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= 029496
(192 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 105 bits (263), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 46/84 (54%), Positives = 66/84 (78%)
Query: 17 IESGTKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIA 76
+E+G KL +SNL++GVS+ DI+ELF+E G LK+ +V +DRSGRS GTA+V RRADA+
Sbjct: 32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALK 91
Query: 77 AVKRYNNVQLDGKPMKIEIIGTNI 100
A+K+Y V LDG+PM I+++ + I
Sbjct: 92 AMKQYKGVPLDGRPMDIQLVASQI 115
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 105 bits (263), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 46/84 (54%), Positives = 66/84 (78%)
Query: 17 IESGTKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIA 76
+E+G KL +SNL++GVS+ DI+ELF+E G LK+ +V +DRSGRS GTA+V RRADA+
Sbjct: 32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALK 91
Query: 77 AVKRYNNVQLDGKPMKIEIIGTNI 100
A+K+Y V LDG+PM I+++ + I
Sbjct: 92 AMKQYKGVPLDGRPMDIQLVASQI 115
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 105 bits (262), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 46/84 (54%), Positives = 66/84 (78%)
Query: 17 IESGTKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIA 76
+E+G KL +SNL++GVS+ DI+ELF+E G LK+ +V +DRSGRS GTA+V RRADA+
Sbjct: 85 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALK 144
Query: 77 AVKRYNNVQLDGKPMKIEIIGTNI 100
A+K+Y V LDG+PM I+++ + I
Sbjct: 145 AMKQYKGVPLDGRPMDIQLVASQI 168
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 102 bits (253), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 44/75 (58%), Positives = 62/75 (82%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVKRY 81
KL +SNL++GVS+ DI+ELF+E G LK+ +VH+DRSGRS GTA+V R+ADA+ A+K+Y
Sbjct: 30 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 89
Query: 82 NNVQLDGKPMKIEII 96
N V LDG+PM I+++
Sbjct: 90 NGVPLDGRPMNIQLV 104
>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex
Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A
Resolution
Length = 107
Score = 98.6 bits (244), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 43/75 (57%), Positives = 60/75 (80%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVKRY 81
KL +SNL++GVS+ DI+ELF+E G LK+ +VH+DRSGRS GTA+V R+ADA+ A K+Y
Sbjct: 31 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQY 90
Query: 82 NNVQLDGKPMKIEII 96
N V LDG+P I+++
Sbjct: 91 NGVPLDGRPXNIQLV 105
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 52.0 bits (123), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 45/76 (59%)
Query: 20 GTKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVK 79
G+ ++++NL+Y V + +KE+FS G + R + D+ G+S+G V + +A+ A+
Sbjct: 15 GSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAIS 74
Query: 80 RYNNVQLDGKPMKIEI 95
+N L +PM +++
Sbjct: 75 MFNGQLLFDRPMHVKM 90
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 45/78 (57%), Gaps = 1/78 (1%)
Query: 19 SGTKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGR-SKGTAEVVLTRRADAIAA 77
S + +Y+SNL + ++N D+ +FS+ G++ + ++ D+ R SKG A ++ + A
Sbjct: 15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNC 74
Query: 78 VKRYNNVQLDGKPMKIEI 95
+ NN QL G+ +K I
Sbjct: 75 TRAINNKQLFGRVIKASI 92
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 43.1 bits (100), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFD-RSGRSKGTAEVVLTRRADAIAAVKR 80
+LY+ +L + ++ + ++ +F G ++ + D +GRSKG + + A A+++
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 81 YNNVQLDGKPMKI 93
N +L G+PMK+
Sbjct: 88 LNGFELAGRPMKV 100
>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 = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 42/78 (53%)
Query: 17 IESGTKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIA 76
++ LY+ NL + + E I ELFS+ G++K+ + D+ + G V RADA
Sbjct: 15 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAEN 74
Query: 77 AVKRYNNVQLDGKPMKIE 94
A++ N +LD + ++ +
Sbjct: 75 AMRYINGTRLDDRIIRTD 92
>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 = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 44/85 (51%), Gaps = 2/85 (2%)
Query: 20 GTKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFD-RSGRSKGTAEVVLTRRADAIAAV 78
G L+++ + + EDI + F+E GE+K ++ D R+G KG V +A AA+
Sbjct: 7 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 79 KRYNNVQLDGKPMKIEIIGTNIGPP 103
+ N L G+P+ ++ GPP
Sbjct: 67 EGLNGQDLMGQPISVDWCFVR-GPP 90
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 33/64 (51%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVKRY 81
KL+I + + DI+ +FS G+++ C + G S+G A V T RA A A+K
Sbjct: 109 KLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAM 168
Query: 82 NNVQ 85
+ Q
Sbjct: 169 HQAQ 172
Score = 32.7 bits (73), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 35/68 (51%), Gaps = 3/68 (4%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSG---RSKGTAEVVLTRRADAIAAV 78
K+++ + S +D++ELF + G + +V DRS +SKG V R A+ A
Sbjct: 17 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 76
Query: 79 KRYNNVQL 86
+N+++
Sbjct: 77 NALHNMKV 84
>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 = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 44/86 (51%), Gaps = 2/86 (2%)
Query: 19 SGTKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFD-RSGRSKGTAEVVLTRRADAIAA 77
G L+++ + + EDI + F+E GE+K ++ D R+G KG V +A AA
Sbjct: 22 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 81
Query: 78 VKRYNNVQLDGKPMKIEIIGTNIGPP 103
++ N L G+P+ ++ GPP
Sbjct: 82 MEGLNGQDLMGQPISVDWCFVR-GPP 106
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 33/64 (51%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVKRY 81
KL+I + + DI+ +FS G+++ C + G S+G A V T RA A A+K
Sbjct: 97 KLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAM 156
Query: 82 NNVQ 85
+ Q
Sbjct: 157 HQAQ 160
Score = 32.3 bits (72), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 35/68 (51%), Gaps = 3/68 (4%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSG---RSKGTAEVVLTRRADAIAAV 78
K+++ + S +D++ELF + G + +V DRS +SKG V R A+ A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 79 KRYNNVQL 86
+N+++
Sbjct: 65 NALHNMKV 72
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 37/76 (48%)
Query: 18 ESGTKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAA 77
E+ +++ NLE V E + ELF + G L + ++ DR G+ K V A
Sbjct: 14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYA 73
Query: 78 VKRYNNVQLDGKPMKI 93
+ N ++L G+P+ +
Sbjct: 74 IALLNGIRLYGRPINV 89
>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 = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 47/87 (54%), Gaps = 4/87 (4%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFD-RSGRSKGTAEVVLTRRADAIAAVKR 80
++Y++++ +S++DIK +F G++K C++ D +G+ KG + + + AV
Sbjct: 112 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 171
Query: 81 YNNVQLDGKPMKIEIIGTNIGPPAAVL 107
N L G+ ++ +G + PP +L
Sbjct: 172 MNLFDLGGQYLR---VGKAVTPPMPLL 195
>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 = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 47/87 (54%), Gaps = 4/87 (4%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFD-RSGRSKGTAEVVLTRRADAIAAVKR 80
++Y++++ +S++DIK +F G++K C++ D +G+ KG + + + AV
Sbjct: 111 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 170
Query: 81 YNNVQLDGKPMKIEIIGTNIGPPAAVL 107
N L G+ ++ +G + PP +L
Sbjct: 171 XNLFDLGGQYLR---VGKAVTPPXPLL 194
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 44/80 (55%), Gaps = 3/80 (3%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVKRYN 82
L +SNL Y + E ++E+F + +K V +++G+SKG A + DA A+ N
Sbjct: 18 LVLSNLSYSATEETLQEVFEKATFIK---VPQNQNGKSKGYAFIEFASFEDAKEALNSCN 74
Query: 83 NVQLDGKPMKIEIIGTNIGP 102
+++G+ +++E+ G P
Sbjct: 75 KREIEGRAIRLELQGPRGSP 94
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 40.4 bits (93), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 6/74 (8%)
Query: 19 SGTKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTAEVVLTRRA--DAI 75
SG K++I L + + E ++E F + GE+K C V D + RS+G V +A D +
Sbjct: 24 SGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV 83
Query: 76 AAVKRYNNVQLDGK 89
A R+ +LD K
Sbjct: 84 LAQSRH---ELDSK 94
>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
pdb|3NNA|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 40.4 bits (93), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 32/64 (50%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVKRY 81
KL+I + + DI+ FS G+++ C + G S+G A V T RA A A+K
Sbjct: 97 KLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAIKAX 156
Query: 82 NNVQ 85
+ Q
Sbjct: 157 HQAQ 160
Score = 29.6 bits (65), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 33/68 (48%), Gaps = 3/68 (4%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSG---RSKGTAEVVLTRRADAIAAV 78
K ++ + S +D++ELF + G + +V DRS +SKG V R A+ A
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 79 KRYNNVQL 86
+N ++
Sbjct: 65 NALHNXKV 72
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 40.4 bits (93), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 41/78 (52%), Gaps = 7/78 (8%)
Query: 18 ESGTKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAA 77
++ TKL++ N+ +N++++ F E G + C + K A V + R DA+ A
Sbjct: 8 KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDI-------VKDYAFVHMERAEDAVEA 60
Query: 78 VKRYNNVQLDGKPMKIEI 95
++ +N + GK M +++
Sbjct: 61 IRGLDNTEFQGKRMHVQL 78
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 40.4 bits (93), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 42/74 (56%), Gaps = 1/74 (1%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTAEVVLTRRADAIAAVKRY 81
L + L + D++E+FS+ G + S+ +D+ S RS+G A V DA A +R
Sbjct: 49 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 108
Query: 82 NNVQLDGKPMKIEI 95
N ++LDG+ ++++
Sbjct: 109 NGMELDGRRIRVDF 122
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 40.0 bits (92), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTAEVVLTRRADAIAAVKRY 81
+++ N+ Y + E +K++FSEVG + + +DR +G+ KG + A++A++
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 82 NNVQLDGKPMKIE 94
N + G+ ++++
Sbjct: 71 NGREFSGRALRVD 83
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 40.0 bits (92), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 42/74 (56%), Gaps = 1/74 (1%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTAEVVLTRRADAIAAVKRY 81
L + L + D++E+FS+ G + S+ +D+ S RS+G A V DA A +R
Sbjct: 15 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 74
Query: 82 NNVQLDGKPMKIEI 95
N ++LDG+ ++++
Sbjct: 75 NGMELDGRRIRVDF 88
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 4/75 (5%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVKRYN 82
L NL Y V+ +++KE+F + E++ S + G+SKG A + ADA +
Sbjct: 96 LLAKNLPYKVTQDELKEVFEDAAEIRLVS----KDGKSKGIAYIEFKTEADAEKTFEEKQ 151
Query: 83 NVQLDGKPMKIEIIG 97
++DG+ + + G
Sbjct: 152 GTEIDGRSISLYYTG 166
>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 = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 42/77 (54%), Gaps = 2/77 (2%)
Query: 14 SSSIESGTKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFD-RSGRSKGTAEVVLTRRA 72
S + E K ++ L + S +D+K+ F++ GE+ C++ D +GRS+G +L + A
Sbjct: 5 SKNEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFG-FILFKDA 63
Query: 73 DAIAAVKRYNNVQLDGK 89
++ V +LDG+
Sbjct: 64 ASVEKVLDQKEHRLDGR 80
>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 = 0.001, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 42/74 (56%), Gaps = 1/74 (1%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTAEVVLTRRADAIAAVKRY 81
L + L + D++E+FS+ G + S+ +D+ S RS+G A V DA A +R
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 82 NNVQLDGKPMKIEI 95
N ++LDG+ ++++
Sbjct: 78 NGMELDGRRIRVDF 91
>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 = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 20 GTKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFD-RSGRSKGTAEVVLTRRADAIAAV 78
G L+++ + + EDI + F+E GE+K ++ D R+G KG V +A AA+
Sbjct: 9 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 68
Query: 79 KRYNNVQLDGKPMKIE 94
+ N L G+P+ ++
Sbjct: 69 EGLNGQDLMGQPISVD 84
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 20 GTKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFD-RSGRSKGTAEVVLTRRADAIAAV 78
G L+++ + + EDI + F+E GE+K ++ D R+G KG V +A AA+
Sbjct: 7 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 79 KRYNNVQLDGKPMKIE 94
+ N L G+P+ ++
Sbjct: 67 EGLNGQDLMGQPISVD 82
>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 = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 20 GTKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFD-RSGRSKGTAEVVLTRRADAIAAV 78
G L+++ + + EDI + F+E GE+K ++ D R+G KG V +A AA+
Sbjct: 7 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 79 KRYNNVQLDGKPMKIE 94
+ N L G+P+ ++
Sbjct: 67 EGLNGQDLMGQPISVD 82
>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 = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
Query: 19 SGTKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFD-RSGRSKGTAEVVLTRRADAIAA 77
G L+++ + + EDI + F+E GE+K ++ D R+G KG V +A AA
Sbjct: 21 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 80
Query: 78 VKRYNNVQLDGKPMKIE 94
++ N L G+P+ ++
Sbjct: 81 MEGLNGQDLMGQPISVD 97
>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
pdb|1HD1|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
Length = 75
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 40/68 (58%), Gaps = 2/68 (2%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTAEVVLTRRADAIAAVKRY 81
++I L + + +D+K+ FS+ GE+ C++ D +GRS+G VL + ++++ V
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFG-FVLFKESESVDKVMDQ 60
Query: 82 NNVQLDGK 89
+L+GK
Sbjct: 61 KEHKLNGK 68
>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 = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 43/80 (53%), Gaps = 1/80 (1%)
Query: 17 IESGTKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSK-GTAEVVLTRRADAI 75
++ LY+ NL + + E I ELFS+ G++K+ + D+ ++ G V RADA
Sbjct: 36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAE 95
Query: 76 AAVKRYNNVQLDGKPMKIEI 95
A++ N +LD + ++ +
Sbjct: 96 NAMRYINGTRLDDRIIRTDW 115
>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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 45/78 (57%), Gaps = 3/78 (3%)
Query: 21 TKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTAEVVLTRRADAIAAVK 79
T LY++NL ++++ + +F + G + + ++ D+ +GR +G A V +R +A A+
Sbjct: 14 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 73
Query: 80 RYNNVQLDG--KPMKIEI 95
NNV +G +P+ + +
Sbjct: 74 ALNNVIPEGGSQPLSVRL 91
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 1/73 (1%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVKRYN 82
LY+ NL+ G+ +E +++ FS G + V + GRSKG V + +A AV N
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMN 76
Query: 83 NVQLDGKPMKIEI 95
+ KP+ + +
Sbjct: 77 GRIVATKPLYVAL 89
>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 = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 41/79 (51%), Gaps = 2/79 (2%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTAEVVLTRRADAIAAVKRY 81
+Y+ N++YG + +D++ FS G + R ++ D+ SG KG A + R AAV
Sbjct: 39 VYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMD 98
Query: 82 NNVQLDGKPMKIEIIGTNI 100
V G+ +K+ TN+
Sbjct: 99 ETV-FRGRTIKVLPKRTNM 116
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 37/73 (50%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVKRY 81
KL+I L + + +K +F + G + + DR+ +S+G A + ADA A K
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDM 68
Query: 82 NNVQLDGKPMKIE 94
N L GK +K+E
Sbjct: 69 NGKSLHGKAIKVE 81
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 33/64 (51%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVKRY 81
KL++ L S +D++ LF G ++ C++ G SKG A V + A+A AA+
Sbjct: 17 KLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINAL 76
Query: 82 NNVQ 85
+ Q
Sbjct: 77 HGSQ 80
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTAEVVLTRRADAIAAVKRY 81
L + L + D++E+FS+ G + S+ +D+ S RS+G A V DA A +R
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 82 NNVQLDGKPMKI 93
N ++LDG+ +++
Sbjct: 78 NGMELDGRRIRV 89
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 45/78 (57%), Gaps = 3/78 (3%)
Query: 21 TKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTAEVVLTRRADAIAAVK 79
T LY++NL ++++ + +F + G + + ++ D+ +GR +G A V +R +A A+
Sbjct: 90 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 149
Query: 80 RYNNVQLDG--KPMKIEI 95
NNV +G +P+ + +
Sbjct: 150 ALNNVIPEGGSQPLSVRL 167
>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 = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 45/78 (57%), Gaps = 3/78 (3%)
Query: 21 TKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTAEVVLTRRADAIAAVK 79
T LY++NL ++++ + +F + G + + ++ D+ +GR +G A V +R +A A+
Sbjct: 101 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 160
Query: 80 RYNNVQLDG--KPMKIEI 95
NNV +G +P+ + +
Sbjct: 161 ALNNVIPEGGSQPLSVRL 178
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 43/76 (56%), Gaps = 1/76 (1%)
Query: 20 GTKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFD-RSGRSKGTAEVVLTRRADAIAAV 78
G L+++++ ++I+E F + GE+K ++ D R+G SKG A V A+AA
Sbjct: 26 GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 85
Query: 79 KRYNNVQLDGKPMKIE 94
+ N ++ G+ ++++
Sbjct: 86 EALNGAEIMGQTIQVD 101
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 21 TKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTAEVVLTRRADAIAAVK 79
+ LY+ +L + ++ + ++ +F G++ + D +GRSKG + + A A++
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 80 RYNNVQLDGKPMKI 93
+ N +L G+PM++
Sbjct: 66 QLNGFELAGRPMRV 79
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 14 SSSIESGTKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTAEVVLTRRA 72
SS + LYIS L ++ +D++++FS G + V D+ +G S+G A + +R+
Sbjct: 82 SSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRS 141
Query: 73 DAIAAVKRYN 82
+A A+ +N
Sbjct: 142 EAEEAITSFN 151
Score = 33.1 bits (74), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 21 TKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTAEVVLTRRADAIAAVK 79
T L ++ L ++ ++++ LFS +GE++ + D+ +G S G V DA A+
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 80 RYNNVQLDGKPMKI 93
N ++L K +K+
Sbjct: 63 TLNGLRLQSKTIKV 76
>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 = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 14 SSSIESGTKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTAEVVLTRRA 72
SS + LYIS L ++ +D++++FS G + V D+ +G S+G A + +R+
Sbjct: 82 SSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRS 141
Query: 73 DAIAAVKRYN 82
+A A+ +N
Sbjct: 142 EAEEAITSFN 151
Score = 33.1 bits (74), Expect = 0.099, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 21 TKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTAEVVLTRRADAIAAVK 79
T L ++ L ++ ++++ LFS +GE++ + D+ +G S G V DA A+
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 80 RYNNVQLDGKPMKI 93
N ++L K +K+
Sbjct: 63 TLNGLRLQSKTIKV 76
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 40/83 (48%), Gaps = 3/83 (3%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTAEVVLTRRADAIAAVKRY 81
+ ++NL D++ELF G + R + D+ +G+SKG A + RR DA A+
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV 77
Query: 82 NNVQLDGKPMKIEII--GTNIGP 102
+ D + +E TN GP
Sbjct: 78 SGFGYDHLILNVEWAKPSTNSGP 100
>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 = 37.4 bits (85), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 26/91 (28%), Positives = 49/91 (53%), Gaps = 3/91 (3%)
Query: 14 SSSIESGTKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRAD 73
S+S+E KL+IS L + + E+++E+ G +K + +R+G+ KG A V +
Sbjct: 12 STSLEK-HKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQ 70
Query: 74 AIAAVKRYNNVQLDGKPMKIEIIGTNIGPPA 104
A AV + + + + +K+ I +N GP +
Sbjct: 71 ASQAVMKMDGMTIKENIIKVAI--SNSGPSS 99
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 37.4 bits (85), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 36/71 (50%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVKRYN 82
+Y+ NL Y ++E +KELFS+ G++ + +DR + V + A+ + +
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAKLD 63
Query: 83 NVQLDGKPMKI 93
N G+ +++
Sbjct: 64 NTDFMGRTIRV 74
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In
Trinucleotide Repeat Containing 4 Variant
Length = 102
Score = 37.4 bits (85), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 31/57 (54%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAV 78
KL++ L ++ED++++F G + C+V G SKG A V A+A AA+
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAI 70
>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 = 37.4 bits (85), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 21/87 (24%), Positives = 46/87 (52%), Gaps = 4/87 (4%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFD-RSGRSKGTAEVVLTRRADAIAAVKR 80
++Y++++ +S++DIK +F G++K ++ D +G+ KG + + + AV
Sbjct: 127 RIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 186
Query: 81 YNNVQLDGKPMKIEIIGTNIGPPAAVL 107
N L G+ ++ +G + PP +L
Sbjct: 187 MNLFDLGGQYLR---VGKAVTPPMPLL 210
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 37.0 bits (84), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/84 (23%), Positives = 42/84 (50%), Gaps = 4/84 (4%)
Query: 14 SSSIESGTKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRAD 73
S + + L NL + ++ +++KE+F + E++ S + G+SKG A + AD
Sbjct: 93 SKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS----QDGKSKGIAYIEFKSEAD 148
Query: 74 AIAAVKRYNNVQLDGKPMKIEIIG 97
A ++ ++DG+ + + G
Sbjct: 149 AEKNLEEKQGAEIDGRSVSLYYTG 172
>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1HL6|C Chain C, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1RK8|A Chain A, Structure Of The Cytosolic Protein Pym Bound To The Mago-
Y14 Core Of The Exon Junction Complex
pdb|2X1G|A Chain A, Crystal Structure Of Importin13 - Mago-Y14 Complex
pdb|2X1G|C Chain C, Crystal Structure Of Importin13 - Mago-Y14 Complex
Length = 165
Score = 37.0 bits (84), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 43/76 (56%), Gaps = 1/76 (1%)
Query: 20 GTKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFD-RSGRSKGTAEVVLTRRADAIAAV 78
G L+++++ ++I+E F + GE+K ++ D R+G SKG A V A+AA
Sbjct: 72 GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 131
Query: 79 KRYNNVQLDGKPMKIE 94
+ N ++ G+ ++++
Sbjct: 132 EALNGAEIMGQTIQVD 147
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 37.0 bits (84), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 41/76 (53%), Gaps = 2/76 (2%)
Query: 21 TKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTAEVVLTRRADAIAAVK 79
TK+++ L Y ++ +++ F G+++ V DR +G+S+G V + RA A A K
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 77
Query: 80 RYNNVQLDGKPMKIEI 95
N + +DG+ + +
Sbjct: 78 DPNPI-IDGRKANVNL 92
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 37.0 bits (84), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 21/88 (23%), Positives = 43/88 (48%), Gaps = 4/88 (4%)
Query: 14 SSSIESGTKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRAD 73
S + + L NL + ++ +++KE+F + E++ S + G+SKG A + AD
Sbjct: 10 SKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS----QDGKSKGIAYIEFKSEAD 65
Query: 74 AIAAVKRYNNVQLDGKPMKIEIIGTNIG 101
A ++ ++DG+ + + G G
Sbjct: 66 AEKNLEEKQGAEIDGRSVSLYYTGEKGG 93
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 37.0 bits (84), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 30/64 (46%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVKRY 81
KL++ L S ED+ LF G + C+V G SKG A V + +A AA+
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHAL 76
Query: 82 NNVQ 85
+ Q
Sbjct: 77 HGSQ 80
>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition
In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 84
Score = 37.0 bits (84), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCSVHFD-RSGRSKGTAEVVLTRRADAIAAVKRY 81
+Y+ ++ Y + E I +L S VG + + FD ++GRSKG A + + +AV+
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 82 NNVQLDGKPMKI 93
N QL + +K
Sbjct: 67 NGYQLGSRFLKC 78
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 37.0 bits (84), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 41/82 (50%), Gaps = 14/82 (17%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLT---------RRAD 73
L+I NL + + E +K +FS+VG +K C++ + K A V+L+ +
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTIS-----KKKNKAGVLLSMGFGFVEYKKPEQ 62
Query: 74 AIAAVKRYNNVQLDGKPMKIEI 95
A A+K+ +DG +++ I
Sbjct: 63 AQKALKQLQGHTVDGHKLEVRI 84
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 37.0 bits (84), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCSVHFD-RSGRSKGTAEVVLTRRADAIAAVKRY 81
+Y+ ++ Y + E I +L S VG + + FD ++GRSKG A + + +AV+
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 82 NNVQLDGKPMKI 93
N QL + +K
Sbjct: 65 NGYQLGSRFLKC 76
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 36.6 bits (83), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCSVHFD-RSGRSKGTAEVVLTRRADAIAAVKRY 81
+Y+ ++ Y + E I +L S VG + + FD ++GRSKG A + + +AV+
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 82 NNVQLDGKPMKI 93
N QL + +K
Sbjct: 66 NGYQLGSRFLKC 77
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 36.6 bits (83), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTAEVVLTRRADAIAAVKR 80
KL++ L + + + ++++FS+ G++ V DR + RS+G V DA A+
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 81 YNNVQLDGKPMKIEIIG 97
N +DG+ ++++ G
Sbjct: 74 MNGKSVDGRQIRVDQAG 90
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 36.6 bits (83), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 1/74 (1%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCSVHFD-RSGRSKGTAEVVLTRRADAIAAVKRY 81
LY+ NL V+ D+ LF+ E K + F +GR +G A + + A A+
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87
Query: 82 NNVQLDGKPMKIEI 95
N +L GK + IE
Sbjct: 88 NGYKLYGKILVIEF 101
>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm
pdb|2LEB|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uccagu-3'
pdb|2LEC|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uggagu-3'
Length = 135
Score = 36.2 bits (82), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 41/80 (51%), Gaps = 1/80 (1%)
Query: 17 IESGTKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTAEVVLTRRADAI 75
+E T L + NL Y S + ++ +F + G + + DR + S+G A V + DA
Sbjct: 44 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAE 103
Query: 76 AAVKRYNNVQLDGKPMKIEI 95
A+ + LDG+ +++++
Sbjct: 104 DAMDAMDGAVLDGRELRVQM 123
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 36.2 bits (82), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 21 TKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFD-RSGRSKGTAEVVLTRRA--DAIAA 77
K++I L + + E ++E F + GE+K C V D + RS+G V +A D + A
Sbjct: 1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60
Query: 78 VKRYNNVQLDGKPM 91
R+ +LD K +
Sbjct: 61 QSRH---ELDSKTI 71
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 36.2 bits (82), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 42/85 (49%), Gaps = 6/85 (7%)
Query: 21 TKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR--SGRSKGTAEVVLTRRADAIAAV 78
TK++I L V+ + I E+FS G++K + +R SKG A V +A A+
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
Query: 79 KRYNNVQLDGKPMKIEIIGTNIGPP 103
K + Q+DG+ EI T + P
Sbjct: 65 KHMDGGQIDGQ----EITATAVLAP 85
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 36.2 bits (82), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 1/82 (1%)
Query: 13 RSSSIESGTKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFD-RSGRSKGTAEVVLTRR 71
+ SS + L++ +L V +E ++ F + V +D ++G S+G V T +
Sbjct: 80 QQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQ 139
Query: 72 ADAIAAVKRYNNVQLDGKPMKI 93
DA A+ L+G+P++I
Sbjct: 140 DDAQNAMDSMQGQDLNGRPLRI 161
Score = 31.2 bits (69), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 36/71 (50%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVKRYN 82
LY+ NL+ ++ + +K+ F G + + D++ ++ A V + DA A++ N
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 83 NVQLDGKPMKI 93
Q++ +KI
Sbjct: 63 GKQIENNIVKI 73
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Rna-Binding Protein 14
Length = 90
Score = 35.8 bits (81), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 39/74 (52%), Gaps = 7/74 (9%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVKRY 81
K+++ N+ ++++++ LF G + C V D A V + + ADA AA+ +
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVVKD-------YAFVHMEKEADAKAAIAQL 63
Query: 82 NNVQLDGKPMKIEI 95
N ++ GK + +E+
Sbjct: 64 NGKEVKGKRINVEL 77
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 35.4 bits (80), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTAEVVLTRRADAIAA 77
KL++ + G+ +D+K LF E G + +V DR +G KG A + R A+ A
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKA 73
>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
pdb|3MD1|B Chain B, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
Length = 83
Score = 35.0 bits (79), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 1/73 (1%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFD-RSGRSKGTAEVVLTRRADAIAAVKR 80
L++ +L V +E ++ F + V +D ++G S+G V T + DA A+
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 81 YNNVQLDGKPMKI 93
L+G+P++I
Sbjct: 63 MQGQDLNGRPLRI 75
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 35.0 bits (79), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTAEVVLTRRADAIAAVKRY 81
+Y+ L+ VS + ELF + G + + DR +G+ +G V DA A+K
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 82 NNVQLDGKPMKI 93
+ ++L GKP+++
Sbjct: 78 DMIKLYGKPIRV 89
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 35.0 bits (79), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 38/78 (48%), Gaps = 8/78 (10%)
Query: 21 TKLYISNLEYG-VSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVK 79
++++I NL V D++ +FS+ G + CSVH KG A V + A AAV
Sbjct: 28 SRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH-------KGYAFVQYSNERHARAAVL 80
Query: 80 RYNNVQLDGKPMKIEIIG 97
N L G+ + I + G
Sbjct: 81 GENGRVLAGQTLDINMAG 98
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 34.7 bits (78), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 41/80 (51%), Gaps = 1/80 (1%)
Query: 17 IESGTKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTAEVVLTRRADAI 75
+E T L + NL Y S + ++ +F + G + + DR + S+G A V + DA
Sbjct: 67 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAE 126
Query: 76 AAVKRYNNVQLDGKPMKIEI 95
A+ + LDG+ +++++
Sbjct: 127 DAMDAMDGAVLDGRELRVQM 146
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 34.7 bits (78), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 37/87 (42%), Gaps = 6/87 (6%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTAEVVLTRRADAIAAVKR 80
+L++ NL Y S ED+++LFS G L D + + KG A V A+ A
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 81 YNNVQLDGK-----PMKIEIIGTNIGP 102
+ G+ P I+ + GP
Sbjct: 70 VDGQVFQGRMLHVLPSTIKKEASQSGP 96
>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 = 0.035, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 41/81 (50%), Gaps = 6/81 (7%)
Query: 23 LYISNLEYGVSNEDIKE----LFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAV 78
+YI+NL + +++K+ +FS+ G++ + RS + +G A V+ + A A+
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNAL 69
Query: 79 KRYNNVQLDGKPMKIEIIGTN 99
+ KPM+I+ T+
Sbjct: 70 RSMQGFPFYDKPMRIQYAKTD 90
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 34.7 bits (78), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTAEVVLTRRADAIAA 77
KL+I + + +D+K LF E G++ +V DR +G KG A + R A+ A
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKA 71
>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 = 34.3 bits (77), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 39/75 (52%), Gaps = 1/75 (1%)
Query: 20 GTKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTAEVVLTRRADAIAAV 78
GT L ++ L + ++++ LFS +GE++ + D+ +G S G V DA A+
Sbjct: 19 GTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 78
Query: 79 KRYNNVQLDGKPMKI 93
N ++L K +K+
Sbjct: 79 NTLNGLRLQSKTIKV 93
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 34.3 bits (77), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 32/61 (52%)
Query: 20 GTKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVK 79
G L + NL VSNE +++ FS+ G +++ V D GR+ G V + A A++
Sbjct: 96 GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALE 155
Query: 80 R 80
R
Sbjct: 156 R 156
Score = 31.6 bits (70), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 32/74 (43%), Gaps = 5/74 (6%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVKRY 81
+L++ NL ++ ED K LF GE ++ DR G + L R A A
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR-----GFGFIRLESRTLAEIAKAEL 78
Query: 82 NNVQLDGKPMKIEI 95
+ L +P++I
Sbjct: 79 DGTILKSRPLRIRF 92
>pdb|2FW2|A Chain A, Catalytic Domain Of Cdy
pdb|2FW2|B Chain B, Catalytic Domain Of Cdy
pdb|2FW2|C Chain C, Catalytic Domain Of Cdy
pdb|2FW2|D Chain D, Catalytic Domain Of Cdy
pdb|2FW2|E Chain E, Catalytic Domain Of Cdy
pdb|2FW2|F Chain F, Catalytic Domain Of Cdy
Length = 260
Score = 34.3 bits (77), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 25/100 (25%), Positives = 46/100 (46%), Gaps = 15/100 (15%)
Query: 40 LFSEVGELKRCSVHFD------RSGRSKGTAEVVLTRRADAIAAVKRYNNVQLD-GKPMK 92
LFS G + C + F R+ R+ + E+V T +K + N + KP+
Sbjct: 53 LFSAAGSVFCCGLDFGYFVRHLRNDRNTASLEMVDT--------IKNFVNTFIQFKKPIV 104
Query: 93 IEIIGTNIGPPAAVLPITNVMYGNEIGMTRSRLRMGGAIP 132
+ + G IG A++LP+ ++++ NE ++ G P
Sbjct: 105 VSVNGPAIGLGASILPLCDLVWANEKAWFQTPYTTFGQSP 144
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 34.3 bits (77), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTAEVVLTRRADAIAAVKRY 81
LY+S L +S +++++LFS+ G + + D+ +G S+G + +R +A A+K
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 82 N 82
N
Sbjct: 64 N 64
>pdb|2FBM|A Chain A, Acetyltransferase Domain Of Cdy1
pdb|2FBM|B Chain B, Acetyltransferase Domain Of Cdy1
pdb|2FBM|C Chain C, Acetyltransferase Domain Of Cdy1
Length = 291
Score = 34.3 bits (77), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 25/100 (25%), Positives = 46/100 (46%), Gaps = 15/100 (15%)
Query: 40 LFSEVGELKRCSVHFD------RSGRSKGTAEVVLTRRADAIAAVKRYNNVQLD-GKPMK 92
LFS G + C + F R+ R+ + E+V T +K + N + KP+
Sbjct: 72 LFSAAGSVFCCGLDFGYFVKHLRNNRNTASLEMVDT--------IKNFVNTFIQFKKPIV 123
Query: 93 IEIIGTNIGPPAAVLPITNVMYGNEIGMTRSRLRMGGAIP 132
+ + G IG A++LP+ ++++ NE ++ G P
Sbjct: 124 VSVNGPAIGLGASILPLCDLVWANEKAWFQTPYTTFGQSP 163
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 33.9 bits (76), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 41/81 (50%), Gaps = 6/81 (7%)
Query: 23 LYISNLEYGVSNEDIKE----LFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAV 78
+YI+NL + +++K+ +FS+ G++ + RS + +G A V+ + A A+
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNAL 69
Query: 79 KRYNNVQLDGKPMKIEIIGTN 99
+ KPM+I+ T+
Sbjct: 70 RSMQGFPFYDKPMRIQYAKTD 90
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 33.9 bits (76), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 26/91 (28%), Positives = 47/91 (51%), Gaps = 11/91 (12%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVKRY 81
K+ I L V+N+++ +L S+ ELK C V + KGTA V L A AA+ +
Sbjct: 24 KILIRGLPGDVTNQEVHDLLSDY-ELKYCFV-----DKYKGTAFVTLLNGEQAEAAINAF 77
Query: 82 NNVQLDGKPMKIEIIGTNIGPPAAVLPITNV 112
+ +L + + +++ T+ A+L + N+
Sbjct: 78 HQSRLRERELSVQLQPTD-----ALLCVANL 103
Score = 32.0 bits (71), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 38/81 (46%), Gaps = 15/81 (18%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCS-VHFDRSGRSKGTAEVVLTRRADAIAAVKRY 81
L ++NL ++ + +EL G L+RC V+ +R+G+SKG ++ A A
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA---- 153
Query: 82 NNVQLDGKPMKIEIIGTNIGP 102
K +++G +GP
Sbjct: 154 ----------KSDLLGKPLGP 164
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 33.9 bits (76), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 26/91 (28%), Positives = 47/91 (51%), Gaps = 11/91 (12%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVKRY 81
K+ I L V+N+++ +L S+ ELK C V + KGTA V L A AA+ +
Sbjct: 24 KILIRGLPGDVTNQEVHDLLSDY-ELKYCFV-----DKYKGTAFVTLLNGEQAEAAINAF 77
Query: 82 NNVQLDGKPMKIEIIGTNIGPPAAVLPITNV 112
+ +L + + +++ T+ A+L + N+
Sbjct: 78 HQSRLRERELSVQLQPTD-----ALLCVANL 103
Score = 32.0 bits (71), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 38/81 (46%), Gaps = 15/81 (18%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCS-VHFDRSGRSKGTAEVVLTRRADAIAAVKRY 81
L ++NL ++ + +EL G L+RC V+ +R+G+SKG ++ A A
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA---- 153
Query: 82 NNVQLDGKPMKIEIIGTNIGP 102
K +++G +GP
Sbjct: 154 ----------KSDLLGKPLGP 164
>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 = 33.9 bits (76), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 26/91 (28%), Positives = 47/91 (51%), Gaps = 11/91 (12%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVKRY 81
K+ I L V+N+++ +L S+ ELK C V + KGTA V L A AA+ +
Sbjct: 22 KILIRGLPGDVTNQEVHDLLSDY-ELKYCFV-----DKYKGTAFVTLLNGEQAEAAINAF 75
Query: 82 NNVQLDGKPMKIEIIGTNIGPPAAVLPITNV 112
+ +L + + +++ T+ A+L + N+
Sbjct: 76 HQSRLRERELSVQLQPTD-----ALLCVANL 101
Score = 31.6 bits (70), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 38/81 (46%), Gaps = 15/81 (18%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCS-VHFDRSGRSKGTAEVVLTRRADAIAAVKRY 81
L ++NL ++ + +EL G L+RC V+ +R+G+SKG ++ A A
Sbjct: 96 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA---- 151
Query: 82 NNVQLDGKPMKIEIIGTNIGP 102
K +++G +GP
Sbjct: 152 ----------KSDLLGKPLGP 162
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 33.9 bits (76), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTAEVVLTRRADAIAAVKRY 81
LY+S L +S +++++LFS+ G + + D+ +G S+G + +R +A A+K
Sbjct: 93 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 152
Query: 82 N 82
N
Sbjct: 153 N 153
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein
U1a117, Nmr, 43 Structures
Length = 116
Score = 33.5 bits (75), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 41/81 (50%), Gaps = 6/81 (7%)
Query: 23 LYISNLEYGVSNEDIKE----LFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAV 78
+YI+NL + +++K+ +FS+ G++ + RS + +G A V+ + A A+
Sbjct: 11 IYINNLNEKIKKDELKKSLYAIFSQFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNAL 68
Query: 79 KRYNNVQLDGKPMKIEIIGTN 99
+ KPM+I+ T+
Sbjct: 69 RSMQGFPFYDKPMRIQYAKTD 89
>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 = 33.5 bits (75), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 21 TKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTAEVVLTRRADAIAAVK 79
T L ++ L ++ ++++ LFS +GE++ + D+ +G S G V DA A+
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 64
Query: 80 RYNNVQLDGKPMKI 93
N ++L K +K+
Sbjct: 65 TLNGLRLQSKTIKV 78
>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 = 33.1 bits (74), Expect = 0.094, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 40/81 (49%), Gaps = 6/81 (7%)
Query: 23 LYISNLEYGVSNEDIKE----LFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAV 78
+YI+NL + +++K+ +FS G++ + RS + +G A V+ + A A+
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNAL 69
Query: 79 KRYNNVQLDGKPMKIEIIGTN 99
+ KPM+I+ T+
Sbjct: 70 RSMQGFPFYDKPMRIQYAKTD 90
>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 = 33.1 bits (74), Expect = 0.095, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 40/81 (49%), Gaps = 6/81 (7%)
Query: 23 LYISNLEYGVSNEDIKE----LFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAV 78
+YI+NL + +++K+ +FS G++ + RS + +G A V+ + A A+
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNAL 69
Query: 79 KRYNNVQLDGKPMKIEIIGTN 99
+ KPM+I+ T+
Sbjct: 70 RSMQGFPFYDKPMRIQYAKTD 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 = 33.1 bits (74), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 40/81 (49%), Gaps = 6/81 (7%)
Query: 23 LYISNLEYGVSNEDIKE----LFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAV 78
+YI+NL + +++K+ +FS G++ + RS + +G A V+ + A A+
Sbjct: 9 IYINNLNEKIKKDELKKSLHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNAL 66
Query: 79 KRYNNVQLDGKPMKIEIIGTN 99
+ KPM+I+ T+
Sbjct: 67 RSMQGFPFYDKPMRIQYAKTD 87
>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 = 33.1 bits (74), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 38/74 (51%), Gaps = 1/74 (1%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCS-VHFDRSGRSKGTAEVVLTRRADAIAAVKRY 81
L+++ + Y + ++ F G +KR V+ RSG+ +G A + D +A K
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 82 NNVQLDGKPMKIEI 95
+ ++DG+ + +++
Sbjct: 165 DGKKIDGRRVLVDV 178
>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 = 33.1 bits (74), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 40/81 (49%), Gaps = 6/81 (7%)
Query: 23 LYISNLEYGVSNEDIKE----LFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAV 78
+YI+NL + +++K+ +FS G++ + RS + +G A V+ + A A+
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNAL 68
Query: 79 KRYNNVQLDGKPMKIEIIGTN 99
+ KPM+I+ T+
Sbjct: 69 RSMQGFPFYDKPMRIQYAKTD 89
>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 = 33.1 bits (74), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 40/81 (49%), Gaps = 6/81 (7%)
Query: 23 LYISNLEYGVSNEDIKE----LFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAV 78
+YI+NL + +++K+ +FS G++ + RS + +G A V+ + A A+
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNAL 68
Query: 79 KRYNNVQLDGKPMKIEIIGTN 99
+ KPM+I+ T+
Sbjct: 69 RSMQGFPFYDKPMRIQYAKTD 89
>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 = 33.1 bits (74), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 40/81 (49%), Gaps = 6/81 (7%)
Query: 23 LYISNLEYGVSNEDIKE----LFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAV 78
+YI+NL + +++K+ +FS G++ + RS + +G A V+ + A A+
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNAL 68
Query: 79 KRYNNVQLDGKPMKIEIIGTN 99
+ KPM+I+ T+
Sbjct: 69 RSMQGFPFYDKPMRIQYAKTD 89
>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 = 32.7 bits (73), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 40/81 (49%), Gaps = 6/81 (7%)
Query: 23 LYISNLEYGVSNEDIKE----LFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAV 78
+YI+NL + +++K+ +FS G++ + RS + +G A V+ + A A+
Sbjct: 6 IYINNLNEKIKKDELKKSLHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNAL 63
Query: 79 KRYNNVQLDGKPMKIEIIGTN 99
+ KPM+I+ T+
Sbjct: 64 RSMQGFPFYDKPMRIQYAKTD 84
>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 = 32.7 bits (73), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 38/74 (51%), Gaps = 1/74 (1%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCS-VHFDRSGRSKGTAEVVLTRRADAIAAVKRY 81
L+++ + Y + ++ F G +KR V+ RSG+ +G A + D +A K
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 82 NNVQLDGKPMKIEI 95
+ ++DG+ + +++
Sbjct: 165 DGKKIDGRRVLVDV 178
>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 = 32.7 bits (73), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 35/68 (51%), Gaps = 3/68 (4%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSG---RSKGTAEVVLTRRADAIAAV 78
K+++ + S +D++ELF + G + +V DRS +SKG V R A+ A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 79 KRYNNVQL 86
+N+++
Sbjct: 65 NALHNMKV 72
>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 = 32.7 bits (73), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 40/81 (49%), Gaps = 6/81 (7%)
Query: 23 LYISNLEYGVSNEDIKE----LFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAV 78
+YI+NL + +++K+ +FS G++ + RS + +G A V+ + A A+
Sbjct: 7 IYINNLNEKIKKDELKKSLHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNAL 64
Query: 79 KRYNNVQLDGKPMKIEIIGTN 99
+ KPM+I+ T+
Sbjct: 65 RSMQGFPFYDKPMRIQYAKTD 85
>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 = 32.7 bits (73), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 40/81 (49%), Gaps = 6/81 (7%)
Query: 23 LYISNLEYGVSNEDIKE----LFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAV 78
+YI+NL + +++K+ +FS G++ + RS + +G A V+ + A A+
Sbjct: 8 IYINNLNEKIKKDELKKSLHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNAL 65
Query: 79 KRYNNVQLDGKPMKIEIIGTN 99
+ KPM+I+ T+
Sbjct: 66 RSMQGFPFYDKPMRIQYAKTD 86
>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 = 32.7 bits (73), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 38/75 (50%), Gaps = 5/75 (6%)
Query: 21 TKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVKR 80
++L++ NL ++ E++++LF + G+ +H D KG + L R A A
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVE 70
Query: 81 YNNVQLDGKPMKIEI 95
+N+ L GK +++
Sbjct: 71 LDNMPLRGKQLRVRF 85
>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
pdb|4F02|D Chain D, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
Length = 213
Score = 32.3 bits (72), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 35/67 (52%), Gaps = 1/67 (1%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVKRYN 82
++I NL+ + N+ + + FS G + C V D +G SKG V + A A+++ N
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMN 164
Query: 83 NVQLDGK 89
+ L+ +
Sbjct: 165 GMLLNDR 171
Score = 30.4 bits (67), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 35/72 (48%), Gaps = 1/72 (1%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTAEVVLTRRADAIAAVKRY 81
LY+ +L V+ + E FS G + V D + RS G A V + ADA A+
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77
Query: 82 NNVQLDGKPMKI 93
N + GKP++I
Sbjct: 78 NFDVIKGKPVRI 89
>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|B Chain B, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|C Chain C, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|D Chain D, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|E Chain E, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|F Chain F, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|G Chain G, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|H Chain H, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
Length = 190
Score = 32.3 bits (72), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 35/67 (52%), Gaps = 1/67 (1%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVKRYN 82
++I NL+ + N+ + + FS G + C V D +G SKG V + A A+++ N
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMN 159
Query: 83 NVQLDGK 89
+ L+ +
Sbjct: 160 GMLLNDR 166
Score = 30.0 bits (66), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 35/72 (48%), Gaps = 1/72 (1%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTAEVVLTRRADAIAAVKRY 81
LY+ +L V+ + E FS G + V D + RS G A V + ADA A+
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 72
Query: 82 NNVQLDGKPMKI 93
N + GKP++I
Sbjct: 73 NFDVIKGKPVRI 84
>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 = 32.3 bits (72), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 37/67 (55%), Gaps = 1/67 (1%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTAEVVLTRRADAIAAVKRY 81
LY+S L ++ +++++LFS+ G + + D+ +G S+G + +R +A A+K
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 82 NNVQLDG 88
N + G
Sbjct: 151 NGQKPSG 157
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 32.3 bits (72), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 5/73 (6%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVKRYN 82
LY+ NL S E I++ F+ + K +V +R + + A V + R DA+ A+K N
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNI---KPGAV--ERVKKIRDYAFVHFSNREDAVEAMKALN 72
Query: 83 NVQLDGKPMKIEI 95
LDG P+++ +
Sbjct: 73 GKVLDGSPIEVTL 85
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 32.3 bits (72), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 38/73 (52%), Gaps = 5/73 (6%)
Query: 21 TKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVKR 80
++L++ NL ++ E++++LF + G+ +H D KG + L R A A
Sbjct: 23 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVE 77
Query: 81 YNNVQLDGKPMKI 93
+N+ L GK +++
Sbjct: 78 LDNMPLRGKQLRV 90
>pdb|2GTR|A Chain A, Human Chromodomain Y-Like Protein
pdb|2GTR|B Chain B, Human Chromodomain Y-Like Protein
pdb|2GTR|C Chain C, Human Chromodomain Y-Like Protein
Length = 261
Score = 32.3 bits (72), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 26/103 (25%), Positives = 43/103 (41%), Gaps = 21/103 (20%)
Query: 40 LFSEVGELKRCSVHF---------DRSGRSKGTAEVVLTRRADAIAAVKRYNNVQLD-GK 89
L S VG + C + F DR S AE A++ + N + K
Sbjct: 54 LLSAVGSVFCCGLDFIYFIRRLTDDRKRESTKMAE-----------AIRNFVNTFIQFKK 102
Query: 90 PMKIEIIGTNIGPPAAVLPITNVMYGNEIGMTRSRLRMGGAIP 132
P+ + + G IG A++LP+ +V++ NE ++ G P
Sbjct: 103 PIIVAVNGPAIGLGASILPLCDVVWANEKAWFQTPYTTFGQSP 145
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 32.0 bits (71), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 15/68 (22%), Positives = 31/68 (45%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVKRY 81
KL++ L++ + E ++ FS+ GE+ C + D++ V + + + V
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 82 NNVQLDGK 89
LDG+
Sbjct: 78 RPHTLDGR 85
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 32.0 bits (71), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 19/82 (23%), Positives = 39/82 (47%), Gaps = 9/82 (10%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKR--------CSVHFDR-SGRSKGTAEVVLTRRAD 73
+++ L V+ E + + F ++G +K +++ DR +G+ KG A V
Sbjct: 16 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 75
Query: 74 AIAAVKRYNNVQLDGKPMKIEI 95
A AA+ ++ + G P+K+
Sbjct: 76 AKAAIDWFDGKEFSGNPIKVSF 97
>pdb|3H2V|E Chain E, Human Raver1 Rrm1 Domain In Complex With Human Vinculin
Tail Domain Vt
pdb|3H2V|F Chain F, Human Raver1 Rrm1 Domain In Complex With Human Vinculin
Tail Domain Vt
pdb|3H2V|G Chain G, Human Raver1 Rrm1 Domain In Complex With Human Vinculin
Tail Domain Vt
pdb|3H2V|H Chain H, Human Raver1 Rrm1 Domain In Complex With Human Vinculin
Tail Domain Vt
Length = 74
Score = 32.0 bits (71), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 40/77 (51%), Gaps = 6/77 (7%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVKRY 81
K+ I L V+N+++ +L S+ ELK C V + KGTA V L A AA+ +
Sbjct: 4 KILIRGLPGDVTNQEVHDLLSDY-ELKYCFV-----DKYKGTAFVTLLNGEQAEAAINAF 57
Query: 82 NNVQLDGKPMKIEIIGT 98
+ +L + + +++ T
Sbjct: 58 HQSRLRERELSVQLQPT 74
>pdb|1A9N|B Chain B, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
pdb|1A9N|D Chain D, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
Length = 96
Score = 32.0 bits (71), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 20/87 (22%), Positives = 41/87 (47%), Gaps = 6/87 (6%)
Query: 17 IESGTKLYISNLEYGVSNEDIKE----LFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRA 72
I +YI+N+ + E++K LFS+ G + + ++ + +G A V+
Sbjct: 3 IRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHV--VDIVALKTMKMRGQAFVIFKELG 60
Query: 73 DAIAAVKRYNNVQLDGKPMKIEIIGTN 99
+ A+++ GKPM+I+ T+
Sbjct: 61 SSTNALRQLQGFPFYGKPMRIQYAKTD 87
>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 = 31.6 bits (70), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 37/71 (52%), Gaps = 1/71 (1%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVKRYN 82
++I NL+ + N+ + + FS G + C V D +G SKG V + A A+++ N
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMN 66
Query: 83 NVQLDGKPMKI 93
+ L+ + + +
Sbjct: 67 GMLLNDRKVFV 77
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 31.6 bits (70), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 36/69 (52%), Gaps = 1/69 (1%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVKRYN 82
++I NL+ + N+ + + FS G + C V D +G SKG V + A A+++ N
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMN 72
Query: 83 NVQLDGKPM 91
+ L+ + +
Sbjct: 73 GMLLNDRKV 81
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 31.2 bits (69), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 38/74 (51%), Gaps = 4/74 (5%)
Query: 21 TKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVKR 80
T LY+ L ++ D++ F + GE++ +V R + TR+A +AA K
Sbjct: 13 TTLYVGGLGDTITETDLRNHFYQFGEIRTITV----VQRQQCAFIQFATRQAAEVAAEKS 68
Query: 81 YNNVQLDGKPMKIE 94
+N + ++G+ + ++
Sbjct: 69 FNKLIVNGRRLNVK 82
>pdb|1WI6|A Chain A, Solution Structure Of The Rna Binding Domain From Mouse
Hypothetical Protein Bab23670
Length = 88
Score = 31.2 bits (69), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 6/77 (7%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVKRYN 82
+ I L V+N+++ +L S+ ELK C V + KGTA V L A AA+ ++
Sbjct: 8 ILIRGLPGDVTNQEVHDLLSDY-ELKYCFVD-----KYKGTAFVTLLNGEQAEAAINTFH 61
Query: 83 NVQLDGKPMKIEIIGTN 99
+L + + +++ T+
Sbjct: 62 QSRLRERELSVQLQPTD 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 = 31.2 bits (69), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTAEVVLT 69
+Y+ N++YG + E+++ F G + R ++ D+ SG KG A + +
Sbjct: 9 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFS 56
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleaoproteins A2B1
Length = 116
Score = 31.2 bits (69), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFD-RSGRSKGTAEVVLTRRADAIAAV 78
KL+I L + + E ++ + + G+L C V D S RS+G V + A+ AA+
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 86
>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 = 31.2 bits (69), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTAEVVLT 69
+Y+ N++YG + E+++ F G + R ++ D+ SG KG A + +
Sbjct: 8 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFS 55
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 31.2 bits (69), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 19/82 (23%), Positives = 39/82 (47%), Gaps = 9/82 (10%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKR--------CSVHFDR-SGRSKGTAEVVLTRRAD 73
+++ L V+ E + + F ++G +K +++ DR +G+ KG A V
Sbjct: 10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 69
Query: 74 AIAAVKRYNNVQLDGKPMKIEI 95
A AA+ ++ + G P+K+
Sbjct: 70 AKAAIDWFDGKEFSGNPIKVSF 91
>pdb|3EGN|A Chain A, C-Terminal Rna Recognition Motif Of The U11U12 65K PROTEIN
Length = 143
Score = 30.8 bits (68), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 27/86 (31%), Positives = 40/86 (46%), Gaps = 10/86 (11%)
Query: 18 ESGTKLYISNLEYGVSNEDIKELFSEV----GELKRCSVHFD----RSGRSKGTAEVVLT 69
E ++Y+ NL V +D+K +F E +R + FD + GR KG A + L
Sbjct: 43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQR--IMFDIRLMKEGRMKGQAFIGLP 100
Query: 70 RRADAIAAVKRYNNVQLDGKPMKIEI 95
A A+K N L GKPM ++
Sbjct: 101 NEKAAAKALKEANGYVLFGKPMVVQF 126
>pdb|1WEZ|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleoprotein H'
Length = 102
Score = 30.8 bits (68), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Query: 19 SGTKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAV 78
+G +++ L Y + DI FS + + R + GR G A+V DA+AA+
Sbjct: 14 TGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAM 72
Query: 79 KR 80
+
Sbjct: 73 AK 74
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 30.8 bits (68), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 39/80 (48%), Gaps = 3/80 (3%)
Query: 18 ESGTKLYISNLEYGVSNEDIKELFSEVGELK--RCSVHFDRSGRSKGTAEVVLTRRADAI 75
++ +K+ + N+ + + +I+ELFS GELK R +G +G V + DA
Sbjct: 13 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAK 72
Query: 76 AAVKRY-NNVQLDGKPMKIE 94
A ++ L G+ + +E
Sbjct: 73 KAFNALCHSTHLYGRRLVLE 92
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 30.8 bits (68), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 8/76 (10%)
Query: 21 TKLYISNLE-YGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVK 79
++++I NL V D++ +FS+ G++ CSVH KG A V +A AAV
Sbjct: 16 SRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH-------KGFAFVQYVNERNARAAVA 68
Query: 80 RYNNVQLDGKPMKIEI 95
+ + G+ + I +
Sbjct: 69 GEDGRMIAGQVLDINL 84
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 30.4 bits (67), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 23/94 (24%), Positives = 41/94 (43%), Gaps = 6/94 (6%)
Query: 13 RSSSIESGTKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRA 72
R + + ++Y+ NL + +DI+++F + G ++ + R G E R
Sbjct: 15 RGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPR-- 72
Query: 73 DAIAAVKRYNNVQLDGKPMKIEII----GTNIGP 102
DA AV + DG +++E GT GP
Sbjct: 73 DAEDAVYGRDGYDYDGYRLRVEFPRSGRGTGSGP 106
>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 = 30.4 bits (67), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 41/80 (51%), Gaps = 5/80 (6%)
Query: 18 ESGTKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTA--EVVLTRRADA 74
+S KL+I L ++++ +KEL + G LK ++ D +G SKG A E V D
Sbjct: 112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTD- 170
Query: 75 IAAVKRYNNVQLDGKPMKIE 94
A+ N +QL K + ++
Sbjct: 171 -QAIAGLNGMQLGDKKLLVQ 189
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 30.4 bits (67), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 15/62 (24%), Positives = 28/62 (45%)
Query: 21 TKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVKR 80
T LYISNL + ++++ + G++ + D SG S+G + A +
Sbjct: 26 TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGH 85
Query: 81 YN 82
+N
Sbjct: 86 FN 87
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 30.4 bits (67), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 16/71 (22%), Positives = 33/71 (46%), Gaps = 2/71 (2%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVKRYN 82
+++ ++ + +I+ F+ G +K + DR+G SKG V D V+ +
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--S 70
Query: 83 NVQLDGKPMKI 93
+ GK +K+
Sbjct: 71 QINFHGKKLKL 81
>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 = 30.0 bits (66), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 16/71 (22%), Positives = 33/71 (46%), Gaps = 2/71 (2%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVKRYN 82
+++ ++ + +I+ F+ G +K + DR+G SKG V D V+ +
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--S 69
Query: 83 NVQLDGKPMKI 93
+ GK +K+
Sbjct: 70 QINFHGKKLKL 80
>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 = 30.0 bits (66), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 16/71 (22%), Positives = 33/71 (46%), Gaps = 2/71 (2%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVKRYN 82
+++ ++ + +I+ F+ G +K + DR+G SKG V D V+ +
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--S 69
Query: 83 NVQLDGKPMKI 93
+ GK +K+
Sbjct: 70 QINFHGKKLKL 80
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 30.0 bits (66), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 16 SIESGTKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFD-RSGRSKGTAEVVLT 69
+++ + L + L + + +D+KE FS GE+ V D ++G SKG V T
Sbjct: 11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFT 65
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 39/86 (45%), Gaps = 11/86 (12%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFD-RSGRSKGTAEVVLTRRADAIAAVKR 80
KL+I L + ++E ++ F + G L C V D + RS+G V + AA
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 71
Query: 81 YNNVQLDGKPMKIEIIGTNIGPPAAV 106
++ +P K++ G + P AV
Sbjct: 72 -----MNARPHKVD--GRVVEPKRAV 90
>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 = 29.3 bits (64), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 39/86 (45%), Gaps = 11/86 (12%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFD-RSGRSKGTAEVVLTRRADAIAAVKR 80
KL+I L + ++E ++ F + G L C V D + RS+G V + AA
Sbjct: 8 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 64
Query: 81 YNNVQLDGKPMKIEIIGTNIGPPAAV 106
++ +P K++ G + P AV
Sbjct: 65 -----MNARPHKVD--GRVVEPKRAV 83
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 29.3 bits (64), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 39/86 (45%), Gaps = 11/86 (12%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFD-RSGRSKGTAEVVLTRRADAIAAVKR 80
KL+I L + ++E ++ F + G L C V D + RS+G V + AA
Sbjct: 13 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 69
Query: 81 YNNVQLDGKPMKIEIIGTNIGPPAAV 106
++ +P K++ G + P AV
Sbjct: 70 -----MNARPHKVD--GRVVEPKRAV 88
>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 = 29.3 bits (64), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 39/86 (45%), Gaps = 11/86 (12%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFD-RSGRSKGTAEVVLTRRADAIAAVKR 80
KL+I L + ++E ++ F + G L C V D + RS+G V + AA
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 71
Query: 81 YNNVQLDGKPMKIEIIGTNIGPPAAV 106
++ +P K++ G + P AV
Sbjct: 72 -----MNARPHKVD--GRVVEPKRAV 90
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 29.3 bits (64), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 39/86 (45%), Gaps = 11/86 (12%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFD-RSGRSKGTAEVVLTRRADAIAAVKR 80
KL+I L + ++E ++ F + G L C V D + RS+G V + AA
Sbjct: 16 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 72
Query: 81 YNNVQLDGKPMKIEIIGTNIGPPAAV 106
++ +P K++ G + P AV
Sbjct: 73 -----MNARPHKVD--GRVVEPKRAV 91
>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 = 29.3 bits (64), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 39/86 (45%), Gaps = 11/86 (12%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFD-RSGRSKGTAEVVLTRRADAIAAVKR 80
KL+I L + ++E ++ F + G L C V D + RS+G V + AA
Sbjct: 14 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 70
Query: 81 YNNVQLDGKPMKIEIIGTNIGPPAAV 106
++ +P K++ G + P AV
Sbjct: 71 -----MNARPHKVD--GRVVEPKRAV 89
>pdb|3BEG|B Chain B, Crystal Structure Of Sr Protein Kinase 1 Complexed To
Its Substrate AsfSF2
Length = 115
Score = 29.3 bits (64), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 33/71 (46%), Gaps = 6/71 (8%)
Query: 16 SIESGTKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAI 75
S S ++ +S L S +D+K+ E G++ V+ D GT V R+ D
Sbjct: 12 SRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMT 65
Query: 76 AAVKRYNNVQL 86
AV++ +N +
Sbjct: 66 YAVRKLDNTKF 76
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 29.3 bits (64), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 37/71 (52%), Gaps = 7/71 (9%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVKRYN 82
L++ NL V+ E +++ FS+ G+L+R + K A + R A+ A++ N
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVK-------KLKDYAFIHFDERDGAVKAMEEMN 66
Query: 83 NVQLDGKPMKI 93
L+G+ ++I
Sbjct: 67 GKDLEGENIEI 77
>pdb|2CPI|A Chain A, Solution Structure Of The Rna Recognition Motif Of Cnot4
Length = 111
Score = 29.3 bits (64), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 30/61 (49%), Gaps = 4/61 (6%)
Query: 39 ELFSEVGELKRC----SVHFDRSGRSKGTAEVVLTRRADAIAAVKRYNNVQLDGKPMKIE 94
E F + G++ + S + S +A V R DA+ A++ NNV +DG+ +K
Sbjct: 37 EYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKAS 96
Query: 95 I 95
+
Sbjct: 97 L 97
>pdb|2O3D|A Chain A, Structure Of Human Sf2ASF RNA RECOGNITION MOTIF 2 (RRM2)
Length = 113
Score = 28.9 bits (63), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 33/71 (46%), Gaps = 6/71 (8%)
Query: 16 SIESGTKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAI 75
S S ++ +S L S +D+K+ E G++ V+ D GT V R+ D
Sbjct: 11 SRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMT 64
Query: 76 AAVKRYNNVQL 86
AV++ +N +
Sbjct: 65 YAVRKLDNTKF 75
>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 = 28.5 bits (62), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 5/76 (6%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTA--EVVLTRRADAIAAV 78
KL+I L ++++ +KEL + G LK ++ D +G SKG A E V D A+
Sbjct: 98 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTD--QAI 155
Query: 79 KRYNNVQLDGKPMKIE 94
N +QL K + ++
Sbjct: 156 AGLNGMQLGDKKLLVQ 171
>pdb|2HGN|A Chain A, Nmr Structure Of The Third Qrrm Domain Of Human Hnrnp F
pdb|2KG1|A Chain A, Structure Of The Third Qrrm Domain Of Hnrnp F In Complex
With A Agggau G-Tract Rna
Length = 139
Score = 28.5 bits (62), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Query: 19 SGTKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAV 78
+G +++ L Y + DI FS + + R + GR G A+V +A+AA+
Sbjct: 45 TGHCVHMRGLPYKATENDIYNFFSPLNPV-RVHIEIGPDGRVTGEADVEFATHEEAVAAM 103
Query: 79 KR 80
+
Sbjct: 104 SK 105
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 28.5 bits (62), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 5/76 (6%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTA--EVVLTRRADAIAAV 78
KL+I L ++++ +KEL + G LK ++ D +G SKG A E V D A+
Sbjct: 96 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTD--QAI 153
Query: 79 KRYNNVQLDGKPMKIE 94
N +QL K + ++
Sbjct: 154 AGLNGMQLGDKKLLVQ 169
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 28.1 bits (61), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 7/43 (16%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRCS-------VHFDRSG 58
L++ NL V+ E +++ FSE G+L+R VHF+ G
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKDYAFVHFEDRG 60
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 28.1 bits (61), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 17/28 (60%)
Query: 23 LYISNLEYGVSNEDIKELFSEVGELKRC 50
LY+ NL V+ I +LFS++G K C
Sbjct: 18 LYVGNLSRDVTEVLILQLFSQIGPCKSC 45
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 27.7 bits (60), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 5/76 (6%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTA--EVVLTRRADAIAAV 78
KL+I L ++++ +KEL + G LK ++ D +G SKG A E V D A+
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTD--QAI 60
Query: 79 KRYNNVQLDGKPMKIE 94
N +QL K + ++
Sbjct: 61 AGLNGMQLGDKKLLVQ 76
>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 = 27.7 bits (60), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 4/75 (5%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDR-SGRSKGTAEVVLTRRADAIAAVKR 80
K+++ + V ++ +E FS+ G + + D+ +G+S+G V ADA+ V
Sbjct: 89 KIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFG-FVTYDSADAVDRV-- 145
Query: 81 YNNVQLDGKPMKIEI 95
N +D K KIEI
Sbjct: 146 CQNKFIDFKDRKIEI 160
>pdb|1JMT|A Chain A, X-Ray Structure Of A Core U2af65U2AF35 HETERODIMER
Length = 104
Score = 27.7 bits (60), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 41/87 (47%), Gaps = 5/87 (5%)
Query: 14 SSSIESGTKLYISNLEYGVS-NEDIKELFSEV----GELKRCSVHFDRSGRSKGTAEVVL 68
SS G + +S++E +E +E+F+E+ GE++ +V + G V
Sbjct: 16 SSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKF 75
Query: 69 TRRADAIAAVKRYNNVQLDGKPMKIEI 95
R DA AV NN +G+P+ E+
Sbjct: 76 RREEDAEKAVIDLNNRWFNGQPIHAEL 102
>pdb|1X4C|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 2
Length = 108
Score = 27.7 bits (60), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 31/65 (47%), Gaps = 6/65 (9%)
Query: 22 KLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADAIAAVKRY 81
++ +S L S +D+K+ E G++ V+ D GT V R+ D AV++
Sbjct: 17 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKL 70
Query: 82 NNVQL 86
+N +
Sbjct: 71 DNTKF 75
>pdb|1A4E|A Chain A, Catalase A From Saccharomyces Cerevisiae
pdb|1A4E|B Chain B, Catalase A From Saccharomyces Cerevisiae
pdb|1A4E|C Chain C, Catalase A From Saccharomyces Cerevisiae
pdb|1A4E|D Chain D, Catalase A From Saccharomyces Cerevisiae
Length = 488
Score = 27.7 bits (60), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 40 LFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRADA 74
+FS++G+ +C F G KG+A+ V R A
Sbjct: 80 MFSKIGKRTKCLTRFSTVGGDKGSADTVRDPRGFA 114
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 27.3 bits (59), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 39/81 (48%), Gaps = 8/81 (9%)
Query: 15 SSIESG-TKLYISNLEYGVSNEDIKELFSEVGELKRCSVHFDRSGRSKGTAEVVLTRRAD 73
SS SG KL+I NL + ++I+ LF + G++ C + K V + +
Sbjct: 2 SSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDI-------IKNYGFVHIEDKTA 54
Query: 74 AIAAVKRYNNVQLDGKPMKIE 94
A A++ ++ +L G + +E
Sbjct: 55 AEDAIRNLHHYKLHGVNINVE 75
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 26.9 bits (58), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 14/30 (46%), Positives = 20/30 (66%), Gaps = 1/30 (3%)
Query: 15 SSIESG-TKLYISNLEYGVSNEDIKELFSE 43
SS SG KLYI NL V+ +D+++LF +
Sbjct: 2 SSGSSGMNKLYIGNLSPAVTADDLRQLFGD 31
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
0.315 0.134 0.370
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,439,549
Number of Sequences: 62578
Number of extensions: 145945
Number of successful extensions: 417
Number of sequences better than 100.0: 155
Number of HSP's better than 100.0 without gapping: 80
Number of HSP's successfully gapped in prelim test: 75
Number of HSP's that attempted gapping in prelim test: 307
Number of HSP's gapped (non-prelim): 170
length of query: 192
length of database: 14,973,337
effective HSP length: 93
effective length of query: 99
effective length of database: 9,153,583
effective search space: 906204717
effective search space used: 906204717
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 49 (23.5 bits)