F G + V ++ D + +GF +I +S+ + V +++
Sbjct: 7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 66
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 42.4 bits (98), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 41/80 (51%), Gaps = 9/80 (11%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+P VF GL TT+ L+ F ++G I DV ++ D ++RSRGF F+ + V
Sbjct: 10 DPNCCLGVF--GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN---V 64
Query: 72 DDAMSNRPH----NIDGRVV 87
DDA + +DGR +
Sbjct: 65 DDAKEAKERANGMELDGRRI 84
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 42.4 bits (98), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 34/59 (57%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
K+FIG + ++ L+ FE++G+I ++ V+KD T +G F+TY E + A S
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQS 73
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 42.0 bits (97), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 42/80 (52%), Gaps = 9/80 (11%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+P VF GL TT+ L+ F ++G I DV ++ D ++RSRGF F+ + + V
Sbjct: 13 DPNCCLGVF--GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF---ENV 67
Query: 72 DDAMSNRPH----NIDGRVV 87
DDA + +DGR +
Sbjct: 68 DDAKEAKERANGMELDGRRI 87
>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 = 42.0 bits (97), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 34/64 (53%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
P+S K+FIGGL D+ ++ +G + ++KD T S+G+ F Y + + D
Sbjct: 111 PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTD 170
Query: 73 DAMS 76
A++
Sbjct: 171 QAIA 174
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 42.0 bits (97), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 42/80 (52%), Gaps = 9/80 (11%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+P VF GL TT+ L+ F ++G I DV ++ D ++RSRGF F+ + + V
Sbjct: 13 DPNCCLGVF--GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF---ENV 67
Query: 72 DDAMSNRPH----NIDGRVV 87
DDA + +DGR +
Sbjct: 68 DDAKEAKERANGMELDGRRI 87
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 42.0 bits (97), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 35/63 (55%), Gaps = 5/63 (7%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+P VF GL TT+ L+ F ++G I DV ++ D ++RSRGF F+ + V
Sbjct: 44 DPNCCLGVF--GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN---V 98
Query: 72 DDA 74
DDA
Sbjct: 99 DDA 101
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 47/95 (49%), Gaps = 5/95 (5%)
Query: 3 PRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGF 62
PR +++ + + +R D L+ F Q+G+I+DV ++ + + S+GFGF
Sbjct: 16 PRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGF 73
Query: 63 ITYSEAKMVDDAMSNRPHN--IDGRVVETKRAVPR 95
+T+ + D A + H ++GR +E A R
Sbjct: 74 VTFENSADADRARE-KLHGTVVEGRKIEVNNATAR 107
>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 = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 1/76 (1%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
VF+G L T E ++A F +G I D V+KD T +S+G+GF+++ ++A+
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 79 PHN-IDGRVVETKRAV 93
+ GR + T A
Sbjct: 78 GGQWLGGRQIRTNWAT 93
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 41.2 bits (95), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 4/74 (5%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKR---SRGFGFITYSEAKMVDDAM 75
+FI L++ TT+E+L+ F + G I + K S GFGF+ Y + + A+
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 76 SN-RPHNIDGRVVE 88
+ H +DG +E
Sbjct: 68 KQLQGHTVDGHKLE 81
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 41.2 bits (95), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 42/83 (50%), Gaps = 1/83 (1%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R +++GGL D+ L A F +G+I D+ + D T++ RGF F+ + A+ A+
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
Query: 77 N-RPHNIDGRVVETKRAVPRDVR 98
N + GR + A P ++
Sbjct: 73 NMNESELFGRTIRVNLAKPMRIK 95
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 40/67 (59%), Gaps = 4/67 (5%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EA 68
+P S RK+F+G L+ + +++ ++ FE +G I + +++ P S+G F+ YS EA
Sbjct: 11 QPPSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGP-DGNSKGCAFVKYSSHAEA 69
Query: 69 KMVDDAM 75
+ +A+
Sbjct: 70 QAAINAL 76
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 31/47 (65%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY 65
VF+G L T E +++ F +G+I D V+KD T +S+G+GF+++
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSF 64
>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 = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 35/63 (55%)
Query: 15 SLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA 74
S R +++GGL D+ L A F +G+I D+ + D T++ RGF F+ + A+ A
Sbjct: 1 SKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 60
Query: 75 MSN 77
+ N
Sbjct: 61 IDN 63
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 34/61 (55%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R +++GGL D+ L A F +G+I D+ + D T++ RGF F+ + A+ A+
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
Query: 77 N 77
N
Sbjct: 124 N 124
>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 = 40.4 bits (93), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 34/61 (55%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R V++G + Y T+E + G ++++ +M DP T RS+G+ FI + + + A+
Sbjct: 5 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 64
Query: 77 N 77
N
Sbjct: 65 N 65
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 40.4 bits (93), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 34/57 (59%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
V++GGLD + ++ L F Q G +V+ + KD +T + +G+GF+ + + D A+
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 74
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 45/81 (55%), Gaps = 5/81 (6%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
+++ + + +R D L+ F Q+G+I+DV ++ + + S+GFGF+T+ + D A
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSADADRARE 73
Query: 77 NRPHN--IDGRVVETKRAVPR 95
+ H ++GR +E A R
Sbjct: 74 -KLHGTVVEGRKIEVNNATAR 93
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 34/61 (55%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R V++G + Y T+E + G ++++ +M DP T RS+G+ FI + + + A+
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 77 N 77
N
Sbjct: 63 N 63
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 34/61 (55%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R +++GGL D+ L A F +G+I D+ + D T++ RGF F+ + A+ A+
Sbjct: 6 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65
Query: 77 N 77
N
Sbjct: 66 N 66
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 39/73 (53%), Gaps = 4/73 (5%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
++F+ L Y +++E L+ F +G + ++ D +TK+ +GF F+T+ M +
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTF----MFPEHAVK 65
Query: 78 RPHNIDGRVVETK 90
+DG+V + +
Sbjct: 66 AYAEVDGQVFQGR 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 = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 34/61 (55%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R +++GGL D+ L A F +G+I D+ + D T++ RGF F+ + A+ A+
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
Query: 77 N 77
N
Sbjct: 68 N 68
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 35/65 (53%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
EP+ LR + + + + L+ FE++G I V ++ D T++SRG+GF+ +
Sbjct: 38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSA 97
Query: 72 DDAMS 76
A++
Sbjct: 98 QQAIA 102
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 40.0 bits (92), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 36/63 (57%), Gaps = 8/63 (12%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
K+FIG L T++ +++ FEQ+G++++ ++K+ +GF+ + +DA+ N
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFVHIEDKTAAEDAIRN 61
Query: 78 RPH 80
H
Sbjct: 62 LHH 64
>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 = 39.7 bits (91), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 34/61 (55%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R V++G + Y T+E + G ++++ +M DP T RS+G+ FI + + + A+
Sbjct: 4 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 63
Query: 77 N 77
N
Sbjct: 64 N 64
>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 = 39.7 bits (91), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 33/47 (70%), Gaps = 1/47 (2%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY 65
VF+GG+D R + +++FF ++G + +V ++ D T S+G+GF+++
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 57
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 39.7 bits (91), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 8 SKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSE 67
S+ + + +F+G L+ DE+L+ F+ + + VM D T SRG+GF++++
Sbjct: 79 SQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTS 138
Query: 68 AKMVDDAM-SNRPHNIDGR 85
+AM S + +++GR
Sbjct: 139 QDDAQNAMDSMQGQDLNGR 157
Score = 32.3 bits (72), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 16/74 (21%), Positives = 39/74 (52%), Gaps = 5/74 (6%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R +++G LD T++ L+ +F+ G I ++ +M D ++ + F+ Y ++ + A+
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIAL- 58
Query: 77 NRPHNIDGRVVETK 90
++G+ +E
Sbjct: 59 ---QTLNGKQIENN 69
>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 = 39.3 bits (90), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 33/47 (70%), Gaps = 1/47 (2%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY 65
VF+GG+D R + +++FF ++G + +V ++ D T S+G+GF+++
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 57
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 33/47 (70%), Gaps = 1/47 (2%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY 65
VF+GG+D R + +++FF ++G + +V ++ D T S+G+GF+++
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 58
>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 = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM-S 76
+F+G L+ DE+L+ F+ + + VM D T SRG+GF++++ +AM S
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 77 NRPHNIDGRVVETKRAV 93
+ +++GR + A
Sbjct: 63 MQGQDLNGRPLRINWAA 79
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 38.9 bits (89), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 30/48 (62%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY 65
K+F+G + ++ L+ FE++G I ++ V+KD +T +G F+TY
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTY 64
>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 = 38.9 bits (89), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 32/57 (56%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+++ GL T + L+ F Q+G I+ ++ D +T SRG GFI + + ++A+
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 147
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 42/88 (47%), Gaps = 14/88 (15%)
Query: 24 LDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNRPHNID 83
L T E ++ F GEI +++D IT +S G+GF+ Y + K + A+ + ++
Sbjct: 10 LPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI----NTLN 65
Query: 84 GRVVETK----------RAVPRDVRLYL 101
G ++TK A RD LY+
Sbjct: 66 GLRLQTKTIKVSYARPSSASIRDANLYV 93
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 3/75 (4%)
Query: 1 MKPRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGF 60
MKP DS+ RK+FIG + + T+ ++ F +G+I + +++ P SRG
Sbjct: 82 MKP--ADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGC 138
Query: 61 GFITYSEAKMVDDAM 75
F+T++ M A+
Sbjct: 139 AFVTFTTRAMAQTAI 153
Score = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 38/67 (56%), Gaps = 3/67 (4%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITK--RSRGFGFITYSEAKMVDDAM 75
K+F+G + +++ L+ FEQ+G + ++ V++D +S+G F+T+ K +A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA- 63
Query: 76 SNRPHNI 82
N HN+
Sbjct: 64 QNALHNM 70
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/98 (25%), Positives = 46/98 (46%), Gaps = 14/98 (14%)
Query: 14 ESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDD 73
+S + + L T + ++ F G+I +++D IT +S G+GF+ YS+ D
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 74 AMSNRPHNIDGRVVETK----------RAVPRDVRLYL 101
A+ + ++G ++TK A RD LY+
Sbjct: 62 AI----NTLNGLKLQTKTIKVSYARPSSASIRDANLYV 95
Score = 35.0 bits (79), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 31/57 (54%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+++ GL + + ++ F Q+G I+ ++ D T SRG GFI + + ++A+
Sbjct: 93 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 149
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 3/75 (4%)
Query: 1 MKPRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGF 60
MKP DS+ RK+FIG + + T+ ++ F +G+I + +++ P SRG
Sbjct: 94 MKPA--DSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGC 150
Query: 61 GFITYSEAKMVDDAM 75
F+T++ M A+
Sbjct: 151 AFVTFTTRAMAQTAI 165
Score = 34.7 bits (78), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 38/67 (56%), Gaps = 3/67 (4%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITK--RSRGFGFITYSEAKMVDDAM 75
K+F+G + +++ L+ FEQ+G + ++ V++D +S+G F+T+ K +A
Sbjct: 17 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA- 75
Query: 76 SNRPHNI 82
N HN+
Sbjct: 76 QNALHNM 82
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 40/77 (51%), Gaps = 4/77 (5%)
Query: 14 ESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDD 73
+S + + L T + ++ F G+I +++D IT +S G+GF+ YS+ D
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 74 AMSNRPHNIDGRVVETK 90
A+ + ++G ++TK
Sbjct: 62 AI----NTLNGLKLQTK 74
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 6/72 (8%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
+++ LD DE L+ F +G I VM + RS+GFGF+ +S + A++
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVT-- 73
Query: 79 PHNIDGRVVETK 90
++GR+V TK
Sbjct: 74 --EMNGRIVATK 83
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 31/60 (51%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
K+FIGGL D+ ++ +G + ++KD T S+G+ F Y + + D A++
Sbjct: 2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 61
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 39/73 (53%), Gaps = 10/73 (13%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
++F+G L T+E + FE++GE +V + +D RGFGFI + + A +
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKA- 76
Query: 78 RPHNIDGRVVETK 90
+DG +++++
Sbjct: 77 ---ELDGTILKSR 86
>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 = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 31/60 (51%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
K+FIGGL D+ ++ +G + ++KD T S+G+ F Y + + D A++
Sbjct: 97 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 156
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 37.0 bits (84), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 31/60 (51%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
K+FIGGL D+ ++ +G + ++KD T S+G+ F Y + + D A++
Sbjct: 95 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 154
>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 = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/80 (22%), Positives = 42/80 (52%), Gaps = 4/80 (5%)
Query: 14 ESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDD 73
++ + +F+ ++Y TT+ L+ FE +G I + ++ + + RG+ FI Y + +
Sbjct: 100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHS 159
Query: 74 AMSNRPHNIDGRVVETKRAV 93
A + DG+ ++ +R +
Sbjct: 160 AYK----HADGKKIDGRRVL 175
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In
Trinucleotide Repeat Containing 4 Variant
Length = 102
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 34/58 (58%), Gaps = 4/58 (6%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFI---TYSEAKMV 71
RK+F+G L + TDE ++ FE +G I + V++ P S+G F+ T++EA+
Sbjct: 13 RKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGP-DGTSKGCAFVKFQTHAEAQAA 69
>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 = 36.6 bits (83), Expect = 0.004, Method: Composition-based stats.
Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 1/75 (1%)
Query: 14 ESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDD 73
++ + +F+ ++Y TT+ L+ FE +G I + ++ + + RG+ FI Y + +
Sbjct: 100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHS 159
Query: 74 AMSNRP-HNIDGRVV 87
A + IDGR V
Sbjct: 160 AYKHADGKKIDGRRV 174
>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 = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 42/83 (50%), Gaps = 5/83 (6%)
Query: 12 EPESLRK----VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSE 67
E E L K +++G L + TT+E + F + G+I +++ D + K + GF F+ Y
Sbjct: 31 EQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYS 90
Query: 68 AKMVDDAMSN-RPHNIDGRVVET 89
++AM +D R++ T
Sbjct: 91 RADAENAMRYINGTRLDDRIIRT 113
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 34/69 (49%)
Query: 7 DSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS 66
D+ E R VF L R L+ FF G++ DV ++ D ++RS+G ++ +
Sbjct: 16 DNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFC 75
Query: 67 EAKMVDDAM 75
E + V A+
Sbjct: 76 EIQSVPLAI 84
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 43/82 (52%), Gaps = 8/82 (9%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAKMVDD 73
+ +F+ GL TT+E+L+ F+ V ++ D T S+GFGF+ ++ +AK +
Sbjct: 16 KTLFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKE 72
Query: 74 AMSNRPHNIDGRVVETKRAVPR 95
AM + IDG V A P+
Sbjct: 73 AMED--GEIDGNKVTLDWAKPK 92
>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 = 0.006, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 30/58 (51%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
++I GL TTD+ L + +G+IV + D T + +G+GF+ + A++
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65
>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 = 35.8 bits (81), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 36/65 (55%), Gaps = 9/65 (13%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFI---TYSEAKMVDDA 74
++F+G L T+E ++ FE++G+ +V + KD +GFGFI T + A++
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 70
Query: 75 MSNRP 79
+ N P
Sbjct: 71 LDNMP 75
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 35.8 bits (81), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 36/65 (55%), Gaps = 9/65 (13%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFI---TYSEAKMVDDA 74
++F+G L T+E ++ FE++G+ +V + KD +GFGFI T + A++
Sbjct: 24 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 77
Query: 75 MSNRP 79
+ N P
Sbjct: 78 LDNMP 82
>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 = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 28/53 (52%)
Query: 24 LDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
L T + L++ F GE+ +++D + S G+GF+ Y AK + A++
Sbjct: 12 LPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 64
>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 = 35.4 bits (80), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 28/53 (52%)
Query: 24 LDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
L T + L++ F GE+ +++D + S G+GF+ Y AK + A++
Sbjct: 27 LPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 79
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 35.0 bits (79), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 43/87 (49%), Gaps = 7/87 (8%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFG---FITYSEAKMVDD 73
+ VFI L + + +E+L +Q+G++ V V+ P T+ S+G F+T A+
Sbjct: 16 KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 75
Query: 74 AMSNRPHN----IDGRVVETKRAVPRD 96
A S +DGR ++ AV RD
Sbjct: 76 AASLEAEGGGLKLDGRQLKVDLAVTRD 102
>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 = 35.0 bits (79), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 28/53 (52%)
Query: 24 LDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
L T + L++ F GE+ +++D + S G+GF+ Y AK + A++
Sbjct: 10 LPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs
Of Human Antigen R
Length = 177
Score = 35.0 bits (79), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 28/53 (52%)
Query: 24 LDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
L T + L++ F GE+ +++D + S G+GF+ Y AK + A++
Sbjct: 10 LPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 35.0 bits (79), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 34/70 (48%), Gaps = 9/70 (12%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVV-VMKDPITKRSRGFGFITYSEAKMVDDA--- 74
+FIG LD ++ L F +G I+ +M+DP T S+G+ FI ++ D A
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 75 -----MSNRP 79
+ NRP
Sbjct: 68 MNGQYLCNRP 77
>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 = 35.0 bits (79), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
RK+FIG + + T+ ++ F +G+I + +++ P SRG F+T++ A+
Sbjct: 96 RKLFIGXISKKCTENDIRVXFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAXAQTAI 153
Score = 33.5 bits (75), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITK--RSRGFGFITYSEAKMVDDAM 75
K F+G + +++ L+ FEQ+G + ++ V++D +S+G F+T+ K +A
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 76 SNRPHN 81
N HN
Sbjct: 65 -NALHN 69
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 35.0 bits (79), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 31/57 (54%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+++ GL + + ++ F Q+G I+ ++ D T SRG GFI + + ++A+
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
pdb|3NNH|C Chain C, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
pdb|3NNH|B Chain B, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
pdb|3NNH|D Chain D, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
Length = 88
Score = 34.7 bits (78), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 38/67 (56%), Gaps = 3/67 (4%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITK--RSRGFGFITYSEAKMVDDAM 75
K+F+G + +++ L+ FEQ+G + ++ V++D +S+G F+T+ K +A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA- 63
Query: 76 SNRPHNI 82
N HN+
Sbjct: 64 QNALHNM 70
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 34.3 bits (77), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 6/77 (7%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
VF+G T++ L+ FF Q+G+++DV I K R F F+T+++ ++ ++
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVF-----IPKPFRAFAFVTFADDQIA-QSLCGE 61
Query: 79 PHNIDGRVVETKRAVPR 95
I G V A P+
Sbjct: 62 DLIIKGISVHISNAEPK 78
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 34.3 bits (77), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 24/41 (58%), Gaps = 2/41 (4%)
Query: 25 DYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY 65
D R TD LQ F +G I + + KD T +S+GF FI++
Sbjct: 26 DTRETD--LQELFRPFGSISRIYLAKDKTTGQSKGFAFISF 64
>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 = 33.9 bits (76), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 42/83 (50%), Gaps = 6/83 (7%)
Query: 12 EPESLRK----VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSE 67
E E L K +++G L + TT+E + F + G+I +++ D + K + GF F+ Y
Sbjct: 10 EQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKM-KTACGFCFVEYYS 68
Query: 68 AKMVDDAMSN-RPHNIDGRVVET 89
++AM +D R++ T
Sbjct: 69 RADAENAMRYINGTRLDDRIIRT 91
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 33.5 bits (75), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 3/44 (6%)
Query: 32 SLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
SL A F Q+G+I+D+V +K T + RG F+ + E +A+
Sbjct: 26 SLYAIFSQFGQILDIVALK---TLKMRGQAFVIFKEIGSASNAL 66
>pdb|1A9N|B Chain B, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
pdb|1A9N|D Chain D, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
Length = 96
Score = 33.1 bits (74), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 7/61 (11%)
Query: 19 VFIGGLDYRTTDE----SLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA 74
++I ++ + E SL A F Q+G +VD+V +K T + RG F+ + E +A
Sbjct: 9 IYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALK---TMKMRGQAFVIFKELGSSTNA 65
Query: 75 M 75
+
Sbjct: 66 L 66
>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 = 32.7 bits (73), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 31/60 (51%)
Query: 16 LRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+ +++G L T+ L F G I+ + V +D IT+RS G+ ++ + + + A+
Sbjct: 15 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL 74
>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 = 32.7 bits (73), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 31/60 (51%)
Query: 16 LRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+ +++G L T+ L F G I+ + V +D IT+RS G+ ++ + + + A+
Sbjct: 10 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL 69
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 32.3 bits (72), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 41/82 (50%), Gaps = 9/82 (10%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITK--RSRGFGFITYSEAKMVDDA 74
+ + + L Y T+E+LQ FE+ +K P + +S+G+ FI ++ + +A
Sbjct: 16 KTLVLSNLSYSATEETLQEVFEK------ATFIKVPQNQNGKSKGYAFIEFASFEDAKEA 69
Query: 75 MSN-RPHNIDGRVVETKRAVPR 95
+++ I+GR + + PR
Sbjct: 70 LNSCNKREIEGRAIRLELQGPR 91
>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 = 0.10, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 30/50 (60%), Gaps = 1/50 (2%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS 66
RK+F+G L+ + ++E + F+ +G I + V++ P S+G F+ +S
Sbjct: 16 RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFS 64
>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 = 31.2 bits (69), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
VF+G L T ++ A F +G I D V+KD T +S+G+GF+++ ++A+
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 79 PHN-IDGRVVETKRAV 93
+ GR + T A
Sbjct: 69 GGQWLGGRQIRTNWAT 84
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 31.2 bits (69), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 33/61 (54%), Gaps = 7/61 (11%)
Query: 19 VFIGGLDYRTTDE----SLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA 74
++I L+ + + SL A F Q+G+I+D++V + + + RG F+ + E +A
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNA 68
Query: 75 M 75
+
Sbjct: 69 L 69
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein
U1a117, Nmr, 43 Structures
Length = 116
Score = 30.8 bits (68), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 34/61 (55%), Gaps = 7/61 (11%)
Query: 19 VFIGGLDYR-TTDE---SLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA 74
++I L+ + DE SL A F Q+G+I+D++V + + + RG F+ + E +A
Sbjct: 11 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNA 67
Query: 75 M 75
+
Sbjct: 68 L 68
>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 = 30.8 bits (68), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 34/61 (55%), Gaps = 7/61 (11%)
Query: 19 VFIGGLDYR-TTDE---SLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA 74
++I L+ + DE SL A F Q+G+I+D++V + + + RG F+ + E +A
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNA 68
Query: 75 M 75
+
Sbjct: 69 L 69
>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 = 30.4 bits (67), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 36/84 (42%), Gaps = 7/84 (8%)
Query: 1 MKPRYD--DSKCTEPESLRKV-----FIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPI 53
M+ YD + EP R V F+ G+ T+E + F ++GEI ++ + D
Sbjct: 1 MREDYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRR 60
Query: 54 TKRSRGFGFITYSEAKMVDDAMSN 77
T +G+ + Y K AM
Sbjct: 61 TGYLKGYTLVEYETYKEAQAAMEG 84
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation
Initiation Factor 4b
Length = 100
Score = 30.0 bits (66), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPIT-KRSRGFGFITY 65
F+G L Y T+ES++ FF I V + ++P +R +GFG+ +
Sbjct: 22 AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEF 68
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of
Eukaryotic Initiation Factor 4b
Length = 104
Score = 30.0 bits (66), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPIT-KRSRGFGFITY 65
F+G L Y T+ES++ FF I V + ++P +R +GFG+ +
Sbjct: 18 AFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEF 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 = 30.0 bits (66), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 15/59 (25%), Positives = 28/59 (47%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
+F+ G+ T+E + F ++GEI ++ + D T +G+ + Y K AM
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 68
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 30.0 bits (66), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 15/59 (25%), Positives = 28/59 (47%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
+F+ G+ T+E + F ++GEI ++ + D T +G+ + Y K AM
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 68
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 29.6 bits (65), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEA 68
VF+ LDY+ + L+ F G +V +++D K SRG G +T+ ++
Sbjct: 18 VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGK-SRGIGTVTFEQS 66
>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 = 29.6 bits (65), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 15/59 (25%), Positives = 28/59 (47%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
+F+ G+ T+E + F ++GEI ++ + D T +G+ + Y K AM
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 70
>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 = 29.6 bits (65), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 15/59 (25%), Positives = 28/59 (47%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
+F+ G+ T+E + F ++GEI ++ + D T +G+ + Y K AM
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 68
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Rna-Binding Protein 14
Length = 90
Score = 29.6 bits (65), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 22/34 (64%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKD 51
K+F+G + T + L++ FE+ G +++ V+KD
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVVKD 44
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 29.6 bits (65), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 10/34 (29%), Positives = 23/34 (67%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKD 51
K+ +G + T++ L+A FE++G +++ ++KD
Sbjct: 12 KLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD 45
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 29.6 bits (65), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 15/59 (25%), Positives = 28/59 (47%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
+F+ G+ T+E + F ++GEI ++ + D T +G+ + Y K AM
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 83
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 28.5 bits (62), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 37/71 (52%), Gaps = 7/71 (9%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM-SN 77
V+ GG+ TD+ ++ F +G+I+++ V + +G+ F+ +S + A+ S
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSV 81
Query: 78 RPHNIDGRVVE 88
I+G VV+
Sbjct: 82 NGTTIEGHVVK 92
>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 = 1.0, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 27/58 (46%), Gaps = 1/58 (1%)
Query: 8 SKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY 65
S+ PE +FI L D+ L F +G +V V D T S+ FGF++Y
Sbjct: 18 SQKEGPEGAN-LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSY 74
>pdb|2M2B|A Chain A, Nmr Structure Of The Rrm2 Domain Of The Protein Rbm10 From
Homo Sapiens
Length = 131
Score = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 28/101 (27%), Positives = 48/101 (47%), Gaps = 11/101 (10%)
Query: 8 SKCTEPESLRK---VFIGGLDYRTTDESLQAFFEQWGEIV--DVVVMKDPITKRSRGFGF 62
S+ +EP S + + L+ +T +S+ + + +V V+KD T+ +RGF F
Sbjct: 12 SQGSEPSSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAF 71
Query: 63 ITYS--EAKMVDDAMS--NRPHNIDGRV--VETKRAVPRDV 97
I S EA + + + P IDG+ VE + RD+
Sbjct: 72 IQLSTIEAAQLLQILQALHPPLTIDGKTINVEFAKGSKRDM 112
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 27.3 bits (59), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 19/39 (48%)
Query: 29 TDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSE 67
TD L A F G I +M+D T S G+ F+ ++
Sbjct: 16 TDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTS 54
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 27.3 bits (59), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 24/39 (61%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMK 50
E +++ +++GGL T+ L+ F Q+GEI + V++
Sbjct: 8 EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ 46
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14
Complex
Length = 110
Score = 27.3 bits (59), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 31/73 (42%), Gaps = 5/73 (6%)
Query: 4 RYDDSKCTEPESLRKV-----FIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSR 58
R +D EP R V F+ + ++ +Q F +GEI ++ + D T S+
Sbjct: 9 RNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSK 68
Query: 59 GFGFITYSEAKMV 71
G+ + Y K
Sbjct: 69 GYALVEYETHKQA 81
>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 = 26.9 bits (58), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 31/73 (42%), Gaps = 5/73 (6%)
Query: 4 RYDDSKCTEPESLRKV-----FIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSR 58
R +D EP R V F+ + ++ +Q F +GEI ++ + D T S+
Sbjct: 55 RNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSK 114
Query: 59 GFGFITYSEAKMV 71
G+ + Y K
Sbjct: 115 GYALVEYETHKQA 127
>pdb|3P5T|L Chain L, Cfim25-Cfim68 Complex
pdb|3P5T|M Chain M, Cfim25-Cfim68 Complex
pdb|3P5T|N Chain N, Cfim25-Cfim68 Complex
pdb|3P5T|O Chain O, Cfim25-Cfim68 Complex
pdb|3P5T|P Chain P, Cfim25-Cfim68 Complex
pdb|3P5T|Q Chain Q, Cfim25-Cfim68 Complex
pdb|3P6Y|C Chain C, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|D Chain D, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|G Chain G, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|H Chain H, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|K Chain K, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|L Chain L, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|O Chain O, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|P Chain P, Cf Im25-Cf Im68-Uguaa Complex
Length = 90
Score = 26.9 bits (58), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 25/47 (53%), Gaps = 2/47 (4%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWG--EIVDVVVMKDPITKRSRGFGFI 63
++IG L + TTDE L G +I+++ ++ +S+GF +
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALV 50
>pdb|2DHA|A Chain A, Solution Structure Of The Second Rna Recognition Motif
In Hypothetical Protein Flj201171
Length = 123
Score = 26.9 bits (58), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 22/53 (41%), Gaps = 10/53 (18%)
Query: 23 GLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
GL + T E + AFF Q PIT G F+TY + + DA
Sbjct: 30 GLPFTATAEEVVAFFGQ----------HCPITGGKEGILFVTYPDGRPTGDAF 72
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 26.9 bits (58), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 19/38 (50%)
Query: 29 TDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS 66
TD L A F G I +M+D T S G+ F+ ++
Sbjct: 16 TDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFT 53
>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 = 26.9 bits (58), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 45 DVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNRPH--NIDGRVVETKRAVPR 95
+V +M++ + +SRGF F+ +S + M H NI G+ V + P+
Sbjct: 31 EVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSDPK 83
>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 26.2 bits (56), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 5/48 (10%)
Query: 45 DVVVMKDPITKRSRGFGFITYSEAKMVDDAMS-----NRPHNIDGRVV 87
++ ++KD T+++RGF F+ S A + + P IDG+ +
Sbjct: 40 NIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTI 87
>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 = 5.1, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 6/59 (10%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRS----RGFGFITYSEAKMV 71
RKVF+GGL ++ + A F ++G + VV +S +G+ F+ + E V
Sbjct: 9 RKVFVGGLPPDIDEDEITASFRRFGPL--VVDWPHKAESKSYFPPKGYAFLLFQEESSV 65
>pdb|2YA1|A Chain A, Product Complex Of A Multi-Modular Glycogen-Degrading
Pneumococcal Virulence Factor Spua
Length = 1014
Score = 25.8 bits (55), Expect = 6.6, Method: Composition-based stats.
Identities = 11/35 (31%), Positives = 20/35 (57%), Gaps = 5/35 (14%)
Query: 39 QWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDD 73
++G +D+ P+ + +R FGF+ E+K DD
Sbjct: 158 KYGRYIDI-----PLNEAAREFGFLLLDESKQGDD 187
>pdb|3Q2S|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2S|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2T|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
pdb|3Q2T|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
Length = 229
Score = 25.4 bits (54), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 25/47 (53%), Gaps = 2/47 (4%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWG--EIVDVVVMKDPITKRSRGFGFI 63
++IG L + TTDE L G +I+++ ++ +S+GF +
Sbjct: 71 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALV 117
>pdb|1F1S|A Chain A, Crystal Structure Of Streptococcus Agalactiae Hyaluronate
Lyase At 2.1 Angstrom Resolution.
pdb|1I8Q|A Chain A, Crystal Structure Of Streptococcus Agalactiae Hyaluronate
Lyase Complexed With Enzyme Product, Unsaturated
Disaccharide Hyaluronan
pdb|1LXM|A Chain A, Crystal Structure Of Streptococcus Agalactiae Hyaluronate
Lyase Complexed With Hexasaccharide Unit Of Hyaluronan
Length = 814
Score = 25.0 bits (53), Expect = 10.0, Method: Composition-based stats.
Identities = 15/72 (20%), Positives = 35/72 (48%), Gaps = 1/72 (1%)
Query: 21 IGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNRPH 80
+ +D+ D +L A + W + D +V K + G G ++ + + DD+ +
Sbjct: 577 LAAMDFTNWDRTLTAQ-KGWVILNDKIVFLGSNIKNTNGIGNVSTTIDQRKDDSKTPYTT 635
Query: 81 NIDGRVVETKRA 92
++G+ ++ K+A
Sbjct: 636 YVNGKTIDLKQA 647
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 0.140 0.417
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,220,938
Number of Sequences: 62578
Number of extensions: 113300
Number of successful extensions: 538
Number of sequences better than 100.0: 136
Number of HSP's better than 100.0 without gapping: 116
Number of HSP's successfully gapped in prelim test: 20
Number of HSP's that attempted gapping in prelim test: 397
Number of HSP's gapped (non-prelim): 156
length of query: 115
length of database: 14,973,337
effective HSP length: 78
effective length of query: 37
effective length of database: 10,092,253
effective search space: 373413361
effective search space used: 373413361
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 45 (21.9 bits)