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= psy7051
(158 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 158 bits (399), Expect = 1e-39, Method: Compositional matrix adjust.
Identities = 75/90 (83%), Positives = 83/90 (92%)
Query: 1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct: 35 MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 94
Query: 61 RFFDKRDAEDALDAMDGRMLDGRELRVQMA 90
RF DKRDAEDA+DAMDG +LDGRELRVQMA
Sbjct: 95 RFHDKRDAEDAMDAMDGAVLDGRELRVQMA 124
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 142 bits (359), Expect = 6e-35, Method: Compositional matrix adjust.
Identities = 67/81 (82%), Positives = 75/81 (92%)
Query: 10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAE 69
+EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFVRF DKRDAE
Sbjct: 67 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAE 126
Query: 70 DALDAMDGRMLDGRELRVQMA 90
DA+DAMDG +LDGRELRVQMA
Sbjct: 127 DAMDAMDGAVLDGRELRVQMA 147
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 123 bits (308), Expect = 5e-29, Method: Compositional matrix adjust.
Identities = 60/89 (67%), Positives = 72/89 (80%)
Query: 2 SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
S G P ++GM++LKVDNLTYRT+PD LRRVFE+ G VGD+YIPR+ T+ RGFAFVR
Sbjct: 2 SSGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVR 61
Query: 62 FFDKRDAEDALDAMDGRMLDGRELRVQMA 90
F D+RDA+DA AMDG LDGRELRVQ+A
Sbjct: 62 FHDRRDAQDAEAAMDGAELDGRELRVQVA 90
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 67.4 bits (163), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 31/75 (41%), Positives = 50/75 (66%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V L++ T L +VF + G++ ++ + +DR T+ SRGF FV F + DA+DA+ AM
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 76 DGRMLDGRELRVQMA 90
+G+ +DGR++RV A
Sbjct: 75 NGKSVDGRQIRVDQA 89
>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In
Cytotoxic Granule-Associated Rna Binding Protein 1
pdb|2RNE|A Chain A, Solution Structure Of The Second Rna Recognition Motif
(Rrm) Of Tia-1
Length = 115
Score = 62.4 bits (150), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 44/73 (60%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V +L+ T +D++ F G + D + +D T +S+G+ FV FF+K DAE+A+ M G
Sbjct: 20 VGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGG 79
Query: 78 RMLDGRELRVQMA 90
+ L GR++R A
Sbjct: 80 QWLGGRQIRTNWA 92
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 60.8 bits (146), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 48/76 (63%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
++ V NL + T +DL R+F + G+V + I +D+ TR+S+G AF+ F DK A++ A
Sbjct: 18 TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRA 77
Query: 75 MDGRMLDGRELRVQMA 90
++ + L GR ++ +A
Sbjct: 78 INNKQLFGRVIKASIA 93
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 60.8 bits (146), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 45/73 (61%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V +L+ T +D++ F G++ D + +D T +S+G+ FV F++K DAE+A+ M G
Sbjct: 20 VGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMGG 79
Query: 78 RMLDGRELRVQMA 90
+ L GR++R A
Sbjct: 80 QWLGGRQIRTNWA 92
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 58.9 bits (141), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 33/74 (44%), Positives = 45/74 (60%)
Query: 14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
L V L+ TT DLR VF + G + D+ I D+ +R SRGFAFV F + DA++A +
Sbjct: 47 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 106
Query: 74 AMDGRMLDGRELRV 87
+G LDGR +RV
Sbjct: 107 RANGMELDGRRIRV 120
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 58.5 bits (140), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 33/75 (44%), Positives = 45/75 (60%)
Query: 14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
L V L+ TT DLR VF + G + D+ I D+ +R SRGFAFV F + DA++A +
Sbjct: 16 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 75
Query: 74 AMDGRMLDGRELRVQ 88
+G LDGR +RV
Sbjct: 76 RANGMELDGRRIRVS 90
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 58.5 bits (140), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 33/77 (42%), Positives = 46/77 (59%)
Query: 14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
L V L+ TT DLR VF + G + D+ I D+ +R SRGFAFV F + DA++A +
Sbjct: 16 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 75
Query: 74 AMDGRMLDGRELRVQMA 90
+G LDGR +RV +
Sbjct: 76 RANGMELDGRRIRVDFS 92
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 58.5 bits (140), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 33/77 (42%), Positives = 46/77 (59%)
Query: 14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
L V L+ TT DLR VF + G + D+ I D+ +R SRGFAFV F + DA++A +
Sbjct: 13 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 72
Query: 74 AMDGRMLDGRELRVQMA 90
+G LDGR +RV +
Sbjct: 73 RANGMELDGRRIRVDFS 89
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 58.2 bits (139), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 42/72 (58%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V NL+Y ++ +DL ++F G + +++ P D T++ +GFAFV F A A +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 76 DGRMLDGRELRV 87
DG++ GR L V
Sbjct: 71 DGQVFQGRMLHV 82
>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|B Chain B, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|C Chain C, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|D Chain D, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
Length = 84
Score = 54.3 bits (129), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 42/79 (53%)
Query: 12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDA 71
G +L V+ L T D+LR +F GEV + RD+ S G+ FV + +DAE A
Sbjct: 3 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 62
Query: 72 LDAMDGRMLDGRELRVQMA 90
++ ++G L + ++V A
Sbjct: 63 INTLNGLRLQSKTIKVSYA 81
>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 = 53.5 bits (127), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 43/76 (56%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L V+ L T ++ R +F GE+ + RD+ T +S G+ FV + D +DAE A++
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 75 MDGRMLDGRELRVQMA 90
++G L + ++V A
Sbjct: 64 LNGLRLQTKTIKVSYA 79
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 41/82 (50%)
Query: 1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
+SY RP +L V L T +L ++F + G + I D+ T SRG F+
Sbjct: 76 VSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFI 135
Query: 61 RFFDKRDAEDALDAMDGRMLDG 82
RF + +AE+A+ ++G+ G
Sbjct: 136 RFDKRIEAEEAIKGLNGQKPSG 157
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs
Of Human Antigen R
Length = 177
Score = 53.5 bits (127), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 42/79 (53%)
Query: 12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDA 71
G +L V+ L T D+LR +F GEV + RD+ S G+ FV + +DAE A
Sbjct: 1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 72 LDAMDGRMLDGRELRVQMA 90
++ ++G L + ++V A
Sbjct: 61 INTLNGLRLQSKTIKVSYA 79
Score = 44.3 bits (103), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 41/78 (52%)
Query: 1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
+SY RP + +L + L T D+ +F R G + + + D+ T SRG AF+
Sbjct: 76 VSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFI 135
Query: 61 RFFDKRDAEDALDAMDGR 78
RF + +AE+A+ + +G
Sbjct: 136 RFDKRSEAEEAITSFNGH 153
>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 = 53.5 bits (127), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 42/79 (53%)
Query: 12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDA 71
G +L V+ L T D+LR +F GEV + RD+ S G+ FV + +DAE A
Sbjct: 1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 72 LDAMDGRMLDGRELRVQMA 90
++ ++G L + ++V A
Sbjct: 61 INTLNGLRLQSKTIKVSYA 79
Score = 44.3 bits (103), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 41/78 (52%)
Query: 1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
+SY RP + +L + L T D+ +F R G + + + D+ T SRG AF+
Sbjct: 76 VSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFI 135
Query: 61 RFFDKRDAEDALDAMDGR 78
RF + +AE+A+ + +G
Sbjct: 136 RFDKRSEAEEAITSFNGH 153
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 53.1 bits (126), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 45/75 (60%), Gaps = 1/75 (1%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L + L T L+ VF + G + ++ + +DR T +SRGFAF+ F + DA++A M
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDM 68
Query: 76 DGRMLDGRELRVQMA 90
+G+ L G+ ++V+ A
Sbjct: 69 NGKSLHGKAIKVEQA 83
>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 = 52.8 bits (125), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 41/76 (53%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L V+ L T D+LR +F GEV + RD+ S G+ FV + +DAE A++
Sbjct: 21 NLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 80
Query: 75 MDGRMLDGRELRVQMA 90
++G L + ++V A
Sbjct: 81 LNGLRLQSKTIKVSYA 96
>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 = 52.8 bits (125), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
S+ V N+ Y +T DL F CG + I I D+F+ +G+A++ F + R++ DA A
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAE-RNSVDAAVA 96
Query: 75 MDGRMLDGRELRV 87
MD + GR ++V
Sbjct: 97 MDETVFRGRTIKV 109
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 52.4 bits (124), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 49/75 (65%), Gaps = 4/75 (5%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L + NL+Y T + L+ VFE+ I +P+++ +S+G+AF+ F DA++AL++
Sbjct: 17 TLVLSNLSYSATEETLQEVFEK---ATFIKVPQNQ-NGKSKGYAFIEFASFEDAKEALNS 72
Query: 75 MDGRMLDGRELRVQM 89
+ R ++GR +R+++
Sbjct: 73 CNKREIEGRAIRLEL 87
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 52.4 bits (124), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 28/85 (32%), Positives = 46/85 (54%)
Query: 6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
P R + +++V NL+ T DL+ +F G + IY+ +D+ T +S+GFAF+ F +
Sbjct: 8 PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 67
Query: 66 RDAEDALDAMDGRMLDGRELRVQMA 90
DA A+ + G D L V+ A
Sbjct: 68 EDAARAIAGVSGFGYDHLILNVEWA 92
>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 = 52.4 bits (124), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 44/74 (59%)
Query: 14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
+L V NL++ TT + + +F + G++ I + D+ + + GF FV ++ + DAE+A+
Sbjct: 40 CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99
Query: 74 AMDGRMLDGRELRV 87
++G LD R +R
Sbjct: 100 YINGTRLDDRIIRT 113
>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2
pdb|3BS9|B Chain B, X-Ray Structure Of Human Tia-1 Rrm2
Length = 87
Score = 52.0 bits (123), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 34/53 (64%)
Query: 38 GEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA 90
G + D + +D T +S+G+ FV FF+K DAE+A+ M G+ L GR++R A
Sbjct: 31 GRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA 83
>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 = 52.0 bits (123), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
S+ V N+ Y T ++L F CG V + I D+F+ +GFA++ F DK +L A
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-A 66
Query: 75 MDGRMLDGRELRV 87
+D + GR+++V
Sbjct: 67 LDESLFRGRQIKV 79
>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 = 52.0 bits (123), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
S+ V N+ Y T ++L F CG V + I D+F+ +GFA++ F DK +L A
Sbjct: 7 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-A 65
Query: 75 MDGRMLDGRELRV 87
+D + GR+++V
Sbjct: 66 LDESLFRGRQIKV 78
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 51.6 bits (122), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 43/77 (55%)
Query: 11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
G L V +L + T D LR +FE G++ +I + +D T S+G+ F+ F D A
Sbjct: 3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62
Query: 71 ALDAMDGRMLDGRELRV 87
AL+ ++G L GR +RV
Sbjct: 63 ALEQLNGFELAGRPMRV 79
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 51.6 bits (122), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 30/75 (40%), Positives = 42/75 (56%), Gaps = 6/75 (8%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V NL T +D +R+FER GE +++I RDR GF F+R + AE A +
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLESRTLAEIAKAEL 78
Query: 76 DGRMLDGRELRVQMA 90
DG +L R LR++ A
Sbjct: 79 DGTILKSRPLRIRFA 93
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 50.8 bits (120), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 26/68 (38%), Positives = 42/68 (61%), Gaps = 2/68 (2%)
Query: 25 TTPDD--LRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDG 82
TT D+ LR++FER G + + I DR TR+SRG+ FV+F A+ A+ ++G +
Sbjct: 52 TTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILN 111
Query: 83 RELRVQMA 90
+ L+V +A
Sbjct: 112 KRLKVALA 119
>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 = 50.4 bits (119), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 28/85 (32%), Positives = 46/85 (54%), Gaps = 4/85 (4%)
Query: 1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
MS P E + L + L++ TT + LR FE+ G + D + RD T+ SRGF FV
Sbjct: 1 MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 60
Query: 61 RFFDKRDAEDALDA----MDGRMLD 81
+ + + A++A +DGR+++
Sbjct: 61 TYATVEEVDAAMNARPHKVDGRVVE 85
Score = 34.7 bits (78), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 33/66 (50%), Gaps = 1/66 (1%)
Query: 25 TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRE 84
T LR FE+ G++ I I DR + + RGFAFV FD D+ D + ++G
Sbjct: 116 TEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVT-FDDHDSVDKIVIQKYHTVNGHN 174
Query: 85 LRVQMA 90
V+ A
Sbjct: 175 CEVRKA 180
>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 = 50.4 bits (119), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 31/92 (33%), Positives = 49/92 (53%), Gaps = 2/92 (2%)
Query: 1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
MSY RP +L V NL T D L +F + G + I RD+ T RG AFV
Sbjct: 1 MSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFV 60
Query: 61 RFFDKRDAEDALDAMDGRMLDG--RELRVQMA 90
R+ + +A++A+ A++ + +G + L V++A
Sbjct: 61 RYNKREEAQEAISALNNVIPEGGSQPLSVRLA 92
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 50.1 bits (118), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 28/85 (32%), Positives = 46/85 (54%), Gaps = 4/85 (4%)
Query: 1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
MS P E + L + L++ TT + LR FE+ G + D + RD T+ SRGF FV
Sbjct: 1 MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 60
Query: 61 RFFDKRDAEDALDA----MDGRMLD 81
+ + + A++A +DGR+++
Sbjct: 61 TYATVEEVDAAMNARPHKVDGRVVE 85
Score = 35.0 bits (79), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 33/66 (50%), Gaps = 1/66 (1%)
Query: 25 TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRE 84
T LR FE+ G++ I I DR + + RGFAFV FD D+ D + ++G
Sbjct: 116 TEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVT-FDDHDSVDKIVIQKYHTVNGHN 174
Query: 85 LRVQMA 90
V+ A
Sbjct: 175 CEVRKA 180
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 49.7 bits (117), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 42/77 (54%)
Query: 14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
+L V+ L T D+ + +F G++ + RD+ T +S G+ FV + D DA+ A++
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 74 AMDGRMLDGRELRVQMA 90
++G L + ++V A
Sbjct: 65 TLNGLKLQTKTIKVSYA 81
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 49.7 bits (117), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 42/76 (55%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
++ V L + + L +F + G V + ++P+DR T + +G+ FV F + DA+ A+
Sbjct: 17 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 76
Query: 75 MDGRMLDGRELRVQMA 90
MD L G+ +RV A
Sbjct: 77 MDMIKLYGKPIRVNKA 92
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With
The Au-Rich Element
Length = 174
Score = 49.7 bits (117), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 42/77 (54%)
Query: 14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
+L V+ L T D+ + +F G++ + RD+ T +S G+ FV + D DA+ A++
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 74 AMDGRMLDGRELRVQMA 90
++G L + ++V A
Sbjct: 65 TLNGLKLQTKTIKVSYA 81
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 40/78 (51%)
Query: 1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
+SY RP +L V L + ++ ++F + G + I D+ T SRG F+
Sbjct: 78 VSYARPSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFI 137
Query: 61 RFFDKRDAEDALDAMDGR 78
RF + +AE+A+ ++G+
Sbjct: 138 RFDKRIEAEEAIKGLNGQ 155
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 49.7 bits (117), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 42/76 (55%)
Query: 12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDA 71
G + L V +L + T D LR +FE G + I + D T S+G+ F+ F D A+ A
Sbjct: 25 GPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKA 84
Query: 72 LDAMDGRMLDGRELRV 87
L+ ++G L GR ++V
Sbjct: 85 LEQLNGFELAGRPMKV 100
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor
9g8
Length = 101
Score = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 42/77 (54%), Gaps = 5/77 (6%)
Query: 14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
+ + V NL +L R F G + ++I R GFAFV F D RDAEDA+
Sbjct: 1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWI-----ARNPPGFAFVEFEDPRDAEDAVR 55
Query: 74 AMDGRMLDGRELRVQMA 90
+DG+++ G +RV+++
Sbjct: 56 GLDGKVICGSRVRVELS 72
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 48.9 bits (115), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 30/75 (40%), Positives = 37/75 (49%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V L L F G++ DI IP D T + RGFAFV F DA A+D M
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 76 DGRMLDGRELRVQMA 90
+ L GR +RV +A
Sbjct: 75 NESELFGRTIRVNLA 89
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 48.5 bits (114), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 28/70 (40%), Positives = 38/70 (54%), Gaps = 4/70 (5%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA- 74
L V L + TT + LR F + GEV D I +D+ T +SRGF FV+F D L +
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASR 78
Query: 75 ---MDGRMLD 81
+DGR +D
Sbjct: 79 PHTLDGRNID 88
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/61 (44%), Positives = 34/61 (55%)
Query: 30 LRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM 89
L F G++ DI IP D T + RGFAFV F DA A+D M+ L GR +RV +
Sbjct: 80 LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 139
Query: 90 A 90
A
Sbjct: 140 A 140
>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 = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 44/74 (59%), Gaps = 1/74 (1%)
Query: 14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
+L V NL++ TT + + +F + G++ I + D+ + + GF FV ++ + DAE+A+
Sbjct: 19 CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKM-KTACGFCFVEYYSRADAENAMR 77
Query: 74 AMDGRMLDGRELRV 87
++G LD R +R
Sbjct: 78 YINGTRLDDRIIRT 91
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 3/82 (3%)
Query: 12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRE---SRGFAFVRFFDKRDA 68
G L + NL + TT + L+ VF + G + I + + S GF FV + A
Sbjct: 4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQA 63
Query: 69 EDALDAMDGRMLDGRELRVQMA 90
+ AL + G +DG +L V+++
Sbjct: 64 QKALKQLQGHTVDGHKLEVRIS 85
>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 = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 30/92 (32%), Positives = 49/92 (53%), Gaps = 2/92 (2%)
Query: 1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
+SY RP +L V NL T D L +F + G + I RD+ T RG AFV
Sbjct: 88 VSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFV 147
Query: 61 RFFDKRDAEDALDAMDGRMLDG--RELRVQMA 90
R+ + +A++A+ A++ + +G + L V++A
Sbjct: 148 RYNKREEAQEAISALNNVIPEGGSQPLSVRLA 179
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/61 (44%), Positives = 34/61 (55%)
Query: 30 LRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM 89
L F G++ DI IP D T + RGFAFV F DA A+D M+ L GR +RV +
Sbjct: 22 LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 81
Query: 90 A 90
A
Sbjct: 82 A 82
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/61 (44%), Positives = 34/61 (55%)
Query: 30 LRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM 89
L F G++ DI IP D T + RGFAFV F DA A+D M+ L GR +RV +
Sbjct: 24 LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 83
Query: 90 A 90
A
Sbjct: 84 A 84
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 30/75 (40%), Positives = 37/75 (49%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V L L F G++ DI IP D T + RGFAFV F DA A+D M
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 76 DGRMLDGRELRVQMA 90
+ L GR +RV +A
Sbjct: 65 NESELFGRTIRVNLA 79
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 30/92 (32%), Positives = 49/92 (53%), Gaps = 2/92 (2%)
Query: 1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
+SY RP +L V NL T D L +F + G + I RD+ T RG AFV
Sbjct: 77 VSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFV 136
Query: 61 RFFDKRDAEDALDAMDGRMLDG--RELRVQMA 90
R+ + +A++A+ A++ + +G + L V++A
Sbjct: 137 RYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 45/84 (53%), Gaps = 4/84 (4%)
Query: 2 SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
S P E + L + L++ TT + LR FE+ G + D + RD T+ SRGF FV
Sbjct: 3 SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT 62
Query: 62 FFDKRDAEDALDA----MDGRMLD 81
+ + + A++A +DGR+++
Sbjct: 63 YATVEEVDAAMNARPHKVDGRVVE 86
Score = 34.7 bits (78), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 33/66 (50%), Gaps = 1/66 (1%)
Query: 25 TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRE 84
T LR FE+ G++ I I DR + + RGFAFV FD D+ D + ++G
Sbjct: 117 TEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVT-FDDHDSVDKIVIQKYHTVNGHN 175
Query: 85 LRVQMA 90
V+ A
Sbjct: 176 CEVRKA 181
>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 = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 45/84 (53%), Gaps = 4/84 (4%)
Query: 2 SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
S P E + L + L++ TT + LR FE+ G + D + RD T+ SRGF FV
Sbjct: 1 SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT 60
Query: 62 FFDKRDAEDALDA----MDGRMLD 81
+ + + A++A +DGR+++
Sbjct: 61 YATVEEVDAAMNARPHKVDGRVVE 84
Score = 34.7 bits (78), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 33/66 (50%), Gaps = 1/66 (1%)
Query: 25 TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRE 84
T LR FE+ G++ I I DR + + RGFAFV FD D+ D + ++G
Sbjct: 115 TEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVT-FDDHDSVDKIVIQKYHTVNGHN 173
Query: 85 LRVQMA 90
V+ A
Sbjct: 174 CEVRKA 179
>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 = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 40/78 (51%)
Query: 13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
M SL V +L T L F G + I + RD TR S G+A+V F DAE AL
Sbjct: 15 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL 74
Query: 73 DAMDGRMLDGRELRVQMA 90
D M+ ++ G+ +R+ +
Sbjct: 75 DTMNFDVIKGKPVRIMWS 92
Score = 32.3 bits (72), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 38/82 (46%), Gaps = 2/82 (2%)
Query: 6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
P R G+ ++ + NL L F G + + D S+G+ FV F +
Sbjct: 96 PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQ 153
Query: 66 RDAEDALDAMDGRMLDGRELRV 87
AE A++ M+G +L+ R++ V
Sbjct: 154 EAAERAIEKMNGMLLNDRKVFV 175
>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 = 47.8 bits (112), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 40/78 (51%)
Query: 13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
M SL V +L T L F G + I + RD TR S G+A+V F DAE AL
Sbjct: 10 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL 69
Query: 73 DAMDGRMLDGRELRVQMA 90
D M+ ++ G+ +R+ +
Sbjct: 70 DTMNFDVIKGKPVRIMWS 87
Score = 32.7 bits (73), Expect = 0.093, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 38/82 (46%), Gaps = 2/82 (2%)
Query: 6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
P R G+ ++ + NL L F G + + D S+G+ FV F +
Sbjct: 91 PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQ 148
Query: 66 RDAEDALDAMDGRMLDGRELRV 87
AE A++ M+G +L+ R++ V
Sbjct: 149 EAAERAIEKMNGMLLNDRKVFV 170
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 47.8 bits (112), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRE-SRGFAFVRFFDKRDAEDALDA 74
+ + LT T D + +F G++ I +P +R S+G+A+V F + +AE AL
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 75 MDGRMLDGREL 85
MDG +DG+E+
Sbjct: 67 MDGGQIDGQEI 77
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 47.4 bits (111), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 39/76 (51%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
S+ V N+ Y T + L+ +F G V + DR T + +G+ F + D+ A A+
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 75 MDGRMLDGRELRVQMA 90
++GR GR LRV A
Sbjct: 70 LNGREFSGRALRVDNA 85
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 47.4 bits (111), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 41/76 (53%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L V +L + LR F+ ++ D T SRG+ FV F + DA++A+D+
Sbjct: 89 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 148
Query: 75 MDGRMLDGRELRVQMA 90
M G+ L+GR LR+ A
Sbjct: 149 MQGQDLNGRPLRINWA 164
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 47.4 bits (111), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 44/79 (55%), Gaps = 4/79 (5%)
Query: 7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKR 66
P E + L + L++ TT + LR FE+ G + D + RD T+ SRGF FV +
Sbjct: 5 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 64
Query: 67 DAEDALDA----MDGRMLD 81
+ + A++A +DGR+++
Sbjct: 65 EVDAAMNARPHKVDGRVVE 83
Score = 35.0 bits (79), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 33/66 (50%), Gaps = 1/66 (1%)
Query: 25 TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRE 84
T LR FE+ G++ I I DR + + RGFAFV FD D+ D + ++G
Sbjct: 114 TEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVT-FDDHDSVDKIVIQKYHTVNGHN 172
Query: 85 LRVQMA 90
V+ A
Sbjct: 173 CEVRKA 178
>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|6 Chain 6, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|7 Chain 7, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|8 Chain 8, Crystal Structure Of Human Spliceosomal U1 Snrnp
Length = 216
Score = 47.4 bits (111), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 40/73 (54%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L V + Y TT LRR FE G + I++ + + + RG+AF+ + +RD A
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 75 MDGRMLDGRELRV 87
DG+ +DGR + V
Sbjct: 164 ADGKKIDGRRVLV 176
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 47.0 bits (110), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 32/55 (58%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
+ L+++TT + LR F + GEV + + RD T+ SRGF FV F D+ + L
Sbjct: 30 IGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 84
>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 = 47.0 bits (110), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 41/76 (53%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L V +L + LR F+ ++ D T SRG+ FV F + DA++A+D+
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 75 MDGRMLDGRELRVQMA 90
M G+ L+GR LR+ A
Sbjct: 63 MQGQDLNGRPLRINWA 78
>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of
Fbp-Interacting Repressor (Fir)
pdb|2KXH|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fir
In The Complex With Fbp Nbox Peptide
Length = 199
Score = 47.0 bits (110), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 39/75 (52%)
Query: 13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
M + V ++ Y D +R+ F G + I + D T + +GFAFV + A+ AL
Sbjct: 13 MCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLAL 72
Query: 73 DAMDGRMLDGRELRV 87
+ M+ ML GR ++V
Sbjct: 73 EQMNSVMLGGRNIKV 87
Score = 42.7 bits (99), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 36/60 (60%)
Query: 28 DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV 87
DD++ VFE G++ + RD T + +G+ F+ + + ++DA+ +M+ L G+ LRV
Sbjct: 125 DDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 184
>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 = 46.6 bits (109), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 44/75 (58%), Gaps = 6/75 (8%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V NL T +++R++FE+ G+ G+++I +D +GF F+R + AE A +
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVEL 71
Query: 76 DGRMLDGRELRVQMA 90
D L G++LRV+ A
Sbjct: 72 DNMPLRGKQLRVRFA 86
>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
pdb|2QFJ|B Chain B, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
Length = 216
Score = 46.6 bits (109), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 39/75 (52%)
Query: 13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
M + V ++ Y D +R+ F G + I + D T + +GFAFV + A+ AL
Sbjct: 28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLAL 87
Query: 73 DAMDGRMLDGRELRV 87
+ M+ ML GR ++V
Sbjct: 88 EQMNSVMLGGRNIKV 102
Score = 43.1 bits (100), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 36/60 (60%)
Query: 28 DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV 87
DD++ VFE G++ + RD T + +G+ F+ + + ++DA+ +M+ L G+ LRV
Sbjct: 140 DDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 199
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 46.6 bits (109), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 44/75 (58%), Gaps = 6/75 (8%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V NL T +++R++FE+ G+ G+++I +D +GF F+R + AE A +
Sbjct: 25 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVEL 78
Query: 76 DGRMLDGRELRVQMA 90
D L G++LRV+ A
Sbjct: 79 DNMPLRGKQLRVRFA 93
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 46.2 bits (108), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 45/75 (60%), Gaps = 2/75 (2%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V N+ +R DLR++F + G++ D+ I + R S+GF FV F + DA+ A + +
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKL 89
Query: 76 DGRMLDGRELRVQMA 90
G +++GR++ V A
Sbjct: 90 HGTVVEGRKIEVNNA 104
>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 = 46.2 bits (108), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 41/75 (54%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L V + Y TT LRR FE G + I++ + + + RG+AF+ + +RD A
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 75 MDGRMLDGRELRVQM 89
DG+ +DGR + V +
Sbjct: 164 ADGKKIDGRRVLVDV 178
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 46.2 bits (108), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 45/75 (60%), Gaps = 2/75 (2%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V N+ +R DLR++F + G++ D+ I + R S+GF FV F + DA+ A + +
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKL 75
Query: 76 DGRMLDGRELRVQMA 90
G +++GR++ V A
Sbjct: 76 HGTVVEGRKIEVNNA 90
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleaoproteins A2B1
Length = 116
Score = 46.2 bits (108), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 41/70 (58%), Gaps = 4/70 (5%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA- 74
L + L++ TT + LR +E+ G++ D + RD ++ SRGF FV F + + A+ A
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAAR 89
Query: 75 ---MDGRMLD 81
+DGR+++
Sbjct: 90 PHSIDGRVVE 99
>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 = 46.2 bits (108), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 27/68 (39%), Positives = 36/68 (52%), Gaps = 4/68 (5%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA--- 74
V L++ T+ DL+ F + GEV D I D T SRGF F+ F D E LD
Sbjct: 16 VGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQKEH 75
Query: 75 -MDGRMLD 81
+DGR++D
Sbjct: 76 RLDGRVID 83
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 46.2 bits (108), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 32/55 (58%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
+ L+++TT + LR F + GEV + + RD T+ SRGF FV F D+ + L
Sbjct: 5 IGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 59
>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 = 45.8 bits (107), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 43/75 (57%), Gaps = 4/75 (5%)
Query: 11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
E + L + L++ TT + LR FE+ G + D + RD T+ SRGF FV + + +
Sbjct: 4 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 63
Query: 71 ALDA----MDGRMLD 81
A++A +DGR+++
Sbjct: 64 AMNARPHKVDGRVVE 78
Score = 34.7 bits (78), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 33/66 (50%), Gaps = 1/66 (1%)
Query: 25 TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRE 84
T LR FE+ G++ I I DR + + RGFAFV FD D+ D + ++G
Sbjct: 109 TEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVT-FDDHDSVDKIVIQKYHTVNGHN 167
Query: 85 LRVQMA 90
V+ A
Sbjct: 168 CEVRKA 173
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 45.4 bits (106), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V L Y TT LR+ FE G++ + + DR T +SRG+ FV D+ AE A +
Sbjct: 22 VGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPN- 80
Query: 78 RMLDGRELRVQMA 90
++DGR+ V +A
Sbjct: 81 PIIDGRKANVNLA 93
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 45.4 bits (106), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 39/73 (53%), Gaps = 5/73 (6%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL +L R F G + +++ R+ GFAFV F D RDA DA+ +DG
Sbjct: 78 VGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDG 132
Query: 78 RMLDGRELRVQMA 90
R L G +RV+++
Sbjct: 133 RTLCGCRVRVELS 145
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/69 (39%), Positives = 37/69 (53%), Gaps = 4/69 (5%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V L ++TT DL+ F GEV + + +D T S+GF FVRF + E + M
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF---TEYETQVKVM 74
Query: 76 DGR-MLDGR 83
R M+DGR
Sbjct: 75 SQRHMIDGR 83
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 39/73 (53%), Gaps = 5/73 (6%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL +L R F G + +++ R+ GFAFV F D RDA DA+ +DG
Sbjct: 78 VGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRDLDG 132
Query: 78 RMLDGRELRVQMA 90
R L G +RV+++
Sbjct: 133 RTLCGCRVRVELS 145
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 44.3 bits (103), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 42/78 (53%), Gaps = 1/78 (1%)
Query: 13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
M ++ V NL Y T + ++ +F + G+V ++ + DR T++ +GF FV + +A+
Sbjct: 1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVE-MQEESVSEAI 59
Query: 73 DAMDGRMLDGRELRVQMA 90
+D GR +RV A
Sbjct: 60 AKLDNTDFMGRTIRVTEA 77
>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 = 43.9 bits (102), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 44/84 (52%), Gaps = 5/84 (5%)
Query: 4 GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFF 63
GR ++ +L NL++ T D+L+ VFE E+ + +D +S+G A++ F
Sbjct: 90 GRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIR--LVSQDG---KSKGIAYIEFK 144
Query: 64 DKRDAEDALDAMDGRMLDGRELRV 87
+ DAE L+ G +DGR + +
Sbjct: 145 SEADAEKNLEEKQGAEIDGRSVSL 168
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 43.5 bits (101), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 44/85 (51%), Gaps = 2/85 (2%)
Query: 8 PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRF-TRESRGFAFVRFFDKR 66
P+ + + V N+ ++ ++R +F GE+ + +P+ T RGF FV F K+
Sbjct: 10 PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQ 69
Query: 67 DAEDALDAM-DGRMLDGRELRVQMA 90
DA+ A +A+ L GR L ++ A
Sbjct: 70 DAKKAFNALCHSTHLYGRRLVLEWA 94
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 42.7 bits (99), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 5/73 (6%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L NL Y+ T D+L+ VFE E+ + +D +S+G A++ F + DAE +
Sbjct: 95 TLLAKNLPYKVTQDELKEVFEDAAEIR--LVSKDG---KSKGIAYIEFKTEADAEKTFEE 149
Query: 75 MDGRMLDGRELRV 87
G +DGR + +
Sbjct: 150 KQGTEIDGRSISL 162
>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 = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 44/82 (53%), Gaps = 1/82 (1%)
Query: 6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
P +EG + L V + T +D+ F GE+ +I++ DR T +G+ V +
Sbjct: 1 PQRSVEGWI-LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 59
Query: 66 RDAEDALDAMDGRMLDGRELRV 87
++A+ A++ ++G+ L G+ + V
Sbjct: 60 KEAQAAMEGLNGQDLMGQPISV 81
>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 = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 36/68 (52%), Gaps = 4/68 (5%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA--- 74
+ L++ TT DL+ F + GEV D + D T SRGF FV F + + +D
Sbjct: 4 IGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEH 63
Query: 75 -MDGRMLD 81
++G+++D
Sbjct: 64 KLNGKVID 71
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 44/82 (53%), Gaps = 1/82 (1%)
Query: 6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
P +EG + L V + T +D+ F GE+ +I++ DR T +G+ V +
Sbjct: 1 PQRSVEGWI-LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 59
Query: 66 RDAEDALDAMDGRMLDGRELRV 87
++A+ A++ ++G+ L G+ + V
Sbjct: 60 KEAQAAMEGLNGQDLMGQPISV 81
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 44/82 (53%), Gaps = 1/82 (1%)
Query: 6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
P +EG + L V + T +D+ F GE+ +I++ DR T +G+ V +
Sbjct: 3 PQRSVEGWI-LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 61
Query: 66 RDAEDALDAMDGRMLDGRELRV 87
++A+ A++ ++G+ L G+ + V
Sbjct: 62 KEAQAAMEGLNGQDLMGQPISV 83
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 44/82 (53%), Gaps = 1/82 (1%)
Query: 6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
P +EG + L V + T +D+ F GE+ +I++ DR T +G+ V +
Sbjct: 16 PQRSVEGWI-LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 74
Query: 66 RDAEDALDAMDGRMLDGRELRV 87
++A+ A++ ++G+ L G+ + V
Sbjct: 75 KEAQAAMEGLNGQDLMGQPISV 96
>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 = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 44/82 (53%), Gaps = 1/82 (1%)
Query: 6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
P +EG + L V + T +D+ F GE+ +I++ DR T +G+ V +
Sbjct: 1 PQRSVEGWI-LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 59
Query: 66 RDAEDALDAMDGRMLDGRELRV 87
++A+ A++ ++G+ L G+ + V
Sbjct: 60 KEAQAAMEGLNGQDLMGQPISV 81
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 45/82 (54%), Gaps = 1/82 (1%)
Query: 6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
P +EG + L V ++ D+++ F GE+ +I++ DR T S+G+A V +
Sbjct: 20 PQRSVEGWI-LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETH 78
Query: 66 RDAEDALDAMDGRMLDGRELRV 87
+ A A +A++G + G+ ++V
Sbjct: 79 KQALAAKEALNGAEIMGQTIQV 100
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 45/83 (54%), Gaps = 5/83 (6%)
Query: 5 RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
R PP + + L + NL Y+ T +++ +F + G + I R T E+RG A+V + D
Sbjct: 2 RLPPEVNRI--LYIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYED 56
Query: 65 KRDAEDALDAMDGRMLDGRELRV 87
DA++A+D + G + R L V
Sbjct: 57 IFDAKNAVDHLSGFNVSNRYLVV 79
>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 = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 44/82 (53%), Gaps = 1/82 (1%)
Query: 6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
P +EG + L V + T +D+ F GE+ +I++ DR T +G+ V +
Sbjct: 17 PQRSVEGWI-LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 75
Query: 66 RDAEDALDAMDGRMLDGRELRV 87
++A+ A++ ++G+ L G+ + V
Sbjct: 76 KEAQAAMEGLNGQDLMGQPISV 97
>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 = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 15 SLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
++ ++NL + D+L++ +F R G++ DI + R + + RG AFV F + A +
Sbjct: 8 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 64
Query: 71 ALDAMDGRMLDGRELRVQMA 90
AL +M G + +R+Q A
Sbjct: 65 ALRSMQGFPFYDKPMRIQYA 84
>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 = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 15 SLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
++ ++NL + D+L++ +F R G++ DI + R + + RG AFV F + A +
Sbjct: 11 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 67
Query: 71 ALDAMDGRMLDGRELRVQMA 90
AL +M G + +R+Q A
Sbjct: 68 ALRSMQGFPFYDKPMRIQYA 87
>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|B Chain B, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|C Chain C, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|D Chain D, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
Length = 96
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 15 SLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
++ ++NL + D+L++ +F R G++ DI + R + + RG AFV F + A +
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 66
Query: 71 ALDAMDGRMLDGRELRVQMA 90
AL +M G + +R+Q A
Sbjct: 67 ALRSMQGFPFYDKPMRIQYA 86
>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 = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 15 SLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
++ ++NL + D+L++ +F R G++ DI + R + + RG AFV F + A +
Sbjct: 5 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 61
Query: 71 ALDAMDGRMLDGRELRVQMA 90
AL +M G + +R+Q A
Sbjct: 62 ALRSMQGFPFYDKPMRIQYA 81
>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 = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 15 SLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
++ ++NL + D+L++ +F R G++ DI + R + + RG AFV F + A +
Sbjct: 11 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 67
Query: 71 ALDAMDGRMLDGRELRVQMA 90
AL +M G + +R+Q A
Sbjct: 68 ALRSMQGFPFYDKPMRIQYA 87
>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|B Chain B, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|C Chain C, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1NU4|A Chain A, U1a Rna Binding Domain At 1.8 Angstrom Resolution
Reveals A Pre- Organized C-Terminal Helix
pdb|1NU4|B Chain B, U1a Rna Binding Domain At 1.8 Angstrom Resolution
Reveals A Pre- Organized C-Terminal Helix
pdb|3HHN|B Chain B, Crystal Structure Of Class I Ligase Ribozyme
Self-Ligation Product, In Complex With U1a Rbd
pdb|3HHN|D Chain D, Crystal Structure Of Class I Ligase Ribozyme
Self-Ligation Product, In Complex With U1a Rbd
Length = 97
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 15 SLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
++ ++NL + D+L++ +F R G++ DI + R + + RG AFV F + A +
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 66
Query: 71 ALDAMDGRMLDGRELRVQMA 90
AL +M G + +R+Q A
Sbjct: 67 ALRSMQGFPFYDKPMRIQYA 86
>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 = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 38/64 (59%), Gaps = 3/64 (4%)
Query: 29 DLRRVFERCGEVGDIYIPRDRFTR--ESRGFAFVRFFDKRDAEDALDAMDG-RMLDGREL 85
DLR +FE+ G V +I + RDR +S+G FV F+ ++ A +A +A+ ++L G
Sbjct: 19 DLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHH 78
Query: 86 RVQM 89
+QM
Sbjct: 79 PIQM 82
>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 = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 15 SLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
++ ++NL + D+L++ +F R G++ DI + R + + RG AFV F + A +
Sbjct: 6 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 62
Query: 71 ALDAMDGRMLDGRELRVQMA 90
AL +M G + +R+Q A
Sbjct: 63 ALRSMQGFPFYDKPMRIQYA 82
>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 = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 15 SLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
++ ++NL + D+L++ +F R G++ DI + R + + RG AFV F + A +
Sbjct: 7 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 63
Query: 71 ALDAMDGRMLDGRELRVQMA 90
AL +M G + +R+Q A
Sbjct: 64 ALRSMQGFPFYDKPMRIQYA 83
>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 = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 15 SLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
++ ++NL + D+L++ +F R G++ DI + R + + RG AFV F + A +
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 66
Query: 71 ALDAMDGRMLDGRELRVQMA 90
AL +M G + +R+Q A
Sbjct: 67 ALRSMQGFPFYDKPMRIQYA 86
>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 = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 45/82 (54%), Gaps = 1/82 (1%)
Query: 6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
P +EG + L V ++ D+++ F GE+ +I++ DR T S+G+A V +
Sbjct: 66 PQRSVEGWI-LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETH 124
Query: 66 RDAEDALDAMDGRMLDGRELRV 87
+ A A +A++G + G+ ++V
Sbjct: 125 KQALAAKEALNGAEIMGQTIQV 146
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 5/73 (6%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L NL++ T D+L+ VFE E+ + +D +S+G A++ F + DAE L+
Sbjct: 18 TLLAKNLSFNITEDELKEVFEDALEIR--LVSQDG---KSKGIAYIEFKSEADAEKNLEE 72
Query: 75 MDGRMLDGRELRV 87
G +DGR + +
Sbjct: 73 KQGAEIDGRSVSL 85
>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 = 40.4 bits (93), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 36/67 (53%), Gaps = 3/67 (4%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA--- 74
+ L + TT D+LR F + G V D+ I +D T SRGF F+ F ++ +
Sbjct: 8 IGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHI 67
Query: 75 MDGRMLD 81
+DG+++D
Sbjct: 68 LDGKVID 74
Score = 31.2 bits (69), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 34/64 (53%), Gaps = 5/64 (7%)
Query: 27 PDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD-AMDGRMLDGREL 85
P + F + G + D + D+ T +SRGF FV + D+ DA+D + +D ++
Sbjct: 101 PKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTY----DSADAVDRVCQNKFIDFKDR 156
Query: 86 RVQM 89
++++
Sbjct: 157 KIEI 160
>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 = 40.4 bits (93), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 36/63 (57%)
Query: 28 DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV 87
DD++ VFE G++ + RD T + +G+ F+ + + ++DA+ + + L G+ LRV
Sbjct: 124 DDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRV 183
Query: 88 QMA 90
A
Sbjct: 184 GKA 186
Score = 39.7 bits (91), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 34/70 (48%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V ++ Y D +R+ F G + I D T + +GFAFV + A+ AL+ +
Sbjct: 17 VGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQXNS 76
Query: 78 RMLDGRELRV 87
L GR ++V
Sbjct: 77 VXLGGRNIKV 86
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 40.4 bits (93), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 29/74 (39%), Positives = 37/74 (50%), Gaps = 3/74 (4%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
+ V NL D+ VF + G + DI + + R FAFV F D RDAEDA+
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDL---KNRRGGPPFAFVEFEDPRDAEDAVYGR 81
Query: 76 DGRMLDGRELRVQM 89
DG DG LRV+
Sbjct: 82 DGYDYDGYRLRVEF 95
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 40.0 bits (92), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 38/64 (59%), Gaps = 3/64 (4%)
Query: 29 DLRRVFERCGEVGDIYIPRDRFTR--ESRGFAFVRFFDKRDAEDALDAMDG-RMLDGREL 85
DLR +FE+ G V +I + RDR +S+G FV F+ ++ A +A +A+ ++L G
Sbjct: 19 DLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHH 78
Query: 86 RVQM 89
+QM
Sbjct: 79 PIQM 82
Score = 30.0 bits (66), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 5/62 (8%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPR--DRFTRESRGFAFVRFFDKRDAEDALD 73
L + ++ + T +D+R +F G++ + I R D SRG AFV F + A+ A+
Sbjct: 98 LFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGL---SRGCAFVTFTTRAMAQTAIK 154
Query: 74 AM 75
AM
Sbjct: 155 AM 156
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 40.0 bits (92), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 38/64 (59%), Gaps = 3/64 (4%)
Query: 29 DLRRVFERCGEVGDIYIPRDRFTR--ESRGFAFVRFFDKRDAEDALDAMDG-RMLDGREL 85
DLR +FE+ G V +I + RDR +S+G FV F+ ++ A +A +A+ ++L G
Sbjct: 31 DLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHH 90
Query: 86 RVQM 89
+QM
Sbjct: 91 PIQM 94
Score = 29.6 bits (65), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 1/60 (1%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L + ++ + T +D+R +F G++ + I R SRG AFV F + A+ A+ AM
Sbjct: 110 LFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAM 168
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 40.0 bits (92), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 8/79 (10%)
Query: 12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDA 71
GMV L + NL T ++R +FE+ G+V + I ++ + FV DK AEDA
Sbjct: 7 GMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFVHIEDKTAAEDA 58
Query: 72 LDAMDGRMLDGRELRVQMA 90
+ + L G + V+ +
Sbjct: 59 IRNLHHYKLHGVNINVEAS 77
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 40.0 bits (92), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 9/74 (12%)
Query: 18 VDNL-TYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
+ NL T D+ +F + G++ + +GFAFV++ ++R+A A+ D
Sbjct: 20 IGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGED 71
Query: 77 GRMLDGRELRVQMA 90
GRM+ G+ L + +A
Sbjct: 72 GRMIAGQVLDINLA 85
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 40.0 bits (92), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 44/83 (53%), Gaps = 5/83 (6%)
Query: 5 RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
R PP + + L + NL Y+ T +++ +F + G + I R T E+RG A+V + D
Sbjct: 6 RLPPEVNRI--LYIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYED 60
Query: 65 KRDAEDALDAMDGRMLDGRELRV 87
DA++A D + G + R L V
Sbjct: 61 IFDAKNACDHLSGFNVCNRYLVV 83
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 39.7 bits (91), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 15 SLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
++ ++NL + D+L++ +F + G++ DI + R + + RG AFV F + A +
Sbjct: 11 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 67
Query: 71 ALDAMDGRMLDGRELRVQMA 90
AL +M G + +R+Q A
Sbjct: 68 ALRSMQGFPFYDKPMRIQYA 87
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 39.7 bits (91), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 43/84 (51%), Gaps = 8/84 (9%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEV------GD--IYIPRDRFTRESRGFAFVRFFDKR 66
++ V L T DDL F++CG V G I+I D+ T + +G A V + D
Sbjct: 17 AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPP 76
Query: 67 DAEDALDAMDGRMLDGRELRVQMA 90
A+ A++ DG+ G +L+V +A
Sbjct: 77 TAKAAVEWFDGKDFQGSKLKVSLA 100
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 39.7 bits (91), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 44/83 (53%), Gaps = 5/83 (6%)
Query: 5 RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
R PP + + L + NL Y+ T +++ +F + G + I R T E+RG A+V + D
Sbjct: 12 RLPPEVNRI--LYIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYED 66
Query: 65 KRDAEDALDAMDGRMLDGRELRV 87
DA++A D + G + R L V
Sbjct: 67 IFDAKNACDHLSGFNVCNRYLVV 89
>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of
The Spliceosomal Protein P14 Bound To A Region Of
Sf3b155
pdb|2F9J|B Chain B, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of
The Spliceosomal Protein P14 Bound To A Region Of
Sf3b155
Length = 125
Score = 39.7 bits (91), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 44/83 (53%), Gaps = 5/83 (6%)
Query: 5 RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
R PP + + L + NL Y+ T +++ +F + G + I R T E+RG A+V + D
Sbjct: 12 RLPPEVNRI--LMIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYED 66
Query: 65 KRDAEDALDAMDGRMLDGRELRV 87
DA++A D + G + R L V
Sbjct: 67 IFDAKNACDHLSGFNVCNRYLVV 89
>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 = 39.7 bits (91), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 15 SLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
++ ++NL + D+L++ +F + G++ DI + R + + RG AFV F + A +
Sbjct: 11 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 67
Query: 71 ALDAMDGRMLDGRELRVQMA 90
AL +M G + +R+Q A
Sbjct: 68 ALRSMQGFPFYDKPMRIQYA 87
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein
U1a117, Nmr, 43 Structures
Length = 116
Score = 39.3 bits (90), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 15 SLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
++ ++NL + D+L++ +F + G++ DI + R + + RG AFV F + A +
Sbjct: 10 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 66
Query: 71 ALDAMDGRMLDGRELRVQMA 90
AL +M G + +R+Q A
Sbjct: 67 ALRSMQGFPFYDKPMRIQYA 86
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 29/85 (34%), Positives = 44/85 (51%), Gaps = 3/85 (3%)
Query: 6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
P R + +L V L+ TT + L+ F+ G V I DR T S+GF FV F +
Sbjct: 8 PNARSQPSKTLFVKGLSEDTTEETLKESFD--GSV-RARIVTDRETGSSKGFGFVDFNSE 64
Query: 66 RDAEDALDAMDGRMLDGRELRVQMA 90
DA+ A +AM+ +DG ++ + A
Sbjct: 65 EDAKAAKEAMEDGEIDGNKVTLDWA 89
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Rna-Binding Protein 14
Length = 90
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 40/73 (54%), Gaps = 8/73 (10%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V N++ T +LR +FER G V + + +D +AFV + DA+ A+ ++G
Sbjct: 14 VGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQLNG 65
Query: 78 RMLDGRELRVQMA 90
+ + G+ + V+++
Sbjct: 66 KEVKGKRINVELS 78
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 28/40 (70%)
Query: 51 TRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA 90
++ R +AFV F ++ DA +A+ A++G++LDG + V +A
Sbjct: 47 VKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA 86
>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
pdb|3NNA|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 38/63 (60%), Gaps = 3/63 (4%)
Query: 29 DLRRVFERCGEVGDIYIPRDRFTR--ESRGFAFVRFFDKRDAEDALDAM-DGRMLDGREL 85
DLR +FE+ G V +I + RDR +S+G FV F+ ++ A +A +A+ + ++L G
Sbjct: 19 DLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNXKVLPGXHH 78
Query: 86 RVQ 88
+Q
Sbjct: 79 PIQ 81
Score = 27.3 bits (59), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPR--DRFTRESRGFAFVRFFDKRDAEDALD 73
L + ++ + T +D+R F G++ + I R D SRG AFV F + A+ A+
Sbjct: 98 LFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDGL---SRGCAFVTFTTRAXAQTAIK 154
Query: 74 A 74
A
Sbjct: 155 A 155
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 36/71 (50%), Gaps = 1/71 (1%)
Query: 20 NLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRM 79
L R P DL F G+V D+ I DR +R S+G A+V F + + A+ + G+
Sbjct: 32 QLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQR 90
Query: 80 LDGRELRVQMA 90
L G + VQ +
Sbjct: 91 LLGVPIIVQAS 101
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 40/78 (51%), Gaps = 7/78 (8%)
Query: 11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
GM L + NL+ T DDLR++F GD +P G+AFV + D+ A
Sbjct: 6 SGMNKLYIGNLSPAVTADDLRQLF------GDRKLPLAGQVLLKSGYAFVDYPDQNWAIR 59
Query: 71 ALDAMDGRM-LDGRELRV 87
A++ + G++ L G+ + V
Sbjct: 60 AIETLSGKVELHGKIMEV 77
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
28
Length = 111
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 6/77 (7%)
Query: 20 NLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD--- 76
NL++ + + L V ++ G++ + + T S+G AF +F + A+ L A
Sbjct: 22 NLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEA 81
Query: 77 ---GRMLDGRELRVQMA 90
G LDGR+L+V +A
Sbjct: 82 EGGGLKLDGRQLKVDLA 98
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V L + + DD+RR+FE G + + I R S+G AFV++ +A+ A++A+
Sbjct: 18 LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGP-DGNSKGCAFVKYSSHAEAQAAINAL 76
Query: 76 DG 77
G
Sbjct: 77 HG 78
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 42/80 (52%), Gaps = 7/80 (8%)
Query: 15 SLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
++ ++NL + D+L++ +F R G++ DI + R + + RG AFV F + A +
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKXRGQAFVIFKEVSSATN 66
Query: 71 ALDAMDGRMLDGRELRVQMA 90
AL + G + R+Q A
Sbjct: 67 ALRSXQGFPFYDKPXRIQYA 86
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 41/83 (49%), Gaps = 2/83 (2%)
Query: 9 RIEGM--VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKR 66
+IEG +L + +L T DL F G V + D+ T S+ F FV F +
Sbjct: 34 QIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPD 93
Query: 67 DAEDALDAMDGRMLDGRELRVQM 89
A+ A+ AM+G + + L+VQ+
Sbjct: 94 SAQVAIKAMNGFQVGTKRLKVQL 116
>pdb|3CUL|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUL|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3EGZ|A Chain A, Crystal Structure Of An In Vitro Evolved Tetracycline
Aptamer And Artificial Riboswitch
Length = 98
Score = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 42/80 (52%), Gaps = 7/80 (8%)
Query: 15 SLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
++ ++NL + D+L++ +F R G++ DI + R + + RG AFV F + A +
Sbjct: 11 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKXRGQAFVIFKEVSSATN 67
Query: 71 ALDAMDGRMLDGRELRVQMA 90
AL + G + R+Q A
Sbjct: 68 ALRSXQGFPFYDKPXRIQYA 87
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 42/80 (52%), Gaps = 7/80 (8%)
Query: 15 SLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
++ ++NL + D+L++ +F R G++ DI + R + + RG AFV F + A +
Sbjct: 8 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKXRGQAFVIFKEVSSATN 64
Query: 71 ALDAMDGRMLDGRELRVQMA 90
AL + G + R+Q A
Sbjct: 65 ALRSXQGFPFYDKPXRIQYA 84
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 33/58 (56%), Gaps = 4/58 (6%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
V L+ TT +D++ FE+ G+V D + D+ T RGF FV F ++ED ++ +
Sbjct: 4 VGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF----ESEDIVEKV 57
>pdb|3P5T|L Chain L, Cfim25-Cfim68 Complex
pdb|3P5T|M Chain M, Cfim25-Cfim68 Complex
pdb|3P5T|N Chain N, Cfim25-Cfim68 Complex
pdb|3P5T|O Chain O, Cfim25-Cfim68 Complex
pdb|3P5T|P Chain P, Cfim25-Cfim68 Complex
pdb|3P5T|Q Chain Q, Cfim25-Cfim68 Complex
pdb|3P6Y|C Chain C, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|D Chain D, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|G Chain G, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|H Chain H, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|K Chain K, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|L Chain L, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|O Chain O, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|P Chain P, Cf Im25-Cf Im68-Uguaa Complex
Length = 90
Score = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 2/72 (2%)
Query: 14 VSLKVDNLTYRTTPDDLRRVFERCG--EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDA 71
++L + NLT+ TT +DL G ++ +I +R +S+GFA V + ++
Sbjct: 2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKL 61
Query: 72 LDAMDGRMLDGR 83
+D + R L G+
Sbjct: 62 MDLLPKRELHGQ 73
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 9/74 (12%)
Query: 18 VDNL-TYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
+ NL T D+ +F + G V + +G+AFV++ ++R A A+ +
Sbjct: 32 IGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGEN 83
Query: 77 GRMLDGRELRVQMA 90
GR+L G+ L + MA
Sbjct: 84 GRVLAGQTLDINMA 97
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 36.6 bits (83), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 35/75 (46%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L + NL+ R T DL +F R E I T RG AF+ F +K A AL +
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87
Query: 76 DGRMLDGRELRVQMA 90
+G L G+ L ++
Sbjct: 88 NGYKLYGKILVIEFG 102
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 36.2 bits (82), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 36/79 (45%), Gaps = 2/79 (2%)
Query: 11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
G + V NL + T L+ F CG V +Y +S+G V+F AE
Sbjct: 6 SGACQIFVRNLPFDFTWKMLKDKFNECGHV--LYADIKMENGKSKGCGVVKFESPEVAER 63
Query: 71 ALDAMDGRMLDGRELRVQM 89
A M+G L GRE+ V++
Sbjct: 64 ACRMMNGMKLSGREIDVRI 82
>pdb|3Q2S|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2S|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2T|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
pdb|3Q2T|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
Length = 229
Score = 36.2 bits (82), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 2/72 (2%)
Query: 14 VSLKVDNLTYRTTPDDLRRVFERCG--EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDA 71
++L + NLT+ TT +DL G ++ +I +R +S+GFA V + ++
Sbjct: 69 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKL 128
Query: 72 LDAMDGRMLDGR 83
+D + R L G+
Sbjct: 129 MDLLPKRELHGQ 140
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 35.8 bits (81), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 35/65 (53%)
Query: 14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
+L V L + ++ ++F + G + I D+ T SRG F+RF + +AE+A+
Sbjct: 2 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 61
Query: 74 AMDGR 78
++G+
Sbjct: 62 GLNGQ 66
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 35.8 bits (81), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 36/62 (58%), Gaps = 1/62 (1%)
Query: 29 DLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM-DGRMLDGRELRV 87
DL+ +FE G++ ++ + +DRFT +G AF+ + ++ A A A+ + + L G +
Sbjct: 29 DLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPI 88
Query: 88 QM 89
Q+
Sbjct: 89 QV 90
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 35.4 bits (80), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 41/76 (53%), Gaps = 2/76 (2%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L V NL+ T + ++F + G + + + + + FV F++ RDA AL A
Sbjct: 17 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAALAA 74
Query: 75 MDGRMLDGRELRVQMA 90
M+GR + G+E++V A
Sbjct: 75 MNGRKILGKEVKVNWA 90
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 35.4 bits (80), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 21/48 (43%), Positives = 29/48 (60%), Gaps = 4/48 (8%)
Query: 45 IPRDRFTRESRGFAFVRF--FDKRDAEDALDAMDGRMLDGRELRVQMA 90
I RD T S+G+AF+ F FD DA A++AM+G+ L R + V A
Sbjct: 38 IMRDPDTGNSKGYAFINFASFDASDA--AIEAMNGQYLCNRPITVSYA 83
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain
In Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 35.4 bits (80), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 36/79 (45%), Gaps = 2/79 (2%)
Query: 11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
G + V NL + T L+ F CG V +Y +S+G V+F AE
Sbjct: 3 SGSSGIFVRNLPFDFTWKMLKDKFNECGHV--LYADIKMENGKSKGCGVVKFESPEVAER 60
Query: 71 ALDAMDGRMLDGRELRVQM 89
A M+G L GRE+ V++
Sbjct: 61 ACRMMNGMKLSGREIDVRI 79
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 35.0 bits (79), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 28/52 (53%)
Query: 30 LRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLD 81
L +F + G+V ++ P D T +++GF FV DA+ + + G+ LD
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLD 80
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 35.0 bits (79), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 8/75 (10%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V N++ T +LR FE G V + I +D +AFV DA +A+ +
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRGL 64
Query: 76 DGRMLDGRELRVQMA 90
D G+ + VQ++
Sbjct: 65 DNTEFQGKRMHVQLS 79
>pdb|3NS6|A Chain A, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
pdb|3NS6|B Chain B, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
Length = 100
Score = 34.7 bits (78), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 28/52 (53%)
Query: 30 LRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLD 81
L +F + G+V ++ P D T +++GF FV DA+ + + G+ LD
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLD 80
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 34.7 bits (78), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 2/73 (2%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL + T D+ +F+ + + + RD+ T + +GF +V F + ++AL DG
Sbjct: 20 VGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDG 77
Query: 78 RMLDGRELRVQMA 90
+L R LRV +A
Sbjct: 78 ALLGDRSLRVDIA 90
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 34.3 bits (77), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 38/78 (48%), Gaps = 2/78 (2%)
Query: 13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
+V+L V NL + LR+ F G + + + S+GF FV F +A A+
Sbjct: 15 VVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAV 72
Query: 73 DAMDGRMLDGRELRVQMA 90
M+GR++ + L V +A
Sbjct: 73 TEMNGRIVATKPLYVALA 90
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet
Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 34.3 bits (77), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 33/62 (53%)
Query: 28 DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV 87
DL ++F G V + D+ T S+ F FV + + A+ A+ +M+G + + L+V
Sbjct: 40 QDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKV 99
Query: 88 QM 89
Q+
Sbjct: 100 QL 101
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 34.3 bits (77), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 30/59 (50%), Gaps = 5/59 (8%)
Query: 11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAE 69
G + V T T D+LR F + G+V D++IP+ R FAFV F D + A+
Sbjct: 3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFADDQIAQ 56
>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 = 33.9 bits (76), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 36/81 (44%)
Query: 10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAE 69
+ G L + L D ++ + G + + +D T S+G+AF + D +
Sbjct: 93 LPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTD 152
Query: 70 DALDAMDGRMLDGRELRVQMA 90
A+ ++G L ++L VQ A
Sbjct: 153 QAIAGLNGMQLGDKKLLVQRA 173
>pdb|1A9N|B Chain B, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
pdb|1A9N|D Chain D, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
Length = 96
Score = 33.9 bits (76), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 42/80 (52%), Gaps = 7/80 (8%)
Query: 15 SLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
++ ++N+ + ++L+R +F + G V DI + T + RG AFV F + + +
Sbjct: 8 TIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALK---TMKMRGQAFVIFKELGSSTN 64
Query: 71 ALDAMDGRMLDGRELRVQMA 90
AL + G G+ +R+Q A
Sbjct: 65 ALRQLQGFPFYGKPMRIQYA 84
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 33.9 bits (76), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 38/82 (46%), Gaps = 2/82 (2%)
Query: 6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
P R G+ ++ + NL L F G + + D S+G+ FV F +
Sbjct: 4 PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQ 61
Query: 66 RDAEDALDAMDGRMLDGRELRV 87
AE A++ M+G +L+ R++ V
Sbjct: 62 EAAERAIEKMNGMLLNDRKVFV 83
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 33.9 bits (76), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 17/75 (22%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L + L + T ++L + + G V D+ + +R + +G A+V + ++ A A+ M
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKP-KGLAYVEYENESQASQAVMKM 78
Query: 76 DGRMLDGRELRVQMA 90
DG + ++V ++
Sbjct: 79 DGMTIKENIIKVAIS 93
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 33.5 bits (75), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 36/81 (44%)
Query: 10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAE 69
+ G L + L D ++ + G + + +D T S+G+AF + D +
Sbjct: 91 LPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTD 150
Query: 70 DALDAMDGRMLDGRELRVQMA 90
A+ ++G L ++L VQ A
Sbjct: 151 QAIAGLNGMQLGDKKLLVQRA 171
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 33.5 bits (75), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 31/63 (49%)
Query: 28 DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV 87
D ++ + G + + +D T S+G+AF + D + A+ ++G L ++L V
Sbjct: 129 DQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLV 188
Query: 88 QMA 90
Q A
Sbjct: 189 QRA 191
>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain
Of Hnrnp D (Auf1) With Telomere Dna
pdb|1X0F|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain
Of Hnrnp D(Auf1) With Telomeric Dna
Length = 79
Score = 33.5 bits (75), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 1/74 (1%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V L+ T + +R F GEV I +P D T + RGF F+ F ++ + ++
Sbjct: 6 VGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYH 65
Query: 78 RM-LDGRELRVQMA 90
+ L E++V M+
Sbjct: 66 NVGLSKCEIKVAMS 79
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 33.1 bits (74), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 21 LTYRTTPDDLRRVFERCG-EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
L T DD+R + G + ++ + R++ + +SRGFAFV F +DA ++A
Sbjct: 9 LPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEA 63
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 33.1 bits (74), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 31/63 (49%)
Query: 28 DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV 87
D ++ + G + + +D T S+G+AF + D + A+ ++G L ++L V
Sbjct: 16 DQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLV 75
Query: 88 QMA 90
Q A
Sbjct: 76 QRA 78
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 33.1 bits (74), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 29/53 (54%), Gaps = 5/53 (9%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
V T T ++L++ F + GEV D++IP+ R FAFV F D + A+
Sbjct: 16 VGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF-----RAFAFVTFADDKVAQS 63
>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 32.7 bits (73), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 6/77 (7%)
Query: 20 NLTYRTTPDDLRRVFERCGE--VGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
N+ T D + V +I + +D+ T+++RGFAFV+ DA L +
Sbjct: 16 NIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQS 75
Query: 78 RM----LDGRELRVQMA 90
+DG+ + V A
Sbjct: 76 LHPPLKIDGKTIGVDFA 92
>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 = 32.7 bits (73), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 39/82 (47%), Gaps = 5/82 (6%)
Query: 6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
PP R+ + + ++ Y T + + + G V ++ + D T S+G+AF+ F D
Sbjct: 2 PPSRV-----VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDL 56
Query: 66 RDAEDALDAMDGRMLDGRELRV 87
+ A+ ++G L R L+
Sbjct: 57 ESSASAVRNLNGYQLGSRFLKC 78
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 32.3 bits (72), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 11/82 (13%)
Query: 12 GMVSLKV---DNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDA 68
GM +KV NL T + L + F + G++ + +D +AF+ F ++ A
Sbjct: 7 GMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGA 58
Query: 69 EDALDAMDGRMLDGRELRVQMA 90
A++ M+G+ L+G + + A
Sbjct: 59 VKAMEEMNGKDLEGENIEIVFA 80
>pdb|2DIT|A Chain A, Solution Structure Of The Rrm_1 Domain Of Hiv Tat
Specific Factor 1 Variant
Length = 112
Score = 32.3 bits (72), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 32/70 (45%), Gaps = 4/70 (5%)
Query: 19 DNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGR 78
D L +DLR + G++ + + F R G A V F D +A+ + +DGR
Sbjct: 32 DPLVLNEIREDLRVECSKFGQIRKLLL----FDRHPDGVASVSFRDPEEADYCIQTLDGR 87
Query: 79 MLDGRELRVQ 88
GR++ Q
Sbjct: 88 WFGGRQITAQ 97
>pdb|3N9U|C Chain C, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
pdb|3N9U|I Chain I, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
Length = 156
Score = 32.0 bits (71), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 18/78 (23%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCG--EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
++ V + ++ TT L +V G +V ++ +R +S+G+A V + L
Sbjct: 57 AVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLL 116
Query: 73 DAMDGRMLDGRELRVQMA 90
+ + G++L+G ++ V+ A
Sbjct: 117 ELLPGKVLNGEKVDVRPA 134
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 32.0 bits (71), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 28/56 (50%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
V L+ T + +R F GEV I +P D T + RGF F+ F ++ + ++
Sbjct: 4 VGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 59
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 31.6 bits (70), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V + + +LR F++ G V ++ + D + RGF F+ F D++ + A++ M
Sbjct: 15 VGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHF 73
Query: 78 RMLDGRELRVQMA 90
+ G+++ V+ A
Sbjct: 74 HDIMGKKVEVKRA 86
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 30.8 bits (68), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V L + + +D+ R+F+ G + + + R S+G AFV+F +A+ A+ A+
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHAL 76
Query: 76 DG 77
G
Sbjct: 77 HG 78
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 30.8 bits (68), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 32 RVFERCGEVGDIYIPRDRF---TRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV 87
++ + C VG + + F T S+G+AF+ F D + A+ ++G L R L+
Sbjct: 19 QILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKC 77
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 30.8 bits (68), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 32 RVFERCGEVGDIYIPRDRF---TRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV 87
++ + C VG + + F T S+G+AF+ F D + A+ ++G L R L+
Sbjct: 18 QILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKC 76
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 30.8 bits (68), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 28 DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM-DGRMLDGRELR 86
DL+ +FE G + ++ + +DR T +G AF+ + + A A A+ + + L G
Sbjct: 30 QDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSALHEQKTLPGMNRP 89
Query: 87 VQM 89
+Q+
Sbjct: 90 IQV 92
>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 = 30.8 bits (68), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 25/48 (52%)
Query: 43 IYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA 90
I + DR T + +G A V F D A+ A+D DG+ G ++V A
Sbjct: 51 INLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98
>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 = 30.0 bits (66), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 23/34 (67%)
Query: 54 SRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV 87
S+G+ FV F + AE A++ M+G +L+ R++ V
Sbjct: 44 SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 77
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 30.0 bits (66), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 25/48 (52%)
Query: 43 IYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA 90
I + DR T + +G A V F D A+ A+D DG+ G ++V A
Sbjct: 45 INLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 92
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In
Trinucleotide Repeat Containing 4 Variant
Length = 102
Score = 30.0 bits (66), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 36/68 (52%), Gaps = 2/68 (2%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V L + T +D+R++FE G + + + R S+G AFV+F +A+ A++ +
Sbjct: 15 LFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGP-DGTSKGCAFVKFQTHAEAQAAINTL 73
Query: 76 -DGRMLDG 82
R L G
Sbjct: 74 HSSRTLPG 81
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 29.6 bits (65), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 13/58 (22%), Positives = 31/58 (53%), Gaps = 6/58 (10%)
Query: 30 LRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV 87
+R+ F G++ +I + ++ G++FVRF A A+ +++G ++G ++
Sbjct: 42 MRQTFSPFGQIMEIRVFPEK------GYSFVRFSTHESAAHAIVSVNGTTIEGHVVKC 93
>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 = 29.6 bits (65), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 21/40 (52%)
Query: 50 FTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM 89
F + +G AFV + AE A++A L REL VQ+
Sbjct: 32 FVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQL 71
>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 = 29.6 bits (65), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 21/40 (52%)
Query: 50 FTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM 89
F + +G AFV + AE A++A L REL VQ+
Sbjct: 50 FVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQL 89
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 29.6 bits (65), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 21/40 (52%)
Query: 50 FTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM 89
F + +G AFV + AE A++A L REL VQ+
Sbjct: 52 FVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQL 91
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 29.6 bits (65), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 21/40 (52%)
Query: 50 FTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM 89
F + +G AFV + AE A++A L REL VQ+
Sbjct: 52 FVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQL 91
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 28.9 bits (63), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/76 (23%), Positives = 36/76 (47%), Gaps = 9/76 (11%)
Query: 16 LKVDNLTYR-TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
L + NL + + +DL R+F G + I I F F++F + + DA++
Sbjct: 13 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIEC 64
Query: 75 MDGRMLDGRELRVQMA 90
M G++L ++++
Sbjct: 65 ESQEMNFGKKLILEVS 80
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 28.5 bits (62), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 10/85 (11%)
Query: 8 PRIEGMVS-LKVDNLTYR-TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
PR M S L + NL + + +DL R+F G + I I F F++F +
Sbjct: 16 PRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNP 67
Query: 66 RDAEDALDAMDGRMLDGRELRVQMA 90
+ DA++ M G++L ++++
Sbjct: 68 QSVRDAIECESQEMNFGKKLILEVS 92
>pdb|2KRB|A Chain A, Solution Structure Of Eif3b-Rrm Bound To Eif3j Peptide
Length = 81
Score = 28.5 bits (62), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 12/55 (21%), Positives = 29/55 (52%), Gaps = 2/55 (3%)
Query: 30 LRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRE 84
+ ++F + G++ + + P + +++G+ F+ + A DA+ DG LD +
Sbjct: 24 IHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQH 76
>pdb|2NLW|A Chain A, Solution Structure Of The Rrm Domain Of Human Eukaryotic
Initiation Factor 3b
Length = 105
Score = 28.5 bits (62), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 21/91 (23%), Positives = 43/91 (47%), Gaps = 10/91 (10%)
Query: 7 PPRIEGMVSLKVDNLTYRTTPDDL-------RRVFERCGEVGDIYIPRDRFTRESRGFAF 59
P +G+ S+ V + + PD L ++F + G++ + + P + +++G+ F
Sbjct: 8 PQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIF 65
Query: 60 VRFFDKRDAEDALDAMDGRMLDGRE-LRVQM 89
+ + A DA+ DG LD + RV +
Sbjct: 66 LEYASPAHAVDAVKNADGYKLDKQHTFRVNL 96
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 28.5 bits (62), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 3/49 (6%)
Query: 29 DLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
L +F + G++ DI + T + RG AFV F + A +AL M G
Sbjct: 26 SLYAIFSQFGQILDIVALK---TLKMRGQAFVIFKEIGSASNALRTMQG 71
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 28.5 bits (62), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 18/76 (23%), Positives = 36/76 (47%), Gaps = 9/76 (11%)
Query: 16 LKVDNLTYR-TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
L + NL + + +DL R+F G + I I F F++F + + DA++
Sbjct: 5 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIEC 56
Query: 75 MDGRMLDGRELRVQMA 90
M G++L ++++
Sbjct: 57 ESQEMNFGKKLILEVS 72
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 28.1 bits (61), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 10/85 (11%)
Query: 8 PRIEGMVS-LKVDNLTYR-TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
PR M S L + NL + + +DL R+F G + I I F F++F +
Sbjct: 16 PRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNP 67
Query: 66 RDAEDALDAMDGRMLDGRELRVQMA 90
+ DA++ M G++L ++++
Sbjct: 68 QSVRDAIEXESQEMNFGKKLILEVS 92
>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 = 2.0, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 8/63 (12%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V NL T + L + F G++ + +D +AFV F D+ A A+D M
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD--------YAFVHFEDRGAAVKAMDEM 69
Query: 76 DGR 78
+G+
Sbjct: 70 NGK 72
>pdb|2WTM|A Chain A, Est1e From Butyrivibrio Proteoclasticus
pdb|2WTM|B Chain B, Est1e From Butyrivibrio Proteoclasticus
pdb|2WTM|C Chain C, Est1e From Butyrivibrio Proteoclasticus
pdb|2WTM|D Chain D, Est1e From Butyrivibrio Proteoclasticus
pdb|2WTN|A Chain A, Ferulic Acid Bound To Est1e From Butyrivibrio
Proteoclasticus
pdb|2WTN|B Chain B, Ferulic Acid Bound To Est1e From Butyrivibrio
Proteoclasticus
Length = 251
Score = 27.3 bits (59), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 20/43 (46%), Gaps = 4/43 (9%)
Query: 45 IPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV 87
IP T E G F D + D LDA DGR L G +RV
Sbjct: 137 IPEIARTGELLGLKF----DPENIPDELDAWDGRKLKGNYVRV 175
>pdb|3KYH|C Chain C, Saccharomyces Cerevisiae Cet1-Ceg1 Capping Apparatus
pdb|3KYH|D Chain D, Saccharomyces Cerevisiae Cet1-Ceg1 Capping Apparatus
Length = 461
Score = 26.6 bits (57), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 23/51 (45%), Gaps = 1/51 (1%)
Query: 38 GEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ 88
GE G I R+ GF F R K+ E DG +LDG EL +Q
Sbjct: 89 GEQGCFMIDRENNYYLVNGFRFPRLPQKKKEELLETLQDGTLLDG-ELVIQ 138
>pdb|3TP2|A Chain A, Crystal Structure Of The Splicing Factor Cwc2 From Yeast
pdb|3TP2|B Chain B, Crystal Structure Of The Splicing Factor Cwc2 From Yeast
Length = 229
Score = 26.2 bits (56), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 28/51 (54%), Gaps = 6/51 (11%)
Query: 30 LRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML 80
+R VF R G+ I R R+ ES+ FV+F + +AE A +AM + L
Sbjct: 162 IRFVFSRLGD-----IDRIRYV-ESKNCGFVKFKYQANAEFAKEAMSNQTL 206
>pdb|3U1L|A Chain A, Structure Of The Mrna Splicing Complex Component Cwc2
pdb|3U1M|A Chain A, Structure Of The Mrna Splicing Complex Component Cwc2
Length = 240
Score = 26.2 bits (56), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 28/51 (54%), Gaps = 6/51 (11%)
Query: 30 LRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML 80
+R VF R G+ I R R+ ES+ FV+F + +AE A +AM + L
Sbjct: 160 IRFVFSRLGD-----IDRIRYV-ESKNCGFVKFKYQANAEFAKEAMSNQTL 204
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.324 0.143 0.426
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,215,605
Number of Sequences: 62578
Number of extensions: 104487
Number of successful extensions: 404
Number of sequences better than 100.0: 184
Number of HSP's better than 100.0 without gapping: 140
Number of HSP's successfully gapped in prelim test: 44
Number of HSP's that attempted gapping in prelim test: 225
Number of HSP's gapped (non-prelim): 206
length of query: 158
length of database: 14,973,337
effective HSP length: 91
effective length of query: 67
effective length of database: 9,278,739
effective search space: 621675513
effective search space used: 621675513
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 47 (22.7 bits)