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= 035722
(80 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 58.5 bits (140), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 28/55 (50%), Positives = 41/55 (74%), Gaps = 2/55 (3%)
Query: 5 AFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFV 59
AFS FG +T A ++M+ G+ SKG+G V FS+ EEA KA+TEMNG+++ + L+V
Sbjct: 35 AFSPFGTITSAKVMMEGGR--SKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYV 87
>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 = 55.8 bits (133), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 26/58 (44%), Positives = 38/58 (65%), Gaps = 2/58 (3%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFV 59
+ D FS FG + ++ D+ N SKGYG V F T+E A++A+ +MNG LL+ R +FV
Sbjct: 115 LYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 170
>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 = 55.5 bits (132), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 26/58 (44%), Positives = 38/58 (65%), Gaps = 2/58 (3%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFV 59
+ D FS FG + ++ D+ N SKGYG V F T+E A++A+ +MNG LL+ R +FV
Sbjct: 120 LYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 175
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 55.1 bits (131), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 26/58 (44%), Positives = 38/58 (65%), Gaps = 2/58 (3%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFV 59
+ D FS FG + ++ D+ N SKGYG V F T+E A++A+ +MNG LL+ R +FV
Sbjct: 28 LYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 83
>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 = 55.1 bits (131), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 26/58 (44%), Positives = 38/58 (65%), Gaps = 2/58 (3%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFV 59
+ D FS FG + ++ D+ N SKGYG V F T+E A++A+ +MNG LL+ R +FV
Sbjct: 22 LYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 77
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 51.6 bits (122), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 39/60 (65%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDNVRPS 65
FS++GQ+++ ++ D+ S+G+G VTF ++A+ A+ MNGK +DGR + VD S
Sbjct: 33 FSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKS 92
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 50.8 bits (120), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/62 (41%), Positives = 37/62 (59%)
Query: 1 MIADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVD 60
M+ F FG++ ++MD SKGYG +TFS E A+KAL ++NG L GR + V
Sbjct: 42 MLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVG 101
Query: 61 NV 62
+V
Sbjct: 102 HV 103
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 34/56 (60%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVL 57
I AF+ FG+++ A ++ D SKGYG V+F + +A+ A+ M G+ L GR +
Sbjct: 32 IKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMGGQWLGGRQI 87
>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 = 47.4 bits (111), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 35/56 (62%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVL 57
I AF+ FG+++ A ++ D SKGYG V+F + +A+ A+ +M G+ L GR +
Sbjct: 32 IKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 87
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 47.4 bits (111), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/62 (38%), Positives = 36/62 (58%)
Query: 1 MIADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVD 60
M+ F FG++ ++ D SKGYG +TFS E A++AL ++NG L GR + V
Sbjct: 21 MLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVG 80
Query: 61 NV 62
+V
Sbjct: 81 HV 82
>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|B Chain B, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|C Chain C, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|D Chain D, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
Length = 84
Score = 46.2 bits (108), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 34/60 (56%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDNVRPS 65
FS G+V A +I DK S GYG V + T ++A++A+ +NG L + + V RPS
Sbjct: 25 FSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPS 84
>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1)
From Homo Sapiens At 1.90 A Resolution
pdb|4FXV|B Chain B, Crystal Structure Of An Elav-Like Protein 1 (Elavl1)
From Homo Sapiens At 1.90 A Resolution
pdb|4FXV|C Chain C, Crystal Structure Of An Elav-Like Protein 1 (Elavl1)
From Homo Sapiens At 1.90 A Resolution
pdb|4FXV|D Chain D, Crystal Structure Of An Elav-Like Protein 1 (Elavl1)
From Homo Sapiens At 1.90 A Resolution
Length = 99
Score = 45.8 bits (107), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 34/60 (56%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDNVRPS 65
FS G+V A +I DK S GYG V + T ++A++A+ +NG L + + V RPS
Sbjct: 40 FSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPS 99
>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 = 45.8 bits (107), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 36/69 (52%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDNVRPS 65
FS G+V A +I DK S GYG V + T ++A++A+ +NG L + + V RPS
Sbjct: 23 FSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPS 82
Query: 66 RRYNTDVPL 74
D L
Sbjct: 83 SEVIKDANL 91
Score = 38.9 bits (89), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 29/48 (60%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNG 49
+ D FS+FG++ + +++D+ S+G + F EA++A+T NG
Sbjct: 105 VEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs
Of Human Antigen R
Length = 177
Score = 45.8 bits (107), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 36/69 (52%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDNVRPS 65
FS G+V A +I DK S GYG V + T ++A++A+ +NG L + + V RPS
Sbjct: 23 FSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPS 82
Query: 66 RRYNTDVPL 74
D L
Sbjct: 83 SEVIKDANL 91
Score = 38.9 bits (89), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 29/48 (60%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNG 49
+ D FS+FG++ + +++D+ S+G + F EA++A+T NG
Sbjct: 105 VEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 45.1 bits (105), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 31/60 (51%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDN 61
+ D FS+ G V ++ D+ KGYG + +E A A+ +NG+ GR L VDN
Sbjct: 25 LKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDN 84
>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
pdb|3MD1|B Chain B, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
Length = 83
Score = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 34/56 (60%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVL 57
+ +AF F ++ D +S+GYG V+F+++++AQ A+ M G+ L+GR L
Sbjct: 18 LRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPL 73
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 26/59 (44%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 1 MIADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFV 59
M+ D F++ G V A I M+ GK SKG G V F + E A++A MNG L GR + V
Sbjct: 24 MLKDKFNECGHVLYADIKMENGK--SKGCGVVKFESPEVAERACRMMNGMKLSGREIDV 80
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain
In Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/59 (44%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 1 MIADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFV 59
M+ D F++ G V A I M+ GK SKG G V F + E A++A MNG L GR + V
Sbjct: 21 MLKDKFNECGHVLYADIKMENGK--SKGCGVVKFESPEVAERACRMMNGMKLSGREIDV 77
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 34/56 (60%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVL 57
+ +AF F ++ D +S+GYG V+F+++++AQ A+ M G+ L+GR L
Sbjct: 104 LRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPL 159
>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 = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 31/49 (63%)
Query: 9 FGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVL 57
FG+++ A ++ D SKGYG V+F + +A+ A+ +M G+ L GR +
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 78
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 42.7 bits (99), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 34/59 (57%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVD 60
+ + FS++G + +I+ D+ S+G+ V F ++A++A NG LDGR + VD
Sbjct: 29 LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD 87
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 42.7 bits (99), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 30/52 (57%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVL 57
FS++G+V K TI+ DK SKG + F ++ AQ +N K L GRV+
Sbjct: 37 FSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVI 88
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 42.0 bits (97), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 34/59 (57%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVD 60
+ + FS++G + +I+ D+ S+G+ V F ++A++A NG LDGR + VD
Sbjct: 32 LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD 90
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 42.0 bits (97), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 34/59 (57%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVD 60
+ + FS++G + +I+ D+ S+G+ V F ++A++A NG LDGR + VD
Sbjct: 63 LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD 121
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 42.0 bits (97), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 25/65 (38%), Positives = 36/65 (55%), Gaps = 7/65 (10%)
Query: 1 MIADAFSQFGQVTKATIIM-DKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFV 59
++ AFSQFG V KA +++ D+G+ T KG+ V F+ + A+KAL DG L
Sbjct: 112 LLEQAFSQFGPVEKAVVVVDDRGRATGKGF--VEFAAKPPARKALERCG----DGAFLLT 165
Query: 60 DNVRP 64
RP
Sbjct: 166 TTPRP 170
>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 = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 33/61 (54%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDNVRPS 65
F ++G+V I D+ S+G+ V F + +A+ A+ M+G +LDGR L V R
Sbjct: 68 FEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYG 127
Query: 66 R 66
R
Sbjct: 128 R 128
>pdb|2XB2|D Chain D, Crystal Structure Of The Core
Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How
The Ejc Is Bridged To The Nmd Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core
Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How
The Ejc Is Bridged To The Nmd Machinery
Length = 90
Score = 41.2 bits (95), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 35/59 (59%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVD 60
I D F+++G++ + +D+ KGY V + T +EAQ A+ +NG+ L G+ + VD
Sbjct: 24 IHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 82
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 41.2 bits (95), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 35/59 (59%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVD 60
I D F+++G++ + +D+ KGY V + T +EAQ A+ +NG+ L G+ + VD
Sbjct: 24 IHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 82
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 41.2 bits (95), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 35/59 (59%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVD 60
I D F+++G++ + +D+ KGY V + T +EAQ A+ +NG+ L G+ + VD
Sbjct: 26 IHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 84
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 33/61 (54%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDNVRPS 65
F ++G+V I D+ S+G+ V F + +A+ A+ M+G +LDGR L V R
Sbjct: 91 FEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYG 150
Query: 66 R 66
R
Sbjct: 151 R 151
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 35/56 (62%), Gaps = 2/56 (3%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDN 61
F QFG++ II ++ SKG+G VTF +A +A +++G +++GR + V+N
Sbjct: 50 FGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN 103
>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX
pdb|1P27|D Chain D, Crystal Structure Of The Human Y14MAGOH COMPLEX
Length = 106
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 35/59 (59%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVD 60
I D F+++G++ + +D+ KGY V + T +EAQ A+ +NG+ L G+ + VD
Sbjct: 40 IHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 98
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 35/56 (62%), Gaps = 2/56 (3%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDN 61
F QFG++ II ++ SKG+G VTF +A +A +++G +++GR + V+N
Sbjct: 36 FGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN 89
>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 = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 35/59 (59%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVD 60
I D F+++G++ + +D+ KGY V + T +EAQ A+ +NG+ L G+ + VD
Sbjct: 24 IHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 82
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 32/54 (59%), Gaps = 4/54 (7%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKA----LTEMNGKLLDGR 55
F QFG+V A ++ DK N +G+G VTF +E+ +K E+N K+++ +
Sbjct: 20 FEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECK 73
>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 = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 35/59 (59%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVD 60
I D F+++G++ + +D+ KGY V + T +EAQ A+ +NG+ L G+ + VD
Sbjct: 39 IHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 97
>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 = 40.4 bits (93), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 3/74 (4%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDNVRPS 65
F Q+G +T ++ D S+G+G VT++T EE A+ K +DGRV V+ R
Sbjct: 27 FEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHK-VDGRV--VEPKRAV 83
Query: 66 RRYNTDVPLARLKI 79
R ++ P A L +
Sbjct: 84 SREDSQRPGAHLTV 97
Score = 30.4 bits (67), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 12/45 (26%), Positives = 23/45 (51%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTE 46
+ D F Q+G++ I+ D+G +G+ VTF + K + +
Sbjct: 114 LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 158
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 40.4 bits (93), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 3/74 (4%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDNVRPS 65
F Q+G +T ++ D S+G+G VT++T EE A+ K +DGRV V+ R
Sbjct: 34 FEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHK-VDGRV--VEPKRAV 90
Query: 66 RRYNTDVPLARLKI 79
R ++ P A L +
Sbjct: 91 SREDSQRPGAHLTV 104
Score = 30.4 bits (67), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 12/45 (26%), Positives = 23/45 (51%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTE 46
+ D F Q+G++ I+ D+G +G+ VTF + K + +
Sbjct: 121 LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 165
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 40.4 bits (93), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 3/74 (4%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDNVRPS 65
F Q+G +T ++ D S+G+G VT++T EE A+ K +DGRV V+ R
Sbjct: 32 FEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHK-VDGRV--VEPKRAV 88
Query: 66 RRYNTDVPLARLKI 79
R ++ P A L +
Sbjct: 89 SREDSQRPGAHLTV 102
Score = 30.4 bits (67), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 12/45 (26%), Positives = 23/45 (51%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTE 46
+ D F Q+G++ I+ D+G +G+ VTF + K + +
Sbjct: 119 LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 163
>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 = 40.4 bits (93), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 3/74 (4%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDNVRPS 65
F Q+G +T ++ D S+G+G VT++T EE A+ K +DGRV V+ R
Sbjct: 34 FEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHK-VDGRV--VEPKRAV 90
Query: 66 RRYNTDVPLARLKI 79
R ++ P A L +
Sbjct: 91 SREDSQRPGAHLTV 104
Score = 30.0 bits (66), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 12/45 (26%), Positives = 23/45 (51%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTE 46
+ D F Q+G++ I+ D+G +G+ VTF + K + +
Sbjct: 121 LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 165
>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 = 40.4 bits (93), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 3/74 (4%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDNVRPS 65
F Q+G +T ++ D S+G+G VT++T EE A+ K +DGRV V+ R
Sbjct: 33 FEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHK-VDGRV--VEPKRAV 89
Query: 66 RRYNTDVPLARLKI 79
R ++ P A L +
Sbjct: 90 SREDSQRPGAHLTV 103
Score = 30.0 bits (66), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 12/45 (26%), Positives = 23/45 (51%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTE 46
+ D F Q+G++ I+ D+G +G+ VTF + K + +
Sbjct: 120 LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 164
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 40.4 bits (93), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 3/74 (4%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDNVRPS 65
F Q+G +T ++ D S+G+G VT++T EE A+ K +DGRV V+ R
Sbjct: 35 FEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHK-VDGRV--VEPKRAV 91
Query: 66 RRYNTDVPLARLKI 79
R ++ P A L +
Sbjct: 92 SREDSQRPGAHLTV 105
Score = 30.0 bits (66), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 12/45 (26%), Positives = 23/45 (51%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTE 46
+ D F Q+G++ I+ D+G +G+ VTF + K + +
Sbjct: 122 LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 166
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 39.7 bits (91), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 27/48 (56%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNG 49
+A F FG V A + +DK + SK +G V+F + AQ A+ MNG
Sbjct: 57 LASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNG 104
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 39.7 bits (91), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 1 MIADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVD 60
M+ F + G +++ +I D+ + S+G+ +TF +A+ A +MNGK L G+ + V+
Sbjct: 23 MLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVE 81
Query: 61 NVR 63
+
Sbjct: 82 QAK 84
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 39.7 bits (91), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 33/55 (60%), Gaps = 1/55 (1%)
Query: 2 IADAFSQFGQVTKATIIMDK-GKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGR 55
I + FS +G++ + +++ + SKGY V F +EA+KAL M+G +DG+
Sbjct: 21 IMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQ 75
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 39.3 bits (90), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDNVRPS 65
F G + ++ DK S GYG V +S +A KA+ +NG L + + V RPS
Sbjct: 25 FGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYARPS 84
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 33/58 (56%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFV 59
+ + FS++G + +I+ D+ S+G+ V F ++A++A NG LDGR + V
Sbjct: 32 LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 89
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 30/54 (55%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFV 59
FS +G +++ +D KG+ VTF E A KA E++G++ GR+L V
Sbjct: 29 FSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHV 82
>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
pdb|1HD1|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
Length = 75
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 4/56 (7%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTE----MNGKLLD 53
+ D FS+FG+V T+ +D S+G+G V F E K + + +NGK++D
Sbjct: 16 LKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVID 71
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With
The Au-Rich Element
Length = 174
Score = 38.9 bits (89), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDNVRPS 65
F G + ++ DK S GYG V +S +A KA+ +NG L + + V RPS
Sbjct: 25 FGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYARPS 84
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 29/45 (64%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGK 50
FSQ+G++ + I++D+ S+G G + F EA++A+ +NG+
Sbjct: 111 FSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQ 155
>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 = 38.9 bits (89), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 31/60 (51%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDNVRPS 65
F G++ ++ DK S GYG V + ++A+KA+ +NG L + + V RPS
Sbjct: 23 FGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPS 82
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 30/49 (61%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDG 54
FSQ+G++ + I++D+ S+G G + F EA++A+ +NG+ G
Sbjct: 109 FSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSG 157
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 38.5 bits (88), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 34/58 (58%), Gaps = 1/58 (1%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFV 59
+ + FS G V +A I+ DK S+G G+VTF EA +A++ NG+LL R + V
Sbjct: 32 LKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHV 88
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 32/56 (57%)
Query: 9 FGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDNVRP 64
F +A I+ D+ +SKG+G V F++EE+A+ A M +DG + +D +P
Sbjct: 36 FDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKP 91
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 30/62 (48%)
Query: 5 AFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDNVRP 64
AF FG +T I +D +G+ V F E+A A+ MN L GR + V+ +P
Sbjct: 32 AFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKP 91
Query: 65 SR 66
R
Sbjct: 92 MR 93
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 29/50 (58%), Gaps = 1/50 (2%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGR 55
F FG + +A +I D+ S+GYG VT + A++A + N ++DGR
Sbjct: 38 FEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPN-PIIDGR 86
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 29/45 (64%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGK 50
FSQ+G++ + I++D+ S+G G + F EA++A+ +NG+
Sbjct: 22 FSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQ 66
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 25/44 (56%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNG 49
F ++G + I+ D+ S+GYG V F + AQ+A+ +NG
Sbjct: 63 FERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNG 106
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 6/57 (10%)
Query: 1 MIADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVL 57
++ FS FGQ+ + + +KG Y V FST E A A+ +NG ++G V+
Sbjct: 41 LMRQTFSPFGQIMEIRVFPEKG------YSFVRFSTHESAAHAIVSVNGTTIEGHVV 91
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 4/67 (5%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALT----EMNGKLLDGRVL 57
+ + F QFG+V + ++ D S+G+G VTF + K L E++ K +D +V
Sbjct: 42 LREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA 101
Query: 58 FVDNVRP 64
F +P
Sbjct: 102 FPRRAQP 108
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 29/62 (46%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDNVRPS 65
F ++G+V I + +G+ V F +AQ A M+G LDGR L V R
Sbjct: 34 FEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARYG 93
Query: 66 RR 67
RR
Sbjct: 94 RR 95
>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 = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 31/64 (48%), Gaps = 2/64 (3%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDN 61
I AF+ FG + + D KG+ V + E AQ AL +MN +L GR + V
Sbjct: 30 IRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVG- 88
Query: 62 VRPS 65
RPS
Sbjct: 89 -RPS 91
Score = 35.0 bits (79), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 28/58 (48%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFV 59
I F FG++ T+ D KGYG + + + +Q A++ MN L G+ L V
Sbjct: 127 IKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 184
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 33/60 (55%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDNVRPS 65
F FG +++ + DK SKG+ ++F E+A +A+ ++G D +L V+ +PS
Sbjct: 36 FRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPS 95
>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 = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 34/59 (57%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVD 60
I + FS+ G + K + +DK K T+ G+ V + + +A+ A+ +NG LD R++ D
Sbjct: 56 IYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTD 114
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug
Triplet Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 37.0 bits (84), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 24/44 (54%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNG 49
F FG V A + +DK N SK +G V++ AQ A+ MNG
Sbjct: 46 FMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNG 89
>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
pdb|3S7R|B Chain B, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
Length = 87
Score = 37.0 bits (84), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVL 57
+ D F++FG+V TI D S+G+G + F +K L + + LDGRV+
Sbjct: 28 LKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQKEHR-LDGRVI 82
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 37.0 bits (84), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 32/60 (53%), Gaps = 1/60 (1%)
Query: 1 MIADAFSQFGQVTKATIIM-DKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFV 59
++ D FS FG + + IM D SKGY + F++ + + A+ MNG+ L R + V
Sbjct: 21 LLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITV 80
>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|6 Chain 6, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|7 Chain 7, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|8 Chain 8, Crystal Structure Of Human Spliceosomal U1 Snrnp
Length = 216
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 14/55 (25%), Positives = 26/55 (47%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVD 60
F +G + + ++ K +GY + + E + A +GK +DGR + VD
Sbjct: 123 FEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD 177
>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
pdb|2QFJ|B Chain B, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
Length = 216
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 31/64 (48%), Gaps = 2/64 (3%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDN 61
I AF+ FG + + D KG+ V + E AQ AL +MN +L GR + V
Sbjct: 45 IRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVG- 103
Query: 62 VRPS 65
RPS
Sbjct: 104 -RPS 106
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 29/58 (50%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFV 59
I F FG++ AT+ D KGYG + + + +Q A++ MN L G+ L V
Sbjct: 142 IKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 199
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 25/65 (38%), Positives = 33/65 (50%), Gaps = 6/65 (9%)
Query: 6 FSQFGQVTKATIIMDKGKNT---SKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDNV 62
FS+ G + TI K K S G+G V + E+AQKAL ++ G +DG L V
Sbjct: 26 FSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKL---EV 82
Query: 63 RPSRR 67
R S R
Sbjct: 83 RISER 87
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 34/64 (53%), Gaps = 5/64 (7%)
Query: 1 MIADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVD 60
++ +AFS FGQV +A +I+D + G G V FS + A+KAL + +G L
Sbjct: 112 LLEEAFSVFGQVERAVVIVD-DRGRPSGKGIVEFSGKPAARKALDRCS----EGSFLLTT 166
Query: 61 NVRP 64
RP
Sbjct: 167 FPRP 170
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVL 57
I + F++FG + KA + D+ S G V F + +A KA+ + NG LDGR +
Sbjct: 45 IQELFAEFGTLKKAAVHYDRS-GRSLGTADVHFERKADALKAMKQYNGVPLDGRPM 99
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 23/39 (58%)
Query: 9 FGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEM 47
+G++ I+DK N KGYG V F + AQKA+T +
Sbjct: 29 YGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 8/64 (12%)
Query: 1 MIADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVD 60
++ AFSQFG++ + + D Y + F + A KA+ EMNGK L+G + +
Sbjct: 27 ILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEMNGKDLEGENIEIV 78
Query: 61 NVRP 64
+P
Sbjct: 79 FAKP 82
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 31/59 (52%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVD 60
I + F +G++ + +D+ SKGY V + T ++A A +NG + G+ + VD
Sbjct: 43 IQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD 101
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 4/61 (6%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALT----EMNGKLLDGRVL 57
+ + F QFG+V + ++ D S+G+G VTF + K L E++ K +D +V
Sbjct: 17 LREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA 76
Query: 58 F 58
F
Sbjct: 77 F 77
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 35.4 bits (80), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 1/65 (1%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDN 61
+ + FSQFG+V +I D+ KG+G V EE +A+ +++ GR + V
Sbjct: 18 VKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAKLDNTDFMGRTIRVTE 76
Query: 62 VRPSR 66
P +
Sbjct: 77 ANPKK 81
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 35.4 bits (80), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 27/56 (48%)
Query: 5 AFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVD 60
AF FG +T I +D +G+ V F E+A A+ MN L GR + V+
Sbjct: 83 AFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN 138
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 35.4 bits (80), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 29/59 (49%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDNVRP 64
F G + I+ D S GY V F++E ++Q+A+ +NG + + L V RP
Sbjct: 24 FRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP 82
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleaoproteins A2B1
Length = 116
Score = 35.0 bits (79), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVL 57
+ Q+G++T ++ D S+G+G VTFS+ E A+ +DGRV+
Sbjct: 48 YEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVV 98
>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 = 35.0 bits (79), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 27/56 (48%)
Query: 5 AFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVD 60
AF FG +T I +D +G+ V F E+A A+ MN L GR + V+
Sbjct: 22 AFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN 77
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 29/59 (49%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDNVRP 64
F G + I+ D S GY V F++E ++Q+A+ +NG + + L V RP
Sbjct: 24 FRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP 82
>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 = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGR 55
I + F++FG + KA + D+ S G V F + +A KA + NG LDGR
Sbjct: 46 IQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAXKQYNGVPLDGR 98
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
28
Length = 111
Score = 34.7 bits (78), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 29/65 (44%), Gaps = 6/65 (9%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKAL------TEMNGKLLDGR 55
+ + QFG + +++ SKG F T+E AQK L E G LDGR
Sbjct: 32 LGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR 91
Query: 56 VLFVD 60
L VD
Sbjct: 92 QLKVD 96
>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 = 34.7 bits (78), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 31/59 (52%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVD 60
I + F +G++ + +D+ SKGY V + T ++A A +NG + G+ + VD
Sbjct: 89 IQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD 147
>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 = 34.7 bits (78), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 27/56 (48%)
Query: 5 AFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVD 60
AF FG +T I +D +G+ V F E+A A+ MN L GR + V+
Sbjct: 27 AFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN 82
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 34.7 bits (78), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 27/56 (48%)
Query: 5 AFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVD 60
AF FG +T I +D +G+ V F E+A A+ MN L GR + V+
Sbjct: 25 AFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN 80
>pdb|3NS6|A Chain A, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
pdb|3NS6|B Chain B, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
Length = 100
Score = 34.3 bits (77), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 36/67 (53%), Gaps = 1/67 (1%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRV-LFVDNVRP 64
FS+ G+V +D+ +KG+ V + +A+K + +GK LD + LF+ ++
Sbjct: 33 FSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLYTMKD 92
Query: 65 SRRYNTD 71
RYN+D
Sbjct: 93 VERYNSD 99
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 34.3 bits (77), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 4/64 (6%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTE----MNGKLLDGRVLFVDN 61
FSQ+G+V I+ DK N S+G+G V F L ++G+ +D +
Sbjct: 37 FSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRNIDPKPCTPRG 96
Query: 62 VRPS 65
++PS
Sbjct: 97 MQPS 100
>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 = 34.3 bits (77), Expect = 0.020, Method: Composition-based stats.
Identities = 15/58 (25%), Positives = 27/58 (46%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDNVR 63
F +G + + ++ K +GY + + E + A +GK +DGR + VD R
Sbjct: 123 FEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 180
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 33.9 bits (76), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFV 59
I + F++FG + KA + D+ S G V F +A KA+ + G LDGR + +
Sbjct: 105 IQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDI 161
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 33.5 bits (75), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 25/44 (56%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALT 45
+ + F +FG VT+ +I D K +G+G +TF E+ +A+
Sbjct: 27 LREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN 70
>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 = 33.5 bits (75), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 28/59 (47%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDNVRP 64
F G + I D S GY V F++E ++Q+A+ +NG + + L V RP
Sbjct: 35 FRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVLNGITVRNKRLKVSYARP 93
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 33.5 bits (75), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 30/55 (54%), Gaps = 8/55 (14%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVD 60
FS++G+V ++ KGY V +S E A+ A+ NG++L G+ L ++
Sbjct: 49 FSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDIN 95
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 33.1 bits (74), Expect = 0.038, Method: Composition-based stats.
Identities = 15/51 (29%), Positives = 28/51 (54%)
Query: 9 FGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFV 59
FG + + ++ + SKGYG + ++ A +A +++ GK L R L+V
Sbjct: 119 FGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 169
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 33.1 bits (74), Expect = 0.038, Method: Composition-based stats.
Identities = 15/51 (29%), Positives = 28/51 (54%)
Query: 9 FGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFV 59
FG + + ++ + SKGYG + ++ A +A +++ GK L R L+V
Sbjct: 119 FGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 169
>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
pdb|3H2U|D Chain D, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
Length = 283
Score = 33.1 bits (74), Expect = 0.039, Method: Composition-based stats.
Identities = 15/51 (29%), Positives = 28/51 (54%)
Query: 9 FGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFV 59
FG + + ++ + SKGYG + ++ A +A +++ GK L R L+V
Sbjct: 117 FGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 167
>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 = 32.7 bits (73), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 28/64 (43%), Gaps = 2/64 (3%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDN 61
I AF+ FG + D KG+ V + E AQ AL + N L GR + V
Sbjct: 29 IRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQXNSVXLGGRNIKVG- 87
Query: 62 VRPS 65
RPS
Sbjct: 88 -RPS 90
Score = 32.7 bits (73), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 27/58 (46%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFV 59
I F FG++ T+ D KGYG + + + +Q A++ N L G+ L V
Sbjct: 126 IKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRV 183
>pdb|3N9U|C Chain C, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
pdb|3N9U|I Chain I, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
Length = 156
Score = 32.7 bits (73), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 3/50 (6%)
Query: 20 DKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDNVRPSRRYN 69
++ SKGY V ++E K L + GK+L+G + +VRP+ R N
Sbjct: 92 NRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKV---DVRPATRQN 138
>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition
In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 84
Score = 32.3 bits (72), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 24/56 (42%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVL 57
I D S G V ++ D SKGY + F E + A+ +NG L R L
Sbjct: 21 ILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFL 76
>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex
With Rna
pdb|2KM8|C Chain C, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 167
Score = 32.0 bits (71), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 23/39 (58%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKAL 44
FSQ+G + A +++DK S+G+G VT+ + + +
Sbjct: 108 FSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVC 146
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 32.0 bits (71), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 22/36 (61%)
Query: 29 YGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDNVRP 64
Y V FS E+A +A+ +NGK+LDG + V +P
Sbjct: 53 YAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKP 88
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 32.0 bits (71), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVL 57
I + F++FG + KA + D+ S G V F +A KA+ + G LDGR +
Sbjct: 52 IQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPM 106
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 32.0 bits (71), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVL 57
I + F++FG + KA + D+ S G V F +A KA+ + G LDGR +
Sbjct: 52 IQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPM 106
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 32.0 bits (71), Expect = 0.093, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 4/70 (5%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDN 61
+ + FS FG+V + D SKG+G V F+ E K +++ + ++DGR + D
Sbjct: 32 LKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRH--MIDGR--WCDC 87
Query: 62 VRPSRRYNTD 71
P+ + + D
Sbjct: 88 KLPNSKQSQD 97
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif In Trna Selenocysteine Associated Protein
Length = 104
Score = 32.0 bits (71), Expect = 0.095, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 23/35 (65%), Gaps = 1/35 (2%)
Query: 17 IIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKL 51
+++D+ SKGYG V F+ E E ++ALTE G +
Sbjct: 42 VVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAV 75
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 32.0 bits (71), Expect = 0.099, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 24/56 (42%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVL 57
I D S G V ++ D SKGY + F E + A+ +NG L R L
Sbjct: 19 ILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFL 74
>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 = 31.6 bits (70), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 24/56 (42%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVL 57
I D S G V ++ D SKGY + F E + A+ +NG L R L
Sbjct: 20 ILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFL 75
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 31.6 bits (70), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 22/43 (51%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKAL 44
I + F FG+V + MD N +G+ +TF EE +K +
Sbjct: 16 IREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 58
>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain
Of Hnrnp D (Auf1) With Telomere Dna
pdb|1X0F|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain
Of Hnrnp D(Auf1) With Telomeric Dna
Length = 79
Score = 31.6 bits (70), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 22/43 (51%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKAL 44
I + F FG+V + MD N +G+ +TF EE +K +
Sbjct: 18 IREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 60
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 31.6 bits (70), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 8/68 (11%)
Query: 2 IADAFSQFGQ-VTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVD 60
I+ AF+ G+ V II ++ GY V F+ A+K L ++NGK L G
Sbjct: 26 ISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPG------ 79
Query: 61 NVRPSRRY 68
P++R+
Sbjct: 80 -ATPAKRF 86
>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 = 31.6 bits (70), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKAL 44
I F+++G V + II D+ SKGYG V+F + + QK +
Sbjct: 26 IRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIV 67
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 31.6 bits (70), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 1/61 (1%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDNVRPS 65
F G V + TI+ DK KG+ + FS +E + +L ++ L GR + V R +
Sbjct: 26 FHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA-LDESLFRGRQIKVIPKRTN 84
Query: 66 R 66
R
Sbjct: 85 R 85
>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 = 31.2 bits (69), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 1/54 (1%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFV 59
FS G + + TI+ DK KGY + F+ E + A M+ + GR + V
Sbjct: 57 FSSCGSINRITILCDKFSGHPKGYAYIEFA-ERNSVDAAVAMDETVFRGRTIKV 109
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of
Hypothetical Polyadenylate-Binding Protein (Pabpn1)
From Homo Sapiens At 1.95 A Resolution
Length = 89
Score = 31.2 bits (69), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 1/61 (1%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDNVRPS 65
F G V + TI+ DK KG+ + FS +E + +L ++ L GR + V R +
Sbjct: 27 FHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA-LDESLFRGRQIKVIPKRTN 85
Query: 66 R 66
R
Sbjct: 86 R 86
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 31.2 bits (69), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKAL 44
I F+++G V + II D+ SKGYG V+F + + QK +
Sbjct: 27 IRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIV 68
>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 = 31.2 bits (69), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKAL 44
I F+++G V + II D+ SKGYG V+F + + QK +
Sbjct: 26 IRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIV 67
>pdb|2DIT|A Chain A, Solution Structure Of The Rrm_1 Domain Of Hiv Tat
Specific Factor 1 Variant
Length = 112
Score = 31.2 bits (69), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 4/49 (8%)
Query: 7 SQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGR 55
S+FGQ+ K ++ D+ + G SV+F EEA + ++G+ GR
Sbjct: 48 SKFGQIRK-LLLFDRHPD---GVASVSFRDPEEADYCIQTLDGRWFGGR 92
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 30.8 bits (68), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 31/60 (51%)
Query: 1 MIADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVD 60
++ + F Q G V + D+ +GYG V F +EE+A A+ M+ L G+ + V+
Sbjct: 31 LLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVN 90
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 30.8 bits (68), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNG 49
F FG + + TI+ N SKG V +S+ EAQ A+ ++G
Sbjct: 36 FEAFGNIEECTILRGPDGN-SKGCAFVKYSSHAEAQAAINALHG 78
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 30.4 bits (67), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 32/49 (65%), Gaps = 2/49 (4%)
Query: 14 KATII-MDKGKN-TSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVD 60
KAT I + + +N SKGY + F++ E+A++AL N + ++GR + ++
Sbjct: 38 KATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLE 86
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 30.0 bits (66), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 26/44 (59%), Gaps = 3/44 (6%)
Query: 6 FSQFGQVTKATIIMDKGKN-TSKGYGSVTFSTEEEAQKALTEMN 48
FS FGQ+ + I+ +G + S+G VTF+T AQ A+ M+
Sbjct: 128 FSSFGQIEECRIL--RGPDGLSRGCAFVTFTTRAMAQTAIKAMH 169
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 29.6 bits (65), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 26/44 (59%), Gaps = 3/44 (6%)
Query: 6 FSQFGQVTKATIIMDKGKN-TSKGYGSVTFSTEEEAQKALTEMN 48
FS FGQ+ + I+ +G + S+G VTF+T AQ A+ M+
Sbjct: 116 FSSFGQIEECRIL--RGPDGLSRGCAFVTFTTRAMAQTAIKAMH 157
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 29.3 bits (64), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 27/45 (60%), Gaps = 3/45 (6%)
Query: 6 FSQFGQVTKATIIMDKGKN-TSKGYGSVTFSTEEEAQKALTEMNG 49
F FG + + T++ +G + +SKG V FS+ EAQ A+ ++G
Sbjct: 36 FQPFGVIDECTVL--RGPDGSSKGCAFVKFSSHTEAQAAIHALHG 78
>pdb|1Q5X|A Chain A, Structure Of Of Rraa (Meng), A Protein Inhibitor Of Rna
Processing
pdb|1Q5X|B Chain B, Structure Of Of Rraa (Meng), A Protein Inhibitor Of Rna
Processing
pdb|1Q5X|C Chain C, Structure Of Of Rraa (Meng), A Protein Inhibitor Of Rna
Processing
pdb|2YJT|A Chain A, Crystal Structure Of E. Coli Dead-Box Protein Srmb Bound
To Regulator Of Ribonuclease Activity A (Rraa)
pdb|2YJT|B Chain B, Crystal Structure Of E. Coli Dead-Box Protein Srmb Bound
To Regulator Of Ribonuclease Activity A (Rraa)
pdb|2YJT|C Chain C, Crystal Structure Of E. Coli Dead-Box Protein Srmb Bound
To Regulator Of Ribonuclease Activity A (Rraa)
pdb|2YJV|A Chain A, Crystal Structure Of E. Coli Regulator Of Ribonuclease
Activity A (Rraa) Bound To Fragment Of Dead-Box Protein
Rhlb
pdb|2YJV|B Chain B, Crystal Structure Of E. Coli Regulator Of Ribonuclease
Activity A (Rraa) Bound To Fragment Of Dead-Box Protein
Rhlb
pdb|2YJV|C Chain C, Crystal Structure Of E. Coli Regulator Of Ribonuclease
Activity A (Rraa) Bound To Fragment Of Dead-Box Protein
Rhlb
pdb|2YJV|D Chain D, Crystal Structure Of E. Coli Regulator Of Ribonuclease
Activity A (Rraa) Bound To Fragment Of Dead-Box Protein
Rhlb
pdb|2YJV|E Chain E, Crystal Structure Of E. Coli Regulator Of Ribonuclease
Activity A (Rraa) Bound To Fragment Of Dead-Box Protein
Rhlb
pdb|2YJV|F Chain F, Crystal Structure Of E. Coli Regulator Of Ribonuclease
Activity A (Rraa) Bound To Fragment Of Dead-Box Protein
Rhlb
pdb|2YJV|G Chain G, Crystal Structure Of E. Coli Regulator Of Ribonuclease
Activity A (Rraa) Bound To Fragment Of Dead-Box Protein
Rhlb
pdb|2YJV|H Chain H, Crystal Structure Of E. Coli Regulator Of Ribonuclease
Activity A (Rraa) Bound To Fragment Of Dead-Box Protein
Rhlb
pdb|2YJV|I Chain I, Crystal Structure Of E. Coli Regulator Of Ribonuclease
Activity A (Rraa) Bound To Fragment Of Dead-Box Protein
Rhlb
pdb|2YJV|J Chain J, Crystal Structure Of E. Coli Regulator Of Ribonuclease
Activity A (Rraa) Bound To Fragment Of Dead-Box Protein
Rhlb
pdb|2YJV|K Chain K, Crystal Structure Of E. Coli Regulator Of Ribonuclease
Activity A (Rraa) Bound To Fragment Of Dead-Box Protein
Rhlb
pdb|2YJV|L Chain L, Crystal Structure Of E. Coli Regulator Of Ribonuclease
Activity A (Rraa) Bound To Fragment Of Dead-Box Protein
Rhlb
Length = 161
Score = 28.9 bits (63), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 17/37 (45%), Positives = 19/37 (51%), Gaps = 3/37 (8%)
Query: 44 LTEMNGKLLDGRVLFVDNVRPSRRYNTDVPLARLKIH 80
L E NG+ GRVL VD RR D LARL +
Sbjct: 51 LLEQNGR---GRVLVVDGGGSVRRALVDAELARLAVQ 84
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 28.9 bits (63), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 6/63 (9%)
Query: 1 MIADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVD 60
++ AFS FG + + MD +N + VT+ E A +A+ E+NG ++ L V+
Sbjct: 53 LLRGAFSPFGNIID--LSMDPPRNCA----FVTYEKMESADQAVAELNGTQVESVQLKVN 106
Query: 61 NVR 63
R
Sbjct: 107 IAR 109
>pdb|2CPI|A Chain A, Solution Structure Of The Rna Recognition Motif Of Cnot4
Length = 111
Score = 28.9 bits (63), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 3/57 (5%)
Query: 4 DAFSQFGQVTKATIIMDKGKNTSKGYGS---VTFSTEEEAQKALTEMNGKLLDGRVL 57
+ F +FG++ K I S+G + VT+ E+A +A+ +N ++DGR L
Sbjct: 37 EYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL 93
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 28.5 bits (62), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 18/32 (56%)
Query: 26 SKGYGSVTFSTEEEAQKALTEMNGKLLDGRVL 57
SKG + F TE +A+K E G +DGR +
Sbjct: 129 SKGIAYIEFKTEADAEKTFEEKQGTEIDGRSI 160
>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 = 28.5 bits (62), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 26 SKGYGSVTFSTEEEAQKALTEMNGKLLDGR 55
SKG + F +E +A+K L E G +DGR
Sbjct: 135 SKGIAYIEFKSEADAEKNLEEKQGAEIDGR 164
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 6/63 (9%)
Query: 1 MIADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVD 60
++ AFS FG + + MD +N + VT+ E A +A+ E+NG ++ L V+
Sbjct: 29 LLRGAFSPFGNIID--LSMDPPRNCA----FVTYEKMESADQAVAELNGTQVESVQLKVN 82
Query: 61 NVR 63
R
Sbjct: 83 IAR 85
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 28.1 bits (61), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 26 SKGYGSVTFSTEEEAQKALTEMNGKLLDGR 55
SKG + F +E +A+K L E G +DGR
Sbjct: 52 SKGIAYIEFKSEADAEKNLEEKQGAEIDGR 81
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 32/68 (47%), Gaps = 9/68 (13%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVL-FVD 60
+ + F FG + + I+ G+ V F E A KA+ E++GK + L V
Sbjct: 48 LNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVY 99
Query: 61 NVRPSRRY 68
+ P++RY
Sbjct: 100 SKLPAKRY 107
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 8/50 (16%)
Query: 1 MIADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGK 50
++ +FS+FG++ + + D Y V F A KA+ EMNGK
Sbjct: 31 ILEKSFSEFGKLERVKKLKD--------YAFVHFEDRGAAVKAMDEMNGK 72
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 28.1 bits (61), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 13/55 (23%), Positives = 30/55 (54%), Gaps = 8/55 (14%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVD 60
FS++G++ ++ KG+ V + E A+ A+ +G+++ G+VL ++
Sbjct: 37 FSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDIN 83
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In
Trinucleotide Repeat Containing 4 Variant
Length = 102
Score = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMN 48
F FG + + T++ TSKG V F T EAQ A+ ++
Sbjct: 33 FEPFGTIDECTVLRGP-DGTSKGCAFVKFQTHAEAQAAINTLH 74
>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 = 27.7 bits (60), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 24/40 (60%), Gaps = 3/40 (7%)
Query: 6 FSQFGQVTKATIIMDKGKN-TSKGYGSVTFSTEEEAQKAL 44
FS FGQ+ + I+ +G + S+G VTF+T AQ A+
Sbjct: 116 FSSFGQIEECRIL--RGPDGLSRGCAFVTFTTRAXAQTAI 153
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 27.7 bits (60), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 22/51 (43%)
Query: 2 IADAFSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLL 52
+ D FS G+V II D+ SKG V F + A+ +LL
Sbjct: 42 LEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLL 92
>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 = 27.3 bits (59), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 25/48 (52%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLD 53
FS+ G+V +D+ +KG+ V + +A+K + +GK LD
Sbjct: 33 FSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLD 80
>pdb|1JMT|A Chain A, X-Ray Structure Of A Core U2af65U2AF35 HETERODIMER
Length = 104
Score = 27.3 bits (59), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 13/53 (24%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 8 QFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVD 60
++G+V + + + G + G V F EE+A+KA+ ++N + +G+ + +
Sbjct: 50 KYGEVEEMNVCDNLGDHLV-GNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAE 101
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 26.6 bits (57), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 9 FGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLL 52
FGQV I+ D TS+G G + E+ + + NGK +
Sbjct: 49 FGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFI 91
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 26.6 bits (57), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 21/34 (61%)
Query: 27 KGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVD 60
+G +TF +E A +AL +NG L G++L ++
Sbjct: 67 RGQAFITFPNKEIAWQALHLVNGYKLYGKILVIE 100
>pdb|3DXB|A Chain A, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|B Chain B, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|C Chain C, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|D Chain D, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|E Chain E, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|F Chain F, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|G Chain G, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|H Chain H, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
Length = 222
Score = 26.6 bits (57), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 20/41 (48%)
Query: 32 VTFSTEEEAQKALTEMNGKLLDGRVLFVDNVRPSRRYNTDV 72
V FS E KA+ +NG+ GR + + R N+D+
Sbjct: 180 VEFSIASETHKAIQALNGRWFAGRKVVAEVYDQERFDNSDL 220
>pdb|2DNY|A Chain A, Solution Structure Of The Third Rna Binding Domain Of Fbp-
Interacting Repressor, Siahbp1
Length = 119
Score = 26.2 bits (56), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 20/41 (48%)
Query: 32 VTFSTEEEAQKALTEMNGKLLDGRVLFVDNVRPSRRYNTDV 72
V FS E KA+ +NG+ GR + + R N+D+
Sbjct: 71 VEFSIASETHKAIQALNGRWFAGRKVVAEVYDQERFDNSDL 111
>pdb|1TVN|A Chain A, Cellulase Cel5g From Pseudoalteromonas Haloplanktis, A
Family Gh 5-2 Enzyme
pdb|1TVN|B Chain B, Cellulase Cel5g From Pseudoalteromonas Haloplanktis, A
Family Gh 5-2 Enzyme
pdb|1TVP|A Chain A, Endoglucanase Cel5g From Pseudoalteromonas Haloplanktis
In Complex With Cellobiose
pdb|1TVP|B Chain B, Endoglucanase Cel5g From Pseudoalteromonas Haloplanktis
In Complex With Cellobiose
Length = 293
Score = 26.2 bits (56), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 31/70 (44%), Gaps = 10/70 (14%)
Query: 18 IMDKGKNTS----------KGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVDNVRPSRR 67
I+ G+NTS G+G+ F T E KA TE N L+ + + S
Sbjct: 12 ILAGGENTSFAGPSLFWSNTGWGAEKFYTAETVAKAKTEFNATLIRAAIGHGTSTGGSLN 71
Query: 68 YNTDVPLARL 77
++ + ++RL
Sbjct: 72 FDWEGNMSRL 81
>pdb|3UE2|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 1.23 A Resolution
pdb|3US5|A Chain A, Crystal Structure Of A Rna-Binding Domain Of A Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 1.38 A Resolution
Length = 118
Score = 26.2 bits (56), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 20/42 (47%)
Query: 32 VTFSTEEEAQKALTEMNGKLLDGRVLFVDNVRPSRRYNTDVP 73
V FS E KA+ +NG+ GR + + R N+D+
Sbjct: 76 VEFSIASETHKAIQALNGRWFAGRKVVAEVYDQERFDNSDLS 117
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Rna-Binding Protein 14
Length = 90
Score = 26.2 bits (56), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 14/55 (25%), Positives = 28/55 (50%), Gaps = 8/55 (14%)
Query: 6 FSQFGQVTKATIIMDKGKNTSKGYGSVTFSTEEEAQKALTEMNGKLLDGRVLFVD 60
F + G+V + ++ D Y V E +A+ A+ ++NGK + G+ + V+
Sbjct: 30 FERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQLNGKEVKGKRINVE 76
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
0.317 0.132 0.361
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,171,861
Number of Sequences: 62578
Number of extensions: 71674
Number of successful extensions: 360
Number of sequences better than 100.0: 154
Number of HSP's better than 100.0 without gapping: 129
Number of HSP's successfully gapped in prelim test: 25
Number of HSP's that attempted gapping in prelim test: 209
Number of HSP's gapped (non-prelim): 168
length of query: 80
length of database: 14,973,337
effective HSP length: 49
effective length of query: 31
effective length of database: 11,907,015
effective search space: 369117465
effective search space used: 369117465
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: 45 (21.9 bits)