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= 015468
(406 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 87.4 bits (215), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 58/183 (31%), Positives = 92/183 (50%), Gaps = 8/183 (4%)
Query: 66 PDASSDGIRSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSH 125
P A S + SL++GDL P + E+ + F G +S +V R+ T S GY ++ F
Sbjct: 8 PSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQP 67
Query: 126 AAAERVLQTFNGTQMPSTEQNFRLNWATYGAGERRQDDGPDFTIFVGDLAADVTDYVLQE 185
A AER L T N + + R+ W+ R+ G IF+ +L + + L +
Sbjct: 68 ADAERALDTMNFDVIKG--KPVRIMWSQRDPSLRKSGVG---NIFIKNLDKSIDNKALYD 122
Query: 186 TFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTEMNGVLCSTRPMRIGPAA 245
TF A + ++ KVV D SKGYGFV F + R++ +MNG+L + R + +G
Sbjct: 123 TFSA-FGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK 179
Query: 246 TKK 248
++K
Sbjct: 180 SRK 182
Score = 67.8 bits (164), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 52/194 (26%), Positives = 87/194 (44%), Gaps = 26/194 (13%)
Query: 165 PDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLR 224
P +++VGDL DVT+ +L E F + +V D T RS GY +V F ++ R
Sbjct: 14 PMASLYVGDLHPDVTEAMLYEKFSPA-GPILSIRVCRDMITRRSLGYAYVNFQQPADAER 72
Query: 225 SMTEMNGVLCSTRPMRIGPAATKKAATGQQYQKATYQNTQGSQGENDPNNTTIFVGGLDP 284
++ MN + +P+RI Q + ++ G+ IF+ LD
Sbjct: 73 ALDTMNFDVIKGKPVRI---------MWSQRDPSLRKSGVGN----------IFIKNLDK 113
Query: 285 SVTDDILKTVFGQYGELVHVKIPA----GKRCGFVQFANRTCAEQALSVLNGTQLGGQSI 340
S+ + L F +G ++ K+ K GFV F + AE+A+ +NG L + +
Sbjct: 114 SIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKV 173
Query: 341 RLSWGRSPSNKQSD 354
+ GR S K+ +
Sbjct: 174 FV--GRFKSRKERE 185
>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 = 86.7 bits (213), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 58/183 (31%), Positives = 92/183 (50%), Gaps = 8/183 (4%)
Query: 66 PDASSDGIRSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSH 125
P A S + SL++GDL P + E+ + F G +S +V R+ T S GY ++ F
Sbjct: 3 PSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQP 62
Query: 126 AAAERVLQTFNGTQMPSTEQNFRLNWATYGAGERRQDDGPDFTIFVGDLAADVTDYVLQE 185
A AER L T N + + R+ W+ R+ G IF+ +L + + L +
Sbjct: 63 ADAERALDTMNFDVIKG--KPVRIMWSQRDPSLRKSGVG---NIFIKNLDKSIDNKALYD 117
Query: 186 TFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTEMNGVLCSTRPMRIGPAA 245
TF A + ++ KVV D SKGYGFV F + R++ +MNG+L + R + +G
Sbjct: 118 TFSA-FGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK 174
Query: 246 TKK 248
++K
Sbjct: 175 SRK 177
Score = 67.4 bits (163), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 52/194 (26%), Positives = 87/194 (44%), Gaps = 26/194 (13%)
Query: 165 PDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLR 224
P +++VGDL DVT+ +L E F + +V D T RS GY +V F ++ R
Sbjct: 9 PMASLYVGDLHPDVTEAMLYEKFSPA-GPILSIRVCRDMITRRSLGYAYVNFQQPADAER 67
Query: 225 SMTEMNGVLCSTRPMRIGPAATKKAATGQQYQKATYQNTQGSQGENDPNNTTIFVGGLDP 284
++ MN + +P+RI Q + ++ G+ IF+ LD
Sbjct: 68 ALDTMNFDVIKGKPVRI---------MWSQRDPSLRKSGVGN----------IFIKNLDK 108
Query: 285 SVTDDILKTVFGQYGELVHVKIPA----GKRCGFVQFANRTCAEQALSVLNGTQLGGQSI 340
S+ + L F +G ++ K+ K GFV F + AE+A+ +NG L + +
Sbjct: 109 SIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKV 168
Query: 341 RLSWGRSPSNKQSD 354
+ GR S K+ +
Sbjct: 169 FV--GRFKSRKERE 180
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 86.7 bits (213), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 59/173 (34%), Positives = 89/173 (51%), Gaps = 9/173 (5%)
Query: 74 RSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQ 133
R L++G+L + E + F G + K++ +K N + Y F+E+ A LQ
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQ 59
Query: 134 TFNGTQMPSTEQNF-RLNWATYGAGERRQDDGPDFTIFVGDLAADVTDYVLQETFRAVYS 192
T NG Q+ E N ++NWA + + + DD F +FVGDL +V D L+ F+ S
Sbjct: 60 TLNGKQI---ENNIVKINWA-FQSQQSSSDDT--FNLFVGDLNVNVDDETLRNAFKDFPS 113
Query: 193 SVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTEMNGVLCSTRPMRIGPAA 245
+ G V+ D TG S+GYGFV F + + +M M G + RP+RI AA
Sbjct: 114 YLSG-HVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAA 165
Score = 52.8 bits (125), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 40/184 (21%), Positives = 84/184 (45%), Gaps = 27/184 (14%)
Query: 168 TIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMT 227
++VG+L +T+ +L++ F+ V + K++ D+ ++ Y FV + + ++
Sbjct: 2 VLYVGNLDKAITEDILKQYFQ-VGGPIANIKIMIDKNN-KNVNYAFVEYHQSHDANIALQ 59
Query: 228 EMNGVLCSTRPMRIGPAATKKAATGQQYQKATYQNTQGSQGENDPNNTTIFVGGLDPSVT 287
+NG ++I A +Q+ Q S + +FVG L+ +V
Sbjct: 60 TLNGKQIENNIVKINWA---------------FQSQQSSSDDT----FNLFVGDLNVNVD 100
Query: 288 DDILKTVFGQYGELV--HV----KIPAGKRCGFVQFANRTCAEQALSVLNGTQLGGQSIR 341
D+ L+ F + + HV + + + GFV F ++ A+ A+ + G L G+ +R
Sbjct: 101 DETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLR 160
Query: 342 LSWG 345
++W
Sbjct: 161 INWA 164
Score = 48.9 bits (115), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 41/84 (48%), Gaps = 5/84 (5%)
Query: 276 TIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRC-----GFVQFANRTCAEQALSVL 330
++VG LD ++T+DILK F G + ++KI K FV++ A AL L
Sbjct: 2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTL 61
Query: 331 NGTQLGGQSIRLSWGRSPSNKQSD 354
NG Q+ ++++W SD
Sbjct: 62 NGKQIENNIVKINWAFQSQQSSSD 85
Score = 48.1 bits (113), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 45/85 (52%), Gaps = 2/85 (2%)
Query: 68 ASSDGIRSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAA 127
+SSD +L++GDL +++ + + F ++SG V+ + QT S GYGF+ F S
Sbjct: 82 SSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDD 141
Query: 128 AERVLQTFNGTQMPSTEQNFRLNWA 152
A+ + + G + R+NWA
Sbjct: 142 AQNAMDSMQGQDLNGRP--LRINWA 164
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 81.3 bits (199), Expect = 9e-16, Method: Compositional matrix adjust.
Identities = 43/87 (49%), Positives = 59/87 (67%), Gaps = 2/87 (2%)
Query: 164 GPDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQL 223
GP++++FVGDL DV D +L E F VY S +G KVV D+ TG SKGYGFV+F DE EQ
Sbjct: 7 GPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQK 65
Query: 224 RSMTEMNGVL-CSTRPMRIGPAATKKA 249
R++TE G + ++P+R+ A K +
Sbjct: 66 RALTECQGAVGLGSKPVRLSVAIPKAS 92
Score = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 30/63 (47%)
Query: 75 SLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQT 134
SL++GDL P +++ + F G + QT S+GYGF++F +R L
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE 70
Query: 135 FNG 137
G
Sbjct: 71 CQG 73
Score = 33.9 bits (76), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 28/86 (32%), Positives = 43/86 (50%), Gaps = 8/86 (9%)
Query: 265 GSQGENDPNNTTIFVGGLDPSVTDDILKTVFGQY------GELVHVKIPAGKRCGFVQFA 318
GS G + P + +FVG L P V D +L F + G++V + K GFV+F
Sbjct: 1 GSSGSSGPEYS-LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFT 59
Query: 319 NRTCAEQALSVLNGTQ-LGGQSIRLS 343
+ ++AL+ G LG + +RLS
Sbjct: 60 DELEQKRALTECQGAVGLGSKPVRLS 85
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 77.4 bits (189), Expect = 1e-14, Method: Composition-based stats.
Identities = 38/83 (45%), Positives = 54/83 (65%), Gaps = 3/83 (3%)
Query: 75 SLWIGDLQPWMEESYIASIFGHTGEFV-SGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQ 133
SLW+GDL+P+M+E++I+ F GE V S K+IRN+ T GY F+EF A AE+ L
Sbjct: 11 SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70
Query: 134 TFNGTQMP--STEQNFRLNWATY 154
NG +P + + F+LN+ATY
Sbjct: 71 KINGKPLPGATPAKRFKLNYATY 93
Score = 37.0 bits (84), Expect = 0.022, Method: Composition-based stats.
Identities = 17/64 (26%), Positives = 34/64 (53%)
Query: 168 TIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMT 227
++++GDL + + + F + +V K++ +R TG GY FV F D + + +
Sbjct: 11 SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70
Query: 228 EMNG 231
++NG
Sbjct: 71 KING 74
Score = 34.3 bits (77), Expect = 0.14, Method: Composition-based stats.
Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 7/71 (9%)
Query: 276 TIFVGGLDPSVTDDILKTVFGQYGELV-HVKIPAGKRCG------FVQFANRTCAEQALS 328
++++G L+P + ++ + F GE V VKI + G FV+FA+ AE+ L
Sbjct: 11 SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70
Query: 329 VLNGTQLGGQS 339
+NG L G +
Sbjct: 71 KINGKPLPGAT 81
>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 = 75.1 bits (183), Expect = 7e-14, Method: Compositional matrix adjust.
Identities = 45/157 (28%), Positives = 83/157 (52%), Gaps = 8/157 (5%)
Query: 75 SLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQT 134
+L + L M + + S+F GE S K+IR+K S GYGF+ +V+ AER + T
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 135 FNGTQMPSTEQNFRLNWATYGAGERRQDDGPDFTIFVGDLAADVTDYVLQETFRAVYSSV 194
NG ++ S + ++++A + + D +++ L +T +++ F + + +
Sbjct: 64 LNGLRLQS--KTIKVSYARPSS-----EVIKDANLYISGLPRTMTQKDVEDMF-SRFGRI 115
Query: 195 KGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTEMNG 231
++V+ D+TTG S+G F+RF SE ++T NG
Sbjct: 116 INSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 57.8 bits (138), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 38/165 (23%), Positives = 81/165 (49%), Gaps = 30/165 (18%)
Query: 184 QETFRAVYSS---VKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTEMNGVLCSTRPMR 240
Q+ R+++SS V+ AK++ D+ G S GYGFV + + R++ +NG+ ++ ++
Sbjct: 16 QDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIK 75
Query: 241 IGPAATKKAATGQQYQKATYQNTQGSQGENDPNNTTIFVGGLDPSVTDDILKTVFGQYGE 300
+ A S+ D N +++ GL ++T ++ +F ++G
Sbjct: 76 VSYA------------------RPSSEVIKDAN---LYISGLPRTMTQKDVEDMFSRFGR 114
Query: 301 LVHVKIPAGKRCG------FVQFANRTCAEQALSVLNGTQLGGQS 339
+++ ++ + G F++F R+ AE+A++ NG + G S
Sbjct: 115 IINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSS 159
Score = 45.1 bits (105), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 27/93 (29%), Positives = 46/93 (49%), Gaps = 6/93 (6%)
Query: 275 TTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRCG------FVQFANRTCAEQALS 328
T + V L ++T D L+++F GE+ K+ K G FV + AE+A++
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 329 VLNGTQLGGQSIRLSWGRSPSNKQSDQAQWNGG 361
LNG +L ++I++S+ R S D + G
Sbjct: 63 TLNGLRLQSKTIKVSYARPSSEVIKDANLYISG 95
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 75.1 bits (183), Expect = 7e-14, Method: Compositional matrix adjust.
Identities = 45/157 (28%), Positives = 83/157 (52%), Gaps = 8/157 (5%)
Query: 75 SLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQT 134
+L + L M + + S+F GE S K+IR+K S GYGF+ +V+ AER + T
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 135 FNGTQMPSTEQNFRLNWATYGAGERRQDDGPDFTIFVGDLAADVTDYVLQETFRAVYSSV 194
NG ++ S + ++++A + + D +++ L +T +++ F + + +
Sbjct: 64 LNGLRLQS--KTIKVSYARPSS-----EVIKDANLYISGLPRTMTQKDVEDMF-SRFGRI 115
Query: 195 KGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTEMNG 231
++V+ D+TTG S+G F+RF SE ++T NG
Sbjct: 116 INSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 57.8 bits (138), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 38/165 (23%), Positives = 81/165 (49%), Gaps = 30/165 (18%)
Query: 184 QETFRAVYSS---VKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTEMNGVLCSTRPMR 240
Q+ R+++SS V+ AK++ D+ G S GYGFV + + R++ +NG+ ++ ++
Sbjct: 16 QDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIK 75
Query: 241 IGPAATKKAATGQQYQKATYQNTQGSQGENDPNNTTIFVGGLDPSVTDDILKTVFGQYGE 300
+ A S+ D N +++ GL ++T ++ +F ++G
Sbjct: 76 VSYA------------------RPSSEVIKDAN---LYISGLPRTMTQKDVEDMFSRFGR 114
Query: 301 LVHVKIPAGKRCG------FVQFANRTCAEQALSVLNGTQLGGQS 339
+++ ++ + G F++F R+ AE+A++ NG + G S
Sbjct: 115 IINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSS 159
Score = 45.1 bits (105), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 27/93 (29%), Positives = 46/93 (49%), Gaps = 6/93 (6%)
Query: 275 TTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRCG------FVQFANRTCAEQALS 328
T + V L ++T D L+++F GE+ K+ K G FV + AE+A++
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 329 VLNGTQLGGQSIRLSWGRSPSNKQSDQAQWNGG 361
LNG +L ++I++S+ R S D + G
Sbjct: 63 TLNGLRLQSKTIKVSYARPSSEVIKDANLYISG 95
>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 = 73.9 bits (180), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 44/157 (28%), Positives = 82/157 (52%), Gaps = 8/157 (5%)
Query: 75 SLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQT 134
+L + L M + S+FG GE S K++R+K T S GYGF+ ++ AE+ + T
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 135 FNGTQMPSTEQNFRLNWATYGAGERRQDDGPDFTIFVGDLAADVTDYVLQETFRAVYSSV 194
NG ++ + + ++++A + R D ++V L +T L++ F + Y +
Sbjct: 64 LNGLRLQT--KTIKVSYARPSSASIR-----DANLYVSGLPKTMTQKELEQLF-SQYGRI 115
Query: 195 KGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTEMNG 231
++++ D+ TG S+G GF+RF E ++ +NG
Sbjct: 116 ITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNG 152
Score = 67.8 bits (164), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 45/163 (27%), Positives = 80/163 (49%), Gaps = 30/163 (18%)
Query: 184 QETFRAVYSSV---KGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTEMNGVLCSTRPMR 240
QE FR+++ S+ + K+V D+ TG+S GYGFV + D + +++ +NG+ T+ ++
Sbjct: 16 QEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIK 75
Query: 241 IGPAATKKAATGQQYQKATYQNTQGSQGENDPNNTTIFVGGLDPSVTDDILKTVFGQYGE 300
+ A A+ D N ++V GL ++T L+ +F QYG
Sbjct: 76 VSYARPSSASI------------------RDAN---LYVSGLPKTMTQKELEQLFSQYGR 114
Query: 301 LVHVKIP------AGKRCGFVQFANRTCAEQALSVLNGTQLGG 337
++ +I + GF++F R AE+A+ LNG + G
Sbjct: 115 IITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSG 157
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 48/95 (50%), Gaps = 6/95 (6%)
Query: 273 NNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRCG------FVQFANRTCAEQA 326
+ T + V L ++T + +++FG GE+ K+ K G FV + + AE+A
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 327 LSVLNGTQLGGQSIRLSWGRSPSNKQSDQAQWNGG 361
++ LNG +L ++I++S+ R S D + G
Sbjct: 61 INTLNGLRLQTKTIKVSYARPSSASIRDANLYVSG 95
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 3/76 (3%)
Query: 69 SSDGIR--SLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHA 126
SS IR +L++ L M + + +F G ++ +++ ++ T S G GFI F
Sbjct: 82 SSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRI 141
Query: 127 AAERVLQTFNGTQMPS 142
AE ++ NG Q PS
Sbjct: 142 EAEEAIKGLNG-QKPS 156
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 70.1 bits (170), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 52/181 (28%), Positives = 81/181 (44%), Gaps = 28/181 (15%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE 228
+ V L D+TD L FRA+ + +++ D TG S GY FV F E + R++
Sbjct: 6 LIVNYLPQDMTDRELYALFRAI-GPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 229 MNGVLCSTRPMRIGPAATKKAATGQQYQKATYQNTQGSQGENDPNNTTIFVGGLDPSVTD 288
+NG+ + +++ A G +T ++V L ++TD
Sbjct: 65 LNGITVRNKRLKVSYA---------------------RPGGESIKDTNLYVTNLPRTITD 103
Query: 289 DILKTVFGQYGELVHVKIPAGKRCG------FVQFANRTCAEQALSVLNGTQLGGQSIRL 342
D L T+FG+YG +V I K G FV++ R A++A+S LN G S L
Sbjct: 104 DQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPL 163
Query: 343 S 343
S
Sbjct: 164 S 164
Score = 67.4 bits (163), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 40/159 (25%), Positives = 81/159 (50%), Gaps = 8/159 (5%)
Query: 75 SLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQT 134
+L + L M + + ++F G + +++R+ +T +S GY F++F S ++R ++
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 135 FNGTQMPSTEQNFRLNWATYGAGERRQDDGPDFTIFVGDLAADVTDYVLQETFRAVYSSV 194
NG + + ++++A G GE +D ++V +L +TD L F Y S+
Sbjct: 65 LNGITV--RNKRLKVSYARPG-GESIKDTN----LYVTNLPRTITDDQLDTIF-GKYGSI 116
Query: 195 KGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTEMNGVL 233
++ D+ TGR +G FVR+ E +++ +N V+
Sbjct: 117 VQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVI 155
>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 = 68.2 bits (165), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 52/181 (28%), Positives = 79/181 (43%), Gaps = 28/181 (15%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE 228
+ V L D TD L FRA+ + ++ D TG S GY FV F E + R++
Sbjct: 17 LIVNYLPQDXTDRELYALFRAI-GPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKV 75
Query: 229 MNGVLCSTRPMRIGPAATKKAATGQQYQKATYQNTQGSQGENDPNNTTIFVGGLDPSVTD 288
+NG+ + +++ A G +T ++V L ++TD
Sbjct: 76 LNGITVRNKRLKVSYA---------------------RPGGESIKDTNLYVTNLPRTITD 114
Query: 289 DILKTVFGQYGELVHVKIPAGKRCG------FVQFANRTCAEQALSVLNGTQLGGQSIRL 342
D L T+FG+YG +V I K G FV++ R A++A+S LN G S L
Sbjct: 115 DQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPL 174
Query: 343 S 343
S
Sbjct: 175 S 175
Score = 63.2 bits (152), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 37/142 (26%), Positives = 73/142 (51%), Gaps = 8/142 (5%)
Query: 92 SIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQTFNGTQMPSTEQNFRLNW 151
++F G + ++ R+ +T +S GY F++F S ++R ++ NG + + ++++
Sbjct: 33 ALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVLNGITV--RNKRLKVSY 90
Query: 152 ATYGAGERRQDDGPDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGY 211
A G GE +D ++V +L +TD L F Y S+ ++ D+ TGR +G
Sbjct: 91 ARPG-GESIKDTN----LYVTNLPRTITDDQLDTIF-GKYGSIVQKNILRDKLTGRPRGV 144
Query: 212 GFVRFGDESEQLRSMTEMNGVL 233
FVR+ E +++ +N V+
Sbjct: 145 AFVRYNKREEAQEAISALNNVI 166
Score = 34.3 bits (77), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 14/64 (21%), Positives = 29/64 (45%)
Query: 75 SLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQT 134
+L++ +L + + + +IFG G V ++R+K T G F+ + A+ +
Sbjct: 102 NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 161
Query: 135 FNGT 138
N
Sbjct: 162 LNNV 165
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 67.8 bits (164), Expect = 9e-12, Method: Compositional matrix adjust.
Identities = 41/161 (25%), Positives = 82/161 (50%), Gaps = 8/161 (4%)
Query: 71 DGIRSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAER 130
D +L + L M + S+FG G+ S K++R+K T S GYGF+ + A++
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 131 VLQTFNGTQMPSTEQNFRLNWATYGAGERRQDDGPDFTIFVGDLAADVTDYVLQETFRAV 190
+ T NG ++ + + ++++A + R D ++V L ++ +++ F +
Sbjct: 62 AINTLNGLKLQT--KTIKVSYARPSSASIR-----DANLYVSGLPKTMSQKEMEQLF-SQ 113
Query: 191 YSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTEMNG 231
Y + ++++ D+ TG S+G GF+RF E ++ +NG
Sbjct: 114 YGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNG 154
Score = 65.9 bits (159), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 43/177 (24%), Positives = 88/177 (49%), Gaps = 32/177 (18%)
Query: 184 QETFRAVYSSV---KGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTEMNGVLCSTRPMR 240
Q+ F++++ S+ + K+V D+ TG+S GYGFV + D ++ +++ +NG+ T+ ++
Sbjct: 18 QDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIK 77
Query: 241 IGPAATKKAATGQQYQKATYQNTQGSQGENDPNNTTIFVGGLDPSVTDDILKTVFGQYGE 300
+ A A+ + ++V GL +++ ++ +F QYG
Sbjct: 78 VSYARPSSASI---------------------RDANLYVSGLPKTMSQKEMEQLFSQYGR 116
Query: 301 LVHVKIP------AGKRCGFVQFANRTCAEQALSVLNGTQ-LG-GQSIRLSWGRSPS 349
++ +I + GF++F R AE+A+ LNG + LG + I + + +PS
Sbjct: 117 IITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQKPLGAAEPITVKFANNPS 173
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/93 (27%), Positives = 48/93 (51%), Gaps = 6/93 (6%)
Query: 275 TTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRC------GFVQFANRTCAEQALS 328
T + V L ++T D K++FG G++ K+ K GFV +++ A++A++
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 329 VLNGTQLGGQSIRLSWGRSPSNKQSDQAQWNGG 361
LNG +L ++I++S+ R S D + G
Sbjct: 65 TLNGLKLQTKTIKVSYARPSSASIRDANLYVSG 97
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 2/71 (2%)
Query: 69 SSDGIR--SLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHA 126
SS IR +L++ L M + + +F G ++ +++ ++ T S G GFI F
Sbjct: 84 SSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRI 143
Query: 127 AAERVLQTFNG 137
AE ++ NG
Sbjct: 144 EAEEAIKGLNG 154
>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 = 61.2 bits (147), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 35/108 (32%), Positives = 58/108 (53%), Gaps = 1/108 (0%)
Query: 155 GAGERRQDDGPDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFV 214
G+ +++D F +FVGDL+ ++T ++ F A + + A+VV D TG+SKGYGFV
Sbjct: 4 GSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAF-APFGRISDARVVKDMATGKSKGYGFV 62
Query: 215 RFGDESEQLRSMTEMNGVLCSTRPMRIGPAATKKAATGQQYQKATYQN 262
F ++ + ++ +M G R +R A K A Y+ T Q+
Sbjct: 63 SFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQS 110
Score = 52.0 bits (123), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 30/94 (31%), Positives = 47/94 (50%), Gaps = 7/94 (7%)
Query: 267 QGENDPNNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPA------GKRCGFVQFANR 320
Q ++ N+ +FVG L P +T + +K F +G + ++ K GFV F N+
Sbjct: 8 QKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNK 67
Query: 321 TCAEQALSVLNGTQLGGQSIRLSWG-RSPSNKQS 353
AE A+ + G LGG+ IR +W R P +S
Sbjct: 68 WDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKS 101
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 2/78 (2%)
Query: 76 LWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQTF 135
+++GDL P + I + F G +V+++ T S+GYGF+ F + AE +Q
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 136 NGTQMPSTEQNFRLNWAT 153
G + + R NWAT
Sbjct: 78 GGQWLGG--RQIRTNWAT 93
>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 = 58.2 bits (139), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 32/79 (40%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 167 FTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSM 226
F +FVGDL +V D L+ F+ S + G V+ D TG S+GYGFV F + + +M
Sbjct: 2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSG-HVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60
Query: 227 TEMNGVLCSTRPMRIGPAA 245
M G + RP+RI AA
Sbjct: 61 DSMQGQDLNGRPLRINWAA 79
Score = 44.7 bits (104), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 42/78 (53%), Gaps = 2/78 (2%)
Query: 75 SLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQT 134
+L++GDL +++ + + F ++SG V+ + QT S GYGF+ F S A+ + +
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 135 FNGTQMPSTEQNFRLNWA 152
G + + R+NWA
Sbjct: 63 MQGQDLNG--RPLRINWA 78
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 6/76 (7%)
Query: 276 TIFVGGLDPSVTDDILKTVFGQYGELV--HV----KIPAGKRCGFVQFANRTCAEQALSV 329
+FVG L+ +V D+ L+ F + + HV + + + GFV F ++ A+ A+
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 330 LNGTQLGGQSIRLSWG 345
+ G L G+ +R++W
Sbjct: 63 MQGQDLNGRPLRINWA 78
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 58.2 bits (139), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 31/85 (36%), Positives = 49/85 (57%), Gaps = 2/85 (2%)
Query: 263 TQGSQGENDPNNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRCGFVQFANRTC 322
+ GS GE D TT++VGGL ++T+ L+ F Q+GE+ + + ++C F+QFA R
Sbjct: 2 SSGSSGE-DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQA 60
Query: 323 AEQAL-SVLNGTQLGGQSIRLSWGR 346
AE A N + G+ + + WGR
Sbjct: 61 AEVAAEKSFNKLIVNGRRLNVKWGR 85
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 57.4 bits (137), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 32/96 (33%), Positives = 52/96 (54%), Gaps = 1/96 (1%)
Query: 155 GAGERRQDDGPDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFV 214
G+ +++D F +FVGDL+ ++T ++ F A + + A+VV D TG+SKGYGFV
Sbjct: 4 GSSGQKKDTSNHFHVFVGDLSPEITTEDIKSAF-APFGKISDARVVKDMATGKSKGYGFV 62
Query: 215 RFGDESEQLRSMTEMNGVLCSTRPMRIGPAATKKAA 250
F ++ + ++ M G R +R A K A
Sbjct: 63 SFYNKLDAENAIVHMGGQWLGGRQIRTNWATRKPPA 98
Score = 52.4 bits (124), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 29/89 (32%), Positives = 47/89 (52%), Gaps = 7/89 (7%)
Query: 267 QGENDPNNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPA------GKRCGFVQFANR 320
Q ++ N+ +FVG L P +T + +K+ F +G++ ++ K GFV F N+
Sbjct: 8 QKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNK 67
Query: 321 TCAEQALSVLNGTQLGGQSIRLSWG-RSP 348
AE A+ + G LGG+ IR +W R P
Sbjct: 68 LDAENAIVHMGGQWLGGRQIRTNWATRKP 96
Score = 45.1 bits (105), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 2/78 (2%)
Query: 76 LWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQTF 135
+++GDL P + I S F G+ +V+++ T S+GYGF+ F + AE +
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 136 NGTQMPSTEQNFRLNWAT 153
G + + R NWAT
Sbjct: 78 GGQWL--GGRQIRTNWAT 93
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 57.0 bits (136), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 45/78 (57%)
Query: 269 ENDPNNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRCGFVQFANRTCAEQALS 328
++ P N T++ GG+ +TD +++ F +G+++ +++ K FV+F+ A A+
Sbjct: 20 QSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIV 79
Query: 329 VLNGTQLGGQSIRLSWGR 346
+NGT + G ++ WG+
Sbjct: 80 SVNGTTIEGHVVKCYWGK 97
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 36/71 (50%), Gaps = 7/71 (9%)
Query: 161 QDDGPDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDES 220
Q + T++ G +A+ +TD ++++TF + + + +V + KGY FVRF
Sbjct: 20 QSSPKNCTVYCGGIASGLTDQLMRQTF-SPFGQIMEIRVFPE------KGYSFVRFSTHE 72
Query: 221 EQLRSMTEMNG 231
++ +NG
Sbjct: 73 SAAHAIVSVNG 83
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 29/81 (35%), Positives = 48/81 (59%), Gaps = 1/81 (1%)
Query: 168 TIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMT 227
++FVG++ + T+ L++ F V V ++V DR TG+ KGYGF + D+ L +M
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEV-GPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68
Query: 228 EMNGVLCSTRPMRIGPAATKK 248
+NG S R +R+ AA++K
Sbjct: 69 NLNGREFSGRALRVDNAASEK 89
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 37/73 (50%)
Query: 68 ASSDGIRSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAA 127
A +RS+++G++ E + IF G VS +++ +++T +GYGF E+
Sbjct: 3 AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62
Query: 128 AERVLQTFNGTQM 140
A ++ NG +
Sbjct: 63 ALSAMRNLNGREF 75
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/94 (25%), Positives = 47/94 (50%), Gaps = 10/94 (10%)
Query: 276 TIFVGGLDPSVTDDILKTVFGQYGELVHVKI--------PAGKRCGFVQFANRTCAEQAL 327
++FVG + T++ LK +F + G +V ++ P G GF ++ ++ A A+
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKG--YGFCEYQDQETALSAM 67
Query: 328 SVLNGTQLGGQSIRLSWGRSPSNKQSDQAQWNGG 361
LNG + G+++R+ S NK+ ++ G
Sbjct: 68 RNLNGREFSGRALRVDNAASEKNKEELKSLGTGA 101
>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 = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 43/187 (22%), Positives = 91/187 (48%), Gaps = 19/187 (10%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFG-DESEQLRSMT 227
++VG + ++ + +++ F A + +K + D T + KG+ FV + E+ QL ++
Sbjct: 31 VYVGSIYYELGEDTIRQAF-APFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQL-ALE 88
Query: 228 EMNGVLCSTRPMRIGPAATKKAATGQQYQKATYQNTQGSQGENDPNNTTIFVGGLDPSVT 287
+MN V+ R +++G + + Q Q Q + ++ N I+V + ++
Sbjct: 89 QMNSVMLGGRNIKVG-----RPSNIGQAQPIIDQLAEEARAFN-----RIYVASVHQDLS 138
Query: 288 DDILKTVFGQYGELVHVKIP------AGKRCGFVQFANRTCAEQALSVLNGTQLGGQSIR 341
DD +K+VF +G++ + K GF+++ ++ A+S +N LGGQ +R
Sbjct: 139 DDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLR 198
Query: 342 LSWGRSP 348
+ +P
Sbjct: 199 VGKAVTP 205
Score = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 40/177 (22%), Positives = 80/177 (45%), Gaps = 9/177 (5%)
Query: 76 LWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQTF 135
+++G + + E I F G S + + T +G+ F+E+ AA+ L+
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 136 NGTQMPSTEQNFRLNW-ATYGAGE----RRQDDGPDFT-IFVGDLAADVTDYVLQETFRA 189
N + +N ++ + G + + ++ F I+V + D++D ++ F A
Sbjct: 91 NSVMLGG--RNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEA 148
Query: 190 VYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTEMNGVLCSTRPMRIGPAAT 246
+ +K A + D TTG+ KGYGF+ + +++ MN + +R+G A T
Sbjct: 149 -FGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVT 204
>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 = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 43/187 (22%), Positives = 91/187 (48%), Gaps = 19/187 (10%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFG-DESEQLRSMT 227
++VG + ++ + +++ F A + +K + D T + KG+ FV + E+ QL ++
Sbjct: 16 VYVGSIYYELGEDTIRQAF-APFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQL-ALE 73
Query: 228 EMNGVLCSTRPMRIGPAATKKAATGQQYQKATYQNTQGSQGENDPNNTTIFVGGLDPSVT 287
+MN V+ R +++G + + Q Q Q + ++ N I+V + ++
Sbjct: 74 QMNSVMLGGRNIKVG-----RPSNIGQAQPIIDQLAEEARAFN-----RIYVASVHQDLS 123
Query: 288 DDILKTVFGQYGELVHVKIP------AGKRCGFVQFANRTCAEQALSVLNGTQLGGQSIR 341
DD +K+VF +G++ + K GF+++ ++ A+S +N LGGQ +R
Sbjct: 124 DDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLR 183
Query: 342 LSWGRSP 348
+ +P
Sbjct: 184 VGKAVTP 190
Score = 45.4 bits (106), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 39/177 (22%), Positives = 77/177 (43%), Gaps = 9/177 (5%)
Query: 76 LWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQTF 135
+++G + + E I F G S + + T +G+ F+E+ AA+ L+
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 136 NGTQMPSTEQNFRL-NWATYGAGERRQDDGPDFT-----IFVGDLAADVTDYVLQETFRA 189
N + +N ++ + G + D + I+V + D++D ++ F A
Sbjct: 76 NSVMLGG--RNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEA 133
Query: 190 VYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTEMNGVLCSTRPMRIGPAAT 246
+ +K + D TTG+ KGYGF+ + +++ MN + +R+G A T
Sbjct: 134 -FGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVT 189
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 53.1 bits (126), Expect = 3e-07, Method: Composition-based stats.
Identities = 26/79 (32%), Positives = 48/79 (60%), Gaps = 2/79 (2%)
Query: 164 GPDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQL 223
GP ++VG L ++T+ +L+ F + ++ +++ D TGRSKGYGF+ F D
Sbjct: 25 GP-MRLYVGSLHFNITEDMLRGIFEP-FGRIESIQLMMDSETGRSKGYGFITFSDSECAK 82
Query: 224 RSMTEMNGVLCSTRPMRIG 242
+++ ++NG + RPM++G
Sbjct: 83 KALEQLNGFELAGRPMKVG 101
Score = 43.9 bits (102), Expect = 2e-04, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 44/72 (61%), Gaps = 6/72 (8%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGELVHVKIPA------GKRCGFVQFANRTCAEQALSVL 330
++VG L ++T+D+L+ +F +G + +++ K GF+ F++ CA++AL L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 331 NGTQLGGQSIRL 342
NG +L G+ +++
Sbjct: 89 NGFELAGRPMKV 100
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 22/71 (30%), Positives = 37/71 (52%)
Query: 70 SDGIRSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAE 129
S G L++G L + E + IF G S +++ + +T S+GYGFI F A+
Sbjct: 23 SAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAK 82
Query: 130 RVLQTFNGTQM 140
+ L+ NG ++
Sbjct: 83 KALEQLNGFEL 93
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 53.1 bits (126), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 46/172 (26%), Positives = 75/172 (43%), Gaps = 13/172 (7%)
Query: 73 IRSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVL 132
+R L+IG L + + S F G V+R+ T S G+GF V++A E V
Sbjct: 14 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF---VTYATVEEVD 70
Query: 133 QTFNGTQMPSTEQNFRLNWATYGAGERRQDDGPDFT---IFVGDLAADVTDYVLQETFRA 189
N P + + E Q G T IFVG + D ++ L++ F
Sbjct: 71 AAMNA--RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQ 128
Query: 190 VYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE----MNGVLCSTR 237
Y ++ +++TDR +G+ +G+ FV F D + + + +NG C R
Sbjct: 129 -YGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVR 179
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 38/152 (25%), Positives = 71/152 (46%), Gaps = 25/152 (16%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE 228
+F+G L+ + TD L+ F + ++ V+ D T RS+G+GFV + ++ E
Sbjct: 17 LFIGGLSFETTDESLRSHFEQ-WGTLTDCVVMRDPNTKRSRGFGFVTYA-------TVEE 68
Query: 229 MNGVLCSTRPMRIGPAAT--KKAATGQQYQKATYQNTQGSQGENDPNNTTIFVGGLDPSV 286
++ + + RP ++ K+A + + Q+ T IFVGG+
Sbjct: 69 VDAAM-NARPHKVDGRVVEPKRAVSREDSQRPGAHLTV----------KKIFVGGIKEDT 117
Query: 287 TDDILKTVFGQYGELVHVKIP----AGKRCGF 314
+ L+ F QYG++ ++I +GK+ GF
Sbjct: 118 EEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGF 149
Score = 30.4 bits (67), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 6/58 (10%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGEL---VHVKIPAGKRC---GFVQFANRTCAEQALS 328
+F+GGL TD+ L++ F Q+G L V ++ P KR GFV +A + A++
Sbjct: 17 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 74
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 52.8 bits (125), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 46/172 (26%), Positives = 75/172 (43%), Gaps = 13/172 (7%)
Query: 73 IRSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVL 132
+R L+IG L + + S F G V+R+ T S G+GF V++A E V
Sbjct: 11 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF---VTYATVEEVD 67
Query: 133 QTFNGTQMPSTEQNFRLNWATYGAGERRQDDGPDFT---IFVGDLAADVTDYVLQETFRA 189
N P + + E Q G T IFVG + D ++ L++ F
Sbjct: 68 AAMNA--RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQ 125
Query: 190 VYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE----MNGVLCSTR 237
Y ++ +++TDR +G+ +G+ FV F D + + + +NG C R
Sbjct: 126 -YGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVR 176
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 38/152 (25%), Positives = 71/152 (46%), Gaps = 25/152 (16%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE 228
+F+G L+ + TD L+ F + ++ V+ D T RS+G+GFV + ++ E
Sbjct: 14 LFIGGLSFETTDESLRSHFEQ-WGTLTDCVVMRDPNTKRSRGFGFVTYA-------TVEE 65
Query: 229 MNGVLCSTRPMRIG--PAATKKAATGQQYQKATYQNTQGSQGENDPNNTTIFVGGLDPSV 286
++ + + RP ++ K+A + + Q+ T IFVGG+
Sbjct: 66 VDAAM-NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKK----------IFVGGIKEDT 114
Query: 287 TDDILKTVFGQYGELVHVKIP----AGKRCGF 314
+ L+ F QYG++ ++I +GK+ GF
Sbjct: 115 EEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGF 146
Score = 30.0 bits (66), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 6/58 (10%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGEL---VHVKIPAGKRC---GFVQFANRTCAEQALS 328
+F+GGL TD+ L++ F Q+G L V ++ P KR GFV +A + A++
Sbjct: 14 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 71
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 52.8 bits (125), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 46/172 (26%), Positives = 75/172 (43%), Gaps = 13/172 (7%)
Query: 73 IRSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVL 132
+R L+IG L + + S F G V+R+ T S G+GF V++A E V
Sbjct: 13 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF---VTYATVEEVD 69
Query: 133 QTFNGTQMPSTEQNFRLNWATYGAGERRQDDGPDFT---IFVGDLAADVTDYVLQETFRA 189
N P + + E Q G T IFVG + D ++ L++ F
Sbjct: 70 AAMNA--RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQ 127
Query: 190 VYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE----MNGVLCSTR 237
Y ++ +++TDR +G+ +G+ FV F D + + + +NG C R
Sbjct: 128 -YGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVR 178
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 38/152 (25%), Positives = 71/152 (46%), Gaps = 25/152 (16%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE 228
+F+G L+ + TD L+ F + ++ V+ D T RS+G+GFV + ++ E
Sbjct: 16 LFIGGLSFETTDESLRSHFEQ-WGTLTDCVVMRDPNTKRSRGFGFVTYA-------TVEE 67
Query: 229 MNGVLCSTRPMRIG--PAATKKAATGQQYQKATYQNTQGSQGENDPNNTTIFVGGLDPSV 286
++ + + RP ++ K+A + + Q+ T IFVGG+
Sbjct: 68 VDAAM-NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKK----------IFVGGIKEDT 116
Query: 287 TDDILKTVFGQYGELVHVKIP----AGKRCGF 314
+ L+ F QYG++ ++I +GK+ GF
Sbjct: 117 EEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGF 148
Score = 30.4 bits (67), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 6/58 (10%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGEL---VHVKIPAGKRC---GFVQFANRTCAEQALS 328
+F+GGL TD+ L++ F Q+G L V ++ P KR GFV +A + A++
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
pdb|1U1K|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt 7da
Ggg); A Human Telomeric Repeat Containing
7-Deaza-Adenine
pdb|1U1L|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt Prn
Ggg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1M|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 7gu
Gg); A Human Telomeric Repeat Containing 7-Deaza-Guanine
pdb|1U1N|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta (Prn)
Gg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1O|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggttag(Di)g); A Human Telomeric Repeat Containing
Inosine
pdb|1U1P|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 2pr
Gg); A Human Telomeric Repeat Containing 2-Aminopurine
pdb|1U1Q|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggtta(Di)gg); A Human Telomeric Repeat Containing
Inosine
pdb|1U1R|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(2pr)
G); A Human Telomeric Repeat Containing 2-Aminopurine
Length = 196
Score = 52.8 bits (125), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 46/172 (26%), Positives = 75/172 (43%), Gaps = 13/172 (7%)
Query: 73 IRSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVL 132
+R L+IG L + + S F G V+R+ T S G+GF V++A E V
Sbjct: 13 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF---VTYATVEEVD 69
Query: 133 QTFNGTQMPSTEQNFRLNWATYGAGERRQDDGPDFT---IFVGDLAADVTDYVLQETFRA 189
N P + + E Q G T IFVG + D ++ L++ F
Sbjct: 70 AAMNAR--PHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQ 127
Query: 190 VYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE----MNGVLCSTR 237
Y ++ +++TDR +G+ +G+ FV F D + + + +NG C R
Sbjct: 128 -YGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVR 178
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 38/152 (25%), Positives = 71/152 (46%), Gaps = 25/152 (16%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE 228
+F+G L+ + TD L+ F + ++ V+ D T RS+G+GFV + ++ E
Sbjct: 16 LFIGGLSFETTDESLRSHFEQ-WGTLTDCVVMRDPNTKRSRGFGFVTYA-------TVEE 67
Query: 229 MNGVLCSTRPMRIG--PAATKKAATGQQYQKATYQNTQGSQGENDPNNTTIFVGGLDPSV 286
++ + + RP ++ K+A + + Q+ T IFVGG+
Sbjct: 68 VDAAM-NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKK----------IFVGGIKEDT 116
Query: 287 TDDILKTVFGQYGELVHVKIP----AGKRCGF 314
+ L+ F QYG++ ++I +GK+ GF
Sbjct: 117 EEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGF 148
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 6/58 (10%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGEL---VHVKIPAGKRC---GFVQFANRTCAEQALS 328
+F+GGL TD+ L++ F Q+G L V ++ P KR GFV +A + A++
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex
pdb|1PO6|A Chain A, Crystal Structure Of Up1 Complexed With
D(Tagg(6mi)ttaggg): A Human Telomeric Repeat Containing
6-Methyl-8-(2-Deoxy-
Beta-Ribofuranosyl)isoxanthopteridine (6mi)
Length = 183
Score = 52.8 bits (125), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 46/172 (26%), Positives = 75/172 (43%), Gaps = 13/172 (7%)
Query: 73 IRSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVL 132
+R L+IG L + + S F G V+R+ T S G+GF V++A E V
Sbjct: 6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF---VTYATVEEVD 62
Query: 133 QTFNGTQMPSTEQNFRLNWATYGAGERRQDDGPDFT---IFVGDLAADVTDYVLQETFRA 189
N P + + E Q G T IFVG + D ++ L++ F
Sbjct: 63 AAMNA--RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQ 120
Query: 190 VYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE----MNGVLCSTR 237
Y ++ +++TDR +G+ +G+ FV F D + + + +NG C R
Sbjct: 121 -YGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVR 171
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 38/152 (25%), Positives = 71/152 (46%), Gaps = 25/152 (16%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE 228
+F+G L+ + TD L+ F + ++ V+ D T RS+G+GFV + ++ E
Sbjct: 9 LFIGGLSFETTDESLRSHFEQ-WGTLTDCVVMRDPNTKRSRGFGFVTYA-------TVEE 60
Query: 229 MNGVLCSTRPMRIG--PAATKKAATGQQYQKATYQNTQGSQGENDPNNTTIFVGGLDPSV 286
++ + + RP ++ K+A + + Q+ T IFVGG+
Sbjct: 61 VDAAM-NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKK----------IFVGGIKEDT 109
Query: 287 TDDILKTVFGQYGELVHVKIP----AGKRCGF 314
+ L+ F QYG++ ++I +GK+ GF
Sbjct: 110 EEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGF 141
Score = 30.4 bits (67), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 6/58 (10%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGEL---VHVKIPAGKRC---GFVQFANRTCAEQALS 328
+F+GGL TD+ L++ F Q+G L V ++ P KR GFV +A + A++
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66
>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi)
G); A Human Telomeric Repeat Containing 6-Methyl-8-(2-
Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi)
Length = 195
Score = 52.8 bits (125), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 46/172 (26%), Positives = 75/172 (43%), Gaps = 13/172 (7%)
Query: 73 IRSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVL 132
+R L+IG L + + S F G V+R+ T S G+GF V++A E V
Sbjct: 12 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF---VTYATVEEVD 68
Query: 133 QTFNGTQMPSTEQNFRLNWATYGAGERRQDDGPDFT---IFVGDLAADVTDYVLQETFRA 189
N P + + E Q G T IFVG + D ++ L++ F
Sbjct: 69 AAMNA--RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQ 126
Query: 190 VYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE----MNGVLCSTR 237
Y ++ +++TDR +G+ +G+ FV F D + + + +NG C R
Sbjct: 127 -YGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVR 177
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 38/152 (25%), Positives = 71/152 (46%), Gaps = 25/152 (16%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE 228
+F+G L+ + TD L+ F + ++ V+ D T RS+G+GFV + ++ E
Sbjct: 15 LFIGGLSFETTDESLRSHFEQ-WGTLTDCVVMRDPNTKRSRGFGFVTYA-------TVEE 66
Query: 229 MNGVLCSTRPMRIG--PAATKKAATGQQYQKATYQNTQGSQGENDPNNTTIFVGGLDPSV 286
++ + + RP ++ K+A + + Q+ T IFVGG+
Sbjct: 67 VDAAM-NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKK----------IFVGGIKEDT 115
Query: 287 TDDILKTVFGQYGELVHVKIP----AGKRCGF 314
+ L+ F QYG++ ++I +GK+ GF
Sbjct: 116 EEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGF 147
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 6/58 (10%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGEL---VHVKIPAGKRC---GFVQFANRTCAEQALS 328
+F+GGL TD+ L++ F Q+G L V ++ P KR GFV +A + A++
Sbjct: 15 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 72
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 52.4 bits (124), Expect = 5e-07, Method: Composition-based stats.
Identities = 26/74 (35%), Positives = 44/74 (59%), Gaps = 1/74 (1%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE 228
++VG L ++T+ +L+ F + + ++ D TGRSKGYGF+ F D R++ +
Sbjct: 8 LYVGSLHFNITEDMLRGIFEP-FGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66
Query: 229 MNGVLCSTRPMRIG 242
+NG + RPMR+G
Sbjct: 67 LNGFELAGRPMRVG 80
Score = 42.7 bits (99), Expect = 4e-04, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 46/75 (61%), Gaps = 6/75 (8%)
Query: 274 NTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPA------GKRCGFVQFANRTCAEQAL 327
++ ++VG L ++T+D+L+ +F +G++ ++ + K GF+ F++ CA +AL
Sbjct: 5 SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
Query: 328 SVLNGTQLGGQSIRL 342
LNG +L G+ +R+
Sbjct: 65 EQLNGFELAGRPMRV 79
Score = 38.9 bits (89), Expect = 0.006, Method: Composition-based stats.
Identities = 22/71 (30%), Positives = 36/71 (50%)
Query: 70 SDGIRSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAE 129
S G L++G L + E + IF G+ + ++++ T S+GYGFI F A
Sbjct: 2 SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECAR 61
Query: 130 RVLQTFNGTQM 140
R L+ NG ++
Sbjct: 62 RALEQLNGFEL 72
>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 = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 45/201 (22%), Positives = 93/201 (46%), Gaps = 19/201 (9%)
Query: 155 GAGERRQDDGPDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFV 214
GA +R++ ++VG + ++ + +++ F A + +K D T + KG+ FV
Sbjct: 1 GAAQRQRALAIXCRVYVGSIYYELGEDTIRQAF-APFGPIKSIDXSWDSVTXKHKGFAFV 59
Query: 215 RFG-DESEQLRSMTEMNGVLCSTRPMRIGPAATKKAATGQQYQKATYQNTQGSQGENDPN 273
+ E+ QL ++ + N V R +++G + + Q Q Q + ++ N
Sbjct: 60 EYEVPEAAQL-ALEQXNSVXLGGRNIKVG-----RPSNIGQAQPIIDQLAEEARAFN--- 110
Query: 274 NTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIP------AGKRCGFVQFANRTCAEQAL 327
I+V + ++DD +K+VF +G++ + K GF+++ ++ A+
Sbjct: 111 --RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAV 168
Query: 328 SVLNGTQLGGQSIRLSWGRSP 348
S N LGGQ +R+ +P
Sbjct: 169 SSXNLFDLGGQYLRVGKAVTP 189
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 38/177 (21%), Positives = 75/177 (42%), Gaps = 9/177 (5%)
Query: 76 LWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQTF 135
+++G + + E I F G S + T +G+ F+E+ AA+ L+
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 136 NGTQMPSTEQNFRL-NWATYGAGERRQDDGPDFT-----IFVGDLAADVTDYVLQETFRA 189
N + +N ++ + G + D + I+V + D++D ++ F A
Sbjct: 75 NSVXLGG--RNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEA 132
Query: 190 VYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTEMNGVLCSTRPMRIGPAAT 246
+ +K + D TTG+ KGYGF+ + +++ N + +R+G A T
Sbjct: 133 -FGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVGKAVT 188
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 49.7 bits (117), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 42/81 (51%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE 228
IF+G+L ++ + +L +TF A ++ K++ D TG SKGY F+ F ++
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 229 MNGVLCSTRPMRIGPAATKKA 249
MNG RP+ + A K +
Sbjct: 68 MNGQYLCNRPITVSYAFKKDS 88
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 38/69 (55%), Gaps = 1/69 (1%)
Query: 70 SDGIRSLWIGDLQPWMEESYIASIFGHTGEFV-SGKVIRNKQTNFSEGYGFIEFVSHAAA 128
S G ++IG+L P ++E + F G + + K++R+ T S+GY FI F S A+
Sbjct: 2 SSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDAS 61
Query: 129 ERVLQTFNG 137
+ ++ NG
Sbjct: 62 DAAIEAMNG 70
Score = 38.1 bits (87), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 40/84 (47%), Gaps = 7/84 (8%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGELVHV-KIPAGKRCG------FVQFANRTCAEQALSV 329
IF+G LDP + + +L F +G ++ KI G F+ FA+ ++ A+
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 330 LNGTQLGGQSIRLSWGRSPSNKQS 353
+NG L + I +S+ +K S
Sbjct: 68 MNGQYLCNRPITVSYAFKKDSKGS 91
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 49.7 bits (117), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 40/165 (24%), Positives = 68/165 (41%), Gaps = 39/165 (23%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE 228
+FVG+L D+T+ E F+ ++ V R +G+GF+R + + E
Sbjct: 25 LFVGNLPTDITE----EDFKRLFERYGEPSEVF---INRDRGFGFIRLESRTLAEIAKAE 77
Query: 229 MNGVLCSTRPMRIGPAATKKAATGQQYQKATYQNTQGSQGENDPNNTTIFVGGLDPSVTD 288
++G + +RP+RI A A T V L P V++
Sbjct: 78 LDGTILKSRPLRIRFATHGAALT---------------------------VKNLSPVVSN 110
Query: 289 DILKTVFGQYGELVHVKIPAGKR-----CGFVQFANRTCAEQALS 328
++L+ F Q+G + + R GFV+FA + A +AL
Sbjct: 111 ELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALE 155
Score = 48.5 bits (114), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 53/205 (25%), Positives = 85/205 (41%), Gaps = 34/205 (16%)
Query: 76 LWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQTF 135
L++G+L + E +F GE +V N+ G+GFI S AE
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGE--PSEVFINR----DRGFGFIRLESRTLAEIAKAEL 78
Query: 136 NGTQMPSTEQNFRLNWATYGAGERRQDDGPDFTIFVGDLAADVTDYVLQETFRAVYSSVK 195
+GT + S + R+ +AT+GA + V +L+ V++ +L++ F K
Sbjct: 79 DGTILKS--RPLRIRFATHGAA-----------LTVKNLSPVVSNELLEQAFSQFGPVEK 125
Query: 196 GAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTEM-NGVLCST---RPMRIGPA------- 244
VV DR GR+ G GFV F + +++ +G T RP+ + P
Sbjct: 126 AVVVVDDR--GRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDDED 183
Query: 245 --ATKKAATGQQYQKATYQNTQGSQ 267
K QQY K Q + +Q
Sbjct: 184 GLPEKLMQKTQQYHKEREQPPRFAQ 208
Score = 48.5 bits (114), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 40/69 (57%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRCGFVQFANRTCAEQALSVLNGTQLG 336
+FVG L +T++ K +F +YGE V I + GF++ +RT AE A + L+GT L
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTILK 84
Query: 337 GQSIRLSWG 345
+ +R+ +
Sbjct: 85 SRPLRIRFA 93
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 49.7 bits (117), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 49/80 (61%), Gaps = 3/80 (3%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE 228
++V +L + D L++ F + + ++ AKV+ + GRSKG+GFV F E +++TE
Sbjct: 18 LYVKNLDDGIDDERLRKAF-SPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTE 74
Query: 229 MNGVLCSTRPMRIGPAATKK 248
MNG + +T+P+ + A K+
Sbjct: 75 MNGRIVATKPLYVALAQRKE 94
Score = 33.1 bits (74), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 40/81 (49%), Gaps = 4/81 (4%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGELVHVKIPA----GKRCGFVQFANRTCAEQALSVLNG 332
++V LD + D+ L+ F +G + K+ K GFV F++ A +A++ +NG
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNG 77
Query: 333 TQLGGQSIRLSWGRSPSNKQS 353
+ + + ++ + +QS
Sbjct: 78 RIVATKPLYVALAQRKEERQS 98
Score = 28.9 bits (63), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 16/65 (24%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 73 IRSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVL 132
+ +L++ +L +++ + F G S KV+ + S+G+GF+ F S A + +
Sbjct: 15 VVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVM--MEGGRSKGFGFVCFSSPEEATKAV 72
Query: 133 QTFNG 137
NG
Sbjct: 73 TEMNG 77
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 49.3 bits (116), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 27/57 (47%), Positives = 37/57 (64%), Gaps = 4/57 (7%)
Query: 165 PDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESE 221
P T+FV L+ D T+ L+E+F SV+ A++VTDR TG SKG+GFV F E +
Sbjct: 14 PSKTLFVKGLSEDTTEETLKESFDG---SVR-ARIVTDRETGSSKGFGFVDFNSEED 66
Score = 35.0 bits (79), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 39/93 (41%), Gaps = 14/93 (15%)
Query: 265 GSQGENDPN-----NTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRCG------ 313
GS G + PN + T+FV GL T++ LK F V +I + G
Sbjct: 1 GSSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFG 57
Query: 314 FVQFANRTCAEQALSVLNGTQLGGQSIRLSWGR 346
FV F + A+ A + ++ G + L W +
Sbjct: 58 FVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAK 90
Score = 31.2 bits (69), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 19/87 (21%), Positives = 41/87 (47%), Gaps = 5/87 (5%)
Query: 66 PDASSDGIRSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSH 125
P+A S ++L++ L E + F + V +++ +++T S+G+GF++F S
Sbjct: 8 PNARSQPSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSE 64
Query: 126 AAAERVLQTFNGTQMPSTEQNFRLNWA 152
A+ + ++ L+WA
Sbjct: 65 EDAKAAKEAMEDGEIDG--NKVTLDWA 89
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 48.5 bits (114), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 40/73 (54%)
Query: 273 NNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRCGFVQFANRTCAEQALSVLNG 332
+ +FVG L P +T++ ++ +F +YG+ V I K GF++ RT AE A L+
Sbjct: 21 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDN 80
Query: 333 TQLGGQSIRLSWG 345
L G+ +R+ +
Sbjct: 81 MPLRGKQLRVRFA 93
>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|B Chain B, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|C Chain C, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|D Chain D, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
Length = 84
Score = 48.5 bits (114), Expect = 7e-06, Method: Composition-based stats.
Identities = 26/71 (36%), Positives = 39/71 (54%)
Query: 72 GIRSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERV 131
G +L + L M + + S+F GE S K+IR+K S GYGF+ +V+ AER
Sbjct: 3 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 62
Query: 132 LQTFNGTQMPS 142
+ T NG ++ S
Sbjct: 63 INTLNGLRLQS 73
Score = 42.4 bits (98), Expect = 4e-04, Method: Composition-based stats.
Identities = 25/81 (30%), Positives = 43/81 (53%), Gaps = 6/81 (7%)
Query: 272 PNNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRCG------FVQFANRTCAEQ 325
P T + V L ++T D L+++F GE+ K+ K G FV + AE+
Sbjct: 2 PGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 61
Query: 326 ALSVLNGTQLGGQSIRLSWGR 346
A++ LNG +L ++I++S+ R
Sbjct: 62 AINTLNGLRLQSKTIKVSYAR 82
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 38/64 (59%), Gaps = 3/64 (4%)
Query: 184 QETFRAVYSS---VKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTEMNGVLCSTRPMR 240
Q+ R+++SS V+ AK++ D+ G S GYGFV + + R++ +NG+ ++ ++
Sbjct: 18 QDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIK 77
Query: 241 IGPA 244
+ A
Sbjct: 78 VSYA 81
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 48.1 bits (113), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 25/65 (38%), Positives = 38/65 (58%), Gaps = 1/65 (1%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE 228
IFVG L TD L++ F + ++ A V+TDR TG+S+GYGFV D + R+ +
Sbjct: 20 IFVGGLPYHTTDASLRKYFEG-FGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 229 MNGVL 233
N ++
Sbjct: 79 PNPII 83
Score = 36.6 bits (83), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 30/61 (49%)
Query: 76 LWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQTF 135
+++G L ++ + F G+ VI ++QT S GYGF+ AAAER +
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79
Query: 136 N 136
N
Sbjct: 80 N 80
Score = 33.9 bits (76), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 32/69 (46%), Gaps = 6/69 (8%)
Query: 269 ENDPNNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRC------GFVQFANRTC 322
+ D T IFVGGL TD L+ F +G++ + ++ GFV A+R
Sbjct: 12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAA 71
Query: 323 AEQALSVLN 331
AE+A N
Sbjct: 72 AERACKDPN 80
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 48.1 bits (113), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE 228
+FVG L+ D + L++ F + Y + VV DR T RS+G+GFV F + + +M
Sbjct: 15 LFVGGLSFDTNEQSLEQVF-SKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 229 MNGVLCSTRPMRIGPA 244
MNG R +R+ A
Sbjct: 74 MNGKSVDGRQIRVDQA 89
Score = 45.4 bits (106), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 30/82 (36%), Positives = 44/82 (53%), Gaps = 7/82 (8%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYG---ELVHVKIPAGKRC---GFVQFANRTCAEQALSVL 330
+FVGGL + L+ VF +YG E+V VK +R GFV F N A+ A+ +
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 331 NGTQLGGQSIRLSW-GRSPSNK 351
NG + G+ IR+ G+S N+
Sbjct: 75 NGKSVDGRQIRVDQAGKSSDNR 96
Score = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 31/62 (50%)
Query: 76 LWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQTF 135
L++G L E + +F G+ V+++++T S G+GF+ F + A+ +
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 136 NG 137
NG
Sbjct: 75 NG 76
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 48.1 bits (113), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 32/89 (35%), Positives = 47/89 (52%), Gaps = 7/89 (7%)
Query: 274 NTTIFVGGLDPS-VTDDILKTVFGQYGELVHVKIPAGKR-CGFVQFANRTCAEQALSVLN 331
N+ + V L+P VT L +FG YG++ VKI K+ VQ A+ A+ A+S LN
Sbjct: 3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLN 62
Query: 332 GTQLGGQSIRLSWGRS-----PSNKQSDQ 355
G +L G+ IR++ + P Q DQ
Sbjct: 63 GHKLHGKPIRITLSKHQNVQLPREGQEDQ 91
>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 = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 32/89 (35%), Positives = 47/89 (52%), Gaps = 7/89 (7%)
Query: 274 NTTIFVGGLDPS-VTDDILKTVFGQYGELVHVKIPAGKR-CGFVQFANRTCAEQALSVLN 331
N+ + V L+P VT L +FG YG++ VKI K+ VQ A+ A+ A+S LN
Sbjct: 34 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLN 93
Query: 332 GTQLGGQSIRLSWGRS-----PSNKQSDQ 355
G +L G+ IR++ + P Q DQ
Sbjct: 94 GHKLHGKPIRITLSKHQNVQLPREGQEDQ 122
>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 = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 41/145 (28%), Positives = 65/145 (44%), Gaps = 24/145 (16%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE 228
+F+G L D T+ L+E F Y +V K++ D TGRS+G+GF+ F E+ S+ E
Sbjct: 6 MFIGGLNWDTTEDNLREYF-GKYGTVTDLKIMKDPATGRSRGFGFLSF----EKPSSVDE 60
Query: 229 MNGVLCSTRPMRIGPAATKKAATGQQYQKATYQNTQGSQGENDPNNTTIFVGGLDPSVTD 288
+ T+ + G K A + Q T + IFVGG+ P V
Sbjct: 61 ----VVKTQHILDGKVIDPKRAIPRDEQDKTGK---------------IFVGGIGPDVRP 101
Query: 289 DILKTVFGQYGELVHVKIPAGKRCG 313
+ F Q+G ++ ++ K G
Sbjct: 102 KEFEEFFSQWGTIIDAQLMLDKDTG 126
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 40/176 (22%), Positives = 78/176 (44%), Gaps = 17/176 (9%)
Query: 75 SLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQT 134
++IG L E + FG G K++++ T S G+GF+ F ++ + V++T
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 135 ---FNGTQMPSTEQNFRLNWATYGAGERRQDDGPDFTIFVGDLAADVTDYVLQETFRAVY 191
+G + R G IFVG + DV +E F + +
Sbjct: 65 QHILDGKVIDPKRAIPRDEQDKTGK------------IFVGGIGPDVRPKEFEEFF-SQW 111
Query: 192 SSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTEMNGVLCSTRPMRIGPAATK 247
++ A+++ D+ TG+S+G+GFV + D ++ + + + + R + I A +
Sbjct: 112 GTIIDAQLMLDKDTGQSRGFGFVTY-DSADAVDRVCQNKFIDFKDRKIEIKRAEPR 166
Score = 34.7 bits (78), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 31/68 (45%)
Query: 66 PDASSDGIRSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSH 125
P D +++G + P + F G + +++ +K T S G+GF+ + S
Sbjct: 80 PRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSA 139
Query: 126 AAAERVLQ 133
A +RV Q
Sbjct: 140 DAVDRVCQ 147
Score = 34.3 bits (77), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 37/69 (53%), Gaps = 9/69 (13%)
Query: 273 NNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKI---PAGKRC---GFVQFANRTCAEQA 326
+ +F+GGL+ T+D L+ FG+YG + +KI PA R GF+ F + ++
Sbjct: 2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61
Query: 327 LS---VLNG 332
+ +L+G
Sbjct: 62 VKTQHILDG 70
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 37/69 (53%)
Query: 70 SDGIRSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAE 129
S G L+I LQP + + + G+ VS K I +K TN +GYGF++F S +AA+
Sbjct: 2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQ 61
Query: 130 RVLQTFNGT 138
+ + +
Sbjct: 62 KAVTALKAS 70
Score = 34.7 bits (78), Expect = 0.098, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE 228
+++ L TD L + + Y + K + D+TT + KGYGFV F S +++T
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQP-YGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA 66
Query: 229 MN 230
+
Sbjct: 67 LK 68
Score = 32.7 bits (73), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 37/73 (50%), Gaps = 6/73 (8%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGK---RC---GFVQFANRTCAEQALSVL 330
+++ GL P TD L + YG++V K K +C GFV F + + A++A++ L
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
Query: 331 NGTQLGGQSIRLS 343
+ + Q + S
Sbjct: 68 KASGVQAQMAKQS 80
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 47.0 bits (110), Expect = 2e-05, Method: Composition-based stats.
Identities = 26/79 (32%), Positives = 45/79 (56%), Gaps = 2/79 (2%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRCGFVQFANRTCAEQALSVLNGTQLG 336
+FV L +VT++IL+ F Q+G+L VK K F+ F R A +A+ +NG L
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVK--KLKDYAFIHFDERDGAVKAMEEMNGKDLE 71
Query: 337 GQSIRLSWGRSPSNKQSDQ 355
G++I + + + P K+ ++
Sbjct: 72 GENIEIVFAKPPDQKRKER 90
Score = 30.4 bits (67), Expect = 1.8, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 34/63 (53%), Gaps = 9/63 (14%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE 228
+FV +LA VT+ +L++ F + + ++ K + D Y F+ F + +++M E
Sbjct: 14 LFVRNLANTVTEEILEKAF-SQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEE 64
Query: 229 MNG 231
MNG
Sbjct: 65 MNG 67
>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 = 46.6 bits (109), Expect = 3e-05, Method: Composition-based stats.
Identities = 22/53 (41%), Positives = 32/53 (60%)
Query: 90 IASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQTFNGTQMPS 142
+ S+F GE S K+IR+K S GYGF+ +V+ AER + T NG ++ S
Sbjct: 36 LRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQS 88
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 38/64 (59%), Gaps = 3/64 (4%)
Query: 184 QETFRAVYSS---VKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTEMNGVLCSTRPMR 240
Q+ R+++SS V+ AK++ D+ G S GYGFV + + R++ +NG+ ++ ++
Sbjct: 33 QDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIK 92
Query: 241 IGPA 244
+ A
Sbjct: 93 VSYA 96
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 24/78 (30%), Positives = 41/78 (52%), Gaps = 6/78 (7%)
Query: 275 TTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRCG------FVQFANRTCAEQALS 328
T + V L + T D L+++F GE+ K+ K G FV + AE+A++
Sbjct: 20 TNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 79
Query: 329 VLNGTQLGGQSIRLSWGR 346
LNG +L ++I++S+ R
Sbjct: 80 TLNGLRLQSKTIKVSYAR 97
>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 = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 28/76 (36%), Positives = 41/76 (53%), Gaps = 6/76 (7%)
Query: 274 NTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRCG------FVQFANRTCAEQAL 327
+T ++V L ++TDD L T+FG+YG +V I K G FV++ R A++A+
Sbjct: 13 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 72
Query: 328 SVLNGTQLGGQSIRLS 343
S LN G S LS
Sbjct: 73 SALNNVIPEGGSQPLS 88
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 166 DFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRS 225
D ++V +L +TD L F Y S+ ++ D+ TGR +G FVR+ E +
Sbjct: 13 DTNLYVTNLPRTITDDQLDTIF-GKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 71
Query: 226 MTEMNGVL 233
++ +N V+
Sbjct: 72 ISALNNVI 79
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 14/62 (22%), Positives = 29/62 (46%)
Query: 75 SLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQT 134
+L++ +L + + + +IFG G V ++R+K T G F+ + A+ +
Sbjct: 15 NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 74
Query: 135 FN 136
N
Sbjct: 75 LN 76
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 46.2 bits (108), Expect = 3e-05, Method: Composition-based stats.
Identities = 27/80 (33%), Positives = 45/80 (56%), Gaps = 3/80 (3%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE 228
IF+ +L + + L +TF A + ++ KVV D SKGYGFV F + R++ +
Sbjct: 14 IFIKNLDKSIDNKALYDTFSA-FGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEK 70
Query: 229 MNGVLCSTRPMRIGPAATKK 248
MNG+L + R + +G ++K
Sbjct: 71 MNGMLLNDRKVFVGRFKSRK 90
Score = 43.5 bits (101), Expect = 2e-04, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 2/75 (2%)
Query: 63 GVAPDASSDGIRSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEF 122
G P G+ +++I +L ++ + F G +S KV+ ++ N S+GYGF+ F
Sbjct: 1 GADPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHF 58
Query: 123 VSHAAAERVLQTFNG 137
+ AAER ++ NG
Sbjct: 59 ETQEAAERAIEKMNG 73
Score = 38.1 bits (87), Expect = 0.009, Method: Composition-based stats.
Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 6/82 (7%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGELVHVKI----PAGKRCGFVQFANRTCAEQALSVLNG 332
IF+ LD S+ + L F +G ++ K+ K GFV F + AE+A+ +NG
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 73
Query: 333 TQLGGQSIRLSWGRSPSNKQSD 354
L + + + GR S K+ +
Sbjct: 74 MLLNDRKVFV--GRFKSRKERE 93
>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 = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 29/84 (34%), Positives = 45/84 (53%), Gaps = 1/84 (1%)
Query: 164 GPDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQL 223
G F +FVGDL+ ++T + F + + A+VV D TG+SKGYGFV F ++ +
Sbjct: 4 GSHFHVFVGDLSPEITTAAIAAAFAP-FGRISDARVVKDMATGKSKGYGFVSFFNKWDAE 62
Query: 224 RSMTEMNGVLCSTRPMRIGPAATK 247
++ +M G R +R A K
Sbjct: 63 NAIQQMGGQWLGGRQIRTNWATRK 86
Score = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 41/78 (52%), Gaps = 2/78 (2%)
Query: 76 LWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQTF 135
+++GDL P + + IA+ F G +V+++ T S+GYGF+ F + AE +Q
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 136 NGTQMPSTEQNFRLNWAT 153
G + + R NWAT
Sbjct: 69 GGQWLGGRQ--IRTNWAT 84
Score = 37.0 bits (84), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 38/79 (48%), Gaps = 7/79 (8%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGELVHVKIPA------GKRCGFVQFANRTCAEQALSVL 330
+FVG L P +T + F +G + ++ K GFV F N+ AE A+ +
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 331 NGTQLGGQSIRLSWG-RSP 348
G LGG+ IR +W R P
Sbjct: 69 GGQWLGGRQIRTNWATRKP 87
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 45.4 bits (106), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 25/94 (26%), Positives = 49/94 (52%), Gaps = 4/94 (4%)
Query: 67 DASSDGIRSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHA 126
+ D +R+L + + ++E + +F G S K++ +++T S GYGF++F S +
Sbjct: 36 NPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGS 95
Query: 127 AAERVLQTFNGTQMPSTEQNFRLNWATYGAGERR 160
+A++ + NG + N RL A +G +R
Sbjct: 96 SAQQAIAGLNGFNI----LNKRLKVALAASGHQR 125
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 44/84 (52%), Gaps = 3/84 (3%)
Query: 165 PDF--TIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQ 222
PD + V + V + L++ F Y ++ K+V DR T +S+GYGFV+F S
Sbjct: 39 PDVLRNLMVNYIPTTVDEVQLRQLFER-YGPIESVKIVCDRETRQSRGYGFVKFQSGSSA 97
Query: 223 LRSMTEMNGVLCSTRPMRIGPAAT 246
+++ +NG + +++ AA+
Sbjct: 98 QQAIAGLNGFNILNKRLKVALAAS 121
Score = 35.4 bits (80), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 40/71 (56%), Gaps = 7/71 (9%)
Query: 284 PSVTDDI-LKTVFGQYGELVHVKIPAGKRC------GFVQFANRTCAEQALSVLNGTQLG 336
P+ D++ L+ +F +YG + VKI + GFV+F + + A+QA++ LNG +
Sbjct: 51 PTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNIL 110
Query: 337 GQSIRLSWGRS 347
+ ++++ S
Sbjct: 111 NKRLKVALAAS 121
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 45.4 bits (106), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 41/185 (22%), Positives = 77/185 (41%), Gaps = 34/185 (18%)
Query: 163 DGPDF---TIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTG--RSKGYGFVRFG 217
D PD +FVG + ++ L+E F Y +V V+ DR+ +SKG FV F
Sbjct: 9 DQPDLDAIKMFVGQVPRTWSEKDLRELFEQ-YGAVYEINVLRDRSQNPPQSKGCCFVTFY 67
Query: 218 DESEQLRSMTEMNGVLC---STRPMRIGPAATKKAATGQQYQKATYQNTQGSQGENDPNN 274
L + ++ + P+++ PA ++K N +
Sbjct: 68 TRKAALEAQNALHNMKVLPGMHHPIQMKPADSEK--------------------NNAVED 107
Query: 275 TTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAG-----KRCGFVQFANRTCAEQALSV 329
+F+G + T++ ++ +F +G++ +I G + C FV F R A+ A+
Sbjct: 108 RKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKA 167
Query: 330 LNGTQ 334
++ Q
Sbjct: 168 MHQAQ 172
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 45.4 bits (106), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 42/184 (22%), Positives = 75/184 (40%), Gaps = 23/184 (12%)
Query: 167 FTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSM 226
F +FVG+L + + L+ V++ K V D G ++ +G+V F + +E L
Sbjct: 8 FNLFVGNLNFNKSAPELKTGISDVFA--KNDLAVVDVRIGMTRKFGYVDF-ESAEDLEKA 64
Query: 227 TEMNGVLCSTRPMRIGPAATKKAATGQQYQKATYQNTQGSQGENDPNNTTIFVGGLDPSV 286
E+ G+ +++ + +G + + + T+ L V
Sbjct: 65 LELTGLKVFGNEIKL-------------------EKPKGKDSKKERDARTLLAKNLPYKV 105
Query: 287 TDDILKTVFGQYGELVHV-KIPAGKRCGFVQFANRTCAEQALSVLNGTQLGGQSIRLSWG 345
T D LK VF E+ V K K +++F AE+ GT++ G+SI L +
Sbjct: 106 TQDELKEVFEDAAEIRLVSKDGKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSISLYYT 165
Query: 346 RSPS 349
P
Sbjct: 166 GEPK 169
>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 = 45.4 bits (106), Expect = 6e-05, Method: Composition-based stats.
Identities = 34/86 (39%), Positives = 48/86 (55%), Gaps = 14/86 (16%)
Query: 168 TIFVG--DLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFG---DESEQ 222
T+FVG D+ D T+ +F A Y SVK K++TDR TG SKGYGFV F D +
Sbjct: 11 TVFVGGIDVRMDETEI---RSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKI 66
Query: 223 LRSMTEMNGVLCSTRPMRIGPAATKK 248
+ S +G + +++GPA K+
Sbjct: 67 VESQINFHG-----KKLKLGPAIRKQ 87
Score = 37.4 bits (85), Expect = 0.014, Method: Composition-based stats.
Identities = 22/88 (25%), Positives = 46/88 (52%), Gaps = 4/88 (4%)
Query: 75 SLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQT 134
++++G + M+E+ I S F G K+I ++ T S+GYGF+ F + ++++++
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVES 69
Query: 135 ---FNGTQMPSTEQNFRLNWATYGAGER 159
F+G ++ + N +TY R
Sbjct: 70 QINFHGKKLKLGPAIRKQNLSTYHVQPR 97
Score = 34.3 bits (77), Expect = 0.13, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 7/58 (12%)
Query: 267 QGENDPNNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKI-----PAGKRCGFVQFAN 319
+G+ PN T+FVGG+D + + +++ F +YG + VKI K GFV F N
Sbjct: 4 EGKIMPN--TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYN 59
>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 = 45.1 bits (105), Expect = 7e-05, Method: Composition-based stats.
Identities = 27/80 (33%), Positives = 45/80 (56%), Gaps = 3/80 (3%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE 228
IF+ +L + + L +TF A + ++ KVV D SKGYGFV F + R++ +
Sbjct: 8 IFIKNLDKSIDNKALYDTFSA-FGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEK 64
Query: 229 MNGVLCSTRPMRIGPAATKK 248
MNG+L + R + +G ++K
Sbjct: 65 MNGMLLNDRKVFVGRFKSRK 84
Score = 37.7 bits (86), Expect = 0.013, Method: Composition-based stats.
Identities = 21/66 (31%), Positives = 37/66 (56%), Gaps = 2/66 (3%)
Query: 72 GIRSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERV 131
G +++I +L ++ + F G +S KV+ ++ N S+GYGF+ F + AAER
Sbjct: 4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERA 61
Query: 132 LQTFNG 137
++ NG
Sbjct: 62 IEKMNG 67
Score = 37.0 bits (84), Expect = 0.018, Method: Composition-based stats.
Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 6/82 (7%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGELVHVKI----PAGKRCGFVQFANRTCAEQALSVLNG 332
IF+ LD S+ + L F +G ++ K+ K GFV F + AE+A+ +NG
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 67
Query: 333 TQLGGQSIRLSWGRSPSNKQSD 354
L + + + GR S K+ +
Sbjct: 68 MLLNDRKVFV--GRFKSRKERE 87
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 45.1 bits (105), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 34/86 (39%), Positives = 48/86 (55%), Gaps = 14/86 (16%)
Query: 168 TIFVG--DLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRF---GDESEQ 222
T+FVG D+ D T+ +F A Y SVK K++TDR TG SKGYGFV F D +
Sbjct: 12 TVFVGGIDVRMDETEI---RSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKI 67
Query: 223 LRSMTEMNGVLCSTRPMRIGPAATKK 248
+ S +G + +++GPA K+
Sbjct: 68 VESQINFHG-----KKLKLGPAIRKQ 88
Score = 37.0 bits (84), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 40/69 (57%), Gaps = 4/69 (5%)
Query: 75 SLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQT 134
++++G + M+E+ I S F G K+I ++ T S+GYGF+ F + ++++++
Sbjct: 12 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVES 70
Query: 135 ---FNGTQM 140
F+G ++
Sbjct: 71 QINFHGKKL 79
Score = 33.1 bits (74), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 34/65 (52%), Gaps = 7/65 (10%)
Query: 268 GENDPNNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIP-----AGKRCGFVQFANRTC 322
G+ PN T+FVGG+D + + +++ F +YG + VKI K GFV F N
Sbjct: 6 GKIMPN--TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVD 63
Query: 323 AEQAL 327
++ +
Sbjct: 64 VQKIV 68
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 44.7 bits (104), Expect = 9e-05, Method: Composition-based stats.
Identities = 20/70 (28%), Positives = 43/70 (61%), Gaps = 3/70 (4%)
Query: 184 QETFRAVYSSV---KGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTEMNGVLCSTRPMR 240
Q+ F++++ S+ + K+V D+ TG+S GYGFV + D ++ +++ +NG+ T+ ++
Sbjct: 18 QDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIK 77
Query: 241 IGPAATKKAA 250
+ A A+
Sbjct: 78 VSYARPSSAS 87
Score = 41.6 bits (96), Expect = 7e-04, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 38/72 (52%)
Query: 71 DGIRSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAER 130
D +L + L M + S+FG G+ S K++R+K T S GYGF+ + A++
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 131 VLQTFNGTQMPS 142
+ T NG ++ +
Sbjct: 62 AINTLNGLKLQT 73
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 24/83 (28%), Positives = 46/83 (55%), Gaps = 6/83 (7%)
Query: 273 NNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRCG------FVQFANRTCAEQA 326
+ T + V L ++T D K++FG G++ K+ K G FV +++ A++A
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 327 LSVLNGTQLGGQSIRLSWGRSPS 349
++ LNG +L ++I++S+ R S
Sbjct: 63 INTLNGLKLQTKTIKVSYARPSS 85
>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 = 44.7 bits (104), Expect = 1e-04, Method: Composition-based stats.
Identities = 34/86 (39%), Positives = 48/86 (55%), Gaps = 14/86 (16%)
Query: 168 TIFVG--DLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFG---DESEQ 222
T+FVG D+ D T+ +F A Y SVK K++TDR TG SKGYGFV F D +
Sbjct: 11 TVFVGGIDVRMDETEI---RSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKI 66
Query: 223 LRSMTEMNGVLCSTRPMRIGPAATKK 248
+ S +G + +++GPA K+
Sbjct: 67 VESQINFHG-----KKLKLGPAIRKQ 87
Score = 35.4 bits (80), Expect = 0.051, Method: Composition-based stats.
Identities = 18/69 (26%), Positives = 40/69 (57%), Gaps = 4/69 (5%)
Query: 75 SLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQT 134
++++G + M+E+ I S F G K+I ++ T S+GYGF+ F + ++++++
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVES 69
Query: 135 ---FNGTQM 140
F+G ++
Sbjct: 70 QINFHGKKL 78
Score = 33.9 bits (76), Expect = 0.17, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 7/58 (12%)
Query: 267 QGENDPNNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKI-----PAGKRCGFVQFAN 319
+G+ PN T+FVGG+D + + +++ F +YG + VKI K GFV F N
Sbjct: 4 EGKIMPN--TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYN 59
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 3/73 (4%)
Query: 159 RRQDDGPDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGD 218
RR DD + TI V +L+ D + LQE FR + S+ + D+TTG+SKG+ F+ F
Sbjct: 10 RRADD--NATIRVTNLSEDTRETDLQELFRP-FGSISRIYLAKDKTTGQSKGFAFISFHR 66
Query: 219 ESEQLRSMTEMNG 231
+ R++ ++G
Sbjct: 67 REDAARAIAGVSG 79
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 44.7 bits (104), Expect = 1e-04, Method: Composition-based stats.
Identities = 26/78 (33%), Positives = 44/78 (56%), Gaps = 5/78 (6%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYG---ELVHVKIPAGKRCG--FVQFANRTCAEQALSVLN 331
+F+GGL+ + +LK VFG++G E++ +K K G F+ F N A+ A +N
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 332 GTQLGGQSIRLSWGRSPS 349
G L G++I++ + PS
Sbjct: 70 GKSLHGKAIKVEQAKKPS 87
Score = 30.4 bits (67), Expect = 1.7, Method: Composition-based stats.
Identities = 17/84 (20%), Positives = 42/84 (50%), Gaps = 2/84 (2%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE 228
+F+G L + + +L+ F + + ++ DRT+ +S+G+ F+ F + ++ + +
Sbjct: 10 LFIGGLNRETNEKMLKAVF-GKHGPISEVLLIKDRTS-KSRGFAFITFENPADAKNAAKD 67
Query: 229 MNGVLCSTRPMRIGPAATKKAATG 252
MNG + +++ A +G
Sbjct: 68 MNGKSLHGKAIKVEQAKKPSFQSG 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 = 1e-04, Method: Composition-based stats.
Identities = 23/71 (32%), Positives = 40/71 (56%)
Query: 275 TTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRCGFVQFANRTCAEQALSVLNGTQ 334
+ +FVG L P +T++ ++ +F +YG+ V I K GF++ RT AE A L+
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMP 75
Query: 335 LGGQSIRLSWG 345
L G+ +R+ +
Sbjct: 76 LRGKQLRVRFA 86
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 38/176 (21%), Positives = 74/176 (42%), Gaps = 31/176 (17%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTG--RSKGYGFVRFGDESEQLRSM 226
+FVG + ++ L+E F Y +V V+ DR+ +SKG FV F L +
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQ-YGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 227 TEMNGVLC---STRPMRIGPAATKKAATGQQYQKATYQNTQGSQGENDPNNTTIFVGGLD 283
++ + P+++ PA ++K N + +F+G +
Sbjct: 65 NALHNMKVLPGMHHPIQMKPADSEK--------------------NNAVEDRKLFIGMIS 104
Query: 284 PSVTDDILKTVFGQYGELVHVKIPAG-----KRCGFVQFANRTCAEQALSVLNGTQ 334
T++ ++ +F +G++ +I G + C FV F R A+ A+ ++ Q
Sbjct: 105 KKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQ 160
>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 = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 40/71 (56%), Gaps = 2/71 (2%)
Query: 276 TIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRCGFVQFANRTCAEQALSVLNGTQL 335
T++V G D +T +L+ F +G ++ + + + C FV + A+QA++ LNGTQ+
Sbjct: 41 TLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQV 98
Query: 336 GGQSIRLSWGR 346
++++ R
Sbjct: 99 ESVQLKVNIAR 109
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 45/86 (52%), Gaps = 4/86 (4%)
Query: 263 TQGSQGENDP--NNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRCGFVQFANR 320
+ GS GE T++V G D +T +L+ F +G ++ + + + C FV +
Sbjct: 2 SSGSSGERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKM 59
Query: 321 TCAEQALSVLNGTQLGGQSIRLSWGR 346
A+QA++ LNGTQ+ ++++ R
Sbjct: 60 ESADQAVAELNGTQVESVQLKVNIAR 85
>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|X Chain X, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|Y Chain Y, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2V|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
pdb|1N52|B Chain B, Cap Binding Complex
pdb|1N54|B Chain B, Cap Binding Complex M7gpppg Free
pdb|3FEX|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex.
pdb|3FEY|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex
Length = 156
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/97 (26%), Positives = 49/97 (50%), Gaps = 6/97 (6%)
Query: 254 QYQKATYQNTQGSQGENDPNNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKR-- 311
QY+ ++ Q + + T++VG L T++ + +F + G++ + + K
Sbjct: 19 QYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKK 78
Query: 312 --CGF--VQFANRTCAEQALSVLNGTQLGGQSIRLSW 344
CGF V++ +R AE A+ +NGT+L + IR W
Sbjct: 79 TACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW 115
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 41/77 (53%), Gaps = 2/77 (2%)
Query: 75 SLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQT 134
+L++G+L + E I +F +G+ + +K + G+ F+E+ S A AE ++
Sbjct: 41 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100
Query: 135 FNGTQMPSTEQNFRLNW 151
NGT++ ++ R +W
Sbjct: 101 INGTRLD--DRIIRTDW 115
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE 228
+ V L D+TD L FRA+ + +++ D TG S GY FV F E + R++
Sbjct: 6 LIVNYLPQDMTDRELYALFRAI-GPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 229 MNGVLCSTRPMRIGPA 244
+NG+ + +++ A
Sbjct: 65 LNGITVRNKRLKVSYA 80
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 4/75 (5%)
Query: 75 SLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQT 134
+L + L M + + ++F G + +++R+ +T +S GY F++F S ++R ++
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 135 FNGTQMPSTEQNFRL 149
NG T +N RL
Sbjct: 65 LNGI----TVRNKRL 75
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 43.1 bits (100), Expect = 3e-04, Method: Composition-based stats.
Identities = 28/73 (38%), Positives = 42/73 (57%), Gaps = 2/73 (2%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE 228
+ V +L V+D +QE F A + ++K A V DR+ GRS G V F +++ L++M +
Sbjct: 31 LLVSNLDFGVSDADIQELF-AEFGTLKKAAVHYDRS-GRSLGTADVHFERKADALKAMKQ 88
Query: 229 MNGVLCSTRPMRI 241
NGV RPM I
Sbjct: 89 YNGVPLDGRPMNI 101
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 42.7 bits (99), Expect = 4e-04, Method: Composition-based stats.
Identities = 28/88 (31%), Positives = 45/88 (51%), Gaps = 5/88 (5%)
Query: 158 ERRQDDGPDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFG 217
ER QD T++VG L V++ +L E F V + DR TG+ +GYGFV F
Sbjct: 11 ERNQDA----TVYVGGLDEKVSEPLLWELFLQA-GPVVNTHMPKDRVTGQHQGYGFVEFL 65
Query: 218 DESEQLRSMTEMNGVLCSTRPMRIGPAA 245
E + ++ M+ + +P+R+ A+
Sbjct: 66 SEEDADYAIKIMDMIKLYGKPIRVNKAS 93
Score = 42.7 bits (99), Expect = 4e-04, Method: Composition-based stats.
Identities = 23/76 (30%), Positives = 45/76 (59%), Gaps = 6/76 (7%)
Query: 274 NTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRC------GFVQFANRTCAEQAL 327
+ T++VGGLD V++ +L +F Q G +V+ +P + GFV+F + A+ A+
Sbjct: 15 DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 74
Query: 328 SVLNGTQLGGQSIRLS 343
+++ +L G+ IR++
Sbjct: 75 KIMDMIKLYGKPIRVN 90
Score = 33.9 bits (76), Expect = 0.18, Method: Composition-based stats.
Identities = 15/62 (24%), Positives = 34/62 (54%)
Query: 75 SLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQT 134
++++G L + E + +F G V+ + +++ T +GYGF+EF+S A+ ++
Sbjct: 17 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 76
Query: 135 FN 136
+
Sbjct: 77 MD 78
>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 = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRCGF------VQFANRTCAEQALSVL 330
+FV G+ T++ + F +YGE+ ++ + +R G+ V++ A+ A+ L
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 331 NGTQLGGQSIRLSW 344
NG L GQ I + W
Sbjct: 86 NGQDLMGQPISVDW 99
Score = 33.5 bits (75), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 1/75 (1%)
Query: 167 FTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSM 226
+ +FV + + T+ + + F A Y +K + DR TG KGY V + E +M
Sbjct: 24 WILFVTGVHEEATEEDIHDKF-AEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 82
Query: 227 TEMNGVLCSTRPMRI 241
+NG +P+ +
Sbjct: 83 EGLNGQDLMGQPISV 97
>pdb|3TP2|A Chain A, Crystal Structure Of The Splicing Factor Cwc2 From Yeast
pdb|3TP2|B Chain B, Crystal Structure Of The Splicing Factor Cwc2 From Yeast
Length = 229
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 42/83 (50%), Gaps = 12/83 (14%)
Query: 258 ATYQNTQGSQGENDPNNTTIFVGGLD---------PSVTDDILKTVFGQYGELVHVKIPA 308
A Y+ G G N T++VGG+D P+ + ++ VF + G++ ++
Sbjct: 120 ADYREDMGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE 179
Query: 309 GKRCGFVQF---ANRTCAEQALS 328
K CGFV+F AN A++A+S
Sbjct: 180 SKNCGFVKFKYQANAEFAKEAMS 202
>pdb|3U1L|A Chain A, Structure Of The Mrna Splicing Complex Component Cwc2
pdb|3U1M|A Chain A, Structure Of The Mrna Splicing Complex Component Cwc2
Length = 240
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 42/83 (50%), Gaps = 12/83 (14%)
Query: 258 ATYQNTQGSQGENDPNNTTIFVGGLD---------PSVTDDILKTVFGQYGELVHVKIPA 308
A Y+ G G N T++VGG+D P+ + ++ VF + G++ ++
Sbjct: 118 ADYREDMGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE 177
Query: 309 GKRCGFVQF---ANRTCAEQALS 328
K CGFV+F AN A++A+S
Sbjct: 178 SKNCGFVKFKYQANAEFAKEAMS 200
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 43/86 (50%), Gaps = 4/86 (4%)
Query: 74 RSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQ 133
R+L++G+L + E I +F G S K+I +N + Y F+EF H A L
Sbjct: 16 RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALA 73
Query: 134 TFNGTQMPSTEQNFRLNWATYGAGER 159
NG ++ E ++NWAT + ++
Sbjct: 74 AMNGRKILGKE--VKVNWATTPSSQK 97
Score = 41.6 bits (96), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 43/77 (55%), Gaps = 3/77 (3%)
Query: 155 GAGERRQDDGPDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFV 214
G+ +DDG T++VG+L+ DVT+ ++ + F + K K++T+ T+ + Y FV
Sbjct: 4 GSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQI-GPCKSCKMITEHTS--NDPYCFV 60
Query: 215 RFGDESEQLRSMTEMNG 231
F + + ++ MNG
Sbjct: 61 EFYEHRDAAAALAAMNG 77
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 28/97 (28%), Positives = 51/97 (52%), Gaps = 6/97 (6%)
Query: 263 TQGSQG--ENDPNNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRCG----FVQ 316
+ GS G E+D T++VG L VT+ ++ +F Q G K+ FV+
Sbjct: 2 SSGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVE 61
Query: 317 FANRTCAEQALSVLNGTQLGGQSIRLSWGRSPSNKQS 353
F A AL+ +NG ++ G+ ++++W +PS+++S
Sbjct: 62 FYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQKS 98
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 41.6 bits (96), Expect = 8e-04, Method: Composition-based stats.
Identities = 23/78 (29%), Positives = 41/78 (52%), Gaps = 6/78 (7%)
Query: 272 PNNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKI------PAGKRCGFVQFANRTCAEQ 325
P+ +T++V L S+T++ L +F +YG++V V I K F+ F ++ A+
Sbjct: 14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQN 73
Query: 326 ALSVLNGTQLGGQSIRLS 343
+N QL G+ I+ S
Sbjct: 74 CTRAINNKQLFGRVIKAS 91
>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1HL6|C Chain C, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1RK8|A Chain A, Structure Of The Cytosolic Protein Pym Bound To The Mago-
Y14 Core Of The Exon Junction Complex
pdb|2X1G|A Chain A, Crystal Structure Of Importin13 - Mago-Y14 Complex
pdb|2X1G|C Chain C, Crystal Structure Of Importin13 - Mago-Y14 Complex
Length = 165
Score = 41.6 bits (96), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 6/74 (8%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRCGF------VQFANRTCAEQALSVL 330
+FV + +D ++ F YGE+ ++ + +R GF V++ A A L
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 331 NGTQLGGQSIRLSW 344
NG ++ GQ+I++ W
Sbjct: 135 NGAEIMGQTIQVDW 148
Score = 35.8 bits (81), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 18/77 (23%), Positives = 37/77 (48%), Gaps = 2/77 (2%)
Query: 76 LWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQTF 135
L++ + +E I F GE + + +++T FS+GY +E+ +H A +
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 136 NGTQMPSTEQNFRLNWA 152
NG ++ Q +++W
Sbjct: 135 NGAEIMG--QTIQVDWC 149
Score = 35.8 bits (81), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 23/89 (25%), Positives = 40/89 (44%), Gaps = 7/89 (7%)
Query: 167 FTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSM 226
+ +FV + + + +QE F Y +K + DR TG SKGY V + + L +
Sbjct: 73 WILFVTSIHEEAQEDEIQEKF-CDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 131
Query: 227 TEMNGVLCSTRPMRI------GPAATKKA 249
+NG + +++ GP KK+
Sbjct: 132 EALNGAEIMGQTIQVDWCFVKGPKRVKKS 160
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 41.6 bits (96), Expect = 8e-04, Method: Composition-based stats.
Identities = 27/75 (36%), Positives = 40/75 (53%), Gaps = 5/75 (6%)
Query: 274 NTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAG-----KRCGFVQFANRTCAEQALS 328
+ T+FVG L+ V ++IL +F Q G L V I K GFV F + A++
Sbjct: 16 DRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIA 75
Query: 329 VLNGTQLGGQSIRLS 343
+LNG +L G+ I +S
Sbjct: 76 LLNGIRLYGRPINVS 90
Score = 38.1 bits (87), Expect = 0.008, Method: Composition-based stats.
Identities = 26/81 (32%), Positives = 41/81 (50%), Gaps = 3/81 (3%)
Query: 166 DFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRS 225
D T+FVG+L A V + +L E F K + DR G+ K +GFV F +
Sbjct: 16 DRTVFVGNLEARVREEILYELFLQAGPLTK-VTICKDR-EGKPKSFGFVCFKHPESVSYA 73
Query: 226 MTEMNGVLCSTRPMRI-GPAA 245
+ +NG+ RP+ + GP++
Sbjct: 74 IALLNGIRLYGRPINVSGPSS 94
>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 = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRCGF------VQFANRTCAEQALSVL 330
+FV G+ T++ + F +YGE+ ++ + +R G+ V++ A+ A+ L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 331 NGTQLGGQSIRLSW 344
NG L GQ I + W
Sbjct: 72 NGQDLMGQPISVDW 85
Score = 33.5 bits (75), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 1/75 (1%)
Query: 167 FTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSM 226
+ +FV + + T+ + + F A Y +K + DR TG KGY V + E +M
Sbjct: 10 WILFVTGVHEEATEEDIHDKF-AEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 68
Query: 227 TEMNGVLCSTRPMRI 241
+NG +P+ +
Sbjct: 69 EGLNGQDLMGQPISV 83
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 7/73 (9%)
Query: 275 TTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPA-------GKRCGFVQFANRTCAEQAL 327
T + +G L +VT D + +F YG++ + +P K +V+F N AE+AL
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
Query: 328 SVLNGTQLGGQSI 340
++G Q+ GQ I
Sbjct: 65 KHMDGGQIDGQEI 77
Score = 30.0 bits (66), Expect = 2.1, Method: Composition-based stats.
Identities = 18/68 (26%), Positives = 33/68 (48%), Gaps = 1/68 (1%)
Query: 78 IGDLQPWMEESYIASIFGHTGEF-VSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQTFN 136
IG L + + +I IF G+ + + + S+GY ++EF + AE+ L+ +
Sbjct: 9 IGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMD 68
Query: 137 GTQMPSTE 144
G Q+ E
Sbjct: 69 GGQIDGQE 76
Score = 30.0 bits (66), Expect = 2.2, Method: Composition-based stats.
Identities = 18/64 (28%), Positives = 32/64 (50%), Gaps = 2/64 (3%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGR-SKGYGFVRFGDESEQLRSMT 227
+ +G L +VT + E F + Y +K + +R SKGY +V F + E +++
Sbjct: 7 VHIGRLTRNVTKDHIMEIF-STYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65
Query: 228 EMNG 231
M+G
Sbjct: 66 HMDG 69
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 28/79 (35%), Positives = 43/79 (54%), Gaps = 2/79 (2%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE 228
+ V +L V+D +QE F A + ++K A V DR+ GRS G V F ++ L++M +
Sbjct: 38 LLVSNLDFGVSDADIQELF-AEFGTLKKAAVDYDRS-GRSLGTADVHFERRADALKAMKQ 95
Query: 229 MNGVLCSTRPMRIGPAATK 247
GV RPM I A++
Sbjct: 96 YKGVPLDGRPMDIQLVASQ 114
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 28/79 (35%), Positives = 43/79 (54%), Gaps = 2/79 (2%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE 228
+ V +L V+D +QE F A + ++K A V DR+ GRS G V F ++ L++M +
Sbjct: 38 LLVSNLDFGVSDADIQELF-AEFGTLKKAAVDYDRS-GRSLGTADVHFERRADALKAMKQ 95
Query: 229 MNGVLCSTRPMRIGPAATK 247
GV RPM I A++
Sbjct: 96 YKGVPLDGRPMDIQLVASQ 114
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 28/79 (35%), Positives = 43/79 (54%), Gaps = 2/79 (2%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE 228
+ V +L V+D +QE F A + ++K A V DR+ GRS G V F ++ L++M +
Sbjct: 91 LLVSNLDFGVSDADIQELF-AEFGTLKKAAVDYDRS-GRSLGTADVHFERRADALKAMKQ 148
Query: 229 MNGVLCSTRPMRIGPAATK 247
GV RPM I A++
Sbjct: 149 YKGVPLDGRPMDIQLVASQ 167
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/70 (38%), Positives = 37/70 (52%), Gaps = 7/70 (10%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRC------GFVQFANRTCAEQALSVL 330
+FVGGLD S T + L++ F QYGE+V I K GFV+F + C L+
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASR 78
Query: 331 NGTQLGGQSI 340
T L G++I
Sbjct: 79 PHT-LDGRNI 87
Score = 36.2 bits (82), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 31/53 (58%), Gaps = 7/53 (13%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYS---SVKGAKVVTDRTTGRSKGYGFVRFGD 218
+FVG L T QET R+ +S V ++ D+TT +S+G+GFV+F D
Sbjct: 19 LFVGGLDWSTT----QETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKD 67
>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 = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/94 (22%), Positives = 42/94 (44%), Gaps = 2/94 (2%)
Query: 63 GVAPDASSDGIRSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEF 122
GV D L+IG L ++ + + + G + ++++ T S+GY F E+
Sbjct: 104 GVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEY 163
Query: 123 VSHAAAERVLQTFNGTQMPSTEQNFRLNWATYGA 156
V ++ + NG Q+ ++ + A+ GA
Sbjct: 164 VDINVTDQAIAGLNGMQL--GDKKLLVQRASVGA 195
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 37/184 (20%), Positives = 78/184 (42%), Gaps = 16/184 (8%)
Query: 169 IFVGDLAADVTDYVLQETFRAV-----YSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQL 223
++VG++ +T+ + + F A + G V+ + + K + F+ F E
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN-QDKNFAFLEFRSVDETT 65
Query: 224 RSMTEMNGVLCSTRPMRIGPAATKKAATGQQYQKATYQNTQGSQGENDPNNT-TIFVGGL 282
++M +G++ + ++I + G + Y G P++ +F+GGL
Sbjct: 66 QAMA-FDGIIFQGQSLKIRRPHDYQPLPGMSENPSVY--VPGVVSTVVPDSAHKLFIGGL 122
Query: 283 DPSVTDDILKTVFGQYGELVHVKIPAGKRCG------FVQFANRTCAEQALSVLNGTQLG 336
+ DD +K + +G L + G F ++ + +QA++ LNG QLG
Sbjct: 123 PNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLG 182
Query: 337 GQSI 340
+ +
Sbjct: 183 DKKL 186
Score = 33.5 bits (75), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 37/73 (50%), Gaps = 1/73 (1%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE 228
+F+G L + D ++E + + +K +V D TG SKGY F + D + +++
Sbjct: 117 LFIGGLPNYLNDDQVKELLTS-FGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 175
Query: 229 MNGVLCSTRPMRI 241
+NG+ + + +
Sbjct: 176 LNGMQLGDKKLLV 188
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 26/83 (31%), Positives = 43/83 (51%), Gaps = 2/83 (2%)
Query: 160 RQDDGPD-FTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGD 218
+Q +GP+ +F+ L + TD L TF + +V AKV D+ T SK +GFV F +
Sbjct: 33 KQIEGPEGCNLFIYHLPQEFTDTDLASTFLP-FGNVISAKVFIDKQTSLSKCFGFVSFDN 91
Query: 219 ESEQLRSMTEMNGVLCSTRPMRI 241
++ MNG T+ +++
Sbjct: 92 PDSAQVAIKAMNGFQVGTKRLKV 114
Score = 37.7 bits (86), Expect = 0.012, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 41/75 (54%)
Query: 75 SLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQT 134
+L+I L ++ +AS F G +S KV +KQT+ S+ +GF+ F + +A+ ++
Sbjct: 42 NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101
Query: 135 FNGTQMPSTEQNFRL 149
NG Q+ + +L
Sbjct: 102 MNGFQVGTKRLKVQL 116
Score = 35.8 bits (81), Expect = 0.049, Method: Composition-based stats.
Identities = 21/77 (27%), Positives = 37/77 (48%), Gaps = 6/77 (7%)
Query: 272 PNNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRC------GFVQFANRTCAEQ 325
P +F+ L TD L + F +G ++ K+ K+ GFV F N A+
Sbjct: 38 PEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQV 97
Query: 326 ALSVLNGTQLGGQSIRL 342
A+ +NG Q+G + +++
Sbjct: 98 AIKAMNGFQVGTKRLKV 114
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet
Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 37/66 (56%)
Query: 75 SLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQT 134
+L+I L + + +F G VS KV +KQTN S+ +GF+ + + +A+ +Q+
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86
Query: 135 FNGTQM 140
NG Q+
Sbjct: 87 MNGFQI 92
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 28/95 (29%), Positives = 47/95 (49%), Gaps = 7/95 (7%)
Query: 265 GSQGENDPNNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGK-----RC-GFVQFA 318
GSQ E P +F+ L D L +F +G +V K+ K +C GFV +
Sbjct: 17 GSQKEG-PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYD 75
Query: 319 NRTCAEQALSVLNGTQLGGQSIRLSWGRSPSNKQS 353
N A+ A+ +NG Q+G + +++ RS ++ +S
Sbjct: 76 NPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSKS 110
Score = 35.8 bits (81), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 40/82 (48%), Gaps = 2/82 (2%)
Query: 161 QDDGPD-FTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDE 219
Q +GP+ +F+ L + D L + F + +V AKV D+ T SK +GFV + +
Sbjct: 19 QKEGPEGANLFIYHLPQEFGDQDLLQMFMP-FGNVVSAKVFIDKQTNLSKCFGFVSYDNP 77
Query: 220 SEQLRSMTEMNGVLCSTRPMRI 241
++ MNG + +++
Sbjct: 78 VSAQAAIQSMNGFQIGMKRLKV 99
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 26/94 (27%), Positives = 48/94 (51%), Gaps = 5/94 (5%)
Query: 263 TQGSQGENDPN--NTTIFVGGLDPSVTDDI-LKTVFGQYGELVHVKIPAGKRCGFVQFAN 319
+ GS G+ DP N+ +F+G L+ V ++ +F +YG++V + G FVQ+ N
Sbjct: 2 SSGSSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKG--FAFVQYVN 59
Query: 320 RTCAEQALSVLNGTQLGGQSIRLSWGRSPSNKQS 353
A A++ +G + GQ + ++ P +S
Sbjct: 60 ERNARAAVAGEDGRMIAGQVLDINLAAEPKVNRS 93
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 39/79 (49%), Gaps = 1/79 (1%)
Query: 164 GPDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQL 223
GP +++G + D T+ + + V V K++ D TGRSKGY F+ F D
Sbjct: 1 GPSRVVYLGSIPYDQTEEQILDLCSNV-GPVINLKMMFDPQTGRSKGYAFIEFRDLESSA 59
Query: 224 RSMTEMNGVLCSTRPMRIG 242
++ +NG +R ++ G
Sbjct: 60 SAVRNLNGYQLGSRFLKCG 78
Score = 37.4 bits (85), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 36/69 (52%)
Query: 74 RSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQ 133
R +++G + E I + + G ++ K++ + QT S+GY FIEF ++ ++
Sbjct: 4 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 63
Query: 134 TFNGTQMPS 142
NG Q+ S
Sbjct: 64 NLNGYQLGS 72
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 26/88 (29%), Positives = 46/88 (52%), Gaps = 5/88 (5%)
Query: 269 ENDPN--NTTIFVGGLDPS-VTDDILKTVFGQYGELVHVKIPAGKRCGFVQFANRTCAEQ 325
+NDP N+ +F+G L+ + V ++T+F +YG + + G FVQ++N A
Sbjct: 20 KNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKGY--AFVQYSNERHARA 77
Query: 326 ALSVLNGTQLGGQSIRLSWGRSPSNKQS 353
A+ NG L GQ++ ++ P +S
Sbjct: 78 AVLGENGRVLAGQTLDINMAGEPKPDRS 105
>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 = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 39/172 (22%), Positives = 67/172 (38%), Gaps = 25/172 (14%)
Query: 170 FVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTG--RSKGYGFVRFGDESEQLRSMT 227
FVG + ++ L+E F Y +V V+ DR+ +SKG FV F L +
Sbjct: 7 FVGQVPRTWSEKDLRELFEQ-YGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 228 EMNGVLCSTRPMRIGPAATKKAATGQQYQKATYQNTQGSQGENDPNNTTIFVGGLDPSVT 287
++ P P K A S+ N + +F+G + T
Sbjct: 66 ALHNX--KVLPGXHHPIQXKPA---------------DSEKNNAVEDRKLFIGXISKKCT 108
Query: 288 DDILKTVFGQYGELVHVKIPAG-----KRCGFVQFANRTCAEQALSVLNGTQ 334
++ ++ F +G++ +I G + C FV F R A+ A+ + Q
Sbjct: 109 ENDIRVXFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAIKAXHQAQ 160
>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 = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRCGF------VQFANRTCAEQALSVL 330
+FV G+ T++ + F +YGE+ ++ + +R G+ V++ A+ A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 331 NGTQLGGQSIRLSW 344
NG L GQ I + W
Sbjct: 70 NGQDLMGQPISVDW 83
Score = 31.6 bits (70), Expect = 0.88, Method: Composition-based stats.
Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 1/75 (1%)
Query: 167 FTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSM 226
+ +FV + + T+ + + F A Y +K + DR TG KGY V + E +M
Sbjct: 8 WILFVTGVHEEATEEDIHDKF-AEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 227 TEMNGVLCSTRPMRI 241
+NG +P+ +
Sbjct: 67 EGLNGQDLMGQPISV 81
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 42/77 (54%), Gaps = 2/77 (2%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRCGFVQFANRTCAEQALSVLNGTQLG 336
+F+G L T+ ++++F QYG+++ I K GFV ++T AE A+ L+ +L
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDII--KNYGFVHIEDKTAAEDAIRNLHHYKLH 68
Query: 337 GQSIRLSWGRSPSNKQS 353
G +I + ++ S S
Sbjct: 69 GVNINVEASKNKSKASS 85
Score = 30.4 bits (67), Expect = 1.8, Method: Composition-based stats.
Identities = 19/69 (27%), Positives = 32/69 (46%), Gaps = 8/69 (11%)
Query: 68 ASSDGIRSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAA 127
+ S G+ L+IG+L E I S+F G+ + +I+N YGF+ A
Sbjct: 3 SGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFVHIEDKTA 54
Query: 128 AERVLQTFN 136
AE ++ +
Sbjct: 55 AEDAIRNLH 63
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRCGF------VQFANRTCAEQALSVL 330
+FV G+ T++ + F +YGE+ ++ + +R G+ V++ A+ A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 331 NGTQLGGQSIRLSW 344
NG L GQ I + W
Sbjct: 70 NGQDLMGQPISVDW 83
Score = 31.2 bits (69), Expect = 0.98, Method: Composition-based stats.
Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 1/75 (1%)
Query: 167 FTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSM 226
+ +FV + + T+ + + F A Y +K + DR TG KGY V + E +M
Sbjct: 8 WILFVTGVHEEATEEDIHDKF-AEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 227 TEMNGVLCSTRPMRI 241
+NG +P+ +
Sbjct: 67 EGLNGQDLMGQPISV 81
>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 = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRCGF------VQFANRTCAEQALSVL 330
+FV G+ T++ + F +YGE+ ++ + +R G+ V++ A+ A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 331 NGTQLGGQSIRLSW 344
NG L GQ I + W
Sbjct: 70 NGQDLMGQPISVDW 83
Score = 31.2 bits (69), Expect = 0.98, Method: Composition-based stats.
Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 1/75 (1%)
Query: 167 FTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSM 226
+ +FV + + T+ + + F A Y +K + DR TG KGY V + E +M
Sbjct: 8 WILFVTGVHEEATEEDIHDKF-AEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 227 TEMNGVLCSTRPMRI 241
+NG +P+ +
Sbjct: 67 EGLNGQDLMGQPISV 81
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 28/87 (32%), Positives = 43/87 (49%), Gaps = 7/87 (8%)
Query: 263 TQGSQGENDPNNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRC------GFVQ 316
+ G++ DPN + V GL T+ L+ VF +YG + V I ++ FV
Sbjct: 5 SSGNRANPDPN-CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVY 63
Query: 317 FANRTCAEQALSVLNGTQLGGQSIRLS 343
F N A++A NG +L G+ IR+S
Sbjct: 64 FENVDDAKEAKERANGMELDGRRIRVS 90
Score = 34.7 bits (78), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 24/92 (26%), Positives = 46/92 (50%), Gaps = 2/92 (2%)
Query: 155 GAGERRQDDGPDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFV 214
G+ R + P+ + V L+ T+ L+E F + Y + +V D+ + RS+G+ FV
Sbjct: 4 GSSGNRANPDPNCCLGVFGLSLYTTERDLREVF-SKYGPIADVSIVYDQQSRRSRGFAFV 62
Query: 215 RFGDESEQLRSMTEMNGVLCSTRPMRI-GPAA 245
F + + + NG+ R +R+ GP++
Sbjct: 63 YFENVDDAKEAKERANGMELDGRRIRVSGPSS 94
>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 = 0.005, Method: Compositional matrix adjust.
Identities = 27/88 (30%), Positives = 43/88 (48%), Gaps = 7/88 (7%)
Query: 263 TQGSQGENDPNNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRC------GFVQ 316
+ G++ DPN + V GL T+ L+ VF +YG + V I ++ FV
Sbjct: 5 SSGNRANPDPN-CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVY 63
Query: 317 FANRTCAEQALSVLNGTQLGGQSIRLSW 344
F N A++A NG +L G+ IR+ +
Sbjct: 64 FENVDDAKEAKERANGMELDGRRIRVDF 91
Score = 37.0 bits (84), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 25/97 (25%), Positives = 47/97 (48%), Gaps = 1/97 (1%)
Query: 155 GAGERRQDDGPDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFV 214
G+ R + P+ + V L+ T+ L+E F + Y + +V D+ + RS+G+ FV
Sbjct: 4 GSSGNRANPDPNCCLGVFGLSLYTTERDLREVF-SKYGPIADVSIVYDQQSRRSRGFAFV 62
Query: 215 RFGDESEQLRSMTEMNGVLCSTRPMRIGPAATKKAAT 251
F + + + NG+ R +R+ + TK+ T
Sbjct: 63 YFENVDDAKEAKERANGMELDGRRIRVDFSITKRPHT 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 = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 39/180 (21%), Positives = 77/180 (42%), Gaps = 25/180 (13%)
Query: 167 FTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSM 226
F +F+G+L + + L+ +++ K V D TG ++ +G+V F + +E L
Sbjct: 14 FNLFIGNLNPNKSVAELKVAISELFA--KNDLAVVDVRTGTNRKFGYVDF-ESAEDLEKA 70
Query: 227 TEMNGVLCSTRPMRIGPAATKKAATGQQYQKATYQNTQGSQGENDPNNTTIFVGGLDPSV 286
E+ G+ +++ + +G + T+ L ++
Sbjct: 71 LELTGLKVFGNEIKL-------------------EKPKGRDSKKVRAARTLLAKNLSFNI 111
Query: 287 TDDILKTVFGQYGELVHVKIPAGKRCG--FVQFANRTCAEQALSVLNGTQLGGQSIRLSW 344
T+D LK VF E+ V GK G +++F + AE+ L G ++ G+S+ L +
Sbjct: 112 TEDELKEVFEDALEIRLVS-QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY 170
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 23/74 (31%), Positives = 41/74 (55%), Gaps = 5/74 (6%)
Query: 276 TIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKR---CGF--VQFANRTCAEQALSVL 330
T++VG L T++ + +F + G++ + + K CGF V++ +R AE A+ +
Sbjct: 20 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMRYI 79
Query: 331 NGTQLGGQSIRLSW 344
NGT+L + IR W
Sbjct: 80 NGTRLDDRIIRTDW 93
Score = 35.0 bits (79), Expect = 0.067, Method: Composition-based stats.
Identities = 19/77 (24%), Positives = 42/77 (54%), Gaps = 3/77 (3%)
Query: 75 SLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQT 134
+L++G+L + E I +F +G+ + ++ + + G+ F+E+ S A AE ++
Sbjct: 20 TLYVGNLSFYTTEEQIYELFSKSGD-IKKIIMGLDKMKTACGFCFVEYYSRADAENAMRY 78
Query: 135 FNGTQMPSTEQNFRLNW 151
NGT++ ++ R +W
Sbjct: 79 INGTRL--DDRIIRTDW 93
>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 = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRCGF------VQFANRTCAEQALSVL 330
+FV G+ T++ + F +YGE+ ++ + +R G+ V++ A+ A+ L
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 331 NGTQLGGQSIRLSW 344
NG L GQ I + W
Sbjct: 85 NGQDLMGQPISVDW 98
Score = 32.0 bits (71), Expect = 0.65, Method: Composition-based stats.
Identities = 23/85 (27%), Positives = 40/85 (47%), Gaps = 3/85 (3%)
Query: 157 GERRQDDGPDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRF 216
G +R +G + +FV + + T+ + + F A Y +K + DR TG KGY V +
Sbjct: 15 GPQRSVEG--WILFVTGVHEEATEEDIHDKF-AEYGEIKNIHLNLDRRTGYLKGYTLVEY 71
Query: 217 GDESEQLRSMTEMNGVLCSTRPMRI 241
E +M +NG +P+ +
Sbjct: 72 ETYKEAQAAMEGLNGQDLMGQPISV 96
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 27/84 (32%), Positives = 45/84 (53%), Gaps = 4/84 (4%)
Query: 274 NTTIFVGGLDPSVTDDILKTVFGQYGELVH--VKIPAGKR--CGFVQFANRTCAEQALSV 329
++ IFV L T +LK F + G +++ +K+ GK CG V+F + AE+A +
Sbjct: 5 SSGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRM 64
Query: 330 LNGTQLGGQSIRLSWGRSPSNKQS 353
+NG +L G+ I + R+ S S
Sbjct: 65 MNGMKLSGREIDVRIDRNASGPSS 88
Score = 29.3 bits (64), Expect = 4.0, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 36/77 (46%), Gaps = 11/77 (14%)
Query: 169 IFVGDLAADVTDYVLQETF----RAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLR 224
IFV +L D T +L++ F +Y+ +K G+SKG G V+F R
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHVLYADIK-------MENGKSKGCGVVKFESPEVAER 60
Query: 225 SMTEMNGVLCSTRPMRI 241
+ MNG+ S R + +
Sbjct: 61 ACRMMNGMKLSGREIDV 77
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 27/81 (33%), Positives = 43/81 (53%), Gaps = 4/81 (4%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGELVH--VKIPAGKR--CGFVQFANRTCAEQALSVLNG 332
IFV L T +LK F + G +++ +K+ GK CG V+F + AE+A ++NG
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNG 70
Query: 333 TQLGGQSIRLSWGRSPSNKQS 353
+L G+ I + R+ S S
Sbjct: 71 MKLSGREIDVRIDRNASGPSS 91
Score = 29.3 bits (64), Expect = 3.7, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 36/77 (46%), Gaps = 11/77 (14%)
Query: 169 IFVGDLAADVTDYVLQETF----RAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLR 224
IFV +L D T +L++ F +Y+ +K G+SKG G V+F R
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADIK-------MENGKSKGCGVVKFESPEVAER 63
Query: 225 SMTEMNGVLCSTRPMRI 241
+ MNG+ S R + +
Sbjct: 64 ACRMMNGMKLSGREIDV 80
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 23/86 (26%), Positives = 47/86 (54%), Gaps = 6/86 (6%)
Query: 274 NTTIFVGGLDPSVTDDILKTVFGQY----GELVHVKIPAGKRCG--FVQFANRTCAEQAL 327
N +++ L P VT+ L ++F ++ G + ++ G+ G F+ F N+ A QAL
Sbjct: 25 NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 84
Query: 328 SVLNGTQLGGQSIRLSWGRSPSNKQS 353
++NG +L G+ + + +G++ + S
Sbjct: 85 HLVNGYKLYGKILVIEFGKNKKQRSS 110
Score = 28.1 bits (61), Expect = 9.4, Method: Composition-based stats.
Identities = 20/81 (24%), Positives = 40/81 (49%), Gaps = 7/81 (8%)
Query: 151 WATYGAGERRQDDGPDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKG 210
+++Y GE P+ +++ +L+ VT+ L F A + KG + TGR +G
Sbjct: 16 FSSYNPGE------PNKVLYLKNLSPRVTERDLVSLF-ARFQEKKGPPIQFRMMTGRMRG 68
Query: 211 YGFVRFGDESEQLRSMTEMNG 231
F+ F ++ +++ +NG
Sbjct: 69 QAFITFPNKEIAWQALHLVNG 89
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 16/65 (24%), Positives = 32/65 (49%)
Query: 75 SLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQT 134
+L++ L M + + +F G ++ +++ ++ T S G GFI F AE ++
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 135 FNGTQ 139
NG +
Sbjct: 63 LNGQK 67
Score = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 45/84 (53%), Gaps = 8/84 (9%)
Query: 274 NTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIP------AGKRCGFVQFANRTCAEQAL 327
+ ++V GL +++ ++ +F QYG ++ +I + GF++F R AE+A+
Sbjct: 1 DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
Query: 328 SVLNGTQ-LG-GQSIRLSWGRSPS 349
LNG + LG + I + + +PS
Sbjct: 61 KGLNGQKPLGAAEPITVKFANNPS 84
Score = 35.4 bits (80), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 36/66 (54%), Gaps = 1/66 (1%)
Query: 166 DFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRS 225
D ++V L ++ +++ F + Y + ++++ D+ TG S+G GF+RF E +
Sbjct: 1 DANLYVSGLPKTMSQKEMEQLF-SQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEA 59
Query: 226 MTEMNG 231
+ +NG
Sbjct: 60 IKGLNG 65
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 38.9 bits (89), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 6/76 (7%)
Query: 276 TIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRC------GFVQFANRTCAEQALSV 329
++VGGL V D +L F +G++ ++IP FV+F A A+
Sbjct: 65 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 124
Query: 330 LNGTQLGGQSIRLSWG 345
+N ++L G++IR++
Sbjct: 125 MNESELFGRTIRVNLA 140
Score = 32.0 bits (71), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 1/77 (1%)
Query: 168 TIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMT 227
++VG LA +V D VL F + + ++ D T + +G+ FV F + ++
Sbjct: 65 VLYVGGLAEEVDDKVLHAAFIP-FGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
Query: 228 EMNGVLCSTRPMRIGPA 244
MN R +R+ A
Sbjct: 124 NMNESELFGRTIRVNLA 140
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 38.5 bits (88), Expect = 0.006, Method: Composition-based stats.
Identities = 27/97 (27%), Positives = 48/97 (49%), Gaps = 8/97 (8%)
Query: 265 GSQGENDPNNT--TIFVGGLDPSVTDDILKTVFGQYGELVHVKIP------AGKRCGFVQ 316
GS G + T ++VGGL V D +L F +G++ ++IP + FV+
Sbjct: 1 GSSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 60
Query: 317 FANRTCAEQALSVLNGTQLGGQSIRLSWGRSPSNKQS 353
F A A+ +N ++L G++IR++ + K+S
Sbjct: 61 FELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIKES 97
Score = 31.2 bits (69), Expect = 1.0, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 1/76 (1%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE 228
++VG LA +V D VL F + + ++ D T + +G+ FV F + ++
Sbjct: 15 LYVGGLAEEVDDKVLHAAF-IPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 73
Query: 229 MNGVLCSTRPMRIGPA 244
MN R +R+ A
Sbjct: 74 MNESELFGRTIRVNLA 89
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 38.5 bits (88), Expect = 0.007, Method: Composition-based stats.
Identities = 24/81 (29%), Positives = 43/81 (53%), Gaps = 2/81 (2%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE 228
I+VG+L T ++E F + + V K++ DR T + KG+GFV +ES ++ +
Sbjct: 4 IYVGNLVYSATSEQVKELF-SQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVS-EAIAK 61
Query: 229 MNGVLCSTRPMRIGPAATKKA 249
++ R +R+ A KK+
Sbjct: 62 LDNTDFMGRTIRVTEANPKKS 82
Score = 36.2 bits (82), Expect = 0.035, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 42/73 (57%), Gaps = 7/73 (9%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGELVHVKI------PAGKRCGFVQFANRTCAEQALSVL 330
I+VG L S T + +K +F Q+G++ +VK+ K GFV+ + +E A++ L
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSE-AIAKL 62
Query: 331 NGTQLGGQSIRLS 343
+ T G++IR++
Sbjct: 63 DNTDFMGRTIRVT 75
Score = 34.3 bits (77), Expect = 0.13, Method: Composition-based stats.
Identities = 21/78 (26%), Positives = 40/78 (51%), Gaps = 4/78 (5%)
Query: 73 IRSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEF----VSHAAA 128
+R++++G+L + +F G+ + K+I +++T +G+GF+E VS A A
Sbjct: 1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIA 60
Query: 129 ERVLQTFNGTQMPSTEQN 146
+ F G + TE N
Sbjct: 61 KLDNTDFMGRTIRVTEAN 78
>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 84
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 38/78 (48%), Gaps = 1/78 (1%)
Query: 165 PDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLR 224
P +++G + D T+ + + V V K++ D TGRSKGY F+ F D
Sbjct: 3 PSRVVYLGSIPYDQTEEQILDLCSNV-GPVINLKMMFDPQTGRSKGYAFIEFRDLESSAS 61
Query: 225 SMTEMNGVLCSTRPMRIG 242
++ +NG +R ++ G
Sbjct: 62 AVRNLNGYQLGSRFLKCG 79
Score = 37.4 bits (85), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 35/67 (52%)
Query: 74 RSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQ 133
R +++G + E I + + G ++ K++ + QT S+GY FIEF ++ ++
Sbjct: 5 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 64
Query: 134 TFNGTQM 140
NG Q+
Sbjct: 65 NLNGYQL 71
>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 = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 16/69 (23%), Positives = 33/69 (47%)
Query: 72 GIRSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERV 131
G L+IG L ++ + + + G + ++++ T S+GY F E+V ++
Sbjct: 95 GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 154
Query: 132 LQTFNGTQM 140
+ NG Q+
Sbjct: 155 IAGLNGMQL 163
Score = 36.2 bits (82), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 36/183 (19%), Positives = 75/183 (40%), Gaps = 34/183 (18%)
Query: 169 IFVGDLAADVTDYVLQETFRAV-----YSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQL 223
++VG++ +T+ + + F A + G V+ + + K + F+ F E
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN-QDKNFAFLEFRSVDETT 67
Query: 224 RSMTEMNGVLCSTRPMRIGPAATKKAATGQQYQKATYQNTQGSQGENDPNNTTIFVGGLD 283
++M +G++ + ++I + YQ G+ +F+GGL
Sbjct: 68 QAMA-FDGIIFQGQSLKI-------------RRPHDYQPLPGAH--------KLFIGGLP 105
Query: 284 PSVTDDILKTVFGQYGELVHVKIPAGKRCG------FVQFANRTCAEQALSVLNGTQLGG 337
+ DD +K + +G L + G F ++ + +QA++ LNG QLG
Sbjct: 106 NYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGD 165
Query: 338 QSI 340
+ +
Sbjct: 166 KKL 168
Score = 35.8 bits (81), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 36/176 (20%), Positives = 68/176 (38%), Gaps = 20/176 (11%)
Query: 74 RSLWIGDLQPWMEESYIASIFGHTGEF-----VSGKVIRNKQTNFSEGYGFIEFVSHAAA 128
R L++G++ + E + F G + Q N + + F+EF S
Sbjct: 7 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 66
Query: 129 ERVLQTFNGTQMPSTEQNFRLNWATYGAGERRQDDGP---DFTIFVGDLAADVTDYVLQE 185
+ + F+G R R D P +F+G L + D ++E
Sbjct: 67 TQAM-AFDGIIFQGQSLKIR----------RPHDYQPLPGAHKLFIGGLPNYLNDDQVKE 115
Query: 186 TFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTEMNGVLCSTRPMRI 241
+ + +K +V D TG SKGY F + D + +++ +NG+ + + +
Sbjct: 116 LLTS-FGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLV 170
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 38.5 bits (88), Expect = 0.007, Method: Composition-based stats.
Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 2/83 (2%)
Query: 269 ENDPNNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRCGFVQFANRTCAEQALS 328
E + +NT +FV V + L +FG +G + VKI G FV+F A +A+
Sbjct: 26 EGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG--FAFVEFEEAESAAKAIE 83
Query: 329 VLNGTQLGGQSIRLSWGRSPSNK 351
++G Q + + + + P+ +
Sbjct: 84 EVHGKSFANQPLEVVYSKLPAKR 106
>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 = 0.007, Method: Composition-based stats.
Identities = 29/93 (31%), Positives = 50/93 (53%), Gaps = 4/93 (4%)
Query: 263 TQGSQGEND--PNNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRCGFVQFANR 320
+ GS G+ + +FV L +VT++IL+ F ++G+L VK K FV F +R
Sbjct: 2 SSGSSGDPEVMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVK--KLKDYAFVHFEDR 59
Query: 321 TCAEQALSVLNGTQLGGQSIRLSWGRSPSNKQS 353
A +A+ +NG ++ G+ I + + P K+S
Sbjct: 60 GAAVKAMDEMNGKEIEGEEIEIVLAKPPDKKRS 92
Score = 34.7 bits (78), Expect = 0.11, Method: Composition-based stats.
Identities = 20/63 (31%), Positives = 35/63 (55%), Gaps = 9/63 (14%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE 228
+FV +LA VT+ +L+++F + + ++ K + D Y FV F D +++M E
Sbjct: 18 LFVRNLATTVTEEILEKSF-SEFGKLERVKKLKD--------YAFVHFEDRGAAVKAMDE 68
Query: 229 MNG 231
MNG
Sbjct: 69 MNG 71
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 38.1 bits (87), Expect = 0.009, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 6/73 (8%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGELVHVKIP------AGKRCGFVQFANRTCAEQALSVL 330
++VGGL V D +L F +G++ ++IP + FV+F A A+ +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 331 NGTQLGGQSIRLS 343
N ++L G++IR++
Sbjct: 65 NESELFGRTIRVN 77
Score = 32.7 bits (73), Expect = 0.37, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 1/76 (1%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE 228
++VG LA +V D VL F + + ++ D T + +G+ FV F + ++
Sbjct: 5 LYVGGLAEEVDDKVLHAAF-IPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 63
Query: 229 MNGVLCSTRPMRIGPA 244
MN R +R+ A
Sbjct: 64 MNESELFGRTIRVNLA 79
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 38.1 bits (87), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 16/69 (23%), Positives = 33/69 (47%)
Query: 72 GIRSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERV 131
G L+IG L ++ + + + G + ++++ T S+GY F E+V ++
Sbjct: 93 GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 152
Query: 132 LQTFNGTQM 140
+ NG Q+
Sbjct: 153 IAGLNGMQL 161
Score = 35.8 bits (81), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 36/183 (19%), Positives = 75/183 (40%), Gaps = 34/183 (18%)
Query: 169 IFVGDLAADVTDYVLQETFRAV-----YSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQL 223
++VG++ +T+ + + F A + G V+ + + K + F+ F E
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN-QDKNFAFLEFRSVDETT 65
Query: 224 RSMTEMNGVLCSTRPMRIGPAATKKAATGQQYQKATYQNTQGSQGENDPNNTTIFVGGLD 283
++M +G++ + ++I + YQ G+ +F+GGL
Sbjct: 66 QAMA-FDGIIFQGQSLKI-------------RRPHDYQPLPGAH--------KLFIGGLP 103
Query: 284 PSVTDDILKTVFGQYGELVHVKIPAGKRCG------FVQFANRTCAEQALSVLNGTQLGG 337
+ DD +K + +G L + G F ++ + +QA++ LNG QLG
Sbjct: 104 NYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGD 163
Query: 338 QSI 340
+ +
Sbjct: 164 KKL 166
Score = 35.4 bits (80), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 37/180 (20%), Positives = 70/180 (38%), Gaps = 20/180 (11%)
Query: 74 RSLWIGDLQPWMEESYIASIFGHTGEF-----VSGKVIRNKQTNFSEGYGFIEFVSHAAA 128
R L++G++ + E + F G + Q N + + F+EF S
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 129 ERVLQTFNGTQMPSTEQNFRLNWATYGAGERRQDDGP---DFTIFVGDLAADVTDYVLQE 185
+ + F+G R R D P +F+G L + D ++E
Sbjct: 65 TQAM-AFDGIIFQGQSLKIR----------RPHDYQPLPGAHKLFIGGLPNYLNDDQVKE 113
Query: 186 TFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTEMNGVLCSTRPMRIGPAA 245
+ + +K +V D TG SKGY F + D + +++ +NG+ + + + A+
Sbjct: 114 LLTS-FGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS 172
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 38.1 bits (87), Expect = 0.009, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 6/74 (8%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRCGF------VQFANRTCAEQALSVL 330
+FV + +D ++ F YGE+ ++ + +R GF V++ A A L
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 331 NGTQLGGQSIRLSW 344
NG ++ GQ+I++ W
Sbjct: 89 NGAEIMGQTIQVDW 102
Score = 35.0 bits (79), Expect = 0.085, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 3/75 (4%)
Query: 157 GERRQDDGPDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRF 216
G +R +G + +FV + + + +QE F Y +K + DR TG SKGY V +
Sbjct: 19 GPQRSVEG--WILFVTSIHEEAQEDEIQEKF-CDYGEIKNIHLNLDRRTGFSKGYALVEY 75
Query: 217 GDESEQLRSMTEMNG 231
+ L + +NG
Sbjct: 76 ETHKQALAAKEALNG 90
Score = 34.3 bits (77), Expect = 0.15, Method: Composition-based stats.
Identities = 18/76 (23%), Positives = 37/76 (48%), Gaps = 2/76 (2%)
Query: 76 LWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQTF 135
L++ + +E I F GE + + +++T FS+GY +E+ +H A +
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 136 NGTQMPSTEQNFRLNW 151
NG ++ Q +++W
Sbjct: 89 NGAEIMG--QTIQVDW 102
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 38.1 bits (87), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 30/99 (30%), Positives = 47/99 (47%), Gaps = 9/99 (9%)
Query: 252 GQQYQKATYQNTQGSQGENDPNNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKR 311
GQQ + + G++ DPN + V GL T+ L+ VF +YG + V I ++
Sbjct: 27 GQQMGRGSRH--VGNRANPDPN-CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQ 83
Query: 312 C------GFVQFANRTCAEQALSVLNGTQLGGQSIRLSW 344
FV F N A++A NG +L G+ IR+ +
Sbjct: 84 SRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF 122
Score = 37.0 bits (84), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 28/112 (25%), Positives = 52/112 (46%), Gaps = 2/112 (1%)
Query: 137 GTQMPSTEQNFRLNWATYGAGERRQDDGPDFTIFVGDLAADVTDYVLQETFRAVYSSVKG 196
G+ M S ++ + G R D P+ + V L+ T+ L+E F + Y +
Sbjct: 18 GSHMASMTGGQQMGRGSRHVGNRANPD-PNCCLGVFGLSLYTTERDLREVF-SKYGPIAD 75
Query: 197 AKVVTDRTTGRSKGYGFVRFGDESEQLRSMTEMNGVLCSTRPMRIGPAATKK 248
+V D+ + RS+G+ FV F + + + NG+ R +R+ + TK+
Sbjct: 76 VSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKR 127
>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 = 38.1 bits (87), Expect = 0.009, Method: Composition-based stats.
Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 6/76 (7%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGELVHVKIP------AGKRCGFVQFANRTCAEQALSVL 330
++VGGL V D +L F +G++ ++IP + FV+F A A+ +
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 331 NGTQLGGQSIRLSWGR 346
N ++L G++IR++ +
Sbjct: 70 NESELFGRTIRVNLAK 85
Score = 32.3 bits (72), Expect = 0.47, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 1/76 (1%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE 228
++VG LA +V D VL F + + ++ D T + +G+ FV F + ++
Sbjct: 10 LYVGGLAEEVDDKVLHAAF-IPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 68
Query: 229 MNGVLCSTRPMRIGPA 244
MN R +R+ A
Sbjct: 69 MNESELFGRTIRVNLA 84
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 38.1 bits (87), Expect = 0.010, Method: Composition-based stats.
Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 6/76 (7%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGELVHVKIP------AGKRCGFVQFANRTCAEQALSVL 330
++VGGL V D +L F +G++ ++IP + FV+F A A+ +
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 331 NGTQLGGQSIRLSWGR 346
N ++L G++IR++ +
Sbjct: 68 NESELFGRTIRVNLAK 83
Score = 32.3 bits (72), Expect = 0.49, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 1/76 (1%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE 228
++VG LA +V D VL F + + ++ D T + +G+ FV F + ++
Sbjct: 8 LYVGGLAEEVDDKVLHAAF-IPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66
Query: 229 MNGVLCSTRPMRIGPA 244
MN R +R+ A
Sbjct: 67 MNESELFGRTIRVNLA 82
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 37.7 bits (86), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 3/63 (4%)
Query: 185 ETFRAV---YSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTEMNGVLCSTRPMRI 241
+T R V Y V + DR T S+G+ FVRF D+ + +M M+G + R +R+
Sbjct: 85 DTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV 144
Query: 242 GPA 244
A
Sbjct: 145 QMA 147
>pdb|2GHP|A Chain A, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|B Chain B, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|C Chain C, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|D Chain D, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|E Chain E, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|F Chain F, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|G Chain G, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|H Chain H, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
Length = 292
Score = 37.4 bits (85), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 9/77 (11%)
Query: 277 IFVGGLDPSVTDD-ILKTVFGQYGELVHVKIPAGKR-------CGFVQFANRTCAEQALS 328
I + L + D+ +L+ F +G + + IPAG++ C F F N+ AE+AL
Sbjct: 213 IXIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFXVFENKDSAERALQ 272
Query: 329 VLNGTQLGGQSIRLSWG 345
N + LG + I +S
Sbjct: 273 X-NRSLLGNREISVSLA 288
>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 = 37.4 bits (85), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 185 ETFRAV---YSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTEMNGVLCSTRPMRI 241
+T R V Y V + DR T S+G+ FVRF D+ + +M M+G + R +R+
Sbjct: 62 DTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV 121
>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 = 37.4 bits (85), Expect = 0.016, Method: Composition-based stats.
Identities = 26/73 (35%), Positives = 40/73 (54%), Gaps = 2/73 (2%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE 228
+ V +L V+D +QE F A + ++K A V DR+ GRS G V F +++ L++ +
Sbjct: 32 LLVSNLDFGVSDADIQELF-AEFGTLKKAAVHYDRS-GRSLGTADVHFERKADALKAXKQ 89
Query: 229 MNGVLCSTRPMRI 241
NGV RP I
Sbjct: 90 YNGVPLDGRPXNI 102
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 37.4 bits (85), Expect = 0.016, Method: Composition-based stats.
Identities = 28/86 (32%), Positives = 42/86 (48%), Gaps = 7/86 (8%)
Query: 265 GSQGENDPNNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRC------GFVQFA 318
GS+ DPN + V GL T+ L+ VF +YG + V I ++ FV F
Sbjct: 4 GSRANPDPN-CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE 62
Query: 319 NRTCAEQALSVLNGTQLGGQSIRLSW 344
N A++A NG +L G+ IR+ +
Sbjct: 63 NVDDAKEAKERANGMELDGRRIRVDF 88
Score = 36.6 bits (83), Expect = 0.024, Method: Composition-based stats.
Identities = 24/92 (26%), Positives = 45/92 (48%), Gaps = 1/92 (1%)
Query: 160 RQDDGPDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDE 219
R + P+ + V L+ T+ L+E F + Y + +V D+ + RS+G+ FV F +
Sbjct: 6 RANPDPNCCLGVFGLSLYTTERDLREVF-SKYGPIADVSIVYDQQSRRSRGFAFVYFENV 64
Query: 220 SEQLRSMTEMNGVLCSTRPMRIGPAATKKAAT 251
+ + NG+ R +R+ + TK+ T
Sbjct: 65 DDAKEAKERANGMELDGRRIRVDFSITKRPHT 96
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 37.4 bits (85), Expect = 0.017, Method: Composition-based stats.
Identities = 22/78 (28%), Positives = 38/78 (48%), Gaps = 1/78 (1%)
Query: 165 PDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLR 224
P +++G + D T+ + + V V K++ D TGRSKGY F+ F D
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNV-GPVINLKMMFDPQTGRSKGYAFIEFRDLESSAS 59
Query: 225 SMTEMNGVLCSTRPMRIG 242
++ +NG +R ++ G
Sbjct: 60 AVRNLNGYQLGSRFLKCG 77
Score = 35.4 bits (80), Expect = 0.063, Method: Composition-based stats.
Identities = 19/69 (27%), Positives = 36/69 (52%)
Query: 74 RSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQ 133
R +++G + E I + + G ++ K++ + QT S+GY FIEF ++ ++
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 134 TFNGTQMPS 142
NG Q+ S
Sbjct: 63 NLNGYQLGS 71
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 37.0 bits (84), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 39/74 (52%), Gaps = 2/74 (2%)
Query: 168 TIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMT 227
T+FV +L V L+E F V+ A ++ D+ G+S+G G V F E +++++
Sbjct: 17 TVFVANLDYKVGWKKLKEVFSMAGVVVR-ADILEDKD-GKSRGIGTVTFEQSIEAVQAIS 74
Query: 228 EMNGVLCSTRPMRI 241
NG L RPM +
Sbjct: 75 MFNGQLLFDRPMHV 88
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 36.6 bits (83), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 4/72 (5%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE 228
+ V L T+ L+E F + + V +V D TG SKG+GFVRF + Q++ M++
Sbjct: 18 LIVLGLPWKTTEQDLKEYF-STFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ 76
Query: 229 ---MNGVLCSTR 237
++G C +
Sbjct: 77 RHMIDGRWCDCK 88
Score = 29.3 bits (64), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 83 PW-MEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVL 132
PW E + F GE + +V ++ +T S+G+GF+ F + +V+
Sbjct: 24 PWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVM 74
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 36.6 bits (83), Expect = 0.026, Method: Composition-based stats.
Identities = 27/99 (27%), Positives = 53/99 (53%), Gaps = 8/99 (8%)
Query: 263 TQGSQG--ENDPNNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAG-----KRCGFV 315
+ GS G P++ +FVG L+ ++D ++ +F +G + I G K C FV
Sbjct: 2 SSGSSGCLRQPPSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFV 61
Query: 316 QFANRTCAEQALSVLNGTQ-LGGQSIRLSWGRSPSNKQS 353
++++ A+ A++ L+G+Q + G S L + ++K+S
Sbjct: 62 KYSSHAEAQAAINALHGSQTMPGASSSLVVKFADTDKES 100
Score = 33.5 bits (75), Expect = 0.21, Method: Composition-based stats.
Identities = 21/80 (26%), Positives = 38/80 (47%), Gaps = 2/80 (2%)
Query: 74 RSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQ 133
R L++G L E + +F G ++R N S+G F+++ SHA A+ +
Sbjct: 16 RKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGN-SKGCAFVKYSSHAEAQAAIN 74
Query: 134 TFNGTQ-MPSTEQNFRLNWA 152
+G+Q MP + + +A
Sbjct: 75 ALHGSQTMPGASSSLVVKFA 94
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 36.6 bits (83), Expect = 0.027, Method: Composition-based stats.
Identities = 21/55 (38%), Positives = 32/55 (58%), Gaps = 3/55 (5%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQL 223
IFVG L+ + T ++ F + V A ++ D+TT R +G+GFV F ESE +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQ-FGKVDDAMLMFDKTTNRHRGFGFVTF--ESEDI 53
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 36.6 bits (83), Expect = 0.028, Method: Composition-based stats.
Identities = 24/79 (30%), Positives = 41/79 (51%), Gaps = 4/79 (5%)
Query: 269 ENDPNNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKR----CGFVQFANRTCAE 324
EN + V + D L+ +FGQ+G+++ V+I +R GFV F N A+
Sbjct: 24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADAD 83
Query: 325 QALSVLNGTQLGGQSIRLS 343
+A L+GT + G+ I ++
Sbjct: 84 RAREKLHGTVVEGRKIEVN 102
Score = 30.8 bits (68), Expect = 1.3, Method: Composition-based stats.
Identities = 15/49 (30%), Positives = 30/49 (61%), Gaps = 2/49 (4%)
Query: 90 IASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQTFNGT 138
+ +FG G+ + ++I N++ S+G+GF+ F + A A+R + +GT
Sbjct: 46 LRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKLHGT 92
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 36.2 bits (82), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 34/72 (47%), Gaps = 2/72 (2%)
Query: 63 GVAPDASSDGIR--SLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFI 120
G+ P S G ++IG L + + FG GE V+R+ T S G+GF+
Sbjct: 13 GLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFV 72
Query: 121 EFVSHAAAERVL 132
F+ A ++VL
Sbjct: 73 TFMDQAGVDKVL 84
Score = 35.4 bits (80), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDES 220
+F+G L+ T L+E F + VK V+ D T RS+G+GFV F D++
Sbjct: 28 MFIGGLSWQTTQEGLREYF-GQFGEVKECLVMRDPLTKRSRGFGFVTFMDQA 78
Score = 32.0 bits (71), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 6/62 (9%)
Query: 273 NNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKI---PAGKRC---GFVQFANRTCAEQA 326
+ +F+GGL T + L+ FGQ+GE+ + P KR GFV F ++ ++
Sbjct: 24 SGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV 83
Query: 327 LS 328
L+
Sbjct: 84 LA 85
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 36.2 bits (82), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 48/233 (20%), Positives = 89/233 (38%), Gaps = 32/233 (13%)
Query: 115 EGYGFIEFVSHAAAERVLQTFNGTQMPSTEQNFRLNWATYGAGERRQDDGPDFTIFVGDL 174
+G F+ ++ AE + F+ +++ E + +L D + V +L
Sbjct: 57 KGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPT-------------DALLCVANL 103
Query: 175 AADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTEMNGVLC 234
+T +E R + S++ +V TG+SKGYGF + + R+ +++ G
Sbjct: 104 PPSLTQQQFEELVRP-FGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLG--- 159
Query: 235 STRPMRIGPAATKKAATGQ-QYQKATYQNTQGSQGENDP--NNTTIFVGGLDPSVTDDIL 291
+P+ GP T Q A + P N+ L +
Sbjct: 160 --KPL--GPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFC 215
Query: 292 KTVFGQYGELVHVKIPAGKRCGFVQFANRTCAEQALSVLNGTQLGGQSIRLSW 344
+ GQ G+L K +++ AE+A +G LGG +R+S+
Sbjct: 216 QLACGQDGQL--------KGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSF 260
>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
pdb|3H2U|D Chain D, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
Length = 283
Score = 36.2 bits (82), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 48/233 (20%), Positives = 89/233 (38%), Gaps = 32/233 (13%)
Query: 115 EGYGFIEFVSHAAAERVLQTFNGTQMPSTEQNFRLNWATYGAGERRQDDGPDFTIFVGDL 174
+G F+ ++ AE + F+ +++ E + +L D + V +L
Sbjct: 55 KGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPT-------------DALLCVANL 101
Query: 175 AADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTEMNGVLC 234
+T +E R + S++ +V TG+SKGYGF + + R+ +++ G
Sbjct: 102 PPSLTQQQFEELVRP-FGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLG--- 157
Query: 235 STRPMRIGPAATKKAATGQ-QYQKATYQNTQGSQGENDP--NNTTIFVGGLDPSVTDDIL 291
+P+ GP T Q A + P N+ L +
Sbjct: 158 --KPL--GPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFC 213
Query: 292 KTVFGQYGELVHVKIPAGKRCGFVQFANRTCAEQALSVLNGTQLGGQSIRLSW 344
+ GQ G+L K +++ AE+A +G LGG +R+S+
Sbjct: 214 QLACGQDGQL--------KGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSF 258
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 36.2 bits (82), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 268 GENDPNNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRCGFVQFANRTCAEQAL 327
G+ +P T ++VGGL P+ + L F ++G + + G ++Q+ + A+ A
Sbjct: 12 GKANPT-TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAAC 70
Query: 328 SVLNGTQLGGQSIRL 342
+ + G LGG RL
Sbjct: 71 AKMRGFPLGGPDRRL 85
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 36.2 bits (82), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 48/233 (20%), Positives = 89/233 (38%), Gaps = 32/233 (13%)
Query: 115 EGYGFIEFVSHAAAERVLQTFNGTQMPSTEQNFRLNWATYGAGERRQDDGPDFTIFVGDL 174
+G F+ ++ AE + F+ +++ E + +L D + V +L
Sbjct: 57 KGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPT-------------DALLCVANL 103
Query: 175 AADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTEMNGVLC 234
+T +E R + S++ +V TG+SKGYGF + + R+ +++ G
Sbjct: 104 PPSLTQQQFEELVRP-FGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLG--- 159
Query: 235 STRPMRIGPAATKKAATGQ-QYQKATYQNTQGSQGENDP--NNTTIFVGGLDPSVTDDIL 291
+P+ GP T Q A + P N+ L +
Sbjct: 160 --KPL--GPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFC 215
Query: 292 KTVFGQYGELVHVKIPAGKRCGFVQFANRTCAEQALSVLNGTQLGGQSIRLSW 344
+ GQ G+L K +++ AE+A +G LGG +R+S+
Sbjct: 216 QLACGQDGQL--------KGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSF 260
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 35.8 bits (81), Expect = 0.042, Method: Composition-based stats.
Identities = 18/49 (36%), Positives = 29/49 (59%), Gaps = 1/49 (2%)
Query: 168 TIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRF 216
T+F LAA + L++ F AV V+ ++++DR + RSKG +V F
Sbjct: 27 TVFCMQLAARIRPRDLEDFFSAV-GKVRDVRIISDRNSRRSKGIAYVEF 74
>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 = 35.8 bits (81), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 32/64 (50%), Gaps = 1/64 (1%)
Query: 168 TIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMT 227
T+FV + D T+ L+ F VY +K +V + +G+ +GY F+ + E + +
Sbjct: 104 TLFVARVNYDTTESKLRREF-EVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 228 EMNG 231
+G
Sbjct: 163 HADG 166
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 20/89 (22%), Positives = 38/89 (42%), Gaps = 11/89 (12%)
Query: 269 ENDPNN-----TTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRCG------FVQF 317
NDPN T+FV ++ T+ L+ F YG + + + KR G F+++
Sbjct: 92 HNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEY 151
Query: 318 ANRTCAEQALSVLNGTQLGGQSIRLSWGR 346
+ A +G ++ G+ + + R
Sbjct: 152 EHERDMHSAYKHADGKKIDGRRVLVDVER 180
>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 = 35.8 bits (81), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 33/70 (47%), Gaps = 1/70 (1%)
Query: 168 TIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMT 227
T+FV + D T+ L+ F VY +K +V + +G+ +GY F+ + E + +
Sbjct: 104 TLFVARVNYDTTESKLRREF-EVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 228 EMNGVLCSTR 237
+G R
Sbjct: 163 HADGKKIDGR 172
Score = 30.0 bits (66), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 20/88 (22%), Positives = 38/88 (43%), Gaps = 11/88 (12%)
Query: 270 NDPNN-----TTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRCG------FVQFA 318
NDPN T+FV ++ T+ L+ F YG + + + KR G F+++
Sbjct: 93 NDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYE 152
Query: 319 NRTCAEQALSVLNGTQLGGQSIRLSWGR 346
+ A +G ++ G+ + + R
Sbjct: 153 HERDMHSAYKHADGKKIDGRRVLVDVER 180
>pdb|2E5J|A Chain A, Solution Structure Of Rna Binding Domain In
Methenyltetrahydrofolate Synthetase Domain Containing
Length = 97
Score = 35.8 bits (81), Expect = 0.048, Method: Composition-based stats.
Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 5/86 (5%)
Query: 269 ENDPNNTTIFVGGL--DPSVTDDILKTVFGQYGEL-VHVKIPAGKRCGFVQFANRTCAEQ 325
E P ++VG L D V+D LK + G + + + +R F+ + + A+Q
Sbjct: 14 EGAPLAADVYVGNLPRDARVSD--LKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQ 71
Query: 326 ALSVLNGTQLGGQSIRLSWGRSPSNK 351
A+S L G +LG ++R++ R +K
Sbjct: 72 AVSCLQGLRLGTDTLRVALARQQRDK 97
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 35.4 bits (80), Expect = 0.062, Method: Composition-based stats.
Identities = 20/52 (38%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDES 220
+F+G L+ T L+E F + VK V+ D T RS+G+GFV F D++
Sbjct: 3 MFIGGLSWQTTQEGLREYF-GQFGEVKECLVMRDPLTKRSRGFGFVTFMDQA 53
Score = 34.7 bits (78), Expect = 0.10, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 29/57 (50%)
Query: 76 LWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVL 132
++IG L + + FG GE V+R+ T S G+GF+ F+ A ++VL
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 59
Score = 32.0 bits (71), Expect = 0.64, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 33/58 (56%), Gaps = 6/58 (10%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGEL---VHVKIPAGKRC---GFVQFANRTCAEQALS 328
+F+GGL T + L+ FGQ+GE+ + ++ P KR GFV F ++ ++ L+
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60
>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D (Auf1) With Telomere Dna
pdb|1X0F|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D(Auf1) With Telomeric Dna
Length = 79
Score = 35.4 bits (80), Expect = 0.065, Method: Composition-based stats.
Identities = 16/42 (38%), Positives = 25/42 (59%), Gaps = 4/42 (9%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGELVHVKIP----AGKRCGF 314
IFVGGL P ++ ++ FG +GE+ +++P KR GF
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGF 45
Score = 33.9 bits (76), Expect = 0.18, Method: Composition-based stats.
Identities = 16/61 (26%), Positives = 31/61 (50%)
Query: 73 IRSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVL 132
++ +++G L P E I FG GE S ++ + +TN G+ FI F ++++
Sbjct: 1 VKKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 60
Query: 133 Q 133
+
Sbjct: 61 E 61
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 35.0 bits (79), Expect = 0.069, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 4/60 (6%)
Query: 288 DDILKTVFGQYGELVHVKIPAGKR----CGFVQFANRTCAEQALSVLNGTQLGGQSIRLS 343
D L+ +FGQ+G+++ V+I +R GFV F N A++A L+GT + G+ I ++
Sbjct: 29 DPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN 88
Score = 30.4 bits (67), Expect = 1.7, Method: Composition-based stats.
Identities = 15/46 (32%), Positives = 29/46 (63%), Gaps = 2/46 (4%)
Query: 93 IFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQTFNGT 138
+FG G+ + ++I N++ S+G+GF+ F + A A+R + +GT
Sbjct: 35 MFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKLHGT 78
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 35.0 bits (79), Expect = 0.074, Method: Composition-based stats.
Identities = 16/42 (38%), Positives = 25/42 (59%), Gaps = 4/42 (9%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGELVHVKIP----AGKRCGF 314
IFVGGL P ++ ++ FG +GE+ +++P KR GF
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGF 43
Score = 32.0 bits (71), Expect = 0.69, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 29/58 (50%)
Query: 76 LWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQ 133
+++G L P E I FG GE S ++ + +TN G+ FI F +++++
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 59
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 35.0 bits (79), Expect = 0.075, Method: Composition-based stats.
Identities = 15/65 (23%), Positives = 32/65 (49%)
Query: 76 LWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQTF 135
L+IG L ++ + + + G + ++++ T S+GY F E+V ++ +
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 136 NGTQM 140
NG Q+
Sbjct: 64 NGMQL 68
Score = 33.9 bits (76), Expect = 0.18, Method: Composition-based stats.
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 6/70 (8%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRCG------FVQFANRTCAEQALSVL 330
+F+GGL + DD +K + +G L + G F ++ + +QA++ L
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 331 NGTQLGGQSI 340
NG QLG + +
Sbjct: 64 NGMQLGDKKL 73
Score = 32.0 bits (71), Expect = 0.59, Method: Composition-based stats.
Identities = 18/64 (28%), Positives = 34/64 (53%), Gaps = 1/64 (1%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE 228
+F+G L + D ++E + + +K +V D TG SKGY F + D + +++
Sbjct: 4 LFIGGLPNYLNDDQVKELLTS-FGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 229 MNGV 232
+NG+
Sbjct: 63 LNGM 66
>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 = 35.0 bits (79), Expect = 0.082, Method: Composition-based stats.
Identities = 21/55 (38%), Positives = 32/55 (58%), Gaps = 2/55 (3%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQL 223
+F+G L+ D T L++ F + + V + D TGRS+G+GFV F ESE +
Sbjct: 2 MFIGGLSWDTTKKDLKDYF-SKFGEVVDCTLKLDPITGRSRGFGFVLF-KESESV 54
>pdb|1U6B|A Chain A, Crystal Structure Of A Self-Splicing Group I Intron With
Both Exons
pdb|1ZZN|A Chain A, Crystal Structure Of A Group I IntronTWO EXON COMPLEX THAT
Includes All Catalytic Metal Ion Ligands.
pdb|3G8S|A Chain A, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|B Chain B, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|C Chain C, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|D Chain D, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8T|A Chain A, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|B Chain B, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|C Chain C, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|D Chain D, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G96|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G9C|A Chain A, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|B Chain B, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|C Chain C, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|D Chain D, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3IRW|P Chain P, Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3MUM|P Chain P, Crystal Structure Of The G20a Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUR|P Chain P, Crystal Structure Of The C92u Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUT|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Gmp
pdb|3MUV|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Amp
pdb|3MXH|P Chain P, Native Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3P49|B Chain B, Crystal Structure Of A Glycine Riboswitch From
Fusobacterium Nucleatum
pdb|3R1H|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1H|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1L|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3R1L|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3UCU|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Pgpg
pdb|3UCZ|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Gpg
pdb|3UD3|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Pgpa
pdb|3UD4|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Gpa
Length = 98
Score = 34.7 bits (78), Expect = 0.090, Method: Composition-based stats.
Identities = 20/82 (24%), Positives = 38/82 (46%)
Query: 165 PDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLR 224
P+ TI++ +L + L+++ A++S + + + +G FV F + S
Sbjct: 8 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 67
Query: 225 SMTEMNGVLCSTRPMRIGPAAT 246
++ M G +PMRI A T
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKT 89
>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures
pdb|1DZ5|A Chain A, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
pdb|1DZ5|B Chain B, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
Length = 101
Score = 34.7 bits (78), Expect = 0.090, Method: Composition-based stats.
Identities = 20/82 (24%), Positives = 38/82 (46%)
Query: 165 PDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLR 224
P+ TI++ +L + L+++ A++S + + + +G FV F + S
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 66
Query: 225 SMTEMNGVLCSTRPMRIGPAAT 246
++ M G +PMRI A T
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKT 88
>pdb|3L3C|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
Length = 90
Score = 34.7 bits (78), Expect = 0.090, Method: Composition-based stats.
Identities = 20/82 (24%), Positives = 38/82 (46%)
Query: 165 PDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLR 224
P+ TI++ +L + L+++ A++S + + + +G FV F + S
Sbjct: 2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 61
Query: 225 SMTEMNGVLCSTRPMRIGPAAT 246
++ M G +PMRI A T
Sbjct: 62 ALRSMQGFPFYDKPMRIQYAKT 83
>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|B Chain B, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|C Chain C, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|D Chain D, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
Length = 96
Score = 34.7 bits (78), Expect = 0.090, Method: Composition-based stats.
Identities = 20/82 (24%), Positives = 38/82 (46%)
Query: 165 PDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLR 224
P+ TI++ +L + L+++ A++S + + + +G FV F + S
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 66
Query: 225 SMTEMNGVLCSTRPMRIGPAAT 246
++ M G +PMRI A T
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKT 88
>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
pdb|3IWN|D Chain D, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
Length = 91
Score = 34.7 bits (78), Expect = 0.090, Method: Composition-based stats.
Identities = 20/82 (24%), Positives = 38/82 (46%)
Query: 165 PDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLR 224
P+ TI++ +L + L+++ A++S + + + +G FV F + S
Sbjct: 3 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 62
Query: 225 SMTEMNGVLCSTRPMRIGPAAT 246
++ M G +PMRI A T
Sbjct: 63 ALRSMQGFPFYDKPMRIQYAKT 84
>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO3|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO4|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3IIN|A Chain A, Plasticity Of The Kink Turn Structural Motif
Length = 95
Score = 34.7 bits (78), Expect = 0.090, Method: Composition-based stats.
Identities = 20/82 (24%), Positives = 38/82 (46%)
Query: 165 PDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLR 224
P+ TI++ +L + L+++ A++S + + + +G FV F + S
Sbjct: 5 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 64
Query: 225 SMTEMNGVLCSTRPMRIGPAAT 246
++ M G +PMRI A T
Sbjct: 65 ALRSMQGFPFYDKPMRIQYAKT 86
>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|B Chain B, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|C Chain C, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|D Chain D, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
Length = 94
Score = 34.7 bits (78), Expect = 0.090, Method: Composition-based stats.
Identities = 20/82 (24%), Positives = 38/82 (46%)
Query: 165 PDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLR 224
P+ TI++ +L + L+++ A++S + + + +G FV F + S
Sbjct: 4 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 63
Query: 225 SMTEMNGVLCSTRPMRIGPAAT 246
++ M G +PMRI A T
Sbjct: 64 ALRSMQGFPFYDKPMRIQYAKT 85
>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|B Chain B, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|C Chain C, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1NU4|A Chain A, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|1NU4|B Chain B, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|3HHN|B Chain B, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
pdb|3HHN|D Chain D, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
Length = 97
Score = 34.7 bits (78), Expect = 0.090, Method: Composition-based stats.
Identities = 20/82 (24%), Positives = 38/82 (46%)
Query: 165 PDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLR 224
P+ TI++ +L + L+++ A++S + + + +G FV F + S
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 66
Query: 225 SMTEMNGVLCSTRPMRIGPAAT 246
++ M G +PMRI A T
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKT 88
>pdb|1M5K|C Chain C, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5K|F Chain F, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5O|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5O|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1SJ3|P Chain P, Hepatitis Delta Virus Gemonic Ribozyme Precursor, With
Mg2+ Bound
pdb|1SJ4|P Chain P, Crystal Structure Of A C75u Mutant Hepatitis Delta Virus
Ribozyme Precursor, In Cu2+ Solution
pdb|1SJF|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Cobalt
Hexammine Solution
pdb|1VBX|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Edta Solution
pdb|1VBY|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, And Mn2+ Bound
pdb|1VBZ|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Ba2+ Solution
pdb|1VC0|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Imidazole And
Sr2+ Solution
pdb|1VC5|A Chain A, Crystal Structure Of The Wild Type Hepatitis Delta Virus
Gemonic Ribozyme Precursor, In Edta Solution
pdb|1VC6|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Product With C75u Mutaion, Cleaved In Imidazole
And Mg2+ Solutions
pdb|1VC7|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Sr2+ Solution
pdb|2OIH|A Chain A, Hepatitis Delta Virus Gemonic Ribozyme Precursor With C75u
Mutation And Bound To Monovalent Cation Tl+
pdb|2OJ3|A Chain A, Hepatitis Delta Virus Ribozyme Precursor Structure, With
C75u Mutation, Bound To Tl+ And Cobalt Hexammine
(Co(Nh3) 63+)
Length = 100
Score = 34.7 bits (78), Expect = 0.090, Method: Composition-based stats.
Identities = 20/82 (24%), Positives = 38/82 (46%)
Query: 165 PDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLR 224
P+ TI++ +L + L+++ A++S + + + +G FV F + S
Sbjct: 8 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 67
Query: 225 SMTEMNGVLCSTRPMRIGPAAT 246
++ M G +PMRI A T
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKT 89
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 34.7 bits (78), Expect = 0.091, Method: Composition-based stats.
Identities = 24/93 (25%), Positives = 46/93 (49%), Gaps = 3/93 (3%)
Query: 263 TQGSQGENDPNNTT--IFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRCGFVQFANR 320
+ GS G+ D ++ ++V L S ++++++ F ++ + FV F+NR
Sbjct: 2 SSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNR 61
Query: 321 TCAEQALSVLNGTQLGGQSIRLSWGRSPSNKQS 353
A +A+ LNG L G I ++ + P +K S
Sbjct: 62 EDAVEAMKALNGKVLDGSPIEVTLAK-PVDKDS 93
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 34.7 bits (78), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 38/80 (47%), Gaps = 7/80 (8%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRC-GFVQFANRTCAEQALSVLNGTQL 335
+FVG +T+D L+ F QYG+++ V IP R FV FA+ A+ L G L
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQS----LCGEDL 63
Query: 336 --GGQSIRLSWGRSPSNKQS 353
G S+ +S N S
Sbjct: 64 IIKGISVHISNAEPKHNSNS 83
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 34.7 bits (78), Expect = 0.093, Method: Composition-based stats.
Identities = 20/81 (24%), Positives = 41/81 (50%), Gaps = 2/81 (2%)
Query: 168 TIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMT 227
+I+VG++ T L+ F SV ++ D+ +G KG+ ++ F D+ E +R+
Sbjct: 7 SIYVGNVDYGATAEELEAHFHGC-GSVNRVTILCDKFSGHPKGFAYIEFSDK-ESVRTSL 64
Query: 228 EMNGVLCSTRPMRIGPAATKK 248
++ L R +++ P T +
Sbjct: 65 ALDESLFRGRQIKVIPKRTNR 85
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 34.3 bits (77), Expect = 0.12, Method: Composition-based stats.
Identities = 20/82 (24%), Positives = 38/82 (46%)
Query: 165 PDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLR 224
P+ TI++ +L + L+++ A++S + + + +G FV F + S
Sbjct: 8 PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATN 67
Query: 225 SMTEMNGVLCSTRPMRIGPAAT 246
++ M G +PMRI A T
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKT 89
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 34.3 bits (77), Expect = 0.14, Method: Composition-based stats.
Identities = 20/82 (24%), Positives = 38/82 (46%)
Query: 165 PDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLR 224
P+ TI++ +L + L+++ A++S + + + +G FV F + S
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATN 66
Query: 225 SMTEMNGVLCSTRPMRIGPAAT 246
++ M G +PMRI A T
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKT 88
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of Hypothetical
Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens
At 1.95 A Resolution
Length = 89
Score = 34.3 bits (77), Expect = 0.14, Method: Composition-based stats.
Identities = 20/81 (24%), Positives = 41/81 (50%), Gaps = 2/81 (2%)
Query: 168 TIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMT 227
+I+VG++ T L+ F SV ++ D+ +G KG+ ++ F D+ E +R+
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGC-GSVNRVTILCDKFSGHPKGFAYIEFSDK-ESVRTSL 65
Query: 228 EMNGVLCSTRPMRIGPAATKK 248
++ L R +++ P T +
Sbjct: 66 ALDESLFRGRQIKVIPKRTNR 86
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 34.3 bits (77), Expect = 0.14, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 2/74 (2%)
Query: 273 NNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRCGFVQFANRTCAEQALSVLNG 332
+NT +FV V + L +FG +G + VKI G FV+F A +A+ ++G
Sbjct: 3 SNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG--FAFVEFEEAESAAKAIEEVHG 60
Query: 333 TQLGGQSIRLSWGR 346
Q + + + +
Sbjct: 61 KSFANQPLEVVYSK 74
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 34.3 bits (77), Expect = 0.14, Method: Composition-based stats.
Identities = 28/80 (35%), Positives = 38/80 (47%), Gaps = 7/80 (8%)
Query: 275 TTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRC-GFVQFANRTCAEQALSVLNGT 333
+ +FVG +T + L+ F QYGE+V V IP R FV FA+ A+ L G
Sbjct: 12 SKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQS----LCGE 67
Query: 334 QL--GGQSIRLSWGRSPSNK 351
L G S+ +S NK
Sbjct: 68 DLIIKGISVHISNAEPKHNK 87
>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 = 33.9 bits (76), Expect = 0.15, Method: Composition-based stats.
Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 4/65 (6%)
Query: 156 AGERRQDDGPDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVR 215
A + +D G F VG L+ D + L++ F + V + D TGRS+G+GF+
Sbjct: 4 ASKNEEDAGKXF---VGGLSWDTSKKDLKDYFTK-FGEVVDCTIKXDPNTGRSRGFGFIL 59
Query: 216 FGDES 220
F D +
Sbjct: 60 FKDAA 64
Score = 28.1 bits (61), Expect = 9.0, Method: Composition-based stats.
Identities = 15/39 (38%), Positives = 20/39 (51%)
Query: 94 FGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVL 132
F GE V + + T S G+GFI F A+ E+VL
Sbjct: 32 FTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVL 70
>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 18/77 (23%), Positives = 36/77 (46%)
Query: 165 PDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLR 224
P+ TI++ +L + L+++ A++S + + + +G FV F + S
Sbjct: 8 PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATN 67
Query: 225 SMTEMNGVLCSTRPMRI 241
++ M G +PMRI
Sbjct: 68 ALRSMQGFPFYDKPMRI 84
Score = 31.6 bits (70), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 39/81 (48%), Gaps = 3/81 (3%)
Query: 269 ENDPNNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKR-CGFVQFANRTCAEQAL 327
EN PN+ +F+ L + +L +F Q+ V++ G+ FV+F N A A
Sbjct: 203 ENPPNHI-LFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAAR 261
Query: 328 SVLNGTQLG-GQSIRLSWGRS 347
L G ++ ++++S+ +
Sbjct: 262 DALQGFKITQNNAMKISFAKK 282
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 33.9 bits (76), Expect = 0.17, Method: Composition-based stats.
Identities = 22/98 (22%), Positives = 45/98 (45%), Gaps = 10/98 (10%)
Query: 68 ASSDGIRSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAA 127
+ S G+ L+IG+L P + + +FG ++G+V+ GY F+++
Sbjct: 3 SGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL------LKSGYAFVDYPDQNW 56
Query: 128 AERVLQTFNGTQMPSTEQNFRLNWATYGAGERRQDDGP 165
A R ++T +G E + ++ Y ++ + GP
Sbjct: 57 AIRAIETLSG----KVELHGKIMEVDYSVSKKLRSSGP 90
Score = 30.8 bits (68), Expect = 1.5, Method: Composition-based stats.
Identities = 23/90 (25%), Positives = 45/90 (50%), Gaps = 3/90 (3%)
Query: 265 GSQGENDPNNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRCGFVQFANRTCAE 324
GS G + N +++G L P+VT D L+ +FG + ++ FV + ++ A
Sbjct: 1 GSSGSSGMNK--LYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAI 58
Query: 325 QALSVLNG-TQLGGQSIRLSWGRSPSNKQS 353
+A+ L+G +L G+ + + + S + S
Sbjct: 59 RAIETLSGKVELHGKIMEVDYSVSKKLRSS 88
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 33.9 bits (76), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 76 LWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQTF 135
L+I +L M+E + ++ G+ +S +++R+ + S G GF S E V+ F
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHF 86
Query: 136 NG 137
NG
Sbjct: 87 NG 88
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 33.5 bits (75), Expect = 0.21, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 39/64 (60%), Gaps = 2/64 (3%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMTE 228
+F+ L T L+E +A + +VK ++VT+R G+ KG +V + +ES+ +++ +
Sbjct: 20 LFISGLPFSCTKEELEEICKA-HGTVKDLRLVTNRA-GKPKGLAYVEYENESQASQAVMK 77
Query: 229 MNGV 232
M+G+
Sbjct: 78 MDGM 81
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 33.1 bits (74), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 34/59 (57%), Gaps = 6/59 (10%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGEL---VHVKIPAGKRC---GFVQFANRTCAEQALSV 329
+F+GGL T++ L+ + Q+G+L V ++ PA KR GFV F++ + A++
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 88
Score = 31.6 bits (70), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 43/85 (50%), Gaps = 10/85 (11%)
Query: 158 ERRQDDGPDF-TIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRF 216
ER++ + F +F+G L+ + T+ L+ + + + V+ D + RS+G+GFV F
Sbjct: 18 ERKKREKEQFRKLFIGGLSFETTEESLRNYYEQ-WGKLTDCVVMRDPASKRSRGFGFVTF 76
Query: 217 GDESEQLRSMTEMNGVLCSTRPMRI 241
SM E++ + + RP I
Sbjct: 77 S-------SMAEVDAAMAA-RPHSI 93
Score = 29.3 bits (64), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 28/60 (46%)
Query: 73 IRSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVL 132
R L+IG L E + + + G+ V+R+ + S G+GF+ F S A + +
Sbjct: 27 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 86
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 33.1 bits (74), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 28/100 (28%), Positives = 46/100 (46%), Gaps = 16/100 (16%)
Query: 263 TQGSQGE--NDPNNTTIFVGGLDPSVTDDILKTVFGQYG----------ELVHVKI--PA 308
+ GS G+ D +N+ I+V GL+ SVT D L F Q G ++H+ +
Sbjct: 2 SSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKET 61
Query: 309 GKRCG--FVQFANRTCAEQALSVLNGTQLGGQSIRLSWGR 346
GK G V + + A+ A+ +G G +++S R
Sbjct: 62 GKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLAR 101
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 33.1 bits (74), Expect = 0.28, Method: Composition-based stats.
Identities = 25/87 (28%), Positives = 41/87 (47%), Gaps = 6/87 (6%)
Query: 264 QGSQGENDPNNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIP---AGKRCGFVQFANR 320
+G G ND I+VG L P + ++ VF +YG + + + G FV+F +
Sbjct: 15 RGPAGNND---CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDP 71
Query: 321 TCAEQALSVLNGTQLGGQSIRLSWGRS 347
AE A+ +G G +R+ + RS
Sbjct: 72 RDAEDAVYGRDGYDYDGYRLRVEFPRS 98
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 32.7 bits (73), Expect = 0.37, Method: Composition-based stats.
Identities = 18/75 (24%), Positives = 34/75 (45%)
Query: 272 PNNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKRCGFVQFANRTCAEQALSVLN 331
P TT ++G + T+ L +F +G ++ K K C F+++ A + L
Sbjct: 25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCIVALA 84
Query: 332 GTQLGGQSIRLSWGR 346
G+++R WG+
Sbjct: 85 NFPFQGRNLRTGWGK 99
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 32.3 bits (72), Expect = 0.47, Method: Composition-based stats.
Identities = 27/83 (32%), Positives = 47/83 (56%), Gaps = 6/83 (7%)
Query: 277 IFVGGLDPSVTD-DILKTV--FGQYGELVHVKIPAG--KRCGFVQFANRTCAEQALSVLN 331
+FVG L+ ++ D+L+ FG E ++ P G K C FV+F++ T A+ A+ L+
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77
Query: 332 GTQ-LGGQSIRLSWGRSPSNKQS 353
G+Q + G S L + ++K+S
Sbjct: 78 GSQTMPGASSSLVVKFADTDKES 100
Score = 31.6 bits (70), Expect = 0.79, Method: Composition-based stats.
Identities = 21/80 (26%), Positives = 37/80 (46%), Gaps = 2/80 (2%)
Query: 74 RSLWIGDLQPWMEESYIASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQ 133
R L++G L E + +F G V+R + S+G F++F SH A+ +
Sbjct: 16 RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGS-SKGCAFVKFSSHTEAQAAIH 74
Query: 134 TFNGTQ-MPSTEQNFRLNWA 152
+G+Q MP + + +A
Sbjct: 75 ALHGSQTMPGASSSLVVKFA 94
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 32.3 bits (72), Expect = 0.53, Method: Composition-based stats.
Identities = 18/75 (24%), Positives = 37/75 (49%), Gaps = 6/75 (8%)
Query: 263 TQGSQGENDPNNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAG------KRCGFVQ 316
+ GS G D + +F+G + ++ + LK +F ++G++ + + K C F+
Sbjct: 2 SSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLT 61
Query: 317 FANRTCAEQALSVLN 331
+ R A +A S L+
Sbjct: 62 YCERESALKAQSALH 76
>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 = 31.6 bits (70), Expect = 0.75, Method: Composition-based stats.
Identities = 18/67 (26%), Positives = 33/67 (49%), Gaps = 8/67 (11%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGELVHVKI--------PAGKRCGFVQFANRTCAEQALS 328
+FVG + + ++ L+ +F QYG + + + P K C FV F R A +A +
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 329 VLNGTQL 335
L+ ++
Sbjct: 66 ALHNMKV 72
>pdb|2VXQ|L Chain L, Crystal Structure Of The Major Grass Pollen Allergen Phl P
2 In Complex With Its Specific Ige-Fab
Length = 214
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 32/72 (44%), Gaps = 6/72 (8%)
Query: 164 GPDFTIFVGDL-AADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQ 222
G DFT+ + L D Y QE+ A Y+ +G KV RT + F EQ
Sbjct: 68 GTDFTLTISSLQPEDFASYYCQESLSASYTFGQGTKVEIKRTVAAPSVF---IFPPSDEQ 124
Query: 223 LRSMTEMNGVLC 234
L+S T V+C
Sbjct: 125 LKSGTA--SVVC 134
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 28/98 (28%), Positives = 46/98 (46%), Gaps = 10/98 (10%)
Query: 160 RQDDGPDFTIFVGDLAADVTDYVLQETFRAVYSSVKGAK--------VVTDRTTGRSKGY 211
QD+ + TIFV L +VT + + F+ + +K K + TDR TG+ KG
Sbjct: 1 EQDNSDNNTIFVQGLGENVTIESVADYFKQI-GIIKTNKKTGQPMINLYTDRETGKLKGE 59
Query: 212 GFVRFGDESEQLRSMTEMNGVLCSTRPMRIGPAATKKA 249
V F D ++ +G S P+++ AT++A
Sbjct: 60 ATVSFDDPPSAKAAIDWFDGKEFSGNPIKVS-FATRRA 96
Score = 28.1 bits (61), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 23/91 (25%), Positives = 41/91 (45%), Gaps = 14/91 (15%)
Query: 269 ENDPNNTTIFVGGLDPSVTDDILKTVFGQYGEL------------VHVKIPAGKRCG--F 314
+++ +N TIFV GL +VT + + F Q G + ++ GK G
Sbjct: 2 QDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEAT 61
Query: 315 VQFANRTCAEQALSVLNGTQLGGQSIRLSWG 345
V F + A+ A+ +G + G I++S+
Sbjct: 62 VSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 92
>pdb|2FR0|A Chain A, The First Ketoreductase Of The Erythromycin Synthase
(Crystal Form 1)
pdb|2FR1|A Chain A, The First Ketoreductase Of The Erythromycin Synthase
(Crystal Form 2)
Length = 486
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 28/90 (31%), Positives = 42/90 (46%), Gaps = 16/90 (17%)
Query: 146 NFRLNWATYGAGERRQDDGPDFTIFVGDLA--ADVTDYVLQETFRAVYSSVKGAKVVTDR 203
+R+ W GAGE + DG T V A AD T +E + + V+ ++V D
Sbjct: 15 RYRIEWRPTGAGEPARLDG---TWLVAKYAGTADETSTAAREALESAGARVR--ELVVDA 69
Query: 204 TTGRSKGYGFVRFGDESEQLRSMTEMNGVL 233
GR + +E+LRS+ E+ GVL
Sbjct: 70 RCGRD---------ELAERLRSVGEVAGVL 90
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation Initiation
Factor 4b
Length = 100
Score = 30.8 bits (68), Expect = 1.3, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 33/58 (56%), Gaps = 3/58 (5%)
Query: 160 RQDDGPDFTIFVGDLAADVTDYVLQETFRAV-YSSVKGAKVVTDRTTGRSKGYGFVRF 216
R P +T F+G+L DVT+ ++E FR + S+V+ + ++ R KG+G+ F
Sbjct: 13 RLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPE--RLKGFGYAEF 68
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 5/74 (6%)
Query: 272 PNNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKI---PAGKRCGFVQFANRTCAEQALS 328
P + ++VG L + L+ FG YG L V + P G FV+F + A A+
Sbjct: 71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG--FAFVEFEDPRDAADAVR 128
Query: 329 VLNGTQLGGQSIRL 342
L+G L G +R+
Sbjct: 129 ELDGRTLCGCRVRV 142
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 5/74 (6%)
Query: 272 PNNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKI---PAGKRCGFVQFANRTCAEQALS 328
P + ++VG L + L+ FG YG L V + P G FV+F + A A+
Sbjct: 71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG--FAFVEFEDPRDAADAVR 128
Query: 329 VLNGTQLGGQSIRL 342
L+G L G +R+
Sbjct: 129 DLDGRTLCGCRVRV 142
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of Eukaryotic
Initiation Factor 4b
Length = 104
Score = 30.4 bits (67), Expect = 1.7, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 33/58 (56%), Gaps = 3/58 (5%)
Query: 160 RQDDGPDFTIFVGDLAADVTDYVLQETFRAV-YSSVKGAKVVTDRTTGRSKGYGFVRF 216
R P +T F+G+L DVT+ ++E FR + S+V+ + ++ R KG+G+ F
Sbjct: 9 RLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPE--RLKGFGYAEF 64
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 30.0 bits (66), Expect = 2.3, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 41/72 (56%), Gaps = 8/72 (11%)
Query: 276 TIFVGGLDPSVTDDILKTVFGQYGELVHVKIPA---GKRCG--FVQFANRTCAEQALSVL 330
T+ + L S T++ L+ VF + +K+P GK G F++FA+ A++AL+
Sbjct: 17 TLVLSNLSYSATEETLQEVFEK---ATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSC 73
Query: 331 NGTQLGGQSIRL 342
N ++ G++IRL
Sbjct: 74 NKREIEGRAIRL 85
Score = 28.5 bits (62), Expect = 7.9, Method: Composition-based stats.
Identities = 19/74 (25%), Positives = 33/74 (44%), Gaps = 5/74 (6%)
Query: 168 TIFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQLRSMT 227
T+ + +L+ T+ LQE F + +K V G+SKGY F+ F + ++
Sbjct: 17 TLVLSNLSYSATEETLQEVFEKA-TFIK----VPQNQNGKSKGYAFIEFASFEDAKEALN 71
Query: 228 EMNGVLCSTRPMRI 241
N R +R+
Sbjct: 72 SCNKREIEGRAIRL 85
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 30.0 bits (66), Expect = 2.3, Method: Composition-based stats.
Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 6/68 (8%)
Query: 276 TIFVGGLDPSVTDDILKTVFGQYGELVHVKI------PAGKRCGFVQFANRTCAEQALSV 329
T+F+ L ++ L V Q+G+L +V++ K C F QF + A++ L+
Sbjct: 17 TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 76
Query: 330 LNGTQLGG 337
+ GG
Sbjct: 77 ASLEAEGG 84
>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 = 3.0, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 169 IFVGDLAADVTDYVLQETFRAVYSSVKGAKVVTDRTTGRSKGYGFVRFGDE 219
IFVG + + + L+E F+ + V ++ D R +G+GF+ F DE
Sbjct: 13 IFVGGIPHNCGETELREYFKK-FGVVTEVVMIYDAEKQRPRGFGFITFEDE 62
>pdb|2M2B|A Chain A, Nmr Structure Of The Rrm2 Domain Of The Protein Rbm10 From
Homo Sapiens
Length = 131
Score = 29.6 bits (65), Expect = 3.5, Method: Composition-based stats.
Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 2/57 (3%)
Query: 104 KVIRNKQTNFSEGYGFIEFVSHAAAERVLQTFNGTQMPSTEQNFRLNWATYGAGERR 160
+VI++KQT + G+ FI+ + AA+ +LQ P T +N + G +R
Sbjct: 56 RVIKDKQTQLNRGFAFIQLSTIEAAQ-LLQILQALHPPLTIDGKTIN-VEFAKGSKR 110
>pdb|2U1A|A Chain A, Rna Binding Domain 2 Of Human U1a Protein, Nmr, 20
Structures
Length = 88
Score = 29.3 bits (64), Expect = 4.0, Method: Composition-based stats.
Identities = 19/68 (27%), Positives = 32/68 (47%), Gaps = 2/68 (2%)
Query: 269 ENDPNNTTIFVGGLDPSVTDDILKTVFGQYGELVHVKIPAGKR-CGFVQFANRTCAEQAL 327
EN PN+ +F+ L + +L +F Q+ V++ G+ FV+F N A A
Sbjct: 9 ENPPNHI-LFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAAR 67
Query: 328 SVLNGTQL 335
L G ++
Sbjct: 68 DALQGFKI 75
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 29.3 bits (64), Expect = 4.5, Method: Composition-based stats.
Identities = 25/83 (30%), Positives = 43/83 (51%), Gaps = 6/83 (7%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYG---ELVHVKIPAG--KRCGFVQFANRTCAEQALSVLN 331
+FVG L TD+ ++ +F +G E ++ P G K C FV+F A+ A++ L+
Sbjct: 15 LFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTLH 74
Query: 332 GTQ-LGGQSIRLSWGRSPSNKQS 353
++ L G S L + + K+S
Sbjct: 75 SSRTLPGASSSLVVKFADTEKES 97
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 28.9 bits (63), Expect = 5.6, Method: Composition-based stats.
Identities = 12/51 (23%), Positives = 32/51 (62%)
Query: 90 IASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQTFNGTQM 140
+ S+F G+ V+ + ++ T ++G+ F+E S A++++++F+G ++
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRL 79
>pdb|3NS6|A Chain A, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
pdb|3NS6|B Chain B, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
Length = 100
Score = 28.9 bits (63), Expect = 5.7, Method: Composition-based stats.
Identities = 12/51 (23%), Positives = 32/51 (62%)
Query: 90 IASIFGHTGEFVSGKVIRNKQTNFSEGYGFIEFVSHAAAERVLQTFNGTQM 140
+ S+F G+ V+ + ++ T ++G+ F+E S A++++++F+G ++
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRL 79
>pdb|3Q2S|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2S|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2T|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
pdb|3Q2T|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
Length = 229
Score = 28.5 bits (62), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 1/64 (1%)
Query: 164 GPDFTIFVGDLAADVTDYVLQETFRAV-YSSVKGAKVVTDRTTGRSKGYGFVRFGDESEQ 222
G +++G+L TD L E ++ + + K +R G+SKG+ V G E+
Sbjct: 66 GKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASS 125
Query: 223 LRSM 226
+ M
Sbjct: 126 KKLM 129
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 28.1 bits (61), Expect = 8.1, Method: Composition-based stats.
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 277 IFVGGLDPSVTDDILKTVFGQYGELV 302
+FVGGL P + +D + F ++G LV
Sbjct: 11 VFVGGLPPDIDEDEITASFRRFGPLV 36
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
0.316 0.134 0.404
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,993,603
Number of Sequences: 62578
Number of extensions: 470380
Number of successful extensions: 1445
Number of sequences better than 100.0: 192
Number of HSP's better than 100.0 without gapping: 123
Number of HSP's successfully gapped in prelim test: 69
Number of HSP's that attempted gapping in prelim test: 983
Number of HSP's gapped (non-prelim): 420
length of query: 406
length of database: 14,973,337
effective HSP length: 101
effective length of query: 305
effective length of database: 8,652,959
effective search space: 2639152495
effective search space used: 2639152495
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: 53 (25.0 bits)