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= psy14193
(239 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 27/111 (24%), Positives = 53/111 (47%), Gaps = 7/111 (6%)
Query: 84 CIKMNKVHEKRTNMNAYVRFKNLESVEKALEMNGHVIDEHTIRVDKALT---TTKSNSH- 139
C+ M + KR+ +V + +E V+ A+ H +D + +A++ + + +H
Sbjct: 43 CVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHL 102
Query: 140 ---SIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
IF+G I LR FE G+I+ + ++ D+ + +GF +V F
Sbjct: 103 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
Score = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 28/52 (53%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+FIG + F LR FE G + + ++RD +T +GFG+V + EE
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 67
Score = 36.2 bits (82), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 27/44 (61%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G ++F+ +E LR FE G + + ++RD +T +GFG+V +
Sbjct: 19 GGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 62
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 48.5 bits (114), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 27/111 (24%), Positives = 53/111 (47%), Gaps = 7/111 (6%)
Query: 84 CIKMNKVHEKRTNMNAYVRFKNLESVEKALEMNGHVIDEHTIRVDKALT---TTKSNSH- 139
C+ M + KR+ +V + +E V+ A+ H +D + +A++ + + +H
Sbjct: 43 CVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHL 102
Query: 140 ---SIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
IF+G I LR FE G+I+ + ++ D+ + +GF +V F
Sbjct: 103 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
Score = 40.4 bits (93), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 28/52 (53%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+FIG + F LR FE G + + ++RD +T +GFG+V + EE
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 67
Score = 35.8 bits (81), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 27/44 (61%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G ++F+ +E LR FE G + + ++RD +T +GFG+V +
Sbjct: 19 GGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 62
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 48.1 bits (113), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 27/111 (24%), Positives = 53/111 (47%), Gaps = 7/111 (6%)
Query: 84 CIKMNKVHEKRTNMNAYVRFKNLESVEKALEMNGHVIDEHTIRVDKALT---TTKSNSH- 139
C+ M + KR+ +V + +E V+ A+ H +D + +A++ + + +H
Sbjct: 44 CVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHL 103
Query: 140 ---SIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
IF+G I LR FE G+I+ + ++ D+ + +GF +V F
Sbjct: 104 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 154
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 28/52 (53%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+FIG + F LR FE G + + ++RD +T +GFG+V + EE
Sbjct: 17 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 68
Score = 35.8 bits (81), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 27/44 (61%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G ++F+ +E LR FE G + + ++RD +T +GFG+V +
Sbjct: 20 GGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 63
>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 = 48.1 bits (113), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 27/111 (24%), Positives = 53/111 (47%), Gaps = 7/111 (6%)
Query: 84 CIKMNKVHEKRTNMNAYVRFKNLESVEKALEMNGHVIDEHTIRVDKALT---TTKSNSH- 139
C+ M + KR+ +V + +E V+ A+ H +D + +A++ + + +H
Sbjct: 42 CVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHL 101
Query: 140 ---SIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
IF+G I LR FE G+I+ + ++ D+ + +GF +V F
Sbjct: 102 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 152
Score = 40.4 bits (93), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 28/52 (53%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+FIG + F LR FE G + + ++RD +T +GFG+V + EE
Sbjct: 15 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 66
Score = 35.8 bits (81), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 27/44 (61%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G ++F+ +E LR FE G + + ++RD +T +GFG+V +
Sbjct: 18 GGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 61
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 48.1 bits (113), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 27/111 (24%), Positives = 53/111 (47%), Gaps = 7/111 (6%)
Query: 84 CIKMNKVHEKRTNMNAYVRFKNLESVEKALEMNGHVIDEHTIRVDKALT---TTKSNSH- 139
C+ M + KR+ +V + +E V+ A+ H +D + +A++ + + +H
Sbjct: 41 CVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHL 100
Query: 140 ---SIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
IF+G I LR FE G+I+ + ++ D+ + +GF +V F
Sbjct: 101 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 151
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 28/52 (53%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+FIG + F LR FE G + + ++RD +T +GFG+V + EE
Sbjct: 14 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 65
Score = 35.8 bits (81), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 27/44 (61%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G ++F+ +E LR FE G + + ++RD +T +GFG+V +
Sbjct: 17 GGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 60
>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 = 48.1 bits (113), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 27/111 (24%), Positives = 53/111 (47%), Gaps = 7/111 (6%)
Query: 84 CIKMNKVHEKRTNMNAYVRFKNLESVEKALEMNGHVIDEHTIRVDKALT---TTKSNSH- 139
C+ M + KR+ +V + +E V+ A+ H +D + +A++ + + +H
Sbjct: 36 CVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHL 95
Query: 140 ---SIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
IF+G I LR FE G+I+ + ++ D+ + +GF +V F
Sbjct: 96 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 146
Score = 40.4 bits (93), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 28/52 (53%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+FIG + F LR FE G + + ++RD +T +GFG+V + EE
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60
Score = 35.8 bits (81), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 27/44 (61%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G ++F+ +E LR FE G + + ++RD +T +GFG+V +
Sbjct: 12 GGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 55
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 47.4 bits (111), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 38/64 (59%), Gaps = 1/64 (1%)
Query: 136 SNSHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
S S +++G++ F LR FE G+IDN+ L++D T KG+G++ F ++ E R
Sbjct: 3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITF-SDSECAR 61
Query: 196 KAFE 199
+A E
Sbjct: 62 RALE 65
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 29/47 (61%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKVS 229
G ++F E+ LR FE G+IDN+ L++D T KG+G++ F S
Sbjct: 11 GSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDS 57
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 47.0 bits (110), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 38/128 (29%), Positives = 63/128 (49%), Gaps = 10/128 (7%)
Query: 99 AYVRFKNLESVEKALEMNGHVIDEHTIRVDKAL---TTTKSNSHSIFIGNIPFXXXXXXL 155
YV F++ E +EKALE+ G + + I+++K + + ++ ++ N+P+ L
Sbjct: 51 GYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGKDSKKERDARTLLAKNLPYKVTQDEL 110
Query: 156 RKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFESCG-EIDNVRLIRDQH 214
++ FE EI RL+ + KG Y+ FK E + + E G EID R I +
Sbjct: 111 KEVFEDAAEI---RLVSKDGKS--KGIAYIEFKTEADAEKTFEEKQGTEIDG-RSISLYY 164
Query: 215 TNIGKGFG 222
T KG G
Sbjct: 165 TGEPKGEG 172
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 36/68 (52%), Gaps = 7/68 (10%)
Query: 127 VDKALTTTKSNSHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVN 186
VD++L S+F+GNIP+ L+ F G + + RL+ D+ T KG+G+
Sbjct: 4 VDRSL-------RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCE 56
Query: 187 FKAEEEEL 194
++ +E L
Sbjct: 57 YQDQETAL 64
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 32/54 (59%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKVSFTTLSSI 236
G + ++A EE+L+ F G + + RL+ D+ T KG+G+ ++ T LS++
Sbjct: 14 GNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAM 67
>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 = 44.3 bits (103), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 38/131 (29%), Positives = 64/131 (48%), Gaps = 11/131 (8%)
Query: 93 KRTNMNAYVRFKNLESVEKALE-MNGHVIDEHTIRV---DKALTTTKSNSHSIFIGNIPF 148
+R+ AYV F+ E+AL+ MN VI +R+ + + KS +IFI N+
Sbjct: 49 RRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDK 108
Query: 149 XXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFESCGEIDNVR 208
L F + G I + +++ D+ N KG+G+V+F+ +E A E E N
Sbjct: 109 SIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQE-----AAERAIEKMNGM 161
Query: 209 LIRDQHTNIGK 219
L+ D+ +G+
Sbjct: 162 LLNDRKVFVGR 172
Score = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 28/56 (50%)
Query: 140 SIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
S+++G++ L + F G I ++R+ RD T G+ YVNF+ + R
Sbjct: 12 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAER 67
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 20/37 (54%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
E L + F G I ++R+ RD T G+ YVNF+
Sbjct: 24 EAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQ 60
>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 = 44.3 bits (103), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 38/131 (29%), Positives = 64/131 (48%), Gaps = 11/131 (8%)
Query: 93 KRTNMNAYVRFKNLESVEKALE-MNGHVIDEHTIRV---DKALTTTKSNSHSIFIGNIPF 148
+R+ AYV F+ E+AL+ MN VI +R+ + + KS +IFI N+
Sbjct: 54 RRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDK 113
Query: 149 XXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFESCGEIDNVR 208
L F + G I + +++ D+ N KG+G+V+F+ +E A E E N
Sbjct: 114 SIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQE-----AAERAIEKMNGM 166
Query: 209 LIRDQHTNIGK 219
L+ D+ +G+
Sbjct: 167 LLNDRKVFVGR 177
Score = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 28/56 (50%)
Query: 140 SIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
S+++G++ L + F G I ++R+ RD T G+ YVNF+ + R
Sbjct: 17 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAER 72
Score = 29.3 bits (64), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 20/37 (54%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
E L + F G I ++R+ RD T G+ YVNF+
Sbjct: 29 EAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQ 65
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 27/45 (60%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYV 185
IF+G +P+ LRK FE G+I+ +I D+ T +G+G+V
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFV 64
Score = 33.1 bits (74), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYV 224
G + + + LRK FE G+I+ +I D+ T +G+G+V
Sbjct: 23 GGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFV 64
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 32/57 (56%)
Query: 135 KSNSHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
++++ SI++GN+ + L F CG ++ V ++ D+ + KGF Y+ F +E
Sbjct: 2 EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKE 58
Score = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 25/44 (56%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G V++ A EEL F CG ++ V ++ D+ + KGF Y+ F
Sbjct: 11 GNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEF 54
>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 = 3e-04, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 32/57 (56%)
Query: 135 KSNSHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
++++ SI++GN+ + L F CG ++ V ++ D+ + KGF Y+ F +E
Sbjct: 3 EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKE 59
Score = 37.7 bits (86), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 25/44 (56%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G V++ A EEL F CG ++ V ++ D+ + KGF Y+ F
Sbjct: 12 GNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEF 55
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 41/82 (50%), Gaps = 9/82 (10%)
Query: 139 HSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAF 198
+I++GN+ + +++ F G++ NV+LI D+ T KGFG+V + E
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEE-----SVS 56
Query: 199 ESCGEIDNV----RLIRDQHTN 216
E+ ++DN R IR N
Sbjct: 57 EAIAKLDNTDFMGRTIRVTEAN 78
Score = 35.4 bits (80), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 28/45 (62%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
G + + A E++++ F G++ NV+LI D+ T KGFG+V +
Sbjct: 7 GNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ 51
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 26/117 (22%), Positives = 58/117 (49%), Gaps = 4/117 (3%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKALTTTKSNSH---SIFIGNIPFXXXXXX 154
A+V + AL+ +NG I+ + ++++ A + +S+S ++F+G++
Sbjct: 44 AFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDET 103
Query: 155 LRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFESCGEIDNVRLIR 211
LR AF+ + ++ D T +G+G+V+F ++++ G+ N R +R
Sbjct: 104 LRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLR 160
Score = 28.9 bits (63), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 24/44 (54%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G +N ++E LR AF+ + ++ D T +G+G+V+F
Sbjct: 93 GDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSF 136
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 40.8 bits (94), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 35/59 (59%), Gaps = 1/59 (1%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
+++G++ F LR FE G I++++L+ D T KG+G++ F ++ E +KA E
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITF-SDSECAKKALE 86
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 28/47 (59%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKVS 229
G ++F E+ LR FE G I++++L+ D T KG+G++ F S
Sbjct: 32 GSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDS 78
>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 = 40.8 bits (94), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 28/51 (54%)
Query: 137 NSHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
+ S+++GN+ + L F SCG I+ + ++ D+ + KG+ Y+ F
Sbjct: 35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEF 85
Score = 36.2 bits (82), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 26/44 (59%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G V++ + ++L F SCG I+ + ++ D+ + KG+ Y+ F
Sbjct: 42 GNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEF 85
>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 = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 35/119 (29%), Positives = 56/119 (47%), Gaps = 12/119 (10%)
Query: 94 RTNMN---AYVRFKNLESVEKALEMNGHVIDEHTIRVDKALTTTKSN---SHSIFIGNIP 147
RT N YV F++ E +EKALE+ G + + I+++K + ++ N+
Sbjct: 49 RTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLS 108
Query: 148 FXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFESCG-EID 205
F L++ FE EI RL+ + KG Y+ FK+E + + E G EID
Sbjct: 109 FNITEDELKEVFEDALEI---RLVSQDGKS--KGIAYIEFKSEADAEKNLEEKQGAEID 162
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 42/76 (55%), Gaps = 7/76 (9%)
Query: 126 RVDKALTTTKSNSHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRD-QHTNIGKGFGY 184
+V K TT+K I + NIPF +R+ F + GE+ VRL + T +GFG+
Sbjct: 8 QVPKKQTTSK-----ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGF 62
Query: 185 VNFKAEEEELRKAFES 200
V+F +++ +KAF +
Sbjct: 63 VDF-ITKQDAKKAFNA 77
Score = 34.7 bits (78), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 27/43 (62%), Gaps = 1/43 (2%)
Query: 185 VNFKAEEEELRKAFESCGEIDNVRLIRD-QHTNIGKGFGYVNF 226
+ F+A + E+R+ F + GE+ VRL + T +GFG+V+F
Sbjct: 23 IPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDF 65
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 31/51 (60%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
IF+G + ++ FE G++D+ L+ D+ TN +GFG+V F++E+
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESED 52
Score = 34.3 bits (77), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 25/36 (69%)
Query: 192 EELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
E+++ FE G++D+ L+ D+ TN +GFG+V F+
Sbjct: 14 EDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFE 49
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 40/73 (54%), Gaps = 2/73 (2%)
Query: 139 HSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAF 198
++ ++GN+PF + F+ I +VRL+RD+ T+ KGF YV F E + L++A
Sbjct: 16 YTAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFD-EVDSLKEAL 73
Query: 199 ESCGEIDNVRLIR 211
G + R +R
Sbjct: 74 TYDGALLGDRSLR 86
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 22/31 (70%)
Query: 100 YVRFKNLESVEKALEMNGHVIDEHTIRVDKA 130
YV F ++S+++AL +G ++ + ++RVD A
Sbjct: 60 YVEFDEVDSLKEALTYDGALLGDRSLRVDIA 90
Score = 28.9 bits (63), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 13/23 (56%), Positives = 17/23 (73%)
Query: 204 IDNVRLIRDQHTNIGKGFGYVNF 226
I +VRL+RD+ T+ KGF YV F
Sbjct: 41 IRSVRLVRDKDTDKFKGFCYVEF 63
>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 = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/90 (17%), Positives = 44/90 (48%), Gaps = 1/90 (1%)
Query: 99 AYVRFKNLESVEKALEMNGHVIDEHTIRVDKALTTTK-SNSHSIFIGNIPFXXXXXXLRK 157
A++ F++++ +A+ +G + ++++ + +H +FIG +P +++
Sbjct: 56 AFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKE 115
Query: 158 AFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
S G + L++D T + KG+ + +
Sbjct: 116 LLTSFGPLKAFNLVKDSATGLSKGYAFCEY 145
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/90 (17%), Positives = 44/90 (48%), Gaps = 1/90 (1%)
Query: 99 AYVRFKNLESVEKALEMNGHVIDEHTIRVDKALTTTK-SNSHSIFIGNIPFXXXXXXLRK 157
A++ F++++ +A+ +G + ++++ + +H +FIG +P +++
Sbjct: 54 AFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKE 113
Query: 158 AFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
S G + L++D T + KG+ + +
Sbjct: 114 LLTSFGPLKAFNLVKDSATGLSKGYAFCEY 143
>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 = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 25/36 (69%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+EE R F S GEI++ +L+RD+ T G+G+VN+
Sbjct: 16 QEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNY 51
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 29/133 (21%), Positives = 49/133 (36%), Gaps = 47/133 (35%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF----KAE------ 190
+ + +P R F S GEI++ +L+RD+ T G+G+VN+ AE
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 191 -------------------------------------EEELRKAFESCGEIDNVRLIRDQ 213
++EL + F G I R++ DQ
Sbjct: 65 NGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQ 124
Query: 214 HTNIGKGFGYVNF 226
T + +G G++ F
Sbjct: 125 VTGVSRGVGFIRF 137
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 32/51 (62%), Gaps = 1/51 (1%)
Query: 178 IGKGF-GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
IGK F G +++ +E LR F GE+ + +++D+ TN +GFG+V FK
Sbjct: 16 IGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFK 66
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 28/48 (58%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 188
+F+G + + LR F GE+ + +++D+ TN +GFG+V FK
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFK 66
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 29/53 (54%)
Query: 136 SNSHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 188
S+ +F+G + F L + F G+I V +++D+ T +GFG+V F+
Sbjct: 10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFE 62
Score = 36.6 bits (83), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 27/45 (60%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
G ++F E+ L + F G+I V +++D+ T +GFG+V F+
Sbjct: 18 GGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFE 62
Score = 31.6 bits (70), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 93 KRTNMNAYVRFKNLESVEKAL-EMNGHVIDEHTIRVDKALTTTKSNS 138
+R+ +V F+N++ + A+ MNG +D IRVD+A ++ + S
Sbjct: 51 QRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNRS 97
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 32/53 (60%)
Query: 184 YVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKVSFTTLSSI 236
Y+ +E +LR+ FE G I++V+++ D+ T +G+G+V F+ + +I
Sbjct: 49 YIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAI 101
Score = 36.2 bits (82), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 29/49 (59%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKA 189
+ + IP LR+ FE G I++V+++ D+ T +G+G+V F++
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQS 93
>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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 27/43 (62%)
Query: 184 YVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
Y+ ++ELR F S GE+++ +LIRD+ G+G+VN+
Sbjct: 11 YLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNY 53
Score = 36.6 bits (83), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 29/55 (52%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
+ + +P LR F S GE+++ +LIRD+ G+G+VN+ ++ R
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 61
>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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 25/36 (69%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
++ELR F S GE+++ +LIRD+ G+G+VN+
Sbjct: 16 QDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNY 51
Score = 36.6 bits (83), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 26/47 (55%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
+ + +P LR F S GE+++ +LIRD+ G+G+VN+
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNY 51
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 42/82 (51%), Gaps = 4/82 (4%)
Query: 140 SIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF--KAEEEELRKA 197
S+ + N+ + LR+ FE G + +V + RD++T +GF +V F K + E+ A
Sbjct: 72 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 131
Query: 198 FESCGEIDNVRLIRDQHTNIGK 219
+ G + + R +R Q G+
Sbjct: 132 MD--GAVLDGRELRVQMARYGR 151
Score = 34.7 bits (78), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 25/42 (59%)
Query: 185 VNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+ ++ + LR+ FE G + +V + RD++T +GF +V F
Sbjct: 78 LTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRF 119
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 25/36 (69%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
++ELR F S GE+++ +LIRD+ G+G+VN+
Sbjct: 16 QDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNY 51
Score = 36.6 bits (83), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 26/47 (55%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
+ + +P LR F S GE+++ +LIRD+ G+G+VN+
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNY 51
>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 = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 25/36 (69%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
++ELR F S GE+++ +LIRD+ G+G+VN+
Sbjct: 33 QDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNY 68
Score = 36.6 bits (83), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 30/55 (54%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
+ + +P LR F S GE+++ +LIRD+ G+G+VN+ ++ R
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 76
>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 = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 42/82 (51%), Gaps = 4/82 (4%)
Query: 140 SIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF--KAEEEELRKA 197
S+ + N+ + LR+ FE G + +V + RD++T +GF +V F K + E+ A
Sbjct: 49 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 108
Query: 198 FESCGEIDNVRLIRDQHTNIGK 219
+ G + + R +R Q G+
Sbjct: 109 MD--GAVLDGRELRVQMARYGR 128
Score = 35.4 bits (80), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 25/42 (59%)
Query: 185 VNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+ ++ + LR+ FE G + +V + RD++T +GF +V F
Sbjct: 55 LTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRF 96
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 30/52 (57%)
Query: 136 SNSHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
SN +F+G++ ++ AF G+I + R+++D T KG+G+V+F
Sbjct: 13 SNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSF 64
Score = 36.2 bits (82), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 24/35 (68%)
Query: 192 EELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
E+++ AF G+I + R+++D T KG+G+V+F
Sbjct: 30 EDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSF 64
>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 = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 29/52 (55%)
Query: 136 SNSHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
SN +F+G++ ++ AF G I + R+++D T KG+G+V+F
Sbjct: 13 SNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSF 64
Score = 35.8 bits (81), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 23/35 (65%)
Query: 192 EELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
E+++ AF G I + R+++D T KG+G+V+F
Sbjct: 30 EDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSF 64
>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 = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/99 (22%), Positives = 48/99 (48%), Gaps = 2/99 (2%)
Query: 94 RTNMNAYVRFKNLESVEKALEMNGHVIDEHTIRVDKALTTTKSN-SHSIFIGNIPFXXXX 152
R+ ++ F+ SV++ ++ H++D I +A+ + + + IF+G I
Sbjct: 43 RSRGFGFLSFEKPSSVDEVVKTQ-HILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRP 101
Query: 153 XXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
+ F G I + +L+ D+ T +GFG+V + + +
Sbjct: 102 KEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSAD 140
Score = 33.9 bits (76), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 30/51 (58%)
Query: 138 SHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 188
S +FIG + + LR+ F G + ++++++D T +GFG+++F+
Sbjct: 3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFE 53
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 27/49 (55%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKA 189
+FIG + F LR +E G++ + ++RD + +GFG+V F +
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSS 78
Score = 36.6 bits (83), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 27/44 (61%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G ++F+ EE LR +E G++ + ++RD + +GFG+V F
Sbjct: 33 GGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTF 76
>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 = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 1/59 (1%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
IF+G + +R+ F GE++++ L D TN +GF ++ FK EEE ++K E
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFK-EEEPVKKIME 61
Score = 32.7 bits (73), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 24/37 (64%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
EE++R+ F GE++++ L D TN +GF ++ FK
Sbjct: 15 EEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFK 51
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 43/77 (55%), Gaps = 6/77 (7%)
Query: 138 SHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE--ELR 195
S ++F+ + L+++F+ G + R++ D+ T KGFG+V+F +EE+ +
Sbjct: 15 SKTLFVKGLSEDTTEETLKESFD--GSV-RARIVTDRETGSSKGFGFVDFNSEEDAKAAK 71
Query: 196 KAFESCGEIDNVRLIRD 212
+A E GEID ++ D
Sbjct: 72 EAMED-GEIDGNKVTLD 87
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 24/36 (66%), Gaps = 3/36 (8%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
EE L+++F+ G + R++ D+ T KGFG+V+F
Sbjct: 29 EETLKESFD--GSV-RARIVTDRETGSSKGFGFVDF 61
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 1/59 (1%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
IF+G + +R+ F GE++++ L D TN +GF ++ FK EEE ++K E
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFK-EEEPVKKIME 59
Score = 32.7 bits (73), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 24/37 (64%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
EE++R+ F GE++++ L D TN +GF ++ FK
Sbjct: 13 EEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFK 49
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 37.0 bits (84), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 27/52 (51%)
Query: 136 SNSHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
S+ +FIG + + LR+ F GE+ ++RD T +GFG+V F
Sbjct: 23 SSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 74
Score = 34.7 bits (78), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 26/44 (59%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G ++++ +E LR+ F GE+ ++RD T +GFG+V F
Sbjct: 31 GGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 74
Score = 28.5 bits (62), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 21/44 (47%)
Query: 82 KACIKMNKVHEKRTNMNAYVRFKNLESVEKALEMNGHVIDEHTI 125
K C+ M KR+ +V F + V+K L + H +D TI
Sbjct: 53 KECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTI 96
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 36.6 bits (83), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 27/51 (52%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
IF+G IP LR+ F+ G + V +I D +GFG++ F+ E+
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQ 63
Score = 28.1 bits (61), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 23/45 (51%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
G + E ELR+ F+ G + V +I D +GFG++ F+
Sbjct: 16 GGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFE 60
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 36.6 bits (83), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 27/43 (62%)
Query: 184 YVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
Y+ ++E + F S G+I++ +L+RD+ T G+G+VN+
Sbjct: 11 YLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNY 53
Score = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 32/60 (53%), Gaps = 1/60 (1%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
+ + +P + F S G+I++ +L+RD+ T G+G+VN+ ++ + KA +
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNY-SDPNDADKAINT 65
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 36.2 bits (82), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 27/43 (62%)
Query: 184 YVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
Y+ ++E + F S G+I++ +L+RD+ T G+G+VN+
Sbjct: 11 YLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNY 53
Score = 35.8 bits (81), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 26/133 (19%), Positives = 49/133 (36%), Gaps = 47/133 (35%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF-------KA---- 189
+ + +P + F S G+I++ +L+RD+ T G+G+VN+ KA
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 190 ------------------------------------EEEELRKAFESCGEIDNVRLIRDQ 213
++E+ + F G I R++ DQ
Sbjct: 67 NGLKLQTKTIKVSYARPSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQ 126
Query: 214 HTNIGKGFGYVNF 226
T + +G G++ F
Sbjct: 127 ATGVSRGVGFIRF 139
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 35.8 bits (81), Expect = 0.020, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 25/47 (53%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
+FIG + + LR+ F GE+ ++RD T +GFG+V F
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49
Score = 34.3 bits (77), Expect = 0.057, Method: Composition-based stats.
Identities = 15/44 (34%), Positives = 26/44 (59%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G ++++ +E LR+ F GE+ ++RD T +GFG+V F
Sbjct: 6 GGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49
Score = 27.3 bits (59), Expect = 7.8, Method: Composition-based stats.
Identities = 14/44 (31%), Positives = 21/44 (47%)
Query: 82 KACIKMNKVHEKRTNMNAYVRFKNLESVEKALEMNGHVIDEHTI 125
K C+ M KR+ +V F + V+K L + H +D TI
Sbjct: 28 KECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTI 71
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 35.8 bits (81), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 31/57 (54%), Gaps = 2/57 (3%)
Query: 132 TTTKSNSHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 188
T KS + + NIPF LR+ F G+I +V +I ++ + KGFG+V F+
Sbjct: 23 TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTFE 77
Score = 28.1 bits (61), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 28/45 (62%), Gaps = 2/45 (4%)
Query: 185 VNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKVS 229
+ F+ + +LR+ F G+I +V +I ++ + KGFG+V F+ S
Sbjct: 37 IPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTFENS 79
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 35.8 bits (81), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 4/79 (5%)
Query: 143 IGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF--KAEEEELRKAFES 200
+ N+ + LR+ FE G + +V + R+ HT +GF +V F + + ++ A +
Sbjct: 18 VDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDG 77
Query: 201 CGEIDNVRLIRDQHTNIGK 219
E+D R +R Q G+
Sbjct: 78 A-ELDG-RELRVQVARYGR 94
Score = 35.4 bits (80), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 24/42 (57%)
Query: 185 VNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+ ++ + LR+ FE G + +V + R+ HT +GF +V F
Sbjct: 21 LTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRF 62
>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 = 35.8 bits (81), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 17/110 (15%), Positives = 46/110 (41%), Gaps = 21/110 (19%)
Query: 99 AYVRFKNLESVEKALEMNGHVIDEHTIRVDKA---------------------LTTTKSN 137
A++ F++++ +A+ +G + ++++ + T +
Sbjct: 54 AFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDS 113
Query: 138 SHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
+H +FIG +P +++ S G + L++D T + KG+ + +
Sbjct: 114 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEY 163
>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 = 35.4 bits (80), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 28/44 (63%), Gaps = 1/44 (2%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G ++ + +E E+R F G + V++I D+ T + KG+G+V+F
Sbjct: 15 GGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 57
Score = 35.0 bits (79), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 130 ALTTTKSNSHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKA 189
+L K +++F+G I +R F G + V++I D+ T + KG+G+V+F
Sbjct: 1 SLPEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF-Y 58
Query: 190 EEEELRKAFES 200
+ +++K ES
Sbjct: 59 NDVDVQKIVES 69
>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|C Chain C, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|B Chain B, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|D Chain D, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
Length = 88
Score = 35.0 bits (79), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 40/84 (47%), Gaps = 6/84 (7%)
Query: 136 SNSHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNI--GKGFGYVNFKAEEEE 193
S++ +F+G +P LR+ FE G + + ++RD+ N KG +V F
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTR--- 57
Query: 194 LRKAFESCGEIDNVRLIRDQHTNI 217
+ A E+ + N++++ H I
Sbjct: 58 -KAALEAQNALHNMKVLPGMHHPI 80
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 35.0 bits (79), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 28/44 (63%), Gaps = 1/44 (2%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G ++ + +E E+R F G + V++I D+ T + KG+G+V+F
Sbjct: 15 GGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 57
Score = 34.7 bits (78), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 130 ALTTTKSNSHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKA 189
+L K +++F+G I +R F G + V++I D+ T + KG+G+V+F
Sbjct: 1 SLPEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF-Y 58
Query: 190 EEEELRKAFES 200
+ +++K ES
Sbjct: 59 NDVDVQKIVES 69
>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 = 0.042, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 38/70 (54%), Gaps = 2/70 (2%)
Query: 131 LTTTKSNSHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAE 190
L + K +++F+G I +R F G + V++I D+ T + KG+G+V+F
Sbjct: 3 LGSGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF-YN 60
Query: 191 EEELRKAFES 200
+ +++K ES
Sbjct: 61 DVDVQKIVES 70
Score = 34.7 bits (78), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 28/44 (63%), Gaps = 1/44 (2%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G ++ + +E E+R F G + V++I D+ T + KG+G+V+F
Sbjct: 16 GGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 58
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 34.3 bits (77), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 40/84 (47%), Gaps = 6/84 (7%)
Query: 136 SNSHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNI--GKGFGYVNFKAEEEE 193
S++ +F+G +P LR+ FE G + + ++RD+ N KG +V F
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTR--- 57
Query: 194 LRKAFESCGEIDNVRLIRDQHTNI 217
+ A E+ + N++++ H I
Sbjct: 58 -KAALEAQNALHNMKVLPGMHHPI 80
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 33.9 bits (76), Expect = 0.076, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 33/74 (44%), Gaps = 8/74 (10%)
Query: 115 MNGHVIDEHTIRVDKALTTTKSNSHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQ 174
M G ID R K T + +F+GN+P +RK FE G+ V + +D
Sbjct: 1 MEGLTIDLKNFR--KPGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD- 57
Query: 175 HTNIGKGFGYVNFK 188
KGFG++ +
Sbjct: 58 -----KGFGFIRLE 66
Score = 27.7 bits (60), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 25/46 (54%), Gaps = 8/46 (17%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKVSFTTLSSI 236
EEE+RK FE G+ V + +D KGFG++ + TL+ I
Sbjct: 36 EEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETR--TLAEI 73
>pdb|3T6C|A Chain A, Crystal Structure Of An Enolase From Pantoea Ananatis (Efi
Target Efi- 501676) With Bound D-Gluconate And Mg
pdb|3T6C|B Chain B, Crystal Structure Of An Enolase From Pantoea Ananatis (Efi
Target Efi- 501676) With Bound D-Gluconate And Mg
Length = 440
Score = 33.9 bits (76), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 33/74 (44%), Gaps = 14/74 (18%)
Query: 155 LRKAFESCGEIDNVRLIRDQHTNIG-KGFGYVNFKAEEEELRKAFESCGEIDNVRLIRDQ 213
+R A+ S G+I + + + H ++ FG + + LR+ F C E+D
Sbjct: 343 VRTAWHSPGDISPIGVCANMHLDLSSPNFGIQEYTPMNDALREVFPGCPEVD-------- 394
Query: 214 HTNIGKGFGYVNFK 227
+G+ YVN K
Sbjct: 395 -----QGYAYVNDK 403
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 33.9 bits (76), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 26/40 (65%)
Query: 187 FKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+K E++L++ F + GE+ V++ +D T KGFG+V F
Sbjct: 25 WKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF 64
Score = 33.5 bits (75), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 28/51 (54%)
Query: 145 NIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
+P+ L++ F + GE+ V++ +D T KGFG+V F E +++
Sbjct: 22 GLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVK 72
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 33.9 bits (76), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 29/55 (52%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
+FIG IP L+ FE G+I + +++D+ T + KG ++ + E L+
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALK 70
Score = 26.9 bits (58), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 13/52 (25%), Positives = 28/52 (53%)
Query: 175 HTNIGKGFGYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
H I G + +E++L+ FE G+I + +++D+ T + KG ++ +
Sbjct: 11 HDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTY 62
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 30/51 (58%)
Query: 185 VNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKVSFTTLSS 235
++ +A+E+E+++ F GEI N+ L D+ T KG+ V ++ L++
Sbjct: 34 IHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 84
Score = 27.7 bits (60), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 14/54 (25%), Positives = 27/54 (50%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEEL 194
+F+ +I +++ F GEI N+ L D+ T KG+ V ++ ++ L
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQAL 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 = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 22/103 (21%), Positives = 48/103 (46%), Gaps = 13/103 (12%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKALTTTKSNS------------HSIFIGN 145
A+V ++ E+ + ALE MN ++ I+V + ++ + I++ +
Sbjct: 58 AFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVAS 117
Query: 146 IPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 188
+ ++ FE+ G+I + L RD T KG+G++ ++
Sbjct: 118 VHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYE 160
Score = 32.3 bits (72), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 12/48 (25%), Positives = 30/48 (62%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKVSFTTLSSIFS 238
+++++ FE+ G+I + L RD T KG+G++ ++ + ++ ++ S
Sbjct: 124 DDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 171
Score = 31.6 bits (70), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 27/51 (52%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
+++G+I + +R+AF G I ++ + D T KGF +V ++ E
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPE 66
Score = 30.4 bits (67), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 26/46 (56%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKV 228
G + ++ E+ +R+AF G I ++ + D T KGF +V ++V
Sbjct: 19 GSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEV 64
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 33.1 bits (74), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 37/79 (46%), Gaps = 6/79 (7%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNI--GKGFGYVNFKAEEEELRKAF 198
+F+G +P LR+ FE G + + ++RD+ N KG +V F + A
Sbjct: 18 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTR----KAAL 73
Query: 199 ESCGEIDNVRLIRDQHTNI 217
E+ + N++++ H I
Sbjct: 74 EAQNALHNMKVLPGMHHPI 92
>pdb|4IHC|A Chain A, Crystal Structure Of Probable Mannonate Dehydratase
Dd703_0947 (target Efi-502222) From Dickeya Dadantii
Ech703
pdb|4IHC|B Chain B, Crystal Structure Of Probable Mannonate Dehydratase
Dd703_0947 (target Efi-502222) From Dickeya Dadantii
Ech703
pdb|4IHC|C Chain C, Crystal Structure Of Probable Mannonate Dehydratase
Dd703_0947 (target Efi-502222) From Dickeya Dadantii
Ech703
pdb|4IHC|D Chain D, Crystal Structure Of Probable Mannonate Dehydratase
Dd703_0947 (target Efi-502222) From Dickeya Dadantii
Ech703
pdb|4IHC|E Chain E, Crystal Structure Of Probable Mannonate Dehydratase
Dd703_0947 (target Efi-502222) From Dickeya Dadantii
Ech703
pdb|4IHC|F Chain F, Crystal Structure Of Probable Mannonate Dehydratase
Dd703_0947 (target Efi-502222) From Dickeya Dadantii
Ech703
pdb|4IHC|G Chain G, Crystal Structure Of Probable Mannonate Dehydratase
Dd703_0947 (target Efi-502222) From Dickeya Dadantii
Ech703
pdb|4IHC|H Chain H, Crystal Structure Of Probable Mannonate Dehydratase
Dd703_0947 (target Efi-502222) From Dickeya Dadantii
Ech703
Length = 440
Score = 33.1 bits (74), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 32/74 (43%), Gaps = 14/74 (18%)
Query: 155 LRKAFESCGEIDNVRLIRDQHTNIG-KGFGYVNFKAEEEELRKAFESCGEIDNVRLIRDQ 213
+R A+ G+I V + + H ++ FG + + LR+ F C EID
Sbjct: 343 VRTAWHGPGDISPVGVCANMHLDMSSPNFGIQEYTPMNDALREVFPGCPEID-------- 394
Query: 214 HTNIGKGFGYVNFK 227
+G+ YVN K
Sbjct: 395 -----QGYAYVNDK 403
>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 = 33.1 bits (74), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 22/103 (21%), Positives = 48/103 (46%), Gaps = 13/103 (12%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKALTTTKSNS------------HSIFIGN 145
A+V ++ E+ + ALE MN ++ I+V + ++ + I++ +
Sbjct: 73 AFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVAS 132
Query: 146 IPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 188
+ ++ FE+ G+I + L RD T KG+G++ ++
Sbjct: 133 VHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYE 175
Score = 32.3 bits (72), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 12/48 (25%), Positives = 30/48 (62%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKVSFTTLSSIFS 238
+++++ FE+ G+I + L RD T KG+G++ ++ + ++ ++ S
Sbjct: 139 DDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 186
Score = 31.6 bits (70), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 27/51 (52%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
+++G+I + +R+AF G I ++ + D T KGF +V ++ E
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPE 81
Score = 30.4 bits (67), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 26/46 (56%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKV 228
G + ++ E+ +R+AF G I ++ + D T KGF +V ++V
Sbjct: 34 GSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEV 79
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 33.1 bits (74), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 29/55 (52%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
+F+G IP L+ FE G I + +++D+ T + KG ++ + A + L+
Sbjct: 18 LFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALK 72
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 33.1 bits (74), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 34/79 (43%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
+F+ N+ + L K F + G + + D T KGF +V F E ++ E
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 201 CGEIDNVRLIRDQHTNIGK 219
G++ R++ + I K
Sbjct: 71 DGQVFQGRMLHVLPSTIKK 89
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 22/42 (52%)
Query: 185 VNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+++ + EE+L K F + G + + D T KGF +V F
Sbjct: 16 LSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTF 57
>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 = 32.7 bits (73), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 30/51 (58%)
Query: 185 VNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKVSFTTLSS 235
++ +A+E+E+++ F GEI N+ L D+ T KG+ V ++ L++
Sbjct: 80 IHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 130
Score = 27.3 bits (59), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 14/54 (25%), Positives = 27/54 (50%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEEL 194
+F+ +I +++ F GEI N+ L D+ T KG+ V ++ ++ L
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQAL 128
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 32.7 bits (73), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 14/60 (23%), Positives = 30/60 (50%)
Query: 136 SNSHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
+++ ++ + +P L F + G I+ R++RD T G+ +V+F +E + R
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Score = 31.6 bits (70), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 20/36 (55%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+ EL F + G I+ R++RD T G+ +V+F
Sbjct: 17 DRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDF 52
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 32.3 bits (72), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 12/48 (25%), Positives = 26/48 (54%)
Query: 140 SIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
++++ N+PF L + F G++ V +++D+ T KG ++ F
Sbjct: 18 TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILF 65
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation Initiation
Factor 4b
Length = 100
Score = 32.3 bits (72), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 134 TKSNSHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRD-QHTNIGKGFGYVNFK 188
KS ++ F+GN+P+ +++ F I VRL R+ + KGFGY F+
Sbjct: 15 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFE 69
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 32.3 bits (72), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 14/60 (23%), Positives = 30/60 (50%)
Query: 136 SNSHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
+++ ++ + +P L F + G I+ R++RD T G+ +V+F +E + R
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Score = 32.0 bits (71), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 29/130 (22%), Positives = 55/130 (42%), Gaps = 6/130 (4%)
Query: 80 PRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALE-MNGHVIDEHTIRVDKALTTTKS-N 137
P C M + A+V F + ++A++ +NG + ++V A +S
Sbjct: 29 PINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPGGESIK 88
Query: 138 SHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKA 197
++++ N+P L F G I ++RD+ T +G +V + EE A
Sbjct: 89 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREE----A 144
Query: 198 FESCGEIDNV 207
E+ ++NV
Sbjct: 145 QEAISALNNV 154
Score = 31.2 bits (69), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 22/43 (51%)
Query: 184 YVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
Y+ + EL F + G I+ R++RD T G+ +V+F
Sbjct: 10 YLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDF 52
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 32.3 bits (72), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 12/50 (24%), Positives = 25/50 (50%)
Query: 138 SHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
+H +FIG +P +++ S G + L++D T + KG+ + +
Sbjct: 1 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEY 50
>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 = 32.3 bits (72), Expect = 0.27, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 25/51 (49%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
+FIG + + L+ F GE+ + L D T +GFG+V FK E
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESE 52
Score = 28.1 bits (61), Expect = 4.3, Method: Composition-based stats.
Identities = 15/47 (31%), Positives = 26/47 (55%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKVS 229
G +++ +++L+ F GE+ + L D T +GFG+V FK S
Sbjct: 5 GGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKES 51
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of Eukaryotic
Initiation Factor 4b
Length = 104
Score = 32.0 bits (71), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 134 TKSNSHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRD-QHTNIGKGFGYVNFK 188
KS ++ F+GN+P+ +++ F I VRL R+ + KGFGY F+
Sbjct: 11 PKSPPYTAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEFE 65
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 32.0 bits (71), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 29/57 (50%)
Query: 131 LTTTKSNSHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
L+ + ++ ++F + L F + G++ +VR+I D+++ KG YV F
Sbjct: 18 LSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEF 74
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 21/34 (61%)
Query: 193 ELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+L F + G++ +VR+I D+++ KG YV F
Sbjct: 41 DLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEF 74
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 32.0 bits (71), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 28/48 (58%), Gaps = 2/48 (4%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 188
+ + NIPF LR+ F G+I +V +I ++ + KGFG+V F+
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTFE 63
Score = 28.5 bits (62), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 28/45 (62%), Gaps = 2/45 (4%)
Query: 185 VNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKVS 229
+ F+ + +LR+ F G+I +V +I ++ + KGFG+V F+ S
Sbjct: 23 IPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTFENS 65
>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 = 32.0 bits (71), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 12/48 (25%), Positives = 30/48 (62%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKVSFTTLSSIFS 238
+++++ FE+ G+I + L RD T KG+G++ ++ + ++ ++ S
Sbjct: 123 DDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 170
Score = 30.4 bits (67), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 26/51 (50%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
+++G+I + +R+AF G I ++ D T KGF +V ++ E
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPE 65
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 21/103 (20%), Positives = 46/103 (44%), Gaps = 13/103 (12%)
Query: 99 AYVRFKNLESVEKALEMNGHV-IDEHTIRVDKALTTTKSNS------------HSIFIGN 145
A+V ++ E+ + ALE V + I+V + ++ + I++ +
Sbjct: 57 AFVEYEVPEAAQLALEQXNSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVAS 116
Query: 146 IPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 188
+ ++ FE+ G+I + L RD T KG+G++ ++
Sbjct: 117 VHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYE 159
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 25/46 (54%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKV 228
G + ++ E+ +R+AF G I ++ D T KGF +V ++V
Sbjct: 18 GSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEV 63
>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|B Chain B, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|C Chain C, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
Length = 184
Score = 31.6 bits (70), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 26/111 (23%), Positives = 51/111 (45%), Gaps = 6/111 (5%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKALTTTKS-NSHSIFIGNIPFXXXXXXLR 156
A+V F + ++A++ +NG + ++V A +S ++++ N+P L
Sbjct: 59 AFVDFTSEXDSQRAIKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLD 118
Query: 157 KAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFESCGEIDNV 207
F G I ++RD+ T +G +V + EE A E+ ++NV
Sbjct: 119 TIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREE----AQEAISALNNV 165
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 31.6 bits (70), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 22/37 (59%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
E +LR+ F G I +V ++ DQ + +GF +V F+
Sbjct: 26 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE 62
Score = 29.3 bits (64), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 155 LRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 188
LR+ F G I +V ++ DQ + +GF +V F+
Sbjct: 29 LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE 62
>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 = 31.6 bits (70), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 38/84 (45%), Gaps = 6/84 (7%)
Query: 136 SNSHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNI--GKGFGYVNFKAEEEE 193
S++ F+G +P LR+ FE G + + ++RD+ N KG +V F
Sbjct: 1 SDAIKXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTR--- 57
Query: 194 LRKAFESCGEIDNVRLIRDQHTNI 217
+ A E+ + N +++ H I
Sbjct: 58 -KAALEAQNALHNXKVLPGXHHPI 80
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 31.6 bits (70), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 13/60 (21%), Positives = 31/60 (51%)
Query: 133 TTKSNSHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+ ++ ++++G + L + F G + N + +D+ T +G+G+V F +EE+
Sbjct: 10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEED 69
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 31.6 bits (70), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 136 SNSHSIFIGNIPFXXXXXXLRKAFESCGEI-DNVRLIRDQHTNIGKGFGYVNFKA 189
S S IFIGN+ L F + G I +++RD T KG+ ++NF +
Sbjct: 3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFAS 57
>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 = 31.2 bits (69), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 12/54 (22%), Positives = 28/54 (51%)
Query: 138 SHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
S +++G+IP+ + + G + N++++ D T KG+ ++ F+ E
Sbjct: 4 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLE 57
Score = 28.1 bits (61), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 11/55 (20%), Positives = 29/55 (52%)
Query: 182 FGYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKVSFTTLSSI 236
G + + EE++ + G + N++++ D T KG+ ++ F+ ++ S++
Sbjct: 9 LGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 63
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 31.2 bits (69), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 22/37 (59%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
E +LR+ F G I +V ++ DQ + +GF +V F+
Sbjct: 29 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE 65
Score = 28.9 bits (63), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 155 LRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 188
LR+ F G I +V ++ DQ + +GF +V F+
Sbjct: 32 LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE 65
>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 = 31.2 bits (69), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 14/75 (18%), Positives = 38/75 (50%), Gaps = 3/75 (4%)
Query: 140 SIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
++F+ + + LR+ FE G I + ++ + + +G+ ++ ++ E ++ A++
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYE-HERDMHSAYK 162
Query: 200 SCG--EIDNVRLIRD 212
+ID R++ D
Sbjct: 163 HADGKKIDGRRVLVD 177
Score = 30.4 bits (67), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 10/43 (23%), Positives = 24/43 (55%)
Query: 185 VNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
VN+ E +LR+ FE G I + ++ + + +G+ ++ ++
Sbjct: 110 VNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYE 152
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 31.2 bits (69), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 12/54 (22%), Positives = 28/54 (51%)
Query: 138 SHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
S +++G+IP+ + + G + N++++ D T KG+ ++ F+ E
Sbjct: 2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLE 55
Score = 28.1 bits (61), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 10/46 (21%), Positives = 24/46 (52%)
Query: 182 FGYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
G + + EE++ + G + N++++ D T KG+ ++ F+
Sbjct: 7 LGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFR 52
>pdb|3TW9|A Chain A, Crystal Structure Of Gluconate Dehydratase (Target
Efi-501679) From Salmonella Enterica Subsp. Enterica
Serovar Enteritidis Str. P125109
pdb|3TW9|B Chain B, Crystal Structure Of Gluconate Dehydratase (Target
Efi-501679) From Salmonella Enterica Subsp. Enterica
Serovar Enteritidis Str. P125109
pdb|3TW9|C Chain C, Crystal Structure Of Gluconate Dehydratase (Target
Efi-501679) From Salmonella Enterica Subsp. Enterica
Serovar Enteritidis Str. P125109
pdb|3TW9|D Chain D, Crystal Structure Of Gluconate Dehydratase (Target
Efi-501679) From Salmonella Enterica Subsp. Enterica
Serovar Enteritidis Str. P125109
pdb|3TWA|A Chain A, Crystal Structure Of Gluconate Dehydratase (Target
Efi-501679) From Salmonella Enterica Subsp. Enterica
Serovar Enteritidis Str. P125109 Complexed With
Magnesium And Glycerol
pdb|3TWA|B Chain B, Crystal Structure Of Gluconate Dehydratase (Target
Efi-501679) From Salmonella Enterica Subsp. Enterica
Serovar Enteritidis Str. P125109 Complexed With
Magnesium And Glycerol
pdb|3TWA|C Chain C, Crystal Structure Of Gluconate Dehydratase (Target
Efi-501679) From Salmonella Enterica Subsp. Enterica
Serovar Enteritidis Str. P125109 Complexed With
Magnesium And Glycerol
pdb|3TWA|D Chain D, Crystal Structure Of Gluconate Dehydratase (Target
Efi-501679) From Salmonella Enterica Subsp. Enterica
Serovar Enteritidis Str. P125109 Complexed With
Magnesium And Glycerol
pdb|3TWA|E Chain E, Crystal Structure Of Gluconate Dehydratase (Target
Efi-501679) From Salmonella Enterica Subsp. Enterica
Serovar Enteritidis Str. P125109 Complexed With
Magnesium And Glycerol
pdb|3TWB|A Chain A, Crystal Structure Of Gluconate Dehydratase (Target
Efi-501679) From Salmonella Enterica Subsp. Enterica
Serovar Enteritidis Str. P125109 Complexed With
Magnesium And Gluconic Acid
pdb|3TWB|B Chain B, Crystal Structure Of Gluconate Dehydratase (Target
Efi-501679) From Salmonella Enterica Subsp. Enterica
Serovar Enteritidis Str. P125109 Complexed With
Magnesium And Gluconic Acid
pdb|3TWB|C Chain C, Crystal Structure Of Gluconate Dehydratase (Target
Efi-501679) From Salmonella Enterica Subsp. Enterica
Serovar Enteritidis Str. P125109 Complexed With
Magnesium And Gluconic Acid
pdb|3TWB|D Chain D, Crystal Structure Of Gluconate Dehydratase (Target
Efi-501679) From Salmonella Enterica Subsp. Enterica
Serovar Enteritidis Str. P125109 Complexed With
Magnesium And Gluconic Acid
pdb|3TWB|E Chain E, Crystal Structure Of Gluconate Dehydratase (Target
Efi-501679) From Salmonella Enterica Subsp. Enterica
Serovar Enteritidis Str. P125109 Complexed With
Magnesium And Gluconic Acid
Length = 442
Score = 31.2 bits (69), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 31/74 (41%), Gaps = 14/74 (18%)
Query: 155 LRKAFESCGEIDNVRLIRDQHTNIG-KGFGYVNFKAEEEELRKAFESCGEIDNVRLIRDQ 213
+R A+ G+I V + + H ++ FG + + LR F C EID+
Sbjct: 345 VRTAWHGPGDISPVGVCANMHLDLSSPNFGIQEYTPMNDALRDVFPGCPEIDH------- 397
Query: 214 HTNIGKGFGYVNFK 227
G+ Y+N K
Sbjct: 398 ------GYAYLNDK 405
>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 = 31.2 bits (69), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 16/71 (22%), Positives = 34/71 (47%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
+F+G++ LR AF+ + ++ D T +G+G+V+F ++++
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 201 CGEIDNVRLIR 211
G+ N R +R
Sbjct: 64 QGQDLNGRPLR 74
Score = 29.3 bits (64), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 24/44 (54%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G +N ++E LR AF+ + ++ D T +G+G+V+F
Sbjct: 7 GDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSF 50
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 31.2 bits (69), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 22/37 (59%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
E +LR+ F G I +V ++ DQ + +GF +V F+
Sbjct: 60 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE 96
Score = 28.5 bits (62), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 155 LRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 188
LR+ F G I +V ++ DQ + +GF +V F+
Sbjct: 63 LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE 96
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 30.8 bits (68), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 2/64 (3%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
+++ N+ LRKAF G I + +++ + + KGFG+V F + EE + E
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRS--KGFGFVCFSSPEEATKAVTEM 75
Query: 201 CGEI 204
G I
Sbjct: 76 NGRI 79
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 30.8 bits (68), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 22/37 (59%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
E +LR+ F G I +V ++ DQ + +GF +V F+
Sbjct: 29 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE 65
Score = 28.1 bits (61), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 155 LRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 188
LR+ F G I +V ++ DQ + +GF +V F+
Sbjct: 32 LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE 65
>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 = 30.8 bits (68), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 12/54 (22%), Positives = 28/54 (51%)
Query: 138 SHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
S +++G+IP+ + + G + N++++ D T KG+ ++ F+ E
Sbjct: 3 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLE 56
Score = 27.3 bits (59), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 10/46 (21%), Positives = 24/46 (52%)
Query: 182 FGYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
G + + EE++ + G + N++++ D T KG+ ++ F+
Sbjct: 8 LGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFR 53
>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 = 30.8 bits (68), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 6/48 (12%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 188
+F+GN+P +RK FE G+ V + +D KGFG++ +
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLE 59
Score = 27.3 bits (59), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 25/46 (54%), Gaps = 8/46 (17%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKVSFTTLSSI 236
EEE+RK FE G+ V + +D KGFG++ + TL+ I
Sbjct: 29 EEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETR--TLAEI 66
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 30.4 bits (67), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 27/56 (48%), Gaps = 6/56 (10%)
Query: 134 TKSNSHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKA 189
T + +F+GN+P ++ FE GE V + RD +GFG++ ++
Sbjct: 18 TYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLES 67
>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 = 30.4 bits (67), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 133 TTKSNSHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+T H +FI +PF L + ++ G + ++RL+ ++ KG YV ++ E +
Sbjct: 12 STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKP-KGLAYVEYENESQ 70
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 30.4 bits (67), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 42/85 (49%), Gaps = 7/85 (8%)
Query: 135 KSNSHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEEL 194
KS +IFI N+ L F + G I + +++ D+ N KG+G+V+F+ +E
Sbjct: 8 KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQE--- 62
Query: 195 RKAFESCGEIDNVRLIRDQHTNIGK 219
A E E N L+ D+ +G+
Sbjct: 63 --AAERAIEKMNGMLLNDRKVFVGR 85
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 26/58 (44%), Gaps = 6/58 (10%)
Query: 136 SNSHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIG--KGFGYVNFKAEE 191
S S IF+ N+PF L+ F CG + L D G KG G V F++ E
Sbjct: 3 SGSSGIFVRNLPFDFTWKMLKDKFNECGHV----LYADIKMENGKSKGCGVVKFESPE 56
>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 = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/52 (25%), Positives = 26/52 (50%)
Query: 137 NSHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 188
++ F+G + + L+ F GE+ + + D +T +GFG++ FK
Sbjct: 10 DAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFK 61
Score = 28.5 bits (62), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 177 NIGKGF-GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
+ GK F G +++ +++L+ F GE+ + + D +T +GFG++ FK
Sbjct: 10 DAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFK 61
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 24/36 (66%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+++L K + G+I + + I D+ TN KG+G+V+F
Sbjct: 19 DQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDF 54
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 27/52 (51%)
Query: 136 SNSHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
S S ++I + L K + G+I + + I D+ TN KG+G+V+F
Sbjct: 3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDF 54
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 29.6 bits (65), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 99 AYVRFKNLESVEKAL-EMNGHVIDEHTIRVDKALTTTKSNS 138
+V +K E +KAL ++ GH +D H + V + TK S
Sbjct: 53 GFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERATKPAS 93
>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 = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 41/82 (50%), Gaps = 7/82 (8%)
Query: 138 SHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKA 197
S +IFI N+ L F + G I + +++ D+ N KG+G+V+F+ +E A
Sbjct: 5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQE-----A 57
Query: 198 FESCGEIDNVRLIRDQHTNIGK 219
E E N L+ D+ +G+
Sbjct: 58 AERAIEKMNGMLLNDRKVFVGR 79
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 28/62 (45%), Gaps = 6/62 (9%)
Query: 132 TTTKSNSHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIG--KGFGYVNFKA 189
++ S + IF+ N+PF L+ F CG + L D G KG G V F++
Sbjct: 2 SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHV----LYADIKMENGKSKGCGVVKFES 57
Query: 190 EE 191
E
Sbjct: 58 PE 59
>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 = 29.3 bits (64), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 10/78 (12%)
Query: 130 ALTTTKSNSHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKA 189
++ TTK +++G + L AF G+I ++++ D T +GF +V F+
Sbjct: 2 SMATTK---RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFEL 58
Query: 190 EEEELRKAFESCGEIDNV 207
E ++ IDN+
Sbjct: 59 AE-------DAAAAIDNM 69
Score = 28.9 bits (63), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 30/56 (53%), Gaps = 3/56 (5%)
Query: 184 YVNFKAEEEE---LRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKVSFTTLSSI 236
YV AEE + L AF G+I ++++ D T +GF +V F+++ ++I
Sbjct: 11 YVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 66
>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 11/39 (28%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 165 IDNVRLIRDQHTNIGKGFGYVNFKA--EEEELRKAFESC 201
++N+RLI+D+ T +GF +V + + +L + +S
Sbjct: 38 VNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSL 76
Score = 28.1 bits (61), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 9/23 (39%), Positives = 16/23 (69%)
Query: 204 IDNVRLIRDQHTNIGKGFGYVNF 226
++N+RLI+D+ T +GF +V
Sbjct: 38 VNNIRLIKDKQTQQNRGFAFVQL 60
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 29.3 bits (64), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 8/77 (10%)
Query: 132 TTTKSNSHSIFIGNIPFXXXXXXLR----KAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
+ + +S+F+G++ L K + SC +++ DQ T + KG+G+V F
Sbjct: 3 SGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSC---RGGKVVLDQ-TGVSKGYGFVKF 58
Query: 188 KAEEEELRKAFESCGEI 204
E E+ R E G +
Sbjct: 59 TDELEQKRALTECQGAV 75
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 28.9 bits (63), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 13/52 (25%), Positives = 26/52 (50%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+++G + L AF G+I ++++ D T +GF +V F+ E+
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 117
Score = 28.5 bits (62), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 30/56 (53%), Gaps = 3/56 (5%)
Query: 184 YVNFKAEEEE---LRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKVSFTTLSSI 236
YV AEE + L AF G+I ++++ D T +GF +V F+++ ++I
Sbjct: 67 YVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 122
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 28.9 bits (63), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 30/56 (53%), Gaps = 3/56 (5%)
Query: 184 YVNFKAEEEE---LRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKVSFTTLSSI 236
YV AEE + L AF G+I ++++ D T +GF +V F+++ ++I
Sbjct: 16 YVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 71
Score = 28.9 bits (63), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 35/78 (44%), Gaps = 10/78 (12%)
Query: 130 ALTTTKSNSHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKA 189
+ TTK +++G + L AF G+I ++++ D T +GF +V F+
Sbjct: 7 GMATTK---RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFEL 63
Query: 190 EEEELRKAFESCGEIDNV 207
E ++ IDN+
Sbjct: 64 AE-------DAAAAIDNM 74
>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 = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 24/43 (55%)
Query: 185 VNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
V+ +A EE++ F GEI N+ L D+ T KG+ V ++
Sbjct: 15 VHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE 57
>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 = 28.9 bits (63), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 24/43 (55%)
Query: 185 VNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
V+ +A EE++ F GEI N+ L D+ T KG+ V ++
Sbjct: 15 VHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE 57
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 28.9 bits (63), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 30/56 (53%), Gaps = 3/56 (5%)
Query: 184 YVNFKAEEEE---LRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKVSFTTLSSI 236
YV AEE + L AF G+I ++++ D T +GF +V F+++ ++I
Sbjct: 9 YVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 64
Score = 28.9 bits (63), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 16/67 (23%), Positives = 31/67 (46%), Gaps = 7/67 (10%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
+++G + L AF G+I ++++ D T +GF +V F+ E ++
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE-------DA 60
Query: 201 CGEIDNV 207
IDN+
Sbjct: 61 AAAIDNM 67
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 28.9 bits (63), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 24/43 (55%)
Query: 185 VNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
V+ +A EE++ F GEI N+ L D+ T KG+ V ++
Sbjct: 15 VHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE 57
>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 = 28.5 bits (62), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 24/43 (55%)
Query: 185 VNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
V+ +A EE++ F GEI N+ L D+ T KG+ V ++
Sbjct: 17 VHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE 59
>pdb|1WV3|A Chain A, Crystal Structure Of N-Terminal Domain Of Hypothetical
Protein Sav0287 From Staphylococcus Aureus
Length = 238
Score = 28.5 bits (62), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 26/42 (61%), Gaps = 5/42 (11%)
Query: 157 KAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAF 198
K F+S E VR++ D++T++ Y+N++ +E+ KA+
Sbjct: 116 KDFQSIQESQYVRIVHDKNTDV-----YINYELQEQLTNKAY 152
>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 = 28.5 bits (62), Expect = 3.8, Method: Composition-based stats.
Identities = 13/52 (25%), Positives = 26/52 (50%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+++G + L AF G+I ++++ D T +GF +V F+ E+
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 56
Score = 27.7 bits (60), Expect = 5.8, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 30/56 (53%), Gaps = 3/56 (5%)
Query: 184 YVNFKAEEEE---LRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKVSFTTLSSI 236
YV AEE + L AF G+I ++++ D T +GF +V F+++ ++I
Sbjct: 6 YVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 61
>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 = 28.5 bits (62), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 34/71 (47%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
+F+G++ + AF G I + R+++D T KG+G+V+F + + +
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 201 CGEIDNVRLIR 211
G+ R IR
Sbjct: 69 GGQWLGGRQIR 79
Score = 27.7 bits (60), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 202 GEIDNVRLIRDQHTNIGKGFGYVNF 226
G I + R+++D T KG+G+V+F
Sbjct: 31 GRISDARVVKDMATGKSKGYGFVSF 55
>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 = 28.1 bits (61), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 24/44 (54%)
Query: 185 VNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKV 228
V+ +A EE++ F GEI N+ L D+ T KG+ V ++
Sbjct: 31 VHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 74
>pdb|2M2B|A Chain A, Nmr Structure Of The Rrm2 Domain Of The Protein Rbm10 From
Homo Sapiens
Length = 131
Score = 28.1 bits (61), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 9/25 (36%), Positives = 16/25 (64%)
Query: 167 NVRLIRDQHTNIGKGFGYVNFKAEE 191
NVR+I+D+ T + +GF ++ E
Sbjct: 54 NVRVIKDKQTQLNRGFAFIQLSTIE 78
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 28.1 bits (61), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 24/43 (55%)
Query: 185 VNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
V+ +A EE++ F GEI N+ L D+ T KG+ V ++
Sbjct: 30 VHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE 72
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 28.1 bits (61), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 24/39 (61%), Gaps = 3/39 (7%)
Query: 94 RTNMN---AYVRFKNLESVEKALEMNGHVIDEHTIRVDK 129
RT N YV F++ E +EKALE+ G + + I+++K
Sbjct: 53 RTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEK 91
Score = 27.7 bits (60), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 5/76 (6%)
Query: 127 VDKALTTTKSNSHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVN 186
V+ + +TT N +FIGN+ L+ A +++ ++ D T + FGYV+
Sbjct: 9 VEGSESTTPFN---LFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVD 64
Query: 187 FKAEEEELRKAFESCG 202
F++ E+L KA E G
Sbjct: 65 FES-AEDLEKALELTG 79
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 28.1 bits (61), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 85 IKMNKVHEKRTNMNAYVRFKNLESVEKALE-MNGHVIDEHTIRVDKALT 132
+ + ++H + AYV F+N + EKAL+ M+G ID I L
Sbjct: 36 MPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVLA 84
>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 = 27.7 bits (60), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 10/43 (23%), Positives = 24/43 (55%)
Query: 185 VNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
VN+ E +LR+ FE G I + ++ + + +G+ ++ ++
Sbjct: 110 VNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYE 152
Score = 27.3 bits (59), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 14/75 (18%), Positives = 38/75 (50%), Gaps = 3/75 (4%)
Query: 140 SIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
++F+ + + LR+ FE G I + ++ + + +G+ ++ ++ E ++ A++
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYE-HERDMHSAYK 162
Query: 200 SCG--EIDNVRLIRD 212
+ID R++ D
Sbjct: 163 HADGKKIDGRRVLVD 177
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 27.3 bits (59), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 25/47 (53%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
+FI ++P L F G + + ++ D+ T++ K FG+V+F
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSF 89
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 27.3 bits (59), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 14/61 (22%), Positives = 27/61 (44%)
Query: 131 LTTTKSNSHSIFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAE 190
L + + ++FI N+ F L + + G++ VR++ T KG + F +
Sbjct: 8 LPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQ 67
Query: 191 E 191
E
Sbjct: 68 E 68
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 27.3 bits (59), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 188
+FIG + L+ F G I V LI+D+ T+ +GF ++ F+
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFE 56
>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second
Rna-Binding Domain Of Sex-Lethal Determined By
Multidimensional Heteronuclear Magnetic Resonance
Spectroscopy
Length = 97
Score = 27.3 bits (59), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 30/67 (44%), Gaps = 4/67 (5%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
+++ N+P L F G I ++RD+ T +G +V + EE A E+
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREE----AQEA 71
Query: 201 CGEIDNV 207
++NV
Sbjct: 72 ISALNNV 78
>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 = 26.9 bits (58), Expect = 10.0, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 26/47 (55%)
Query: 141 IFIGNIPFXXXXXXLRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
+FI ++P L + F G + + ++ D+ TN+ K FG+V++
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSY 74
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.320 0.134 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,154,604
Number of Sequences: 62578
Number of extensions: 221636
Number of successful extensions: 749
Number of sequences better than 100.0: 136
Number of HSP's better than 100.0 without gapping: 103
Number of HSP's successfully gapped in prelim test: 33
Number of HSP's that attempted gapping in prelim test: 486
Number of HSP's gapped (non-prelim): 287
length of query: 239
length of database: 14,973,337
effective HSP length: 96
effective length of query: 143
effective length of database: 8,965,849
effective search space: 1282116407
effective search space used: 1282116407
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 bits)