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= psy2347
(207 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor
9g8
Length = 101
Score = 54.7 bits (130), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 27/70 (38%), Positives = 38/70 (54%)
Query: 11 RVYVGGLTETVXXXXXXXXXXXXXXXNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
+VYVG L +VW+A NPPGFAFVEF + DAE A ++ +
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKV 61
Query: 71 LMGSKLRVEI 80
+ GS++RVE+
Sbjct: 62 ICGSRVRVEL 71
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 52.0 bits (123), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 28/70 (40%), Positives = 36/70 (51%)
Query: 11 RVYVGGLTETVXXXXXXXXXXXXXXXNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
+VYVG L SVWVA NPPGFAFVEF + DA A ++ +
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRT 134
Query: 71 LMGSKLRVEI 80
L G ++RVE+
Sbjct: 135 LCGCRVRVEL 144
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 52.0 bits (123), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 28/70 (40%), Positives = 36/70 (51%)
Query: 11 RVYVGGLTETVXXXXXXXXXXXXXXXNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
+VYVG L SVWVA NPPGFAFVEF + DA A ++ +
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRDLDGRT 134
Query: 71 LMGSKLRVEI 80
L G ++RVE+
Sbjct: 135 LCGCRVRVEL 144
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 28/84 (33%), Positives = 37/84 (44%), Gaps = 5/84 (5%)
Query: 2 SDGMMERGTRVYVGGLTETVXXXXXXXXXXXXXXXNSVWVAFN-----PPGFAFVEFSNQ 56
S GM +YVGGL E V + + + GFAFVEF
Sbjct: 5 SSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELA 64
Query: 57 IDAEAACDSMNDQDLMGSKLRVEI 80
DA AA D+MN+ +L G +RV +
Sbjct: 65 EDAAAAIDNMNESELFGRTIRVNL 88
>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 = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 29/83 (34%), Positives = 37/83 (44%), Gaps = 6/83 (7%)
Query: 4 GMMERGTRV-YVGGLTETVXXXXXXXXXXXXXXXNSVWVAFN-----PPGFAFVEFSNQI 57
G M RV YVGGL E V + + + GFAFVEF
Sbjct: 1 GSMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 60
Query: 58 DAEAACDSMNDQDLMGSKLRVEI 80
DA AA D+MN+ +L G +RV +
Sbjct: 61 DAAAAIDNMNESELFGRTIRVNL 83
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 40.8 bits (94), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 34/74 (45%), Gaps = 5/74 (6%)
Query: 12 VYVGGLTETVXXXXXXXXXXXXXXXNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSM 66
+YVGGL E V + + + GFAFVEF DA AA D+M
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 67 NDQDLMGSKLRVEI 80
N+ +L G +RV +
Sbjct: 68 NESELFGRTIRVNL 81
>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 = 40.8 bits (94), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 34/74 (45%), Gaps = 5/74 (6%)
Query: 12 VYVGGLTETVXXXXXXXXXXXXXXXNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSM 66
+YVGGL E V + + + GFAFVEF DA AA D+M
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 67 NDQDLMGSKLRVEI 80
N+ +L G +RV +
Sbjct: 65 NESELFGRTIRVNL 78
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 34/74 (45%), Gaps = 5/74 (6%)
Query: 12 VYVGGLTETVXXXXXXXXXXXXXXXNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSM 66
+YVGGL E V + + + GFAFVEF DA AA D+M
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 67 NDQDLMGSKLRVEI 80
N+ +L G +RV +
Sbjct: 126 NESELFGRTIRVNL 139
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 37.4 bits (85), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 17/32 (53%), Positives = 22/32 (68%)
Query: 47 GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV 78
G+ FV F++Q DA+ A DSM QDL G LR+
Sbjct: 130 GYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRI 161
>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 = 37.4 bits (85), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 17/32 (53%), Positives = 22/32 (68%)
Query: 47 GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV 78
G+ FV F++Q DA+ A DSM QDL G LR+
Sbjct: 44 GYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRI 75
>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm
pdb|2LEB|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uccagu-3'
pdb|2LEC|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uggagu-3'
Length = 135
Score = 36.6 bits (83), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 17/34 (50%), Positives = 24/34 (70%)
Query: 47 GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI 80
GFAFV F ++ DAE A D+M+ L G +LRV++
Sbjct: 90 GFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM 123
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 36.2 bits (82), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 20/33 (60%)
Query: 47 GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE 79
GFAF+ F N DA+ A MN + L G ++VE
Sbjct: 49 GFAFITFENPADAKNAAKDMNGKSLHGKAIKVE 81
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 36.2 bits (82), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 17/34 (50%), Positives = 24/34 (70%)
Query: 47 GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI 80
GFAFV F ++ DAE A D+M+ L G +LRV++
Sbjct: 113 GFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM 146
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 35.4 bits (80), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 25/36 (69%)
Query: 45 PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI 80
P GFAFV F ++ DA+ A +M+ +L G +LRV++
Sbjct: 54 PRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQV 89
>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 = 33.1 bits (74), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 21/33 (63%)
Query: 47 GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE 79
G+ VE+ +A+AA + +N QDLMG + V+
Sbjct: 50 GYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 82
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 33.1 bits (74), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 25/34 (73%)
Query: 47 GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI 80
G+AF+EF++ DA+ A +S N +++ G +R+E+
Sbjct: 54 GYAFIEFASFEDAKEALNSCNKREIEGRAIRLEL 87
>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 = 32.7 bits (73), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 21/33 (63%)
Query: 47 GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE 79
G+ VE+ +A+AA + +N QDLMG + V+
Sbjct: 52 GYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 84
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 32.7 bits (73), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 21/33 (63%)
Query: 47 GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE 79
G+ VE+ +A+AA + +N QDLMG + V+
Sbjct: 50 GYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 82
>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 = 32.7 bits (73), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 21/33 (63%)
Query: 47 GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE 79
G+ VE+ +A+AA + +N QDLMG + V+
Sbjct: 66 GYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 98
>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 = 32.7 bits (73), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 21/33 (63%)
Query: 47 GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE 79
G+ VE+ +A+AA + +N QDLMG + V+
Sbjct: 50 GYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 82
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 32.3 bits (72), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 26/33 (78%)
Query: 47 GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE 79
GF FV+F+++ DA+AA ++M D ++ G+K+ ++
Sbjct: 55 GFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLD 87
>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 = 32.3 bits (72), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 21/33 (63%)
Query: 47 GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE 79
G+ VE+ +A+AA + +N QDLMG + V+
Sbjct: 65 GYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 97
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 32.0 bits (71), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 17/35 (48%), Positives = 20/35 (57%)
Query: 46 PGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI 80
P FAFVEF + DAE A + D G +LRVE
Sbjct: 61 PPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF 95
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 30.4 bits (67), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 21/33 (63%)
Query: 47 GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE 79
GFAFV F N DA+ A + N +L G ++RV+
Sbjct: 89 GFAFVYFENVDDAKEAKERANGMELDGRRIRVD 121
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 30.4 bits (67), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 21/33 (63%)
Query: 47 GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE 79
GFAFV F N DA+ A + N +L G ++RV+
Sbjct: 55 GFAFVYFENVDDAKEAKERANGMELDGRRIRVD 87
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 30.4 bits (67), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 15/34 (44%), Positives = 21/34 (61%)
Query: 47 GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI 80
GFAFV F N DA+ A + N +L G ++RV+
Sbjct: 58 GFAFVYFENVDDAKEAKERANGMELDGRRIRVDF 91
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Rna-Binding Protein 14
Length = 90
Score = 29.6 bits (65), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 11/33 (33%), Positives = 21/33 (63%)
Query: 48 FAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI 80
+AFV + DA+AA +N +++ G ++ VE+
Sbjct: 45 YAFVHMEKEADAKAAIAQLNGKEVKGKRINVEL 77
>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 = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 47 GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV 78
G+A+V F DAE A D+MN + G +R+
Sbjct: 58 GYAYVNFQQPADAERALDTMNFDVIKGKPVRI 89
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 29.6 bits (65), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 20/32 (62%)
Query: 47 GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV 78
GFAFV F N DA+ A + N +L G ++RV
Sbjct: 58 GFAFVYFENVDDAKEAKERANGMELDGRRIRV 89
>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein
In Complex With Polyadenylate Rna
pdb|1CVJ|B Chain B, X-Ray Crystal Structure Of The Poly(A)-Binding Protein
In Complex With Polyadenylate Rna
pdb|1CVJ|C Chain C, X-Ray Crystal Structure Of The Poly(A)-Binding Protein
In Complex With Polyadenylate Rna
pdb|1CVJ|D Chain D, X-Ray Crystal Structure Of The Poly(A)-Binding Protein
In Complex With Polyadenylate Rna
pdb|1CVJ|E Chain E, X-Ray Crystal Structure Of The Poly(A)-Binding Protein
In Complex With Polyadenylate Rna
pdb|1CVJ|F Chain F, X-Ray Crystal Structure Of The Poly(A)-Binding Protein
In Complex With Polyadenylate Rna
pdb|1CVJ|G Chain G, X-Ray Crystal Structure Of The Poly(A)-Binding Protein
In Complex With Polyadenylate Rna
pdb|1CVJ|H Chain H, X-Ray Crystal Structure Of The Poly(A)-Binding Protein
In Complex With Polyadenylate Rna
Length = 190
Score = 29.6 bits (65), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 47 GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV 78
G+A+V F DAE A D+MN + G +R+
Sbjct: 53 GYAYVNFQQPADAERALDTMNFDVIKGKPVRI 84
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 28.5 bits (62), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 21/36 (58%)
Query: 44 NPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE 79
P G+ F E+ +Q A +A ++N ++ G LRV+
Sbjct: 48 KPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVD 83
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 28.5 bits (62), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 21/33 (63%)
Query: 48 FAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI 80
+AFV FSN+ DA A ++N + L GS + V +
Sbjct: 53 YAFVHFSNREDAVEAMKALNGKVLDGSPIEVTL 85
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 28.5 bits (62), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 21/33 (63%)
Query: 47 GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE 79
GF FV F N DA+ A +MN + + G ++RV+
Sbjct: 55 GFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVD 87
>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 = 28.5 bits (62), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 20/33 (60%)
Query: 48 FAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI 80
F FV + N + A+AA SMN + +L+V++
Sbjct: 69 FGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL 101
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 28.5 bits (62), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 11/33 (33%), Positives = 21/33 (63%)
Query: 47 GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE 79
G+A VE+ A AA +++N ++MG ++V+
Sbjct: 69 GYALVEYETHKQALAAKEALNGAEIMGQTIQVD 101
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 28.1 bits (61), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 10/32 (31%), Positives = 22/32 (68%)
Query: 47 GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV 78
G+AFV+F++++D++ A +N + +L+V
Sbjct: 46 GYAFVDFTSEMDSQRAIKVLNGITVRNKRLKV 77
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 28.1 bits (61), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 10/33 (30%), Positives = 22/33 (66%)
Query: 47 GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE 79
G+AFV+F++++D++ A +N + +L+V
Sbjct: 46 GYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVS 78
>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 = 28.1 bits (61), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 21/34 (61%)
Query: 46 PGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE 79
G+A VE+ A AA +++N ++MG ++V+
Sbjct: 114 KGYALVEYETHKQALAAKEALNGAEIMGQTIQVD 147
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 27.7 bits (60), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 47 GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI 80
G+AFV++SN+ A AA N + L G L + +
Sbjct: 63 GYAFVQYSNERHARAAVLGENGRVLAGQTLDINM 96
>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 = 27.7 bits (60), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 18/32 (56%)
Query: 47 GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV 78
G+ F+E+ ++ A SMN DL G LRV
Sbjct: 168 GYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 199
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 27.3 bits (59), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 39 VWVAFN---PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV 78
V + FN GF FV F N DA+ A + ++ + G K+ V
Sbjct: 59 VEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV 101
>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 = 27.3 bits (59), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 18/32 (56%)
Query: 47 GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV 78
G+ F+E+ ++ A SMN DL G LRV
Sbjct: 153 GYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 184
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 26.9 bits (58), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 39 VWVAFN---PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV 78
V + FN GF FV F N DA+ A + ++ + G K+ V
Sbjct: 45 VEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV 87
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 26.9 bits (58), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 21/36 (58%)
Query: 45 PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI 80
P G A V + + A+AA + + +D GSKL+V +
Sbjct: 64 PKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSL 99
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
0.319 0.134 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,661,210
Number of Sequences: 62578
Number of extensions: 55975
Number of successful extensions: 188
Number of sequences better than 100.0: 45
Number of HSP's better than 100.0 without gapping: 45
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 136
Number of HSP's gapped (non-prelim): 49
length of query: 207
length of database: 14,973,337
effective HSP length: 94
effective length of query: 113
effective length of database: 9,091,005
effective search space: 1027283565
effective search space used: 1027283565
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)