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= 042899
(93 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 53.1 bits (126), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 26/64 (40%), Positives = 39/64 (60%), Gaps = 2/64 (3%)
Query: 4 STTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVR 63
S + L D FS FG + ++ D +N SKGYG++ T+E A++A+ MN MLL+ R
Sbjct: 16 SIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDR 73
Query: 64 VIFV 67
+FV
Sbjct: 74 KVFV 77
>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 = 53.1 bits (126), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 26/64 (40%), Positives = 39/64 (60%), Gaps = 2/64 (3%)
Query: 4 STTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVR 63
S + L D FS FG + ++ D +N SKGYG++ T+E A++A+ MN MLL+ R
Sbjct: 114 SIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDR 171
Query: 64 VIFV 67
+FV
Sbjct: 172 KVFV 175
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 53.1 bits (126), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 26/64 (40%), Positives = 39/64 (60%), Gaps = 2/64 (3%)
Query: 4 STTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVR 63
S + L D FS FG + ++ D +N SKGYG++ T+E A++A+ MN MLL+ R
Sbjct: 22 SIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDR 79
Query: 64 VIFV 67
+FV
Sbjct: 80 KVFV 83
>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|B Chain B, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|C Chain C, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|D Chain D, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|E Chain E, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|F Chain F, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|G Chain G, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|H Chain H, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
Length = 190
Score = 53.1 bits (126), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 26/64 (40%), Positives = 39/64 (60%), Gaps = 2/64 (3%)
Query: 4 STTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVR 63
S + L D FS FG + ++ D +N SKGYG++ T+E A++A+ MN MLL+ R
Sbjct: 109 SIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDR 166
Query: 64 VIFV 67
+FV
Sbjct: 167 KVFV 170
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 52.0 bits (123), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 25/60 (41%), Positives = 40/60 (66%), Gaps = 2/60 (3%)
Query: 8 EMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVRVIFV 67
E L AFS FG +T A ++M+ G RSKG+G++ S+ EEA KA+ +MN ++ + ++V
Sbjct: 30 ERLRKAFSPFGTITSAKVMMEGG--RSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYV 87
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 51.6 bits (122), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 27/70 (38%), Positives = 41/70 (58%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
+ F+ T++ML F FG++ ++MD RSKGYG++T S E A+KAL +N L
Sbjct: 34 LHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFEL 93
Query: 61 DVRVIFVDYV 70
R + V +V
Sbjct: 94 AGRPMKVGHV 103
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 49.3 bits (116), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 43/68 (63%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
+SF T ++ L FS++GQ+++ ++ D RS+G+G++T ++A+ A++ MN +
Sbjct: 20 LSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSV 79
Query: 61 DVRVIFVD 68
D R I VD
Sbjct: 80 DGRQIRVD 87
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs
Of Human Antigen R
Length = 177
Score = 48.5 bits (114), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 42/77 (54%)
Query: 6 TKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVRVI 65
T++ L FS G+V A +I D S GYG++ T ++A++A+ +N + L + I
Sbjct: 15 TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTI 74
Query: 66 FVDYVRPNRHYNTDASL 82
V Y RP+ DA+L
Sbjct: 75 KVSYARPSSEVIKDANL 91
Score = 31.2 bits (69), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 13/51 (25%), Positives = 29/51 (56%)
Query: 6 TKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMN 56
T++ + D FS+FG++ + +++D S+G ++ EA++A+ N
Sbjct: 101 TQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFN 151
>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 = 48.5 bits (114), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 42/77 (54%)
Query: 6 TKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVRVI 65
T++ L FS G+V A +I D S GYG++ T ++A++A+ +N + L + I
Sbjct: 15 TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTI 74
Query: 66 FVDYVRPNRHYNTDASL 82
V Y RP+ DA+L
Sbjct: 75 KVSYARPSSEVIKDANL 91
Score = 31.2 bits (69), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 13/51 (25%), Positives = 29/51 (56%)
Query: 6 TKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMN 56
T++ + D FS+FG++ + +++D S+G ++ EA++A+ N
Sbjct: 101 TQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFN 151
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 48.1 bits (113), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 25/70 (35%), Positives = 40/70 (57%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
+ F+ T++ML F FG++ ++ D RSKGYG++T S E A++AL +N L
Sbjct: 13 LHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFEL 72
Query: 61 DVRVIFVDYV 70
R + 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 = 46.6 bits (109), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 38/65 (58%)
Query: 6 TKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVRVI 65
T E + AF+ FG+++ A ++ D+ +SKGYG+++ + +A+ A+V M L R I
Sbjct: 28 TTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMGGQWLGGRQI 87
Query: 66 FVDYV 70
++
Sbjct: 88 RTNWA 92
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 45.4 bits (106), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 29/90 (32%), Positives = 46/90 (51%), Gaps = 12/90 (13%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
+SF TT E L F Q+G +T ++ D RS+G+G++T +T EE A+ + +
Sbjct: 19 LSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHKV 77
Query: 61 DVRVIFVDYVRPNRHYNTDASLVRQPAQSP 90
D RV V P R ++ R+ +Q P
Sbjct: 78 DGRV-----VEPKR------AVSREDSQRP 96
Score = 30.8 bits (68), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 12/49 (24%), Positives = 25/49 (51%)
Query: 5 TTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALV 53
T + L D F Q+G++ I+ D G + +G+ ++T + K ++
Sbjct: 114 TEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 162
>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 = 45.4 bits (106), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 37/67 (55%)
Query: 6 TKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVRVI 65
T++ L FS G+V A +I D S GYG++ T ++A++A+ +N + L + I
Sbjct: 17 TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTI 76
Query: 66 FVDYVRP 72
V Y RP
Sbjct: 77 KVSYARP 83
>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 = 45.4 bits (106), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 29/90 (32%), Positives = 46/90 (51%), Gaps = 12/90 (13%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
+SF TT E L F Q+G +T ++ D RS+G+G++T +T EE A+ + +
Sbjct: 14 LSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHKV 72
Query: 61 DVRVIFVDYVRPNRHYNTDASLVRQPAQSP 90
D RV V P R ++ R+ +Q P
Sbjct: 73 DGRV-----VEPKR------AVSREDSQRP 91
Score = 30.4 bits (67), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 12/49 (24%), Positives = 25/49 (51%)
Query: 5 TTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALV 53
T + L D F Q+G++ I+ D G + +G+ ++T + K ++
Sbjct: 109 TEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 157
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 45.4 bits (106), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 29/90 (32%), Positives = 46/90 (51%), Gaps = 12/90 (13%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
+SF TT E L F Q+G +T ++ D RS+G+G++T +T EE A+ + +
Sbjct: 21 LSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHKV 79
Query: 61 DVRVIFVDYVRPNRHYNTDASLVRQPAQSP 90
D RV V P R ++ R+ +Q P
Sbjct: 80 DGRV-----VEPKR------AVSREDSQRP 98
Score = 30.8 bits (68), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 12/49 (24%), Positives = 25/49 (51%)
Query: 5 TTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALV 53
T + L D F Q+G++ I+ D G + +G+ ++T + K ++
Sbjct: 116 TEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 164
>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 = 45.4 bits (106), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 37/67 (55%)
Query: 6 TKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVRVI 65
T++ L FS G+V A +I D S GYG++ T ++A++A+ +N + L + I
Sbjct: 32 TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTI 91
Query: 66 FVDYVRP 72
V Y RP
Sbjct: 92 KVSYARP 98
>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 = 45.4 bits (106), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 29/90 (32%), Positives = 46/90 (51%), Gaps = 12/90 (13%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
+SF TT E L F Q+G +T ++ D RS+G+G++T +T EE A+ + +
Sbjct: 20 LSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHKV 78
Query: 61 DVRVIFVDYVRPNRHYNTDASLVRQPAQSP 90
D RV V P R ++ R+ +Q P
Sbjct: 79 DGRV-----VEPKR------AVSREDSQRP 97
Score = 30.0 bits (66), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 12/49 (24%), Positives = 25/49 (51%)
Query: 5 TTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALV 53
T + L D F Q+G++ I+ D G + +G+ ++T + K ++
Sbjct: 115 TEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 163
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 45.1 bits (105), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 29/90 (32%), Positives = 46/90 (51%), Gaps = 12/90 (13%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
+SF TT E L F Q+G +T ++ D RS+G+G++T +T EE A+ + +
Sbjct: 22 LSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHKV 80
Query: 61 DVRVIFVDYVRPNRHYNTDASLVRQPAQSP 90
D RV V P R ++ R+ +Q P
Sbjct: 81 DGRV-----VEPKR------AVSREDSQRP 99
Score = 30.0 bits (66), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 12/49 (24%), Positives = 25/49 (51%)
Query: 5 TTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALV 53
T + L D F Q+G++ I+ D G + +G+ ++T + K ++
Sbjct: 117 TEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 165
>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 = 45.1 bits (105), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 29/90 (32%), Positives = 46/90 (51%), Gaps = 12/90 (13%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
+SF TT E L F Q+G +T ++ D RS+G+G++T +T EE A+ + +
Sbjct: 21 LSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHKV 79
Query: 61 DVRVIFVDYVRPNRHYNTDASLVRQPAQSP 90
D RV V P R ++ R+ +Q P
Sbjct: 80 DGRV-----VEPKR------AVSREDSQRP 98
Score = 30.0 bits (66), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 12/49 (24%), Positives = 25/49 (51%)
Query: 5 TTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALV 53
T + L D F Q+G++ I+ D G + +G+ ++T + K ++
Sbjct: 116 TEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 164
>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 = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 37/65 (56%), Gaps = 1/65 (1%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
+S+ T+K+ L D F++FG+V TI D RS+G+G++ +K L D + L
Sbjct: 19 LSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVL-DQKEHRL 77
Query: 61 DVRVI 65
D RVI
Sbjct: 78 DGRVI 82
>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 = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 37/65 (56%)
Query: 6 TKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVRVI 65
T E + AF+ FG+++ A ++ D+ +SKGYG+++ + +A+ A+ M L R I
Sbjct: 28 TTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 87
Query: 66 FVDYV 70
++
Sbjct: 88 RTNWA 92
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 39/69 (56%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
+S TT+ L + FS++G + +I+ D RS+G+ ++ ++A++A N M L
Sbjct: 20 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 79
Query: 61 DVRVIFVDY 69
D R I VD+
Sbjct: 80 DGRRIRVDF 88
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 42.7 bits (99), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 39/69 (56%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
+S TT+ L + FS++G + +I+ D RS+G+ ++ ++A++A N M L
Sbjct: 23 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 82
Query: 61 DVRVIFVDY 69
D R I VD+
Sbjct: 83 DGRRIRVDF 91
>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 = 42.7 bits (99), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 38/65 (58%), Gaps = 1/65 (1%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
+S+ TTK+ L D FS+FG+V T+ +D RS+G+G++ E K + D + L
Sbjct: 7 LSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM-DQKEHKL 65
Query: 61 DVRVI 65
+ +VI
Sbjct: 66 NGKVI 70
>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 = 42.7 bits (99), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 39/77 (50%)
Query: 6 TKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVRVI 65
T+E F G++ ++ D +S GYG++ ++A+KA+ +N + L + I
Sbjct: 15 TQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTI 74
Query: 66 FVDYVRPNRHYNTDASL 82
V Y RP+ DA+L
Sbjct: 75 KVSYARPSSASIRDANL 91
Score = 31.6 bits (70), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 30/51 (58%)
Query: 6 TKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMN 56
T++ L FSQ+G++ + I++D S+G G++ EA++A+ +N
Sbjct: 101 TQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLN 151
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 42.7 bits (99), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 39/69 (56%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
+S TT+ L + FS++G + +I+ D RS+G+ ++ ++A++A N M L
Sbjct: 54 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 113
Query: 61 DVRVIFVDY 69
D R I VD+
Sbjct: 114 DGRRIRVDF 122
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleaoproteins A2B1
Length = 116
Score = 42.4 bits (98), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 38/65 (58%), Gaps = 1/65 (1%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
+SF TT+E L + + Q+G++T ++ D RS+G+G++T S+ E A+ +
Sbjct: 35 LSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSI 93
Query: 61 DVRVI 65
D RV+
Sbjct: 94 DGRVV 98
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 42.0 bits (97), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 41/77 (53%), Gaps = 4/77 (5%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALV----DMN 56
+S+ TT+E L + F QFG+V + ++ D RS+G+G++T + K L +++
Sbjct: 33 LSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELD 92
Query: 57 KMLLDVRVIFVDYVRPN 73
+D +V F +P
Sbjct: 93 SKTIDPKVAFPRRAQPK 109
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With
The Au-Rich Element
Length = 174
Score = 41.2 bits (95), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 37/77 (48%)
Query: 6 TKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVRVI 65
T++ F G + ++ D +S GYG++ S +A KA+ +N + L + I
Sbjct: 17 TQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTI 76
Query: 66 FVDYVRPNRHYNTDASL 82
V Y RP+ DA+L
Sbjct: 77 KVSYARPSSASIRDANL 93
Score = 31.2 bits (69), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 5 TTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMN 56
+ KEM FSQ+G++ + I++D S+G G++ EA++A+ +N
Sbjct: 103 SQKEM-EQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLN 153
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 40.4 bits (93), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 33/68 (48%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
+ + T+E L D FS+ G V ++ D + KGYG+ +E A A+ ++N
Sbjct: 16 IPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREF 75
Query: 61 DVRVIFVD 68
R + VD
Sbjct: 76 SGRALRVD 83
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 39/70 (55%), Gaps = 4/70 (5%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALV----DMN 56
+S+ TT+E L + F QFG+V + ++ D RS+G+G++T + K L +++
Sbjct: 8 LSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELD 67
Query: 57 KMLLDVRVIF 66
+D +V F
Sbjct: 68 SKTIDPKVAF 77
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 39.7 bits (91), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 27/67 (40%), Positives = 36/67 (53%), Gaps = 2/67 (2%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
+ F T +ML D F++ G V A I M+ GK SKG G + + E A++A MN M L
Sbjct: 16 LPFDFTWKMLKDKFNECGHVLYADIKMENGK--SKGCGVVKFESPEVAERACRMMNGMKL 73
Query: 61 DVRVIFV 67
R I V
Sbjct: 74 SGREIDV 80
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 39.7 bits (91), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 31/47 (65%), Gaps = 1/47 (2%)
Query: 6 TKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKAL 52
+ E+L AFSQFG V KA +++D + R+ G G++ + + A+KAL
Sbjct: 109 SNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKAL 154
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain
In Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 39.7 bits (91), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 27/67 (40%), Positives = 36/67 (53%), Gaps = 2/67 (2%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
+ F T +ML D F++ G V A I M+ GK SKG G + + E A++A MN M L
Sbjct: 13 LPFDFTWKMLKDKFNECGHVLYADIKMENGK--SKGCGVVKFESPEVAERACRMMNGMKL 70
Query: 61 DVRVIFV 67
R I V
Sbjct: 71 SGREIDV 77
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 39.3 bits (90), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 32/59 (54%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKML 59
+ + TT L F FG + +A +I D +S+GYG++T + A++A D N ++
Sbjct: 25 LPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPII 83
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 39.3 bits (90), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 31/52 (59%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKAL 52
+S +TT E + F QFG+V A ++ D NR +G+G++T +E+ +K
Sbjct: 7 LSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC 58
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 39.3 bits (90), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 32/67 (47%)
Query: 6 TKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVRVI 65
T++ F G + ++ D +S GYG++ S +A KA+ +N + L + I
Sbjct: 17 TQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTI 76
Query: 66 FVDYVRP 72
V Y RP
Sbjct: 77 KVSYARP 83
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 38.9 bits (89), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 37/67 (55%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
+S TT+ L + FS++G + +I+ D RS+G+ ++ ++A++A N M L
Sbjct: 23 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 82
Query: 61 DVRVIFV 67
D R I V
Sbjct: 83 DGRRIRV 89
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 27/40 (67%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYM 40
+ +STT+E L FSQ+G+V I+ D N+S+G+G++
Sbjct: 24 LDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFV 63
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 41/72 (56%), Gaps = 3/72 (4%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
+S TT+E L ++F G V +A I+ D SKG+G++ ++EE+A+ A M +
Sbjct: 23 LSEDTTEETLKESFD--GSV-RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEI 79
Query: 61 DVRVIFVDYVRP 72
D + +D+ +P
Sbjct: 80 DGNKVTLDWAKP 91
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/48 (41%), Positives = 30/48 (62%), Gaps = 1/48 (2%)
Query: 5 TTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKAL 52
+ E+L +AFS FGQV +A +I+D + R G G + S + A+KAL
Sbjct: 108 VSNELLEEAFSVFGQVERAVVIVD-DRGRPSGKGIVEFSGKPAARKAL 154
Score = 25.4 bits (54), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 34/67 (50%), Gaps = 9/67 (13%)
Query: 6 TKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL---DV 62
T+E + F ++G+ + I ++ KG+G++ T A+ A V+++ M L +
Sbjct: 35 TEEEMRKLFEKYGKAGEVFI------HKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQL 88
Query: 63 RVIFVDY 69
RV F +
Sbjct: 89 RVRFACH 95
>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 = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 31/54 (57%)
Query: 17 FGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVRVIFVDYV 70
FG+++ A ++ D+ +SKGYG+++ + +A+ A+ M L R I ++
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA 83
>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 = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 43/84 (51%), Gaps = 3/84 (3%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
+SF TT+E + + FS+ G + K + +D K + G+ ++ + +A+ A+ +N L
Sbjct: 47 LSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRL 106
Query: 61 DVRVIFVDY---VRPNRHYNTDAS 81
D R+I D+ + R Y S
Sbjct: 107 DDRIIRTDWDAGFKEGRQYGRGRS 130
>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 = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 36/68 (52%)
Query: 8 EMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVRVIFV 67
E L +AF F ++ D+ S+GYG+++ +++++AQ A+ M L+ R + +
Sbjct: 16 ETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRI 75
Query: 68 DYVRPNRH 75
++ H
Sbjct: 76 NWAAKLEH 83
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/87 (26%), Positives = 40/87 (45%), Gaps = 8/87 (9%)
Query: 4 STTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVR 63
+ T+E+L AFSQFG++ + + D Y ++ + A KA+ +MN L+
Sbjct: 22 TVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEMNGKDLEGE 73
Query: 64 VIFVDYVRPNRHYNTDASLVRQPAQSP 90
I + + +P + RQ A P
Sbjct: 74 NIEIVFAKPPDQKRKERKAQRQAASGP 100
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 28/76 (36%), Positives = 41/76 (53%), Gaps = 16/76 (21%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNR-----SKGYGYMTSSTEEEAQKAL--- 52
++FSTT+E L FS+ G + TI KN+ S G+G++ E+AQKAL
Sbjct: 13 LNFSTTEETLKGVFSKVGAIKSCTISKK--KNKAGVLLSMGFGFVEYKKPEQAQKALKQL 70
Query: 53 ----VDMNKMLLDVRV 64
VD +K L+VR+
Sbjct: 71 QGHTVDGHK--LEVRI 84
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 36.2 bits (82), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 35/67 (52%)
Query: 8 EMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVRVIFV 67
++L AF FG +T I +D + +G+ ++ E+A A+ +MN+ L R I V
Sbjct: 27 KVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV 86
Query: 68 DYVRPNR 74
+ +P R
Sbjct: 87 NLAKPMR 93
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 35/62 (56%)
Query: 8 EMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVRVIFV 67
E L +AF F ++ D+ S+GYG+++ +++++AQ A+ M L+ R + +
Sbjct: 102 ETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRI 161
Query: 68 DY 69
++
Sbjct: 162 NW 163
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 35.8 bits (81), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 45/84 (53%), Gaps = 10/84 (11%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKN---RSKGYGYMTSSTEEEAQKALVDMNK 57
+S+S T+E L + F KAT I + +N +SKGY ++ ++ E+A++AL NK
Sbjct: 23 LSYSATEETLQEVFE------KATFI-KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNK 75
Query: 58 MLLDVRVIFVDYVRPNRHYNTDAS 81
++ R I ++ P N+ S
Sbjct: 76 REIEGRAIRLELQGPRGSPNSGPS 99
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 35.8 bits (81), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 1/72 (1%)
Query: 3 FSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDV 62
+S T E + + FSQFG+V +I D + KG+G++ EE +A+ ++
Sbjct: 11 YSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFV-EMQEESVSEAIAKLDNTDFMG 69
Query: 63 RVIFVDYVRPNR 74
R I V P +
Sbjct: 70 RTIRVTEANPKK 81
>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex
With Rna
pdb|2KM8|C Chain C, Interdomain Rrm Packing Contributes To Rna Recognition
In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 167
Score = 35.8 bits (81), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 38/65 (58%), Gaps = 2/65 (3%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
+++ TT++ L + F ++G VT I+ D RS+G+G++ S E+ + V + +L
Sbjct: 11 LNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFL--SFEKPSSVDEVVKTQHIL 68
Query: 61 DVRVI 65
D +VI
Sbjct: 69 DGKVI 73
Score = 30.0 bits (66), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 12/54 (22%), Positives = 29/54 (53%), Gaps = 4/54 (7%)
Query: 14 FSQFGQVTKATIIMDIGKNRSKGYGYMT----SSTEEEAQKALVDMNKMLLDVR 63
FSQ+G + A +++D +S+G+G++T + + Q +D ++++
Sbjct: 108 FSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIK 161
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 35.8 bits (81), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 32/63 (50%)
Query: 3 FSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDV 62
FS T L FS++G+V K TI+ D +SKG ++ ++ AQ +N L
Sbjct: 26 FSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFG 85
Query: 63 RVI 65
RVI
Sbjct: 86 RVI 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 = 35.4 bits (80), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 41/70 (58%), Gaps = 3/70 (4%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSK-GYGYMTSSTEEEAQKALVDMNKML 59
+SF TT+E + + FS+ G + K IIM + K ++ G+ ++ + +A+ A+ +N
Sbjct: 26 LSFYTTEEQIYELFSKSGDIKK--IIMGLDKMKTACGFCFVEYYSRADAENAMRYINGTR 83
Query: 60 LDVRVIFVDY 69
LD R+I D+
Sbjct: 84 LDDRIIRTDW 93
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 35.0 bits (79), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 26/43 (60%)
Query: 10 LADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKAL 52
L + F +FG VT+ +I D K R +G+G++T E+ +A+
Sbjct: 27 LREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV 69
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 35.0 bits (79), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 6/60 (10%)
Query: 6 TKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVRVI 65
T +++ FS FGQ IM+I KGY ++ ST E A A+V +N ++ V+
Sbjct: 38 TDQLMRQTFSPFGQ------IMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVV 91
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 40/78 (51%), Gaps = 4/78 (5%)
Query: 3 FSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDV 62
+ TT++ L + FS FG+V + D+ SKG+G++ TE E Q ++ M +D
Sbjct: 25 WKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFV-RFTEYETQVKVMSQRHM-IDG 82
Query: 63 RVIFVDYVRPNRHYNTDA 80
R + D PN + D+
Sbjct: 83 R--WCDCKLPNSKQSQDS 98
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
28
Length = 111
Score = 34.7 bits (78), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 6/74 (8%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKAL------VD 54
+SF + +E L + QFG + +++ SKG + T+E AQK L +
Sbjct: 23 LSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAE 82
Query: 55 MNKMLLDVRVIFVD 68
+ LD R + VD
Sbjct: 83 GGGLKLDGRQLKVD 96
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 34.7 bits (78), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 36/67 (53%), Gaps = 1/67 (1%)
Query: 5 TTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVRV 64
T ++ML F + G +++ +I D ++S+G+ ++T +A+ A DMN L +
Sbjct: 19 TNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKA 77
Query: 65 IFVDYVR 71
I V+ +
Sbjct: 78 IKVEQAK 84
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 34.7 bits (78), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 14/64 (21%), Positives = 35/64 (54%)
Query: 10 LADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVRVIFVDY 69
L + F FG +++ + D +SKG+ +++ E+A +A+ ++ D ++ V++
Sbjct: 32 LQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW 91
Query: 70 VRPN 73
+P+
Sbjct: 92 AKPS 95
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 33.9 bits (76), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 1/65 (1%)
Query: 7 KEMLADAFSQFGQVTKATIIM-DIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVRVI 65
+++L D FS FG + + IM D SKGY ++ ++ + + A+ MN L R I
Sbjct: 19 EKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPI 78
Query: 66 FVDYV 70
V Y
Sbjct: 79 TVSYA 83
>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 = 33.9 bits (76), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 34/74 (45%), Gaps = 1/74 (1%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
V + T E L F G V + TI+ D KG+ Y+ S +E + +L +++ L
Sbjct: 14 VDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA-LDESLF 72
Query: 61 DVRVIFVDYVRPNR 74
R I V R NR
Sbjct: 73 RGRQIKVIPKRTNR 86
>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 = 33.9 bits (76), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 31/69 (44%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
+ + T+E + D S G V ++ D RSKGY ++ E + A+ ++N L
Sbjct: 12 IPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQL 71
Query: 61 DVRVIFVDY 69
R + Y
Sbjct: 72 GSRFLKCGY 80
>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 = 33.9 bits (76), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 34/74 (45%), Gaps = 1/74 (1%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
V + T E L F G V + TI+ D KG+ Y+ S +E + +L +++ L
Sbjct: 13 VDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA-LDESLF 71
Query: 61 DVRVIFVDYVRPNR 74
R I V R NR
Sbjct: 72 RGRQIKVIPKRTNR 85
>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 = 33.9 bits (76), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 35/70 (50%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
V T+E + D F+++G++ + +D KGY + T +EAQ A+ +N L
Sbjct: 31 VHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDL 90
Query: 61 DVRVIFVDYV 70
+ I VD+
Sbjct: 91 MGQPISVDWC 100
>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm
pdb|2LEB|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uccagu-3'
pdb|2LEC|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uggagu-3'
Length = 135
Score = 33.5 bits (75), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 41/81 (50%), Gaps = 4/81 (4%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
+++ T+ + L F ++G+V I D S+G+ ++ + +A+ A+ M+ +L
Sbjct: 55 LTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVL 114
Query: 61 DVRVIFVDYVR----PNRHYN 77
D R + V R P+ H++
Sbjct: 115 DGRELRVQMARYGRPPDSHHS 135
>pdb|2XB2|D Chain D, Crystal Structure Of The Core
Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How
The Ejc Is Bridged To The Nmd Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core
Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How
The Ejc Is Bridged To The Nmd Machinery
Length = 90
Score = 33.5 bits (75), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 35/70 (50%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
V T+E + D F+++G++ + +D KGY + T +EAQ A+ +N L
Sbjct: 15 VHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDL 74
Query: 61 DVRVIFVDYV 70
+ I VD+
Sbjct: 75 MGQPISVDWC 84
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 33.5 bits (75), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 35/70 (50%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
V T+E + D F+++G++ + +D KGY + T +EAQ A+ +N L
Sbjct: 17 VHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDL 76
Query: 61 DVRVIFVDYV 70
+ I VD+
Sbjct: 77 MGQPISVDWC 86
>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 = 33.5 bits (75), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 35/70 (50%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
V T+E + D F+++G++ + +D KGY + T +EAQ A+ +N L
Sbjct: 30 VHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDL 89
Query: 61 DVRVIFVDYV 70
+ I VD+
Sbjct: 90 MGQPISVDWC 99
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 33.5 bits (75), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 35/70 (50%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
V T+E + D F+++G++ + +D KGY + T +EAQ A+ +N L
Sbjct: 15 VHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDL 74
Query: 61 DVRVIFVDYV 70
+ I VD+
Sbjct: 75 MGQPISVDWC 84
>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 = 33.1 bits (74), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 31/69 (44%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
+ + T+E + D S G V ++ D RSKGY ++ E + A+ ++N L
Sbjct: 11 IPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQL 70
Query: 61 DVRVIFVDY 69
R + Y
Sbjct: 71 GSRFLKCGY 79
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 33.1 bits (74), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 31/69 (44%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
+ + T+E + D S G V ++ D RSKGY ++ E + A+ ++N L
Sbjct: 10 IPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQL 69
Query: 61 DVRVIFVDY 69
R + Y
Sbjct: 70 GSRFLKCGY 78
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 32.7 bits (73), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 41/81 (50%), Gaps = 4/81 (4%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
+++ T+ + L F ++G+V I D S+G+ ++ + +A+ A+ M+ +L
Sbjct: 78 LTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVL 137
Query: 61 DVRVIFVDYVR----PNRHYN 77
D R + V R P+ H++
Sbjct: 138 DGRELRVQMARYGRPPDSHHS 158
>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
pdb|2QFJ|B Chain B, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
Length = 216
Score = 32.7 bits (73), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 2/49 (4%)
Query: 14 FSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDV 62
F FG++ AT+ D + KGYG++ + +Q A+ MN L D+
Sbjct: 146 FEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN--LFDL 192
Score = 32.0 bits (71), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 2/73 (2%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
+ + ++ + AF+ FG + + D + KG+ ++ E AQ AL MN ++L
Sbjct: 36 IYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVML 95
Query: 61 DVRVIFVDYVRPN 73
R I V RP+
Sbjct: 96 GGRNIKVG--RPS 106
>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 = 32.7 bits (73), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 35/70 (50%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
V T+E + D F+++G++ + +D KGY + T +EAQ A+ +N L
Sbjct: 15 VHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDL 74
Query: 61 DVRVIFVDYV 70
+ I VD+
Sbjct: 75 MGQPISVDWC 84
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 32.7 bits (73), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 38/78 (48%), Gaps = 1/78 (1%)
Query: 5 TTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVRV 64
T +E+ A F G + I+ D S GY ++ ++E ++Q+A+ +N + + +
Sbjct: 16 TDRELYA-LFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKR 74
Query: 65 IFVDYVRPNRHYNTDASL 82
+ V Y RP D +L
Sbjct: 75 LKVSYARPGGESIKDTNL 92
>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 = 32.3 bits (72), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 34/73 (46%), Gaps = 1/73 (1%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
V + +T + L FS G + + TI+ D KGY Y+ + E + A V M++ +
Sbjct: 44 VDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFA-ERNSVDAAVAMDETVF 102
Query: 61 DVRVIFVDYVRPN 73
R I V R N
Sbjct: 103 RGRTIKVLPKRTN 115
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 32.3 bits (72), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 5 TTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVRV 64
T +E+ A F G + I+ D S GY ++ ++E ++Q+A+ +N + + +
Sbjct: 16 TDRELYA-LFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKR 74
Query: 65 IFVDYVRP 72
+ V Y RP
Sbjct: 75 LKVSYARP 82
>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of
Fbp-Interacting Repressor (Fir)
pdb|2KXH|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fir
In The Complex With Fbp Nbox Peptide
Length = 199
Score = 32.3 bits (72), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 2/73 (2%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
+ + ++ + AF+ FG + + D + KG+ ++ E AQ AL MN ++L
Sbjct: 21 IYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVML 80
Query: 61 DVRVIFVDYVRPN 73
R I V RP+
Sbjct: 81 GGRNIKVG--RPS 91
Score = 31.6 bits (70), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 22/43 (51%)
Query: 14 FSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMN 56
F FG++ T+ D + KGYG++ + +Q A+ MN
Sbjct: 131 FEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 173
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 32.0 bits (71), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 25/47 (53%)
Query: 10 LADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMN 56
L F ++G + I+ D +S+GYG++ + AQ+A+ +N
Sbjct: 59 LRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLN 105
>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 = 32.0 bits (71), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 1/78 (1%)
Query: 5 TTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVRV 64
T +E+ A F G + I D S GY ++ ++E ++Q+A+ +N + + +
Sbjct: 27 TDRELYA-LFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVLNGITVRNKR 85
Query: 65 IFVDYVRPNRHYNTDASL 82
+ V Y RP D +L
Sbjct: 86 LKVSYARPGGESIKDTNL 103
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 32.0 bits (71), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 28/52 (53%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKAL 52
+S T +E + + F FG+V + MD N+ +G+ ++T EE +K +
Sbjct: 7 LSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 58
>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 = 32.0 bits (71), Expect = 0.093, Method: Compositional matrix adjust.
Identities = 15/71 (21%), Positives = 31/71 (43%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
V++ TT+ L F +G + + ++ + +GY ++ E + A + +
Sbjct: 110 VNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKI 169
Query: 61 DVRVIFVDYVR 71
D R + VD R
Sbjct: 170 DGRRVLVDVER 180
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 32.0 bits (71), Expect = 0.099, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 31/60 (51%)
Query: 9 MLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVRVIFVD 68
+L AF FG +T I +D + +G+ ++ E+A A+ +MN+ L R I V+
Sbjct: 79 VLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN 138
>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 = 32.0 bits (71), Expect = 0.100, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 28/52 (53%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKAL 52
+S T +E + + F FG+V + MD N+ +G+ ++T EE +K +
Sbjct: 9 LSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 60
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 32.0 bits (71), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 25/47 (53%)
Query: 10 LADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMN 56
LA F FG V A + +D + SK +G+++ + AQ A+ MN
Sbjct: 57 LASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMN 103
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 31.6 bits (70), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 34/59 (57%), Gaps = 1/59 (1%)
Query: 4 STTKEMLADAFSQFGQVTKATIIMD-IGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLD 61
+ TK+ + + FS +G++ + ++ + + SKGY Y+ +EA+KAL M+ +D
Sbjct: 15 NVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQID 73
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 31.6 bits (70), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 32/63 (50%)
Query: 9 MLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVRVIFVD 68
+L AF FG +T I +D + +G+ ++ E+A A+ +MN+ L R I V+
Sbjct: 21 VLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN 80
Query: 69 YVR 71
+
Sbjct: 81 LAK 83
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 31.6 bits (70), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 5 TTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMN 56
+ KEM FSQ+G++ + I++D S+G G++ EA++A+ +N
Sbjct: 14 SQKEM-EQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLN 64
>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 = 31.6 bits (70), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 29/62 (46%)
Query: 10 LADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVRVIFVDY 69
L F FG V A + +D N SK +G+++ AQ A+ MN + ++ + V
Sbjct: 42 LLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL 101
Query: 70 VR 71
R
Sbjct: 102 KR 103
>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 = 31.6 bits (70), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 32/63 (50%)
Query: 9 MLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVRVIFVD 68
+L AF FG +T I +D + +G+ ++ E+A A+ +MN+ L R I V+
Sbjct: 23 VLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN 82
Query: 69 YVR 71
+
Sbjct: 83 LAK 85
>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 = 31.6 bits (70), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 31/60 (51%)
Query: 9 MLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVRVIFVD 68
+L AF FG +T I +D + +G+ ++ E+A A+ +MN+ L R I V+
Sbjct: 18 VLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN 77
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 31.2 bits (69), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 32/59 (54%), Gaps = 2/59 (3%)
Query: 10 LADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVRVIFVD 68
L F QFG++ II + + SKG+G++T +A +A ++ +++ R I V+
Sbjct: 32 LRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN 88
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 31.2 bits (69), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 32/59 (54%), Gaps = 2/59 (3%)
Query: 10 LADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVRVIFVD 68
L F QFG++ II + + SKG+G++T +A +A ++ +++ R I V+
Sbjct: 46 LRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN 102
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 30.8 bits (68), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 26/51 (50%)
Query: 5 TTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDM 55
TT + L +G++ I+D N+ KGYG++ + AQKA+ +
Sbjct: 17 TTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 30.0 bits (66), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 25/56 (44%)
Query: 10 LADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVRVI 65
L D FS G+V II D RSKG Y+ + A+ + LL V +I
Sbjct: 42 LEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPII 97
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 29.6 bits (65), Expect = 0.46, Method: Composition-based stats.
Identities = 15/71 (21%), Positives = 31/71 (43%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
V++ TT+ L F +G + + ++ + +GY ++ E + A + +
Sbjct: 110 VNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKI 169
Query: 61 DVRVIFVDYVR 71
D R + VD R
Sbjct: 170 DGRRVLVDVER 180
>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 = 29.6 bits (65), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 2/49 (4%)
Query: 14 FSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDV 62
F FG++ T+ D + KGYG++ + +Q A+ N L D+
Sbjct: 130 FEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXN--LFDL 176
Score = 28.5 bits (62), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 32/73 (43%), Gaps = 2/73 (2%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
+ + ++ + AF+ FG + D + KG+ ++ E AQ AL N + L
Sbjct: 20 IYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQXNSVXL 79
Query: 61 DVRVIFVDYVRPN 73
R I V RP+
Sbjct: 80 GGRNIKVG--RPS 90
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 29.3 bits (64), Expect = 0.57, Method: Composition-based stats.
Identities = 15/66 (22%), Positives = 31/66 (46%)
Query: 4 STTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVR 63
S T++ + FG + + ++ +SKGYG+ ++ A +A D+ L R
Sbjct: 106 SLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPR 165
Query: 64 VIFVDY 69
++V +
Sbjct: 166 TLYVHW 171
>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 = 29.3 bits (64), Expect = 0.57, Method: Composition-based stats.
Identities = 15/66 (22%), Positives = 31/66 (46%)
Query: 4 STTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVR 63
S T++ + FG + + ++ +SKGYG+ ++ A +A D+ L R
Sbjct: 104 SLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPR 163
Query: 64 VIFVDY 69
++V +
Sbjct: 164 TLYVHW 169
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 29.3 bits (64), Expect = 0.59, Method: Composition-based stats.
Identities = 15/66 (22%), Positives = 31/66 (46%)
Query: 4 STTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVR 63
S T++ + FG + + ++ +SKGYG+ ++ A +A D+ L R
Sbjct: 106 SLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPR 165
Query: 64 VIFVDY 69
++V +
Sbjct: 166 TLYVHW 171
>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 = 28.9 bits (63), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 38/74 (51%), Gaps = 1/74 (1%)
Query: 7 KEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVR-VI 65
K+ L FS+ G+V +D ++KG+ ++ + +A+K + + LD++ +
Sbjct: 26 KKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRL 85
Query: 66 FVDYVRPNRHYNTD 79
F+ ++ YN+D
Sbjct: 86 FLYTMKDVERYNSD 99
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 33/74 (44%)
Query: 1 VSFSTTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
+++ T+ + L F ++G+V I + +G+ ++ +AQ A M+ L
Sbjct: 21 LTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAEL 80
Query: 61 DVRVIFVDYVRPNR 74
D R + V R R
Sbjct: 81 DGRELRVQVARYGR 94
>pdb|1JMT|A Chain A, X-Ray Structure Of A Core U2af65U2AF35 HETERODIMER
Length = 104
Score = 27.7 bits (60), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 14/62 (22%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 7 KEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVRVIF 66
+E+ + ++G+V + + ++G + G Y+ EE+A+KA++D+N + + I
Sbjct: 41 EEVFTEMEEKYGEVEEMNVCDNLG-DHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH 99
Query: 67 VD 68
+
Sbjct: 100 AE 101
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 26.9 bits (58), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 5 TTKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKA--LVDMNKM 58
++ +L + F Q G V + D + +GYG++ +EE+A A ++DM K+
Sbjct: 27 VSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKL 82
>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 = 26.6 bits (57), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 13/57 (22%), Positives = 29/57 (50%)
Query: 7 KEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLLDVR 63
K+ L FS+ G+V +D ++KG+ ++ + +A+K + + LD++
Sbjct: 26 KKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLK 82
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 26.2 bits (56), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 33/72 (45%), Gaps = 10/72 (13%)
Query: 3 FSTTKEMLADAFSQF--GQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL 60
ST++EM+ F+ G V + I D Y ++ S E+A +A+ +N +L
Sbjct: 25 LSTSEEMIEKEFNNIKPGAVERVKKIRD--------YAFVHFSNREDAVEAMKALNGKVL 76
Query: 61 DVRVIFVDYVRP 72
D I V +P
Sbjct: 77 DGSPIEVTLAKP 88
>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 = 25.8 bits (55), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 14 FSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKAL 52
F+++G V + II D SKGYG+++ + + QK +
Sbjct: 30 FARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIV 67
>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 = 25.4 bits (54), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 14 FSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKAL 52
F+++G V + II D SKGYG+++ + + QK +
Sbjct: 30 FARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIV 67
>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 = 25.4 bits (54), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 34/67 (50%), Gaps = 9/67 (13%)
Query: 6 TKEMLADAFSQFGQVTKATIIMDIGKNRSKGYGYMTSSTEEEAQKALVDMNKMLL---DV 62
T+E + F ++G+ + I ++ KG+G++ T A+ A V+++ M L +
Sbjct: 28 TEEEMRKLFEKYGKAGEVFI------HKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQL 81
Query: 63 RVIFVDY 69
RV F +
Sbjct: 82 RVRFACH 88
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
0.315 0.128 0.346
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,436,616
Number of Sequences: 62578
Number of extensions: 76479
Number of successful extensions: 335
Number of sequences better than 100.0: 118
Number of HSP's better than 100.0 without gapping: 100
Number of HSP's successfully gapped in prelim test: 18
Number of HSP's that attempted gapping in prelim test: 210
Number of HSP's gapped (non-prelim): 136
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 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 45 (21.9 bits)