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= 025583
(250 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3BEG|B Chain B, Crystal Structure Of Sr Protein Kinase 1 Complexed To Its
Substrate AsfSF2
Length = 115
Score = 82.4 bits (202), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 37/63 (58%), Positives = 50/63 (79%), Gaps = 3/63 (4%)
Query: 85 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSE 144
V+V+GLP S SWQDLKDHMR AGDVC++ V+RD TG+V++ +DM YA+RKLD ++
Sbjct: 19 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD---GTGVVEFVRKEDMTYAVRKLDNTK 75
Query: 145 FRN 147
FR+
Sbjct: 76 FRS 78
>pdb|2O3D|A Chain A, Structure Of Human Sf2ASF RNA RECOGNITION MOTIF 2 (RRM2)
Length = 113
Score = 82.4 bits (202), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 37/63 (58%), Positives = 50/63 (79%), Gaps = 3/63 (4%)
Query: 85 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSE 144
V+V+GLP S SWQDLKDHMR AGDVC++ V+RD TG+V++ +DM YA+RKLD ++
Sbjct: 18 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD---GTGVVEFVRKEDMTYAVRKLDNTK 74
Query: 145 FRN 147
FR+
Sbjct: 75 FRS 77
>pdb|1X4C|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 2
Length = 108
Score = 82.0 bits (201), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 37/63 (58%), Positives = 50/63 (79%), Gaps = 3/63 (4%)
Query: 85 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSE 144
V+V+GLP S SWQDLKDHMR AGDVC++ V+RD TG+V++ +DM YA+RKLD ++
Sbjct: 18 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD---GTGVVEFVRKEDMTYAVRKLDNTK 74
Query: 145 FRN 147
FR+
Sbjct: 75 FRS 77
>pdb|1WG4|A Chain A, Solution Structure Of Rrm Domain In Protein Bab31986
Length = 98
Score = 79.0 bits (193), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 39/63 (61%), Positives = 51/63 (80%), Gaps = 3/63 (4%)
Query: 85 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSE 144
VLV+GLP S SWQDLKDHMR AGDVC++ V +D GM G+V+Y +DM+YA+RKLD ++
Sbjct: 18 VLVSGLPPSGSWQDLKDHMREAGDVCYADVQKD--GM-GMVEYLRKEDMEYALRKLDDTK 74
Query: 145 FRN 147
FR+
Sbjct: 75 FRS 77
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 65.9 bits (159), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 35/54 (64%), Positives = 40/54 (74%)
Query: 3 YGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG 56
YG I DIDLK P +AF+EFED RDAEDA+ GRDGY++DGYRLRVE G
Sbjct: 46 YGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSG 99
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor
9g8
Length = 101
Score = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 30/53 (56%), Positives = 37/53 (69%), Gaps = 2/53 (3%)
Query: 3 YGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG 55
YGP+ + I PPG+AF+EFED RDAEDA+RG DG G R+RVEL+ G
Sbjct: 24 YGPLRTV--WIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTG 74
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 55.5 bits (132), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 27/53 (50%), Positives = 36/53 (67%), Gaps = 2/53 (3%)
Query: 3 YGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG 55
YGP+ + + PPG+AF+EFED RDA DA+R DG G R+RVEL++G
Sbjct: 97 YGPLRSV--WVARNPPGFAFVEFEDPRDAADAVRDLDGRTLCGCRVRVELSNG 147
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 55.5 bits (132), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 27/53 (50%), Positives = 36/53 (67%), Gaps = 2/53 (3%)
Query: 3 YGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG 55
YGP+ + + PPG+AF+EFED RDA DA+R DG G R+RVEL++G
Sbjct: 97 YGPLRSV--WVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNG 147
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 29/51 (56%), Gaps = 5/51 (9%)
Query: 3 YGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
YGP+++ D+ YAF+ E DA +AIRG D F G R+ V+L+
Sbjct: 34 YGPVIECDI-----VKDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLS 79
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 24/57 (42%), Positives = 32/57 (56%), Gaps = 3/57 (5%)
Query: 3 YGPIVDIDLKIPPR---PPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG 56
YG + D+ + P P G+AF+ F D RDA+DA DG DG LRV++A G
Sbjct: 37 YGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARYG 93
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 20/38 (52%), Positives = 25/38 (65%)
Query: 19 GYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG 56
G+AF+ F D RDAEDA+ DG DG LRV++A G
Sbjct: 113 GFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYG 150
>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 = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 19/35 (54%), Positives = 24/35 (68%)
Query: 19 GYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
G+AF+ F D RDAEDA+ DG DG LRV++A
Sbjct: 90 GFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA 124
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 32/54 (59%), Gaps = 3/54 (5%)
Query: 3 YGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
YGPI D+ + + R G+AF+ FE+ DA++A +G DG R+RV+ +
Sbjct: 70 YGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS 123
>pdb|2OSR|A Chain A, Nmr Structure Of Rrm-2 Of Yeast Npl3 Protein
Length = 87
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 35/64 (54%), Gaps = 3/64 (4%)
Query: 85 VLVTGLPSSASWQDLKDHMRRAG-DVCFSQV-FRDRGGMTGIVDYTSYDDMKYAIRKLDR 142
+ + LP SWQDLKD R + FS V RD G TG +++ S + + A+ +L+
Sbjct: 9 ITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDG-TGALEFPSEEILVEALERLNN 67
Query: 143 SEFR 146
EFR
Sbjct: 68 IEFR 71
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 32/54 (59%), Gaps = 3/54 (5%)
Query: 3 YGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
YGPI D+ + + R G+AF+ FE+ DA++A +G DG R+RV+ +
Sbjct: 39 YGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS 92
>pdb|2JVR|A Chain A, Segmental Isotope Labeling Of Npl3p
Length = 111
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 35/64 (54%), Gaps = 3/64 (4%)
Query: 85 VLVTGLPSSASWQDLKDHMRRAG-DVCFSQV-FRDRGGMTGIVDYTSYDDMKYAIRKLDR 142
+ + LP SWQDLKD R + FS V RD G TG +++ S + + A+ +L+
Sbjct: 31 ITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDG-TGALEFPSEEILVEALERLNN 89
Query: 143 SEFR 146
EFR
Sbjct: 90 IEFR 93
>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 = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 32/57 (56%), Gaps = 3/57 (5%)
Query: 2 MYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG 55
+YGPI I + K +P GYAF+E+E RD A + DG DG R+ V++ G
Sbjct: 125 VYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERG 181
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 32/54 (59%), Gaps = 3/54 (5%)
Query: 3 YGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
YGPI D+ + + R G+AF+ FE+ DA++A +G DG R+RV+ +
Sbjct: 36 YGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS 89
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 31/57 (54%), Gaps = 3/57 (5%)
Query: 3 YGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG 56
YGPI D+ + + R G+AF+ FE+ DA++A +G DG R+RV G
Sbjct: 39 YGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGPSSG 95
>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 = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 32/57 (56%), Gaps = 3/57 (5%)
Query: 2 MYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG 55
+YGPI I + K +P GYAF+E+E RD A + DG DG R+ V++ G
Sbjct: 125 VYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERG 181
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 37.4 bits (85), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 31/57 (54%), Gaps = 3/57 (5%)
Query: 3 YGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG 56
YGPI + + + + GY F++F+ A+ AI G +G+N RL+V LA G
Sbjct: 66 YGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASG 122
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 37.0 bits (84), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 26/50 (52%), Gaps = 3/50 (6%)
Query: 4 GPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRV 50
GP++++ + P R GYAF+EF D + A+R +GY L+
Sbjct: 27 GPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKC 76
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 36.6 bits (83), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 3/43 (6%)
Query: 4 GPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAIRGRDGYNF 43
GP++++ + P R GYAF+EF D + A+R +GY
Sbjct: 28 GPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQL 70
>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 = 36.2 bits (82), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 26/50 (52%), Gaps = 3/50 (6%)
Query: 4 GPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRV 50
GP++++ + P R GYAF+EF D + A+R +GY L+
Sbjct: 29 GPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKC 78
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 36.2 bits (82), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 32/54 (59%), Gaps = 3/54 (5%)
Query: 3 YGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
YG I ++ + + R G+ F+ FE+ DA+DA+ +G + DG ++RV+ A
Sbjct: 36 YGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA 89
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 35.4 bits (80), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 28/53 (52%), Gaps = 3/53 (5%)
Query: 4 GPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
GP+V L + +P GY F E++D A A+R +G F G LRV+ A
Sbjct: 33 GPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA 85
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 35.4 bits (80), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 28/50 (56%), Gaps = 4/50 (8%)
Query: 3 YGPIVDIDLKI----PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRL 48
YG I ID+ + P GYA++EFE+ +AE A++ DG DG +
Sbjct: 28 YGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEI 77
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 34.3 bits (77), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 27/46 (58%), Gaps = 4/46 (8%)
Query: 11 LKIPP----RPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL 52
+K+P + GYAF+EF + DA++A+ + +G +R+EL
Sbjct: 42 IKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLEL 87
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 33.5 bits (75), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 24/52 (46%), Gaps = 5/52 (9%)
Query: 2 MYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
YG +++ D+ Y F+ ED AEDAIR Y G + VE +
Sbjct: 31 QYGKVLECDI-----IKNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEAS 77
>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 = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 28/51 (54%), Gaps = 3/51 (5%)
Query: 3 YGPIVDIDLKIPPRP---PGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRV 50
YG I +I L + R GY +E+E Y++A+ A+ G +G + G + V
Sbjct: 31 YGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV 81
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 32.7 bits (73), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 32/54 (59%), Gaps = 4/54 (7%)
Query: 3 YGPIVDIDLKIPPRPP---GYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
+GPI ++ L I R G+AF+ FE+ DA++A + +G + G ++VE A
Sbjct: 31 HGPISEV-LLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA 83
>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 = 0.19, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 3/52 (5%)
Query: 3 YGPIVDIDLKIPPRP---PGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVE 51
YG I +I L + R GY +E+E Y++A+ A+ G +G + G + V+
Sbjct: 31 YGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 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 = 32.3 bits (72), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 3/52 (5%)
Query: 3 YGPIVDIDLKIPPRP---PGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVE 51
YG I +I L + R GY +E+E Y++A+ A+ G +G + G + V+
Sbjct: 33 YGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 84
>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 = 32.3 bits (72), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 3/52 (5%)
Query: 3 YGPIVDIDLKIPPRP---PGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVE 51
YG I +I L + R GY +E+E Y++A+ A+ G +G + G + V+
Sbjct: 31 YGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 82
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 32.3 bits (72), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 28/51 (54%), Gaps = 3/51 (5%)
Query: 3 YGPIVDIDLKIPPRP---PGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRV 50
YG I +I L + R GY +E+E Y++A+ A+ G +G + G + V
Sbjct: 46 YGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV 96
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 32.0 bits (71), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 23/38 (60%)
Query: 16 RPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
+P G A + +ED A+ A+ DG +F G +L+V LA
Sbjct: 63 KPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLA 100
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 31.6 bits (70), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 10/35 (28%), Positives = 22/35 (62%)
Query: 19 GYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
G+ F+E++ A+ A++ G+ DG++L V ++
Sbjct: 51 GFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRIS 85
>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 = 31.6 bits (70), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 3/52 (5%)
Query: 3 YGPIVDIDLKIPPRP---PGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVE 51
YG I +I L + R GY +E+E Y++A+ A+ G +G + G + V+
Sbjct: 47 YGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 98
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 31.6 bits (70), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 3/54 (5%)
Query: 3 YGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
+G I DI + + + G+AF+EFE DA AI + G +RV LA
Sbjct: 87 FGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 31.2 bits (69), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 5/51 (9%)
Query: 3 YGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
YG IV + G+AF+++ + R+A A+ G DG G L + LA
Sbjct: 40 YGKIVGCSVH-----KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLA 85
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Rna-Binding Protein 14
Length = 90
Score = 31.2 bits (69), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 20/37 (54%)
Query: 20 YAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG 56
YAF+ E DA+ AI +G G R+ VEL+ G
Sbjct: 45 YAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKG 81
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 31.2 bits (69), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 31/150 (20%), Positives = 61/150 (40%), Gaps = 30/150 (20%)
Query: 2 MYGPIVDIDL------KIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG 55
++G I DI+ KI + GY F+ + D DA+ AI +G ++V A
Sbjct: 24 LFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYAR- 82
Query: 56 GXXXXXXXXXXXXXXXXXXXXXXXXXXXXVLVTGLPSSASWQDLKDHMRRAGDVCFSQVF 115
+ V+GLP + S ++++ + G + S++
Sbjct: 83 -------------------PSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRIL 123
Query: 116 RDRG-GMTGIVDYTSYD---DMKYAIRKLD 141
D+ G++ V + +D + + AI+ L+
Sbjct: 124 LDQATGVSRGVGFIRFDKRIEAEEAIKGLN 153
>pdb|1WHX|A Chain A, Solution Structure Of The Second Rna Binding Domain From
Hypothetical Protein Bab23448
Length = 111
Score = 30.8 bits (68), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 31/63 (49%), Gaps = 2/63 (3%)
Query: 85 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSE 144
+L LP+ ++++ R G + +V GG+T IV++ + + A R L S+
Sbjct: 13 ILAKNLPAGTLAAEIQETFSRFGSL--GRVLLPEGGITAIVEFLEPLEARKAFRHLAYSK 70
Query: 145 FRN 147
F +
Sbjct: 71 FHH 73
>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 = 30.8 bits (68), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 3/54 (5%)
Query: 3 YGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
+G I DI + + + G+AF+EFE DA AI + G +RV LA
Sbjct: 31 FGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 84
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 30.4 bits (67), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 3/54 (5%)
Query: 3 YGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
+G I DI + + + G+AF+EFE DA AI + G +RV LA
Sbjct: 36 FGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 89
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 20/38 (52%)
Query: 19 GYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG 56
G+A LE+E AE+A + DG + G LRV G
Sbjct: 227 GFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPG 264
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 20/38 (52%)
Query: 19 GYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG 56
G+A LE+E AE+A + DG + G LRV G
Sbjct: 227 GFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPG 264
>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 = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 20/38 (52%)
Query: 19 GYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG 56
G+A LE+E AE+A + DG + G LRV G
Sbjct: 225 GFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPG 262
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 20 YAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
YAF+ F + DA +A++ +G DG + V LA
Sbjct: 53 YAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA 86
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 11/41 (26%), Positives = 22/41 (53%)
Query: 16 RPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG 56
+P G A++E+E+ A A+ DG ++V +++ G
Sbjct: 56 KPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISNSG 96
>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
pdb|3IWN|D Chain D, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
Length = 91
Score = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 28/51 (54%)
Query: 3 YGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
+G I+DI + + G AF+ F++ A +A+R G+ F +R++ A
Sbjct: 32 FGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 82
>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 = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 29/129 (22%), Positives = 48/129 (37%), Gaps = 28/129 (21%)
Query: 19 GYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGGXXXXXXXXXXXXXXXXXXXXXX 78
GYAF++F D++ AI+ +G RL+V A G
Sbjct: 57 GYAFVDFTSEXDSQRAIKVLNGITVRNKRLKVSYARPG--------------------GE 96
Query: 79 XXXXXXVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTG------IVDYTSYDD 132
+ VT LP + + L + G + + RD+ +TG V Y ++
Sbjct: 97 SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDK--LTGRPRGVAFVRYNKREE 154
Query: 133 MKYAIRKLD 141
+ AI L+
Sbjct: 155 AQEAISALN 163
>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To
Its Catalytic Cofactor
pdb|2NZ4|B Chain B, Structural Investigation Of The Glms Ribozyme Bound To
Its Catalytic Cofactor
pdb|2NZ4|C Chain C, Structural Investigation Of The Glms Ribozyme Bound To
Its Catalytic Cofactor
pdb|2NZ4|D Chain D, Structural Investigation Of The Glms Ribozyme Bound To
Its Catalytic Cofactor
Length = 94
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 28/51 (54%)
Query: 3 YGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
+G I+DI + + G AF+ F++ A +A+R G+ F +R++ A
Sbjct: 33 FGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 83
>pdb|1M5K|C Chain C, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5K|F Chain F, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5O|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5O|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1SJ3|P Chain P, Hepatitis Delta Virus Gemonic Ribozyme Precursor, With
Mg2+ Bound
pdb|1SJ4|P Chain P, Crystal Structure Of A C75u Mutant Hepatitis Delta Virus
Ribozyme Precursor, In Cu2+ Solution
pdb|1SJF|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Cobalt
Hexammine Solution
pdb|1VBX|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Edta Solution
pdb|1VBY|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, And Mn2+ Bound
pdb|1VBZ|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Ba2+ Solution
pdb|1VC0|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Imidazole And
Sr2+ Solution
pdb|1VC5|A Chain A, Crystal Structure Of The Wild Type Hepatitis Delta Virus
Gemonic Ribozyme Precursor, In Edta Solution
pdb|1VC6|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Product With C75u Mutaion, Cleaved In
Imidazole And Mg2+ Solutions
pdb|1VC7|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Sr2+ Solution
pdb|2OIH|A Chain A, Hepatitis Delta Virus Gemonic Ribozyme Precursor With
C75u Mutation And Bound To Monovalent Cation Tl+
pdb|2OJ3|A Chain A, Hepatitis Delta Virus Ribozyme Precursor Structure, With
C75u Mutation, Bound To Tl+ And Cobalt Hexammine
(Co(Nh3) 63+)
Length = 100
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 28/51 (54%)
Query: 3 YGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
+G I+DI + + G AF+ F++ A +A+R G+ F +R++ A
Sbjct: 37 FGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 87
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 29/129 (22%), Positives = 48/129 (37%), Gaps = 28/129 (21%)
Query: 19 GYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGGXXXXXXXXXXXXXXXXXXXXXX 78
GYAF++F D++ AI+ +G RL+V A G
Sbjct: 46 GYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPG--------------------GE 85
Query: 79 XXXXXXVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTG------IVDYTSYDD 132
+ VT LP + + L + G + + RD+ +TG V Y ++
Sbjct: 86 SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDK--LTGRPRGVAFVRYNKREE 143
Query: 133 MKYAIRKLD 141
+ AI L+
Sbjct: 144 AQEAISALN 152
>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures
pdb|1DZ5|A Chain A, The Nmr Structure Of The 38kda U1a Protein-Pie Rna
Complex Reveals The Basis Of Cooperativity In
Regulation Of Polyadenylation By Human U1a Protein
pdb|1DZ5|B Chain B, The Nmr Structure Of The 38kda U1a Protein-Pie Rna
Complex Reveals The Basis Of Cooperativity In
Regulation Of Polyadenylation By Human U1a Protein
Length = 101
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 28/51 (54%)
Query: 3 YGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
+G I+DI + + G AF+ F++ A +A+R G+ F +R++ A
Sbjct: 36 FGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 86
>pdb|3L3C|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Glc6p
pdb|3L3C|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Glc6p
pdb|3L3C|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Glc6p
pdb|3L3C|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Glc6p
Length = 90
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 28/51 (54%)
Query: 3 YGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
+G I+DI + + G AF+ F++ A +A+R G+ F +R++ A
Sbjct: 31 FGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 81
>pdb|1U6B|A Chain A, Crystal Structure Of A Self-Splicing Group I Intron With
Both Exons
pdb|1ZZN|A Chain A, Crystal Structure Of A Group I IntronTWO EXON COMPLEX
THAT Includes All Catalytic Metal Ion Ligands.
pdb|3G8S|A Chain A, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|B Chain B, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|C Chain C, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|D Chain D, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8T|A Chain A, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|B Chain B, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|C Chain C, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|D Chain D, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G96|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Man6p
pdb|3G96|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Man6p
pdb|3G96|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Man6p
pdb|3G96|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Man6p
pdb|3G9C|A Chain A, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|B Chain B, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|C Chain C, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|D Chain D, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3IRW|P Chain P, Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3MUM|P Chain P, Crystal Structure Of The G20a Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUR|P Chain P, Crystal Structure Of The C92u Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUT|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Gmp
pdb|3MUV|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Amp
pdb|3MXH|P Chain P, Native Structure Of A C-Di-Gmp Riboswitch From V.
Cholerae
pdb|3P49|B Chain B, Crystal Structure Of A Glycine Riboswitch From
Fusobacterium Nucleatum
pdb|3R1H|A Chain A, Crystal Structure Of The Class I Ligase
Ribozyme-Substrate Preligation Complex, C47u Mutant,
Ca2+ Bound
pdb|3R1H|D Chain D, Crystal Structure Of The Class I Ligase
Ribozyme-Substrate Preligation Complex, C47u Mutant,
Ca2+ Bound
pdb|3R1L|A Chain A, Crystal Structure Of The Class I Ligase
Ribozyme-Substrate Preligation Complex, C47u Mutant,
Mg2+ Bound
pdb|3R1L|D Chain D, Crystal Structure Of The Class I Ligase
Ribozyme-Substrate Preligation Complex, C47u Mutant,
Mg2+ Bound
pdb|3UCU|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Pgpg
pdb|3UCZ|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Gpg
pdb|3UD3|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Pgpa
pdb|3UD4|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Gpa
Length = 98
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 28/51 (54%)
Query: 3 YGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
+G I+DI + + G AF+ F++ A +A+R G+ F +R++ A
Sbjct: 37 FGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 87
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 25/48 (52%)
Query: 3 YGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRV 50
YGPI I + P G A++ +ED DA++A+ G+N L V
Sbjct: 32 YGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVV 79
>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|B Chain B, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|C Chain C, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|D Chain D, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
Length = 96
Score = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 28/51 (54%)
Query: 3 YGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
+G I+DI + + G AF+ F++ A +A+R G+ F +R++ A
Sbjct: 36 FGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 86
>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|B Chain B, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|C Chain C, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1NU4|A Chain A, U1a Rna Binding Domain At 1.8 Angstrom Resolution
Reveals A Pre- Organized C-Terminal Helix
pdb|1NU4|B Chain B, U1a Rna Binding Domain At 1.8 Angstrom Resolution
Reveals A Pre- Organized C-Terminal Helix
pdb|3HHN|B Chain B, Crystal Structure Of Class I Ligase Ribozyme
Self-Ligation Product, In Complex With U1a Rbd
pdb|3HHN|D Chain D, Crystal Structure Of Class I Ligase Ribozyme
Self-Ligation Product, In Complex With U1a Rbd
Length = 97
Score = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 28/51 (54%)
Query: 3 YGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
+G I+DI + + G AF+ F++ A +A+R G+ F +R++ A
Sbjct: 36 FGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 86
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 28/51 (54%)
Query: 3 YGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
+G I+DI + + G AF+ F++ A +A+R G+ F +R++ A
Sbjct: 37 FGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 87
>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group
I Intron
pdb|3BO3|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group
I Intron
pdb|3BO4|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group
I Intron
pdb|3IIN|A Chain A, Plasticity Of The Kink Turn Structural Motif
Length = 95
Score = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 28/51 (54%)
Query: 3 YGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
+G I+DI + + G AF+ F++ A +A+R G+ F +R++ A
Sbjct: 34 FGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 84
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 29.3 bits (64), Expect = 1.9, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 3/54 (5%)
Query: 3 YGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
+G I DI + + + G+AF+EFE DA AI + G +RV LA
Sbjct: 29 FGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 82
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 21/38 (55%)
Query: 19 GYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG 56
GYAF++F D++ AI+ +G RL+V A G
Sbjct: 46 GYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPG 83
>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 = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 20/32 (62%)
Query: 19 GYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRV 50
GY F+E+E + ++DA+ + ++ G LRV
Sbjct: 168 GYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 199
>pdb|1A9N|B Chain B, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
pdb|1A9N|D Chain D, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
Length = 96
Score = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 28/51 (54%)
Query: 3 YGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
+G +VDI + G AF+ F++ + +A+R G+ F G +R++ A
Sbjct: 34 FGHVVDIVALKTMKMRGQAFVIFKELGSSTNALRQLQGFPFYGKPMRIQYA 84
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 29.3 bits (64), Expect = 2.0, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 3/54 (5%)
Query: 3 YGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
+G I DI + + + G+AF+EFE DA AI + G +RV LA
Sbjct: 26 FGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 79
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 29.3 bits (64), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 6/58 (10%)
Query: 2 MYGPIVDIDL------KIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
++G I DI+ KI + GY F+ + D DA+ AI +G ++V A
Sbjct: 24 LFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYA 81
>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 = 29.3 bits (64), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 20/32 (62%)
Query: 19 GYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRV 50
GY F+E+E + ++DA+ + ++ G LRV
Sbjct: 153 GYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 184
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 20/35 (57%)
Query: 19 GYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
GYAF+++ + R A A+ G +G G L + +A
Sbjct: 63 GYAFVQYSNERHARAAVLGENGRVLAGQTLDINMA 97
>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 = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 20/32 (62%)
Query: 19 GYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRV 50
GY F+E+E + ++DA+ + ++ G LRV
Sbjct: 152 GYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRV 183
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 29/51 (56%), Gaps = 4/51 (7%)
Query: 85 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRD-RGGMT---GIVDYTSYD 131
++V GLP + QDLK++ G+V QV +D + G + G V +T Y+
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYE 68
>pdb|2NLW|A Chain A, Solution Structure Of The Rrm Domain Of Human Eukaryotic
Initiation Factor 3b
Length = 105
Score = 28.9 bits (63), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 16 RPPGYAFLEFEDYRDAEDAIRGRDGYNFDG-YRLRVEL 52
+ GY FLE+ A DA++ DGY D + RV L
Sbjct: 59 KTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVNL 96
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein
U1a117, Nmr, 43 Structures
Length = 116
Score = 28.5 bits (62), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 28/52 (53%)
Query: 3 YGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH 54
+G I+DI + + G AF+ F++ A +A+R G+ F +R++ A
Sbjct: 36 FGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAK 87
>pdb|2KRB|A Chain A, Solution Structure Of Eif3b-Rrm Bound To Eif3j Peptide
Length = 81
Score = 28.5 bits (62), Expect = 3.3, Method: Composition-based stats.
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 19 GYAFLEFEDYRDAEDAIRGRDGYNFD 44
GY FLE+ A DA++ DGY D
Sbjct: 48 GYIFLEYASPAHAVDAVKNADGYKLD 73
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 28.5 bits (62), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 22/40 (55%)
Query: 3 YGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYN 42
YGPI I + P G A++ +ED DA++A G+N
Sbjct: 36 YGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFN 75
>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of
The Spliceosomal Protein P14 Bound To A Region Of
Sf3b155
pdb|2F9J|B Chain B, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of
The Spliceosomal Protein P14 Bound To A Region Of
Sf3b155
Length = 125
Score = 28.5 bits (62), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 22/40 (55%)
Query: 3 YGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYN 42
YGPI I + P G A++ +ED DA++A G+N
Sbjct: 42 YGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFN 81
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 28.5 bits (62), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 22/40 (55%)
Query: 3 YGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYN 42
YGPI I + P G A++ +ED DA++A G+N
Sbjct: 42 YGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFN 81
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 28.1 bits (61), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 27/51 (52%)
Query: 3 YGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
+G I+DI + + G AF+ F++ A +A+R G+ F R++ A
Sbjct: 36 FGQILDILVSRSLKXRGQAFVIFKEVSSATNALRSXQGFPFYDKPXRIQYA 86
>pdb|3CUL|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUL|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3EGZ|A Chain A, Crystal Structure Of An In Vitro Evolved Tetracycline
Aptamer And Artificial Riboswitch
Length = 98
Score = 28.1 bits (61), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 27/51 (52%)
Query: 3 YGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
+G I+DI + + G AF+ F++ A +A+R G+ F R++ A
Sbjct: 37 FGQILDILVSRSLKXRGQAFVIFKEVSSATNALRSXQGFPFYDKPXRIQYA 87
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 28.1 bits (61), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 27/51 (52%)
Query: 3 YGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
+G I+DI + + G AF+ F++ A +A+R G+ F R++ A
Sbjct: 34 FGQILDILVSRSLKXRGQAFVIFKEVSSATNALRSXQGFPFYDKPXRIQYA 84
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 27.7 bits (60), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 2/59 (3%)
Query: 85 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGM--TGIVDYTSYDDMKYAIRKLD 141
+ V LP +W+ LKD G V ++ + + G G+V + S + + A R ++
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMN 66
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 27.7 bits (60), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 2/59 (3%)
Query: 85 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGM--TGIVDYTSYDDMKYAIRKLD 141
+ V LP +W+ LKD G V ++ + + G G+V + S + + A R ++
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMN 69
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 27.7 bits (60), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 3/56 (5%)
Query: 1 MMYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
+ GP+V+ + ++ + GY F+EF DA+ AI+ D G +RV A
Sbjct: 37 LQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA 92
>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 = 27.7 bits (60), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 19 GYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
GY F+ F DA++A+ G + +G LR+ A
Sbjct: 44 GYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 78
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 27.3 bits (59), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 19 GYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 53
GY F+ F DA++A+ G + +G LR+ A
Sbjct: 130 GYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 164
>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 = 27.3 bits (59), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 24/44 (54%), Gaps = 6/44 (13%)
Query: 4 GPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFD 44
GPI+ I + I R GYA++ F+ DAE A+ D NFD
Sbjct: 35 GPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL---DTMNFD 75
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.324 0.144 0.459
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,552,356
Number of Sequences: 62578
Number of extensions: 149922
Number of successful extensions: 350
Number of sequences better than 100.0: 91
Number of HSP's better than 100.0 without gapping: 75
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 263
Number of HSP's gapped (non-prelim): 99
length of query: 250
length of database: 14,973,337
effective HSP length: 96
effective length of query: 154
effective length of database: 8,965,849
effective search space: 1380740746
effective search space used: 1380740746
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 50 (23.9 bits)