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= 022814
(291 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 68.2 bits (165), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 33/76 (43%), Positives = 47/76 (61%), Gaps = 6/76 (7%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
V+VG IP++ TE L +F++ G +V LV D+ TGKP+G+ F Y+DQ NL
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 92 NGAQILGRTIRVDHVA 107
NG + GR +RVD+ A
Sbjct: 71 NGREFSGRALRVDNAA 86
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 58.9 bits (141), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 31/78 (39%), Positives = 45/78 (57%), Gaps = 6/78 (7%)
Query: 34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYE------DQ 87
D ++VGG+ FD E L VF++ G+I +V +V+D+ T + RGF FV +E D
Sbjct: 11 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 70
Query: 88 RNNLNGAQILGRTIRVDH 105
+NG + GR IRVD
Sbjct: 71 MMAMNGKSVDGRQIRVDQ 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 = 56.6 bits (135), Expect = 2e-08, Method: Composition-based stats.
Identities = 26/71 (36%), Positives = 43/71 (60%), Gaps = 6/71 (8%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
VYV +PF LT DL +F++ G++V V +++DK T K +G AF+ + D+ + +
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 92 NGAQILGRTIR 102
N Q+ GR I+
Sbjct: 79 NNKQLFGRVIK 89
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 54.3 bits (129), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 46/79 (58%), Gaps = 6/79 (7%)
Query: 35 SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ------R 88
S+ +YVG + F++TE L +F G+I ++ L++D TG+ +G+ F+ + D
Sbjct: 5 SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
Query: 89 NNLNGAQILGRTIRVDHVA 107
LNG ++ GR +RV HV
Sbjct: 65 EQLNGFELAGRPMRVGHVT 83
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 52.0 bits (123), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 41/76 (53%), Gaps = 6/76 (7%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ------RNNL 91
+YVG + F++TE L +F G I + L+ D TG+ +G+ F+ + D L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 92 NGAQILGRTIRVDHVA 107
NG ++ GR ++V HV
Sbjct: 89 NGFELAGRPMKVGHVT 104
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 50.8 bits (120), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 44/74 (59%), Gaps = 6/74 (8%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
VY+G IP+D TE +L + + G ++++ ++ D TG+ +G+AF+ + D + NL
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 92 NGAQILGRTIRVDH 105
NG Q+ R ++ +
Sbjct: 66 NGYQLGSRFLKCGY 79
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
Length = 124
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 44/72 (61%), Gaps = 7/72 (9%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNLNGAQIL 97
VYVG + + T DL A F+ CG I + ++ DK +G P+G+A++ + +RN+++ A +
Sbjct: 39 VYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFA-ERNSVDAAVAM 97
Query: 98 ------GRTIRV 103
GRTI+V
Sbjct: 98 DETVFRGRTIKV 109
>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 84
Score = 50.1 bits (118), Expect = 1e-06, Method: Composition-based stats.
Identities = 24/74 (32%), Positives = 44/74 (59%), Gaps = 6/74 (8%)
Query: 35 SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN----- 89
S VY+G IP+D TE +L + + G ++++ ++ D TG+ +G+AF+ + D +
Sbjct: 4 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 63
Query: 90 -NLNGAQILGRTIR 102
NLNG Q+ R ++
Sbjct: 64 RNLNGYQLGSRFLK 77
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 50.1 bits (118), Expect = 1e-06, Method: Composition-based stats.
Identities = 24/74 (32%), Positives = 44/74 (59%), Gaps = 6/74 (8%)
Query: 35 SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN----- 89
S VY+G IP+D TE +L + + G ++++ ++ D TG+ +G+AF+ + D +
Sbjct: 2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61
Query: 90 -NLNGAQILGRTIR 102
NLNG Q+ R ++
Sbjct: 62 RNLNGYQLGSRFLK 75
>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 = 50.1 bits (118), Expect = 2e-06, Method: Composition-based stats.
Identities = 28/73 (38%), Positives = 43/73 (58%), Gaps = 6/73 (8%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
+YVGG+ ++ + L A F G+I D+ + D T K RGFAFV +E +N+
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 92 NGAQILGRTIRVD 104
N +++ GRTIRV+
Sbjct: 70 NESELFGRTIRVN 82
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 43/73 (58%), Gaps = 6/73 (8%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
+YVGG+ ++ + L A F G+I D+ + D T K RGFAFV +E +N+
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 92 NGAQILGRTIRVD 104
N +++ GRTIRV+
Sbjct: 126 NESELFGRTIRVN 138
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 46/75 (61%), Gaps = 7/75 (9%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYE---DQRN---NL 91
+++GG+ + E L AVF + G I +V L++D+ T K RGFAF+ +E D +N ++
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDM 68
Query: 92 NGAQILGRTIRVDHV 106
NG + G+ I+V+
Sbjct: 69 NGKSLHGKAIKVEQA 83
>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 = 49.7 bits (117), Expect = 2e-06, Method: Composition-based stats.
Identities = 28/73 (38%), Positives = 43/73 (58%), Gaps = 6/73 (8%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
+YVGG+ ++ + L A F G+I D+ + D T K RGFAFV +E +N+
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 92 NGAQILGRTIRVD 104
N +++ GRTIRV+
Sbjct: 65 NESELFGRTIRVN 77
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 43/73 (58%), Gaps = 6/73 (8%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
+YVGG+ ++ + L A F G+I D+ + D T K RGFAFV +E +N+
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 92 NGAQILGRTIRVD 104
N +++ GRTIRV+
Sbjct: 75 NESELFGRTIRVN 87
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 29/72 (40%), Positives = 42/72 (58%), Gaps = 6/72 (8%)
Query: 40 VGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYE------DQRNNLNG 93
V G+ TE DL VF++ G I DV++V D+ + + RGFAFV +E + + NG
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 94 AQILGRTIRVDH 105
++ GR IRVD
Sbjct: 80 MELDGRRIRVDF 91
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 49.3 bits (116), Expect = 2e-06, Method: Composition-based stats.
Identities = 28/73 (38%), Positives = 43/73 (58%), Gaps = 6/73 (8%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
+YVGG+ ++ + L A F G+I D+ + D T K RGFAFV +E +N+
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 92 NGAQILGRTIRVD 104
N +++ GRTIRV+
Sbjct: 68 NESELFGRTIRVN 80
>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 = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 6/74 (8%)
Query: 37 YVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY------EDQRNN 90
+V+VG + ++T D+ A FA G I D +V+D TGK +G+ FV++ E+
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 91 LNGAQILGRTIRVD 104
+ G + GR IR +
Sbjct: 77 MGGQWLGGRQIRTN 90
>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The
Second Rna-Binding Domain Of Sex-Lethal Determined By
Multidimensional Heteronuclear Magnetic Resonance
Spectroscopy
Length = 97
Score = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/47 (46%), Positives = 31/47 (65%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY 84
+YV +P +T+ L +F + G IV N++RDK TG+PRG AFV Y
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRY 62
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 42/71 (59%), Gaps = 5/71 (7%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLN 92
++VGGIP + E +L F + G + +V ++ D +PRGF F+ +ED+++ N++
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMH 72
Query: 93 GAQILGRTIRV 103
I+G+ + V
Sbjct: 73 FHDIMGKKVEV 83
>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 = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 22/47 (46%), Positives = 31/47 (65%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY 84
+YV +P +T+ L +F + G IV N++RDK TG+PRG AFV Y
Sbjct: 103 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRY 149
Score = 35.0 bits (79), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 1/66 (1%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNLNGAQIL 97
+ V +P D T+ +L A+F G I + RD TG G+AFV + + ++ ++L
Sbjct: 17 LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 98 -GRTIR 102
G T+R
Sbjct: 77 NGITVR 82
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 49.3 bits (116), Expect = 3e-06, Method: Composition-based stats.
Identities = 24/71 (33%), Positives = 41/71 (57%), Gaps = 5/71 (7%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR-----NNLN 92
+YVG + + T + +F+Q G++ +V L+ D+ T KP+GF FV +++ L+
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAKLD 63
Query: 93 GAQILGRTIRV 103
+GRTIRV
Sbjct: 64 NTDFMGRTIRV 74
>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 = 48.9 bits (115), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 42/74 (56%), Gaps = 6/74 (8%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
+ V +P ++T+ + ++F GEI LVRDK TG+ G+ FV Y D + N L
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 92 NGAQILGRTIRVDH 105
NG ++ +TI+V +
Sbjct: 65 NGLRLQTKTIKVSY 78
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 38/71 (53%), Gaps = 6/71 (8%)
Query: 36 AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY------EDQRN 89
A +YV G+P +T+ +L +F+Q G I+ ++ D+ TG RG F+ + E+
Sbjct: 89 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 148
Query: 90 NLNGAQILGRT 100
LNG + G T
Sbjct: 149 GLNGQKPSGAT 159
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 29/72 (40%), Positives = 42/72 (58%), Gaps = 6/72 (8%)
Query: 40 VGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYE------DQRNNLNG 93
V G+ TE DL VF++ G I DV++V D+ + + RGFAFV +E + + NG
Sbjct: 17 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 76
Query: 94 AQILGRTIRVDH 105
++ GR IRVD
Sbjct: 77 MELDGRRIRVDF 88
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 48.5 bits (114), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 29/71 (40%), Positives = 42/71 (59%), Gaps = 6/71 (8%)
Query: 40 VGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED------QRNNLNG 93
V G+ TE DL VF++ G I DV++V D+ + + RGFAFV +E+ + NG
Sbjct: 51 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 110
Query: 94 AQILGRTIRVD 104
++ GR IRVD
Sbjct: 111 MELDGRRIRVD 121
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 48.5 bits (114), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 22/47 (46%), Positives = 31/47 (65%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY 84
+YV +P +T+ L +F + G IV N++RDK TG+PRG AFV Y
Sbjct: 92 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRY 138
Score = 37.7 bits (86), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 37/66 (56%), Gaps = 1/66 (1%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNLNGAQIL 97
+ V +P D+T+ +L A+F G I ++RD TG G+AFV + + ++ ++L
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 98 -GRTIR 102
G T+R
Sbjct: 66 NGITVR 71
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 48.1 bits (113), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 6/74 (8%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
+ V +P ++T+ + ++F G+I LVRDK TG+ G+ FV Y D N L
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 92 NGAQILGRTIRVDH 105
NG ++ +TI+V +
Sbjct: 67 NGLKLQTKTIKVSY 80
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 38/69 (55%), Gaps = 6/69 (8%)
Query: 36 AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY------EDQRN 89
A +YV G+P +++ ++ +F+Q G I+ ++ D+ TG RG F+ + E+
Sbjct: 91 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 150
Query: 90 NLNGAQILG 98
LNG + LG
Sbjct: 151 GLNGQKPLG 159
>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex
With Rna
pdb|2KM8|C Chain C, Interdomain Rrm Packing Contributes To Rna Recognition
In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 167
Score = 48.1 bits (113), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 36/53 (67%)
Query: 33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYE 85
K+S +++GG+ +D TE +L F + G + D+ +++D TG+ RGF F+++E
Sbjct: 1 KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFE 53
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/48 (43%), Positives = 30/48 (62%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYE 85
++VGGI D+ + F+Q G I+D L+ DK TG+ RGF FV Y+
Sbjct: 90 IFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYD 137
>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1HL6|C Chain C, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1RK8|A Chain A, Structure Of The Cytosolic Protein Pym Bound To The Mago-
Y14 Core Of The Exon Junction Complex
pdb|2X1G|A Chain A, Crystal Structure Of Importin13 - Mago-Y14 Complex
pdb|2X1G|C Chain C, Crystal Structure Of Importin13 - Mago-Y14 Complex
Length = 165
Score = 47.4 bits (111), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 6/73 (8%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
++V I + E ++ F GEI +++L D+ TG +G+A V YE + L
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 92 NGAQILGRTIRVD 104
NGA+I+G+TI+VD
Sbjct: 135 NGAEIMGQTIQVD 147
>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi)
G); A Human Telomeric Repeat Containing 6-Methyl-8-(2-
Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi)
Length = 195
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 22/49 (44%), Positives = 32/49 (65%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
++VGGI D E L F Q G+I + ++ D+G+GK RGFAFV ++D
Sbjct: 106 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 154
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 29/47 (61%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY 84
+++GG+ F+ T+ L + F Q G + D ++RD T + RGF FV Y
Sbjct: 15 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 61
>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
pdb|1U1K|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt 7da
Ggg); A Human Telomeric Repeat Containing
7-Deaza-Adenine
pdb|1U1L|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt Prn
Ggg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1M|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 7gu
Gg); A Human Telomeric Repeat Containing 7-Deaza-Guanine
pdb|1U1N|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta (Prn)
Gg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1O|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggttag(Di)g); A Human Telomeric Repeat Containing
Inosine
pdb|1U1P|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 2pr
Gg); A Human Telomeric Repeat Containing 2-Aminopurine
pdb|1U1Q|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggtta(Di)gg); A Human Telomeric Repeat Containing
Inosine
pdb|1U1R|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(2pr)
G); A Human Telomeric Repeat Containing 2-Aminopurine
Length = 196
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 22/49 (44%), Positives = 32/49 (65%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
++VGGI D E L F Q G+I + ++ D+G+GK RGFAFV ++D
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 155
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 29/47 (61%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY 84
+++GG+ F+ T+ L + F Q G + D ++RD T + RGF FV Y
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 62
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 22/49 (44%), Positives = 32/49 (65%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
++VGGI D E L F Q G+I + ++ D+G+GK RGFAFV ++D
Sbjct: 108 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 156
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 29/47 (61%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY 84
+++GG+ F+ T+ L + F Q G + D ++RD T + RGF FV Y
Sbjct: 17 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 63
>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 = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 6/73 (8%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
++V + +D TE L F G I +++V K +GKPRG+AF+ YE +R+ +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 92 NGAQILGRTIRVD 104
+G +I GR + VD
Sbjct: 165 DGKKIDGRRVLVD 177
>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 = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 6/73 (8%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
++V + +D TE L F G I +++V K +GKPRG+AF+ YE +R+ +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 92 NGAQILGRTIRVD 104
+G +I GR + VD
Sbjct: 165 DGKKIDGRRVLVD 177
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 43/74 (58%), Gaps = 6/74 (8%)
Query: 37 YVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY------EDQRNN 90
+V+VG + ++T D+ + FA G+I D +V+D TGK +G+ FV++ E+ +
Sbjct: 17 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 91 LNGAQILGRTIRVD 104
+ G + GR IR +
Sbjct: 77 MGGQWLGGRQIRTN 90
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 29/72 (40%), Positives = 44/72 (61%), Gaps = 8/72 (11%)
Query: 39 YVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNL------N 92
YVG +PF+ +GD+ A+F I V LVRDK T K +GF +V + D+ ++L +
Sbjct: 19 YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEF-DEVDSLKEALTYD 76
Query: 93 GAQILGRTIRVD 104
GA + R++RVD
Sbjct: 77 GALLGDRSLRVD 88
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 46.6 bits (109), Expect = 1e-05, Method: Composition-based stats.
Identities = 25/72 (34%), Positives = 40/72 (55%), Gaps = 6/72 (8%)
Query: 40 VGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNLNG 93
V +P ++T+ + ++F G+I LVRDK TG+ G+ FV Y D N LNG
Sbjct: 9 VNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNG 68
Query: 94 AQILGRTIRVDH 105
++ +TI+V +
Sbjct: 69 LKLQTKTIKVSY 80
>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
pdb|3S7R|B Chain B, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
Length = 87
Score = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 33/53 (62%)
Query: 34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
D+ +VGG+ +D ++ DL F + GE+VD + D TG+ RGF F+ ++D
Sbjct: 10 DAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKD 62
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 28/70 (40%), Positives = 41/70 (58%), Gaps = 6/70 (8%)
Query: 40 VGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED------QRNNLNG 93
V G+ TE DL VF++ G I DV++V D+ + + RGFAFV +E+ + NG
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 94 AQILGRTIRV 103
++ GR IRV
Sbjct: 80 MELDGRRIRV 89
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/49 (44%), Positives = 32/49 (65%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
++VGGI D E L F Q G+I + ++ D+G+GK RGFAFV ++D
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 155
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 29/47 (61%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY 84
+++GG+ F+ T+ L + F Q G + D ++RD T + RGF FV Y
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 62
>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex
pdb|1PO6|A Chain A, Crystal Structure Of Up1 Complexed With
D(Tagg(6mi)ttaggg): A Human Telomeric Repeat Containing
6-Methyl-8-(2-Deoxy-
Beta-Ribofuranosyl)isoxanthopteridine (6mi)
Length = 183
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/49 (44%), Positives = 32/49 (65%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
++VGGI D E L F Q G+I + ++ D+G+GK RGFAFV ++D
Sbjct: 100 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 148
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 29/47 (61%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY 84
+++GG+ F+ T+ L + F Q G + D ++RD T + RGF FV Y
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 55
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/49 (44%), Positives = 32/49 (65%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
++VGGI D E L F Q G+I + ++ D+G+GK RGFAFV ++D
Sbjct: 105 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 153
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 29/47 (61%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY 84
+++GG+ F+ T+ L + F Q G + D ++RD T + RGF FV Y
Sbjct: 14 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 60
>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
pdb|4ED5|B Chain B, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
Length = 177
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 41/74 (55%), Gaps = 6/74 (8%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY------EDQRNNL 91
+ V +P ++T+ +L ++F+ GE+ L+RDK G G+ FV Y E N L
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 92 NGAQILGRTIRVDH 105
NG ++ +TI+V +
Sbjct: 65 NGLRLQSKTIKVSY 78
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 33/50 (66%)
Query: 36 AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYE 85
A +Y+ G+P +T+ D+ +F++ G I++ ++ D+ TG RG AF+ ++
Sbjct: 89 ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFD 138
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 41/74 (55%), Gaps = 6/74 (8%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY------EDQRNNL 91
+ V +P ++T+ +L ++F+ GE+ L+RDK G G+ FV Y E N L
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 92 NGAQILGRTIRVDH 105
NG ++ +TI+V +
Sbjct: 65 NGLRLQSKTIKVSY 78
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 33/50 (66%)
Query: 36 AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYE 85
A +Y+ G+P +T+ D+ +F++ G I++ ++ D+ TG RG AF+ ++
Sbjct: 89 ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFD 138
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 40/67 (59%), Gaps = 2/67 (2%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNLNGAQIL 97
++VGG+ + T+ L + F+Q GE+VD +++DK T + RGF FV ++D N G +
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDP--NCVGTVLA 76
Query: 98 GRTIRVD 104
R +D
Sbjct: 77 SRPHTLD 83
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 6/73 (8%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
++V I + E ++ F GEI +++L D+ TG +G+A V YE + L
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 92 NGAQILGRTIRVD 104
NGA+I+G+TI+VD
Sbjct: 89 NGAEIMGQTIQVD 101
>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
pdb|1HD1|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
Length = 75
Score = 44.7 bits (104), Expect = 6e-05, Method: Composition-based stats.
Identities = 20/52 (38%), Positives = 34/52 (65%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN 89
+++GG+ +D T+ DL F++ GE+VD L D TG+ RGF FV +++ +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESES 53
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 44.3 bits (103), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 39/64 (60%)
Query: 34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNLNG 93
D+ +++G IP +L E DL +F + G+I ++ +++D+ TG +G AF+ Y ++ + L
Sbjct: 12 DAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKA 71
Query: 94 AQIL 97
L
Sbjct: 72 QSAL 75
>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|B Chain B, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|C Chain C, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|D Chain D, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
Length = 84
Score = 44.3 bits (103), Expect = 8e-05, Method: Composition-based stats.
Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 6/72 (8%)
Query: 40 VGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY------EDQRNNLNG 93
V +P ++T+ +L ++F+ GE+ L+RDK G G+ FV Y E N LNG
Sbjct: 9 VNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNG 68
Query: 94 AQILGRTIRVDH 105
++ +TI+V +
Sbjct: 69 LRLQSKTIKVSY 80
>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|B Chain B, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|C Chain C, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|D Chain D, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
Length = 99
Score = 44.3 bits (103), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 6/74 (8%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
+ V +P + T+ +L ++F+ GE+ L+RDK G G+ FV Y + N L
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 92 NGAQILGRTIRVDH 105
NG ++ +TI+V +
Sbjct: 82 NGLRLQSKTIKVSY 95
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of Hypothetical
Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens
At 1.95 A Resolution
Length = 89
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 42/75 (56%), Gaps = 5/75 (6%)
Query: 34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN---- 89
D+ +YVG + + T +L A F CG + V ++ DK +G P+GFA++ + D+ +
Sbjct: 5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 64
Query: 90 -NLNGAQILGRTIRV 103
L+ + GR I+V
Sbjct: 65 LALDESLFRGRQIKV 79
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 42/75 (56%), Gaps = 5/75 (6%)
Query: 34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN---- 89
D+ +YVG + + T +L A F CG + V ++ DK +G P+GFA++ + D+ +
Sbjct: 4 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 63
Query: 90 -NLNGAQILGRTIRV 103
L+ + GR I+V
Sbjct: 64 LALDESLFRGRQIKV 78
>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 = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 6/73 (8%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
++V G+ + TE D+ FA+ GEI +++L D+ TG +G+ V YE + L
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 92 NGAQILGRTIRVD 104
NG ++G+ I VD
Sbjct: 85 NGQDLMGQPISVD 97
>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 = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 6/73 (8%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
++V G+ + TE D+ FA+ GEI +++L D+ TG +G+ V YE + L
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 92 NGAQILGRTIRVD 104
NG ++G+ I VD
Sbjct: 86 NGQDLMGQPISVD 98
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 44/75 (58%), Gaps = 6/75 (8%)
Query: 36 AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNN----- 90
A VYVGG+ ++E L +F Q G +V+ ++ +D+ TG+ +G+ FV + + +
Sbjct: 16 ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIK 75
Query: 91 -LNGAQILGRTIRVD 104
++ ++ G+ IRV+
Sbjct: 76 IMDMIKLYGKPIRVN 90
>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 = 42.7 bits (99), Expect = 3e-04, Method: Composition-based stats.
Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 6/73 (8%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
++V G+ + TE D+ FA+ GEI +++L D+ TG +G+ V YE + L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 92 NGAQILGRTIRVD 104
NG ++G+ I VD
Sbjct: 70 NGQDLMGQPISVD 82
>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 = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 6/72 (8%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYE------DQRNNL 91
+YV + DL++ D+ +VF G+I L RD TGK +G+ F+ YE D +++
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 92 NGAQILGRTIRV 103
N + G+ +RV
Sbjct: 188 NLFDLGGQYLRV 199
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 36/72 (50%), Gaps = 6/72 (8%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED------QRNNL 91
VYVG I ++L E + FA G I +++ D T K +GFAFV YE +
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 92 NGAQILGRTIRV 103
N + GR I+V
Sbjct: 91 NSVMLGGRNIKV 102
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 42.4 bits (98), Expect = 3e-04, Method: Composition-based stats.
Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 6/73 (8%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
++V G+ + TE D+ FA+ GEI +++L D+ TG +G+ V YE + L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 92 NGAQILGRTIRVD 104
NG ++G+ I VD
Sbjct: 70 NGQDLMGQPISVD 82
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 42.4 bits (98), Expect = 3e-04, Method: Composition-based stats.
Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 6/73 (8%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
++V G+ + TE D+ FA+ GEI +++L D+ TG +G+ V YE + L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 92 NGAQILGRTIRVD 104
NG ++G+ I VD
Sbjct: 72 NGQDLMGQPISVD 84
>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|X Chain X, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|Y Chain Y, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2V|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
pdb|1N52|B Chain B, Cap Binding Complex
pdb|1N54|B Chain B, Cap Binding Complex M7gpppg Free
pdb|3FEX|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex.
pdb|3FEY|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex
Length = 156
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 38/78 (48%), Gaps = 6/78 (7%)
Query: 33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY------ED 86
K S +YVG + F TE + +F++ G+I + + DK GF FV Y E+
Sbjct: 37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAEN 96
Query: 87 QRNNLNGAQILGRTIRVD 104
+NG ++ R IR D
Sbjct: 97 AMRYINGTRLDDRIIRTD 114
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 8/74 (10%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ------RNNL 91
++V IPF + DL +F Q G+I+DV ++ ++ K GF FV +E+ R L
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSK--GFGFVTFENSADADRAREKL 89
Query: 92 NGAQILGRTIRVDH 105
+G + GR I V++
Sbjct: 90 HGTVVEGRKIEVNN 103
>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 = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 36/72 (50%), Gaps = 6/72 (8%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED------QRNNL 91
VYVG I ++L E + FA G I +++ D T K +GFAFV YE +
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 92 NGAQILGRTIRV 103
N + GR I+V
Sbjct: 76 NSVMLGGRNIKV 87
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 6/72 (8%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYE------DQRNNL 91
+YV + DL++ D+ +VF G+I L RD TGK +G+ F+ YE D +++
Sbjct: 113 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 172
Query: 92 NGAQILGRTIRV 103
N + G+ +RV
Sbjct: 173 NLFDLGGQYLRV 184
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 8/74 (10%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ------RNNL 91
++V IPF + DL +F Q G+I+DV ++ ++ K GF FV +E+ R L
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSK--GFGFVTFENSADADRAREKL 75
Query: 92 NGAQILGRTIRVDH 105
+G + GR I V++
Sbjct: 76 HGTVVEGRKIEVNN 89
>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 = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 6/73 (8%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
++V G+ + TE D+ FA+ GEI +++L D+ TG +G+ V YE + L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 92 NGAQILGRTIRVD 104
NG ++G+ I VD
Sbjct: 70 NGQDLMGQPISVD 82
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 34/55 (61%), Gaps = 6/55 (10%)
Query: 55 VFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRV 103
VF + G + DV + R+ T PRGFAFV + D+R+ ++GA++ GR +RV
Sbjct: 33 VFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRV 87
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleaoproteins A2B1
Length = 116
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 29/47 (61%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY 84
+++GG+ F+ TE L + Q G++ D ++RD + + RGF FV +
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTF 76
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 33 KDSAY--VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
KD+ + ++VGG+P+ T+ L F G+I + ++ D+ TGK RG+ FV D
Sbjct: 13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMAD 68
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 40.8 bits (94), Expect = 8e-04, Method: Composition-based stats.
Identities = 19/50 (38%), Positives = 30/50 (60%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ 87
++VGG+ + T D+ F Q G++ D L+ DK T + RGF FV +E +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESE 51
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/62 (40%), Positives = 35/62 (56%), Gaps = 10/62 (16%)
Query: 34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVN---------LVRDKGTGKPRGFAFVAY 84
D++ +YV G+ +T DL F QCG +V +N + DK TGKP+G A V+Y
Sbjct: 14 DNSAIYVQGLNDSVTLDDLADFFKQCG-VVKMNKRTGQPMIHIYLDKETGKPKGDATVSY 72
Query: 85 ED 86
ED
Sbjct: 73 ED 74
>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 = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 6/72 (8%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYE------DQRNNL 91
+YV + DL++ D+ +VF G+I L RD TGK +G+ F+ YE D ++
Sbjct: 112 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSX 171
Query: 92 NGAQILGRTIRV 103
N + G+ +RV
Sbjct: 172 NLFDLGGQYLRV 183
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 34/72 (47%), Gaps = 6/72 (8%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
VYVG I ++L E + FA G I ++ D T K +GFAFV YE
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 92 NGAQILGRTIRV 103
N + GR I+V
Sbjct: 75 NSVXLGGRNIKV 86
>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm
pdb|2LEB|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uccagu-3'
pdb|2LEC|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uggagu-3'
Length = 135
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 34/55 (61%), Gaps = 6/55 (10%)
Query: 55 VFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNLNGAQILGRTIRV 103
VF + G + DV + RD+ T + RGFAFV + D+R + ++GA + GR +RV
Sbjct: 67 VFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV 121
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 30/54 (55%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNL 91
+ V G+P+ TE DL F+ GE++ V + +D TG +GF FV + + +
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQV 71
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 37/66 (56%), Gaps = 2/66 (3%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNLNGAQIL 97
+++ G+PF T+ +L + G + D+ LV ++ GKP+G A+V YE++ +
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRA-GKPKGLAYVEYENESQASQAVMKM 78
Query: 98 -GRTIR 102
G TI+
Sbjct: 79 DGMTIK 84
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 30/50 (60%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ 87
+++GG+ + T+ L F Q GE+ + ++RD T + RGF FV + DQ
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 77
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 34/55 (61%), Gaps = 6/55 (10%)
Query: 55 VFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNLNGAQILGRTIRV 103
VF + G + DV + RD+ T + RGFAFV + D+R + ++GA + GR +RV
Sbjct: 90 VFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV 144
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 21/69 (30%), Positives = 38/69 (55%), Gaps = 6/69 (8%)
Query: 36 AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY------EDQRN 89
A +YV G+P +++ ++ +F+Q G I+ ++ D+ TG RG F+ + E+
Sbjct: 2 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 61
Query: 90 NLNGAQILG 98
LNG + LG
Sbjct: 62 GLNGQKPLG 70
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 39.7 bits (91), Expect = 0.002, Method: Composition-based stats.
Identities = 18/50 (36%), Positives = 30/50 (60%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ 87
+++GG+ + T+ L F Q GE+ + ++RD T + RGF FV + DQ
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 52
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 35/68 (51%), Gaps = 3/68 (4%)
Query: 34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY---EDQRNN 90
D+A + V + D E DL +F G I + L +DK TG+ +GFAF+++ ED
Sbjct: 14 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 73
Query: 91 LNGAQILG 98
+ G G
Sbjct: 74 IAGVSGFG 81
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 40/73 (54%), Gaps = 8/73 (10%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
+YVG + D+TE +L +F+Q G ++ + + P + FV + + R+ +
Sbjct: 18 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAALAAM 75
Query: 92 NGAQILGRTIRVD 104
NG +ILG+ ++V+
Sbjct: 76 NGRKILGKEVKVN 88
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 43/89 (48%), Gaps = 5/89 (5%)
Query: 20 LGISDDASWHAKYKDSAY-----VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTG 74
+G + D K + Y ++VG +P D+TE D +F + GE +V + RD+G G
Sbjct: 2 MGFTIDIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFG 61
Query: 75 KPRGFAFVAYEDQRNNLNGAQILGRTIRV 103
R + E + L+G + R +R+
Sbjct: 62 FIRLESRTLAEIAKAELDGTILKSRPLRI 90
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 2/66 (3%)
Query: 34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKP--RGFAFVAYEDQRNNL 91
D+ ++VG +P +E DL +F Q G + ++N++RD+ P +G FV + ++ L
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 92 NGAQIL 97
L
Sbjct: 62 EAQNAL 67
Score = 28.5 bits (62), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY 84
+++G I TE D+ +F+ G+I + ++R G RG AFV +
Sbjct: 98 LFIGMISKKCTENDIRVMFSSFGQIEECRILRGPD-GLSRGCAFVTF 143
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 2/66 (3%)
Query: 34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKP--RGFAFVAYEDQRNNL 91
D+ ++VG +P +E DL +F Q G + ++N++RD+ P +G FV + ++ L
Sbjct: 14 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 73
Query: 92 NGAQIL 97
L
Sbjct: 74 EAQNAL 79
Score = 28.5 bits (62), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY 84
+++G I TE D+ +F+ G+I + ++R G RG AFV +
Sbjct: 110 LFIGMISKKCTENDIRVMFSSFGQIEECRILRGPD-GLSRGCAFVTF 155
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 38.1 bits (87), Expect = 0.006, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 7/72 (9%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNN------L 91
V+VG + + E L +F Q G + V + +D+ GKP+ F FV ++ + L
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYAIALL 77
Query: 92 NGAQILGRTIRV 103
NG ++ GR I V
Sbjct: 78 NGIRLYGRPINV 89
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 38/78 (48%), Gaps = 7/78 (8%)
Query: 33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY------ED 86
K S +YVG + F TE + +F++ G+I + + DK GF FV Y E+
Sbjct: 16 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDK-MKTACGFCFVEYYSRADAEN 74
Query: 87 QRNNLNGAQILGRTIRVD 104
+NG ++ R IR D
Sbjct: 75 AMRYINGTRLDDRIIRTD 92
>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
pdb|3NNA|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 34/66 (51%), Gaps = 2/66 (3%)
Query: 34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKP--RGFAFVAYEDQRNNL 91
D+ +VG +P +E DL +F Q G + ++N++RD+ P +G FV + ++ L
Sbjct: 2 DAIKXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 92 NGAQIL 97
L
Sbjct: 62 EAQNAL 67
Score = 27.7 bits (60), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY 84
+++G I TE D+ F+ G+I + ++R G RG AFV +
Sbjct: 98 LFIGXISKKCTENDIRVXFSSFGQIEECRILRGPD-GLSRGCAFVTF 143
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 43/89 (48%), Gaps = 13/89 (14%)
Query: 21 GISDDASWHAK------YKDSAY-VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGT 73
G+S++ S + DSA+ +++GG+P L + + + G + NLV+D T
Sbjct: 93 GMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSAT 152
Query: 74 GKPRGFAFVAYEDQRNN------LNGAQI 96
G +G+AF Y D LNG Q+
Sbjct: 153 GLSKGYAFCEYVDINVTDQAIAGLNGMQL 181
>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
pdb|3NNH|C Chain C, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
pdb|3NNH|B Chain B, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
pdb|3NNH|D Chain D, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
Length = 88
Score = 37.7 bits (86), Expect = 0.008, Method: Composition-based stats.
Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 2/66 (3%)
Query: 34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKP--RGFAFVAYEDQRNNL 91
D+ ++VG +P +E DL +F Q G + ++N++RD+ P +G FV + ++ L
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 92 NGAQIL 97
L
Sbjct: 62 EAQNAL 67
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 37.4 bits (85), Expect = 0.009, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 6/65 (9%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
+++GG+P L + + + G + NLV+D TG +G+AF Y D L
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 92 NGAQI 96
NG Q+
Sbjct: 64 NGMQL 68
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 37.0 bits (84), Expect = 0.013, Method: Composition-based stats.
Identities = 21/64 (32%), Positives = 36/64 (56%), Gaps = 1/64 (1%)
Query: 40 VGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNLNGAQIL-G 98
V +P D+T+ +L A+F G I ++RD TG G+AFV + + ++ ++L G
Sbjct: 8 VNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNG 67
Query: 99 RTIR 102
T+R
Sbjct: 68 ITVR 71
>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|B Chain B, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|C Chain C, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|D Chain D, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|E Chain E, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|F Chain F, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|G Chain G, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|H Chain H, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
Length = 190
Score = 37.0 bits (84), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 36 AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY------EDQRN 89
A +YVG + D+TE L F+ G I+ + + RD T + G+A+V + E +
Sbjct: 11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 70
Query: 90 NLNGAQILGRTIRV 103
+N I G+ +R+
Sbjct: 71 TMNFDVIKGKPVRI 84
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 36.6 bits (83), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 6/65 (9%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNN------L 91
+++GG+P L + + + G + NLV+D TG +G+AF Y D L
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 92 NGAQI 96
NG Q+
Sbjct: 157 NGMQL 161
>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 = 36.6 bits (83), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 36 AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY------EDQRN 89
A +YVG + D+TE L F+ G I+ + + RD T + G+A+V + E +
Sbjct: 16 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 75
Query: 90 NLNGAQILGRTIRV 103
+N I G+ +R+
Sbjct: 76 TMNFDVIKGKPVRI 89
>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAF|B Chain B, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAG|A Chain A, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAG|B Chain B, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAH|A Chain A, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAH|B Chain B, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAI|A Chain A, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAI|B Chain B, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAJ|A Chain A, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAJ|B Chain B, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAK|A Chain A, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAK|B Chain B, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAL|A Chain A, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|B Chain B, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|D Chain D, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|I Chain I, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAM|A Chain A, Structure Of U2af65 Variant With Bru5c2 Dna
pdb|3VAM|B Chain B, Structure Of U2af65 Variant With Bru5c2 Dna
Length = 174
Score = 36.6 bits (83), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 6/65 (9%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNN------L 91
+++GG+P L + + + G + NLV+D TG +G+AF Y D L
Sbjct: 99 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 158
Query: 92 NGAQI 96
NG Q+
Sbjct: 159 NGMQL 163
>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain
Of Hnrnp D (Auf1) With Telomere Dna
pdb|1X0F|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain
Of Hnrnp D(Auf1) With Telomeric Dna
Length = 79
Score = 35.8 bits (81), Expect = 0.027, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 27/50 (54%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ 87
++VGG+ D E + F GE+ + L D T K RGF F+ ++++
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEE 53
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 35.4 bits (80), Expect = 0.033, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 27/50 (54%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ 87
++VGG+ D E + F GE+ + L D T K RGF F+ ++++
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEE 51
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 35.4 bits (80), Expect = 0.033, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 31/47 (65%), Gaps = 1/47 (2%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY 84
V+VGGI + E ++ + FA+ G + +V ++ D+ TG +G+ FV++
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 57
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet
Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 35.4 bits (80), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 40/76 (52%), Gaps = 6/76 (7%)
Query: 34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN---- 89
+ A +++ +P + + DLL +F G +V + DK T + F FV+Y++ +
Sbjct: 24 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 83
Query: 90 --NLNGAQILGRTIRV 103
++NG QI + ++V
Sbjct: 84 IQSMNGFQIGMKRLKV 99
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 35.4 bits (80), Expect = 0.039, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 31/47 (65%), Gaps = 1/47 (2%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY 84
V+VGGI + E ++ + FA+ G + +V ++ D+ TG +G+ FV++
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 58
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 34.7 bits (78), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 37/73 (50%), Gaps = 11/73 (15%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
VYVG + +G+L F+ G + V + R+ P GFAFV +ED R+ L
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGL 57
Query: 92 NGAQILGRTIRVD 104
+G I G +RV+
Sbjct: 58 DGKVICGSRVRVE 70
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 34.3 bits (77), Expect = 0.086, Method: Composition-based stats.
Identities = 26/73 (35%), Positives = 39/73 (53%), Gaps = 10/73 (13%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKP-RGFAFVAYEDQR--NNLNGA 94
V+VG D+T +L F Q GE+VDV + KP R FAFV + D + +L G
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFI------PKPFRAFAFVTFADDKVAQSLCGE 67
Query: 95 QILGRTIRVDHVA 107
++ + I V H++
Sbjct: 68 DLIIKGISV-HIS 79
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 33.9 bits (76), Expect = 0.098, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 40/72 (55%), Gaps = 9/72 (12%)
Query: 35 SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKP-RGFAFVAYEDQR--NNL 91
S+ V+VG D+TE +L F+Q G+++DV + KP R FAFV + D + +L
Sbjct: 5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFI------PKPFRAFAFVTFADDQIAQSL 58
Query: 92 NGAQILGRTIRV 103
G ++ + I V
Sbjct: 59 CGEDLIIKGISV 70
>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Rna, Uuguucuu
Length = 102
Score = 33.5 bits (75), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 31/47 (65%), Gaps = 1/47 (2%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY 84
V+VGGI + E ++ + FA+ G + +V ++ D+ TG +G+ FV++
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 57
>pdb|3NS6|A Chain A, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
pdb|3NS6|B Chain B, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
Length = 100
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 29/52 (55%), Gaps = 6/52 (11%)
Query: 37 YVYVGGIPF------DLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFV 82
Y+ V G P + + L ++F++ G++V++ D+ TGK +GF FV
Sbjct: 8 YIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFV 59
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 33.1 bits (74), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 39/72 (54%), Gaps = 3/72 (4%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNLNG-AQI 96
++V + + +E DL +F+ G + +++ D T KP+GFAFV + + + A++
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 97 LGRTI--RVDHV 106
G+ R+ HV
Sbjct: 71 DGQVFQGRMLHV 82
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 33.1 bits (74), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 36/66 (54%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNLNGAQIL 97
++VG +P D+TE ++ +F + G+ +V + +DKG G R E + L+ +
Sbjct: 25 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLR 84
Query: 98 GRTIRV 103
G+ +RV
Sbjct: 85 GKQLRV 90
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 32.3 bits (72), Expect = 0.28, Method: Composition-based stats.
Identities = 16/52 (30%), Positives = 29/52 (55%), Gaps = 6/52 (11%)
Query: 37 YVYVGGIPF------DLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFV 82
Y+ V G P + + L ++F++ G++V++ D+ TGK +GF FV
Sbjct: 8 YIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFV 59
>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2
pdb|3BS9|B Chain B, X-Ray Structure Of Human Tia-1 Rrm2
Length = 87
Score = 32.3 bits (72), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 27/51 (52%), Gaps = 6/51 (11%)
Query: 60 GEIVDVNLVRDKGTGKPRGFAFVAY------EDQRNNLNGAQILGRTIRVD 104
G I D +V+D TGK +G+ FV++ E+ + G + GR IR +
Sbjct: 31 GRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTN 81
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 32.3 bits (72), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 4/67 (5%)
Query: 31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDK-GTGKPRGFAFVAY---ED 86
K + ++ + V IPF + ++ +F+ GE+ V L + GTG RGF FV + +D
Sbjct: 11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQD 70
Query: 87 QRNNLNG 93
+ N
Sbjct: 71 AKKAFNA 77
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 32.0 bits (71), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 33/55 (60%), Gaps = 4/55 (7%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNL---VRDKGTGKPRGFAFVAYEDQRN 89
V+VGG+P D+ E ++ A F + G +V V+ K P+G+AF+ ++++ +
Sbjct: 11 VFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESS 64
>pdb|3D2N|A Chain A, Crystal Structure Of Mbnl1 Tandem Zinc Finger 1 And 2
Domain
Length = 83
Score = 32.0 bits (71), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 14/21 (66%), Positives = 16/21 (76%), Gaps = 1/21 (4%)
Query: 129 VCRAFQRGECTRGDG-CKFSH 148
VCR FQRG C+R D CKF+H
Sbjct: 11 VCREFQRGTCSRPDTECKFAH 31
>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
pdb|2RS8|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
Length = 99
Score = 32.0 bits (71), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 36/66 (54%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNLNGAQIL 97
++VG +P D+TE ++ +F + G+ +V + +DKG G R E + L+ +
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLR 77
Query: 98 GRTIRV 103
G+ +RV
Sbjct: 78 GKQLRV 83
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 31.6 bits (70), Expect = 0.52, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 29/51 (56%)
Query: 35 SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYE 85
S+ +Y+ G+ T+ DL+ + G+IV + DK T K +G+ FV ++
Sbjct: 5 SSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFD 55
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 31.6 bits (70), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 8/75 (10%)
Query: 35 SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------ 88
S+ ++V +PFD T L F +CG ++ ++ + GK +G V +E
Sbjct: 5 SSGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERAC 62
Query: 89 NNLNGAQILGRTIRV 103
+NG ++ GR I V
Sbjct: 63 RMMNGMKLSGREIDV 77
>pdb|2RPP|A Chain A, Solution Structure Of Tandem Zinc Finger Domain 12 In
Muscleblind-Like Protein 2
Length = 89
Score = 31.6 bits (70), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 14/21 (66%), Positives = 16/21 (76%), Gaps = 1/21 (4%)
Query: 129 VCRAFQRGECTRGD-GCKFSH 148
VCR FQRG C+R D CKF+H
Sbjct: 19 VCRQFQRGTCSRSDEECKFAH 39
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 31.2 bits (69), Expect = 0.65, Method: Composition-based stats.
Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 3/49 (6%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
+Y+ +P+ +T ++ +F + G I +R T + RG A+V YED
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPI---RQIRVGNTPETRGTAYVVYED 60
>pdb|2E5S|A Chain A, Solution Structure Of The Zf-Ccchx2 Domain Of Muscleblind-
Like 2, Isoform 1 [homo Sapiens]
Length = 98
Score = 31.2 bits (69), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 13/21 (61%), Positives = 16/21 (76%), Gaps = 1/21 (4%)
Query: 129 VCRAFQRGECTRGDG-CKFSH 148
VCR FQRG C RG+ C+F+H
Sbjct: 22 VCREFQRGNCARGETDCRFAH 42
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 31.2 bits (69), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 8/75 (10%)
Query: 35 SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------ 88
+ ++V +PFD T L F +CG ++ ++ + GK +G V +E
Sbjct: 8 ACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERAC 65
Query: 89 NNLNGAQILGRTIRV 103
+NG ++ GR I V
Sbjct: 66 RMMNGMKLSGREIDV 80
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 30.8 bits (68), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 3/49 (6%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
+Y+ +P+ +T ++ +F + G I + R T + RG A+V YED
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYED 66
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 30.8 bits (68), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 3/49 (6%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
+Y+ +P+ +T ++ +F + G I + R T + RG A+V YED
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYED 56
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 11/73 (15%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
VYVG + + + +L F G + V + R+ P GFAFV +ED R+ +L
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRDL 130
Query: 92 NGAQILGRTIRVD 104
+G + G +RV+
Sbjct: 131 DGRTLCGCRVRVE 143
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 19/35 (54%)
Query: 39 YVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGT 73
Y+G IP TE DL+ +F G I+D +KG
Sbjct: 31 YIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGC 65
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 38/73 (52%), Gaps = 14/73 (19%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
++VG + T +L ++F + G +++ ++V+D +AFV E + + L
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQL 63
Query: 92 NGAQILGRTIRVD 104
NG ++ G+ I V+
Sbjct: 64 NGKEVKGKRINVE 76
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 7/73 (9%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
+YVG + +TE L F G I ++ ++ DK K +AFV Y + L
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKN-NKNVNYAFVEYHQSHDANIALQTL 61
Query: 92 NGAQILGRTIRVD 104
NG QI ++++
Sbjct: 62 NGKQIENNIVKIN 74
Score = 27.3 bits (59), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 18/80 (22%), Positives = 39/80 (48%), Gaps = 6/80 (7%)
Query: 34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ------ 87
D+ ++VG + ++ + L F + +++ D TG RG+ FV++ Q
Sbjct: 86 DTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNA 145
Query: 88 RNNLNGAQILGRTIRVDHVA 107
+++ G + GR +R++ A
Sbjct: 146 MDSMQGQDLNGRPLRINWAA 165
>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 = 1.6, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 11/73 (15%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
VYVG + + + +L F G + V + R+ P GFAFV +ED R+ L
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVREL 130
Query: 92 NGAQILGRTIRVD 104
+G + G +RV+
Sbjct: 131 DGRTLCGCRVRVE 143
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 30.0 bits (66), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 30/53 (56%), Gaps = 9/53 (16%)
Query: 38 VYVGGI-PFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN 89
V++G + + + D+ A+F++ G+IV G +GFAFV Y ++RN
Sbjct: 18 VFIGNLNTLVVKKSDVEAIFSKYGKIV--------GCSVHKGFAFVQYVNERN 62
>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 = 1.7, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 35 SAYVYVGGIPFDLTEGDLLAVFAQCG-EIVDVNLVRDKGTGKPRGFAFVAY 84
S V + +P TE D+ G + +V L+R+K +G+ RGFAFV +
Sbjct: 1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEF 51
>pdb|3D2Q|A Chain A, Crystal Structure Of Mbnl1 Tandem Zinc Finger 3 And 4
Domain
pdb|3D2Q|B Chain B, Crystal Structure Of Mbnl1 Tandem Zinc Finger 3 And 4
Domain
pdb|3D2Q|C Chain C, Crystal Structure Of Mbnl1 Tandem Zinc Finger 3 And 4
Domain
pdb|3D2Q|D Chain D, Crystal Structure Of Mbnl1 Tandem Zinc Finger 3 And 4
Domain
pdb|3D2S|A Chain A, Crystal Structure Of Mbnl1 Tandem Zinc Finger 3 And 4
Domain In Complex With Cgcugu Rna
pdb|3D2S|B Chain B, Crystal Structure Of Mbnl1 Tandem Zinc Finger 3 And 4
Domain In Complex With Cgcugu Rna
pdb|3D2S|C Chain C, Crystal Structure Of Mbnl1 Tandem Zinc Finger 3 And 4
Domain In Complex With Cgcugu Rna
pdb|3D2S|D Chain D, Crystal Structure Of Mbnl1 Tandem Zinc Finger 3 And 4
Domain In Complex With Cgcugu Rna
Length = 70
Score = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 12/21 (57%), Positives = 16/21 (76%), Gaps = 1/21 (4%)
Query: 129 VCRAFQRGECTRGDG-CKFSH 148
VCR +QRG C RG+ C+F+H
Sbjct: 8 VCREYQRGNCNRGENDCRFAH 28
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 29.6 bits (65), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 35/71 (49%), Gaps = 12/71 (16%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
VY GGI LT+ + F+ G+I+++ + +K G++FV + + ++
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFSTHESAAHAIVSV 81
Query: 92 NGAQILGRTIR 102
NG I G ++
Sbjct: 82 NGTTIEGHVVK 92
>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 29.3 bits (64), Expect = 2.8, Method: Composition-based stats.
Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 10/51 (19%)
Query: 64 DVNLVRDKGTGKPRGFAFVAYEDQRNNLNGAQIL----------GRTIRVD 104
++ L++DK T + RGFAFV + QIL G+TI VD
Sbjct: 40 NIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVD 90
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 29.3 bits (64), Expect = 2.9, Method: Composition-based stats.
Identities = 20/78 (25%), Positives = 38/78 (48%), Gaps = 7/78 (8%)
Query: 35 SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDV-NLVRDKGTGKPRGFAFV------AYEDQ 87
S+ +++G + ++ E L F+ G I+ ++RD TG +G+AF+ A +
Sbjct: 5 SSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAA 64
Query: 88 RNNLNGAQILGRTIRVDH 105
+NG + R I V +
Sbjct: 65 IEAMNGQYLCNRPITVSY 82
>pdb|2RHK|C Chain C, Crystal Structure Of Influenza A Ns1a Protein In Complex
With F2f3 Fragment Of Human Cellular Factor Cpsf30,
Northeast Structural Genomics Targets Or8c And Hr6309a
pdb|2RHK|D Chain D, Crystal Structure Of Influenza A Ns1a Protein In Complex
With F2f3 Fragment Of Human Cellular Factor Cpsf30,
Northeast Structural Genomics Targets Or8c And Hr6309a
Length = 72
Score = 29.3 bits (64), Expect = 3.0, Method: Composition-based stats.
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 129 VCRAFQRGECTRGDGCKFSH 148
VC+ + RG C +GD C+F H
Sbjct: 18 VCKHWLRGLCKKGDQCEFLH 37
>pdb|2DIS|A Chain A, Solution Structure Of The Rrm Domain Of Unnamed Protein
Product
Length = 109
Score = 28.9 bits (63), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 34/77 (44%), Gaps = 10/77 (12%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGE-IVDVNLVRDKG-TGKPRGFAFVAYEDQRNNLNG-- 93
+++GGIP ++L A+ E ++DV + K RGFAFV YE R
Sbjct: 11 LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 70
Query: 94 ------AQILGRTIRVD 104
Q+ G I VD
Sbjct: 71 KLMPGRIQLWGHQIAVD 87
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 28.9 bits (63), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 13/54 (24%), Positives = 26/54 (48%), Gaps = 1/54 (1%)
Query: 33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
+D +Y+ +P + E +L + G+++ ++RD +G RG F E
Sbjct: 23 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMES 75
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 28.5 bits (62), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 3/61 (4%)
Query: 29 HAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR 88
+A+ + S ++V G+ D TE L F V +V D+ TG +GF FV + +
Sbjct: 9 NARSQPSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEE 65
Query: 89 N 89
+
Sbjct: 66 D 66
>pdb|2D9N|A Chain A, Solution Structure Of Ccch Type Zinc-Finger Domain 2 In
Cleavage And Polyadenylation Specificity Factor
Length = 77
Score = 28.1 bits (61), Expect = 5.2, Method: Composition-based stats.
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 129 VCRAFQRGECTRGDGCKFSH 148
VC+ + RG C +GD C+F H
Sbjct: 12 VCKHWLRGLCKKGDQCEFLH 31
>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of
The Spliceosomal Protein P14 Bound To A Region Of
Sf3b155
pdb|2F9J|B Chain B, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of
The Spliceosomal Protein P14 Bound To A Region Of
Sf3b155
Length = 125
Score = 27.7 bits (60), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 3/49 (6%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
+ + +P+ +T ++ +F + G I + R T + RG A+V YED
Sbjct: 21 LMIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYED 66
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 27.7 bits (60), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 21/37 (56%)
Query: 33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVR 69
K +YVGG+ +TE DL F Q GEI + +V+
Sbjct: 10 KTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ 46
>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
pdb|3MD1|B Chain B, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
Length = 83
Score = 27.7 bits (60), Expect = 8.3, Method: Composition-based stats.
Identities = 17/76 (22%), Positives = 37/76 (48%), Gaps = 6/76 (7%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ------RNNL 91
++VG + ++ + L F + +++ D TG RG+ FV++ Q +++
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 92 NGAQILGRTIRVDHVA 107
G + GR +R++ A
Sbjct: 64 QGQDLNGRPLRINWAA 79
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
0.314 0.133 0.399
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,934,226
Number of Sequences: 62578
Number of extensions: 372066
Number of successful extensions: 732
Number of sequences better than 100.0: 152
Number of HSP's better than 100.0 without gapping: 118
Number of HSP's successfully gapped in prelim test: 34
Number of HSP's that attempted gapping in prelim test: 549
Number of HSP's gapped (non-prelim): 183
length of query: 291
length of database: 14,973,337
effective HSP length: 98
effective length of query: 193
effective length of database: 8,840,693
effective search space: 1706253749
effective search space used: 1706253749
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 51 (24.3 bits)