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= 030175
(182 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 45.8 bits (107), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 10 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVD 69
LFV F P+ +E ++ F P+G + V+I FAFV+FE E A KA+E +
Sbjct: 34 LFVRPF-PLDVQESELNEIFGPFGPMKEVKILNGFAFVEFEEAESAAKAIEEVHGKSFAN 92
Query: 70 RVISVEYA 77
+ + V Y+
Sbjct: 93 QPLEVVYS 100
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 43.9 bits (102), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 10 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVD 69
LFV F P+ +E ++ F P+G + V+I FAFV+FE E A KA+E +
Sbjct: 7 LFVRPF-PLDVQESELNEIFGPFGPMKEVKILNGFAFVEFEEAESAAKAIEEVHGKSFAN 65
Query: 70 RVISVEYA 77
+ + V Y+
Sbjct: 66 QPLEVVYS 73
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 43.9 bits (102), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 35/68 (51%)
Query: 10 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVD 69
+F+ N + + ++ D++ F YG ++ + + FAFVQ+ + A A+ D +
Sbjct: 18 VFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERNARAAVAGEDGRMIAG 77
Query: 70 RVISVEYA 77
+V+ + A
Sbjct: 78 QVLDINLA 85
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 43.5 bits (101), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 37/77 (48%)
Query: 1 MANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALE 60
M N P LF+ N + D+ R F PYG+++ + I+ F F+QF+ + A+E
Sbjct: 4 MHNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIE 63
Query: 61 STDRSKLVDRVISVEYA 77
+ + + +E +
Sbjct: 64 CESQEMNFGKKLILEVS 80
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 43/83 (51%), Gaps = 10/83 (12%)
Query: 10 LFVINFDPIRTRERDIKRHFEPYGNVLHV-RIRRN--------FAFVQFETQEEATKALE 60
+F+ N DP E+ + F +G +L +I R+ +AF+ F + + + A+E
Sbjct: 8 IFIGNLDP-EIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66
Query: 61 STDRSKLVDRVISVEYALKDDSE 83
+ + L +R I+V YA K DS+
Sbjct: 67 AMNGQYLCNRPITVSYAFKKDSK 89
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 30/59 (50%)
Query: 6 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDR 64
P LF+ N + D+ R F PYG+++ + I+ F F+QF+ + A+E +
Sbjct: 1 PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECESQ 59
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 40.4 bits (93), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 29/55 (52%)
Query: 10 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDR 64
LF+ N + D+ R F PYG+++ + I+ F F+QF+ + A+E +
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECESQ 79
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 40.0 bits (92), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 28/85 (32%), Positives = 41/85 (48%), Gaps = 9/85 (10%)
Query: 2 ANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQE 53
AN P L V + T ERD++ F YG + V I R FAFV FE +
Sbjct: 41 ANPDPNCCLGVFGLS-LYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 99
Query: 54 EATKALESTDRSKLVDRVISVEYAL 78
+A +A E + +L R I V++++
Sbjct: 100 DAKEAKERANGMELDGRRIRVDFSI 124
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 40.0 bits (92), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 34/66 (51%), Gaps = 1/66 (1%)
Query: 10 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVD 69
LF+ N P E++I+ FE YG VL I +N+ FV E + A A+ + KL
Sbjct: 11 LFIGNL-PREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAIRNLHHYKLHG 69
Query: 70 RVISVE 75
I+VE
Sbjct: 70 VNINVE 75
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 39.7 bits (91), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 28/85 (32%), Positives = 41/85 (48%), Gaps = 9/85 (10%)
Query: 2 ANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQE 53
AN P L V + T ERD++ F YG + V I R FAFV FE +
Sbjct: 10 ANPDPNCCLGVFGL-SLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 68
Query: 54 EATKALESTDRSKLVDRVISVEYAL 78
+A +A E + +L R I V++++
Sbjct: 69 DAKEAKERANGMELDGRRIRVDFSI 93
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 39.7 bits (91), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 8/57 (14%)
Query: 29 FEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA 77
F P+G++ ++I R FAFV+FE E+A A+++ + S+L R I V A
Sbjct: 33 FIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 89
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 39.7 bits (91), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 28/51 (54%)
Query: 10 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALE 60
LF+ N + D+ R F PYG+++ + I+ F F+QF+ + A+E
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIE 75
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 28/85 (32%), Positives = 41/85 (48%), Gaps = 9/85 (10%)
Query: 2 ANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQE 53
AN P L V + T ERD++ F YG + V I R FAFV FE +
Sbjct: 7 ANPDPNCCLGVFGLS-LYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 65
Query: 54 EATKALESTDRSKLVDRVISVEYAL 78
+A +A E + +L R I V++++
Sbjct: 66 DAKEAKERANGMELDGRRIRVDFSI 90
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 8/57 (14%)
Query: 29 FEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA 77
F P+G++ ++I R FAFV+FE E+A A+++ + S+L R I V A
Sbjct: 84 FIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140
>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 = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 8/57 (14%)
Query: 29 FEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA 77
F P+G++ ++I R FAFV+FE E+A A+++ + S+L R I V A
Sbjct: 28 FIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 84
>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 = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 7/71 (9%)
Query: 10 LFVINFDPIRTRERDIKRHFEPYGNVLHVRI------RRNFAFVQFETQEEATKALESTD 63
+F+ N D + + F +GN+L ++ + + FV FETQE A +A+E +
Sbjct: 106 IFIKNLDK-SIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 164
Query: 64 RSKLVDRVISV 74
L DR + V
Sbjct: 165 GMLLNDRKVFV 175
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 8/57 (14%)
Query: 29 FEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA 77
F P+G++ ++I R FAFV+FE E+A A+++ + S+L R I V A
Sbjct: 26 FIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 82
>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human
Pabpc1 At Ph 6.0
pdb|4F26|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human
Pabpc1 A Ph 9.0
Length = 115
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 7/71 (9%)
Query: 10 LFVINFDPIRTRERDIKRHFEPYGNVLHVRI------RRNFAFVQFETQEEATKALESTD 63
+F+ N D + + F +GN+L ++ + + FV FETQE A +A+E +
Sbjct: 8 IFIKNLDK-SIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 66
Query: 64 RSKLVDRVISV 74
L DR + V
Sbjct: 67 GMLLNDRKVFV 77
>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 = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 8/57 (14%)
Query: 29 FEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA 77
F P+G++ ++I R FAFV+FE E+A A+++ + S+L R I V A
Sbjct: 23 FIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 79
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 5 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDR 64
+ + L V N P T + +++ FE YG V+ I +++AFV E E+A +A+ D
Sbjct: 8 KASTKLHVGNISPTCTNQ-ELRAKFEEYGPVIECDIVKDYAFVHMERAEDAVEAIRGLDN 66
Query: 65 SKLVDRVISVEYA 77
++ + + V+ +
Sbjct: 67 TEFQGKRMHVQLS 79
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 7/71 (9%)
Query: 10 LFVINFDPIRTRERDIKRHFEPYGNVLHVRI------RRNFAFVQFETQEEATKALESTD 63
+F+ N D + + F +GN+L ++ + + FV FETQE A +A+E +
Sbjct: 14 IFIKNLDK-SIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 72
Query: 64 RSKLVDRVISV 74
L DR + V
Sbjct: 73 GMLLNDRKVFV 83
>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 = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 7/71 (9%)
Query: 10 LFVINFDPIRTRERDIKRHFEPYGNVLHVRI------RRNFAFVQFETQEEATKALESTD 63
+F+ N D + + F +GN+L ++ + + FV FETQE A +A+E +
Sbjct: 101 IFIKNLDK-SIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 159
Query: 64 RSKLVDRVISV 74
L DR + V
Sbjct: 160 GMLLNDRKVFV 170
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 1/81 (1%)
Query: 7 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSK 66
K LFV N T E +++ F +G + V+ +++AF+ F+ ++ A KA+E +
Sbjct: 11 VKVLFVRNLANTVTEEI-LEKAFSQFGKLERVKKLKDYAFIHFDERDGAVKAMEEMNGKD 69
Query: 67 LVDRVISVEYALKDDSERDDR 87
L I + +A D +R +R
Sbjct: 70 LEGENIEIVFAKPPDQKRKER 90
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 35/72 (48%), Gaps = 6/72 (8%)
Query: 25 IKRHFEPYGNVLHVRI--RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDS 82
+++ F P+G ++ +R+ + ++FV+F T E A A+ S + + + V+ +
Sbjct: 42 MRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG----K 97
Query: 83 ERDDRYDSPRRG 94
E D P G
Sbjct: 98 ESPDMTSGPSSG 109
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 28/81 (34%), Positives = 37/81 (45%), Gaps = 9/81 (11%)
Query: 2 ANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQE 53
AN P L V + T ERD++ F YG + V I R FAFV FE +
Sbjct: 10 ANPDPNCCLGVFGLS-LYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 68
Query: 54 EATKALESTDRSKLVDRVISV 74
+A +A E + +L R I V
Sbjct: 69 DAKEAKERANGMELDGRRIRV 89
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 37.0 bits (84), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 21/90 (23%), Positives = 48/90 (53%), Gaps = 9/90 (10%)
Query: 8 KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI-------RRNFAFVQFETQEEATKALE 60
+ L+V N D T E +K++F+ G + +++I N+AFV++ +A AL+
Sbjct: 1 RVLYVGNLDKAIT-EDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQ 59
Query: 61 STDRSKLVDRVISVEYALKD-DSERDDRYD 89
+ + ++ + ++ + +A + S DD ++
Sbjct: 60 TLNGKQIENNIVKINWAFQSQQSSSDDTFN 89
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 36.6 bits (83), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 15/68 (22%), Positives = 32/68 (47%)
Query: 10 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVD 69
+F+ N + ++ D++ F YG V + + +AFVQ+ + A A+ + L
Sbjct: 30 VFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKGYAFVQYSNERHARAAVLGENGRVLAG 89
Query: 70 RVISVEYA 77
+ + + A
Sbjct: 90 QTLDINMA 97
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 36.6 bits (83), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 24/91 (26%), Positives = 43/91 (47%), Gaps = 11/91 (12%)
Query: 10 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIR------RNFAFVQFETQEEATKALESTD 63
L+V N D ER +++ F P+G + ++ + F FV F + EEATKA+ +
Sbjct: 18 LYVKNLDDGIDDER-LRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMN 76
Query: 64 RSKLVDRVISVEYALKDDSERDDRYDSPRRG 94
+ + + V A + +++R P G
Sbjct: 77 GRIVATKPLYVALAQR----KEERQSGPSSG 103
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 36.6 bits (83), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 42/89 (47%), Gaps = 10/89 (11%)
Query: 6 PTKTLFVINFDPIRTRERDIKRHF----EPYGNVLHVRIR----RNFAFVQFETQEEATK 57
P K L++ N P R ERD+ F E G + R+ R AF+ F +E A +
Sbjct: 24 PNKVLYLKNLSP-RVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQ 82
Query: 58 ALESTDRSKLVDRVISVEYALKDDSERDD 86
AL + KL +++ +E+ K+ +R
Sbjct: 83 ALHLVNGYKLYGKILVIEFG-KNKKQRSS 110
>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 = 36.2 bits (82), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 9/78 (11%)
Query: 9 TLFVINFDPIRTRERDIKRHFEPYGNV--LHVRIRR------NFAFVQFETQEEATKALE 60
LFV T E DI F YG + +H+ + R + V++ET +EA A+E
Sbjct: 25 ILFVTGVHEEATEE-DIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 83
Query: 61 STDRSKLVDRVISVEYAL 78
+ L+ + ISV++
Sbjct: 84 GLNGQDLMGQPISVDWCF 101
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 35.8 bits (81), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 35/66 (53%), Gaps = 8/66 (12%)
Query: 20 TRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKALESTDRSKLVDRV 71
TRE D++ F P+G++ + + ++ FAF+ F +E+A +A+ +
Sbjct: 27 TRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLI 86
Query: 72 ISVEYA 77
++VE+A
Sbjct: 87 LNVEWA 92
>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 = 35.8 bits (81), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 13/78 (16%)
Query: 8 KTLFV--INFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATK 57
KTLFV +N+D T E ++R FE YG + + + R +AF+++E + +
Sbjct: 103 KTLFVARVNYD---TTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHS 159
Query: 58 ALESTDRSKLVDRVISVE 75
A + D K+ R + V+
Sbjct: 160 AYKHADGKKIDGRRVLVD 177
>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 = 35.4 bits (80), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 9/78 (11%)
Query: 9 TLFVINFDPIRTRERDIKRHFEPYGNV--LHVRIRR------NFAFVQFETQEEATKALE 60
LFV T E DI F YG + +H+ + R + V++ET +EA A+E
Sbjct: 24 ILFVTGVHEEATEE-DIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 82
Query: 61 STDRSKLVDRVISVEYAL 78
+ L+ + ISV++
Sbjct: 83 GLNGQDLMGQPISVDWCF 100
>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 = 35.0 bits (79), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 34/67 (50%), Gaps = 8/67 (11%)
Query: 19 RTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDR 70
RT ++R FE YG V V I R FAFV+F + +A A+++ D + L R
Sbjct: 58 RTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGR 117
Query: 71 VISVEYA 77
+ V+ A
Sbjct: 118 ELRVQMA 124
>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 = 35.0 bits (79), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 9/78 (11%)
Query: 9 TLFVINFDPIRTRERDIKRHFEPYGNV--LHVRIRR------NFAFVQFETQEEATKALE 60
LFV T E DI F YG + +H+ + R + V++ET +EA A+E
Sbjct: 11 ILFVTGVHEEATEE-DIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 69
Query: 61 STDRSKLVDRVISVEYAL 78
+ L+ + ISV++
Sbjct: 70 GLNGQDLMGQPISVDWCF 87
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 35.0 bits (79), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 17/75 (22%), Positives = 37/75 (49%), Gaps = 8/75 (10%)
Query: 11 FVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALEST 62
++N+ P E +++ FE YG + V+I R + FV+F++ A +A+
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 63 DRSKLVDRVISVEYA 77
+ ++++ + V A
Sbjct: 105 NGFNILNKRLKVALA 119
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 35.0 bits (79), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 27/90 (30%), Positives = 44/90 (48%), Gaps = 14/90 (15%)
Query: 4 QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI---------RRNFAFVQFETQEE 54
++ T + V N P + +R+I+ F +G + VR+ R F FV F T+++
Sbjct: 12 KQTTSKILVRNI-PFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQD 70
Query: 55 ATKALESTDRSK-LVDRVISVEYALKDDSE 83
A KA + S L R + +E+A DSE
Sbjct: 71 AKKAFNALCHSTHLYGRRLVLEWA---DSE 97
>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 = 35.0 bits (79), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 9/78 (11%)
Query: 9 TLFVINFDPIRTRERDIKRHFEPYGNV--LHVRIRR------NFAFVQFETQEEATKALE 60
LFV T E DI F YG + +H+ + R + V++ET +EA A+E
Sbjct: 9 ILFVTGVHEEATEE-DIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 67
Query: 61 STDRSKLVDRVISVEYAL 78
+ L+ + ISV++
Sbjct: 68 GLNGQDLMGQPISVDWCF 85
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 34.7 bits (78), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 9/78 (11%)
Query: 9 TLFVINFDPIRTRERDIKRHFEPYGNV--LHVRIRR------NFAFVQFETQEEATKALE 60
LFV T E DI F YG + +H+ + R + V++ET +EA A+E
Sbjct: 9 ILFVTGVHEEATEE-DIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 67
Query: 61 STDRSKLVDRVISVEYAL 78
+ L+ + ISV++
Sbjct: 68 GLNGQDLMGQPISVDWCF 85
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In
Trinucleotide Repeat Containing 4 Variant
Length = 102
Score = 34.7 bits (78), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 39/83 (46%), Gaps = 8/83 (9%)
Query: 10 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN-------FAFVQFETQEEATKALEST 62
LFV +T E D+++ FEP+G + + R AFV+F+T EA A+ +
Sbjct: 15 LFVGMLGKQQTDE-DVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTL 73
Query: 63 DRSKLVDRVISVEYALKDDSERD 85
S+ + S D+E++
Sbjct: 74 HSSRTLPGASSSLVVKFADTEKE 96
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 34.7 bits (78), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 28/103 (27%), Positives = 46/103 (44%), Gaps = 23/103 (22%)
Query: 8 KTLFV--INFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATK 57
KT+F+ ++FD + E + + +G++ +VR+ + AF QF TQE A K
Sbjct: 16 KTVFIRNLSFD---SEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQK 72
Query: 58 ALESTDRS------KLVDRVISVEYALKDDSERDDRYDSPRRG 94
L + KL R + V+ A+ RD+ P G
Sbjct: 73 CLAAASLEAEGGGLKLDGRQLKVDLAVT----RDEAASGPSSG 111
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 34.7 bits (78), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 7 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTD 63
K LFV N T E +++ F +G + V+ +++AFV FE + A KA++ +
Sbjct: 15 VKVLFVRNLATTVTEEI-LEKSFSEFGKLERVKKLKDYAFVHFEDRGAAVKAMDEMN 70
>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic
Granule-Associated Rna Binding Protein 1
pdb|2RNE|A Chain A, Solution Structure Of The Second Rna Recognition Motif
(Rrm) Of Tia-1
Length = 115
Score = 34.3 bits (77), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 38/89 (42%), Gaps = 9/89 (10%)
Query: 10 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFA--------FVQFETQEEATKALES 61
+FV + P T E DIK F P+G + R+ ++ A FV F + +A A++
Sbjct: 18 VFVGDLSPEITTE-DIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 62 TDRSKLVDRVISVEYALKDDSERDDRYDS 90
L R I +A + Y+S
Sbjct: 77 MGGQWLGGRQIRTNWATRKPPAPKSTYES 105
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 34.3 bits (77), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 38/81 (46%), Gaps = 7/81 (8%)
Query: 3 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI------RRNFAFVQFETQEEAT 56
N+ K L V N P R R+ D+++ F +G +L V I + F FV FE +A
Sbjct: 25 NKSQPKRLHVSNI-PFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADAD 83
Query: 57 KALESTDRSKLVDRVISVEYA 77
+A E + + R I V A
Sbjct: 84 RAREKLHGTVVEGRKIEVNNA 104
>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 = 34.3 bits (77), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 9/78 (11%)
Query: 9 TLFVINFDPIRTRERDIKRHFEPYGNV--LHVRIRR------NFAFVQFETQEEATKALE 60
LFV T E DI F YG + +H+ + R + V++ET +EA A+E
Sbjct: 9 ILFVTGVHEEATEE-DIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 67
Query: 61 STDRSKLVDRVISVEYAL 78
+ L+ + ISV++
Sbjct: 68 GLNGQDLMGQPISVDWCF 85
>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 = 0.048, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 5 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 55
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 7 RPNHTIYINNLNE-KIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSA 65
Query: 56 TKALESTDRSKLVDRVISVEYALKDDSE 83
T AL S D+ + ++YA K DS+
Sbjct: 66 TNALRSMQGFPFYDKPMRIQYA-KTDSD 92
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor
9g8
Length = 101
Score = 33.9 bits (76), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 34/71 (47%), Gaps = 5/71 (7%)
Query: 24 DIKRHFEPYGNVLHVRIRRN---FAFVQFETQEEATKALESTDRSKLVDRVISVEYALKD 80
+++R F YG + V I RN FAFV+FE +A A+ D + + VE L
Sbjct: 16 ELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVE--LST 73
Query: 81 DSERDDRYDSP 91
R R+D P
Sbjct: 74 GMPRRSRFDRP 84
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 33.9 bits (76), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 37/79 (46%), Gaps = 8/79 (10%)
Query: 7 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKA 58
+KT ++N+ P + + K F G++ ++ R+ + FV + +A KA
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 59 LESTDRSKLVDRVISVEYA 77
+ + + KL + I V YA
Sbjct: 63 INTLNGLKLQTKTIKVSYA 81
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 33.5 bits (75), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 37/77 (48%), Gaps = 9/77 (11%)
Query: 9 TLFVINFDPIRTRERDIKRHFEPYGNVL--------HVRIRRNFAFVQFETQEEATKALE 60
TL V N RT ++R FE YG V H + R FAFV+F + +A A
Sbjct: 15 TLKVDNL-TYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEA 73
Query: 61 STDRSKLVDRVISVEYA 77
+ D ++L R + V+ A
Sbjct: 74 AMDGAELDGRELRVQVA 90
>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 = 33.5 bits (75), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 13/78 (16%)
Query: 8 KTLFV--INFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATK 57
KTLFV +N+D T E ++R FE YG + + + R +AF+++E + +
Sbjct: 103 KTLFVARVNYD---TTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHS 159
Query: 58 ALESTDRSKLVDRVISVE 75
A + D K+ R + V+
Sbjct: 160 AYKHADGKKIDGRRVLVD 177
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 33.5 bits (75), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 6/67 (8%)
Query: 17 PIRTRERDIKRHFEPYGNVLHVRI------RRNFAFVQFETQEEATKALESTDRSKLVDR 70
P R R+ D+++ F +G +L V I + F FV FE +A +A E + + R
Sbjct: 24 PFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGR 83
Query: 71 VISVEYA 77
I V A
Sbjct: 84 KIEVNNA 90
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With
The Au-Rich Element
Length = 174
Score = 33.1 bits (74), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 37/79 (46%), Gaps = 8/79 (10%)
Query: 7 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKA 58
+KT ++N+ P + + K F G++ ++ R+ + FV + +A KA
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 59 LESTDRSKLVDRVISVEYA 77
+ + + KL + I V YA
Sbjct: 63 INTLNGLKLQTKTIKVSYA 81
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 33.1 bits (74), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 5 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 55
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 7 RPNHTIYINNLNE-KIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSA 65
Query: 56 TKALESTDRSKLVDRVISVEYALKDDSE 83
T AL S D+ + ++YA K DS+
Sbjct: 66 TNALRSMQGFPFYDKPMRIQYA-KTDSD 92
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 33.1 bits (74), Expect = 0.091, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 40/84 (47%), Gaps = 12/84 (14%)
Query: 2 ANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQE 53
A +P+KTLFV T E +K F+ + RI + F FV F ++E
Sbjct: 10 ARSQPSKTLFVKGLSE-DTTEETLKESFD---GSVRARIVTDRETGSSKGFGFVDFNSEE 65
Query: 54 EATKALESTDRSKLVDRVISVEYA 77
+A A E+ + ++ +++++A
Sbjct: 66 DAKAAKEAMEDGEIDGNKVTLDWA 89
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 32.7 bits (73), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 40/85 (47%), Gaps = 13/85 (15%)
Query: 10 LFV--INFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKAL 59
LFV ++FD T E+ +++ F YG + V + R F FV FE ++A A+
Sbjct: 15 LFVGGLSFD---TNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 71
Query: 60 ESTDRSKLVDRVISVEYALKDDSER 84
+ + + R I V+ A K R
Sbjct: 72 MAMNGKSVDGRQIRVDQAGKSSDNR 96
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 32.7 bits (73), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 25/70 (35%), Positives = 34/70 (48%), Gaps = 3/70 (4%)
Query: 10 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--FAFVQFETQEEATKALESTDRSKL 67
LFV N P E D KR FE YG V I R+ F F++ E++ A A D + L
Sbjct: 25 LFVGNL-PTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTIL 83
Query: 68 VDRVISVEYA 77
R + + +A
Sbjct: 84 KSRPLRIRFA 93
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein
U1a117, Nmr, 43 Structures
Length = 116
Score = 32.7 bits (73), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 5 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 55
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 6 RPNHTIYINNLNE-KIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSA 64
Query: 56 TKALESTDRSKLVDRVISVEYALKDDSE 83
T AL S D+ + ++YA K DS+
Sbjct: 65 TNALRSMQGFPFYDKPMRIQYA-KTDSD 91
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 32.7 bits (73), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 34/67 (50%), Gaps = 8/67 (11%)
Query: 19 RTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDR 70
RT ++R FE YG V V I R FAFV+F + +A A+++ D + L R
Sbjct: 81 RTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGR 140
Query: 71 VISVEYA 77
+ V+ A
Sbjct: 141 ELRVQMA 147
>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 = 32.7 bits (73), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 8/61 (13%)
Query: 22 ERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVIS 73
E I++ F P+G + + + + FAFV++E E A ALE + L R I
Sbjct: 42 EDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIK 101
Query: 74 V 74
V
Sbjct: 102 V 102
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 32.3 bits (72), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 33/76 (43%), Gaps = 9/76 (11%)
Query: 10 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFA--------FVQFETQEEATKALES 61
+FV + P T E DIK F P+G + R+ ++ A FV F + +A A+
Sbjct: 18 VFVGDLSPEITTE-DIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 62 TDRSKLVDRVISVEYA 77
L R I +A
Sbjct: 77 MGGQWLGGRQIRTNWA 92
>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 = 32.3 bits (72), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 5 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 55
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 7 RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 65
Query: 56 TKALESTDRSKLVDRVISVEYALKDDSE 83
T AL S D+ + ++YA K DS+
Sbjct: 66 TNALRSMQGFPFYDKPMRIQYA-KTDSD 92
>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 = 32.3 bits (72), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 5 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 55
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 1 RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 59
Query: 56 TKALESTDRSKLVDRVISVEYALKDDSE 83
T AL S D+ + ++YA K DS+
Sbjct: 60 TNALRSMQGFPFYDKPMRIQYA-KTDSD 86
>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 = 32.3 bits (72), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 5 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 55
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 4 RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 62
Query: 56 TKALESTDRSKLVDRVISVEYALKDDSE 83
T AL S D+ + ++YA K DS+
Sbjct: 63 TNALRSMQGFPFYDKPMRIQYA-KTDSD 89
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 32.3 bits (72), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 37/82 (45%), Gaps = 10/82 (12%)
Query: 6 PTK-TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEAT 56
P+K T++V N P D+ R F YG V+ V I ++ AF+ F ++ A
Sbjct: 14 PSKSTVYVSNL-PFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQ 72
Query: 57 KALESTDRSKLVDRVISVEYAL 78
+ + +L RVI A+
Sbjct: 73 NCTRAINNKQLFGRVIKASIAI 94
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 32.3 bits (72), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 8/66 (12%)
Query: 10 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRR-------NFAFVQFETQEEATKALEST 62
LFV + + E D++R FE +GN+ I R AFV++ + EA A+ +
Sbjct: 18 LFVGMLNK-QQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINAL 76
Query: 63 DRSKLV 68
S+ +
Sbjct: 77 HGSQTM 82
>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 = 32.0 bits (71), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 5 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 55
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 6 RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 64
Query: 56 TKALESTDRSKLVDRVISVEYALKDDSE 83
T AL S D+ + ++YA K DS+
Sbjct: 65 TNALRSMQGFPFYDKPMRIQYA-KTDSD 91
>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 = 32.0 bits (71), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 5 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 55
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 2 RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 60
Query: 56 TKALESTDRSKLVDRVISVEYALKDDSE 83
T AL S D+ + ++YA K DS+
Sbjct: 61 TNALRSMQGFPFYDKPMRIQYA-KTDSD 87
>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 = 32.0 bits (71), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 8/61 (13%)
Query: 22 ERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVIS 73
E I++ F P+G + + + + FAFV++E E A ALE + L R I
Sbjct: 27 EDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIK 86
Query: 74 V 74
V
Sbjct: 87 V 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 = 32.0 bits (71), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 5 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 55
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 7 RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 65
Query: 56 TKALESTDRSKLVDRVISVEYALKDDSE 83
T AL S D+ + ++YA K DS+
Sbjct: 66 TNALRSMQGFPFYDKPMRIQYA-KTDSD 92
>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 = 32.0 bits (71), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 5 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 55
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 6 RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 64
Query: 56 TKALESTDRSKLVDRVISVEYALKDDSE 83
T AL S D+ + ++YA K DS+
Sbjct: 65 TNALRSMQGFPFYDKPMRIQYA-KTDSD 91
>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 = 32.0 bits (71), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 5 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 55
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 6 RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 64
Query: 56 TKALESTDRSKLVDRVISVEYALKDDSE 83
T AL S D+ + ++YA K DS+
Sbjct: 65 TNALRSMQGFPFYDKPMRIQYA-KTDSD 91
>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 = 32.0 bits (71), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 5 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 55
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 3 RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 61
Query: 56 TKALESTDRSKLVDRVISVEYALKDDSE 83
T AL S D+ + ++YA K DS+
Sbjct: 62 TNALRSMQGFPFYDKPMRIQYA-KTDSD 88
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 31.6 bits (70), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 3/73 (4%)
Query: 7 TKTLFVINFDPIRTRERDIKRHFEPY--GNVLHVRIRRNFAFVQFETQEEATKALESTDR 64
K L+V N + T E I++ F G V V+ R++AFV F +E+A +A+++ +
Sbjct: 15 VKILYVRNL-MLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNG 73
Query: 65 SKLVDRVISVEYA 77
L I V A
Sbjct: 74 KVLDGSPIEVTLA 86
>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 = 31.2 bits (69), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 19/85 (22%), Positives = 42/85 (49%), Gaps = 8/85 (9%)
Query: 1 MANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNF--------AFVQFETQ 52
M + R + T ++N+ P +R++ F G + RI R++ AFV F ++
Sbjct: 7 MNDPRASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSE 66
Query: 53 EEATKALESTDRSKLVDRVISVEYA 77
++ +A++ + + ++ + V YA
Sbjct: 67 XDSQRAIKVLNGITVRNKRLKVSYA 91
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 31.2 bits (69), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 30/67 (44%), Gaps = 7/67 (10%)
Query: 20 TRERDIKRHFEPYGNVLHVRI-------RRNFAFVQFETQEEATKALESTDRSKLVDRVI 72
T E+ +K F +G + V + R FAF+ FE +A A + + L + I
Sbjct: 19 TNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAI 78
Query: 73 SVEYALK 79
VE A K
Sbjct: 79 KVEQAKK 85
>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 = 30.8 bits (68), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 28/61 (45%), Gaps = 8/61 (13%)
Query: 22 ERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVIS 73
E I++ F P+G + + + FAFV++E E A ALE + L R I
Sbjct: 26 EDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQXNSVXLGGRNIK 85
Query: 74 V 74
V
Sbjct: 86 V 86
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 30.8 bits (68), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 9/63 (14%)
Query: 25 IKRHFEPYGNV---------LHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISVE 75
I F YG + +H + + +A+V+FE +EA KAL+ D ++ + I+
Sbjct: 21 IMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITAT 80
Query: 76 YAL 78
L
Sbjct: 81 AVL 83
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 30.8 bits (68), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 44/88 (50%), Gaps = 11/88 (12%)
Query: 5 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 55
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 4 RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSA 62
Query: 56 TKALESTDRSKLVDRVISVEYALKDDSE 83
T AL S D+ ++YA K DS+
Sbjct: 63 TNALRSXQGFPFYDKPXRIQYA-KTDSD 89
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 30.4 bits (67), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 44/88 (50%), Gaps = 11/88 (12%)
Query: 5 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 55
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 6 RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSA 64
Query: 56 TKALESTDRSKLVDRVISVEYALKDDSE 83
T AL S D+ ++YA K DS+
Sbjct: 65 TNALRSXQGFPFYDKPXRIQYA-KTDSD 91
>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 = 30.4 bits (67), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 44/88 (50%), Gaps = 11/88 (12%)
Query: 5 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 55
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 7 RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSA 65
Query: 56 TKALESTDRSKLVDRVISVEYALKDDSE 83
T AL S D+ ++YA K DS+
Sbjct: 66 TNALRSXQGFPFYDKPXRIQYA-KTDSD 92
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 30.4 bits (67), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 39/78 (50%), Gaps = 10/78 (12%)
Query: 10 LFVINFDPIRTRERDIKRHFEPYG-NVLHVRIRRN--------FAFVQFETQEEATKALE 60
+ ++ P E DI+ + +G VR+ RN FAFV+F ++AT+ +E
Sbjct: 3 IVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWME 62
Query: 61 STDRS-KLVDRVISVEYA 77
+ S ++ + +S+ Y+
Sbjct: 63 ANQHSLNILGQKVSMHYS 80
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 30.0 bits (66), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 3/57 (5%)
Query: 24 DIKRHFEPYGNVLHVRIRRN---FAFVQFETQEEATKALESTDRSKLVDRVISVEYA 77
+++R F YG + V + RN FAFV+FE +A A+ D L + VE +
Sbjct: 89 ELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELS 145
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 30.0 bits (66), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 3/57 (5%)
Query: 24 DIKRHFEPYGNVLHVRIRRN---FAFVQFETQEEATKALESTDRSKLVDRVISVEYA 77
+++R F YG + V + RN FAFV+FE +A A+ D L + VE +
Sbjct: 89 ELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRDLDGRTLCGCRVRVELS 145
>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 = 29.6 bits (65), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 18/80 (22%), Positives = 37/80 (46%), Gaps = 9/80 (11%)
Query: 5 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHV--------RIRRNFAFVQFETQEEAT 56
+ + TL+V N T E I F G++ + + F FV++ ++ +A
Sbjct: 37 KKSCTLYVGNL-SFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAE 95
Query: 57 KALESTDRSKLVDRVISVEY 76
A+ + ++L DR+I ++
Sbjct: 96 NAMRYINGTRLDDRIIRTDW 115
>pdb|1S79|A Chain A, Solution Structure Of The Central Rrm Of Human La
Protein
Length = 103
Score = 29.6 bits (65), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 33/68 (48%), Gaps = 8/68 (11%)
Query: 1 MANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNF-------AFVQFETQE 53
+ N +++++ F P DIK E G VL++++RR FV F++ E
Sbjct: 5 LKNDVKNRSVYIKGF-PTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIE 63
Query: 54 EATKALES 61
A K +E+
Sbjct: 64 SAKKFVET 71
>pdb|2VOD|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auauuuu
pdb|2VOD|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auauuuu
pdb|2VON|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auaauuu
pdb|2VON|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auaauuu
pdb|2VOO|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Uuuuuuuu
pdb|2VOO|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Uuuuuuuu
pdb|2VOP|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auuuu
Length = 193
Score = 29.3 bits (64), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 7/45 (15%)
Query: 24 DIKRHFEPYGNVLHVRIRRNF-------AFVQFETQEEATKALES 61
DIK E G VL++++RR FV F++ E A K +E+
Sbjct: 125 DIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVET 169
>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 = 28.9 bits (63), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 17/79 (21%), Positives = 37/79 (46%), Gaps = 8/79 (10%)
Query: 7 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKA 58
+KT ++N+ P + + + F G + ++ R+ + FV + ++A KA
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 59 LESTDRSKLVDRVISVEYA 77
+ + + +L + I V YA
Sbjct: 61 INTLNGLRLQTKTIKVSYA 79
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 28.5 bits (62), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 17/80 (21%), Positives = 39/80 (48%), Gaps = 8/80 (10%)
Query: 6 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNF--------AFVQFETQEEATK 57
+ T ++N+ P +R++ F G + RI R++ AFV F ++ ++ +
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 58 ALESTDRSKLVDRVISVEYA 77
A++ + + ++ + V YA
Sbjct: 61 AIKVLNGITVRNKRLKVSYA 80
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 28.5 bits (62), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 17/79 (21%), Positives = 39/79 (49%), Gaps = 8/79 (10%)
Query: 7 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNF--------AFVQFETQEEATKA 58
+ T ++N+ P +R++ F G + RI R++ AFV F ++ ++ +A
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 59 LESTDRSKLVDRVISVEYA 77
++ + + ++ + V YA
Sbjct: 62 IKVLNGITVRNKRLKVSYA 80
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 28.1 bits (61), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 6/59 (10%)
Query: 10 LFVINFDPIRTRERDIKRHFEPYGNV--LHVRIRRN---FAFVQFETQEEATKALESTD 63
++V N P R +DI+ F YG + + ++ RR FAFV+FE +A A+ D
Sbjct: 25 IYVGNLPP-DIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRD 82
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 28.1 bits (61), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 11/77 (14%)
Query: 7 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN-------FAFVQFETQEEATKAL 59
+KTL + N T E ++ FE +++ +N +AF++F + E+A +AL
Sbjct: 15 SKTLVLSNLSYSATEE-TLQEVFE---KATFIKVPQNQNGKSKGYAFIEFASFEDAKEAL 70
Query: 60 ESTDRSKLVDRVISVEY 76
S ++ ++ R I +E
Sbjct: 71 NSCNKREIEGRAIRLEL 87
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 27.3 bits (59), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 23/52 (44%), Gaps = 8/52 (15%)
Query: 17 PIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALE 60
+ T D+K +FE +G V + R F FV FE+++ K E
Sbjct: 8 SVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 27.3 bits (59), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 15/30 (50%), Positives = 19/30 (63%), Gaps = 2/30 (6%)
Query: 35 VLHVRI--RRNFAFVQFETQEEATKALEST 62
V+ VRI R F +V FE+ E+ KALE T
Sbjct: 39 VVDVRIGMTRKFGYVDFESAEDLEKALELT 68
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
0.320 0.139 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,008,810
Number of Sequences: 62578
Number of extensions: 180930
Number of successful extensions: 411
Number of sequences better than 100.0: 93
Number of HSP's better than 100.0 without gapping: 40
Number of HSP's successfully gapped in prelim test: 53
Number of HSP's that attempted gapping in prelim test: 360
Number of HSP's gapped (non-prelim): 97
length of query: 182
length of database: 14,973,337
effective HSP length: 93
effective length of query: 89
effective length of database: 9,153,583
effective search space: 814668887
effective search space used: 814668887
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)