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= psy3721
(207 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 84.7 bits (208), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 37/85 (43%), Positives = 59/85 (69%)
Query: 31 SSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYGFVHMENDEEGRTAIKELN 90
SS T+KIF+GNV+ + + +R LFE+ G+V+ECDVVK+Y FVHME + + + AI +LN
Sbjct: 5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKDYAFVHMEKEADAKAAIAQLN 64
Query: 91 GQIVNEKPLKIEAATSRKGPNTPTT 115
G+ V K + +E +T + + P++
Sbjct: 65 GKEVKGKRINVELSTKGQKKSGPSS 89
Score = 70.1 bits (170), Expect = 7e-13, Method: Compositional matrix adjust.
Identities = 33/76 (43%), Positives = 48/76 (63%), Gaps = 1/76 (1%)
Query: 109 GPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHID-SPDINKCIKEL 167
G + T K+FVGN+S + E+R LF G V+ECD+V++Y FVH++ D I +L
Sbjct: 4 GSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKDYAFVHMEKEADAKAAIAQL 63
Query: 168 NGMMVDGKPMKVQIST 183
NG V GK + V++ST
Sbjct: 64 NGKEVKGKRINVELST 79
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 70.9 bits (172), Expect = 5e-13, Method: Compositional matrix adjust.
Identities = 34/85 (40%), Positives = 56/85 (65%), Gaps = 1/85 (1%)
Query: 32 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYGFVHMENDEEGRTAIKELNG 91
S G K+FIGN+ + + IR LFE+YGKV+ECD++KNYGFVH+E+ AI+ L+
Sbjct: 5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAIRNLHH 64
Query: 92 QIVNEKPLKIEAATSR-KGPNTPTT 115
++ + +EA+ ++ K + P++
Sbjct: 65 YKLHGVNINVEASKNKSKASSGPSS 89
Score = 63.2 bits (152), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 30/77 (38%), Positives = 44/77 (57%), Gaps = 1/77 (1%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHI-DSPDINKCIKELNGMMVDG 174
K+F+GNL E+R LF YG V+ECDI++NYGFVHI D I+ L+ + G
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAIRNLHHYKLHG 69
Query: 175 KPMKVQISTSRVRQRPG 191
+ V+ S ++ + G
Sbjct: 70 VNINVEASKNKSKASSG 86
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 69.7 bits (169), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 35/79 (44%), Positives = 50/79 (63%), Gaps = 1/79 (1%)
Query: 114 TTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHID-SPDINKCIKELNGMMV 172
+TK+ VGN+S E+R F YG V+ECDIV++Y FVH++ + D + I+ L+
Sbjct: 10 STKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKDYAFVHMERAEDAVEAIRGLDNTEF 69
Query: 173 DGKPMKVQISTSRVRQRPG 191
GK M VQ+STSR+R G
Sbjct: 70 QGKRMHVQLSTSRLRTASG 88
Score = 67.4 bits (163), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 31/80 (38%), Positives = 51/80 (63%), Gaps = 4/80 (5%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYGFVHMENDEEGRTAIKELNGQIVNE 96
K+ +GN++P + + +R FE+YG V+ECD+VK+Y FVHME E+ AI+ L+
Sbjct: 12 KLHVGNISPTCTNQELRAKFEEYGPVIECDIVKDYAFVHMERAEDAVEAIRGLDNTEFQG 71
Query: 97 KPLKIEAATSR----KGPNT 112
K + ++ +TSR GP++
Sbjct: 72 KRMHVQLSTSRLRTASGPSS 91
>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 = 58.9 bits (141), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 45/171 (26%), Positives = 77/171 (45%), Gaps = 27/171 (15%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIKE 88
K+FIG +N T+ + +R F KYG V + ++K+ +GF+ E +K
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 89 ---LNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECD 145
L+G++++ K A R T K+FVG + + R E E F +GT+++
Sbjct: 65 QHILDGKVIDPK-----RAIPRD-EQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQ 118
Query: 146 IV--------RNYGFVHIDSPDINKCIKELNGMMVDGKPMKVQISTSRVRQ 188
++ R +GFV DS D + +D K K++I + R
Sbjct: 119 LMLDKDTGQSRGFGFVTYDSADAVDRV--CQNKFIDFKDRKIEIKRAEPRH 167
>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 = 58.2 bits (139), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 38/143 (26%), Positives = 69/143 (48%), Gaps = 20/143 (13%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAI-- 86
K+FIG ++ T+ E +R FE++G + +C V+++ +GFV EE A+
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 87 --KELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVEC 144
+++G++V K + R G + K+FVG + ++T +R+ F YG +
Sbjct: 75 RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI 134
Query: 145 DIV--------RNYGFVHIDSPD 159
+I+ R + FV D D
Sbjct: 135 EIMTDRGSGKKRGFAFVTFDDHD 157
>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 = 58.2 bits (139), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 38/143 (26%), Positives = 69/143 (48%), Gaps = 20/143 (13%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAI-- 86
K+FIG ++ T+ E +R FE++G + +C V+++ +GFV EE A+
Sbjct: 8 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67
Query: 87 --KELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVEC 144
+++G++V K + R G + K+FVG + ++T +R+ F YG +
Sbjct: 68 RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI 127
Query: 145 DIV--------RNYGFVHIDSPD 159
+I+ R + FV D D
Sbjct: 128 EIMTDRGSGKKRGFAFVTFDDHD 150
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 58.2 bits (139), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 38/143 (26%), Positives = 69/143 (48%), Gaps = 20/143 (13%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAI-- 86
K+FIG ++ T+ E +R FE++G + +C V+++ +GFV EE A+
Sbjct: 16 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 75
Query: 87 --KELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVEC 144
+++G++V K + R G + K+FVG + ++T +R+ F YG +
Sbjct: 76 RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI 135
Query: 145 DIV--------RNYGFVHIDSPD 159
+I+ R + FV D D
Sbjct: 136 EIMTDRGSGKKRGFAFVTFDDHD 158
>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 = 57.8 bits (138), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 38/143 (26%), Positives = 69/143 (48%), Gaps = 20/143 (13%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAI-- 86
K+FIG ++ T+ E +R FE++G + +C V+++ +GFV EE A+
Sbjct: 14 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 73
Query: 87 --KELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVEC 144
+++G++V K + R G + K+FVG + ++T +R+ F YG +
Sbjct: 74 RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI 133
Query: 145 DIV--------RNYGFVHIDSPD 159
+I+ R + FV D D
Sbjct: 134 EIMTDRGSGKKRGFAFVTFDDHD 156
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 57.8 bits (138), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 38/143 (26%), Positives = 69/143 (48%), Gaps = 20/143 (13%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAI-- 86
K+FIG ++ T+ E +R FE++G + +C V+++ +GFV EE A+
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 87 --KELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVEC 144
+++G++V K + R G + K+FVG + ++T +R+ F YG +
Sbjct: 75 RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI 134
Query: 145 DIV--------RNYGFVHIDSPD 159
+I+ R + FV D D
Sbjct: 135 EIMTDRGSGKKRGFAFVTFDDHD 157
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 57.8 bits (138), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 38/143 (26%), Positives = 69/143 (48%), Gaps = 20/143 (13%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAI-- 86
K+FIG ++ T+ E +R FE++G + +C V+++ +GFV EE A+
Sbjct: 13 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 72
Query: 87 --KELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVEC 144
+++G++V K + R G + K+FVG + ++T +R+ F YG +
Sbjct: 73 RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI 132
Query: 145 DIV--------RNYGFVHIDSPD 159
+I+ R + FV D D
Sbjct: 133 EIMTDRGSGKKRGFAFVTFDDHD 155
>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 = 55.8 bits (133), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 36/176 (20%), Positives = 84/176 (47%), Gaps = 20/176 (11%)
Query: 28 PGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMEND 79
P S +++G+++P + ++ F G ++ V ++ Y +V+ +
Sbjct: 3 PSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQP 62
Query: 80 EEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPTTKV---FVGNLSDNTRAPEVRELFV 136
+ A+ +N ++ KP++I S++ P+ + V F+ NL + + + F
Sbjct: 63 ADAERALDTMNFDVIKGKPVRI--MWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFS 120
Query: 137 PYGTVVECDIV------RNYGFVHIDSPD-INKCIKELNGMMVDGKPMKVQISTSR 185
+G ++ C +V + YGFVH ++ + + I+++NGM+++ + + V SR
Sbjct: 121 AFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR 176
Score = 52.4 bits (124), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/87 (31%), Positives = 43/87 (49%), Gaps = 6/87 (6%)
Query: 28 PGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV------KNYGFVHMENDEE 81
P G IFI N++ + + F +G ++ C VV K YGFVH E E
Sbjct: 91 PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEA 150
Query: 82 GRTAIKELNGQIVNEKPLKIEAATSRK 108
AI+++NG ++N++ + + SRK
Sbjct: 151 AERAIEKMNGMLLNDRKVFVGRFKSRK 177
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 55.8 bits (133), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 34/163 (20%), Positives = 75/163 (46%), Gaps = 17/163 (10%)
Query: 38 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------KNYGFVHMENDEEGRTAIKELN 90
+++GN++ + ++++ F+ G + ++ NY FV + A++ LN
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 91 GQIVNEKPLKIEAA-TSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-- 147
G+ + +KI A S++ + T +FVG+L+ N +R F + + + ++
Sbjct: 63 GKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWD 122
Query: 148 ------RNYGFVHIDS-PDINKCIKELNGMMVDGKPMKVQIST 183
R YGFV S D + + G ++G+P+++ +
Sbjct: 123 MQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAA 165
Score = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 42/83 (50%), Gaps = 8/83 (9%)
Query: 31 SSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEG 82
SS TF +F+G++N E +R F+ + + V+ + YGFV + ++
Sbjct: 83 SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDA 142
Query: 83 RTAIKELNGQIVNEKPLKIEAAT 105
+ A+ + GQ +N +PL+I A
Sbjct: 143 QNAMDSMQGQDLNGRPLRINWAA 165
>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 = 55.5 bits (132), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 36/176 (20%), Positives = 84/176 (47%), Gaps = 20/176 (11%)
Query: 28 PGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMEND 79
P S +++G+++P + ++ F G ++ V ++ Y +V+ +
Sbjct: 8 PSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQP 67
Query: 80 EEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPTTKV---FVGNLSDNTRAPEVRELFV 136
+ A+ +N ++ KP++I S++ P+ + V F+ NL + + + F
Sbjct: 68 ADAERALDTMNFDVIKGKPVRI--MWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFS 125
Query: 137 PYGTVVECDIV------RNYGFVHIDSPD-INKCIKELNGMMVDGKPMKVQISTSR 185
+G ++ C +V + YGFVH ++ + + I+++NGM+++ + + V SR
Sbjct: 126 AFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR 181
Score = 52.0 bits (123), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/87 (31%), Positives = 43/87 (49%), Gaps = 6/87 (6%)
Query: 28 PGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV------KNYGFVHMENDEE 81
P G IFI N++ + + F +G ++ C VV K YGFVH E E
Sbjct: 96 PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEA 155
Query: 82 GRTAIKELNGQIVNEKPLKIEAATSRK 108
AI+++NG ++N++ + + SRK
Sbjct: 156 AERAIEKMNGMLLNDRKVFVGRFKSRK 182
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 51.6 bits (122), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 27/87 (31%), Positives = 43/87 (49%), Gaps = 6/87 (6%)
Query: 28 PGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV------KNYGFVHMENDEE 81
P G IFI N++ + + F +G ++ C VV K YGFVH E E
Sbjct: 4 PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEA 63
Query: 82 GRTAIKELNGQIVNEKPLKIEAATSRK 108
AI+++NG ++N++ + + SRK
Sbjct: 64 AERAIEKMNGMLLNDRKVFVGRFKSRK 90
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 41/76 (53%), Gaps = 7/76 (9%)
Query: 117 VFVGNLSDNTRAPEVRELFVPYGTVVECDIV------RNYGFVHIDSPD-INKCIKELNG 169
+F+ NL + + + F +G ++ C +V + YGFVH ++ + + I+++NG
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 73
Query: 170 MMVDGKPMKVQISTSR 185
M+++ + + V SR
Sbjct: 74 MLLNDRKVFVGRFKSR 89
>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 = 51.2 bits (121), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 44/82 (53%), Gaps = 6/82 (7%)
Query: 33 VGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV------KNYGFVHMENDEEGRTAI 86
+G+ IFI N++ + + F +G ++ C VV K YGFVH E E AI
Sbjct: 3 LGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAI 62
Query: 87 KELNGQIVNEKPLKIEAATSRK 108
+++NG ++N++ + + SRK
Sbjct: 63 EKMNGMLLNDRKVFVGRFKSRK 84
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 41/76 (53%), Gaps = 7/76 (9%)
Query: 117 VFVGNLSDNTRAPEVRELFVPYGTVVECDIV------RNYGFVHIDSPD-INKCIKELNG 169
+F+ NL + + + F +G ++ C +V + YGFVH ++ + + I+++NG
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 67
Query: 170 MMVDGKPMKVQISTSR 185
M+++ + + V SR
Sbjct: 68 MLLNDRKVFVGRFKSR 83
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 50.8 bits (120), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 33/136 (24%), Positives = 61/136 (44%), Gaps = 13/136 (9%)
Query: 26 NMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYG------------- 72
+ P + K+F+G V S + +R LFE+YG V E +V+++
Sbjct: 6 DHPDQPDLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVT 65
Query: 73 FVHMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVR 132
F + E + A+ + P++++ A S K K+F+G +S ++R
Sbjct: 66 FYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIR 125
Query: 133 ELFVPYGTVVECDIVR 148
+F +G + EC I+R
Sbjct: 126 VMFSSFGQIEECRILR 141
Score = 33.1 bits (74), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 23/40 (57%)
Query: 110 PNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN 149
P+ K+FVG + ++RELF YG V E +++R+
Sbjct: 11 PDLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRD 50
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 50.8 bits (120), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 30/84 (35%), Positives = 43/84 (51%), Gaps = 11/84 (13%)
Query: 37 KIFIGNVNPG----TSVELIRPLFEKYGKVVECDVVKNYGFVHMENDEEGRTAIKELNGQ 92
++FIGN+N + VE I F KYG+V C V K Y FV N+ R A+ NG+
Sbjct: 29 RVFIGNLNTALVKKSDVETI---FSKYGRVAGCSVHKGYAFVQYSNERHARAAVLGENGR 85
Query: 93 IVNEKPLKIEAAT----SRKGPNT 112
++ + L I A R GP++
Sbjct: 86 VLAGQTLDINMAGEPKPDRSGPSS 109
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/88 (25%), Positives = 47/88 (53%), Gaps = 4/88 (4%)
Query: 99 LKIEAA--TSRKGPNTPTTKVFVGNLSDN-TRAPEVRELFVPYGTVVECDIVRNYGFV-H 154
LK++A+ T++ P + ++VF+GNL+ + +V +F YG V C + + Y FV +
Sbjct: 10 LKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKGYAFVQY 69
Query: 155 IDSPDINKCIKELNGMMVDGKPMKVQIS 182
+ + NG ++ G+ + + ++
Sbjct: 70 SNERHARAAVLGENGRVLAGQTLDINMA 97
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 50.4 bits (119), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 32/125 (25%), Positives = 58/125 (46%), Gaps = 13/125 (10%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYG-------------FVHMENDEEGR 83
K+F+G V S + +R LFE+YG V E +V+++ F + E +
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 84 TAIKELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVE 143
A+ + P++++ A S K K+F+G +S ++R +F +G + E
Sbjct: 65 NALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEE 124
Query: 144 CDIVR 148
C I+R
Sbjct: 125 CRILR 129
Score = 31.2 bits (69), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 21/34 (61%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN 149
K+FVG + ++RELF YG V E +++R+
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRD 38
>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 = 49.7 bits (117), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 40/155 (25%), Positives = 70/155 (45%), Gaps = 26/155 (16%)
Query: 50 ELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIKELNGQIVNEKPLKI 101
E R LF G++ C +V++ YGFV+ + ++ AI LNG + K +K+
Sbjct: 17 EEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKV 76
Query: 102 EAATSRKGPNTPTTK---VFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNY 150
A P++ + + ++V L E+ +LF YG ++ I+ R
Sbjct: 77 SYAR----PSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGV 132
Query: 151 GFVHIDSP-DINKCIKELNGMMVDG--KPMKVQIS 182
GF+ D + + IK LNG G +P+ V+ +
Sbjct: 133 GFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167
>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 = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 47/88 (53%), Gaps = 9/88 (10%)
Query: 36 FKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIK 87
F +F+G+++P + E I+ F +G++ + VVK+ YGFV N + AI+
Sbjct: 16 FHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 75
Query: 88 ELNGQIVNEKPLKIEAATSRKGPNTPTT 115
++ GQ + + ++ AT RK P +T
Sbjct: 76 QMGGQWLGGRQIRTNWAT-RKPPAPKST 102
Score = 40.4 bits (93), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 39/78 (50%), Gaps = 9/78 (11%)
Query: 117 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVH-IDSPDINKCIKEL 167
VFVG+LS +++ F P+G + + +V++ YGFV + D I+++
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 168 NGMMVDGKPMKVQISTSR 185
G + G+ ++ +T +
Sbjct: 78 GGQWLGGRQIRTNWATRK 95
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 52/88 (59%), Gaps = 12/88 (13%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIKE 88
K+F+G ++ T+ + + +F KYG++ E VVK+ +GFV EN ++ + A+
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 89 LNGQIVNEKPLKIEAA----TSRKGPNT 112
+NG+ V+ + ++++ A +R GP++
Sbjct: 74 MNGKSVDGRQIRVDQAGKSSDNRSGPSS 101
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 42/85 (49%), Gaps = 9/85 (10%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPDINK-CIKE 166
K+FVG LS +T + ++F YG + E +V R +GFV ++ D K +
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 167 LNGMMVDGKPMKVQISTSRVRQRPG 191
+NG VDG+ ++V + R G
Sbjct: 74 MNGKSVDGRQIRVDQAGKSSDNRSG 98
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 48.1 bits (113), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 29/84 (34%), Positives = 45/84 (53%), Gaps = 11/84 (13%)
Query: 37 KIFIGNVNP----GTSVELIRPLFEKYGKVVECDVVKNYGFVHMENDEEGRTAIKELNGQ 92
++FIGN+N + VE I F KYGK+V C V K + FV N+ R A+ +G+
Sbjct: 17 RVFIGNLNTLVVKKSDVEAI---FSKYGKIVGCSVHKGFAFVQYVNERNARAAVAGEDGR 73
Query: 93 IVNEKPLKIEAAT----SRKGPNT 112
++ + L I A +R GP++
Sbjct: 74 MIAGQVLDINLAAEPKVNRSGPSS 97
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/94 (22%), Positives = 47/94 (50%), Gaps = 6/94 (6%)
Query: 102 EAATSRKGPNTPTTKVFVGNLSDNT---RAPEVRELFVPYGTVVECDIVRNYGFV-HIDS 157
++ + P + ++VF+GNL NT + +V +F YG +V C + + + FV +++
Sbjct: 3 SGSSGKTDPRSMNSRVFIGNL--NTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNE 60
Query: 158 PDINKCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
+ + +G M+ G+ + + ++ R G
Sbjct: 61 RNARAAVAGEDGRMIAGQVLDINLAAEPKVNRSG 94
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 47.8 bits (112), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 46/75 (61%), Gaps = 7/75 (9%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-------YGFVHMENDEEGRTAIKEL 89
K+FIG +N T+ ++++ +F K+G + E ++K+ + F+ EN + + A K++
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDM 68
Query: 90 NGQIVNEKPLKIEAA 104
NG+ ++ K +K+E A
Sbjct: 69 NGKSLHGKAIKVEQA 83
Score = 37.0 bits (84), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 44/88 (50%), Gaps = 13/88 (14%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-------RNYGFVHIDSP-DINKCIKEL 167
K+F+G L+ T ++ +F +G + E ++ R + F+ ++P D K++
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDM 68
Query: 168 NGMMVDGKPMKVQIST-----SRVRQRP 190
NG + GK +KV+ + S R+RP
Sbjct: 69 NGKSLHGKAIKVEQAKKPSFQSGGRRRP 96
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 47.4 bits (111), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 46/89 (51%), Gaps = 9/89 (10%)
Query: 36 FKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIK 87
F +F+G+++P + E I+ F +GK+ + VVK+ YGFV N + AI
Sbjct: 16 FHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIV 75
Query: 88 ELNGQIVNEKPLKIEAATSR-KGPNTPTT 115
+ GQ + + ++ AT + P+ P++
Sbjct: 76 HMGGQWLGGRQIRTNWATRKPPAPSGPSS 104
Score = 37.4 bits (85), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 37/78 (47%), Gaps = 9/78 (11%)
Query: 117 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHI-DSPDINKCIKEL 167
VFVG+LS +++ F P+G + + +V++ YGFV + D I +
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 168 NGMMVDGKPMKVQISTSR 185
G + G+ ++ +T +
Sbjct: 78 GGQWLGGRQIRTNWATRK 95
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 42/71 (59%), Gaps = 2/71 (2%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--YGFVHMENDEEGRTAIKELNGQIV 94
++F+GN+ + E + LFE+YG+ E + ++ +GF+ +E+ A EL+G I+
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTIL 83
Query: 95 NEKPLKIEAAT 105
+PL+I AT
Sbjct: 84 KSRPLRIRFAT 94
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 43/75 (57%), Gaps = 3/75 (4%)
Query: 112 TPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--YGFVHIDSPDINKCIK-ELN 168
T ++FVGNL + + + LF YG E I R+ +GF+ ++S + + K EL+
Sbjct: 20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELD 79
Query: 169 GMMVDGKPMKVQIST 183
G ++ +P++++ +T
Sbjct: 80 GTILKSRPLRIRFAT 94
>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 = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 34/125 (27%), Positives = 55/125 (44%), Gaps = 13/125 (10%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYG----------FVHMENDEEGRTAI 86
K F+G V S + +R LFE+YG V E +V+++ FV + A
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 87 KELNGQIV---NEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVE 143
L+ V P++ + A S K K+F+G +S ++R F +G + E
Sbjct: 65 NALHNXKVLPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQIEE 124
Query: 144 CDIVR 148
C I+R
Sbjct: 125 CRILR 129
Score = 30.0 bits (66), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN 149
K FVG + ++RELF YG V E +++R+
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRD 38
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 46.2 bits (108), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 35/138 (25%), Positives = 60/138 (43%), Gaps = 24/138 (17%)
Query: 52 IRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIKELNGQIVNEKPLKIEA 103
+ LF G + C +V++ YGFV+ + + AI LNG + K +K+
Sbjct: 21 FKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSY 80
Query: 104 ATSRKGPNTPTTK---VFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGF 152
A P++ + + ++V L E+ +LF YG ++ I+ R GF
Sbjct: 81 AR----PSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGF 136
Query: 153 VHIDSP-DINKCIKELNG 169
+ D + + IK LNG
Sbjct: 137 IRFDKRIEAEEAIKGLNG 154
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 37/147 (25%), Positives = 70/147 (47%), Gaps = 20/147 (13%)
Query: 55 LFEKYGKVVECDVVKNY--------GFVHMENDEEGRTAIKELNGQIVNEKPLKIEAATS 106
LF G + C ++++Y FV ++ + + AIK LNG V K LK+ A
Sbjct: 23 LFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP 82
Query: 107 RKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDS- 157
G + T ++V NL ++ +F YG++V+ +I+R+ FV +
Sbjct: 83 -GGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKR 141
Query: 158 PDINKCIKELNGMMVDG--KPMKVQIS 182
+ + I LN ++ +G +P+ V+++
Sbjct: 142 EEAQEAISALNNVIPEGGSQPLSVRLA 168
Score = 33.9 bits (76), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 26/90 (28%), Positives = 40/90 (44%), Gaps = 15/90 (16%)
Query: 115 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN------YGFVHID---SPDINKCIK 165
T + V L + E+ LF G + C I+R+ YG+ +D D + IK
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 166 ELNGMMVDGKPMKVQISTSRVRQRPGVDEV 195
LNG+ V K +KV + RPG + +
Sbjct: 64 VLNGITVRNKRLKVSYA------RPGGESI 87
Score = 32.7 bits (73), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 28/116 (24%), Positives = 52/116 (44%), Gaps = 14/116 (12%)
Query: 2 SRFDQQQLVKVSR---YSNNQINISCRNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEK 58
S D Q+ +KV N ++ +S PG S+ +++ N+ + + + +F K
Sbjct: 54 SEMDSQRAIKVLNGITVRNKRLKVSYAR-PGGESIKDTNLYVTNLPRTITDDQLDTIFGK 112
Query: 59 YGKVVECDVVKN--------YGFVHMENDEEGRTAIKELNGQIV--NEKPLKIEAA 104
YG +V+ +++++ FV EE + AI LN I +PL + A
Sbjct: 113 YGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 6/73 (8%)
Query: 38 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV------KNYGFVHMENDEEGRTAIKELNG 91
+++ N++ G E +R F +G + V+ K +GFV + EE A+ E+NG
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNG 77
Query: 92 QIVNEKPLKIEAA 104
+IV KPL + A
Sbjct: 78 RIVATKPLYVALA 90
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 43/82 (52%), Gaps = 7/82 (8%)
Query: 117 VFVGNLSDNTRAPEVRELFVPYGTVVECDIV------RNYGFVHIDSP-DINKCIKELNG 169
++V NL D +R+ F P+GT+ ++ + +GFV SP + K + E+NG
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNG 77
Query: 170 MMVDGKPMKVQISTSRVRQRPG 191
+V KP+ V ++ + ++ G
Sbjct: 78 RIVATKPLYVALAQRKEERQSG 99
>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 = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 49/169 (28%), Positives = 77/169 (45%), Gaps = 21/169 (12%)
Query: 27 MPGFSSVGTFKIFIGNVNPGTSV-EL---IRPLFEKYGKVVECDVV----KNYGFVHMEN 78
+ G S F +FIGN+NP SV EL I LF K V DV + +G+V E+
Sbjct: 5 VEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAV-VDVRTGTNRKFGYVDFES 63
Query: 79 DEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVG-NLSDNTRAPEVRELFVP 137
E+ A+ EL G V +K+E R + + NLS N E++E+F
Sbjct: 64 AEDLEKAL-ELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFED 122
Query: 138 YGTVVECDIV----RNYGFVHID---SPDINKCIKELNGMMVDGKPMKV 179
+E +V ++ G +I+ D K ++E G +DG+ + +
Sbjct: 123 ---ALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSL 168
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 20/84 (23%), Positives = 47/84 (55%), Gaps = 8/84 (9%)
Query: 32 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGR 83
S G ++++G+++ + +++R +FE +G++ ++ K YGF+ + E +
Sbjct: 23 SAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAK 82
Query: 84 TAIKELNGQIVNEKPLKIEAATSR 107
A+++LNG + +P+K+ T R
Sbjct: 83 KALEQLNGFELAGRPMKVGHVTER 106
Score = 43.9 bits (102), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 27/89 (30%), Positives = 45/89 (50%), Gaps = 10/89 (11%)
Query: 107 RKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHI-DS 157
+KG P +++VG+L N +R +F P+G + ++ + YGF+ DS
Sbjct: 20 QKGSAGPM-RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDS 78
Query: 158 PDINKCIKELNGMMVDGKPMKVQISTSRV 186
K +++LNG + G+PMKV T R
Sbjct: 79 ECAKKALEQLNGFELAGRPMKVGHVTERT 107
>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 = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 37/147 (25%), Positives = 69/147 (46%), Gaps = 20/147 (13%)
Query: 55 LFEKYGKVVECDVVKNY--------GFVHMENDEEGRTAIKELNGQIVNEKPLKIEAATS 106
LF G + C + ++Y FV ++ + + AIK LNG V K LK+ A
Sbjct: 34 LFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVLNGITVRNKRLKVSYARP 93
Query: 107 RKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDS- 157
G + T ++V NL ++ +F YG++V+ +I+R+ FV +
Sbjct: 94 -GGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKR 152
Query: 158 PDINKCIKELNGMMVDG--KPMKVQIS 182
+ + I LN ++ +G +P+ V+++
Sbjct: 153 EEAQEAISALNNVIPEGGSQPLSVRLA 179
Score = 35.4 bits (80), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 27/95 (28%), Positives = 40/95 (42%), Gaps = 15/95 (15%)
Query: 110 PNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNY------GFVHID---SPDI 160
P T + V L + E+ LF G + C I R+Y G+ +D D
Sbjct: 10 PRASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDS 69
Query: 161 NKCIKELNGMMVDGKPMKVQISTSRVRQRPGVDEV 195
+ IK LNG+ V K +KV + RPG + +
Sbjct: 70 QRAIKVLNGITVRNKRLKVSYA------RPGGESI 98
Score = 31.6 bits (70), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 28/116 (24%), Positives = 52/116 (44%), Gaps = 14/116 (12%)
Query: 2 SRFDQQQLVKVSR---YSNNQINISCRNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEK 58
S D Q+ +KV N ++ +S PG S+ +++ N+ + + + +F K
Sbjct: 65 SEXDSQRAIKVLNGITVRNKRLKVSYAR-PGGESIKDTNLYVTNLPRTITDDQLDTIFGK 123
Query: 59 YGKVVECDVVKN--------YGFVHMENDEEGRTAIKELNGQIVN--EKPLKIEAA 104
YG +V+ +++++ FV EE + AI LN I +PL + A
Sbjct: 124 YGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 179
>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 = 44.7 bits (104), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 40/79 (50%), Gaps = 8/79 (10%)
Query: 35 TFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGRTAI 86
TF +F+G++N E +R F+ + + V+ + YGFV + ++ + A+
Sbjct: 1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60
Query: 87 KELNGQIVNEKPLKIEAAT 105
+ GQ +N +PL+I A
Sbjct: 61 DSMQGQDLNGRPLRINWAA 79
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 44.7 bits (104), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/93 (24%), Positives = 51/93 (54%), Gaps = 9/93 (9%)
Query: 32 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKV--------VECDVVKNYGFVHMENDEEGR 83
S G+ +++G+++ + +++R +FE +GK+ + K YGF+ + E R
Sbjct: 2 SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECAR 61
Query: 84 TAIKELNGQIVNEKPLKIEAATSR-KGPNTPTT 115
A+++LNG + +P+++ T R G + P++
Sbjct: 62 RALEQLNGFELAGRPMRVGHVTERLDGGSGPSS 94
Score = 40.0 bits (92), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 25/90 (27%), Positives = 47/90 (52%), Gaps = 9/90 (10%)
Query: 111 NTPTTKVFVGNLSDNTRAPEVRELFVPYGTV------VECDIVRN--YGFVHI-DSPDIN 161
++ ++ ++VG+L N +R +F P+G + + D R+ YGF+ DS
Sbjct: 2 SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECAR 61
Query: 162 KCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
+ +++LNG + G+PM+V T R+ G
Sbjct: 62 RALEQLNGFELAGRPMRVGHVTERLDGGSG 91
>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 = 44.3 bits (103), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 45/82 (54%), Gaps = 6/82 (7%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--YGFVHMENDEEGRTAIKELNGQIV 94
++F+GN+ P + E +R LFEKYGK E + K+ +GF+ +E A EL+ +
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPL 76
Query: 95 NEKPLKI----EAATSRKGPNT 112
K L++ +A+ GP++
Sbjct: 77 RGKQLRVRFACHSASLTSGPSS 98
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 44/74 (59%), Gaps = 3/74 (4%)
Query: 112 TPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--YGFVHIDSPDINKCIK-ELN 168
T +++FVGNL + E+R+LF YG E I ++ +GF+ +++ + + K EL+
Sbjct: 13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELD 72
Query: 169 GMMVDGKPMKVQIS 182
M + GK ++V+ +
Sbjct: 73 NMPLRGKQLRVRFA 86
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 44.3 bits (103), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 50/83 (60%), Gaps = 7/83 (8%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN------YGFVHID-SPDINKCIKELN 168
++ V N+ R P++R++F +G +++ +I+ N +GFV + S D ++ ++L+
Sbjct: 17 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLH 76
Query: 169 GMMVDGKPMKVQISTSRVRQRPG 191
G +V+G+ ++V +T+RV G
Sbjct: 77 GTVVEGRKIEVNNATARVMTNSG 99
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 38/62 (61%), Gaps = 6/62 (9%)
Query: 52 IRPLFEKYGKVVECDVV------KNYGFVHMENDEEGRTAIKELNGQIVNEKPLKIEAAT 105
+R +F ++GK+++ +++ K +GFV EN + A ++L+G +V + +++ AT
Sbjct: 32 LRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT 91
Query: 106 SR 107
+R
Sbjct: 92 AR 93
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 43.9 bits (102), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 31/107 (28%), Positives = 50/107 (46%), Gaps = 9/107 (8%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--YGFVHMENDEEGRTAIKELNGQIV 94
++F+GN+ P + E +R LFEKYGK E + K+ +GF+ +E A EL+ +
Sbjct: 24 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPL 83
Query: 95 NEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTV 141
K L++ A + + V NL + E F +G V
Sbjct: 84 RGKQLRVRFACH-------SASLTVRNLPQYVSNELLEEAFSVFGQV 123
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 44/74 (59%), Gaps = 3/74 (4%)
Query: 112 TPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--YGFVHIDSPDINKCIK-ELN 168
T +++FVGNL + E+R+LF YG E I ++ +GF+ +++ + + K EL+
Sbjct: 20 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELD 79
Query: 169 GMMVDGKPMKVQIS 182
M + GK ++V+ +
Sbjct: 80 NMPLRGKQLRVRFA 93
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 43.9 bits (102), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 44/77 (57%), Gaps = 2/77 (2%)
Query: 113 PTTKVFVGNLS-DNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSP-DINKCIKELNGM 170
P +++F+GNL N ++ +F PYG +++ +I +GF+ D+P + I+ +
Sbjct: 1 PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECESQE 60
Query: 171 MVDGKPMKVQISTSRVR 187
M GK + +++S+S R
Sbjct: 61 MNFGKKLILEVSSSNAR 77
Score = 33.5 bits (75), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 37 KIFIGNVN-PGTSVELIRPLFEKYGKVVECDVVKNYGFVHMENDEEGRTAIKELNGQIVN 95
++FIGN+ S E + +F YG +++ ++ +GF+ +N + R AI+ + ++
Sbjct: 4 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECESQEMNF 63
Query: 96 EKPLKIEAATS 106
K L +E ++S
Sbjct: 64 GKKLILEVSSS 74
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 43.9 bits (102), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 49/78 (62%), Gaps = 7/78 (8%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN------YGFVHID-SPDINKCIKELN 168
++ V N+ R P++R++F +G +++ +I+ N +GFV + S D ++ ++L+
Sbjct: 31 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLH 90
Query: 169 GMMVDGKPMKVQISTSRV 186
G +V+G+ ++V +T+RV
Sbjct: 91 GTVVEGRKIEVNNATARV 108
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 38/62 (61%), Gaps = 6/62 (9%)
Query: 52 IRPLFEKYGKVVECDVV------KNYGFVHMENDEEGRTAIKELNGQIVNEKPLKIEAAT 105
+R +F ++GK+++ +++ K +GFV EN + A ++L+G +V + +++ AT
Sbjct: 46 LRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT 105
Query: 106 SR 107
+R
Sbjct: 106 AR 107
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 43.5 bits (101), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 44/77 (57%), Gaps = 2/77 (2%)
Query: 113 PTTKVFVGNLS-DNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSP-DINKCIKELNGM 170
P +++F+GNL N ++ +F PYG +++ +I +GF+ D+P + I+ +
Sbjct: 9 PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECESQE 68
Query: 171 MVDGKPMKVQISTSRVR 187
M GK + +++S+S R
Sbjct: 69 MNFGKKLILEVSSSNAR 85
Score = 35.0 bits (79), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 37 KIFIGNVN-PGTSVELIRPLFEKYGKVVECDVVKNYGFVHMENDEEGRTAIKELNGQIVN 95
++FIGN+ S E + +F YG +++ ++ +GF+ +N + R AI+ + ++
Sbjct: 12 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECESQEMNF 71
Query: 96 EKPLKIEAATSRKGP 110
K L +E ++S P
Sbjct: 72 GKKLILEVSSSNARP 86
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 43.5 bits (101), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 41/81 (50%), Gaps = 11/81 (13%)
Query: 32 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVK-----------NYGFVHMENDE 80
S G+ +FI N+N T+ E ++ +F K G + C + K +GFV + E
Sbjct: 2 SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPE 61
Query: 81 EGRTAIKELNGQIVNEKPLKI 101
+ + A+K+L G V+ L++
Sbjct: 62 QAQKALKQLQGHTVDGHKLEV 82
Score = 40.0 bits (92), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 42/84 (50%), Gaps = 12/84 (14%)
Query: 111 NTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVR-----------NYGFVHIDSPD 159
++ ++ +F+ NL+ +T ++ +F G + C I + +GFV P+
Sbjct: 2 SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPE 61
Query: 160 -INKCIKELNGMMVDGKPMKVQIS 182
K +K+L G VDG ++V+IS
Sbjct: 62 QAQKALKQLQGHTVDGHKLEVRIS 85
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 39/69 (56%), Gaps = 2/69 (2%)
Query: 38 IFIGNVNPGTSVELIRPLFE--KYGKVVECDVVKNYGFVHMENDEEGRTAIKELNGQIVN 95
+++ N+ TS E+I F K G V +++Y FVH N E+ A+K LNG++++
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLD 77
Query: 96 EKPLKIEAA 104
P+++ A
Sbjct: 78 GSPIEVTLA 86
Score = 35.8 bits (81), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 38/69 (55%), Gaps = 3/69 (4%)
Query: 117 VFVGNLSDNTRAPEVRELF--VPYGTVVECDIVRNYGFVHIDS-PDINKCIKELNGMMVD 173
++V NL +T + + F + G V +R+Y FVH + D + +K LNG ++D
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLD 77
Query: 174 GKPMKVQIS 182
G P++V ++
Sbjct: 78 GSPIEVTLA 86
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 43/75 (57%), Gaps = 2/75 (2%)
Query: 115 TKVFVGNLS-DNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSP-DINKCIKELNGMMV 172
+++F+GNL N ++ +F PYG +++ +I +GF+ D+P + I+ + M
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIEXESQEMN 82
Query: 173 DGKPMKVQISTSRVR 187
GK + +++S+S R
Sbjct: 83 FGKKLILEVSSSNAR 97
Score = 34.7 bits (78), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 37 KIFIGNVN-PGTSVELIRPLFEKYGKVVECDVVKNYGFVHMENDEEGRTAIKELNGQIVN 95
++FIGN+ S E + +F YG +++ ++ +GF+ +N + R AI+ + ++
Sbjct: 24 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIEXESQEMNF 83
Query: 96 EKPLKIEAATS 106
K L +E ++S
Sbjct: 84 GKKLILEVSSS 94
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 38/166 (22%), Positives = 73/166 (43%), Gaps = 24/166 (14%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKV-------------VECDVVKNYGFVHMENDEEGR 83
++++GN+ G + E + F ++ V+ + KN+ F+ + +E
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 84 TAIKELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVE 143
A+ +G I + LKI + P K+F+G L + +V+EL +G +
Sbjct: 66 QAMA-FDGIIFQGQSLKIRRPHDYQ-PLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKA 123
Query: 144 CDIVRNY------GFVHIDSPDIN---KCIKELNGMMVDGKPMKVQ 180
++V++ G+ + DIN + I LNGM + K + VQ
Sbjct: 124 FNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQ 169
>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 = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 38/166 (22%), Positives = 73/166 (43%), Gaps = 24/166 (14%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKV-------------VECDVVKNYGFVHMENDEEGR 83
++++GN+ G + E + F ++ V+ + KN+ F+ + +E
Sbjct: 8 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67
Query: 84 TAIKELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVE 143
A+ +G I + LKI + P K+F+G L + +V+EL +G +
Sbjct: 68 QAMA-FDGIIFQGQSLKIRRPHDYQ-PLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKA 125
Query: 144 CDIVRNY------GFVHIDSPDIN---KCIKELNGMMVDGKPMKVQ 180
++V++ G+ + DIN + I LNGM + K + VQ
Sbjct: 126 FNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQ 171
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 42/77 (54%), Gaps = 8/77 (10%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-----RNYGF--VHID-SPDINKCIKEL 167
K+ V NL +++ELF +GT+ + + R+ G VH + D K +K+
Sbjct: 30 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 89
Query: 168 NGMMVDGKPMKVQISTS 184
NG+ +DG+PM +Q+ TS
Sbjct: 90 NGVPLDGRPMNIQLVTS 106
Score = 33.5 bits (75), Expect = 0.091, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 38/77 (49%), Gaps = 7/77 (9%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-------YGFVHMENDEEGRTAIKEL 89
K+ + N++ G S I+ LF ++G + + V + VH E + A+K+
Sbjct: 30 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 89
Query: 90 NGQIVNEKPLKIEAATS 106
NG ++ +P+ I+ TS
Sbjct: 90 NGVPLDGRPMNIQLVTS 106
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 4/76 (5%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN---YGFVHIDSP-DINKCIKELNGMM 171
KV+VGNL +N E+ F YG + + RN + FV + P D ++EL+G
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRT 134
Query: 172 VDGKPMKVQISTSRVR 187
+ G ++V++S R
Sbjct: 135 LCGCRVRVELSNGEKR 150
>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 = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/98 (24%), Positives = 49/98 (50%), Gaps = 11/98 (11%)
Query: 103 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVV--------ECDIVRNYGFVH 154
A + ++GP +F+ +L ++ ++F+P+G VV + ++ + +GFV
Sbjct: 16 AGSQKEGPEG--ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVS 73
Query: 155 IDSP-DINKCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
D+P I+ +NG + K +KVQ+ S+ + G
Sbjct: 74 YDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSKSG 111
Score = 30.0 bits (66), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 12/70 (17%)
Query: 55 LFEKYGKVVECDVV--------KNYGFVHMENDEEGRTAIKELNGQIVNEKPLKIEAA-- 104
+F +G VV V K +GFV +N + AI+ +NG + K LK++
Sbjct: 45 MFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRS 104
Query: 105 --TSRKGPNT 112
S+ GP++
Sbjct: 105 KNDSKSGPSS 114
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 43/75 (57%), Gaps = 2/75 (2%)
Query: 115 TKVFVGNLS-DNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSP-DINKCIKELNGMMV 172
+++F+GNL N ++ +F PYG +++ +I +GF+ D+P + I+ + M
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECESQEMN 82
Query: 173 DGKPMKVQISTSRVR 187
GK + +++S+S R
Sbjct: 83 FGKKLILEVSSSNAR 97
Score = 33.5 bits (75), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 37 KIFIGNVN-PGTSVELIRPLFEKYGKVVECDVVKNYGFVHMENDEEGRTAIKELNGQIVN 95
++FIGN+ S E + +F YG +++ ++ +GF+ +N + R AI+ + ++
Sbjct: 24 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECESQEMNF 83
Query: 96 EKPLKIEAATS 106
K L +E ++S
Sbjct: 84 GKKLILEVSSS 94
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 41/82 (50%), Gaps = 9/82 (10%)
Query: 32 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV---------KNYGFVHMENDEEG 82
S G+ IFIGN++P +L+ F +G +++ + K Y F++ + +
Sbjct: 2 SSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDAS 61
Query: 83 RTAIKELNGQIVNEKPLKIEAA 104
AI+ +NGQ + +P+ + A
Sbjct: 62 DAAIEAMNGQYLCNRPITVSYA 83
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 40.8 bits (94), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 42/79 (53%), Gaps = 8/79 (10%)
Query: 38 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGRTAIKEL 89
+F+GN+ + E ++ +F + G VV +V K YGF ++ E +A++ L
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 90 NGQIVNEKPLKIEAATSRK 108
NG+ + + L+++ A S K
Sbjct: 71 NGREFSGRALRVDNAASEK 89
Score = 30.0 bits (66), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 9/77 (11%)
Query: 117 VFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFV-HIDSPDINKCIKEL 167
VFVGN+ +++++F G VV +V + YGF + D ++ L
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 168 NGMMVDGKPMKVQISTS 184
NG G+ ++V + S
Sbjct: 71 NGREFSGRALRVDNAAS 87
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 40.0 bits (92), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 4/77 (5%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN---YGFVHIDSP-DINKCIKELNGMM 171
KV+VGNL E+ F YG + I RN + FV + P D ++ L+G +
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKV 61
Query: 172 VDGKPMKVQISTSRVRQ 188
+ G ++V++ST R+
Sbjct: 62 ICGSRVRVELSTGMPRR 78
Score = 35.8 bits (81), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 16/73 (21%), Positives = 37/73 (50%), Gaps = 3/73 (4%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN---YGFVHMENDEEGRTAIKELNGQI 93
K+++GN+ G + F YG + + +N + FV E+ + A++ L+G++
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKV 61
Query: 94 VNEKPLKIEAATS 106
+ +++E +T
Sbjct: 62 ICGSRVRVELSTG 74
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 40.0 bits (92), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 29/89 (32%), Positives = 46/89 (51%), Gaps = 10/89 (11%)
Query: 106 SRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDS 157
SR P+ P + V LS T ++RE+F YG + + IV R + FV+ ++
Sbjct: 5 SRANPD-PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 63
Query: 158 PDINKCIKE-LNGMMVDGKPMKVQISTSR 185
D K KE NGM +DG+ ++V S ++
Sbjct: 64 VDDAKEAKERANGMELDGRRIRVDFSITK 92
Score = 32.7 bits (73), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 16/74 (21%), Positives = 41/74 (55%), Gaps = 9/74 (12%)
Query: 47 TSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGRTAIKELNGQIVNEKP 98
T+ +R +F KYG + + +V + + FV+ EN ++ + A + NG ++ +
Sbjct: 24 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR 83
Query: 99 LKIEAATSRKGPNT 112
++++ + +++ P+T
Sbjct: 84 IRVDFSITKR-PHT 96
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 40.0 bits (92), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 4/76 (5%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN---YGFVHIDSP-DINKCIKELNGMM 171
KV+VGNL +N E+ F YG + + RN + FV + P D +++L+G
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRDLDGRT 134
Query: 172 VDGKPMKVQISTSRVR 187
+ G ++V++S R
Sbjct: 135 LCGCRVRVELSNGEKR 150
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 28/92 (30%), Positives = 48/92 (52%), Gaps = 10/92 (10%)
Query: 103 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVH 154
++ +R P+ P + V LS T ++RE+F YG + + IV R + FV+
Sbjct: 5 SSGNRANPD-PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVY 63
Query: 155 IDSPDINKCIKE-LNGMMVDGKPMKVQISTSR 185
++ D K KE NGM +DG+ ++V S ++
Sbjct: 64 FENVDDAKEAKERANGMELDGRRIRVDFSITK 95
Score = 32.7 bits (73), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 16/74 (21%), Positives = 41/74 (55%), Gaps = 9/74 (12%)
Query: 47 TSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGRTAIKELNGQIVNEKP 98
T+ +R +F KYG + + +V + + FV+ EN ++ + A + NG ++ +
Sbjct: 27 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR 86
Query: 99 LKIEAATSRKGPNT 112
++++ + +++ P+T
Sbjct: 87 IRVDFSITKR-PHT 99
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 41/80 (51%), Gaps = 8/80 (10%)
Query: 115 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSPDIN--------KCIKE 166
K+ V NL +++ELF +GT+ + + + + + D++ K +K+
Sbjct: 36 AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQ 95
Query: 167 LNGMMVDGKPMKVQISTSRV 186
G+ +DG+PM +Q+ S++
Sbjct: 96 YKGVPLDGRPMDIQLVASQI 115
Score = 29.3 bits (64), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 21/101 (20%), Positives = 47/101 (46%), Gaps = 9/101 (8%)
Query: 14 RYSNNQINISCRNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDV-----V 68
++ ++ + C G + K+ + N++ G S I+ LF ++G + + V
Sbjct: 16 KWQHDLFDSGCGGGEGVET--GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSG 73
Query: 69 KNYGF--VHMENDEEGRTAIKELNGQIVNEKPLKIEAATSR 107
++ G VH E + A+K+ G ++ +P+ I+ S+
Sbjct: 74 RSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQ 114
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 41/80 (51%), Gaps = 8/80 (10%)
Query: 115 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSPDIN--------KCIKE 166
K+ V NL +++ELF +GT+ + + + + + D++ K +K+
Sbjct: 36 AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQ 95
Query: 167 LNGMMVDGKPMKVQISTSRV 186
G+ +DG+PM +Q+ S++
Sbjct: 96 YKGVPLDGRPMDIQLVASQI 115
Score = 29.3 bits (64), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 21/101 (20%), Positives = 47/101 (46%), Gaps = 9/101 (8%)
Query: 14 RYSNNQINISCRNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDV-----V 68
++ ++ + C G + K+ + N++ G S I+ LF ++G + + V
Sbjct: 16 KWQHDLFDSGCGGGEGVET--GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSG 73
Query: 69 KNYGF--VHMENDEEGRTAIKELNGQIVNEKPLKIEAATSR 107
++ G VH E + A+K+ G ++ +P+ I+ S+
Sbjct: 74 RSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQ 114
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 43/80 (53%), Gaps = 4/80 (5%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSPDIN---KCIKELNGMM- 171
K+++GNLS A ++R+LF + ++ G+ +D PD N + I+ L+G +
Sbjct: 10 KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVE 69
Query: 172 VDGKPMKVQISTSRVRQRPG 191
+ GK M+V S S+ + G
Sbjct: 70 LHGKIMEVDYSVSKKLRSSG 89
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 32/62 (51%), Gaps = 7/62 (11%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------KNYGFVHMENDEEGRTAIKEL 89
K+F+G +N S + +R LFE +G + EC ++ K FV + E + AI L
Sbjct: 17 KLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINAL 76
Query: 90 NG 91
+G
Sbjct: 77 HG 78
Score = 32.7 bits (73), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 20/33 (60%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVR 148
K+FVG L+ +VR LF +G + EC I+R
Sbjct: 17 KLFVGMLNKQQSEDDVRRLFEAFGNIEECTILR 49
>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 = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/103 (20%), Positives = 53/103 (51%), Gaps = 9/103 (8%)
Query: 103 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVH 154
+A R+G ++V+VG++ +R+ F P+G + D+ + + FV
Sbjct: 17 SAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVE 76
Query: 155 IDSPDINK-CIKELNGMMVDGKPMKVQISTSRVRQRPGVDEVV 196
+ P+ + ++++N +M+ G+ +KV ++ + +P +D++
Sbjct: 77 YEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLA 119
Score = 33.1 bits (74), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 15/62 (24%), Positives = 31/62 (50%), Gaps = 8/62 (12%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGRTAIKE 88
+I++ +V+ S + I+ +FE +GK+ + K YGF+ E + + A+
Sbjct: 127 RIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 186
Query: 89 LN 90
+N
Sbjct: 187 MN 188
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 9/74 (12%)
Query: 117 VFVGNLSDNTRAPEVRELFVPYGTVV--------ECDIVRNYGFVHIDSPDINK-CIKEL 167
+F+ +L ++ F+P+G V+ + + + +GFV D+PD + IK +
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 168 NGMMVDGKPMKVQI 181
NG V K +KVQ+
Sbjct: 103 NGFQVGTKRLKVQL 116
Score = 32.3 bits (72), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 8/55 (14%)
Query: 56 FEKYGKVVECDVV--------KNYGFVHMENDEEGRTAIKELNGQIVNEKPLKIE 102
F +G V+ V K +GFV +N + + AIK +NG V K LK++
Sbjct: 61 FLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQ 115
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 10/71 (14%)
Query: 115 TKVFVGNLSDNTRAPEVRELFVPYGTVVECD---------IVRNYGFVHIDSPD-INKCI 164
TKV +G L+ N + E+F YG + D + + Y +V ++PD K +
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
Query: 165 KELNGMMVDGK 175
K ++G +DG+
Sbjct: 65 KHMDGGQIDGQ 75
Score = 34.3 bits (77), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 32/69 (46%), Gaps = 9/69 (13%)
Query: 32 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECD---------VVKNYGFVHMENDEEG 82
S+ K+ IG + + + I +F YGK+ D + K Y +V EN +E
Sbjct: 1 SMKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEA 60
Query: 83 RTAIKELNG 91
A+K ++G
Sbjct: 61 EKALKHMDG 69
>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 = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 41/80 (51%), Gaps = 8/80 (10%)
Query: 36 FKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIK 87
F +F+G+++P + I F +G++ + VVK+ YGFV N + AI+
Sbjct: 7 FHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 66
Query: 88 ELNGQIVNEKPLKIEAATSR 107
++ GQ + + ++ AT +
Sbjct: 67 QMGGQWLGGRQIRTNWATRK 86
Score = 33.9 bits (76), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 21/86 (24%), Positives = 39/86 (45%), Gaps = 9/86 (10%)
Query: 109 GPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFV-HIDSPD 159
GP VFVG+LS + F P+G + + +V++ YGFV + D
Sbjct: 1 GPLGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWD 60
Query: 160 INKCIKELNGMMVDGKPMKVQISTSR 185
I+++ G + G+ ++ +T +
Sbjct: 61 AENAIQQMGGQWLGGRQIRTNWATRK 86
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 41/80 (51%), Gaps = 8/80 (10%)
Query: 115 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSPDIN--------KCIKE 166
K+ V NL +++ELF +GT+ + + + + + D++ K +K+
Sbjct: 89 AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQ 148
Query: 167 LNGMMVDGKPMKVQISTSRV 186
G+ +DG+PM +Q+ S++
Sbjct: 149 YKGVPLDGRPMDIQLVASQI 168
Score = 28.9 bits (63), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 21/101 (20%), Positives = 47/101 (46%), Gaps = 9/101 (8%)
Query: 14 RYSNNQINISCRNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDV-----V 68
++ ++ + C G + K+ + N++ G S I+ LF ++G + + V
Sbjct: 69 KWQHDLFDSGCGGGEGVET--GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSG 126
Query: 69 KNYGF--VHMENDEEGRTAIKELNGQIVNEKPLKIEAATSR 107
++ G VH E + A+K+ G ++ +P+ I+ S+
Sbjct: 127 RSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQ 167
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 31/55 (56%)
Query: 38 IFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYGFVHMENDEEGRTAIKELNGQ 92
+F+ N+ + E++ F ++GK+ +K+Y FVH E+ A+ E+NG+
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKDYAFVHFEDRGAAVKAMDEMNGK 72
Score = 28.5 bits (62), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 1/54 (1%)
Query: 117 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHI-DSPDINKCIKELNG 169
+FV NL+ + + F +G + +++Y FVH D K + E+NG
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKDYAFVHFEDRGAAVKAMDEMNG 71
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 42/82 (51%), Gaps = 9/82 (10%)
Query: 113 PTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPDINKCI 164
P + V LS T ++RE+F YG + + IV R + FV+ ++ D K
Sbjct: 45 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 104
Query: 165 KE-LNGMMVDGKPMKVQISTSR 185
KE NGM +DG+ ++V S ++
Sbjct: 105 KERANGMELDGRRIRVDFSITK 126
Score = 32.7 bits (73), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 23/112 (20%), Positives = 55/112 (49%), Gaps = 22/112 (19%)
Query: 7 QQLVKVSRYSNNQINI--SCRNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVE 64
QQ+ + SR+ N+ N +C +G F + + T+ +R +F KYG + +
Sbjct: 28 QQMGRGSRHVGNRANPDPNC-------CLGVFGLSLY-----TTERDLREVFSKYGPIAD 75
Query: 65 CDVV--------KNYGFVHMENDEEGRTAIKELNGQIVNEKPLKIEAATSRK 108
+V + + FV+ EN ++ + A + NG ++ + ++++ + +++
Sbjct: 76 VSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKR 127
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 41/74 (55%), Gaps = 12/74 (16%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIKE 88
K+F+G ++ T+ E +R F +YG+VV+C ++K+ +GFV ++ T +
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 89 ----LNGQIVNEKP 98
L+G+ ++ KP
Sbjct: 78 RPHTLDGRNIDPKP 91
Score = 37.4 bits (85), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 37/84 (44%), Gaps = 8/84 (9%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPDINKCIKEL 167
K+FVG L +T +R F YG VV+C I+ R +GFV P+ +
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 168 NGMMVDGKPMKVQISTSRVRQRPG 191
+DG+ + + T R Q G
Sbjct: 78 RPHTLDGRNIDPKPCTPRGMQPSG 101
>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex
Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A
Resolution
Length = 107
Score = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 8/77 (10%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-----RNYGF--VHID-SPDINKCIKEL 167
K+ V NL +++ELF +GT+ + + R+ G VH + D K K+
Sbjct: 31 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQY 90
Query: 168 NGMMVDGKPMKVQISTS 184
NG+ +DG+P +Q+ TS
Sbjct: 91 NGVPLDGRPXNIQLVTS 107
Score = 30.8 bits (68), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 7/77 (9%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-------YGFVHMENDEEGRTAIKEL 89
K+ + N++ G S I+ LF ++G + + V + VH E + A K+
Sbjct: 31 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQY 90
Query: 90 NGQIVNEKPLKIEAATS 106
NG ++ +P I+ TS
Sbjct: 91 NGVPLDGRPXNIQLVTS 107
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 8/76 (10%)
Query: 117 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-------YGFVHIDSPD-INKCIKELN 168
VFVGNL R + ELF+ G + + I ++ +GFV P+ ++ I LN
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLN 78
Query: 169 GMMVDGKPMKVQISTS 184
G+ + G+P+ V +S
Sbjct: 79 GIRLYGRPINVSGPSS 94
Score = 32.0 bits (71), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 37/76 (48%), Gaps = 7/76 (9%)
Query: 38 IFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-------YGFVHMENDEEGRTAIKELN 90
+F+GN+ E++ LF + G + + + K+ +GFV ++ E AI LN
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLN 78
Query: 91 GQIVNEKPLKIEAATS 106
G + +P+ + +S
Sbjct: 79 GIRLYGRPINVSGPSS 94
>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 = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 18/87 (20%), Positives = 45/87 (51%), Gaps = 8/87 (9%)
Query: 34 GTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTA 85
G + + N+ TS + +R +FEKYG+V + + ++ + FV + + A
Sbjct: 46 GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDA 105
Query: 86 IKELNGQIVNEKPLKIEAATSRKGPNT 112
+ ++G +++ + L+++ A + P++
Sbjct: 106 MDAMDGAVLDGRELRVQMARYGRPPDS 132
Score = 33.5 bits (75), Expect = 0.095, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 38/77 (49%), Gaps = 9/77 (11%)
Query: 115 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHI-DSPDINKCIK 165
T + V NL+ T +R +F YG V + I R+ + FV D D +
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 166 ELNGMMVDGKPMKVQIS 182
++G ++DG+ ++VQ++
Sbjct: 108 AMDGAVLDGRELRVQMA 124
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 37.7 bits (86), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 14/55 (25%), Positives = 32/55 (58%)
Query: 38 IFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYGFVHMENDEEGRTAIKELNGQ 92
+F+ N+ + E++ F ++GK+ +K+Y F+H + + A++E+NG+
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKDYAFIHFDERDGAVKAMEEMNGK 68
Score = 36.2 bits (82), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 16/64 (25%), Positives = 36/64 (56%), Gaps = 1/64 (1%)
Query: 117 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSPD-INKCIKELNGMMVDGK 175
+FV NL++ + + F +G + +++Y F+H D D K ++E+NG ++G+
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKDYAFIHFDERDGAVKAMEEMNGKDLEGE 73
Query: 176 PMKV 179
+++
Sbjct: 74 NIEI 77
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 37.4 bits (85), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 37/69 (53%), Gaps = 1/69 (1%)
Query: 115 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSPD-INKCIKELNGMMVD 173
T++FV + + E+ E+F P+G + E I+ + FV + + K I+E++G
Sbjct: 5 TRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNGFAFVEFEEAESAAKAIEEVHGKSFA 64
Query: 174 GKPMKVQIS 182
+P++V S
Sbjct: 65 NQPLEVVYS 73
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 37.4 bits (85), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 37/69 (53%), Gaps = 1/69 (1%)
Query: 115 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSPD-INKCIKELNGMMVD 173
T++FV + + E+ E+F P+G + E I+ + FV + + K I+E++G
Sbjct: 32 TRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNGFAFVEFEEAESAAKAIEEVHGKSFA 91
Query: 174 GKPMKVQIS 182
+P++V S
Sbjct: 92 NQPLEVVYS 100
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 37.4 bits (85), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 31/63 (49%), Gaps = 8/63 (12%)
Query: 52 IRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGRTAIKELNGQIVNEKPLKIEA 103
+R LFE+YG + +V + YGFV ++ + AI LNG + K LK+
Sbjct: 59 LRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL 118
Query: 104 ATS 106
A S
Sbjct: 119 AAS 121
>pdb|2ADC|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd34 Complexed With Cucucu Rna
pdb|2EVZ|A Chain A, Structure Of Rna Binding Domains 3 And 4 Of Polypyrimidine
Tract Binding Protein
Length = 229
Score = 37.0 bits (84), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 39/83 (46%), Gaps = 12/83 (14%)
Query: 27 MPGFSSVGTFKIFIGNVNPGTSVELIRP-----LFEKYGKVVECDVV---KNYGFVHMEN 78
+PG + G + + N+NP E + P LF YG V ++ K V M +
Sbjct: 26 IPGLAGAGNSVLLVSNLNP----ERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMAD 81
Query: 79 DEEGRTAIKELNGQIVNEKPLKI 101
+ + A+ LNG ++ KP++I
Sbjct: 82 GNQAQLAMSHLNGHKLHGKPIRI 104
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 37.0 bits (84), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 28/91 (30%), Positives = 47/91 (51%), Gaps = 10/91 (10%)
Query: 103 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVH 154
++ +R P+ P + V LS T ++RE+F YG + + IV R + FV+
Sbjct: 5 SSGNRANPD-PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVY 63
Query: 155 IDSPDINKCIKE-LNGMMVDGKPMKVQISTS 184
++ D K KE NGM +DG+ ++V +S
Sbjct: 64 FENVDDAKEAKERANGMELDGRRIRVSGPSS 94
Score = 32.3 bits (72), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 15/68 (22%), Positives = 35/68 (51%), Gaps = 8/68 (11%)
Query: 47 TSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGRTAIKELNGQIVNEKP 98
T+ +R +F KYG + + +V + + FV+ EN ++ + A + NG ++ +
Sbjct: 27 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR 86
Query: 99 LKIEAATS 106
+++ +S
Sbjct: 87 IRVSGPSS 94
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 37.0 bits (84), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 29/138 (21%), Positives = 57/138 (41%), Gaps = 24/138 (17%)
Query: 52 IRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIKELNGQIVNEKPLKIEA 103
+R LF G+V ++++ YGFV+ ++ AI LNG + K +K+
Sbjct: 19 LRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSY 78
Query: 104 ATSRKGPNTPTTK---VFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGF 152
A P++ K +++ L +V ++F +G ++ ++ R F
Sbjct: 79 AR----PSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAF 134
Query: 153 VHIDS-PDINKCIKELNG 169
+ D + + I NG
Sbjct: 135 IRFDKRSEAEEAITSFNG 152
>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 = 37.0 bits (84), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 29/138 (21%), Positives = 57/138 (41%), Gaps = 24/138 (17%)
Query: 52 IRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIKELNGQIVNEKPLKIEA 103
+R LF G+V ++++ YGFV+ ++ AI LNG + K +K+
Sbjct: 19 LRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSY 78
Query: 104 ATSRKGPNTPTTK---VFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGF 152
A P++ K +++ L +V ++F +G ++ ++ R F
Sbjct: 79 AR----PSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAF 134
Query: 153 VHIDS-PDINKCIKELNG 169
+ D + + I NG
Sbjct: 135 IRFDKRSEAEEAITSFNG 152
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 36.6 bits (83), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 18/87 (20%), Positives = 45/87 (51%), Gaps = 8/87 (9%)
Query: 34 GTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTA 85
G + + N+ TS + +R +FEKYG+V + + ++ + FV + + A
Sbjct: 69 GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDA 128
Query: 86 IKELNGQIVNEKPLKIEAATSRKGPNT 112
+ ++G +++ + L+++ A + P++
Sbjct: 129 MDAMDGAVLDGRELRVQMARYGRPPDS 155
Score = 33.9 bits (76), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 38/77 (49%), Gaps = 9/77 (11%)
Query: 115 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHI-DSPDINKCIK 165
T + V NL+ T +R +F YG V + I R+ + FV D D +
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 166 ELNGMMVDGKPMKVQIS 182
++G ++DG+ ++VQ++
Sbjct: 131 AMDGAVLDGRELRVQMA 147
>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 = 36.6 bits (83), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 22/88 (25%), Positives = 43/88 (48%), Gaps = 9/88 (10%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGRTAIKE 88
+I++ +V+ S + I+ +FE +GK+ C + K YGF+ E + + A+
Sbjct: 112 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 171
Query: 89 LNGQIVNEKPLKIEAATSRKGP-NTPTT 115
+N + + L++ A + P TP T
Sbjct: 172 MNLFDLGGQYLRVGKAVTPPMPLLTPAT 199
Score = 33.9 bits (76), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 18/90 (20%), Positives = 47/90 (52%), Gaps = 9/90 (10%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPDINK-CIKE 166
+V+VG++ +R+ F P+G + D+ + + FV + P+ + +++
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 167 LNGMMVDGKPMKVQISTSRVRQRPGVDEVV 196
+N +M+ G+ +KV ++ + +P +D++
Sbjct: 75 MNSVMLGGRNIKVGRPSNIGQAQPIIDQLA 104
>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 = 36.2 bits (82), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 13/71 (18%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTVVECDI--------VRNYGFVHI-DSPDINKCIKE 166
K FVG LS +T ++++ F +G VV+C I R +GF+ D+ + K + +
Sbjct: 13 KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQ 72
Query: 167 ----LNGMMVD 173
L+G ++D
Sbjct: 73 KEHRLDGRVID 83
Score = 29.6 bits (65), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 13/50 (26%), Positives = 28/50 (56%), Gaps = 8/50 (16%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDV--------VKNYGFVHMEN 78
K F+G ++ TS + ++ F K+G+VV+C + + +GF+ ++
Sbjct: 13 KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKD 62
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 36.2 bits (82), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 42/84 (50%), Gaps = 9/84 (10%)
Query: 117 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVH-IDSPDINKCIKEL 167
V+VG L + P + ELF+ G VV + ++ YGFV + D + IK +
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 168 NGMMVDGKPMKVQISTSRVRQRPG 191
+ + + GKP++V +++ + G
Sbjct: 78 DMIKLYGKPIRVNKASAHNKNLSG 101
Score = 32.7 bits (73), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 40/78 (51%), Gaps = 8/78 (10%)
Query: 38 IFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIKEL 89
+++G ++ S L+ LF + G VV + K+ YGFV ++E+ AIK +
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 90 NGQIVNEKPLKIEAATSR 107
+ + KP+++ A++
Sbjct: 78 DMIKLYGKPIRVNKASAH 95
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 36.2 bits (82), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 22/34 (64%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN 149
K+FVG L +VR++F P+GT+ EC ++R
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRG 47
Score = 34.7 bits (78), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 7/61 (11%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------KNYGFVHMENDEEGRTAIKEL 89
K+F+G + + E +R +FE +G + EC V+ K FV + E + AI L
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTL 73
Query: 90 N 90
+
Sbjct: 74 H 74
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 35.8 bits (81), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 2/65 (3%)
Query: 38 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFVHMENDEEGRTAIKELNGQIVN 95
++ G + G + +L+R F +G+++E V K Y FV E AI +NG +
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIE 87
Query: 96 EKPLK 100
+K
Sbjct: 88 GHVVK 92
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 35.8 bits (81), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 9/78 (11%)
Query: 36 FKIFIGNVNPGTSVELIRPLFEKY------GKVV--ECDVVKNYGFVHMENDEEGRTAIK 87
+ +F+G++ P ++ F K GKVV + V K YGFV ++ E + A+
Sbjct: 10 YSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALT 69
Query: 88 ELNGQI-VNEKPLKIEAA 104
E G + + KP+++ A
Sbjct: 70 ECQGAVGLGSKPVRLSVA 87
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 35.8 bits (81), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 7/62 (11%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------KNYGFVHMENDEEGRTAIKEL 89
K+F+G +N S E + LF+ +G + EC V+ K FV + E + AI L
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHAL 76
Query: 90 NG 91
+G
Sbjct: 77 HG 78
Score = 32.0 bits (71), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN 149
K+FVG L+ +V LF P+G + EC ++R
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRG 50
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 35.8 bits (81), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 37/71 (52%), Gaps = 8/71 (11%)
Query: 117 VFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPDINKCIKELN 168
++VGNL + + +V+ELF +G V ++ + +GFV + +++ I +L+
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAKLD 63
Query: 169 GMMVDGKPMKV 179
G+ ++V
Sbjct: 64 NTDFMGRTIRV 74
Score = 32.3 bits (72), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 40/79 (50%), Gaps = 9/79 (11%)
Query: 38 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGRTAIKEL 89
I++GN+ + E ++ LF ++GKV ++ K +GFV M+ +E AI +L
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAKL 62
Query: 90 NGQIVNEKPLKIEAATSRK 108
+ + +++ A +K
Sbjct: 63 DNTDFMGRTIRVTEANPKK 81
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 35.4 bits (80), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 42/78 (53%), Gaps = 11/78 (14%)
Query: 113 PTTK--VFVGNLSDNTRAPEVR----ELFVPYGTV---VECDIVRNYGFVHIDSP-DINK 162
PTT +FVGNL+ N APE++ ++F V + R +G+V +S D+ K
Sbjct: 4 PTTAFNLFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRIGMTRKFGYVDFESAEDLEK 63
Query: 163 CIKELNGMMVDGKPMKVQ 180
+ EL G+ V G +K++
Sbjct: 64 AL-ELTGLKVFGNEIKLE 80
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 35.4 bits (80), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 37/83 (44%), Gaps = 8/83 (9%)
Query: 32 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGR 83
S G+ ++I + PGT+ + + L + YGK+V + K YGFV ++ +
Sbjct: 2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQ 61
Query: 84 TAIKELNGQIVNEKPLKIEAATS 106
A+ L V + K +S
Sbjct: 62 KAVTALKASGVQAQMAKQSGPSS 84
Score = 28.5 bits (62), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 14/56 (25%), Positives = 27/56 (48%), Gaps = 8/56 (14%)
Query: 111 NTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSP 158
++ ++ +++ L T ++ +L PYG +V + + YGFV DSP
Sbjct: 2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSP 57
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 35.4 bits (80), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 6/75 (8%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYG-----FVHIDSP-DINKCIKELNG 169
+++VGNL + R ++ ++F YG + + D+ G FV + P D + +G
Sbjct: 24 RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDG 83
Query: 170 MMVDGKPMKVQISTS 184
DG ++V+ S
Sbjct: 84 YDYDGYRLRVEFPRS 98
Score = 34.7 bits (78), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 5/78 (6%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYG-----FVHMENDEEGRTAIKELNG 91
+I++GN+ P + I +F KYG + + D+ G FV E+ + A+ +G
Sbjct: 24 RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDG 83
Query: 92 QIVNEKPLKIEAATSRKG 109
+ L++E S +G
Sbjct: 84 YDYDGYRLRVEFPRSGRG 101
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 35.0 bits (79), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 13/73 (17%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFV-HIDSPDINKCI-- 164
K+F+G LS T +RE F +G V EC ++R+ +GFV +D ++K +
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 86
Query: 165 --KELNGMMVDGK 175
EL+ +D K
Sbjct: 87 SRHELDSKTIDPK 99
Score = 32.0 bits (71), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 28/46 (60%), Gaps = 8/46 (17%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 74
K+FIG ++ T+ E +R F ++G+V EC V+++ +GFV
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFV 72
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 35.0 bits (79), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 13/73 (17%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFV-HIDSPDINKCI-- 164
K+F+G LS T +RE F +G V EC ++R+ +GFV +D ++K +
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 165 --KELNGMMVDGK 175
EL+ +D K
Sbjct: 62 SRHELDSKTIDPK 74
Score = 32.0 bits (71), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 28/46 (60%), Gaps = 8/46 (17%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 74
K+FIG ++ T+ E +R F ++G+V EC V+++ +GFV
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFV 47
>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 2.50 A Resolution
Length = 200
Score = 35.0 bits (79), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 22/88 (25%), Positives = 42/88 (47%), Gaps = 9/88 (10%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGRTAIKE 88
+I++ +V+ S + I+ +FE +GK+ C + K YGF+ E + + A+
Sbjct: 111 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 170
Query: 89 LNGQIVNEKPLKIEAATSRKGP-NTPTT 115
N + + L++ A + P TP T
Sbjct: 171 XNLFDLGGQYLRVGKAVTPPXPLLTPAT 198
Score = 29.3 bits (64), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 17/90 (18%), Positives = 44/90 (48%), Gaps = 9/90 (10%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPDINK-CIKE 166
+V+VG++ +R+ F P+G + D + + FV + P+ + +++
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 167 LNGMMVDGKPMKVQISTSRVRQRPGVDEVV 196
N + + G+ +KV ++ + +P +D++
Sbjct: 74 XNSVXLGGRNIKVGRPSNIGQAQPIIDQLA 103
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 35.0 bits (79), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 15/80 (18%), Positives = 42/80 (52%), Gaps = 2/80 (2%)
Query: 35 TFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVK--NYGFVHMENDEEGRTAIKELNGQ 92
T ++++G + P TS+ + F+++G + D VK ++ ++ E+ + + A ++ G
Sbjct: 17 TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGF 76
Query: 93 IVNEKPLKIEAATSRKGPNT 112
+ ++ ++ GP++
Sbjct: 77 PLGGPDRRLRVDFAKSGPSS 96
Score = 32.3 bits (72), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 38/81 (46%), Gaps = 5/81 (6%)
Query: 109 GPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSPDIN----KCI 164
G PTT+++VG L NT + F +G++ D V+ F +I ++ C
Sbjct: 12 GKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACA 71
Query: 165 KELNGMMVDGKPMKVQISTSR 185
K + G + G ++++ ++
Sbjct: 72 K-MRGFPLGGPDRRLRVDFAK 91
>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
pdb|1HD1|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
Length = 75
Score = 34.7 bits (78), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 13/72 (18%)
Query: 117 VFVGNLSDNTRAPEVRELFVPYGTVVECDI--------VRNYGFVHI-DSPDINKCIKE- 166
+F+G LS +T ++++ F +G VV+C + R +GFV +S ++K + +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 167 ---LNGMMVDGK 175
LNG ++D K
Sbjct: 62 EHKLNGKVIDPK 73
Score = 32.0 bits (71), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 38/72 (52%), Gaps = 12/72 (16%)
Query: 38 IFIGNVNPGTSVELIRPLFEKYGKVVECDV--------VKNYGFVHMENDEEGRTAIKE- 88
+FIG ++ T+ + ++ F K+G+VV+C + + +GFV + E + +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 89 ---LNGQIVNEK 97
LNG++++ K
Sbjct: 62 EHKLNGKVIDPK 73
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 34.3 bits (77), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 24/36 (66%)
Query: 35 TFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN 70
K+F+G + G + ++PLFE++G++ E V+K+
Sbjct: 15 AIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKD 50
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 34.3 bits (77), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 10/81 (12%)
Query: 111 NTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHI-DSPDIN 161
+T TK+FVG L +T +R+ F +G + E ++ R YGFV + D
Sbjct: 14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAE 73
Query: 162 KCIKELNGMMVDGKPMKVQIS 182
+ K+ N ++DG+ V ++
Sbjct: 74 RACKDPN-PIIDGRKANVNLA 93
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 33.9 bits (76), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 31/88 (35%), Positives = 43/88 (48%), Gaps = 8/88 (9%)
Query: 29 GFSSVGTFKIFIGNVNPGTSV-ELIRPLFEKYGK----VVECDVVKN--YGFVHMENDEE 81
G S F +FIGN+NP SV EL + E + K VV+ N +G+V E+ E+
Sbjct: 11 GSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAED 70
Query: 82 GRTAIKELNGQIVNEKPLKIEAATSRKG 109
A+ EL G V +K+E R G
Sbjct: 71 LEKAL-ELTGLKVFGNEIKLEKPKGRDG 97
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 33.9 bits (76), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 40/73 (54%), Gaps = 12/73 (16%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAI-- 86
K+FIG ++ T+ E +R +E++GK+ +C V+++ +GFV + E A+
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 88
Query: 87 --KELNGQIVNEK 97
++G++V K
Sbjct: 89 RPHSIDGRVVEPK 101
Score = 29.6 bits (65), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 25/50 (50%), Gaps = 8/50 (16%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDS 157
K+F+G LS T +R + +G + +C ++R+ +GFV S
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSS 78
>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 = 33.9 bits (76), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 39/186 (20%), Positives = 75/186 (40%), Gaps = 44/186 (23%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKV-------------VECDVVKNYGFVHMENDEEGR 83
++++GN+ G + E + F ++ V+ + KN+ F+ + +E
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 84 TAIKELNGQIVNEKPLKIE--------------------AATSRKGPNTPTTKVFVGNLS 123
A+ +G I + LKI S P++ K+F+G L
Sbjct: 66 QAMA-FDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDS-AHKLFIGGLP 123
Query: 124 DNTRAPEVRELFVPYGTVVECDIVRNY------GFVHIDSPDIN---KCIKELNGMMVDG 174
+ +V+EL +G + ++V++ G+ + DIN + I LNGM +
Sbjct: 124 NYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGD 183
Query: 175 KPMKVQ 180
K + VQ
Sbjct: 184 KKLLVQ 189
>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Rna, Uuguucuu
Length = 102
Score = 33.9 bits (76), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 29/96 (30%), Positives = 44/96 (45%), Gaps = 21/96 (21%)
Query: 110 PNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-------RNYGFVHI-DSPDIN 161
PNT VFVG + E+R F YG+V E I+ + YGFV + D+
Sbjct: 9 PNT----VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQ 64
Query: 162 KCIKELNGMMVDGKPMKV-------QISTSRVRQRP 190
K ++ + + GK +K+ +ST V+ RP
Sbjct: 65 KIVE--SQINFHGKKLKLGPAIRKQNLSTYHVQPRP 98
Score = 30.8 bits (68), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 7/49 (14%)
Query: 38 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------KNYGFVHMEND 79
+F+G ++ IR F +YG V E ++ K YGFV ND
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYND 60
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 33.9 bits (76), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 26/90 (28%), Positives = 40/90 (44%), Gaps = 15/90 (16%)
Query: 115 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNY------GFVHID---SPDINKCIK 165
T + V L + E+ LF G + C I+R+Y G+ +D D + IK
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 166 ELNGMMVDGKPMKVQISTSRVRQRPGVDEV 195
LNG+ V K +KV + RPG + +
Sbjct: 64 VLNGITVRNKRLKVSYA------RPGGESI 87
Score = 31.6 bits (70), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 8/61 (13%)
Query: 52 IRPLFEKYGKVVECDVVKNY--------GFVHMENDEEGRTAIKELNGQIVNEKPLKIEA 103
+ LF G + C ++++Y FV ++ + + AIK LNG V K LK+
Sbjct: 20 LYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSY 79
Query: 104 A 104
A
Sbjct: 80 A 80
>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX
pdb|1P27|D Chain D, Crystal Structure Of The Human Y14MAGOH COMPLEX
Length = 106
Score = 33.5 bits (75), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 41/87 (47%), Gaps = 8/87 (9%)
Query: 32 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDV--------VKNYGFVHMENDEEGR 83
SV + +F+ V+ + E I F +YG++ + +K Y V E +E +
Sbjct: 20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 79
Query: 84 TAIKELNGQIVNEKPLKIEAATSRKGP 110
A++ LNGQ + +P+ ++ R P
Sbjct: 80 AAMEGLNGQDLMGQPISVDWCFVRGPP 106
>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 90
Score = 33.5 bits (75), Expect = 0.089, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 41/87 (47%), Gaps = 8/87 (9%)
Query: 32 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDV--------VKNYGFVHMENDEEGR 83
SV + +F+ V+ + E I F +YG++ + +K Y V E +E +
Sbjct: 4 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 63
Query: 84 TAIKELNGQIVNEKPLKIEAATSRKGP 110
A++ LNGQ + +P+ ++ R P
Sbjct: 64 AAMEGLNGQDLMGQPISVDWCFVRGPP 90
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 33.5 bits (75), Expect = 0.095, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 30/62 (48%), Gaps = 4/62 (6%)
Query: 51 LIRPLFEKYGKVVEC--DVVKNYGFVHMENDEEGRTAIKELNGQIVNEKPLKIEAATSRK 108
L+R F +G +++ D +N FV E E A+ ELNG V LK+ A RK
Sbjct: 29 LLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA--RK 86
Query: 109 GP 110
P
Sbjct: 87 QP 88
Score = 31.6 bits (70), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 36/66 (54%), Gaps = 7/66 (10%)
Query: 131 VRELFVPYGTVVEC--DIVRNYGFVHIDSPD-INKCIKELNGMMVDGKPMKVQISTSRVR 187
+R F P+G +++ D RN FV + + ++ + ELNG V+ +KV I+ R
Sbjct: 30 LRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA----R 85
Query: 188 QRPGVD 193
++P +D
Sbjct: 86 KQPMLD 91
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 33.1 bits (74), Expect = 0.098, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 9/74 (12%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNY------GFVHIDSPDIN---KCIKE 166
K+F+G L + +V+EL +G + ++V++ G+ + DIN + I
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 167 LNGMMVDGKPMKVQ 180
LNGM + K + VQ
Sbjct: 63 LNGMQLGDKKLLVQ 76
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 33.1 bits (74), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 29 GFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN 70
G K+FIG + + ++PLFE++GK+ E V+K+
Sbjct: 7 GMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKD 48
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 33.1 bits (74), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 30/62 (48%), Gaps = 4/62 (6%)
Query: 51 LIRPLFEKYGKVVEC--DVVKNYGFVHMENDEEGRTAIKELNGQIVNEKPLKIEAATSRK 108
L+R F +G +++ D +N FV E E A+ ELNG V LK+ A RK
Sbjct: 53 LLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA--RK 110
Query: 109 GP 110
P
Sbjct: 111 QP 112
Score = 31.2 bits (69), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 36/69 (52%), Gaps = 7/69 (10%)
Query: 131 VRELFVPYGTVVEC--DIVRNYGFVHIDSPD-INKCIKELNGMMVDGKPMKVQISTSRVR 187
+R F P+G +++ D RN FV + + ++ + ELNG V+ +KV I+ R
Sbjct: 54 LRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA----R 109
Query: 188 QRPGVDEVV 196
++P +D
Sbjct: 110 KQPMLDAAT 118
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 33.1 bits (74), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 23/87 (26%), Positives = 42/87 (48%), Gaps = 9/87 (10%)
Query: 32 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDV--------VKNYGFVHMENDEEGR 83
SV + +F+ V+ + E I F +YG++ + +K Y V E +E +
Sbjct: 4 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 63
Query: 84 TAIKELNGQIVNEKPLKIEAATSRKGP 110
A++ LNGQ + +P+ ++ R GP
Sbjct: 64 AAMEGLNGQDLMGQPISVDWCFVR-GP 89
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 32.7 bits (73), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 6/73 (8%)
Query: 115 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDI---VRNYGFVHIDSPDINKCIKELNGMM 171
+KVFVG +++ A E+++ F YG VV+ I R + FV +K + L G
Sbjct: 12 SKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFAD---DKVAQSLCGED 68
Query: 172 VDGKPMKVQISTS 184
+ K + V IS +
Sbjct: 69 LIIKGISVHISNA 81
Score = 28.1 bits (61), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 35/71 (49%), Gaps = 9/71 (12%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDV---VKNYGFVHMENDEEGRTA------IK 87
K+F+G + E ++ F +YG+VV+ + + + FV +D+ ++ IK
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQSLCGEDLIIK 72
Query: 88 ELNGQIVNEKP 98
++ I N +P
Sbjct: 73 GISVHISNAEP 83
>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 = 32.7 bits (73), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 23/87 (26%), Positives = 42/87 (48%), Gaps = 9/87 (10%)
Query: 32 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDV--------VKNYGFVHMENDEEGR 83
SV + +F+ V+ + E I F +YG++ + +K Y V E +E +
Sbjct: 6 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 65
Query: 84 TAIKELNGQIVNEKPLKIEAATSRKGP 110
A++ LNGQ + +P+ ++ R GP
Sbjct: 66 AAMEGLNGQDLMGQPISVDWCFVR-GP 91
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 32.3 bits (72), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 36/72 (50%), Gaps = 7/72 (9%)
Query: 38 IFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-------YGFVHMENDEEGRTAIKELN 90
+F+ N++ + ++ +F G VV D++++ G V E E AI N
Sbjct: 18 VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFN 77
Query: 91 GQIVNEKPLKIE 102
GQ++ ++P+ ++
Sbjct: 78 GQLLFDRPMHVK 89
Score = 31.2 bits (69), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 8/75 (10%)
Query: 115 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-------RNYGFVHID-SPDINKCIKE 166
+ VFV NL +++E+F G VV DI+ R G V + S + + I
Sbjct: 16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISM 75
Query: 167 LNGMMVDGKPMKVQI 181
NG ++ +PM V++
Sbjct: 76 FNGQLLFDRPMHVKM 90
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 32.0 bits (71), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 21/85 (24%), Positives = 38/85 (44%), Gaps = 12/85 (14%)
Query: 38 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGRTAIKEL 89
+++ + S + + LF +YG+++ ++ + GF+ + E AIK L
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 90 NGQIVNEKPLKIEAATSRKGPNTPT 114
NGQ KPL + K N P+
Sbjct: 64 NGQ----KPLGAAEPITVKFANNPS 84
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 32.0 bits (71), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 17/79 (21%), Positives = 38/79 (48%), Gaps = 8/79 (10%)
Query: 34 GTFKIFIGNVNPGTSVELIRPLFEKYGKVVE--------CDVVKNYGFVHMENDEEGRTA 85
G + + N+ TS + +R +FEKYG+V + + + FV + + + A
Sbjct: 12 GMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDA 71
Query: 86 IKELNGQIVNEKPLKIEAA 104
++G ++ + L+++ A
Sbjct: 72 EAAMDGAELDGRELRVQVA 90
Score = 30.0 bits (66), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 33/73 (45%), Gaps = 9/73 (12%)
Query: 119 VGNLSDNTRAPEVRELFVPYGTVVECDI--------VRNYGFVHI-DSPDINKCIKELNG 169
V NL+ T +R +F YG V + I R + FV D D ++G
Sbjct: 18 VDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDG 77
Query: 170 MMVDGKPMKVQIS 182
+DG+ ++VQ++
Sbjct: 78 AELDGRELRVQVA 90
>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
pdb|2J0Q|G Chain G, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
Length = 109
Score = 32.0 bits (71), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 39/79 (49%), Gaps = 8/79 (10%)
Query: 32 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDV--------VKNYGFVHMENDEEGR 83
SV + +F+ V+ + E I F +YG++ + +K Y V E +E +
Sbjct: 4 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 63
Query: 84 TAIKELNGQIVNEKPLKIE 102
A++ LNGQ + +P+ ++
Sbjct: 64 AAMEGLNGQDLMGQPISVD 82
>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 = 32.0 bits (71), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 30/64 (46%), Gaps = 12/64 (18%)
Query: 110 PNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-------RNYGFVHI-DSPDIN 161
PNT VFVG + E+R F YG+V E I+ + YGFV + D+
Sbjct: 9 PNT----VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQ 64
Query: 162 KCIK 165
K ++
Sbjct: 65 KIVE 68
Score = 31.2 bits (69), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 7/49 (14%)
Query: 38 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------KNYGFVHMEND 79
+F+G ++ IR F +YG V E ++ K YGFV ND
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYND 60
>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 = 32.0 bits (71), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 39/79 (49%), Gaps = 8/79 (10%)
Query: 32 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDV--------VKNYGFVHMENDEEGR 83
SV + +F+ V+ + E I F +YG++ + +K Y V E +E +
Sbjct: 19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 78
Query: 84 TAIKELNGQIVNEKPLKIE 102
A++ LNGQ + +P+ ++
Sbjct: 79 AAMEGLNGQDLMGQPISVD 97
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 32.0 bits (71), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 22/89 (24%), Positives = 39/89 (43%), Gaps = 13/89 (14%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDV--------VKNYGFVHMENDEEGRTAIKE 88
++F+ N++ +S E + LF YG + E K + FV E A E
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 89 LNGQIVNEK-----PLKIEAATSRKGPNT 112
++GQ+ + P I+ S+ GP++
Sbjct: 70 VDGQVFQGRMLHVLPSTIKKEASQSGPSS 98
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 32.0 bits (71), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 30/64 (46%), Gaps = 12/64 (18%)
Query: 110 PNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-------RNYGFVHI-DSPDIN 161
PNT VFVG + E+R F YG+V E I+ + YGFV + D+
Sbjct: 10 PNT----VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQ 65
Query: 162 KCIK 165
K ++
Sbjct: 66 KIVE 69
Score = 31.2 bits (69), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 7/49 (14%)
Query: 38 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------KNYGFVHMEND 79
+F+G ++ IR F +YG V E ++ K YGFV ND
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYND 61
>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 = 32.0 bits (71), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 23/34 (67%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN 70
K+F+G V S + +R LFE+YG V E +V+++
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRD 38
Score = 31.2 bits (69), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 21/34 (61%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN 149
K+FVG + ++RELF YG V E +++R+
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRD 38
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 31.6 bits (70), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 8/61 (13%)
Query: 52 IRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIKELNGQIVNEKPLKIEA 103
+ LF G + C +V++ YGFV+ + + AI LNG + K +K+
Sbjct: 21 FKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSY 80
Query: 104 A 104
A
Sbjct: 81 A 81
>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 = 31.6 bits (70), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 16/66 (24%), Positives = 32/66 (48%), Gaps = 8/66 (12%)
Query: 38 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGRTAIKEL 89
+F+ VN T+ +R FE YG + +V + Y F+ E++ + +A K
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 90 NGQIVN 95
+G+ ++
Sbjct: 165 DGKKID 170
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 31.6 bits (70), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 22/92 (23%), Positives = 42/92 (45%), Gaps = 12/92 (13%)
Query: 103 AATSRKGPN---TPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN------YGFV 153
++ GPN + V NLS++TR +++ELF P+G++ + ++ GF
Sbjct: 1 GSSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFA 60
Query: 154 HID---SPDINKCIKELNGMMVDGKPMKVQIS 182
I D + I ++G D + V+ +
Sbjct: 61 FISFHRREDAARAIAGVSGFGYDHLILNVEWA 92
>pdb|1JMT|A Chain A, X-Ray Structure Of A Core U2af65U2AF35 HETERODIMER
Length = 104
Score = 31.2 bits (69), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 7/62 (11%)
Query: 50 ELIRPLFEKYGKVVECDVVKNYG-------FVHMENDEEGRTAIKELNGQIVNEKPLKIE 102
E+ + EKYG+V E +V N G +V +E+ A+ +LN + N +P+ E
Sbjct: 42 EVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAE 101
Query: 103 AA 104
+
Sbjct: 102 LS 103
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 30.8 bits (68), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 36/77 (46%), Gaps = 12/77 (15%)
Query: 33 VGTFKIFIGNVNPGTSVELIRP-----LFEKYGKVVECDVV---KNYGFVHMENDEEGRT 84
+G + + N+NP E + P LF YG V ++ K V M + + +
Sbjct: 1 MGNSVLLVSNLNP----ERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQL 56
Query: 85 AIKELNGQIVNEKPLKI 101
A+ LNG ++ KP++I
Sbjct: 57 AMSHLNGHKLHGKPIRI 73
>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 = 30.8 bits (68), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 8/61 (13%)
Query: 52 IRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIKELNGQIVNEKPLKIEA 103
+R LF G+V ++++ YGFV+ ++ AI LNG + K +K+
Sbjct: 21 LRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSY 80
Query: 104 A 104
A
Sbjct: 81 A 81
>pdb|3IPQ|A Chain A, X-Ray Structure Of Gw3965 Synthetic Agonist Bound To The
Lxr
pdb|3IPS|A Chain A, X-Ray Structure Of Benzisoxazole Synthetic Agonist Bound
To Alpha
pdb|3IPS|B Chain B, X-Ray Structure Of Benzisoxazole Synthetic Agonist Bound
To Alpha
pdb|3IPU|A Chain A, X-Ray Structure Of Benzisoxazole Urea Synthetic Agonist
Boun Lxr-Alpha
pdb|3IPU|B Chain B, X-Ray Structure Of Benzisoxazole Urea Synthetic Agonist
Boun Lxr-Alpha
Length = 283
Score = 30.4 bits (67), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 27/61 (44%), Gaps = 4/61 (6%)
Query: 1 MSRFDQQQLVKVSRYSNNQINISCRNMPGFSSVGTFKIFIGN----VNPGTSVELIRPLF 56
+SR DQ L+K S + S R PG S+ K F N G VE I P+F
Sbjct: 117 LSREDQIALLKTSAIEVMLLETSRRYNPGSESITFLKDFSYNREDFAKAGLQVEFINPIF 176
Query: 57 E 57
E
Sbjct: 177 E 177
>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 = 30.4 bits (67), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 21/87 (24%), Positives = 40/87 (45%), Gaps = 10/87 (11%)
Query: 28 PGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMEND 79
PG S+ +++ N+ + + + +F KYG +V+ +++++ FV
Sbjct: 6 PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKR 65
Query: 80 EEGRTAIKELNGQIV--NEKPLKIEAA 104
EE + AI LN I +PL + A
Sbjct: 66 EEAQEAISALNNVIPEGGSQPLSVRLA 92
>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 = 30.4 bits (67), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 8/61 (13%)
Query: 52 IRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIKELNGQIVNEKPLKIEA 103
+R LF G+V ++++ YGFV+ ++ AI LNG + K +K+
Sbjct: 36 LRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSY 95
Query: 104 A 104
A
Sbjct: 96 A 96
>pdb|1UHL|B Chain B, Crystal Structure Of The Lxralfa-Rxrbeta Lbd Heterodimer
Length = 242
Score = 30.4 bits (67), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 27/61 (44%), Gaps = 4/61 (6%)
Query: 1 MSRFDQQQLVKVSRYSNNQINISCRNMPGFSSVGTFKIFIGN----VNPGTSVELIRPLF 56
+SR DQ L+K S + S R PG S+ K F N G VE I P+F
Sbjct: 76 LSREDQIALLKTSAIEVMLLETSRRYNPGSESITFLKDFSYNREDFAKAGLQVEFINPIF 135
Query: 57 E 57
E
Sbjct: 136 E 136
>pdb|3FC6|B Chain B, Hrxralpha & Mlxralpha With An Indole Pharmacophore,
Sb786875
pdb|3FC6|D Chain D, Hrxralpha & Mlxralpha With An Indole Pharmacophore,
Sb786875
pdb|3FAL|B Chain B, Humanrxr Alpha & Mouse Lxr Alpha Complexed With Retenoic
Acid And Gsk2186
pdb|3FAL|D Chain D, Humanrxr Alpha & Mouse Lxr Alpha Complexed With Retenoic
Acid And Gsk2186
Length = 266
Score = 30.4 bits (67), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 27/61 (44%), Gaps = 4/61 (6%)
Query: 1 MSRFDQQQLVKVSRYSNNQINISCRNMPGFSSVGTFKIFIGN----VNPGTSVELIRPLF 56
+SR DQ L+K S + S R PG S+ K F N G VE I P+F
Sbjct: 100 LSREDQIALLKTSAIEVMLLETSRRYNPGSESITFLKDFSYNREDFAKAGLQVEFINPIF 159
Query: 57 E 57
E
Sbjct: 160 E 160
>pdb|2ACL|B Chain B, Liver X-Receptor Alpha Ligand Binding Domain With Sb313987
pdb|2ACL|D Chain D, Liver X-Receptor Alpha Ligand Binding Domain With Sb313987
pdb|2ACL|F Chain F, Liver X-Receptor Alpha Ligand Binding Domain With Sb313987
pdb|2ACL|H Chain H, Liver X-Receptor Alpha Ligand Binding Domain With Sb313987
Length = 244
Score = 30.4 bits (67), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 27/61 (44%), Gaps = 4/61 (6%)
Query: 1 MSRFDQQQLVKVSRYSNNQINISCRNMPGFSSVGTFKIFIGN----VNPGTSVELIRPLF 56
+SR DQ L+K S + S R PG S+ K F N G VE I P+F
Sbjct: 78 LSREDQIALLKTSAIEVMLLETSRRYNPGSESITFLKDFSYNREDFAKAGLQVEFINPIF 137
Query: 57 E 57
E
Sbjct: 138 E 138
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 30.0 bits (66), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 42/75 (56%), Gaps = 9/75 (12%)
Query: 38 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGRTAIKEL 89
IF+G ++ T+VE ++ FE++GKV + ++ + +GFV E+ E+ + E+
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFES-EDIVEKVCEI 60
Query: 90 NGQIVNEKPLKIEAA 104
+ +N K ++ + A
Sbjct: 61 HFHEINNKMVECKKA 75
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 30.0 bits (66), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 37/82 (45%), Gaps = 7/82 (8%)
Query: 117 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN------YGFVHI-DSPDINKCIKELNG 169
++VGNLS + + +LF G C ++ Y FV + D + +NG
Sbjct: 18 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNG 77
Query: 170 MMVDGKPMKVQISTSRVRQRPG 191
+ GK +KV +T+ Q+ G
Sbjct: 78 RKILGKEVKVNWATTPSSQKSG 99
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 29.6 bits (65), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 34/70 (48%), Gaps = 9/70 (12%)
Query: 35 TFK-IFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGRTA 85
FK +F+ VN T+ +R FE YG + +V + Y F+ E++ + +A
Sbjct: 101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSA 160
Query: 86 IKELNGQIVN 95
K +G+ ++
Sbjct: 161 YKHADGKKID 170
>pdb|2DGX|A Chain A, Solution Structure Of The Rna Recognition Motif In
Kiaa0430 Protein
Length = 96
Score = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 5/68 (7%)
Query: 50 ELIRPLFEKYGKV--VECDVVKNY---GFVHMENDEEGRTAIKELNGQIVNEKPLKIEAA 104
+L++ F ++GKV VE +Y V MEN ++ A+ L+ + K + + A
Sbjct: 28 QLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLA 87
Query: 105 TSRKGPNT 112
T GP++
Sbjct: 88 TGASGPSS 95
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 21/85 (24%), Positives = 41/85 (48%), Gaps = 10/85 (11%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHI-DSPDINKCIKE 166
K+FVG + N E+RE F +G V E ++ R +GF+ D +++ +
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN- 70
Query: 167 LNGMMVDGKPMKVQISTSRVRQRPG 191
++ + GK ++V+ + R + G
Sbjct: 71 MHFHDIMGKKVEVKRAEPRDSKSSG 95
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 29.3 bits (64), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/87 (21%), Positives = 41/87 (47%), Gaps = 6/87 (6%)
Query: 32 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDV------VKNYGFVHMENDEEGRTA 85
S G +IF+ N+ + ++++ F + G V+ D+ K G V E+ E A
Sbjct: 5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERA 64
Query: 86 IKELNGQIVNEKPLKIEAATSRKGPNT 112
+ +NG ++ + + + + GP++
Sbjct: 65 CRMMNGMKLSGREIDVRIDRNASGPSS 91
>pdb|2OQY|A Chain A, The Crystal Structure Of Muconate Cycloisomerase From
Oceanobacillus Iheyensis
pdb|2OQY|B Chain B, The Crystal Structure Of Muconate Cycloisomerase From
Oceanobacillus Iheyensis
pdb|2OQY|C Chain C, The Crystal Structure Of Muconate Cycloisomerase From
Oceanobacillus Iheyensis
pdb|2OQY|D Chain D, The Crystal Structure Of Muconate Cycloisomerase From
Oceanobacillus Iheyensis
pdb|2OQY|E Chain E, The Crystal Structure Of Muconate Cycloisomerase From
Oceanobacillus Iheyensis
pdb|2OQY|F Chain F, The Crystal Structure Of Muconate Cycloisomerase From
Oceanobacillus Iheyensis
pdb|2OQY|G Chain G, The Crystal Structure Of Muconate Cycloisomerase From
Oceanobacillus Iheyensis
pdb|2OQY|H Chain H, The Crystal Structure Of Muconate Cycloisomerase From
Oceanobacillus Iheyensis
pdb|3ES7|A Chain A, Crystal Structure Of Divergent Enolase From Oceanobacillus
Iheyensis Complexed With Mg And L-Malate.
pdb|3ES7|B Chain B, Crystal Structure Of Divergent Enolase From Oceanobacillus
Iheyensis Complexed With Mg And L-Malate.
pdb|3ES8|A Chain A, Crystal Structure Of Divergent Enolase From Oceanobacillus
Iheyensis Complexed With Mg And L-Malate.
pdb|3ES8|B Chain B, Crystal Structure Of Divergent Enolase From Oceanobacillus
Iheyensis Complexed With Mg And L-Malate.
pdb|3ES8|C Chain C, Crystal Structure Of Divergent Enolase From Oceanobacillus
Iheyensis Complexed With Mg And L-Malate.
pdb|3ES8|D Chain D, Crystal Structure Of Divergent Enolase From Oceanobacillus
Iheyensis Complexed With Mg And L-Malate.
pdb|3ES8|E Chain E, Crystal Structure Of Divergent Enolase From Oceanobacillus
Iheyensis Complexed With Mg And L-Malate.
pdb|3ES8|F Chain F, Crystal Structure Of Divergent Enolase From Oceanobacillus
Iheyensis Complexed With Mg And L-Malate.
pdb|3ES8|G Chain G, Crystal Structure Of Divergent Enolase From Oceanobacillus
Iheyensis Complexed With Mg And L-Malate.
pdb|3ES8|H Chain H, Crystal Structure Of Divergent Enolase From Oceanobacillus
Iheyensis Complexed With Mg And L-Malate.
pdb|3FYY|A Chain A, Crystal Structure Of Divergent Enolase From Oceanobacillus
Iheyensis Complexed With Mg
pdb|3FYY|B Chain B, Crystal Structure Of Divergent Enolase From Oceanobacillus
Iheyensis Complexed With Mg
pdb|3GD6|A Chain A, Crystal Structure Of Divergent Enolase From Oceanobacillus
Iheyensis Complexed With Phosphate
Length = 391
Score = 28.5 bits (62), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 29/54 (53%), Gaps = 4/54 (7%)
Query: 36 FKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYGFVHMENDEEGRTAIKEL 89
F++++G N E + + E++G V +K+Y F H+ N ++ AIK L
Sbjct: 161 FRLYVGK-NLDADEEFLSRVKEEFGSRVR---IKSYDFSHLLNWKDAHRAIKRL 210
>pdb|3HPF|A Chain A, Crystal Structure Of The Mutant Y90f Of Divergent
Galactarate Dehydratase From Oceanobacillus Iheyensis
Complexed With Mg And Galactarate
pdb|3HPF|B Chain B, Crystal Structure Of The Mutant Y90f Of Divergent
Galactarate Dehydratase From Oceanobacillus Iheyensis
Complexed With Mg And Galactarate
Length = 391
Score = 28.5 bits (62), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 29/54 (53%), Gaps = 4/54 (7%)
Query: 36 FKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYGFVHMENDEEGRTAIKEL 89
F++++G N E + + E++G V +K+Y F H+ N ++ AIK L
Sbjct: 161 FRLYVGK-NLDADEEFLSRVKEEFGSRVR---IKSYDFSHLLNWKDAHRAIKRL 210
>pdb|3FAN|A Chain A, Crystal Structure Of Chymotrypsin-Like ProteasePROTEINASE
(3clspNSP4) OF PORCINE REPRODUCTIVE AND RESPIRATORY
Syndrome Virus (Prrsv)
Length = 213
Score = 28.1 bits (61), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 3/60 (5%)
Query: 74 VHMENDEEGRTAIKELNGQIVNEKPLKI-EAATSRKGPNTPTTKVFVGN--LSDNTRAPE 130
VH ++++G + +GQ N KP+K+ E + GP P V +G+ + D P
Sbjct: 141 VHTGSNKQGGGIVTRPSGQFCNVKPIKLSELSEFFAGPKVPLGDVKIGSHIIKDTCEVPS 200
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 28.1 bits (61), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 19/87 (21%), Positives = 41/87 (47%), Gaps = 6/87 (6%)
Query: 32 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDV------VKNYGFVHMENDEEGRTA 85
S G+ IF+ N+ + ++++ F + G V+ D+ K G V E+ E A
Sbjct: 2 SSGSSGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERA 61
Query: 86 IKELNGQIVNEKPLKIEAATSRKGPNT 112
+ +NG ++ + + + + GP++
Sbjct: 62 CRMMNGMKLSGREIDVRIDRNASGPSS 88
>pdb|3FAO|A Chain A, Crystal Structure Of S118a Mutant 3clsp Of Prrsv
Length = 213
Score = 28.1 bits (61), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 3/60 (5%)
Query: 74 VHMENDEEGRTAIKELNGQIVNEKPLKI-EAATSRKGPNTPTTKVFVGN--LSDNTRAPE 130
VH ++++G + +GQ N KP+K+ E + GP P V +G+ + D P
Sbjct: 141 VHTGSNKQGGGIVTRPSGQFCNVKPIKLSELSEFFAGPKVPLGDVKIGSHIIKDTCEVPS 200
>pdb|3DG3|A Chain A, Crystal Structure Of Muconate Lactonizing Enzyme From
Mucobacterium Smegmatis
pdb|3DG6|A Chain A, Crystal Structure Of Muconate Lactonizing Enzyme From
Mucobacterium Smegmatis Complexed With Muconolactone
pdb|3DG7|A Chain A, Crystal Structure Of Muconate Lactonizing Enzyme From
Mucobacterium Smegmatis Complexed With Muconolactone
pdb|3DG7|B Chain B, Crystal Structure Of Muconate Lactonizing Enzyme From
Mucobacterium Smegmatis Complexed With Muconolactone
pdb|3DG7|C Chain C, Crystal Structure Of Muconate Lactonizing Enzyme From
Mucobacterium Smegmatis Complexed With Muconolactone
pdb|3DG7|D Chain D, Crystal Structure Of Muconate Lactonizing Enzyme From
Mucobacterium Smegmatis Complexed With Muconolactone
Length = 367
Score = 28.1 bits (61), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 36/154 (23%), Positives = 62/154 (40%), Gaps = 9/154 (5%)
Query: 33 VGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYGFVHMENDEEGRTAIKELN-- 90
+ TFK+ +G ++R L E++G +E V N G+ + E A++E+
Sbjct: 156 INTFKVKVGRRPVQLDTAVVRALRERFGDAIELYVDGNRGW----SAAESLRAMREMADL 211
Query: 91 GQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNY 150
+ E+ + SR+ F+ + S T A RE+ T + R
Sbjct: 212 DLLFAEELCPADDVLSRRRLVGQLDMPFIADESVPTPADVTREVLGGSATAISIKTART- 270
Query: 151 GFVHIDSPDINKCIKELNGMMVDGKPMKVQISTS 184
GF S ++ + L MV G + QI T+
Sbjct: 271 GFT--GSTRVHHLAEGLGLDMVMGNQIDGQIGTA 302
>pdb|1QAP|A Chain A, Quinolinic Acid Phosphoribosyltransferase With Bound
Quinolinic Acid
pdb|1QAP|B Chain B, Quinolinic Acid Phosphoribosyltransferase With Bound
Quinolinic Acid
Length = 296
Score = 28.1 bits (61), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 29/58 (50%)
Query: 78 NDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELF 135
N ++ R A+K +NGQ E + A T R+ T + VG L+ + RA ++ F
Sbjct: 238 NTDQMREAVKRVNGQARLEVSGNVTAETLREFAETGVDFISVGALTKHVRALDLSMRF 295
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 27.7 bits (60), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 17/88 (19%), Positives = 39/88 (44%), Gaps = 9/88 (10%)
Query: 104 ATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNY------GFVHID- 156
++ G T ++VG L++ + F+P+G + + I +Y GF ++
Sbjct: 2 SSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 61
Query: 157 --SPDINKCIKELNGMMVDGKPMKVQIS 182
+ D I +N + G+ ++V ++
Sbjct: 62 ELAEDAAAAIDNMNESELFGRTIRVNLA 89
>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 = 27.7 bits (60), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 18/83 (21%), Positives = 39/83 (46%), Gaps = 11/83 (13%)
Query: 111 NTPTTK--VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNY------GFVHID---SPD 159
+ TTK ++VG L++ + F+P+G + + I +Y GF ++ + D
Sbjct: 2 SMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 61
Query: 160 INKCIKELNGMMVDGKPMKVQIS 182
I +N + G+ ++V ++
Sbjct: 62 AAAAIDNMNESELFGRTIRVNLA 84
>pdb|2O0R|A Chain A, The Three-Dimensional Structure Of
N-Succinyldiaminopimelate Aminotransferase From
Mycobacterium Tuberculosis
pdb|2O0R|B Chain B, The Three-Dimensional Structure Of
N-Succinyldiaminopimelate Aminotransferase From
Mycobacterium Tuberculosis
Length = 411
Score = 27.7 bits (60), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 40 IGNVNPGTSVELIRPLFEKYGKVV 63
+G V PG+ V LI P ++ Y VV
Sbjct: 104 LGLVEPGSEVLLIEPFYDSYSPVV 127
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 27.7 bits (60), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 18/80 (22%), Positives = 38/80 (47%), Gaps = 11/80 (13%)
Query: 114 TTK--VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNY------GFVHID---SPDINK 162
TTK ++VG L++ + F+P+G + + I +Y GF ++ + D
Sbjct: 3 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 62
Query: 163 CIKELNGMMVDGKPMKVQIS 182
I +N + G+ ++V ++
Sbjct: 63 AIDNMNESELFGRTIRVNLA 82
>pdb|2E44|A Chain A, Solution Structure Of Rna Binding Domain In Insulin-Like
Growth Factor 2 Mrna Binding Protein 3
Length = 96
Score = 27.3 bits (59), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 5/60 (8%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYGF-----VHMENDEEGRTAIKELNG 91
K+ I N+ P E++ L +YG V C+ V V + ++ R A+ +LNG
Sbjct: 17 KLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNG 76
>pdb|3KH2|A Chain A, Crystal Structure Of The P1 Bacteriophage Doc Toxin
(F68s) In Complex With The Phd Antitoxin (L17mV39A).
NORTHEAST STRUCTURAL GENOMICS Targets Er385-Er386
pdb|3KH2|B Chain B, Crystal Structure Of The P1 Bacteriophage Doc Toxin
(F68s) In Complex With The Phd Antitoxin (L17mV39A).
NORTHEAST STRUCTURAL GENOMICS Targets Er385-Er386
pdb|3KH2|C Chain C, Crystal Structure Of The P1 Bacteriophage Doc Toxin
(F68s) In Complex With The Phd Antitoxin (L17mV39A).
NORTHEAST STRUCTURAL GENOMICS Targets Er385-Er386
pdb|3KH2|D Chain D, Crystal Structure Of The P1 Bacteriophage Doc Toxin
(F68s) In Complex With The Phd Antitoxin (L17mV39A).
NORTHEAST STRUCTURAL GENOMICS Targets Er385-Er386
Length = 134
Score = 27.3 bits (59), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 25/60 (41%), Gaps = 5/60 (8%)
Query: 27 MPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYGFVHMENDEEGRTAI 86
+PG S G + IG V + E I LFE V + H+ ND RTA+
Sbjct: 23 LPGXSDPGRAEAIIGRVQARVAYEEITDLFE-----VSATYLVATARGHISNDANKRTAL 77
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 26.9 bits (58), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 13/68 (19%), Positives = 31/68 (45%), Gaps = 7/68 (10%)
Query: 38 IFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNY-------GFVHMENDEEGRTAIKELN 90
++I N+ + + + + +G+V+ ++++ GF ME+ E+ I N
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFN 87
Query: 91 GQIVNEKP 98
G+ + P
Sbjct: 88 GKFIKTPP 95
>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 = 26.9 bits (58), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 12/26 (46%), Positives = 17/26 (65%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTV 141
K+FVG LS +T ++RE F +G V
Sbjct: 3 KIFVGGLSPDTPEEKIREYFGGFGEV 28
Score = 26.6 bits (57), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 12/26 (46%), Positives = 17/26 (65%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKV 62
KIF+G ++P T E IR F +G+V
Sbjct: 3 KIFVGGLSPDTPEEKIREYFGGFGEV 28
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
0.317 0.136 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,215,640
Number of Sequences: 62578
Number of extensions: 257109
Number of successful extensions: 1071
Number of sequences better than 100.0: 166
Number of HSP's better than 100.0 without gapping: 93
Number of HSP's successfully gapped in prelim test: 73
Number of HSP's that attempted gapping in prelim test: 801
Number of HSP's gapped (non-prelim): 265
length of query: 207
length of database: 14,973,337
effective HSP length: 94
effective length of query: 113
effective length of database: 9,091,005
effective search space: 1027283565
effective search space used: 1027283565
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)