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= psy14686
(306 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 154 bits (388), Expect = 9e-38, Method: Compositional matrix adjust.
Identities = 78/145 (53%), Positives = 100/145 (68%), Gaps = 13/145 (8%)
Query: 39 EPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMV 98
EPE LRKLFIGGL + T D+SL++ FEQWG + D VVM+DP TKRSRGFGF+TY+ + V
Sbjct: 10 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 69
Query: 99 DEAMSNRPHEIDGRVVETKRAVPRE----------VKVRRVTKVQIALEQ---MDYFGQY 145
D AM+ RPH++DGRVVE KRAV RE VK V ++ E+ DYF QY
Sbjct: 70 DAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 129
Query: 146 GTIESVNMVTNKETGAKRGFAFIEF 170
G IE + ++T++ +G KRGFAF+ F
Sbjct: 130 GKIEVIEIMTDRGSGKKRGFAFVTF 154
Score = 59.7 bits (143), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 32/109 (29%), Positives = 64/109 (58%), Gaps = 3/109 (2%)
Query: 16 EVAGTVVPLAMIINKAMEDSQCSEPE-SLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVV 74
+V G VV +++ EDSQ +++K+F+GG+ T + L+ +FEQ+G+I +
Sbjct: 79 KVDGRVVEPKRAVSR--EDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIE 136
Query: 75 VMKDPVTKRSRGFGFITYSESKMVDEAMSNRPHEIDGRVVETKRAVPRE 123
+M D + + RGF F+T+ + VD+ + + H ++G E ++A+ ++
Sbjct: 137 IMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQ 185
>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 = 153 bits (387), Expect = 9e-38, Method: Compositional matrix adjust.
Identities = 78/145 (53%), Positives = 100/145 (68%), Gaps = 13/145 (8%)
Query: 39 EPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMV 98
EPE LRKLFIGGL + T D+SL++ FEQWG + D VVM+DP TKRSRGFGF+TY+ + V
Sbjct: 9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 68
Query: 99 DEAMSNRPHEIDGRVVETKRAVPRE----------VKVRRVTKVQIALEQ---MDYFGQY 145
D AM+ RPH++DGRVVE KRAV RE VK V ++ E+ DYF QY
Sbjct: 69 DAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 128
Query: 146 GTIESVNMVTNKETGAKRGFAFIEF 170
G IE + ++T++ +G KRGFAF+ F
Sbjct: 129 GKIEVIEIMTDRGSGKKRGFAFVTF 153
Score = 59.7 bits (143), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 32/109 (29%), Positives = 64/109 (58%), Gaps = 3/109 (2%)
Query: 16 EVAGTVVPLAMIINKAMEDSQCSEPE-SLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVV 74
+V G VV +++ EDSQ +++K+F+GG+ T + L+ +FEQ+G+I +
Sbjct: 78 KVDGRVVEPKRAVSR--EDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIE 135
Query: 75 VMKDPVTKRSRGFGFITYSESKMVDEAMSNRPHEIDGRVVETKRAVPRE 123
+M D + + RGF F+T+ + VD+ + + H ++G E ++A+ ++
Sbjct: 136 IMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQ 184
>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 = 153 bits (387), Expect = 9e-38, Method: Compositional matrix adjust.
Identities = 78/145 (53%), Positives = 100/145 (68%), Gaps = 13/145 (8%)
Query: 39 EPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMV 98
EPE LRKLFIGGL + T D+SL++ FEQWG + D VVM+DP TKRSRGFGF+TY+ + V
Sbjct: 8 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 67
Query: 99 DEAMSNRPHEIDGRVVETKRAVPRE----------VKVRRVTKVQIALEQ---MDYFGQY 145
D AM+ RPH++DGRVVE KRAV RE VK V ++ E+ DYF QY
Sbjct: 68 DAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 127
Query: 146 GTIESVNMVTNKETGAKRGFAFIEF 170
G IE + ++T++ +G KRGFAF+ F
Sbjct: 128 GKIEVIEIMTDRGSGKKRGFAFVTF 152
Score = 59.7 bits (143), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 32/109 (29%), Positives = 64/109 (58%), Gaps = 3/109 (2%)
Query: 16 EVAGTVVPLAMIINKAMEDSQCSEPE-SLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVV 74
+V G VV +++ EDSQ +++K+F+GG+ T + L+ +FEQ+G+I +
Sbjct: 77 KVDGRVVEPKRAVSR--EDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIE 134
Query: 75 VMKDPVTKRSRGFGFITYSESKMVDEAMSNRPHEIDGRVVETKRAVPRE 123
+M D + + RGF F+T+ + VD+ + + H ++G E ++A+ ++
Sbjct: 135 IMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQ 183
>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 = 153 bits (387), Expect = 1e-37, Method: Compositional matrix adjust.
Identities = 78/145 (53%), Positives = 100/145 (68%), Gaps = 13/145 (8%)
Query: 39 EPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMV 98
EPE LRKLFIGGL + T D+SL++ FEQWG + D VVM+DP TKRSRGFGF+TY+ + V
Sbjct: 2 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 61
Query: 99 DEAMSNRPHEIDGRVVETKRAVPRE----------VKVRRVTKVQIALEQ---MDYFGQY 145
D AM+ RPH++DGRVVE KRAV RE VK V ++ E+ DYF QY
Sbjct: 62 DAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 121
Query: 146 GTIESVNMVTNKETGAKRGFAFIEF 170
G IE + ++T++ +G KRGFAF+ F
Sbjct: 122 GKIEVIEIMTDRGSGKKRGFAFVTF 146
Score = 60.1 bits (144), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 32/109 (29%), Positives = 64/109 (58%), Gaps = 3/109 (2%)
Query: 16 EVAGTVVPLAMIINKAMEDSQCSEPE-SLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVV 74
+V G VV +++ EDSQ +++K+F+GG+ T + L+ +FEQ+G+I +
Sbjct: 71 KVDGRVVEPKRAVSR--EDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIE 128
Query: 75 VMKDPVTKRSRGFGFITYSESKMVDEAMSNRPHEIDGRVVETKRAVPRE 123
+M D + + RGF F+T+ + VD+ + + H ++G E ++A+ ++
Sbjct: 129 IMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQ 177
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 153 bits (386), Expect = 1e-37, Method: Compositional matrix adjust.
Identities = 78/145 (53%), Positives = 100/145 (68%), Gaps = 13/145 (8%)
Query: 39 EPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMV 98
EPE LRKLFIGGL + T D+SL++ FEQWG + D VVM+DP TKRSRGFGF+TY+ + V
Sbjct: 9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 68
Query: 99 DEAMSNRPHEIDGRVVETKRAVPRE----------VKVRRVTKVQIALEQM---DYFGQY 145
D AM+ RPH++DGRVVE KRAV RE VK V ++ E+ DYF QY
Sbjct: 69 DAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 128
Query: 146 GTIESVNMVTNKETGAKRGFAFIEF 170
G IE + ++T++ +G KRGFAF+ F
Sbjct: 129 GKIEVIEIMTDRGSGKKRGFAFVTF 153
Score = 59.7 bits (143), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 32/109 (29%), Positives = 64/109 (58%), Gaps = 3/109 (2%)
Query: 16 EVAGTVVPLAMIINKAMEDSQCSEPE-SLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVV 74
+V G VV +++ EDSQ +++K+F+GG+ T + L+ +FEQ+G+I +
Sbjct: 78 KVDGRVVEPKRAVSR--EDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIE 135
Query: 75 VMKDPVTKRSRGFGFITYSESKMVDEAMSNRPHEIDGRVVETKRAVPRE 123
+M D + + RGF F+T+ + VD+ + + H ++G E ++A+ ++
Sbjct: 136 IMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQ 184
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 153 bits (386), Expect = 1e-37, Method: Compositional matrix adjust.
Identities = 78/145 (53%), Positives = 100/145 (68%), Gaps = 13/145 (8%)
Query: 39 EPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMV 98
EPE LRKLFIGGL + T D+SL++ FEQWG + D VVM+DP TKRSRGFGF+TY+ + V
Sbjct: 7 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 66
Query: 99 DEAMSNRPHEIDGRVVETKRAVPRE----------VKVRRVTKVQIALEQM---DYFGQY 145
D AM+ RPH++DGRVVE KRAV RE VK V ++ E+ DYF QY
Sbjct: 67 DAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 126
Query: 146 GTIESVNMVTNKETGAKRGFAFIEF 170
G IE + ++T++ +G KRGFAF+ F
Sbjct: 127 GKIEVIEIMTDRGSGKKRGFAFVTF 151
Score = 59.7 bits (143), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 32/109 (29%), Positives = 64/109 (58%), Gaps = 3/109 (2%)
Query: 16 EVAGTVVPLAMIINKAMEDSQCSEPE-SLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVV 74
+V G VV +++ EDSQ +++K+F+GG+ T + L+ +FEQ+G+I +
Sbjct: 76 KVDGRVVEPKRAVSR--EDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIE 133
Query: 75 VMKDPVTKRSRGFGFITYSESKMVDEAMSNRPHEIDGRVVETKRAVPRE 123
+M D + + RGF F+T+ + VD+ + + H ++G E ++A+ ++
Sbjct: 134 IMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQ 182
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 121 bits (303), Expect = 6e-28, Method: Compositional matrix adjust.
Identities = 53/85 (62%), Positives = 66/85 (77%)
Query: 39 EPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMV 98
E E RKLFIGGL + T ++SL+ ++EQWG++ D VVM+DP +KRSRGFGF+T+S V
Sbjct: 23 EKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEV 82
Query: 99 DEAMSNRPHEIDGRVVETKRAVPRE 123
D AM+ RPH IDGRVVE KRAV RE
Sbjct: 83 DAAMAARPHSIDGRVVEPKRAVARE 107
>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 = 104 bits (260), Expect = 5e-23, Method: Compositional matrix adjust.
Identities = 50/134 (37%), Positives = 87/134 (64%), Gaps = 10/134 (7%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
K+FIGGL++ T +D+L+ +F ++G + D+ +MKDP T RSRGFGF+++ + VDE +
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 105 RPHEIDGRVVETKRAVPREVKVRRVTKVQIA--------LEQMDYFGQYGTIESVNMVTN 156
+ H +DG+V++ KRA+PR+ + + K+ + E ++F Q+GTI ++ +
Sbjct: 65 Q-HILDGKVIDPKRAIPRDEQ-DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLD 122
Query: 157 KETGAKRGFAFIEF 170
K+TG RGF F+ +
Sbjct: 123 KDTGQSRGFGFVTY 136
Score = 67.8 bits (164), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 33/85 (38%), Positives = 46/85 (54%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
E + K+F+GG+ + FF QWG I+D +M D T +SRGFGF+TY +
Sbjct: 82 DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADA 141
Query: 98 VDEAMSNRPHEIDGRVVETKRAVPR 122
VD N+ + R +E KRA PR
Sbjct: 142 VDRVCQNKFIDFKDRKIEIKRAEPR 166
>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 = 1e-19, Method: Compositional matrix adjust.
Identities = 36/82 (43%), Positives = 58/82 (70%)
Query: 41 ESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDE 100
+ + KLF+GGLD+ T ++L+++F Q+GE+VD V+MKD T +SRGFGF+ + + V
Sbjct: 14 DEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGT 73
Query: 101 AMSNRPHEIDGRVVETKRAVPR 122
+++RPH +DGR ++ K PR
Sbjct: 74 VLASRPHTLDGRNIDPKPCTPR 95
Score = 31.6 bits (70), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 141 YFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
YF QYG + ++ +K T RGF F++F
Sbjct: 36 YFSQYGEVVDCVIMKDKTTNQSRGFGFVKF 65
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 87.8 bits (216), Expect = 7e-18, Method: Compositional matrix adjust.
Identities = 35/83 (42%), Positives = 59/83 (71%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
K+FIGGL ++T + L+ +F Q+GE+ + +VM+DP+TKRSRGFGF+T+ + VD+ ++
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 86
Query: 105 RPHEIDGRVVETKRAVPREVKVR 127
HE+D + ++ K A PR + +
Sbjct: 87 SRHELDSKTIDPKVAFPRRAQPK 109
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 19/31 (61%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
+YFGQ+G ++ ++ + T RGF F+ F
Sbjct: 44 EYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 74
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 82.0 bits (201), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 33/75 (44%), Positives = 55/75 (73%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
K+FIGGL ++T + L+ +F Q+GE+ + +VM+DP+TKRSRGFGF+T+ + VD+ ++
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 105 RPHEIDGRVVETKRA 119
HE+D + ++ K A
Sbjct: 62 SRHELDSKTIDPKVA 76
Score = 29.6 bits (65), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 19/31 (61%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
+YFGQ+G ++ ++ + T RGF F+ F
Sbjct: 19 EYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49
>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 = 82.0 bits (201), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 34/74 (45%), Positives = 53/74 (71%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
+FIGGL + T LK +F ++GE+VD + DP+T RSRGFGF+ + ES+ VD+ M +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 106 PHEIDGRVVETKRA 119
H+++G+V++ KRA
Sbjct: 62 EHKLNGKVIDPKRA 75
Score = 28.9 bits (63), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
DYF ++G + + + TG RGF F+ F
Sbjct: 18 DYFSKFGEVVDCTLKLDPITGRSRGFGFVLF 48
>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 = 77.4 bits (189), Expect = 1e-14, Method: Composition-based stats.
Identities = 33/79 (41%), Positives = 52/79 (65%)
Query: 41 ESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDE 100
E K F+GGL + T+ LK +F ++GE+VD + DP T RSRGFGFI + ++ V++
Sbjct: 9 EDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEK 68
Query: 101 AMSNRPHEIDGRVVETKRA 119
+ + H +DGRV++ K+A
Sbjct: 69 VLDQKEHRLDGRVIDPKKA 87
Score = 29.6 bits (65), Expect = 2.1, Method: Composition-based stats.
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
DYF ++G + + + TG RGF FI F
Sbjct: 30 DYFTKFGEVVDCTIKXDPNTGRSRGFGFILF 60
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 72.4 bits (176), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 32/81 (39%), Positives = 56/81 (69%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
K+F+GG+ + + L+ +F+++G + +VV++ D +R RGFGFIT+ + + VD+A++
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
Query: 105 RPHEIDGRVVETKRAVPREVK 125
H+I G+ VE KRA PR+ K
Sbjct: 72 HFHDIMGKKVEVKRAEPRDSK 92
Score = 29.6 bits (65), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 19/34 (55%)
Query: 137 EQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
E +YF ++G + V M+ + E RGF FI F
Sbjct: 26 ELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITF 59
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 67.8 bits (164), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 29/74 (39%), Positives = 48/74 (64%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
+F+GGL T + +K +FEQ+G++ D ++M D T R RGFGF+T+ +V++
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 106 PHEIDGRVVETKRA 119
HEI+ ++VE K+A
Sbjct: 62 FHEINNKMVECKKA 75
Score = 29.6 bits (65), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 141 YFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
YF Q+G ++ ++ +K T RGF F+ F
Sbjct: 19 YFEQFGKVDDAMLMFDKTTNRHRGFGFVTF 48
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 67.0 bits (162), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 33/76 (43%), Positives = 49/76 (64%), Gaps = 1/76 (1%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSE-SKMVDEAMS 103
KLF+GGL + TN+ SL+ F ++G+I +VVV+KD T+RSRGFGF+T+ D M+
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 104 NRPHEIDGRVVETKRA 119
+DGR + +A
Sbjct: 74 MNGKSVDGRQIRVDQA 89
Score = 32.0 bits (71), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 23/36 (63%), Gaps = 2/36 (5%)
Query: 135 ALEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
+LEQ+ F +YG I V +V ++ET RGF F+ F
Sbjct: 28 SLEQV--FSKYGQISEVVVVKDRETQRSRGFGFVTF 61
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 63.5 bits (153), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 29/71 (40%), Positives = 45/71 (63%)
Query: 42 SLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEA 101
+ K+F+GGL Y T D SL+ +FE +G+I + VV+ D T +SRG+GF+T ++ + A
Sbjct: 16 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA 75
Query: 102 MSNRPHEIDGR 112
+ IDGR
Sbjct: 76 CKDPNPIIDGR 86
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 11/28 (39%), Positives = 19/28 (67%)
Query: 141 YFGQYGTIESVNMVTNKETGAKRGFAFI 168
YF +G IE ++T+++TG RG+ F+
Sbjct: 37 YFEGFGDIEEAVVITDRQTGKSRGYGFV 64
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 57.8 bits (138), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 40/144 (27%), Positives = 67/144 (46%), Gaps = 20/144 (13%)
Query: 41 ESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDE 100
+S L + L D K+ F G+I +++D +T +S G+GF+ YS+ D+
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 101 AMSNRPHEIDGRVVETKR-----AVPREVKVRRV---------TKVQIALEQMDYFGQYG 146
A+ + ++G ++TK A P +R T Q +EQ+ F QYG
Sbjct: 62 AI----NTLNGLKLQTKTIKVSYARPSSASIRDANLYVSGLPKTMSQKEMEQL--FSQYG 115
Query: 147 TIESVNMVTNKETGAKRGFAFIEF 170
I + ++ ++ TG RG FI F
Sbjct: 116 RIITSRILLDQATGVSRGVGFIRF 139
Score = 36.6 bits (83), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 30/57 (52%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM 102
L++ GL + ++ F Q+G I+ ++ D T SRG GFI + + +EA+
Sbjct: 93 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 149
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 56.6 bits (135), Expect = 2e-08, Method: Composition-based stats.
Identities = 28/78 (35%), Positives = 46/78 (58%), Gaps = 1/78 (1%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN- 104
L++G L + +D L+ FE +G+I ++V+MKD T RS+G+GFIT+S+S+ A+
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 105 RPHEIDGRVVETKRAVPR 122
E+ GR + R
Sbjct: 68 NGFELAGRPMRVGHVTER 85
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 55.1 bits (131), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 29/72 (40%), Positives = 44/72 (61%), Gaps = 1/72 (1%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
L + GL ++T + LK +F +GE++ V V KD T S+GFGF+ ++E + + MS R
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 77
Query: 106 PHEIDGRVVETK 117
H IDGR + K
Sbjct: 78 -HMIDGRWCDCK 88
>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 = 54.7 bits (130), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 46/77 (59%), Gaps = 4/77 (5%)
Query: 41 ESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDE 100
E + L + L YRT+ D+L+ FE++G + DV + +D TK SRGF F+ + + + ++
Sbjct: 45 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 104
Query: 101 AMSNRPHEIDGRVVETK 117
AM +DG V++ +
Sbjct: 105 AMD----AMDGAVLDGR 117
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 54.3 bits (129), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 45/79 (56%), Gaps = 1/79 (1%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
+L++G L + +D L+ FE +G I + +M D T RS+G+GFIT+S+S+ +A+
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 105 -RPHEIDGRVVETKRAVPR 122
E+ GR ++ R
Sbjct: 88 LNGFELAGRPMKVGHVTER 106
Score = 31.2 bits (69), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 19/29 (65%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEF 170
F +G IES+ ++ + ETG +G+ FI F
Sbjct: 47 FEPFGRIESIQLMMDSETGRSKGYGFITF 75
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 53.5 bits (127), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 45/75 (60%), Gaps = 4/75 (5%)
Query: 41 ESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDE 100
E + L + L YRT+ D+L+ FE++G + DV + +D TK SRGF F+ + + + ++
Sbjct: 68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 127
Query: 101 AMSNRPHEIDGRVVE 115
AM +DG V++
Sbjct: 128 AMD----AMDGAVLD 138
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/48 (54%), Positives = 35/48 (72%), Gaps = 1/48 (2%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY 92
KLFIGGL+ TN+ LKA F + G I +V+++KD T +SRGF FIT+
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITF 55
Score = 28.9 bits (63), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 19/29 (65%), Gaps = 1/29 (3%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEF 170
FG++G I V ++ ++ T RGFAFI F
Sbjct: 28 FGKHGPISEVLLIKDR-TSKSRGFAFITF 55
>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 = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 35/135 (25%), Positives = 62/135 (45%), Gaps = 12/135 (8%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN- 104
L + L + ++ F GEI +++D +T +S G+GF+ Y + K ++A++
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 105 RPHEIDGRVVETKRAVPREVKVRRV---------TKVQIALEQMDYFGQYGTIESVNMVT 155
+ + ++ A P +R T Q LEQ+ F QYG I + ++
Sbjct: 65 NGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQL--FSQYGRIITSRILV 122
Query: 156 NKETGAKRGFAFIEF 170
++ TG RG FI F
Sbjct: 123 DQVTGVSRGVGFIRF 137
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 30/57 (52%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM 102
L++ GL L+ F Q+G I+ ++ D VT SRG GFI + + +EA+
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 147
>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 = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 36/64 (56%)
Query: 40 PESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVD 99
P+S KLFIGGL NDD +K +G + ++KD T S+G+ F Y + + D
Sbjct: 111 PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTD 170
Query: 100 EAMS 103
+A++
Sbjct: 171 QAIA 174
Score = 28.9 bits (63), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 9/26 (34%), Positives = 18/26 (69%)
Query: 145 YGTIESVNMVTNKETGAKRGFAFIEF 170
+G +++ N+V + TG +G+AF E+
Sbjct: 138 FGPLKAFNLVKDSATGLSKGYAFCEY 163
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 25/68 (36%), Positives = 41/68 (60%), Gaps = 1/68 (1%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEA-MSN 104
L + L YRT+ DSL+ FE++G + DV + ++P TK RGF F+ + + + +A +
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75
Query: 105 RPHEIDGR 112
E+DGR
Sbjct: 76 DGAELDGR 83
>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 = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 41/71 (57%)
Query: 34 DSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYS 93
D E + ++++ + +DD +K+ FE +G+I + +DP T + +G+GFI Y
Sbjct: 116 DQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYE 175
Query: 94 ESKMVDEAMSN 104
+++ +A+S+
Sbjct: 176 KAQSSQDAVSS 186
Score = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 31/149 (20%), Positives = 64/149 (42%), Gaps = 23/149 (15%)
Query: 43 LRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM 102
+ ++++G + Y +D+++ F +G I + + D VT + +GF F+ Y + A+
Sbjct: 28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLAL 87
Query: 103 SNRPH-EIDGRVVETKRAVPREV------------KVRRVTKVQIALEQMDY-------- 141
+ GR ++ R P + + R ++ +A D
Sbjct: 88 EQMNSVMLGGRNIKVGR--PSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSV 145
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEF 170
F +G I+S + + TG +G+ FIE+
Sbjct: 146 FEAFGKIKSATLARDPTTGKHKGYGFIEY 174
>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 = 2e-06, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 41/71 (57%)
Query: 34 DSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYS 93
D E + ++++ + +DD +K+ FE +G+I + +DP T + +G+GFI Y
Sbjct: 101 DQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYE 160
Query: 94 ESKMVDEAMSN 104
+++ +A+S+
Sbjct: 161 KAQSSQDAVSS 171
Score = 44.7 bits (104), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 34/146 (23%), Positives = 66/146 (45%), Gaps = 21/146 (14%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY---SESKMVDEA 101
++++G + Y +D+++ F +G I + + D VT + +GF F+ Y +++ E
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 102 MSN-----------RPHEID------GRVVETKRAVPREVKVRRVTKVQIALEQMDYFGQ 144
M++ RP I ++ E RA R + V V + + F
Sbjct: 75 MNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNR-IYVASVHQDLSDDDIKSVFEA 133
Query: 145 YGTIESVNMVTNKETGAKRGFAFIEF 170
+G I+S + + TG +G+ FIE+
Sbjct: 134 FGKIKSCTLARDPTTGKHKGYGFIEY 159
>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 = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 44/78 (56%)
Query: 43 LRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM 102
++K+F+GGL T ++ ++ +F +GE+ + + D T + RGF FIT+ E + V + M
Sbjct: 1 VKKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 60
Query: 103 SNRPHEIDGRVVETKRAV 120
+ H + E K A+
Sbjct: 61 EKKYHNVGLSKCEIKVAM 78
Score = 36.2 bits (82), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 21/31 (67%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
+YFG +G +ES+ + + +T +RGF FI F
Sbjct: 20 EYFGGFGEVESIELPMDNKTNKRRGFCFITF 50
>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 = 2e-06, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 41/71 (57%)
Query: 34 DSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYS 93
D E + ++++ + +DD +K+ FE +G+I + +DP T + +G+GFI Y
Sbjct: 100 DQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYE 159
Query: 94 ESKMVDEAMSN 104
+++ +A+S+
Sbjct: 160 KAQSSQDAVSS 170
Score = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 31/147 (21%), Positives = 62/147 (42%), Gaps = 23/147 (15%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
++++G + Y +D+++ F +G I + D VT + +GF F+ Y + A+
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 105 RPH-EIDGRVVETKRAVPREV------------KVRRVTKVQIALEQMDY--------FG 143
+ GR ++ R P + + R ++ +A D F
Sbjct: 74 XNSVXLGGRNIKVGR--PSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFE 131
Query: 144 QYGTIESVNMVTNKETGAKRGFAFIEF 170
+G I+S + + TG +G+ FIE+
Sbjct: 132 AFGKIKSCTLARDPTTGKHKGYGFIEY 158
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 47.8 bits (112), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 46/82 (56%), Gaps = 2/82 (2%)
Query: 43 LRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM 102
+R +++G L Y + +K F Q+G++ +V ++ D TK+ +GFGF+ E V EA+
Sbjct: 1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAI 59
Query: 103 SNRPH-EIDGRVVETKRAVPRE 123
+ + + GR + A P++
Sbjct: 60 AKLDNTDFMGRTIRVTEANPKK 81
Score = 29.6 bits (65), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 10/30 (33%), Positives = 20/30 (66%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIE 169
+ F Q+G + +V ++ ++ET +GF F+E
Sbjct: 20 ELFSQFGKVFNVKLIYDRETKKPKGFGFVE 49
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 31/133 (23%), Positives = 58/133 (43%), Gaps = 8/133 (6%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN- 104
L + L D L++ F GE+ +++D V S G+GF+ Y +K + A++
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 105 RPHEIDGRVVETKRAVPREVKVRRVTKVQIALEQM-------DYFGQYGTIESVNMVTNK 157
+ + ++ A P ++ L + D F ++G I + ++ ++
Sbjct: 65 NGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQ 124
Query: 158 ETGAKRGFAFIEF 170
TG RG AFI F
Sbjct: 125 TTGLSRGVAFIRF 137
Score = 35.0 bits (79), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 31/59 (52%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
L+I GL ++ F ++G I++ V+ D T SRG FI + + +EA+++
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITS 149
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 1/80 (1%)
Query: 42 SLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEA 101
SLR +F+G + Y ++ LK F + G +V ++ D T + +G+GF Y + + A
Sbjct: 7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSA 66
Query: 102 MSN-RPHEIDGRVVETKRAV 120
M N E GR + A
Sbjct: 67 MRNLNGREFSGRALRVDNAA 86
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 22/35 (62%), Gaps = 1/35 (2%)
Query: 137 EQM-DYFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
EQ+ D F + G + S +V ++ETG +G+ F E+
Sbjct: 23 EQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEY 57
>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 = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 31/133 (23%), Positives = 58/133 (43%), Gaps = 8/133 (6%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN- 104
L + L D L++ F GE+ +++D V S G+GF+ Y +K + A++
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 105 RPHEIDGRVVETKRAVPREVKVRRVTKVQIALEQM-------DYFGQYGTIESVNMVTNK 157
+ + ++ A P ++ L + D F ++G I + ++ ++
Sbjct: 65 NGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQ 124
Query: 158 ETGAKRGFAFIEF 170
TG RG AFI F
Sbjct: 125 TTGLSRGVAFIRF 137
Score = 35.0 bits (79), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 31/59 (52%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
L+I GL ++ F ++G I++ V+ D T SRG FI + + +EA+++
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITS 149
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 40/74 (54%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
+F+GGL T ++ ++ +F +GE+ + + D T + RGF FIT+ E + V + M +
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Query: 106 PHEIDGRVVETKRA 119
H + E K A
Sbjct: 62 YHNVGLSKCEIKVA 75
Score = 35.8 bits (81), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 21/31 (67%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
+YFG +G +ES+ + + +T +RGF FI F
Sbjct: 18 EYFGGFGEVESIELPMDNKTNKRRGFCFITF 48
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 35/59 (59%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
KLFIG + ++ LK FE++G+I ++ V+KD T +G F+TY E + +A S
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQS 73
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 43/83 (51%), Gaps = 1/83 (1%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
R L++GGL +D L A F +G+I D+ + D T++ RGF F+ + ++ A+
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
Query: 104 N-RPHEIDGRVVETKRAVPREVK 125
N E+ GR + A P +K
Sbjct: 73 NMNESELFGRTIRVNLAKPMRIK 95
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 27/94 (28%), Positives = 49/94 (52%), Gaps = 2/94 (2%)
Query: 28 INKAMEDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGF 87
IN A + Q S ++ LF+G L+ +D++L+ F+ + + VM D T SRG+
Sbjct: 73 INWAFQSQQSSSDDTFN-LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGY 131
Query: 88 GFITYSESKMVDEAM-SNRPHEIDGRVVETKRAV 120
GF++++ AM S + +++GR + A
Sbjct: 132 GFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAA 165
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 31/137 (22%), Positives = 64/137 (46%), Gaps = 11/137 (8%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
R L++G LD +D LK +F+ G I ++ +M D ++ + F+ Y +S + A+
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQ 59
Query: 104 N-RPHEIDGRVVETKRAVPREVKVRRVT--------KVQIALEQM-DYFGQYGTIESVNM 153
+I+ +V+ A + T V + E + + F + + S ++
Sbjct: 60 TLNGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHV 119
Query: 154 VTNKETGAKRGFAFIEF 170
+ + +TG+ RG+ F+ F
Sbjct: 120 MWDMQTGSSRGYGFVSF 136
>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 = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 33/59 (55%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
KLFIGGL NDD +K +G + ++KD T S+G+ F Y + + D+A++
Sbjct: 98 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 156
Score = 31.2 bits (69), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 28/151 (18%), Positives = 60/151 (39%), Gaps = 32/151 (21%)
Query: 42 SLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVV-VMKDPV----TKRSRGFGFITYSESK 96
S R+L++G + + ++++ FF + + +PV + + F F+ +
Sbjct: 5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 64
Query: 97 MVDEAMSNRPHEIDGRVVETKRAVPREVKVRRVTKVQIALEQMDYF-------------- 142
+AM+ DG + + + +K+RR Q F
Sbjct: 65 ETTQAMA-----FDGIIFQGQ-----SLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVK 114
Query: 143 ---GQYGTIESVNMVTNKETGAKRGFAFIEF 170
+G +++ N+V + TG +G+AF E+
Sbjct: 115 ELLTSFGPLKAFNLVKDSATGLSKGYAFCEY 145
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 33/59 (55%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
KLFIGGL NDD +K +G + ++KD T S+G+ F Y + + D+A++
Sbjct: 96 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 154
Score = 30.8 bits (68), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 28/151 (18%), Positives = 60/151 (39%), Gaps = 32/151 (21%)
Query: 42 SLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVV-VMKDPV----TKRSRGFGFITYSESK 96
S R+L++G + + ++++ FF + + +PV + + F F+ +
Sbjct: 3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62
Query: 97 MVDEAMSNRPHEIDGRVVETKRAVPREVKVRRVTKVQIALEQMDYF-------------- 142
+AM+ DG + + + +K+RR Q F
Sbjct: 63 ETTQAMA-----FDGIIFQGQ-----SLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVK 112
Query: 143 ---GQYGTIESVNMVTNKETGAKRGFAFIEF 170
+G +++ N+V + TG +G+AF E+
Sbjct: 113 ELLTSFGPLKAFNLVKDSATGLSKGYAFCEY 143
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 44.7 bits (104), Expect = 6e-05, Method: Composition-based stats.
Identities = 21/59 (35%), Positives = 33/59 (55%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
KLFIGGL NDD +K +G + ++KD T S+G+ F Y + + D+A++
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 61
Score = 28.5 bits (62), Expect = 5.5, Method: Composition-based stats.
Identities = 9/26 (34%), Positives = 18/26 (69%)
Query: 145 YGTIESVNMVTNKETGAKRGFAFIEF 170
+G +++ N+V + TG +G+AF E+
Sbjct: 25 FGPLKAFNLVKDSATGLSKGYAFCEY 50
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 44.7 bits (104), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 37/66 (56%)
Query: 38 SEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
EP+ LR L + + ++ L+ FE++G I V ++ D T++SRG+GF+ +
Sbjct: 37 PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSS 96
Query: 98 VDEAMS 103
+A++
Sbjct: 97 AQQAIA 102
Score = 36.2 bits (82), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 26/38 (68%), Gaps = 2/38 (5%)
Query: 133 QIALEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
++ L Q+ F +YG IESV +V ++ET RG+ F++F
Sbjct: 56 EVQLRQL--FERYGPIESVKIVCDRETRQSRGYGFVKF 91
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 44.7 bits (104), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 37/134 (27%), Positives = 65/134 (48%), Gaps = 21/134 (15%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
+LF+G L ++ K FE++GE +V + +D RGFGFI + + A +
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKA- 76
Query: 105 RPHEIDGRVVETKRAVPR------EVKVRRVTKV--QIALEQMDYFGQYGTIESVNMVTN 156
E+DG +++++ R + V+ ++ V LEQ F Q+G +E +V +
Sbjct: 77 ---ELDGTILKSRPLRIRFATHGAALTVKNLSPVVSNELLEQA--FSQFGPVEKAVVVVD 131
Query: 157 KETGAKRGFAFIEF 170
+ G G F+EF
Sbjct: 132 -DRGRATGKGFVEF 144
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 44.7 bits (104), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 28/90 (31%), Positives = 44/90 (48%), Gaps = 14/90 (15%)
Query: 29 NKAMEDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFG 88
N+A D C L + GL T + L+ F ++G I DV ++ D ++RSRGF
Sbjct: 39 NRANPDPNCC-------LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 91
Query: 89 FITYSESKMVDEAMSNRPH----EIDGRVV 114
F+ + VD+A + E+DGR +
Sbjct: 92 FVYFEN---VDDAKEAKERANGMELDGRRI 118
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 20/29 (68%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEF 170
F +YG I V++V ++++ RGFAF+ F
Sbjct: 67 FSKYGPIADVSIVYDQQSRRSRGFAFVYF 95
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 44.7 bits (104), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 34/55 (61%), Gaps = 1/55 (1%)
Query: 39 EPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYS 93
+P S RKLF+G L+ + ++D ++ FE +G I + +++ P S+G F+ YS
Sbjct: 11 QPPSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGP-DGNSKGCAFVKYS 64
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 44.7 bits (104), Expect = 7e-05, Method: Composition-based stats.
Identities = 28/98 (28%), Positives = 47/98 (47%), Gaps = 14/98 (14%)
Query: 29 NKAMEDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFG 88
N+A D C L + GL T + L+ F ++G I DV ++ D ++RSRGF
Sbjct: 8 NRANPDPNCC-------LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 60
Query: 89 FITYSESKMVDEAMSNRPH----EIDGRVVETKRAVPR 122
F+ + VD+A + E+DGR + ++ +
Sbjct: 61 FVYFEN---VDDAKEAKERANGMELDGRRIRVDFSITK 95
Score = 30.8 bits (68), Expect = 0.87, Method: Composition-based stats.
Identities = 12/31 (38%), Positives = 21/31 (67%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
+ F +YG I V++V ++++ RGFAF+ F
Sbjct: 34 EVFSKYGPIADVSIVYDQQSRRSRGFAFVYF 64
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 44.3 bits (103), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 28/93 (30%), Positives = 49/93 (52%), Gaps = 8/93 (8%)
Query: 32 MEDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFIT 91
M S+P ++L + + +R D L+ F Q+G+I+DV ++ + + S+GFGF+T
Sbjct: 21 MNTENKSQP---KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVT 75
Query: 92 YSESKMVDEAMSNRPHE--IDGRVVETKRAVPR 122
+ S D A + H ++GR +E A R
Sbjct: 76 FENSADADRARE-KLHGTVVEGRKIEVNNATAR 107
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 44.3 bits (103), Expect = 9e-05, Method: Composition-based stats.
Identities = 28/90 (31%), Positives = 44/90 (48%), Gaps = 14/90 (15%)
Query: 29 NKAMEDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFG 88
N+A D C L + GL T + L+ F ++G I DV ++ D ++RSRGF
Sbjct: 8 NRANPDPNCC-------LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 60
Query: 89 FITYSESKMVDEAMSNRPH----EIDGRVV 114
F+ + VD+A + E+DGR +
Sbjct: 61 FVYFEN---VDDAKEAKERANGMELDGRRI 87
Score = 30.8 bits (68), Expect = 0.87, Method: Composition-based stats.
Identities = 12/31 (38%), Positives = 21/31 (67%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
+ F +YG I V++V ++++ RGFAF+ F
Sbjct: 34 EVFSKYGPIADVSIVYDQQSRRSRGFAFVYF 64
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 46/93 (49%), Gaps = 10/93 (10%)
Query: 10 KLVPGLEVAGTVVPLAMIINKAMEDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGE 69
K++PG+ + P N A+ED RKLFIG + + ++ ++ F +G+
Sbjct: 71 KVLPGMHHPIQMKPADSEKNNAVED---------RKLFIGMISKKCTENDIRVMFSSFGQ 121
Query: 70 IVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM 102
I + +++ P SRG F+T++ M A+
Sbjct: 122 IEECRILRGP-DGLSRGCAFVTFTTRAMAQTAI 153
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 33/140 (23%), Positives = 64/140 (45%), Gaps = 15/140 (10%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPV--TKRSRGFGFITYSESKMVDEAM 102
K+F+G + ++ L+ FEQ+G + ++ V++D +S+G F+T+ K EA
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 103 S-----------NRPHEIDGRVVETKRAVP-REVKVRRVTKVQIALEQMDYFGQYGTIES 150
+ + P ++ E AV R++ + ++K + F +G IE
Sbjct: 65 NALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEE 124
Query: 151 VNMVTNKETGAKRGFAFIEF 170
++ + G RG AF+ F
Sbjct: 125 CRILRGPD-GLSRGCAFVTF 143
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 46/93 (49%), Gaps = 10/93 (10%)
Query: 10 KLVPGLEVAGTVVPLAMIINKAMEDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGE 69
K++PG+ + P N A+ED RKLFIG + + ++ ++ F +G+
Sbjct: 83 KVLPGMHHPIQMKPADSEKNNAVED---------RKLFIGMISKKCTENDIRVMFSSFGQ 133
Query: 70 IVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM 102
I + +++ P SRG F+T++ M A+
Sbjct: 134 IEECRILRGP-DGLSRGCAFVTFTTRAMAQTAI 165
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 33/140 (23%), Positives = 64/140 (45%), Gaps = 15/140 (10%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPV--TKRSRGFGFITYSESKMVDEAM 102
K+F+G + ++ L+ FEQ+G + ++ V++D +S+G F+T+ K EA
Sbjct: 17 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 76
Query: 103 S-----------NRPHEIDGRVVETKRAVP-REVKVRRVTKVQIALEQMDYFGQYGTIES 150
+ + P ++ E AV R++ + ++K + F +G IE
Sbjct: 77 NALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEE 136
Query: 151 VNMVTNKETGAKRGFAFIEF 170
++ + G RG AF+ F
Sbjct: 137 CRILRGPD-GLSRGCAFVTF 155
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 43.1 bits (100), Expect = 2e-04, Method: Composition-based stats.
Identities = 24/81 (29%), Positives = 42/81 (51%), Gaps = 7/81 (8%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
L + GL T + L+ F ++G I DV ++ D ++RSRGF F+ + VD+A +
Sbjct: 15 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN---VDDAKEAK 71
Query: 106 PH----EIDGRVVETKRAVPR 122
E+DGR + ++ +
Sbjct: 72 ERANGMELDGRRIRVDFSITK 92
Score = 31.2 bits (69), Expect = 0.76, Method: Composition-based stats.
Identities = 12/31 (38%), Positives = 21/31 (67%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
+ F +YG I V++V ++++ RGFAF+ F
Sbjct: 31 EVFSKYGPIADVSIVYDQQSRRSRGFAFVYF 61
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 45/81 (55%), Gaps = 5/81 (6%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
++L + + +R D L+ F Q+G+I+DV ++ + + S+GFGF+T+ S D A
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSADADRARE 73
Query: 104 NRPHE--IDGRVVETKRAVPR 122
+ H ++GR +E A R
Sbjct: 74 -KLHGTVVEGRKIEVNNATAR 93
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 1/77 (1%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
R L++GGL +D L A F +G+I D+ + D T++ RGF F+ + ++ A+
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
Query: 104 N-RPHEIDGRVVETKRA 119
N E+ GR + A
Sbjct: 124 NMNESELFGRTIRVNLA 140
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 1/77 (1%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
R L++GGL +D L A F +G+I D+ + D T++ RGF F+ + ++ A+
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
Query: 104 N-RPHEIDGRVVETKRA 119
N E+ GR + A
Sbjct: 68 NMNESELFGRTIRVNLA 84
>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 = 42.7 bits (99), Expect = 2e-04, Method: Composition-based stats.
Identities = 25/79 (31%), Positives = 41/79 (51%), Gaps = 1/79 (1%)
Query: 42 SLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEA 101
S R L++GGL +D L A F +G+I D+ + D T++ RGF F+ + ++ A
Sbjct: 1 SKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 60
Query: 102 MSN-RPHEIDGRVVETKRA 119
+ N E+ GR + A
Sbjct: 61 IDNMNESELFGRTIRVNLA 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 = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 33/59 (55%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
KLF+G + ++ LK FE++G I ++ V+KD +T +G F+TY +A S
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQS 75
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 39/137 (28%), Positives = 61/137 (44%), Gaps = 16/137 (11%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
L + L D L A F G I +M+D T S G+ F+ ++ A+
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI--- 62
Query: 106 PHEIDGRVVETKR-----AVPREVKVR----RVTKVQ--IALEQMD-YFGQYGTIESVNM 153
++G V KR A P ++ VT + I +Q+D FG+YG+I N+
Sbjct: 63 -KVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNI 121
Query: 154 VTNKETGAKRGFAFIEF 170
+ +K TG RG AF+ +
Sbjct: 122 LRDKLTGRPRGVAFVRY 138
>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 = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 37/72 (51%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
R +++G +DY + L+A F G I + ++ D + +G+ +I ++E VD A++
Sbjct: 37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVA 96
Query: 104 NRPHEIDGRVVE 115
GR ++
Sbjct: 97 MDETVFRGRTIK 108
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 26/49 (53%)
Query: 122 REVKVRRVTKVQIALEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
R V V V A + +F G+I + ++ +K +G +G+A+IEF
Sbjct: 37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEF 85
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 41/72 (56%), Gaps = 6/72 (8%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
L++ LD +D+ L+ F +G I VM + RS+GFGF+ +S + +A++
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVT-- 73
Query: 106 PHEIDGRVVETK 117
E++GR+V TK
Sbjct: 74 --EMNGRIVATK 83
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 42.0 bits (97), Expect = 5e-04, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 1/77 (1%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
R L++GGL +D L A F +G+I D+ + D T++ RGF F+ + ++ A+
Sbjct: 6 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65
Query: 104 N-RPHEIDGRVVETKRA 119
N E+ GR + A
Sbjct: 66 NMNESELFGRTIRVNLA 82
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 41.6 bits (96), Expect = 5e-04, Method: Composition-based stats.
Identities = 21/82 (25%), Positives = 46/82 (56%), Gaps = 5/82 (6%)
Query: 42 SLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY---SESKMV 98
S +++ L + ++ L F ++G++V V +MKD T++S+G FI + ++
Sbjct: 15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNC 74
Query: 99 DEAMSNRPHEIDGRVVETKRAV 120
A++N+ ++ GRV++ A+
Sbjct: 75 TRAINNK--QLFGRVIKASIAI 94
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 41.6 bits (96), Expect = 5e-04, Method: Composition-based stats.
Identities = 22/83 (26%), Positives = 44/83 (53%), Gaps = 6/83 (7%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
+LF+ L Y ++++ L+ F +G + ++ D +TK+ +GF F+T+ M E
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTF----MFPEHAVK 65
Query: 105 RPHEIDGRVVETK--RAVPREVK 125
E+DG+V + + +P +K
Sbjct: 66 AYAEVDGQVFQGRMLHVLPSTIK 88
>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 = 40.8 bits (94), Expect = 9e-04, Method: Composition-based stats.
Identities = 23/79 (29%), Positives = 42/79 (53%), Gaps = 1/79 (1%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM-SN 104
LF+G L+ +D++L+ F+ + + VM D T SRG+GF++++ AM S
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 105 RPHEIDGRVVETKRAVPRE 123
+ +++GR + A E
Sbjct: 64 QGQDLNGRPLRINWAAKLE 82
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 41/82 (50%), Gaps = 6/82 (7%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
K+F+G + L+ FF Q+GE+VDV + K R F F+T+++ K V +++
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYGEVVDVF-----IPKPFRAFAFVTFADDK-VAQSLCG 66
Query: 105 RPHEIDGRVVETKRAVPREVKV 126
I G V A P+ K+
Sbjct: 67 EDLIIKGISVHISNAEPKHNKL 88
>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|B Chain B, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|C Chain C, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
Length = 184
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 41/151 (27%), Positives = 64/151 (42%), Gaps = 20/151 (13%)
Query: 32 MEDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFIT 91
M D + S L + L D L A F G I + +D T S G+ F+
Sbjct: 7 MNDPRASNTN----LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVD 62
Query: 92 YSESKMVDEAMSNRPHEIDGRVVETKR-----AVPREVKVRR----VTKVQ--IALEQMD 140
++ A+ ++G V KR A P ++ VT + I +Q+D
Sbjct: 63 FTSEXDSQRAI----KVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLD 118
Query: 141 -YFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
FG+YG+I N++ +K TG RG AF+ +
Sbjct: 119 TIFGKYGSIVQKNILRDKLTGRPRGVAFVRY 149
>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 = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 36/151 (23%), Positives = 68/151 (45%), Gaps = 16/151 (10%)
Query: 31 AMEDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFI 90
+M S S P + L++G L + L F G I+ + V +D +T+RS G+ ++
Sbjct: 5 SMNPSAPSYP--MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYV 62
Query: 91 TYSESKMVDEAMSNRPHE-IDGRVVETKRAVPREVKVRRVTKVQIALEQM---------- 139
+ + + A+ + I G+ V + R+ +R+ I ++ +
Sbjct: 63 NFQQPADAERALDTMNFDVIKGKPVRIMWSQ-RDPSLRKSGVGNIFIKNLDKSIDNKALY 121
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
D F +G I S +V + E G+K G+ F+ F
Sbjct: 122 DTFSAFGNILSCKVVCD-ENGSK-GYGFVHF 150
>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 = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 34/47 (72%), Gaps = 1/47 (2%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY 92
+F+GG+D R ++ +++FF ++G + +V ++ D T S+G+GF+++
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSF 57
>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 = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 34/47 (72%), Gaps = 1/47 (2%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY 92
+F+GG+D R ++ +++FF ++G + +V ++ D T S+G+GF+++
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 57
>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 = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/93 (25%), Positives = 43/93 (46%), Gaps = 10/93 (10%)
Query: 10 KLVPGLEVAGTVVPLAMIINKAMEDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGE 69
K++PG P N A+ED RKLFIG + + ++ ++ F +G+
Sbjct: 71 KVLPGXHHPIQXKPADSEKNNAVED---------RKLFIGXISKKCTENDIRVXFSSFGQ 121
Query: 70 IVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM 102
I + +++ P SRG F+T++ A+
Sbjct: 122 IEECRILRGP-DGLSRGCAFVTFTTRAXAQTAI 153
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 31/140 (22%), Positives = 61/140 (43%), Gaps = 15/140 (10%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPV--TKRSRGFGFITYSESKMVDEA- 101
K F+G + ++ L+ FEQ+G + ++ V++D +S+G F+T+ K EA
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 102 --------MSNRPHEIDGRVVETKRAVPREVKVRRVTKVQIALEQMD---YFGQYGTIES 150
+ H I + ++++ E + + + + D F +G IE
Sbjct: 65 NALHNXKVLPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQIEE 124
Query: 151 VNMVTNKETGAKRGFAFIEF 170
++ + G RG AF+ F
Sbjct: 125 CRILRGPD-GLSRGCAFVTF 143
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 34/47 (72%), Gaps = 1/47 (2%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY 92
+F+GG+D R ++ +++FF ++G + +V ++ D T S+G+GF+++
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 58
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 21/88 (23%), Positives = 42/88 (47%), Gaps = 1/88 (1%)
Query: 41 ESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDE 100
+S L + L D K+ F G+I +++D +T +S G+GF+ YS+ D+
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 101 AMSN-RPHEIDGRVVETKRAVPREVKVR 127
A++ ++ + ++ A P +R
Sbjct: 62 AINTLNGLKLQTKTIKVSYARPSSASIR 89
Score = 29.6 bits (65), Expect = 2.3, Method: Composition-based stats.
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEF 170
FG G IES +V +K TG G+ F+ +
Sbjct: 25 FGSIGDIESCKLVRDKITGQSLGYGFVNY 53
>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 = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 29/47 (61%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY 92
+F+G L + +KA F +G I D V+KD T +S+G+GF+++
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSF 64
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 34/57 (59%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM 102
+++GGLD + ++ L F Q G +V+ + KD VT + +G+GF+ + + D A+
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 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 = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 36/150 (24%), Positives = 67/150 (44%), Gaps = 16/150 (10%)
Query: 32 MEDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFIT 91
M S S P + L++G L + L F G I+ + V +D +T+RS G+ ++
Sbjct: 1 MNPSAPSYP--MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVN 58
Query: 92 YSESKMVDEAMSNRPHE-IDGRVVETKRAVPREVKVRRVTKVQIALEQM----------D 140
+ + + A+ + I G+ V + R+ +R+ I ++ + D
Sbjct: 59 FQQPADAERALDTMNFDVIKGKPVRIMWSQ-RDPSLRKSGVGNIFIKNLDKSIDNKALYD 117
Query: 141 YFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
F +G I S +V + E G+K G+ F+ F
Sbjct: 118 TFSAFGNILSCKVVCD-ENGSK-GYGFVHF 145
>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 = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 33/60 (55%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
R +++G +DY + L+A F G + V ++ D + +GF +I +S+ + V +++
Sbjct: 6 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 65
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 27/52 (51%)
Query: 119 AVPREVKVRRVTKVQIALEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
A R + V V A E +F G++ V ++ +K +G +GFA+IEF
Sbjct: 3 ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEF 54
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 30/47 (63%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY 92
+F+G L + +K+ F +G+I D V+KD T +S+G+GF+++
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSF 64
>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 = 38.1 bits (87), Expect = 0.006, Method: Composition-based stats.
Identities = 18/79 (22%), Positives = 40/79 (50%), Gaps = 3/79 (3%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
R +++G +DY + L+A F G + V ++ D + +GF +I +S+ + V +++
Sbjct: 7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 66
Query: 104 NRPHEIDGRVVETKRAVPR 122
GR + + +P+
Sbjct: 67 LDESLFRGRQI---KVIPK 82
Score = 29.3 bits (64), Expect = 2.6, Method: Composition-based stats.
Identities = 16/49 (32%), Positives = 26/49 (53%)
Query: 122 REVKVRRVTKVQIALEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
R + V V A E +F G++ V ++ +K +G +GFA+IEF
Sbjct: 7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEF 55
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 27/82 (32%), Positives = 43/82 (52%), Gaps = 8/82 (9%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYS---ESKMVDE 100
+ LF+ GL T +++LK F+ V ++ D T S+GFGF+ ++ ++K E
Sbjct: 16 KTLFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKE 72
Query: 101 AMSNRPHEIDGRVVETKRAVPR 122
AM + EIDG V A P+
Sbjct: 73 AMED--GEIDGNKVTLDWAKPK 92
Score = 28.5 bits (62), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 9/18 (50%), Positives = 16/18 (88%)
Query: 153 MVTNKETGAKRGFAFIEF 170
+VT++ETG+ +GF F++F
Sbjct: 44 IVTDRETGSSKGFGFVDF 61
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 37.7 bits (86), Expect = 0.008, Method: Composition-based stats.
Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 4/76 (5%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTK---RSRGFGFITYSESKMVDEAM 102
LFI L++ T +++LK F + G I + K S GFGF+ Y + + +A+
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 103 SN-RPHEIDGRVVETK 117
+ H +DG +E +
Sbjct: 68 KQLQGHTVDGHKLEVR 83
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 37.0 bits (84), Expect = 0.013, Method: Composition-based stats.
Identities = 24/70 (34%), Positives = 36/70 (51%), Gaps = 9/70 (12%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDV-VVMKDPVTKRSRGFGFITYSESKMVD---EA 101
+FIG LD ++ L F +G I+ +M+DP T S+G+ FI ++ D EA
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 102 MS-----NRP 106
M+ NRP
Sbjct: 68 MNGQYLCNRP 77
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 37.0 bits (84), Expect = 0.015, Method: Composition-based stats.
Identities = 17/57 (29%), Positives = 30/57 (52%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM 102
L++ GL + ++ F Q+G I+ ++ D T SRG GFI + + +EA+
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
Score = 31.2 bits (69), Expect = 0.82, Method: Composition-based stats.
Identities = 16/41 (39%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 130 TKVQIALEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
T Q +EQ+ F QYG I + ++ ++ TG RG FI F
Sbjct: 12 TMSQKEMEQL--FSQYGRIITSRILLDQATGVSRGVGFIRF 50
>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 = 36.6 bits (83), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 21/29 (72%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEF 170
F YG I+ ++MV +K +G RG+AFIE+
Sbjct: 123 FEVYGPIKRIHMVYSKRSGKPRGYAFIEY 151
Score = 36.6 bits (83), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 18/80 (22%), Positives = 41/80 (51%), Gaps = 4/80 (5%)
Query: 41 ESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDE 100
++ + LF+ ++Y T + L+ FE +G I + ++ + + RG+ FI Y + +
Sbjct: 100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHS 159
Query: 101 AMSNRPHEIDGRVVETKRAV 120
A + DG+ ++ +R +
Sbjct: 160 AYKH----ADGKKIDGRRVL 175
>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 = 36.2 bits (82), Expect = 0.021, Method: Composition-based stats.
Identities = 15/61 (24%), Positives = 33/61 (54%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
R +++G + Y ++ + G ++++ +M DP T RS+G+ FI + + + A+
Sbjct: 5 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 64
Query: 104 N 104
N
Sbjct: 65 N 65
Score = 28.9 bits (63), Expect = 3.4, Method: Composition-based stats.
Identities = 11/32 (34%), Positives = 20/32 (62%)
Query: 139 MDYFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
+D G + ++ M+ + +TG +G+AFIEF
Sbjct: 22 LDLCSNVGPVINLKMMFDPQTGRSKGYAFIEF 53
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 36.2 bits (82), Expect = 0.025, Method: Composition-based stats.
Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 6/77 (7%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
+F+G +D L+ FF Q+G+++DV + K R F F+T+++ ++ +++
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVF-----IPKPFRAFAFVTFADDQIA-QSLCGE 61
Query: 106 PHEIDGRVVETKRAVPR 122
I G V A P+
Sbjct: 62 DLIIKGISVHISNAEPK 78
>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 = 36.2 bits (82), Expect = 0.025, Method: Composition-based stats.
Identities = 15/61 (24%), Positives = 33/61 (54%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
R +++G + Y ++ + G ++++ +M DP T RS+G+ FI + + + A+
Sbjct: 4 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 63
Query: 104 N 104
N
Sbjct: 64 N 64
Score = 28.9 bits (63), Expect = 4.0, Method: Composition-based stats.
Identities = 11/32 (34%), Positives = 20/32 (62%)
Query: 139 MDYFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
+D G + ++ M+ + +TG +G+AFIEF
Sbjct: 21 LDLCSNVGPVINLKMMFDPQTGRSKGYAFIEF 52
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 36.2 bits (82), Expect = 0.026, Method: Composition-based stats.
Identities = 15/61 (24%), Positives = 33/61 (54%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
R +++G + Y ++ + G ++++ +M DP T RS+G+ FI + + + A+
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 104 N 104
N
Sbjct: 63 N 63
Score = 28.9 bits (63), Expect = 4.1, Method: Composition-based stats.
Identities = 11/32 (34%), Positives = 20/32 (62%)
Query: 139 MDYFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
+D G + ++ M+ + +TG +G+AFIEF
Sbjct: 20 LDLCSNVGPVINLKMMFDPQTGRSKGYAFIEF 51
>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 = 35.8 bits (81), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 21/29 (72%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEF 170
F YG I+ ++MV +K +G RG+AFIE+
Sbjct: 123 FEVYGPIKRIHMVYSKRSGKPRGYAFIEY 151
Score = 35.0 bits (79), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 18/80 (22%), Positives = 41/80 (51%), Gaps = 4/80 (5%)
Query: 41 ESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDE 100
++ + LF+ ++Y T + L+ FE +G I + ++ + + RG+ FI Y + +
Sbjct: 100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHS 159
Query: 101 AMSNRPHEIDGRVVETKRAV 120
A + DG+ ++ +R +
Sbjct: 160 AYKH----ADGKKIDGRRVL 175
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 35.8 bits (81), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 34/69 (49%)
Query: 34 DSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYS 93
D+ E R +F L R L+ FF G++ DV ++ D ++RS+G ++ +
Sbjct: 16 DNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFC 75
Query: 94 ESKMVDEAM 102
E + V A+
Sbjct: 76 EIQSVPLAI 84
Score = 29.3 bits (64), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 14/55 (25%), Positives = 28/55 (50%), Gaps = 5/55 (9%)
Query: 121 PREVKVRRVTKVQIAL-----EQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
P E R V +Q+A + D+F G + V +++++ + +G A++EF
Sbjct: 20 PEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEF 74
>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 = 0.034, Method: Composition-based stats.
Identities = 16/63 (25%), Positives = 34/63 (53%), Gaps = 8/63 (12%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
KLFIG L + +++ FEQ+G++++ ++K+ +GF+ + ++A+ N
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFVHIEDKTAAEDAIRN 61
Query: 105 RPH 107
H
Sbjct: 62 LHH 64
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 35.4 bits (80), Expect = 0.036, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 29/58 (50%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
L+I GL T D L + +G+IV + D T + +G+GF+ + +A++
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65
>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 = 35.4 bits (80), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 34/61 (55%), Gaps = 2/61 (3%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPV--TKRSRGFGFITYSESKMVDEAM 102
K+F+G + ++ L+ FEQ+G + ++ V++D +S+G F+T+ K EA
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 103 S 103
+
Sbjct: 65 N 65
>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 = 0.043, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 29/58 (50%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
L + L D L++ F GE+ +++D V S G+GF+ Y +K + A++
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 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 = 0.043, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 29/58 (50%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
L + L D L++ F GE+ +++D V S G+GF+ Y +K + A++
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 79
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In
Trinucleotide Repeat Containing 4 Variant
Length = 102
Score = 35.0 bits (79), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY 92
RKLF+G L + D+ ++ FE +G I + V++ P S+G F+ +
Sbjct: 13 RKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGP-DGTSKGCAFVKF 60
>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 = 34.7 bits (78), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 5/83 (6%)
Query: 39 EPESLRK----LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSE 94
E E L K L++G L + T ++ + F + G+I +++ D + K + GF F+ Y
Sbjct: 31 EQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYS 90
Query: 95 SKMVDEAMSN-RPHEIDGRVVET 116
+ AM +D R++ T
Sbjct: 91 RADAENAMRYINGTRLDDRIIRT 113
>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second
Rna-Binding Domain Of Sex-Lethal Determined By
Multidimensional Heteronuclear Magnetic Resonance
Spectroscopy
Length = 97
Score = 33.9 bits (76), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 25/38 (65%), Gaps = 1/38 (2%)
Query: 134 IALEQMD-YFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
I +Q+D FG+YG+I N++ +K TG RG AF+ +
Sbjct: 25 ITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRY 62
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 20/87 (22%), Positives = 43/87 (49%), Gaps = 7/87 (8%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
+ +FI L + + +++L +Q+G++ V V+ P T+ S+G F + + + ++
Sbjct: 16 KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 75
Query: 104 NRPHE-------IDGRVVETKRAVPRE 123
E +DGR ++ AV R+
Sbjct: 76 AASLEAEGGGLKLDGRQLKVDLAVTRD 102
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 27/46 (58%), Gaps = 6/46 (13%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFI 90
+LF+G L ++ ++ FE++G+ +V + KD +GFGFI
Sbjct: 24 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFI 63
>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 = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 27/46 (58%), Gaps = 6/46 (13%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFI 90
+LF+G L ++ ++ FE++G+ +V + KD +GFGFI
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFI 56
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 32.3 bits (72), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 30/50 (60%), Gaps = 1/50 (2%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYS 93
RKLF+G L+ + +++ + F+ +G I + V++ P S+G F+ +S
Sbjct: 16 RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFS 64
>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 = 32.3 bits (72), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 7/61 (11%)
Query: 46 LFIGGLDYRTNDDSLK----AFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEA 101
++I L+ + D LK A F Q+G+I+D++V + + + RG F+ + E A
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNA 68
Query: 102 M 102
+
Sbjct: 69 L 69
>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 = 32.3 bits (72), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 22/36 (61%), Gaps = 3/36 (8%)
Query: 59 SLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSE 94
SL A F Q+G +VD+V +K T + RG F+ + E
Sbjct: 26 SLYALFSQFGHVVDIVALK---TMKMRGQAFVIFKE 58
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 32.3 bits (72), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 23/36 (63%), Gaps = 3/36 (8%)
Query: 59 SLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSE 94
SL A F Q+G+I+D+V +K T + RG F+ + E
Sbjct: 26 SLYAIFSQFGQILDIVALK---TLKMRGQAFVIFKE 58
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug
Triplet Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 32.0 bits (71), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 26/58 (44%), Gaps = 1/58 (1%)
Query: 35 SQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY 92
SQ PE LFI L D L F +G +V V D T S+ FGF++Y
Sbjct: 18 SQKEGPEGAN-LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSY 74
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 31.6 bits (70), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 3/46 (6%)
Query: 128 RVTKVQIALEQMDY---FGQYGTIESVNMVTNKETGAKRGFAFIEF 170
RVT + + D F +G+I + + +K TG +GFAFI F
Sbjct: 19 RVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISF 64
Score = 31.6 bits (70), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 22/38 (57%)
Query: 55 TNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY 92
T + L+ F +G I + + KD T +S+GF FI++
Sbjct: 27 TRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISF 64
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 31.6 bits (70), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
+F+ LDY+ LK F G +V +++D K SRG G +T+ +S +A+S
Sbjct: 18 VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGK-SRGIGTVTFEQSIEAVQAIS 74
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein
U1a117, Nmr, 43 Structures
Length = 116
Score = 31.2 bits (69), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 30/53 (56%), Gaps = 7/53 (13%)
Query: 46 LFIGGLDYRTNDDSLK----AFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSE 94
++I L+ + D LK A F Q+G+I+D++V + + + RG F+ + E
Sbjct: 11 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKE 60
>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 = 0.82, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 28/47 (59%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY 92
+F+G L ++ A F +G I D V+KD T +S+G+GF+++
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSF 55
>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 = 31.2 bits (69), Expect = 0.85, Method: Composition-based stats.
Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 6/83 (7%)
Query: 39 EPESLRK----LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSE 94
E E L K L++G L + T ++ + F + G+I +++ D + K + GF F+ Y
Sbjct: 10 EQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKM-KTACGFCFVEYYS 68
Query: 95 SKMVDEAMSN-RPHEIDGRVVET 116
+ AM +D R++ T
Sbjct: 69 RADAENAMRYINGTRLDDRIIRT 91
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 30.4 bits (67), Expect = 1.2, Method: Composition-based stats.
Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 7/61 (11%)
Query: 46 LFIGGLDYRTNDDSLK----AFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEA 101
++I L+ + D LK A F Q+G+I+D++V + + + RG F+ + E A
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNA 68
Query: 102 M 102
+
Sbjct: 69 L 69
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 29.6 bits (65), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 7/74 (9%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRS----RGFGFITYSESKMVD 99
RK+F+GGL ++D + A F ++G + VV +S +G+ F+ + E V
Sbjct: 9 RKVFVGGLPPDIDEDEITASFRRFGPL--VVDWPHKAESKSYFPPKGYAFLLFQEESSV- 65
Query: 100 EAMSNRPHEIDGRV 113
+A+ + E DG++
Sbjct: 66 QALIDACLEEDGKL 79
>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 = 29.6 bits (65), Expect = 2.1, Method: Composition-based stats.
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 151 VNMVTNKETGAKRGFAFIEF 170
V ++ NK +G RGFAF+EF
Sbjct: 32 VRLMRNKSSGQSRGFAFVEF 51
>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 = 2.4, Method: Compositional matrix adjust.
Identities = 10/34 (29%), Positives = 21/34 (61%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKD 78
KL +G + + L+A FE++G +++ ++KD
Sbjct: 12 KLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD 45
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 29.6 bits (65), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 121 PREVKVRRVTKVQIALEQMDYFGQYGTIESVNM-VTNKETGAKRGFAFIEF 170
P +V + R+T+ M+ F YG I+ ++M V +G+A++EF
Sbjct: 4 PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEF 54
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 29.3 bits (64), Expect = 3.1, Method: Composition-based stats.
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 3/55 (5%)
Query: 40 PESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSE 94
PE R L+I L Y+ + + F ++G I + V P T RG ++ Y +
Sbjct: 9 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYED 60
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 28.9 bits (63), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 3/55 (5%)
Query: 40 PESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSE 94
PE R L+I L Y+ + + F ++G I + V P T RG ++ Y +
Sbjct: 15 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYED 66
>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 = 28.9 bits (63), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 9/31 (29%), Positives = 21/31 (67%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
D F +YG I+++++ ++ TG +G+ +E+
Sbjct: 42 DKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 72
>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 = 28.9 bits (63), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 9/31 (29%), Positives = 21/31 (67%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
D F +YG I+++++ ++ TG +G+ +E+
Sbjct: 26 DKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 56
>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 = 28.9 bits (63), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 9/31 (29%), Positives = 21/31 (67%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
D F +YG I+++++ ++ TG +G+ +E+
Sbjct: 41 DKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 71
>pdb|4DXF|A Chain A, Crystal Structure Of Staphylococcal Superantigen-Like
Protein 4
pdb|4DXF|B Chain B, Crystal Structure Of Staphylococcal Superantigen-Like
Protein 4
pdb|4DXG|A Chain A, Crystal Structure Of Staphylococcal Superantigen-Like
Protein 4 Complexed With Sialyl Lewis X
Length = 204
Score = 28.9 bits (63), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 5/73 (6%)
Query: 88 GFITYSESKMVDEAMSNRPHEIDGRVVETKRAVPREVKVRRVTKVQIALEQMDYFGQYGT 147
G IT S SK VD R + D K + +V ++TK QI+L+++D+ +
Sbjct: 95 GGITKSNSKKVDHKAGVRITKED-----NKGTISHDVSEFKITKEQISLKELDFKLRKQL 149
Query: 148 IESVNMVTNKETG 160
IE N+ N +G
Sbjct: 150 IEKNNLYGNVGSG 162
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 28.9 bits (63), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 9/31 (29%), Positives = 21/31 (67%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
D F +YG I+++++ ++ TG +G+ +E+
Sbjct: 26 DKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 56
>pdb|3URY|A Chain A, Crystal Structure Of Superantigen-Like Protein, Exotoxin
From Staphylococcus Aureus Subsp. Aureus Nctc 8325
pdb|3URY|B Chain B, Crystal Structure Of Superantigen-Like Protein, Exotoxin
From Staphylococcus Aureus Subsp. Aureus Nctc 8325
Length = 193
Score = 28.9 bits (63), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 5/73 (6%)
Query: 88 GFITYSESKMVDEAMSNRPHEIDGRVVETKRAVPREVKVRRVTKVQIALEQMDYFGQYGT 147
G IT S SK VD R + D K + +V ++TK QI+L+++D+ +
Sbjct: 84 GGITKSNSKKVDHKAGVRITKED-----NKGTISHDVSEFKITKEQISLKELDFKLRKQL 138
Query: 148 IESVNMVTNKETG 160
IE N+ N +G
Sbjct: 139 IEKNNLYGNVGSG 151
>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 = 28.9 bits (63), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 9/31 (29%), Positives = 21/31 (67%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
D F +YG I+++++ ++ TG +G+ +E+
Sbjct: 26 DKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 56
>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 = 28.9 bits (63), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 9/31 (29%), Positives = 21/31 (67%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
D F +YG I+++++ ++ TG +G+ +E+
Sbjct: 28 DKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 58
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 28.9 bits (63), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 9/29 (31%), Positives = 20/29 (68%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEF 170
F YG I+++++ ++ TG +G+A +E+
Sbjct: 47 FCDYGEIKNIHLNLDRRTGFSKGYALVEY 75
Score = 27.7 bits (60), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 13/53 (24%), Positives = 25/53 (47%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMV 98
LF+ + +D ++ F +GEI ++ + D T S+G+ + Y K
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQA 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 = 28.5 bits (62), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 9/29 (31%), Positives = 20/29 (68%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEF 170
F YG I+++++ ++ TG +G+A +E+
Sbjct: 93 FCDYGEIKNIHLNLDRRTGFSKGYALVEY 121
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 28.5 bits (62), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 3/55 (5%)
Query: 40 PESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSE 94
PE R L+I L Y+ + + F ++G I + V P T RG ++ Y +
Sbjct: 5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYED 56
>pdb|2GAO|A Chain A, Crystal Structure Of Human Sar1a In Complex With Gdp
pdb|2GAO|B Chain B, Crystal Structure Of Human Sar1a In Complex With Gdp
Length = 208
Score = 28.1 bits (61), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 35/153 (22%), Positives = 60/153 (39%), Gaps = 17/153 (11%)
Query: 14 GLEVAGTVVPLAMIINKAMEDSQCSEPESLRKLFIGGLDYRTND----DSLKAFFEQWGE 69
GL+ AG L M+ + + + + +L I G+ + T D + + ++ +
Sbjct: 42 GLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMTFTTFDLGGHEQARRVWKNYLP 101
Query: 70 IVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNRPHEIDGRVVETKRAVPREVKVRRV 129
++ +V SR + M DE +SN P I G ++ A+ E K+R +
Sbjct: 102 AINGIVFLVDCADHSRLVESKVELNALMTDETISNVPILILGNKIDRTDAISEE-KLREI 160
Query: 130 TKVQIALEQMDYFGQYGTIESVNMVTNKETGAK 162
FG YG VT KE A+
Sbjct: 161 ------------FGLYGQTTGKGNVTLKELNAR 181
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of
Eukaryotic Initiation Factor 4b
Length = 104
Score = 27.7 bits (60), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 2/47 (4%)
Query: 47 FIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVT-KRSRGFGFITY 92
F+G L Y ++S+K FF I V + ++P +R +GFG+ +
Sbjct: 19 FLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEF 64
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation Initiation
Factor 4b
Length = 100
Score = 27.7 bits (60), Expect = 8.3, Method: Composition-based stats.
Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 9/72 (12%)
Query: 47 FIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVT-KRSRGFGFITYSESKMV------- 98
F+G L Y ++S+K FF I V + ++P +R +GFG+ + + +
Sbjct: 23 FLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLN 81
Query: 99 DEAMSNRPHEID 110
+E++ NR +D
Sbjct: 82 EESLGNRRIRVD 93
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 0.135 0.385
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,709,622
Number of Sequences: 62578
Number of extensions: 219288
Number of successful extensions: 805
Number of sequences better than 100.0: 138
Number of HSP's better than 100.0 without gapping: 112
Number of HSP's successfully gapped in prelim test: 26
Number of HSP's that attempted gapping in prelim test: 567
Number of HSP's gapped (non-prelim): 232
length of query: 306
length of database: 14,973,337
effective HSP length: 98
effective length of query: 208
effective length of database: 8,840,693
effective search space: 1838864144
effective search space used: 1838864144
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: 51 (24.3 bits)