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= 021599
(310 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 = 75.1 bits (183), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 38/72 (52%), Positives = 50/72 (69%), Gaps = 5/72 (6%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKR-----DFAFVEFSDPRDADDARYSLNG 66
R+YVG L R++D+E++F +YG IRD+D+K FAFVEF DPRDA+DA Y +G
Sbjct: 24 RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDG 83
Query: 67 RDVDGSRIIVEF 78
D DG R+ VEF
Sbjct: 84 YDYDGYRLRVEF 95
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor
9g8
Length = 101
Score = 60.1 bits (144), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 33/72 (45%), Positives = 46/72 (63%), Gaps = 3/72 (4%)
Query: 11 TRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD---FAFVEFSDPRDADDARYSLNGR 67
++YVG L + +LE FS YG +R V + R+ FAFVEF DPRDA+DA L+G+
Sbjct: 1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGK 60
Query: 68 DVDGSRIIVEFA 79
+ GSR+ VE +
Sbjct: 61 VICGSRVRVELS 72
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 58.5 bits (140), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 32/71 (45%), Positives = 43/71 (60%), Gaps = 3/71 (4%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD---FAFVEFSDPRDADDARYSLNGRD 68
++YVG L + +LE F YG +R V + R+ FAFVEF DPRDA DA L+GR
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRT 134
Query: 69 VDGSRIIVEFA 79
+ G R+ VE +
Sbjct: 135 LCGCRVRVELS 145
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 58.5 bits (140), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 30/76 (39%), Positives = 47/76 (61%), Gaps = 8/76 (10%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDARYS 63
+L+VG L+ T + LE++FS+YG+I +V + +D F FV F + DA DA +
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 64 LNGRDVDGSRIIVEFA 79
+NG+ VDG +I V+ A
Sbjct: 74 MNGKSVDGRQIRVDQA 89
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 58.2 bits (139), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 32/71 (45%), Positives = 43/71 (60%), Gaps = 3/71 (4%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD---FAFVEFSDPRDADDARYSLNGRD 68
++YVG L + +LE F YG +R V + R+ FAFVEF DPRDA DA L+GR
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRDLDGRT 134
Query: 69 VDGSRIIVEFA 79
+ G R+ VE +
Sbjct: 135 LCGCRVRVELS 145
>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 = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 33/82 (40%), Positives = 44/82 (53%), Gaps = 8/82 (9%)
Query: 6 DRYGGTRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDA 57
D G T L V L RT L +F +YGR+ DV + RD FAFV F D RDA
Sbjct: 43 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDA 102
Query: 58 DDARYSLNGRDVDGSRIIVEFA 79
+DA +++G +DG + V+ A
Sbjct: 103 EDAMDAMDGAVLDGRELRVQMA 124
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 52.4 bits (124), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 32/75 (42%), Positives = 43/75 (57%), Gaps = 8/75 (10%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIRDVDM--------KRDFAFVEFSDPRDADDARYSL 64
L V L+ T RDL E+FS+YG I DV + R FAFV F + DA +A+
Sbjct: 49 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 108
Query: 65 NGRDVDGSRIIVEFA 79
NG ++DG RI V+F+
Sbjct: 109 NGMELDGRRIRVDFS 123
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 52.0 bits (123), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 32/79 (40%), Positives = 43/79 (54%), Gaps = 8/79 (10%)
Query: 9 GGTRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDA 60
G T L V L RT L +F +YGR+ DV + RD FAFV F D RDA+DA
Sbjct: 69 GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDA 128
Query: 61 RYSLNGRDVDGSRIIVEFA 79
+++G +DG + V+ A
Sbjct: 129 MDAMDGAVLDGRELRVQMA 147
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 52.0 bits (123), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 42/75 (56%), Gaps = 7/75 (9%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD-------FAFVEFSDPRDADDARYSL 64
+L++G L T + L+ +F ++G I +V + +D FAF+ F +P DA +A +
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDM 68
Query: 65 NGRDVDGSRIIVEFA 79
NG+ + G I VE A
Sbjct: 69 NGKSLHGKAIKVEQA 83
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 51.6 bits (122), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 32/75 (42%), Positives = 43/75 (57%), Gaps = 8/75 (10%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDARYSL 64
L V L+ T RDL E+FS+YG I DV + D FAFV F + DA +A+
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 65 NGRDVDGSRIIVEFA 79
NG ++DG RI V+F+
Sbjct: 78 NGMELDGRRIRVDFS 92
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Rna-Binding Protein 14
Length = 90
Score = 51.6 bits (122), Expect = 6e-07, Method: Composition-based stats.
Identities = 25/68 (36%), Positives = 42/68 (61%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRDFAFVEFSDPRDADDARYSLNGRDVDG 71
+++VG +++ S++L +F R GR+ + D+ +D+AFV DA A LNG++V G
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVVKDYAFVHMEKEADAKAAIAQLNGKEVKG 70
Query: 72 SRIIVEFA 79
RI VE +
Sbjct: 71 KRINVELS 78
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 51.2 bits (121), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 32/75 (42%), Positives = 43/75 (57%), Gaps = 8/75 (10%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDARYSL 64
L V L+ T RDL E+FS+YG I DV + D FAFV F + DA +A+
Sbjct: 15 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 74
Query: 65 NGRDVDGSRIIVEFA 79
NG ++DG RI V+F+
Sbjct: 75 NGMELDGRRIRVDFS 89
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 41/70 (58%), Gaps = 1/70 (1%)
Query: 11 TRLYVGRL-ASRTRSRDLEEIFSRYGRIRDVDMKRDFAFVEFSDPRDADDARYSLNGRDV 69
+R+++G L + + D+E IFS+YGR+ + + +AFV++S+ R A A NGR +
Sbjct: 28 SRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKGYAFVQYSNERHARAAVLGENGRVL 87
Query: 70 DGSRIIVEFA 79
G + + A
Sbjct: 88 AGQTLDINMA 97
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 49.7 bits (117), Expect = 2e-06, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 41/73 (56%), Gaps = 9/73 (12%)
Query: 11 TRLYVGRLASRTRSRDLEEIFSRYGRIRDVDM---------KRDFAFVEFSDPRDADDAR 61
T++++GRL + EIFS YG+I+ +DM + +A+VEF +P +A+ A
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
Query: 62 YSLNGRDVDGSRI 74
++G +DG I
Sbjct: 65 KHMDGGQIDGQEI 77
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 30/79 (37%), Positives = 42/79 (53%), Gaps = 8/79 (10%)
Query: 9 GGTRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDA 60
G L V L RT L +F +YGR+ DV + R+ FAFV F D RDA DA
Sbjct: 12 GMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDA 71
Query: 61 RYSLNGRDVDGSRIIVEFA 79
+++G ++DG + V+ A
Sbjct: 72 EAAMDGAELDGRELRVQVA 90
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 31/72 (43%), Positives = 40/72 (55%), Gaps = 8/72 (11%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIRDVDM--------KRDFAFVEFSDPRDADDARYSL 64
L V L+ T RDL E+FS+YG I DV + R FAFV F + DA +A+
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 65 NGRDVDGSRIIV 76
NG ++DG RI V
Sbjct: 78 NGMELDGRRIRV 89
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 48.1 bits (113), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 44/78 (56%), Gaps = 1/78 (1%)
Query: 3 RYDDRYGGTRLYVGRLASRT-RSRDLEEIFSRYGRIRDVDMKRDFAFVEFSDPRDADDAR 61
+ D R +R+++G L + + D+E IFS+YG+I + + FAFV++ + R+A A
Sbjct: 8 KTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERNARAAV 67
Query: 62 YSLNGRDVDGSRIIVEFA 79
+GR + G + + A
Sbjct: 68 AGEDGRMIAGQVLDINLA 85
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 48.1 bits (113), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 41/71 (57%), Gaps = 6/71 (8%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRYGRIRDVDM------KRDFAFVEFSDPRDADDARYSLN 65
RL+V + R R DL ++F ++G+I DV++ + F FV F + DAD AR L+
Sbjct: 31 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLH 90
Query: 66 GRDVDGSRIIV 76
G V+G +I V
Sbjct: 91 GTVVEGRKIEV 101
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 48.1 bits (113), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 41/71 (57%), Gaps = 6/71 (8%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRYGRIRDVDM------KRDFAFVEFSDPRDADDARYSLN 65
RL+V + R R DL ++F ++G+I DV++ + F FV F + DAD AR L+
Sbjct: 17 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLH 76
Query: 66 GRDVDGSRIIV 76
G V+G +I V
Sbjct: 77 GTVVEGRKIEV 87
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 44.7 bits (104), Expect = 7e-05, Method: Composition-based stats.
Identities = 26/90 (28%), Positives = 43/90 (47%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRDFAFVEFSDPRDADDARYSLNGRDVDGS 72
L+V LA+ LE+ FS++G++ V +D+AF+ F + A A +NG+D++G
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKDYAFIHFDERDGAVKAMEEMNGKDLEGE 73
Query: 73 RIIVEFAXXXXXXXXXSREYLGRGPPPGSG 102
I + FA + P SG
Sbjct: 74 NIEIVFAKPPDQKRKERKAQRQAASGPSSG 103
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 43.1 bits (100), Expect = 2e-04, Method: Composition-based stats.
Identities = 20/51 (39%), Positives = 32/51 (62%), Gaps = 1/51 (1%)
Query: 11 TRLYVGRLASRTRSR-DLEEIFSRYGRIRDVDMKRDFAFVEFSDPRDADDA 60
+RL++G L + S+ DL IFS YG I +++K F F++F +P+ DA
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDA 73
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 43.1 bits (100), Expect = 2e-04, Method: Composition-based stats.
Identities = 20/51 (39%), Positives = 32/51 (62%), Gaps = 1/51 (1%)
Query: 11 TRLYVGRLASRTRSR-DLEEIFSRYGRIRDVDMKRDFAFVEFSDPRDADDA 60
+RL++G L + S+ DL IFS YG I +++K F F++F +P+ DA
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDA 73
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 43.1 bits (100), Expect = 2e-04, Method: Composition-based stats.
Identities = 20/51 (39%), Positives = 32/51 (62%), Gaps = 1/51 (1%)
Query: 11 TRLYVGRLASRTRSR-DLEEIFSRYGRIRDVDMKRDFAFVEFSDPRDADDA 60
+RL++G L + S+ DL IFS YG I +++K F F++F +P+ DA
Sbjct: 3 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDA 53
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 40/73 (54%), Gaps = 9/73 (12%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDARYSL 64
++ +LA+R R RDLE+ FS G++RDV + D A+VEF + + A L
Sbjct: 28 VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLA-IGL 86
Query: 65 NGRDVDGSRIIVE 77
G+ + G IIV+
Sbjct: 87 TGQRLLGVPIIVQ 99
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 42.4 bits (98), Expect = 3e-04, Method: Composition-based stats.
Identities = 20/51 (39%), Positives = 32/51 (62%), Gaps = 1/51 (1%)
Query: 11 TRLYVGRLASRTRSR-DLEEIFSRYGRIRDVDMKRDFAFVEFSDPRDADDA 60
+RL++G L + S+ DL IFS YG I +++K F F++F +P+ DA
Sbjct: 11 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDA 61
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 42.0 bits (97), Expect = 5e-04, Method: Composition-based stats.
Identities = 19/69 (27%), Positives = 38/69 (55%)
Query: 9 GGTRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRDFAFVEFSDPRDADDARYSLNGRD 68
G +L++G L +++ +F +YG++ + D+ +++ FV D A+DA +L+
Sbjct: 7 GMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAIRNLHHYK 66
Query: 69 VDGSRIIVE 77
+ G I VE
Sbjct: 67 LHGVNINVE 75
>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 = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 37/71 (52%), Gaps = 9/71 (12%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDARYSL 64
LYVG L+ T + E+FS+ G I+ + M D F FVE+ DA++A +
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 65 NGRDVDGSRII 75
NG +D RII
Sbjct: 102 NGTRLD-DRII 111
>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 = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 35/74 (47%), Gaps = 8/74 (10%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIRDVDM--------KRDFAFVEFSDPRDADDARYSL 64
L+V R+ T L F YG I+ + M R +AF+E+ RD A
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 65 NGRDVDGSRIIVEF 78
+G+ +DG R++V+
Sbjct: 165 DGKKIDGRRVLVDV 178
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 33/66 (50%)
Query: 3 RYDDRYGGTRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRDFAFVEFSDPRDADDARY 62
R + TRL+V + +L EIF +G +++V + FAFVEF + A A
Sbjct: 24 RQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNGFAFVEFEEAESAAKAIE 83
Query: 63 SLNGRD 68
++G+
Sbjct: 84 EVHGKS 89
>pdb|1BJ6|A Chain A, 1h Nmr Of (12-53) Ncp7D(ACGCC) COMPLEX, 10 STRUCTURES
pdb|1ESK|A Chain A, Solution Structure Of Ncp7 From Hiv-1
Length = 42
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 18/37 (48%), Positives = 27/37 (72%), Gaps = 1/37 (2%)
Query: 103 RCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNC 139
+CFNCG +GH AR+C+A K C++CG+ GH ++C
Sbjct: 3 KCFNCGKEGHTARNCRAPR-KKGCWKCGKEGHQMKDC 38
Score = 27.7 bits (60), Expect = 8.2, Method: Composition-based stats.
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 125 KCYRCGERGHIERNCQNSPKK 145
KC+ CG+ GH RNC+ KK
Sbjct: 3 KCFNCGKEGHTARNCRAPRKK 23
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 28/69 (40%), Positives = 39/69 (56%), Gaps = 2/69 (2%)
Query: 13 LYVGRLASRTRSRDLEEIFS--RYGRIRDVDMKRDFAFVEFSDPRDADDARYSLNGRDVD 70
LYV L T +E+ F+ + G + V RD+AFV FS+ DA +A +LNG+ +D
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLD 77
Query: 71 GSRIIVEFA 79
GS I V A
Sbjct: 78 GSPIEVTLA 86
>pdb|2EXF|A Chain A, Solution Structure Of The Hiv-1 Nucleocapsid (Ncp7(12-55))
Complexed With The Dna (-) Primer Binding Site
pdb|2JZW|A Chain A, How The Hiv-1 Nucleocapsid Protein Binds And Destabilises
The (-)primer Binding Site During Reverse Transcription
Length = 44
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 18/37 (48%), Positives = 27/37 (72%), Gaps = 1/37 (2%)
Query: 103 RCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNC 139
+CFNCG +GH AR+C+A K C++CG+ GH ++C
Sbjct: 3 KCFNCGKEGHTARNCRAPR-KKGCWKCGKEGHQMKDC 38
Score = 27.7 bits (60), Expect = 8.5, Method: Composition-based stats.
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 125 KCYRCGERGHIERNCQNSPKK 145
KC+ CG+ GH RNC+ KK
Sbjct: 3 KCFNCGKEGHTARNCRAPRKK 23
>pdb|2L4L|A Chain A, Structural Insights Into The Ctar Dna Recognition By The
Hiv-1 Nucleocapsid Protein: Role Of Sugar Deoxyriboses
In The Binding Polarity Of Nc
Length = 45
Score = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 18/37 (48%), Positives = 27/37 (72%), Gaps = 1/37 (2%)
Query: 103 RCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNC 139
+CFNCG +GH AR+C+A K C++CG+ GH ++C
Sbjct: 4 KCFNCGKEGHTARNCRAPR-KKGCWKCGKEGHQMKDC 39
Score = 27.7 bits (60), Expect = 9.2, Method: Composition-based stats.
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 125 KCYRCGERGHIERNCQNSPKK 145
KC+ CG+ GH RNC+ KK
Sbjct: 4 KCFNCGKEGHTARNCRAPRKK 24
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 8/77 (10%)
Query: 10 GTRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDAR 61
G L+V + + +++E F YG I+++ + D +A VE+ + A A+
Sbjct: 26 GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 85
Query: 62 YSLNGRDVDGSRIIVEF 78
+LNG ++ G I V++
Sbjct: 86 EALNGAEIMGQTIQVDW 102
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 25/90 (27%), Positives = 43/90 (47%), Gaps = 8/90 (8%)
Query: 11 TRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRDFAFVEFSDPRDADDARYSLNGRDVD 70
T+L+VG ++ +++L F YG + + D+ +D+AFV DA +A L+ +
Sbjct: 11 TKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKDYAFVHMERAEDAVEAIRGLDNTEFQ 70
Query: 71 GSRIIVEFAXXXXXXXXXSREYLGRGPPPG 100
G R+ V+ + SR GP G
Sbjct: 71 GKRMHVQLS--------TSRLRTASGPSSG 92
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 36/64 (56%), Gaps = 2/64 (3%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIRDVDM--KRDFAFVEFSDPRDADDARYSLNGRDVD 70
+Y G +AS + + + FS +G+I ++ + ++ ++FV FS A A S+NG ++
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIE 87
Query: 71 GSRI 74
G +
Sbjct: 88 GHVV 91
>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 = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 39/76 (51%), Gaps = 8/76 (10%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRDFA--------FVEFSDPRDADDARYS 63
++VG L+ + D++ F+ +GRI D + +D A FV F + DA++A
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 64 LNGRDVDGSRIIVEFA 79
+ G+ + G +I +A
Sbjct: 77 MGGQWLGGRQIRTNWA 92
>pdb|2M3Z|A Chain A, Nmr Solution Structure Of Hiv-1 Nucleocapsid Protein In
Complex With An Inhibitor Displaying A 2 Inhibitors:1 Nc
Stoichiometry
Length = 55
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 17/37 (45%), Positives = 27/37 (72%), Gaps = 1/37 (2%)
Query: 103 RCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNC 139
+CFNCG +GH A++C+A K C++CG+ GH ++C
Sbjct: 14 KCFNCGKEGHIAKNCRAPR-KKGCWKCGKEGHQMKDC 49
Score = 28.5 bits (62), Expect = 4.6, Method: Composition-based stats.
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 125 KCYRCGERGHIERNCQNSPKK 145
KC+ CG+ GHI +NC+ KK
Sbjct: 14 KCFNCGKEGHIAKNCRAPRKK 34
>pdb|1F6U|A Chain A, Nmr Structure Of The Hiv-1 Nucleocapsid Protein Bound To
Stem-Loop Sl2 Of The Psi-Rna Packaging Signal.
Implications For Genome Recognition
Length = 56
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 17/37 (45%), Positives = 27/37 (72%), Gaps = 1/37 (2%)
Query: 103 RCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNC 139
+CFNCG +GH A++C+A K C++CG+ GH ++C
Sbjct: 14 KCFNCGKEGHIAKNCRAPR-KKGCWKCGKEGHQMKDC 49
Score = 28.5 bits (62), Expect = 5.1, Method: Composition-based stats.
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 125 KCYRCGERGHIERNCQNSPKK 145
KC+ CG+ GHI +NC+ KK
Sbjct: 14 KCFNCGKEGHIAKNCRAPRKK 34
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 35/63 (55%), Gaps = 7/63 (11%)
Query: 10 GTRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMK---RDFAFVEFSDPRDADDARYSLNG 66
G++++VGR + +L++ F +YG + DV + R FAFV F+D D SL G
Sbjct: 11 GSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFAD----DKVAQSLCG 66
Query: 67 RDV 69
D+
Sbjct: 67 EDL 69
>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 = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 41/77 (53%), Gaps = 10/77 (12%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIRD----VD----MKRDFAFVEFSDPRDADDARYSL 64
LY+ L +D+E++FSR+GRI + VD + R AF+ F +A++A S
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 65 NGRDVDGSR--IIVEFA 79
NG GS I V+FA
Sbjct: 151 NGHKPPGSSEPITVKFA 167
Score = 33.5 bits (75), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 33/79 (41%), Gaps = 8/79 (10%)
Query: 9 GGTRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDA 60
G T L V L +L +FS G + + RD + FV + +DA+ A
Sbjct: 1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 61 RYSLNGRDVDGSRIIVEFA 79
+LNG + I V +A
Sbjct: 61 INTLNGLRLQSKTIKVSYA 79
>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 = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 8/73 (10%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIRDVDM--------KRDFAFVEFSDPRDADDARYSL 64
L+V R+ T L F YG I+ + M R +AF+E+ RD A
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 65 NGRDVDGSRIIVE 77
+G+ +DG R++V+
Sbjct: 165 DGKKIDGRRVLVD 177
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 6/73 (8%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD------FAFVEFSDPRDADDARYSLNG 66
LYVG L+ + ++FS+ G + M + + FVEF + RDA A ++NG
Sbjct: 18 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNG 77
Query: 67 RDVDGSRIIVEFA 79
R + G + V +A
Sbjct: 78 RKILGKEVKVNWA 90
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 31/71 (43%), Gaps = 8/71 (11%)
Query: 9 GGTRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDA 60
G RLYVG L L IF +GRI + + D + F+ FSD A A
Sbjct: 25 GPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKA 84
Query: 61 RYSLNGRDVDG 71
LNG ++ G
Sbjct: 85 LEQLNGFELAG 95
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With
The Au-Rich Element
Length = 174
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 33/77 (42%), Gaps = 8/77 (10%)
Query: 11 TRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDARY 62
T L V L + + +F G I + RD + FV +SDP DAD A
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 63 SLNGRDVDGSRIIVEFA 79
+LNG + I V +A
Sbjct: 65 TLNGLKLQTKTIKVSYA 81
Score = 37.4 bits (85), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 10/77 (12%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRI--------RDVDMKRDFAFVEFSDPRDADDARYSL 64
LYV L +++E++FS+YGRI + + R F+ F +A++A L
Sbjct: 93 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 152
Query: 65 NGRDVDGSR--IIVEFA 79
NG+ G+ I V+FA
Sbjct: 153 NGQKPLGAAEPITVKFA 169
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 34/71 (47%), Gaps = 12/71 (16%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDAR-- 61
+L+VG L T L FS+YG + D + +D F FV+F DP
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 62 --YSLNGRDVD 70
++L+GR++D
Sbjct: 78 RPHTLDGRNID 88
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 39/76 (51%), Gaps = 8/76 (10%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRDFA--------FVEFSDPRDADDARYS 63
++VG L+ + D++ F+ +G+I D + +D A FV F + DA++A
Sbjct: 17 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 64 LNGRDVDGSRIIVEFA 79
+ G+ + G +I +A
Sbjct: 77 MGGQWLGGRQIRTNWA 92
>pdb|1A1T|A Chain A, Structure Of The Hiv-1 Nucleocapsid Protein Bound To The
Sl3 Psi-Rna Recognition Element, Nmr, 25 Structures
pdb|1MFS|A Chain A, Dynamical Behavior Of The Hiv-1 Nucleocapsid Protein; Nmr,
30 Structures
Length = 55
Score = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 17/37 (45%), Positives = 27/37 (72%), Gaps = 1/37 (2%)
Query: 103 RCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNC 139
+CFNCG +GH A++C+A K C++CG+ GH ++C
Sbjct: 14 KCFNCGKEGHIAKNCRAPR-KKGCWKCGKEGHQMKDC 49
Score = 28.1 bits (61), Expect = 6.4, Method: Composition-based stats.
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 125 KCYRCGERGHIERNCQNSPKK 145
KC+ CG+ GHI +NC+ KK
Sbjct: 14 KCFNCGKEGHIAKNCRAPRKK 34
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 40/77 (51%), Gaps = 10/77 (12%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIRD----VD----MKRDFAFVEFSDPRDADDARYSL 64
LY+ L +D+E++FSR+GRI + VD + R AF+ F +A++A S
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 65 NGRDVDGSR--IIVEFA 79
NG GS I V FA
Sbjct: 151 NGHKPPGSSEPITVXFA 167
Score = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 33/79 (41%), Gaps = 8/79 (10%)
Query: 9 GGTRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDA 60
G T L V L +L +FS G + + RD + FV + +DA+ A
Sbjct: 1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 61 RYSLNGRDVDGSRIIVEFA 79
+LNG + I V +A
Sbjct: 61 INTLNGLRLQSKTIKVSYA 79
>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 = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 8/77 (10%)
Query: 10 GTRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDAR 61
G L+V + D+ + F+ YG I+++ + D + VE+ ++A A
Sbjct: 23 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 82
Query: 62 YSLNGRDVDGSRIIVEF 78
LNG+D+ G I V++
Sbjct: 83 EGLNGQDLMGQPISVDW 99
>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 = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 8/77 (10%)
Query: 10 GTRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDAR 61
G L+V + + +++E F YG I+++ + D +A VE+ + A A+
Sbjct: 72 GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 131
Query: 62 YSLNGRDVDGSRIIVEF 78
+LNG ++ G I V++
Sbjct: 132 EALNGAEIMGQTIQVDW 148
>pdb|1AAF|A Chain A, Nucleocapsid Zinc Fingers Detected In Retroviruses: Exafs
Studies On Intact Viruses And The Solution-State
Structure Of The Nucleocapsid Protein From Hiv-1
Length = 55
Score = 38.9 bits (89), Expect = 0.003, Method: Composition-based stats.
Identities = 17/37 (45%), Positives = 27/37 (72%), Gaps = 1/37 (2%)
Query: 103 RCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNC 139
+CFNCG +GH A++C+A K C++CG+ GH ++C
Sbjct: 14 KCFNCGKEGHIAKNCRAPR-KRGCWKCGKEGHQMKDC 49
>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos
Rna
pdb|1G2E|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The Tumor
Necrosis Factor Alpha Rna
Length = 167
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 40/77 (51%), Gaps = 10/77 (12%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIRD----VD----MKRDFAFVEFSDPRDADDARYSL 64
LYV L ++LE++FS+YGRI VD + R F+ F +A++A L
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 65 NGRDVDGSR--IIVEFA 79
NG+ G+ I V+FA
Sbjct: 151 NGQKPSGATEPITVKFA 167
Score = 36.6 bits (83), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 32/77 (41%), Gaps = 8/77 (10%)
Query: 11 TRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDARY 62
T L V L + +F G I + RD + FV + DP+DA+ A
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 63 SLNGRDVDGSRIIVEFA 79
+LNG + I V +A
Sbjct: 63 TLNGLRLQTKTIKVSYA 79
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 33/64 (51%), Gaps = 7/64 (10%)
Query: 9 GGTRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMK---RDFAFVEFSDPRDADDARYSLN 65
G + ++VGR +L E FS+YG + DV + R FAFV F+D D SL
Sbjct: 4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFAD----DQIAQSLC 59
Query: 66 GRDV 69
G D+
Sbjct: 60 GEDL 63
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 8/77 (10%)
Query: 10 GTRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDAR 61
G L+V + D+ + F+ YG I+++ + D + VE+ ++A A
Sbjct: 22 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 81
Query: 62 YSLNGRDVDGSRIIVEF 78
LNG+D+ G I V++
Sbjct: 82 EGLNGQDLMGQPISVDW 98
>pdb|2EC7|A Chain A, Solution Structure Of Human Immunodificiency Virus Type-2
Nucleocapsid Protein
Length = 49
Score = 38.5 bits (88), Expect = 0.005, Method: Composition-based stats.
Identities = 17/37 (45%), Positives = 25/37 (67%), Gaps = 1/37 (2%)
Query: 103 RCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNC 139
RC+NCG +GH AR C+A + C++CG+ GH+ C
Sbjct: 8 RCWNCGKEGHSARQCRAPR-RQGCWKCGKTGHVMAKC 43
>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 = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 8/77 (10%)
Query: 10 GTRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDAR 61
G L+V + D+ + F+ YG I+++ + D + VE+ ++A A
Sbjct: 7 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 62 YSLNGRDVDGSRIIVEF 78
LNG+D+ G I V++
Sbjct: 67 EGLNGQDLMGQPISVDW 83
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 38.1 bits (87), Expect = 0.006, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 31/57 (54%)
Query: 11 TRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRDFAFVEFSDPRDADDARYSLNGR 67
TRL+V + +L EIF +G +++V + FAFVEF + A A ++G+
Sbjct: 5 TRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNGFAFVEFEEAESAAKAIEEVHGK 61
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 7/74 (9%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD-------FAFVEFSDPRDADDARYSLN 65
LYVG L L++ F G I ++ + D +AFVE+ DA+ A +LN
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 66 GRDVDGSRIIVEFA 79
G+ ++ + + + +A
Sbjct: 63 GKQIENNIVKINWA 76
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 34/75 (45%), Gaps = 8/75 (10%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDARYSL 64
LYVG LA + L F +G I D+ + D FAFVEF DA A ++
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 65 NGRDVDGSRIIVEFA 79
N ++ G I V A
Sbjct: 126 NESELFGRTIRVNLA 140
>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 = 37.7 bits (86), Expect = 0.007, Method: Composition-based stats.
Identities = 26/70 (37%), Positives = 37/70 (52%), Gaps = 8/70 (11%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD-------FAFVEFSDPRDADDARYSLN 65
LYVG L+ T + E+FS+ G I+ + M D F FVE+ DA++A +N
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMRYIN 80
Query: 66 GRDVDGSRII 75
G +D RII
Sbjct: 81 GTRLD-DRII 89
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 37.7 bits (86), Expect = 0.008, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 33/77 (42%), Gaps = 8/77 (10%)
Query: 11 TRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDARY 62
T L V L + + +F G I + RD + FV +SDP DAD A
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 63 SLNGRDVDGSRIIVEFA 79
+LNG + I V +A
Sbjct: 65 TLNGLKLQTKTIKVSYA 81
>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex
With Rna
pdb|2KM8|C Chain C, Interdomain Rrm Packing Contributes To Rna Recognition
In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 167
Score = 37.0 bits (84), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 11/75 (14%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDA--- 60
++++G L T +L E F +YG + D+ + +D F F+ F P D+
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 61 RYSLNGRDVDGSRII 75
++ L+G+ +D R I
Sbjct: 65 QHILDGKVIDPKRAI 79
Score = 30.8 bits (68), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 9/56 (16%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADD 59
+++VG + R ++ EE FS++G I D + D F FV + D DA D
Sbjct: 89 KIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTY-DSADAVD 143
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet
Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 37.0 bits (84), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 18/77 (23%), Positives = 35/77 (45%), Gaps = 8/77 (10%)
Query: 10 GTRLYVGRLASRTRSRDLEEIFSRYGRI--------RDVDMKRDFAFVEFSDPRDADDAR 61
G L++ L +DL ++F +G + + ++ + F FV + +P A A
Sbjct: 25 GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAI 84
Query: 62 YSLNGRDVDGSRIIVEF 78
S+NG + R+ V+
Sbjct: 85 QSMNGFQIGMKRLKVQL 101
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 37.0 bits (84), Expect = 0.015, Method: Composition-based stats.
Identities = 22/82 (26%), Positives = 35/82 (42%), Gaps = 11/82 (13%)
Query: 9 GGTRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD-----------FAFVEFSDPRDA 57
G + L++ L T L+ +FS+ G I+ + + F FVE+ P A
Sbjct: 4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQA 63
Query: 58 DDARYSLNGRDVDGSRIIVEFA 79
A L G VDG ++ V +
Sbjct: 64 QKALKQLQGHTVDGHKLEVRIS 85
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 37.0 bits (84), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 8/74 (10%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIRDVDMK--------RDFAFVEFSDPRDADDARYSL 64
LY+ L+ R RDL +F+R+ + ++ R AF+ F + A A + +
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87
Query: 65 NGRDVDGSRIIVEF 78
NG + G +++EF
Sbjct: 88 NGYKLYGKILVIEF 101
>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 = 36.6 bits (83), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 34/74 (45%), Gaps = 8/74 (10%)
Query: 11 TRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDARY 62
+R+YVG + + + F+ +G I+ +DM D FAFVE+ P A A
Sbjct: 29 SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 88
Query: 63 SLNGRDVDGSRIIV 76
+N + G I V
Sbjct: 89 QMNSVMLGGRNIKV 102
Score = 36.6 bits (83), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 34/71 (47%), Gaps = 8/71 (11%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDARYS 63
R+YV + D++ +F +G+I+ + RD + F+E+ + + DA S
Sbjct: 127 RIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 186
Query: 64 LNGRDVDGSRI 74
+N D+ G +
Sbjct: 187 MNLFDLGGQYL 197
>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 = 36.6 bits (83), Expect = 0.017, Method: Composition-based stats.
Identities = 26/75 (34%), Positives = 34/75 (45%), Gaps = 8/75 (10%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIRDVDM--------KRDFAFVEFSDPRDADDARYSL 64
LYVG LA + L F +G I D+ + R FAFVEF DA A ++
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 65 NGRDVDGSRIIVEFA 79
N ++ G I V A
Sbjct: 70 NESELFGRTIRVNLA 84
>pdb|1Q3Y|A Chain A, Nmr Structure Of The Cys28his Mutant (D Form) Of The
Nucleocapsid Protein Ncp7 Of Hiv-1.
pdb|1Q3Z|A Chain A, Nmr Structure Of The Cys28his Mutant (e Form) Of The
Nucleocapsid Protein Ncp7 Of Hiv-1
Length = 42
Score = 36.6 bits (83), Expect = 0.019, Method: Composition-based stats.
Identities = 17/37 (45%), Positives = 26/37 (70%), Gaps = 1/37 (2%)
Query: 103 RCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNC 139
+CFNCG +GH AR+ +A K C++CG+ GH ++C
Sbjct: 3 KCFNCGKEGHTARNHRAPR-KKGCWKCGKEGHQMKDC 38
>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 = 36.2 bits (82), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 17/77 (22%), Positives = 38/77 (49%), Gaps = 8/77 (10%)
Query: 9 GGTRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDA 60
G +L++G L + ++E+ + +G ++ ++ +D +AF E+ D D A
Sbjct: 95 GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 154
Query: 61 RYSLNGRDVDGSRIIVE 77
LNG + +++V+
Sbjct: 155 IAGLNGMQLGDKKLLVQ 171
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 36.2 bits (82), Expect = 0.023, Method: Composition-based stats.
Identities = 26/75 (34%), Positives = 34/75 (45%), Gaps = 8/75 (10%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIRDVDM--------KRDFAFVEFSDPRDADDARYSL 64
LYVG LA + L F +G I D+ + R FAFVEF DA A ++
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 65 NGRDVDGSRIIVEFA 79
N ++ G I V A
Sbjct: 68 NESELFGRTIRVNLA 82
>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 = 36.2 bits (82), Expect = 0.023, Method: Composition-based stats.
Identities = 26/75 (34%), Positives = 34/75 (45%), Gaps = 8/75 (10%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIRDVDM--------KRDFAFVEFSDPRDADDARYSL 64
LYVG LA + L F +G I D+ + R FAFVEF DA A ++
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 65 NGRDVDGSRIIVEFA 79
N ++ G I V A
Sbjct: 65 NESELFGRTIRVNLA 79
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 36.2 bits (82), Expect = 0.026, Method: Composition-based stats.
Identities = 20/55 (36%), Positives = 30/55 (54%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRDFAFVEFSDPRDADDARYSLNGR 67
L+V LA+ LE+ FS +G++ V +D+AFV F D A A +NG+
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKDYAFVHFEDRGAAVKAMDEMNGK 72
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 36.2 bits (82), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 17/77 (22%), Positives = 38/77 (49%), Gaps = 8/77 (10%)
Query: 9 GGTRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDA 60
G +L++G L + ++E+ + +G ++ ++ +D +AF E+ D D A
Sbjct: 93 GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 152
Query: 61 RYSLNGRDVDGSRIIVE 77
LNG + +++V+
Sbjct: 153 IAGLNGMQLGDKKLLVQ 169
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 35.8 bits (81), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 2/70 (2%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--FAFVEFSDPRDADDARYSLNGRDV 69
RL+VG L + D + +F RYG +V + RD F F+ A+ A+ L+G +
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTIL 83
Query: 70 DGSRIIVEFA 79
+ + FA
Sbjct: 84 KSRPLRIRFA 93
>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 = 35.8 bits (81), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 33/73 (45%), Gaps = 8/73 (10%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDARYS 63
R+YVG + + + F+ +G I+ +DM D FAFVE+ P A A
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 64 LNGRDVDGSRIIV 76
+N + G I V
Sbjct: 75 MNSVMLGGRNIKV 87
Score = 35.8 bits (81), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 34/71 (47%), Gaps = 8/71 (11%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDARYS 63
R+YV + D++ +F +G+I+ + RD + F+E+ + + DA S
Sbjct: 112 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 171
Query: 64 LNGRDVDGSRI 74
+N D+ G +
Sbjct: 172 MNLFDLGGQYL 182
>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
pdb|1HD1|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
Length = 75
Score = 35.8 bits (81), Expect = 0.030, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 12/73 (16%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIRDVDMK--------RDFAFVEFSDPRDADDA---- 60
+++G L+ T +DL++ FS++G + D +K R F FV F + D
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 61 RYSLNGRDVDGSR 73
+ LNG+ +D R
Sbjct: 62 EHKLNGKVIDPKR 74
>pdb|3TRZ|A Chain A, Mouse Lin28a In Complex With Let-7d Microrna Pre-Element
pdb|3TRZ|B Chain B, Mouse Lin28a In Complex With Let-7d Microrna Pre-Element
pdb|3TRZ|C Chain C, Mouse Lin28a In Complex With Let-7d Microrna Pre-Element
pdb|3TRZ|D Chain D, Mouse Lin28a In Complex With Let-7d Microrna Pre-Element
pdb|3TRZ|E Chain E, Mouse Lin28a In Complex With Let-7d Microrna Pre-Element
pdb|3TRZ|F Chain F, Mouse Lin28a In Complex With Let-7d Microrna Pre-Element
pdb|3TS2|A Chain A, Mouse Lin28a In Complex With Let-7g Microrna Pre-Element
pdb|3TS2|B Chain B, Mouse Lin28a In Complex With Let-7g Microrna Pre-Element
Length = 148
Score = 35.8 bits (81), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 22/42 (52%)
Query: 98 PPGSGRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNC 139
P G RC+NCG H A++CK KC+ C H+ +C
Sbjct: 94 PKGGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSINHMVASC 135
>pdb|3TS0|A Chain A, Mouse Lin28a In Complex With Let-7f-1 Microrna Pre-Element
pdb|3TS0|B Chain B, Mouse Lin28a In Complex With Let-7f-1 Microrna Pre-Element
Length = 146
Score = 35.8 bits (81), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 22/42 (52%)
Query: 98 PPGSGRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNC 139
P G RC+NCG H A++CK KC+ C H+ +C
Sbjct: 92 PKGGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSINHMVASC 133
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 35.8 bits (81), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 37/71 (52%), Gaps = 2/71 (2%)
Query: 11 TRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--FAFVEFSDPRDADDARYSLNGRD 68
+RL+VG L ++ ++F +YG+ +V + +D F F+ A+ A+ L+
Sbjct: 23 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMP 82
Query: 69 VDGSRIIVEFA 79
+ G ++ V FA
Sbjct: 83 LRGKQLRVRFA 93
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 35.8 bits (81), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 38/78 (48%), Gaps = 10/78 (12%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD-------FAFVEFSDPRDADDARYSL 64
+L+VG L + D+ +F +G I + + R AFV+FS +A A ++L
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHAL 76
Query: 65 NGRDV---DGSRIIVEFA 79
+G S ++V+FA
Sbjct: 77 HGSQTMPGASSSLVVKFA 94
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 35.4 bits (80), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 31/75 (41%), Gaps = 8/75 (10%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIRDVDM--------KRDFAFVEFSDPRDADDARYSL 64
L V + + L ++F RYG I V + R + FV+F A A L
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 65 NGRDVDGSRIIVEFA 79
NG ++ R+ V A
Sbjct: 105 NGFNILNKRLKVALA 119
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 35.4 bits (80), Expect = 0.041, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 10/77 (12%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRI--------RDVDMKRDFAFVEFSDPRDADDARYSL 64
LYV L +++E++FS+YGRI + + R F+ F +A++A L
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 65 NGRDVDGSR--IIVEFA 79
NG+ G+ I V+FA
Sbjct: 64 NGQKPLGAAEPITVKFA 80
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 35.4 bits (80), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 37/71 (52%), Gaps = 5/71 (7%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIRDVDM-----KRDFAFVEFSDPRDADDARYSLNGR 67
LY+ L + + ++ +IF +YG IR + + R A+V + D DA +A L+G
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGF 70
Query: 68 DVDGSRIIVEF 78
+V ++V +
Sbjct: 71 NVSNRYLVVLY 81
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 35.4 bits (80), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 32/79 (40%), Gaps = 6/79 (7%)
Query: 7 RYGGTRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD------FAFVEFSDPRDADDA 60
RY LYV L L + FS +G I + + F FV FS P +A A
Sbjct: 12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKA 71
Query: 61 RYSLNGRDVDGSRIIVEFA 79
+NGR V + V A
Sbjct: 72 VTEMNGRIVATKPLYVALA 90
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 35.0 bits (79), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 33/71 (46%), Gaps = 8/71 (11%)
Query: 9 GGTRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDA 60
G + LYVG L L IF +G+I ++ + +D + F+ FSD A A
Sbjct: 4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRA 63
Query: 61 RYSLNGRDVDG 71
LNG ++ G
Sbjct: 64 LEQLNGFELAG 74
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 35.0 bits (79), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 36/73 (49%), Gaps = 4/73 (5%)
Query: 11 TRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKR--DFAFVEFSDPRDADDARYSLNGRD 68
TRL+VG L T L F R+G IR +D + FA++++ A A + G
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFP 77
Query: 69 VDGS--RIIVEFA 79
+ G R+ V+FA
Sbjct: 78 LGGPDRRLRVDFA 90
>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 = 35.0 bits (79), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 16/74 (21%), Positives = 37/74 (50%), Gaps = 8/74 (10%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDARYS 63
+L++G L + ++E+ + +G ++ ++ +D +AF E+ D D A
Sbjct: 116 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 175
Query: 64 LNGRDVDGSRIIVE 77
LNG + +++V+
Sbjct: 176 LNGMQLGDKKLLVQ 189
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 34.7 bits (78), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 26/51 (50%), Gaps = 2/51 (3%)
Query: 31 FSRYGRIRDVDM--KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 79
FS +G I D+ M R+ AFV + AD A LNG V+ ++ V A
Sbjct: 34 FSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA 84
>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1)
From Homo Sapiens At 1.90 A Resolution
pdb|4FXV|B Chain B, Crystal Structure Of An Elav-Like Protein 1 (Elavl1)
From Homo Sapiens At 1.90 A Resolution
pdb|4FXV|C Chain C, Crystal Structure Of An Elav-Like Protein 1 (Elavl1)
From Homo Sapiens At 1.90 A Resolution
pdb|4FXV|D Chain D, Crystal Structure Of An Elav-Like Protein 1 (Elavl1)
From Homo Sapiens At 1.90 A Resolution
Length = 99
Score = 34.7 bits (78), Expect = 0.066, Method: Composition-based stats.
Identities = 22/80 (27%), Positives = 34/80 (42%), Gaps = 8/80 (10%)
Query: 8 YGGTRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADD 59
+ GT L V L +L +FS G + + RD + FV + +DA+
Sbjct: 17 FQGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 76
Query: 60 ARYSLNGRDVDGSRIIVEFA 79
A +LNG + I V +A
Sbjct: 77 AINTLNGLRLQSKTIKVSYA 96
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 34.7 bits (78), Expect = 0.067, Method: Composition-based stats.
Identities = 26/75 (34%), Positives = 34/75 (45%), Gaps = 8/75 (10%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIRDVDM--------KRDFAFVEFSDPRDADDARYSL 64
LYVG LA + L F +G I D+ + R FAFVEF DA A ++
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 65 NGRDVDGSRIIVEFA 79
N ++ G I V A
Sbjct: 75 NESELFGRTIRVNLA 89
>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 = 34.3 bits (77), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 33/71 (46%), Gaps = 8/71 (11%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDARYS 63
R+YV + D++ +F +G+I+ + RD + F+E+ + + DA S
Sbjct: 111 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 170
Query: 64 LNGRDVDGSRI 74
N D+ G +
Sbjct: 171 XNLFDLGGQYL 181
Score = 32.0 bits (71), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 31/73 (42%), Gaps = 8/73 (10%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDARYS 63
R+YVG + + + F+ +G I+ +D D FAFVE+ P A A
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 64 LNGRDVDGSRIIV 76
N + G I V
Sbjct: 74 XNSVXLGGRNIKV 86
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 34.3 bits (77), Expect = 0.091, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 36/74 (48%), Gaps = 9/74 (12%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDARYS 63
+++VG + +L E F ++G + +V M D F F+ F D + D A +
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQA-VN 70
Query: 64 LNGRDVDGSRIIVE 77
++ D+ G ++ V+
Sbjct: 71 MHFHDIMGKKVEVK 84
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 34.3 bits (77), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 35/73 (47%), Gaps = 8/73 (10%)
Query: 15 VGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDARYSLNG 66
V L+ TR DL+E+F +G I + + +D FAF+ F DA A ++G
Sbjct: 20 VTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSG 79
Query: 67 RDVDGSRIIVEFA 79
D + VE+A
Sbjct: 80 FGYDHLILNVEWA 92
>pdb|2BL6|A Chain A, Solution Structure Of The Zn Complex Of Eiav Ncp11(22-58)
Peptide, Including Two Cchc Zn-Binding Motifs
Length = 37
Score = 34.3 bits (77), Expect = 0.092, Method: Composition-based stats.
Identities = 13/38 (34%), Positives = 22/38 (57%), Gaps = 3/38 (7%)
Query: 104 CFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQN 141
C+NCG GH + C+A C++C + GH + C++
Sbjct: 3 CYNCGKPGHLSSQCRA---PKVCFKCKQPGHFSKQCRS 37
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 34.3 bits (77), Expect = 0.094, Method: Composition-based stats.
Identities = 22/68 (32%), Positives = 33/68 (48%), Gaps = 8/68 (11%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDARYS 63
RL+V L+ + DLE++FS YG + ++ D FAFV F P A A
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 64 LNGRDVDG 71
++G+ G
Sbjct: 70 VDGQVFQG 77
>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 = 34.3 bits (77), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 35/83 (42%), Gaps = 8/83 (9%)
Query: 5 DDRYGGTRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRDF--------AFVEFSDPRD 56
D R T L V L R+L +F G I + RD+ AFV+F+ D
Sbjct: 9 DPRASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXD 68
Query: 57 ADDARYSLNGRDVDGSRIIVEFA 79
+ A LNG V R+ V +A
Sbjct: 69 SQRAIKVLNGITVRNKRLKVSYA 91
Score = 30.8 bits (68), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 29/63 (46%), Gaps = 8/63 (12%)
Query: 11 TRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDARY 62
T LYV L L+ IF +YG I ++ RD AFV ++ +A +A
Sbjct: 101 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 160
Query: 63 SLN 65
+LN
Sbjct: 161 ALN 163
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 34.3 bits (77), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 26/51 (50%), Gaps = 2/51 (3%)
Query: 31 FSRYGRIRDVDM--KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 79
FS +G I D+ M R+ AFV + AD A LNG V+ ++ V A
Sbjct: 58 FSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA 108
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 34.3 bits (77), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 35/70 (50%), Gaps = 10/70 (14%)
Query: 10 GTRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD----------FAFVEFSDPRDADD 59
+++VG++ +DL E+F +YG + ++++ RD FV F + A +
Sbjct: 3 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALE 62
Query: 60 ARYSLNGRDV 69
A+ +L+ V
Sbjct: 63 AQNALHNMKV 72
Score = 32.3 bits (72), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 41/78 (52%), Gaps = 10/78 (12%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRYGRIRDV-------DMKRDFAFVEFSDPRDADDARYSL 64
+L++G ++ + D+ +FS +G+I + + R AFV F+ A A ++
Sbjct: 97 KLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAM 156
Query: 65 N-GRDVDG--SRIIVEFA 79
+ + ++G S ++V+FA
Sbjct: 157 HQAQTMEGCSSPMVVKFA 174
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 33.9 bits (76), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 35/70 (50%), Gaps = 10/70 (14%)
Query: 10 GTRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD----------FAFVEFSDPRDADD 59
+++VG++ +DL E+F +YG + ++++ RD FV F + A +
Sbjct: 15 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALE 74
Query: 60 ARYSLNGRDV 69
A+ +L+ V
Sbjct: 75 AQNALHNMKV 84
Score = 32.3 bits (72), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 41/78 (52%), Gaps = 10/78 (12%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRYGRIRDV-------DMKRDFAFVEFSDPRDADDARYSL 64
+L++G ++ + D+ +FS +G+I + + R AFV F+ A A ++
Sbjct: 109 KLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAM 168
Query: 65 N-GRDVDG--SRIIVEFA 79
+ + ++G S ++V+FA
Sbjct: 169 HQAQTMEGCSSPMVVKFA 186
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 33.9 bits (76), Expect = 0.11, Method: Composition-based stats.
Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 8/77 (10%)
Query: 10 GTRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDAR 61
G L+V + D+ + F+ YG I+++ + D + VE+ ++A A
Sbjct: 7 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 62 YSLNGRDVDGSRIIVEF 78
LNG+D+ G I V++
Sbjct: 67 EGLNGQDLMGQPISVDW 83
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 31/77 (40%), Gaps = 8/77 (10%)
Query: 10 GTRLYVGRLASRTRSRDLEEIFSRYGRI--------RDVDMKRDFAFVEFSDPRDADDAR 61
G L++ L DL F +G + + + + F FV F +P A A
Sbjct: 40 GCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAI 99
Query: 62 YSLNGRDVDGSRIIVEF 78
++NG V R+ V+
Sbjct: 100 KAMNGFQVGTKRLKVQL 116
>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 = 33.9 bits (76), Expect = 0.11, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 37/71 (52%), Gaps = 2/71 (2%)
Query: 11 TRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--FAFVEFSDPRDADDARYSLNGRD 68
+RL+VG L ++ ++F +YG+ +V + +D F F+ A+ A+ L+
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMP 75
Query: 69 VDGSRIIVEFA 79
+ G ++ V FA
Sbjct: 76 LRGKQLRVRFA 86
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 33.9 bits (76), Expect = 0.12, Method: Composition-based stats.
Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 8/77 (10%)
Query: 11 TRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDARY 62
+ +YV L + DL IFS+YG++ V + +D AF+ F D A +
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
Query: 63 SLNGRDVDGSRIIVEFA 79
++N + + G I A
Sbjct: 77 AINNKQLFGRVIKASIA 93
>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 = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 37/71 (52%), Gaps = 5/71 (7%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIRDVDM-----KRDFAFVEFSDPRDADDARYSLNGR 67
LY+ L + + ++ +IF +YG IR + + R A+V + D DA +A L+G
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGF 80
Query: 68 DVDGSRIIVEF 78
+V ++V +
Sbjct: 81 NVCNRYLVVLY 91
>pdb|2LI8|A Chain A, The Solution Structure Of The Lin28-Znf Domains Bound To
Aggagau Of Pre-Let-7 Mirna
Length = 74
Score = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 20/37 (54%)
Query: 103 RCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNC 139
RC+NCG H A++CK KC+ C H+ +C
Sbjct: 26 RCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASC 62
>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 = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 9/63 (14%)
Query: 13 LYVGRLASRTRSRDLEE----IFSRYGRIRDVDMKRDF-----AFVEFSDPRDADDARYS 63
+Y+ L + + +L++ IFS++G+I D+ + R AFV F + A +A S
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 71
Query: 64 LNG 66
+ G
Sbjct: 72 MQG 74
Score = 32.0 bits (71), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 30/61 (49%), Gaps = 3/61 (4%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIRDVDM---KRDFAFVEFSDPRDADDARYSLNGRDV 69
L++ L T L +F+++ ++V + + D AFVEF + A AR +L G +
Sbjct: 210 LFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKI 269
Query: 70 D 70
Sbjct: 270 T 270
>pdb|2XB2|D Chain D, Crystal Structure Of The Core
Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How
The Ejc Is Bridged To The Nmd Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core
Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How
The Ejc Is Bridged To The Nmd Machinery
Length = 90
Score = 33.5 bits (75), Expect = 0.14, Method: Composition-based stats.
Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 8/77 (10%)
Query: 10 GTRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDAR 61
G L+V + D+ + F+ YG I+++ + D + VE+ ++A A
Sbjct: 7 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 62 YSLNGRDVDGSRIIVEF 78
LNG+D+ G I V++
Sbjct: 67 EGLNGQDLMGQPISVDW 83
>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 = 33.5 bits (75), Expect = 0.14, Method: Composition-based stats.
Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 8/77 (10%)
Query: 10 GTRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDAR 61
G L+V + D+ + F+ YG I+++ + D + VE+ ++A A
Sbjct: 9 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 68
Query: 62 YSLNGRDVDGSRIIVEF 78
LNG+D+ G I V++
Sbjct: 69 EGLNGQDLMGQPISVDW 85
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 33.5 bits (75), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 12/69 (17%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRYGRIRDVDM--------KRDFAFVEFSDPRDADDAR-- 61
+++VG + T L + F +YG+I +++ KR FAFV F D D
Sbjct: 107 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 166
Query: 62 --YSLNGRD 68
+++NG +
Sbjct: 167 KYHTVNGHN 175
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 33.5 bits (75), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 12/69 (17%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRYGRIRDVDM--------KRDFAFVEFSDPRDADDAR-- 61
+++VG + T L + F +YG+I +++ KR FAFV F D D
Sbjct: 104 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 163
Query: 62 --YSLNGRD 68
+++NG +
Sbjct: 164 KYHTVNGHN 172
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 33.5 bits (75), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 12/69 (17%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRYGRIRDVDM--------KRDFAFVEFSDPRDADDAR-- 61
+++VG + T L + F +YG+I +++ KR FAFV F D D
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 165
Query: 62 --YSLNGRD 68
+++NG +
Sbjct: 166 KYHTVNGHN 174
>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 = 33.5 bits (75), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 12/69 (17%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRYGRIRDVDM--------KRDFAFVEFSDPRDADDAR-- 61
+++VG + T L + F +YG+I +++ KR FAFV F D D
Sbjct: 105 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 164
Query: 62 --YSLNGRD 68
+++NG +
Sbjct: 165 KYHTVNGHN 173
>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 = 33.1 bits (74), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 12/69 (17%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRYGRIRDVDM--------KRDFAFVEFSDPRDADDAR-- 61
+++VG + T L + F +YG+I +++ KR FAFV F D D
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 165
Query: 62 --YSLNGRD 68
+++NG +
Sbjct: 166 KYHTVNGHN 174
>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 = 33.1 bits (74), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 12/69 (17%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRYGRIRDVDM--------KRDFAFVEFSDPRDADDAR-- 61
+++VG + T L + F +YG+I +++ KR FAFV F D D
Sbjct: 99 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 158
Query: 62 --YSLNGRD 68
+++NG +
Sbjct: 159 KYHTVNGHN 167
>pdb|1SJR|A Chain A, Nmr Structure Of Rrm2 From Human Polypyrimidine Tract
Binding Protein Isoform 1 (Ptb1)
Length = 164
Score = 33.1 bits (74), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 28/47 (59%), Gaps = 4/47 (8%)
Query: 27 LEEIFSRYGRIRDVDM---KRDF-AFVEFSDPRDADDARYSLNGRDV 69
L +IFS++G + + F A ++++DP A A+ SL+G+++
Sbjct: 63 LHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNI 109
>pdb|2ADB|A Chain A, Solution Structure Of Polypyrimidine Tract Binding
Protein Rbd2 Complexed With Cucucu Rna
Length = 148
Score = 33.1 bits (74), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRYGRIRDVDM---KRDF-AFVEFSDPRDADDARYSLNGR 67
R+ V L L +IFS++G + + F A ++++DP A A+ SL+G+
Sbjct: 35 RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQ 94
Query: 68 DV 69
++
Sbjct: 95 NI 96
>pdb|2CQF|A Chain A, Solution Structure Of The Zinc-Finger Domain In Lin-28
Length = 63
Score = 32.7 bits (73), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 20/37 (54%)
Query: 103 RCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNC 139
RC+NCG H A++CK KC+ C H+ +C
Sbjct: 9 RCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASC 45
>pdb|3ZZY|A Chain A, Crystal Structure Of A Raver1 Pri3 Peptide In Complex
With Polypyrimidine Tract Binding Protein Rrm2
pdb|3ZZY|B Chain B, Crystal Structure Of A Raver1 Pri3 Peptide In Complex
With Polypyrimidine Tract Binding Protein Rrm2
pdb|3ZZZ|A Chain A, Crystal Structure Of A Raver1 Pri4 Peptide In Complex
With Polypyrimidine Tract Binding Protein Rrm2
pdb|3ZZZ|B Chain B, Crystal Structure Of A Raver1 Pri4 Peptide In Complex
With Polypyrimidine Tract Binding Protein Rrm2
Length = 130
Score = 32.7 bits (73), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRYGRIRDVDM---KRDF-AFVEFSDPRDADDARYSLNGR 67
R+ V L L +IFS++G + + F A ++++DP A A+ SL+G+
Sbjct: 30 RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQ 89
Query: 68 DV 69
++
Sbjct: 90 NI 91
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 32.7 bits (73), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 33/77 (42%), Gaps = 8/77 (10%)
Query: 11 TRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRDF--------AFVEFSDPRDADDARY 62
T L V L R+L +F G I + RD+ AFV+F+ D+ A
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 63 SLNGRDVDGSRIIVEFA 79
LNG V R+ V +A
Sbjct: 64 VLNGITVRNKRLKVSYA 80
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 29/63 (46%), Gaps = 8/63 (12%)
Query: 11 TRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDARY 62
T LYV L L+ IF +YG I ++ RD AFV ++ +A +A
Sbjct: 90 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 149
Query: 63 SLN 65
+LN
Sbjct: 150 ALN 152
>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 = 32.7 bits (73), Expect = 0.28, Method: Composition-based stats.
Identities = 22/79 (27%), Positives = 33/79 (41%), Gaps = 8/79 (10%)
Query: 9 GGTRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDA 60
G T L V L +L +FS G + + RD + FV + +DA+ A
Sbjct: 3 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 62
Query: 61 RYSLNGRDVDGSRIIVEFA 79
+LNG + I V +A
Sbjct: 63 INTLNGLRLQSKTIKVSYA 81
>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 = 32.3 bits (72), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 34/70 (48%), Gaps = 10/70 (14%)
Query: 10 GTRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD----------FAFVEFSDPRDADD 59
+ +VG++ +DL E+F +YG + ++++ RD FV F + A +
Sbjct: 3 AIKXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALE 62
Query: 60 ARYSLNGRDV 69
A+ +L+ V
Sbjct: 63 AQNALHNXKV 72
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 32.3 bits (72), Expect = 0.33, Method: Composition-based stats.
Identities = 17/76 (22%), Positives = 38/76 (50%), Gaps = 8/76 (10%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDARYS 63
+L++G L + ++E+ + +G ++ ++ +D +AF E+ D D A
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 64 LNGRDVDGSRIIVEFA 79
LNG + +++V+ A
Sbjct: 63 LNGMQLGDKKLLVQRA 78
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein
U1a117, Nmr, 43 Structures
Length = 116
Score = 32.3 bits (72), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 9/63 (14%)
Query: 13 LYVGRLASRTRSRDLEE----IFSRYGRIRDVDMKRDF-----AFVEFSDPRDADDARYS 63
+Y+ L + + +L++ IFS++G+I D+ + R AFV F + A +A S
Sbjct: 11 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 70
Query: 64 LNG 66
+ G
Sbjct: 71 MQG 73
>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 = 32.0 bits (71), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 29/63 (46%), Gaps = 8/63 (12%)
Query: 11 TRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDARY 62
T LYV L L+ IF +YG I ++ RD AFV ++ +A +A
Sbjct: 14 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 73
Query: 63 SLN 65
+LN
Sbjct: 74 ALN 76
>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 = 31.2 bits (69), Expect = 0.77, Method: Composition-based stats.
Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 12/71 (16%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDA----DD 59
+ +VG L+ T +DL++ F+++G + D +K D F F+ F D D
Sbjct: 13 KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQ 72
Query: 60 ARYSLNGRDVD 70
+ L+GR +D
Sbjct: 73 KEHRLDGRVID 83
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 31.2 bits (69), Expect = 0.78, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 33/77 (42%), Gaps = 8/77 (10%)
Query: 11 TRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRDF--------AFVEFSDPRDADDARY 62
T L V L R+L +F G I + RD+ AFV+F+ D+ A
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 63 SLNGRDVDGSRIIVEFA 79
LNG V R+ V +A
Sbjct: 64 VLNGITVRNKRLKVSYA 80
>pdb|1HVN|E Chain E, Zinc-And Sequence-Dependent Binding To Nucleic Acids By
The N-Terminal Zinc Finger Domain Of The Hiv-1
Nucleocapsid Protein: Nmr Structure Of The Complex With
The Psi-Site Analog, DACGCC
pdb|1HVO|E Chain E, Zinc-And Sequence-Dependent Binding To Nucleic Acids By
The N-Terminal Zinc Finger Domain Of The Hiv-1
Nucleocapsid Protein: Nmr Structure Of The Complex With
The Psi-Site Analog, DACGCC
pdb|2ZNF|A Chain A, High-Resolution Structure Of An Hiv Zinc Fingerlike Domain
Via A New Nmr-Based Distance Geometry Approach
Length = 18
Score = 31.2 bits (69), Expect = 0.78, Method: Composition-based stats.
Identities = 11/17 (64%), Positives = 15/17 (88%)
Query: 103 RCFNCGIDGHWARDCKA 119
+CFNCG +GH AR+C+A
Sbjct: 2 KCFNCGKEGHIARNCRA 18
Score = 29.6 bits (65), Expect = 2.1, Method: Composition-based stats.
Identities = 10/16 (62%), Positives = 13/16 (81%)
Query: 125 KCYRCGERGHIERNCQ 140
KC+ CG+ GHI RNC+
Sbjct: 2 KCFNCGKEGHIARNCR 17
>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 = 31.2 bits (69), Expect = 0.81, Method: Composition-based stats.
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 9/63 (14%)
Query: 13 LYVGRLASRTRSRDLEE----IFSRYGRIRDVDMKRDF-----AFVEFSDPRDADDARYS 63
+Y+ L + + +L++ IFSR+G+I D+ + R AFV F + A +A S
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 70
Query: 64 LNG 66
+ G
Sbjct: 71 MQG 73
>pdb|2DGX|A Chain A, Solution Structure Of The Rna Recognition Motif In
Kiaa0430 Protein
Length = 96
Score = 31.2 bits (69), Expect = 0.82, Method: Composition-based stats.
Identities = 19/68 (27%), Positives = 38/68 (55%), Gaps = 5/68 (7%)
Query: 17 RLASRTRSRDLEEIFSRYGRIRDVDMK--RDF---AFVEFSDPRDADDARYSLNGRDVDG 71
RL+ + + L+E F+R+G+++ V++ D+ A V+ + +DA A SL+ +
Sbjct: 20 RLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGS 79
Query: 72 SRIIVEFA 79
+I+V A
Sbjct: 80 KKILVSLA 87
>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 = 30.8 bits (68), Expect = 0.90, Method: Composition-based stats.
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 9/63 (14%)
Query: 13 LYVGRLASRTRSRDLEE----IFSRYGRIRDVDMKRDF-----AFVEFSDPRDADDARYS 63
+Y+ L + + +L++ IFSR+G+I D+ + R AFV F + A +A S
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 71
Query: 64 LNG 66
+ G
Sbjct: 72 MQG 74
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 30.8 bits (68), Expect = 0.91, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 9/72 (12%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDARYSL 64
+YVG L S ++E+FS++G++ +V + D F FVE + +A L
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAKL 62
Query: 65 NGRDVDGSRIIV 76
+ D G I V
Sbjct: 63 DNTDFMGRTIRV 74
>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 = 30.8 bits (68), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 5/71 (7%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIRDVDM-----KRDFAFVEFSDPRDADDARYSLNGR 67
L + L + + ++ +IF +YG IR + + R A+V + D DA +A L+G
Sbjct: 21 LMIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGF 80
Query: 68 DVDGSRIIVEF 78
+V ++V +
Sbjct: 81 NVCNRYLVVLY 91
>pdb|1M5K|C Chain C, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5K|F Chain F, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5O|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5O|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1SJ3|P Chain P, Hepatitis Delta Virus Gemonic Ribozyme Precursor, With
Mg2+ Bound
pdb|1SJ4|P Chain P, Crystal Structure Of A C75u Mutant Hepatitis Delta Virus
Ribozyme Precursor, In Cu2+ Solution
pdb|1SJF|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Cobalt
Hexammine Solution
pdb|1VBX|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Edta Solution
pdb|1VBY|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, And Mn2+ Bound
pdb|1VBZ|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Ba2+ Solution
pdb|1VC0|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Imidazole And
Sr2+ Solution
pdb|1VC5|A Chain A, Crystal Structure Of The Wild Type Hepatitis Delta Virus
Gemonic Ribozyme Precursor, In Edta Solution
pdb|1VC6|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Product With C75u Mutaion, Cleaved In
Imidazole And Mg2+ Solutions
pdb|1VC7|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Sr2+ Solution
pdb|2OIH|A Chain A, Hepatitis Delta Virus Gemonic Ribozyme Precursor With
C75u Mutation And Bound To Monovalent Cation Tl+
pdb|2OJ3|A Chain A, Hepatitis Delta Virus Ribozyme Precursor Structure, With
C75u Mutation, Bound To Tl+ And Cobalt Hexammine
(Co(Nh3) 63+)
Length = 100
Score = 30.8 bits (68), Expect = 0.97, Method: Composition-based stats.
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 9/63 (14%)
Query: 13 LYVGRLASRTRSRDLEE----IFSRYGRIRDVDMKRDF-----AFVEFSDPRDADDARYS 63
+Y+ L + + +L++ IFSR+G+I D+ + R AFV F + A +A S
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 71
Query: 64 LNG 66
+ G
Sbjct: 72 MQG 74
>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 = 30.8 bits (68), Expect = 1.00, Method: Composition-based stats.
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 9/63 (14%)
Query: 13 LYVGRLASRTRSRDLEE----IFSRYGRIRDVDMKRDF-----AFVEFSDPRDADDARYS 63
+Y+ L + + +L++ IFSR+G+I D+ + R AFV F + A +A S
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 70
Query: 64 LNG 66
+ G
Sbjct: 71 MQG 73
>pdb|2A51|A Chain A, Structure Of The (13-51) Domain Of The Nucleocapsid
Protein Ncp8 From Sivlhoest
Length = 39
Score = 30.8 bits (68), Expect = 1.1, Method: Composition-based stats.
Identities = 15/36 (41%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 104 CFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNC 139
CFNCG GH AR C+ + C+ CG + H C
Sbjct: 3 CFNCGKPGHTARMCRQPR-QEGCWNCGSKEHRFAQC 37
>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 = 30.8 bits (68), Expect = 1.1, Method: Composition-based stats.
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 9/63 (14%)
Query: 13 LYVGRLASRTRSRDLEE----IFSRYGRIRDVDMKRDF-----AFVEFSDPRDADDARYS 63
+Y+ L + + +L++ IFSR+G+I D+ + R AFV F + A +A S
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 70
Query: 64 LNG 66
+ G
Sbjct: 71 MQG 73
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 30.8 bits (68), Expect = 1.1, Method: Composition-based stats.
Identities = 20/71 (28%), Positives = 37/71 (52%), Gaps = 5/71 (7%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIRDVDM-----KRDFAFVEFSDPRDADDARYSLNGR 67
LY+ L + + ++ +IF +YG IR + + R A+V + D DA +A L+G
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGF 74
Query: 68 DVDGSRIIVEF 78
+V ++V +
Sbjct: 75 NVCNRYLVVLY 85
>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
pdb|3IWN|D Chain D, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
Length = 91
Score = 30.4 bits (67), Expect = 1.2, Method: Composition-based stats.
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 9/63 (14%)
Query: 13 LYVGRLASRTRSRDLEE----IFSRYGRIRDVDMKRDF-----AFVEFSDPRDADDARYS 63
+Y+ L + + +L++ IFSR+G+I D+ + R AFV F + A +A S
Sbjct: 7 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 66
Query: 64 LNG 66
+ G
Sbjct: 67 MQG 69
>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To
Its Catalytic Cofactor
pdb|2NZ4|B Chain B, Structural Investigation Of The Glms Ribozyme Bound To
Its Catalytic Cofactor
pdb|2NZ4|C Chain C, Structural Investigation Of The Glms Ribozyme Bound To
Its Catalytic Cofactor
pdb|2NZ4|D Chain D, Structural Investigation Of The Glms Ribozyme Bound To
Its Catalytic Cofactor
Length = 94
Score = 30.4 bits (67), Expect = 1.2, Method: Composition-based stats.
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 9/63 (14%)
Query: 13 LYVGRLASRTRSRDLEE----IFSRYGRIRDVDMKRDF-----AFVEFSDPRDADDARYS 63
+Y+ L + + +L++ IFSR+G+I D+ + R AFV F + A +A S
Sbjct: 8 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 67
Query: 64 LNG 66
+ G
Sbjct: 68 MQG 70
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 8/58 (13%)
Query: 11 TRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDA 60
+YVG L + L E+F + G + + M +D + FVEF DAD A
Sbjct: 16 ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA 73
>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 = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 31/72 (43%), Gaps = 8/72 (11%)
Query: 8 YGGTRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADD 59
Y LYVG L L E FS G I + + RD +A+V F P DA+
Sbjct: 13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAER 72
Query: 60 ARYSLNGRDVDG 71
A ++N + G
Sbjct: 73 ALDTMNFDVIKG 84
>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 = 30.4 bits (67), Expect = 1.3, Method: Composition-based stats.
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 9/63 (14%)
Query: 13 LYVGRLASRTRSRDLEE----IFSRYGRIRDVDMKRDF-----AFVEFSDPRDADDARYS 63
+Y+ L + + +L++ IFSR+G+I D+ + R AFV F + A +A S
Sbjct: 6 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 65
Query: 64 LNG 66
+ G
Sbjct: 66 MQG 68
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 29/67 (43%), Gaps = 8/67 (11%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADDARYSL 64
++VG + L++IFS G + + D + F E+ D A A +L
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 65 NGRDVDG 71
NGR+ G
Sbjct: 71 NGREFSG 77
>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 = 30.4 bits (67), Expect = 1.4, Method: Composition-based stats.
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 9/63 (14%)
Query: 13 LYVGRLASRTRSRDLEE----IFSRYGRIRDVDMKRDF-----AFVEFSDPRDADDARYS 63
+Y+ L + + +L++ IFSR+G+I D+ + R AFV F + A +A S
Sbjct: 9 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 68
Query: 64 LNG 66
+ G
Sbjct: 69 MQG 71
>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 = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 31/72 (43%), Gaps = 8/72 (11%)
Query: 8 YGGTRLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSDPRDADD 59
Y LYVG L L E FS G I + + RD +A+V F P DA+
Sbjct: 8 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAER 67
Query: 60 ARYSLNGRDVDG 71
A ++N + G
Sbjct: 68 ALDTMNFDVIKG 79
>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 = 29.6 bits (65), Expect = 2.1, Method: Composition-based stats.
Identities = 10/34 (29%), Positives = 23/34 (67%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD 45
+++VG++ +DL E+F +YG + ++++ RD
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRD 38
>pdb|2IHX|A Chain A, Solution Structure Of The Rous Sarcoma Virus Nucleocapsid
Protein:upsi Rna Packaging Signal Complex
Length = 61
Score = 29.6 bits (65), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 21/42 (50%), Gaps = 4/42 (9%)
Query: 102 GRCFNCGIDGHWARDC----KAGDWKNKCYRCGERGHIERNC 139
G C+ CG GH+ C K+G+ + +C C GH + C
Sbjct: 5 GLCYTCGSPGHYQAQCPKKRKSGNSRERCQLCNGMGHNAKQC 46
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 29.3 bits (64), Expect = 2.6, Method: Composition-based stats.
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 4/70 (5%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIR----DVDMKRDFAFVEFSDPRDADDARYSLNGRD 68
L + L+ L+E+F + I+ + +AF+EF+ DA +A S N R+
Sbjct: 18 LVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKRE 77
Query: 69 VDGSRIIVEF 78
++G I +E
Sbjct: 78 IEGRAIRLEL 87
>pdb|3EGN|A Chain A, C-Terminal Rna Recognition Motif Of The U11U12 65K PROTEIN
Length = 143
Score = 29.3 bits (64), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 13/81 (16%)
Query: 12 RLYVGRLASRTRSRDLEEIFSRY-------GRIR-DVDMKRD-----FAFVEFSDPRDAD 58
R+YV LA + +DL+ IF RY RI D+ + ++ AF+ + + A
Sbjct: 47 RIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAA 106
Query: 59 DARYSLNGRDVDGSRIIVEFA 79
A NG + G ++V+FA
Sbjct: 107 KALKEANGYVLFGKPMVVQFA 127
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 29.3 bits (64), Expect = 2.6, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 9/63 (14%)
Query: 13 LYVGRLASRTRSRDLEE----IFSRYGRIRDVDMKRDF-----AFVEFSDPRDADDARYS 63
+Y+ L + + +L++ IFS++G+I D+ + R AFV F + A +A S
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 71
Query: 64 LNG 66
+ G
Sbjct: 72 MQG 74
>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 = 2.7, Method: Composition-based stats.
Identities = 23/71 (32%), Positives = 32/71 (45%), Gaps = 7/71 (9%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD-------FAFVEFSDPRDADDARYSLN 65
++VG L +R R L E+F + G + V + +D F FV F P A LN
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLN 78
Query: 66 GRDVDGSRIIV 76
G + G I V
Sbjct: 79 GIRLYGRPINV 89
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 29.3 bits (64), Expect = 2.9, Method: Composition-based stats.
Identities = 19/72 (26%), Positives = 38/72 (52%), Gaps = 5/72 (6%)
Query: 13 LYVGRLASRTRSRDLEEIF-----SRYGRIRDVDMKRDFAFVEFSDPRDADDARYSLNGR 67
L+V L+ T L+E F +R R+ + F FV+F+ DA A+ ++
Sbjct: 18 LFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDG 77
Query: 68 DVDGSRIIVEFA 79
++DG+++ +++A
Sbjct: 78 EIDGNKVTLDWA 89
>pdb|2U1A|A Chain A, Rna Binding Domain 2 Of Human U1a Protein, Nmr, 20
Structures
Length = 88
Score = 28.9 bits (63), Expect = 3.6, Method: Composition-based stats.
Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 3/57 (5%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIRDVDM---KRDFAFVEFSDPRDADDARYSLNG 66
L++ L T L +F+++ ++V + + D AFVEF + A AR +L G
Sbjct: 16 LFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQG 72
>pdb|1NCP|N Chain N, Structural Characterization Of A 39 Residue Synthetic
Peptide Containing The Two Zinc Binding Domains From The
Hiv-1 P7 Nucleocapsid Protein By Cd And Nmr Spectroscopy
Length = 17
Score = 28.9 bits (63), Expect = 4.0, Method: Composition-based stats.
Identities = 10/16 (62%), Positives = 14/16 (87%)
Query: 103 RCFNCGIDGHWARDCK 118
+CFNCG +GH AR+C+
Sbjct: 2 KCFNCGKEGHTARNCR 17
>pdb|1NC8|A Chain A, High-Resolution Solution Nmr Structure Of The Minimal
Active Domain Of The Human Immunodeficiency Virus Type-2
Nucleocapsid Protein, 15 Structures
Length = 29
Score = 28.9 bits (63), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 11/17 (64%), Positives = 14/17 (82%)
Query: 103 RCFNCGIDGHWARDCKA 119
RC+NCG +GH AR C+A
Sbjct: 8 RCWNCGKEGHSARQCRA 24
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 28.5 bits (62), Expect = 5.4, Method: Composition-based stats.
Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 9/63 (14%)
Query: 13 LYVGRLASRTRSRDLEE----IFSRYGRIRDVDMKRDF-----AFVEFSDPRDADDARYS 63
+Y+ L + + +L++ IFSR+G+I D+ + R AFV F + A +A S
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATNALRS 70
Query: 64 LNG 66
G
Sbjct: 71 XQG 73
>pdb|3CUL|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUL|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3EGZ|A Chain A, Crystal Structure Of An In Vitro Evolved Tetracycline
Aptamer And Artificial Riboswitch
Length = 98
Score = 28.5 bits (62), Expect = 5.4, Method: Composition-based stats.
Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 9/63 (14%)
Query: 13 LYVGRLASRTRSRDLEE----IFSRYGRIRDVDMKRDF-----AFVEFSDPRDADDARYS 63
+Y+ L + + +L++ IFSR+G+I D+ + R AFV F + A +A S
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATNALRS 71
Query: 64 LNG 66
G
Sbjct: 72 XQG 74
>pdb|2B0G|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd2
pdb|2AYM|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd2
Length = 83
Score = 28.1 bits (61), Expect = 6.0, Method: Composition-based stats.
Identities = 15/57 (26%), Positives = 30/57 (52%), Gaps = 3/57 (5%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIRDVDM---KRDFAFVEFSDPRDADDARYSLNG 66
L++ L T L +F+++ ++V + + D AFVEF+ ++ A+ +L G
Sbjct: 11 LFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQG 67
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 28.1 bits (61), Expect = 6.4, Method: Composition-based stats.
Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 9/63 (14%)
Query: 13 LYVGRLASRTRSRDLEE----IFSRYGRIRDVDMKRDF-----AFVEFSDPRDADDARYS 63
+Y+ L + + +L++ IFSR+G+I D+ + R AFV F + A +A S
Sbjct: 9 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATNALRS 68
Query: 64 LNG 66
G
Sbjct: 69 XQG 71
>pdb|1CL4|A Chain A, Nucleocapsid Protein From Mason-Pfizer Monkey Virus (Mpmv)
Length = 60
Score = 28.1 bits (61), Expect = 7.2, Method: Composition-based stats.
Identities = 15/47 (31%), Positives = 20/47 (42%), Gaps = 7/47 (14%)
Query: 102 GRCFNCGIDGHWARDCKAGDWKNK-------CYRCGERGHIERNCQN 141
G CF CG GH+A++C N C RC H C++
Sbjct: 2 GSCFKCGKKGHFAKNCHEHAHNNAEPKVPGLCPRCKRGKHWANECKS 48
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 27.3 bits (59), Expect = 9.7, Method: Composition-based stats.
Identities = 17/49 (34%), Positives = 26/49 (53%), Gaps = 8/49 (16%)
Query: 13 LYVGRLASRTRSRDLEEIFSRYGRIRDVDMKRD--------FAFVEFSD 53
L V L +T +DL+E FS +G + V +K+D F FV F++
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTE 66
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.316 0.138 0.430
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,637,222
Number of Sequences: 62578
Number of extensions: 284489
Number of successful extensions: 789
Number of sequences better than 100.0: 172
Number of HSP's better than 100.0 without gapping: 84
Number of HSP's successfully gapped in prelim test: 88
Number of HSP's that attempted gapping in prelim test: 600
Number of HSP's gapped (non-prelim): 222
length of query: 310
length of database: 14,973,337
effective HSP length: 99
effective length of query: 211
effective length of database: 8,778,115
effective search space: 1852182265
effective search space used: 1852182265
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)