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= 026341
(240 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 = 47.0 bits (110), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 30/90 (33%), Positives = 46/90 (51%), Gaps = 6/90 (6%)
Query: 46 RGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFV 105
RG HR + ++N R LFV F P+ +E ++ F P+G + V+I FAFV
Sbjct: 17 RGSHMHHRQEGE-LSNTR----LFVRPF-PLDVQESELNEIFGPFGPMKEVKILNGFAFV 70
Query: 106 QFETQEEATKALESTDRSKLVDRVISVEYA 135
+FE E A KA+E ++ + V Y+
Sbjct: 71 EFEEAESAAKAIEEVHGKSFANQPLEVVYS 100
>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 = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 34/131 (25%), Positives = 60/131 (45%), Gaps = 20/131 (15%)
Query: 9 GFAFVYFEDDRDAADAIRGLDNIPFGYDRRR-LSVEWARGERGRHRDGSKSMANQRPTKT 67
G+A+V F+ ADA R LD + F + + + + W++ + + G
Sbjct: 58 GYAYVNFQQ---PADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSG---------VGN 105
Query: 68 LFVINFDPIRTRERDIKRHFEPYGNVLHVRI------RRNFAFVQFETQEEATKALESTD 121
+F+ N D + + F +GN+L ++ + + FV FETQE A +A+E +
Sbjct: 106 IFIKNLDK-SIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 164
Query: 122 RSKLVDRVISV 132
L DR + V
Sbjct: 165 GMLLNDRKVFV 175
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 45.8 bits (107), Expect = 2e-05, Method: Composition-based stats.
Identities = 24/68 (35%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 68 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVD 127
LFV F P+ +E ++ F P+G + V+I FAFV+FE E A KA+E +
Sbjct: 7 LFVRPF-PLDVQESELNEIFGPFGPMKEVKILNGFAFVEFEEAESAAKAIEEVHGKSFAN 65
Query: 128 RVISVEYA 135
+ + V Y+
Sbjct: 66 QPLEVVYS 73
>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 = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 34/131 (25%), Positives = 60/131 (45%), Gaps = 20/131 (15%)
Query: 9 GFAFVYFEDDRDAADAIRGLDNIPFGYDRRR-LSVEWARGERGRHRDGSKSMANQRPTKT 67
G+A+V F+ ADA R LD + F + + + + W++ + + G
Sbjct: 53 GYAYVNFQQ---PADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSG---------VGN 100
Query: 68 LFVINFDPIRTRERDIKRHFEPYGNVLHVRI------RRNFAFVQFETQEEATKALESTD 121
+F+ N D + + F +GN+L ++ + + FV FETQE A +A+E +
Sbjct: 101 IFIKNLDK-SIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 159
Query: 122 RSKLVDRVISV 132
L DR + V
Sbjct: 160 GMLLNDRKVFV 170
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 37/77 (48%)
Query: 59 MANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALE 118
M N P LF+ N + D+ R F PYG+++ + I+ F F+QF+ + A+E
Sbjct: 4 MHNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIE 63
Query: 119 STDRSKLVDRVISVEYA 135
+ + + +E +
Sbjct: 64 CESQEMNFGKKLILEVS 80
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 35/68 (51%)
Query: 68 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVD 127
+F+ N + + ++ D++ F YG ++ + + FAFVQ+ + A A+ D +
Sbjct: 18 VFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERNARAAVAGEDGRMIAG 77
Query: 128 RVISVEYA 135
+V+ + A
Sbjct: 78 QVLDINLA 85
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 42.4 bits (98), Expect = 3e-04, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 29/55 (52%)
Query: 64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALE 118
P LF+ N + D+ R F PYG+++ + I+ F F+QF+ + A+E
Sbjct: 1 PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIE 55
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 42/89 (47%), Gaps = 8/89 (8%)
Query: 55 GSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQ 106
GS + TK + + ++ + F P+G++ ++I R FAFV+
Sbjct: 1 GSSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 60
Query: 107 FETQEEATKALESTDRSKLVDRVISVEYA 135
FE E+A A+++ + S+L R I V A
Sbjct: 61 FELAEDAAAAIDNMNESELFGRTIRVNLA 89
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 43/83 (51%), Gaps = 10/83 (12%)
Query: 68 LFVINFDPIRTRERDIKRHFEPYGNVLHV-RIRRN--------FAFVQFETQEEATKALE 118
+F+ N DP E+ + F +G +L +I R+ +AF+ F + + + A+E
Sbjct: 8 IFIGNLDP-EIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66
Query: 119 STDRSKLVDRVISVEYALKDDSE 141
+ + L +R I+V YA K DS+
Sbjct: 67 AMNGQYLCNRPITVSYAFKKDSK 89
>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 = 0.001, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 29/55 (52%)
Query: 68 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDR 122
LF+ N + D+ R F PYG+++ + I+ F F+QF+ + A+E +
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECESQ 79
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/91 (29%), Positives = 46/91 (50%), Gaps = 4/91 (4%)
Query: 55 GSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEAT 114
GS MA K LFV N T E +++ F +G + V+ +++AF+ F+ ++ A
Sbjct: 4 GSSGMAK---VKVLFVRNLANTVTEE-ILEKAFSQFGKLERVKKLKDYAFIHFDERDGAV 59
Query: 115 KALESTDRSKLVDRVISVEYALKDDSERDDR 145
KA+E + L I + +A D +R +R
Sbjct: 60 KAMEEMNGKDLEGENIEIVFAKPPDQKRKER 90
>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 = 0.001, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 34/66 (51%), Gaps = 1/66 (1%)
Query: 68 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVD 127
LF+ N P E++I+ FE YG VL I +N+ FV E + A A+ + KL
Sbjct: 11 LFIGNL-PREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAIRNLHHYKLHG 69
Query: 128 RVISVE 133
I+VE
Sbjct: 70 VNINVE 75
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 28/85 (32%), Positives = 41/85 (48%), Gaps = 9/85 (10%)
Query: 60 ANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQE 111
AN P L V + T ERD++ F YG + V I R FAFV FE +
Sbjct: 41 ANPDPNCCLGVFGLS-LYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 99
Query: 112 EATKALESTDRSKLVDRVISVEYAL 136
+A +A E + +L R I V++++
Sbjct: 100 DAKEAKERANGMELDGRRIRVDFSI 124
Score = 27.3 bits (59), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 25/41 (60%), Gaps = 2/41 (4%)
Query: 9 GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER 49
GFAFVYFE+ DA +A + + D RR+ V+++ +R
Sbjct: 89 GFAFVYFENVDDAKEAKERANGMEL--DGRRIRVDFSITKR 127
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 28/51 (54%)
Query: 68 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALE 118
LF+ N + D+ R F PYG+++ + I+ F F+QF+ + A+E
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIE 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 = 0.002, Method: Compositional matrix adjust.
Identities = 29/89 (32%), Positives = 43/89 (48%), Gaps = 9/89 (10%)
Query: 56 SKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQF 107
S + AN P L V + T ERD++ F YG + V I R FAFV F
Sbjct: 6 SGNRANPDPNCCLGVFGLS-LYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF 64
Query: 108 ETQEEATKALESTDRSKLVDRVISVEYAL 136
E ++A +A E + +L R I V++++
Sbjct: 65 ENVDDAKEAKERANGMELDGRRIRVDFSI 93
Score = 26.9 bits (58), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 25/41 (60%), Gaps = 2/41 (4%)
Query: 9 GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER 49
GFAFVYFE+ DA +A + + D RR+ V+++ +R
Sbjct: 58 GFAFVYFENVDDAKEAKERANGMEL--DGRRIRVDFSITKR 96
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 29/87 (33%), Positives = 42/87 (48%), Gaps = 9/87 (10%)
Query: 58 SMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFET 109
S AN P L V + T ERD++ F YG + V I R FAFV FE
Sbjct: 5 SRANPDPNCCLGVFGLS-LYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 63
Query: 110 QEEATKALESTDRSKLVDRVISVEYAL 136
++A +A E + +L R I V++++
Sbjct: 64 VDDAKEAKERANGMELDGRRIRVDFSI 90
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/38 (52%), Positives = 24/38 (63%), Gaps = 2/38 (5%)
Query: 9 GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR 46
GFAF+ F DAA AI G+ FGYD L+VEWA+
Sbjct: 58 GFAFISFHRREDAARAIAGVSG--FGYDHLILNVEWAK 93
Score = 35.0 bits (79), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 35/66 (53%), Gaps = 8/66 (12%)
Query: 78 TRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKALESTDRSKLVDRV 129
TRE D++ F P+G++ + + ++ FAF+ F +E+A +A+ +
Sbjct: 27 TRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLI 86
Query: 130 ISVEYA 135
++VE+A
Sbjct: 87 LNVEWA 92
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/41 (56%), Positives = 26/41 (63%), Gaps = 2/41 (4%)
Query: 9 GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER 49
GFAFV FED RDAADA+R LD R R VE + GE+
Sbjct: 111 GFAFVEFEDPRDAADAVRELDGRTLCGCRVR--VELSNGEK 149
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 3/57 (5%)
Query: 82 DIKRHFEPYGNVLHVRIRRN---FAFVQFETQEEATKALESTDRSKLVDRVISVEYA 135
+++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 = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/41 (56%), Positives = 26/41 (63%), Gaps = 2/41 (4%)
Query: 9 GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER 49
GFAFV FED RDAADA+R LD R R VE + GE+
Sbjct: 111 GFAFVEFEDPRDAADAVRDLDGRTLCGCRVR--VELSNGEK 149
Score = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 3/57 (5%)
Query: 82 DIKRHFEPYGNVLHVRIRRN---FAFVQFETQEEATKALESTDRSKLVDRVISVEYA 135
+++R F YG + V + RN FAFV+FE +A A+ D L + VE +
Sbjct: 89 ELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRDLDGRTLCGCRVRVELS 145
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 8/57 (14%)
Query: 87 FEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA 135
F P+G++ ++I R FAFV+FE E+A A+++ + S+L R I V A
Sbjct: 26 FIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 82
>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 = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 8/57 (14%)
Query: 87 FEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA 135
F P+G++ ++I R FAFV+FE E+A A+++ + S+L R I V A
Sbjct: 28 FIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 84
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 8/57 (14%)
Query: 87 FEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA 135
F P+G++ ++I R FAFV+FE E+A A+++ + S+L R I V A
Sbjct: 84 FIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDR 122
+ + L V N P T + +++ FE YG V+ I +++AFV E E+A +A+ D
Sbjct: 8 KASTKLHVGNISPTCTNQ-ELRAKFEEYGPVIECDIVKDYAFVHMERAEDAVEAIRGLDN 66
Query: 123 SKLVDRVISVEYA 135
++ + + V+ +
Sbjct: 67 TEFQGKRMHVQLS 79
Score = 35.4 bits (80), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 16/37 (43%), Positives = 22/37 (59%)
Query: 10 FAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR 46
+AFV+ E DA +AIRGLDN F R + + +R
Sbjct: 46 YAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSR 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 = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 7/71 (9%)
Query: 68 LFVINFDPIRTRERDIKRHFEPYGNVLHVRI------RRNFAFVQFETQEEATKALESTD 121
+F+ N D + + F +GN+L ++ + + FV FETQE A +A+E +
Sbjct: 8 IFIKNLDK-SIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 66
Query: 122 RSKLVDRVISV 132
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 = 38.1 bits (87), Expect = 0.004, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 8/57 (14%)
Query: 87 FEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA 135
F P+G++ ++I R FAFV+FE E+A A+++ + S+L R I V A
Sbjct: 23 FIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 79
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor
9g8
Length = 101
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/30 (60%), Positives = 22/30 (73%)
Query: 1 MCISLHYAGFAFVYFEDDRDAADAIRGLDN 30
+ I+ + GFAFV FED RDA DA+RGLD
Sbjct: 30 VWIARNPPGFAFVEFEDPRDAEDAVRGLDG 59
Score = 33.5 bits (75), Expect = 0.099, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 34/71 (47%), Gaps = 5/71 (7%)
Query: 82 DIKRHFEPYGNVLHVRIRRN---FAFVQFETQEEATKALESTDRSKLVDRVISVEYALKD 138
+++R F YG + V I RN FAFV+FE +A A+ D + + VE L
Sbjct: 16 ELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVE--LST 73
Query: 139 DSERDDRYDSP 149
R R+D P
Sbjct: 74 GMPRRSRFDRP 84
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 37.7 bits (86), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 23/41 (56%), Positives = 26/41 (63%), Gaps = 2/41 (4%)
Query: 10 FAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG 50
FAFV FED RDA DA+ G D + YD RL VE+ R RG
Sbjct: 63 FAFVEFEDPRDAEDAVYGRDG--YDYDGYRLRVEFPRSGRG 101
Score = 28.1 bits (61), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 6/59 (10%)
Query: 68 LFVINFDPIRTRERDIKRHFEPYGNV--LHVRIRRN---FAFVQFETQEEATKALESTD 121
++V N P R +DI+ F YG + + ++ RR FAFV+FE +A A+ D
Sbjct: 25 IYVGNLPP-DIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRD 82
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 37.7 bits (86), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 7/72 (9%)
Query: 67 TLFVINFDPIRTRERDIKRHFEPYGNVLHVRI------RRNFAFVQFETQEEATKALEST 120
+F+ N D + + F +GN+L ++ + + FV FETQE A +A+E
Sbjct: 13 NIFIKNLDK-SIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKM 71
Query: 121 DRSKLVDRVISV 132
+ L DR + V
Sbjct: 72 NGMLLNDRKVFV 83
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 35/72 (48%), Gaps = 6/72 (8%)
Query: 83 IKRHFEPYGNVLHVRI--RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDS 140
+++ F P+G ++ +R+ + ++FV+F T E A A+ S + + + V+ +
Sbjct: 42 MRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG----K 97
Query: 141 ERDDRYDSPRRG 152
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 = 0.006, Method: Compositional matrix adjust.
Identities = 29/85 (34%), Positives = 39/85 (45%), Gaps = 9/85 (10%)
Query: 56 SKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQF 107
S + AN P L V + T ERD++ F YG + V I R FAFV F
Sbjct: 6 SGNRANPDPNCCLGVFGLS-LYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF 64
Query: 108 ETQEEATKALESTDRSKLVDRVISV 132
E ++A +A E + +L R I V
Sbjct: 65 ENVDDAKEAKERANGMELDGRRIRV 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 = 0.009, Method: Compositional matrix adjust.
Identities = 21/90 (23%), Positives = 48/90 (53%), Gaps = 9/90 (10%)
Query: 66 KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI-------RRNFAFVQFETQEEATKALE 118
+ L+V N D T E +K++F+ G + +++I N+AFV++ +A AL+
Sbjct: 1 RVLYVGNLDKAIT-EDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQ 59
Query: 119 STDRSKLVDRVISVEYALKD-DSERDDRYD 147
+ + ++ + ++ + +A + S DD ++
Sbjct: 60 TLNGKQIENNIVKINWAFQSQQSSSDDTFN 89
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 37.0 bits (84), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 33/121 (27%), Positives = 57/121 (47%), Gaps = 22/121 (18%)
Query: 9 GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTL 68
G+AFV F + D+ AI+ L+ I +RL V +AR G +S+ + L
Sbjct: 46 GYAFVDFTSEMDSQRAIKVLNGITV--RNKRLKVSYAR-------PGGESIKD----TNL 92
Query: 69 FVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKALEST 120
+V N P + + F YG+++ I R+ AFV++ +EEA +A+ +
Sbjct: 93 YVTNL-PRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151
Query: 121 D 121
+
Sbjct: 152 N 152
Score = 28.5 bits (62), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 17/79 (21%), Positives = 39/79 (49%), Gaps = 8/79 (10%)
Query: 65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNF--------AFVQFETQEEATKA 116
+ T ++N+ P +R++ F G + RI R++ AFV F ++ ++ +A
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 117 LESTDRSKLVDRVISVEYA 135
++ + + ++ + V YA
Sbjct: 62 IKVLNGITVRNKRLKVSYA 80
>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 = 37.0 bits (84), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 33/121 (27%), Positives = 57/121 (47%), Gaps = 22/121 (18%)
Query: 9 GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTL 68
G+AFV F + D+ AI+ L+ I +RL V +AR G +S+ + L
Sbjct: 57 GYAFVDFTSEXDSQRAIKVLNGITV--RNKRLKVSYAR-------PGGESIKDT----NL 103
Query: 69 FVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKALEST 120
+V N P + + F YG+++ I R+ AFV++ +EEA +A+ +
Sbjct: 104 YVTNL-PRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 162
Query: 121 D 121
+
Sbjct: 163 N 163
Score = 31.6 bits (70), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 19/85 (22%), Positives = 42/85 (49%), Gaps = 8/85 (9%)
Query: 59 MANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNF--------AFVQFETQ 110
M + R + T ++N+ P +R++ F G + RI R++ AFV F ++
Sbjct: 7 MNDPRASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSE 66
Query: 111 EEATKALESTDRSKLVDRVISVEYA 135
++ +A++ + + ++ + V YA
Sbjct: 67 XDSQRAIKVLNGITVRNKRLKVSYA 91
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 36.6 bits (83), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 42/89 (47%), Gaps = 10/89 (11%)
Query: 64 PTKTLFVINFDPIRTRERDIKRHF----EPYGNVLHVRIR----RNFAFVQFETQEEATK 115
P K L++ N P R ERD+ F E G + R+ R AF+ F +E A +
Sbjct: 24 PNKVLYLKNLSP-RVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQ 82
Query: 116 ALESTDRSKLVDRVISVEYALKDDSERDD 144
AL + KL +++ +E+ K+ +R
Sbjct: 83 ALHLVNGYKLYGKILVIEFG-KNKKQRSS 110
>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 = 0.012, Method: Compositional matrix adjust.
Identities = 24/91 (26%), Positives = 43/91 (47%), Gaps = 11/91 (12%)
Query: 68 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIR------RNFAFVQFETQEEATKALESTD 121
L+V N D ER +++ F P+G + ++ + F FV F + EEATKA+ +
Sbjct: 18 LYVKNLDDGIDDER-LRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMN 76
Query: 122 RSKLVDRVISVEYALKDDSERDDRYDSPRRG 152
+ + + V A + +++R P G
Sbjct: 77 GRIVATKPLYVALAQR----KEERQSGPSSG 103
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 36.6 bits (83), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 27/98 (27%), Positives = 46/98 (46%), Gaps = 13/98 (13%)
Query: 54 DGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI---------RRNFAF 104
GS ++ T + ++ P + +R+I+ F +G + VR+ R F F
Sbjct: 3 SGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGF 62
Query: 105 VQFETQEEATKALESTDRSK-LVDRVISVEYALKDDSE 141
V F T+++A KA + S L R + +E+A DSE
Sbjct: 63 VDFITKQDAKKAFNALCHSTHLYGRRLVLEWA---DSE 97
Score = 28.9 bits (63), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 17/40 (42%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 9 GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE 48
GF FV F +DA A L + Y RRL +EWA E
Sbjct: 59 GFGFVDFITKQDAKKAFNALCHSTHLYG-RRLVLEWADSE 97
>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm
pdb|2LEB|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uccagu-3'
pdb|2LEC|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uggagu-3'
Length = 135
Score = 36.2 bits (82), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 30/99 (30%), Positives = 47/99 (47%), Gaps = 13/99 (13%)
Query: 50 GRHRDGSKSMANQRP---TKTLFVINFDPI--RTRERDIKRHFEPYGNVLHVRI------ 98
G + G SM+ RP + + + D + RT ++R FE YG V V I
Sbjct: 26 GGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYT 85
Query: 99 --RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA 135
R FAFV+F + +A A+++ D + L R + V+ A
Sbjct: 86 KESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA 124
Score = 34.3 bits (77), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 19/38 (50%), Positives = 22/38 (57%), Gaps = 2/38 (5%)
Query: 9 GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR 46
GFAFV F D RDA DA+ +D D R L V+ AR
Sbjct: 90 GFAFVRFHDKRDAEDAMDAMDGAVL--DGRELRVQMAR 125
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 35.8 bits (81), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 15/68 (22%), Positives = 32/68 (47%)
Query: 68 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVD 127
+F+ N + ++ D++ F YG V + + +AFVQ+ + A A+ + L
Sbjct: 30 VFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKGYAFVQYSNERHARAAVLGENGRVLAG 89
Query: 128 RVISVEYA 135
+ + + A
Sbjct: 90 QTLDINMA 97
>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 = 35.4 bits (80), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 13/78 (16%)
Query: 66 KTLFV--INFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATK 115
KTLFV +N+D T E ++R FE YG + + + R +AF+++E + +
Sbjct: 103 KTLFVARVNYD---TTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHS 159
Query: 116 ALESTDRSKLVDRVISVE 133
A + D K+ R + V+
Sbjct: 160 AYKHADGKKIDGRRVLVD 177
>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 = 35.0 bits (79), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 9/78 (11%)
Query: 67 TLFVINFDPIRTRERDIKRHFEPYGNV--LHVRIRR------NFAFVQFETQEEATKALE 118
LFV T E DI F YG + +H+ + R + V++ET +EA A+E
Sbjct: 25 ILFVTGVHEEATEE-DIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 83
Query: 119 STDRSKLVDRVISVEYAL 136
+ L+ + ISV++
Sbjct: 84 GLNGQDLMGQPISVDWCF 101
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 34.7 bits (78), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 17/75 (22%), Positives = 37/75 (49%), Gaps = 8/75 (10%)
Query: 69 FVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALEST 120
++N+ P E +++ FE YG + V+I R + FV+F++ A +A+
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 121 DRSKLVDRVISVEYA 135
+ ++++ + V A
Sbjct: 105 NGFNILNKRLKVALA 119
>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 = 34.7 bits (78), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 9/78 (11%)
Query: 67 TLFVINFDPIRTRERDIKRHFEPYGNV--LHVRIRR------NFAFVQFETQEEATKALE 118
LFV T E DI F YG + +H+ + R + V++ET +EA A+E
Sbjct: 24 ILFVTGVHEEATEE-DIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 82
Query: 119 STDRSKLVDRVISVEYAL 136
+ L+ + ISV++
Sbjct: 83 GLNGQDLMGQPISVDWCF 100
>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 = 34.7 bits (78), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 9/78 (11%)
Query: 67 TLFVINFDPIRTRERDIKRHFEPYGNV--LHVRIRR------NFAFVQFETQEEATKALE 118
LFV T E DI F YG + +H+ + R + V++ET +EA A+E
Sbjct: 11 ILFVTGVHEEATEE-DIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 69
Query: 119 STDRSKLVDRVISVEYAL 136
+ L+ + ISV++
Sbjct: 70 GLNGQDLMGQPISVDWCF 87
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 34.7 bits (78), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 29/93 (31%), Positives = 42/93 (45%), Gaps = 11/93 (11%)
Query: 49 RGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI------RRNF 102
RG H + N+ K L V N P R R+ D+++ F +G +L V I + F
Sbjct: 17 RGSHMN----TENKSQPKRLHVSNI-PFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGF 71
Query: 103 AFVQFETQEEATKALESTDRSKLVDRVISVEYA 135
FV FE +A +A E + + R I V A
Sbjct: 72 GFVTFENSADADRAREKLHGTVVEGRKIEVNNA 104
>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 = 0.053, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 39/83 (46%), Gaps = 8/83 (9%)
Query: 68 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN-------FAFVQFETQEEATKALEST 120
LFV +T E D+++ FEP+G + + R AFV+F+T EA A+ +
Sbjct: 15 LFVGMLGKQQTDE-DVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTL 73
Query: 121 DRSKLVDRVISVEYALKDDSERD 143
S+ + S D+E++
Sbjct: 74 HSSRTLPGASSSLVVKFADTEKE 96
>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 = 0.055, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 38/89 (42%), Gaps = 9/89 (10%)
Query: 68 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFA--------FVQFETQEEATKALES 119
+FV + P T E DIK F P+G + R+ ++ A FV F + +A A++
Sbjct: 18 VFVGDLSPEITTE-DIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 120 TDRSKLVDRVISVEYALKDDSERDDRYDS 148
L R I +A + Y+S
Sbjct: 77 MGGQWLGGRQIRTNWATRKPPAPKSTYES 105
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 34.3 bits (77), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTD 121
K LFV N T E +++ F +G + V+ +++AFV FE + A KA++ +
Sbjct: 15 VKVLFVRNLATTVTEEI-LEKSFSEFGKLERVKKLKDYAFVHFEDRGAAVKAMDEMN 70
>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 = 34.3 bits (77), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 9/78 (11%)
Query: 67 TLFVINFDPIRTRERDIKRHFEPYGNV--LHVRIRR------NFAFVQFETQEEATKALE 118
LFV T E DI F YG + +H+ + R + V++ET +EA A+E
Sbjct: 9 ILFVTGVHEEATEE-DIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 67
Query: 119 STDRSKLVDRVISVEYAL 136
+ 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 = 33.9 bits (76), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 9/78 (11%)
Query: 67 TLFVINFDPIRTRERDIKRHFEPYGNV--LHVRIRR------NFAFVQFETQEEATKALE 118
LFV T E DI F YG + +H+ + R + V++ET +EA A+E
Sbjct: 9 ILFVTGVHEEATEE-DIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 67
Query: 119 STDRSKLVDRVISVEYAL 136
+ L+ + ISV++
Sbjct: 68 GLNGQDLMGQPISVDWCF 85
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 33.9 bits (76), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 28/103 (27%), Positives = 46/103 (44%), Gaps = 23/103 (22%)
Query: 66 KTLFV--INFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATK 115
KT+F+ ++FD + E + + +G++ +VR+ + AF QF TQE A K
Sbjct: 16 KTVFIRNLSFD---SEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQK 72
Query: 116 ALESTDRS------KLVDRVISVEYALKDDSERDDRYDSPRRG 152
L + KL R + V+ A+ RD+ P G
Sbjct: 73 CLAAASLEAEGGGLKLDGRQLKVDLAVT----RDEAASGPSSG 111
>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 = 0.087, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 37/79 (46%), Gaps = 8/79 (10%)
Query: 65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKA 116
+KT ++N+ P + + K F G++ ++ R+ + FV + +A KA
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 117 LESTDRSKLVDRVISVEYA 135
+ + + KL + I V YA
Sbjct: 63 INTLNGLKLQTKTIKVSYA 81
>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 = 33.5 bits (75), Expect = 0.100, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 63 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 113
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 7 RPNHTIYINNLNE-KIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSA 65
Query: 114 TKALESTDRSKLVDRVISVEYALKDDSE 141
T AL S D+ + ++YA K DS+
Sbjct: 66 TNALRSMQGFPFYDKPMRIQYA-KTDSD 92
Score = 30.4 bits (67), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 26/43 (60%), Gaps = 2/43 (4%)
Query: 4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR 46
SL G AFV F++ A +A+R + PF YD + + +++A+
Sbjct: 48 SLKMRGQAFVIFKEVSSATNALRSMQGFPF-YD-KPMRIQYAK 88
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 33.5 bits (75), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 19/38 (50%), Positives = 22/38 (57%), Gaps = 2/38 (5%)
Query: 9 GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR 46
GFAFV F D RDA DA+ +D D R L V+ AR
Sbjct: 113 GFAFVRFHDKRDAEDAMDAMDGAVL--DGRELRVQMAR 148
Score = 32.3 bits (72), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 34/67 (50%), Gaps = 8/67 (11%)
Query: 77 RTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDR 128
RT ++R FE YG V V I R FAFV+F + +A A+++ D + L R
Sbjct: 81 RTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGR 140
Query: 129 VISVEYA 135
+ V+ A
Sbjct: 141 ELRVQMA 147
>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
pdb|2J0Q|G Chain G, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
Length = 109
Score = 33.5 bits (75), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 9/78 (11%)
Query: 67 TLFVINFDPIRTRERDIKRHFEPYGNV--LHVRIRR------NFAFVQFETQEEATKALE 118
LFV T E DI F YG + +H+ + R + V++ET +EA A+E
Sbjct: 9 ILFVTGVHEEATEE-DIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 67
Query: 119 STDRSKLVDRVISVEYAL 136
+ L+ + ISV++
Sbjct: 68 GLNGQDLMGQPISVDWCF 85
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 37/77 (48%), Gaps = 9/77 (11%)
Query: 67 TLFVINFDPIRTRERDIKRHFEPYGNV--------LHVRIRRNFAFVQFETQEEATKALE 118
TL V N RT ++R FE YG V H + R FAFV+F + +A A
Sbjct: 15 TLKVDNL-TYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEA 73
Query: 119 STDRSKLVDRVISVEYA 135
+ D ++L R + V+ A
Sbjct: 74 AMDGAELDGRELRVQVA 90
Score = 30.8 bits (68), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 19/38 (50%), Positives = 21/38 (55%), Gaps = 2/38 (5%)
Query: 9 GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR 46
GFAFV F D RDA DA +D D R L V+ AR
Sbjct: 56 GFAFVRFHDRRDAQDAEAAMDGAEL--DGRELRVQVAR 91
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 34/80 (42%), Gaps = 7/80 (8%)
Query: 54 DGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRR-------NFAFVQ 106
GS Q P+ + + E D++R FE +GN+ I R AFV+
Sbjct: 3 SGSSGCLRQPPSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVK 62
Query: 107 FETQEEATKALESTDRSKLV 126
+ + EA A+ + S+ +
Sbjct: 63 YSSHAEAQAAINALHGSQTM 82
>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 = 0.12, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 63 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 113
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 7 RPNHTIYINNLNE-KIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSA 65
Query: 114 TKALESTDRSKLVDRVISVEYALKDDSE 141
T AL S D+ + ++YA K DS+
Sbjct: 66 TNALRSMQGFPFYDKPMRIQYA-KTDSD 92
Score = 28.5 bits (62), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 27/45 (60%), Gaps = 2/45 (4%)
Query: 4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE 48
SL G AFV F++ A +A+R + PF YD + + +++A+ +
Sbjct: 48 SLKMRGQAFVIFKEVSSATNALRSMQGFPF-YD-KPMRIQYAKTD 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 = 0.13, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 37/79 (46%), Gaps = 8/79 (10%)
Query: 65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKA 116
+KT ++N+ P + + K F G++ ++ R+ + FV + +A KA
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 117 LESTDRSKLVDRVISVEYA 135
+ + + KL + I V YA
Sbjct: 63 INTLNGLKLQTKTIKVSYA 81
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 33.1 bits (74), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 36/76 (47%), Gaps = 7/76 (9%)
Query: 66 KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI------RRNFAFVQFETQEEATKALES 119
K L V N P R R+ D+++ F +G +L V I + F FV FE +A +A E
Sbjct: 16 KRLHVSNI-PFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREK 74
Query: 120 TDRSKLVDRVISVEYA 135
+ + R I V A
Sbjct: 75 LHGTVVEGRKIEVNNA 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 = 33.1 bits (74), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 13/78 (16%)
Query: 66 KTLFV--INFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATK 115
KTLFV +N+D T E ++R FE YG + + + R +AF+++E + +
Sbjct: 103 KTLFVARVNYD---TTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHS 159
Query: 116 ALESTDRSKLVDRVISVE 133
A + D K+ R + V+
Sbjct: 160 AYKHADGKKIDGRRVLVD 177
>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 = 0.17, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 63 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 113
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 6 RPNHTIYINNLNE-KIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSA 64
Query: 114 TKALESTDRSKLVDRVISVEYALKDDSE 141
T AL S D+ + ++YA K DS+
Sbjct: 65 TNALRSMQGFPFYDKPMRIQYA-KTDSD 91
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 26/43 (60%), Gaps = 2/43 (4%)
Query: 4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR 46
SL G AFV F++ A +A+R + PF YD + + +++A+
Sbjct: 47 SLKMRGQAFVIFKEVSSATNALRSMQGFPF-YD-KPMRIQYAK 87
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 32.7 bits (73), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 25/70 (35%), Positives = 34/70 (48%), Gaps = 3/70 (4%)
Query: 68 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--FAFVQFETQEEATKALESTDRSKL 125
LFV N P E D KR FE YG V I R+ F F++ E++ A A D + L
Sbjct: 25 LFVGNL-PTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTIL 83
Query: 126 VDRVISVEYA 135
R + + +A
Sbjct: 84 KSRPLRIRFA 93
>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 = 0.18, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 8/61 (13%)
Query: 80 ERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVIS 131
E I++ F P+G + + + + FAFV++E E A ALE + L R I
Sbjct: 42 EDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIK 101
Query: 132 V 132
V
Sbjct: 102 V 102
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 32.7 bits (73), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 40/85 (47%), Gaps = 13/85 (15%)
Query: 68 LFV--INFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKAL 117
LFV ++FD T E+ +++ F YG + V + R F FV FE ++A A+
Sbjct: 15 LFVGGLSFD---TNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 71
Query: 118 ESTDRSKLVDRVISVEYALKDDSER 142
+ + + R I V+ A K R
Sbjct: 72 MAMNGKSVDGRQIRVDQAGKSSDNR 96
>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 = 0.21, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 63 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 113
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 1 RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 59
Query: 114 TKALESTDRSKLVDRVISVEYALKDDSE 141
T AL S D+ + ++YA K DS+
Sbjct: 60 TNALRSMQGFPFYDKPMRIQYA-KTDSD 86
Score = 28.5 bits (62), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 27/45 (60%), Gaps = 2/45 (4%)
Query: 4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE 48
SL G AFV F++ A +A+R + PF YD + + +++A+ +
Sbjct: 42 SLKMRGQAFVIFKEVSSATNALRSMQGFPF-YD-KPMRIQYAKTD 84
>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 = 0.23, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 63 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 113
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 7 RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 65
Query: 114 TKALESTDRSKLVDRVISVEYALKDDSE 141
T AL S D+ + ++YA K DS+
Sbjct: 66 TNALRSMQGFPFYDKPMRIQYA-KTDSD 92
Score = 28.9 bits (63), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 26/43 (60%), Gaps = 2/43 (4%)
Query: 4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR 46
SL G AFV F++ A +A+R + PF YD + + +++A+
Sbjct: 48 SLKMRGQAFVIFKEVSSATNALRSMQGFPF-YD-KPMRIQYAK 88
>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 = 0.24, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 35/81 (43%), Gaps = 8/81 (9%)
Query: 64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATK 115
P+K+ ++ P D+ R F YG V+ V I ++ AF+ F ++ A
Sbjct: 14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQN 73
Query: 116 ALESTDRSKLVDRVISVEYAL 136
+ + +L RVI A+
Sbjct: 74 CTRAINNKQLFGRVIKASIAI 94
>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 = 32.3 bits (72), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 63 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 113
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 2 RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 60
Query: 114 TKALESTDRSKLVDRVISVEYALKDDSE 141
T AL S D+ + ++YA K DS+
Sbjct: 61 TNALRSMQGFPFYDKPMRIQYA-KTDSD 87
Score = 28.5 bits (62), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 27/45 (60%), Gaps = 2/45 (4%)
Query: 4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE 48
SL G AFV F++ A +A+R + PF YD + + +++A+ +
Sbjct: 43 SLKMRGQAFVIFKEVSSATNALRSMQGFPF-YD-KPMRIQYAKTD 85
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 32.3 bits (72), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 40/84 (47%), Gaps = 12/84 (14%)
Query: 60 ANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQE 111
A +P+KTLFV T E +K F+ + RI + F FV F ++E
Sbjct: 10 ARSQPSKTLFVKGLSE-DTTEETLKESFD---GSVRARIVTDRETGSSKGFGFVDFNSEE 65
Query: 112 EATKALESTDRSKLVDRVISVEYA 135
+A A E+ + ++ +++++A
Sbjct: 66 DAKAAKEAMEDGEIDGNKVTLDWA 89
>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 = 0.25, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 63 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 113
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 4 RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 62
Query: 114 TKALESTDRSKLVDRVISVEYALKDDSE 141
T AL S D+ + ++YA K DS+
Sbjct: 63 TNALRSMQGFPFYDKPMRIQYA-KTDSD 89
Score = 28.9 bits (63), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 27/45 (60%), Gaps = 2/45 (4%)
Query: 4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE 48
SL G AFV F++ A +A+R + PF YD + + +++A+ +
Sbjct: 45 SLKMRGQAFVIFKEVSSATNALRSMQGFPF-YD-KPMRIQYAKTD 87
>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 = 32.3 bits (72), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 63 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 113
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 6 RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 64
Query: 114 TKALESTDRSKLVDRVISVEYALKDDSE 141
T AL S D+ + ++YA K DS+
Sbjct: 65 TNALRSMQGFPFYDKPMRIQYA-KTDSD 91
Score = 28.9 bits (63), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 26/43 (60%), Gaps = 2/43 (4%)
Query: 4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR 46
SL G AFV F++ A +A+R + PF YD + + +++A+
Sbjct: 47 SLKMRGQAFVIFKEVSSATNALRSMQGFPF-YD-KPMRIQYAK 87
>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|B Chain B, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|C Chain C, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|D Chain D, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
Length = 96
Score = 32.3 bits (72), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 63 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 113
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 6 RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 64
Query: 114 TKALESTDRSKLVDRVISVEYALKDDSE 141
T AL S D+ + ++YA K DS+
Sbjct: 65 TNALRSMQGFPFYDKPMRIQYA-KTDSD 91
Score = 28.9 bits (63), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 27/45 (60%), Gaps = 2/45 (4%)
Query: 4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE 48
SL G AFV F++ A +A+R + PF YD + + +++A+ +
Sbjct: 47 SLKMRGQAFVIFKEVSSATNALRSMQGFPF-YD-KPMRIQYAKTD 89
>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 = 32.3 bits (72), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 63 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 113
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 6 RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 64
Query: 114 TKALESTDRSKLVDRVISVEYALKDDSE 141
T AL S D+ + ++YA K DS+
Sbjct: 65 TNALRSMQGFPFYDKPMRIQYA-KTDSD 91
Score = 28.9 bits (63), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 27/45 (60%), Gaps = 2/45 (4%)
Query: 4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE 48
SL G AFV F++ A +A+R + PF YD + + +++A+ +
Sbjct: 47 SLKMRGQAFVIFKEVSSATNALRSMQGFPF-YD-KPMRIQYAKTD 89
>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 = 0.27, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 8/61 (13%)
Query: 80 ERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVIS 131
E I++ F P+G + + + + FAFV++E E A ALE + L R I
Sbjct: 27 EDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIK 86
Query: 132 V 132
V
Sbjct: 87 V 87
>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 = 0.28, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 63 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 113
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 3 RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 61
Query: 114 TKALESTDRSKLVDRVISVEYALKDDSE 141
T AL S D+ + ++YA K DS+
Sbjct: 62 TNALRSMQGFPFYDKPMRIQYA-KTDSD 88
Score = 28.9 bits (63), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 27/45 (60%), Gaps = 2/45 (4%)
Query: 4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE 48
SL G AFV F++ A +A+R + PF YD + + +++A+ +
Sbjct: 44 SLKMRGQAFVIFKEVSSATNALRSMQGFPF-YD-KPMRIQYAKTD 86
>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 = 0.28, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 63 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 113
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 7 RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 65
Query: 114 TKALESTDRSKLVDRVISVEYALKDDSE 141
T AL S D+ + ++YA K DS+
Sbjct: 66 TNALRSMQGFPFYDKPMRIQYA-KTDSD 92
Score = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 27/45 (60%), Gaps = 2/45 (4%)
Query: 4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE 48
SL G AFV F++ A +A+R + PF YD + + +++A+ +
Sbjct: 48 SLKMRGQAFVIFKEVSSATNALRSMQGFPF-YD-KPMRIQYAKTD 90
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 32.0 bits (71), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 33/76 (43%), Gaps = 9/76 (11%)
Query: 68 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFA--------FVQFETQEEATKALES 119
+FV + P T E DIK F P+G + R+ ++ A FV F + +A A+
Sbjct: 18 VFVGDLSPEITTE-DIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 120 TDRSKLVDRVISVEYA 135
L R I +A
Sbjct: 77 MGGQWLGGRQIRTNWA 92
>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 = 0.40, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 3/73 (4%)
Query: 65 TKTLFVINFDPIRTRERDIKRHFEPY--GNVLHVRIRRNFAFVQFETQEEATKALESTDR 122
K L+V N + T E I++ F G V V+ R++AFV F +E+A +A+++ +
Sbjct: 15 VKILYVRNL-MLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNG 73
Query: 123 SKLVDRVISVEYA 135
L I V A
Sbjct: 74 KVLDGSPIEVTLA 86
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 31.2 bits (69), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 30/67 (44%), Gaps = 7/67 (10%)
Query: 78 TRERDIKRHFEPYGNVLHVRI-------RRNFAFVQFETQEEATKALESTDRSKLVDRVI 130
T E+ +K F +G + V + R FAF+ FE +A A + + L + I
Sbjct: 19 TNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAI 78
Query: 131 SVEYALK 137
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 = 0.65, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 28/61 (45%), Gaps = 8/61 (13%)
Query: 80 ERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVIS 131
E I++ F P+G + + + FAFV++E E A ALE + L R I
Sbjct: 26 EDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQXNSVXLGGRNIK 85
Query: 132 V 132
V
Sbjct: 86 V 86
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 30.8 bits (68), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 44/88 (50%), Gaps = 11/88 (12%)
Query: 63 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 113
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 4 RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSA 62
Query: 114 TKALESTDRSKLVDRVISVEYALKDDSE 141
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 = 0.81, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 44/88 (50%), Gaps = 11/88 (12%)
Query: 63 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 113
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 6 RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSA 64
Query: 114 TKALESTDRSKLVDRVISVEYALKDDSE 141
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 = 0.81, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 44/88 (50%), Gaps = 11/88 (12%)
Query: 63 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 113
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 7 RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSA 65
Query: 114 TKALESTDRSKLVDRVISVEYALKDDSE 141
T AL S D+ ++YA K DS+
Sbjct: 66 TNALRSXQGFPFYDKPXRIQYA-KTDSD 92
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 30.4 bits (67), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 9/63 (14%)
Query: 83 IKRHFEPYGNV---------LHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISVE 133
I F YG + +H + + +A+V+FE +EA KAL+ D ++ + I+
Sbjct: 21 IMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITAT 80
Query: 134 YAL 136
L
Sbjct: 81 AVL 83
>pdb|2ADC|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd34 Complexed With Cucucu Rna
pdb|2EVZ|A Chain A, Structure Of Rna Binding Domains 3 And 4 Of Polypyrimidine
Tract Binding Protein
Length = 229
Score = 30.4 bits (67), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 33/70 (47%), Gaps = 6/70 (8%)
Query: 53 RDGSKSMANQ-RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLH----VRIRRNFAFVQF 107
+ GSK+ N P+ TL + N P E D+K F G V+ + R A +Q
Sbjct: 138 KPGSKNFQNIFPPSATLHLSNIPP-SVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQM 196
Query: 108 ETQEEATKAL 117
+ EEA +AL
Sbjct: 197 GSVEEAVQAL 206
>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 = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 39/78 (50%), Gaps = 10/78 (12%)
Query: 68 LFVINFDPIRTRERDIKRHFEPYG-NVLHVRIRRN--------FAFVQFETQEEATKALE 118
+ ++ P E DI+ + +G VR+ RN FAFV+F ++AT+ +E
Sbjct: 3 IVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWME 62
Query: 119 STDRS-KLVDRVISVEYA 135
+ S ++ + +S+ Y+
Sbjct: 63 ANQHSLNILGQKVSMHYS 80
>pdb|1S79|A Chain A, Solution Structure Of The Central Rrm Of Human La Protein
Length = 103
Score = 29.3 bits (64), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 33/68 (48%), Gaps = 8/68 (11%)
Query: 59 MANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNF-------AFVQFETQE 111
+ N +++++ F P DIK E G VL++++RR FV F++ E
Sbjct: 5 LKNDVKNRSVYIKGF-PTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIE 63
Query: 112 EATKALES 119
A K +E+
Sbjct: 64 SAKKFVET 71
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 29.3 bits (64), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 33/70 (47%), Gaps = 6/70 (8%)
Query: 53 RDGSKSMANQ-RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLH----VRIRRNFAFVQF 107
+ GSK+ N P+ TL + N P E D+K F G V+ + R A +Q
Sbjct: 107 KPGSKNFQNIFPPSATLHLSNIPP-SVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQM 165
Query: 108 ETQEEATKAL 117
+ EEA +AL
Sbjct: 166 GSVEEAVQAL 175
>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 = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 18/80 (22%), Positives = 37/80 (46%), Gaps = 9/80 (11%)
Query: 63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHV--------RIRRNFAFVQFETQEEAT 114
+ + TL+V N T E I F G++ + + F FV++ ++ +A
Sbjct: 37 KKSCTLYVGNL-SFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAE 95
Query: 115 KALESTDRSKLVDRVISVEY 134
A+ + ++L DR+I ++
Sbjct: 96 NAMRYINGTRLDDRIIRTDW 115
>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 = 2.4, Method: Compositional matrix adjust.
Identities = 17/79 (21%), Positives = 37/79 (46%), Gaps = 8/79 (10%)
Query: 65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKA 116
+KT ++N+ P + + + F G + ++ R+ + FV + ++A KA
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 117 LESTDRSKLVDRVISVEYA 135
+ + + +L + I V YA
Sbjct: 61 INTLNGLRLQTKTIKVSYA 79
>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 = 28.9 bits (63), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 7/45 (15%)
Query: 82 DIKRHFEPYGNVLHVRIRRNF-------AFVQFETQEEATKALES 119
DIK E G VL++++RR FV F++ E A K +E+
Sbjct: 125 DIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVET 169
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 28.9 bits (63), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 17/79 (21%), Positives = 39/79 (49%), Gaps = 8/79 (10%)
Query: 65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNF--------AFVQFETQEEATKA 116
+ T ++N+ P +R++ F G + RI R++ AFV F ++ ++ +A
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 117 LESTDRSKLVDRVISVEYA 135
++ + + ++ + V YA
Sbjct: 62 IKVLNGITVRNKRLKVSYA 80
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 28.1 bits (61), Expect = 4.2, Method: Composition-based stats.
Identities = 15/51 (29%), Positives = 23/51 (45%), Gaps = 8/51 (15%)
Query: 76 IRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALE 118
+ T D+K +FE +G V + R F FV FE+++ K E
Sbjct: 9 VNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 28.1 bits (61), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 11/77 (14%)
Query: 65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN-------FAFVQFETQEEATKAL 117
+KTL + N T E ++ FE +++ +N +AF++F + E+A +AL
Sbjct: 15 SKTLVLSNLSYSATEE-TLQEVFE---KATFIKVPQNQNGKSKGYAFIEFASFEDAKEAL 70
Query: 118 ESTDRSKLVDRVISVEY 134
S ++ ++ R I +E
Sbjct: 71 NSCNKREIEGRAIRLEL 87
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 26.9 bits (58), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 15/30 (50%), Positives = 19/30 (63%), Gaps = 2/30 (6%)
Query: 93 VLHVRI--RRNFAFVQFETQEEATKALEST 120
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
0.322 0.140 0.431
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,911,650
Number of Sequences: 62578
Number of extensions: 265760
Number of successful extensions: 580
Number of sequences better than 100.0: 99
Number of HSP's better than 100.0 without gapping: 44
Number of HSP's successfully gapped in prelim test: 55
Number of HSP's that attempted gapping in prelim test: 477
Number of HSP's gapped (non-prelim): 156
length of query: 240
length of database: 14,973,337
effective HSP length: 96
effective length of query: 144
effective length of database: 8,965,849
effective search space: 1291082256
effective search space used: 1291082256
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 bits)