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= 040243
(797 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1K1G|A Chain A, Structural Basis For Recognition Of The Intron Branch Site
Rna By Splicing Factor 1
Length = 131
Score = 110 bits (274), Expect = 4e-24, Method: Compositional matrix adjust.
Identities = 61/127 (48%), Positives = 88/127 (69%), Gaps = 8/127 (6%)
Query: 250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDL 309
++ K+ IP EYP NF+GL+IGPRGNT K +E+E AKI+IRGKGSVKEG++ +K D
Sbjct: 6 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRK-DG 64
Query: 310 KPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQ-----PVDEVLNEHKRQQLRELAALN 364
+ P E+E LH LV A T E+++ A + +L+ P D+ N+ ++ QLRELA LN
Sbjct: 65 QMLPGEDEPLHALVTANTMENVKKAVEQIRNILKQGIETPEDQ--NDLRKMQLRELARLN 122
Query: 365 GTIRDEE 371
GT+R+++
Sbjct: 123 GTLREDD 129
>pdb|2BL5|A Chain A, Solution Structure Of The Kh-Qua2 Region Of The Xenopus
Star-Gsg Quaking Protein
Length = 140
Score = 109 bits (273), Expect = 5e-24, Method: Compositional matrix adjust.
Identities = 60/126 (47%), Positives = 87/126 (69%), Gaps = 6/126 (4%)
Query: 250 KLQKKLYIPMKEYPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDL 309
+LQ+KLY+P+KEYP +NF+G I+GPRG T K++E ETG KI++RGKGS+++ + +++
Sbjct: 1 QLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRG 60
Query: 310 KPDPSE-NEDLHVLVEAETQES-----LEGAAAMVEKLLQPVDEVLNEHKRQQLRELAAL 363
KP+ NEDLHVL+ E ++ L+ A V+KLL P E + K+ +L ELA L
Sbjct: 61 KPNWEHLNEDLHVLITVEDAQNRAELKLKRAVEEVKKLLVPAAEGEDSLKKMKLMELAIL 120
Query: 364 NGTIRD 369
NGT RD
Sbjct: 121 NGTYRD 126
>pdb|2M0G|A Chain A, Structure, Phosphorylation And U2af65 Binding Of The
Nterminal Domain Of Splicing Factor 1 During 3 Splice
Site Recognition
Length = 145
Score = 82.0 bits (201), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 50/129 (38%), Positives = 80/129 (62%), Gaps = 5/129 (3%)
Query: 134 RKRRSRWADDEPKPVIQLPDFMKDFTGGIEFDPEIQALNSRLLE-ISRMLQSG-LPLDDR 191
+++RSRW D + +P G+ + E + +E ++R L++G L +
Sbjct: 16 KRKRSRWNQDTMEQKTVIPGMPTVIPPGLTREQERAYIVQLQIEDLTRKLRTGDLGIPPN 75
Query: 192 PEGQRSPSPEPIYDNMGIRINTREYRARERLNKERQEIISQIIKRNPAFKPPADYRPP-- 249
PE RSPSPEPIY++ G R+NTRE+R R++L +ER +I++++ NP FKPPADY+PP
Sbjct: 76 PED-RSPSPEPIYNSEGKRLNTREFRTRKKLEEERHNLITEMVALNPDFKPPADYKPPAT 134
Query: 250 KLQKKLYIP 258
++ K+ IP
Sbjct: 135 RVCDKVMIP 143
>pdb|2M09|A Chain A, Structure, Phosphorylation And U2af65 Binding Of The
Nterminal Domain Of Splicing Factor 1 During 3 Splice
Site Recognition
Length = 121
Score = 78.6 bits (192), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 41/85 (48%), Positives = 63/85 (74%), Gaps = 4/85 (4%)
Query: 177 EISRMLQSG-LPLDDRPEGQRSPSPEPIYDNMGIRINTREYRARERLNKERQEIISQIIK 235
+++R L++G L + PE RSPSPEPIY++ G R+NTRE+R R++L +ER +I++++
Sbjct: 36 DLTRKLRTGDLGIPPNPE-DRSPSPEPIYNSEGKRLNTREFRTRKKLEEERHNLITEMVA 94
Query: 236 RNPAFKPPADYRPP--KLQKKLYIP 258
NP FKPPADY+PP ++ K+ IP
Sbjct: 95 LNPDFKPPADYKPPATRVSDKVMIP 119
>pdb|4FXX|A Chain A, Structure Of Sf1 Coiled-coil Domain
pdb|4FXX|B Chain B, Structure Of Sf1 Coiled-coil Domain
pdb|4FXX|C Chain C, Structure Of Sf1 Coiled-coil Domain
pdb|4FXX|D Chain D, Structure Of Sf1 Coiled-coil Domain
Length = 112
Score = 77.0 bits (188), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 38/74 (51%), Positives = 57/74 (77%), Gaps = 2/74 (2%)
Query: 177 EISRMLQSG-LPLDDRPEGQRSPSPEPIYDNMGIRINTREYRARERLNKERQEIISQIIK 235
+++R L++G L + PE RSPSPEPIY++ G R+NTRE+R R++L +ER +I++++
Sbjct: 40 DLTRKLRTGDLGIPPNPE-DRSPSPEPIYNSEGKRLNTREFRTRKKLEEERHNLITEMVA 98
Query: 236 RNPAFKPPADYRPP 249
NP FKPPADY+PP
Sbjct: 99 LNPDFKPPADYKPP 112
>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|B Chain B, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|C Chain C, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|D Chain D, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
Length = 84
Score = 73.6 bits (179), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 36/77 (46%), Positives = 49/77 (63%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
TNL + YLP + D L LFS+ G++ AK+I+D+V G S GYGFV Y + A AI
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 64
Query: 552 SMNGYRLEGRTIAVRVA 568
++NG RL+ +TI V A
Sbjct: 65 TLNGLRLQSKTIKVSYA 81
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 72.8 bits (177), Expect = 6e-13, Method: Compositional matrix adjust.
Identities = 34/77 (44%), Positives = 49/77 (63%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
TNL + YLP + D LF + GDI K+++D++TG S GYGFV Y+D A+ AI
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 552 SMNGYRLEGRTIAVRVA 568
++NG +L+ +TI V A
Sbjct: 65 TLNGLKLQTKTIKVSYA 81
Score = 55.5 bits (132), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 42/67 (62%)
Query: 489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANN 548
+ D NLY+ LP T+ + +LFS +G I+ ++++ D+ TG+S+G GF+++ A
Sbjct: 88 IRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEE 147
Query: 549 AIASMNG 555
AI +NG
Sbjct: 148 AIKGLNG 154
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 72.8 bits (177), Expect = 7e-13, Method: Compositional matrix adjust.
Identities = 34/77 (44%), Positives = 49/77 (63%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
TNL + YLP + D LF + GDI K+++D++TG S GYGFV Y+D A+ AI
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 552 SMNGYRLEGRTIAVRVA 568
++NG +L+ +TI V A
Sbjct: 65 TLNGLKLQTKTIKVSYA 81
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 72.4 bits (176), Expect = 9e-13, Method: Composition-based stats.
Identities = 36/77 (46%), Positives = 49/77 (63%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
TNL + YLP + D L LFS+ G++ AK+I+D+V G S GYGFV Y + A AI
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 552 SMNGYRLEGRTIAVRVA 568
++NG RL+ +TI V A
Sbjct: 63 TLNGLRLQSKTIKVSYA 79
Score = 59.7 bits (143), Expect = 6e-09, Method: Composition-based stats.
Identities = 31/86 (36%), Positives = 50/86 (58%), Gaps = 1/86 (1%)
Query: 483 AKPIKE-LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYA 541
A+P E + D NLYI LP T+ + +FS FG I+ ++V+ D+ TG+S+G F+++
Sbjct: 79 ARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFD 138
Query: 542 DIQMANNAIASMNGYRLEGRTIAVRV 567
A AI S NG++ G + + V
Sbjct: 139 KRSEAEEAITSFNGHKPPGSSEPITV 164
>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 = 72.4 bits (176), Expect = 9e-13, Method: Composition-based stats.
Identities = 36/77 (46%), Positives = 49/77 (63%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
TNL + YLP + D L LFS+ G++ AK+I+D+V G S GYGFV Y + A AI
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 552 SMNGYRLEGRTIAVRVA 568
++NG RL+ +TI V A
Sbjct: 63 TLNGLRLQSKTIKVSYA 79
Score = 59.7 bits (143), Expect = 7e-09, Method: Composition-based stats.
Identities = 31/86 (36%), Positives = 50/86 (58%), Gaps = 1/86 (1%)
Query: 483 AKPIKE-LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYA 541
A+P E + D NLYI LP T+ + +FS FG I+ ++V+ D+ TG+S+G F+++
Sbjct: 79 ARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFD 138
Query: 542 DIQMANNAIASMNGYRLEGRTIAVRV 567
A AI S NG++ G + + V
Sbjct: 139 KRSEAEEAITSFNGHKPPGSSEPITV 164
>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|B Chain B, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|C Chain C, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|D Chain D, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
Length = 99
Score = 72.0 bits (175), Expect = 1e-12, Method: Composition-based stats.
Identities = 36/77 (46%), Positives = 48/77 (62%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
TNL + YLP D L LFS+ G++ AK+I+D+V G S GYGFV Y + A AI
Sbjct: 20 TNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 79
Query: 552 SMNGYRLEGRTIAVRVA 568
++NG RL+ +TI V A
Sbjct: 80 TLNGLRLQSKTIKVSYA 96
>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 = 69.3 bits (168), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 33/77 (42%), Positives = 48/77 (62%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
TNL + YLP + + LF + G+I K+++D++TG S GYGFV Y D + A AI
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 552 SMNGYRLEGRTIAVRVA 568
++NG RL+ +TI V A
Sbjct: 63 TLNGLRLQTKTIKVSYA 79
Score = 60.8 bits (146), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 31/82 (37%), Positives = 50/82 (60%), Gaps = 2/82 (2%)
Query: 489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANN 548
+ D NLY+ LP T+ L +LFS +G I+ ++++ D+VTG+S+G GF+++ A
Sbjct: 86 IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEE 145
Query: 549 AIASMNGYRLEGRT--IAVRVA 568
AI +NG + G T I V+ A
Sbjct: 146 AIKGLNGQKPSGATEPITVKFA 167
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 67.0 bits (162), Expect = 4e-11, Method: Composition-based stats.
Identities = 31/75 (41%), Positives = 48/75 (64%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
L+IG LP L+DD + L ++FG + ++KD TG+SKGY F +Y DI + + AIA +
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 554 NGYRLEGRTIAVRVA 568
NG +L + + V+ A
Sbjct: 64 NGMQLGDKKLLVQRA 78
>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 = 65.1 bits (157), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 31/75 (41%), Positives = 48/75 (64%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
L+IG LP L+DD + L ++FG + ++KD TG+SKGY F +Y DI + + AIA +
Sbjct: 99 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 158
Query: 554 NGYRLEGRTIAVRVA 568
NG +L + + V+ A
Sbjct: 159 NGMQLGDKKLLVQRA 173
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 64.7 bits (156), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 31/75 (41%), Positives = 48/75 (64%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
L+IG LP L+DD + L ++FG + ++KD TG+SKGY F +Y DI + + AIA +
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 554 NGYRLEGRTIAVRVA 568
NG +L + + V+ A
Sbjct: 157 NGMQLGDKKLLVQRA 171
>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 = 64.7 bits (156), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 31/75 (41%), Positives = 48/75 (64%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
L+IG LP L+DD + L ++FG + ++KD TG+SKGY F +Y DI + + AIA +
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176
Query: 554 NGYRLEGRTIAVRVA 568
NG +L + + V+ A
Sbjct: 177 NGMQLGDKKLLVQRA 191
>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 = 63.5 bits (153), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 30/78 (38%), Positives = 49/78 (62%)
Query: 490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNA 549
+ NL+I +LP D L+++F FG++V AKV D+ T +SK +GFV Y + A A
Sbjct: 24 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 83
Query: 550 IASMNGYRLEGRTIAVRV 567
I SMNG+++ + + V++
Sbjct: 84 IQSMNGFQIGMKRLKVQL 101
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 62.4 bits (150), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 30/76 (39%), Positives = 46/76 (60%)
Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
NL + Y+P T+D+ L +LF +G I K++ DR T S+GYGFVK+ A AIA
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 553 MNGYRLEGRTIAVRVA 568
+NG+ + + + V +A
Sbjct: 104 LNGFNILNKRLKVALA 119
>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 = 62.0 bits (149), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 31/82 (37%), Positives = 51/82 (62%), Gaps = 2/82 (2%)
Query: 489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANN 548
+ DTNLY+ LP T+ DD L +F +G IV +++D++TG +G FV+Y + A
Sbjct: 11 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQE 70
Query: 549 AIASMNGYRLEGRT--IAVRVA 568
AI+++N EG + ++VR+A
Sbjct: 71 AISALNNVIPEGGSQPLSVRLA 92
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 61.6 bits (148), Expect = 2e-09, Method: Composition-based stats.
Identities = 32/81 (39%), Positives = 50/81 (61%)
Query: 490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNA 549
D+ L++G L ++ L ++FS +G I V+KDR T S+G+GFV + +I A +A
Sbjct: 11 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 70
Query: 550 IASMNGYRLEGRTIAVRVAGK 570
+ +MNG ++GR I V AGK
Sbjct: 71 MMAMNGKSVDGRQIRVDQAGK 91
>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 = 61.2 bits (147), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 37/93 (39%), Positives = 52/93 (55%), Gaps = 4/93 (4%)
Query: 479 GSNGAKPIKELDDTN---LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGY 535
GS+G+ K+ D +N +++G L P + + + F+ FG I A+V+KD TG SKGY
Sbjct: 1 GSSGSSGQKK-DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGY 59
Query: 536 GFVKYADIQMANNAIASMNGYRLEGRTIAVRVA 568
GFV + + A NAI M G L GR I A
Sbjct: 60 GFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA 92
>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 = 60.8 bits (146), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 34/89 (38%), Positives = 54/89 (60%), Gaps = 5/89 (5%)
Query: 482 GAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYA 541
G + IK DTNLY+ LP T+ DD L +F +G IV +++D++TG +G FV+Y
Sbjct: 94 GGESIK---DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYN 150
Query: 542 DIQMANNAIASMNGYRLEGRT--IAVRVA 568
+ A AI+++N EG + ++VR+A
Sbjct: 151 KREEAQEAISALNNVIPEGGSQPLSVRLA 179
Score = 47.0 bits (110), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 37/78 (47%)
Query: 491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
+TNL + YLP D L LF G I ++ +D TG S GY FV + + AI
Sbjct: 14 NTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAI 73
Query: 551 ASMNGYRLEGRTIAVRVA 568
+NG + + + V A
Sbjct: 74 KVLNGITVRNKRLKVSYA 91
>pdb|4FXW|B Chain B, Structure Of Phosphorylated Sf1 Complex With U2af65-uhm
Domain
pdb|4FXW|D Chain D, Structure Of Phosphorylated Sf1 Complex With U2af65-uhm
Domain
Length = 124
Score = 60.5 bits (145), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 25/47 (53%), Positives = 37/47 (78%)
Query: 203 IYDNMGIRINTREYRARERLNKERQEIISQIIKRNPAFKPPADYRPP 249
IY++ G R+NTRE+R R++L +ER +I++ + NP FKPPADY+PP
Sbjct: 78 IYNSEGKRLNTREFRTRKKLEEERHNLITEXVALNPDFKPPADYKPP 124
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 60.1 bits (144), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 30/76 (39%), Positives = 45/76 (59%)
Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
GS+G+ +K+ D L+IG +P LD+ L LF FG I V+KDR TGM KG F+
Sbjct: 1 GSSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFL 60
Query: 539 KYADIQMANNAIASMN 554
Y + + A A ++++
Sbjct: 61 TYCERESALKAQSALH 76
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 59.7 bits (143), Expect = 7e-09, Method: Composition-based stats.
Identities = 30/75 (40%), Positives = 50/75 (66%), Gaps = 1/75 (1%)
Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMA-KVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
+L++G L P +D++ + R F+T G+ VM+ K+I++R+TG+ GY FV++AD+ A +
Sbjct: 11 SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70
Query: 552 SMNGYRLEGRTIAVR 566
+NG L G T A R
Sbjct: 71 KINGKPLPGATPAKR 85
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 59.3 bits (142), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 31/84 (36%), Positives = 52/84 (61%), Gaps = 2/84 (2%)
Query: 487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMA 546
+ + DTNLY+ LP T+ DD L +F +G IV +++D++TG +G FV+Y + A
Sbjct: 85 ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 144
Query: 547 NNAIASMNGYRLEGRT--IAVRVA 568
AI+++N EG + ++VR+A
Sbjct: 145 QEAISALNNVIPEGGSQPLSVRLA 168
Score = 48.9 bits (115), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 39/78 (50%)
Query: 491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
+TNL + YLP + D L LF G I ++++D TG S GY FV + + AI
Sbjct: 3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62
Query: 551 ASMNGYRLEGRTIAVRVA 568
+NG + + + V A
Sbjct: 63 KVLNGITVRNKRLKVSYA 80
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 58.2 bits (139), Expect = 2e-08, Method: Composition-based stats.
Identities = 29/74 (39%), Positives = 44/74 (59%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
+ LY+G L + +D L +F FG I ++KD TG SKGYGF+ ++D + A A+
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 552 SMNGYRLEGRTIAV 565
+NG+ L GR + V
Sbjct: 66 QLNGFELAGRPMRV 79
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 57.4 bits (137), Expect = 3e-08, Method: Composition-based stats.
Identities = 28/72 (38%), Positives = 43/72 (59%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
LY+G L + +D L +F FG I +++ D TG SKGYGF+ ++D + A A+ +
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 554 NGYRLEGRTIAV 565
NG+ L GR + V
Sbjct: 89 NGFELAGRPMKV 100
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 57.4 bits (137), Expect = 3e-08, Method: Composition-based stats.
Identities = 33/82 (40%), Positives = 44/82 (53%), Gaps = 1/82 (1%)
Query: 490 DDT-NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANN 548
DDT NL++G L +DD+ L F F + V+ D TG S+GYGFV + A N
Sbjct: 85 DDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQN 144
Query: 549 AIASMNGYRLEGRTIAVRVAGK 570
A+ SM G L GR + + A K
Sbjct: 145 AMDSMQGQDLNGRPLRINWAAK 166
Score = 37.7 bits (86), Expect = 0.027, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
LY+G L + +D L + F G I K++ D+ + Y FV+Y AN A+ ++
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTL 61
Query: 554 NGYRLEGRTIAVRVA 568
NG ++E + + A
Sbjct: 62 NGKQIENNIVKINWA 76
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 56.6 bits (135), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 42/67 (62%)
Query: 491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
D NLY+ LP T+ + +LFS +G I+ ++++ D+ TG+S+G GF+++ A AI
Sbjct: 1 DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
Query: 551 ASMNGYR 557
+NG +
Sbjct: 61 KGLNGQK 67
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 56.2 bits (134), Expect = 7e-08, Method: Composition-based stats.
Identities = 36/88 (40%), Positives = 51/88 (57%), Gaps = 4/88 (4%)
Query: 479 GSNGAKPIKELDDTN---LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGY 535
GS+G+ K+ D +N +++G L P + + + F+ FG I A+V+KD TG SKGY
Sbjct: 1 GSSGSSGQKK-DTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGY 59
Query: 536 GFVKYADIQMANNAIASMNGYRLEGRTI 563
GFV + + A NAI M G L GR I
Sbjct: 60 GFVSFYNKLDAENAIVHMGGQWLGGRQI 87
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 55.8 bits (133), Expect = 8e-08, Method: Composition-based stats.
Identities = 26/77 (33%), Positives = 44/77 (57%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
+ +Y+ LP +L ++ L R+FS +G +V ++KD+ T SKG F+ + D A N
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
Query: 552 SMNGYRLEGRTIAVRVA 568
++N +L GR I +A
Sbjct: 77 AINNKQLFGRVIKASIA 93
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 55.5 bits (132), Expect = 1e-07, Method: Composition-based stats.
Identities = 29/85 (34%), Positives = 49/85 (57%)
Query: 483 AKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYAD 542
K I+ + NL+I +LP D L F FG+++ AKV D+ T +SK +GFV + +
Sbjct: 32 GKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDN 91
Query: 543 IQMANNAIASMNGYRLEGRTIAVRV 567
A AI +MNG+++ + + V++
Sbjct: 92 PDSAQVAIKAMNGFQVGTKRLKVQL 116
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 55.1 bits (131), Expect = 2e-07, Method: Composition-based stats.
Identities = 32/80 (40%), Positives = 46/80 (57%), Gaps = 1/80 (1%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMA-KVIKDRVTGMSKGYGFVKYADIQMANNAI 550
+ ++IG L P +D+ L FS FG I+ K+++D TG SKGY F+ +A ++ AI
Sbjct: 6 SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAI 65
Query: 551 ASMNGYRLEGRTIAVRVAGK 570
+MNG L R I V A K
Sbjct: 66 EAMNGQYLCNRPITVSYAFK 85
>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 = 55.1 bits (131), Expect = 2e-07, Method: Composition-based stats.
Identities = 30/78 (38%), Positives = 41/78 (52%)
Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
NL++G L +DD+ L F F + V+ D TG S+GYGFV + A NA+ S
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 553 MNGYRLEGRTIAVRVAGK 570
M G L GR + + A K
Sbjct: 63 MQGQDLNGRPLRINWAAK 80
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 54.7 bits (130), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 29/76 (38%), Positives = 44/76 (57%), Gaps = 1/76 (1%)
Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
GS+G P+K+ D L++G +P LD+ L LF FG I V+KDR+TG+ KG F+
Sbjct: 4 GSSGV-PMKDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFL 62
Query: 539 KYADIQMANNAIASMN 554
Y A A ++++
Sbjct: 63 TYCARDSALKAQSALH 78
>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 = 54.7 bits (130), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 42/72 (58%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
+Y+ + L DD + +F FG I A + +D TG KGYGF++Y Q + +A++SM
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 554 NGYRLEGRTIAV 565
N + L G+ + V
Sbjct: 188 NLFDLGGQYLRV 199
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 38/74 (51%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
+ +Y+G + L +D + + F+ FG I + D VT KG+ FV+Y + A A+
Sbjct: 29 SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 88
Query: 552 SMNGYRLEGRTIAV 565
MN L GR I V
Sbjct: 89 QMNSVMLGGRNIKV 102
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 53.9 bits (128), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 44/73 (60%)
Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
++++G +P ++ L +FS G +V +++ DR TG KGYGF +Y D + A +A+ +
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 553 MNGYRLEGRTIAV 565
+NG GR + V
Sbjct: 70 LNGREFSGRALRV 82
>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 = 53.1 bits (126), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 29/73 (39%), Positives = 40/73 (54%), Gaps = 2/73 (2%)
Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
N++I L ++D+ L FS FG+I+ KV+ D SKGYGFV + + A AI
Sbjct: 100 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEK 157
Query: 553 MNGYRLEGRTIAV 565
MNG L R + V
Sbjct: 158 MNGMLLNDRKVFV 170
Score = 37.7 bits (86), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 39/74 (52%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
+LY+G L P + + L FS G I+ +V +D +T S GY +V + A A+
Sbjct: 11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 70
Query: 552 SMNGYRLEGRTIAV 565
+MN ++G+ + +
Sbjct: 71 TMNFDVIKGKPVRI 84
>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 = 53.1 bits (126), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 41/72 (56%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
+Y+ + L DD + +F FG I + +D TG KGYGF++Y Q + +A++SM
Sbjct: 113 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 172
Query: 554 NGYRLEGRTIAV 565
N + L G+ + V
Sbjct: 173 NLFDLGGQYLRV 184
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 37/72 (51%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
+Y+G + L +D + + F+ FG I + D VT KG+ FV+Y + A A+ M
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 554 NGYRLEGRTIAV 565
N L GR I V
Sbjct: 76 NSVMLGGRNIKV 87
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 53.1 bits (126), Expect = 7e-07, Method: Composition-based stats.
Identities = 32/85 (37%), Positives = 46/85 (54%), Gaps = 3/85 (3%)
Query: 482 GAKP-IKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKY 540
GA P +++ N++I L ++D+ L FS FG+I+ KV+ D SKGYGFV +
Sbjct: 1 GADPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHF 58
Query: 541 ADIQMANNAIASMNGYRLEGRTIAV 565
+ A AI MNG L R + V
Sbjct: 59 ETQEAAERAIEKMNGMLLNDRKVFV 83
>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 = 52.8 bits (125), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 29/73 (39%), Positives = 40/73 (54%), Gaps = 2/73 (2%)
Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
N++I L ++D+ L FS FG+I+ KV+ D SKGYGFV + + A AI
Sbjct: 105 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEK 162
Query: 553 MNGYRLEGRTIAV 565
MNG L R + V
Sbjct: 163 MNGMLLNDRKVFV 175
Score = 38.1 bits (87), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 39/74 (52%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
+LY+G L P + + L FS G I+ +V +D +T S GY +V + A A+
Sbjct: 16 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 75
Query: 552 SMNGYRLEGRTIAV 565
+MN ++G+ + +
Sbjct: 76 TMNFDVIKGKPVRI 89
>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 = 52.8 bits (125), Expect = 8e-07, Method: Composition-based stats.
Identities = 30/77 (38%), Positives = 41/77 (53%), Gaps = 2/77 (2%)
Query: 489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANN 548
L N++I L ++D+ L FS FG+I+ KV+ D SKGYGFV + + A
Sbjct: 3 LGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAER 60
Query: 549 AIASMNGYRLEGRTIAV 565
AI MNG L R + V
Sbjct: 61 AIEKMNGMLLNDRKVFV 77
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 52.4 bits (124), Expect = 1e-06, Method: Composition-based stats.
Identities = 34/82 (41%), Positives = 43/82 (52%), Gaps = 1/82 (1%)
Query: 487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMA 546
K+ T +++G LP D L + F FGDI A VI DR TG S+GYGFV AD A
Sbjct: 13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAA 72
Query: 547 NNAIASMNGYRLEGRTIAVRVA 568
A N ++GR V +A
Sbjct: 73 ERACKDPNPI-IDGRKANVNLA 93
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 51.2 bits (121), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 31/77 (40%), Positives = 44/77 (57%), Gaps = 3/77 (3%)
Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
GS+G + I NLY+ L +DD+ L + FS FG I AKV+ + G SKG+GFV
Sbjct: 4 GSSGDR-ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFV 60
Query: 539 KYADIQMANNAIASMNG 555
++ + A A+ MNG
Sbjct: 61 CFSSPEEATKAVTEMNG 77
>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 = 51.2 bits (121), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 40/72 (55%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
+Y+ + L DD + +F FG I + +D TG KGYGF++Y Q + +A++S
Sbjct: 112 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSX 171
Query: 554 NGYRLEGRTIAV 565
N + L G+ + V
Sbjct: 172 NLFDLGGQYLRV 183
Score = 39.3 bits (90), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 35/72 (48%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
+Y+G + L +D + + F+ FG I D VT KG+ FV+Y + A A+
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 554 NGYRLEGRTIAV 565
N L GR I V
Sbjct: 75 NSVXLGGRNIKV 86
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 50.4 bits (119), Expect = 4e-06, Method: Composition-based stats.
Identities = 26/78 (33%), Positives = 39/78 (50%)
Query: 491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
+TNL + YLP + D L LF G I ++++D TG S GY FV + + AI
Sbjct: 3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62
Query: 551 ASMNGYRLEGRTIAVRVA 568
+NG + + + V A
Sbjct: 63 KVLNGITVRNKRLKVSYA 80
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 50.4 bits (119), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 32/85 (37%), Positives = 47/85 (55%), Gaps = 1/85 (1%)
Query: 485 PIKELD-DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADI 543
PI E + D +Y+G L + + L LF G +V + KDRVTG +GYGFV++
Sbjct: 8 PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSE 67
Query: 544 QMANNAIASMNGYRLEGRTIAVRVA 568
+ A+ AI M+ +L G+ I V A
Sbjct: 68 EDADYAIKIMDMIKLYGKPIRVNKA 92
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 50.4 bits (119), Expect = 4e-06, Method: Composition-based stats.
Identities = 22/68 (32%), Positives = 44/68 (64%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
+Y+G +P ++ ++ L S G ++ K++ D TG SKGY F+++ D++ + +A+ ++
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 554 NGYRLEGR 561
NGY+L R
Sbjct: 65 NGYQLGSR 72
>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 = 50.4 bits (119), Expect = 4e-06, Method: Composition-based stats.
Identities = 22/68 (32%), Positives = 44/68 (64%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
+Y+G +P ++ ++ L S G ++ K++ D TG SKGY F+++ D++ + +A+ ++
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 554 NGYRLEGR 561
NGY+L R
Sbjct: 66 NGYQLGSR 73
>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 = 49.7 bits (117), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 45/70 (64%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
+Y+G +P ++ ++ L S G ++ K++ D TG SKGY F+++ D++ + +A+ ++
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 554 NGYRLEGRTI 563
NGY+L R +
Sbjct: 67 NGYQLGSRFL 76
>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 = 49.7 bits (117), Expect = 6e-06, Method: Composition-based stats.
Identities = 30/71 (42%), Positives = 41/71 (57%)
Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
++++G L P + + F+ FG I A+V+KD TG SKGYGFV + + A NAI
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 553 MNGYRLEGRTI 563
M G L GR I
Sbjct: 68 MGGQWLGGRQI 78
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 48.9 bits (115), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 45/88 (51%), Gaps = 5/88 (5%)
Query: 472 TPGHPGLGSNGAKPI----KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDR 527
+ G GL ++G + +E D TNLYI LP ++D+ L + FG ++ ++++D
Sbjct: 2 SSGSSGLKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS 61
Query: 528 VTGMSKGYGFVKYADIQMANNAIASMNG 555
+G S+G GF + + I NG
Sbjct: 62 -SGTSRGVGFARMESTEKCEAVIGHFNG 88
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 48.1 bits (113), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
L++G L + + L FS +G++V ++KD+ T S+G+GFVK+ D +AS
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS- 77
Query: 554 NGYRLEGRTI 563
+ L+GR I
Sbjct: 78 RPHTLDGRNI 87
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 47.4 bits (111), Expect = 3e-05, Method: Composition-based stats.
Identities = 28/76 (36%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
N+Y+G L + + + LFS FG + K+I DR T KG+GFV+ + + + AIA
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61
Query: 553 MNGYRLEGRTIAVRVA 568
++ GRTI V A
Sbjct: 62 LDNTDFMGRTIRVTEA 77
>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 = 47.4 bits (111), Expect = 3e-05, Method: Composition-based stats.
Identities = 29/75 (38%), Positives = 40/75 (53%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
LY+G L +DD L F FGDI ++ D T +G+ FV++ + A AI +M
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 554 NGYRLEGRTIAVRVA 568
N L GRTI V +A
Sbjct: 65 NESELFGRTIRVNLA 79
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 47.4 bits (111), Expect = 3e-05, Method: Composition-based stats.
Identities = 29/75 (38%), Positives = 40/75 (53%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
LY+G L +DD L F FGDI ++ D T +G+ FV++ + A AI +M
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 554 NGYRLEGRTIAVRVA 568
N L GRTI V +A
Sbjct: 126 NESELFGRTIRVNLA 140
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 47.4 bits (111), Expect = 3e-05, Method: Composition-based stats.
Identities = 29/75 (38%), Positives = 40/75 (53%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
LY+G L +DD L F FGDI ++ D T +G+ FV++ + A AI +M
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 554 NGYRLEGRTIAVRVA 568
N L GRTI V +A
Sbjct: 68 NESELFGRTIRVNLA 82
>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 = 47.4 bits (111), Expect = 3e-05, Method: Composition-based stats.
Identities = 29/75 (38%), Positives = 40/75 (53%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
LY+G L +DD L F FGDI ++ D T +G+ FV++ + A AI +M
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 554 NGYRLEGRTIAVRVA 568
N L GRTI V +A
Sbjct: 70 NESELFGRTIRVNLA 84
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 46.6 bits (109), Expect = 5e-05, Method: Composition-based stats.
Identities = 33/90 (36%), Positives = 46/90 (51%), Gaps = 4/90 (4%)
Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
GS+G K + LY+G L +DD L F FGDI ++ D T +G+ FV
Sbjct: 4 GSSGMATTKRV----LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFV 59
Query: 539 KYADIQMANNAIASMNGYRLEGRTIAVRVA 568
++ + A AI +MN L GRTI V +A
Sbjct: 60 EFELAEDAAAAIDNMNESELFGRTIRVNLA 89
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 46.6 bits (109), Expect = 5e-05, Method: Composition-based stats.
Identities = 25/68 (36%), Positives = 41/68 (60%), Gaps = 2/68 (2%)
Query: 479 GSNGAKPIKEL--DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYG 536
GS+G+ +K ++L + LP + L FSTFG+++M +V KD TG SKG+G
Sbjct: 1 GSSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFG 60
Query: 537 FVKYADIQ 544
FV++ + +
Sbjct: 61 FVRFTEYE 68
>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 = 46.6 bits (109), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 45/77 (58%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
T+L + L D L R+F +G + + +DR T S+G+ FV++ D + A +A+
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 552 SMNGYRLEGRTIAVRVA 568
+M+G L+GR + V++A
Sbjct: 108 AMDGAVLDGRELRVQMA 124
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 46.2 bits (108), Expect = 8e-05, Method: Composition-based stats.
Identities = 25/77 (32%), Positives = 45/77 (58%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
T+L + L D L R+F +G + + +DR T S+G+ FV++ D + A +A+
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 552 SMNGYRLEGRTIAVRVA 568
+M+G L+GR + V++A
Sbjct: 131 AMDGAVLDGRELRVQMA 147
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 45.8 bits (107), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
L+IG L ++ L +F G I +IKDR T S+G+ F+ + + A NA M
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDM 68
Query: 554 NGYRLEGRTIAVRVAGK 570
NG L G+ I V A K
Sbjct: 69 NGKSLHGKAIKVEQAKK 85
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 44/74 (59%), Gaps = 1/74 (1%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVT-GMSKGYGFVKYADIQMANNAI 550
T ++IG L + D ++ +FST+G I M + +R+ +SKGY +V++ + A A+
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
Query: 551 ASMNGYRLEGRTIA 564
M+G +++G+ I
Sbjct: 65 KHMDGGQIDGQEIT 78
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 44.7 bits (104), Expect = 2e-04, Method: Composition-based stats.
Identities = 28/81 (34%), Positives = 42/81 (51%), Gaps = 1/81 (1%)
Query: 485 PIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQ 544
P +E D +++G L + ++ L LF G + + KDR G K +GFV + +
Sbjct: 10 PAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPE 68
Query: 545 MANNAIASMNGYRLEGRTIAV 565
+ AIA +NG RL GR I V
Sbjct: 69 SVSYAIALLNGIRLYGRPINV 89
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 43.5 bits (101), Expect = 5e-04, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
++IG L +GL F FG++ V++D +T S+G+GFV + D Q + + +
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMD-QAGVDKVLAQ 61
Query: 554 NGYRLEGRTIAVRVA 568
+ + L+ +TI +VA
Sbjct: 62 SRHELDSKTIDPKVA 76
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 43.5 bits (101), Expect = 5e-04, Method: Composition-based stats.
Identities = 23/62 (37%), Positives = 32/62 (51%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
+ LYI L P D L++L +G IV K I D+ T KGYGFV + A A+
Sbjct: 6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65
Query: 552 SM 553
++
Sbjct: 66 AL 67
>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 = 43.1 bits (100), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 42/79 (53%), Gaps = 1/79 (1%)
Query: 487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMA 546
KE+D ++Y+G + L FS+ G I ++ D+ +G KGY ++++A+
Sbjct: 32 KEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSV 91
Query: 547 NNAIASMNGYRLEGRTIAV 565
+ A+A M+ GRTI V
Sbjct: 92 DAAVA-MDETVFRGRTIKV 109
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 42.4 bits (98), Expect = 0.001, Method: Composition-based stats.
Identities = 28/96 (29%), Positives = 49/96 (51%), Gaps = 10/96 (10%)
Query: 473 PGHPGLGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMS 532
P +GS+G K ++IG L +GL F FG++ V++D +T S
Sbjct: 16 PRGSHMGSSGCK---------MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRS 66
Query: 533 KGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA 568
+G+GFV + D Q + + + + + L+ +TI +VA
Sbjct: 67 RGFGFVTFMD-QAGVDKVLAQSRHELDSKTIDPKVA 101
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 37/66 (56%), Gaps = 1/66 (1%)
Query: 489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANN 548
++D L+IG + ++ + +FS+FG I ++++ G+S+G FV + MA
Sbjct: 93 VEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQT 151
Query: 549 AIASMN 554
AI +M+
Sbjct: 152 AIKAMH 157
Score = 32.7 bits (73), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 2/53 (3%)
Query: 490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTG--MSKGYGFVKY 540
D +++G +P T + L LF +G + V++DR SKG FV +
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTF 54
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 6/77 (7%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
+ L++G LPP + ++ + +LF +G + KD KG+GF++ +A A
Sbjct: 23 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKV 76
Query: 552 SMNGYRLEGRTIAVRVA 568
++ L G+ + VR A
Sbjct: 77 ELDNMPLRGKQLRVRFA 93
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 39/76 (51%), Gaps = 6/76 (7%)
Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
L++G LP + ++ RLF +G+ + +DR G+GF++ +A A A
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLESRTLAEIAKAE 77
Query: 553 MNGYRLEGRTIAVRVA 568
++G L+ R + +R A
Sbjct: 78 LDGTILKSRPLRIRFA 93
>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 = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 34/75 (45%)
Query: 491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
D L + LPP+L L FG + ++ TG SKGYGF +Y A A
Sbjct: 93 DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAK 152
Query: 551 ASMNGYRLEGRTIAV 565
+ + G L RT+ V
Sbjct: 153 SDLLGKPLGPRTLYV 167
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 34/75 (45%)
Query: 491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
D L + LPP+L L FG + ++ TG SKGYGF +Y A A
Sbjct: 95 DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAK 154
Query: 551 ASMNGYRLEGRTIAV 565
+ + G L RT+ V
Sbjct: 155 SDLLGKPLGPRTLYV 169
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 34/75 (45%)
Query: 491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
D L + LPP+L L FG + ++ TG SKGYGF +Y A A
Sbjct: 95 DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAK 154
Query: 551 ASMNGYRLEGRTIAV 565
+ + G L RT+ V
Sbjct: 155 SDLLGKPLGPRTLYV 169
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 37/66 (56%), Gaps = 1/66 (1%)
Query: 489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANN 548
++D L+IG + ++ + +FS+FG I ++++ G+S+G FV + MA
Sbjct: 105 VEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQT 163
Query: 549 AIASMN 554
AI +M+
Sbjct: 164 AIKAMH 169
Score = 34.7 bits (78), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 28/55 (50%), Gaps = 2/55 (3%)
Query: 488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTG--MSKGYGFVKY 540
+LD +++G +P T + L LF +G + V++DR SKG FV +
Sbjct: 12 DLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTF 66
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 40.8 bits (94), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 38/63 (60%)
Query: 506 DGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAV 565
D L R+F +G + + ++ T +G+ FV++ D + A +A A+M+G L+GR + V
Sbjct: 28 DSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRV 87
Query: 566 RVA 568
+VA
Sbjct: 88 QVA 90
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 40.4 bits (93), Expect = 0.004, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 6/73 (8%)
Query: 491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
+ +Y G + L D + + FS FG I+ +V + KGY FV+++ + A +AI
Sbjct: 25 NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAI 78
Query: 551 ASMNGYRLEGRTI 563
S+NG +EG +
Sbjct: 79 VSVNGTTIEGHVV 91
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 40.0 bits (92), Expect = 0.004, Method: Composition-based stats.
Identities = 24/81 (29%), Positives = 41/81 (50%)
Query: 485 PIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQ 544
P + ++ L++ + +D + F +G+I + DR TG SKGY V+Y +
Sbjct: 20 PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHK 79
Query: 545 MANNAIASMNGYRLEGRTIAV 565
A A ++NG + G+TI V
Sbjct: 80 QALAAKEALNGAEIMGQTIQV 100
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 39.7 bits (91), Expect = 0.006, Method: Composition-based stats.
Identities = 26/89 (29%), Positives = 44/89 (49%), Gaps = 2/89 (2%)
Query: 479 GSNGAKPIKELDDTNLYIGYLPPTL--DDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYG 536
GS+G+ + D N +G +L + L +FS +G I ++ D+ + S+G+
Sbjct: 1 GSSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 60
Query: 537 FVKYADIQMANNAIASMNGYRLEGRTIAV 565
FV + ++ A A NG L+GR I V
Sbjct: 61 FVYFENVDDAKEAKERANGMELDGRRIRV 89
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 39.7 bits (91), Expect = 0.006, Method: Composition-based stats.
Identities = 22/78 (28%), Positives = 43/78 (55%), Gaps = 4/78 (5%)
Query: 485 PIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKY---A 541
P ++ +++G + +D+ + F+ +G + K+I DR TG+SKGYGFV +
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDV 61
Query: 542 DIQMANNAIASMNGYRLE 559
D+Q + + +G +L+
Sbjct: 62 DVQKIVESQINFHGKKLK 79
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 39.7 bits (91), Expect = 0.006, Method: Composition-based stats.
Identities = 28/93 (30%), Positives = 47/93 (50%), Gaps = 4/93 (4%)
Query: 479 GSNGAKPIKELDDTNLYIGYLPPTL--DDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYG 536
GS+G+ + D N +G +L + L +FS +G I ++ D+ + S+G+
Sbjct: 1 GSSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 60
Query: 537 FVKYADIQMANNAIASMNGYRLEGRTIAVRVAG 569
FV + ++ A A NG L+GR I RV+G
Sbjct: 61 FVYFENVDDAKEAKERANGMELDGRRI--RVSG 91
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 39.7 bits (91), Expect = 0.006, Method: Composition-based stats.
Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 2/80 (2%)
Query: 479 GSNGAK-PIKELDD-TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYG 536
GS+G+ P + DD + + L + L LF FG I + KD+ TG SKG+
Sbjct: 1 GSSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFA 60
Query: 537 FVKYADIQMANNAIASMNGY 556
F+ + + A AIA ++G+
Sbjct: 61 FISFHRREDAARAIAGVSGF 80
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 39.7 bits (91), Expect = 0.007, Method: Composition-based stats.
Identities = 25/85 (29%), Positives = 44/85 (51%), Gaps = 10/85 (11%)
Query: 478 LGSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGF 537
LGS P +++G + +D+ + F+ +G + K+I DR TG+SKGYGF
Sbjct: 3 LGSGKIMP------NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGF 55
Query: 538 VKY---ADIQMANNAIASMNGYRLE 559
V + D+Q + + +G +L+
Sbjct: 56 VSFYNDVDVQKIVESQINFHGKKLK 80
>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 = 39.7 bits (91), Expect = 0.007, Method: Composition-based stats.
Identities = 24/81 (29%), Positives = 41/81 (50%)
Query: 485 PIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQ 544
P + ++ L++ + +D + F +G+I + DR TG SKGY V+Y +
Sbjct: 66 PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHK 125
Query: 545 MANNAIASMNGYRLEGRTIAV 565
A A ++NG + G+TI V
Sbjct: 126 QALAAKEALNGAEIMGQTIQV 146
>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|X Chain X, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|Y Chain Y, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2V|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
pdb|1N52|B Chain B, Cap Binding Complex
pdb|1N54|B Chain B, Cap Binding Complex M7gpppg Free
pdb|3FEX|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex.
pdb|3FEY|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex
Length = 156
Score = 39.7 bits (91), Expect = 0.007, Method: Composition-based stats.
Identities = 24/70 (34%), Positives = 37/70 (52%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
LY+G L ++ + LFS GDI + D++ + G+ FV+Y A NA+ +
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 554 NGYRLEGRTI 563
NG RL+ R I
Sbjct: 102 NGTRLDDRII 111
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 39.3 bits (90), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 39/72 (54%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
LY+ L P + + L+ LF+ F + + +TG +G F+ + + ++A A+ +
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87
Query: 554 NGYRLEGRTIAV 565
NGY+L G+ + +
Sbjct: 88 NGYKLYGKILVI 99
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 39.3 bits (90), Expect = 0.009, Method: Composition-based stats.
Identities = 27/92 (29%), Positives = 46/92 (50%), Gaps = 5/92 (5%)
Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
GS P + L+IG L D+ L F +G + V++D T S+G+GFV
Sbjct: 2 GSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 61
Query: 539 KYADIQMANNAIASMNG--YRLEGRTIAVRVA 568
YA ++ + A+MN ++++GR + + A
Sbjct: 62 TYATVEEVD---AAMNARPHKVDGRVVEPKRA 90
Score = 32.0 bits (71), Expect = 1.2, Method: Composition-based stats.
Identities = 18/85 (21%), Positives = 40/85 (47%), Gaps = 4/85 (4%)
Query: 481 NGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKY 540
+ +P L +++G + ++ L F +G I + +++ DR +G +G+ FV +
Sbjct: 95 DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 154
Query: 541 ADIQMANNAIA----SMNGYRLEGR 561
D + + ++NG+ E R
Sbjct: 155 DDHDSVDKIVIQKYHTVNGHNCEVR 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 = 39.3 bits (90), Expect = 0.010, Method: Composition-based stats.
Identities = 21/59 (35%), Positives = 34/59 (57%), Gaps = 1/59 (1%)
Query: 483 AKPIKELDDT-NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKY 540
A P E D T +++G + P + FS +G I+ A+++ D+ TG S+G+GFV Y
Sbjct: 78 AIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTY 136
Score = 36.2 bits (82), Expect = 0.076, Method: Composition-based stats.
Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 2/74 (2%)
Query: 490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNA 549
+ ++IG L +D L F +G + K++KD TG S+G+GF+ + +
Sbjct: 2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61
Query: 550 IASMNGYRLEGRTI 563
+ + + L+G+ I
Sbjct: 62 VKTQ--HILDGKVI 73
>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 = 38.9 bits (89), Expect = 0.010, Method: Composition-based stats.
Identities = 22/78 (28%), Positives = 43/78 (55%), Gaps = 4/78 (5%)
Query: 485 PIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKY---A 541
P ++ +++G + +D+ + F+ +G + K+I DR TG+SKGYGFV +
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDV 61
Query: 542 DIQMANNAIASMNGYRLE 559
D+Q + + +G +L+
Sbjct: 62 DVQKIVESQINFHGKKLK 79
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 38.9 bits (89), Expect = 0.011, Method: Composition-based stats.
Identities = 26/90 (28%), Positives = 43/90 (47%), Gaps = 13/90 (14%)
Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
GS+G+ + L+IG LP + + LF +G ++ +IK+ YGFV
Sbjct: 1 GSSGSSGM-----VKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFV 47
Query: 539 KYADIQMANNAIASMNGYRLEGRTIAVRVA 568
D A +AI +++ Y+L G I V +
Sbjct: 48 HIEDKTAAEDAIRNLHHYKLHGVNINVEAS 77
>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 = 38.9 bits (89), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 32/60 (53%)
Query: 508 LIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV 567
L R F +G I ++ + +G +GY F++Y + ++A +G +++GR + V V
Sbjct: 119 LRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV 178
>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 = 38.1 bits (87), Expect = 0.018, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 5/77 (6%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
L+IG L D+ L F +G + V++D T S+G+GFV YA ++ + A+M
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD---AAM 65
Query: 554 NG--YRLEGRTIAVRVA 568
N ++++GR + + A
Sbjct: 66 NARPHKVDGRVVEPKRA 82
Score = 32.3 bits (72), Expect = 0.93, Method: Composition-based stats.
Identities = 18/85 (21%), Positives = 40/85 (47%), Gaps = 4/85 (4%)
Query: 481 NGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKY 540
+ +P L +++G + ++ L F +G I + +++ DR +G +G+ FV +
Sbjct: 87 DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 146
Query: 541 ADIQMANNAIA----SMNGYRLEGR 561
D + + ++NG+ E R
Sbjct: 147 DDHDSVDKIVIQKYHTVNGHNCEVR 171
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 37.7 bits (86), Expect = 0.023, Method: Composition-based stats.
Identities = 28/89 (31%), Positives = 43/89 (48%), Gaps = 7/89 (7%)
Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
GS+G+ ++ NL + L D F+ G ++ A + + G SKG G V
Sbjct: 1 GSSGSSGACQIFVRNLPFDFTWKMLKDK-----FNECGHVLYADIKME--NGKSKGCGVV 53
Query: 539 KYADIQMANNAIASMNGYRLEGRTIAVRV 567
K+ ++A A MNG +L GR I VR+
Sbjct: 54 KFESPEVAERACRMMNGMKLSGREIDVRI 82
>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 = 37.7 bits (86), Expect = 0.023, Method: Composition-based stats.
Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 6/77 (7%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
+ L++G LPP + ++ + +LF +G + KD KG+GF++ +A A
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKV 69
Query: 552 SMNGYRLEGRTIAVRVA 568
++ L G+ + VR A
Sbjct: 70 ELDNMPLRGKQLRVRFA 86
>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 = 37.7 bits (86), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 30/54 (55%)
Query: 512 FSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAV 565
F+ +G+I + DR TG KGY V+Y + A A+ +NG L G+ I+V
Sbjct: 44 FAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV 97
>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 = 37.7 bits (86), Expect = 0.024, Method: Composition-based stats.
Identities = 20/54 (37%), Positives = 30/54 (55%)
Query: 512 FSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAV 565
F+ +G+I + DR TG KGY V+Y + A A+ +NG L G+ I+V
Sbjct: 28 FAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV 81
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 37.7 bits (86), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 24/40 (60%)
Query: 530 GMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAG 569
G SKGY F+++A + A A+ S N +EGR I + + G
Sbjct: 50 GKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQG 89
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 37.7 bits (86), Expect = 0.024, Method: Composition-based stats.
Identities = 24/75 (32%), Positives = 40/75 (53%), Gaps = 2/75 (2%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
L++ +P D L ++F FG I+ ++I + SKG+GFV + + A+ A +
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKL 89
Query: 554 NGYRLEGRTIAVRVA 568
+G +EGR I V A
Sbjct: 90 HGTVVEGRKIEVNNA 104
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 37.7 bits (86), Expect = 0.025, Method: Composition-based stats.
Identities = 24/75 (32%), Positives = 40/75 (53%), Gaps = 2/75 (2%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
L++ +P D L ++F FG I+ ++I + SKG+GFV + + A+ A +
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKL 75
Query: 554 NGYRLEGRTIAVRVA 568
+G +EGR I V A
Sbjct: 76 HGTVVEGRKIEVNNA 90
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 37.7 bits (86), Expect = 0.026, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 5/77 (6%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
L+IG L D+ L F +G + V++D T S+G+GFV YA ++ + A+M
Sbjct: 14 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD---AAM 70
Query: 554 NG--YRLEGRTIAVRVA 568
N ++++GR + + A
Sbjct: 71 NARPHKVDGRVVEPKRA 87
Score = 32.3 bits (72), Expect = 1.1, Method: Composition-based stats.
Identities = 18/85 (21%), Positives = 40/85 (47%), Gaps = 4/85 (4%)
Query: 481 NGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKY 540
+ +P L +++G + ++ L F +G I + +++ DR +G +G+ FV +
Sbjct: 92 DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 151
Query: 541 ADIQMANNAIA----SMNGYRLEGR 561
D + + ++NG+ E R
Sbjct: 152 DDHDSVDKIVIQKYHTVNGHNCEVR 176
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 37.7 bits (86), Expect = 0.026, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 5/77 (6%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
L+IG L D+ L F +G + V++D T S+G+GFV YA ++ + A+M
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD---AAM 72
Query: 554 NG--YRLEGRTIAVRVA 568
N ++++GR + + A
Sbjct: 73 NARPHKVDGRVVEPKRA 89
Score = 32.3 bits (72), Expect = 1.1, Method: Composition-based stats.
Identities = 18/85 (21%), Positives = 40/85 (47%), Gaps = 4/85 (4%)
Query: 481 NGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKY 540
+ +P L +++G + ++ L F +G I + +++ DR +G +G+ FV +
Sbjct: 94 DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
Query: 541 ADIQMANNAIA----SMNGYRLEGR 561
D + + ++NG+ E R
Sbjct: 154 DDHDSVDKIVIQKYHTVNGHNCEVR 178
>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|6 Chain 6, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|7 Chain 7, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|8 Chain 8, Crystal Structure Of Human Spliceosomal U1 Snrnp
Length = 216
Score = 37.7 bits (86), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 17/75 (22%), Positives = 37/75 (49%)
Query: 493 NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIAS 552
L++ + + L R F +G I ++ + +G +GY F++Y + ++A
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 553 MNGYRLEGRTIAVRV 567
+G +++GR + V V
Sbjct: 164 ADGKKIDGRRVLVDV 178
>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 = 37.7 bits (86), Expect = 0.028, Method: Composition-based stats.
Identities = 25/85 (29%), Positives = 39/85 (45%), Gaps = 3/85 (3%)
Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
G N +K E D ++G L L F+ FG++V + D TG S+G+GF+
Sbjct: 1 GINASK--NEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFI 58
Query: 539 KYADIQMANNAIASMNGYRLEGRTI 563
+ D + +RL+GR I
Sbjct: 59 LFKDAASVEKVL-DQKEHRLDGRVI 82
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 37.7 bits (86), Expect = 0.028, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 31/58 (53%)
Query: 508 LIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAV 565
L +FS +G I ++ D+ + S+G+ FV + ++ A A NG L+GR I V
Sbjct: 63 LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 120
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 37.7 bits (86), Expect = 0.028, Method: Composition-based stats.
Identities = 21/56 (37%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 512 FSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRV 567
F+ G ++ A + + G SKG G VK+ ++A A MNG +L GR I VR+
Sbjct: 26 FNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRI 79
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 37.4 bits (85), Expect = 0.029, Method: Composition-based stats.
Identities = 24/64 (37%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 493 NLYIGYLPPTLDDDGLIRLF-STFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
+L++G L P +DD L F + KV+ D+ TG+SKGYGFVK+ D A+
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALT 69
Query: 552 SMNG 555
G
Sbjct: 70 ECQG 73
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 37.4 bits (85), Expect = 0.029, Method: Composition-based stats.
Identities = 26/75 (34%), Positives = 37/75 (49%), Gaps = 11/75 (14%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSK-----GYGFVKYADIQMANN 548
LY+G L ++ + LFS GDI K + G+ K G+ FV+Y A N
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDI------KKIIMGLDKMKTACGFCFVEYYSRADAEN 74
Query: 549 AIASMNGYRLEGRTI 563
A+ +NG RL+ R I
Sbjct: 75 AMRYINGTRLDDRII 89
>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 = 37.4 bits (85), Expect = 0.030, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 5/77 (6%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
L+IG L D+ L F +G + V++D T S+G+GFV YA ++ + A+M
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD---AAM 72
Query: 554 NG--YRLEGRTIAVRVA 568
N ++++GR + + A
Sbjct: 73 NARPHKVDGRVVEPKRA 89
Score = 32.0 bits (71), Expect = 1.2, Method: Composition-based stats.
Identities = 18/85 (21%), Positives = 40/85 (47%), Gaps = 4/85 (4%)
Query: 481 NGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKY 540
+ +P L +++G + ++ L F +G I + +++ DR +G +G+ FV +
Sbjct: 94 DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
Query: 541 ADIQMANNAIA----SMNGYRLEGR 561
D + + ++NG+ E R
Sbjct: 154 DDHDSVDKIVIQKYHTVNGHNCEVR 178
>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 = 37.4 bits (85), Expect = 0.030, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 5/77 (6%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
L+IG L D+ L F +G + V++D T S+G+GFV YA ++ + A+M
Sbjct: 15 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD---AAM 71
Query: 554 NG--YRLEGRTIAVRVA 568
N ++++GR + + A
Sbjct: 72 NARPHKVDGRVVEPKRA 88
Score = 32.0 bits (71), Expect = 1.2, Method: Composition-based stats.
Identities = 18/85 (21%), Positives = 40/85 (47%), Gaps = 4/85 (4%)
Query: 481 NGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKY 540
+ +P L +++G + ++ L F +G I + +++ DR +G +G+ FV +
Sbjct: 93 DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 152
Query: 541 ADIQMANNAIA----SMNGYRLEGR 561
D + + ++NG+ E R
Sbjct: 153 DDHDSVDKIVIQKYHTVNGHNCEVR 177
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 37.4 bits (85), Expect = 0.032, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 31/58 (53%)
Query: 508 LIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAV 565
L +FS +G I ++ D+ + S+G+ FV + ++ A A NG L+GR I V
Sbjct: 29 LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 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 = 0.035, Method: Composition-based stats.
Identities = 20/54 (37%), Positives = 30/54 (55%)
Query: 512 FSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAV 565
F+ +G+I + DR TG KGY V+Y + A A+ +NG L G+ I+V
Sbjct: 28 FAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV 81
>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 = 37.0 bits (84), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 30/54 (55%)
Query: 512 FSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAV 565
F+ +G+I + DR TG KGY V+Y + A A+ +NG L G+ I+V
Sbjct: 28 FAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV 81
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 36.6 bits (83), Expect = 0.053, Method: Composition-based stats.
Identities = 20/54 (37%), Positives = 30/54 (55%)
Query: 512 FSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAV 565
F+ +G+I + DR TG KGY V+Y + A A+ +NG L G+ I+V
Sbjct: 30 FAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV 83
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 36.6 bits (83), Expect = 0.057, Method: Composition-based stats.
Identities = 20/54 (37%), Positives = 30/54 (55%)
Query: 512 FSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAV 565
F+ +G+I + DR TG KGY V+Y + A A+ +NG L G+ I+V
Sbjct: 43 FAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV 96
>pdb|3N9U|C Chain C, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
pdb|3N9U|I Chain I, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
Length = 156
Score = 36.6 bits (83), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 36/79 (45%), Gaps = 2/79 (2%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFG--DIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
+Y+G D LI++ + G D+V K ++R G SKGY V A + +
Sbjct: 58 VYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLE 117
Query: 552 SMNGYRLEGRTIAVRVAGK 570
+ G L G + VR A +
Sbjct: 118 LLPGKVLNGEKVDVRPATR 136
>pdb|2YQR|A Chain A, Solution Structure Of The Kh Domain In Kiaa0907 Protein
Length = 119
Score = 36.2 bits (82), Expect = 0.082, Method: Composition-based stats.
Identities = 26/96 (27%), Positives = 46/96 (47%), Gaps = 8/96 (8%)
Query: 251 LQKKLYIPMKE-YPGYNFIGLIIGPRGNTQKRMERETGAKIVIRGKGSVKEGRLQQKRDL 309
+Q KL++ ++ P +N + GP + + ++ ETGAK+ +RGKGS +
Sbjct: 12 VQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAF 71
Query: 310 KPDPSENEDLHVLVEAETQESLEGAAAMVEKLLQPV 345
+P +++ + E L A + E LLQ V
Sbjct: 72 EP-------MYIYISHPKPEGLAAAKKLCENLLQTV 100
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 36.2 bits (82), Expect = 0.082, Method: Composition-based stats.
Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
L++G L +D + RLF FG+I +++ G SKG FVKY+ A AI ++
Sbjct: 18 LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGP-DGNSKGCAFVKYSSHAEAQAAINAL 76
Query: 554 NG 555
+G
Sbjct: 77 HG 78
>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 = 35.8 bits (81), Expect = 0.094, Method: Composition-based stats.
Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 1/70 (1%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
++IG L L FS FG++V + D +TG S+G+GFV + + + + +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDK-VMDQ 60
Query: 554 NGYRLEGRTI 563
++L G+ I
Sbjct: 61 KEHKLNGKVI 70
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 35.4 bits (80), Expect = 0.11, Method: Composition-based stats.
Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 491 DTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAI 550
D L++G L ++ ++RLF FG I V++ G SKG FVK++ A AI
Sbjct: 15 DRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAI 73
Query: 551 ASMNG 555
+++G
Sbjct: 74 HALHG 78
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 35.4 bits (80), Expect = 0.11, Method: Composition-based stats.
Identities = 21/80 (26%), Positives = 41/80 (51%), Gaps = 3/80 (3%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTG---MSKGYGFVKYADIQMANN 548
+ L+I L + ++ L +FS G I + K + +S G+GFV+Y + A
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 549 AIASMNGYRLEGRTIAVRVA 568
A+ + G+ ++G + VR++
Sbjct: 66 ALKQLQGHTVDGHKLEVRIS 85
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 35.4 bits (80), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 36/72 (50%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
L++ L T ++ L +LFS +G + D +T KG+ FV + + A A A +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 554 NGYRLEGRTIAV 565
+G +GR + V
Sbjct: 71 DGQVFQGRMLHV 82
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 35.0 bits (79), Expect = 0.18, Method: Composition-based stats.
Identities = 19/46 (41%), Positives = 29/46 (63%), Gaps = 2/46 (4%)
Query: 527 RVTGMS--KGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGK 570
RV G S KGY FV+Y++ + A A+ NG L G+T+ + +AG+
Sbjct: 54 RVAGCSVHKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGE 99
>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 34.7 bits (78), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 41/85 (48%), Gaps = 13/85 (15%)
Query: 491 DTNLYIGYLPPTLDDD----GLIRLFSTFG---DIVMAKVIKDRVTGMSKGYGFVKYADI 543
+ +YI L + D L +FS FG DI++++ +K R G FV + ++
Sbjct: 9 NHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMR------GQAFVIFKEV 62
Query: 544 QMANNAIASMNGYRLEGRTIAVRVA 568
A NA+ SM G+ + + ++ A
Sbjct: 63 SSATNALRSMQGFPFYDKPMRIQYA 87
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 34.7 bits (78), Expect = 0.23, Method: Composition-based stats.
Identities = 26/92 (28%), Positives = 46/92 (50%), Gaps = 3/92 (3%)
Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRV-TGMSKGYGF 537
GS+G P K+ + + + +P + + LFSTFG++ ++ K TG +G+GF
Sbjct: 4 GSSGQVPKKQ-TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGF 62
Query: 538 VKYADIQMANNAIASM-NGYRLEGRTIAVRVA 568
V + Q A A ++ + L GR + + A
Sbjct: 63 VDFITKQDAKKAFNALCHSTHLYGRRLVLEWA 94
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 34.3 bits (77), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 35/70 (50%), Gaps = 13/70 (18%)
Query: 494 LYIGYLPPTLDDD----GLIRLFSTFG---DIVMAKVIKDRVTGMSKGYGFVKYADIQMA 546
+YI L + D L +FS FG DI++++ +K R G FV + ++ A
Sbjct: 11 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMR------GQAFVIFKEVSSA 64
Query: 547 NNAIASMNGY 556
NA+ SM G+
Sbjct: 65 TNALRSMQGF 74
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 34.3 bits (77), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 27/92 (29%), Positives = 50/92 (54%), Gaps = 4/92 (4%)
Query: 479 GSNGAKPIKELDDT--NLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYG 536
GS+G+ + E D LY+G L + + +++LFS G K+I + + + Y
Sbjct: 1 GSSGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYC 58
Query: 537 FVKYADIQMANNAIASMNGYRLEGRTIAVRVA 568
FV++ + + A A+A+MNG ++ G+ + V A
Sbjct: 59 FVEFYEHRDAAAALAAMNGRKILGKEVKVNWA 90
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 33.9 bits (76), Expect = 0.32, Method: Composition-based stats.
Identities = 27/90 (30%), Positives = 42/90 (46%), Gaps = 13/90 (14%)
Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
GS+G +K L ++ L T+ ++ L + FS FG + K +KD Y F+
Sbjct: 4 GSSGMAKVKVL-----FVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFI 50
Query: 539 KYADIQMANNAIASMNGYRLEGRTIAVRVA 568
+ + A A+ MNG LEG I + A
Sbjct: 51 HFDERDGAVKAMEEMNGKDLEGENIEIVFA 80
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 33.9 bits (76), Expect = 0.36, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 30/55 (54%)
Query: 511 LFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAV 565
L +F V A+++ DR TG SKG+GFV + + A A +M ++G + +
Sbjct: 32 LKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTL 86
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 33.9 bits (76), Expect = 0.36, Method: Composition-based stats.
Identities = 19/53 (35%), Positives = 27/53 (50%)
Query: 507 GLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLE 559
L LFS G +V + D TG +KG+ FV+ + A I S +G RL+
Sbjct: 28 ALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLD 80
>pdb|2IHX|A Chain A, Solution Structure Of The Rous Sarcoma Virus Nucleocapsid
Protein:upsi Rna Packaging Signal Complex
Length = 61
Score = 33.9 bits (76), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 20/45 (44%)
Query: 368 RDEEYCRLCGEPGHRQYACPSRTSTFKSDVLCKICGDGGHPTIDC 412
R C CG PGH Q CP + + S C++C GH C
Sbjct: 2 RARGLCYTCGSPGHYQAQCPKKRKSGNSRERCQLCNGMGHNAKQC 46
>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 = 33.9 bits (76), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 5/69 (7%)
Query: 490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTG--MSKGYGFVKYADIQM-- 545
D +++G +P T + L LF +G + V++DR SKG FV + +
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 546 -ANNAIASM 553
A NA+ +M
Sbjct: 62 EAQNALHNM 70
>pdb|3NS6|A Chain A, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
pdb|3NS6|B Chain B, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
Length = 100
Score = 33.5 bits (75), Expect = 0.44, Method: Composition-based stats.
Identities = 19/53 (35%), Positives = 27/53 (50%)
Query: 507 GLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLE 559
L LFS G +V + D TG +KG+ FV+ + A I S +G RL+
Sbjct: 28 ALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLD 80
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 33.5 bits (75), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 3/72 (4%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
LYI LP + + + +F +G I +V T ++G +V Y DI A NA+ +
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNAVDHL 67
Query: 554 NGYRLEGRTIAV 565
+G+ + R + V
Sbjct: 68 SGFNVSNRYLVV 79
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 33.5 bits (75), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 18/77 (23%), Positives = 36/77 (46%), Gaps = 8/77 (10%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
T L++G + PT + L F +G ++ ++KD Y FV + A AI
Sbjct: 11 TKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIR 62
Query: 552 SMNGYRLEGRTIAVRVA 568
++ +G+ + V+++
Sbjct: 63 GLDNTEFQGKRMHVQLS 79
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 33.1 bits (74), Expect = 0.67, Method: Composition-based stats.
Identities = 25/76 (32%), Positives = 34/76 (44%), Gaps = 6/76 (7%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
T L++G L P L R F FG I D V G S + +++Y + A A A
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIRTI----DHVKGDS--FAYIQYESLDAAQAACA 71
Query: 552 SMNGYRLEGRTIAVRV 567
M G+ L G +RV
Sbjct: 72 KMRGFPLGGPDRRLRV 87
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 33.1 bits (74), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 27/89 (30%), Positives = 44/89 (49%), Gaps = 2/89 (2%)
Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
GS+GA L T +++ L + L +FS G +V A +++D+ G S+G G V
Sbjct: 4 GSSGALQAGRLGST-VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTV 61
Query: 539 KYADIQMANNAIASMNGYRLEGRTIAVRV 567
+ A AI+ NG L R + V++
Sbjct: 62 TFEQSIEAVQAISMFNGQLLFDRPMHVKM 90
>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO3|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO4|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3IIN|A Chain A, Plasticity Of The Kink Turn Structural Motif
Length = 95
Score = 32.7 bits (73), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 13/70 (18%)
Query: 494 LYIGYLPPTLDDDGLIR----LFSTFG---DIVMAKVIKDRVTGMSKGYGFVKYADIQMA 546
+YI L + D L + +FS FG DI++++ +K R G FV + ++ A
Sbjct: 9 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR------GQAFVIFKEVSSA 62
Query: 547 NNAIASMNGY 556
NA+ SM G+
Sbjct: 63 TNALRSMQGF 72
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 32.7 bits (73), Expect = 0.74, Method: Composition-based stats.
Identities = 18/75 (24%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
+++G +P + L F FG + +I D +G+GF+ + D Q + A+ +M
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV-NM 71
Query: 554 NGYRLEGRTIAVRVA 568
+ + + G+ + V+ A
Sbjct: 72 HFHDIMGKKVEVKRA 86
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 32.7 bits (73), Expect = 0.86, Method: Composition-based stats.
Identities = 21/68 (30%), Positives = 34/68 (50%), Gaps = 1/68 (1%)
Query: 490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNA 549
+D L++G L D+ + ++F FG I V++ G SKG FVK+ A A
Sbjct: 11 EDRKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGP-DGTSKGCAFVKFQTHAEAQAA 69
Query: 550 IASMNGYR 557
I +++ R
Sbjct: 70 INTLHSSR 77
>pdb|2DGR|A Chain A, Solution Structure Of The Second Kh Domain In Ring Finger
And Kh Domain Containing Protein 1
Length = 83
Score = 32.7 bits (73), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 21/31 (67%)
Query: 265 YNFIGLIIGPRGNTQKRMERETGAKIVIRGK 295
Y +GL++GP+G T KR+++ T IV G+
Sbjct: 18 YRVVGLVVGPKGATIKRIQQRTHTYIVTPGR 48
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 32.3 bits (72), Expect = 1.00, Method: Composition-based stats.
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 1/82 (1%)
Query: 487 KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMA 546
+E D ++ L + L FS G + ++I DR + SKG +V++ +IQ
Sbjct: 21 EERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSV 80
Query: 547 NNAIASMNGYRLEGRTIAVRVA 568
AI + G RL G I V+ +
Sbjct: 81 PLAIG-LTGQRLLGVPIIVQAS 101
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 32.3 bits (72), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 35/70 (50%), Gaps = 13/70 (18%)
Query: 494 LYIGYLPPTLDDD----GLIRLFSTFG---DIVMAKVIKDRVTGMSKGYGFVKYADIQMA 546
+YI L + D L +FS FG DI++++ +K R G FV + ++ A
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMR------GQAFVIFKEVSSA 65
Query: 547 NNAIASMNGY 556
NA+ SM G+
Sbjct: 66 TNALRSMQGF 75
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 32.0 bits (71), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 27/88 (30%), Positives = 42/88 (47%), Gaps = 12/88 (13%)
Query: 479 GSNGAKPIKELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFV 538
GS+G+ + +L YIG L P + D L +LF + +V+ + GY FV
Sbjct: 1 GSSGSSGMNKL-----YIGNLSPAVTADDLRQLFGDRKLPLAGQVL------LKSGYAFV 49
Query: 539 KYADIQMANNAIASMNG-YRLEGRTIAV 565
Y D A AI +++G L G+ + V
Sbjct: 50 DYPDQNWAIRAIETLSGKVELHGKIMEV 77
>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 = 32.0 bits (71), Expect = 1.5, Method: Composition-based stats.
Identities = 22/94 (23%), Positives = 45/94 (47%), Gaps = 5/94 (5%)
Query: 479 GSNGAKPI----KELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKG 534
GS+G+ + L+ L+I LP + + L + G + +++ +R G KG
Sbjct: 1 GSSGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKG 59
Query: 535 YGFVKYADIQMANNAIASMNGYRLEGRTIAVRVA 568
+V+Y + A+ A+ M+G ++ I V ++
Sbjct: 60 LAYVEYENESQASQAVMKMDGMTIKENIIKVAIS 93
>pdb|3L3C|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
Length = 90
Score = 32.0 bits (71), Expect = 1.6, Method: Composition-based stats.
Identities = 23/82 (28%), Positives = 41/82 (50%), Gaps = 13/82 (15%)
Query: 494 LYIGYLPPTLDDDGLIR----LFSTFG---DIVMAKVIKDRVTGMSKGYGFVKYADIQMA 546
+YI L + D L + +FS FG DI++++ +K R G FV + ++ A
Sbjct: 6 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR------GQAFVIFKEVSSA 59
Query: 547 NNAIASMNGYRLEGRTIAVRVA 568
NA+ SM G+ + + ++ A
Sbjct: 60 TNALRSMQGFPFYDKPMRIQYA 81
>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
pdb|3IWN|D Chain D, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
Length = 91
Score = 32.0 bits (71), Expect = 1.6, Method: Composition-based stats.
Identities = 23/82 (28%), Positives = 41/82 (50%), Gaps = 13/82 (15%)
Query: 494 LYIGYLPPTLDDDGLIR----LFSTFG---DIVMAKVIKDRVTGMSKGYGFVKYADIQMA 546
+YI L + D L + +FS FG DI++++ +K R G FV + ++ A
Sbjct: 7 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR------GQAFVIFKEVSSA 60
Query: 547 NNAIASMNGYRLEGRTIAVRVA 568
NA+ SM G+ + + ++ A
Sbjct: 61 TNALRSMQGFPFYDKPMRIQYA 82
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 31.6 bits (70), Expect = 1.6, Method: Composition-based stats.
Identities = 21/77 (27%), Positives = 34/77 (44%), Gaps = 8/77 (10%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
+++G + L LF G ++ V+KD Y FV A AIA +
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQL 63
Query: 554 NGYRLEGRTIAVRVAGK 570
NG ++G+ I V ++ K
Sbjct: 64 NGKEVKGKRINVELSTK 80
>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures
pdb|1DZ5|A Chain A, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
pdb|1DZ5|B Chain B, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
Length = 101
Score = 31.6 bits (70), Expect = 1.8, Method: Composition-based stats.
Identities = 23/82 (28%), Positives = 41/82 (50%), Gaps = 13/82 (15%)
Query: 494 LYIGYLPPTLDDDGLIR----LFSTFG---DIVMAKVIKDRVTGMSKGYGFVKYADIQMA 546
+YI L + D L + +FS FG DI++++ +K R G FV + ++ A
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR------GQAFVIFKEVSSA 64
Query: 547 NNAIASMNGYRLEGRTIAVRVA 568
NA+ SM G+ + + ++ A
Sbjct: 65 TNALRSMQGFPFYDKPMRIQYA 86
>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|B Chain B, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|C Chain C, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|D Chain D, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
Length = 94
Score = 31.6 bits (70), Expect = 1.8, Method: Composition-based stats.
Identities = 23/82 (28%), Positives = 41/82 (50%), Gaps = 13/82 (15%)
Query: 494 LYIGYLPPTLDDDGLIR----LFSTFG---DIVMAKVIKDRVTGMSKGYGFVKYADIQMA 546
+YI L + D L + +FS FG DI++++ +K R G FV + ++ A
Sbjct: 8 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR------GQAFVIFKEVSSA 61
Query: 547 NNAIASMNGYRLEGRTIAVRVA 568
NA+ SM G+ + + ++ A
Sbjct: 62 TNALRSMQGFPFYDKPMRIQYA 83
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 31.6 bits (70), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 3/72 (4%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
LYI LP + + + +F +G I + I+ T ++G +V Y DI A NA +
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPI---RQIRVGNTPETRGTAYVVYEDIFDAKNACDHL 77
Query: 554 NGYRLEGRTIAV 565
+G+ + R + V
Sbjct: 78 SGFNVCNRYLVV 89
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 31.2 bits (69), Expect = 2.2, Method: Composition-based stats.
Identities = 18/75 (24%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
L+IG L ++ L + +G + V++D + S+G+GFV ++ + + A+A+
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA- 88
Query: 554 NGYRLEGRTIAVRVA 568
+ ++GR + + A
Sbjct: 89 RPHSIDGRVVEPKRA 103
>pdb|1U6B|A Chain A, Crystal Structure Of A Self-Splicing Group I Intron With
Both Exons
pdb|1ZZN|A Chain A, Crystal Structure Of A Group I IntronTWO EXON COMPLEX THAT
Includes All Catalytic Metal Ion Ligands.
pdb|3G8S|A Chain A, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|B Chain B, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|C Chain C, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|D Chain D, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8T|A Chain A, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|B Chain B, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|C Chain C, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|D Chain D, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G96|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G9C|A Chain A, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|B Chain B, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|C Chain C, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|D Chain D, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3IRW|P Chain P, Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3MUM|P Chain P, Crystal Structure Of The G20a Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUR|P Chain P, Crystal Structure Of The C92u Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUT|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Gmp
pdb|3MUV|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Amp
pdb|3MXH|P Chain P, Native Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3P49|B Chain B, Crystal Structure Of A Glycine Riboswitch From
Fusobacterium Nucleatum
pdb|3R1H|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1H|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1L|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3R1L|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3UCU|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Pgpg
pdb|3UCZ|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Gpg
pdb|3UD3|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Pgpa
pdb|3UD4|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Gpa
Length = 98
Score = 31.2 bits (69), Expect = 2.5, Method: Composition-based stats.
Identities = 23/82 (28%), Positives = 41/82 (50%), Gaps = 13/82 (15%)
Query: 494 LYIGYLPPTLDDDGLIR----LFSTFG---DIVMAKVIKDRVTGMSKGYGFVKYADIQMA 546
+YI L + D L + +FS FG DI++++ +K R G FV + ++ A
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR------GQAFVIFKEVSSA 65
Query: 547 NNAIASMNGYRLEGRTIAVRVA 568
NA+ SM G+ + + ++ A
Sbjct: 66 TNALRSMQGFPFYDKPMRIQYA 87
>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|B Chain B, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|C Chain C, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|D Chain D, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
Length = 96
Score = 31.2 bits (69), Expect = 2.5, Method: Composition-based stats.
Identities = 23/82 (28%), Positives = 41/82 (50%), Gaps = 13/82 (15%)
Query: 494 LYIGYLPPTLDDDGLIR----LFSTFG---DIVMAKVIKDRVTGMSKGYGFVKYADIQMA 546
+YI L + D L + +FS FG DI++++ +K R G FV + ++ A
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR------GQAFVIFKEVSSA 64
Query: 547 NNAIASMNGYRLEGRTIAVRVA 568
NA+ SM G+ + + ++ A
Sbjct: 65 TNALRSMQGFPFYDKPMRIQYA 86
>pdb|1M5K|C Chain C, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5K|F Chain F, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5O|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5O|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1SJ3|P Chain P, Hepatitis Delta Virus Gemonic Ribozyme Precursor, With
Mg2+ Bound
pdb|1SJ4|P Chain P, Crystal Structure Of A C75u Mutant Hepatitis Delta Virus
Ribozyme Precursor, In Cu2+ Solution
pdb|1SJF|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Cobalt
Hexammine Solution
pdb|1VBX|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Edta Solution
pdb|1VBY|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, And Mn2+ Bound
pdb|1VBZ|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Ba2+ Solution
pdb|1VC0|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Imidazole And
Sr2+ Solution
pdb|1VC5|A Chain A, Crystal Structure Of The Wild Type Hepatitis Delta Virus
Gemonic Ribozyme Precursor, In Edta Solution
pdb|1VC6|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Product With C75u Mutaion, Cleaved In Imidazole
And Mg2+ Solutions
pdb|1VC7|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Sr2+ Solution
pdb|2OIH|A Chain A, Hepatitis Delta Virus Gemonic Ribozyme Precursor With C75u
Mutation And Bound To Monovalent Cation Tl+
pdb|2OJ3|A Chain A, Hepatitis Delta Virus Ribozyme Precursor Structure, With
C75u Mutation, Bound To Tl+ And Cobalt Hexammine
(Co(Nh3) 63+)
Length = 100
Score = 31.2 bits (69), Expect = 2.5, Method: Composition-based stats.
Identities = 23/82 (28%), Positives = 41/82 (50%), Gaps = 13/82 (15%)
Query: 494 LYIGYLPPTLDDDGLIR----LFSTFG---DIVMAKVIKDRVTGMSKGYGFVKYADIQMA 546
+YI L + D L + +FS FG DI++++ +K R G FV + ++ A
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR------GQAFVIFKEVSSA 65
Query: 547 NNAIASMNGYRLEGRTIAVRVA 568
NA+ SM G+ + + ++ A
Sbjct: 66 TNALRSMQGFPFYDKPMRIQYA 87
>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|B Chain B, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|C Chain C, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1NU4|A Chain A, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|1NU4|B Chain B, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|3HHN|B Chain B, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
pdb|3HHN|D Chain D, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
Length = 97
Score = 31.2 bits (69), Expect = 2.5, Method: Composition-based stats.
Identities = 23/82 (28%), Positives = 41/82 (50%), Gaps = 13/82 (15%)
Query: 494 LYIGYLPPTLDDDGLIR----LFSTFG---DIVMAKVIKDRVTGMSKGYGFVKYADIQMA 546
+YI L + D L + +FS FG DI++++ +K R G FV + ++ A
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR------GQAFVIFKEVSSA 64
Query: 547 NNAIASMNGYRLEGRTIAVRVA 568
NA+ SM G+ + + ++ A
Sbjct: 65 TNALRSMQGFPFYDKPMRIQYA 86
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 31.2 bits (69), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 6/59 (10%)
Query: 512 FSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGK 570
FS FG+I+ D + FV Y ++ A+ A+A +NG ++E + V +A K
Sbjct: 58 FSPFGNII------DLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARK 110
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 30.8 bits (68), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 10/72 (13%)
Query: 499 LPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRL 558
+ PTL L FS FG+I+ D + FV Y ++ A+ A+A +NG ++
Sbjct: 25 MTPTL----LRGAFSPFGNII------DLSMDPPRNCAFVTYEKMESADQAVAELNGTQV 74
Query: 559 EGRTIAVRVAGK 570
E + V +A K
Sbjct: 75 ESVQLKVNIARK 86
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 30.8 bits (68), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 28/52 (53%), Gaps = 9/52 (17%)
Query: 508 LIRLFSTFG---DIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGY 556
L +FS FG DIV K +K R G FV + +I A+NA+ +M G+
Sbjct: 27 LYAIFSQFGQILDIVALKTLKMR------GQAFVIFKEIGSASNALRTMQGF 72
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 30.8 bits (68), Expect = 2.8, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 3/72 (4%)
Query: 494 LYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASM 553
LYI LP + + + +F +G I +V T ++G +V Y DI A NA +
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNACDHL 71
Query: 554 NGYRLEGRTIAV 565
+G+ + R + V
Sbjct: 72 SGFNVCNRYLVV 83
>pdb|2KRB|A Chain A, Solution Structure Of Eif3b-Rrm Bound To Eif3j Peptide
Length = 81
Score = 30.8 bits (68), Expect = 3.4, Method: Composition-based stats.
Identities = 17/50 (34%), Positives = 30/50 (60%), Gaps = 2/50 (4%)
Query: 510 RLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLE 559
++FS FG I ++ G +KGY F++YA A +A+ + +GY+L+
Sbjct: 26 KIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAVDAVKNADGYKLD 73
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 30.4 bits (67), Expect = 3.5, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 8/60 (13%)
Query: 511 LFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLEGRTIAVRVAGK 570
+FS +G IV V KG+ FV+Y + + A A+A +G + G+ + + +A +
Sbjct: 36 IFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAE 87
>pdb|2NLW|A Chain A, Solution Structure Of The Rrm Domain Of Human Eukaryotic
Initiation Factor 3b
Length = 105
Score = 30.4 bits (67), Expect = 3.9, Method: Composition-based stats.
Identities = 17/50 (34%), Positives = 30/50 (60%), Gaps = 2/50 (4%)
Query: 510 RLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMNGYRLE 559
++FS FG I ++ G +KGY F++YA A +A+ + +GY+L+
Sbjct: 40 KIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAVDAVKNADGYKLD 87
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 30.4 bits (67), Expect = 4.3, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 33/72 (45%), Gaps = 6/72 (8%)
Query: 492 TNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIA 551
T YIG +P + LI LF FG I+ K + KG F+KY + A I
Sbjct: 28 TTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIKYDTHEQAAVCIV 81
Query: 552 SMNGYRLEGRTI 563
++ + +GR +
Sbjct: 82 ALANFPFQGRNL 93
>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 = 30.0 bits (66), Expect = 4.7, Method: Composition-based stats.
Identities = 17/64 (26%), Positives = 33/64 (51%), Gaps = 1/64 (1%)
Query: 489 LDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANN 548
++D L+IG + ++ + FS+FG I ++++ G+S+G FV + A
Sbjct: 93 VEDRKLFIGXISKKCTENDIRVXFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAXAQT 151
Query: 549 AIAS 552
AI +
Sbjct: 152 AIKA 155
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 30.0 bits (66), Expect = 4.8, Method: Composition-based stats.
Identities = 21/76 (27%), Positives = 39/76 (51%), Gaps = 3/76 (3%)
Query: 490 DDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNA 549
+D +Y+G LPP + + +F +G I +K+R G + FV++ D + A +A
Sbjct: 21 NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDID-LKNRRGG--PPFAFVEFEDPRDAEDA 77
Query: 550 IASMNGYRLEGRTIAV 565
+ +GY +G + V
Sbjct: 78 VYGRDGYDYDGYRLRV 93
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 29.6 bits (65), Expect = 6.5, Method: Composition-based stats.
Identities = 18/71 (25%), Positives = 35/71 (49%), Gaps = 6/71 (8%)
Query: 504 DDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMANNAIASMN------GYR 557
+++ L + FGD+ +V+ T SKG F ++ + A +A+ + G +
Sbjct: 28 EEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLK 87
Query: 558 LEGRTIAVRVA 568
L+GR + V +A
Sbjct: 88 LDGRQLKVDLA 98
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 29.6 bits (65), Expect = 6.6, Method: Composition-based stats.
Identities = 17/78 (21%), Positives = 38/78 (48%), Gaps = 1/78 (1%)
Query: 488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMAN 547
E D ++Y+G + + L F G + ++ D+ +G KG+ +++++D +
Sbjct: 2 EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 61
Query: 548 NAIASMNGYRLEGRTIAV 565
++A ++ GR I V
Sbjct: 62 TSLA-LDESLFRGRQIKV 78
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of Hypothetical
Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens
At 1.95 A Resolution
Length = 89
Score = 29.6 bits (65), Expect = 7.3, Method: Composition-based stats.
Identities = 17/78 (21%), Positives = 38/78 (48%), Gaps = 1/78 (1%)
Query: 488 ELDDTNLYIGYLPPTLDDDGLIRLFSTFGDIVMAKVIKDRVTGMSKGYGFVKYADIQMAN 547
E D ++Y+G + + L F G + ++ D+ +G KG+ +++++D +
Sbjct: 3 EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62
Query: 548 NAIASMNGYRLEGRTIAV 565
++A ++ GR I V
Sbjct: 63 TSLA-LDESLFRGRQIKV 79
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
0.313 0.133 0.394
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,929,869
Number of Sequences: 62578
Number of extensions: 760091
Number of successful extensions: 1440
Number of sequences better than 100.0: 183
Number of HSP's better than 100.0 without gapping: 127
Number of HSP's successfully gapped in prelim test: 56
Number of HSP's that attempted gapping in prelim test: 1252
Number of HSP's gapped (non-prelim): 214
length of query: 797
length of database: 14,973,337
effective HSP length: 107
effective length of query: 690
effective length of database: 8,277,491
effective search space: 5711468790
effective search space used: 5711468790
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 55 (25.8 bits)