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= 013926
(434 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 142 bits (358), Expect = 3e-34, Method: Compositional matrix adjust.
Identities = 70/172 (40%), Positives = 111/172 (64%), Gaps = 5/172 (2%)
Query: 15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTT---RASRCCFVICPSRQEADKA 71
+K+FVGQVP+ +E L +F+++ V E+N+++D++ ++ CCFV +R+ A +A
Sbjct: 16 IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 75
Query: 72 VNACHNKKTLPGASSPLQVKYADGELERL--EHKLFIGMLPKNVSEAEVSALFSIYGTIK 129
NA HN K LPG P+Q+K AD E + KLFIGM+ K +E ++ +FS +G I+
Sbjct: 76 QNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIE 135
Query: 130 DLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWAD 181
+ +ILRG S+GCAF+ + T+ A A++A++ MEG S P+VVK+AD
Sbjct: 136 ECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD 187
Score = 60.8 bits (146), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 30/85 (35%), Positives = 50/85 (58%), Gaps = 3/85 (3%)
Query: 103 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT---SKGCAFLKYETKEQALAAL 159
K+F+G +P+ SE ++ LF YG + ++ +LR Q SKGC F+ + T++ AL A
Sbjct: 17 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 76
Query: 160 EAINGKHKMEGSSVPLVVKWADTEK 184
A++ + G P+ +K AD+EK
Sbjct: 77 NALHNMKVLPGMHHPIQMKPADSEK 101
Score = 31.6 bits (70), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 351 LFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAMM 410
LFI I ++ + ++ F +FG++ ++ + G+S+ FV++ + A AQ AI M
Sbjct: 110 LFIGMISKKCTENDIRVMFSSFGQIEECRI-LRGPDGLSRGCAFVTFTTRAMAQTAIKAM 168
Query: 411 N 411
+
Sbjct: 169 H 169
Score = 29.6 bits (65), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 34/65 (52%), Gaps = 5/65 (7%)
Query: 351 LFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATG--VSK--CF-GFVSYESPASAQN 405
+F+ +P+ + +++L F+ +G V V D++ SK CF F + ++ AQN
Sbjct: 18 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 77
Query: 406 AIAMM 410
A+ M
Sbjct: 78 ALHNM 82
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 142 bits (357), Expect = 4e-34, Method: Compositional matrix adjust.
Identities = 70/172 (40%), Positives = 111/172 (64%), Gaps = 5/172 (2%)
Query: 15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTT---RASRCCFVICPSRQEADKA 71
+K+FVGQVP+ +E L +F+++ V E+N+++D++ ++ CCFV +R+ A +A
Sbjct: 4 IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Query: 72 VNACHNKKTLPGASSPLQVKYADGELERL--EHKLFIGMLPKNVSEAEVSALFSIYGTIK 129
NA HN K LPG P+Q+K AD E + KLFIGM+ K +E ++ +FS +G I+
Sbjct: 64 QNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIE 123
Query: 130 DLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWAD 181
+ +ILRG S+GCAF+ + T+ A A++A++ MEG S P+VVK+AD
Sbjct: 124 ECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD 175
Score = 60.1 bits (144), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 34/88 (38%), Positives = 52/88 (59%), Gaps = 9/88 (10%)
Query: 103 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT---SKGCAFLKYETKEQALAAL 159
K+F+G +P+ SE ++ LF YG + ++ +LR Q SKGC F+ + T++ AAL
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRK---AAL 61
Query: 160 EAINGKHKME---GSSVPLVVKWADTEK 184
EA N H M+ G P+ +K AD+EK
Sbjct: 62 EAQNALHNMKVLPGMHHPIQMKPADSEK 89
Score = 31.2 bits (69), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 351 LFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAMM 410
LFI I ++ + ++ F +FG++ ++ + G+S+ FV++ + A AQ AI M
Sbjct: 98 LFIGMISKKCTENDIRVMFSSFGQIEECRI-LRGPDGLSRGCAFVTFTTRAMAQTAIKAM 156
Query: 411 N 411
+
Sbjct: 157 H 157
Score = 29.3 bits (64), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 34/65 (52%), Gaps = 5/65 (7%)
Query: 351 LFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATG--VSK--CF-GFVSYESPASAQN 405
+F+ +P+ + +++L F+ +G V V D++ SK CF F + ++ AQN
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 406 AIAMM 410
A+ M
Sbjct: 66 ALHNM 70
>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 = 131 bits (329), Expect = 8e-31, Method: Compositional matrix adjust.
Identities = 68/172 (39%), Positives = 104/172 (60%), Gaps = 5/172 (2%)
Query: 15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTT---RASRCCFVICPSRQEADKA 71
+K FVGQVP+ +E L +F+++ V E+N+++D++ ++ CCFV +R+ A +A
Sbjct: 4 IKXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Query: 72 VNACHNKKTLPGASSPLQVKYADGELERL--EHKLFIGMLPKNVSEAEVSALFSIYGTIK 129
NA HN K LPG P+Q K AD E + KLFIG + K +E ++ FS +G I+
Sbjct: 64 QNALHNXKVLPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQIE 123
Query: 130 DLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWAD 181
+ +ILRG S+GCAF+ + T+ A A++A + EG S P VVK+AD
Sbjct: 124 ECRILRGPDGLSRGCAFVTFTTRAXAQTAIKAXHQAQTXEGCSSPXVVKFAD 175
Score = 58.9 bits (141), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 30/85 (35%), Positives = 48/85 (56%), Gaps = 3/85 (3%)
Query: 103 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT---SKGCAFLKYETKEQALAAL 159
K F+G +P+ SE ++ LF YG + ++ +LR Q SKGC F+ + T++ AL A
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 160 EAINGKHKMEGSSVPLVVKWADTEK 184
A++ + G P+ K AD+EK
Sbjct: 65 NALHNXKVLPGXHHPIQXKPADSEK 89
>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 = 107 bits (267), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 50/71 (70%), Positives = 57/71 (80%)
Query: 342 QIEGPPGANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPA 401
Q EGP GANLFIYH+PQEFGDQ+L F FG V+SAKVF+DK T +SKCFGFVSY++P
Sbjct: 19 QKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPV 78
Query: 402 SAQNAIAMMNG 412
SAQ AI MNG
Sbjct: 79 SAQAAIQSMNG 89
Score = 32.0 bits (71), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 20/41 (48%)
Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRC 57
LF+ +P+ + LL MF F V + DK T S+C
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKC 68
Score = 30.0 bits (66), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGC-AFLKYETKEQALAALEAI 162
LFI LP+ + ++ +F +G + ++ Q C F+ Y+ A AA++++
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 163 NG 164
NG
Sbjct: 88 NG 89
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 103 bits (258), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 47/71 (66%), Positives = 56/71 (78%)
Query: 342 QIEGPPGANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPA 401
QIEGP G NLFIYH+PQEF D +L + F FG V+SAKVF+DK T +SKCFGFVS+++P
Sbjct: 34 QIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPD 93
Query: 402 SAQNAIAMMNG 412
SAQ AI MNG
Sbjct: 94 SAQVAIKAMNG 104
Score = 32.3 bits (72), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 15/62 (24%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGC-AFLKYETKEQALAALEAI 162
LFI LP+ ++ ++++ F +G + ++ Q + C F+ ++ + A A++A+
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 163 NG 164
NG
Sbjct: 103 NG 104
Score = 30.4 bits (67), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 28/61 (45%), Gaps = 4/61 (6%)
Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRCCFVIC----PSRQEADKAV 72
LF+ +P+ T+ L + F F V + DK T S+C + S Q A KA+
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 73 N 73
N
Sbjct: 103 N 103
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 89.0 bits (219), Expect = 5e-18, Method: Compositional matrix adjust.
Identities = 43/83 (51%), Positives = 57/83 (68%)
Query: 103 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 162
KLF+GML K SE +V LF +G I++ ILRG SKGCAF+KY + +A AA+ A+
Sbjct: 17 KLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINAL 76
Query: 163 NGKHKMEGSSVPLVVKWADTEKE 185
+G M G+S LVVK+ADT+KE
Sbjct: 77 HGSQTMPGASSSLVVKFADTDKE 99
Score = 66.6 bits (161), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 33/83 (39%), Positives = 48/83 (57%)
Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRCCFVICPSRQEADKAVNAC 75
KLFVG + K +E + +F+ F ++E I++ + C FV S EA A+NA
Sbjct: 17 KLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINAL 76
Query: 76 HNKKTLPGASSPLQVKYADGELE 98
H +T+PGASS L VK+AD + E
Sbjct: 77 HGSQTMPGASSSLVVKFADTDKE 99
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 82.4 bits (202), Expect = 4e-16, Method: Composition-based stats.
Identities = 41/85 (48%), Positives = 58/85 (68%)
Query: 101 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALE 160
+ KLF+GML K SE +V LF +G I + +LRG +SKGCAF+K+ + +A AA+
Sbjct: 15 DRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIH 74
Query: 161 AINGKHKMEGSSVPLVVKWADTEKE 185
A++G M G+S LVVK+ADT+KE
Sbjct: 75 ALHGSQTMPGASSSLVVKFADTDKE 99
Score = 67.4 bits (163), Expect = 2e-11, Method: Composition-based stats.
Identities = 33/83 (39%), Positives = 50/83 (60%)
Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRCCFVICPSRQEADKAVNAC 75
KLFVG + K +E +L +F+ F ++DE +++ + C FV S EA A++A
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHAL 76
Query: 76 HNKKTLPGASSPLQVKYADGELE 98
H +T+PGASS L VK+AD + E
Sbjct: 77 HGSQTMPGASSSLVVKFADTDKE 99
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 82.0 bits (201), Expect = 6e-16, Method: Composition-based stats.
Identities = 39/85 (45%), Positives = 58/85 (68%)
Query: 101 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALE 160
+ KLF+GML K ++ +V +F +GTI + +LRG TSKGCAF+K++T +A AA+
Sbjct: 12 DRKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAIN 71
Query: 161 AINGKHKMEGSSVPLVVKWADTEKE 185
++ + G+S LVVK+ADTEKE
Sbjct: 72 TLHSSRTLPGASSSLVVKFADTEKE 96
Score = 68.2 bits (165), Expect = 1e-11, Method: Composition-based stats.
Identities = 34/83 (40%), Positives = 48/83 (57%)
Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRCCFVICPSRQEADKAVNAC 75
KLFVG + K T+ + MF+ F +DE +++ + C FV + EA A+N
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTL 73
Query: 76 HNKKTLPGASSPLQVKYADGELE 98
H+ +TLPGASS L VK+AD E E
Sbjct: 74 HSSRTLPGASSSLVVKFADTEKE 96
>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 = 77.4 bits (189), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 53/171 (30%), Positives = 96/171 (56%), Gaps = 9/171 (5%)
Query: 14 RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASR-CCFVICPSRQEADKAV 72
R L V +P++MT+ +L ++F V+ +I+DK S FV + ++A++A+
Sbjct: 2 RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Query: 73 NACHNKKTLPGASSPLQVKYADGELERLEH-KLFIGMLPKNVSEAEVSALFSIYGTIKDL 131
N + L S ++V YA E ++ L+I LP+ +++ +V +FS +G I +
Sbjct: 62 NTLNG---LRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINS 118
Query: 132 QILRGSQQT--SKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA 180
++L Q T S+G AF++++ + +A A+ + NG HK GSS P+ VK+A
Sbjct: 119 RVL-VDQTTGLSRGVAFIRFDKRSEAEEAITSFNG-HKPPGSSEPITVKFA 167
Score = 55.8 bits (133), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 41/64 (64%)
Query: 349 ANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIA 408
ANL+I +P+ +++ + F FGR+++++V VD+ TG+S+ F+ ++ + A+ AI
Sbjct: 89 ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAIT 148
Query: 409 MMNG 412
NG
Sbjct: 149 SFNG 152
Score = 51.6 bits (122), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 25/65 (38%), Positives = 36/65 (55%)
Query: 349 ANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIA 408
NL + ++PQ EL + F + G V SAK+ DK G S +GFV+Y + A+ AI
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 409 MMNGC 413
+NG
Sbjct: 63 TLNGL 67
>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 = 75.5 bits (184), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 35/85 (41%), Positives = 56/85 (65%), Gaps = 3/85 (3%)
Query: 15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTT---RASRCCFVICPSRQEADKA 71
+K+FVGQVP+ +E L +F+++ V E+N+++D++ ++ CCFV +R+ A +A
Sbjct: 4 IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Query: 72 VNACHNKKTLPGASSPLQVKYADGE 96
NA HN K LPG P+Q+K AD E
Sbjct: 64 QNALHNMKVLPGMHHPIQMKPADSE 88
Score = 59.3 bits (142), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 29/84 (34%), Positives = 49/84 (58%), Gaps = 3/84 (3%)
Query: 103 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT---SKGCAFLKYETKEQALAAL 159
K+F+G +P+ SE ++ LF YG + ++ +LR Q SKGC F+ + T++ AL A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 160 EAINGKHKMEGSSVPLVVKWADTE 183
A++ + G P+ +K AD+E
Sbjct: 65 NALHNMKVLPGMHHPIQMKPADSE 88
Score = 30.0 bits (66), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 34/65 (52%), Gaps = 5/65 (7%)
Query: 351 LFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATG--VSK--CF-GFVSYESPASAQN 405
+F+ +P+ + +++L F+ +G V V D++ SK CF F + ++ AQN
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 406 AIAMM 410
A+ M
Sbjct: 66 ALHNM 70
>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 = 8e-14, Method: Compositional matrix adjust.
Identities = 52/171 (30%), Positives = 95/171 (55%), Gaps = 9/171 (5%)
Query: 14 RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASR-CCFVICPSRQEADKAV 72
R L V +P++MT+ +L ++F V+ +I+DK S FV + ++A++A+
Sbjct: 2 RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Query: 73 NACHNKKTLPGASSPLQVKYADGELERL-EHKLFIGMLPKNVSEAEVSALFSIYGTIKDL 131
N + L S ++V YA E + + L+I LP+ +++ +V +FS +G I +
Sbjct: 62 NTLNG---LRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINS 118
Query: 132 QILRGSQQT--SKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA 180
++L Q T S+G AF++++ + +A A+ + NG HK GSS P+ V +A
Sbjct: 119 RVL-VDQTTGLSRGVAFIRFDKRSEAEEAITSFNG-HKPPGSSEPITVXFA 167
Score = 55.8 bits (133), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 41/64 (64%)
Query: 349 ANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIA 408
ANL+I +P+ +++ + F FGR+++++V VD+ TG+S+ F+ ++ + A+ AI
Sbjct: 89 ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAIT 148
Query: 409 MMNG 412
NG
Sbjct: 149 SFNG 152
Score = 51.6 bits (122), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 25/65 (38%), Positives = 36/65 (55%)
Query: 349 ANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIA 408
NL + ++PQ EL + F + G V SAK+ DK G S +GFV+Y + A+ AI
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 409 MMNGC 413
+NG
Sbjct: 63 TLNGL 67
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 71.2 bits (173), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 35/83 (42%), Positives = 53/83 (63%), Gaps = 1/83 (1%)
Query: 15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASR-CCFVICPSRQEADKAVN 73
+KLFVGQ+P+ + E L +F+EF + E+ ++KD+ T + C F+ +R A KA +
Sbjct: 16 IKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQS 75
Query: 74 ACHNKKTLPGASSPLQVKYADGE 96
A H +KTLPG + P+QVK A E
Sbjct: 76 ALHEQKTLPGMNRPIQVKPAASE 98
Score = 55.1 bits (131), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 29/82 (35%), Positives = 48/82 (58%), Gaps = 1/82 (1%)
Query: 103 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEA 161
KLF+G +P+ + E ++ LF +G I +L +L+ KGCAFL Y ++ AL A A
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSA 76
Query: 162 INGKHKMEGSSVPLVVKWADTE 183
++ + + G + P+ VK A +E
Sbjct: 77 LHEQKTLPGMNRPIQVKPAASE 98
Score = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 34/61 (55%), Gaps = 3/61 (4%)
Query: 350 NLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSY---ESPASAQNA 406
LF+ IP+ +Q+L F+ FGR+ V D+ TG+ K F++Y +S AQ+A
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSA 76
Query: 407 I 407
+
Sbjct: 77 L 77
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 70.9 bits (172), Expect = 1e-12, Method: Composition-based stats.
Identities = 34/81 (41%), Positives = 54/81 (66%), Gaps = 1/81 (1%)
Query: 15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASR-CCFVICPSRQEADKAVN 73
+KLF+GQ+P+++ E L +F+EF + E+ ++KD+ T + C F+ R+ A KA +
Sbjct: 14 IKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQS 73
Query: 74 ACHNKKTLPGASSPLQVKYAD 94
A H +KTLPG + P+QVK AD
Sbjct: 74 ALHEQKTLPGMNRPIQVKPAD 94
Score = 58.9 bits (141), Expect = 5e-09, Method: Composition-based stats.
Identities = 32/80 (40%), Positives = 48/80 (60%), Gaps = 1/80 (1%)
Query: 103 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEA 161
KLFIG +P+N+ E ++ LF +G I +L +L+ KGCAFL Y +E AL A A
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74
Query: 162 INGKHKMEGSSVPLVVKWAD 181
++ + + G + P+ VK AD
Sbjct: 75 LHEQKTLPGMNRPIQVKPAD 94
Score = 39.3 bits (90), Expect = 0.005, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 34/60 (56%), Gaps = 3/60 (5%)
Query: 351 LFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSY---ESPASAQNAI 407
LFI IP+ +++L F+ FG++ V D+ TG+ K F++Y ES AQ+A+
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSAL 75
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 70.5 bits (171), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 47/171 (27%), Positives = 92/171 (53%), Gaps = 7/171 (4%)
Query: 14 RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRCC-FVICPSRQEADKAV 72
+ L V +P++MT+ + ++F ++ +++DK T S FV +ADKA+
Sbjct: 4 KTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI 63
Query: 73 NACHNKKTLPGASSPLQVKYADGELERL-EHKLFIGMLPKNVSEAEVSALFSIYGTIKDL 131
N + K + ++V YA + + L++ LPK +S+ E+ LFS YG I
Sbjct: 64 NTLNGLKL---QTKTIKVSYARPSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITS 120
Query: 132 QILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWAD 181
+IL + S+G F++++ + +A A++ +NG+ + G++ P+ VK+A+
Sbjct: 121 RILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQKPL-GAAEPITVKFAN 170
Score = 57.8 bits (138), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 42/64 (65%)
Query: 349 ANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIA 408
ANL++ +P+ +E+ F +GR++++++ +D+ATGVS+ GF+ ++ A+ AI
Sbjct: 91 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 150
Query: 409 MMNG 412
+NG
Sbjct: 151 GLNG 154
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 34/65 (52%)
Query: 349 ANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIA 408
NL + ++PQ E + F + G + S K+ DK TG S +GFV+Y P A AI
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 409 MMNGC 413
+NG
Sbjct: 65 TLNGL 69
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 67.8 bits (164), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 47/167 (28%), Positives = 86/167 (51%), Gaps = 7/167 (4%)
Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKD-KTTRASRCCFVICPSRQEADKAVNAC 75
L V +P+ MT+ +L A+F+ ++ I++D KT + FV S ++ +A+
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 76 HNKKTLPGASSPLQVKYADGELERL-EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL 134
+ + + L+V YA E + + L++ LP+ +++ ++ +F YG+I IL
Sbjct: 66 NG---ITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNIL 122
Query: 135 RGSQQTS-KGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA 180
R +G AF++Y +E+A A+ A+N EG S PL V+ A
Sbjct: 123 RDKLTGRPRGVAFVRYNKREEAQEAISALNNVIP-EGGSQPLSVRLA 168
Score = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 37/65 (56%)
Query: 349 ANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIA 408
NL + ++PQ+ D+EL F+A G + + ++ D TG S + FV + S +Q AI
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 409 MMNGC 413
++NG
Sbjct: 64 VLNGI 68
>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 = 65.9 bits (159), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 46/170 (27%), Positives = 90/170 (52%), Gaps = 7/170 (4%)
Query: 14 RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASR-CCFVICPSRQEADKAV 72
+ L V +P++MT+ + ++F ++ +++DK T S FV ++A+KA+
Sbjct: 2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61
Query: 73 NACHNKKTLPGASSPLQVKYADGELERL-EHKLFIGMLPKNVSEAEVSALFSIYGTIKDL 131
N + L + ++V YA + + L++ LPK +++ E+ LFS YG I
Sbjct: 62 NTLNG---LRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITS 118
Query: 132 QILRGSQQ-TSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA 180
+IL S+G F++++ + +A A++ +NG K G++ P+ VK+A
Sbjct: 119 RILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNG-QKPSGATEPITVKFA 167
Score = 58.2 bits (139), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 41/64 (64%)
Query: 349 ANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIA 408
ANL++ +P+ +EL F +GR++++++ VD+ TGVS+ GF+ ++ A+ AI
Sbjct: 89 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 148
Query: 409 MMNG 412
+NG
Sbjct: 149 GLNG 152
Score = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 36/65 (55%)
Query: 349 ANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIA 408
NL + ++PQ +E + F + G + S K+ DK TG S +GFV+Y P A+ AI
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 409 MMNGC 413
+NG
Sbjct: 63 TLNGL 67
>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 = 63.9 bits (154), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 46/168 (27%), Positives = 85/168 (50%), Gaps = 7/168 (4%)
Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKD-KTTRASRCCFVICPSRQEADKAVNAC 75
L V +P+ T+ +L A+F+ ++ I +D KT + FV S ++ +A+
Sbjct: 17 LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 76 HNKKTLPGASSPLQVKYADGELERL-EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL 134
+ + + L+V YA E + + L++ LP+ +++ ++ +F YG+I IL
Sbjct: 77 NG---ITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNIL 133
Query: 135 RGSQQTS-KGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWAD 181
R +G AF++Y +E+A A+ A+N EG S PL V+ A+
Sbjct: 134 RDKLTGRPRGVAFVRYNKREEAQEAISALNNVIP-EGGSQPLSVRLAE 180
Score = 49.3 bits (116), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 37/65 (56%)
Query: 349 ANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIA 408
NL + ++PQ+ D+EL F+A G + + ++ D TG S + FV + S +Q AI
Sbjct: 15 TNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIK 74
Query: 409 MMNGC 413
++NG
Sbjct: 75 VLNGI 79
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 57.4 bits (137), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 42/64 (65%)
Query: 349 ANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIA 408
ANL++ +P+ +E+ F +GR++++++ +D+ATGVS+ GF+ ++ A+ AI
Sbjct: 2 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 61
Query: 409 MMNG 412
+NG
Sbjct: 62 GLNG 65
Score = 48.9 bits (115), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 50/79 (63%), Gaps = 2/79 (2%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAI 162
L++ LPK +S+ E+ LFS YG I +IL + S+G F++++ + +A A++ +
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 163 NGKHKMEGSSVPLVVKWAD 181
NG+ + G++ P+ VK+A+
Sbjct: 64 NGQKPL-GAAEPITVKFAN 81
Score = 45.4 bits (106), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 46/79 (58%), Gaps = 2/79 (2%)
Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASR-CCFVICPSRQEADKAVNAC 75
L+V +PK M++ ++ +F ++ + I+ D+ T SR F+ R EA++A+
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 76 HNKKTLPGASSPLQVKYAD 94
+ +K L GA+ P+ VK+A+
Sbjct: 64 NGQKPL-GAAEPITVKFAN 81
>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 = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 39/62 (62%)
Query: 350 NLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAM 409
+++ + Q+ D ++ + F+AFG++ SA + D TG K +GF+ YE S+Q+A++
Sbjct: 127 RIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 186
Query: 410 MN 411
MN
Sbjct: 187 MN 188
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 32/65 (49%)
Query: 349 ANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIA 408
+ +++ I E G+ + AF FG + S + D T K F FV YE P +AQ A+
Sbjct: 29 SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 88
Query: 409 MMNGC 413
MN
Sbjct: 89 QMNSV 93
Score = 33.1 bits (74), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 103 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEA 161
++++G + + E + F+ +G IK + + S KG AF++YE E A ALE
Sbjct: 30 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 89
Query: 162 IN 163
+N
Sbjct: 90 MN 91
>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 = 53.1 bits (126), Expect = 3e-07, Method: Composition-based stats.
Identities = 27/68 (39%), Positives = 38/68 (55%)
Query: 345 GPPGANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQ 404
GP NL + ++PQ EL + F + G V SAK+ DK G S +GFV+Y + A+
Sbjct: 1 GPGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAE 60
Query: 405 NAIAMMNG 412
AI +NG
Sbjct: 61 RAINTLNG 68
Score = 36.2 bits (82), Expect = 0.041, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAI 162
L + LP+N+++ E+ +LFS G ++ +++R S G F+ Y T + A A+ +
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 163 NG 164
NG
Sbjct: 67 NG 68
Score = 33.5 bits (75), Expect = 0.22, Method: Composition-based stats.
Identities = 22/81 (27%), Positives = 42/81 (51%), Gaps = 4/81 (4%)
Query: 14 RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASR-CCFVICPSRQEADKAV 72
R L V +P++MT+ +L ++F V+ +I+DK S FV + ++A++A+
Sbjct: 4 RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 63
Query: 73 NACHNKKTLPGASSPLQVKYA 93
N + + S ++V YA
Sbjct: 64 NTLNGLRL---QSKTIKVSYA 81
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 52.4 bits (124), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 39/63 (61%)
Query: 350 NLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAM 409
NL + +IP + +L F+ +G + S K+ D+ T S+ +GFV ++S +SAQ AIA
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 410 MNG 412
+NG
Sbjct: 104 LNG 106
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 37/65 (56%), Gaps = 3/65 (4%)
Query: 102 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL--RGSQQTSKGCAFLKYETKEQALAAL 159
L + +P V E ++ LF YG I+ ++I+ R ++Q S+G F+K+++ A A+
Sbjct: 43 RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQ-SRGYGFVKFQSGSSAQQAI 101
Query: 160 EAING 164
+NG
Sbjct: 102 AGLNG 106
>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 = 52.0 bits (123), Expect = 6e-07, Method: Composition-based stats.
Identities = 26/65 (40%), Positives = 37/65 (56%)
Query: 348 GANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAI 407
G NL + ++PQ EL + F + G V SAK+ DK G S +GFV+Y + A+ AI
Sbjct: 19 GTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 78
Query: 408 AMMNG 412
+NG
Sbjct: 79 NTLNG 83
Score = 36.2 bits (82), Expect = 0.041, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAI 162
L + LP+N ++ E+ +LFS G ++ +++R S G F+ Y T + A A+ +
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 163 NG 164
NG
Sbjct: 82 NG 83
>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 = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 38/62 (61%)
Query: 350 NLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAM 409
+++ + Q+ D ++ + F+AFG++ S + D TG K +GF+ YE S+Q+A++
Sbjct: 112 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 171
Query: 410 MN 411
MN
Sbjct: 172 MN 173
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 31/62 (50%)
Query: 350 NLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAM 409
+++ I E G+ + AF FG + S + D T K F FV YE P +AQ A+
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 410 MN 411
MN
Sbjct: 75 MN 76
Score = 32.7 bits (73), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 103 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEA 161
++++G + + E + F+ +G IK + + S KG AF++YE E A ALE
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 162 IN 163
+N
Sbjct: 75 MN 76
>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 = 50.8 bits (120), Expect = 1e-06, Method: Composition-based stats.
Identities = 28/69 (40%), Positives = 43/69 (62%), Gaps = 3/69 (4%)
Query: 345 GPPGA-NLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASA 403
GP G+ N+FI ++ + ++ L + F AFG +LS KV D+ SK +GFV +E+ +A
Sbjct: 1 GPLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAA 58
Query: 404 QNAIAMMNG 412
+ AI MNG
Sbjct: 59 ERAIEKMNG 67
Score = 36.2 bits (82), Expect = 0.037, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 163
+FI L K++ + FS +G I +++ + SKG F+ +ET+E A A+E +N
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVV-CDENGSKGYGFVHFETQEAAERAIEKMN 66
Query: 164 G 164
G
Sbjct: 67 G 67
>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 = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 38/63 (60%)
Query: 350 NLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAM 409
++F+ + E +++ AF FGR+ A+V D ATG SK +GFVS+ + A+NAI
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 410 MNG 412
M G
Sbjct: 77 MGG 79
Score = 30.4 bits (67), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRC-CFVICPSRQEADKAV 72
+FVG + +T + A F F + + ++KD T S+ FV ++ +A+ A+
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAI 74
>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 = 50.8 bits (120), Expect = 2e-06, Method: Composition-based stats.
Identities = 27/63 (42%), Positives = 35/63 (55%)
Query: 350 NLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAM 409
NLF+ + D+ L NAF+ F LS V D TG S+ +GFVS+ S AQNA+
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 410 MNG 412
M G
Sbjct: 63 MQG 65
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/63 (42%), Positives = 35/63 (55%)
Query: 350 NLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAM 409
NLF+ + D+ L NAF+ F LS V D TG S+ +GFVS+ S AQNA+
Sbjct: 89 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 148
Query: 410 MNG 412
M G
Sbjct: 149 MQG 151
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 36/168 (21%), Positives = 77/168 (45%), Gaps = 10/168 (5%)
Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRCCFVICPSRQEADKAVNACH 76
L+VG + K +TE L F+ + + I+ DK + FV +A+ A+ +
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 77 NKKTLPGASSPLQVKYADGELERLEHK---LFIGMLPKNVSEAEVSALFSIYGTIKDLQI 133
K+ ++ +++ +A + LF+G L NV + + F + + +
Sbjct: 63 GKQI---ENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHV 119
Query: 134 LRGSQQ-TSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA 180
+ Q +S+G F+ + +++ A A++++ G+ + G PL + WA
Sbjct: 120 MWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQ-DLNGR--PLRINWA 164
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 39/63 (61%)
Query: 350 NLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAM 409
++F+ + E +++ +AF FG++ A+V D ATG SK +GFVS+ + A+NAI
Sbjct: 17 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 410 MNG 412
M G
Sbjct: 77 MGG 79
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 49.7 bits (117), Expect = 3e-06, Method: Composition-based stats.
Identities = 25/64 (39%), Positives = 39/64 (60%), Gaps = 2/64 (3%)
Query: 349 ANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIA 408
N+FI ++ + ++ L + F AFG +LS KV D+ SK +GFV +E+ +A+ AI
Sbjct: 12 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIE 69
Query: 409 MMNG 412
MNG
Sbjct: 70 KMNG 73
Score = 37.0 bits (84), Expect = 0.021, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 163
+FI L K++ + FS +G I +++ + SKG F+ +ET+E A A+E +N
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVV-CDENGSKGYGFVHFETQEAAERAIEKMN 72
Query: 164 G 164
G
Sbjct: 73 G 73
>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 = 49.7 bits (117), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 39/63 (61%), Gaps = 2/63 (3%)
Query: 350 NLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAM 409
N+FI ++ + ++ L + F AFG +LS KV D+ SK +GFV +E+ +A+ AI
Sbjct: 105 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEK 162
Query: 410 MNG 412
MNG
Sbjct: 163 MNG 165
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 39/150 (26%), Positives = 69/150 (46%), Gaps = 4/150 (2%)
Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASR-CCFVICPSRQEADKAVNAC 75
L+VG + +TEA L F + + + +D TR S +V +A++A++
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77
Query: 76 HNKKTLPGASSPLQVKYADGELERL-EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL 134
N + G + D L + +FI L K++ + FS +G I +++
Sbjct: 78 -NFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVV 136
Query: 135 RGSQQTSKGCAFLKYETKEQALAALEAING 164
+ SKG F+ +ET+E A A+E +NG
Sbjct: 137 -CDENGSKGYGFVHFETQEAAERAIEKMNG 165
Score = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 34/65 (52%)
Query: 347 PGANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNA 406
P A+L++ + + + L F G +LS +V D T S + +V+++ PA A+ A
Sbjct: 14 PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERA 73
Query: 407 IAMMN 411
+ MN
Sbjct: 74 LDTMN 78
>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 = 49.7 bits (117), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 39/63 (61%), Gaps = 2/63 (3%)
Query: 350 NLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAM 409
N+FI ++ + ++ L + F AFG +LS KV D+ SK +GFV +E+ +A+ AI
Sbjct: 100 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEK 157
Query: 410 MNG 412
MNG
Sbjct: 158 MNG 160
Score = 45.1 bits (105), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 39/150 (26%), Positives = 69/150 (46%), Gaps = 4/150 (2%)
Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASR-CCFVICPSRQEADKAVNAC 75
L+VG + +TEA L F + + + +D TR S +V +A++A++
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 72
Query: 76 HNKKTLPGASSPLQVKYADGELERL-EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL 134
N + G + D L + +FI L K++ + FS +G I +++
Sbjct: 73 -NFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVV 131
Query: 135 RGSQQTSKGCAFLKYETKEQALAALEAING 164
+ SKG F+ +ET+E A A+E +NG
Sbjct: 132 -CDENGSKGYGFVHFETQEAAERAIEKMNG 160
Score = 33.9 bits (76), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 34/65 (52%)
Query: 347 PGANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNA 406
P A+L++ + + + L F G +LS +V D T S + +V+++ PA A+ A
Sbjct: 9 PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERA 68
Query: 407 IAMMN 411
+ MN
Sbjct: 69 LDTMN 73
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 49.3 bits (116), Expect = 4e-06, Method: Composition-based stats.
Identities = 24/63 (38%), Positives = 34/63 (53%)
Query: 350 NLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAM 409
NL + ++PQ E + F + G + S K+ DK TG S +GFV+Y P A AI
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 410 MNG 412
+NG
Sbjct: 66 LNG 68
Score = 33.1 bits (74), Expect = 0.32, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAI 162
L + LP+N+++ E +LF G I+ +++R S G F+ Y A A+ +
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 163 NG 164
NG
Sbjct: 67 NG 68
Score = 32.7 bits (73), Expect = 0.41, Method: Composition-based stats.
Identities = 21/81 (25%), Positives = 40/81 (49%), Gaps = 4/81 (4%)
Query: 14 RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASR-CCFVICPSRQEADKAV 72
+ L V +P++MT+ + ++F ++ +++DK T S FV +ADKA+
Sbjct: 4 KTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI 63
Query: 73 NACHNKKTLPGASSPLQVKYA 93
N + K + ++V YA
Sbjct: 64 NTLNGLKL---QTKTIKVSYA 81
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 48.9 bits (115), Expect = 5e-06, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 37/63 (58%)
Query: 350 NLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAM 409
NL + ++PQ+ D+EL F+A G + + ++ D TG S + FV + S +Q AI +
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 410 MNG 412
+NG
Sbjct: 65 LNG 67
Score = 34.7 bits (78), Expect = 0.12, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 36/62 (58%), Gaps = 1/62 (1%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT-SKGCAFLKYETKEQALAALEAI 162
L + LP+++++ E+ ALF G I +I+R + S G AF+ + ++ + A++ +
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 163 NG 164
NG
Sbjct: 66 NG 67
Score = 29.6 bits (65), Expect = 3.7, Method: Composition-based stats.
Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 10/81 (12%)
Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKD-KTTRASRCCFVICPSRQEADKAVNAC 75
L V +P+ MT+ +L A+F+ ++ I++D KT + FV S ++ +A+
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI--- 62
Query: 76 HNKKTLPGAS---SPLQVKYA 93
K L G + L+V YA
Sbjct: 63 ---KVLNGITVRNKRLKVSYA 80
>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 = 48.9 bits (115), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 37/62 (59%)
Query: 350 NLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAM 409
+++ + Q+ D ++ + F+AFG++ S + D TG K +GF+ YE S+Q+A++
Sbjct: 111 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 170
Query: 410 MN 411
N
Sbjct: 171 XN 172
Score = 38.1 bits (87), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 29/62 (46%)
Query: 350 NLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAM 409
+++ I E G+ + AF FG + S D T K F FV YE P +AQ A+
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 410 MN 411
N
Sbjct: 74 XN 75
Score = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 103 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEA 161
++++G + + E + F+ +G IK + S KG AF++YE E A ALE
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 162 IN 163
N
Sbjct: 74 XN 75
>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 = 48.5 bits (114), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 30/77 (38%), Positives = 43/77 (55%), Gaps = 4/77 (5%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQI-LRGSQQTSKGCAFLKYETKEQALAALEAI 162
LF+ + + E E+ F YG IK++ + L SKG A ++YET +QALAA EA+
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 163 NGKHKMEGSSVPLVVKW 179
NG M G ++ V W
Sbjct: 135 NGAEIM-GQTIQ--VDW 148
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 33/67 (49%)
Query: 347 PGANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNA 406
G LF+ I +E + E+ F +G + + + +D+ TG SK + V YE+ A A
Sbjct: 71 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 130
Query: 407 IAMMNGC 413
+NG
Sbjct: 131 KEALNGA 137
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 48.5 bits (114), Expect = 7e-06, Method: Composition-based stats.
Identities = 26/63 (41%), Positives = 36/63 (57%), Gaps = 2/63 (3%)
Query: 350 NLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAM 409
NL++ ++ D+ L AF FG + SAKV ++ G SK FGFV + SP A A+
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG--GRSKGFGFVCFSSPEEATKAVTE 74
Query: 410 MNG 412
MNG
Sbjct: 75 MNG 77
Score = 30.8 bits (68), Expect = 1.7, Method: Composition-based stats.
Identities = 21/82 (25%), Positives = 42/82 (51%), Gaps = 4/82 (4%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 163
L++ L + + + FS +GTI +++ + SKG F+ + + E+A A+ +N
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGR-SKGFGFVCFSSPEEATKAVTEMN 76
Query: 164 GKHKMEGSSVPLVVKWADTEKE 185
G+ ++ PL V A ++E
Sbjct: 77 GRIV---ATKPLYVALAQRKEE 95
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 37/63 (58%)
Query: 349 ANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIA 408
+ L+I + DQ+L Q +G+++S K +DK T K +GFV ++SP++AQ A+
Sbjct: 6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65
Query: 409 MMN 411
+
Sbjct: 66 ALK 68
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 47.4 bits (111), Expect = 2e-05, Method: Composition-based stats.
Identities = 27/66 (40%), Positives = 38/66 (57%), Gaps = 1/66 (1%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQI-LRGSQQTSKGCAFLKYETKEQALAALEAI 162
LF+ + + E E+ F YG IK++ + L SKG A ++YET +QALAA EA+
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 163 NGKHKM 168
NG M
Sbjct: 89 NGAEIM 94
Score = 37.4 bits (85), Expect = 0.015, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 32/62 (51%)
Query: 351 LFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAMM 410
LF+ I +E + E+ F +G + + + +D+ TG SK + V YE+ A A +
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 411 NG 412
NG
Sbjct: 89 NG 90
>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 = 46.6 bits (109), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 40/64 (62%)
Query: 101 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALE 160
+HKLFI LP + ++ E+ + +GT+KDL+++ KG A+++YE + QA A+
Sbjct: 17 KHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVM 76
Query: 161 AING 164
++G
Sbjct: 77 KMDG 80
Score = 31.6 bits (70), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 351 LFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAMM 410
LFI +P +EL +A G V ++ ++A G K +V YE+ + A A+ M
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRA-GKPKGLAYVEYENESQASQAVMKM 78
Query: 411 NG 412
+G
Sbjct: 79 DG 80
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 46.6 bits (109), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 35/64 (54%), Gaps = 1/64 (1%)
Query: 349 ANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIA 408
NL+I ++P +QEL N + FG+V+S ++ D ++G S+ GF ES + I
Sbjct: 26 TNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIG 84
Query: 409 MMNG 412
NG
Sbjct: 85 HFNG 88
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 34/62 (54%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 163
L+I LP ++ E E+ + +G + +ILR S TS+G F + E+ E+ A + N
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFN 87
Query: 164 GK 165
GK
Sbjct: 88 GK 89
>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 = 46.6 bits (109), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 47/180 (26%), Positives = 79/180 (43%), Gaps = 39/180 (21%)
Query: 16 KLFVGQVPKHMTEAQLLAMF-------------------------KEFALVDEVNIIKDK 50
+L+VG +P +TE ++ F K FA ++ ++ D+
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV--DE 63
Query: 51 TTRASRCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERL----EHKLFI 106
TT+A +I Q + H+ + LPG S V Y G + + HKLFI
Sbjct: 64 TTQAMAFDGIIF---QGQSLKIRRPHDYQPLPGMSENPSV-YVPGVVSTVVPDSAHKLFI 119
Query: 107 GMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQ-TSKGCAFLKY---ETKEQALAALEAI 162
G LP +++ +V L + +G +K +++ S SKG AF +Y +QA+A L +
Sbjct: 120 GGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGM 179
Score = 37.4 bits (85), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 30/62 (48%)
Query: 351 LFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAMM 410
LFI +P D ++ +FG + + + D ATG+SK + F Y AIA +
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176
Query: 411 NG 412
NG
Sbjct: 177 NG 178
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 36/141 (25%), Positives = 69/141 (48%), Gaps = 7/141 (4%)
Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRCC-FVICPSRQEADKAVNA 74
KLF+G + T+ L + F+++ + + +++D T+ SR FV + +E D A+NA
Sbjct: 16 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 75
Query: 75 CHNKKTLPGASSPLQVKYADGEL---ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDL 131
+K V D + K+F+G + ++ E + F YG I+ +
Sbjct: 76 RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI 135
Query: 132 QIL--RGSQQTSKGCAFLKYE 150
+I+ RGS + +G AF+ ++
Sbjct: 136 EIMTDRGSGK-KRGFAFVTFD 155
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 3/72 (4%)
Query: 103 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEA 161
KLFIG L ++ + + F +GT+ D ++R + + S+G F+ Y T E+ AA+ A
Sbjct: 16 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 75
Query: 162 INGKHKMEGSSV 173
HK++G V
Sbjct: 76 --RPHKVDGRVV 85
Score = 35.0 bits (79), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 15/66 (22%), Positives = 34/66 (51%), Gaps = 5/66 (7%)
Query: 347 PGANL-----FIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPA 401
PGA+L F+ I ++ + L + F+ +G++ ++ D+ +G + F FV+++
Sbjct: 99 PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD 158
Query: 402 SAQNAI 407
S +
Sbjct: 159 SVDKIV 164
Score = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 3/62 (4%)
Query: 350 NLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAM 409
LFI + E D+ L + F+ +G + V D T S+ FGFV+Y A+ + A
Sbjct: 16 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY---ATVEEVDAA 72
Query: 410 MN 411
MN
Sbjct: 73 MN 74
>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 = 45.4 bits (106), Expect = 6e-05, Method: Composition-based stats.
Identities = 26/79 (32%), Positives = 45/79 (56%), Gaps = 2/79 (2%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAI 162
L++ LP+ +++ ++ +F YG+I ILR +G AF++Y +E+A A+ A+
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 163 NGKHKMEGSSVPLVVKWAD 181
N EG S PL V+ A+
Sbjct: 76 NNVIP-EGGSQPLSVRLAE 93
Score = 45.1 bits (105), Expect = 8e-05, Method: Composition-based stats.
Identities = 28/80 (35%), Positives = 48/80 (60%), Gaps = 4/80 (5%)
Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTT-RASRCCFVICPSRQEADKAVNAC 75
L+V +P+ +T+ QL +F ++ + + NI++DK T R FV R+EA +A++A
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 76 HNKKTLP-GASSPLQVKYAD 94
+N +P G S PL V+ A+
Sbjct: 76 NN--VIPEGGSQPLSVRLAE 93
>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi)
G); A Human Telomeric Repeat Containing 6-Methyl-8-(2-
Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi)
Length = 195
Score = 45.4 bits (106), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 36/141 (25%), Positives = 69/141 (48%), Gaps = 7/141 (4%)
Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRCC-FVICPSRQEADKAVNA 74
KLF+G + T+ L + F+++ + + +++D T+ SR FV + +E D A+NA
Sbjct: 14 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 73
Query: 75 CHNKKTLPGASSPLQVKYADGEL---ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDL 131
+K V D + K+F+G + ++ E + F YG I+ +
Sbjct: 74 RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI 133
Query: 132 QIL--RGSQQTSKGCAFLKYE 150
+I+ RGS + +G AF+ ++
Sbjct: 134 EIMTDRGSGK-KRGFAFVTFD 153
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 3/72 (4%)
Query: 103 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEA 161
KLFIG L ++ + + F +GT+ D ++R + + S+G F+ Y T E+ AA+ A
Sbjct: 14 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 73
Query: 162 INGKHKMEGSSV 173
HK++G V
Sbjct: 74 --RPHKVDGRVV 83
Score = 35.0 bits (79), Expect = 0.076, Method: Compositional matrix adjust.
Identities = 15/66 (22%), Positives = 34/66 (51%), Gaps = 5/66 (7%)
Query: 347 PGANL-----FIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPA 401
PGA+L F+ I ++ + L + F+ +G++ ++ D+ +G + F FV+++
Sbjct: 97 PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD 156
Query: 402 SAQNAI 407
S +
Sbjct: 157 SVDKIV 162
Score = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 3/62 (4%)
Query: 350 NLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAM 409
LFI + E D+ L + F+ +G + V D T S+ FGFV+Y A+ + A
Sbjct: 14 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY---ATVEEVDAA 70
Query: 410 MN 411
MN
Sbjct: 71 MN 72
>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
pdb|1U1K|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt 7da
Ggg); A Human Telomeric Repeat Containing
7-Deaza-Adenine
pdb|1U1L|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt Prn
Ggg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1M|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 7gu
Gg); A Human Telomeric Repeat Containing 7-Deaza-Guanine
pdb|1U1N|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta (Prn)
Gg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1O|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggttag(Di)g); A Human Telomeric Repeat Containing
Inosine
pdb|1U1P|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 2pr
Gg); A Human Telomeric Repeat Containing 2-Aminopurine
pdb|1U1Q|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggtta(Di)gg); A Human Telomeric Repeat Containing
Inosine
pdb|1U1R|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(2pr)
G); A Human Telomeric Repeat Containing 2-Aminopurine
Length = 196
Score = 45.4 bits (106), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 36/141 (25%), Positives = 69/141 (48%), Gaps = 7/141 (4%)
Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRCC-FVICPSRQEADKAVNA 74
KLF+G + T+ L + F+++ + + +++D T+ SR FV + +E D A+NA
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 75 CHNKKTLPGASSPLQVKYADGEL---ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDL 131
+K V D + K+F+G + ++ E + F YG I+ +
Sbjct: 75 RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI 134
Query: 132 QIL--RGSQQTSKGCAFLKYE 150
+I+ RGS + +G AF+ ++
Sbjct: 135 EIMTDRGSGK-KRGFAFVTFD 154
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 3/72 (4%)
Query: 103 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEA 161
KLFIG L ++ + + F +GT+ D ++R + + S+G F+ Y T E+ AA+ A
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 162 INGKHKMEGSSV 173
HK++G V
Sbjct: 75 --RPHKVDGRVV 84
Score = 35.0 bits (79), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 15/66 (22%), Positives = 34/66 (51%), Gaps = 5/66 (7%)
Query: 347 PGANL-----FIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPA 401
PGA+L F+ I ++ + L + F+ +G++ ++ D+ +G + F FV+++
Sbjct: 98 PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD 157
Query: 402 SAQNAI 407
S +
Sbjct: 158 SVDKIV 163
Score = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 3/62 (4%)
Query: 350 NLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAM 409
LFI + E D+ L + F+ +G + V D T S+ FGFV+Y A+ + A
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY---ATVEEVDAA 71
Query: 410 MN 411
MN
Sbjct: 72 MN 73
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 45.4 bits (106), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 36/141 (25%), Positives = 69/141 (48%), Gaps = 7/141 (4%)
Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRCC-FVICPSRQEADKAVNA 74
KLF+G + T+ L + F+++ + + +++D T+ SR FV + +E D A+NA
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 75 CHNKKTLPGASSPLQVKYADGEL---ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDL 131
+K V D + K+F+G + ++ E + F YG I+ +
Sbjct: 75 RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI 134
Query: 132 QIL--RGSQQTSKGCAFLKYE 150
+I+ RGS + +G AF+ ++
Sbjct: 135 EIMTDRGSGK-KRGFAFVTFD 154
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 3/72 (4%)
Query: 103 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEA 161
KLFIG L ++ + + F +GT+ D ++R + + S+G F+ Y T E+ AA+ A
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 162 INGKHKMEGSSV 173
HK++G V
Sbjct: 75 --RPHKVDGRVV 84
Score = 35.0 bits (79), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 15/66 (22%), Positives = 34/66 (51%), Gaps = 5/66 (7%)
Query: 347 PGANL-----FIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPA 401
PGA+L F+ I ++ + L + F+ +G++ ++ D+ +G + F FV+++
Sbjct: 98 PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD 157
Query: 402 SAQNAI 407
S +
Sbjct: 158 SVDKIV 163
Score = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 3/62 (4%)
Query: 350 NLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAM 409
LFI + E D+ L + F+ +G + V D T S+ FGFV+Y A+ + A
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY---ATVEEVDAA 71
Query: 410 MN 411
MN
Sbjct: 72 MN 73
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 45.1 bits (105), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 36/141 (25%), Positives = 69/141 (48%), Gaps = 7/141 (4%)
Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRCC-FVICPSRQEADKAVNA 74
KLF+G + T+ L + F+++ + + +++D T+ SR FV + +E D A+NA
Sbjct: 13 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 72
Query: 75 CHNKKTLPGASSPLQVKYADGEL---ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDL 131
+K V D + K+F+G + ++ E + F YG I+ +
Sbjct: 73 RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI 132
Query: 132 QIL--RGSQQTSKGCAFLKYE 150
+I+ RGS + +G AF+ ++
Sbjct: 133 EIMTDRGSGK-KRGFAFVTFD 152
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 3/72 (4%)
Query: 103 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEA 161
KLFIG L ++ + + F +GT+ D ++R + + S+G F+ Y T E+ AA+ A
Sbjct: 13 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 72
Query: 162 INGKHKMEGSSV 173
HK++G V
Sbjct: 73 --RPHKVDGRVV 82
Score = 35.0 bits (79), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 15/66 (22%), Positives = 34/66 (51%), Gaps = 5/66 (7%)
Query: 347 PGANL-----FIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPA 401
PGA+L F+ I ++ + L + F+ +G++ ++ D+ +G + F FV+++
Sbjct: 96 PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD 155
Query: 402 SAQNAI 407
S +
Sbjct: 156 SVDKIV 161
Score = 34.3 bits (77), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 3/62 (4%)
Query: 350 NLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAM 409
LFI + E D+ L + F+ +G + V D T S+ FGFV+Y A+ + A
Sbjct: 13 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY---ATVEEVDAA 69
Query: 410 MN 411
MN
Sbjct: 70 MN 71
>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex
pdb|1PO6|A Chain A, Crystal Structure Of Up1 Complexed With
D(Tagg(6mi)ttaggg): A Human Telomeric Repeat Containing
6-Methyl-8-(2-Deoxy-
Beta-Ribofuranosyl)isoxanthopteridine (6mi)
Length = 183
Score = 45.1 bits (105), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 36/141 (25%), Positives = 69/141 (48%), Gaps = 7/141 (4%)
Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRCC-FVICPSRQEADKAVNA 74
KLF+G + T+ L + F+++ + + +++D T+ SR FV + +E D A+NA
Sbjct: 8 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67
Query: 75 CHNKKTLPGASSPLQVKYADGEL---ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDL 131
+K V D + K+F+G + ++ E + F YG I+ +
Sbjct: 68 RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI 127
Query: 132 QIL--RGSQQTSKGCAFLKYE 150
+I+ RGS + +G AF+ ++
Sbjct: 128 EIMTDRGSGK-KRGFAFVTFD 147
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 3/72 (4%)
Query: 103 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEA 161
KLFIG L ++ + + F +GT+ D ++R + + S+G F+ Y T E+ AA+ A
Sbjct: 8 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67
Query: 162 INGKHKMEGSSV 173
HK++G V
Sbjct: 68 --RPHKVDGRVV 77
Score = 35.0 bits (79), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 15/66 (22%), Positives = 34/66 (51%), Gaps = 5/66 (7%)
Query: 347 PGANL-----FIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPA 401
PGA+L F+ I ++ + L + F+ +G++ ++ D+ +G + F FV+++
Sbjct: 91 PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD 150
Query: 402 SAQNAI 407
S +
Sbjct: 151 SVDKIV 156
Score = 33.9 bits (76), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 3/62 (4%)
Query: 350 NLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAM 409
LFI + E D+ L + F+ +G + V D T S+ FGFV+Y A+ + A
Sbjct: 8 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY---ATVEEVDAA 64
Query: 410 MN 411
MN
Sbjct: 65 MN 66
>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 = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 39/141 (27%), Positives = 60/141 (42%), Gaps = 12/141 (8%)
Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASR----CCFVICPSRQEADKA 71
K+F+G + TE L F ++ V ++ I+KD T SR F S E K
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 72 VNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDL 131
+ K P + P + G K+F+G + +V E FS +GTI D
Sbjct: 65 QHILDGKVIDPKRAIPRDEQDKTG-------KIFVGGIGPDVRPKEFEEFFSQWGTIIDA 117
Query: 132 QI-LRGSQQTSKGCAFLKYET 151
Q+ L S+G F+ Y++
Sbjct: 118 QLMLDKDTGQSRGFGFVTYDS 138
Score = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 4/72 (5%)
Query: 103 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEA 161
K+FIG L + +E + F YGT+ DL+I++ + S+G FL + E+ + E
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSF---EKPSSVDEV 61
Query: 162 INGKHKMEGSSV 173
+ +H ++G +
Sbjct: 62 VKTQHILDGKVI 73
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 30/58 (51%)
Query: 350 NLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAI 407
+FI + + + L F +G V K+ D ATG S+ FGF+S+E P+S +
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVV 62
Score = 37.7 bits (86), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 26/44 (59%)
Query: 363 QELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNA 406
+E F +G ++ A++ +DK TG S+ FGFV+Y+S +
Sbjct: 102 KEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRV 145
>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 = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 44/176 (25%), Positives = 74/176 (42%), Gaps = 51/176 (28%)
Query: 16 KLFVGQVPKHMTEAQLLAMF-------------------------KEFALVDEVNIIKDK 50
+L+VG +P +TE ++ F K FA ++ ++ D+
Sbjct: 8 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV--DE 65
Query: 51 TTRASRCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLP 110
TT+A +I Q + H+ + LPGA HKLFIG LP
Sbjct: 66 TTQAMAFDGIIF---QGQSLKIRRPHDYQPLPGA-----------------HKLFIGGLP 105
Query: 111 KNVSEAEVSALFSIYGTIKDLQILRGSQQ-TSKGCAFLKY---ETKEQALAALEAI 162
+++ +V L + +G +K +++ S SKG AF +Y +QA+A L +
Sbjct: 106 NYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGM 161
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 34/67 (50%), Gaps = 1/67 (1%)
Query: 347 PGAN-LFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQN 405
PGA+ LFI +P D ++ +FG + + + D ATG+SK + F Y
Sbjct: 94 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 153
Query: 406 AIAMMNG 412
AIA +NG
Sbjct: 154 AIAGLNG 160
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 43.9 bits (102), Expect = 2e-04, Method: Composition-based stats.
Identities = 23/66 (34%), Positives = 40/66 (60%), Gaps = 1/66 (1%)
Query: 101 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAAL 159
E KLF+G L + +E + +FS YG I ++ +++ + Q S+G F+ +E + A A+
Sbjct: 12 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 71
Query: 160 EAINGK 165
A+NGK
Sbjct: 72 MAMNGK 77
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 20/62 (32%), Positives = 35/62 (56%)
Query: 351 LFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAMM 410
LF+ + + +Q L F +G++ V D+ T S+ FGFV++E+ A++A+ M
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 411 NG 412
NG
Sbjct: 75 NG 76
Score = 32.7 bits (73), Expect = 0.43, Method: Composition-based stats.
Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 1/64 (1%)
Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASR-CCFVICPSRQEADKAVNA 74
KLFVG + E L +F ++ + EV ++KD+ T+ SR FV + +A A+ A
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 75 CHNK 78
+ K
Sbjct: 74 MNGK 77
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 44/176 (25%), Positives = 74/176 (42%), Gaps = 51/176 (28%)
Query: 16 KLFVGQVPKHMTEAQLLAMF-------------------------KEFALVDEVNIIKDK 50
+L+VG +P +TE ++ F K FA ++ ++ D+
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV--DE 63
Query: 51 TTRASRCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLP 110
TT+A +I Q + H+ + LPGA HKLFIG LP
Sbjct: 64 TTQAMAFDGIIF---QGQSLKIRRPHDYQPLPGA-----------------HKLFIGGLP 103
Query: 111 KNVSEAEVSALFSIYGTIKDLQILRGSQQ-TSKGCAFLKY---ETKEQALAALEAI 162
+++ +V L + +G +K +++ S SKG AF +Y +QA+A L +
Sbjct: 104 NYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGM 159
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 34/67 (50%), Gaps = 1/67 (1%)
Query: 347 PGAN-LFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQN 405
PGA+ LFI +P D ++ +FG + + + D ATG+SK + F Y
Sbjct: 92 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 151
Query: 406 AIAMMNG 412
AIA +NG
Sbjct: 152 AIAGLNG 158
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 43.5 bits (101), Expect = 2e-04, Method: Composition-based stats.
Identities = 23/64 (35%), Positives = 40/64 (62%), Gaps = 2/64 (3%)
Query: 103 KLFIGMLPKNVSEAEVSALFSIYGTIK--DLQILRGSQQTSKGCAFLKYETKEQALAALE 160
K+ IG L +NV++ + +FS YG IK D+ + R SKG A++++E ++A AL+
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65
Query: 161 AING 164
++G
Sbjct: 66 HMDG 69
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 38/63 (60%)
Query: 350 NLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAM 409
++F+ +IP E +++L + F G V+S ++ D+ TG K +GF Y+ +A +A+
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 410 MNG 412
+NG
Sbjct: 70 LNG 72
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 47/89 (52%), Gaps = 4/89 (4%)
Query: 97 LERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTS-KGCAFLKYETKEQA 155
++R +F+G +P +E ++ +FS G + +++ + KG F +Y+ +E A
Sbjct: 4 VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETA 63
Query: 156 LAALEAINGKHKMEGSSVPLVVKWADTEK 184
L+A+ +NG+ E S L V A +EK
Sbjct: 64 LSAMRNLNGR---EFSGRALRVDNAASEK 89
Score = 29.6 bits (65), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 39/87 (44%), Gaps = 2/87 (2%)
Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRCCFVICPSRQEADKAVNACH 76
+FVG +P TE QL +F E V ++ D+ T + + C Q+ + A++A
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPK-GYGFC-EYQDQETALSAMR 68
Query: 77 NKKTLPGASSPLQVKYADGELERLEHK 103
N + L+V A E + E K
Sbjct: 69 NLNGREFSGRALRVDNAASEKNKEELK 95
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 43/72 (59%), Gaps = 9/72 (12%)
Query: 94 DGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKE 153
+GEL +LF+ P +V E+E++ +F +G +K+++IL G AF+++E E
Sbjct: 26 EGELSNT--RLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAE 76
Query: 154 QALAALEAINGK 165
A A+E ++GK
Sbjct: 77 SAAKAIEEVHGK 88
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 36/63 (57%)
Query: 103 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 162
KLFIG L + +E + A+F +G I ++ +++ S+G AF+ +E A A + +
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDM 68
Query: 163 NGK 165
NGK
Sbjct: 69 NGK 71
Score = 38.1 bits (87), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 1/70 (1%)
Query: 343 IEGPPGANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPAS 402
+E LFI + +E ++ L F G + S + + T S+ F F+++E+PA
Sbjct: 2 VEADHPGKLFIGGLNRETNEKMLKAVFGKHGPI-SEVLLIKDRTSKSRGFAFITFENPAD 60
Query: 403 AQNAIAMMNG 412
A+NA MNG
Sbjct: 61 AKNAAKDMNG 70
Score = 36.6 bits (83), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 36/68 (52%), Gaps = 1/68 (1%)
Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRCCFVICPSRQEADKAVNAC 75
KLF+G + + E L A+F + + EV +IKD+T+++ F+ + +A A
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDM 68
Query: 76 HNKKTLPG 83
N K+L G
Sbjct: 69 -NGKSLHG 75
>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 = 42.7 bits (99), Expect = 4e-04, Method: Composition-based stats.
Identities = 28/70 (40%), Positives = 40/70 (57%), Gaps = 2/70 (2%)
Query: 345 GPPGAN--LFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPAS 402
GP G++ +F+ + E + AF FGR+ A+V D ATG SK +GFVS+ +
Sbjct: 1 GPLGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWD 60
Query: 403 AQNAIAMMNG 412
A+NAI M G
Sbjct: 61 AENAIQQMGG 70
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 41.6 bits (96), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 39/63 (61%), Gaps = 7/63 (11%)
Query: 103 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 162
+LF+ P +V E+E++ +F +G +K+++IL G AF+++E E A A+E +
Sbjct: 6 RLFVRPFPLDVQESELNEIFGPFGPMKEVKILN-------GFAFVEFEEAESAAKAIEEV 58
Query: 163 NGK 165
+GK
Sbjct: 59 HGK 61
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 21/63 (33%), Positives = 37/63 (58%), Gaps = 1/63 (1%)
Query: 103 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQ-TSKGCAFLKYETKEQALAALEA 161
+L++G L N++E + +F +G I+ +Q++ S+ SKG F+ + E A ALE
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 162 ING 164
+NG
Sbjct: 88 LNG 90
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 16/44 (36%), Positives = 28/44 (63%)
Query: 369 FQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAMMNG 412
F+ FGR+ S ++ +D TG SK +GF+++ A+ A+ +NG
Sbjct: 47 FEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNG 90
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 4/77 (5%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQI-LRGSQQTSKGCAFLKYETKEQALAALEAI 162
LF+ + + +E ++ F+ YG IK++ + L KG ++YET ++A AA+E +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 163 NGKHKMEGSSVPLVVKW 179
NG+ M P+ V W
Sbjct: 70 NGQDLM---GQPISVDW 83
Score = 37.7 bits (86), Expect = 0.012, Method: Composition-based stats.
Identities = 17/62 (27%), Positives = 35/62 (56%)
Query: 351 LFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAMM 410
LF+ + +E ++++ + F +G + + + +D+ TG K + V YE+ AQ A+ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 411 NG 412
NG
Sbjct: 70 NG 71
>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 = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 4/77 (5%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQI-LRGSQQTSKGCAFLKYETKEQALAALEAI 162
LF+ + + +E ++ F+ YG IK++ + L KG ++YET ++A AA+E +
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 163 NGKHKMEGSSVPLVVKW 179
NG+ M P+ V W
Sbjct: 85 NGQDLM---GQPISVDW 98
Score = 37.7 bits (86), Expect = 0.012, Method: Composition-based stats.
Identities = 17/62 (27%), Positives = 35/62 (56%)
Query: 351 LFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAMM 410
LF+ + +E ++++ + F +G + + + +D+ TG K + V YE+ AQ A+ +
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 411 NG 412
NG
Sbjct: 85 NG 86
>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 = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 4/77 (5%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQI-LRGSQQTSKGCAFLKYETKEQALAALEAI 162
LF+ + + +E ++ F+ YG IK++ + L KG ++YET ++A AA+E +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 163 NGKHKMEGSSVPLVVKW 179
NG+ M P+ V W
Sbjct: 70 NGQDLM---GQPISVDW 83
Score = 37.7 bits (86), Expect = 0.012, Method: Composition-based stats.
Identities = 17/62 (27%), Positives = 35/62 (56%)
Query: 351 LFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAMM 410
LF+ + +E ++++ + F +G + + + +D+ TG K + V YE+ AQ A+ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 411 NG 412
NG
Sbjct: 70 NG 71
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 37/147 (25%), Positives = 67/147 (45%), Gaps = 13/147 (8%)
Query: 14 RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRCCFVICPSRQEADKAVN 73
R +LFVG +P +TE ++ +F+++ EV I KDK F+ +R A+ A
Sbjct: 22 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG-----FGFIRLETRTLAEIAKV 76
Query: 74 ACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQI 133
N +P L+V++A L + LP+ VS + FS++G ++ +
Sbjct: 77 ELDN---MPLRGKQLRVRFACHSA-----SLTVRNLPQYVSNELLEEAFSVFGQVERAVV 128
Query: 134 LRGSQQTSKGCAFLKYETKEQALAALE 160
+ + G +++ K A AL+
Sbjct: 129 IVDDRGRPSGKGIVEFSGKPAARKALD 155
Score = 32.0 bits (71), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 35/63 (55%), Gaps = 6/63 (9%)
Query: 349 ANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIA 408
+ LF+ ++P + ++E+ F+ +G+ + +VF+ K G FGF+ E+ A+ A
Sbjct: 23 SRLFVGNLPPDITEEEMRKLFEKYGK--AGEVFIHKDKG----FGFIRLETRTLAEIAKV 76
Query: 409 MMN 411
++
Sbjct: 77 ELD 79
Score = 29.6 bits (65), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 349 ANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAI 407
A+L + ++PQ ++ L AF FG+V A V VD G G V + +A+ A+
Sbjct: 97 ASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDD-RGRPSGKGIVEFSGKPAARKAL 154
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 26/69 (37%), Positives = 38/69 (55%), Gaps = 3/69 (4%)
Query: 345 GPPGA-NLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASA 403
G GA +F+ ++P +F + L + F G VL A + ++ G SK G V +ESP A
Sbjct: 4 GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVA 61
Query: 404 QNAIAMMNG 412
+ A MMNG
Sbjct: 62 ERACRMMNG 70
>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 = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 4/77 (5%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQI-LRGSQQTSKGCAFLKYETKEQALAALEAI 162
LF+ + + +E ++ F+ YG IK++ + L KG ++YET ++A AA+E +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 163 NGKHKMEGSSVPLVVKW 179
NG+ M P+ V W
Sbjct: 70 NGQDLM---GQPISVDW 83
Score = 37.4 bits (85), Expect = 0.017, Method: Composition-based stats.
Identities = 17/62 (27%), Positives = 35/62 (56%)
Query: 351 LFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAMM 410
LF+ + +E ++++ + F +G + + + +D+ TG K + V YE+ AQ A+ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 411 NG 412
NG
Sbjct: 70 NG 71
>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 = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 95 GELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQI-LRGSQQTSKGCAFLKYETKE 153
G + + L++G L + V + + A F +G I D+QI L + +G AF+++E E
Sbjct: 1 GSMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 60
Query: 154 QALAALEAIN 163
A AA++ +N
Sbjct: 61 DAAAAIDNMN 70
Score = 33.9 bits (76), Expect = 0.18, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 30/61 (49%)
Query: 351 LFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAMM 410
L++ + +E D+ L AF FG + ++ +D T + F FV +E A AI M
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 411 N 411
N
Sbjct: 70 N 70
>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 = 40.0 bits (92), Expect = 0.003, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 4/77 (5%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQI-LRGSQQTSKGCAFLKYETKEQALAALEAI 162
LF+ + + +E ++ F+ YG IK++ + L KG ++YET ++A AA+E +
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 163 NGKHKMEGSSVPLVVKW 179
NG+ M P+ V W
Sbjct: 72 NGQDLM---GQPISVDW 85
Score = 37.4 bits (85), Expect = 0.019, Method: Composition-based stats.
Identities = 17/62 (27%), Positives = 35/62 (56%)
Query: 351 LFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAMM 410
LF+ + +E ++++ + F +G + + + +D+ TG K + V YE+ AQ A+ +
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 411 NG 412
NG
Sbjct: 72 NG 73
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 45/82 (54%), Gaps = 2/82 (2%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQ-TSKGCAFLKYETKEQALAALEAI 162
LF+ + + +E+++ F +YG IK + ++ + +G AF++YE + +A +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 163 NGKHKMEGSSVPLVVKWADTEK 184
+GK K++G V + V+ T K
Sbjct: 165 DGK-KIDGRRVLVDVERGRTVK 185
>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 = 40.0 bits (92), Expect = 0.003, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 4/77 (5%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQI-LRGSQQTSKGCAFLKYETKEQALAALEAI 162
LF+ + + +E ++ F+ YG IK++ + L KG ++YET ++A AA+E +
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 163 NGKHKMEGSSVPLVVKW 179
NG+ M P+ V W
Sbjct: 86 NGQDLM---GQPISVDW 99
Score = 37.0 bits (84), Expect = 0.020, Method: Composition-based stats.
Identities = 17/62 (27%), Positives = 35/62 (56%)
Query: 351 LFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAMM 410
LF+ + +E ++++ + F +G + + + +D+ TG K + V YE+ AQ A+ +
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 411 NG 412
NG
Sbjct: 86 NG 87
>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 = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 45/82 (54%), Gaps = 2/82 (2%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQ-TSKGCAFLKYETKEQALAALEAI 162
LF+ + + +E+++ F +YG IK + ++ + +G AF++YE + +A +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 163 NGKHKMEGSSVPLVVKWADTEK 184
+GK K++G V + V+ T K
Sbjct: 165 DGK-KIDGRRVLVDVERGRTVK 185
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 2/64 (3%)
Query: 349 ANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIA 408
+ +F+ ++P +F + L + F G VL A + ++ G SK G V +ESP A+ A
Sbjct: 6 SGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACR 63
Query: 409 MMNG 412
MMNG
Sbjct: 64 MMNG 67
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 23/67 (34%), Positives = 35/67 (52%), Gaps = 3/67 (4%)
Query: 349 ANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFV---SYESPASAQN 405
++L + +P + +Q+L F FG VL +V D TG SK FGFV YE+ +
Sbjct: 16 SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 75
Query: 406 AIAMMNG 412
M++G
Sbjct: 76 QRHMIDG 82
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 37/65 (56%), Gaps = 4/65 (6%)
Query: 102 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQ-TSKGCAFLKY---ETKEQALA 157
HKLFIG LP +++ +V L + +G +K +++ S SKG AF +Y +QA+A
Sbjct: 2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 61
Query: 158 ALEAI 162
L +
Sbjct: 62 GLNGM 66
Score = 37.0 bits (84), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 30/62 (48%)
Query: 351 LFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAMM 410
LFI +P D ++ +FG + + + D ATG+SK + F Y AIA +
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 411 NG 412
NG
Sbjct: 64 NG 65
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 6/72 (8%)
Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASR----CCFVICPSRQEADKA 71
KLF+G +P ++ + Q+ + F + N++KD T S+ C +V +A
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 72 VNACH--NKKTL 81
+N +KK L
Sbjct: 63 LNGMQLGDKKLL 74
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 39.3 bits (90), Expect = 0.005, Method: Composition-based stats.
Identities = 21/62 (33%), Positives = 35/62 (56%), Gaps = 2/62 (3%)
Query: 351 LFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAMM 410
L + +IP F D +L F FG++L ++ ++ SK FGFV++E+ A A A +
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKL 89
Query: 411 NG 412
+G
Sbjct: 90 HG 91
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 39.3 bits (90), Expect = 0.005, Method: Composition-based stats.
Identities = 21/62 (33%), Positives = 35/62 (56%), Gaps = 2/62 (3%)
Query: 351 LFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAMM 410
L + +IP F D +L F FG++L ++ ++ SK FGFV++E+ A A A +
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKL 75
Query: 411 NG 412
+G
Sbjct: 76 HG 77
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 39.3 bits (90), Expect = 0.005, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 5/58 (8%)
Query: 105 FIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 162
+IG +P +EA++ LF +G I D + KGC F+KY+T EQA + A+
Sbjct: 31 YIGNIPHFATEADLIPLFQNFGFILDFK-----HYPEKGCCFIKYDTHEQAAVCIVAL 83
Score = 29.6 bits (65), Expect = 3.2, Method: Composition-based stats.
Identities = 15/60 (25%), Positives = 29/60 (48%), Gaps = 5/60 (8%)
Query: 18 FVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRCCFVICPSRQEADKAVNACHN 77
++G +P TEA L+ +F+ F + + +K CCF+ + ++A + A N
Sbjct: 31 YIGNIPHFATEADLIPLFQNFGFILDFKHYPEKG-----CCFIKYDTHEQAAVCIVALAN 85
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 36/61 (59%), Gaps = 1/61 (1%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQI-LRGSQQTSKGCAFLKYETKEQALAALEAI 162
L++G L + V + + A F +G I D+QI L + +G AF+++E E A AA++ +
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 163 N 163
N
Sbjct: 68 N 68
Score = 33.9 bits (76), Expect = 0.18, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 30/61 (49%)
Query: 351 LFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAMM 410
L++ + +E D+ L AF FG + ++ +D T + F FV +E A AI M
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 411 N 411
N
Sbjct: 68 N 68
>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 = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 36/61 (59%), Gaps = 1/61 (1%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQI-LRGSQQTSKGCAFLKYETKEQALAALEAI 162
L++G L + V + + A F +G I D+QI L + +G AF+++E E A AA++ +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 163 N 163
N
Sbjct: 65 N 65
Score = 33.9 bits (76), Expect = 0.18, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 30/61 (49%)
Query: 351 LFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAMM 410
L++ + +E D+ L AF FG + ++ +D T + F FV +E A AI M
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 411 N 411
N
Sbjct: 65 N 65
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 36/61 (59%), Gaps = 1/61 (1%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQI-LRGSQQTSKGCAFLKYETKEQALAALEAI 162
L++G L + V + + A F +G I D+QI L + +G AF+++E E A AA++ +
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 163 N 163
N
Sbjct: 126 N 126
Score = 33.9 bits (76), Expect = 0.18, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 30/61 (49%)
Query: 351 LFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAMM 410
L++ + +E D+ L AF FG + ++ +D T + F FV +E A AI M
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 411 N 411
N
Sbjct: 126 N 126
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 37/65 (56%), Gaps = 1/65 (1%)
Query: 349 ANLFIYHIPQEFGDQELGNAFQAFGRVLSA-KVFVDKATGVSKCFGFVSYESPASAQNAI 407
+ +FI ++ E ++ L + F AFG +L K+ D TG SK + F+++ S ++ AI
Sbjct: 6 SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAI 65
Query: 408 AMMNG 412
MNG
Sbjct: 66 EAMNG 70
Score = 38.1 bits (87), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 43/79 (54%), Gaps = 5/79 (6%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDL-QILRG-SQQTSKGCAFLKYETKEQALAALEA 161
+FIG L + E + FS +G I +I+R SKG AF+ + + + + AA+EA
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 162 INGKHKMEGSSVPLVVKWA 180
+NG++ + P+ V +A
Sbjct: 68 MNGQYLC---NRPITVSYA 83
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 38.9 bits (89), Expect = 0.006, Method: Composition-based stats.
Identities = 22/57 (38%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASR-CCFVICPSRQEADKA 71
K+FVG +P H T+A L F+ F ++E +I D+ T SR FV R A++A
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA 75
Score = 38.1 bits (87), Expect = 0.009, Method: Composition-based stats.
Identities = 19/56 (33%), Positives = 30/56 (53%)
Query: 351 LFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNA 406
+F+ +P D L F+ FG + A V D+ TG S+ +GFV+ A+A+ A
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA 75
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 38.5 bits (88), Expect = 0.007, Method: Composition-based stats.
Identities = 22/59 (37%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASR-CCFVICPSRQEADKAVN 73
K+FVG +P + E +L FK+F +V EV +I D + R F+ Q D+AVN
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN 70
Score = 36.6 bits (83), Expect = 0.028, Method: Composition-based stats.
Identities = 18/59 (30%), Positives = 28/59 (47%)
Query: 351 LFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAM 409
+F+ IP G+ EL F+ FG V + D + FGF+++E S A+ M
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
Score = 33.1 bits (74), Expect = 0.32, Method: Composition-based stats.
Identities = 15/59 (25%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 102 HKLFIGMLPKNVSEAEVSALFSIYGTIKD-LQILRGSQQTSKGCAFLKYETKEQALAAL 159
+K+F+G +P N E E+ F +G + + + I +Q +G F+ +E ++ A+
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV 69
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 37.7 bits (86), Expect = 0.013, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 36/61 (59%), Gaps = 1/61 (1%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQI-LRGSQQTSKGCAFLKYETKEQALAALEAI 162
L++G L + V + + A F +G I D+QI L + +G AF+++E E A AA++ +
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 163 N 163
N
Sbjct: 75 N 75
Score = 32.7 bits (73), Expect = 0.37, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 30/61 (49%)
Query: 351 LFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAMM 410
L++ + +E D+ L AF FG + ++ +D T + F FV +E A AI M
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 411 N 411
N
Sbjct: 75 N 75
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 37.7 bits (86), Expect = 0.013, Method: Composition-based stats.
Identities = 21/62 (33%), Positives = 33/62 (53%)
Query: 103 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 162
KL + L VS+A++ LF+ +GT+K + S G A + +E K AL A++
Sbjct: 30 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 89
Query: 163 NG 164
NG
Sbjct: 90 NG 91
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 37.7 bits (86), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 43/171 (25%), Positives = 75/171 (43%), Gaps = 24/171 (14%)
Query: 14 RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRCCFVICPSRQEADKAVN 73
R +LFVG +P +TE +F+ + EV I +D+ F+ SR A+ A
Sbjct: 22 RCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRG-----FGFIRLESRTLAEIA-- 74
Query: 74 ACHNKKTLPGA---SSPLQVKYADGELERLEH--KLFIGMLPKNVSEAEVSALFSIYGTI 128
K L G S PL++++A H L + L VS + FS +G +
Sbjct: 75 ----KAELDGTILKSRPLRIRFAT-------HGAALTVKNLSPVVSNELLEQAFSQFGPV 123
Query: 129 KDLQILRGSQQTSKGCAFLKYETKEQALAALEAI-NGKHKMEGSSVPLVVK 178
+ ++ + + G F+++ K A ALE +G + + P++V+
Sbjct: 124 EKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVE 174
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 37.4 bits (85), Expect = 0.015, Method: Composition-based stats.
Identities = 20/62 (32%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQ-TSKGCAFLKYETKEQALAALEAI 162
L++G L N++E + +F +G I ++ +++ S SKG F+ + E A ALE +
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 163 NG 164
NG
Sbjct: 68 NG 69
Score = 34.3 bits (77), Expect = 0.15, Method: Composition-based stats.
Identities = 14/44 (31%), Positives = 26/44 (59%)
Query: 369 FQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAMMNG 412
F+ FG++ + + D TG SK +GF+++ A+ A+ +NG
Sbjct: 26 FEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNG 69
Score = 28.5 bits (62), Expect = 7.0, Method: Composition-based stats.
Identities = 13/40 (32%), Positives = 24/40 (60%)
Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASR 56
L+VG + ++TE L +F+ F +D + ++KD T S+
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSK 47
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 37.4 bits (85), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 41/73 (56%), Gaps = 8/73 (10%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 163
LF+ L V+E + FS +G ++ ++ L K AF+ ++ ++ A+ A+E +N
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKL-------KDYAFIHFDERDGAVKAMEEMN 66
Query: 164 GKHKMEGSSVPLV 176
GK +EG ++ +V
Sbjct: 67 GKD-LEGENIEIV 78
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 37.0 bits (84), Expect = 0.023, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 36/65 (55%), Gaps = 7/65 (10%)
Query: 15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRCCFVICPSRQEADKAVNA 74
VKLF+G +P+ TE ++ ++F+++ V E +IIK+ FV + A+ A+
Sbjct: 9 VKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYG-------FVHIEDKTAAEDAIRN 61
Query: 75 CHNKK 79
H+ K
Sbjct: 62 LHHYK 66
Score = 36.2 bits (82), Expect = 0.035, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 33/57 (57%), Gaps = 8/57 (14%)
Query: 351 LFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAI 407
LFI ++P+E +QE+ + F+ +G+VL + K +GFV E +A++AI
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAI 59
Score = 35.4 bits (80), Expect = 0.064, Method: Composition-based stats.
Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 8/71 (11%)
Query: 103 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 162
KLFIG LP+ +E E+ +LF YG + + I+ K F+ E K A A+ +
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDAIRNL 62
Query: 163 NGKHKMEGSSV 173
+ +K+ G ++
Sbjct: 63 H-HYKLHGVNI 72
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 37.0 bits (84), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 32/62 (51%)
Query: 103 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 162
KL + L VS+A++ LF+ +GT+K + S G A + +E + AL A++
Sbjct: 90 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQY 149
Query: 163 NG 164
G
Sbjct: 150 KG 151
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 36.6 bits (83), Expect = 0.025, Method: Composition-based stats.
Identities = 17/67 (25%), Positives = 32/67 (47%)
Query: 345 GPPGANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQ 404
P + +++ ++P + +L F +G+V+ + DK T SK F+ + SAQ
Sbjct: 13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQ 72
Query: 405 NAIAMMN 411
N +N
Sbjct: 73 NCTRAIN 79
Score = 34.7 bits (78), Expect = 0.10, Method: Composition-based stats.
Identities = 18/64 (28%), Positives = 35/64 (54%), Gaps = 1/64 (1%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEAI 162
+++ LP +++ ++ +FS YG + + I++ + SKG AF+ + K+ A AI
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 163 NGKH 166
N K
Sbjct: 79 NNKQ 82
>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 = 36.2 bits (82), Expect = 0.035, Method: Composition-based stats.
Identities = 21/62 (33%), Positives = 32/62 (51%)
Query: 103 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 162
KL + L VS+A++ LF+ +GT+K + S G A + +E K AL A +
Sbjct: 31 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQY 90
Query: 163 NG 164
NG
Sbjct: 91 NG 92
>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 = 35.8 bits (81), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 37/63 (58%), Gaps = 4/63 (6%)
Query: 102 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA 161
H LF+ LP+ +E +S LF+ + K+++++ G AF++++ + QA AA +A
Sbjct: 208 HILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHD----IAFVEFDNEVQAGAARDA 263
Query: 162 ING 164
+ G
Sbjct: 264 LQG 266
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 35.4 bits (80), Expect = 0.061, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 3/72 (4%)
Query: 96 ELERLEHK---LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETK 152
E E+L K L++G L +E ++ LFS G IK + + +T+ G F++Y ++
Sbjct: 10 EQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSR 69
Query: 153 EQALAALEAING 164
A A+ ING
Sbjct: 70 ADAENAMRYING 81
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 35.4 bits (80), Expect = 0.068, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 34/64 (53%)
Query: 349 ANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIA 408
A + + ++ ++ + +L F+ FG + + DK TG SK F F+S+ A AIA
Sbjct: 16 ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 75
Query: 409 MMNG 412
++G
Sbjct: 76 GVSG 79
Score = 29.6 bits (65), Expect = 3.2, Method: Composition-based stats.
Identities = 15/57 (26%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 109 LPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAING 164
L ++ E ++ LF +G+I + + + + SKG AF+ + +E A A+ ++G
Sbjct: 23 LSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSG 79
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 35.0 bits (79), Expect = 0.074, Method: Composition-based stats.
Identities = 13/50 (26%), Positives = 30/50 (60%)
Query: 100 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKY 149
+ + +F+G + + E E+ + F+ YG++K+++I+ SKG F+ +
Sbjct: 8 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF 57
Score = 33.9 bits (76), Expect = 0.18, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 351 LFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAI 407
+F+ I + E+ + F +G V K+ D+ TGVSK +GFVS+ + Q +
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIV 67
Score = 30.4 bits (67), Expect = 2.2, Method: Composition-based stats.
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKT 51
+FVG + M E ++ + F + V EV II D+T
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRT 46
>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 = 35.0 bits (79), Expect = 0.075, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 13/73 (17%)
Query: 103 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 162
+LF+G LP +++E E+ LF YG ++ I KG F++ ET+ A A
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFI-----HKDKGFGFIRLETRTLAEIA---- 67
Query: 163 NGKHKMEGSSVPL 175
K+E ++PL
Sbjct: 68 ----KVELDNMPL 76
Score = 34.3 bits (77), Expect = 0.15, Method: Composition-based stats.
Identities = 25/84 (29%), Positives = 39/84 (46%), Gaps = 11/84 (13%)
Query: 14 RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDK-------TTRA----SRCCFVIC 62
R +LFVG +P +TE ++ +F+++ EV I KDK TR ++
Sbjct: 15 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNM 74
Query: 63 PSRQEADKAVNACHNKKTLPGASS 86
P R + + ACH+ G SS
Sbjct: 75 PLRGKQLRVRFACHSASLTSGPSS 98
Score = 30.4 bits (67), Expect = 1.8, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 33/58 (56%), Gaps = 6/58 (10%)
Query: 349 ANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNA 406
+ LF+ ++P + ++E+ F+ +G+ + +VF+ K G FGF+ E+ A+ A
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGK--AGEVFIHKDKG----FGFIRLETRTLAEIA 67
>pdb|2U1A|A Chain A, Rna Binding Domain 2 Of Human U1a Protein, Nmr, 20
Structures
Length = 88
Score = 35.0 bits (79), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 37/63 (58%), Gaps = 4/63 (6%)
Query: 102 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA 161
H LF+ LP+ +E +S LF+ + K+++++ G AF++++ + QA AA +A
Sbjct: 14 HILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRH----DIAFVEFDNEVQAGAARDA 69
Query: 162 ING 164
+ G
Sbjct: 70 LQG 72
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 34.7 bits (78), Expect = 0.095, Method: Composition-based stats.
Identities = 13/50 (26%), Positives = 30/50 (60%)
Query: 100 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKY 149
+ + +F+G + + E E+ + F+ YG++K+++I+ SKG F+ +
Sbjct: 9 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF 58
Score = 33.9 bits (76), Expect = 0.17, Method: Composition-based stats.
Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 7/69 (10%)
Query: 345 GPPGA------NLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYE 398
GP G+ +F+ I + E+ + F +G V K+ D+ TGVSK +GFVS+
Sbjct: 1 GPLGSGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFY 59
Query: 399 SPASAQNAI 407
+ Q +
Sbjct: 60 NDVDVQKIV 68
Score = 30.0 bits (66), Expect = 2.6, Method: Composition-based stats.
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKT 51
+FVG + M E ++ + F + V EV II D+T
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRT 47
>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 = 34.7 bits (78), Expect = 0.11, Method: Composition-based stats.
Identities = 13/50 (26%), Positives = 30/50 (60%)
Query: 100 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKY 149
+ + +F+G + + E E+ + F+ YG++K+++I+ SKG F+ +
Sbjct: 8 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF 57
Score = 33.5 bits (75), Expect = 0.25, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 351 LFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAI 407
+F+ I + E+ + F +G V K+ D+ TGVSK +GFVS+ + Q +
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIV 67
Score = 30.0 bits (66), Expect = 2.9, Method: Composition-based stats.
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKT 51
+FVG + M E ++ + F + V EV II D+T
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRT 46
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 25/49 (51%)
Query: 365 LGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAMMNGC 413
L F+ +GRV + D+ T S+ F FV + A++A+ M+G
Sbjct: 87 LRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGA 135
Score = 32.3 bits (72), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAI 162
L + L S + +F YG + D+ I R + S+G AF+++ K A A++A+
Sbjct: 73 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132
Query: 163 NG 164
+G
Sbjct: 133 DG 134
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 34.3 bits (77), Expect = 0.15, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 32/62 (51%)
Query: 103 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 162
KL + L VS+A++ LF+ +GT+K + S G A + +E + AL A++
Sbjct: 37 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQY 96
Query: 163 NG 164
G
Sbjct: 97 KG 98
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 34.3 bits (77), Expect = 0.15, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 32/62 (51%)
Query: 103 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 162
KL + L VS+A++ LF+ +GT+K + S G A + +E + AL A++
Sbjct: 37 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQY 96
Query: 163 NG 164
G
Sbjct: 97 KG 98
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 33.9 bits (76), Expect = 0.17, Method: Composition-based stats.
Identities = 14/37 (37%), Positives = 24/37 (64%)
Query: 363 QELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYES 399
+++ + F+ FG+V A + DK T + FGFV++ES
Sbjct: 14 EDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFES 50
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 33.5 bits (75), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 1/64 (1%)
Query: 103 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQI-LRGSQQTSKGCAFLKYETKEQALAALEA 161
+LF+ L SE ++ LFS YG + +L + + KG AF+ + E A+ A
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 162 INGK 165
++G+
Sbjct: 70 VDGQ 73
Score = 30.0 bits (66), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 30/63 (47%)
Query: 350 NLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAM 409
LF+ ++ +++L F A+G + +D T K F FV++ P A A A
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 410 MNG 412
++G
Sbjct: 70 VDG 72
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 33.5 bits (75), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 31/67 (46%)
Query: 99 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAA 158
RL +F+ L V ++ +FS+ G + IL S+G + +E +A+ A
Sbjct: 13 RLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQA 72
Query: 159 LEAINGK 165
+ NG+
Sbjct: 73 ISMFNGQ 79
>pdb|1OWX|A Chain A, Solution Structure Of The C-Terminal Rrm Of Human La
(La225- 334)
Length = 121
Score = 33.5 bits (75), Expect = 0.24, Method: Composition-based stats.
Identities = 24/81 (29%), Positives = 37/81 (45%), Gaps = 3/81 (3%)
Query: 105 FIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAING 164
F G L ++ LFS +G IK + +RG+++ G K + KE A +A NG
Sbjct: 23 FSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKE---GIILFKEKAKEALGKAKDANNG 79
Query: 165 KHKMEGSSVPLVVKWADTEKE 185
++ V V + EKE
Sbjct: 80 NLQLRNKEVTWEVLEGEVEKE 100
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 33.5 bits (75), Expect = 0.24, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 6/73 (8%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQI-LRGSQQTSKGCAFLKYETKEQ-----ALA 157
+FI L + E + + +G +K +++ L + SKGCAF ++ T+E A A
Sbjct: 18 VFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAA 77
Query: 158 ALEAINGKHKMEG 170
+LEA G K++G
Sbjct: 78 SLEAEGGGLKLDG 90
Score = 28.5 bits (62), Expect = 8.4, Method: Composition-based stats.
Identities = 16/61 (26%), Positives = 29/61 (47%)
Query: 348 GANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAI 407
G +FI ++ + ++ LG Q FG + +V + T SK F + + +AQ +
Sbjct: 15 GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCL 74
Query: 408 A 408
A
Sbjct: 75 A 75
>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 = 33.5 bits (75), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 40/73 (54%), Gaps = 4/73 (5%)
Query: 96 ELERLEHK---LFIGMLPKNVSEAEVSALFSIYGTIKDLQI-LRGSQQTSKGCAFLKYET 151
E E+L K L++G L +E ++ LFS G IK + + L ++T+ G F++Y +
Sbjct: 31 EQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYS 90
Query: 152 KEQALAALEAING 164
+ A A+ ING
Sbjct: 91 RADAENAMRYING 103
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 33.5 bits (75), Expect = 0.25, Method: Composition-based stats.
Identities = 19/52 (36%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 114 SEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEAING 164
+E ++ +FS YG I D+ I+ Q + S+G AF+ +E + A A E NG
Sbjct: 25 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 76
Score = 28.1 bits (61), Expect = 9.5, Method: Composition-based stats.
Identities = 15/66 (22%), Positives = 30/66 (45%)
Query: 347 PGANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNA 406
P L ++ + +++L F +G + + D+ + S+ F FV +E+ A+ A
Sbjct: 11 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 70
Query: 407 IAMMNG 412
NG
Sbjct: 71 KERANG 76
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 33.5 bits (75), Expect = 0.25, Method: Composition-based stats.
Identities = 19/52 (36%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 114 SEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEAING 164
+E ++ +FS YG I D+ I+ Q + S+G AF+ +E + A A E NG
Sbjct: 28 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Score = 28.1 bits (61), Expect = 9.6, Method: Composition-based stats.
Identities = 15/66 (22%), Positives = 30/66 (45%)
Query: 347 PGANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNA 406
P L ++ + +++L F +G + + D+ + S+ F FV +E+ A+ A
Sbjct: 14 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 73
Query: 407 IAMMNG 412
NG
Sbjct: 74 KERANG 79
>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 = 33.1 bits (74), Expect = 0.27, Method: Composition-based stats.
Identities = 15/56 (26%), Positives = 29/56 (51%)
Query: 352 FIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAI 407
F+ + + ++L + F FG V+ + D TG S+ FGF+ ++ AS + +
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVL 70
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 33.1 bits (74), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 8/67 (11%)
Query: 100 LEHKLFIGMLPKN-VSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAA 158
+ ++FIG L V +++V +FS YG + + KG AF++Y + A AA
Sbjct: 26 INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQYSNERHARAA 78
Query: 159 LEAINGK 165
+ NG+
Sbjct: 79 VLGENGR 85
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 33.1 bits (74), Expect = 0.33, Method: Composition-based stats.
Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 350 NLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAM 409
N+++ ++ +++ F FG+V + K+ D+ T K FGFV + S AIA
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61
Query: 410 MN 411
++
Sbjct: 62 LD 63
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 33.1 bits (74), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 31/67 (46%), Gaps = 6/67 (8%)
Query: 346 PPGANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQN 405
P ++ I DQ + F FG+++ +VF +K + FV + + SA +
Sbjct: 23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG------YSFVRFSTHESAAH 76
Query: 406 AIAMMNG 412
AI +NG
Sbjct: 77 AIVSVNG 83
Score = 30.0 bits (66), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 37/70 (52%), Gaps = 6/70 (8%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 163
++ G + +++ + FS +G I ++++ KG +F+++ T E A A+ ++N
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVF-----PEKGYSFVRFSTHESAAHAIVSVN 82
Query: 164 GKHKMEGSSV 173
G +EG V
Sbjct: 83 GT-TIEGHVV 91
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 33.1 bits (74), Expect = 0.33, Method: Composition-based stats.
Identities = 19/52 (36%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 114 SEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEAING 164
+E ++ +FS YG I D+ I+ Q + S+G AF+ +E + A A E NG
Sbjct: 59 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 110
>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 = 32.7 bits (73), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 37/62 (59%), Gaps = 1/62 (1%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQ-TSKGCAFLKYETKEQALAALEAI 162
+++G +P + +E ++ L S G + +L+++ Q SKG AF+++ E + +A+ +
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 163 NG 164
NG
Sbjct: 67 NG 68
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 32.7 bits (73), Expect = 0.42, Method: Composition-based stats.
Identities = 20/62 (32%), Positives = 30/62 (48%), Gaps = 8/62 (12%)
Query: 351 LFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAMM 410
+F+ ++ QEL + F+ GRV+ V D + FV E A A+ AIA +
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQL 63
Query: 411 NG 412
NG
Sbjct: 64 NG 65
Score = 28.1 bits (61), Expect = 9.6, Method: Composition-based stats.
Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 7/63 (11%)
Query: 103 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 162
K+F+G + + E+ +LF G + + ++ K AF+ E + A AA+ +
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVV-------KDYAFVHMEKEADAKAAIAQL 63
Query: 163 NGK 165
NGK
Sbjct: 64 NGK 66
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 32.7 bits (73), Expect = 0.44, Method: Composition-based stats.
Identities = 19/52 (36%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 114 SEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEAING 164
+E ++ +FS YG I D+ I+ Q + S+G AF+ +E + A A E NG
Sbjct: 28 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 32.7 bits (73), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 8/67 (11%)
Query: 100 LEHKLFIGMLPK-NVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAA 158
+ ++FIG L V +++V A+FS YG I + KG AF++Y + A AA
Sbjct: 14 MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV-------HKGFAFVQYVNERNARAA 66
Query: 159 LEAINGK 165
+ +G+
Sbjct: 67 VAGEDGR 73
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 32.3 bits (72), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 35/66 (53%), Gaps = 4/66 (6%)
Query: 100 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAAL 159
L+ K+++G L N ++ E+ F YG ++ + + R G AF+++E A A+
Sbjct: 72 LDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVAR----NPPGFAFVEFEDPRDAADAV 127
Query: 160 EAINGK 165
++G+
Sbjct: 128 RELDGR 133
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 32.3 bits (72), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 35/66 (53%), Gaps = 4/66 (6%)
Query: 100 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAAL 159
L+ K+++G L N ++ E+ F YG ++ + + R G AF+++E A A+
Sbjct: 72 LDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVAR----NPPGFAFVEFEDPRDAADAV 127
Query: 160 EAINGK 165
++G+
Sbjct: 128 RDLDGR 133
>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
pdb|1HD1|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
Length = 75
Score = 32.3 bits (72), Expect = 0.60, Method: Composition-based stats.
Identities = 16/57 (28%), Positives = 29/57 (50%)
Query: 351 LFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAI 407
+FI + + ++L + F FG V+ + +D TG S+ FGFV ++ S +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM 58
>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 = 32.0 bits (71), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 37/62 (59%), Gaps = 1/62 (1%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQ-TSKGCAFLKYETKEQALAALEAI 162
+++G +P + +E ++ L S G + +L+++ Q SKG AF+++ E + +A+ +
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 163 NG 164
NG
Sbjct: 66 NG 67
>pdb|3HLR|A Chain A, Donor Strand Complemented Faeg Of F4ad Fimbriae
Length = 276
Score = 32.0 bits (71), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 36/88 (40%), Gaps = 10/88 (11%)
Query: 57 CCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERL----EHKLFIGMLPKN 112
+ + P + V + + GA V ADGEL L H +F G LP N
Sbjct: 87 LAYFVLPMKNAEGTKVGSVKVNASYAGALGRGGVTSADGELMSLFAEGSHAIFYGGLPTN 146
Query: 113 VSEAEV------SALFSIYGTIKDLQIL 134
V +E+ +A ++G++ IL
Sbjct: 147 VKNSELKGGSAAAARTELFGSLSKNDIL 174
>pdb|3GGH|A Chain A, Donor Strand Complemented Faeg Of F4ad Fimbriae
pdb|3GGH|B Chain B, Donor Strand Complemented Faeg Of F4ad Fimbriae
Length = 275
Score = 32.0 bits (71), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 36/88 (40%), Gaps = 10/88 (11%)
Query: 57 CCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERL----EHKLFIGMLPKN 112
+ + P + V + + GA V ADGEL L H +F G LP N
Sbjct: 96 LAYFVLPMKNAEGTKVGSVKVNASYAGALGRGGVTSADGELMSLFAEGSHAIFYGGLPTN 155
Query: 113 VSEAEV------SALFSIYGTIKDLQIL 134
V +E+ +A ++G++ IL
Sbjct: 156 VKNSELKGGSAAAARTELFGSLSKNDIL 183
>pdb|3GEA|A Chain A, Donor Strand Complemented Faeg Monomer Of F4 Variant Ad
pdb|3GEA|B Chain B, Donor Strand Complemented Faeg Monomer Of F4 Variant Ad
Length = 274
Score = 32.0 bits (71), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 36/88 (40%), Gaps = 10/88 (11%)
Query: 57 CCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERL----EHKLFIGMLPKN 112
+ + P + V + + GA V ADGEL L H +F G LP N
Sbjct: 95 LAYFVLPMKNAEGTKVGSVKVNASYAGALGRGGVTSADGELMSLFAEGSHAIFYGGLPTN 154
Query: 113 VSEAEV------SALFSIYGTIKDLQIL 134
V +E+ +A ++G++ IL
Sbjct: 155 VKNSELKGGSAAAARTELFGSLSKNDIL 182
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 32.0 bits (71), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 8/60 (13%)
Query: 103 KLFIGMLP-KNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA 161
+LFIG LP KNVS+ ++ +FS YG I + I F++++ + A+E
Sbjct: 12 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIEC 64
>pdb|3GEW|D Chain D, Faee-Faeg Chaperone-Major Pilin Complex Of F4 Ad Fimbriae
pdb|3GEW|A Chain A, Faee-Faeg Chaperone-Major Pilin Complex Of F4 Ad Fimbriae
Length = 253
Score = 32.0 bits (71), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 36/88 (40%), Gaps = 10/88 (11%)
Query: 57 CCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERL----EHKLFIGMLPKN 112
+ + P + V + + GA V ADGEL L H +F G LP N
Sbjct: 95 LAYFVLPMKNAEGTKVGSVKVNASYAGALGRGGVTSADGELMSLFAEGSHAIFYGGLPTN 154
Query: 113 VSEAEV------SALFSIYGTIKDLQIL 134
V +E+ +A ++G++ IL
Sbjct: 155 VKNSELKGGSAAAARTELFGSLSKNDIL 182
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 32.0 bits (71), Expect = 0.74, Method: Composition-based stats.
Identities = 17/61 (27%), Positives = 35/61 (57%), Gaps = 2/61 (3%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 163
L+I LP ++ E+ +F YG I+ +++ G+ ++G A++ YE A A++ ++
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRV--GNTPETRGTAYVVYEDIFDAKNAVDHLS 68
Query: 164 G 164
G
Sbjct: 69 G 69
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 31.6 bits (70), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 37/62 (59%), Gaps = 1/62 (1%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQ-TSKGCAFLKYETKEQALAALEAI 162
+++G +P + +E ++ L S G + +L+++ Q SKG AF+++ E + +A+ +
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 163 NG 164
NG
Sbjct: 65 NG 66
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 31.6 bits (70), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 8/62 (12%)
Query: 100 LEHKLFIGMLP-KNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAA 158
++ +LFIG LP KNVS+ ++ +FS YG I + I F++++ + A
Sbjct: 21 MKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDA 73
Query: 159 LE 160
+E
Sbjct: 74 IE 75
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 31.6 bits (70), Expect = 0.91, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 4/63 (6%)
Query: 103 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 162
K+++G L + E+ FS YG ++ + I R G AF+++E A A+ +
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIAR----NPPGFAFVEFEDPRDAEDAVRGL 57
Query: 163 NGK 165
+GK
Sbjct: 58 DGK 60
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 31.6 bits (70), Expect = 0.93, Method: Composition-based stats.
Identities = 17/61 (27%), Positives = 34/61 (55%), Gaps = 2/61 (3%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 163
L+I LP ++ E+ +F YG I+ +++ G+ ++G A++ YE A A + ++
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRV--GNTPETRGTAYVVYEDIFDAKNACDHLS 72
Query: 164 G 164
G
Sbjct: 73 G 73
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 31.2 bits (69), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 8/63 (12%)
Query: 100 LEHKLFIGMLP-KNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAA 158
++ +LFIG LP KNVS+ ++ +FS YG I + I F++++ + A
Sbjct: 21 MKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDA 73
Query: 159 LEA 161
+E
Sbjct: 74 IEC 76
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 7/70 (10%)
Query: 102 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQI-LRGSQQTSKGCAFLKYETKEQALAALE 160
+KL+IG L V+ ++ LF D ++ L G G AF+ Y + A+ A+E
Sbjct: 9 NKLYIGNLSPAVTADDLRQLFG------DRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIE 62
Query: 161 AINGKHKMEG 170
++GK ++ G
Sbjct: 63 TLSGKVELHG 72
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 31.2 bits (69), Expect = 1.2, Method: Composition-based stats.
Identities = 17/41 (41%), Positives = 24/41 (58%)
Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASR 56
KLFVG + T+ L + F ++ V + I+KDKTT SR
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSR 58
Score = 31.2 bits (69), Expect = 1.3, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 27/58 (46%)
Query: 351 LFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIA 408
LF+ + + L + F +G V+ + DK T S+ FGFV ++ P +A
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLA 76
Score = 29.3 bits (64), Expect = 4.6, Method: Composition-based stats.
Identities = 15/49 (30%), Positives = 29/49 (59%), Gaps = 1/49 (2%)
Query: 103 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYE 150
KLF+G L + ++ + + FS YG + D I++ + S+G F+K++
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFK 66
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 30.8 bits (68), Expect = 1.4, Method: Composition-based stats.
Identities = 17/61 (27%), Positives = 34/61 (55%), Gaps = 2/61 (3%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 163
L+I LP ++ E+ +F YG I+ +++ G+ ++G A++ YE A A + ++
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRV--GNTPETRGTAYVVYEDIFDAKNACDHLS 78
Query: 164 G 164
G
Sbjct: 79 G 79
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 31/67 (46%), Gaps = 3/67 (4%)
Query: 349 ANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDK-ATGV--SKCFGFVSYESPASAQN 405
+ LFI ++ ++ L F G + S + K GV S FGFV Y+ P AQ
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 406 AIAMMNG 412
A+ + G
Sbjct: 66 ALKQLQG 72
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 28/100 (28%), Positives = 50/100 (50%), Gaps = 7/100 (7%)
Query: 87 PLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQI-LRGSQQTSKGCA 145
P+ Y GE ++ L++ L V+E ++ +LF+ + K I R +G A
Sbjct: 14 PMFSSYNPGEPNKV---LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQA 70
Query: 146 FLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKE 185
F+ + KE A AL +NG +K+ G LV+++ +K+
Sbjct: 71 FITFPNKEIAWQALHLVNG-YKLYGKI--LVIEFGKNKKQ 107
>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 = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 22/45 (48%), Gaps = 5/45 (11%)
Query: 122 FSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKH 166
FS +G I DL S + CAF+ YE E A A+ +NG
Sbjct: 58 FSPFGNIIDL-----SMDPPRNCAFVTYEKMESADQAVAELNGTQ 97
Score = 28.5 bits (62), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 30/66 (45%), Gaps = 8/66 (12%)
Query: 348 GANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAI 407
G L++Y ++ L AF FG + +D + + FV+YE SA A+
Sbjct: 39 GNTLYVYG--EDMTPTLLRGAFSPFGNI------IDLSMDPPRNCAFVTYEKMESADQAV 90
Query: 408 AMMNGC 413
A +NG
Sbjct: 91 AELNGT 96
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 30.4 bits (67), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 8/60 (13%)
Query: 103 KLFIGMLP-KNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA 161
+LFIG LP KNVS+ ++ +FS YG I + I F++++ + A+E
Sbjct: 4 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIEC 56
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 30.4 bits (67), Expect = 2.0, Method: Composition-based stats.
Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 7/77 (9%)
Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRCCFVICPSRQEADKAVNACH 76
L+VG + +TE L F +F + + +++ + +C F+ +RQ A+ A
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ-----QCAFIQFATRQAAEVAAEKSF 69
Query: 77 NKKTLPGASSPLQVKYA 93
NK + G L VK+
Sbjct: 70 NKLIVNGRR--LNVKWG 84
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 30.4 bits (67), Expect = 2.1, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 27/64 (42%)
Query: 345 GPPGANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQ 404
G G +FI + + + L F FG V V D T S+ FGFV++ A
Sbjct: 22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVD 81
Query: 405 NAIA 408
+A
Sbjct: 82 KVLA 85
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 30.4 bits (67), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 16/65 (24%), Positives = 33/65 (50%), Gaps = 1/65 (1%)
Query: 349 ANLFIYHIPQEFGDQELGNAFQAFGR-VLSAKVFVDKATGVSKCFGFVSYESPASAQNAI 407
A+L++ + + + AF G V+S K+ ++ TG+ + FV + A+A+ +
Sbjct: 10 ASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCL 69
Query: 408 AMMNG 412
+NG
Sbjct: 70 HKING 74
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 30.4 bits (67), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 22/45 (48%), Gaps = 5/45 (11%)
Query: 122 FSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKH 166
FS +G I DL S + CAF+ YE E A A+ +NG
Sbjct: 34 FSPFGNIIDL-----SMDPPRNCAFVTYEKMESADQAVAELNGTQ 73
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 30.4 bits (67), Expect = 2.3, Method: Composition-based stats.
Identities = 13/26 (50%), Positives = 17/26 (65%)
Query: 387 GVSKCFGFVSYESPASAQNAIAMMNG 412
G K FGFV ++ P S AIA++NG
Sbjct: 54 GKPKSFGFVCFKHPESVSYAIALLNG 79
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 30.0 bits (66), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 20/33 (60%)
Query: 380 VFVDKATGVSKCFGFVSYESPASAQNAIAMMNG 412
+++DK TG K VSYE P +A+ A+ +G
Sbjct: 55 IYLDKETGKPKGDATVSYEDPPTAKAAVEWFDG 87
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 29.6 bits (65), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 32/63 (50%)
Query: 349 ANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIA 408
A +++ + ++ + L F G V++ + D+ TG + +GFV + S A AI
Sbjct: 16 ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIK 75
Query: 409 MMN 411
+M+
Sbjct: 76 IMD 78
>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 = 29.6 bits (65), Expect = 3.3, Method: Composition-based stats.
Identities = 15/48 (31%), Positives = 25/48 (52%)
Query: 365 LGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQNAIAMMNG 412
L F+ +GRV + D+ T S+ F FV + A++A+ M+G
Sbjct: 64 LRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 111
Score = 28.5 bits (62), Expect = 7.4, Method: Composition-based stats.
Identities = 15/45 (33%), Positives = 27/45 (60%), Gaps = 1/45 (2%)
Query: 121 LFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAING 164
+F YG + D+ I R + S+G AF+++ K A A++A++G
Sbjct: 67 VFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 111
>pdb|2B0G|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd2
pdb|2AYM|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd2
Length = 83
Score = 29.6 bits (65), Expect = 3.3, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 35/61 (57%), Gaps = 4/61 (6%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 163
LF+ LP+ +E +S LF+ + K+++++ AF+++ T+ Q+ AA EA+
Sbjct: 11 LFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDI----AFVEFTTELQSNAAKEALQ 66
Query: 164 G 164
G
Sbjct: 67 G 67
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 29.3 bits (64), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 29/67 (43%)
Query: 346 PPGANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQN 405
P A L + ++P Q+ + FG + + + TG SK +GF Y SA
Sbjct: 93 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAAR 152
Query: 406 AIAMMNG 412
A + + G
Sbjct: 153 AKSDLLG 159
>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
pdb|3H2U|D Chain D, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
Length = 283
Score = 29.3 bits (64), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 29/67 (43%)
Query: 346 PPGANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQN 405
P A L + ++P Q+ + FG + + + TG SK +GF Y SA
Sbjct: 91 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAAR 150
Query: 406 AIAMMNG 412
A + + G
Sbjct: 151 AKSDLLG 157
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 29.3 bits (64), Expect = 4.8, Method: Composition-based stats.
Identities = 20/81 (24%), Positives = 39/81 (48%), Gaps = 7/81 (8%)
Query: 104 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 163
LF+ L V+E + FS +G ++ ++ L K AF+ +E + A+ A++ +N
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKL-------KDYAFVHFEDRGAAVKAMDEMN 70
Query: 164 GKHKMEGSSVPLVVKWADTEK 184
GK ++ K D ++
Sbjct: 71 GKEIEGEEIEIVLAKPPDKKR 91
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 29.3 bits (64), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 29/67 (43%)
Query: 346 PPGANLFIYHIPQEFGDQELGNAFQAFGRVLSAKVFVDKATGVSKCFGFVSYESPASAQN 405
P A L + ++P Q+ + FG + + + TG SK +GF Y SA
Sbjct: 93 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAAR 152
Query: 406 AIAMMNG 412
A + + G
Sbjct: 153 AKSDLLG 159
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 28.5 bits (62), Expect = 7.1, Method: Composition-based stats.
Identities = 14/34 (41%), Positives = 20/34 (58%)
Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKD 49
KL VG + T +L A F+E+ V E +I+KD
Sbjct: 12 KLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD 45
>pdb|4AH6|A Chain A, Human Mitochondrial Aspartyl-Trna Synthetase
pdb|4AH6|B Chain B, Human Mitochondrial Aspartyl-Trna Synthetase
pdb|4AH6|C Chain C, Human Mitochondrial Aspartyl-Trna Synthetase
pdb|4AH6|D Chain D, Human Mitochondrial Aspartyl-Trna Synthetase
Length = 617
Score = 28.5 bits (62), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 27/60 (45%), Gaps = 7/60 (11%)
Query: 270 LSSNMGPRNYAMPPSGFVGSGYPAV-------PGLQYPMPYPGGMLGHRPLNNSPGSVSP 322
LS + +Y PP G + G + P ++ + +P GH ++N+P SV P
Sbjct: 525 LSHLLQALDYGAPPHGGIALGLDRLICLVTGSPSIRDVIAFPKSFRGHDLMSNTPDSVPP 584
>pdb|1X4F|A Chain A, Solution Structure Of The Second Rrm Domain In Matrin 3
Length = 112
Score = 28.1 bits (61), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 36/66 (54%), Gaps = 9/66 (13%)
Query: 96 ELERLEHKLFIGMLPKN-VSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQ 154
EL R+ H + LP + S++ V L YG IK+ ++R Q AF++ ET+E
Sbjct: 23 ELGRVIH---LSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQ-----AFIEMETRED 74
Query: 155 ALAALE 160
A+A ++
Sbjct: 75 AMAMVD 80
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 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,139,490
Number of Sequences: 62578
Number of extensions: 488550
Number of successful extensions: 1269
Number of sequences better than 100.0: 163
Number of HSP's better than 100.0 without gapping: 119
Number of HSP's successfully gapped in prelim test: 44
Number of HSP's that attempted gapping in prelim test: 884
Number of HSP's gapped (non-prelim): 343
length of query: 434
length of database: 14,973,337
effective HSP length: 102
effective length of query: 332
effective length of database: 8,590,381
effective search space: 2852006492
effective search space used: 2852006492
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)