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= 022425
(297 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 95.5 bits (236), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 48/75 (64%), Positives = 58/75 (77%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
+YVGNLP D R +++ED+FYKYG I DIDLK P +AF+EFED RDAEDA+ GRDGY
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 84
Query: 69 NFDGYRLRVELAHGG 83
++DGYRLRVE G
Sbjct: 85 DYDGYRLRVEFPRSG 99
>pdb|3BEG|B Chain B, Crystal Structure Of Sr Protein Kinase 1 Complexed To Its
Substrate AsfSF2
Length = 115
Score = 83.2 bits (204), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 37/63 (58%), Positives = 50/63 (79%), Gaps = 3/63 (4%)
Query: 112 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSE 171
V+V+GLP S SWQDLKDHMR AGDVC++ V+RD TG+V++ +DM YA+RKLD ++
Sbjct: 19 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD---GTGVVEFVRKEDMTYAVRKLDNTK 75
Query: 172 FRN 174
FR+
Sbjct: 76 FRS 78
>pdb|2O3D|A Chain A, Structure Of Human Sf2ASF RNA RECOGNITION MOTIF 2 (RRM2)
Length = 113
Score = 83.2 bits (204), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 37/63 (58%), Positives = 50/63 (79%), Gaps = 3/63 (4%)
Query: 112 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSE 171
V+V+GLP S SWQDLKDHMR AGDVC++ V+RD TG+V++ +DM YA+RKLD ++
Sbjct: 18 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD---GTGVVEFVRKEDMTYAVRKLDNTK 74
Query: 172 FRN 174
FR+
Sbjct: 75 FRS 77
>pdb|1X4C|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 2
Length = 108
Score = 82.8 bits (203), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 37/63 (58%), Positives = 50/63 (79%), Gaps = 3/63 (4%)
Query: 112 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSE 171
V+V+GLP S SWQDLKDHMR AGDVC++ V+RD TG+V++ +DM YA+RKLD ++
Sbjct: 18 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD---GTGVVEFVRKEDMTYAVRKLDNTK 74
Query: 172 FRN 174
FR+
Sbjct: 75 FRS 77
>pdb|1WG4|A Chain A, Solution Structure Of Rrm Domain In Protein Bab31986
Length = 98
Score = 79.7 bits (195), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 39/63 (61%), Positives = 51/63 (80%), Gaps = 3/63 (4%)
Query: 112 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSE 171
VLV+GLP S SWQDLKDHMR AGDVC++ V +D GM G+V+Y +DM+YA+RKLD ++
Sbjct: 18 VLVSGLPPSGSWQDLKDHMREAGDVCYADVQKD--GM-GMVEYLRKEDMEYALRKLDDTK 74
Query: 172 FRN 174
FR+
Sbjct: 75 FRS 77
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 67.8 bits (164), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 35/74 (47%), Positives = 47/74 (63%), Gaps = 2/74 (2%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
+YVGNL + E+E F YGP+ + + PPG+AF+EFED RDA DA+R DG
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSV--WVARNPPGFAFVEFEDPRDAADAVRELDGR 133
Query: 69 NFDGYRLRVELAHG 82
G R+RVEL++G
Sbjct: 134 TLCGCRVRVELSNG 147
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 67.8 bits (164), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 35/74 (47%), Positives = 47/74 (63%), Gaps = 2/74 (2%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
+YVGNL + E+E F YGP+ + + PPG+AF+EFED RDA DA+R DG
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSV--WVARNPPGFAFVEFEDPRDAADAVRDLDGR 133
Query: 69 NFDGYRLRVELAHG 82
G R+RVEL++G
Sbjct: 134 TLCGCRVRVELSNG 147
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor
9g8
Length = 101
Score = 66.6 bits (161), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 38/74 (51%), Positives = 47/74 (63%), Gaps = 2/74 (2%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
+YVGNL E+E F YGP+ + I PPG+AF+EFED RDAEDA+RG DG
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTV--WIARNPPGFAFVEFEDPRDAEDAVRGLDGK 60
Query: 69 NFDGYRLRVELAHG 82
G R+RVEL+ G
Sbjct: 61 VICGSRVRVELSTG 74
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 56.6 bits (135), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 29/80 (36%), Positives = 47/80 (58%), Gaps = 3/80 (3%)
Query: 4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAED 60
RS R+++VGN+P + +++D+F + GP+V L + +P GY F E++D A
Sbjct: 6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALS 65
Query: 61 AIRGRDGYNFDGYRLRVELA 80
A+R +G F G LRV+ A
Sbjct: 66 AMRNLNGREFSGRALRVDNA 85
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 53.5 bits (127), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 45/75 (60%), Gaps = 3/75 (4%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGR 65
L+VG L DT + +E +F KYG I ++ + + R G+ F+ FE+ DA+DA+
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 66 DGYNFDGYRLRVELA 80
+G + DG ++RV+ A
Sbjct: 75 NGKSVDGRQIRVDQA 89
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 52.4 bits (124), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 40/75 (53%), Gaps = 3/75 (4%)
Query: 6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAI 62
SR +Y+G++P D ++ DL GP++++ + P R GYAF+EF D + A+
Sbjct: 2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61
Query: 63 RGRDGYNFDGYRLRV 77
R +GY L+
Sbjct: 62 RNLNGYQLGSRFLKC 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 = 52.4 bits (124), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 38/68 (55%), Gaps = 3/68 (4%)
Query: 6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAI 62
SR +Y+G++P D ++ DL GP++++ + P R GYAF+EF D + A+
Sbjct: 3 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 62
Query: 63 RGRDGYNF 70
R +GY
Sbjct: 63 RNLNGYQL 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 = 51.6 bits (122), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 40/75 (53%), Gaps = 3/75 (4%)
Query: 6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAI 62
SR +Y+G++P D ++ DL GP++++ + P R GYAF+EF D + A+
Sbjct: 4 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 63
Query: 63 RGRDGYNFDGYRLRV 77
R +GY L+
Sbjct: 64 RNLNGYQLGSRFLKC 78
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 51.6 bits (122), Expect = 5e-07, Method: Composition-based stats.
Identities = 27/77 (35%), Positives = 43/77 (55%), Gaps = 5/77 (6%)
Query: 4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIR 63
++S L+VGN+ +E+ F +YGP+++ D+ YAF+ E DA +AIR
Sbjct: 8 KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV-----KDYAFVHMERAEDAVEAIR 62
Query: 64 GRDGYNFDGYRLRVELA 80
G D F G R+ V+L+
Sbjct: 63 GLDNTEFQGKRMHVQLS 79
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 50.4 bits (119), Expect = 1e-06, Method: Composition-based stats.
Identities = 25/70 (35%), Positives = 37/70 (52%), Gaps = 5/70 (7%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
L++GNLP + +E+ LF +YG +++ D+ Y F+ ED AEDAIR Y
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDII-----KNYGFVHIEDKTAAEDAIRNLHHY 65
Query: 69 NFDGYRLRVE 78
G + VE
Sbjct: 66 KLHGVNINVE 75
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 32/79 (40%), Positives = 42/79 (53%), Gaps = 3/79 (3%)
Query: 8 TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPR---PPGYAFLEFEDYRDAEDAIRG 64
TL V NL T + +F KYG + D+ + P P G+AF+ F D RDA+DA
Sbjct: 15 TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74
Query: 65 RDGYNFDGYRLRVELAHGG 83
DG DG LRV++A G
Sbjct: 75 MDGAELDGRELRVQVARYG 93
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 47.4 bits (111), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 29/76 (38%), Positives = 40/76 (52%), Gaps = 3/76 (3%)
Query: 8 TLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRG 64
T+ V NL DTR ++++LF +G I I L K + G+AF+ F DA AI G
Sbjct: 17 TIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAG 76
Query: 65 RDGYNFDGYRLRVELA 80
G+ +D L VE A
Sbjct: 77 VSGFGYDHLILNVEWA 92
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 47.4 bits (111), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 40/77 (51%)
Query: 1 MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAED 60
+ +R LY+ NLP E+ D+F KYGPI I + P G A++ +ED DA++
Sbjct: 3 LPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKN 62
Query: 61 AIRGRDGYNFDGYRLRV 77
A+ G+N L V
Sbjct: 63 AVDHLSGFNVSNRYLVV 79
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 47.0 bits (110), Expect = 1e-05, Method: Composition-based stats.
Identities = 25/64 (39%), Positives = 36/64 (56%)
Query: 6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGR 65
+R LY+ NLP E+ D+F KYGPI I + P G A++ +ED DA++A
Sbjct: 12 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHL 71
Query: 66 DGYN 69
G+N
Sbjct: 72 SGFN 75
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 30/79 (37%), Positives = 42/79 (53%), Gaps = 3/79 (3%)
Query: 8 TLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRG 64
+L V NL T + +F KYG + D+ + + G+AF+ F D RDAEDA+
Sbjct: 72 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 131
Query: 65 RDGYNFDGYRLRVELAHGG 83
DG DG LRV++A G
Sbjct: 132 MDGAVLDGRELRVQMARYG 150
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 40/66 (60%), Gaps = 3/66 (4%)
Query: 18 TRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYR 74
T R++ ++F KYGPI D+ + + R G+AF+ FE+ DA++A +G DG R
Sbjct: 58 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR 117
Query: 75 LRVELA 80
+RV+ +
Sbjct: 118 IRVDFS 123
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 40/66 (60%), Gaps = 3/66 (4%)
Query: 18 TRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYR 74
T R++ ++F KYGPI D+ + + R G+AF+ FE+ DA++A +G DG R
Sbjct: 27 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR 86
Query: 75 LRVELA 80
+RV+ +
Sbjct: 87 IRVDFS 92
>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 = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/64 (39%), Positives = 36/64 (56%)
Query: 6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGR 65
+R LY+ NLP E+ D+F KYGPI I + P G A++ +ED DA++A
Sbjct: 18 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHL 77
Query: 66 DGYN 69
G+N
Sbjct: 78 SGFN 81
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 39/69 (56%), Gaps = 3/69 (4%)
Query: 18 TRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYR 74
T R++ ++F KYGPI D+ + + R G+AF+ FE+ DA++A +G DG R
Sbjct: 27 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR 86
Query: 75 LRVELAHGG 83
+RV G
Sbjct: 87 IRVSGPSSG 95
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 3/80 (3%)
Query: 7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIR 63
R L V +P ++ LF +YGPI + + + + GY F++F+ A+ AI
Sbjct: 43 RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA 102
Query: 64 GRDGYNFDGYRLRVELAHGG 83
G +G+N RL+V LA G
Sbjct: 103 GLNGFNILNKRLKVALAASG 122
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 40/66 (60%), Gaps = 3/66 (4%)
Query: 18 TRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYR 74
T R++ ++F KYGPI D+ + + R G+AF+ FE+ DA++A +G DG R
Sbjct: 24 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR 83
Query: 75 LRVELA 80
+RV+ +
Sbjct: 84 IRVDFS 89
>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 = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 29/79 (36%), Positives = 42/79 (53%), Gaps = 3/79 (3%)
Query: 7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIR 63
+TL+V + DT ++ F YGPI I + K +P GYAF+E+E RD A +
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 64 GRDGYNFDGYRLRVELAHG 82
DG DG R+ V++ G
Sbjct: 163 HADGKKIDGRRVLVDVERG 181
>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 = 45.1 bits (105), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 29/76 (38%), Positives = 41/76 (53%), Gaps = 3/76 (3%)
Query: 8 TLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRG 64
+L V NL T + +F KYG + D+ + + G+AF+ F D RDAEDA+
Sbjct: 49 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 108
Query: 65 RDGYNFDGYRLRVELA 80
DG DG LRV++A
Sbjct: 109 MDGAVLDGRELRVQMA 124
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 44.7 bits (104), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 45/75 (60%), Gaps = 4/75 (5%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPP---GYAFLEFEDYRDAEDAIRGR 65
L++G L +T + ++ +F K+GPI ++ L I R G+AF+ FE+ DA++A +
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEV-LLIKDRTSKSRGFAFITFENPADAKNAAKDM 68
Query: 66 DGYNFDGYRLRVELA 80
+G + G ++VE A
Sbjct: 69 NGKSLHGKAIKVEQA 83
>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 = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 35/64 (54%)
Query: 6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGR 65
+R L + NLP E+ D+F KYGPI I + P G A++ +ED DA++A
Sbjct: 18 NRILMIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHL 77
Query: 66 DGYN 69
G+N
Sbjct: 78 SGFN 81
>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 = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 29/79 (36%), Positives = 42/79 (53%), Gaps = 3/79 (3%)
Query: 7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIR 63
+TL+V + DT ++ F YGPI I + K +P GYAF+E+E RD A +
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 64 GRDGYNFDGYRLRVELAHG 82
DG DG R+ V++ G
Sbjct: 163 HADGKKIDGRRVLVDVERG 181
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 28/82 (34%), Positives = 42/82 (51%), Gaps = 3/82 (3%)
Query: 4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAED 60
+ S TLYVGNL T ++ +LF K G I I + K+ G+ F+E+ DAE+
Sbjct: 37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAEN 96
Query: 61 AIRGRDGYNFDGYRLRVELAHG 82
A+R +G D +R + G
Sbjct: 97 AMRYINGTRLDDRIIRTDWDAG 118
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 39/81 (48%), Gaps = 3/81 (3%)
Query: 3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAE 59
+ + R LYVG L + + + F +G I DI + + + G+AF+EFE DA
Sbjct: 60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 119
Query: 60 DAIRGRDGYNFDGYRLRVELA 80
AI + G +RV LA
Sbjct: 120 AAIDNMNESELFGRTIRVNLA 140
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 42.0 bits (97), Expect = 4e-04, Method: Composition-based stats.
Identities = 22/68 (32%), Positives = 37/68 (54%), Gaps = 4/68 (5%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI----PPRPPGYAFLEFEDYRDAEDAIRG 64
+++G L + + ++F YG I ID+ + P GYA++EFE+ +AE A++
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 65 RDGYNFDG 72
DG DG
Sbjct: 67 MDGGQIDG 74
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Rna-Binding Protein 14
Length = 90
Score = 41.6 bits (96), Expect = 5e-04, Method: Composition-based stats.
Identities = 25/82 (30%), Positives = 42/82 (51%), Gaps = 5/82 (6%)
Query: 2 SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDA 61
SS ++ ++VGN+ +E+ LF + G +++ D+ YAF+ E DA+ A
Sbjct: 5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV-----KDYAFVHMEKEADAKAA 59
Query: 62 IRGRDGYNFDGYRLRVELAHGG 83
I +G G R+ VEL+ G
Sbjct: 60 IAQLNGKEVKGKRINVELSTKG 81
>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 = 41.2 bits (95), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 20/84 (23%), Positives = 40/84 (47%), Gaps = 2/84 (2%)
Query: 2 SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAE 59
+S L++ LP E+E++ +G + D+ L +P G A++E+E+ A
Sbjct: 13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQAS 72
Query: 60 DAIRGRDGYNFDGYRLRVELAHGG 83
A+ DG ++V +++ G
Sbjct: 73 QAVMKMDGMTIKENIIKVAISNSG 96
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 40.8 bits (94), Expect = 9e-04, Method: Composition-based stats.
Identities = 23/78 (29%), Positives = 42/78 (53%), Gaps = 4/78 (5%)
Query: 7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIR 63
R +YVGNL +V++LF ++G + ++ L + +P G+ F+E ++ +AI
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIA 60
Query: 64 GRDGYNFDGYRLRVELAH 81
D +F G +RV A+
Sbjct: 61 KLDNTDFMGRTIRVTEAN 78
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 39/81 (48%), Gaps = 3/81 (3%)
Query: 3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAE 59
+ + R LYVG L + + + F +G I DI + + + G+AF+EFE DA
Sbjct: 9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 68
Query: 60 DAIRGRDGYNFDGYRLRVELA 80
AI + G +RV LA
Sbjct: 69 AAIDNMNESELFGRTIRVNLA 89
>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 = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 35/67 (52%), Gaps = 3/67 (4%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGR 65
LYV LP +E+E LF +YG I+ + ++ G F+ F+ +AE+AI+G
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 66 DGYNFDG 72
+G G
Sbjct: 151 NGQKPSG 157
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 40/173 (23%), Positives = 68/173 (39%), Gaps = 31/173 (17%)
Query: 5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDA 61
S L V LP + E LF G I L KI + GY F+ + D +DAE A
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 62 IRGRDGYNFDGYRLRVELAHGGXXXXXXXXXXXXXXXXXXXXXXXXXXXXVLVTGLPSSA 121
I +G ++V A + V+GLP +
Sbjct: 61 INTLNGLRLQTKTIKVSYAR--------------------PSSASIRDANLYVSGLPKTM 100
Query: 122 SWQDLKDHMRRAGDVCFSQVFRDRGGMTGI---VDYTSYD---DMKYAIRKLD 168
+ ++L+ + G + S++ D+ +TG+ V + +D + + AI+ L+
Sbjct: 101 TQKELEQLFSQYGRIITSRILVDQ--VTGVSRGVGFIRFDKRIEAEEAIKGLN 151
>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures
pdb|1DZ5|A Chain A, The Nmr Structure Of The 38kda U1a Protein-Pie Rna
Complex Reveals The Basis Of Cooperativity In
Regulation Of Polyadenylation By Human U1a Protein
pdb|1DZ5|B Chain B, The Nmr Structure Of The 38kda U1a Protein-Pie Rna
Complex Reveals The Basis Of Cooperativity In
Regulation Of Polyadenylation By Human U1a Protein
Length = 101
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 43/82 (52%), Gaps = 4/82 (4%)
Query: 3 SRSSRTLYVGNL----PGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDA 58
+R + T+Y+ NL D + + +F ++G I+DI + + G AF+ F++ A
Sbjct: 5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 64
Query: 59 EDAIRGRDGYNFDGYRLRVELA 80
+A+R G+ F +R++ A
Sbjct: 65 TNALRSMQGFPFYDKPMRIQYA 86
>pdb|1M5K|C Chain C, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5K|F Chain F, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5O|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5O|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1SJ3|P Chain P, Hepatitis Delta Virus Gemonic Ribozyme Precursor, With
Mg2+ Bound
pdb|1SJ4|P Chain P, Crystal Structure Of A C75u Mutant Hepatitis Delta Virus
Ribozyme Precursor, In Cu2+ Solution
pdb|1SJF|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Cobalt
Hexammine Solution
pdb|1VBX|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Edta Solution
pdb|1VBY|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, And Mn2+ Bound
pdb|1VBZ|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Ba2+ Solution
pdb|1VC0|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Imidazole And
Sr2+ Solution
pdb|1VC5|A Chain A, Crystal Structure Of The Wild Type Hepatitis Delta Virus
Gemonic Ribozyme Precursor, In Edta Solution
pdb|1VC6|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Product With C75u Mutaion, Cleaved In
Imidazole And Mg2+ Solutions
pdb|1VC7|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Sr2+ Solution
pdb|2OIH|A Chain A, Hepatitis Delta Virus Gemonic Ribozyme Precursor With
C75u Mutation And Bound To Monovalent Cation Tl+
pdb|2OJ3|A Chain A, Hepatitis Delta Virus Ribozyme Precursor Structure, With
C75u Mutation, Bound To Tl+ And Cobalt Hexammine
(Co(Nh3) 63+)
Length = 100
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 43/82 (52%), Gaps = 4/82 (4%)
Query: 3 SRSSRTLYVGNL----PGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDA 58
+R + T+Y+ NL D + + +F ++G I+DI + + G AF+ F++ A
Sbjct: 6 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 65
Query: 59 EDAIRGRDGYNFDGYRLRVELA 80
+A+R G+ F +R++ A
Sbjct: 66 TNALRSMQGFPFYDKPMRIQYA 87
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 40.0 bits (92), Expect = 0.001, Method: Composition-based stats.
Identities = 27/81 (33%), Positives = 39/81 (48%), Gaps = 3/81 (3%)
Query: 3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAE 59
S + R LYVG L + + + F +G I DI + + + G+AF+EFE DA
Sbjct: 2 STTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 61
Query: 60 DAIRGRDGYNFDGYRLRVELA 80
AI + G +RV LA
Sbjct: 62 AAIDNMNESELFGRTIRVNLA 82
>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 = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 40/81 (49%), Gaps = 3/81 (3%)
Query: 3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRP---PGYAFLEFEDYRDAE 59
S L+V + + ++ D F +YG I +I L + R GY +E+E Y++A+
Sbjct: 4 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 63
Query: 60 DAIRGRDGYNFDGYRLRVELA 80
A+ G +G + G + V+
Sbjct: 64 AAMEGLNGQDLMGQPISVDWC 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 = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 27/79 (34%), Positives = 38/79 (48%), Gaps = 3/79 (3%)
Query: 5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDA 61
S R LYVG L + + + F +G I DI + + + G+AF+EFE DA A
Sbjct: 1 SKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 60
Query: 62 IRGRDGYNFDGYRLRVELA 80
I + G +RV LA
Sbjct: 61 IDNMNESELFGRTIRVNLA 79
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 38/74 (51%), Gaps = 1/74 (1%)
Query: 6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGR 65
S+TL + NL ++++F K + + + GYAF+EF + DA++A+
Sbjct: 15 SKTLVLSNLSYSATEETLQEVFEK-ATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSC 73
Query: 66 DGYNFDGYRLRVEL 79
+ +G +R+EL
Sbjct: 74 NKREIEGRAIRLEL 87
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein
U1a117, Nmr, 43 Structures
Length = 116
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 44/82 (53%), Gaps = 4/82 (4%)
Query: 3 SRSSRTLYVGNLPGDTRMREVED----LFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDA 58
+R + T+Y+ NL + E++ +F ++G I+DI + + G AF+ F++ A
Sbjct: 5 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSA 64
Query: 59 EDAIRGRDGYNFDGYRLRVELA 80
+A+R G+ F +R++ A
Sbjct: 65 TNALRSMQGFPFYDKPMRIQYA 86
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 5/73 (6%)
Query: 5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRG 64
S+ L+V P D + E+ ++F +GP+ ++ + G+AF+EFE+ A AI
Sbjct: 30 SNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-----NGFAFVEFEEAESAAKAIEE 84
Query: 65 RDGYNFDGYRLRV 77
G +F L V
Sbjct: 85 VHGKSFANQPLEV 97
>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 = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 40/81 (49%), Gaps = 3/81 (3%)
Query: 3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRP---PGYAFLEFEDYRDAE 59
S L+V + + ++ D F +YG I +I L + R GY +E+E Y++A+
Sbjct: 19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 78
Query: 60 DAIRGRDGYNFDGYRLRVELA 80
A+ G +G + G + V+
Sbjct: 79 AAMEGLNGQDLMGQPISVDWC 99
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 37/73 (50%), Gaps = 6/73 (8%)
Query: 9 LYVGNL-PGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDG 67
+++GNL + +VE +F KYG + + GYAF+++ + R A A+ G +G
Sbjct: 30 VFIGNLNTALVKKSDVETIFSKYGRVAGCSVH-----KGYAFVQYSNERHARAAVLGENG 84
Query: 68 YNFDGYRLRVELA 80
G L + +A
Sbjct: 85 RVLAGQTLDINMA 97
>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 = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 26/79 (32%), Positives = 38/79 (48%), Gaps = 3/79 (3%)
Query: 5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDA 61
+ R LYVG L + + + F +G I DI + + + G+AF+EFE DA A
Sbjct: 6 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 65
Query: 62 IRGRDGYNFDGYRLRVELA 80
I + G +RV LA
Sbjct: 66 IDNMNESELFGRTIRVNLA 84
>pdb|1U6B|A Chain A, Crystal Structure Of A Self-Splicing Group I Intron With
Both Exons
pdb|1ZZN|A Chain A, Crystal Structure Of A Group I IntronTWO EXON COMPLEX
THAT Includes All Catalytic Metal Ion Ligands.
pdb|3G8S|A Chain A, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|B Chain B, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|C Chain C, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|D Chain D, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8T|A Chain A, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|B Chain B, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|C Chain C, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|D Chain D, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G96|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Man6p
pdb|3G96|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Man6p
pdb|3G96|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Man6p
pdb|3G96|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Man6p
pdb|3G9C|A Chain A, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|B Chain B, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|C Chain C, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|D Chain D, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3IRW|P Chain P, Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3MUM|P Chain P, Crystal Structure Of The G20a Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUR|P Chain P, Crystal Structure Of The C92u Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUT|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Gmp
pdb|3MUV|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Amp
pdb|3MXH|P Chain P, Native Structure Of A C-Di-Gmp Riboswitch From V.
Cholerae
pdb|3P49|B Chain B, Crystal Structure Of A Glycine Riboswitch From
Fusobacterium Nucleatum
pdb|3R1H|A Chain A, Crystal Structure Of The Class I Ligase
Ribozyme-Substrate Preligation Complex, C47u Mutant,
Ca2+ Bound
pdb|3R1H|D Chain D, Crystal Structure Of The Class I Ligase
Ribozyme-Substrate Preligation Complex, C47u Mutant,
Ca2+ Bound
pdb|3R1L|A Chain A, Crystal Structure Of The Class I Ligase
Ribozyme-Substrate Preligation Complex, C47u Mutant,
Mg2+ Bound
pdb|3R1L|D Chain D, Crystal Structure Of The Class I Ligase
Ribozyme-Substrate Preligation Complex, C47u Mutant,
Mg2+ Bound
pdb|3UCU|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Pgpg
pdb|3UCZ|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Gpg
pdb|3UD3|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Pgpa
pdb|3UD4|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Gpa
Length = 98
Score = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 22/82 (26%), Positives = 43/82 (52%), Gaps = 4/82 (4%)
Query: 3 SRSSRTLYVGNL----PGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDA 58
+R + T+Y+ NL D + + +F ++G I+DI + + G AF+ F++ A
Sbjct: 6 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 65
Query: 59 EDAIRGRDGYNFDGYRLRVELA 80
+A+R G+ F +R++ A
Sbjct: 66 TNALRSMQGFPFYDKPMRIQYA 87
>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|B Chain B, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|C Chain C, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|D Chain D, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
Length = 96
Score = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 22/82 (26%), Positives = 43/82 (52%), Gaps = 4/82 (4%)
Query: 3 SRSSRTLYVGNL----PGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDA 58
+R + T+Y+ NL D + + +F ++G I+DI + + G AF+ F++ A
Sbjct: 5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 64
Query: 59 EDAIRGRDGYNFDGYRLRVELA 80
+A+R G+ F +R++ A
Sbjct: 65 TNALRSMQGFPFYDKPMRIQYA 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 = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 22/82 (26%), Positives = 43/82 (52%), Gaps = 4/82 (4%)
Query: 3 SRSSRTLYVGNL----PGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDA 58
+R + T+Y+ NL D + + +F ++G I+DI + + G AF+ F++ A
Sbjct: 5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 64
Query: 59 EDAIRGRDGYNFDGYRLRVELA 80
+A+R G+ F +R++ A
Sbjct: 65 TNALRSMQGFPFYDKPMRIQYA 86
>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 = 38.9 bits (89), Expect = 0.003, Method: Composition-based stats.
Identities = 22/82 (26%), Positives = 43/82 (52%), Gaps = 4/82 (4%)
Query: 3 SRSSRTLYVGNL----PGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDA 58
+R + T+Y+ NL D + + +F ++G I+DI + + G AF+ F++ A
Sbjct: 2 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 61
Query: 59 EDAIRGRDGYNFDGYRLRVELA 80
+A+R G+ F +R++ A
Sbjct: 62 TNALRSMQGFPFYDKPMRIQYA 83
>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 = 38.9 bits (89), Expect = 0.003, Method: Composition-based stats.
Identities = 22/82 (26%), Positives = 43/82 (52%), Gaps = 4/82 (4%)
Query: 3 SRSSRTLYVGNL----PGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDA 58
+R + T+Y+ NL D + + +F ++G I+DI + + G AF+ F++ A
Sbjct: 1 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 60
Query: 59 EDAIRGRDGYNFDGYRLRVELA 80
+A+R G+ F +R++ A
Sbjct: 61 TNALRSMQGFPFYDKPMRIQYA 82
>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 = 38.9 bits (89), Expect = 0.003, Method: Composition-based stats.
Identities = 22/82 (26%), Positives = 43/82 (52%), Gaps = 4/82 (4%)
Query: 3 SRSSRTLYVGNL----PGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDA 58
+R + T+Y+ NL D + + +F ++G I+DI + + G AF+ F++ A
Sbjct: 3 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 62
Query: 59 EDAIRGRDGYNFDGYRLRVELA 80
+A+R G+ F +R++ A
Sbjct: 63 TNALRSMQGFPFYDKPMRIQYA 84
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 38/82 (46%), Gaps = 3/82 (3%)
Query: 5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDA 61
S+ L++G LP +V++L +GP+ +L GYAF E+ D + A
Sbjct: 113 SAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 172
Query: 62 IRGRDGYNFDGYRLRVELAHGG 83
I G +G +L V+ A G
Sbjct: 173 IAGLNGMQLGDKKLLVQRASVG 194
Score = 29.3 bits (64), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 35/87 (40%), Gaps = 15/87 (17%)
Query: 6 SRTLYVGNLPGDTRMREVEDLFYKY-----------GPIVDIDLKIPPRPPGYAFLEFED 54
+R LYVGN+P + D F P++ + + + +AFLEF
Sbjct: 4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN---QDKNFAFLEFRS 60
Query: 55 YRDAEDAIRGRDGYNFDGYRLRVELAH 81
+ A+ DG F G L++ H
Sbjct: 61 VDETTQAM-AFDGIIFQGQSLKIRRPH 86
>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 = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 34/154 (22%), Positives = 59/154 (38%), Gaps = 24/154 (15%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGR 65
L V LP + E+ LF G + L K+ GY F+ + +DAE AI
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 66 DGYNFDGYRLRVELAHGGXXXXXXXXXXXXXXXXXXXXXXXXXXXXVLVTGLPSSASWQD 125
+G ++V A + ++GLP + + +D
Sbjct: 65 NGLRLQSKTIKVSYAR--------------------PSSEVIKDANLYISGLPRTMTQKD 104
Query: 126 LKDHMRRAGDVCFSQVFRDR-GGMTGIVDYTSYD 158
++D R G + S+V D+ G++ V + +D
Sbjct: 105 VEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFD 138
Score = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 35/63 (55%), Gaps = 3/63 (4%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPP---GYAFLEFEDYRDAEDAIRGR 65
LY+ LP ++VED+F ++G I++ + + G AF+ F+ +AE+AI
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 66 DGY 68
+G+
Sbjct: 151 NGH 153
>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 = 38.9 bits (89), Expect = 0.004, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 3/73 (4%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRP---PGYAFLEFEDYRDAEDAIRGR 65
L+V + + ++ D F +YG I +I L + R GY +E+E Y++A+ A+ G
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 66 DGYNFDGYRLRVE 78
+G + G + V+
Sbjct: 70 NGQDLMGQPISVD 82
>pdb|2JVR|A Chain A, Segmental Isotope Labeling Of Npl3p
Length = 111
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 112 VLVTGLPSSASWQDLKDHMRRAG-DVCFSQV-FRDRGGMTGIVDYTSYDDMKYAIRKLDR 169
+ + LP SWQDLKD R + FS V RD G TG +++ S + + A+ +L+
Sbjct: 31 ITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDG-TGALEFPSEEILVEALERLNN 89
Query: 170 SEFRNA 175
EFR +
Sbjct: 90 IEFRGS 95
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 38.9 bits (89), Expect = 0.004, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 3/73 (4%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRP---PGYAFLEFEDYRDAEDAIRGR 65
L+V + + ++ D F +YG I +I L + R GY +E+E Y++A+ A+ G
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 66 DGYNFDGYRLRVE 78
+G + G + V+
Sbjct: 70 NGQDLMGQPISVD 82
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 33/57 (57%), Gaps = 3/57 (5%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAI 62
LYV NLP +++ +F KYG IV ++ K+ RP G AF+ + +A++AI
Sbjct: 92 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 148
Score = 37.0 bits (84), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 42/173 (24%), Positives = 65/173 (37%), Gaps = 31/173 (17%)
Query: 5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPP---GYAFLEFEDYRDAEDA 61
S+ L V LP D RE+ LF GPI + + GYAF++F D++ A
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 62 IRGRDGYNFDGYRLRVELAHGGXXXXXXXXXXXXXXXXXXXXXXXXXXXXVLVTGLPSSA 121
I+ +G RL+V A G + VT LP +
Sbjct: 62 IKVLNGITVRNKRLKVSYARPG--------------------GESIKDTNLYVTNLPRTI 101
Query: 122 SWQDLKDHMRRAGDVCFSQVFRDRGGMTG------IVDYTSYDDMKYAIRKLD 168
+ L + G + + RD+ +TG V Y ++ + AI L+
Sbjct: 102 TDDQLDTIFGKYGSIVQKNILRDK--LTGRPRGVAFVRYNKREEAQEAISALN 152
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 34/154 (22%), Positives = 59/154 (38%), Gaps = 24/154 (15%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGR 65
L V LP + E+ LF G + L K+ GY F+ + +DAE AI
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 66 DGYNFDGYRLRVELAHGGXXXXXXXXXXXXXXXXXXXXXXXXXXXXVLVTGLPSSASWQD 125
+G ++V A + ++GLP + + +D
Sbjct: 65 NGLRLQSKTIKVSYAR--------------------PSSEVIKDANLYISGLPRTMTQKD 104
Query: 126 LKDHMRRAGDVCFSQVFRDR-GGMTGIVDYTSYD 158
++D R G + S+V D+ G++ V + +D
Sbjct: 105 VEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFD 138
Score = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 35/63 (55%), Gaps = 3/63 (4%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPP---GYAFLEFEDYRDAEDAIRGR 65
LY+ LP ++VED+F ++G I++ + + G AF+ F+ +AE+AI
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 66 DGY 68
+G+
Sbjct: 151 NGH 153
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 38.5 bits (88), Expect = 0.004, Method: Composition-based stats.
Identities = 27/81 (33%), Positives = 41/81 (50%), Gaps = 2/81 (2%)
Query: 4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPP--GYAFLEFEDYRDAEDA 61
+ S TLYVGNL T ++ +LF K G I I + + G+ F+E+ DAE+A
Sbjct: 16 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENA 75
Query: 62 IRGRDGYNFDGYRLRVELAHG 82
+R +G D +R + G
Sbjct: 76 MRYINGTRLDDRIIRTDWDAG 96
>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition
Motif Of Nono
pdb|2RS8|A Chain A, Solution Structure Of The N-Terminal Rna Recognition
Motif Of Nono
Length = 99
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 34/72 (47%), Gaps = 3/72 (4%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
L+VGNLP D E+ LF KYG ++ + + G+ F+ E AE A D
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIH---KDKGFGFIRLETRTLAEIAKVELDNM 74
Query: 69 NFDGYRLRVELA 80
G +LRV A
Sbjct: 75 PLRGKQLRVRFA 86
>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 = 38.5 bits (88), Expect = 0.004, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 3/73 (4%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRP---PGYAFLEFEDYRDAEDAIRGR 65
L+V + + ++ D F +YG I +I L + R GY +E+E Y++A+ A+ G
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 66 DGYNFDGYRLRVE 78
+G + G + V+
Sbjct: 72 NGQDLMGQPISVD 84
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 38.5 bits (88), Expect = 0.004, Method: Composition-based stats.
Identities = 22/82 (26%), Positives = 44/82 (53%), Gaps = 4/82 (4%)
Query: 3 SRSSRTLYVGNLPGDTRMREVED----LFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDA 58
+R + T+Y+ NL + E++ +F ++G I+DI + + G AF+ F++ A
Sbjct: 6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSA 65
Query: 59 EDAIRGRDGYNFDGYRLRVELA 80
+A+R G+ F +R++ A
Sbjct: 66 TNALRSMQGFPFYDKPMRIQYA 87
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 38.5 bits (88), Expect = 0.004, Method: Composition-based stats.
Identities = 27/81 (33%), Positives = 43/81 (53%), Gaps = 10/81 (12%)
Query: 1 MSSRSSRTLYVGNLPG-DTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAE 59
M+SR +++GNL + +VE +F KYG IV + G+AF+++ + R+A
Sbjct: 14 MNSR----VFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH-----KGFAFVQYVNERNAR 64
Query: 60 DAIRGRDGYNFDGYRLRVELA 80
A+ G DG G L + LA
Sbjct: 65 AAVAGEDGRMIAGQVLDINLA 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 = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 40/81 (49%), Gaps = 3/81 (3%)
Query: 3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRP---PGYAFLEFEDYRDAE 59
S L+V + + ++ D F +YG I +I L + R GY +E+E Y++A+
Sbjct: 20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 79
Query: 60 DAIRGRDGYNFDGYRLRVELA 80
A+ G +G + G + V+
Sbjct: 80 AAMEGLNGQDLMGQPISVDWC 100
>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 = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 33/58 (56%), Gaps = 3/58 (5%)
Query: 8 TLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAI 62
LYV NLP +++ +F KYG IV ++ K+ RP G AF+ + +A++AI
Sbjct: 102 NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 159
Score = 37.4 bits (85), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 42/173 (24%), Positives = 65/173 (37%), Gaps = 31/173 (17%)
Query: 5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPP---GYAFLEFEDYRDAEDA 61
S+ L V LP D RE+ LF GPI + + GYAF++F D++ A
Sbjct: 13 SNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRA 72
Query: 62 IRGRDGYNFDGYRLRVELAHGGXXXXXXXXXXXXXXXXXXXXXXXXXXXXVLVTGLPSSA 121
I+ +G RL+V A G + VT LP +
Sbjct: 73 IKVLNGITVRNKRLKVSYARPG--------------------GESIKDTNLYVTNLPRTI 112
Query: 122 SWQDLKDHMRRAGDVCFSQVFRDRGGMTG------IVDYTSYDDMKYAIRKLD 168
+ L + G + + RD+ +TG V Y ++ + AI L+
Sbjct: 113 TDDQLDTIFGKYGSIVQKNILRDK--LTGRPRGVAFVRYNKREEAQEAISALN 163
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 37/71 (52%), Gaps = 5/71 (7%)
Query: 2 SSRSSR--TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPP---GYAFLEFEDYR 56
SS S R LYV LP +E+E LF +YG I+ + + G F+ F+
Sbjct: 84 SSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRI 143
Query: 57 DAEDAIRGRDG 67
+AE+AI+G +G
Sbjct: 144 EAEEAIKGLNG 154
Score = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 38/171 (22%), Positives = 67/171 (39%), Gaps = 27/171 (15%)
Query: 5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDA 61
S L V LP + E + LF G I L KI + GY F+ + D DA+ A
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 62 IRGRDGYNFDGYRLRVELAHGGXXXXXXXXXXXXXXXXXXXXXXXXXXXXVLVTGLPSSA 121
I +G ++V A + V+GLP +
Sbjct: 63 INTLNGLKLQTKTIKVSYAR--------------------PSSASIRDANLYVSGLPKTM 102
Query: 122 SWQDLKDHMRRAGDVCFSQVFRDRG-GMTGIVDYTSYD---DMKYAIRKLD 168
S ++++ + G + S++ D+ G++ V + +D + + AI+ L+
Sbjct: 103 SQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLN 153
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 38.5 bits (88), Expect = 0.005, Method: Composition-based stats.
Identities = 22/82 (26%), Positives = 42/82 (51%), Gaps = 4/82 (4%)
Query: 3 SRSSRTLYVGNL----PGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDA 58
+R + T+Y+ NL D + + +F ++G I+DI + + G AF+ F++ A
Sbjct: 5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSA 64
Query: 59 EDAIRGRDGYNFDGYRLRVELA 80
+A+R G+ F R++ A
Sbjct: 65 TNALRSXQGFPFYDKPXRIQYA 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 = 38.5 bits (88), Expect = 0.005, Method: Composition-based stats.
Identities = 22/82 (26%), Positives = 42/82 (51%), Gaps = 4/82 (4%)
Query: 3 SRSSRTLYVGNL----PGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDA 58
+R + T+Y+ NL D + + +F ++G I+DI + + G AF+ F++ A
Sbjct: 6 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSA 65
Query: 59 EDAIRGRDGYNFDGYRLRVELA 80
+A+R G+ F R++ A
Sbjct: 66 TNALRSXQGFPFYDKPXRIQYA 87
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 2/76 (2%)
Query: 7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP--RPPGYAFLEFEDYRDAEDAIRG 64
R LYVGNL ++ F GPI +I + I + YAF+E+ DA A++
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQT 60
Query: 65 RDGYNFDGYRLRVELA 80
+G + +++ A
Sbjct: 61 LNGKQIENNIVKINWA 76
Score = 27.7 bits (60), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 46 GYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 80
GY F+ F DA++A+ G + +G LR+ A
Sbjct: 130 GYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 164
>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 = 38.5 bits (88), Expect = 0.005, Method: Composition-based stats.
Identities = 22/81 (27%), Positives = 42/81 (51%), Gaps = 4/81 (4%)
Query: 4 RSSRTLYVGNL----PGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAE 59
R + T+Y+ NL D + + +F ++G I+DI + + G AF+ F++ A
Sbjct: 1 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 60
Query: 60 DAIRGRDGYNFDGYRLRVELA 80
+A+R G+ F +R++ A
Sbjct: 61 NALRSMQGFPFYDKPMRIQYA 81
>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 = 38.5 bits (88), Expect = 0.005, Method: Composition-based stats.
Identities = 23/84 (27%), Positives = 44/84 (52%), Gaps = 4/84 (4%)
Query: 1 MSSRSSRTLYVGNLPGDTRMREVED----LFYKYGPIVDIDLKIPPRPPGYAFLEFEDYR 56
M R + T+Y+ N+ + E++ LF ++G +VDI + G AF+ F++
Sbjct: 1 MDIRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELG 60
Query: 57 DAEDAIRGRDGYNFDGYRLRVELA 80
+ +A+R G+ F G +R++ A
Sbjct: 61 SSTNALRQLQGFPFYGKPMRIQYA 84
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 38.1 bits (87), Expect = 0.005, Method: Composition-based stats.
Identities = 22/82 (26%), Positives = 42/82 (51%), Gaps = 4/82 (4%)
Query: 3 SRSSRTLYVGNL----PGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDA 58
+R + T+Y+ NL D + + +F ++G I+DI + + G AF+ F++ A
Sbjct: 3 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSA 62
Query: 59 EDAIRGRDGYNFDGYRLRVELA 80
+A+R G+ F R++ A
Sbjct: 63 TNALRSXQGFPFYDKPXRIQYA 84
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 37.7 bits (86), Expect = 0.008, Method: Composition-based stats.
Identities = 21/62 (33%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPR---PPGYAFLEFEDYRDAEDAIRGR 65
LYV LP +E+E LF +YG I+ + + G F+ F+ +AE+AI+G
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 66 DG 67
+G
Sbjct: 64 NG 65
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 37.7 bits (86), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 34/72 (47%), Gaps = 3/72 (4%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
L+VGNLP D E+ LF KYG ++ + + G+ F+ E AE A D
Sbjct: 25 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIH---KDKGFGFIRLETRTLAEIAKVELDNM 81
Query: 69 NFDGYRLRVELA 80
G +LRV A
Sbjct: 82 PLRGKQLRVRFA 93
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 37.7 bits (86), Expect = 0.008, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 5/73 (6%)
Query: 5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRG 64
S+ L+V P D + E+ ++F +GP+ ++ + G+AF+EFE+ A AI
Sbjct: 3 SNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-----NGFAFVEFEEAESAAKAIEE 57
Query: 65 RDGYNFDGYRLRV 77
G +F L V
Sbjct: 58 VHGKSFANQPLEV 70
>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 = 37.4 bits (85), Expect = 0.009, Method: Composition-based stats.
Identities = 21/66 (31%), Positives = 36/66 (54%), Gaps = 4/66 (6%)
Query: 10 YVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAIRGRD 66
+VG L DT ++++D F K+G +VD +K P R G+ F+ F+D E + ++
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQKE 74
Query: 67 GYNFDG 72
+ DG
Sbjct: 75 -HRLDG 79
>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The
Second Rna-Binding Domain Of Sex-Lethal Determined By
Multidimensional Heteronuclear Magnetic Resonance
Spectroscopy
Length = 97
Score = 37.4 bits (85), Expect = 0.009, Method: Composition-based stats.
Identities = 21/57 (36%), Positives = 33/57 (57%), Gaps = 3/57 (5%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAI 62
LYV NLP +++ +F KYG IV ++ K+ RP G AF+ + +A++AI
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 72
>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 37.4 bits (85), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 44/82 (53%), Gaps = 4/82 (4%)
Query: 3 SRSSRTLYVGNLPGDTRMREVED----LFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDA 58
+R + T+Y+ NL + E++ +F ++G I+DI + + G AF+ F++ A
Sbjct: 6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSA 65
Query: 59 EDAIRGRDGYNFDGYRLRVELA 80
+A+R G+ F +R++ A
Sbjct: 66 TNALRSMQGFPFYDKPMRIQYA 87
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 37.4 bits (85), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 27/82 (32%), Positives = 38/82 (46%), Gaps = 3/82 (3%)
Query: 5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPP---GYAFLEFEDYRDAEDA 61
S+ L V LP D RE+ LF GPI + + GYAF++F D++ A
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 62 IRGRDGYNFDGYRLRVELAHGG 83
I+ +G RL+V A G
Sbjct: 62 IKVLNGITVRNKRLKVSYARPG 83
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 37.4 bits (85), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 34/72 (47%), Gaps = 3/72 (4%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGR 65
L+V NL + ++E LF YGP+ ++ I +P G+AF+ F A A
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 66 DGYNFDGYRLRV 77
DG F G L V
Sbjct: 71 DGQVFQGRMLHV 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 = 37.0 bits (84), Expect = 0.012, Method: Composition-based stats.
Identities = 17/49 (34%), Positives = 31/49 (63%), Gaps = 3/49 (6%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFED 54
+++G L DT ++++D F K+G +VD LK+ P R G+ F+ F++
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKE 50
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 37.0 bits (84), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 3/78 (3%)
Query: 6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAI 62
+ L++G LP +V++L +GP+ +L GYAF E+ D + AI
Sbjct: 94 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 153
Query: 63 RGRDGYNFDGYRLRVELA 80
G +G +L V+ A
Sbjct: 154 AGLNGMQLGDKKLLVQRA 171
Score = 30.8 bits (68), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 36/88 (40%), Gaps = 15/88 (17%)
Query: 5 SSRTLYVGNLPGDTRMREVEDLFYKY-----------GPIVDIDLKIPPRPPGYAFLEFE 53
S+R LYVGN+P + D F P++ + + + +AFLEF
Sbjct: 3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN---QDKNFAFLEFR 59
Query: 54 DYRDAEDAIRGRDGYNFDGYRLRVELAH 81
+ A+ DG F G L++ H
Sbjct: 60 SVDETTQAM-AFDGIIFQGQSLKIRRPH 86
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 37.0 bits (84), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 37/76 (48%), Gaps = 3/76 (3%)
Query: 7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL--KIPPRPPGYAFLEFEDYRDAEDAIRG 64
RTLYVGNL D + LF + GP + + P Y F+EF ++RDA A+
Sbjct: 16 RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP-YCFVEFYEHRDAAAALAA 74
Query: 65 RDGYNFDGYRLRVELA 80
+G G ++V A
Sbjct: 75 MNGRKILGKEVKVNWA 90
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 37.0 bits (84), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
Query: 5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPR-PPGYAFLEFEDYRDAEDAIR 63
+ + L+V N+P R ++ +F ++G I+D+++ R G+ F+ FE+ DA+ A
Sbjct: 14 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRARE 73
Query: 64 GRDGYNFDGYRLRVELA 80
G +G ++ V A
Sbjct: 74 KLHGTVVEGRKIEVNNA 90
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 36.6 bits (83), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 38/76 (50%), Gaps = 3/76 (3%)
Query: 8 TLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRG 64
T+YVG L + +LF + GP+V+ + ++ + GY F+EF DA+ AI+
Sbjct: 17 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 76
Query: 65 RDGYNFDGYRLRVELA 80
D G +RV A
Sbjct: 77 MDMIKLYGKPIRVNKA 92
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 36.6 bits (83), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPR-PPGYAFLEFEDYRDAEDAIRGR 65
+ L+V N+P R ++ +F ++G I+D+++ R G+ F+ FE+ DA+ A
Sbjct: 30 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKL 89
Query: 66 DGYNFDGYRLRVELA 80
G +G ++ V A
Sbjct: 90 HGTVVEGRKIEVNNA 104
>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAF|B Chain B, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAG|A Chain A, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAG|B Chain B, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAH|A Chain A, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAH|B Chain B, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAI|A Chain A, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAI|B Chain B, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAJ|A Chain A, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAJ|B Chain B, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAK|A Chain A, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAK|B Chain B, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAL|A Chain A, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|B Chain B, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|D Chain D, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|I Chain I, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAM|A Chain A, Structure Of U2af65 Variant With Bru5c2 Dna
pdb|3VAM|B Chain B, Structure Of U2af65 Variant With Bru5c2 Dna
Length = 174
Score = 36.6 bits (83), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 3/78 (3%)
Query: 6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAI 62
+ L++G LP +V++L +GP+ +L GYAF E+ D + AI
Sbjct: 96 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 155
Query: 63 RGRDGYNFDGYRLRVELA 80
G +G +L V+ A
Sbjct: 156 AGLNGMQLGDKKLLVQRA 173
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 36/88 (40%), Gaps = 15/88 (17%)
Query: 5 SSRTLYVGNLPGDTRMREVEDLFYKY-----------GPIVDIDLKIPPRPPGYAFLEFE 53
S+R LYVGN+P + D F P++ + + + +AFLEF
Sbjct: 5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN---QDKNFAFLEFR 61
Query: 54 DYRDAEDAIRGRDGYNFDGYRLRVELAH 81
+ A+ DG F G L++ H
Sbjct: 62 SVDETTQAM-AFDGIIFQGQSLKIRRPH 88
>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 = 36.6 bits (83), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 39/74 (52%), Gaps = 4/74 (5%)
Query: 7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIR 63
R++YVGN+ + +++E F G I I + K P GYA++EF + R++ DA
Sbjct: 37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAE-RNSVDAAV 95
Query: 64 GRDGYNFDGYRLRV 77
D F G ++V
Sbjct: 96 AMDETVFRGRTIKV 109
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 36.6 bits (83), Expect = 0.018, Method: Composition-based stats.
Identities = 23/81 (28%), Positives = 37/81 (45%), Gaps = 3/81 (3%)
Query: 6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAI 62
+ L++G LP +V++L +GP+ +L GYAF E+ D + AI
Sbjct: 1 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 60
Query: 63 RGRDGYNFDGYRLRVELAHGG 83
G +G +L V+ A G
Sbjct: 61 AGLNGMQLGDKKLLVQRASVG 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 = 36.6 bits (83), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 40/78 (51%), Gaps = 3/78 (3%)
Query: 3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAE 59
+R+ +YV ++ D +++ +F +G I L P + GY F+E+E + ++
Sbjct: 107 ARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQ 166
Query: 60 DAIRGRDGYNFDGYRLRV 77
DA+ + ++ G LRV
Sbjct: 167 DAVSSMNLFDLGGQYLRV 184
Score = 30.8 bits (68), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 35/72 (48%), Gaps = 3/72 (4%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGR 65
+YVG++ + + F +GPI ID+ + + G+AF+E+E A+ A+
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 66 DGYNFDGYRLRV 77
+ G ++V
Sbjct: 76 NSVMLGGRNIKV 87
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 36.2 bits (82), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 3/72 (4%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPR---PPGYAFLEFEDYRDAEDAIRGR 65
L+V ++ + + E+++ F YG I +I L + R GYA +E+E ++ A A
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 66 DGYNFDGYRLRV 77
+G G ++V
Sbjct: 89 NGAEIMGQTIQV 100
>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 = 35.8 bits (81), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 40/78 (51%), Gaps = 3/78 (3%)
Query: 3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAE 59
+R+ +YV ++ D +++ +F +G I L P + GY F+E+E + ++
Sbjct: 106 ARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQ 165
Query: 60 DAIRGRDGYNFDGYRLRV 77
DA+ + ++ G LRV
Sbjct: 166 DAVSSXNLFDLGGQYLRV 183
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 34/72 (47%), Gaps = 3/72 (4%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGR 65
+YVG++ + + F +GPI ID + + G+AF+E+E A+ A+
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 66 DGYNFDGYRLRV 77
+ G ++V
Sbjct: 75 NSVXLGGRNIKV 86
>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1HL6|C Chain C, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1RK8|A Chain A, Structure Of The Cytosolic Protein Pym Bound To The Mago-
Y14 Core Of The Exon Junction Complex
pdb|2X1G|A Chain A, Crystal Structure Of Importin13 - Mago-Y14 Complex
pdb|2X1G|C Chain C, Crystal Structure Of Importin13 - Mago-Y14 Complex
Length = 165
Score = 35.8 bits (81), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 3/72 (4%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPR---PPGYAFLEFEDYRDAEDAIRGR 65
L+V ++ + + E+++ F YG I +I L + R GYA +E+E ++ A A
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 66 DGYNFDGYRLRV 77
+G G ++V
Sbjct: 135 NGAEIMGQTIQV 146
>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 = 35.8 bits (81), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 40/78 (51%), Gaps = 3/78 (3%)
Query: 3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAE 59
+R+ +YV ++ D +++ +F +G I L P + GY F+E+E + ++
Sbjct: 122 ARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQ 181
Query: 60 DAIRGRDGYNFDGYRLRV 77
DA+ + ++ G LRV
Sbjct: 182 DAVSSMNLFDLGGQYLRV 199
Score = 30.8 bits (68), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 35/72 (48%), Gaps = 3/72 (4%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGR 65
+YVG++ + + F +GPI ID+ + + G+AF+E+E A+ A+
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 66 DGYNFDGYRLRV 77
+ G ++V
Sbjct: 91 NSVMLGGRNIKV 102
>pdb|2OSR|A Chain A, Nmr Structure Of Rrm-2 Of Yeast Npl3 Protein
Length = 87
Score = 35.8 bits (81), Expect = 0.029, Method: Composition-based stats.
Identities = 24/66 (36%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 112 VLVTGLPSSASWQDLKDHMRRAG-DVCFSQV-FRDRGGMTGIVDYTSYDDMKYAIRKLDR 169
+ + LP SWQDLKD R + FS V RD G TG +++ S + + A+ +L+
Sbjct: 9 ITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDG-TGALEFPSEEILVEALERLNN 67
Query: 170 SEFRNA 175
EFR +
Sbjct: 68 IEFRGS 73
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 35.8 bits (81), Expect = 0.031, Method: Composition-based stats.
Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 3/79 (3%)
Query: 5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDA 61
S T+YV NLP ++ +F KYG +V + + K + G AF+ F D A++
Sbjct: 15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNC 74
Query: 62 IRGRDGYNFDGYRLRVELA 80
R + G ++ +A
Sbjct: 75 TRAINNKQLFGRVIKASIA 93
>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 = 35.8 bits (81), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 35/67 (52%), Gaps = 6/67 (8%)
Query: 8 TLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRG 64
+LYVG+L D + + F GPI+ I + I R GYA++ F+ DAE A+
Sbjct: 12 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL-- 69
Query: 65 RDGYNFD 71
D NFD
Sbjct: 70 -DTMNFD 75
>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 = 35.0 bits (79), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 4/77 (5%)
Query: 7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIR 63
+ ++VG + DT + D F +YG I I++ + G+AF+ F+D+ D+ D I
Sbjct: 105 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH-DSVDKIV 163
Query: 64 GRDGYNFDGYRLRVELA 80
+ + +G+ V A
Sbjct: 164 IQKYHTVNGHNCEVRKA 180
>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 = 35.0 bits (79), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 35/67 (52%), Gaps = 6/67 (8%)
Query: 8 TLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRG 64
+LYVG+L D + + F GPI+ I + I R GYA++ F+ DAE A+
Sbjct: 17 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL-- 74
Query: 65 RDGYNFD 71
D NFD
Sbjct: 75 -DTMNFD 80
>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 = 35.0 bits (79), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 4/77 (5%)
Query: 7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIR 63
+ ++VG + DT + D F +YG I I++ + G+AF+ F+D+ D+ D I
Sbjct: 98 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH-DSVDKIV 156
Query: 64 GRDGYNFDGYRLRVELA 80
+ + +G+ V A
Sbjct: 157 IQKYHTVNGHNCEVRKA 173
>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 = 35.0 bits (79), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 4/77 (5%)
Query: 7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIR 63
+ ++VG + DT + D F +YG I I++ + G+AF+ F+D+ D+ D I
Sbjct: 104 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH-DSVDKIV 162
Query: 64 GRDGYNFDGYRLRVELA 80
+ + +G+ V A
Sbjct: 163 IQKYHTVNGHNCEVRKA 179
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 34.7 bits (78), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 4/77 (5%)
Query: 7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIR 63
+ ++VG + DT + D F +YG I I++ + G+AF+ F+D+ D+ D I
Sbjct: 106 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH-DSVDKIV 164
Query: 64 GRDGYNFDGYRLRVELA 80
+ + +G+ V A
Sbjct: 165 IQKYHTVNGHNCEVRKA 181
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 34.7 bits (78), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 41/86 (47%), Gaps = 11/86 (12%)
Query: 6 SRTLYVGNLPGDTRMREVEDLFYKYG----------PIVDIDL-KIPPRPPGYAFLEFED 54
+ +YV L + ++ D F + G P++ I L K +P G A + +ED
Sbjct: 15 NSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYED 74
Query: 55 YRDAEDAIRGRDGYNFDGYRLRVELA 80
A+ A+ DG +F G +L+V LA
Sbjct: 75 PPTAKAAVEWFDGKDFQGSKLKVSLA 100
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 34.7 bits (78), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 4/77 (5%)
Query: 7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIR 63
+ ++VG + DT + D F +YG I I++ + G+AF+ F+D+ D+ D I
Sbjct: 105 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH-DSVDKIV 163
Query: 64 GRDGYNFDGYRLRVELA 80
+ + +G+ V A
Sbjct: 164 IQKYHTVNGHNCEVRKA 180
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 34.7 bits (78), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 31/57 (54%), Gaps = 3/57 (5%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAI 62
++VG +P + E+ + F K+G + ++ + RP G+ F+ FED + + A+
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV 69
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 34.7 bits (78), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 40/79 (50%), Gaps = 4/79 (5%)
Query: 5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDA 61
+ + ++VG + DT + D F +YG I I++ + G+AF+ F+D+ D+ D
Sbjct: 101 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH-DSVDK 159
Query: 62 IRGRDGYNFDGYRLRVELA 80
I + + +G+ V A
Sbjct: 160 IVIQKYHTVNGHNCEVRKA 178
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 34.3 bits (77), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 35/76 (46%), Gaps = 4/76 (5%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
L+VGNLP D + + LF +YG ++ + R G+ F+ E AE A DG
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFIN---RDRGFGFIRLESRTLAEIAKAELDGT 81
Query: 69 NFDGYRLRVELA-HGG 83
LR+ A HG
Sbjct: 82 ILKSRPLRIRFATHGA 97
>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 = 34.3 bits (77), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 3/75 (4%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVD---IDLKIPPRPPGYAFLEFEDYRDAEDAIRGR 65
++VG+L + +++ F +G I D + + GY F+ F + DAE+AI+
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 66 DGYNFDGYRLRVELA 80
G G ++R A
Sbjct: 78 GGQWLGGRQIRTNWA 92
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 34.3 bits (77), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 3/72 (4%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGR 65
LYVG+L + + +F +G I I L + R GY F+ F D A+ A+
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 66 DGYNFDGYRLRV 77
+G+ G ++V
Sbjct: 89 NGFELAGRPMKV 100
>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 = 33.9 bits (76), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 31/75 (41%), Gaps = 3/75 (4%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGR 65
L V LP + E+ LF G + L K+ GY F+ + +DAE AI
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 66 DGYNFDGYRLRVELA 80
+G ++V A
Sbjct: 82 NGLRLQSKTIKVSYA 96
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 3/75 (4%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVD---IDLKIPPRPPGYAFLEFEDYRDAEDAIRGR 65
++VG+L + +++ F +G I D + + GY F+ F + DAE+AI
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 66 DGYNFDGYRLRVELA 80
G G ++R A
Sbjct: 78 GGQWLGGRQIRTNWA 92
>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 = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 4/75 (5%)
Query: 6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAI 62
+R++YVGN+ E+E F+ G + + + K P G+A++EF D ++
Sbjct: 5 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 64
Query: 63 RGRDGYNFDGYRLRV 77
D F G +++V
Sbjct: 65 -ALDESLFRGRQIKV 78
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 35/78 (44%), Gaps = 3/78 (3%)
Query: 3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAE 59
S S LYVG+L + + +F +G I +I L R GY F+ F D A
Sbjct: 2 SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECAR 61
Query: 60 DAIRGRDGYNFDGYRLRV 77
A+ +G+ G +RV
Sbjct: 62 RALEQLNGFELAGRPMRV 79
>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 = 33.5 bits (75), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 3/63 (4%)
Query: 4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAED 60
+ S +++G L DT + + F KYG + D+ + P R G+ FL FE ++
Sbjct: 1 KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDE 60
Query: 61 AIR 63
++
Sbjct: 61 VVK 63
Score = 31.6 bits (70), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 4/76 (5%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGR 65
++VG + D R +E E+ F ++G I+D L K + G+ F+ + D DA D +
Sbjct: 90 IFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTY-DSADAVDRVCQN 148
Query: 66 DGYNFDGYRLRVELAH 81
+F ++ ++ A
Sbjct: 149 KFIDFKDRKIEIKRAE 164
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 33.1 bits (74), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 35/76 (46%), Gaps = 3/76 (3%)
Query: 5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRG 64
S + LYV NL T +E F P +K + YAF+ F + DA +A++
Sbjct: 14 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK---KIRDYAFVHFSNREDAVEAMKA 70
Query: 65 RDGYNFDGYRLRVELA 80
+G DG + V LA
Sbjct: 71 LNGKVLDGSPIEVTLA 86
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 33.1 bits (74), Expect = 0.17, Method: Composition-based stats.
Identities = 20/84 (23%), Positives = 38/84 (45%), Gaps = 6/84 (7%)
Query: 3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPG------YAFLEFEDYR 56
S S L++ NL T ++ +F K G I + G + F+E++
Sbjct: 2 SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPE 61
Query: 57 DAEDAIRGRDGYNFDGYRLRVELA 80
A+ A++ G+ DG++L V ++
Sbjct: 62 QAQKALKQLQGHTVDGHKLEVRIS 85
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 33.1 bits (74), Expect = 0.17, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 31/57 (54%), Gaps = 2/57 (3%)
Query: 3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAE 59
S S ++VG GD E+ + F +YG ++D+ + P R +AF+ F D + A+
Sbjct: 2 SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFR--AFAFVTFADDQIAQ 56
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 32.7 bits (73), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 35/71 (49%), Gaps = 12/71 (16%)
Query: 7 RTLYVGNLPGDTRMREVEDLFYKYGP-IVDIDLK------IPPRPPGYAFLEFEDYRDAE 59
R ++VG LP D E+ F ++GP +VD K PP+ GYAFL F++ +
Sbjct: 9 RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPK--GYAFLLFQEESSVQ 66
Query: 60 ---DAIRGRDG 67
DA DG
Sbjct: 67 ALIDACLEEDG 77
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 32.7 bits (73), Expect = 0.22, Method: Composition-based stats.
Identities = 24/79 (30%), Positives = 33/79 (41%), Gaps = 3/79 (3%)
Query: 5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDA 61
S L V LP + E + LF G I L KI + GY F+ + D DA+ A
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 62 IRGRDGYNFDGYRLRVELA 80
I +G ++V A
Sbjct: 63 INTLNGLKLQTKTIKVSYA 81
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 32.7 bits (73), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 15/58 (25%), Positives = 32/58 (55%), Gaps = 5/58 (8%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDL-----KIPPRPPGYAFLEFEDYRDAEDA 61
++VG +P +++ +LF +YG + +I++ + PP+ G F+ F + A +A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 32.7 bits (73), Expect = 0.26, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 28/51 (54%), Gaps = 2/51 (3%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAE 59
++VG D E++ F +YG +VD+ + P R +AF+ F D + A+
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFR--AFAFVTFADDKVAQ 62
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 32.3 bits (72), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 32/71 (45%), Gaps = 6/71 (8%)
Query: 4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPI--VDIDLKIPPRPPGYAFLEFEDYRDAEDA 61
R +RTL NLP E++++F I V D + G A++EF+ DAE
Sbjct: 91 RDARTLLAKNLPYKVTQDELKEVFEDAAEIRLVSKD----GKSKGIAYIEFKTEADAEKT 146
Query: 62 IRGRDGYNFDG 72
+ G DG
Sbjct: 147 FEEKQGTEIDG 157
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain
In Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 32.0 bits (71), Expect = 0.44, Method: Composition-based stats.
Identities = 22/78 (28%), Positives = 38/78 (48%), Gaps = 1/78 (1%)
Query: 3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP-RPPGYAFLEFEDYRDAEDA 61
S S ++V NLP D + ++D F + G ++ D+K+ + G ++FE AE A
Sbjct: 2 SSGSSGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERA 61
Query: 62 IRGRDGYNFDGYRLRVEL 79
R +G G + V +
Sbjct: 62 CRMMNGMKLSGREIDVRI 79
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 32.0 bits (71), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 15/58 (25%), Positives = 32/58 (55%), Gaps = 5/58 (8%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDL-----KIPPRPPGYAFLEFEDYRDAEDA 61
++VG +P +++ +LF +YG + +I++ + PP+ G F+ F + A +A
Sbjct: 18 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 75
>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 = 31.6 bits (70), Expect = 0.57, Method: Composition-based stats.
Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 4/75 (5%)
Query: 6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAI 62
+R++YVGN+ E+E F+ G + + + K P G+A++EF D ++
Sbjct: 6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 65
Query: 63 RGRDGYNFDGYRLRV 77
D F G +++V
Sbjct: 66 -ALDESLFRGRQIKV 79
>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 = 31.6 bits (70), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 31/57 (54%), Gaps = 5/57 (8%)
Query: 10 YVGNLPGDTRMREVEDLFYKYGPIVDIDL-----KIPPRPPGYAFLEFEDYRDAEDA 61
+VG +P +++ +LF +YG + +I++ + PP+ G F+ F + A +A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 31.2 bits (69), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 32/70 (45%), Gaps = 3/70 (4%)
Query: 8 TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDG 67
T Y+GN+P ++ LF +G I+D P + G F++++ + A I
Sbjct: 29 TAYIGNIPHFATEADLIPLFQNFGFILDFK-HYPEK--GCCFIKYDTHEQAAVCIVALAN 85
Query: 68 YNFDGYRLRV 77
+ F G LR
Sbjct: 86 FPFQGRNLRT 95
>pdb|2KRB|A Chain A, Solution Structure Of Eif3b-Rrm Bound To Eif3j Peptide
Length = 81
Score = 31.2 bits (69), Expect = 0.64, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 7/70 (10%)
Query: 9 LYVGNLP--GDTRMREVED----LFYKYGPIV-DIDLKIPPRPPGYAFLEFEDYRDAEDA 61
+ V N+P G R+ ++++ +F K+G I D + + GY FLE+ A DA
Sbjct: 4 IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDA 63
Query: 62 IRGRDGYNFD 71
++ DGY D
Sbjct: 64 VKNADGYKLD 73
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 31.2 bits (69), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 38/82 (46%), Gaps = 4/82 (4%)
Query: 4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAED 60
R +RT++ L R R++ED F G + D+ + + R G A++EF + +
Sbjct: 23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPL 82
Query: 61 AIRGRDGYNFDGYRLRVELAHG 82
AI G G G + V+ +
Sbjct: 83 AI-GLTGQRLLGVPIIVQASQA 103
>pdb|2NLW|A Chain A, Solution Structure Of The Rrm Domain Of Human Eukaryotic
Initiation Factor 3b
Length = 105
Score = 31.2 bits (69), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 40/80 (50%), Gaps = 8/80 (10%)
Query: 8 TLYVGNLP--GDTRMREVED----LFYKYGPIV-DIDLKIPPRPPGYAFLEFEDYRDAED 60
+ V N+P G R+ ++++ +F K+G I D + + GY FLE+ A D
Sbjct: 17 VIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVD 76
Query: 61 AIRGRDGYNFDG-YRLRVEL 79
A++ DGY D + RV L
Sbjct: 77 AVKNADGYKLDKQHTFRVNL 96
>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
pdb|3NNH|C Chain C, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
pdb|3NNH|B Chain B, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
pdb|3NNH|D Chain D, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
Length = 88
Score = 30.8 bits (68), Expect = 0.93, Method: Composition-based stats.
Identities = 15/58 (25%), Positives = 32/58 (55%), Gaps = 5/58 (8%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDL-----KIPPRPPGYAFLEFEDYRDAEDA 61
++VG +P +++ +LF +YG + +I++ + PP+ G F+ F + A +A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 30.8 bits (68), Expect = 1.0, Method: Composition-based stats.
Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP-RPPGYAFLEFEDYRDAEDAIRGRDG 67
++V NLP D + ++D F + G ++ D+K+ + G ++FE AE A R +G
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNG 70
Query: 68 YNFDGYRLRVEL 79
G + V +
Sbjct: 71 MKLSGREIDVRI 82
>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: 46 GYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG 83
G+A LE+E AE+A + DG + G LRV G
Sbjct: 227 GFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPG 264
>pdb|2E5J|A Chain A, Solution Structure Of Rna Binding Domain In
Methenyltetrahydrofolate Synthetase Domain Containing
Length = 97
Score = 30.4 bits (67), Expect = 1.1, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 4/73 (5%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPI-VDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDG 67
+YVGNLP D R+ +++ + G + + + + P R AFL + D A+ A+ G
Sbjct: 22 VYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRR---RAFLHYPDSAAAQQAVSCLQG 78
Query: 68 YNFDGYRLRVELA 80
LRV LA
Sbjct: 79 LRLGTDTLRVALA 91
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 4/74 (5%)
Query: 1 MSSRSSRTLYVGNL----PGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYR 56
M ++T+Y+ NL + + + +F ++G I+DI + G AF+ F++
Sbjct: 1 MEMLPNQTIYINNLNEKIKKEELKKSLYAIFSQFGQILDIVALKTLKMRGQAFVIFKEIG 60
Query: 57 DAEDAIRGRDGYNF 70
A +A+R G+ F
Sbjct: 61 SASNALRTMQGFPF 74
>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: 46 GYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG 83
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: 46 GYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG 83
G+A LE+E AE+A + DG + G LRV G
Sbjct: 225 GFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPG 262
>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 = 30.4 bits (67), Expect = 1.2, Method: Composition-based stats.
Identities = 21/75 (28%), Positives = 31/75 (41%), Gaps = 3/75 (4%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGR 65
L V LP + E+ LF G + L K+ GY F+ + +DAE AI
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 66 DGYNFDGYRLRVELA 80
+G ++V A
Sbjct: 67 NGLRLQSKTIKVSYA 81
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 20/84 (23%), Positives = 40/84 (47%), Gaps = 9/84 (10%)
Query: 4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPP------GYAFLEFEDYRD 57
+++ + V N+P RE+ +LF +G + + ++P + G+ F++F +D
Sbjct: 13 QTTSKILVRNIPFQANQREIRELFSTFGELKTV--RLPKKMTGTGAHRGFGFVDFITKQD 70
Query: 58 AEDAIRGR-DGYNFDGYRLRVELA 80
A+ A + G RL +E A
Sbjct: 71 AKKAFNALCHSTHLYGRRLVLEWA 94
>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 = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 6/71 (8%)
Query: 4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPI--VDIDLKIPPRPPGYAFLEFEDYRDAEDA 61
R++RTL NL + E++++F I V D + G A++EF+ DAE
Sbjct: 97 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQD----GKSKGIAYIEFKSEADAEKN 152
Query: 62 IRGRDGYNFDG 72
+ + G DG
Sbjct: 153 LEEKQGAEIDG 163
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 29.3 bits (64), Expect = 2.5, Method: Composition-based stats.
Identities = 19/75 (25%), Positives = 34/75 (45%), Gaps = 2/75 (2%)
Query: 5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL--KIPPRPPGYAFLEFEDYRDAEDAI 62
+ RT++VGNL R + +LF + GP+ + + +P + F+ F+ AI
Sbjct: 15 ADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAI 74
Query: 63 RGRDGYNFDGYRLRV 77
+G G + V
Sbjct: 75 ALLNGIRLYGRPINV 89
>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 = 3.2, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 29/51 (56%), Gaps = 4/51 (7%)
Query: 112 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRD-RGGMT---GIVDYTSYD 158
++V GLP + QDLK++ G+V QV +D + G + G V +T Y+
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYE 68
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 28.9 bits (63), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 31/70 (44%), Gaps = 7/70 (10%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGR 65
L+VG L T + F +YG +VD + K + G+ F++F+D + R
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASR 78
Query: 66 ----DGYNFD 71
DG N D
Sbjct: 79 PHTLDGRNID 88
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 28.5 bits (62), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 40/78 (51%), Gaps = 5/78 (6%)
Query: 8 TLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRG 64
T YVGNLP +T ++ D +K I + L K + G+ ++EF++ ++A+
Sbjct: 17 TAYVGNLPFNTVQGDI-DAIFKDLSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT- 74
Query: 65 RDGYNFDGYRLRVELAHG 82
DG LRV++A G
Sbjct: 75 YDGALLGDRSLRVDIAEG 92
>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 = 28.1 bits (61), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 10/75 (13%)
Query: 8 TLYVGNLPGDTRMREVE--DLFYKYGPIVDIDLKIPPRP---PGYAFLEFEDYRDAEDAI 62
T++VG + D RM E E F +YG + ++ + I R GY F+ F + D + +
Sbjct: 11 TVFVGGI--DVRMDETEIRSFFARYGSVKEVKI-ITDRTGVSKGYGFVSFYNDVDVQKIV 67
Query: 63 RGRDGYNFDGYRLRV 77
+ NF G +L++
Sbjct: 68 ESQ--INFHGKKLKL 80
>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 = 27.7 bits (60), Expect = 7.1, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 10/75 (13%)
Query: 8 TLYVGNLPGDTRMREVE--DLFYKYGPIVDIDLKIPPR---PPGYAFLEFEDYRDAEDAI 62
T++VG + D RM E E F +YG + ++ + I R GY F+ F + D + +
Sbjct: 11 TVFVGGI--DVRMDETEIRSFFARYGSVKEVKI-ITDRTGVSKGYGFVSFYNDVDVQKIV 67
Query: 63 RGRDGYNFDGYRLRV 77
+ NF G +L++
Sbjct: 68 ESQ--INFHGKKLKL 80
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 27.7 bits (60), Expect = 7.5, Method: Composition-based stats.
Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 2/69 (2%)
Query: 4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIR 63
R++RTL NL + E++++F I + + G A++EF+ DAE +
Sbjct: 14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQD--GKSKGIAYIEFKSEADAEKNLE 71
Query: 64 GRDGYNFDG 72
+ G DG
Sbjct: 72 EKQGAEIDG 80
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 27.7 bits (60), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 2/73 (2%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPI--VDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRD 66
L V NL ++++LF ++G + +D R G A + FE DA A++
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 97
Query: 67 GYNFDGYRLRVEL 79
G DG + ++L
Sbjct: 98 GVPLDGRPMDIQL 110
>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 = 7.8, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 46 GYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 80
GY F+ F DA++A+ G + +G LR+ A
Sbjct: 44 GYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 78
>pdb|2HZC|A Chain A, Crystal Structure Of The N-terminal Rrm Of The U2af
Large Subunit
Length = 87
Score = 27.7 bits (60), Expect = 8.1, Method: Composition-based stats.
Identities = 22/84 (26%), Positives = 35/84 (41%), Gaps = 15/84 (17%)
Query: 5 SSRTLYVGNLPGDTRMREVEDLFYKY-----------GPIVDIDLKIPPRPPGYAFLEFE 53
S+R LYVGN+P + D F P++ + + + +AFLEF
Sbjct: 5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN---QDKNFAFLEFR 61
Query: 54 DYRDAEDAIRGRDGYNFDGYRLRV 77
+ A+ DG F G L++
Sbjct: 62 SVDETTQAM-AFDGIIFQGQSLKI 84
>pdb|1U2F|A Chain A, Solution Structure Of The First Rna-Binding Domain Of
Hu2af65
Length = 90
Score = 27.7 bits (60), Expect = 8.4, Method: Composition-based stats.
Identities = 22/87 (25%), Positives = 35/87 (40%), Gaps = 15/87 (17%)
Query: 6 SRTLYVGNLPGDTRMREVEDLFYKY-----------GPIVDIDLKIPPRPPGYAFLEFED 54
+R LYVGN+P + D F P++ + + + +AFLEF
Sbjct: 1 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN---QDKNFAFLEFRS 57
Query: 55 YRDAEDAIRGRDGYNFDGYRLRVELAH 81
+ A+ DG F G L++ H
Sbjct: 58 VDETTQAM-AFDGIIFQGQSLKIRRPH 83
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 27.7 bits (60), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 2/73 (2%)
Query: 9 LYVGNLPGDTRMREVEDLFYKYGPI--VDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRD 66
L V NL ++++LF ++G + +D R G A + FE DA A++
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 97
Query: 67 GYNFDGYRLRVEL 79
G DG + ++L
Sbjct: 98 GVPLDGRPMDIQL 110
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 27.7 bits (60), Expect = 8.4, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 10/75 (13%)
Query: 8 TLYVGNLPGDTRMREVE--DLFYKYGPIVDIDLKIPPR---PPGYAFLEFEDYRDAEDAI 62
T++VG + D RM E E F +YG + ++ + I R GY F+ F + D + +
Sbjct: 12 TVFVGGI--DVRMDETEIRSFFARYGSVKEVKI-ITDRTGVSKGYGFVSFYNDVDVQKIV 68
Query: 63 RGRDGYNFDGYRLRV 77
+ NF G +L++
Sbjct: 69 ESQ--INFHGKKLKL 81
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 27.3 bits (59), Expect = 9.3, Method: Composition-based stats.
Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 6/70 (8%)
Query: 3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRP-----PGYAFLEFEDYRD 57
S S +++GNL + + + D F +G I+ KI P GYAF+ F +
Sbjct: 2 SSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTP-KIMRDPDTGNSKGYAFINFASFDA 60
Query: 58 AEDAIRGRDG 67
++ AI +G
Sbjct: 61 SDAAIEAMNG 70
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
0.323 0.142 0.435
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,151,078
Number of Sequences: 62578
Number of extensions: 195690
Number of successful extensions: 517
Number of sequences better than 100.0: 164
Number of HSP's better than 100.0 without gapping: 92
Number of HSP's successfully gapped in prelim test: 72
Number of HSP's that attempted gapping in prelim test: 331
Number of HSP's gapped (non-prelim): 199
length of query: 297
length of database: 14,973,337
effective HSP length: 98
effective length of query: 199
effective length of database: 8,840,693
effective search space: 1759297907
effective search space used: 1759297907
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)