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= psy15045
(363 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 94.4 bits (233), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 46/99 (46%), Positives = 63/99 (63%), Gaps = 8/99 (8%)
Query: 83 GNSSATQSKRSYPDNSGPVQNT-DLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNT 141
G+S ++ KR+ VQ T DL+VLG+PW T+ DLKEYF FG + VK D T
Sbjct: 1 GSSGSSGVKRA-------VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKT 53
Query: 142 GRSKGFGFIRFSSHESALKAMLKKHKIGNRICDVRIPES 180
G SKGFGF+RF+ +E+ +K M ++H I R CD ++P S
Sbjct: 54 GHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNS 92
Score = 30.0 bits (66), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 6/65 (9%)
Query: 190 ASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFRE-----FAFVTF-ELDSVAKSL 243
S + V L TE DL+E+F +G V+ V + K + F FV F E ++ K +
Sbjct: 15 TSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVM 74
Query: 244 IGQHV 248
+H+
Sbjct: 75 SQRHM 79
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 88.2 bits (217), Expect = 6e-18, Method: Compositional matrix adjust.
Identities = 62/178 (34%), Positives = 96/178 (53%), Gaps = 12/178 (6%)
Query: 100 PVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESAL 159
P Q L + G+ + TD L+ +FEQ+GTL V D NT RS+GFGF+ +++ E
Sbjct: 11 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 70
Query: 160 KAM-LKKHKIGNRICD----VRIPESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYY 214
AM + HK+ R+ + V +S + G V K+FVG + D E LR++FE Y
Sbjct: 71 AAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTV-KKIFVGGIKEDTEEHHLRDYFEQY 129
Query: 215 GA--VVDVLIPK---PFREFAFVTF-ELDSVAKSLIGQHVNIKDKKVVVMEATPKKKM 266
G V++++ + R FAFVTF + DSV K +I ++ + V +A K++M
Sbjct: 130 GKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEM 187
>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 = 88.2 bits (217), Expect = 7e-18, Method: Compositional matrix adjust.
Identities = 62/178 (34%), Positives = 96/178 (53%), Gaps = 12/178 (6%)
Query: 100 PVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESAL 159
P Q L + G+ + TD L+ +FEQ+GTL V D NT RS+GFGF+ +++ E
Sbjct: 9 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 68
Query: 160 KAM-LKKHKIGNRICD----VRIPESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYY 214
AM + HK+ R+ + V +S + G V K+FVG + D E LR++FE Y
Sbjct: 69 AAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTV-KKIFVGGIKEDTEEHHLRDYFEQY 127
Query: 215 GA--VVDVLIPK---PFREFAFVTF-ELDSVAKSLIGQHVNIKDKKVVVMEATPKKKM 266
G V++++ + R FAFVTF + DSV K +I ++ + V +A K++M
Sbjct: 128 GKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEM 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 = 88.2 bits (217), Expect = 7e-18, Method: Compositional matrix adjust.
Identities = 62/178 (34%), Positives = 96/178 (53%), Gaps = 12/178 (6%)
Query: 100 PVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESAL 159
P Q L + G+ + TD L+ +FEQ+GTL V D NT RS+GFGF+ +++ E
Sbjct: 10 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 69
Query: 160 KAM-LKKHKIGNRICD----VRIPESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYY 214
AM + HK+ R+ + V +S + G V K+FVG + D E LR++FE Y
Sbjct: 70 AAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTV-KKIFVGGIKEDTEEHHLRDYFEQY 128
Query: 215 GA--VVDVLIPK---PFREFAFVTF-ELDSVAKSLIGQHVNIKDKKVVVMEATPKKKM 266
G V++++ + R FAFVTF + DSV K +I ++ + V +A K++M
Sbjct: 129 GKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEM 186
>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 = 87.4 bits (215), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 62/178 (34%), Positives = 96/178 (53%), Gaps = 12/178 (6%)
Query: 100 PVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESAL 159
P Q L + G+ + TD L+ +FEQ+GTL V D NT RS+GFGF+ +++ E
Sbjct: 3 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 62
Query: 160 KAM-LKKHKIGNRICD----VRIPESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYY 214
AM + HK+ R+ + V +S + G V K+FVG + D E LR++FE Y
Sbjct: 63 AAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTV-KKIFVGGIKEDTEEHHLRDYFEQY 121
Query: 215 GA--VVDVLIPK---PFREFAFVTF-ELDSVAKSLIGQHVNIKDKKVVVMEATPKKKM 266
G V++++ + R FAFVTF + DSV K +I ++ + V +A K++M
Sbjct: 122 GKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEM 179
>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 = 85.9 bits (211), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 47/168 (27%), Positives = 91/168 (54%), Gaps = 9/168 (5%)
Query: 102 QNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKA 161
++ + + G+ W T+++L+EYF ++GT+ + D TGRS+GFGF+ F S +
Sbjct: 2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61
Query: 162 MLKKHKIGNRICDVRIPESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVD-- 219
+ +H + ++ D P+ E+ K+FVG + PD+ + E F +G ++D
Sbjct: 62 VKTQHILDGKVID---PKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQ 118
Query: 220 VLIPKPF---REFAFVTFE-LDSVAKSLIGQHVNIKDKKVVVMEATPK 263
+++ K R F FVT++ D+V + + ++ KD+K+ + A P+
Sbjct: 119 LMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAEPR 166
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 84.7 bits (208), Expect = 8e-17, Method: Compositional matrix adjust.
Identities = 61/176 (34%), Positives = 94/176 (53%), Gaps = 12/176 (6%)
Query: 100 PVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESAL 159
P Q L + G+ + TD L+ +FEQ+GTL V D NT RS+GFGF+ +++ E
Sbjct: 10 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 69
Query: 160 KAM-LKKHKIGNRICD----VRIPESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYY 214
AM + HK+ R+ + V +S + G V K+FVG + D E LR++FE Y
Sbjct: 70 AAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTV-KKIFVGGIKEDTEEHHLRDYFEQY 128
Query: 215 GA--VVDVLIPK---PFREFAFVTF-ELDSVAKSLIGQHVNIKDKKVVVMEATPKK 264
G V++++ + R FAFVTF + DSV K +I ++ + V +A K+
Sbjct: 129 GKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQ 184
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 84.7 bits (208), Expect = 8e-17, Method: Compositional matrix adjust.
Identities = 61/176 (34%), Positives = 94/176 (53%), Gaps = 12/176 (6%)
Query: 100 PVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESAL 159
P Q L + G+ + TD L+ +FEQ+GTL V D NT RS+GFGF+ +++ E
Sbjct: 8 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 67
Query: 160 KAM-LKKHKIGNRICD----VRIPESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYY 214
AM + HK+ R+ + V +S + G V K+FVG + D E LR++FE Y
Sbjct: 68 AAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTV-KKIFVGGIKEDTEEHHLRDYFEQY 126
Query: 215 GA--VVDVLIPK---PFREFAFVTF-ELDSVAKSLIGQHVNIKDKKVVVMEATPKK 264
G V++++ + R FAFVTF + DSV K +I ++ + V +A K+
Sbjct: 127 GKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQ 182
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 80.9 bits (198), Expect = 1e-15, Method: Composition-based stats.
Identities = 41/74 (55%), Positives = 50/74 (67%)
Query: 190 ASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKSLIGQHVN 249
+S VFVG T D+TE +LRE F YG V+DV IPKPFR FAFVTF D +A+SL G+ +
Sbjct: 5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGEDLI 64
Query: 250 IKDKKVVVMEATPK 263
IK V + A PK
Sbjct: 65 IKGISVHISNAEPK 78
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 80.5 bits (197), Expect = 1e-15, Method: Composition-based stats.
Identities = 41/74 (55%), Positives = 49/74 (66%)
Query: 190 ASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKSLIGQHVN 249
SKVFVG T D+T +L++ F YG VVDV IPKPFR FAFVTF D VA+SL G+ +
Sbjct: 11 GSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQSLCGEDLI 70
Query: 250 IKDKKVVVMEATPK 263
IK V + A PK
Sbjct: 71 IKGISVHISNAEPK 84
>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 = 60.1 bits (144), Expect = 2e-09, Method: Composition-based stats.
Identities = 29/70 (41%), Positives = 43/70 (61%), Gaps = 1/70 (1%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM-LK 164
+ + G+ W T DLK+YF +FG + +K+D TGRS+GFGF+ F ES K M K
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 165 KHKIGNRICD 174
+HK+ ++ D
Sbjct: 62 EHKLNGKVID 71
Score = 33.9 bits (76), Expect = 0.13, Method: Composition-based stats.
Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 5/69 (7%)
Query: 193 VFVGSLTPDLTESDLREHFEYYGAVVDVL-----IPKPFREFAFVTFELDSVAKSLIGQH 247
+F+G L+ D T+ DL+++F +G VVD I R F FV F+ ++ Q
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 248 VNIKDKKVV 256
+ + KV+
Sbjct: 62 EHKLNGKVI 70
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 59.7 bits (143), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 45/150 (30%), Positives = 78/150 (52%), Gaps = 13/150 (8%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDK--NTGRSKGFGFIRFSSHESALKAML 163
+ V +P T+++ DL+E FEQ+G + NV D+ N +SKG F+ F + ++AL+A
Sbjct: 18 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 77
Query: 164 KKHKIG-----NRICDVRIPESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVV 218
H + + ++ +S K E K+F+G ++ TE+D+R F +G +
Sbjct: 78 ALHNMKVLPGMHHPIQMKPADSEKNNAVE--DRKLFIGMISKKCTENDIRVMFSSFGQIE 135
Query: 219 DVLI---PKPF-REFAFVTFELDSVAKSLI 244
+ I P R AFVTF ++A++ I
Sbjct: 136 ECRILRGPDGLSRGCAFVTFTTRAMAQTAI 165
Score = 36.6 bits (83), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 28/52 (53%), Gaps = 7/52 (13%)
Query: 190 ASKVFVGSLTPDLTESDLREHFEYYGAVVDVLI-------PKPFREFAFVTF 234
A K+FVG + +E DLRE FE YGAV ++ + P + FVTF
Sbjct: 15 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTF 66
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 41/83 (49%), Gaps = 4/83 (4%)
Query: 83 GNSSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTG 142
G Q K + + + V++ L + I T+ND++ F FG +E + + G
Sbjct: 87 GMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRI-LRGPDG 145
Query: 143 RSKGFGFIRFSSH---ESALKAM 162
S+G F+ F++ ++A+KAM
Sbjct: 146 LSRGCAFVTFTTRAMAQTAIKAM 168
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 59.3 bits (142), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 44/150 (29%), Positives = 78/150 (52%), Gaps = 13/150 (8%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDK--NTGRSKGFGFIRFSSHESALKAML 163
+ V +P T+++ DL+E FEQ+G + NV D+ N +SKG F+ F + ++AL+A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 164 KKHKIG-----NRICDVRIPESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVV 218
H + + ++ +S K E K+F+G ++ TE+D+R F +G +
Sbjct: 66 ALHNMKVLPGMHHPIQMKPADSEKNNAVED--RKLFIGMISKKCTENDIRVMFSSFGQIE 123
Query: 219 DVLIPK----PFREFAFVTFELDSVAKSLI 244
+ I + R AFVTF ++A++ I
Sbjct: 124 ECRILRGPDGLSRGCAFVTFTTRAMAQTAI 153
Score = 36.6 bits (83), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 28/52 (53%), Gaps = 7/52 (13%)
Query: 190 ASKVFVGSLTPDLTESDLREHFEYYGAVVDVLI-------PKPFREFAFVTF 234
A K+FVG + +E DLRE FE YGAV ++ + P + FVTF
Sbjct: 3 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTF 54
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 41/83 (49%), Gaps = 4/83 (4%)
Query: 83 GNSSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTG 142
G Q K + + + V++ L + I T+ND++ F FG +E + + G
Sbjct: 75 GMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRI-LRGPDG 133
Query: 143 RSKGFGFIRFSSH---ESALKAM 162
S+G F+ F++ ++A+KAM
Sbjct: 134 LSRGCAFVTFTTRAMAQTAIKAM 156
>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 = 58.9 bits (141), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 29/68 (42%), Positives = 41/68 (60%), Gaps = 1/68 (1%)
Query: 108 VLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM-LKKH 166
V G+ W + DLK+YF +FG + +K D NTGRS+GFGFI F S K + K+H
Sbjct: 16 VGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQKEH 75
Query: 167 KIGNRICD 174
++ R+ D
Sbjct: 76 RLDGRVID 83
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 42/83 (50%), Gaps = 9/83 (10%)
Query: 187 EPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKP-----FREFAFVTFELDSVAK 241
E A K FVG L+ D ++ DL+++F +G VVD I R F F+ F+ + +
Sbjct: 8 EEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVE 67
Query: 242 SLIGQHVNIKDKKVVVMEATPKK 264
++ Q + D +V+ PKK
Sbjct: 68 KVLDQKEHRLDGRVI----DPKK 86
>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 = 56.6 bits (135), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 44/151 (29%), Positives = 74/151 (49%), Gaps = 25/151 (16%)
Query: 111 IPWTFTDNDLKEYFEQFGTLEFANVKVDK--NTGRSKGFGFIRFSSHESALKAM--LKKH 166
+P T+++ DL+E FEQ+G + NV D+ N +SKG F+ F + ++AL+A L
Sbjct: 11 VPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNX 70
Query: 167 KIGNRICDVRIPESTKIGTEEPVAS---------KVFVGSLTPDLTESDLREHFEYYGAV 217
K+ +P +P S K+F+G ++ TE+D+R F +G +
Sbjct: 71 KV--------LPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQI 122
Query: 218 VDVLIPKP----FREFAFVTFELDSVAKSLI 244
+ I + R AFVTF + A++ I
Sbjct: 123 EECRILRGPDGLSRGCAFVTFTTRAXAQTAI 153
Score = 35.8 bits (81), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 27/52 (51%), Gaps = 7/52 (13%)
Query: 190 ASKVFVGSLTPDLTESDLREHFEYYGAVVDVLI-------PKPFREFAFVTF 234
A K FVG + +E DLRE FE YGAV ++ + P + FVTF
Sbjct: 3 AIKXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTF 54
Score = 35.0 bits (79), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 21/85 (24%), Positives = 39/85 (45%), Gaps = 1/85 (1%)
Query: 83 GNSSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTG 142
G Q K + + + V++ L + I T+ND++ F FG +E + + G
Sbjct: 75 GXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQIEECRI-LRGPDG 133
Query: 143 RSKGFGFIRFSSHESALKAMLKKHK 167
S+G F+ F++ A A+ H+
Sbjct: 134 LSRGCAFVTFTTRAXAQTAIKAXHQ 158
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 24/59 (40%), Positives = 38/59 (64%)
Query: 104 TDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
T + V G+P+ TD L++YFE FG +E A V D+ TG+S+G+GF+ + +A +A
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERAC 76
Score = 29.6 bits (65), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 22/32 (68%)
Query: 191 SKVFVGSLTPDLTESDLREHFEYYGAVVDVLI 222
+K+FVG L T++ LR++FE +G + + ++
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVV 49
>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 = 52.0 bits (123), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 42/69 (60%), Gaps = 3/69 (4%)
Query: 97 NSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSH- 155
+S +++ +L V G+P T T +L++ F Q+G + + + VD+ TG S+G GFIRF
Sbjct: 82 SSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRI 141
Query: 156 --ESALKAM 162
E A+K +
Sbjct: 142 EAEEAIKGL 150
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 31/121 (25%), Positives = 58/121 (47%), Gaps = 13/121 (10%)
Query: 104 TDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAML 163
T+L+V +P T + + F G +E + DK TG+S G+GF+ + + A KA+
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI- 61
Query: 164 KKHKIGNRICDVRIPEST-KIGTEEPVASKV-----FVGSLTPDLTESDLREHFEYYGAV 217
N + +R+ T K+ P ++ + +V L +T+ +L + F YG +
Sbjct: 62 ------NTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRI 115
Query: 218 V 218
+
Sbjct: 116 I 116
>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 = 51.2 bits (121), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 48/83 (57%), Gaps = 4/83 (4%)
Query: 101 VQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALK 160
+++T+L V +P T TD+ L F ++G++ N+ DK TGR +G F+R++ E A +
Sbjct: 11 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQE 70
Query: 161 AMLKKHKI----GNRICDVRIPE 179
A+ + + G++ VR+ E
Sbjct: 71 AISALNNVIPEGGSQPLSVRLAE 93
>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 = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 48/83 (57%), Gaps = 4/83 (4%)
Query: 101 VQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALK 160
+++T+L V +P T TD+ L F ++G++ N+ DK TGR +G F+R++ E A +
Sbjct: 98 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQE 157
Query: 161 AMLKKHKI----GNRICDVRIPE 179
A+ + + G++ VR+ E
Sbjct: 158 AISALNNVIPEGGSQPLSVRLAE 180
Score = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 41/154 (26%), Positives = 71/154 (46%), Gaps = 8/154 (5%)
Query: 103 NTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
NT+L+V +P TD +L F G + + D TG S G+ F+ F+S + +A+
Sbjct: 14 NTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAI 73
Query: 163 LKKHKIGNRICDVRIPESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVV---- 218
+ I R +++ + + G E + ++V +L +T+ L F YG++V
Sbjct: 74 KVLNGITVRNKRLKVSYA-RPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNI 132
Query: 219 --DVLIPKPFREFAFVTFELDSVAKSLIGQHVNI 250
D L +P R AFV + A+ I N+
Sbjct: 133 LRDKLTGRP-RGVAFVRYNKREEAQEAISALNNV 165
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 50.8 bits (120), Expect = 1e-06, Method: Composition-based stats.
Identities = 27/66 (40%), Positives = 41/66 (62%), Gaps = 3/66 (4%)
Query: 97 NSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHE 156
++GP++ L V + + T++ L+ FE FG +E + +D TGRSKG+GFI FS E
Sbjct: 23 SAGPMR---LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSE 79
Query: 157 SALKAM 162
A KA+
Sbjct: 80 CAKKAL 85
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 39/62 (62%)
Query: 101 VQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALK 160
+++T+L V +P T TD+ L F ++G++ N+ DK TGR +G F+R++ E A +
Sbjct: 87 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQE 146
Query: 161 AM 162
A+
Sbjct: 147 AI 148
Score = 49.7 bits (117), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 41/154 (26%), Positives = 71/154 (46%), Gaps = 8/154 (5%)
Query: 103 NTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
NT+L+V +P TD +L F G + + D TG S G+ F+ F+S + +A+
Sbjct: 3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62
Query: 163 LKKHKIGNRICDVRIPESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVV---- 218
+ I R +++ + + G E + ++V +L +T+ L F YG++V
Sbjct: 63 KVLNGITVRNKRLKVSYA-RPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNI 121
Query: 219 --DVLIPKPFREFAFVTFELDSVAKSLIGQHVNI 250
D L +P R AFV + A+ I N+
Sbjct: 122 LRDKLTGRP-RGVAFVRYNKREEAQEAISALNNV 154
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 38/62 (61%)
Query: 101 VQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALK 160
+++ +L + G+P T T D+++ F +FG + + V VD+ TG S+G FIRF A +
Sbjct: 86 IKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEE 145
Query: 161 AM 162
A+
Sbjct: 146 AI 147
>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 = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 38/62 (61%)
Query: 101 VQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALK 160
+++ +L + G+P T T D+++ F +FG + + V VD+ TG S+G FIRF A +
Sbjct: 86 IKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEE 145
Query: 161 AM 162
A+
Sbjct: 146 AI 147
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 50.1 bits (118), Expect = 2e-06, Method: Composition-based stats.
Identities = 26/72 (36%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM-LK 164
+ V G+ T D+K YFEQFG ++ A + DK T R +GFGF+ F S + K +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 165 KHKIGNRICDVR 176
H+I N++ + +
Sbjct: 62 FHEINNKMVECK 73
Score = 38.5 bits (88), Expect = 0.005, Method: Composition-based stats.
Identities = 21/69 (30%), Positives = 37/69 (53%), Gaps = 5/69 (7%)
Query: 193 VFVGSLTPDLTESDLREHFEYYGAVVDVLI-----PKPFREFAFVTFELDSVAKSLIGQH 247
+FVG L+ + T D++ +FE +G V D ++ R F FVTFE + + + + H
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 248 VNIKDKKVV 256
+ + K+V
Sbjct: 62 FHEINNKMV 70
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 49.7 bits (117), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 45/76 (59%), Gaps = 3/76 (3%)
Query: 97 NSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSH- 155
+S +++ +L V G+P T + ++++ F Q+G + + + +D+ TG S+G GFIRF
Sbjct: 84 SSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRI 143
Query: 156 --ESALKAMLKKHKIG 169
E A+K + + +G
Sbjct: 144 EAEEAIKGLNGQKPLG 159
Score = 48.1 bits (113), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 39/159 (24%), Positives = 73/159 (45%), Gaps = 22/159 (13%)
Query: 104 TDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAML 163
T+L+V +P T ++ K F G +E + DK TG+S G+GF+ +S A KA+
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI- 63
Query: 164 KKHKIGNRICDVRIPEST-KIGTEEPVASKV-----FVGSLTPDLTESDLREHFEYYGAV 217
N + +++ T K+ P ++ + +V L +++ ++ + F YG +
Sbjct: 64 ------NTLNGLKLQTKTIKVSYARPSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRI 117
Query: 218 VD--VLIPKPF---REFAFVTF----ELDSVAKSLIGQH 247
+ +L+ + R F+ F E + K L GQ
Sbjct: 118 ITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQK 156
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 48.9 bits (115), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 38/58 (65%)
Query: 105 DLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
+L+V IP T + L++ FE++G +E + D+ T +S+G+GF++F S SA +A+
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAI 101
Score = 30.0 bits (66), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 39/88 (44%), Gaps = 7/88 (7%)
Query: 181 TKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLI-----PKPFREFAFVTFE 235
T++ E V + V + + E LR+ FE YG + V I + R + FV F+
Sbjct: 33 TQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQ 92
Query: 236 LDSVAKSLIG--QHVNIKDKKVVVMEAT 261
S A+ I NI +K++ V A
Sbjct: 93 SGSSAQQAIAGLNGFNILNKRLKVALAA 120
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 47.8 bits (112), Expect = 1e-05, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAMLK- 164
+ + G+ W T L+EYF QFG ++ V D T RS+GFGF+ F K + +
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62
Query: 165 KHKIGNRICDVRI 177
+H++ ++ D ++
Sbjct: 63 RHELDSKTIDPKV 75
Score = 36.2 bits (82), Expect = 0.030, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 35/70 (50%), Gaps = 5/70 (7%)
Query: 192 KVFVGSLTPDLTESDLREHFEYYGAVVDVLI-----PKPFREFAFVTFELDSVAKSLIGQ 246
K+F+G L+ T+ LRE+F +G V + L+ K R F FVTF + ++ Q
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 247 HVNIKDKKVV 256
+ D K +
Sbjct: 62 SRHELDSKTI 71
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 47.4 bits (111), Expect = 1e-05, Method: Composition-based stats.
Identities = 28/67 (41%), Positives = 38/67 (56%), Gaps = 4/67 (5%)
Query: 99 GPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHES- 157
GP + +L + +P FTD DL F FG + A V +DK T SK FGF+ F + +S
Sbjct: 37 GP-EGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSA 95
Query: 158 --ALKAM 162
A+KAM
Sbjct: 96 QVAIKAM 102
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 47.4 bits (111), Expect = 1e-05, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAMLK- 164
+ + G+ W T L+EYF QFG ++ V D T RS+GFGF+ F K + +
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 87
Query: 165 KHKIGNRICDVRI 177
+H++ ++ D ++
Sbjct: 88 RHELDSKTIDPKV 100
Score = 37.7 bits (86), Expect = 0.010, Method: Composition-based stats.
Identities = 24/85 (28%), Positives = 41/85 (48%), Gaps = 8/85 (9%)
Query: 177 IPESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLI-----PKPFREFAF 231
+P + +G+ K+F+G L+ T+ LRE+F +G V + L+ K R F F
Sbjct: 15 VPRGSHMGSS---GCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGF 71
Query: 232 VTFELDSVAKSLIGQHVNIKDKKVV 256
VTF + ++ Q + D K +
Sbjct: 72 VTFMDQAGVDKVLAQSRHELDSKTI 96
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 41/70 (58%), Gaps = 3/70 (4%)
Query: 103 NTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSH---ESAL 159
+ +L V G+P T + ++++ F Q+G + + + +D+ TG S+G GFIRF E A+
Sbjct: 1 DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
Query: 160 KAMLKKHKIG 169
K + + +G
Sbjct: 61 KGLNGQKPLG 70
>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of
Fbp-Interacting Repressor (Fir)
pdb|2KXH|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fir In
The Complex With Fbp Nbox Peptide
Length = 199
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/119 (21%), Positives = 62/119 (52%), Gaps = 14/119 (11%)
Query: 111 IPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAMLKKHKI-- 168
I + ++ +++ F FG ++ ++ D T + KGF F+ + E+A A+ + + +
Sbjct: 21 IYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVML 80
Query: 169 GNRICDVRIPESTKIGTEEPVA----------SKVFVGSLTPDLTESDLREHFEYYGAV 217
G R ++++ + IG +P+ ++++V S+ DL++ D++ FE +G +
Sbjct: 81 GGR--NIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKI 137
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 29/48 (60%)
Query: 115 FTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
+D+D+K FE FG ++ + D TG+ KG+GFI + +S+ A+
Sbjct: 122 LSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAV 169
Score = 29.3 bits (64), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 32/63 (50%), Gaps = 5/63 (7%)
Query: 189 VASKVFVGSLTPDLTESDLREHFEYYGAVVDV-----LIPKPFREFAFVTFELDSVAKSL 243
+ +V+VGS+ +L E +R+ F +G + + + + FAFV +E+ A+
Sbjct: 12 IMCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLA 71
Query: 244 IGQ 246
+ Q
Sbjct: 72 LEQ 74
>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
pdb|2QFJ|B Chain B, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
Length = 216
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/119 (21%), Positives = 62/119 (52%), Gaps = 14/119 (11%)
Query: 111 IPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAMLKKHKI-- 168
I + ++ +++ F FG ++ ++ D T + KGF F+ + E+A A+ + + +
Sbjct: 36 IYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVML 95
Query: 169 GNRICDVRIPESTKIGTEEPVA----------SKVFVGSLTPDLTESDLREHFEYYGAV 217
G R ++++ + IG +P+ ++++V S+ DL++ D++ FE +G +
Sbjct: 96 GGR--NIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKI 152
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 30/48 (62%)
Query: 115 FTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
+D+D+K FE FG ++ A + D TG+ KG+GFI + +S+ A+
Sbjct: 137 LSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAV 184
>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 = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/117 (20%), Positives = 59/117 (50%), Gaps = 10/117 (8%)
Query: 111 IPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAMLKKHKIGN 170
I + ++ +++ F FG ++ + D T + KGF F+ + E+A A+ + + +
Sbjct: 20 IYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQXNSVXL 79
Query: 171 RICDVRIPESTKIGTEEPVA----------SKVFVGSLTPDLTESDLREHFEYYGAV 217
++++ + IG +P+ ++++V S+ DL++ D++ FE +G +
Sbjct: 80 GGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKI 136
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 29/48 (60%)
Query: 115 FTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
+D+D+K FE FG ++ + D TG+ KG+GFI + +S+ A+
Sbjct: 121 LSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAV 168
Score = 29.6 bits (65), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 32/63 (50%), Gaps = 5/63 (7%)
Query: 189 VASKVFVGSLTPDLTESDLREHFEYYGAVVDV-----LIPKPFREFAFVTFELDSVAKSL 243
+ +V+VGS+ +L E +R+ F +G + + + + FAFV +E+ A+
Sbjct: 11 IXCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLA 70
Query: 244 IGQ 246
+ Q
Sbjct: 71 LEQ 73
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 46.2 bits (108), Expect = 2e-05, Method: Composition-based stats.
Identities = 29/83 (34%), Positives = 47/83 (56%), Gaps = 4/83 (4%)
Query: 97 NSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHE 156
+SG + V +P+ FT LK+ F + G + +A++K++ G+SKG G ++F S E
Sbjct: 2 SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPE 59
Query: 157 SALKA--MLKKHKIGNRICDVRI 177
A +A M+ K+ R DVRI
Sbjct: 60 VAERACRMMNGMKLSGREIDVRI 82
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 45/80 (56%), Gaps = 8/80 (10%)
Query: 191 SKVFVGSLTPDLTESDLREHFEYYGAVVDVLI------PKPFREFAFVTFELDSVAKSLI 244
+K+FVG + + E++LRE+F+ +G V +V++ +P R F F+TFE + +
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRP-RGFGFITFEDEQSVDQAV 69
Query: 245 GQHV-NIKDKKVVVMEATPK 263
H +I KKV V A P+
Sbjct: 70 NMHFHDIMGKKVEVKRAEPR 89
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM-LK 164
+ V GIP + +L+EYF++FG + + D R +GFGFI F +S +A+ +
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMH 72
Query: 165 KHKIGNRICDVRIPE 179
H I + +V+ E
Sbjct: 73 FHDIMGKKVEVKRAE 87
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 45.8 bits (107), Expect = 4e-05, Method: Composition-based stats.
Identities = 24/64 (37%), Positives = 38/64 (59%)
Query: 99 GPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESA 158
G ++ L V + + T++ L+ FE FG ++ + D +TGRSKG+GFI FS E A
Sbjct: 1 GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60
Query: 159 LKAM 162
+A+
Sbjct: 61 RRAL 64
Score = 29.6 bits (65), Expect = 2.4, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 34/62 (54%), Gaps = 5/62 (8%)
Query: 190 ASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKP-----FREFAFVTFELDSVAKSLI 244
+S ++VGSL ++TE LR FE +G + ++++ K + + F+TF A+ +
Sbjct: 5 SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
Query: 245 GQ 246
Q
Sbjct: 65 EQ 66
>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 = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 33/104 (31%), Positives = 52/104 (50%), Gaps = 5/104 (4%)
Query: 81 ASGNSSATQSK--RSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVD 138
+SG+S TQ + GP + +L + +P F D DL + F FG + A V +D
Sbjct: 2 SSGSSGLTQQSIGAAGSQKEGP-EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFID 60
Query: 139 KNTGRSKGFGFIRFSSHESALKAM--LKKHKIGNRICDVRIPES 180
K T SK FGF+ + + SA A+ + +IG + V++ S
Sbjct: 61 KQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRS 104
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 45.4 bits (106), Expect = 5e-05, Method: Composition-based stats.
Identities = 28/81 (34%), Positives = 47/81 (58%), Gaps = 4/81 (4%)
Query: 99 GPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESA 158
G ++ + V +P+ FT LK+ F + G + +A++K++ G+SKG G ++F S E A
Sbjct: 1 GSSGSSGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVA 58
Query: 159 LKA--MLKKHKIGNRICDVRI 177
+A M+ K+ R DVRI
Sbjct: 59 ERACRMMNGMKLSGREIDVRI 79
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 45.1 bits (105), Expect = 6e-05, Method: Composition-based stats.
Identities = 26/74 (35%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 102 QNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKA 161
Q L + G+ + T+ L+ Y+EQ+G L V D + RS+GFGF+ FSS A
Sbjct: 26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAA 85
Query: 162 MLKK-HKIGNRICD 174
M + H I R+ +
Sbjct: 86 MAARPHSIDGRVVE 99
>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 = 45.1 bits (105), Expect = 7e-05, Method: Composition-based stats.
Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 117 DNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAMLKK-HKIGNRICDV 175
+ ++EYF FG +E + +D T + +GF FI F E K M KK H +G C++
Sbjct: 15 EEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEI 74
Query: 176 RIPES 180
++ S
Sbjct: 75 KVAMS 79
Score = 39.7 bits (91), Expect = 0.002, Method: Composition-based stats.
Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 5/58 (8%)
Query: 192 KVFVGSLTPDLTESDLREHFEYYGAVVDVLIP-----KPFREFAFVTFELDSVAKSLI 244
K+FVG L+PD E +RE+F +G V + +P R F F+TF+ + K ++
Sbjct: 3 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 60
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 44.7 bits (104), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 29/47 (61%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRF 152
L V G+ W+ T L+ YF Q+G + + DK T +S+GFGF++F
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF 65
Score = 37.0 bits (84), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 36/78 (46%), Gaps = 6/78 (7%)
Query: 192 KVFVGSLTPDLTESDLREHFEYYGAVVDVLIPK-----PFREFAFVTF-ELDSVAKSLIG 245
K+FVG L T+ LR +F YG VVD +I K R F FV F + + V L
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 246 QHVNIKDKKVVVMEATPK 263
+ + + + TP+
Sbjct: 78 RPHTLDGRNIDPKPCTPR 95
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 44.7 bits (104), Expect = 9e-05, Method: Composition-based stats.
Identities = 21/62 (33%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 117 DNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAMLKK-HKIGNRICDV 175
+ ++EYF FG +E + +D T + +GF FI F E K M KK H +G C++
Sbjct: 13 EEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEI 72
Query: 176 RI 177
++
Sbjct: 73 KV 74
Score = 38.1 bits (87), Expect = 0.008, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 5/57 (8%)
Query: 193 VFVGSLTPDLTESDLREHFEYYGAVVDVLIP-----KPFREFAFVTFELDSVAKSLI 244
+FVG L+PD E +RE+F +G V + +P R F F+TF+ + K ++
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 58
>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 = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 21/51 (41%), Positives = 34/51 (66%), Gaps = 1/51 (1%)
Query: 191 SKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAK 241
S++FVG+L PD+TE ++R+ FE YG +V I K + F F+ E ++A+
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-KGFGFIRLETRTLAE 65
Score = 30.4 bits (67), Expect = 1.6, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 31/57 (54%), Gaps = 6/57 (10%)
Query: 102 QNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESA 158
Q + L V +P T+ ++++ FE++G + V + K+ KGFGFIR + A
Sbjct: 14 QRSRLFVGNLPPDITEEEMRKLFEKYG--KAGEVFIHKD----KGFGFIRLETRTLA 64
>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 = 1e-04, Method: Compositional matrix adjust.
Identities = 27/91 (29%), Positives = 47/91 (51%), Gaps = 8/91 (8%)
Query: 85 SSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRS 144
SS + R+ PD N L V G+ T+ DL+E F ++G + ++ D+ + RS
Sbjct: 2 SSGSSGNRANPD-----PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRS 56
Query: 145 KGFGFIRFSSHESALKAMLKKHKI---GNRI 172
+GF F+ F + + A +A + + + G RI
Sbjct: 57 RGFAFVYFENVDDAKEAKERANGMELDGRRI 87
Score = 33.5 bits (75), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 19/38 (50%), Positives = 21/38 (55%), Gaps = 5/38 (13%)
Query: 203 TESDLREHFEYYGAVVDVLI-----PKPFREFAFVTFE 235
TE DLRE F YG + DV I + R FAFV FE
Sbjct: 28 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE 65
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 41/80 (51%)
Query: 82 SGNSSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNT 141
+G + R + + P N L V G+ T+ DL+E F ++G + ++ D+ +
Sbjct: 25 TGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQS 84
Query: 142 GRSKGFGFIRFSSHESALKA 161
RS+GF F+ F + + A +A
Sbjct: 85 RRSRGFAFVYFENVDDAKEA 104
Score = 33.1 bits (74), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 19/38 (50%), Positives = 21/38 (55%), Gaps = 5/38 (13%)
Query: 203 TESDLREHFEYYGAVVDVLI-----PKPFREFAFVTFE 235
TE DLRE F YG + DV I + R FAFV FE
Sbjct: 59 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE 96
>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 = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 39/65 (60%), Gaps = 2/65 (3%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDK--NTGRSKGFGFIRFSSHESALKAML 163
+ V +P T+++ DL+E FEQ+G + NV D+ N +SKG F+ F + ++AL+A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 164 KKHKI 168
H +
Sbjct: 66 ALHNM 70
Score = 36.6 bits (83), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 28/52 (53%), Gaps = 7/52 (13%)
Query: 190 ASKVFVGSLTPDLTESDLREHFEYYGAVVDVLI-------PKPFREFAFVTF 234
A K+FVG + +E DLRE FE YGAV ++ + P + FVTF
Sbjct: 3 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTF 54
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 30/52 (57%)
Query: 111 IPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
IP+ T+ LK+ F + G + + D+ TG+ KG+GF + E+AL AM
Sbjct: 16 IPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAM 67
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 34/51 (66%), Gaps = 1/51 (1%)
Query: 191 SKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAK 241
S++FVG+L PD+TE ++R+ FE YG +V I K + F F+ E ++A+
Sbjct: 23 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-KGFGFIRLETRTLAE 72
Score = 31.6 bits (70), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 6/57 (10%)
Query: 102 QNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESA 158
Q + L V +P T+ ++++ FE++G V + K+ KGFGFIR + A
Sbjct: 21 QRSRLFVGNLPPDITEEEMRKLFEKYGKA--GEVFIHKD----KGFGFIRLETRTLA 71
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/91 (29%), Positives = 47/91 (51%), Gaps = 8/91 (8%)
Query: 85 SSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRS 144
SS + R+ PD N L V G+ T+ DL+E F ++G + ++ D+ + RS
Sbjct: 2 SSGSSGNRANPD-----PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRS 56
Query: 145 KGFGFIRFSSHESALKAMLKKHKI---GNRI 172
+GF F+ F + + A +A + + + G RI
Sbjct: 57 RGFAFVYFENVDDAKEAKERANGMELDGRRI 87
Score = 32.7 bits (73), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 19/38 (50%), Positives = 21/38 (55%), Gaps = 5/38 (13%)
Query: 203 TESDLREHFEYYGAVVDVLI-----PKPFREFAFVTFE 235
TE DLRE F YG + DV I + R FAFV FE
Sbjct: 28 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE 65
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/61 (42%), Positives = 35/61 (57%), Gaps = 2/61 (3%)
Query: 102 QNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKA 161
Q +L V + D L++ F FGT+ A V ++ GRSKGFGF+ FSS E A KA
Sbjct: 14 QVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG--GRSKGFGFVCFSSPEEATKA 71
Query: 162 M 162
+
Sbjct: 72 V 72
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 43.5 bits (101), Expect = 2e-04, Method: Composition-based stats.
Identities = 24/62 (38%), Positives = 32/62 (51%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAMLKK 165
L + IP + DLK FE+FG + V D+ TG KG F+ + ESALKA
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSAL 75
Query: 166 HK 167
H+
Sbjct: 76 HE 77
Score = 29.6 bits (65), Expect = 2.8, Method: Composition-based stats.
Identities = 13/41 (31%), Positives = 25/41 (60%)
Query: 184 GTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPK 224
G ++ A K+F+G + +L E DL+ FE +G + ++ + K
Sbjct: 7 GMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLK 47
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 43.1 bits (100), Expect = 2e-04, Method: Composition-based stats.
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 2/74 (2%)
Query: 93 SYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRF 152
S+ + Q L V IP+ F D DL++ F QFG + +V++ N SKGFGF+ F
Sbjct: 19 SHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKI--LDVEIIFNERGSKGFGFVTF 76
Query: 153 SSHESALKAMLKKH 166
+ A +A K H
Sbjct: 77 ENSADADRAREKLH 90
Score = 29.6 bits (65), Expect = 2.8, Method: Composition-based stats.
Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 4/63 (6%)
Query: 177 IPESTKIGTEEPVASK-VFVGSLTPDLTESDLREHFEYYGAVVDVLI---PKPFREFAFV 232
+P + + TE K + V ++ + DLR+ F +G ++DV I + + F FV
Sbjct: 15 VPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFV 74
Query: 233 TFE 235
TFE
Sbjct: 75 TFE 77
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 42.7 bits (99), Expect = 3e-04, Method: Composition-based stats.
Identities = 25/70 (35%), Positives = 37/70 (52%), Gaps = 4/70 (5%)
Query: 97 NSGPVQNTD----LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRF 152
+SGP + D + V + + DL+E F FG++ + DK TG+SKGF FI F
Sbjct: 5 SSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISF 64
Query: 153 SSHESALKAM 162
E A +A+
Sbjct: 65 HRREDAARAI 74
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 34/57 (59%), Gaps = 1/57 (1%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
L+V + + +D D++E F +FGTL+ A V D+ +GRS G + F ALKAM
Sbjct: 91 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAM 146
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 42.4 bits (98), Expect = 4e-04, Method: Composition-based stats.
Identities = 26/71 (36%), Positives = 38/71 (53%), Gaps = 3/71 (4%)
Query: 100 PVQNTD---LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHE 156
P+++ D L V IP + DLK FE+FG + V D+ TG KG F+ + + +
Sbjct: 9 PMKDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARD 68
Query: 157 SALKAMLKKHK 167
SALKA H+
Sbjct: 69 SALKAQSALHE 79
Score = 28.1 bits (61), Expect = 7.2, Method: Composition-based stats.
Identities = 14/45 (31%), Positives = 26/45 (57%)
Query: 180 STKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPK 224
S+ + ++ A K+FVG + L E DL+ FE +G + ++ + K
Sbjct: 5 SSGVPMKDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLK 49
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 89 QSKRSYPDNSGPVQNTD--LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKG 146
QS+ + S +Q TD L V +P + T +E FG+LE + + TG+SKG
Sbjct: 79 QSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKG 138
Query: 147 FGFIRFSSHESALKA 161
+GF + +SA +A
Sbjct: 139 YGFAEYMKKDSAARA 153
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 89 QSKRSYPDNSGPVQNTD--LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKG 146
QS+ + S +Q TD L V +P + T +E FG+LE + + TG+SKG
Sbjct: 79 QSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKG 138
Query: 147 FGFIRFSSHESALKA 161
+GF + +SA +A
Sbjct: 139 YGFAEYMKKDSAARA 153
>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
pdb|3H2U|D Chain D, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
Length = 283
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 89 QSKRSYPDNSGPVQNTD--LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKG 146
QS+ + S +Q TD L V +P + T +E FG+LE + + TG+SKG
Sbjct: 77 QSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKG 136
Query: 147 FGFIRFSSHESALKA 161
+GF + +SA +A
Sbjct: 137 YGFAEYMKKDSAARA 151
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 45/78 (57%), Gaps = 5/78 (6%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAMLKK 165
L+V + + +D D++E F +FGTL+ A V D+ +GRS G + F ALKAM K+
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAM-KQ 95
Query: 166 HK---IGNRICDVRIPES 180
+K + R D+++ S
Sbjct: 96 YKGVPLDGRPMDIQLVAS 113
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 45/78 (57%), Gaps = 5/78 (6%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAMLKK 165
L+V + + +D D++E F +FGTL+ A V D+ +GRS G + F ALKAM K+
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAM-KQ 95
Query: 166 HK---IGNRICDVRIPES 180
+K + R D+++ S
Sbjct: 96 YKGVPLDGRPMDIQLVAS 113
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 42.4 bits (98), Expect = 5e-04, Method: Composition-based stats.
Identities = 25/61 (40%), Positives = 35/61 (57%), Gaps = 2/61 (3%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAMLKK 165
L V IP+ F D DL++ F QFG + +V++ N SKGFGF+ F + A +A K
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKI--LDVEIIFNERGSKGFGFVTFENSADADRAREKL 75
Query: 166 H 166
H
Sbjct: 76 H 76
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 33/59 (55%)
Query: 104 TDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
T+L+V +P T ++ K F G +E + DK TG+S G+GF+ +S A KA+
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI 63
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 36/64 (56%)
Query: 98 SGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHES 157
+ P N L V G+ T+ DL+E F ++G + ++ D+ + RS+GF F+ F + +
Sbjct: 7 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 66
Query: 158 ALKA 161
A +A
Sbjct: 67 AKEA 70
Score = 32.3 bits (72), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 19/38 (50%), Positives = 21/38 (55%), Gaps = 5/38 (13%)
Query: 203 TESDLREHFEYYGAVVDVLI-----PKPFREFAFVTFE 235
TE DLRE F YG + DV I + R FAFV FE
Sbjct: 25 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE 62
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 34/57 (59%), Gaps = 1/57 (1%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
L+V + + +D D++E F +FGTL+ A V D+ +GRS G + F ALKAM
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAM 86
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 40/71 (56%), Gaps = 6/71 (8%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHE---SALKAM 162
L V G+ T+ LKE F+ G++ A + D+ TG SKGFGF+ F+S E +A +AM
Sbjct: 18 LFVKGLSEDTTEETLKESFD--GSVR-ARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAM 74
Query: 163 LKKHKIGNRIC 173
GN++
Sbjct: 75 EDGEIDGNKVT 85
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 35/60 (58%), Gaps = 1/60 (1%)
Query: 99 GPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESA 158
P ++T + V +P++ T+NDL F ++G + + DK+T +SKG FI F +SA
Sbjct: 13 APSKST-VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSA 71
Score = 29.6 bits (65), Expect = 2.8, Method: Composition-based stats.
Identities = 17/37 (45%), Positives = 20/37 (54%)
Query: 188 PVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPK 224
P S V+V +L LT +DL F YG VV V I K
Sbjct: 14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMK 50
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 43/76 (56%), Gaps = 5/76 (6%)
Query: 192 KVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKSLIGQ--HVN 249
K+FVG+++ T +LR FE G V++ + K ++AFV E ++ AK+ I Q
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVVK---DYAFVHMEKEADAKAAIAQLNGKE 67
Query: 250 IKDKKVVVMEATPKKK 265
+K K++ V +T +K
Sbjct: 68 VKGKRINVELSTKGQK 83
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 31/60 (51%)
Query: 103 NTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
NT+L+V +P TD +L F G + + D TG S G+ F+ F+S + +A+
Sbjct: 3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 34/64 (53%)
Query: 99 GPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESA 158
G ++ L + G+ TD DL + + +G + +DK T + KG+GF+ F S +A
Sbjct: 1 GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60
Query: 159 LKAM 162
KA+
Sbjct: 61 QKAV 64
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 33/58 (56%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAML 163
L V G+ + + L++ F ++G + V D+ T RS+GFGF+ F + + A AM+
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 72
Score = 38.1 bits (87), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 34/77 (44%), Gaps = 18/77 (23%)
Query: 192 KVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKP-----FREFAFVTFELDSVAKSLIGQ 246
K+FVG L+ D E L + F YG + +V++ K R F FVTFE
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFE----------- 62
Query: 247 HVNIKDKKVVVMEATPK 263
NI D K +M K
Sbjct: 63 --NIDDAKDAMMAMNGK 77
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 34/122 (27%), Positives = 56/122 (45%), Gaps = 13/122 (10%)
Query: 101 VQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALK 160
Q L V +P T+ D K FE++G E + V ++ R +GFGFIR ES
Sbjct: 20 TQRCRLFVGNLPTDITEEDFKRLFERYG--EPSEVFIN----RDRGFGFIRL---ESRTL 70
Query: 161 AMLKKHKIGNRICDVRIPESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDV 220
A + K ++ I R P + T + + V +L+P ++ L + F +G V
Sbjct: 71 AEIAKAELDGTILKSR-PLRIRFATH---GAALTVKNLSPVVSNELLEQAFSQFGPVEKA 126
Query: 221 LI 222
++
Sbjct: 127 VV 128
Score = 37.4 bits (85), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 191 SKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAK 241
++FVG+L D+TE D + FE YG +V I + R F F+ E ++A+
Sbjct: 23 CRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-RGFGFIRLESRTLAE 72
Score = 35.8 bits (81), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
L V + ++ L++ F QFG +E A V VD + GR+ G GF+ F++ A KA+
Sbjct: 99 LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKAL 154
>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 = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 44/93 (47%), Gaps = 10/93 (10%)
Query: 96 DNSGP---VQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRF 152
D GP V+ L V G+ T+ D+ + F ++G ++ ++ +D+ TG KG+ + +
Sbjct: 13 DEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 72
Query: 153 SSHESALKAM-------LKKHKIGNRICDVRIP 178
+++ A AM L I C VR P
Sbjct: 73 ETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGP 105
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 31/56 (55%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKA 161
L V + +T ++ DL++ F +G L + +D T + KGF F+ F E A+KA
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKA 66
Score = 29.3 bits (64), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 28/49 (57%), Gaps = 7/49 (14%)
Query: 192 KVFVGSLTPDLTESDLREHFEYYGAV------VDVLIPKPFREFAFVTF 234
++FV +L+ +E DL + F YG + +D L KP + FAFVTF
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKP-KGFAFVTF 57
>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 = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 38/70 (54%), Gaps = 3/70 (4%)
Query: 96 DNSGP---VQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRF 152
D GP V+ L V G+ T+ D+ + F ++G ++ ++ +D+ TG KG+ + +
Sbjct: 12 DEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 71
Query: 153 SSHESALKAM 162
+++ A AM
Sbjct: 72 ETYKEAQAAM 81
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 38.1 bits (87), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 36/67 (53%)
Query: 95 PDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSS 154
P V+ L V I +++++E F +G ++ ++ +D+ TG SKG+ + + +
Sbjct: 18 PGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYET 77
Query: 155 HESALKA 161
H+ AL A
Sbjct: 78 HKQALAA 84
>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 = 37.7 bits (86), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 37/70 (52%), Gaps = 3/70 (4%)
Query: 106 LVVLG-IPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM-- 162
+V LG IP+ T+ + + G + + D TGRSKG+ FI F ES+ A+
Sbjct: 6 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 65
Query: 163 LKKHKIGNRI 172
L +++G+R
Sbjct: 66 LNGYQLGSRF 75
>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 = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 38/66 (57%), Gaps = 3/66 (4%)
Query: 99 GPVQNTD---LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSH 155
GP ++ + L V I +++++E F +G ++ ++ +D+ TG SKG+ + + +H
Sbjct: 65 GPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETH 124
Query: 156 ESALKA 161
+ AL A
Sbjct: 125 KQALAA 130
>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 = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 37/70 (52%), Gaps = 3/70 (4%)
Query: 106 LVVLG-IPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM-- 162
+V LG IP+ T+ + + G + + D TGRSKG+ FI F ES+ A+
Sbjct: 5 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 64
Query: 163 LKKHKIGNRI 172
L +++G+R
Sbjct: 65 LNGYQLGSRF 74
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 9/73 (12%)
Query: 188 PVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFE-----LDSV--- 239
P+ KV+VG+L + +++L F YYG + V + + FAFV FE D+V
Sbjct: 71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRDL 130
Query: 240 -AKSLIGQHVNIK 251
++L G V ++
Sbjct: 131 DGRTLCGCRVRVE 143
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 37/70 (52%), Gaps = 3/70 (4%)
Query: 106 LVVLG-IPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM-- 162
+V LG IP+ T+ + + G + + D TGRSKG+ FI F ES+ A+
Sbjct: 4 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63
Query: 163 LKKHKIGNRI 172
L +++G+R
Sbjct: 64 LNGYQLGSRF 73
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 37.7 bits (86), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 9/73 (12%)
Query: 188 PVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFE-----LDSV--- 239
P+ KV+VG+L + +++L F YYG + V + + FAFV FE D+V
Sbjct: 71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVREL 130
Query: 240 -AKSLIGQHVNIK 251
++L G V ++
Sbjct: 131 DGRTLCGCRVRVE 143
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 37.4 bits (85), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 44/85 (51%), Gaps = 9/85 (10%)
Query: 81 ASGNSSATQSKRSYPD--NSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVD 138
+SG+S T+ R + D N +N + GI TD +++ F FG + ++V
Sbjct: 2 SSGSSGNTKQLR-FEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFG--QIMEIRVF 58
Query: 139 KNTGRSKGFGFIRFSSHESALKAML 163
KG+ F+RFS+HESA A++
Sbjct: 59 PE----KGYSFVRFSTHESAAHAIV 79
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 37.4 bits (85), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 39/76 (51%), Gaps = 5/76 (6%)
Query: 87 ATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKG 146
A QS++S D++ + DL V D L+ F+ F + +V D TG S+G
Sbjct: 76 AFQSQQSSSDDTFNLFVGDLNV-----NVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRG 130
Query: 147 FGFIRFSSHESALKAM 162
+GF+ F+S + A AM
Sbjct: 131 YGFVSFTSQDDAQNAM 146
Score = 36.2 bits (82), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 35/155 (22%), Positives = 70/155 (45%), Gaps = 13/155 (8%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM--L 163
L V + T++ LK+YF+ G + + +DKN ++ + F+ + A A+ L
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNN-KNVNYAFVEYHQSHDANIALQTL 61
Query: 164 KKHKIGNRICDVRIPESTKIGTEEPVASKVFVGSLTPDLTESDLREHFEYY-----GAVV 218
+I N I + ++ + + + +FVG L ++ + LR F+ + G V+
Sbjct: 62 NGKQIENNIVKINWAFQSQQSSSDDTFN-LFVGDLNVNVDDETLRNAFKDFPSYLSGHVM 120
Query: 219 DVLIPKPFREFAFVTF----ELDSVAKSLIGQHVN 249
+ R + FV+F + + S+ GQ +N
Sbjct: 121 WDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLN 155
>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 = 37.4 bits (85), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 23/91 (25%), Positives = 42/91 (46%), Gaps = 7/91 (7%)
Query: 95 PDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSS 154
P V+ L V G+ T+ D+ + F ++G ++ ++ +D+ TG KG+ + + +
Sbjct: 1 PGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 60
Query: 155 HESALKAM-------LKKHKIGNRICDVRIP 178
++ A AM L I C VR P
Sbjct: 61 YKEAQAAMEGLNGQDLMGQPISVDWCFVRGP 91
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 37.4 bits (85), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 37/75 (49%), Gaps = 4/75 (5%)
Query: 116 TDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAMLKKHKIGNRICDV 175
T D+K F FG + A V D TG+SKG+GF+ F + A A++ H G +
Sbjct: 28 TTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIV--HMGGQWLGGR 85
Query: 176 RIPESTKIGTEEPVA 190
+I T T +P A
Sbjct: 86 QI--RTNWATRKPPA 98
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 5/47 (10%)
Query: 193 VFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPF-----REFAFVTF 234
VFVG L+P++T D++ F +G + D + K + + FV+F
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSF 64
>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 90
Score = 37.4 bits (85), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 7/85 (8%)
Query: 101 VQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALK 160
V+ L V G+ T+ D+ + F ++G ++ ++ +D+ TG KG+ + + +++ A
Sbjct: 5 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQA 64
Query: 161 AM-------LKKHKIGNRICDVRIP 178
AM L I C VR P
Sbjct: 65 AMEGLNGQDLMGQPISVDWCFVRGP 89
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 37.4 bits (85), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 41/86 (47%), Gaps = 5/86 (5%)
Query: 99 GPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTG---RSKGFGFIRFSSH 155
G ++ L + + ++ T+ LK F + G ++ + KN S GFGF+ +
Sbjct: 1 GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60
Query: 156 ESALKAM--LKKHKIGNRICDVRIPE 179
E A KA+ L+ H + +VRI E
Sbjct: 61 EQAQKALKQLQGHTVDGHKLEVRISE 86
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 37.4 bits (85), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 7/85 (8%)
Query: 101 VQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALK 160
V+ L V G+ T+ D+ + F ++G ++ ++ +D+ TG KG+ + + +++ A
Sbjct: 5 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQA 64
Query: 161 AM-------LKKHKIGNRICDVRIP 178
AM L I C VR P
Sbjct: 65 AMEGLNGQDLMGQPISVDWCFVRGP 89
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 37.0 bits (84), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 29/47 (61%), Gaps = 3/47 (6%)
Query: 189 VASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFE 235
++K+ VG+++P T +LR FE YG V++ I K ++AFV E
Sbjct: 9 ASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK---DYAFVHME 52
>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 = 37.0 bits (84), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 39/80 (48%), Gaps = 10/80 (12%)
Query: 116 TDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSH---ESALKAMLKKHKIGNRI 172
T D+K F FG + A V D TG+SKG+GF+ F + E+A++ M + G +I
Sbjct: 28 TTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 87
Query: 173 CDVRIPESTKIGTEEPVASK 192
T T +P A K
Sbjct: 88 -------RTNWATRKPPAPK 100
Score = 33.9 bits (76), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 5/47 (10%)
Query: 193 VFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPF-----REFAFVTF 234
VFVG L+P++T D++ F +G + D + K + + FV+F
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSF 64
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 36.6 bits (83), Expect = 0.026, Method: Composition-based stats.
Identities = 19/51 (37%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 116 TDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAMLKKH 166
TD D+++ FE FGT++ V + G SKG F++F +H A A+ H
Sbjct: 25 TDEDVRKMFEPFGTIDECTV-LRGPDGTSKGCAFVKFQTHAEAQAAINTLH 74
Score = 28.1 bits (61), Expect = 7.1, Method: Composition-based stats.
Identities = 17/57 (29%), Positives = 31/57 (54%), Gaps = 4/57 (7%)
Query: 192 KVFVGSLTPDLTESDLREHFEYYGAVVDVLIPK----PFREFAFVTFELDSVAKSLI 244
K+FVG L T+ D+R+ FE +G + + + + + AFV F+ + A++ I
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAI 70
>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 = 36.2 bits (82), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 34/71 (47%), Gaps = 3/71 (4%)
Query: 92 RSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIR 151
R PD G T L V + + + + L+ FE++G + + D+ T S+GF F+R
Sbjct: 39 RPPPDVEG---MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVR 95
Query: 152 FSSHESALKAM 162
F A AM
Sbjct: 96 FHDKRDAEDAM 106
Score = 31.2 bits (69), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 21/46 (45%), Positives = 23/46 (50%), Gaps = 5/46 (10%)
Query: 195 VGSLTPDLTESDLREHFEYYGAVVDVLIP-----KPFREFAFVTFE 235
V +LT + LR FE YG V DV IP K R FAFV F
Sbjct: 52 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFH 97
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 36.2 bits (82), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 5/63 (7%)
Query: 103 NTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDK---NTGRSKGFGFIRFSSHESAL 159
+ ++V IP+ +++E F FG E V++ K TG +GFGF+ F + + A
Sbjct: 15 TSKILVRNIPFQANQREIRELFSTFG--ELKTVRLPKKMTGTGAHRGFGFVDFITKQDAK 72
Query: 160 KAM 162
KA
Sbjct: 73 KAF 75
>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 = 36.2 bits (82), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 25/47 (53%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRF 152
L + G+P D+ +KE FG L+ N+ D TG SKG+ F +
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEY 163
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 36.2 bits (82), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 43/85 (50%), Gaps = 8/85 (9%)
Query: 95 PDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSS 154
P SG + + V GI + +++ +F ++G+++ + D+ TG SKG+GF+ F +
Sbjct: 2 PLGSGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYN 60
Query: 155 H-------ESALKAMLKKHKIGNRI 172
ES + KK K+G I
Sbjct: 61 DVDVQKIVESQINFHGKKLKLGPAI 85
Score = 33.9 bits (76), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 44/86 (51%), Gaps = 4/86 (4%)
Query: 183 IGTEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLI----PKPFREFAFVTFELDS 238
+G+ + + + VFVG + + E+++R F YG+V +V I + + FV+F D
Sbjct: 3 LGSGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDV 62
Query: 239 VAKSLIGQHVNIKDKKVVVMEATPKK 264
+ ++ +N KK+ + A K+
Sbjct: 63 DVQKIVESQINFHGKKLKLGPAIRKQ 88
>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 = 35.8 bits (81), Expect = 0.037, Method: Composition-based stats.
Identities = 15/57 (26%), Positives = 33/57 (57%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
L V G+ T+ D+ + F ++G ++ ++ +D+ TG KG+ + + +++ A AM
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
>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 = 35.8 bits (81), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 26/46 (56%)
Query: 117 DNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
D L+ F+ F + +V D TG S+G+GF+ F+S + A AM
Sbjct: 15 DETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 35.8 bits (81), Expect = 0.041, Method: Composition-based stats.
Identities = 17/47 (36%), Positives = 25/47 (53%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRF 152
L + G+P D+ +KE FG L+ N+ D TG SKG+ F +
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEY 50
>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 = 35.4 bits (80), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 25/47 (53%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRF 152
L + G+P D+ +KE FG L+ N+ D TG SKG+ F +
Sbjct: 99 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEY 145
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 35.4 bits (80), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 25/47 (53%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRF 152
L + G+P D+ +KE FG L+ N+ D TG SKG+ F +
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEY 143
>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
At Ph 6.0
pdb|4F26|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
A Ph 9.0
Length = 115
Score = 35.4 bits (80), Expect = 0.049, Method: Composition-based stats.
Identities = 19/66 (28%), Positives = 36/66 (54%), Gaps = 2/66 (3%)
Query: 99 GPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESA 158
GP+ + ++ + + + + L + F FG + V D+N SKG+GF+ F + E+A
Sbjct: 1 GPLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAA 58
Query: 159 LKAMLK 164
+A+ K
Sbjct: 59 ERAIEK 64
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 35.0 bits (79), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 30/53 (56%), Gaps = 3/53 (5%)
Query: 192 KVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKSLI 244
K+F+G+L + TE ++R FE YG V++ I + + FV E + A+ I
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDI---IKNYGFVHIEDKTAAEDAI 59
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 35.0 bits (79), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 30/59 (50%)
Query: 104 TDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
T L V + + + + L+ FE++G + + D+ T S+GF F+RF A AM
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAM 129
Score = 31.2 bits (69), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 21/45 (46%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 195 VGSLTPDLTESDLREHFEYYGAVVDVLIP-----KPFREFAFVTF 234
V +LT + LR FE YG V DV IP K R FAFV F
Sbjct: 75 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRF 119
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 34.7 bits (78), Expect = 0.081, Method: Composition-based stats.
Identities = 23/68 (33%), Positives = 33/68 (48%), Gaps = 8/68 (11%)
Query: 99 GPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESA 158
G + NT L V P +++L E F FG ++ VK+ GF F+ F ESA
Sbjct: 27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMK--EVKI------LNGFAFVEFEEAESA 78
Query: 159 LKAMLKKH 166
KA+ + H
Sbjct: 79 AKAIEEVH 86
Score = 29.3 bits (64), Expect = 3.2, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 4/58 (6%)
Query: 191 SKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTF-ELDSVAKSLIGQH 247
+++FV D+ ES+L E F +G + +V K FAFV F E +S AK++ H
Sbjct: 32 TRLFVRPFPLDVQESELNEIFGPFGPMKEV---KILNGFAFVEFEEAESAAKAIEEVH 86
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 34.7 bits (78), Expect = 0.082, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 37/61 (60%), Gaps = 4/61 (6%)
Query: 102 QNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKA 161
++ LV+ + ++ T+ L+E FE+ F V ++N G+SKG+ FI F+S E A +A
Sbjct: 14 ESKTLVLSNLSYSATEETLQEVFEK---ATFIKVPQNQN-GKSKGYAFIEFASFEDAKEA 69
Query: 162 M 162
+
Sbjct: 70 L 70
>pdb|1WG5|A Chain A, Solution Structure Of The First Rrm Domain In
Heterogeneous Nuclear Ribonucleoprotein H
Length = 104
Score = 34.3 bits (77), Expect = 0.11, Method: Composition-based stats.
Identities = 24/81 (29%), Positives = 40/81 (49%), Gaps = 3/81 (3%)
Query: 110 GIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAMLKKHK-- 167
G+P+ + ++ ++F + GRS G F++F+S E A KA LKKHK
Sbjct: 22 GLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKA-LKKHKER 80
Query: 168 IGNRICDVRIPESTKIGTEEP 188
IG+R ++ ++ T P
Sbjct: 81 IGHRYIEIFKSSRAEVRTSGP 101
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 34.3 bits (77), Expect = 0.11, Method: Composition-based stats.
Identities = 16/43 (37%), Positives = 25/43 (58%)
Query: 120 LKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
L E +QFG L++ V + +T SKG F +F + E+A K +
Sbjct: 32 LGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCL 74
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 34.3 bits (77), Expect = 0.12, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 116 TDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAMLKKH 166
+++D++ FE FG +E + + G SKG F+++SSH A A+ H
Sbjct: 28 SEDDVRRLFEAFGNIEECTI-LRGPDGNSKGCAFVKYSSHAEAQAAINALH 77
Score = 28.1 bits (61), Expect = 7.7, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 20/37 (54%)
Query: 186 EEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLI 222
+ P K+FVG L +E D+R FE +G + + I
Sbjct: 11 QPPSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTI 47
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 33.9 bits (76), Expect = 0.14, Method: Composition-based stats.
Identities = 25/82 (30%), Positives = 43/82 (52%), Gaps = 10/82 (12%)
Query: 192 KVFVGSLTPDLTESDLREHFEYYGAVVDVLIPK--------PFREFAFVTFELDSVAKSL 243
KVFVG L PD+ E ++ F +G +V V P P + +AF+ F+ +S ++L
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQAL 68
Query: 244 IGQHVNIKDKKVVVMEATPKKK 265
I + +D K+ + ++P K
Sbjct: 69 IDACLE-EDGKLYLCVSSPTIK 89
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 33.9 bits (76), Expect = 0.15, Method: Composition-based stats.
Identities = 18/44 (40%), Positives = 24/44 (54%)
Query: 192 KVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFE 235
KV+VG+L + +L F YYG + V I + FAFV FE
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFE 45
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAMLKK 165
L+ +P+ T ++LKE FE + A +++ G+SKG +I F + A K +K
Sbjct: 96 LLAKNLPYKVTQDELKEVFE-----DAAEIRLVSKDGKSKGIAYIEFKTEADAEKTFEEK 150
Query: 166 H 166
Sbjct: 151 Q 151
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 33.5 bits (75), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 1/60 (1%)
Query: 105 DLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAMLK 164
++ V + ++ T +KE F QFG + + D+ T + KGFGF+ ES +A+ K
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEM-QEESVSEAIAK 61
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 33.1 bits (74), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 31/57 (54%)
Query: 102 QNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESA 158
Q+ + V G+ ++ L E F Q G + ++ D+ TG+ +G+GF+ F S E A
Sbjct: 14 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDA 70
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 33.1 bits (74), Expect = 0.23, Method: Composition-based stats.
Identities = 17/46 (36%), Positives = 28/46 (60%), Gaps = 2/46 (4%)
Query: 192 KVFVGSLTPDLTESDLREHFEYYGAVVDVLIP--KPFREFAFVTFE 235
+++VG+L PD+ D+ + F YGA+ D+ + + FAFV FE
Sbjct: 24 RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFE 69
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 33.1 bits (74), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 16/67 (23%), Positives = 36/67 (53%), Gaps = 1/67 (1%)
Query: 98 SGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHES 157
S ++ L + G+P++ T +L+E + GT++ + V G+ KG ++ + +
Sbjct: 12 STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRL-VTNRAGKPKGLAYVEYENESQ 70
Query: 158 ALKAMLK 164
A +A++K
Sbjct: 71 ASQAVMK 77
>pdb|2HGN|A Chain A, Nmr Structure Of The Third Qrrm Domain Of Human Hnrnp F
pdb|2KG1|A Chain A, Structure Of The Third Qrrm Domain Of Hnrnp F In Complex
With A Agggau G-Tract Rna
Length = 139
Score = 33.1 bits (74), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 41/79 (51%), Gaps = 5/79 (6%)
Query: 89 QSKRSYPDNSGPVQNTD---LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSK 145
Q R D+ VQ+T + + G+P+ T+ND+ +F + ++++ + GR
Sbjct: 29 QMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVR-VHIEIGPD-GRVT 86
Query: 146 GFGFIRFSSHESALKAMLK 164
G + F++HE A+ AM K
Sbjct: 87 GEADVEFATHEEAVAAMSK 105
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 33.1 bits (74), Expect = 0.27, Method: Composition-based stats.
Identities = 16/56 (28%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 186 EEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAK 241
E+ + ++VG L +TE+DLR HF +G + + + + ++ AF+ F A+
Sbjct: 8 EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-QQCAFIQFATRQAAE 62
Score = 28.1 bits (61), Expect = 7.9, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 6/55 (10%)
Query: 104 TDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESA 158
T L V G+ T T+ DL+ +F QFG + V + + FI+F++ ++A
Sbjct: 13 TTLYVGGLGDTITETDLRNHFYQFGEIRTITVV------QRQQCAFIQFATRQAA 61
>pdb|3Q2S|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2S|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2T|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
pdb|3Q2T|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
Length = 229
Score = 33.1 bits (74), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 27/59 (45%), Gaps = 2/59 (3%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKN--TGRSKGFGFIRFSSHESALKAM 162
L + + W TD DL E G + +K +N G+SKGF + S S+ K M
Sbjct: 71 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 129
>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 = 32.7 bits (73), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 41/81 (50%), Gaps = 8/81 (9%)
Query: 99 GPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSH--- 155
G + + V GI + +++ +F ++G+++ + D+ TG SKG+GF+ F +
Sbjct: 5 GKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDV 63
Query: 156 ----ESALKAMLKKHKIGNRI 172
ES + KK K+G I
Sbjct: 64 QKIVESQINFHGKKLKLGPAI 84
Score = 31.6 bits (70), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 4/76 (5%)
Query: 193 VFVGSLTPDLTESDLREHFEYYGAVVDVLI----PKPFREFAFVTFELDSVAKSLIGQHV 248
VFVG + + E+++R F YG+V +V I + + FV+F D + ++ +
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQI 71
Query: 249 NIKDKKVVVMEATPKK 264
N KK+ + A K+
Sbjct: 72 NFHGKKLKLGPAIRKQ 87
>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Rna, Uuguucuu
Length = 102
Score = 32.7 bits (73), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 41/81 (50%), Gaps = 8/81 (9%)
Query: 99 GPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSH--- 155
G + + V GI + +++ +F ++G+++ + D+ TG SKG+GF+ F +
Sbjct: 5 GKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDV 63
Query: 156 ----ESALKAMLKKHKIGNRI 172
ES + KK K+G I
Sbjct: 64 QKIVESQINFHGKKLKLGPAI 84
Score = 32.0 bits (71), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 4/78 (5%)
Query: 193 VFVGSLTPDLTESDLREHFEYYGAVVDVLI----PKPFREFAFVTFELDSVAKSLIGQHV 248
VFVG + + E+++R F YG+V +V I + + FV+F D + ++ +
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQI 71
Query: 249 NIKDKKVVVMEATPKKKM 266
N KK+ + A K+ +
Sbjct: 72 NFHGKKLKLGPAIRKQNL 89
>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
pdb|4F02|D Chain D, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
Length = 213
Score = 32.7 bits (73), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 26/45 (57%), Gaps = 2/45 (4%)
Query: 120 LKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAMLK 164
L + F FG + V D+N SKG+GF+ F + E+A +A+ K
Sbjct: 120 LYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEK 162
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 44/78 (56%), Gaps = 8/78 (10%)
Query: 188 PVASKVFVGSLTPDLTESDLREHFEYYGAVVDV-----LIPKPFREFAFVTFELDSVA-K 241
P+AS ++VG L PD+TE+ L E F G ++ + +I + +A+V F+ + A +
Sbjct: 14 PMAS-LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAER 72
Query: 242 SLIGQHVN-IKDKKVVVM 258
+L + + IK K V +M
Sbjct: 73 ALDTMNFDVIKGKPVRIM 90
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 32.7 bits (73), Expect = 0.33, Method: Composition-based stats.
Identities = 22/66 (33%), Positives = 32/66 (48%), Gaps = 8/66 (12%)
Query: 101 VQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALK 160
+ NT L V P +++L E F FG ++ VK+ GF F+ F ESA K
Sbjct: 2 LSNTRLFVRPFPLDVQESELNEIFGPFGPMK--EVKI------LNGFAFVEFEEAESAAK 53
Query: 161 AMLKKH 166
A+ + H
Sbjct: 54 AIEEVH 59
Score = 29.3 bits (64), Expect = 3.7, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 4/58 (6%)
Query: 191 SKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTF-ELDSVAKSLIGQH 247
+++FV D+ ES+L E F +G + +V K FAFV F E +S AK++ H
Sbjct: 5 TRLFVRPFPLDVQESELNEIFGPFGPMKEV---KILNGFAFVEFEEAESAAKAIEEVH 59
>pdb|1WEZ|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein H'
Length = 102
Score = 32.7 bits (73), Expect = 0.37, Method: Composition-based stats.
Identities = 16/55 (29%), Positives = 31/55 (56%), Gaps = 2/55 (3%)
Query: 110 GIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAMLK 164
G+P+ T+ND+ +F + ++++ + GR G + F++HE A+ AM K
Sbjct: 22 GLPYRATENDIYNFFSPLNPMR-VHIEIGPD-GRVTGEADVEFATHEDAVAAMAK 74
>pdb|3P5T|L Chain L, Cfim25-Cfim68 Complex
pdb|3P5T|M Chain M, Cfim25-Cfim68 Complex
pdb|3P5T|N Chain N, Cfim25-Cfim68 Complex
pdb|3P5T|O Chain O, Cfim25-Cfim68 Complex
pdb|3P5T|P Chain P, Cfim25-Cfim68 Complex
pdb|3P5T|Q Chain Q, Cfim25-Cfim68 Complex
pdb|3P6Y|C Chain C, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|D Chain D, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|G Chain G, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|H Chain H, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|K Chain K, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|L Chain L, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|O Chain O, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|P Chain P, Cf Im25-Cf Im68-Uguaa Complex
Length = 90
Score = 32.3 bits (72), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 27/59 (45%), Gaps = 2/59 (3%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKN--TGRSKGFGFIRFSSHESALKAM 162
L + + W TD DL E G + +K +N G+SKGF + S S+ K M
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62
>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 = 32.3 bits (72), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 24/47 (51%)
Query: 116 TDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
T DL+ +F G++ + DK +G KG+ +I F+ S A+
Sbjct: 49 TAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV 95
>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|B Chain B, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|C Chain C, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|D Chain D, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|E Chain E, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|F Chain F, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|G Chain G, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|H Chain H, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
Length = 190
Score = 32.3 bits (72), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 26/45 (57%), Gaps = 2/45 (4%)
Query: 120 LKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAMLK 164
L + F FG + V D+N SKG+GF+ F + E+A +A+ K
Sbjct: 115 LYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEK 157
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 31/53 (58%), Gaps = 6/53 (11%)
Query: 188 PVASKVFVGSLTPDLTESDLREHFEYYGAVVDV-----LIPKPFREFAFVTFE 235
P+AS ++VG L PD+TE+ L E F G ++ + +I + +A+V F+
Sbjct: 9 PMAS-LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQ 60
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 32.0 bits (71), Expect = 0.54, Method: Composition-based stats.
Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 13/76 (17%)
Query: 192 KVFVGSLTPDLTESDLREHFEYYGAVVDVLIPK----PFREFAFVTFE---------LDS 238
K+F+G L + E L+ F +G + +VL+ K R FAF+TFE D
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDM 68
Query: 239 VAKSLIGQHVNIKDKK 254
KSL G+ + ++ K
Sbjct: 69 NGKSLHGKAIKVEQAK 84
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 32.0 bits (71), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 31/66 (46%), Gaps = 8/66 (12%)
Query: 97 NSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHE 156
+SG + L V + T T+ L++ F QFG LE + K + FI F +
Sbjct: 5 SSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLE--------RVKKLKDYAFIHFDERD 56
Query: 157 SALKAM 162
A+KAM
Sbjct: 57 GAVKAM 62
>pdb|2HGM|A Chain A, Nmr Structure Of The Second Qrrm Domain Of Human Hnrnp F
pdb|2KG0|A Chain A, Structure Of The Second Qrrm Domain Of Hnrnp F In Complex
With A Agggau G-Tract Rna
Length = 126
Score = 32.0 bits (71), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 28/85 (32%), Positives = 43/85 (50%), Gaps = 10/85 (11%)
Query: 97 NSGPVQNTDLVVL-GIPWTFTDNDLKEYFEQFGTLEFA----NVKVDKNTGRSKGFGFIR 151
NS N V L G+P+ T ++ ++F LE + VD G+ G F++
Sbjct: 35 NSADSANDGFVRLRGLPFGCTKEEIVQFFS---GLEIVPNGITLPVDPE-GKITGEAFVQ 90
Query: 152 FSSHESALKAMLK-KHKIGNRICDV 175
F+S E A KA+ K K +IG+R +V
Sbjct: 91 FASQELAEKALGKHKERIGHRYIEV 115
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 31.6 bits (70), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAMLKK 165
L+ + + T+++LKE FE LE V D G+SKG +I F S A K + +K
Sbjct: 102 LLAKNLSFNITEDELKEVFED--ALEIRLVSQD---GKSKGIAYIEFKSEADAEKNLEEK 156
Query: 166 H 166
Sbjct: 157 Q 157
Score = 29.6 bits (65), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 34/124 (27%), Positives = 55/124 (44%), Gaps = 24/124 (19%)
Query: 94 YPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFS 153
+ N P ++ + + I F NDL VD TG ++ FG++ F
Sbjct: 17 FIGNLNPNKSVAELKVAISELFAKNDL--------------AVVDVRTGTNRKFGYVDFE 62
Query: 154 SHESALKAM-LKKHKI-GNRICDVRIP---ESTKIGTEEPVASKVFVGSLTPDLTESDLR 208
S E KA+ L K+ GN I + P +S K+ A + +L+ ++TE +L+
Sbjct: 63 SAEDLEKALELTGLKVFGNEI-KLEKPKGRDSKKV----RAARTLLAKNLSFNITEDELK 117
Query: 209 EHFE 212
E FE
Sbjct: 118 EVFE 121
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 31.6 bits (70), Expect = 0.67, Method: Composition-based stats.
Identities = 17/45 (37%), Positives = 26/45 (57%), Gaps = 2/45 (4%)
Query: 120 LKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAMLK 164
L + F FG + V D+N SKG+GF+ F + E+A +A+ K
Sbjct: 28 LYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEK 70
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 31.6 bits (70), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 3/59 (5%)
Query: 120 LKEYFEQFGT-LEFANVKVDKNTGRSKGFGFIRFSSHESALKAMLKKHKIGNRICDVRI 177
L + F FG L+ + D +TG SKG+ FI F+S +++ A+ + G +C+ I
Sbjct: 22 LYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMN--GQYLCNRPI 78
Score = 30.0 bits (66), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 37/71 (52%), Gaps = 14/71 (19%)
Query: 190 ASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFRE--------FAFVTF----ELD 237
+S +F+G+L P++ E L + F +G ++ PK R+ +AF+ F D
Sbjct: 5 SSGIFIGNLDPEIDEKLLYDTFSAFGVILQT--PKIMRDPDTGNSKGYAFINFASFDASD 62
Query: 238 SVAKSLIGQHV 248
+ +++ GQ++
Sbjct: 63 AAIEAMNGQYL 73
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 31.2 bits (69), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 21/45 (46%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 195 VGSLTPDLTESDLREHFEYYGAVVDVLIP-----KPFREFAFVTF 234
V +LT + LR FE YG V DV IP K R FAFV F
Sbjct: 18 VDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRF 62
Score = 29.3 bits (64), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 33/72 (45%), Gaps = 3/72 (4%)
Query: 90 SKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGF 149
S S PD G + L V + + + + L+ FE++G + + + +T +GF F
Sbjct: 3 SGSSGPDVDGMIT---LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAF 59
Query: 150 IRFSSHESALKA 161
+RF A A
Sbjct: 60 VRFHDRRDAQDA 71
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 31.2 bits (69), Expect = 0.97, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 116 TDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAMLKKH 166
++ D+ F+ FG ++ V + G SKG F++FSSH A A+ H
Sbjct: 28 SEEDVLRLFQPFGVIDECTV-LRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77
>pdb|2DNN|A Chain A, Solution Structure Of Rna Binding Domain In Rna-Binding
Protein 12
Length = 109
Score = 31.2 bits (69), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 41/72 (56%), Gaps = 7/72 (9%)
Query: 100 PVQNTDLVVL--GIPWTFTDNDLKEYFEQFGTLEFANVKVDKN-TGRSKGFGFIRFSSHE 156
P+ DL V G+P++ +ND++++F L V + K+ GR+ G G ++F S +
Sbjct: 11 PINPDDLYVSVHGMPFSAMENDVRDFFH---GLRVDAVHLLKDHVGRNNGNGLVKFLSPQ 67
Query: 157 SALKAMLKKHKI 168
+A LK++++
Sbjct: 68 DTFEA-LKRNRM 78
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 31.2 bits (69), Expect = 1.1, Method: Composition-based stats.
Identities = 12/39 (30%), Positives = 22/39 (56%)
Query: 119 DLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHES 157
DL+++F G + + D+N+ RSKG ++ F +S
Sbjct: 41 DLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQS 79
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 30.4 bits (67), Expect = 1.8, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAMLKK 165
L+ + + T+++LKE FE LE V D G+SKG +I F S A K + +K
Sbjct: 19 LLAKNLSFNITEDELKEVFED--ALEIRLVSQD---GKSKGIAYIEFKSEADAEKNLEEK 73
Query: 166 H 166
Sbjct: 74 Q 74
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 30.0 bits (66), Expect = 2.0, Method: Composition-based stats.
Identities = 26/110 (23%), Positives = 44/110 (40%), Gaps = 14/110 (12%)
Query: 81 ASGNSSATQSKRSYPDNSGPVQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKN 140
+SG+S +KR L V G+ D L F FG + + +D
Sbjct: 2 SSGSSGMATTKRV------------LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYE 49
Query: 141 TGRSKGFGFIRFSSHESALKAM--LKKHKIGNRICDVRIPESTKIGTEEP 188
T + +GF F+ F E A A+ + + ++ R V + + +I P
Sbjct: 50 TEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIKESGP 99
>pdb|1WEX|A Chain A, Solution Structure Of Rrm Domain In Protein Bab28521
Length = 104
Score = 30.0 bits (66), Expect = 2.3, Method: Composition-based stats.
Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 189 VASKVFVGSLTPDLTESDLREHFEYYGAVVDVLIPKPFREFAFVTFELDSVAKSLI 244
V+ V V L + E+DL E E +G + V++ PF+ A V FE AK +
Sbjct: 14 VSPVVHVRGLCESVVEADLVEALEKFGTICYVMM-MPFKRQALVEFENIDSAKECV 68
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 29.6 bits (65), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 25/57 (43%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
L V G+ D L F FG + + +D T + +GF F+ F E A A+
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 122
>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 = 29.6 bits (65), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 37/75 (49%), Gaps = 13/75 (17%)
Query: 193 VFVGSLTPDLTESDLREHFEYYGAVVDVLI------PKPFREFAFVTFE----LDSVAKS 242
+FV + D TES LR FE YG + + + KP R +AF+ +E + S K
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKP-RGYAFIEYEHERDMHSAYKH 163
Query: 243 LIGQHVNIKDKKVVV 257
G+ I ++V+V
Sbjct: 164 ADGK--KIDGRRVLV 176
>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 = 2.7, Method: Composition-based stats.
Identities = 15/54 (27%), Positives = 33/54 (61%), Gaps = 3/54 (5%)
Query: 111 IPWTFTDNDLKEYFEQFGTLEFANVKV--DKNTGRSKGFGFIRFSSHESALKAM 162
+P T++D++ + G ++ V++ +K++G+S+GF F+ FS + A + M
Sbjct: 9 LPQAATEDDIRGQLQSHG-VQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWM 61
>pdb|2M2B|A Chain A, Nmr Structure Of The Rrm2 Domain Of The Protein Rbm10 From
Homo Sapiens
Length = 131
Score = 29.6 bits (65), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 22/34 (64%), Gaps = 2/34 (5%)
Query: 127 FGTLEFANVKV--DKNTGRSKGFGFIRFSSHESA 158
+ L +NV+V DK T ++GF FI+ S+ E+A
Sbjct: 47 YAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIEAA 80
>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 = 29.3 bits (64), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 26/49 (53%), Gaps = 7/49 (14%)
Query: 193 VFVGSLTPDLTESDLREHFEYYGAVVDVLIP------KPFREFAFVTFE 235
+FV + D TES LR FE YG + + + KP R +AF+ +E
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKP-RGYAFIEYE 152
>pdb|2VOD|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auauuuu
pdb|2VOD|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auauuuu
pdb|2VON|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auaauuu
pdb|2VON|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auaauuu
pdb|2VOO|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Uuuuuuuu
pdb|2VOO|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Uuuuuuuu
pdb|2VOP|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auuuu
Length = 193
Score = 29.3 bits (64), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 3/61 (4%)
Query: 101 VQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRS-KGFGFIRFSSHESAL 159
V+N + + G P T +D+KE+ E G + N+++ + ++ KG F+ F S ESA
Sbjct: 107 VKNRSVYIKGFPTDATLDDIKEWLEDKG--QVLNIQMRRTLHKAFKGSIFVVFDSIESAK 164
Query: 160 K 160
K
Sbjct: 165 K 165
>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 = 29.3 bits (64), Expect = 3.7, Method: Composition-based stats.
Identities = 17/57 (29%), Positives = 25/57 (43%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
L V G+ D L F FG + + +D T + +GF F+ F E A A+
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 61
>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 = 29.3 bits (64), Expect = 3.9, Method: Composition-based stats.
Identities = 17/57 (29%), Positives = 25/57 (43%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
L V G+ D L F FG + + +D T + +GF F+ F E A A+
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 66
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 29.3 bits (64), Expect = 3.9, Method: Composition-based stats.
Identities = 20/62 (32%), Positives = 29/62 (46%), Gaps = 8/62 (12%)
Query: 98 SGPVQNTDLVVLGIPWTFTDNDLKEYFEQFG-TLEFANVKVDKNTGRSKGFGFIRFSSHE 156
S P + T + IP T+ DL F+ FG L+F + KG FI++ +HE
Sbjct: 22 SAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP-------EKGCCFIKYDTHE 74
Query: 157 SA 158
A
Sbjct: 75 QA 76
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 29.3 bits (64), Expect = 4.1, Method: Composition-based stats.
Identities = 17/57 (29%), Positives = 25/57 (43%)
Query: 106 LVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAM 162
L V G+ D L F FG + + +D T + +GF F+ F E A A+
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 64
>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2
pdb|3BS9|B Chain B, X-Ray Structure Of Human Tia-1 Rrm2
Length = 87
Score = 28.9 bits (63), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 28/49 (57%), Gaps = 3/49 (6%)
Query: 127 FGTLEFANVKVDKNTGRSKGFGFIRFSSH---ESALKAMLKKHKIGNRI 172
FG + A V D TG+SKG+GF+ F + E+A++ M + G +I
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 78
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 28.9 bits (63), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 35/68 (51%), Gaps = 8/68 (11%)
Query: 103 NTDLVVLGIPWTFTDNDLKEYFEQFGTLE--------FANVKVDKNTGRSKGFGFIRFSS 154
N+ + V G+ + T +DL ++F+Q G ++ ++ +DK TG+ KG + +
Sbjct: 15 NSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYED 74
Query: 155 HESALKAM 162
+A A+
Sbjct: 75 PPTAKAAV 82
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 28.5 bits (62), Expect = 5.8, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 33/58 (56%), Gaps = 3/58 (5%)
Query: 116 TDNDLKEYFEQFGTLEFANVKVDK-NTGRSKGFGFIRFSSHESALKAMLKKHKIGNRI 172
T + + E F +G ++ ++ V++ + SKG+ ++ F + + A KA+ KH G +I
Sbjct: 17 TKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL--KHMDGGQI 72
>pdb|1S79|A Chain A, Solution Structure Of The Central Rrm Of Human La Protein
Length = 103
Score = 28.5 bits (62), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 3/61 (4%)
Query: 101 VQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRS-KGFGFIRFSSHESAL 159
V+N + + G P T +D+KE+ E G + N+++ + ++ KG F+ F S ESA
Sbjct: 9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQV--LNIQMRRTLHKAFKGSIFVVFDSIESAK 66
Query: 160 K 160
K
Sbjct: 67 K 67
>pdb|1ZH5|A Chain A, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
pdb|1ZH5|B Chain B, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
Length = 195
Score = 28.1 bits (61), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 3/61 (4%)
Query: 101 VQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRS-KGFGFIRFSSHESAL 159
V+N + + G P T +D+KE+ E G + N++ + ++ KG F+ F S ESA
Sbjct: 109 VKNRSVYIKGFPTDATLDDIKEWLEDKGQV--LNIQXRRTLHKAFKGSIFVVFDSIESAK 166
Query: 160 K 160
K
Sbjct: 167 K 167
>pdb|1YTY|A Chain A, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
pdb|1YTY|B Chain B, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
Length = 194
Score = 28.1 bits (61), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 3/61 (4%)
Query: 101 VQNTDLVVLGIPWTFTDNDLKEYFEQFGTLEFANVKVDKNTGRS-KGFGFIRFSSHESAL 159
V+N + + G P T +D+KE+ E G + N++ + ++ KG F+ F S ESA
Sbjct: 108 VKNRSVYIKGFPTDATLDDIKEWLEDKGQV--LNIQXRRTLHKAFKGSIFVVFDSIESAK 165
Query: 160 K 160
K
Sbjct: 166 K 166
>pdb|1HL6|B Chain B, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1HL6|D Chain D, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
Length = 149
Score = 28.1 bits (61), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 35/130 (26%), Positives = 57/130 (43%), Gaps = 21/130 (16%)
Query: 128 GTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAMLKKHKIGNRIC---DVRIPESTKIG 184
G L +AN KN + F+ H+S ++ LK+ I + I D+ P ++G
Sbjct: 31 GKLRYANNSNYKNDTMIRKEAFV----HQSVMEE-LKRIIIDSEIMQEDDLPWPPPDRVG 85
Query: 185 TEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDV---LIPKPFREFAFVTFELDSVAK 241
+E ++ +G T S G++VDV P+ R F ++ +L +
Sbjct: 86 RQE---LEIVIGDEHISFTTSKT-------GSLVDVNRSKDPEGLRCFYYLVQDLKCLVF 135
Query: 242 SLIGQHVNIK 251
SLIG H IK
Sbjct: 136 SLIGLHFKIK 145
>pdb|1OO0|A Chain A, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
pdb|1RK8|B Chain B, Structure Of The Cytosolic Protein Pym Bound To The Mago-
Y14 Core Of The Exon Junction Complex
pdb|2X1G|B Chain B, Crystal Structure Of Importin13 - Mago-Y14 Complex
pdb|2X1G|D Chain D, Crystal Structure Of Importin13 - Mago-Y14 Complex
Length = 147
Score = 27.7 bits (60), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 35/130 (26%), Positives = 57/130 (43%), Gaps = 21/130 (16%)
Query: 128 GTLEFANVKVDKNTGRSKGFGFIRFSSHESALKAMLKKHKIGNRIC---DVRIPESTKIG 184
G L +AN KN + F+ H+S ++ LK+ I + I D+ P ++G
Sbjct: 31 GKLRYANNSNYKNDTMIRKEAFV----HQSVMEE-LKRIIIDSEIMQEDDLPWPPPDRVG 85
Query: 185 TEEPVASKVFVGSLTPDLTESDLREHFEYYGAVVDV---LIPKPFREFAFVTFELDSVAK 241
+E ++ +G T S G++VDV P+ R F ++ +L +
Sbjct: 86 RQE---LEIVIGDEHISFTTSKT-------GSLVDVNRSKDPEGLRCFYYLVQDLKCLVF 135
Query: 242 SLIGQHVNIK 251
SLIG H IK
Sbjct: 136 SLIGLHFKIK 145
>pdb|2GHP|A Chain A, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|B Chain B, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|C Chain C, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|D Chain D, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|E Chain E, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|F Chain F, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|G Chain G, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|H Chain H, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
Length = 292
Score = 27.7 bits (60), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 24/94 (25%), Positives = 46/94 (48%), Gaps = 6/94 (6%)
Query: 89 QSKRSYPDNSGPVQNTDLVVLGIPWTFTD-NDLKEYFEQFGTLEFANVKV-DKNTGRSKG 146
+SKR+ +S ++ ++ + + D N L+E FE FG++E N+ K +
Sbjct: 199 KSKRT---DSATLEGREIXIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNC 255
Query: 147 FGFIRFSSHESALKAM-LKKHKIGNRICDVRIPE 179
F F + +SA +A+ + +GNR V + +
Sbjct: 256 CAFXVFENKDSAERALQXNRSLLGNREISVSLAD 289
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
0.314 0.132 0.384
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,836,401
Number of Sequences: 62578
Number of extensions: 454525
Number of successful extensions: 1020
Number of sequences better than 100.0: 163
Number of HSP's better than 100.0 without gapping: 112
Number of HSP's successfully gapped in prelim test: 51
Number of HSP's that attempted gapping in prelim test: 775
Number of HSP's gapped (non-prelim): 257
length of query: 363
length of database: 14,973,337
effective HSP length: 100
effective length of query: 263
effective length of database: 8,715,537
effective search space: 2292186231
effective search space used: 2292186231
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 52 (24.6 bits)