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= 048030
(93 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 66.6 bits (161), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 30/73 (41%), Positives = 48/73 (65%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+SF T ++ L FS++GQ++E ++ D+ RS+G+G+VTF ++A+ A+ MNGK +
Sbjct: 20 LSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSV 79
Query: 61 DGRVIFVDNVRPS 73
DGR I VD S
Sbjct: 80 DGRQIRVDQAGKS 92
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 60.8 bits (146), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 30/70 (42%), Positives = 44/70 (62%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+ F+ T++ML F FG++ ++MD RSKGYG++TFS E A+KAL +NG L
Sbjct: 34 LHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFEL 93
Query: 61 DGRVIFVDNV 70
GR + V +V
Sbjct: 94 AGRPMKVGHV 103
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 60.1 bits (144), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 28/60 (46%), Positives = 43/60 (71%), Gaps = 2/60 (3%)
Query: 8 EMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 67
E L AFS FG +T A ++M+ G RSKG+G+V FS+ EEA KA+ +MNG+++ + ++V
Sbjct: 30 ERLRKAFSPFGTITSAKVMMEGG--RSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYV 87
>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 = 59.3 bits (142), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 28/64 (43%), Positives = 40/64 (62%), Gaps = 2/64 (3%)
Query: 4 STTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGR 63
S + L D FS FG + ++ D+ N SKGYG+V F T+E A++A+ MNG LL+ R
Sbjct: 109 SIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDR 166
Query: 64 VIFV 67
+FV
Sbjct: 167 KVFV 170
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 31/61 (50%)
Query: 5 TTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRV 64
T+ ML + FS G + + D RS GY YV F +A++AL MN ++ G+
Sbjct: 22 VTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKP 81
Query: 65 I 65
+
Sbjct: 82 V 82
>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 = 58.9 bits (141), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 28/64 (43%), Positives = 40/64 (62%), Gaps = 2/64 (3%)
Query: 4 STTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGR 63
S + L D FS FG + ++ D+ N SKGYG+V F T+E A++A+ MNG LL+ R
Sbjct: 114 SIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDR 171
Query: 64 VIFV 67
+FV
Sbjct: 172 KVFV 175
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 31/61 (50%)
Query: 5 TTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRV 64
T+ ML + FS G + + D RS GY YV F +A++AL MN ++ G+
Sbjct: 27 VTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKP 86
Query: 65 I 65
+
Sbjct: 87 V 87
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 58.9 bits (141), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 28/64 (43%), Positives = 40/64 (62%), Gaps = 2/64 (3%)
Query: 4 STTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGR 63
S + L D FS FG + ++ D+ N SKGYG+V F T+E A++A+ MNG LL+ R
Sbjct: 22 SIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDR 79
Query: 64 VIFV 67
+FV
Sbjct: 80 KVFV 83
>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 = 58.9 bits (141), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 28/64 (43%), Positives = 40/64 (62%), Gaps = 2/64 (3%)
Query: 4 STTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGR 63
S + L D FS FG + ++ D+ N SKGYG+V F T+E A++A+ MNG LL+ R
Sbjct: 16 SIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDR 73
Query: 64 VIFV 67
+FV
Sbjct: 74 KVFV 77
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 57.4 bits (137), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 28/70 (40%), Positives = 43/70 (61%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+ F+ T++ML F FG++ ++ D RSKGYG++TFS E A++AL +NG L
Sbjct: 13 LHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFEL 72
Query: 61 DGRVIFVDNV 70
GR + V +V
Sbjct: 73 AGRPMRVGHV 82
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 54.7 bits (130), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 39/60 (65%)
Query: 6 TKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 65
T E + AF+ FG++++A ++ D +SKGYG+V+F + +A+ A+ M G+ L GR I
Sbjct: 28 TTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMGGQWLGGRQI 87
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 54.3 bits (129), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 39/69 (56%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+ + T+E L D FS+ G V ++ D+ + KGYG+ + +E A A+ ++NG+
Sbjct: 16 IPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREF 75
Query: 61 DGRVIFVDN 69
GR + VDN
Sbjct: 76 SGRALRVDN 84
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleaoproteins A2B1
Length = 116
Score = 53.5 bits (127), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 25/65 (38%), Positives = 42/65 (64%), Gaps = 1/65 (1%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+SF TT+E L + + Q+G++T+ ++ D RS+G+G+VTFS+ E A+A +
Sbjct: 35 LSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSI 93
Query: 61 DGRVI 65
DGRV+
Sbjct: 94 DGRVV 98
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs
Of Human Antigen R
Length = 177
Score = 53.5 bits (127), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 29/77 (37%), Positives = 42/77 (54%)
Query: 6 TKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 65
T++ L FS G+V A +I DK S GYG+V + T ++A++A+ +NG L + I
Sbjct: 15 TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTI 74
Query: 66 FVDNVRPSRRYNTDAPL 82
V RPS DA L
Sbjct: 75 KVSYARPSSEVIKDANL 91
Score = 39.7 bits (91), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 33/55 (60%)
Query: 4 STTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGK 58
+ T++ + D FS+FG++ + +++D+ S+G ++ F EA++A+ NG
Sbjct: 99 TMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGH 153
>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 = 53.5 bits (127), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 29/77 (37%), Positives = 42/77 (54%)
Query: 6 TKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 65
T++ L FS G+V A +I DK S GYG+V + T ++A++A+ +NG L + I
Sbjct: 15 TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTI 74
Query: 66 FVDNVRPSRRYNTDAPL 82
V RPS DA L
Sbjct: 75 KVSYARPSSEVIKDANL 91
Score = 39.7 bits (91), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 33/54 (61%)
Query: 4 STTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNG 57
+ T++ + D FS+FG++ + +++D+ S+G ++ F EA++A+ NG
Sbjct: 99 TMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
>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 = 53.5 bits (127), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 39/60 (65%)
Query: 6 TKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 65
T E + AF+ FG++++A ++ D +SKGYG+V+F + +A+ A+ M G+ L GR I
Sbjct: 28 TTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 87
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 53.1 bits (126), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 26/65 (40%), Positives = 40/65 (61%), Gaps = 1/65 (1%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+SF TT E L F Q+G +T+ ++ D RS+G+G+VT++T EE A+ K +
Sbjct: 21 LSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHK-V 79
Query: 61 DGRVI 65
DGRV+
Sbjct: 80 DGRVV 84
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 26/48 (54%)
Query: 5 TTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKAL 52
T + L D F Q+G++ I+ D+G + +G+ +VTF + K +
Sbjct: 116 TEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 53.1 bits (126), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 26/65 (40%), Positives = 40/65 (61%), Gaps = 1/65 (1%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+SF TT E L F Q+G +T+ ++ D RS+G+G+VT++T EE A+ K +
Sbjct: 19 LSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHK-V 77
Query: 61 DGRVI 65
DGRV+
Sbjct: 78 DGRVV 82
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 26/48 (54%)
Query: 5 TTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKAL 52
T + L D F Q+G++ I+ D+G + +G+ +VTF + K +
Sbjct: 114 TEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 161
>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 = 52.8 bits (125), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 26/65 (40%), Positives = 40/65 (61%), Gaps = 1/65 (1%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+SF TT E L F Q+G +T+ ++ D RS+G+G+VT++T EE A+ K +
Sbjct: 20 LSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHK-V 78
Query: 61 DGRVI 65
DGRV+
Sbjct: 79 DGRVV 83
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 26/48 (54%)
Query: 5 TTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKAL 52
T + L D F Q+G++ I+ D+G + +G+ +VTF + K +
Sbjct: 115 TEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 162
>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 = 52.8 bits (125), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 26/65 (40%), Positives = 40/65 (61%), Gaps = 1/65 (1%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+SF TT E L F Q+G +T+ ++ D RS+G+G+VT++T EE A+ K +
Sbjct: 21 LSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHK-V 79
Query: 61 DGRVI 65
DGRV+
Sbjct: 80 DGRVV 84
Score = 36.2 bits (82), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 26/48 (54%)
Query: 5 TTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKAL 52
T + L D F Q+G++ I+ D+G + +G+ +VTF + K +
Sbjct: 116 TEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 52.8 bits (125), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 25/68 (36%), Positives = 42/68 (61%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+S TT+ L + FS++G + + +I+ D+ RS+G+ +V F ++A++A NG L
Sbjct: 20 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 79
Query: 61 DGRVIFVD 68
DGR I VD
Sbjct: 80 DGRRIRVD 87
>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 = 52.8 bits (125), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 26/65 (40%), Positives = 40/65 (61%), Gaps = 1/65 (1%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+SF TT E L F Q+G +T+ ++ D RS+G+G+VT++T EE A+ K +
Sbjct: 14 LSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHK-V 72
Query: 61 DGRVI 65
DGRV+
Sbjct: 73 DGRVV 77
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 26/48 (54%)
Query: 5 TTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKAL 52
T + L D F Q+G++ I+ D+G + +G+ +VTF + K +
Sbjct: 109 TEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 156
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 52.8 bits (125), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 26/65 (40%), Positives = 40/65 (61%), Gaps = 1/65 (1%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+SF TT E L F Q+G +T+ ++ D RS+G+G+VT++T EE A+ K +
Sbjct: 22 LSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHK-V 80
Query: 61 DGRVI 65
DGRV+
Sbjct: 81 DGRVV 85
Score = 36.2 bits (82), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 26/48 (54%)
Query: 5 TTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKAL 52
T + L D F Q+G++ I+ D+G + +G+ +VTF + K +
Sbjct: 117 TEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 164
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 52.4 bits (124), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 44/76 (57%), Gaps = 4/76 (5%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALA----DMN 56
+S+ TT+E L + F QFG+V E ++ D RS+G+G+VTF + K LA +++
Sbjct: 33 LSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELD 92
Query: 57 GKLLDGRVIFVDNVRP 72
K +D +V F +P
Sbjct: 93 SKTIDPKVAFPRRAQP 108
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 52.4 bits (124), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 25/68 (36%), Positives = 42/68 (61%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+S TT+ L + FS++G + + +I+ D+ RS+G+ +V F ++A++A NG L
Sbjct: 23 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 82
Query: 61 DGRVIFVD 68
DGR I VD
Sbjct: 83 DGRRIRVD 90
>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 = 52.4 bits (124), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 25/65 (38%), Positives = 40/65 (61%), Gaps = 4/65 (6%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKAL----ADMN 56
+S+ TTK+ L D FS+FG+V + T+ +D RS+G+G+V F E K + +N
Sbjct: 7 LSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLN 66
Query: 57 GKLLD 61
GK++D
Sbjct: 67 GKVID 71
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 52.0 bits (123), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 25/68 (36%), Positives = 42/68 (61%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+S TT+ L + FS++G + + +I+ D+ RS+G+ +V F ++A++A NG L
Sbjct: 54 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 113
Query: 61 DGRVIFVD 68
DGR I VD
Sbjct: 114 DGRRIRVD 121
>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 = 52.0 bits (123), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 26/65 (40%), Positives = 39/65 (60%), Gaps = 1/65 (1%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+S+ T+K+ L D F++FG+V + TI D RS+G+G++ F +K L D L
Sbjct: 19 LSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVL-DQKEHRL 77
Query: 61 DGRVI 65
DGRVI
Sbjct: 78 DGRVI 82
>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 = 52.0 bits (123), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 26/68 (38%), Positives = 39/68 (57%)
Query: 6 TKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 65
T++ L FS G+V A +I DK S GYG+V + T ++A++A+ +NG L + I
Sbjct: 17 TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTI 76
Query: 66 FVDNVRPS 73
V RPS
Sbjct: 77 KVSYARPS 84
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 52.0 bits (123), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 41/67 (61%), Gaps = 1/67 (1%)
Query: 5 TTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRV 64
T ++ML F + G ++E +I D+ ++S+G+ ++TF +A+ A DMNGK L G+
Sbjct: 19 TNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKA 77
Query: 65 IFVDNVR 71
I V+ +
Sbjct: 78 IKVEQAK 84
>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1)
From Homo Sapiens At 1.90 A Resolution
pdb|4FXV|B Chain B, Crystal Structure Of An Elav-Like Protein 1 (Elavl1)
From Homo Sapiens At 1.90 A Resolution
pdb|4FXV|C Chain C, Crystal Structure Of An Elav-Like Protein 1 (Elavl1)
From Homo Sapiens At 1.90 A Resolution
pdb|4FXV|D Chain D, Crystal Structure Of An Elav-Like Protein 1 (Elavl1)
From Homo Sapiens At 1.90 A Resolution
Length = 99
Score = 51.6 bits (122), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 26/68 (38%), Positives = 39/68 (57%)
Query: 6 TKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 65
T++ L FS G+V A +I DK S GYG+V + T ++A++A+ +NG L + I
Sbjct: 32 TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTI 91
Query: 66 FVDNVRPS 73
V RPS
Sbjct: 92 KVSYARPS 99
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 50.4 bits (119), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/70 (37%), Positives = 42/70 (60%), Gaps = 4/70 (5%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALA----DMN 56
+S+ TT+E L + F QFG+V E ++ D RS+G+G+VTF + K LA +++
Sbjct: 8 LSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELD 67
Query: 57 GKLLDGRVIF 66
K +D +V F
Sbjct: 68 SKTIDPKVAF 77
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 49.7 bits (117), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 41/67 (61%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+S TT+ L + FS++G + + +I+ D+ RS+G+ +V F ++A++A NG L
Sbjct: 23 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 82
Query: 61 DGRVIFV 67
DGR I V
Sbjct: 83 DGRRIRV 89
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 49.7 bits (117), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 42/67 (62%), Gaps = 4/67 (5%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKA----LADMN 56
+S +TT E + F QFG+V +A ++ DK NR +G+G+VTF +E+ +K ++N
Sbjct: 7 LSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEIN 66
Query: 57 GKLLDGR 63
K+++ +
Sbjct: 67 NKMVECK 73
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 49.3 bits (116), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 30/65 (46%), Positives = 37/65 (56%), Gaps = 2/65 (3%)
Query: 3 FSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG 62
F T +ML D F++ G V A I M+ GK SKG G V F + E A++A MNG L G
Sbjct: 18 FDFTWKMLKDKFNECGHVLYADIKMENGK--SKGCGVVKFESPEVAERACRMMNGMKLSG 75
Query: 63 RVIFV 67
R I V
Sbjct: 76 REIDV 80
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 49.3 bits (116), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 26/65 (40%), Positives = 37/65 (56%), Gaps = 1/65 (1%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+ +STT+E L FSQ+G+V + I+ DK N+S+G+G+V F LA L
Sbjct: 24 LDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRP-HTL 82
Query: 61 DGRVI 65
DGR I
Sbjct: 83 DGRNI 87
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 49.3 bits (116), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 32/85 (37%), Positives = 45/85 (52%), Gaps = 10/85 (11%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNR-----SKGYGYVTFSTEEEAQKALADM 55
++FSTT+E L FS+ G + TI K KN+ S G+G+V + E+AQKAL +
Sbjct: 13 LNFSTTEETLKGVFSKVGAIKSCTI--SKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQL 70
Query: 56 NGKLLDGRVIFVDNVRPSRRYNTDA 80
G +DG + VR S R A
Sbjct: 71 QGHTVDGHKL---EVRISERATKPA 92
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain
In Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 49.3 bits (116), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 30/65 (46%), Positives = 37/65 (56%), Gaps = 2/65 (3%)
Query: 3 FSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG 62
F T +ML D F++ G V A I M+ GK SKG G V F + E A++A MNG L G
Sbjct: 15 FDFTWKMLKDKFNECGHVLYADIKMENGK--SKGCGVVKFESPEVAERACRMMNGMKLSG 72
Query: 63 RVIFV 67
R I V
Sbjct: 73 REIDV 77
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 49.3 bits (116), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 42/67 (62%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+S+++++E L FS +G ++E +D + KG+ +VTF E A KA A+++G++
Sbjct: 16 LSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVF 75
Query: 61 DGRVIFV 67
GR++ V
Sbjct: 76 QGRMLHV 82
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 49.3 bits (116), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 36/63 (57%)
Query: 3 FSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG 62
FS T L FS++G+V + TI+ DK +SKG ++ F ++ AQ +N K L G
Sbjct: 26 FSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFG 85
Query: 63 RVI 65
RVI
Sbjct: 86 RVI 88
>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 = 48.1 bits (113), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 33/49 (67%)
Query: 17 FGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 65
FG++++A ++ D +SKGYG+V+F + +A+ A+ M G+ L GR I
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 78
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+ + TT L F FG + EA +I D+ +S+GYG+VT + A++A D N ++
Sbjct: 25 LPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPN-PII 83
Query: 61 DGR 63
DGR
Sbjct: 84 DGR 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 = 47.0 bits (110), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 42/74 (56%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+++ T+ + L F ++G+V + I D+ S+G+ +V F + +A+ A+ M+G +L
Sbjct: 55 LTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVL 114
Query: 61 DGRVIFVDNVRPSR 74
DGR + V R R
Sbjct: 115 DGRELRVQMARYGR 128
>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 = 46.2 bits (108), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 34/56 (60%)
Query: 8 EMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGR 63
E L +AF F ++ D S+GYG+V+F+++++AQ A+ M G+ L+GR
Sbjct: 16 ETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGR 71
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 46.2 bits (108), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 42/74 (56%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+++ T+ + L F ++G+V + I D+ S+G+ +V F + +A+ A+ M+G +L
Sbjct: 78 LTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVL 137
Query: 61 DGRVIFVDNVRPSR 74
DGR + V R R
Sbjct: 138 DGRELRVQMARYGR 151
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 46.2 bits (108), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 34/56 (60%)
Query: 8 EMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGR 63
E L +AF F ++ D S+GYG+V+F+++++AQ A+ M G+ L+GR
Sbjct: 102 ETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGR 157
>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 = 46.2 bits (108), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 34/68 (50%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
V++ TT+ L F +G + ++ K + +GY ++ + E + A +GK +
Sbjct: 110 VNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKI 169
Query: 61 DGRVIFVD 68
DGR + VD
Sbjct: 170 DGRRVLVD 177
>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 = 45.8 bits (107), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 39/77 (50%)
Query: 6 TKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 65
T+E F G++ ++ DK +S GYG+V + ++A+KA+ +NG L + I
Sbjct: 15 TQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTI 74
Query: 66 FVDNVRPSRRYNTDAPL 82
V RPS DA L
Sbjct: 75 KVSYARPSSASIRDANL 91
Score = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 35/55 (63%)
Query: 4 STTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGK 58
+ T++ L FSQ+G++ + I++D+ S+G G++ F EA++A+ +NG+
Sbjct: 99 TMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQ 153
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 45.4 bits (106), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 3 FSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG 62
+S T E + + FSQFG+V +I D+ + KG+G+V EE +A+A ++ G
Sbjct: 11 YSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAKLDNTDFMG 69
Query: 63 RVIFVDNVRPSR 74
R I V P +
Sbjct: 70 RTIRVTEANPKK 81
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 45.4 bits (106), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 33/60 (55%), Gaps = 6/60 (10%)
Query: 6 TKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 65
T +++ FS FGQ+ E + +KG Y +V FST E A A+ +NG ++G V+
Sbjct: 38 TDQLMRQTFSPFGQIMEIRVFPEKG------YSFVRFSTHESAAHAIVSVNGTTIEGHVV 91
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 45.4 bits (106), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 37/60 (61%), Gaps = 2/60 (3%)
Query: 10 LADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDN 69
L F QFG++ + II ++ SKG+G+VTF +A +A ++G +++GR I V+N
Sbjct: 46 LRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN 103
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 45.4 bits (106), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 37/60 (61%), Gaps = 2/60 (3%)
Query: 10 LADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDN 69
L F QFG++ + II ++ SKG+G+VTF +A +A ++G +++GR I V+N
Sbjct: 32 LRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN 89
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 39/63 (61%), Gaps = 1/63 (1%)
Query: 4 STTKEMLADAFSQFGQVTEATIIMDK-GKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG 62
+ TK+ + + FS +G++ + +++ + SKGY YV F +EA+KAL M+G +DG
Sbjct: 15 NVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDG 74
Query: 63 RVI 65
+ I
Sbjct: 75 QEI 77
>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 = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 39/68 (57%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
V T+E + D F+++G++ + +D+ KGY V + T +EAQ A+ +NG+ L
Sbjct: 31 VHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDL 90
Query: 61 DGRVIFVD 68
G+ I VD
Sbjct: 91 MGQPISVD 98
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With
The Au-Rich Element
Length = 174
Score = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 37/77 (48%)
Query: 6 TKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 65
T++ F G + ++ DK +S GYG+V +S +A KA+ +NG L + I
Sbjct: 17 TQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTI 76
Query: 66 FVDNVRPSRRYNTDAPL 82
V RPS DA L
Sbjct: 77 KVSYARPSSASIRDANL 93
Score = 40.4 bits (93), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 33/52 (63%), Gaps = 1/52 (1%)
Query: 7 KEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGK 58
KEM FSQ+G++ + I++D+ S+G G++ F EA++A+ +NG+
Sbjct: 105 KEM-EQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQ 155
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
28
Length = 111
Score = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 37/74 (50%), Gaps = 6/74 (8%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKAL------AD 54
+SF + +E L + QFG + +++ SKG + F T+E AQK L A+
Sbjct: 23 LSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAE 82
Query: 55 MNGKLLDGRVIFVD 68
G LDGR + VD
Sbjct: 83 GGGLKLDGRQLKVD 96
>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 = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 41/68 (60%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+SF TT+E + + FS+ G + + + +DK K + G+ +V + + +A+ A+ +NG L
Sbjct: 47 LSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRL 106
Query: 61 DGRVIFVD 68
D R+I D
Sbjct: 107 DDRIIRTD 114
>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 = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 39/68 (57%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
V T+E + D F+++G++ + +D+ KGY V + T +EAQ A+ +NG+ L
Sbjct: 15 VHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDL 74
Query: 61 DGRVIFVD 68
G+ I VD
Sbjct: 75 MGQPISVD 82
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 42/87 (48%), Gaps = 8/87 (9%)
Query: 4 STTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGR 63
+ T+E+L AFSQFG++ + D Y ++ F + A KA+ +MNGK L+G
Sbjct: 22 TVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEMNGKDLEGE 73
Query: 64 VIFVDNVRPSRRYNTDAPLARQLPQSP 90
I + +P + + RQ P
Sbjct: 74 NIEIVFAKPPDQKRKERKAQRQAASGP 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 = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 39/68 (57%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
V T+E + D F+++G++ + +D+ KGY V + T +EAQ A+ +NG+ L
Sbjct: 17 VHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDL 76
Query: 61 DGRVIFVD 68
G+ I VD
Sbjct: 77 MGQPISVD 84
>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 = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 39/68 (57%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
V T+E + D F+++G++ + +D+ KGY V + T +EAQ A+ +NG+ L
Sbjct: 30 VHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDL 89
Query: 61 DGRVIFVD 68
G+ I VD
Sbjct: 90 MGQPISVD 97
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 39/68 (57%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
V T+E + D F+++G++ + +D+ KGY V + T +EAQ A+ +NG+ L
Sbjct: 15 VHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDL 74
Query: 61 DGRVIFVD 68
G+ I VD
Sbjct: 75 MGQPISVD 82
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 37/67 (55%)
Query: 8 EMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 67
++L AF FG +T+ I +D + +G+ +V F E+A A+ +MN L GR I V
Sbjct: 27 KVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV 86
Query: 68 DNVRPSR 74
+ +P R
Sbjct: 87 NLAKPMR 93
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 43.9 bits (102), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 34/68 (50%)
Query: 6 TKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 65
T++ F G + ++ DK +S GYG+V +S +A KA+ +NG L + I
Sbjct: 17 TQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTI 76
Query: 66 FVDNVRPS 73
V RPS
Sbjct: 77 KVSYARPS 84
>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 = 43.9 bits (102), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 39/68 (57%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
V T+E + D F+++G++ + +D+ KGY V + T +EAQ A+ +NG+ L
Sbjct: 15 VHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDL 74
Query: 61 DGRVIFVD 68
G+ I VD
Sbjct: 75 MGQPISVD 82
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 42/72 (58%), Gaps = 3/72 (4%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+S TT+E L ++F G V A I+ D+ SKG+G+V F++EE+A+ A M +
Sbjct: 23 LSEDTTEETLKESFD--GSV-RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEI 79
Query: 61 DGRVIFVDNVRP 72
DG + +D +P
Sbjct: 80 DGNKVTLDWAKP 91
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 43.1 bits (100), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 5/72 (6%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+S + E+L AFSQFG V +A +++D + R+ G G+V F+ + A+KAL
Sbjct: 104 LSPVVSNELLEQAFSQFGPVEKAVVVVDD-RGRATGKGFVEFAAKPPARKALERCG---- 158
Query: 61 DGRVIFVDNVRP 72
DG + RP
Sbjct: 159 DGAFLLTTTPRP 170
Score = 31.6 bits (70), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 33/62 (53%), Gaps = 6/62 (9%)
Query: 6 TKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 65
T+E F ++G+ +E I NR +G+G++ + A+ A A+++G +L R +
Sbjct: 35 TEEDFKRLFERYGEPSEVFI------NRDRGFGFIRLESRTLAEIAKAELDGTILKSRPL 88
Query: 66 FV 67
+
Sbjct: 89 RI 90
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 39/75 (52%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+++ T+ + L F ++G+V + I + +G+ +V F +AQ A A M+G L
Sbjct: 21 LTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAEL 80
Query: 61 DGRVIFVDNVRPSRR 75
DGR + V R RR
Sbjct: 81 DGRELRVQVARYGRR 95
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 20/48 (41%), Positives = 28/48 (58%)
Query: 10 LADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNG 57
LA F FG V A + +DK + SK +G+V+F + AQ A+ MNG
Sbjct: 57 LASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNG 104
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 34/56 (60%), Gaps = 1/56 (1%)
Query: 10 LADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNG-KLLDGRV 64
L F ++G + I+ D+ +S+GYG+V F + AQ+A+A +NG +L+ R+
Sbjct: 59 LRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRL 114
>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 = 42.7 bits (99), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 41/64 (64%), Gaps = 3/64 (4%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTF---STEEEAQKALADMNG 57
+++ TT++ L + F ++G VT+ I+ D RS+G+G+++F S+ +E K ++G
Sbjct: 11 LNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDG 70
Query: 58 KLLD 61
K++D
Sbjct: 71 KVID 74
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 26/39 (66%)
Query: 14 FSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKAL 52
FSQ+G + +A +++DK +S+G+G+VT+ + + +
Sbjct: 108 FSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVC 146
>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 = 42.4 bits (98), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 36/74 (48%), Gaps = 1/74 (1%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
V + T E L F G V TI+ DK KG+ Y+ FS +E + +LA ++ L
Sbjct: 13 VDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA-LDESLF 71
Query: 61 DGRVIFVDNVRPSR 74
GR I V R +R
Sbjct: 72 RGRQIKVIPKRTNR 85
>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 = 42.0 bits (97), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 36/74 (48%), Gaps = 1/74 (1%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
V + T E L F G V TI+ DK KG+ Y+ FS +E + +LA ++ L
Sbjct: 14 VDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA-LDESLF 72
Query: 61 DGRVIFVDNVRPSR 74
GR I V R +R
Sbjct: 73 RGRQIKVIPKRTNR 86
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 42.0 bits (97), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 37/64 (57%)
Query: 10 LADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDN 69
L + F FG ++ + DK +SKG+ +++F E+A +A+A ++G D ++ V+
Sbjct: 32 LQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW 91
Query: 70 VRPS 73
+PS
Sbjct: 92 AKPS 95
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 42.0 bits (97), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 7 KEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIF 66
+E+L + F Q G +T+ TI D+ + + K +G+V F E A+A +NG L GR I
Sbjct: 30 EEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPIN 88
Query: 67 VDN 69
V
Sbjct: 89 VSG 91
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 42.0 bits (97), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 10 LADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDN 69
L + F +FG VTE +I D K R +G+G++TF E+ +A+ +M+ + G+ + V
Sbjct: 27 LREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV-NMHFHDIMGKKVEVKR 85
Query: 70 VRP 72
P
Sbjct: 86 AEP 88
>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 = 41.2 bits (95), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 41/68 (60%), Gaps = 1/68 (1%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+SF TT+E + + FS+ G + + + +DK K + G+ +V + + +A+ A+ +NG L
Sbjct: 26 LSFYTTEEQIYELFSKSGDIKKIIMGLDKMKT-ACGFCFVEYYSRADAENAMRYINGTRL 84
Query: 61 DGRVIFVD 68
D R+I D
Sbjct: 85 DDRIIRTD 92
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 41.2 bits (95), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 7 KEMLADAFSQFGQVTEATIIM-DKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 65
+++L D FS FG + + IM D SKGY ++ F++ + + A+ MNG+ L R I
Sbjct: 19 EKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPI 78
Query: 66 FV 67
V
Sbjct: 79 TV 80
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/48 (45%), Positives = 30/48 (62%), Gaps = 1/48 (2%)
Query: 5 TTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKAL 52
+ E+L +AFS FGQV A +I+D + R G G V FS + A+KAL
Sbjct: 108 VSNELLEEAFSVFGQVERAVVIVD-DRGRPSGKGIVEFSGKPAARKAL 154
Score = 26.9 bits (58), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 15/62 (24%), Positives = 31/62 (50%), Gaps = 6/62 (9%)
Query: 6 TKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 65
T+E + F ++G+ E I ++ KG+G++ T A+ A +++ L G+ +
Sbjct: 35 TEEEMRKLFEKYGKAGEVFI------HKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQL 88
Query: 66 FV 67
V
Sbjct: 89 RV 90
>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 = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 32/65 (49%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+ + T+E + D S G V ++ D RSKGY ++ F E + A+ ++NG L
Sbjct: 12 IPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQL 71
Query: 61 DGRVI 65
R +
Sbjct: 72 GSRFL 76
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 40.8 bits (94), Expect = 2e-04, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 35/71 (49%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
V++ TT+ L F +G + ++ K + +GY ++ + E + A +GK +
Sbjct: 110 VNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKI 169
Query: 61 DGRVIFVDNVR 71
DGR + VD R
Sbjct: 170 DGRRVLVDVER 180
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 33/60 (55%)
Query: 9 MLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 68
+L AF FG +T+ I +D + +G+ +V F E+A A+ +MN L GR I V+
Sbjct: 79 VLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN 138
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 34/54 (62%), Gaps = 1/54 (1%)
Query: 5 TTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGK 58
+ KEM FSQ+G++ + I++D+ S+G G++ F EA++A+ +NG+
Sbjct: 14 SQKEM-EQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQ 66
>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 = 40.4 bits (93), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 2/73 (2%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+ + ++ + AF+ FG + + D + KG+ +V + E AQ AL MN +L
Sbjct: 21 IYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVML 80
Query: 61 DGRVIFVDNVRPS 73
GR I V RPS
Sbjct: 81 GGRNIKVG--RPS 91
Score = 36.2 bits (82), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 30/58 (51%)
Query: 10 LADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 67
+ F FG++ T+ D + KGYG++ + + +Q A++ MN L G+ + V
Sbjct: 127 IKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 184
>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 = 40.4 bits (93), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 32/67 (47%), Gaps = 1/67 (1%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
V + +T + L FS G + TI+ DK KGY Y+ F+ A+A M+ +
Sbjct: 44 VDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVA-MDETVF 102
Query: 61 DGRVIFV 67
GR I V
Sbjct: 103 RGRTIKV 109
>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 = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 26/48 (54%)
Query: 10 LADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNG 57
L F FG V A + +DK N SK +G+V++ AQ A+ MNG
Sbjct: 42 LLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNG 89
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 32/65 (49%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+ + T+E + D S G V ++ D RSKGY ++ F E + A+ ++NG L
Sbjct: 10 IPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQL 69
Query: 61 DGRVI 65
R +
Sbjct: 70 GSRFL 74
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 33/60 (55%)
Query: 9 MLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 68
+L AF FG +T+ I +D + +G+ +V F E+A A+ +MN L GR I V+
Sbjct: 18 VLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN 77
>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 = 40.0 bits (92), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 2/73 (2%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+ + ++ + AF+ FG + + D + KG+ +V + E AQ AL MN +L
Sbjct: 36 IYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVML 95
Query: 61 DGRVIFVDNVRPS 73
GR I V RPS
Sbjct: 96 GGRNIKVG--RPS 106
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 31/58 (53%)
Query: 10 LADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 67
+ F FG++ AT+ D + KGYG++ + + +Q A++ MN L G+ + V
Sbjct: 142 IKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 199
>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 = 40.0 bits (92), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 32/65 (49%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+ + T+E + D S G V ++ D RSKGY ++ F E + A+ ++NG L
Sbjct: 11 IPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQL 70
Query: 61 DGRVI 65
R +
Sbjct: 71 GSRFL 75
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 40.0 bits (92), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 34/61 (55%)
Query: 8 EMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 67
++L AF FG +T+ I +D + +G+ +V F E+A A+ +MN L GR I V
Sbjct: 20 KVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV 79
Query: 68 D 68
+
Sbjct: 80 N 80
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 39.7 bits (91), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 28/51 (54%)
Query: 5 TTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADM 55
TT + L +G++ I+DK N+ KGYG+V F + AQKA+ +
Sbjct: 17 TTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 39.7 bits (91), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 34/61 (55%)
Query: 8 EMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 67
++L AF FG +T+ I +D + +G+ +V F E+A A+ +MN L GR I V
Sbjct: 22 KVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV 81
Query: 68 D 68
+
Sbjct: 82 N 82
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 39.7 bits (91), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 42/78 (53%), Gaps = 4/78 (5%)
Query: 3 FSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG 62
+ TT++ L + FS FG+V + D SKG+G+V F+ E K ++ + ++DG
Sbjct: 25 WKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRH--MIDG 82
Query: 63 RVIFVDNVRPSRRYNTDA 80
R + D P+ + + D+
Sbjct: 83 R--WCDCKLPNSKQSQDS 98
>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 = 39.7 bits (91), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 7 KEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRV-I 65
K+ L FS+ G+V +D+ ++KG+ +V + +A+K + +GK LD + +
Sbjct: 26 KKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRL 85
Query: 66 FVDNVRPSRRYNTD 79
F+ ++ RYN+D
Sbjct: 86 FLYTMKDVERYNSD 99
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 38.9 bits (89), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 44/70 (62%), Gaps = 8/70 (11%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATII-MDKGKN-RSKGYGYVTFSTEEEAQKALADMNGK 58
+S+S T+E L + F + AT I + + +N +SKGY ++ F++ E+A++AL N +
Sbjct: 23 LSYSATEETLQEVFEK------ATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKR 76
Query: 59 LLDGRVIFVD 68
++GR I ++
Sbjct: 77 EIEGRAIRLE 86
>pdb|3N9U|C Chain C, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
pdb|3N9U|I Chain I, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
Length = 156
Score = 38.9 bits (89), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 37/78 (47%), Gaps = 5/78 (6%)
Query: 2 SFSTTKEMLADAFSQFG--QVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKL 59
S+ TT + L G V E ++ +SKGY V ++E K L + GK+
Sbjct: 64 SWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKV 123
Query: 60 LDGRVIFVDNVRPSRRYN 77
L+G + +VRP+ R N
Sbjct: 124 LNGEKV---DVRPATRQN 138
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 38.5 bits (88), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 36/72 (50%), Gaps = 10/72 (13%)
Query: 3 FSTTKEMLADAFSQF--GQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
ST++EM+ F+ G V I D Y +V FS E+A +A+ +NGK+L
Sbjct: 25 LSTSEEMIEKEFNNIKPGAVERVKKIRD--------YAFVHFSNREDAVEAMKALNGKVL 76
Query: 61 DGRVIFVDNVRP 72
DG I V +P
Sbjct: 77 DGSPIEVTLAKP 88
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/58 (41%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 10 LADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 67
L + FS G V A I+ DK +S+G G VTF EA +A++ NG+LL R + V
Sbjct: 32 LKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHV 88
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 29/58 (50%), Gaps = 1/58 (1%)
Query: 10 LADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 67
L D FS G+V + II D+ RSKG YV F + A+ + G+ L G I V
Sbjct: 42 LEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIV 98
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 37.4 bits (85), Expect = 0.002, Method: Composition-based stats.
Identities = 17/64 (26%), Positives = 34/64 (53%)
Query: 4 STTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGR 63
S T++ + FG + ++ + +SKGYG+ + ++ A +A +D+ GK L R
Sbjct: 106 SLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPR 165
Query: 64 VIFV 67
++V
Sbjct: 166 TLYV 169
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 37.4 bits (85), Expect = 0.002, Method: Composition-based stats.
Identities = 17/64 (26%), Positives = 34/64 (53%)
Query: 4 STTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGR 63
S T++ + FG + ++ + +SKGYG+ + ++ A +A +D+ GK L R
Sbjct: 106 SLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPR 165
Query: 64 VIFV 67
++V
Sbjct: 166 TLYV 169
>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
pdb|3H2U|D Chain D, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
Length = 283
Score = 37.4 bits (85), Expect = 0.002, Method: Composition-based stats.
Identities = 17/64 (26%), Positives = 34/64 (53%)
Query: 4 STTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGR 63
S T++ + FG + ++ + +SKGYG+ + ++ A +A +D+ GK L R
Sbjct: 104 SLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPR 163
Query: 64 VIFV 67
++V
Sbjct: 164 TLYV 167
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Rna-Binding Protein 14
Length = 90
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 8/68 (11%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
VS + T + L F + G+V E ++ D Y +V E +A+ A+A +NGK +
Sbjct: 17 VSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQLNGKEV 68
Query: 61 DGRVIFVD 68
G+ I V+
Sbjct: 69 KGKRINVE 76
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 36.6 bits (83), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 5 TTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRV 64
T +E+ A F G + I+ D S GY +V F++E ++Q+A+ +NG + +
Sbjct: 16 TDRELYA-LFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKR 74
Query: 65 IFVDNVRP 72
+ V RP
Sbjct: 75 LKVSYARP 82
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 36.6 bits (83), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 5 TTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRV 64
T +E+ A F G + I+ D S GY +V F++E ++Q+A+ +NG + +
Sbjct: 16 TDRELYA-LFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKR 74
Query: 65 IFVDNVRP 72
+ V RP
Sbjct: 75 LKVSYARP 82
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 36.2 bits (82), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 35/64 (54%)
Query: 5 TTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRV 64
++ +L + F Q G V + D+ + +GYG+V F +EE+A A+ M+ L G+
Sbjct: 27 VSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKP 86
Query: 65 IFVD 68
I V+
Sbjct: 87 IRVN 90
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 29/52 (55%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKAL 52
+S T +E + + F FG+V + MD N+ +G+ ++TF EE +K +
Sbjct: 7 LSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 58
>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 = 0.006, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 27/48 (56%)
Query: 5 TTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKAL 52
T +E + + F FG+V + MD N+ +G+ ++TF EE +K +
Sbjct: 13 TPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 60
>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 2.50 A Resolution
Length = 200
Score = 35.8 bits (81), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 33/73 (45%), Gaps = 2/73 (2%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+ + ++ + AF+ FG + D + KG+ +V + E AQ AL N L
Sbjct: 20 IYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQXNSVXL 79
Query: 61 DGRVIFVDNVRPS 73
GR I V RPS
Sbjct: 80 GGRNIKVG--RPS 90
Score = 33.9 bits (76), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 15/58 (25%), Positives = 29/58 (50%)
Query: 10 LADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 67
+ F FG++ T+ D + KGYG++ + + +Q A++ N L G+ + V
Sbjct: 126 IKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRV 183
>pdb|1JMT|A Chain A, X-Ray Structure Of A Core U2af65U2AF35 HETERODIMER
Length = 104
Score = 35.8 bits (81), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 7 KEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIF 66
+E+ + ++G+V E + + G + G YV F EE+A+KA+ D+N + +G+ I
Sbjct: 41 EEVFTEMEEKYGEVEEMNVCDNLG-DHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH 99
Query: 67 VD 68
+
Sbjct: 100 AE 101
>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 = 35.4 bits (80), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 34/68 (50%), Gaps = 1/68 (1%)
Query: 5 TTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRV 64
T +E+ A F G + I D S GY +V F++E ++Q+A+ +NG + +
Sbjct: 27 TDRELYA-LFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVLNGITVRNKR 85
Query: 65 IFVDNVRP 72
+ V RP
Sbjct: 86 LKVSYARP 93
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 35.4 bits (80), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 31/59 (52%)
Query: 10 LADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 68
+ + F +G++ + +D+ SKGY V + T ++A A +NG + G+ I VD
Sbjct: 43 IQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD 101
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 35.4 bits (80), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 35/65 (53%), Gaps = 5/65 (7%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+SF+ T++ L + F E ++ GK SKG Y+ F +E +A+K L + G +
Sbjct: 107 LSFNITEDELKEVFED---ALEIRLVSQDGK--SKGIAYIEFKSEADAEKNLEEKQGAEI 161
Query: 61 DGRVI 65
DGR +
Sbjct: 162 DGRSV 166
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 35.4 bits (80), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 35/65 (53%), Gaps = 5/65 (7%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+SF+ T++ L + F E ++ GK SKG Y+ F +E +A+K L + G +
Sbjct: 24 LSFNITEDELKEVFED---ALEIRLVSQDGK--SKGIAYIEFKSEADAEKNLEEKQGAEI 78
Query: 61 DGRVI 65
DGR +
Sbjct: 79 DGRSV 83
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 35.4 bits (80), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 31/55 (56%), Gaps = 8/55 (14%)
Query: 14 FSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 68
FS++G+V ++ KGY +V +S E A+ A+ NG++L G+ + ++
Sbjct: 49 FSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDIN 95
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 35.0 bits (79), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+ F + + + F++FG + +A + D+ RS G V F + +A KA+ NG L
Sbjct: 36 LDFGVSDADIQELFAEFGTLKKAAVHYDRS-GRSLGTADVHFERKADALKAMKQYNGVPL 94
Query: 61 DGR 63
DGR
Sbjct: 95 DGR 97
>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 = 35.0 bits (79), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 3/73 (4%)
Query: 3 FSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG 62
FS TKE L + G V + ++ ++ + KG YV + E +A +A+ M+G +
Sbjct: 27 FSCTKEELEEICKAHGTVKDLRLVTNRA-GKPKGLAYVEYENESQASQAVMKMDGMTIKE 85
Query: 63 RVIFV--DNVRPS 73
+I V N PS
Sbjct: 86 NIIKVAISNSGPS 98
>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 = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 30/50 (60%), Gaps = 4/50 (8%)
Query: 14 FSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKAL---ADMNGKLL 60
F+++G V E II D+ SKGYG+V+F + + QK + + +GK L
Sbjct: 30 FARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQINFHGKKL 78
>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 = 34.7 bits (78), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 31/59 (52%)
Query: 10 LADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 68
+ + F +G++ + +D+ SKGY V + T ++A A +NG + G+ I VD
Sbjct: 89 IQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD 147
>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 = 34.7 bits (78), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 30/50 (60%), Gaps = 4/50 (8%)
Query: 14 FSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKAL---ADMNGKLL 60
F+++G V E II D+ SKGYG+V+F + + QK + + +GK L
Sbjct: 30 FARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQINFHGKKL 78
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 34.7 bits (78), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 30/50 (60%), Gaps = 4/50 (8%)
Query: 14 FSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKAL---ADMNGKLL 60
F+++G V E II D+ SKGYG+V+F + + QK + + +GK L
Sbjct: 31 FARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQINFHGKKL 79
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 34.3 bits (77), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 14 FSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNG 57
F FG + E TI+ N SKG +V +S+ EAQ A+ ++G
Sbjct: 36 FEAFGNIEECTILRGPDGN-SKGCAFVKYSSHAEAQAAINALHG 78
>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex
Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A
Resolution
Length = 107
Score = 33.9 bits (76), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 1/63 (1%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+ F + + + F++FG + +A + D+ RS G V F + +A KA NG L
Sbjct: 37 LDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAXKQYNGVPL 95
Query: 61 DGR 63
DGR
Sbjct: 96 DGR 98
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 33.9 bits (76), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 3/57 (5%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKN-RSKGYGYVTFSTEEEAQKALADMN 56
+S T+ + FS FGQ+ E I+ +G + S+G +VTF+T AQ A+ M+
Sbjct: 115 ISKKCTENDIRVMFSSFGQIEECRIL--RGPDGLSRGCAFVTFTTRAMAQTAIKAMH 169
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 33.5 bits (75), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 3/57 (5%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKN-RSKGYGYVTFSTEEEAQKALADMN 56
+S T+ + FS FGQ+ E I+ +G + S+G +VTF+T AQ A+ M+
Sbjct: 103 ISKKCTENDIRVMFSSFGQIEECRIL--RGPDGLSRGCAFVTFTTRAMAQTAIKAMH 157
>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 = 33.5 bits (75), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 30/55 (54%)
Query: 7 KEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD 61
K+ L FS+ G+V +D+ ++KG+ +V + +A+K + +GK LD
Sbjct: 26 KKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLD 80
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 33.5 bits (75), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 8/55 (14%)
Query: 4 STTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGK 58
+ T+E+L +FS+FG++ + D Y +V F A KA+ +MNGK
Sbjct: 26 TVTEEILEKSFSEFGKLERVKKLKD--------YAFVHFEDRGAAVKAMDEMNGK 72
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 33.1 bits (74), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 5/65 (7%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+ + T++ L + F E ++ GK SKG Y+ F TE +A+K + G +
Sbjct: 101 LPYKVTQDELKEVFED---AAEIRLVSKDGK--SKGIAYIEFKTEADAEKTFEEKQGTEI 155
Query: 61 DGRVI 65
DGR I
Sbjct: 156 DGRSI 160
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 32.7 bits (73), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 27/45 (60%), Gaps = 3/45 (6%)
Query: 14 FSQFGQVTEATIIMDKGKN-RSKGYGYVTFSTEEEAQKALADMNG 57
F FG + E T++ +G + SKG +V FS+ EAQ A+ ++G
Sbjct: 36 FQPFGVIDECTVL--RGPDGSSKGCAFVKFSSHTEAQAAIHALHG 78
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 32.7 bits (73), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 33/67 (49%), Gaps = 1/67 (1%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+ F + + + F++FG + +A + D+ RS G V F +A KA+ G L
Sbjct: 96 LDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPL 154
Query: 61 DGRVIFV 67
DGR + +
Sbjct: 155 DGRPMDI 161
>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
pdb|3NNA|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 32.3 bits (72), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 3/53 (5%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKN-RSKGYGYVTFSTEEEAQKAL 52
+S T+ + FS FGQ+ E I+ +G + S+G +VTF+T AQ A+
Sbjct: 103 ISKKCTENDIRVXFSSFGQIEECRIL--RGPDGLSRGCAFVTFTTRAXAQTAI 153
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 32.3 bits (72), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 32/64 (50%)
Query: 5 TTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRV 64
T+ L F++F + I R +G ++TF +E A +AL +NG L G++
Sbjct: 37 VTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKI 96
Query: 65 IFVD 68
+ ++
Sbjct: 97 LVIE 100
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 32.0 bits (71), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 29/52 (55%), Gaps = 6/52 (11%)
Query: 6 TKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNG 57
T +L AFS FG + + + MD +N +VT+ E A +A+A++NG
Sbjct: 50 TPTLLRGAFSPFGNIID--LSMDPPRN----CAFVTYEKMESADQAVAELNG 95
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 32.0 bits (71), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 36/68 (52%), Gaps = 9/68 (13%)
Query: 14 FSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPS 73
FS++G++ ++ KG+ +V + E A+ A+A +G+++ G+V+ + N+
Sbjct: 37 FSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDI-NLAAE 87
Query: 74 RRYNTDAP 81
+ N P
Sbjct: 88 PKVNRSGP 95
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 32.0 bits (71), Expect = 0.094, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 34/71 (47%), Gaps = 8/71 (11%)
Query: 10 LADAFSQFGQ-VTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 68
++ AF+ G+ V II ++ GY +V F+ A+K L +NGK L G
Sbjct: 26 ISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPG------ 79
Query: 69 NVRPSRRYNTD 79
P++R+ +
Sbjct: 80 -ATPAKRFKLN 89
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 31.6 bits (70), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 35/66 (53%), Gaps = 6/66 (9%)
Query: 6 TKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 65
T +L AFS FG + + + MD +N +VT+ E A +A+A++NG ++ +
Sbjct: 26 TPTLLRGAFSPFGNIID--LSMDPPRN----CAFVTYEKMESADQAVAELNGTQVESVQL 79
Query: 66 FVDNVR 71
V+ R
Sbjct: 80 KVNIAR 85
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 31.2 bits (69), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 1/63 (1%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+ F + + + F++FG + +A + D+ RS G V F +A KA+ G L
Sbjct: 43 LDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPL 101
Query: 61 DGR 63
DGR
Sbjct: 102 DGR 104
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 30.8 bits (68), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 1/63 (1%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+ F + + + F++FG + +A + D+ RS G V F +A KA+ G L
Sbjct: 43 LDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPL 101
Query: 61 DGR 63
DGR
Sbjct: 102 DGR 104
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In
Trinucleotide Repeat Containing 4 Variant
Length = 102
Score = 30.4 bits (67), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 1/51 (1%)
Query: 6 TKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMN 56
T E + F FG + E T++ SKG +V F T EAQ A+ ++
Sbjct: 25 TDEDVRKMFEPFGTIDECTVLRGP-DGTSKGCAFVKFQTHAEAQAAINTLH 74
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 30.4 bits (67), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 33/68 (48%), Gaps = 9/68 (13%)
Query: 10 LADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI-FVD 68
L + F FG + E I+ G+ +V F E A KA+ +++GK + + V
Sbjct: 48 LNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVY 99
Query: 69 NVRPSRRY 76
+ P++RY
Sbjct: 100 SKLPAKRY 107
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 30.4 bits (67), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 27/60 (45%), Gaps = 1/60 (1%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+ S ++ L + FGQV I+ D S+G G+ + E+ + + NGK +
Sbjct: 33 LPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFI 91
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 30.0 bits (66), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 39/72 (54%), Gaps = 6/72 (8%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDK---GKNRSKGYGYVTFSTEEEAQKAL-ADMN 56
+ F + + + FS FG++ T+ + K G +G+G+V F T+++A+KA A +
Sbjct: 23 IPFQANQREIRELFSTFGEL--KTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCH 80
Query: 57 GKLLDGRVIFVD 68
L GR + ++
Sbjct: 81 STHLYGRRLVLE 92
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif In Trna Selenocysteine Associated Protein
Length = 104
Score = 30.0 bits (66), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 23/35 (65%), Gaps = 1/35 (2%)
Query: 25 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKL 59
+++D+ SKGYG+V F+ E E ++AL + G +
Sbjct: 42 VVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAV 75
>pdb|2CPI|A Chain A, Solution Structure Of The Rna Recognition Motif Of Cnot4
Length = 111
Score = 29.3 bits (64), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 3/55 (5%)
Query: 14 FSQFGQVTEATIIMDKGKNRSKG---YGYVTFSTEEEAQKALADMNGKLLDGRVI 65
F +FG++ + I S+G YVT+ E+A +A+ +N ++DGR +
Sbjct: 39 FGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL 93
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 28.9 bits (63), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 31/64 (48%), Gaps = 8/64 (12%)
Query: 5 TTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRV 64
T++ + F Q+G+V E II K YG+V + A+ A+ +++ L G
Sbjct: 20 ATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVN 71
Query: 65 IFVD 68
I V+
Sbjct: 72 INVE 75
>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 = 28.5 bits (62), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 28/62 (45%), Gaps = 4/62 (6%)
Query: 6 TKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 65
KE+L + FG + ++ D SKGY + + +A+A +NG L + +
Sbjct: 131 VKELL----TSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKL 186
Query: 66 FV 67
V
Sbjct: 187 LV 188
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 28.5 bits (62), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 7 KEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNG 57
K+ L FSQFGQ+ + I+ + +G +V F A AL M G
Sbjct: 27 KKSLYAIFSQFGQILD---ILVSRSLKMRGQAFVIFKEVSSATNALRSMQG 74
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 28.5 bits (62), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 8/49 (16%)
Query: 10 LADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGK 58
L + F FG + E I+ G+ +V F E A KA+ +++GK
Sbjct: 21 LNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGK 61
>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 = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 28/62 (45%), Gaps = 4/62 (6%)
Query: 6 TKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 65
KE+L + FG + ++ D SKGY + + +A+A +NG L + +
Sbjct: 113 VKELL----TSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKL 168
Query: 66 FV 67
V
Sbjct: 169 LV 170
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 28/62 (45%), Gaps = 4/62 (6%)
Query: 6 TKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 65
KE+L + FG + ++ D SKGY + + +A+A +NG L + +
Sbjct: 111 VKELL----TSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKL 166
Query: 66 FV 67
V
Sbjct: 167 LV 168
>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 = 27.7 bits (60), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 7 KEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNG 57
K+ L FSQFGQ+ + I+ + +G +V F A AL M G
Sbjct: 27 KKSLYAIFSQFGQILD---ILVSRSLKMRGQAFVIFKEVSSATNALRSMQG 74
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein
U1a117, Nmr, 43 Structures
Length = 116
Score = 27.7 bits (60), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 7 KEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNG 57
K+ L FSQFGQ+ + I+ + +G +V F A AL M G
Sbjct: 26 KKSLYAIFSQFGQILD---ILVSRSLKMRGQAFVIFKEVSSATNALRSMQG 73
>pdb|2PE8|A Chain A, Crystal Structure Of The Uhm Domain Of Human Spf45 (free
Form)
pdb|2PEH|A Chain A, Crystal Structure Of The Uhm Domain Of Human Spf45 In
Complex With Sf3b155-Ulm5
pdb|2PEH|B Chain B, Crystal Structure Of The Uhm Domain Of Human Spf45 In
Complex With Sf3b155-Ulm5
Length = 105
Score = 27.7 bits (60), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 39 YVTFSTEEEAQKALADMNGKLLDGRVI 65
++ F E A KA+ D+NG+ GRV+
Sbjct: 60 FLEFERVESAIKAVVDLNGRYFGGRVV 86
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 27.7 bits (60), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 28/62 (45%), Gaps = 4/62 (6%)
Query: 6 TKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 65
KE+L + FG + ++ D SKGY + + +A+A +NG L + +
Sbjct: 18 VKELL----TSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKL 73
Query: 66 FV 67
V
Sbjct: 74 LV 75
>pdb|2DNY|A Chain A, Solution Structure Of The Third Rna Binding Domain Of Fbp-
Interacting Repressor, Siahbp1
Length = 119
Score = 27.3 bits (59), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 20/41 (48%)
Query: 39 YVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTD 79
+V FS E KA+ +NG+ GR + + R N+D
Sbjct: 70 FVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQERFDNSD 110
>pdb|3UE2|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 1.23 A Resolution
pdb|3US5|A Chain A, Crystal Structure Of A Rna-Binding Domain Of A Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 1.38 A Resolution
Length = 118
Score = 26.9 bits (58), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 20/41 (48%)
Query: 39 YVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTD 79
+V FS E KA+ +NG+ GR + + R N+D
Sbjct: 75 FVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQERFDNSD 115
>pdb|3DXB|A Chain A, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|B Chain B, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|C Chain C, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|D Chain D, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|E Chain E, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|F Chain F, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|G Chain G, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|H Chain H, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
Length = 222
Score = 26.9 bits (58), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 20/41 (48%)
Query: 39 YVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTD 79
+V FS E KA+ +NG+ GR + + R N+D
Sbjct: 179 FVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQERFDNSD 219
>pdb|2DGW|A Chain A, Solution Structure Of The Second Rna Recognition Motif
In Rna-Binding Protein 19
Length = 91
Score = 26.9 bits (58), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 23 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 67
A I+ GY +V FS EEE ++AL N + + GR I V
Sbjct: 38 AIRIVRNAHGNKTGYIFVDFSNEEEVKQAL-KCNREYMGGRYIEV 81
>pdb|2D1S|A Chain A, Crystal Structure Of The Thermostable Japanese Firefly
Luciferase Complexed With High-Energy Intermediate
Analogue
Length = 548
Score = 26.6 bits (57), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 32/75 (42%), Gaps = 12/75 (16%)
Query: 18 GQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADM--NGKLLDGRVIFVDNVRPSRR 75
G++ A ++++ GKN TE+E +A N K L G V FVD V
Sbjct: 480 GELPGAVVVLESGKNM----------TEKEVMDYVASQVSNAKRLRGGVRFVDEVPKGLT 529
Query: 76 YNTDAPLARQLPQSP 90
D R++ + P
Sbjct: 530 GKIDGRAIREILKKP 544
>pdb|2D1Q|A Chain A, Crystal Structure Of The Thermostable Japanese Firefly
Luciferase Complexed With Mgatp
pdb|2D1R|A Chain A, Crystal Structure Of The Thermostable Japanese Firefly
Luciferase Complexed With Oxyluciferin And Amp
Length = 548
Score = 26.2 bits (56), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 32/75 (42%), Gaps = 12/75 (16%)
Query: 18 GQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADM--NGKLLDGRVIFVDNVRPSRR 75
G++ A ++++ GKN TE+E +A N K L G V FVD V
Sbjct: 480 GELPGAVVVLESGKNM----------TEKEVMDYVASQVSNAKRLRGGVRFVDEVPKGLT 529
Query: 76 YNTDAPLARQLPQSP 90
D R++ + P
Sbjct: 530 GKIDGRAIREILKKP 544
>pdb|2D1T|A Chain A, Crystal Structure Of The Thermostable Japanese Firefly
Luciferase Red-Color Emission S286n Mutant Complexed
With High-Energy Intermediate Analogue
Length = 548
Score = 26.2 bits (56), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 32/75 (42%), Gaps = 12/75 (16%)
Query: 18 GQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADM--NGKLLDGRVIFVDNVRPSRR 75
G++ A ++++ GKN TE+E +A N K L G V FVD V
Sbjct: 480 GELPGAVVVLESGKNM----------TEKEVMDYVASQVSNAKRLRGGVRFVDEVPKGLT 529
Query: 76 YNTDAPLARQLPQSP 90
D R++ + P
Sbjct: 530 GKIDGRAIREILKKP 544
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 26.2 bits (56), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 33/68 (48%), Gaps = 2/68 (2%)
Query: 1 VSFSTTKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL 60
+S T+ ++ FSQ G +I + N Y +V F +A ALA MNG+ +
Sbjct: 23 LSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAALAAMNGRKI 80
Query: 61 DGRVIFVD 68
G+ + V+
Sbjct: 81 LGKEVKVN 88
>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 = 26.2 bits (56), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 15/62 (24%), Positives = 31/62 (50%), Gaps = 6/62 (9%)
Query: 6 TKEMLADAFSQFGQVTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 65
T+E + F ++G+ E I ++ KG+G++ T A+ A +++ L G+ +
Sbjct: 28 TEEEMRKLFEKYGKAGEVFI------HKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQL 81
Query: 66 FV 67
V
Sbjct: 82 RV 83
>pdb|4H63|Q Chain Q, Structure Of The Schizosaccharomyces Pombe Mediator Head
Module
Length = 469
Score = 25.8 bits (55), Expect = 6.4, Method: Composition-based stats.
Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 2/55 (3%)
Query: 21 TEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 75
TE+ DK N +VT E+E K L D + ++F+ + R S R
Sbjct: 278 TESGFTEDKKSNEDTSTNFVTIKQEKELLKCLCDTLNAI--AHILFLKHCRKSDR 330
>pdb|2LDK|A Chain A, Solution Nmr Structure Of Protein Aaur_3427 From
Arthrobacter Aurescens, Northeast Structural Genomics
Consortium Target Aar96
Length = 172
Score = 25.4 bits (54), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 24/37 (64%), Gaps = 1/37 (2%)
Query: 20 VTEATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMN 56
VT AT+ ++ +NR++ TF +EE+ QK +A+M
Sbjct: 107 VTHATVKLEPLENRTRMTIISTFESEEQMQK-MAEMG 142
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
0.313 0.129 0.352
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,676,233
Number of Sequences: 62578
Number of extensions: 95973
Number of successful extensions: 344
Number of sequences better than 100.0: 176
Number of HSP's better than 100.0 without gapping: 147
Number of HSP's successfully gapped in prelim test: 29
Number of HSP's that attempted gapping in prelim test: 160
Number of HSP's gapped (non-prelim): 196
length of query: 93
length of database: 14,973,337
effective HSP length: 60
effective length of query: 33
effective length of database: 11,218,657
effective search space: 370215681
effective search space used: 370215681
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 45 (21.9 bits)