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= 026078
(244 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 99.0 bits (245), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 48/82 (58%), Positives = 64/82 (78%)
Query: 55 LAPSKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDA 114
LAPSKSTVYVSNL ++LTN+DL+ +FS +GK+ +VT++KD+ TRKS+GVAFI F+ A
Sbjct: 12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSA 71
Query: 115 LSAARAIHGKVLNGRTVNASIA 136
+ RAI+ K L GR + ASIA
Sbjct: 72 QNCTRAINNKQLFGRVIKASIA 93
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 64.3 bits (155), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 31/88 (35%), Positives = 51/88 (57%), Gaps = 3/88 (3%)
Query: 55 LAPSKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDA 114
+A + ++V L + L +FS +G+I+ V V+KDR T++SRG F+ F I DA
Sbjct: 8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDA 67
Query: 115 LSAARAIHGKVLNGRTV---NASIAADN 139
A A++GK ++GR + A ++DN
Sbjct: 68 KDAMMAMNGKSVDGRQIRVDQAGKSSDN 95
>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 = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 29/73 (39%), Positives = 45/73 (61%), Gaps = 1/73 (1%)
Query: 59 KSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAA 118
K +VYV N+DY T DL FS+ G I R+T+L D+ + +G A+I+F + +++ AA
Sbjct: 36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAER-NSVDAA 94
Query: 119 RAIHGKVLNGRTV 131
A+ V GRT+
Sbjct: 95 VAMDETVFRGRTI 107
>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 = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 43/75 (57%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
V+V +L +T D+ F+ FG+I+ V+KD AT KS+G F+ F DA +A + +
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 122 HGKVLNGRTVNASIA 136
G+ L GR + + A
Sbjct: 78 GGQWLGGRQIRTNWA 92
>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 = 55.5 bits (132), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 45/77 (58%)
Query: 60 STVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAAR 119
+++ V NL Y + L +F +G++ V + +DR T++SRG AF++F DA A
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 120 AIHGKVLNGRTVNASIA 136
A+ G VL+GR + +A
Sbjct: 108 AMDGAVLDGRELRVQMA 124
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 55.1 bits (131), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 33/86 (38%), Positives = 43/86 (50%), Gaps = 3/86 (3%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
++V + L DL LF FG+I +TVLKDR T +G AF+ + AL A A+
Sbjct: 18 LFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSAL 77
Query: 122 H-GKVLNG--RTVNASIAADNGRASS 144
H K L G R + AA GR S
Sbjct: 78 HEQKTLPGMNRPIQVKPAASEGRGES 103
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 54.7 bits (130), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 28/75 (37%), Positives = 43/75 (57%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
V+V +L +T D+ + F+ FGKI+ V+KD AT KS+G F+ F DA +A +
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 122 HGKVLNGRTVNASIA 136
G+ L GR + + A
Sbjct: 78 GGQWLGGRQIRTNWA 92
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 54.7 bits (130), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 45/77 (58%)
Query: 60 STVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAAR 119
+++ V NL Y + L +F +G++ V + +DR T++SRG AF++F DA A
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 120 AIHGKVLNGRTVNASIA 136
A+ G VL+GR + +A
Sbjct: 131 AMDGAVLDGRELRVQMA 147
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 53.1 bits (126), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 45/75 (60%), Gaps = 1/75 (1%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
+ VSNLD+ ++++D+ LF+ FG + + V DR+ R S G A + F + DAL A +
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGR-SLGTADVHFERKADALKAMKQY 89
Query: 122 HGKVLNGRTVNASIA 136
+G L+GR +N +
Sbjct: 90 NGVPLDGRPMNIQLV 104
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 47/80 (58%), Gaps = 1/80 (1%)
Query: 58 SKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSA 117
+ + + VSNLD+ ++++D+ LF+ FG + + V DR+ R S G A + F + DAL A
Sbjct: 87 TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGR-SLGTADVHFERRADALKA 145
Query: 118 ARAIHGKVLNGRTVNASIAA 137
+ G L+GR ++ + A
Sbjct: 146 MKQYKGVPLDGRPMDIQLVA 165
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 52.4 bits (124), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 40/71 (56%)
Query: 64 VSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAIHG 123
V L T DL +FS +G IA V+++ D+ +R+SRG AF+ F + DA A +G
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 124 KVLNGRTVNAS 134
L+GR + S
Sbjct: 80 MELDGRRIRVS 90
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 52.4 bits (124), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 47/80 (58%), Gaps = 1/80 (1%)
Query: 58 SKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSA 117
+ + + VSNLD+ ++++D+ LF+ FG + + V DR+ R S G A + F + DAL A
Sbjct: 34 TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGR-SLGTADVHFERRADALKA 92
Query: 118 ARAIHGKVLNGRTVNASIAA 137
+ G L+GR ++ + A
Sbjct: 93 MKQYKGVPLDGRPMDIQLVA 112
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 52.4 bits (124), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 47/80 (58%), Gaps = 1/80 (1%)
Query: 58 SKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSA 117
+ + + VSNLD+ ++++D+ LF+ FG + + V DR+ R S G A + F + DAL A
Sbjct: 34 TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGR-SLGTADVHFERRADALKA 92
Query: 118 ARAIHGKVLNGRTVNASIAA 137
+ G L+GR ++ + A
Sbjct: 93 MKQYKGVPLDGRPMDIQLVA 112
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 52.4 bits (124), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 43/83 (51%), Gaps = 1/83 (1%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
++V LD++ T L + FS +G++ ++KD+ T +SRG F++F + P+ + A
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF-KDPNCVGTVLAS 77
Query: 122 HGKVLNGRTVNASIAADNGRASS 144
L+GR ++ G S
Sbjct: 78 RPHTLDGRNIDPKPCTPRGMQPS 100
>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex
Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A
Resolution
Length = 107
Score = 52.4 bits (124), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 44/74 (59%), Gaps = 1/74 (1%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
+ VSNLD+ ++++D+ LF+ FG + + V DR+ R S G A + F + DAL A +
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGR-SLGTADVHFERKADALKAXKQY 90
Query: 122 HGKVLNGRTVNASI 135
+G L+GR N +
Sbjct: 91 NGVPLDGRPXNIQL 104
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 51.2 bits (121), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 40/73 (54%)
Query: 64 VSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAIHG 123
V L T DL +FS +G IA V+++ D+ +R+SRG AF+ F + DA A +G
Sbjct: 17 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 76
Query: 124 KVLNGRTVNASIA 136
L+GR + +
Sbjct: 77 MELDGRRIRVDFS 89
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 51.2 bits (121), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 26/68 (38%), Positives = 39/68 (57%)
Query: 64 VSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAIHG 123
V L T DL +FS +G IA V+++ D+ +R+SRG AF+ F + DA A +G
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 124 KVLNGRTV 131
L+GR +
Sbjct: 80 MELDGRRI 87
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 50.8 bits (120), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 26/68 (38%), Positives = 39/68 (57%)
Query: 64 VSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAIHG 123
V L T DL +FS +G IA V+++ D+ +R+SRG AF+ F + DA A +G
Sbjct: 51 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 110
Query: 124 KVLNGRTV 131
L+GR +
Sbjct: 111 MELDGRRI 118
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 50.8 bits (120), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 26/70 (37%), Positives = 41/70 (58%), Gaps = 1/70 (1%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
+++ L+ L +F G I+ V ++KDR T KSRG AFI F DA +AA+ +
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDM 68
Query: 122 HGKVLNGRTV 131
+GK L+G+ +
Sbjct: 69 NGKSLHGKAI 78
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 50.4 bits (119), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 29/68 (42%), Positives = 40/68 (58%), Gaps = 3/68 (4%)
Query: 56 APSKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDAL 115
A +T+ V+NL +DL LF FG I+R+ + KD+ T +S+G AFI F + D
Sbjct: 12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRED-- 69
Query: 116 SAARAIHG 123
AARAI G
Sbjct: 70 -AARAIAG 76
>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 = 8e-07, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 51/84 (60%), Gaps = 2/84 (2%)
Query: 60 STVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAAR 119
+ +YV+NL +T+ L T+F +G I + +L+D+ T + RGVAF+++ + +A A
Sbjct: 14 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 73
Query: 120 AIHGKVLNG--RTVNASIAADNGR 141
A++ + G + ++ +A ++G+
Sbjct: 74 ALNNVIPEGGSQPLSVRLAEEHGK 97
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 50.4 bits (119), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 34/61 (55%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
+++ + L DL LF FGKI +TVLKDR T +G AF+ + + AL A A+
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSAL 75
Query: 122 H 122
H
Sbjct: 76 H 76
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 39/72 (54%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
++V NL Y + DL LFS +G ++ + D T+K +G AF+ F+ A+ A +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 122 HGKVLNGRTVNA 133
G+V GR ++
Sbjct: 71 DGQVFQGRMLHV 82
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 40/77 (51%)
Query: 61 TVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARA 120
+V+V N+ Y T L +FS G + ++ DR T K +G F ++ ALSA R
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 121 IHGKVLNGRTVNASIAA 137
++G+ +GR + AA
Sbjct: 70 LNGREFSGRALRVDNAA 86
>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 = 49.7 bits (117), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 51/84 (60%), Gaps = 2/84 (2%)
Query: 60 STVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAAR 119
+ +YV+NL +T+ L T+F +G I + +L+D+ T + RGVAF+++ + +A A
Sbjct: 101 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 160
Query: 120 AIHGKVLNG--RTVNASIAADNGR 141
A++ + G + ++ +A ++G+
Sbjct: 161 ALNNVIPEGGSQPLSVRLAEEHGK 184
>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 = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 42/71 (59%)
Query: 60 STVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAAR 119
+ +YVS L +T +L LFS +G+I +L D+ T SRGV FI+F + +A A +
Sbjct: 89 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 148
Query: 120 AIHGKVLNGRT 130
++G+ +G T
Sbjct: 149 GLNGQKPSGAT 159
Score = 43.9 bits (102), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 42/79 (53%)
Query: 58 SKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSA 117
SK+ + V+ L +T + +LF + G+I +++D+ T +S G F+ ++ DA A
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 118 ARAIHGKVLNGRTVNASIA 136
++G L +T+ S A
Sbjct: 61 INTLNGLRLQTKTIKVSYA 79
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 41/81 (50%)
Query: 56 APSKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDAL 115
A +K +YV L + + LH F FG I + + D T K RG AF++F DA
Sbjct: 60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 119
Query: 116 SAARAIHGKVLNGRTVNASIA 136
+A ++ L GRT+ ++A
Sbjct: 120 AAIDNMNESELFGRTIRVNLA 140
>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 = 2e-06, Method: Compositional matrix adjust.
Identities = 27/82 (32%), Positives = 42/82 (51%)
Query: 55 LAPSKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDA 114
+A +K +YV L + + LH F FG I + + D T K RG AF++F DA
Sbjct: 8 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 67
Query: 115 LSAARAIHGKVLNGRTVNASIA 136
+A ++ L GRT+ ++A
Sbjct: 68 AAAIDNMNESELFGRTIRVNLA 89
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 48.9 bits (115), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 42/69 (60%)
Query: 60 STVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAAR 119
+ +YV+NL +T+ L T+F +G I + +L+D+ T + RGVAF+++ + +A A
Sbjct: 90 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 149
Query: 120 AIHGKVLNG 128
A++ + G
Sbjct: 150 ALNNVIPEG 158
>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 = 48.9 bits (115), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 40/71 (56%)
Query: 61 TVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARA 120
T++V+ ++Y T S L F +G I R+ ++ + + K RG AFI++ D SA +
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 121 IHGKVLNGRTV 131
GK ++GR V
Sbjct: 164 ADGKKIDGRRV 174
>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 = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 27/82 (32%), Positives = 42/82 (51%)
Query: 55 LAPSKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDA 114
+A +K +YV L + + LH F FG I + + D T K RG AF++F DA
Sbjct: 3 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 62
Query: 115 LSAARAIHGKVLNGRTVNASIA 136
+A ++ L GRT+ ++A
Sbjct: 63 AAAIDNMNESELFGRTIRVNLA 84
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 44/76 (57%), Gaps = 1/76 (1%)
Query: 60 STVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAAR 119
STV+V+NLDY + L +FS G + R +L+D+ KSRG+ + F Q +A+ A
Sbjct: 16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAIS 74
Query: 120 AIHGKVLNGRTVNASI 135
+G++L R ++ +
Sbjct: 75 MFNGQLLFDRPMHVKM 90
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 48.1 bits (113), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 2/76 (2%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
++VSN+ + + DL +F FGKI V ++ + R S+G F+ F DA A +
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKL 89
Query: 122 HGKVLNGRTVNASIAA 137
HG V+ GR + + A
Sbjct: 90 HGTVVEGRKIEVNNAT 105
>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 = 48.1 bits (113), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 41/83 (49%)
Query: 55 LAPSKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDA 114
L T+YV NL + T ++ LFS G I ++ + D+ + + G F+++ DA
Sbjct: 35 LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADA 94
Query: 115 LSAARAIHGKVLNGRTVNASIAA 137
+A R I+G L+ R + A
Sbjct: 95 ENAMRYINGTRLDDRIIRTDWDA 117
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 48.1 bits (113), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 40/65 (61%)
Query: 60 STVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAAR 119
+ +YVS L ++ ++ LFS +G+I +L D+AT SRGV FI+F + +A A +
Sbjct: 2 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 61
Query: 120 AIHGK 124
++G+
Sbjct: 62 GLNGQ 66
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 47.8 bits (112), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 2/76 (2%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
++VSN+ + + DL +F FGKI V ++ + R S+G F+ F DA A +
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKL 75
Query: 122 HGKVLNGRTVNASIAA 137
HG V+ GR + + A
Sbjct: 76 HGTVVEGRKIEVNNAT 91
>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 = 47.8 bits (112), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 25/64 (39%), Positives = 38/64 (59%)
Query: 60 STVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAAR 119
+ +Y+S L +T D+ +FS FG+I VL D+ T SRGVAFI+F + +A A
Sbjct: 89 ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAIT 148
Query: 120 AIHG 123
+ +G
Sbjct: 149 SFNG 152
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 47.8 bits (112), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 25/64 (39%), Positives = 38/64 (59%)
Query: 60 STVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAAR 119
+ +Y+S L +T D+ +FS FG+I VL D+ T SRGVAFI+F + +A A
Sbjct: 89 ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAIT 148
Query: 120 AIHG 123
+ +G
Sbjct: 149 SFNG 152
>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 = 7e-06, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 41/75 (54%)
Query: 61 TVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARA 120
T++V+ ++Y T S L F +G I R+ ++ + + K RG AFI++ D SA +
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 121 IHGKVLNGRTVNASI 135
GK ++GR V +
Sbjct: 164 ADGKKIDGRRVLVDV 178
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 47.4 bits (111), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 40/65 (61%)
Query: 60 STVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAAR 119
+ +YVS L ++ ++ LFS +G+I +L D+AT SRGV FI+F + +A A +
Sbjct: 91 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 150
Query: 120 AIHGK 124
++G+
Sbjct: 151 GLNGQ 155
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 47.4 bits (111), Expect = 8e-06, Method: Composition-based stats.
Identities = 27/79 (34%), Positives = 40/79 (50%)
Query: 58 SKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSA 117
SK +YV L + + LH F FG I + + D T K RG AF++F DA +A
Sbjct: 1 SKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 60
Query: 118 ARAIHGKVLNGRTVNASIA 136
++ L GRT+ ++A
Sbjct: 61 IDNMNESELFGRTIRVNLA 79
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 47.4 bits (111), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
+YV NL Y+ T+ + LFS FGK+ V ++ DR T+K +G F++ +Q A +
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVE-MQEESVSEAIAKL 62
Query: 122 HGKVLNGRTVNASIA 136
GRT+ + A
Sbjct: 63 DNTDFMGRTIRVTEA 77
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 47.4 bits (111), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 40/76 (52%)
Query: 61 TVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARA 120
T+ V NL Y + L +F +G++ V + ++ T+ RG AF++F DA A A
Sbjct: 15 TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74
Query: 121 IHGKVLNGRTVNASIA 136
+ G L+GR + +A
Sbjct: 75 MDGAELDGRELRVQVA 90
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 40/79 (50%)
Query: 58 SKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSA 117
+K +YV L + + LH F FG I + + D T K RG AF++F DA +A
Sbjct: 4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 63
Query: 118 ARAIHGKVLNGRTVNASIA 136
++ L GRT+ ++A
Sbjct: 64 IDNMNESELFGRTIRVNLA 82
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 38/72 (52%)
Query: 60 STVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAAR 119
S +YV +L + +T L +F FGKI + ++KD T +S+G FI F A A
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 120 AIHGKVLNGRTV 131
++G L GR +
Sbjct: 66 QLNGFELAGRPM 77
>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 = 3e-05, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 39/77 (50%), Gaps = 5/77 (6%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
++V L Y T++ L F FG I V+ DR T KSRG FV + D +A RA
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYG---FVTMADRAAAERAC 76
Query: 122 H--GKVLNGRTVNASIA 136
+++GR N ++A
Sbjct: 77 KDPNPIIDGRKANVNLA 93
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 27/87 (31%), Positives = 43/87 (49%), Gaps = 3/87 (3%)
Query: 60 STVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPD---ALS 116
S + V L + T DL FSTFG++ V V KD T S+G F++F + +S
Sbjct: 16 SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 75
Query: 117 AARAIHGKVLNGRTVNASIAADNGRAS 143
I G+ + + N+ + D+G +S
Sbjct: 76 QRHMIDGRWCDCKLPNSKQSQDSGPSS 102
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 41/78 (52%), Gaps = 1/78 (1%)
Query: 60 STVYVSNLDYALTNSDLHTLFSTFGKIARVT-VLKDRATRKSRGVAFIQFVQIPDALSAA 118
S +++ NLD + L+ FS FG I + +++D T S+G AFI F + +A
Sbjct: 6 SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAI 65
Query: 119 RAIHGKVLNGRTVNASIA 136
A++G+ L R + S A
Sbjct: 66 EAMNGQYLCNRPITVSYA 83
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 44/81 (54%), Gaps = 3/81 (3%)
Query: 61 TVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARA 120
TV+ L + DL FS GK+ V ++ DR +R+S+G+A+++F +I ++ A
Sbjct: 27 TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEI-QSVPLAIG 85
Query: 121 IHGKVLNGR--TVNASIAADN 139
+ G+ L G V AS A N
Sbjct: 86 LTGQRLLGVPIIVQASQAEKN 106
>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 = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 43/78 (55%), Gaps = 2/78 (2%)
Query: 56 APS--KSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPD 113
APS +++YV +L +T + L+ FS G I + V +D TR+S G A++ F Q D
Sbjct: 10 APSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPAD 69
Query: 114 ALSAARAIHGKVLNGRTV 131
A A ++ V+ G+ V
Sbjct: 70 AERALDTMNFDVIKGKPV 87
Score = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 2/71 (2%)
Query: 61 TVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARA 120
+++ NLD ++ N L+ FS FG I V+ D S+G F+ F A A
Sbjct: 105 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEK 162
Query: 121 IHGKVLNGRTV 131
++G +LN R V
Sbjct: 163 MNGMLLNDRKV 173
>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 = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 43/78 (55%), Gaps = 2/78 (2%)
Query: 56 APS--KSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPD 113
APS +++YV +L +T + L+ FS G I + V +D TR+S G A++ F Q D
Sbjct: 5 APSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPAD 64
Query: 114 ALSAARAIHGKVLNGRTV 131
A A ++ V+ G+ V
Sbjct: 65 AERALDTMNFDVIKGKPV 82
Score = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 2/71 (2%)
Query: 61 TVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARA 120
+++ NLD ++ N L+ FS FG I V+ D S+G F+ F A A
Sbjct: 100 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEK 157
Query: 121 IHGKVLNGRTV 131
++G +LN R V
Sbjct: 158 MNGMLLNDRKV 168
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 44.7 bits (104), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 47/80 (58%), Gaps = 9/80 (11%)
Query: 60 STVYVSNLDYALTN-SDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAA 118
S V++ NL+ AL SD+ T+FS +G++A +V K G AF+Q+ A +A
Sbjct: 28 SRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHK--------GYAFVQYSNERHARAAV 79
Query: 119 RAIHGKVLNGRTVNASIAAD 138
+G+VL G+T++ ++A +
Sbjct: 80 LGENGRVLAGQTLDINMAGE 99
>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 = 43.9 bits (102), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 43/75 (57%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
V+V +L +T + + F+ FG+I+ V+KD AT KS+G F+ F DA +A + +
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 122 HGKVLNGRTVNASIA 136
G+ L GR + + A
Sbjct: 69 GGQWLGGRQIRTNWA 83
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 41/83 (49%), Gaps = 1/83 (1%)
Query: 55 LAPSKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDA 114
L T+YV NL + T ++ LFS G I ++ + D+ + + G F+++ DA
Sbjct: 14 LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKM-KTACGFCFVEYYSRADA 72
Query: 115 LSAARAIHGKVLNGRTVNASIAA 137
+A R I+G L+ R + A
Sbjct: 73 ENAMRYINGTRLDDRIIRTDWDA 95
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/90 (27%), Positives = 46/90 (51%), Gaps = 2/90 (2%)
Query: 60 STVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALS-AA 118
S VYV ++ Y L + F+ FG I + + D T K +G AF+++ ++P+A A
Sbjct: 29 SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEY-EVPEAAQLAL 87
Query: 119 RAIHGKVLNGRTVNASIAADNGRASSFIKK 148
++ +L GR + ++ G+A I +
Sbjct: 88 EQMNSVMLGGRNIKVGRPSNIGQAQPIIDQ 117
Score = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 30/47 (63%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQF 108
+YV+++ L++ D+ ++F FGKI T+ +D T K +G FI++
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEY 174
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 45/86 (52%), Gaps = 4/86 (4%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIP--DALSAAR 119
+++ L + T L + +GK+ V++D A+++SRG F+ F + DA AAR
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAAR 89
Query: 120 --AIHGKVLNGRTVNASIAADNGRAS 143
+I G+V+ + A + +G +S
Sbjct: 90 PHSIDGRVVEPKRAVAREESGSGPSS 115
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 61 TVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARA 120
++YV N+DY T +L F G + RVT+L D+ + +G A+I+F +++ + A
Sbjct: 7 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSD-KESVRTSLA 65
Query: 121 IHGKVLNGRTV 131
+ + GR +
Sbjct: 66 LDESLFRGRQI 76
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 61 TVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARA 120
++YV N+DY T +L F G + RVT+L D+ + +G A+I+F +++ + A
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSD-KESVRTSLA 66
Query: 121 IHGKVLNGRTV 131
+ + GR +
Sbjct: 67 LDESLFRGRQI 77
>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 = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 2/88 (2%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALS-AARA 120
VYV ++ Y L + F+ FG I + + D T K +G AF+++ ++P+A A
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEY-EVPEAAQLALEQ 74
Query: 121 IHGKVLNGRTVNASIAADNGRASSFIKK 148
++ +L GR + ++ G+A I +
Sbjct: 75 MNSVMLGGRNIKVGRPSNIGQAQPIIDQ 102
Score = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 30/47 (63%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQF 108
+YV+++ L++ D+ ++F FGKI T+ +D T K +G FI++
Sbjct: 113 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEY 159
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 37/84 (44%), Gaps = 5/84 (5%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
VYV NL +L FS +G + V + R G AF++F DA A R +
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWI-----ARNPPGFAFVEFEDPRDAEDAVRGL 57
Query: 122 HGKVLNGRTVNASIAADNGRASSF 145
GKV+ G V ++ R S F
Sbjct: 58 DGKVICGSRVRVELSTGMPRRSRF 81
>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 = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 41/82 (50%)
Query: 57 PSKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALS 116
P VY+ ++ Y T + L S G + + ++ D T +S+G AFI+F + + S
Sbjct: 2 PPSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSAS 61
Query: 117 AARAIHGKVLNGRTVNASIAAD 138
A R ++G L R + +++
Sbjct: 62 AVRNLNGYQLGSRFLKCGYSSN 83
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 36/70 (51%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
+YV +L + +T L +F FG+I + ++ D T +S+G FI F A A +
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 122 HGKVLNGRTV 131
+G L GR +
Sbjct: 89 NGFELAGRPM 98
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 44/84 (52%), Gaps = 1/84 (1%)
Query: 61 TVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARA 120
+YV NLD A+T L F G IA + ++ D+ K+ AF+++ Q DA A +
Sbjct: 2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQT 60
Query: 121 IHGKVLNGRTVNASIAADNGRASS 144
++GK + V + A + ++SS
Sbjct: 61 LNGKQIENNIVKINWAFQSQQSSS 84
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 37/77 (48%)
Query: 61 TVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARA 120
++V +L+ + + L F F V+ D T SRG F+ F DA +A +
Sbjct: 89 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 148
Query: 121 IHGKVLNGRTVNASIAA 137
+ G+ LNGR + + AA
Sbjct: 149 MQGQDLNGRPLRINWAA 165
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 2/71 (2%)
Query: 61 TVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARA 120
+++ NLD ++ N L+ FS FG I V+ D S+G F+ F A A
Sbjct: 13 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEK 70
Query: 121 IHGKVLNGRTV 131
++G +LN R V
Sbjct: 71 MNGMLLNDRKV 81
>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 = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 37/71 (52%), Gaps = 2/71 (2%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
+++ L++ T +L F +G + + ++KD AT +SRG F+ F + +
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65
Query: 122 HGKVLNGRTVN 132
H +L+G+ ++
Sbjct: 66 H--ILDGKVID 74
>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 = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 3/70 (4%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATR--KSRGVAFIQFVQIPDALSAAR 119
++V + + DL LF +G + + VL+DR+ +S+G F+ F AL A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 120 AIHG-KVLNG 128
A+H KVL G
Sbjct: 66 ALHNMKVLPG 75
>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 = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 43/83 (51%), Gaps = 1/83 (1%)
Query: 56 APSKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDAL 115
PS+ VY+ ++ Y T + L S G + + ++ D T +S+G AFI+F + +
Sbjct: 1 GPSR-VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSA 59
Query: 116 SAARAIHGKVLNGRTVNASIAAD 138
SA R ++G L R + +++
Sbjct: 60 SAVRNLNGYQLGSRFLKCGYSSN 82
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 35/76 (46%), Gaps = 8/76 (10%)
Query: 61 TVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARA 120
++V NL +T L FS FGK+ RV LKD AFI F + A+ A
Sbjct: 13 VLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEE 64
Query: 121 IHGKVLNGRTVNASIA 136
++GK L G + A
Sbjct: 65 MNGKDLEGENIEIVFA 80
>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 = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 35/72 (48%), Gaps = 2/72 (2%)
Query: 60 STVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAAR 119
+++ NLD ++ N L+ FS FG I V+ D S+G F+ F A A
Sbjct: 6 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIE 63
Query: 120 AIHGKVLNGRTV 131
++G +LN R V
Sbjct: 64 KMNGMLLNDRKV 75
>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 = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 37/77 (48%)
Query: 61 TVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARA 120
++V +L+ + + L F F V+ D T SRG F+ F DA +A +
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 121 IHGKVLNGRTVNASIAA 137
+ G+ LNGR + + AA
Sbjct: 63 MQGQDLNGRPLRINWAA 79
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 44/83 (53%), Gaps = 1/83 (1%)
Query: 57 PSKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALS 116
PS+ VY+ ++ Y T + L S G + + ++ D T +S+G AFI+F + + S
Sbjct: 1 PSR-VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSAS 59
Query: 117 AARAIHGKVLNGRTVNASIAADN 139
A R ++G L R + ++++
Sbjct: 60 AVRNLNGYQLGSRFLKCGYSSNS 82
>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 2.50 A Resolution
Length = 200
Score = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 42/88 (47%), Gaps = 2/88 (2%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
VYV ++ Y L + F+ FG I + D T K +G AF+++ ++P+A A
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEY-EVPEAAQLALEQ 73
Query: 122 HGKV-LNGRTVNASIAADNGRASSFIKK 148
V L GR + ++ G+A I +
Sbjct: 74 XNSVXLGGRNIKVGRPSNIGQAQPIIDQ 101
Score = 40.8 bits (94), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 30/47 (63%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQF 108
+YV+++ L++ D+ ++F FGKI T+ +D T K +G FI++
Sbjct: 112 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEY 158
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 42/75 (56%), Gaps = 3/75 (4%)
Query: 61 TVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARA 120
TV+V NL+ + L+ LF G + +VT+ KDR K + F+ F P+++S A A
Sbjct: 18 TVFVGNLEARVREEILYELFLQAGPLTKVTICKDREG-KPKSFGFVCFKH-PESVSYAIA 75
Query: 121 -IHGKVLNGRTVNAS 134
++G L GR +N S
Sbjct: 76 LLNGIRLYGRPINVS 90
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 3/70 (4%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATR--KSRGVAFIQFVQIPDALSAAR 119
++V + + DL LF +G + + VL+DR+ +S+G F+ F AL A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 120 AIHG-KVLNG 128
A+H KVL G
Sbjct: 66 ALHNMKVLPG 75
Score = 37.0 bits (84), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
+++ + T +D+ +FS+FG+I +L+ SRG AF+ F A +A +A+
Sbjct: 98 LFIGMISKKCTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAFVTFTTRAMAQTAIKAM 156
Query: 122 H 122
H
Sbjct: 157 H 157
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 20/85 (23%), Positives = 41/85 (48%), Gaps = 7/85 (8%)
Query: 55 LAPSKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQ---I 111
+ S +++ L + T L F FG++ V++D T++SRG F+ F+ +
Sbjct: 21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGV 80
Query: 112 PDALSAARAIHGKVLNGRTVNASIA 136
L+ +R L+ +T++ +A
Sbjct: 81 DKVLAQSR----HELDSKTIDPKVA 101
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 1/67 (1%)
Query: 57 PSKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALS 116
PS ++V L+ + D+ LF FG I T+L+ S+G AF+++ +A +
Sbjct: 13 PSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRG-PDGNSKGCAFVKYSSHAEAQA 71
Query: 117 AARAIHG 123
A A+HG
Sbjct: 72 AINALHG 78
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 40.8 bits (94), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 3/70 (4%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATR--KSRGVAFIQFVQIPDALSAAR 119
++V + + DL LF +G + + VL+DR+ +S+G F+ F AL A
Sbjct: 18 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 77
Query: 120 AIHG-KVLNG 128
A+H KVL G
Sbjct: 78 ALHNMKVLPG 87
Score = 37.0 bits (84), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
+++ + T +D+ +FS+FG+I +L+ SRG AF+ F A +A +A+
Sbjct: 110 LFIGMISKKCTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAFVTFTTRAMAQTAIKAM 168
Query: 122 H 122
H
Sbjct: 169 H 169
>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 = 40.8 bits (94), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 39/67 (58%), Gaps = 7/67 (10%)
Query: 61 TVYVSNLDYALTNSDL----HTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALS 116
T+Y++NL+ + +L H +FS FG+I + V + + K RG AF+ F ++ A +
Sbjct: 8 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 64
Query: 117 AARAIHG 123
A R++ G
Sbjct: 65 ALRSMQG 71
>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 = 40.8 bits (94), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 39/67 (58%), Gaps = 7/67 (10%)
Query: 61 TVYVSNLDYALTNSDL----HTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALS 116
T+Y++NL+ + +L H +FS FG+I + V + + K RG AF+ F ++ A +
Sbjct: 7 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 63
Query: 117 AARAIHG 123
A R++ G
Sbjct: 64 ALRSMQG 70
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 40.8 bits (94), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 37/67 (55%), Gaps = 7/67 (10%)
Query: 61 TVYVSNLDYALTNS----DLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALS 116
T+Y++NL+ + L+ +FS FG+I + LK T K RG AF+ F +I A +
Sbjct: 8 TIYINNLNEKIKKEELKKSLYAIFSQFGQILDIVALK---TLKMRGQAFVIFKEIGSASN 64
Query: 117 AARAIHG 123
A R + G
Sbjct: 65 ALRTMQG 71
>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
pdb|3NNA|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 40.8 bits (94), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 3/69 (4%)
Query: 63 YVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATR--KSRGVAFIQFVQIPDALSAARA 120
+V + + DL LF +G + + VL+DR+ +S+G F+ F AL A A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 121 IHG-KVLNG 128
+H KVL G
Sbjct: 67 LHNXKVLPG 75
Score = 35.4 bits (80), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 1/61 (1%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
+++ + T +D+ FS+FG+I +L+ SRG AF+ F A +A +A
Sbjct: 98 LFIGXISKKCTENDIRVXFSSFGQIEECRILRG-PDGLSRGCAFVTFTTRAXAQTAIKAX 156
Query: 122 H 122
H
Sbjct: 157 H 157
>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 = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 39/67 (58%), Gaps = 7/67 (10%)
Query: 61 TVYVSNLDYALTNSDL----HTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALS 116
T+Y++NL+ + +L H +FS FG+I + V + + K RG AF+ F ++ A +
Sbjct: 11 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 67
Query: 117 AARAIHG 123
A R++ G
Sbjct: 68 ALRSMQG 74
>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 = 40.4 bits (93), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 39/67 (58%), Gaps = 7/67 (10%)
Query: 61 TVYVSNLDYALTNSDL----HTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALS 116
T+Y++NL+ + +L H +FS FG+I + V + + K RG AF+ F ++ A +
Sbjct: 11 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 67
Query: 117 AARAIHG 123
A R++ G
Sbjct: 68 ALRSMQG 74
>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 = 40.4 bits (93), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 39/67 (58%), Gaps = 7/67 (10%)
Query: 61 TVYVSNLDYALTNSDL----HTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALS 116
T+Y++NL+ + +L H +FS FG+I + V + + K RG AF+ F ++ A +
Sbjct: 5 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 61
Query: 117 AARAIHG 123
A R++ G
Sbjct: 62 ALRSMQG 68
>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 = 40.4 bits (93), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 39/67 (58%), Gaps = 7/67 (10%)
Query: 61 TVYVSNLDYALTNSDL----HTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALS 116
T+Y++NL+ + +L H +FS FG+I + V + + K RG AF+ F ++ A +
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 66
Query: 117 AARAIHG 123
A R++ G
Sbjct: 67 ALRSMQG 73
>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 = 40.4 bits (93), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 39/67 (58%), Gaps = 7/67 (10%)
Query: 61 TVYVSNLDYALTNSDL----HTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALS 116
T+Y++NL+ + +L H +FS FG+I + V + + K RG AF+ F ++ A +
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 66
Query: 117 AARAIHG 123
A R++ G
Sbjct: 67 ALRSMQG 73
>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 = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 38/77 (49%)
Query: 55 LAPSKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDA 114
L P+ + + V+NL +LT L FG + R ++ T +S+G F ++++ A
Sbjct: 89 LQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSA 148
Query: 115 LSAARAIHGKVLNGRTV 131
A + GK L RT+
Sbjct: 149 ARAKSDLLGKPLGPRTL 165
>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 = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 39/67 (58%), Gaps = 7/67 (10%)
Query: 61 TVYVSNLDYALTNSDL----HTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALS 116
T+Y++NL+ + +L H +FS FG+I + V + + K RG AF+ F ++ A +
Sbjct: 6 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 62
Query: 117 AARAIHG 123
A R++ G
Sbjct: 63 ALRSMQG 69
>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 = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 39/67 (58%), Gaps = 7/67 (10%)
Query: 61 TVYVSNLDYALTNSDL----HTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALS 116
T+Y++NL+ + +L H +FS FG+I + V + + K RG AF+ F ++ A +
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 66
Query: 117 AARAIHG 123
A R++ G
Sbjct: 67 ALRSMQG 73
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 38/77 (49%)
Query: 55 LAPSKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDA 114
L P+ + + V+NL +LT L FG + R ++ T +S+G F ++++ A
Sbjct: 91 LQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSA 150
Query: 115 LSAARAIHGKVLNGRTV 131
A + GK L RT+
Sbjct: 151 ARAKSDLLGKPLGPRTL 167
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 38/77 (49%)
Query: 55 LAPSKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDA 114
L P+ + + V+NL +LT L FG + R ++ T +S+G F ++++ A
Sbjct: 91 LQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSA 150
Query: 115 LSAARAIHGKVLNGRTV 131
A + GK L RT+
Sbjct: 151 ARAKSDLLGKPLGPRTL 167
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 39/78 (50%)
Query: 60 STVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAAR 119
+TVYV LD ++ L LF G + + KDR T + +G F++F+ DA A +
Sbjct: 16 ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIK 75
Query: 120 AIHGKVLNGRTVNASIAA 137
+ L G+ + + A+
Sbjct: 76 IMDMIKLYGKPIRVNKAS 93
>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 = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 5/72 (6%)
Query: 63 YVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAIH 122
+V L + + DL F+ FG++ T+ D T +SRG FI F DA S + +
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILF---KDAASVEKVLD 71
Query: 123 GKV--LNGRTVN 132
K L+GR ++
Sbjct: 72 QKEHRLDGRVID 83
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 45/80 (56%), Gaps = 9/80 (11%)
Query: 60 STVYVSNLD-YALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAA 118
S V++ NL+ + SD+ +FS +GKI +V K G AF+Q+V +A +A
Sbjct: 16 SRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK--------GFAFVQYVNERNARAAV 67
Query: 119 RAIHGKVLNGRTVNASIAAD 138
G+++ G+ ++ ++AA+
Sbjct: 68 AGEDGRMIAGQVLDINLAAE 87
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 41/86 (47%), Gaps = 8/86 (9%)
Query: 61 TVYVSNLDYALTNSDLHTLF--STFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAA 118
T+ +SNL Y+ T L +F +TF K+ + KS+G AFI+F DA A
Sbjct: 17 TLVLSNLSYSATEETLQEVFEKATFIKVPQ------NQNGKSKGYAFIEFASFEDAKEAL 70
Query: 119 RAIHGKVLNGRTVNASIAADNGRASS 144
+ + + + GR + + G +S
Sbjct: 71 NSCNKREIEGRAIRLELQGPRGSPNS 96
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 38/67 (56%), Gaps = 7/67 (10%)
Query: 61 TVYVSNLDYALTNSDL----HTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALS 116
T+Y++NL+ + +L H +FS FG+I + V + + K RG AF+ F ++ A +
Sbjct: 8 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKXRGQAFVIFKEVSSATN 64
Query: 117 AARAIHG 123
A R+ G
Sbjct: 65 ALRSXQG 71
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 38/67 (56%), Gaps = 7/67 (10%)
Query: 61 TVYVSNLDYALTNSDL----HTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALS 116
T+Y++NL+ + +L H +FS FG+I + V + + K RG AF+ F ++ A +
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKXRGQAFVIFKEVSSATN 66
Query: 117 AARAIHG 123
A R+ G
Sbjct: 67 ALRSXQG 73
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 39/67 (58%), Gaps = 7/67 (10%)
Query: 61 TVYVSNLDYALTNSDL----HTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALS 116
T+Y++NL+ + +L + +FS FG+I + V + + K RG AF+ F ++ A +
Sbjct: 10 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 66
Query: 117 AARAIHG 123
A R++ G
Sbjct: 67 ALRSMQG 73
>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 = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 38/67 (56%), Gaps = 7/67 (10%)
Query: 61 TVYVSNLDYALTNSDL----HTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALS 116
T+Y++NL+ + +L H +FS FG+I + V + + K RG AF+ F ++ A +
Sbjct: 11 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKXRGQAFVIFKEVSSATN 67
Query: 117 AARAIHG 123
A R+ G
Sbjct: 68 ALRSXQG 74
>pdb|1A9N|B Chain B, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
pdb|1A9N|D Chain D, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
Length = 96
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 41/80 (51%), Gaps = 7/80 (8%)
Query: 61 TVYVSNLDYALTNSDL----HTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALS 116
T+Y++N++ + +L + LFS FG + + LK T K RG AF+ F ++ + +
Sbjct: 8 TIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALK---TMKMRGQAFVIFKELGSSTN 64
Query: 117 AARAIHGKVLNGRTVNASIA 136
A R + G G+ + A
Sbjct: 65 ALRQLQGFPFYGKPMRIQYA 84
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 40/79 (50%), Gaps = 4/79 (5%)
Query: 67 LDYALTNSD---LHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAIHG 123
++Y T D L LF +G I V ++ DR TR+SRG F++F A A ++G
Sbjct: 47 VNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNG 106
Query: 124 -KVLNGRTVNASIAADNGR 141
+LN R A A+ + R
Sbjct: 107 FNILNKRLKVALAASGHQR 125
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 41/85 (48%), Gaps = 7/85 (8%)
Query: 60 STVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAA- 118
S +Y+ L T+ DL L +GKI + D+ T K +G F+ F D+ SAA
Sbjct: 6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDF----DSPSAAQ 61
Query: 119 RAIHGKVLNGRTVNASIAADNGRAS 143
+A+ L V A +A +G +S
Sbjct: 62 KAVT--ALKASGVQAQMAKQSGPSS 84
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 7/75 (9%)
Query: 60 STVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDA-LSAA 118
+T+YV L +T +DL F FG+I +TV++ + AFIQF A ++A
Sbjct: 13 TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQ------CAFIQFATRQAAEVAAE 66
Query: 119 RAIHGKVLNGRTVNA 133
++ + ++NGR +N
Sbjct: 67 KSFNKLIVNGRRLNV 81
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 8/75 (10%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
++V N+ A T+ +L +LF G++ V+KD AF+ + DA +A +
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQL 63
Query: 122 HGKVLNGRTVNASIA 136
+GK + G+ +N ++
Sbjct: 64 NGKEVKGKRINVELS 78
>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 = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 39/67 (58%), Gaps = 7/67 (10%)
Query: 61 TVYVSNLDYALTNSDL----HTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALS 116
T+Y++NL+ + +L + +FS FG+I + V + + K RG AF+ F ++ A +
Sbjct: 11 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 67
Query: 117 AARAIHG 123
A R++ G
Sbjct: 68 ALRSMQG 74
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 39/67 (58%), Gaps = 7/67 (10%)
Query: 61 TVYVSNLDYALTNSDL----HTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALS 116
T+Y++NL+ + +L + +FS FG+I + V + + K RG AF+ F ++ A +
Sbjct: 11 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 67
Query: 117 AARAIHG 123
A R++ G
Sbjct: 68 ALRSMQG 74
>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 = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 16/73 (21%), Positives = 38/73 (52%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
++V+ + T D+H F+ +G+I + + DR T +G +++ +A +A +
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 122 HGKVLNGRTVNAS 134
+G+ L G+ ++
Sbjct: 86 NGQDLMGQPISVD 98
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 18/83 (21%), Positives = 41/83 (49%), Gaps = 4/83 (4%)
Query: 56 APSKST----VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQI 111
P +S ++V+ + T D+H F+ +G+I + + DR T +G +++
Sbjct: 15 GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 74
Query: 112 PDALSAARAIHGKVLNGRTVNAS 134
+A +A ++G+ L G+ ++
Sbjct: 75 KEAQAAMEGLNGQDLMGQPISVD 97
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 6/76 (7%)
Query: 56 APSKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDAL 115
+P TVY + LT+ + FS FG+I + V + +G +F++F A
Sbjct: 22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAA 75
Query: 116 SAARAIHGKVLNGRTV 131
A +++G + G V
Sbjct: 76 HAIVSVNGTTIEGHVV 91
>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1HL6|C Chain C, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1RK8|A Chain A, Structure Of The Cytosolic Protein Pym Bound To The Mago-
Y14 Core Of The Exon Junction Complex
pdb|2X1G|A Chain A, Crystal Structure Of Importin13 - Mago-Y14 Complex
pdb|2X1G|C Chain C, Crystal Structure Of Importin13 - Mago-Y14 Complex
Length = 165
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 26/107 (24%), Positives = 50/107 (46%), Gaps = 14/107 (13%)
Query: 56 APSKST----VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQI 111
P +S ++V+++ ++ F +G+I + + DR T S+G A +++
Sbjct: 65 GPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETH 124
Query: 112 PDALSAARAIHGKVLNGRTVNASIAADNGRASSFIK--KRVYKDKSR 156
AL+A A++G + G+T+ F+K KRV K + R
Sbjct: 125 KQALAAKEALNGAEIMGQTIQVDWC--------FVKGPKRVKKSEKR 163
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 38/75 (50%), Gaps = 2/75 (2%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
+YV NLD + + L FS FG I V+ + +S+G F+ F +A A +
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGG--RSKGFGFVCFSSPEEATKAVTEM 75
Query: 122 HGKVLNGRTVNASIA 136
+G+++ + + ++A
Sbjct: 76 NGRIVATKPLYVALA 90
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 37.7 bits (86), Expect = 0.006, Method: Composition-based stats.
Identities = 19/78 (24%), Positives = 39/78 (50%), Gaps = 7/78 (8%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQ---IPDALSAA 118
+++ L + T L F FG++ V++D T++SRG F+ F+ + L+ +
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62
Query: 119 RAIHGKVLNGRTVNASIA 136
R L+ +T++ +A
Sbjct: 63 R----HELDSKTIDPKVA 76
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 38/72 (52%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
++V+++ ++ F +G+I + + DR T S+G A +++ AL+A A+
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 122 HGKVLNGRTVNA 133
+G + G+T+
Sbjct: 89 NGAEIMGQTIQV 100
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 4/70 (5%)
Query: 60 STVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQF---VQIPDALS 116
+TV+V +D + +++ + F+ +G + V ++ DR T S+G F+ F V + +
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE 68
Query: 117 AARAIHGKVL 126
+ HGK L
Sbjct: 69 SQINFHGKKL 78
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 44/81 (54%), Gaps = 3/81 (3%)
Query: 55 LAPSKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRA-TRKSRGVAFIQFVQIPD 113
+ P+K V++ L +T + +FST+GKI + + +R S+G A+++F +
Sbjct: 2 MKPTK--VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDE 59
Query: 114 ALSAARAIHGKVLNGRTVNAS 134
A A + + G ++G+ + A+
Sbjct: 60 AEKALKHMDGGQIDGQEITAT 80
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 4/70 (5%)
Query: 60 STVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQF---VQIPDALS 116
+TV+V +D + +++ + F+ +G + V ++ DR T S+G F+ F V + +
Sbjct: 11 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE 69
Query: 117 AARAIHGKVL 126
+ HGK L
Sbjct: 70 SQINFHGKKL 79
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 37.0 bits (84), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
++V L+ + D+ LF FG I TVL+ S+G AF++F +A +A A+
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRG-PDGSSKGCAFVKFSSHTEAQAAIHAL 76
Query: 122 HG 123
HG
Sbjct: 77 HG 78
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 37.0 bits (84), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 16/72 (22%), Positives = 38/72 (52%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
++V+ + T D+H F+ +G+I + + DR T +G +++ +A +A +
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 122 HGKVLNGRTVNA 133
+G+ L G+ ++
Sbjct: 72 NGQDLMGQPISV 83
>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 90
Score = 37.0 bits (84), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 16/72 (22%), Positives = 38/72 (52%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
++V+ + T D+H F+ +G+I + + DR T +G +++ +A +A +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 122 HGKVLNGRTVNA 133
+G+ L G+ ++
Sbjct: 70 NGQDLMGQPISV 81
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 37.0 bits (84), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 36/74 (48%), Gaps = 2/74 (2%)
Query: 58 SKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKD-RATRKSRGVAFIQFVQIPDALS 116
+ S + V N+ + ++ LFSTFG++ V + K T RG F+ F+ DA
Sbjct: 14 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKK 73
Query: 117 AARAI-HGKVLNGR 129
A A+ H L GR
Sbjct: 74 AFNALCHSTHLYGR 87
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 37.0 bits (84), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 16/72 (22%), Positives = 38/72 (52%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
++V+ + T D+H F+ +G+I + + DR T +G +++ +A +A +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 122 HGKVLNGRTVNA 133
+G+ L G+ ++
Sbjct: 70 NGQDLMGQPISV 81
>pdb|2CPI|A Chain A, Solution Structure Of The Rna Recognition Motif Of Cnot4
Length = 111
Score = 37.0 bits (84), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 45/84 (53%), Gaps = 6/84 (7%)
Query: 59 KSTVYVSNLDYALTNSDL---HTLFSTFGKIARVTVLKDRATRKSRG---VAFIQFVQIP 112
K+ V+V L L + ++ F FGKI +V + + S+G A++ +++
Sbjct: 15 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSE 74
Query: 113 DALSAARAIHGKVLNGRTVNASIA 136
DAL A + ++ V++GRT+ AS+
Sbjct: 75 DALRAIQCVNNVVVDGRTLKASLG 98
>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 = 37.0 bits (84), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 34/70 (48%)
Query: 57 PSKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALS 116
P +++ L L + + L ++FG + ++KD AT S+G AF ++V I
Sbjct: 94 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 153
Query: 117 AARAIHGKVL 126
A ++G L
Sbjct: 154 AIAGLNGMQL 163
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 36.6 bits (83), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 10/77 (12%)
Query: 62 VYVSNLDYALTNSDLHTLFSTF--GKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAAR 119
+YV NL + + + F+ G + RV +K R AF+ F DA+ A +
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERV--------KKIRDYAFVHFSNREDAVEAMK 69
Query: 120 AIHGKVLNGRTVNASIA 136
A++GKVL+G + ++A
Sbjct: 70 ALNGKVLDGSPIEVTLA 86
>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 = 36.6 bits (83), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 35/62 (56%), Gaps = 3/62 (4%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
+Y+ NL Y +T +++ +F +G I ++ V T ++RG A++ + I DA +A +
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDIFDAKNACDHL 77
Query: 122 HG 123
G
Sbjct: 78 SG 79
>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 = 36.6 bits (83), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 16/72 (22%), Positives = 38/72 (52%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
++V+ + T D+H F+ +G+I + + DR T +G +++ +A +A +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 122 HGKVLNGRTVNA 133
+G+ L G+ ++
Sbjct: 70 NGQDLMGQPISV 81
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 36.6 bits (83), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 34/70 (48%)
Query: 57 PSKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALS 116
P +++ L L + + L ++FG + ++KD AT S+G AF ++V I
Sbjct: 92 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 151
Query: 117 AARAIHGKVL 126
A ++G L
Sbjct: 152 AIAGLNGMQL 161
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 36.6 bits (83), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 35/62 (56%), Gaps = 3/62 (4%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
+Y+ NL Y +T +++ +F +G I ++ V T ++RG A++ + I DA +A +
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDIFDAKNAVDHL 67
Query: 122 HG 123
G
Sbjct: 68 SG 69
>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Rna, Uuguucuu
Length = 102
Score = 36.6 bits (83), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 4/70 (5%)
Query: 60 STVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQF---VQIPDALS 116
+TV+V +D + +++ + F+ +G + V ++ DR T S+G F+ F V + +
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE 68
Query: 117 AARAIHGKVL 126
+ HGK L
Sbjct: 69 SQINFHGKKL 78
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 36.2 bits (82), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 41/85 (48%), Gaps = 3/85 (3%)
Query: 58 SKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSA 117
S +++ L L + + L ++FG + ++KD AT S+G AF ++V I A
Sbjct: 113 SAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 172
Query: 118 ARAIHGKVLNGRTV---NASIAADN 139
++G L + + AS+ A N
Sbjct: 173 IAGLNGMQLGDKKLLVQRASVGAKN 197
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 36.2 bits (82), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 32/68 (47%)
Query: 56 APSKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDAL 115
P +++ +L T++DL + F FG + V D+ T S+ F+ F A
Sbjct: 37 GPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQ 96
Query: 116 SAARAIHG 123
A +A++G
Sbjct: 97 VAIKAMNG 104
>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 = 35.8 bits (81), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 36/72 (50%), Gaps = 5/72 (6%)
Query: 56 APSKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDAL 115
AP + V L ALT +LFS GK+ + D AT K++G F++ + DA
Sbjct: 14 APVIPSAKVPVLKKALT-----SLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAK 68
Query: 116 SAARAIHGKVLN 127
++ HGK L+
Sbjct: 69 KIIKSFHGKRLD 80
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 35.8 bits (81), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 40/81 (49%), Gaps = 3/81 (3%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
+++ L L + + L ++FG + ++KD AT S+G AF ++V I A +
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 122 HGKVLNGRTV---NASIAADN 139
+G L + + AS+ A N
Sbjct: 64 NGMQLGDKKLLVQRASVGAKN 84
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 35.8 bits (81), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 38/80 (47%), Gaps = 3/80 (3%)
Query: 60 STVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDR---ATRKSRGVAFIQFVQIPDALS 116
S +++ NL+++ T L +FS G I T+ K + S G F+++ + A
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 117 AARAIHGKVLNGRTVNASIA 136
A + + G ++G + I+
Sbjct: 66 ALKQLQGHTVDGHKLEVRIS 85
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 35.4 bits (80), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 27/46 (58%), Gaps = 1/46 (2%)
Query: 60 STVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAF 105
+ +Y+SNL ++ +L + FG++ +L+D ++ SRGV F
Sbjct: 26 TNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGF 70
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 35.4 bits (80), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 35/63 (55%), Gaps = 3/63 (4%)
Query: 61 TVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARA 120
+Y+ NL Y +T +++ +F +G I ++ V T ++RG A++ + I DA +A
Sbjct: 14 ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNACDH 70
Query: 121 IHG 123
+ G
Sbjct: 71 LSG 73
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 35.4 bits (80), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 1/61 (1%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
++V L T+ D+ +F FG I TVL+ S+G AF++F +A +A +
Sbjct: 15 LFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRG-PDGTSKGCAFVKFQTHAEAQAAINTL 73
Query: 122 H 122
H
Sbjct: 74 H 74
>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 = 0.035, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 36/72 (50%), Gaps = 5/72 (6%)
Query: 56 APSKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDAL 115
AP + V L ALT +LFS GK+ + D AT K++G F++ + DA
Sbjct: 14 APVIPSAKVPVLKKALT-----SLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAK 68
Query: 116 SAARAIHGKVLN 127
++ HGK L+
Sbjct: 69 KIIKSFHGKRLD 80
>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
pdb|1HD1|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
Length = 75
Score = 35.0 bits (79), Expect = 0.041, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 25/47 (53%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQF 108
+++ L + T DL FS FG++ T+ D T +SRG F+ F
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLF 48
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 34.7 bits (78), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 23/47 (48%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQF 108
++V + L F +GKI + ++ DR + K RG AF+ F
Sbjct: 108 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 154
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 34.7 bits (78), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 31/67 (46%), Gaps = 8/67 (11%)
Query: 58 SKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSA 117
S + ++V + S+L+ +F FG + V +L G AF++F + A A
Sbjct: 30 SNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAKA 81
Query: 118 ARAIHGK 124
+HGK
Sbjct: 82 IEEVHGK 88
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 34.7 bits (78), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 5/72 (6%)
Query: 61 TVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARA 120
T+ NL Y +T +L +F +I V+ KD KS+G+A+I+F DA
Sbjct: 95 TLLAKNLPYKVTQDELKEVFEDAAEIRLVS--KDG---KSKGIAYIEFKTEADAEKTFEE 149
Query: 121 IHGKVLNGRTVN 132
G ++GR+++
Sbjct: 150 KQGTEIDGRSIS 161
>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 = 34.7 bits (78), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 23/47 (48%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQF 108
++V + L F +GKI + ++ DR + K RG AF+ F
Sbjct: 106 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 152
>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 = 34.7 bits (78), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 23/47 (48%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQF 108
++V + L F +GKI + ++ DR + K RG AF+ F
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 34.3 bits (77), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 23/47 (48%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQF 108
++V + L F +GKI + ++ DR + K RG AF+ F
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 34.3 bits (77), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 23/47 (48%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQF 108
++V + L F +GKI + ++ DR + K RG AF+ F
Sbjct: 105 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 151
>pdb|2M2B|A Chain A, Nmr Structure Of The Rrm2 Domain Of The Protein Rbm10 From
Homo Sapiens
Length = 131
Score = 34.3 bits (77), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 41/78 (52%), Gaps = 12/78 (15%)
Query: 71 LTNSDLH-TLFSTFGKIA--------RVTVLKDRATRKSRGVAFIQFVQIPDA--LSAAR 119
L N + H T+ S G +A V V+KD+ T+ +RG AFIQ I A L +
Sbjct: 28 LRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIEAAQLLQILQ 87
Query: 120 AIHGKV-LNGRTVNASIA 136
A+H + ++G+T+N A
Sbjct: 88 ALHPPLTIDGKTINVEFA 105
>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 = 34.3 bits (77), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 23/47 (48%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQF 108
++V + L F +GKI + ++ DR + K RG AF+ F
Sbjct: 100 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 146
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 34.3 bits (77), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 39/86 (45%), Gaps = 14/86 (16%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPD---ALSAA 118
+++ NL T ++ +LF +GK+ ++K+ FV I D A A
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYG-----------FVHIEDKTAAEDAI 59
Query: 119 RAIHGKVLNGRTVNASIAADNGRASS 144
R +H L+G +N + + +ASS
Sbjct: 60 RNLHHYKLHGVNINVEASKNKSKASS 85
>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 = 33.5 bits (75), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 33/60 (55%), Gaps = 3/60 (5%)
Query: 64 VSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAIHG 123
+ NL Y +T +++ +F +G I ++ V T ++RG A++ + I DA +A + G
Sbjct: 23 IRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDIFDAKNACDHLSG 79
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 18/87 (20%), Positives = 38/87 (43%), Gaps = 8/87 (9%)
Query: 58 SKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSA 117
+ + ++V N+ TN +L F +G + ++KD AF+ + DA+ A
Sbjct: 9 ASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEA 60
Query: 118 ARAIHGKVLNGRTVNASIAADNGRASS 144
R + G+ ++ ++ R +S
Sbjct: 61 IRGLDNTEFQGKRMHVQLSTSRLRTAS 87
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 30/64 (46%), Gaps = 8/64 (12%)
Query: 61 TVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARA 120
++V NL +T L FS FGK+ RV LKD AF+ F A+ A
Sbjct: 17 VLFVRNLATTVTEEILEKSFSEFGKLERVKKLKD--------YAFVHFEDRGAAVKAMDE 68
Query: 121 IHGK 124
++GK
Sbjct: 69 MNGK 72
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 28/90 (31%), Positives = 42/90 (46%), Gaps = 6/90 (6%)
Query: 61 TVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDA---LSA 117
TV++ NL + L + FG + V V+ T S+G AF QF+ A L+A
Sbjct: 17 TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 76
Query: 118 A--RAIHGKV-LNGRTVNASIAADNGRASS 144
A A G + L+GR + +A A+S
Sbjct: 77 ASLEAEGGGLKLDGRQLKVDLAVTRDEAAS 106
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 33.1 bits (74), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 37/80 (46%), Gaps = 5/80 (6%)
Query: 61 TVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARA 120
T+ NL + +T +L +F +I V+ KS+G+A+I+F DA
Sbjct: 18 TLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEE 72
Query: 121 IHGKVLNGRTVNASIAADNG 140
G ++GR+V+ + G
Sbjct: 73 KQGAEIDGRSVSLYYTGEKG 92
>pdb|2ADC|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd34 Complexed With Cucucu Rna
pdb|2EVZ|A Chain A, Structure Of Rna Binding Domains 3 And 4 Of Polypyrimidine
Tract Binding Protein
Length = 229
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 36/66 (54%), Gaps = 4/66 (6%)
Query: 57 PSKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALS 116
P +T+++SN+ +++ DL LFS+ G + + + +K R +A IQ + +A+
Sbjct: 149 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVK----GFKFFQKDRKMALIQMGSVEEAVQ 204
Query: 117 AARAIH 122
A +H
Sbjct: 205 ALIDLH 210
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 32.7 bits (73), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 36/66 (54%), Gaps = 4/66 (6%)
Query: 57 PSKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALS 116
P +T+++SN+ +++ DL LFS+ G + + + +K R +A IQ + +A+
Sbjct: 118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVK----GFKFFQKDRKMALIQMGSVEEAVQ 173
Query: 117 AARAIH 122
A +H
Sbjct: 174 ALIDLH 179
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 32.7 bits (73), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 60 STVYVSNLDYALTNSDLHTLFSTFGK-IARVTVLKDRATRKSRGVAFIQFVQIPDALSAA 118
+++++ +L+ + + + F+T G+ + V ++++R T G F++F + A
Sbjct: 10 ASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCL 69
Query: 119 RAIHGKVLNGRT 130
I+GK L G T
Sbjct: 70 HKINGKPLPGAT 81
>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 = 32.7 bits (73), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 32/56 (57%), Gaps = 1/56 (1%)
Query: 60 STVYVSNLDYALTNSDLHTLFSTFGKIAR-VTVLKDRATRKSRGVAFIQFVQIPDA 114
+ V + L A T D+ + G AR V +++++++ +SRG AF++F + DA
Sbjct: 2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDA 57
>pdb|1U6P|A Chain A, Nmr Structure Of The Mlv Encapsidation Signal Bound To The
Nucleocapsid Protein
pdb|1WWD|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
Sequence Aacagu
pdb|1WWE|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
Sequence Uuuugcu
pdb|1WWF|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
Sequence Ccuccgu
pdb|1WWG|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
Sequence Uaucug
Length = 56
Score = 32.3 bits (72), Expect = 0.28, Method: Composition-based stats.
Identities = 13/38 (34%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 147 KKRVYKDKSRCYECGDEGHLSYECPRNQLGPRERPMPK 184
++R D+ +C C ++GH + +CP+ GPR P P+
Sbjct: 16 RRRSQLDRDQCAYCKEKGHWAKDCPKKPRGPRG-PRPQ 52
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 32.0 bits (71), Expect = 0.35, Method: Composition-based stats.
Identities = 18/67 (26%), Positives = 31/67 (46%), Gaps = 8/67 (11%)
Query: 58 SKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSA 117
S + ++V + S+L+ +F FG + V +L G AF++F + A A
Sbjct: 3 SNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAKA 54
Query: 118 ARAIHGK 124
+HGK
Sbjct: 55 IEEVHGK 61
>pdb|1A6B|B Chain B, Nmr Structure Of The Complex Between The Zinc Finger
Protein Ncp10 Of Moloney Murine Leukemia Virus And A
Sequence Of The Psi-Packaging Domain Of Hiv-1, 20
Structures
Length = 40
Score = 32.0 bits (71), Expect = 0.36, Method: Composition-based stats.
Identities = 13/38 (34%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 147 KKRVYKDKSRCYECGDEGHLSYECPRNQLGPRERPMPK 184
++R D+ +C C ++GH + +CP+ GPR P P+
Sbjct: 3 RRRSQLDRDQCAYCKEKGHWAKDCPKKPRGPRG-PRPQ 39
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 31.6 bits (70), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 37/80 (46%), Gaps = 5/80 (6%)
Query: 61 TVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARA 120
T+ NL + +T +L +F +I V+ KS+G+A+I+F DA
Sbjct: 101 TLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEE 155
Query: 121 IHGKVLNGRTVNASIAADNG 140
G ++GR+V+ + G
Sbjct: 156 KQGAEIDGRSVSLYYTGEKG 175
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 31.6 bits (70), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 2/76 (2%)
Query: 60 STVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAAR 119
S ++V NL + T L F+ G + + + KS+G ++F A A R
Sbjct: 6 SGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENG--KSKGCGVVKFESPEVAERACR 63
Query: 120 AIHGKVLNGRTVNASI 135
++G L+GR ++ I
Sbjct: 64 MMNGMKLSGREIDVRI 79
>pdb|2ADB|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd2 Complexed With Cucucu Rna
Length = 148
Score = 31.6 bits (70), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 30/101 (29%), Positives = 52/101 (51%), Gaps = 15/101 (14%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
+ V NL Y +T LH +FS FG + ++ T+ ++ A +Q+ D +SA
Sbjct: 36 IIVENLFYPVTLDVLHQIFSKFGTVLKIITF----TKNNQFQALLQYA---DPVSAQ--- 85
Query: 122 HGKV-LNGRTV-NA--SIAADNGRASSFIKKRVYKDKSRCY 158
H K+ L+G+ + NA ++ D + +S + + DKSR Y
Sbjct: 86 HAKLSLDGQNIYNACCTLRIDFSKLTS-LNVKYNNDKSRDY 125
>pdb|3ZZY|A Chain A, Crystal Structure Of A Raver1 Pri3 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
pdb|3ZZY|B Chain B, Crystal Structure Of A Raver1 Pri3 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
pdb|3ZZZ|A Chain A, Crystal Structure Of A Raver1 Pri4 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
pdb|3ZZZ|B Chain B, Crystal Structure Of A Raver1 Pri4 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
Length = 130
Score = 31.2 bits (69), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 30/101 (29%), Positives = 52/101 (51%), Gaps = 15/101 (14%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
+ V NL Y +T LH +FS FG + ++ T+ ++ A +Q+ D +SA
Sbjct: 31 IIVENLFYPVTLDVLHQIFSKFGTVLKIITF----TKNNQFQALLQYA---DPVSAQ--- 80
Query: 122 HGKV-LNGRTV-NA--SIAADNGRASSFIKKRVYKDKSRCY 158
H K+ L+G+ + NA ++ D + +S + + DKSR Y
Sbjct: 81 HAKLSLDGQNIYNACCTLRIDFSKLTS-LNVKYNNDKSRDY 120
>pdb|1SJR|A Chain A, Nmr Structure Of Rrm2 From Human Polypyrimidine Tract
Binding Protein Isoform 1 (Ptb1)
Length = 164
Score = 31.2 bits (69), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 30/101 (29%), Positives = 52/101 (51%), Gaps = 15/101 (14%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
+ V NL Y +T LH +FS FG + ++ T+ ++ A +Q+ D +SA
Sbjct: 49 IIVENLFYPVTLDVLHQIFSKFGTVLKIITF----TKNNQFQALLQYA---DPVSAQ--- 98
Query: 122 HGKV-LNGRTV-NA--SIAADNGRASSFIKKRVYKDKSRCY 158
H K+ L+G+ + NA ++ D + +S + + DKSR Y
Sbjct: 99 HAKLSLDGQNIYNACCTLRIDFSKLTS-LNVKYNNDKSRDY 138
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 30.8 bits (68), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 6/51 (11%)
Query: 58 SKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQF 108
+S ++V NL +T ++ LF +GK V + KD +G FI+
Sbjct: 21 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRL 65
>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 30.8 bits (68), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 42/82 (51%), Gaps = 6/82 (7%)
Query: 61 TVYVSNLDYALTNSDLHTLFSTFGKIA--RVTVLKDRATRKSRGVAFIQFVQIPDA---L 115
T+ + N+ + T S + +A + ++KD+ T+++RG AF+Q DA L
Sbjct: 11 TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLL 70
Query: 116 SAARAIHGKV-LNGRTVNASIA 136
+++H + ++G+T+ A
Sbjct: 71 QILQSLHPPLKIDGKTIGVDFA 92
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 30.8 bits (68), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 2/74 (2%)
Query: 62 VYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARAI 121
++V NL + T L F+ G + + + KS+G ++F A A R +
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENG--KSKGCGVVKFESPEVAERACRMM 68
Query: 122 HGKVLNGRTVNASI 135
+G L+GR ++ I
Sbjct: 69 NGMKLSGREIDVRI 82
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 30.4 bits (67), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 6/52 (11%)
Query: 57 PSKSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQF 108
P +T Y+ N+ + T +DL LF FG I D +G FI++
Sbjct: 25 PRVTTAYIGNIPHFATEADLIPLFQNFGFIL------DFKHYPEKGCCFIKY 70
>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 = 29.6 bits (65), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 21/86 (24%), Positives = 36/86 (41%), Gaps = 6/86 (6%)
Query: 59 KSTVYVSNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAA 118
+S ++V NL +T ++ LF +GK V + KD +G FI+ A A
Sbjct: 15 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAK 68
Query: 119 RAIHGKVLNGRTVNASIAADNGRASS 144
+ L G+ + A + +S
Sbjct: 69 VELDNMPLRGKQLRVRFACHSASLTS 94
>pdb|2DGX|A Chain A, Solution Structure Of The Rna Recognition Motif In
Kiaa0430 Protein
Length = 96
Score = 29.3 bits (64), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 1/76 (1%)
Query: 62 VYVSNLDYALTNSDLHTLFS-TFGKIARVTVLKDRATRKSRGVAFIQFVQIPDALSAARA 120
V VSN+DY L+ +L L F + +V ++ + A +Q + DA+ A +
Sbjct: 12 VQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNS 71
Query: 121 IHGKVLNGRTVNASIA 136
+H + + + S+A
Sbjct: 72 LHRYKIGSKKILVSLA 87
>pdb|2EC7|A Chain A, Solution Structure Of Human Immunodificiency Virus Type-2
Nucleocapsid Protein
Length = 49
Score = 28.9 bits (63), Expect = 2.9, Method: Composition-based stats.
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 157 CYECGDEGHLSYECPRNQLG 176
C++CG GH+ +CP Q G
Sbjct: 30 CWKCGKTGHVMAKCPERQAG 49
Score = 28.5 bits (62), Expect = 3.2, Method: Composition-based stats.
Identities = 11/21 (52%), Positives = 14/21 (66%), Gaps = 2/21 (9%)
Query: 156 RCYECGDEGHLSYEC--PRNQ 174
RC+ CG EGH + +C PR Q
Sbjct: 8 RCWNCGKEGHSARQCRAPRRQ 28
>pdb|3N9I|A Chain A, Crystal Structure Of Tryptophanyl-Trna Synthetase From
Yersinia Pestis Co92
pdb|3N9I|B Chain B, Crystal Structure Of Tryptophanyl-Trna Synthetase From
Yersinia Pestis Co92
Length = 346
Score = 28.9 bits (63), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 29/54 (53%), Gaps = 13/54 (24%)
Query: 57 PSKSTVYV-------SNLDYALTNSDLHTLFSTFGKIARVTVLKDRATRKSRGV 103
P KST++V S L +AL ++ FG+++R+T KD++ R + +
Sbjct: 86 PKKSTIFVQSHVPEHSQLSWALN------CYTYFGELSRMTQFKDKSARYAENI 133
>pdb|2E1X|A Chain A, Nmr Structure Of The Hiv-2 Nucleocapsid Protein
pdb|2IWJ|A Chain A, Solution Structure Of The Zn Complex Of Hiv-2 Ncp(23-49)
Peptide, Encompassing Protein Cchc-Linker, Distal Cchc
Zn- Binding Motif And C-Terminal Tail
Length = 27
Score = 28.5 bits (62), Expect = 3.1, Method: Composition-based stats.
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 157 CYECGDEGHLSYECPRNQLG 176
C++CG GH+ +CP Q G
Sbjct: 8 CWKCGKTGHVMAKCPERQAG 27
>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 = 28.5 bits (62), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 2/80 (2%)
Query: 59 KSTVYVSNLDYALTNSDLHTLFSTFG--KIARVTVLKDRATRKSRGVAFIQFVQIPDALS 116
++ VYV + + T+ L + + G + + ++RA +S+G A +
Sbjct: 55 RAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHK 114
Query: 117 AARAIHGKVLNGRTVNASIA 136
+ GKVLNG V+ A
Sbjct: 115 LLELLPGKVLNGEKVDVRPA 134
>pdb|2BL6|A Chain A, Solution Structure Of The Zn Complex Of Eiav Ncp11(22-58)
Peptide, Including Two Cchc Zn-Binding Motifs
Length = 37
Score = 28.1 bits (61), Expect = 5.2, Method: Composition-based stats.
Identities = 9/14 (64%), Positives = 10/14 (71%)
Query: 157 CYECGDEGHLSYEC 170
CY CG GHLS +C
Sbjct: 3 CYNCGKPGHLSSQC 16
>pdb|2IHX|A Chain A, Solution Structure Of The Rous Sarcoma Virus Nucleocapsid
Protein:upsi Rna Packaging Signal Complex
Length = 61
Score = 27.7 bits (60), Expect = 6.9, Method: Composition-based stats.
Identities = 12/31 (38%), Positives = 15/31 (48%), Gaps = 2/31 (6%)
Query: 152 KDKSRCYECGDEGHLSYECP--RNQLGPRER 180
+ + CY CG GH +CP R RER
Sbjct: 2 RARGLCYTCGSPGHYQAQCPKKRKSGNSRER 32
>pdb|1NC8|A Chain A, High-Resolution Solution Nmr Structure Of The Minimal
Active Domain Of The Human Immunodeficiency Virus Type-2
Nucleocapsid Protein, 15 Structures
Length = 29
Score = 27.3 bits (59), Expect = 7.3, Method: Composition-based stats.
Identities = 11/21 (52%), Positives = 14/21 (66%), Gaps = 2/21 (9%)
Query: 156 RCYECGDEGHLSYEC--PRNQ 174
RC+ CG EGH + +C PR Q
Sbjct: 8 RCWNCGKEGHSARQCRAPRRQ 28
>pdb|2DI2|A Chain A, Nmr Structure Of The Hiv-2 Nucleocapsid Protein
Length = 29
Score = 26.9 bits (58), Expect = 10.0, Method: Composition-based stats.
Identities = 11/21 (52%), Positives = 14/21 (66%), Gaps = 2/21 (9%)
Query: 156 RCYECGDEGHLSYEC--PRNQ 174
RC+ CG EGH + +C PR Q
Sbjct: 8 RCWACGKEGHSARQCRAPRRQ 28
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
0.316 0.131 0.375
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,084,036
Number of Sequences: 62578
Number of extensions: 166949
Number of successful extensions: 545
Number of sequences better than 100.0: 181
Number of HSP's better than 100.0 without gapping: 134
Number of HSP's successfully gapped in prelim test: 47
Number of HSP's that attempted gapping in prelim test: 363
Number of HSP's gapped (non-prelim): 197
length of query: 244
length of database: 14,973,337
effective HSP length: 96
effective length of query: 148
effective length of database: 8,965,849
effective search space: 1326945652
effective search space used: 1326945652
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)