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= 032044
(148 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 91.3 bits (225), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 39/142 (27%), Positives = 88/142 (61%), Gaps = 4/142 (2%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPL 61
++ + ++ D+ ++ +AFV D N ++ L+G++ I+++N++ + +
Sbjct: 27 IANIKIMIDKNN-KNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQQS--- 82
Query: 62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEM 121
++ F LFVG+L+ +V E+L AF+++ + + V++D ++G SRGYGFV ++++ +
Sbjct: 83 SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDA 142
Query: 122 ETALESLNGVELEGRAMRVSLA 143
+ A++S+ G +L GR +R++ A
Sbjct: 143 QNAMDSMQGQDLNGRPLRINWA 164
Score = 50.1 bits (118), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 44/75 (58%), Gaps = 1/75 (1%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
L+VGNL ++T + L Q FQ G + +++ D ++ ++ Y FV Y + AL++L
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQTL 61
Query: 129 NGVELEGRAMRVSLA 143
NG ++E ++++ A
Sbjct: 62 NGKQIENNIVKINWA 76
Score = 45.4 bits (106), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 34/48 (70%)
Query: 7 VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK 54
V++D +TG SRG+ FV+ ++ +D ++++ G++ GR LR+N++ K
Sbjct: 119 VMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 73.2 bits (178), Expect = 6e-14, Method: Compositional matrix adjust.
Identities = 38/133 (28%), Positives = 72/133 (54%), Gaps = 5/133 (3%)
Query: 10 DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKL 69
D+ TG+S G+ FV S D + I L+G + + ++V+++ + D L
Sbjct: 39 DKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYARPSSASI-----RDANL 93
Query: 70 FVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLN 129
+V L +++ + + Q F +YG ++ +R+L D +G SRG GF+ + + E E A++ LN
Sbjct: 94 YVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLN 153
Query: 130 GVELEGRAMRVSL 142
G + G A +++
Sbjct: 154 GQKPLGAAEPITV 166
Score = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 45/76 (59%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
L V L ++T + F G++ +++ D +G+S GYGFV YS + + A+ +L
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 129 NGVELEGRAMRVSLAQ 144
NG++L+ + ++VS A+
Sbjct: 67 NGLKLQTKTIKVSYAR 82
Score = 30.8 bits (68), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 2/51 (3%)
Query: 7 VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLG--RILRVNFSDKP 55
+L D+ TG SRG F+ + I+ L+G++ LG + V F++ P
Sbjct: 122 ILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQKPLGAAEPITVKFANNP 172
>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 = 72.8 bits (177), Expect = 6e-14, Method: Compositional matrix adjust.
Identities = 29/77 (37%), Positives = 55/77 (71%)
Query: 67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
F LFVG+L+ +V E+L AF+++ + + V++D ++G SRGYGFV ++++ + + A++
Sbjct: 2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 127 SLNGVELEGRAMRVSLA 143
S+ G +L GR +R++ A
Sbjct: 62 SMQGQDLNGRPLRINWA 78
Score = 45.4 bits (106), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 34/48 (70%)
Query: 7 VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK 54
V++D +TG SRG+ FV+ ++ +D ++++ G++ GR LR+N++ K
Sbjct: 33 VMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 80
>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 = 70.5 bits (171), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 38/126 (30%), Positives = 66/126 (52%), Gaps = 5/126 (3%)
Query: 10 DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKL 69
D+ TG+S G+ FV +D I L+G + ++V+++ + D L
Sbjct: 37 DKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASI-----RDANL 91
Query: 70 FVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLN 129
+V L ++T + L Q F +YG ++ +R+L D +G SRG GF+ + + E E A++ LN
Sbjct: 92 YVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLN 151
Query: 130 GVELEG 135
G + G
Sbjct: 152 GQKPSG 157
Score = 49.3 bits (116), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 42/76 (55%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
L V L ++T E F G + +++ D +G+S GYGFV Y + E A+ +L
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 129 NGVELEGRAMRVSLAQ 144
NG+ L+ + ++VS A+
Sbjct: 65 NGLRLQTKTIKVSYAR 80
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 70.1 bits (170), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 43/136 (31%), Positives = 76/136 (55%), Gaps = 5/136 (3%)
Query: 7 VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETD 66
++ D +TG S G+AFV ++ D I+ L+G + L+V+++ +P + + D
Sbjct: 35 IMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYA-RPGGE----SIKD 89
Query: 67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
L+V NL ++T + L F +YG++V +L D +GR RG FV Y+ + E + A+
Sbjct: 90 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 149
Query: 127 SLNGVELEGRAMRVSL 142
+LN V EG + +S+
Sbjct: 150 ALNNVIPEGGSQPLSV 165
Score = 45.8 bits (107), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 45/80 (56%)
Query: 65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
++ L V L +T L F+ G + R++ D ++G S GY FV ++++ + + A
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 125 LESLNGVELEGRAMRVSLAQ 144
++ LNG+ + + ++VS A+
Sbjct: 62 IKVLNGITVRNKRLKVSYAR 81
>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 = 69.7 bits (169), Expect = 6e-13, Method: Compositional matrix adjust.
Identities = 32/77 (41%), Positives = 49/77 (63%)
Query: 67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
F +FVG+LS +TTE + AF +G + ARV+ D +G+S+GYGFV + K + E A++
Sbjct: 16 FHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 75
Query: 127 SLNGVELEGRAMRVSLA 143
+ G L GR +R + A
Sbjct: 76 QMGGQWLGGRQIRTNWA 92
Score = 39.7 bits (91), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLP 60
+S V+ D TG+S+G+ FV+ D I+ + G+ GR +R N++ + KP P
Sbjct: 42 ISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATR-KPPAP 99
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 69.3 bits (168), Expect = 7e-13, Method: Compositional matrix adjust.
Identities = 33/80 (41%), Positives = 48/80 (60%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
+FVGN+ + T E L F E G VV R++YD E+G+ +GYGF Y + +A+ +L
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 129 NGVELEGRAMRVSLAQGRRS 148
NG E GRA+RV A ++
Sbjct: 71 NGREFSGRALRVDNAASEKN 90
Score = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 32/52 (61%)
Query: 7 VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
++YDRETG+ +G+ F E + + NL+GRE+ GR LRV+ + K K
Sbjct: 40 LVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEKNK 91
>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|B Chain B, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|C Chain C, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
Length = 184
Score = 68.9 bits (167), Expect = 9e-13, Method: Compositional matrix adjust.
Identities = 45/137 (32%), Positives = 76/137 (55%), Gaps = 7/137 (5%)
Query: 10 DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKL 69
D +TG S G+AFV ++ D I+ L+G + L+V+++ +P + + D L
Sbjct: 49 DYKTGYSFGYAFVDFTSEXDSQRAIKVLNGITVRNKRLKVSYA-RPGGE----SIKDTNL 103
Query: 70 FVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLN 129
+V NL ++T + L F +YG++V +L D +GR RG FV Y+ + E + A+ +LN
Sbjct: 104 YVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 163
Query: 130 GVELEG--RAMRVSLAQ 144
V EG + + V LA+
Sbjct: 164 NVIPEGGSQPLSVRLAE 180
Score = 43.5 bits (101), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 41/76 (53%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
L V L T L F+ G + R+ D ++G S GY FV ++++ + + A++ L
Sbjct: 17 LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 129 NGVELEGRAMRVSLAQ 144
NG+ + + ++VS A+
Sbjct: 77 NGITVRNKRLKVSYAR 92
Score = 27.3 bits (59), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 18/33 (54%)
Query: 6 TVLYDRETGRSRGFAFVTMSTVEDCNAVIENLD 38
+L D+ TGR RG AFV + E+ I L+
Sbjct: 131 NILRDKLTGRPRGVAFVRYNKREEAQEAISALN 163
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 68.6 bits (166), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 32/77 (41%), Positives = 48/77 (62%)
Query: 67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
F +FVG+LS +TTE + AF +G + ARV+ D +G+S+GYGFV + K + E A+
Sbjct: 16 FHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIV 75
Query: 127 SLNGVELEGRAMRVSLA 143
+ G L GR +R + A
Sbjct: 76 HMGGQWLGGRQIRTNWA 92
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLP 60
+S V+ D TG+S+G+ FV+ D I ++ G+ GR +R N++ + KP P
Sbjct: 42 ISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMGGQWLGGRQIRTNWATR-KPPAP 99
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 68.2 bits (165), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 30/73 (41%), Positives = 49/73 (67%)
Query: 68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
+L+VG+L +++T + L F+ +G + +++ D E+GRS+GYGF+ +S + ALE
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 128 LNGVELEGRAMRV 140
LNG EL GR M+V
Sbjct: 88 LNGFELAGRPMKV 100
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 29/48 (60%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRV 49
+ + ++ D ETGRS+G+ F+T S E +E L+G E GR ++V
Sbjct: 53 IESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKV 100
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 66.6 bits (161), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 35/136 (25%), Positives = 71/136 (52%), Gaps = 5/136 (3%)
Query: 7 VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETD 66
++ D+ G S G+ FV T +D I L+G + ++V+++ +P ++ D
Sbjct: 34 LIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYA-RPSSEVI----KD 88
Query: 67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
L++ L ++T + + F +G ++ +RVL D +G SRG F+ + ++E E A+
Sbjct: 89 ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAIT 148
Query: 127 SLNGVELEGRAMRVSL 142
S NG + G + +++
Sbjct: 149 SFNGHKPPGSSEPITV 164
Score = 55.8 bits (133), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 28/76 (36%), Positives = 44/76 (57%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
L V L ++T + L F G V A+++ D +G S GYGFV Y T + E A+ +L
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 129 NGVELEGRAMRVSLAQ 144
NG+ L+ + ++VS A+
Sbjct: 65 NGLRLQSKTIKVSYAR 80
>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 = 66.6 bits (161), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 35/136 (25%), Positives = 71/136 (52%), Gaps = 5/136 (3%)
Query: 7 VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETD 66
++ D+ G S G+ FV T +D I L+G + ++V+++ +P ++ D
Sbjct: 34 LIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYA-RPSSEVI----KD 88
Query: 67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
L++ L ++T + + F +G ++ +RVL D +G SRG F+ + ++E E A+
Sbjct: 89 ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAIT 148
Query: 127 SLNGVELEGRAMRVSL 142
S NG + G + +++
Sbjct: 149 SFNGHKPPGSSEPITV 164
Score = 55.8 bits (133), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 28/76 (36%), Positives = 44/76 (57%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
L V L ++T + L F G V A+++ D +G S GYGFV Y T + E A+ +L
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 129 NGVELEGRAMRVSLAQ 144
NG+ L+ + ++VS A+
Sbjct: 65 NGLRLQSKTIKVSYAR 80
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 65.5 bits (158), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 32/81 (39%), Positives = 49/81 (60%)
Query: 63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
A + KLFVG LS+ +SL Q F +YG + V+ D E+ RSRG+GFV + + +
Sbjct: 9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAK 68
Query: 123 TALESLNGVELEGRAMRVSLA 143
A+ ++NG ++GR +RV A
Sbjct: 69 DAMMAMNGKSVDGRQIRVDQA 89
Score = 47.0 bits (110), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 32/49 (65%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVN 50
+S++ V+ DRET RSRGF FVT ++D + ++G+ GR +RV+
Sbjct: 39 ISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVD 87
>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 = 64.3 bits (155), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 37/150 (24%), Positives = 75/150 (50%), Gaps = 16/150 (10%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIEN---LDGREYLGRILRVNFSDKPKPK 58
++ L ++ D TGRSRGF F++ + V++ LDG+ PK
Sbjct: 30 VTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDGKVI-----------DPKRA 78
Query: 59 LPLYAETDF-KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYST 117
+P + K+FVG + V + + F ++G ++ A+++ D ++G+SRG+GFV Y +
Sbjct: 79 IPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDS 138
Query: 118 KAEMETALESLNGVELEGRAMRVSLAQGRR 147
++ ++ ++ + R + + A+ R
Sbjct: 139 ADAVDRVCQN-KFIDFKDRKIEIKRAEPRH 167
Score = 53.5 bits (127), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 40/62 (64%)
Query: 68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
K+F+G L+W T ++L + F +YG V +++ D +GRSRG+GF+ + + ++ +++
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 128 LN 129
+
Sbjct: 65 QH 66
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 63.9 bits (154), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 30/72 (41%), Positives = 46/72 (63%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
L+VG+L +++T + L F+ +G + ++ D ++GRS+GYGF+ +S ALE L
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 129 NGVELEGRAMRV 140
NG EL GR MRV
Sbjct: 68 NGFELAGRPMRV 79
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 29/48 (60%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRV 49
+ + ++ D +TGRS+G+ F+T S E +E L+G E GR +RV
Sbjct: 32 IDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRV 79
>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 = 63.2 bits (152), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 42/143 (29%), Positives = 75/143 (52%), Gaps = 5/143 (3%)
Query: 5 LTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAE 64
+ V D T RS G+A+V D ++ ++ G+ +R+ +S + P L
Sbjct: 40 IRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR-DPSLRKSGV 98
Query: 65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
+ +F+ NL S+ ++L F +GN++ +V+ D E+G S+GYGFV + T+ E A
Sbjct: 99 GN--IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENG-SKGYGFVHFETQEAAERA 154
Query: 125 LESLNGVELEGRAMRVSLAQGRR 147
+E +NG+ L R + V + R+
Sbjct: 155 IEKMNGMLLNDRKVFVGRFKSRK 177
Score = 50.4 bits (119), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 28/88 (31%), Positives = 46/88 (52%), Gaps = 2/88 (2%)
Query: 57 PKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYS 116
P P Y L+VG+L VT L + F G ++ RV D + RS GY +V +
Sbjct: 3 PSAPSYPMA--SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQ 60
Query: 117 TKAEMETALESLNGVELEGRAMRVSLAQ 144
A+ E AL+++N ++G+ +R+ +Q
Sbjct: 61 QPADAERALDTMNFDVIKGKPVRIMWSQ 88
>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 = 63.2 bits (152), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 42/143 (29%), Positives = 75/143 (52%), Gaps = 5/143 (3%)
Query: 5 LTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAE 64
+ V D T RS G+A+V D ++ ++ G+ +R+ +S + P L
Sbjct: 45 IRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR-DPSLRKSGV 103
Query: 65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
+ +F+ NL S+ ++L F +GN++ +V+ D E+G S+GYGFV + T+ E A
Sbjct: 104 GN--IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENG-SKGYGFVHFETQEAAERA 159
Query: 125 LESLNGVELEGRAMRVSLAQGRR 147
+E +NG+ L R + V + R+
Sbjct: 160 IEKMNGMLLNDRKVFVGRFKSRK 182
Score = 50.4 bits (119), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 28/88 (31%), Positives = 46/88 (52%), Gaps = 2/88 (2%)
Query: 57 PKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYS 116
P P Y L+VG+L VT L + F G ++ RV D + RS GY +V +
Sbjct: 8 PSAPSYPMA--SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQ 65
Query: 117 TKAEMETALESLNGVELEGRAMRVSLAQ 144
A+ E AL+++N ++G+ +R+ +Q
Sbjct: 66 QPADAERALDTMNFDVIKGKPVRIMWSQ 93
>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 = 63.2 bits (152), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 42/143 (29%), Positives = 69/143 (48%), Gaps = 12/143 (8%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILR----VNFSDKPKP 57
L+ V+ D T RSRGF FVT +TVE+ +A + N + GR++ V+ D +P
Sbjct: 33 LTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHKVDGRVVEPKRAVSREDSQRP 91
Query: 58 KLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYST 117
L + K+FVG + L F++YG + ++ D SG+ RG+ FV +
Sbjct: 92 GAHLTVK---KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 148
Query: 118 KAEMETAL----ESLNGVELEGR 136
++ + ++NG E R
Sbjct: 149 HDSVDKIVIQKYHTVNGHNCEVR 171
Score = 56.6 bits (135), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 29/79 (36%), Positives = 47/79 (59%), Gaps = 1/79 (1%)
Query: 68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
KLF+G LS+ T ESL F+++G + V+ D + RSRG+GFV Y+T E++ A+ +
Sbjct: 8 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67
Query: 128 LNGVELEGRAMRVSLAQGR 146
+++GR + A R
Sbjct: 68 RPH-KVDGRVVEPKRAVSR 85
>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 = 62.8 bits (151), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 42/143 (29%), Positives = 69/143 (48%), Gaps = 12/143 (8%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILR----VNFSDKPKP 57
L+ V+ D T RSRGF FVT +TVE+ +A + N + GR++ V+ D +P
Sbjct: 39 LTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHKVDGRVVEPKRAVSREDSQRP 97
Query: 58 KLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYST 117
L + K+FVG + L F++YG + ++ D SG+ RG+ FV +
Sbjct: 98 GAHLTVK---KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 154
Query: 118 KAEMETAL----ESLNGVELEGR 136
++ + ++NG E R
Sbjct: 155 HDSVDKIVIQKYHTVNGHNCEVR 177
Score = 57.4 bits (137), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 32/91 (35%), Positives = 51/91 (56%), Gaps = 1/91 (1%)
Query: 56 KPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCY 115
K + P E KLF+G LS+ T ESL F+++G + V+ D + RSRG+GFV Y
Sbjct: 2 KSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 61
Query: 116 STKAEMETALESLNGVELEGRAMRVSLAQGR 146
+T E++ A+ + +++GR + A R
Sbjct: 62 ATVEEVDAAMNARPH-KVDGRVVEPKRAVSR 91
>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 = 62.8 bits (151), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 42/143 (29%), Positives = 69/143 (48%), Gaps = 12/143 (8%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILR----VNFSDKPKP 57
L+ V+ D T RSRGF FVT +TVE+ +A + N + GR++ V+ D +P
Sbjct: 40 LTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHKVDGRVVEPKRAVSREDSQRP 98
Query: 58 KLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYST 117
L + K+FVG + L F++YG + ++ D SG+ RG+ FV +
Sbjct: 99 GAHLTVK---KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 155
Query: 118 KAEMETAL----ESLNGVELEGR 136
++ + ++NG E R
Sbjct: 156 HDSVDKIVIQKYHTVNGHNCEVR 178
Score = 57.4 bits (137), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 32/91 (35%), Positives = 51/91 (56%), Gaps = 1/91 (1%)
Query: 56 KPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCY 115
K + P E KLF+G LS+ T ESL F+++G + V+ D + RSRG+GFV Y
Sbjct: 3 KSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 62
Query: 116 STKAEMETALESLNGVELEGRAMRVSLAQGR 146
+T E++ A+ + +++GR + A R
Sbjct: 63 ATVEEVDAAMNA-RPHKVDGRVVEPKRAVSR 92
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 62.8 bits (151), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 42/143 (29%), Positives = 69/143 (48%), Gaps = 12/143 (8%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILR----VNFSDKPKP 57
L+ V+ D T RSRGF FVT +TVE+ +A + N + GR++ V+ D +P
Sbjct: 38 LTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHKVDGRVVEPKRAVSREDSQRP 96
Query: 58 KLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYST 117
L + K+FVG + L F++YG + ++ D SG+ RG+ FV +
Sbjct: 97 GAHLTVK---KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 153
Query: 118 KAEMETAL----ESLNGVELEGR 136
++ + ++NG E R
Sbjct: 154 HDSVDKIVIQKYHTVNGHNCEVR 176
Score = 57.8 bits (138), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 32/91 (35%), Positives = 51/91 (56%), Gaps = 1/91 (1%)
Query: 56 KPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCY 115
K + P E KLF+G LS+ T ESL F+++G + V+ D + RSRG+GFV Y
Sbjct: 1 KSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 60
Query: 116 STKAEMETALESLNGVELEGRAMRVSLAQGR 146
+T E++ A+ + +++GR + A R
Sbjct: 61 ATVEEVDAAMNARPH-KVDGRVVEPKRAVSR 90
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 62.8 bits (151), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 42/143 (29%), Positives = 69/143 (48%), Gaps = 12/143 (8%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILR----VNFSDKPKP 57
L+ V+ D T RSRGF FVT +TVE+ +A + N + GR++ V+ D +P
Sbjct: 41 LTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHKVDGRVVEPKRAVSREDSQRP 99
Query: 58 KLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYST 117
L + K+FVG + L F++YG + ++ D SG+ RG+ FV +
Sbjct: 100 GAHLTVK---KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 156
Query: 118 KAEMETAL----ESLNGVELEGR 136
++ + ++NG E R
Sbjct: 157 HDSVDKIVIQKYHTVNGHNCEVR 179
Score = 57.4 bits (137), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 32/91 (35%), Positives = 51/91 (56%), Gaps = 1/91 (1%)
Query: 56 KPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCY 115
K + P E KLF+G LS+ T ESL F+++G + V+ D + RSRG+GFV Y
Sbjct: 4 KSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 63
Query: 116 STKAEMETALESLNGVELEGRAMRVSLAQGR 146
+T E++ A+ + +++GR + A R
Sbjct: 64 ATVEEVDAAMNARPH-KVDGRVVEPKRAVSR 93
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 62.8 bits (151), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 42/143 (29%), Positives = 69/143 (48%), Gaps = 12/143 (8%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILR----VNFSDKPKP 57
L+ V+ D T RSRGF FVT +TVE+ +A + N + GR++ V+ D +P
Sbjct: 40 LTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHKVDGRVVEPKRAVSREDSQRP 98
Query: 58 KLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYST 117
L + K+FVG + L F++YG + ++ D SG+ RG+ FV +
Sbjct: 99 GAHLTVK---KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 155
Query: 118 KAEMETAL----ESLNGVELEGR 136
++ + ++NG E R
Sbjct: 156 HDSVDKIVIQKYHTVNGHNCEVR 178
Score = 57.8 bits (138), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 32/91 (35%), Positives = 51/91 (56%), Gaps = 1/91 (1%)
Query: 56 KPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCY 115
K + P E KLF+G LS+ T ESL F+++G + V+ D + RSRG+GFV Y
Sbjct: 3 KSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 62
Query: 116 STKAEMETALESLNGVELEGRAMRVSLAQGR 146
+T E++ A+ + +++GR + A R
Sbjct: 63 ATVEEVDAAMNARPH-KVDGRVVEPKRAVSR 92
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 60.1 bits (144), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 29/76 (38%), Positives = 47/76 (61%), Gaps = 2/76 (2%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
L+V NL + E L +AF +G + A+V+ +G GRS+G+GFVC+S+ E A+ +
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG--GRSKGFGFVCFSSPEEATKAVTEM 75
Query: 129 NGVELEGRAMRVSLAQ 144
NG + + + V+LAQ
Sbjct: 76 NGRIVATKPLYVALAQ 91
Score = 30.4 bits (67), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 18/29 (62%)
Query: 12 ETGRSRGFAFVTMSTVEDCNAVIENLDGR 40
E GRS+GF FV S+ E+ + ++GR
Sbjct: 50 EGGRSKGFGFVCFSSPEEATKAVTEMNGR 78
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 58.9 bits (141), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 30/76 (39%), Positives = 48/76 (63%), Gaps = 1/76 (1%)
Query: 68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
K+FVG L + T SL + F+ +G++ A V+ D ++G+SRGYGFV + +A E A +
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 128 LNGVELEGRAMRVSLA 143
N + ++GR V+LA
Sbjct: 79 PNPI-IDGRKANVNLA 93
Score = 35.4 bits (80), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 36/67 (53%), Gaps = 19/67 (28%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMS-------TVEDCNAVIENLDGRE------YLG---R 45
+ + V+ DR+TG+SRG+ FVTM+ +D N +I DGR+ YLG R
Sbjct: 44 IEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPII---DGRKANVNLAYLGAKPR 100
Query: 46 ILRVNFS 52
L+ F+
Sbjct: 101 SLQTGFA 107
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 58.5 bits (140), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 50/80 (62%), Gaps = 1/80 (1%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
++VGNL +S T+E + + F ++G V +++YD E+ + +G+GFV ++ E A+ L
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSE-AIAKL 62
Query: 129 NGVELEGRAMRVSLAQGRRS 148
+ + GR +RV+ A ++S
Sbjct: 63 DNTDFMGRTIRVTEANPKKS 82
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 33/55 (60%), Gaps = 2/55 (3%)
Query: 5 LTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKL 59
+ ++YDRET + +GF FV M E + I LD +++GR +RV ++ PK L
Sbjct: 31 VKLIYDRETKKPKGFGFVEMQE-ESVSEAIAKLDNTDFMGRTIRVTEAN-PKKSL 83
>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 = 57.4 bits (137), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 45/78 (57%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
LFV +++ T L + F+ YG + ++Y SG+ RGY F+ Y + +M +A +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 129 NGVELEGRAMRVSLAQGR 146
+G +++GR + V + +GR
Sbjct: 165 DGKKIDGRRVLVDVERGR 182
Score = 34.7 bits (78), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 12/49 (24%), Positives = 30/49 (61%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVN 50
+ ++ ++Y + +G+ RG+AF+ D ++ ++ DG++ GR + V+
Sbjct: 129 IKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD 177
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 56.6 bits (135), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 29/79 (36%), Positives = 44/79 (55%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
L V LS T L + F +YG + ++YD +S RSRG+ FV + + + A E
Sbjct: 15 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 74
Query: 129 NGVELEGRAMRVSLAQGRR 147
NG+EL+GR +RV + +R
Sbjct: 75 NGMELDGRRIRVDFSITKR 93
Score = 48.5 bits (114), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 36/57 (63%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
++ ++++YD+++ RSRGFAFV V+D E +G E GR +RV+FS +P
Sbjct: 39 IADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRPH 95
>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 = 56.6 bits (135), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 30/81 (37%), Positives = 47/81 (58%), Gaps = 2/81 (2%)
Query: 66 DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETAL 125
D L+V NL ++T + L F +YG++V +L D +GR RG FV Y+ + E + A+
Sbjct: 13 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 72
Query: 126 ESLNGVELEG--RAMRVSLAQ 144
+LN V EG + + V LA+
Sbjct: 73 SALNNVIPEGGSQPLSVRLAE 93
Score = 27.7 bits (60), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 18/33 (54%)
Query: 6 TVLYDRETGRSRGFAFVTMSTVEDCNAVIENLD 38
+L D+ TGR RG AFV + E+ I L+
Sbjct: 44 NILRDKLTGRPRGVAFVRYNKREEAQEAISALN 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 = 56.2 bits (134), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 29/79 (36%), Positives = 44/79 (55%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
L V LS T L + F +YG + ++YD +S RSRG+ FV + + + A E
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 129 NGVELEGRAMRVSLAQGRR 147
NG+EL+GR +RV + +R
Sbjct: 78 NGMELDGRRIRVDFSITKR 96
Score = 48.9 bits (115), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 36/57 (63%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
++ ++++YD+++ RSRGFAFV V+D E +G E GR +RV+FS +P
Sbjct: 42 IADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRPH 98
>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 = 55.8 bits (133), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 34/148 (22%), Positives = 71/148 (47%), Gaps = 6/148 (4%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD---KPKPK 58
+ + + +D T + +GFAFV E +E ++ GR ++V + +P
Sbjct: 55 IKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPI 114
Query: 59 LPLYAETD---FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCY 115
+ AE +++V ++ ++ + + F+ +G + A + D +G+ +GYGF+ Y
Sbjct: 115 IDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEY 174
Query: 116 STKAEMETALESLNGVELEGRAMRVSLA 143
+ A+ S+N +L G+ +RV A
Sbjct: 175 EKAQSSQDAVSSMNLFDLGGQYLRVGKA 202
Score = 45.8 bits (107), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 42/73 (57%)
Query: 68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
+++VG++ + + +++ QAF +G + + +D + + +G+ FV Y + ALE
Sbjct: 30 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 89
Query: 128 LNGVELEGRAMRV 140
+N V L GR ++V
Sbjct: 90 MNSVMLGGRNIKV 102
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 55.8 bits (133), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 30/75 (40%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
KL V NL + V+ + + F E+G + A V YD SGRS G V + KA+ A++
Sbjct: 30 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQ 88
Query: 128 LNGVELEGRAMRVSL 142
NGV L+GR M + L
Sbjct: 89 YNGVPLDGRPMNIQL 103
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 55.8 bits (133), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 46/77 (59%)
Query: 66 DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETAL 125
D L+V L +++ + + Q F +YG ++ +R+L D +G SRG GF+ + + E E A+
Sbjct: 1 DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
Query: 126 ESLNGVELEGRAMRVSL 142
+ LNG + G A +++
Sbjct: 61 KGLNGQKPLGAAEPITV 77
Score = 31.2 bits (69), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 2/51 (3%)
Query: 7 VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLG--RILRVNFSDKP 55
+L D+ TG SRG F+ + I+ L+G++ LG + V F++ P
Sbjct: 33 ILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQKPLGAAEPITVKFANNP 83
>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 = 55.5 bits (132), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 31/79 (39%), Positives = 50/79 (63%)
Query: 65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
+ F +FVG+LS +TT ++ AF +G + ARV+ D +G+S+GYGFV + K + E A
Sbjct: 5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENA 64
Query: 125 LESLNGVELEGRAMRVSLA 143
++ + G L GR +R + A
Sbjct: 65 IQQMGGQWLGGRQIRTNWA 83
Score = 37.0 bits (84), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP 57
+S V+ D TG+S+G+ FV+ D I+ + G+ GR +R N++ + KP
Sbjct: 33 ISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATR-KP 87
>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 = 55.5 bits (132), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 28/76 (36%), Positives = 44/76 (57%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
L V L ++T + L F G V A+++ D +G S GYGFV Y T + E A+ +L
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 129 NGVELEGRAMRVSLAQ 144
NG+ L+ + ++VS A+
Sbjct: 67 NGLRLQSKTIKVSYAR 82
>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 = 55.1 bits (131), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 27/87 (31%), Positives = 50/87 (57%)
Query: 58 KLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYST 117
+ P E L V NL++ + ++L + F++YG V + D + SRG+ FV +
Sbjct: 39 RPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHD 98
Query: 118 KAEMETALESLNGVELEGRAMRVSLAQ 144
K + E A+++++G L+GR +RV +A+
Sbjct: 99 KRDAEDAMDAMDGAVLDGRELRVQMAR 125
Score = 34.7 bits (78), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 24/48 (50%)
Query: 10 DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP 57
DR T SRGFAFV D ++ +DG GR LRV + +P
Sbjct: 82 DRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRP 129
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 55.1 bits (131), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 29/79 (36%), Positives = 44/79 (55%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
L V LS T L + F +YG + ++YD +S RSRG+ FV + + + A E
Sbjct: 49 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 108
Query: 129 NGVELEGRAMRVSLAQGRR 147
NG+EL+GR +RV + +R
Sbjct: 109 NGMELDGRRIRVDFSITKR 127
Score = 49.3 bits (116), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 36/57 (63%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
++ ++++YD+++ RSRGFAFV V+D E +G E GR +RV+FS +P
Sbjct: 73 IADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRPH 129
>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 = 55.1 bits (131), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 45/78 (57%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
LFV +++ T L + F+ YG + ++Y SG+ RGY F+ Y + +M +A +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 129 NGVELEGRAMRVSLAQGR 146
+G +++GR + V + +GR
Sbjct: 165 DGKKIDGRRVLVDVERGR 182
Score = 35.0 bits (79), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 12/49 (24%), Positives = 30/49 (61%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVN 50
+ ++ ++Y + +G+ RG+AF+ D ++ ++ DG++ GR + V+
Sbjct: 129 IKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD 177
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 55.1 bits (131), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 25/58 (43%), Positives = 39/58 (67%)
Query: 68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETAL 125
KLF+G LS+ T ESL ++++G + V+ D S RSRG+GFV +S+ AE++ A+
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 86
Score = 33.1 bits (74), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 26/43 (60%), Gaps = 4/43 (9%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVI----ENLDGR 40
L+ V+ D + RSRGF FVT S++ + +A + ++DGR
Sbjct: 54 LTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGR 96
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 55.1 bits (131), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 47/76 (61%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
L V NL++ + ++L + F++YG V + D + SRG+ FV + K + E A++++
Sbjct: 73 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132
Query: 129 NGVELEGRAMRVSLAQ 144
+G L+GR +RV +A+
Sbjct: 133 DGAVLDGRELRVQMAR 148
Score = 35.0 bits (79), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 24/48 (50%)
Query: 10 DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP 57
DR T SRGFAFV D ++ +DG GR LRV + +P
Sbjct: 105 DRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRP 152
>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 = 54.7 bits (130), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
K FVG LSW + + L F ++G VV + D +GRSRG+GF+ + A +E L+
Sbjct: 13 KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQ 72
Query: 128 LNGVELEGRAM 138
L+GR +
Sbjct: 73 KEH-RLDGRVI 82
Score = 29.3 bits (64), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 26/44 (59%), Gaps = 5/44 (11%)
Query: 6 TVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYL--GRIL 47
T+ D TGRSRGF F+ +D +V + LD +E+ GR++
Sbjct: 42 TIKXDPNTGRSRGFGFILF---KDAASVEKVLDQKEHRLDGRVI 82
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 54.7 bits (130), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 29/73 (39%), Positives = 42/73 (57%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
L V LS T L + F +YG + ++YD +S RSRG+ FV + + + A E
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 129 NGVELEGRAMRVS 141
NG+EL+GR +RVS
Sbjct: 78 NGMELDGRRIRVS 90
Score = 42.7 bits (99), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 32/49 (65%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVN 50
++ ++++YD+++ RSRGFAFV V+D E +G E GR +RV+
Sbjct: 42 IADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVS 90
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 54.7 bits (130), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 28/79 (35%), Positives = 48/79 (60%), Gaps = 2/79 (2%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
+F+ NL S+ ++L F +GN++ +V+ D E+G S+GYGFV + T+ E A+E +
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENG-SKGYGFVHFETQEAAERAIEKM 71
Query: 129 NGVELEGRAMRVSLAQGRR 147
NG+ L R + V + R+
Sbjct: 72 NGMLLNDRKVFVGRFKSRK 90
>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 = 54.3 bits (129), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 28/76 (36%), Positives = 43/76 (56%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
L V L + T + L F G V A+++ D +G S GYGFV Y T + E A+ +L
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 129 NGVELEGRAMRVSLAQ 144
NG+ L+ + ++VS A+
Sbjct: 82 NGLRLQSKTIKVSYAR 97
>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 = 54.3 bits (129), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 33/148 (22%), Positives = 70/148 (47%), Gaps = 6/148 (4%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD---KPKPK 58
+ + + +D T + +GFAFV E +E ++ GR ++V + +P
Sbjct: 40 IKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPI 99
Query: 59 LPLYAETD---FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCY 115
+ AE +++V ++ ++ + + F+ +G + + D +G+ +GYGF+ Y
Sbjct: 100 IDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEY 159
Query: 116 STKAEMETALESLNGVELEGRAMRVSLA 143
+ A+ S+N +L G+ +RV A
Sbjct: 160 EKAQSSQDAVSSMNLFDLGGQYLRVGKA 187
Score = 46.6 bits (109), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 42/73 (57%)
Query: 68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
+++VG++ + + +++ QAF +G + + +D + + +G+ FV Y + ALE
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 128 LNGVELEGRAMRV 140
+N V L GR ++V
Sbjct: 75 MNSVMLGGRNIKV 87
>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 = 54.3 bits (129), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 42/74 (56%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
LF+ +L + L Q F +GNVV A+V D ++ S+ +GFV Y + A++S+
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 129 NGVELEGRAMRVSL 142
NG ++ + ++V L
Sbjct: 88 NGFQIGMKRLKVQL 101
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 53.9 bits (128), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 43/75 (57%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
++V NL +S+T L + F +YG VV ++ D ++ +S+G F+ + K + ++
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 129 NGVELEGRAMRVSLA 143
N +L GR ++ S+A
Sbjct: 79 NNKQLFGRVIKASIA 93
Score = 32.0 bits (71), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 13/52 (25%), Positives = 31/52 (59%), Gaps = 6/52 (11%)
Query: 4 KLTVLYDRETGRSRGFAFVTM---STVEDCNAVIENLDGREYLGRILRVNFS 52
K+T++ D++T +S+G AF+ + ++C I N ++ GR+++ + +
Sbjct: 45 KVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINN---KQLFGRVIKASIA 93
>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
At Ph 6.0
pdb|4F26|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
A Ph 9.0
Length = 115
Score = 53.9 bits (128), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 28/79 (35%), Positives = 48/79 (60%), Gaps = 2/79 (2%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
+F+ NL S+ ++L F +GN++ +V+ D E+G S+GYGFV + T+ E A+E +
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENG-SKGYGFVHFETQEAAERAIEKM 65
Query: 129 NGVELEGRAMRVSLAQGRR 147
NG+ L R + V + R+
Sbjct: 66 NGMLLNDRKVFVGRFKSRK 84
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 53.5 bits (127), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 29/71 (40%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
KLFVG L WS T E+L F +YG VV ++ D + +SRG+GFV + + T L S
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 128 LNGVELEGRAM 138
L+GR +
Sbjct: 78 RPHT-LDGRNI 87
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 53.5 bits (127), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 34/132 (25%), Positives = 68/132 (51%), Gaps = 9/132 (6%)
Query: 7 VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETD 66
+ D TG +R F +V + ED +E L G + G +++ +KPK +
Sbjct: 44 AVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKL---EKPKGRDSKKVRAA 99
Query: 67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
L NLS+++T + L + F+ + + R++ + G+S+G ++ + ++A+ E LE
Sbjct: 100 RTLLAKNLSFNITEDELKEVFE---DALEIRLV--SQDGKSKGIAYIEFKSEADAEKNLE 154
Query: 127 SLNGVELEGRAM 138
G E++GR++
Sbjct: 155 EKQGAEIDGRSV 166
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 46/84 (54%), Gaps = 2/84 (2%)
Query: 65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
T F LF+GNL+ + + L A E V+ D +G +R +G+V + + ++E A
Sbjct: 12 TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDLEKA 70
Query: 125 LESLNGVELEGRAMRVSLAQGRRS 148
LE L G+++ G +++ +GR S
Sbjct: 71 LE-LTGLKVFGNEIKLEKPKGRDS 93
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 53.5 bits (127), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 29/83 (34%), Positives = 42/83 (50%), Gaps = 1/83 (1%)
Query: 59 LPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTK 118
P E D +FVGNL V E L + F + G + + D E G+ + +GFVC+
Sbjct: 9 FPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHP 67
Query: 119 AEMETALESLNGVELEGRAMRVS 141
+ A+ LNG+ L GR + VS
Sbjct: 68 ESVSYAIALLNGIRLYGRPINVS 90
Score = 31.2 bits (69), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVN 50
L+K+T+ DRE G+ + F FV E + I L+G GR + V+
Sbjct: 43 LTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVS 90
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 53.5 bits (127), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 30/79 (37%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMET 123
ET KL V NL + V+ + + F E+G + A V YD SGRS G V + +A+
Sbjct: 86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADALK 144
Query: 124 ALESLNGVELEGRAMRVSL 142
A++ GV L+GR M + L
Sbjct: 145 AMKQYKGVPLDGRPMDIQL 163
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 52.8 bits (125), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 46/79 (58%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
L+VG L+ V + L AF +G++ ++ D E+ + RG+ FV + + A++++
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 129 NGVELEGRAMRVSLAQGRR 147
N EL GR +RV+LA+ R
Sbjct: 75 NESELFGRTIRVNLAKPMR 93
Score = 47.4 bits (111), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 22/54 (40%), Positives = 32/54 (59%), Gaps = 1/54 (1%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP 55
++ + + D ET + RGFAFV ED A I+N++ E GR +RVN + KP
Sbjct: 39 ITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA-KP 91
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 52.8 bits (125), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 39/112 (34%), Positives = 51/112 (45%), Gaps = 12/112 (10%)
Query: 15 RSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNL 74
R RGF F+ + + LDG R LR+ F A L V NL
Sbjct: 56 RDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRF-----------ATHGAALTVKNL 104
Query: 75 SWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
S V+ E L QAF ++G V A V+ D + GR+ G GFV ++ K ALE
Sbjct: 105 SPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALE 155
Score = 45.8 bits (107), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 6/76 (7%)
Query: 68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
+LFVGNL +T E + F+ YG + R RG+GF+ ++ E A
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFI------NRDRGFGFIRLESRTLAEIAKAE 77
Query: 128 LNGVELEGRAMRVSLA 143
L+G L+ R +R+ A
Sbjct: 78 LDGTILKSRPLRIRFA 93
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 52.8 bits (125), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 45/76 (59%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
L+VG L+ V + L AF +G++ ++ D E+ + RG+ FV + + A++++
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 129 NGVELEGRAMRVSLAQ 144
N EL GR +RV+LA+
Sbjct: 68 NESELFGRTIRVNLAK 83
Score = 46.2 bits (108), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 30/51 (58%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
++ + + D ET + RGFAFV ED A I+N++ E GR +RVN +
Sbjct: 32 ITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 82
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 52.8 bits (125), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 34/132 (25%), Positives = 62/132 (46%), Gaps = 9/132 (6%)
Query: 7 VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETD 66
+ D G +R F +V + ED +E L G + G +++ +KPK K
Sbjct: 38 AVVDVRIGMTRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKL---EKPKGKDSKKERDA 93
Query: 67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
L NL + VT + L + F++ A + + G+S+G ++ + T+A+ E E
Sbjct: 94 RTLLAKNLPYKVTQDELKEVFED-----AAEIRLVSKDGKSKGIAYIEFKTEADAEKTFE 148
Query: 127 SLNGVELEGRAM 138
G E++GR++
Sbjct: 149 EKQGTEIDGRSI 160
Score = 36.6 bits (83), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 47/87 (54%), Gaps = 8/87 (9%)
Query: 65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGAR---VLYDGESGRSRGYGFVCYSTKAEM 121
T F LFVGNL+++ + L + V A+ + D G +R +G+V + + ++
Sbjct: 6 TAFNLFVGNLNFNKSAPELKTGISD----VFAKNDLAVVDVRIGMTRKFGYVDFESAEDL 61
Query: 122 ETALESLNGVELEGRAMRVSLAQGRRS 148
E ALE L G+++ G +++ +G+ S
Sbjct: 62 EKALE-LTGLKVFGNEIKLEKPKGKDS 87
>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 = 52.8 bits (125), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 45/76 (59%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
L+VG L+ V + L AF +G++ ++ D E+ + RG+ FV + + A++++
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 129 NGVELEGRAMRVSLAQ 144
N EL GR +RV+LA+
Sbjct: 70 NESELFGRTIRVNLAK 85
Score = 46.6 bits (109), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 30/51 (58%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
++ + + D ET + RGFAFV ED A I+N++ E GR +RVN +
Sbjct: 34 ITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 84
>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 = 52.4 bits (124), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 44/75 (58%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
L+VG L+ V + L AF +G++ ++ D E+ + RG+ FV + + A++++
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 129 NGVELEGRAMRVSLA 143
N EL GR +RV+LA
Sbjct: 65 NESELFGRTIRVNLA 79
Score = 46.6 bits (109), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 30/51 (58%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
++ + + D ET + RGFAFV ED A I+N++ E GR +RVN +
Sbjct: 29 ITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 79
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 52.4 bits (124), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 48/80 (60%), Gaps = 1/80 (1%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
L V NL++ + +SL + F++YG V + + + RG+ FV + + + + A ++
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75
Query: 129 NGVELEGRAMRVSLAQ-GRR 147
+G EL+GR +RV +A+ GRR
Sbjct: 76 DGAELDGRELRVQVARYGRR 95
Score = 29.3 bits (64), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 18/41 (43%)
Query: 12 ETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
T RGFAFV D +DG E GR LRV +
Sbjct: 50 HTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVA 90
>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 = 52.0 bits (123), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 33/141 (23%), Positives = 65/141 (46%), Gaps = 6/141 (4%)
Query: 9 YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD---KPKPKLPLYAET 65
+D T + +GFAFV E +E + GR ++V + +P + AE
Sbjct: 46 WDSVTXKHKGFAFVEYEVPEAAQLALEQXNSVXLGGRNIKVGRPSNIGQAQPIIDQLAEE 105
Query: 66 D---FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
+++V ++ ++ + + F+ +G + + D +G+ +GYGF+ Y +
Sbjct: 106 ARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQ 165
Query: 123 TALESLNGVELEGRAMRVSLA 143
A+ S N +L G+ +RV A
Sbjct: 166 DAVSSXNLFDLGGQYLRVGKA 186
Score = 45.4 bits (106), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 40/73 (54%)
Query: 68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
+++VG++ + + +++ QAF +G + +D + + +G+ FV Y + ALE
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 128 LNGVELEGRAMRV 140
N V L GR ++V
Sbjct: 74 XNSVXLGGRNIKV 86
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 52.0 bits (123), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 45/76 (59%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
L V L ++T + F G++ +++ D +G+S GYGFV YS + + A+ +L
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 129 NGVELEGRAMRVSLAQ 144
NG++L+ + ++VS A+
Sbjct: 67 NGLKLQTKTIKVSYAR 82
Score = 30.8 bits (68), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 25/43 (58%)
Query: 10 DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
D+ TG+S G+ FV S D + I L+G + + ++V+++
Sbjct: 39 DKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYA 81
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 52.0 bits (123), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 30/79 (37%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMET 123
ET KL V NL + V+ + + F E+G + A V YD SGRS G V + +A+
Sbjct: 33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADALK 91
Query: 124 ALESLNGVELEGRAMRVSL 142
A++ GV L+GR M + L
Sbjct: 92 AMKQYKGVPLDGRPMDIQL 110
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 52.0 bits (123), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 30/79 (37%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMET 123
ET KL V NL + V+ + + F E+G + A V YD SGRS G V + +A+
Sbjct: 33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADALK 91
Query: 124 ALESLNGVELEGRAMRVSL 142
A++ GV L+GR M + L
Sbjct: 92 AMKQYKGVPLDGRPMDIQL 110
>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 = 51.6 bits (122), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 29/75 (38%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
KL V NL + V+ + + F E+G + A V YD SGRS G V + KA+ A +
Sbjct: 31 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAXKQ 89
Query: 128 LNGVELEGRAMRVSL 142
NGV L+GR + L
Sbjct: 90 YNGVPLDGRPXNIQL 104
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 51.6 bits (122), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 28/81 (34%), Positives = 47/81 (58%), Gaps = 1/81 (1%)
Query: 68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
K+F+G LSW T E L + F ++G V V+ D + RSRG+GFV + +A ++ L +
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-A 85
Query: 128 LNGVELEGRAMRVSLAQGRRS 148
+ EL+ + + +A RR+
Sbjct: 86 QSRHELDSKTIDPKVAFPRRA 106
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 44/75 (58%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
L+VG L+ V + L AF +G++ ++ D E+ + RG+ FV + + A++++
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 129 NGVELEGRAMRVSLA 143
N EL GR +RV+LA
Sbjct: 126 NESELFGRTIRVNLA 140
Score = 45.8 bits (107), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 30/51 (58%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
++ + + D ET + RGFAFV ED A I+N++ E GR +RVN +
Sbjct: 90 ITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 41/74 (55%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
LF+ +L T L F +GNV+ A+V D ++ S+ +GFV + + A++++
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 129 NGVELEGRAMRVSL 142
NG ++ + ++V L
Sbjct: 103 NGFQVGTKRLKVQL 116
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/89 (30%), Positives = 47/89 (52%), Gaps = 2/89 (2%)
Query: 57 PKLPLYAETDF--KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVC 114
P + E D L V + +V L Q F+ YG + +++ D E+ +SRGYGFV
Sbjct: 31 PPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVK 90
Query: 115 YSTKAEMETALESLNGVELEGRAMRVSLA 143
+ + + + A+ LNG + + ++V+LA
Sbjct: 91 FQSGSSAQQAIAGLNGFNILNKRLKVALA 119
Score = 32.0 bits (71), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 26/51 (50%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
+ + ++ DRET +SRG+ FV + I L+G L + L+V +
Sbjct: 69 IESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA 119
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 29/99 (29%), Positives = 52/99 (52%), Gaps = 11/99 (11%)
Query: 48 RVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRS 107
+N +K +PK +L V N+ + L Q F ++G ++ ++++ E G S
Sbjct: 20 HMNTENKSQPK---------RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERG-S 68
Query: 108 RGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR 146
+G+GFV + A+ + A E L+G +EGR + V+ A R
Sbjct: 69 KGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107
Score = 26.9 bits (58), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 17/35 (48%)
Query: 16 SRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVN 50
S+GF FVT D + E L G GR + VN
Sbjct: 68 SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN 102
>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 = 50.8 bits (120), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 25/66 (37%), Positives = 35/66 (53%), Gaps = 4/66 (6%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCY----STKAEMETA 124
+F+G LSW T + L F ++G VV + D +GRSRG+GFV + S M+
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 125 LESLNG 130
LNG
Sbjct: 62 EHKLNG 67
Score = 27.7 bits (60), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 17/31 (54%)
Query: 6 TVLYDRETGRSRGFAFVTMSTVEDCNAVIEN 36
T+ D TGRSRGF FV E + V++
Sbjct: 30 TLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 50.8 bits (120), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 41/139 (29%), Positives = 70/139 (50%), Gaps = 13/139 (9%)
Query: 4 KLTVLYDRETG--RSRGFAFVTMST----VEDCNAVIENLDGREYLGRILRVNFSDKPKP 57
++ VL DR +S+G FVT T +E NA + N+ + +++ +D K
Sbjct: 44 EINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA-LHNMKVLPGMHHPIQMKPADSEKN 102
Query: 58 KLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYST 117
A D KLF+G +S T + F +G + R+L G G SRG FV ++T
Sbjct: 103 N----AVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILR-GPDGLSRGCAFVTFTT 157
Query: 118 KAEMETALESLNGVE-LEG 135
+A +TA+++++ + +EG
Sbjct: 158 RAMAQTAIKAMHQAQTMEG 176
Score = 34.3 bits (77), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 36/68 (52%), Gaps = 5/68 (7%)
Query: 67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYD--GESGRSRGYGFVCYSTKAEMETA 124
K+FVG + + + + L + F++YG V VL D +S+G FV + T+ + A
Sbjct: 16 IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTR---KAA 72
Query: 125 LESLNGVE 132
LE+ N +
Sbjct: 73 LEAQNALH 80
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 50.8 bits (120), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 41/139 (29%), Positives = 70/139 (50%), Gaps = 13/139 (9%)
Query: 4 KLTVLYDRETG--RSRGFAFVTMST----VEDCNAVIENLDGREYLGRILRVNFSDKPKP 57
++ VL DR +S+G FVT T +E NA + N+ + +++ +D K
Sbjct: 32 EINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA-LHNMKVLPGMHHPIQMKPADSEKN 90
Query: 58 KLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYST 117
A D KLF+G +S T + F +G + R+L G G SRG FV ++T
Sbjct: 91 N----AVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILR-GPDGLSRGCAFVTFTT 145
Query: 118 KAEMETALESLNGVE-LEG 135
+A +TA+++++ + +EG
Sbjct: 146 RAMAQTAIKAMHQAQTMEG 164
Score = 33.9 bits (76), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 36/68 (52%), Gaps = 5/68 (7%)
Query: 67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYD--GESGRSRGYGFVCYSTKAEMETA 124
K+FVG + + + + L + F++YG V VL D +S+G FV + T+ + A
Sbjct: 4 IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTR---KAA 60
Query: 125 LESLNGVE 132
LE+ N +
Sbjct: 61 LEAQNALH 68
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 50.4 bits (119), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 46/82 (56%), Gaps = 2/82 (2%)
Query: 65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
T +L V N+ + L Q F ++G ++ ++++ E G S+G+GFV + A+ + A
Sbjct: 14 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERG-SKGFGFVTFENSADADRA 71
Query: 125 LESLNGVELEGRAMRVSLAQGR 146
E L+G +EGR + V+ A R
Sbjct: 72 REKLHGTVVEGRKIEVNNATAR 93
Score = 27.3 bits (59), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 17/35 (48%)
Query: 16 SRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVN 50
S+GF FVT D + E L G GR + VN
Sbjct: 54 SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN 88
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 50.1 bits (118), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 35/58 (60%)
Query: 68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETAL 125
K+F+G LSW T E L + F ++G V V+ D + RSRG+GFV + +A ++ L
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 59
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 50.1 bits (118), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 28/79 (35%), Positives = 49/79 (62%), Gaps = 5/79 (6%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
L + NLS+S T E+L + F++ + + ++G+S+GY F+ +++ + + AL S
Sbjct: 18 LVLSNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGYAFIEFASFEDAKEALNSC 73
Query: 129 NGVELEGRAMRVSLAQGRR 147
N E+EGRA+R+ L QG R
Sbjct: 74 NKREIEGRAIRLEL-QGPR 91
Score = 34.3 bits (77), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 12/38 (31%), Positives = 24/38 (63%)
Query: 12 ETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRV 49
+ G+S+G+AF+ ++ ED + + + RE GR +R+
Sbjct: 48 QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRL 85
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 49.7 bits (117), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 45/82 (54%), Gaps = 1/82 (1%)
Query: 63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
A+ KLF+G L+ + L F ++G + ++ D + +SRG+ F+ + A+ +
Sbjct: 4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAK 62
Query: 123 TALESLNGVELEGRAMRVSLAQ 144
A + +NG L G+A++V A+
Sbjct: 63 NAAKDMNGKSLHGKAIKVEQAK 84
Score = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 33/54 (61%), Gaps = 1/54 (1%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP 55
+S++ ++ DR T +SRGFAF+T D ++++G+ G+ ++V + KP
Sbjct: 34 ISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKP 86
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 43/89 (48%), Gaps = 3/89 (3%)
Query: 53 DKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGF 112
D+P P+ + + LFV + T E + F EYG + + D +G +GY
Sbjct: 12 DEPGPQRSVEG---WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTL 68
Query: 113 VCYSTKAEMETALESLNGVELEGRAMRVS 141
V Y T E + A+E LNG +L G+ + V
Sbjct: 69 VEYETYKEAQAAMEGLNGQDLMGQPISVD 97
Score = 32.7 bits (73), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 26/42 (61%)
Query: 10 DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNF 51
DR TG +G+ V T ++ A +E L+G++ +G+ + V++
Sbjct: 57 DRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 98
>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 = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 43/89 (48%), Gaps = 3/89 (3%)
Query: 53 DKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGF 112
D+P P+ + + LFV + T E + F EYG + + D +G +GY
Sbjct: 13 DEPGPQRSVEG---WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTL 69
Query: 113 VCYSTKAEMETALESLNGVELEGRAMRVS 141
V Y T E + A+E LNG +L G+ + V
Sbjct: 70 VEYETYKEAQAAMEGLNGQDLMGQPISVD 98
Score = 33.1 bits (74), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 13/50 (26%), Positives = 29/50 (58%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNF 51
+ + + DR TG +G+ V T ++ A +E L+G++ +G+ + V++
Sbjct: 50 IKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 99
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 47/78 (60%), Gaps = 3/78 (3%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
LFV LS T E+L ++F V AR++ D E+G S+G+GFV ++++ + + A E++
Sbjct: 18 LFVKGLSEDTTEETLKESFD---GSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAM 74
Query: 129 NGVELEGRAMRVSLAQGR 146
E++G + + A+ +
Sbjct: 75 EDGEIDGNKVTLDWAKPK 92
Score = 39.7 bits (91), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 31/50 (62%), Gaps = 1/50 (2%)
Query: 7 VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK 56
++ DRETG S+GF FV ++ ED A E ++ E G + ++++ KPK
Sbjct: 44 IVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWA-KPK 92
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 47.8 bits (112), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 35/58 (60%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
+FVG LS + T E + F+++G V A +++D + R RG+GFV + ++ +E E
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59
Score = 26.9 bits (58), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 7 VLYDRETGRSRGFAFVTMST 26
+++D+ T R RGF FVT +
Sbjct: 31 LMFDKTTNRHRGFGFVTFES 50
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 47.4 bits (111), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 44/76 (57%), Gaps = 1/76 (1%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVV-GARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
+F+GNL + + L F +G ++ +++ D ++G S+GY F+ +++ + A+E+
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 128 LNGVELEGRAMRVSLA 143
+NG L R + VS A
Sbjct: 68 MNGQYLCNRPITVSYA 83
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 34/58 (58%)
Query: 1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
+L ++ D +TG S+G+AF+ ++ + +A IE ++G+ R + V+++ K K
Sbjct: 32 ILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSK 89
>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 = 47.0 bits (110), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 40/137 (29%), Positives = 62/137 (45%), Gaps = 16/137 (11%)
Query: 4 KLTVLYDRETG--RSRGFAFVTMST----VEDCNAVIEN--LDGREYLGRILRVNFSDKP 55
++ VL DR +S+G FVT T +E NA+ L G + KP
Sbjct: 32 EINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNXKVLPGXHH-------PIQXKP 84
Query: 56 KPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCY 115
A D KLF+G +S T + F +G + R+L G G SRG FV +
Sbjct: 85 ADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQIEECRILR-GPDGLSRGCAFVTF 143
Query: 116 STKAEMETALESLNGVE 132
+T+A +TA+++ + +
Sbjct: 144 TTRAXAQTAIKAXHQAQ 160
Score = 32.0 bits (71), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 5/68 (7%)
Query: 67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYD--GESGRSRGYGFVCYSTKAEMETA 124
K FVG + + + + L + F++YG V VL D +S+G FV + T+ + A
Sbjct: 4 IKXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTR---KAA 60
Query: 125 LESLNGVE 132
LE+ N +
Sbjct: 61 LEAQNALH 68
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 47.0 bits (110), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 43/77 (55%), Gaps = 8/77 (10%)
Query: 67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
+K+FVGN+S + T++ L F+ G V+ V+ D Y FV +A+ + A+
Sbjct: 10 WKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIA 61
Query: 127 SLNGVELEGRAMRVSLA 143
LNG E++G+ + V L+
Sbjct: 62 QLNGKEVKGKRINVELS 78
Score = 32.0 bits (71), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 22/42 (52%)
Query: 17 RGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
+ +AFV M D A I L+G+E G+ + V S K + K
Sbjct: 43 KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQKK 84
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 46.6 bits (109), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 31/132 (23%), Positives = 61/132 (46%), Gaps = 6/132 (4%)
Query: 12 ETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFV 71
+ + + FAF+ +V++ + DG + G+ L++ +P PL KLF+
Sbjct: 46 QINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR---RPHDYQPLPGAH--KLFI 99
Query: 72 GNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGV 131
G L + + + + +G + ++ D +G S+GY F Y + A+ LNG+
Sbjct: 100 GGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGM 159
Query: 132 ELEGRAMRVSLA 143
+L + + V A
Sbjct: 160 QLGDKKLLVQRA 171
>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 = 46.6 bits (109), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 36/73 (49%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
LFV + T E + F EYG + + D +G +GY V Y T E + A+E L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 129 NGVELEGRAMRVS 141
NG +L G+ + V
Sbjct: 70 NGQDLMGQPISVD 82
Score = 33.5 bits (75), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 26/42 (61%)
Query: 10 DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNF 51
DR TG +G+ V T ++ A +E L+G++ +G+ + V++
Sbjct: 42 DRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 83
>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 = 46.6 bits (109), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 31/132 (23%), Positives = 61/132 (46%), Gaps = 6/132 (4%)
Query: 12 ETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFV 71
+ + + FAF+ +V++ + DG + G+ L++ +P PL KLF+
Sbjct: 48 QINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR---RPHDYQPLPGAH--KLFI 101
Query: 72 GNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGV 131
G L + + + + +G + ++ D +G S+GY F Y + A+ LNG+
Sbjct: 102 GGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGM 161
Query: 132 ELEGRAMRVSLA 143
+L + + V A
Sbjct: 162 QLGDKKLLVQRA 173
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 46.2 bits (108), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 46/81 (56%), Gaps = 1/81 (1%)
Query: 68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
K+FVG + + L + F+++G V ++YD E R RG+GF+ + + ++ A+ +
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV-N 70
Query: 128 LNGVELEGRAMRVSLAQGRRS 148
++ ++ G+ + V A+ R S
Sbjct: 71 MHFHDIMGKKVEVKRAEPRDS 91
Score = 30.8 bits (68), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 12/49 (24%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRV 49
+++++ ++YD E R RGF F+T + + + N+ + +G+ + V
Sbjct: 36 VVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV-NMHFHDIMGKKVEV 83
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 46.2 bits (108), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 36/73 (49%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
LFV + T E + F EYG + + D +G +GY V Y T E + A+E L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 129 NGVELEGRAMRVS 141
NG +L G+ + V
Sbjct: 70 NGQDLMGQPISVD 82
Score = 33.1 bits (74), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 26/42 (61%)
Query: 10 DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNF 51
DR TG +G+ V T ++ A +E L+G++ +G+ + V++
Sbjct: 42 DRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 83
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 46.2 bits (108), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 36/73 (49%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
LFV + T E + F EYG + + D +G +GY V Y T E + A+E L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 129 NGVELEGRAMRVS 141
NG +L G+ + V
Sbjct: 72 NGQDLMGQPISVD 84
Score = 33.5 bits (75), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 26/42 (61%)
Query: 10 DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNF 51
DR TG +G+ V T ++ A +E L+G++ +G+ + V++
Sbjct: 44 DRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 85
>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 = 46.2 bits (108), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 36/73 (49%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
LFV + T E + F EYG + + D +G +GY V Y T E + A+E L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 129 NGVELEGRAMRVS 141
NG +L G+ + V
Sbjct: 70 NGQDLMGQPISVD 82
Score = 33.1 bits (74), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 26/42 (61%)
Query: 10 DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNF 51
DR TG +G+ V T ++ A +E L+G++ +G+ + V++
Sbjct: 42 DRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 83
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 45.8 bits (107), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 43/76 (56%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
L V L +T L F+ G + R++ D ++G S GY FV ++++ + + A++ L
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 129 NGVELEGRAMRVSLAQ 144
NG+ + + ++VS A+
Sbjct: 66 NGITVRNKRLKVSYAR 81
Score = 27.7 bits (60), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 27/46 (58%)
Query: 7 VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
++ D +TG S G+AFV ++ D I+ L+G + L+V+++
Sbjct: 35 IMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYA 80
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 45.8 bits (107), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 38/79 (48%), Gaps = 8/79 (10%)
Query: 68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
KL VGN+S + T + L F+EYG V+ ++ D Y FV + A+
Sbjct: 12 KLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRG 63
Query: 128 LNGVELEGRAMRVSLAQGR 146
L+ E +G+ M V L+ R
Sbjct: 64 LDNTEFQGKRMHVQLSTSR 82
Score = 29.3 bits (64), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 18/36 (50%)
Query: 17 RGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
+ +AFV M ED I LD E+ G+ + V S
Sbjct: 44 KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLS 79
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 45.4 bits (106), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 6/76 (7%)
Query: 68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
+LFVGNL +T E + + F++YG G ++ + +G+GF+ T+ E A
Sbjct: 24 RLFVGNLPPDITEEEMRKLFEKYGK-AGEVFIH-----KDKGFGFIRLETRTLAEIAKVE 77
Query: 128 LNGVELEGRAMRVSLA 143
L+ + L G+ +RV A
Sbjct: 78 LDNMPLRGKQLRVRFA 93
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 35/112 (31%), Positives = 47/112 (41%), Gaps = 12/112 (10%)
Query: 15 RSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNL 74
+ +GF F+ + T LD G+ LRV F A L V NL
Sbjct: 56 KDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRF-----------ACHSASLTVRNL 104
Query: 75 SWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
V+ E L +AF +G V A V+ D + GR G G V +S K AL+
Sbjct: 105 PQYVSNELLEEAFSVFGQVERAVVIVD-DRGRPSGKGIVEFSGKPAARKALD 155
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 45.4 bits (106), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 46/81 (56%)
Query: 66 DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETAL 125
D ++VG L V+ L + F + G VV + D +G+ +GYGFV + ++ + + A+
Sbjct: 15 DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 74
Query: 126 ESLNGVELEGRAMRVSLAQGR 146
+ ++ ++L G+ +RV+ A
Sbjct: 75 KIMDMIKLYGKPIRVNKASAH 95
Score = 33.9 bits (76), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 25/41 (60%)
Query: 10 DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVN 50
DR TG+ +G+ FV + ED + I+ +D + G+ +RVN
Sbjct: 50 DRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVN 90
>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 = 45.4 bits (106), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 38/73 (52%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
LFV ++ + + + F +YG + + D +G S+GY V Y T + A E+L
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 129 NGVELEGRAMRVS 141
NG E+ G+ ++V
Sbjct: 135 NGAEIMGQTIQVD 147
Score = 33.5 bits (75), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 31/57 (54%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
+ + + DR TG S+G+A V T + A E L+G E +G+ ++V++ PK
Sbjct: 99 IKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPK 155
>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 = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 41/72 (56%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
+++G++ + T E + G V+ ++++D ++GRS+GY F+ + +A+ +L
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 129 NGVELEGRAMRV 140
NG +L R ++
Sbjct: 67 NGYQLGSRFLKC 78
Score = 40.4 bits (93), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 30/49 (61%)
Query: 4 KLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
L +++D +TGRS+G+AF+ +E + + NL+G + R L+ +S
Sbjct: 33 NLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYS 81
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 38/73 (52%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
LFV ++ + + + F +YG + + D +G S+GY V Y T + A E+L
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 129 NGVELEGRAMRVS 141
NG E+ G+ ++V
Sbjct: 89 NGAEIMGQTIQVD 101
Score = 34.7 bits (78), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 31/57 (54%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
+ + + DR TG S+G+A V T + A E L+G E +G+ ++V++ PK
Sbjct: 53 IKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPK 109
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 39/65 (60%), Gaps = 1/65 (1%)
Query: 68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
KLFVG L+ + + + + F+ +GN+ +L G G S+G FV YS+ AE + A+ +
Sbjct: 17 KLFVGMLNKQQSEDDVRRLFEAFGNIEECTILR-GPDGNSKGCAFVKYSSHAEAQAAINA 75
Query: 128 LNGVE 132
L+G +
Sbjct: 76 LHGSQ 80
>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
pdb|2RS8|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
Length = 99
Score = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 6/76 (7%)
Query: 68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
+LFVGNL +T E + + F++YG + D +G+GF+ T+ E A
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 70
Query: 128 LNGVELEGRAMRVSLA 143
L+ + L G+ +RV A
Sbjct: 71 LDNMPLRGKQLRVRFA 86
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 41/71 (57%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
+++G++ + T E + G V+ ++++D ++GRS+GY F+ + +A+ +L
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 129 NGVELEGRAMR 139
NG +L R ++
Sbjct: 65 NGYQLGSRFLK 75
Score = 40.4 bits (93), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 30/49 (61%)
Query: 4 KLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
L +++D +TGRS+G+AF+ +E + + NL+G + R L+ +S
Sbjct: 31 NLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYS 79
>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 = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 41/72 (56%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
+++G++ + T E + G V+ ++++D ++GRS+GY F+ + +A+ +L
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 129 NGVELEGRAMRV 140
NG +L R ++
Sbjct: 66 NGYQLGSRFLKC 77
Score = 40.4 bits (93), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 30/49 (61%)
Query: 4 KLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
L +++D +TGRS+G+AF+ +E + + NL+G + R L+ +S
Sbjct: 32 NLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYS 80
>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 = 44.3 bits (103), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 31/147 (21%), Positives = 65/147 (44%), Gaps = 16/147 (10%)
Query: 12 ETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRV----------NFSDKPKPKLP- 60
+ + + FAF+ +V++ + DG + G+ L++ S+ P +P
Sbjct: 46 QINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPG 104
Query: 61 ----LYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYS 116
+ ++ KLF+G L + + + + +G + ++ D +G S+GY F Y
Sbjct: 105 VVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYV 164
Query: 117 TKAEMETALESLNGVELEGRAMRVSLA 143
+ A+ LNG++L + + V A
Sbjct: 165 DINVTDQAIAGLNGMQLGDKKLLVQRA 191
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 44.3 bits (103), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 35/124 (28%), Positives = 50/124 (40%), Gaps = 11/124 (8%)
Query: 17 RGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSW 76
+G AFVT+ E A I R L V TD L V NL
Sbjct: 57 KGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQ-----------PTDALLCVANLPP 105
Query: 77 SVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGR 136
S+T + + + +G++ ++Y +G+S+GYGF Y K A L G L R
Sbjct: 106 SLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPR 165
Query: 137 AMRV 140
+ V
Sbjct: 166 TLYV 169
Score = 34.7 bits (78), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 35/145 (24%), Positives = 64/145 (44%), Gaps = 8/145 (5%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK--PKL 59
L + ++Y TG+S+G+ F + +L G+ R L V+++D + P L
Sbjct: 122 LERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPAL 181
Query: 60 PLYAETDFKLFVGNLSWSVT-TESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTK 118
L++ L V L ++L +A + + L G+ G+ +G+ + Y T
Sbjct: 182 -LHSRC---LCVDRLPPGFNDVDALCRALSAVHSPTFCQ-LACGQDGQLKGFAVLEYETA 236
Query: 119 AEMETALESLNGVELEGRAMRVSLA 143
E A + +G+ L G +RVS
Sbjct: 237 EMAEEAQQQADGLSLGGSHLRVSFC 261
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 44.3 bits (103), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 8/76 (10%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
LFV NL+ +VT E L +AF ++G + + L D Y F+ + + A+E +
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEM 65
Query: 129 NGVELEGRAMRVSLAQ 144
NG +LEG + + A+
Sbjct: 66 NGKDLEGENIEIVFAK 81
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 43.9 bits (102), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 35/124 (28%), Positives = 50/124 (40%), Gaps = 11/124 (8%)
Query: 17 RGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSW 76
+G AFVT+ E A I R L V TD L V NL
Sbjct: 57 KGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQ-----------PTDALLCVANLPP 105
Query: 77 SVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGR 136
S+T + + + +G++ ++Y +G+S+GYGF Y K A L G L R
Sbjct: 106 SLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPR 165
Query: 137 AMRV 140
+ V
Sbjct: 166 TLYV 169
Score = 34.7 bits (78), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 35/145 (24%), Positives = 64/145 (44%), Gaps = 8/145 (5%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK--PKL 59
L + ++Y TG+S+G+ F + +L G+ R L V+++D + P L
Sbjct: 122 LERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPAL 181
Query: 60 PLYAETDFKLFVGNLSWSVT-TESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTK 118
L++ L V L ++L +A + + L G+ G+ +G+ + Y T
Sbjct: 182 -LHSRC---LCVDRLPPGFNDVDALCRALSAVHSPTFCQ-LACGQDGQLKGFAVLEYETA 236
Query: 119 AEMETALESLNGVELEGRAMRVSLA 143
E A + +G+ L G +RVS
Sbjct: 237 EMAEEAQQQADGLSLGGSHLRVSFC 261
>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|X Chain X, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|Y Chain Y, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2V|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
pdb|1N52|B Chain B, Cap Binding Complex
pdb|1N54|B Chain B, Cap Binding Complex M7gpppg Free
pdb|3FEX|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex.
pdb|3FEY|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex
Length = 156
Score = 43.9 bits (102), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 41/77 (53%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
L+VGNLS+ T E + + F + G++ + D + G+ FV Y ++A+ E A+ +
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 129 NGVELEGRAMRVSLAQG 145
NG L+ R +R G
Sbjct: 102 NGTRLDDRIIRTDWDAG 118
>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 = 43.9 bits (102), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 35/124 (28%), Positives = 50/124 (40%), Gaps = 11/124 (8%)
Query: 17 RGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSW 76
+G AFVT+ E A I R L V TD L V NL
Sbjct: 55 KGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQ-----------PTDALLCVANLPP 103
Query: 77 SVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGR 136
S+T + + + +G++ ++Y +G+S+GYGF Y K A L G L R
Sbjct: 104 SLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPR 163
Query: 137 AMRV 140
+ V
Sbjct: 164 TLYV 167
Score = 34.7 bits (78), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 35/145 (24%), Positives = 64/145 (44%), Gaps = 8/145 (5%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK--PKL 59
L + ++Y TG+S+G+ F + +L G+ R L V+++D + P L
Sbjct: 120 LERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPAL 179
Query: 60 PLYAETDFKLFVGNLSWSVT-TESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTK 118
L++ L V L ++L +A + + L G+ G+ +G+ + Y T
Sbjct: 180 -LHSRC---LCVDRLPPGFNDVDALCRALSAVHSPTFCQ-LACGQDGQLKGFAVLEYETA 234
Query: 119 AEMETALESLNGVELEGRAMRVSLA 143
E A + +G+ L G +RVS
Sbjct: 235 EMAEEAQQQADGLSLGGSHLRVSFC 259
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 43.5 bits (101), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
+FV NL + V + L + F G VV A +L D + G+SRG G V + E A+
Sbjct: 18 VFVANLDYKVGWKKLKEVFSMAGVVVRADILED-KDGKSRGIGTVTFEQSIEAVQAISMF 76
Query: 129 NGVELEGRAMRVSL 142
NG L R M V +
Sbjct: 77 NGQLLFDRPMHVKM 90
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 43.5 bits (101), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 42/75 (56%), Gaps = 2/75 (2%)
Query: 68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
++FV NL + T + L F E G+V+ A + E+G+S+G G V + + E A
Sbjct: 10 QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKM--ENGKSKGCGVVKFESPEVAERACRM 67
Query: 128 LNGVELEGRAMRVSL 142
+NG++L GR + V +
Sbjct: 68 MNGMKLSGREIDVRI 82
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 43.1 bits (100), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 38/67 (56%), Gaps = 1/67 (1%)
Query: 66 DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETAL 125
D KLFVG L+ + E + + FQ +G + VL G G S+G FV +S+ E + A+
Sbjct: 15 DRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLR-GPDGSSKGCAFVKFSSHTEAQAAI 73
Query: 126 ESLNGVE 132
+L+G +
Sbjct: 74 HALHGSQ 80
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 43.1 bits (100), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 2/74 (2%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
+FV NL + T + L F E G+V+ A + E+G+S+G G V + + E A +
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKM--ENGKSKGCGVVKFESPEVAERACRMM 65
Query: 129 NGVELEGRAMRVSL 142
NG++L GR + V +
Sbjct: 66 NGMKLSGREIDVRI 79
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 42.7 bits (99), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 28/81 (34%), Positives = 43/81 (53%), Gaps = 7/81 (8%)
Query: 68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
KL++GNLS +VT + L Q F + + +VL GY FV Y + A+E+
Sbjct: 10 KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIET 63
Query: 128 LNG-VELEGRAMRVSLAQGRR 147
L+G VEL G+ M V + ++
Sbjct: 64 LSGKVELHGKIMEVDYSVSKK 84
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 42.7 bits (99), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 42/88 (47%), Gaps = 3/88 (3%)
Query: 61 LYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAE 120
L E + L++ NL + +T E + F +YG + RV G + +RG +V Y +
Sbjct: 3 LPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDIFD 59
Query: 121 METALESLNGVELEGRAMRVSLAQGRRS 148
+ A++ L+G + R + V R+
Sbjct: 60 AKNAVDHLSGFNVSNRYLVVLYYNANRA 87
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 42.7 bits (99), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 24/95 (25%), Positives = 45/95 (47%), Gaps = 5/95 (5%)
Query: 58 KLPLYA-----ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGF 112
K+P+++ E + L++ NLS VT L F + G + + +GR RG F
Sbjct: 12 KIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAF 71
Query: 113 VCYSTKAEMETALESLNGVELEGRAMRVSLAQGRR 147
+ + K AL +NG +L G+ + + + ++
Sbjct: 72 ITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKK 106
Score = 29.6 bits (65), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 22/44 (50%)
Query: 13 TGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK 56
TGR RG AF+T E + ++G + G+IL + F K
Sbjct: 63 TGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKK 106
>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 = 42.4 bits (98), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 1/77 (1%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
L+VGNLS+ T E + + F + G++ + D + + G+ FV Y ++A+ E A+ +
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLD-KMKTACGFCFVEYYSRADAENAMRYI 79
Query: 129 NGVELEGRAMRVSLAQG 145
NG L+ R +R G
Sbjct: 80 NGTRLDDRIIRTDWDAG 96
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 46/84 (54%), Gaps = 6/84 (7%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
+F+ NLS+ E+L + Q++G++ RV+ ++ S+G F + T+ + L +
Sbjct: 18 VFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAA 77
Query: 129 N------GVELEGRAMRVSLAQGR 146
+ G++L+GR ++V LA R
Sbjct: 78 SLEAEGGGLKLDGRQLKVDLAVTR 101
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 29/85 (34%), Positives = 50/85 (58%), Gaps = 3/85 (3%)
Query: 66 DFKLFVGNLSWSVTTESLTQAF-QEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
++ LFVG+L+ V L + F + Y + G +V+ D ++G S+GYGFV ++ + E + A
Sbjct: 9 EYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFVKFTDELEQKRA 67
Query: 125 LESLNG-VELEGRAMRVSLAQGRRS 148
L G V L + +R+S+A + S
Sbjct: 68 LTECQGAVGLGSKPVRLSVAIPKAS 92
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
++VGN+ + T E L F G+V +L D SG +G+ ++ +S K + T+L +L
Sbjct: 8 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-AL 66
Query: 129 NGVELEGRAMRV 140
+ GR ++V
Sbjct: 67 DESLFRGRQIKV 78
Score = 28.1 bits (61), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRV 49
++++T+L D+ +G +GFA++ S E + LD + GR ++V
Sbjct: 32 VNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA-LDESLFRGRQIKV 78
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 8/79 (10%)
Query: 68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
KLF+GNL T + + F++YG V+ ++ + YGFV K E A+ +
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRN 61
Query: 128 LNGVELEGRAMRVSLAQGR 146
L+ +L G + V ++ +
Sbjct: 62 LHHYKLHGVNINVEASKNK 80
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of Hypothetical
Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens
At 1.95 A Resolution
Length = 89
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
++VGN+ + T E L F G+V +L D SG +G+ ++ +S K + T+L +L
Sbjct: 9 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-AL 67
Query: 129 NGVELEGRAMRV 140
+ GR ++V
Sbjct: 68 DESLFRGRQIKV 79
Score = 28.1 bits (61), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRV 49
++++T+L D+ +G +GFA++ S E + LD + GR ++V
Sbjct: 33 VNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA-LDESLFRGRQIKV 79
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 27/95 (28%), Positives = 47/95 (49%), Gaps = 14/95 (14%)
Query: 50 NFSDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQA-FQEYGNVVGARVLYDGESGRSR 108
N ++K PK + ++F+GNL+ ++ +S + F +YG V G V +
Sbjct: 16 NVTNKNDPK-----SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HK 62
Query: 109 GYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA 143
GY FV YS + A+ NG L G+ + +++A
Sbjct: 63 GYAFVQYSNERHARAAVLGENGRVLAGQTLDINMA 97
Score = 32.0 bits (71), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 2/51 (3%)
Query: 9 YDRETGRS--RGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP 57
Y R G S +G+AFV S A + +GR G+ L +N + +PKP
Sbjct: 52 YGRVAGCSVHKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPKP 102
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 40.4 bits (93), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 37/57 (64%), Gaps = 2/57 (3%)
Query: 4 KLTVLYDRETGRSRGFAFVTMSTVEDCNAVIE-NLDGREYLGRILRVNFSDKPKPKL 59
++ ++ ++ +G+SRGFAFV S ++D +E N LG+ + +++SD PKPK+
Sbjct: 31 EVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSD-PKPKI 86
>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 = 40.4 bits (93), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 41/88 (46%), Gaps = 3/88 (3%)
Query: 61 LYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAE 120
L E + L++ NL + +T E + F +YG + RV G + +RG +V Y +
Sbjct: 13 LPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDIFD 69
Query: 121 METALESLNGVELEGRAMRVSLAQGRRS 148
+ A + L+G + R + V R+
Sbjct: 70 AKNACDHLSGFNVCNRYLVVLYYNANRA 97
>pdb|3P5T|L Chain L, Cfim25-Cfim68 Complex
pdb|3P5T|M Chain M, Cfim25-Cfim68 Complex
pdb|3P5T|N Chain N, Cfim25-Cfim68 Complex
pdb|3P5T|O Chain O, Cfim25-Cfim68 Complex
pdb|3P5T|P Chain P, Cfim25-Cfim68 Complex
pdb|3P5T|Q Chain Q, Cfim25-Cfim68 Complex
pdb|3P6Y|C Chain C, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|D Chain D, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|G Chain G, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|H Chain H, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|K Chain K, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|L Chain L, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|O Chain O, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|P Chain P, Cf Im25-Cf Im68-Uguaa Complex
Length = 90
Score = 40.0 bits (92), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 39/70 (55%), Gaps = 2/70 (2%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYG--NVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
L++GNL+W T E LT+A G +++ + + +G+S+G+ V ++A + ++
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63
Query: 127 SLNGVELEGR 136
L EL G+
Sbjct: 64 LLPKRELHGQ 73
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 40.0 bits (92), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 35/73 (47%)
Query: 68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
+LFV NLS++ + E L + F YG + D + + +G+ FV + A
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 128 LNGVELEGRAMRV 140
++G +GR + V
Sbjct: 70 VDGQVFQGRMLHV 82
Score = 35.8 bits (81), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 25/48 (52%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRV 49
LS+L D T + +GFAFVT E +DG+ + GR+L V
Sbjct: 35 LSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHV 82
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 40.0 bits (92), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 45/86 (52%), Gaps = 8/86 (9%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNV-----VGARVLY---DGESGRSRGYGFVCYSTKAE 120
++V L+ SVT + L F++ G V G +++ D E+G+ +G V Y
Sbjct: 18 IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPT 77
Query: 121 METALESLNGVELEGRAMRVSLAQGR 146
+ A+E +G + +G ++VSLA+ +
Sbjct: 78 AKAAVEWFDGKDFQGSKLKVSLARKK 103
Score = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 29/53 (54%)
Query: 5 LTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP 57
+ + D+ETG+ +G A V+ A +E DG+++ G L+V+ + K P
Sbjct: 53 IHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPP 105
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 40.0 bits (92), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 42/70 (60%), Gaps = 5/70 (7%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
L NLS+++T + L + F+ + + R++ + G+S+G ++ + ++A+ E LE
Sbjct: 19 LLAKNLSFNITEDELKEVFE---DALEIRLV--SQDGKSKGIAYIEFKSEADAEKNLEEK 73
Query: 129 NGVELEGRAM 138
G E++GR++
Sbjct: 74 QGAEIDGRSV 83
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
Length = 124
Score = 40.0 bits (92), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/89 (24%), Positives = 45/89 (50%), Gaps = 6/89 (6%)
Query: 57 PKLPLYAETDFKL-----FVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYG 111
P PL AE ++ +VGN+ + T + L F G++ +L D SG +GY
Sbjct: 22 PPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYA 81
Query: 112 FVCYSTKAEMETALESLNGVELEGRAMRV 140
++ ++ + ++ A+ +++ GR ++V
Sbjct: 82 YIEFAERNSVDAAV-AMDETVFRGRTIKV 109
Score = 28.9 bits (63), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 11/48 (22%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRV 49
++++T+L D+ +G +G+A++ + +A + +D + GR ++V
Sbjct: 63 INRITILCDKFSGHPKGYAYIEFAERNSVDAAVA-MDETVFRGRTIKV 109
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 40.0 bits (92), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 37/73 (50%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
L++ L T + L + Q YG +V + + D + + +GYGFV + + + + A+ +L
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
Query: 129 NGVELEGRAMRVS 141
++ + + S
Sbjct: 68 KASGVQAQMAKQS 80
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 39.7 bits (91), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 41/83 (49%), Gaps = 5/83 (6%)
Query: 58 KLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYST 117
+LP E + L++ NL + +T E + F +YG + RV G + +RG +V Y
Sbjct: 6 RLP--PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYED 60
Query: 118 KAEMETALESLNGVELEGRAMRV 140
+ + A + L+G + R + V
Sbjct: 61 IFDAKNACDHLSGFNVCNRYLVV 83
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 39.7 bits (91), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 43/81 (53%), Gaps = 4/81 (4%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
L V L W T + L + F +G V+ +V D ++G S+G+GFV ++ E ET ++ +
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFT---EYETQVKVM 74
Query: 129 NGVEL-EGRAMRVSLAQGRRS 148
+ + +GR L ++S
Sbjct: 75 SQRHMIDGRWCDCKLPNSKQS 95
>pdb|3N9U|C Chain C, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
pdb|3N9U|I Chain I, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
Length = 156
Score = 39.7 bits (91), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 31/106 (29%), Positives = 50/106 (47%), Gaps = 9/106 (8%)
Query: 47 LRVNFSDKPKPKLP--LYAETDFK-----LFVGNLSWSVTTESLTQAFQEYG--NVVGAR 97
+R S KP K P LY + + ++VG+ SW T + L Q + G +VV +
Sbjct: 29 VRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELK 88
Query: 98 VLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA 143
+ +G+S+GY V +++ + LE L G L G + V A
Sbjct: 89 FAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPA 134
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 39.3 bits (90), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
L++ NL S+ + L + +G V+ R+L D SG SRG GF + + E +
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHF 86
Query: 129 NG 130
NG
Sbjct: 87 NG 88
Score = 31.2 bits (69), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 7 VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGR 40
+L D +G SRG F M + E C AVI + +G+
Sbjct: 57 ILRD-SSGTSRGVGFARMESTEKCEAVIGHFNGK 89
>pdb|3Q2S|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2S|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2T|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
pdb|3Q2T|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
Length = 229
Score = 39.3 bits (90), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 41/75 (54%), Gaps = 2/75 (2%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYG--NVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
L++GNL+W T E LT+A G +++ + + +G+S+G+ V ++A + ++
Sbjct: 71 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 130
Query: 127 SLNGVELEGRAMRVS 141
L EL G+ V+
Sbjct: 131 LLPKRELHGQNPVVT 145
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 3/79 (3%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGR---SRGYGFVCYSTKAEMETAL 125
LF+ NL++S T E+L F + G + + S G+GFV Y + + AL
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 126 ESLNGVELEGRAMRVSLAQ 144
+ L G ++G + V +++
Sbjct: 68 KQLQGHTVDGHKLEVRISE 86
>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
pdb|2F9J|B Chain B, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
Length = 125
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 40/88 (45%), Gaps = 3/88 (3%)
Query: 61 LYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAE 120
L E + L + NL + +T E + F +YG + RV G + +RG +V Y +
Sbjct: 13 LPPEVNRILMIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDIFD 69
Query: 121 METALESLNGVELEGRAMRVSLAQGRRS 148
+ A + L+G + R + V R+
Sbjct: 70 AKNACDHLSGFNVCNRYLVVLYYNANRA 97
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/89 (25%), Positives = 49/89 (55%), Gaps = 6/89 (6%)
Query: 61 LYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAE 120
L E + +VGNL ++ + F++ ++ R++ D ++ + +G+ CY E
Sbjct: 10 LPTEPPYTAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGF---CYVEFDE 65
Query: 121 METALESL--NGVELEGRAMRVSLAQGRR 147
+++ E+L +G L R++RV +A+GR+
Sbjct: 66 VDSLKEALTYDGALLGDRSLRVDIAEGRK 94
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 37/72 (51%), Gaps = 6/72 (8%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
++ G ++ +T + + Q F +G ++ RV + +GY FV +ST A+ S+
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSV 81
Query: 129 NGVELEGRAMRV 140
NG +EG ++
Sbjct: 82 NGTTIEGHVVKC 93
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 44/82 (53%), Gaps = 2/82 (2%)
Query: 65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
T F LF+GNL+ + + L A E + D +G +R +G+V + + ++E A
Sbjct: 16 TPFNLFIGNLNPNKSVAELKVAISELF-AKNDLAVVDVRTGTNRKFGYVDFESAEDLEKA 74
Query: 125 LESLNGVELEGRAMRVSLAQGR 146
LE L G+++ G +++ +GR
Sbjct: 75 LE-LTGLKVFGNEIKLEKPKGR 95
>pdb|2E5J|A Chain A, Solution Structure Of Rna Binding Domain In
Methenyltetrahydrofolate Synthetase Domain Containing
Length = 97
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 27/88 (30%), Positives = 44/88 (50%), Gaps = 9/88 (10%)
Query: 60 PLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKA 119
PL A+ ++VGNL L +A +E G+ V R+ + G R+ F+ Y A
Sbjct: 17 PLAAD----VYVGNLPRDARVSDLKRALRELGS-VPLRLTWQGPRRRA----FLHYPDSA 67
Query: 120 EMETALESLNGVELEGRAMRVSLAQGRR 147
+ A+ L G+ L +RV+LA+ +R
Sbjct: 68 AAQQAVSCLQGLRLGTDTLRVALARQQR 95
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 37/76 (48%)
Query: 68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
KLF+G L + + + + +G + ++ D +G S+GY F Y + A+
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 128 LNGVELEGRAMRVSLA 143
LNG++L + + V A
Sbjct: 63 LNGMQLGDKKLLVQRA 78
>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 = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 39/75 (52%), Gaps = 3/75 (4%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
+FVG + + + F YG+V +++ D +G S+GYGFV + +++ +ES
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVES- 69
Query: 129 NGVELEGRAMRVSLA 143
+ G+ +++ A
Sbjct: 70 -QINFHGKKLKLGPA 83
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 37.0 bits (84), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 3/66 (4%)
Query: 67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
KLF+G + ++ + L F+E+G + VL D +G +G F+ Y E E+AL+
Sbjct: 14 IKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTY---CERESALK 70
Query: 127 SLNGVE 132
+ + +
Sbjct: 71 AQSALH 76
Score = 26.2 bits (56), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 12/20 (60%), Positives = 15/20 (75%)
Query: 4 KLTVLYDRETGRSRGFAFVT 23
+LTVL DR TG +G AF+T
Sbjct: 42 ELTVLKDRFTGMHKGCAFLT 61
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 37.0 bits (84), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 39/75 (52%), Gaps = 3/75 (4%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
+FVG + + + F YG+V +++ D +G S+GYGFV + +++ +ES
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVESQ 71
Query: 129 NGVELEGRAMRVSLA 143
+ G+ +++ A
Sbjct: 72 --INFHGKKLKLGPA 84
>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 = 37.0 bits (84), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 39/75 (52%), Gaps = 3/75 (4%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
+FVG + + + F YG+V +++ D +G S+GYGFV + +++ +ES
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 129 NGVELEGRAMRVSLA 143
+ G+ +++ A
Sbjct: 71 --INFHGKKLKLGPA 83
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 37.0 bits (84), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 28/48 (58%)
Query: 5 LTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
+ + DRETG+ +G A V+ A I+ DG+E+ G ++V+F+
Sbjct: 51 INLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 37.0 bits (84), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 33/71 (46%)
Query: 59 LPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTK 118
+P+ KLFVG + + + L F+E+G + VL D +G +G F+ Y +
Sbjct: 8 VPMKDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCAR 67
Query: 119 AEMETALESLN 129
A +L+
Sbjct: 68 DSALKAQSALH 78
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 28/48 (58%)
Query: 5 LTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
+ + DRETG+ +G A V+ A I+ DG+E+ G ++V+F+
Sbjct: 45 INLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 92
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 36.6 bits (83), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 32/62 (51%), Gaps = 8/62 (12%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
LFV NL+ +VT E L ++F E+G + + L D Y FV + + A++ +
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD--------YAFVHFEDRGAAVKAMDEM 69
Query: 129 NG 130
NG
Sbjct: 70 NG 71
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 36.2 bits (82), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 6/76 (7%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
L+V NL S + E + + F RV + R Y FV +S + + A+++L
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVHFSNREDAVEAMKAL 71
Query: 129 NGVELEGRAMRVSLAQ 144
NG L+G + V+LA+
Sbjct: 72 NGKVLDGSPIEVTLAK 87
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 35.8 bits (81), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 1/54 (1%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP 55
+S++ + D+ TG+S+GFAF++ ED I + G Y IL V ++ KP
Sbjct: 42 ISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA-KP 94
Score = 31.6 bits (70), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 17/82 (20%), Positives = 40/82 (48%)
Query: 63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
A+ + + V NLS L + F+ +G++ + D +G+S+G+ F+ + + +
Sbjct: 12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAA 71
Query: 123 TALESLNGVELEGRAMRVSLAQ 144
A+ ++G + + V A+
Sbjct: 72 RAIAGVSGFGYDHLILNVEWAK 93
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 34.7 bits (78), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 41/83 (49%), Gaps = 7/83 (8%)
Query: 68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
K++VGNL L +AF YG + R ++ + G+ FV + + E A+
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPL---RTVWIARN--PPGFAFVEFEDPRDAEDAVRG 56
Query: 128 LNGVELEGRAMRVSLAQG--RRS 148
L+G + G +RV L+ G RRS
Sbjct: 57 LDGKVICGSRVRVELSTGMPRRS 79
Score = 27.3 bits (59), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 16/35 (45%)
Query: 18 GFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
GFAFV D + LDG+ G +RV S
Sbjct: 38 GFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELS 72
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 34.3 bits (77), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 21/88 (23%), Positives = 39/88 (44%), Gaps = 9/88 (10%)
Query: 63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRG---YGFVCYSTKA 119
D +++VGNL + T+ + F +YG + D + RG + FV +
Sbjct: 19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYG------AIRDIDLKNRRGGPPFAFVEFEDPR 72
Query: 120 EMETALESLNGVELEGRAMRVSLAQGRR 147
+ E A+ +G + +G +RV + R
Sbjct: 73 DAEDAVYGRDGYDYDGYRLRVEFPRSGR 100
>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 = 34.3 bits (77), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 36/68 (52%), Gaps = 5/68 (7%)
Query: 67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYD--GESGRSRGYGFVCYSTKAEMETA 124
K+FVG + + + + L + F++YG V VL D +S+G FV + T+ + A
Sbjct: 4 IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTR---KAA 60
Query: 125 LESLNGVE 132
LE+ N +
Sbjct: 61 LEAQNALH 68
>pdb|1WG4|A Chain A, Solution Structure Of Rrm Domain In Protein Bab31986
Length = 98
Score = 34.3 bits (77), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 33/74 (44%), Gaps = 7/74 (9%)
Query: 60 PLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKA 119
P +DF++ V L S + + L +E G+V A V D G G V Y K
Sbjct: 9 PPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKD-------GMGMVEYLRKE 61
Query: 120 EMETALESLNGVEL 133
+ME AL L+ +
Sbjct: 62 DMEYALRKLDDTKF 75
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 33.5 bits (75), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 38/82 (46%), Gaps = 5/82 (6%)
Query: 66 DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETAL 125
D K++VGNL + L +AF YG + V + G+ FV + + A+
Sbjct: 73 DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAV 127
Query: 126 ESLNGVELEGRAMRVSLAQGRR 147
L+G L G +RV L+ G +
Sbjct: 128 RDLDGRTLCGCRVRVELSNGEK 149
Score = 28.9 bits (63), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 19/39 (48%)
Query: 18 GFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK 56
GFAFV D + +LDGR G +RV S+ K
Sbjct: 111 GFAFVEFEDPRDAADAVRDLDGRTLCGCRVRVELSNGEK 149
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 33.1 bits (74), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 38/82 (46%), Gaps = 5/82 (6%)
Query: 66 DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETAL 125
D K++VGNL + L +AF YG + V + G+ FV + + A+
Sbjct: 73 DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAV 127
Query: 126 ESLNGVELEGRAMRVSLAQGRR 147
L+G L G +RV L+ G +
Sbjct: 128 RELDGRTLCGCRVRVELSNGEK 149
Score = 28.1 bits (61), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 18/39 (46%)
Query: 18 GFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK 56
GFAFV D + LDGR G +RV S+ K
Sbjct: 111 GFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEK 149
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 33.1 bits (74), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 14/59 (23%), Positives = 29/59 (49%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
+FVG LS E + + F +G V + D ++ + RG+ F+ + + ++ +E
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 32.7 bits (73), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 22/40 (55%)
Query: 17 RGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK 56
+GFAFV + A + DGR G++L +N + +PK
Sbjct: 50 KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPK 89
>pdb|2NLW|A Chain A, Solution Structure Of The Rrm Domain Of Human Eukaryotic
Initiation Factor 3b
Length = 105
Score = 32.7 bits (73), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 35/61 (57%), Gaps = 3/61 (4%)
Query: 83 LTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGR-AMRVS 141
+ + F ++G + Y E G+++GY F+ Y++ A A+++ +G +L+ + RV+
Sbjct: 38 IHKIFSKFGKITND--FYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVN 95
Query: 142 L 142
L
Sbjct: 96 L 96
>pdb|2M2B|A Chain A, Nmr Structure Of The Rrm2 Domain Of The Protein Rbm10
From Homo Sapiens
Length = 131
Score = 32.7 bits (73), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 12/26 (46%), Positives = 20/26 (76%)
Query: 3 SKLTVLYDRETGRSRGFAFVTMSTVE 28
S + V+ D++T +RGFAF+ +ST+E
Sbjct: 53 SNVRVIKDKQTQLNRGFAFIQLSTIE 78
Score = 32.7 bits (73), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 46/84 (54%), Gaps = 5/84 (5%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGA--RVLYDGESGRSRGYGFVCYST--KAEMETA 124
+ + NL+ T +S+ A Y + + RV+ D ++ +RG+ F+ ST A++
Sbjct: 26 IILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIEAAQLLQI 85
Query: 125 LESLN-GVELEGRAMRVSLAQGRR 147
L++L+ + ++G+ + V A+G +
Sbjct: 86 LQALHPPLTIDGKTINVEFAKGSK 109
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 32.0 bits (71), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 41/83 (49%), Gaps = 11/83 (13%)
Query: 68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
K+FVG + +T E L Q F +YG VV + R + FV ++ + +S
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYGEVVDVFI-----PKPFRAFAFVTFAD----DKVAQS 63
Query: 128 LNGVEL--EGRAMRVSLAQGRRS 148
L G +L +G ++ +S A+ + +
Sbjct: 64 LCGEDLIIKGISVHISNAEPKHN 86
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 32.0 bits (71), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYG-NVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
L++G+L + +++AF G V+ +++ + +G GY FV ++ A E L
Sbjct: 12 LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71
Query: 128 LNGVELEG 135
+NG L G
Sbjct: 72 INGKPLPG 79
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 31.6 bits (70), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 39/82 (47%), Gaps = 2/82 (2%)
Query: 64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGE-SGRSRGYGFVCYSTKAEME 122
+T K+ V N+ + + + F +G + R+ +G RG+GFV + TK + +
Sbjct: 13 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAK 72
Query: 123 TALESL-NGVELEGRAMRVSLA 143
A +L + L GR + + A
Sbjct: 73 KAFNALCHSTHLYGRRLVLEWA 94
>pdb|2KRB|A Chain A, Solution Structure Of Eif3b-Rrm Bound To Eif3j Peptide
Length = 81
Score = 31.2 bits (69), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 13/54 (24%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 83 LTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGR 136
+ + F ++G + Y E G+++GY F+ Y++ A A+++ +G +L+ +
Sbjct: 24 IHKIFSKFGKITND--FYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ 75
>pdb|3EGN|A Chain A, C-Terminal Rna Recognition Motif Of The U11U12 65K PROTEIN
Length = 143
Score = 31.2 bits (69), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 24/91 (26%), Positives = 41/91 (45%), Gaps = 5/91 (5%)
Query: 63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVG--ARVLYD---GESGRSRGYGFVCYST 117
E + +++V NL+ V + L F Y + R+++D + GR +G F+
Sbjct: 42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPN 101
Query: 118 KAEMETALESLNGVELEGRAMRVSLAQGRRS 148
+ AL+ NG L G+ M V A+ R
Sbjct: 102 EKAAAKALKEANGYVLFGKPMVVQFARSARP 132
>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 30.8 bits (68), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 11/36 (30%), Positives = 26/36 (72%)
Query: 2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENL 37
++ + ++ D++T ++RGFAFV +S+ D + +++ L
Sbjct: 38 VNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQIL 73
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 30.8 bits (68), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
L+VGNLS VT + Q F + G +++ + S Y FV + + AL ++
Sbjct: 18 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAALAAM 75
Query: 129 NGVELEGRAMRVSLA 143
NG ++ G+ ++V+ A
Sbjct: 76 NGRKILGKEVKVNWA 90
>pdb|2E44|A Chain A, Solution Structure Of Rna Binding Domain In Insulin-Like
Growth Factor 2 Mrna Binding Protein 3
Length = 96
Score = 30.4 bits (67), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 5/75 (6%)
Query: 68 KLFVGNLSWSVTTESLTQAFQEYGNVVGA-RVLYDGESGRSRGYGFVCYSTKAEMETALE 126
KL + N+ + E L +YG V +V D E+ V YS+K + AL+
Sbjct: 17 KLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVN----VTYSSKDQARQALD 72
Query: 127 SLNGVELEGRAMRVS 141
LNG +LE ++V+
Sbjct: 73 KLNGFQLENFTLKVA 87
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 30.4 bits (67), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 10/31 (32%), Positives = 19/31 (61%)
Query: 10 DRETGRSRGFAFVTMSTVEDCNAVIENLDGR 40
D TG+++GF FV ++ D +I++ G+
Sbjct: 47 DEATGKTKGFLFVECGSMNDAKKIIKSFHGK 77
>pdb|2GHP|A Chain A, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|B Chain B, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|C Chain C, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|D Chain D, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|E Chain E, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|F Chain F, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|G Chain G, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|H Chain H, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
Length = 292
Score = 30.0 bits (66), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 35/139 (25%), Positives = 61/139 (43%), Gaps = 13/139 (9%)
Query: 16 SRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDF------KL 69
SR FA++ +++ ED +E L+G + G L S+ L TD ++
Sbjct: 158 SRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSN----PLEKSKRTDSATLEGREI 213
Query: 70 FVGNLSWSVTTESLT-QAFQEYGNVVGARVLY-DGESGRSRGYGFVCYSTKAEMETALES 127
+ NLS + E+L ++F+ +G++ + E + F + K E AL+
Sbjct: 214 XIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFXVFENKDSAERALQX 273
Query: 128 LNGVELEGRAMRVSLAQGR 146
N L R + VSLA +
Sbjct: 274 -NRSLLGNREISVSLADKK 291
Score = 28.1 bits (61), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 33/71 (46%)
Query: 65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
T+ L+ N S T ++ Q+ V + L SR + ++ ++K +
Sbjct: 116 TECTLWXTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYC 175
Query: 125 LESLNGVELEG 135
+E LNG+++EG
Sbjct: 176 VEKLNGLKIEG 186
>pdb|3NS6|A Chain A, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
pdb|3NS6|B Chain B, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
Length = 100
Score = 29.6 bits (65), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 10/31 (32%), Positives = 19/31 (61%)
Query: 10 DRETGRSRGFAFVTMSTVEDCNAVIENLDGR 40
D TG+++GF FV ++ D +I++ G+
Sbjct: 47 DEATGKTKGFLFVECGSMNDAKKIIKSFHGK 77
>pdb|2KH9|A Chain A, Solution Structure Of Yeast Prp24-Rrm2 Bound To A Fragment
Of U6 Rna
Length = 92
Score = 29.6 bits (65), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 35/74 (47%)
Query: 65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
T+ L++ N S T ++ Q+ V + L SR + ++ ++K +
Sbjct: 2 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYC 61
Query: 125 LESLNGVELEGRAM 138
+E LNG+++EG +
Sbjct: 62 VEKLNGLKIEGYTL 75
>pdb|2GO9|A Chain A, Rrm Domains 1 And 2 Of Prp24 From S. Cerevisiae
Length = 161
Score = 29.3 bits (64), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 35/74 (47%)
Query: 65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
T+ L++ N S T ++ Q+ V + L SR + ++ ++K +
Sbjct: 79 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYC 138
Query: 125 LESLNGVELEGRAM 138
+E LNG+++EG +
Sbjct: 139 VEKLNGLKIEGYTL 152
>pdb|1LKX|A Chain A, Motor Domain Of Myoe, A Class-I Myosin
pdb|1LKX|B Chain B, Motor Domain Of Myoe, A Class-I Myosin
pdb|1LKX|C Chain C, Motor Domain Of Myoe, A Class-I Myosin
pdb|1LKX|D Chain D, Motor Domain Of Myoe, A Class-I Myosin
Length = 697
Score = 28.9 bits (63), Expect = 1.1, Method: Composition-based stats.
Identities = 26/99 (26%), Positives = 44/99 (44%), Gaps = 15/99 (15%)
Query: 21 FVTMSTVEDCNAVIENLDGRE-------YLGRILRVNFSDKPKPKLPLYAETDFKLFVGN 73
FV ++ + + NA IENL R Y+G ++ S P L +Y E+D K + G
Sbjct: 13 FVLLNQITE-NAFIENLTMRHKSDNIYTYIGDVV---ISTNPFKNLNIYKESDIKAYNGR 68
Query: 74 LSWSVTTESLTQAFQEYGNVVGAR----VLYDGESGRSR 108
+ + A Y ++ ++ V+ GESG +
Sbjct: 69 YKYEMPPHMYALANDAYRSMRQSQENQCVIISGESGAGK 107
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 28.9 bits (63), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 18/38 (47%)
Query: 18 GFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP 55
GFAFV E IE + G+ + + L V +S P
Sbjct: 66 GFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLP 103
>pdb|4A7F|C Chain C, Structure Of The Actin-Tropomyosin-Myosin Complex (Rigor
Atm 3)
pdb|4A7F|G Chain G, Structure Of The Actin-Tropomyosin-Myosin Complex (Rigor
Atm 3)
pdb|4A7F|J Chain J, Structure Of The Actin-Tropomyosin-Myosin Complex (Rigor
Atm 3)
pdb|4A7H|C Chain C, Structure Of The Actin-Tropomyosin-Myosin Complex (Rigor
Atm 2)
pdb|4A7H|I Chain I, Structure Of The Actin-Tropomyosin-Myosin Complex (Rigor
Atm 2)
pdb|4A7H|J Chain J, Structure Of The Actin-Tropomyosin-Myosin Complex (Rigor
Atm 2)
pdb|4A7L|C Chain C, Structure Of The Actin-Tropomyosin-Myosin Complex (Rigor
Atm 1)
pdb|4A7L|G Chain G, Structure Of The Actin-Tropomyosin-Myosin Complex (Rigor
Atm 1)
pdb|4A7L|J Chain J, Structure Of The Actin-Tropomyosin-Myosin Complex (Rigor
Atm 1)
Length = 697
Score = 28.9 bits (63), Expect = 1.2, Method: Composition-based stats.
Identities = 26/99 (26%), Positives = 44/99 (44%), Gaps = 15/99 (15%)
Query: 21 FVTMSTVEDCNAVIENLDGRE-------YLGRILRVNFSDKPKPKLPLYAETDFKLFVGN 73
FV ++ + + NA IENL R Y+G ++ S P L +Y E+D K + G
Sbjct: 13 FVLLNQITE-NAFIENLTMRHKSDNIYTYIGDVV---ISTNPFKNLNIYKESDIKAYNGR 68
Query: 74 LSWSVTTESLTQAFQEYGNVVGAR----VLYDGESGRSR 108
+ + A Y ++ ++ V+ GESG +
Sbjct: 69 YKYEMPPHMYALANDAYRSMRQSQENQCVIISGESGAGK 107
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation Initiation
Factor 4b
Length = 100
Score = 28.9 bits (63), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 42/88 (47%), Gaps = 8/88 (9%)
Query: 57 PKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESG-RSRGYGFVCY 115
PK P Y F+GNL + VT ES+ + F+ N+ R+ + + R +G+G+ +
Sbjct: 15 PKSPPYT-----AFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEF 68
Query: 116 STKAEMETALESLNGVELEGRAMRVSLA 143
+ SLN L R +RV +A
Sbjct: 69 EDLD-SLLSALSLNEESLGNRRIRVDVA 95
>pdb|3K3T|A Chain A, E185a Mutant Of Peptidoglycan Hydrolase From Sphingomonas
Sp. A1
Length = 170
Score = 28.5 bits (62), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 20/33 (60%)
Query: 81 ESLTQAFQEYGNVVGARVLYDGESGRSRGYGFV 113
+S QAFQ+Y ++VG Y +G++ G+ F
Sbjct: 90 DSYEQAFQDYADLVGNSPRYAKVAGKTDGHAFA 122
>pdb|2ZYC|A Chain A, Crystal Structure Of Peptidoglycan Hydrolase From
Sphingomonas Sp. A1
Length = 170
Score = 28.5 bits (62), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 20/33 (60%)
Query: 81 ESLTQAFQEYGNVVGARVLYDGESGRSRGYGFV 113
+S QAFQ+Y ++VG Y +G++ G+ F
Sbjct: 90 DSYEQAFQDYADLVGNSPRYAKVAGKTDGHAFA 122
>pdb|1OPI|A Chain A, Solution Structure Of The Third Rna Recognition Motif
(Rrm) Of U2af65 In Complex With An N-Terminal Sf1
Peptide
pdb|2M0G|B Chain B, Structure, Phosphorylation And U2af65 Binding Of The
Nterminal Domain Of Splicing Factor 1 During 3 Splice
Site Recognition
Length = 104
Score = 28.5 bits (62), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 18 GFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD 53
G FV ++V DC ++ L GR++ R++ + D
Sbjct: 59 GKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCD 94
>pdb|1O0P|A Chain A, Solution Structure Of The Third Rna Recognition Motif
(Rrm) Of U2af65 In Complex With An N-Terminal Sf1
Peptide
Length = 104
Score = 28.5 bits (62), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 18 GFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD 53
G FV ++V DC ++ L GR++ R++ + D
Sbjct: 59 GKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCD 94
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of Eukaryotic
Initiation Factor 4b
Length = 104
Score = 28.1 bits (61), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 31/60 (51%), Gaps = 7/60 (11%)
Query: 57 PKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESG-RSRGYGFVCY 115
PK P Y F+GNL + VT ES+ + F+ N+ R+ + + R +G+G+ +
Sbjct: 11 PKSPPYT-----AFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEF 64
>pdb|3O8O|B Chain B, Structure Of Phosphofructokinase From Saccharomyces
Cerevisiae
pdb|3O8O|D Chain D, Structure Of Phosphofructokinase From Saccharomyces
Cerevisiae
pdb|3O8O|F Chain F, Structure Of Phosphofructokinase From Saccharomyces
Cerevisiae
pdb|3O8O|H Chain H, Structure Of Phosphofructokinase From Saccharomyces
Cerevisiae
Length = 766
Score = 28.1 bits (61), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 19/78 (24%)
Query: 41 EYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLS----------WSVTTESLTQAFQEY 90
E+L + +N +D +PKLP + K+ + N+ +S+ T ++Q + Y
Sbjct: 370 EHLNNFMAINSADHNEPKLP--KDKRLKIAIVNVGAPAGGINSAVYSMATYCMSQGHRPY 427
Query: 91 GNVVGARVLYDGESGRSR 108
+Y+G SG +R
Sbjct: 428 A-------IYNGWSGLAR 438
>pdb|4FXW|A Chain A, Structure Of Phosphorylated Sf1 Complex With U2af65-uhm
Domain
pdb|4FXW|C Chain C, Structure Of Phosphorylated Sf1 Complex With U2af65-uhm
Domain
Length = 106
Score = 27.7 bits (60), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 11/36 (30%), Positives = 19/36 (52%)
Query: 18 GFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD 53
G FV ++V DC + L GR++ R++ + D
Sbjct: 61 GKIFVEFTSVFDCQKAXQGLTGRKFANRVVVTKYCD 96
>pdb|3V4M|A Chain A, Crystal Structure Of A Rna Binding Domain Of A U2 Small
Nuclear Ribonucleoprotein Auxiliary Factor 2 (U2af)
From Mus Musculus At 1.80 A Resolution
pdb|3V4M|B Chain B, Crystal Structure Of A Rna Binding Domain Of A U2 Small
Nuclear Ribonucleoprotein Auxiliary Factor 2 (U2af)
From Mus Musculus At 1.80 A Resolution
Length = 105
Score = 27.7 bits (60), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 11/36 (30%), Positives = 19/36 (52%)
Query: 18 GFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD 53
G FV ++V DC + L GR++ R++ + D
Sbjct: 60 GKIFVEFTSVFDCQKAXQGLTGRKFANRVVVTKYCD 95
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 26.9 bits (58), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 19/42 (45%)
Query: 11 RETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
+E GFAFV E IE + G+ + + L V +S
Sbjct: 32 KEVKILNGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYS 73
>pdb|1X4F|A Chain A, Solution Structure Of The Second Rrm Domain In Matrin 3
Length = 112
Score = 26.9 bits (58), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 25/42 (59%), Gaps = 2/42 (4%)
Query: 15 RSRGFAFVTMSTVEDCNAVIENLDGRE--YLGRILRVNFSDK 54
R + AF+ M T ED A++++ + + GR ++V+ S+K
Sbjct: 60 RMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEK 101
>pdb|2GJP|A Chain A, Structure Of Bacillus Halmapalus Alpha-Amylase,
Crystallized With The Substrate Analogue Acarbose And
Maltose
pdb|2GJR|A Chain A, Structure Of Bacillus Halmapalus Alpha-Amylase Without Any
Substrate Analogues
Length = 485
Score = 26.6 bits (57), Expect = 5.7, Method: Composition-based stats.
Identities = 15/43 (34%), Positives = 25/43 (58%), Gaps = 2/43 (4%)
Query: 95 GARVLYDGESGRSRGYGFVCYSTKAEMETALESL--NGVELEG 135
GA LYD +G Y T++++E+A+ +L NGV++ G
Sbjct: 59 GAYDLYDLGEFNQKGTVRTKYGTRSQLESAIHALKNNGVQVYG 101
>pdb|1W9X|A Chain A, Bacillus Halmapalus Alpha Amylase
Length = 481
Score = 26.6 bits (57), Expect = 5.7, Method: Composition-based stats.
Identities = 15/43 (34%), Positives = 25/43 (58%), Gaps = 2/43 (4%)
Query: 95 GARVLYDGESGRSRGYGFVCYSTKAEMETALESL--NGVELEG 135
GA LYD +G Y T++++E+A+ +L NGV++ G
Sbjct: 55 GAYDLYDLGEFNQKGTVRTKYGTRSQLESAIHALKNNGVQVYG 97
>pdb|2IAH|A Chain A, Crystal Structure Of The Ferripyoverdine Receptor Of The
Outer Membrane Of Pseudomonas Aeruginosa Bound To
Ferripyoverdine.
pdb|2O5P|A Chain A, Crystal Structure Of The Full Length Ferric Pyoverdine
Outer Membrane Receptor Fpva Of Pseudomonas Aeruginosa
In Its Apo Form
pdb|2O5P|B Chain B, Crystal Structure Of The Full Length Ferric Pyoverdine
Outer Membrane Receptor Fpva Of Pseudomonas Aeruginosa
In Its Apo Form
pdb|2W16|A Chain A, Structures Of Fpva Bound To Heterologous Pyoverdines
pdb|2W16|B Chain B, Structures Of Fpva Bound To Heterologous Pyoverdines
pdb|2W6T|A Chain A, Structures Of P. Aeruginosa Fpva Bound To Heterologous
Pyoverdines: Fpva-Pvd(Dsm50106)-Fe Complex
pdb|2W6T|B Chain B, Structures Of P. Aeruginosa Fpva Bound To Heterologous
Pyoverdines: Fpva-Pvd(Dsm50106)-Fe Complex
pdb|2W6U|A Chain A, Structures Of P. Aeruginosa Fpva Bound To Heterologous
Pyoverdines: Fpva-Pvd(G173)-Fe Complex
pdb|2W6U|B Chain B, Structures Of P. Aeruginosa Fpva Bound To Heterologous
Pyoverdines: Fpva-Pvd(G173)-Fe Complex
pdb|2W75|A Chain A, Structures Of P. Aeruginosa Fpva Bound To Heterologous
Pyoverdines: Apo-Fpva
pdb|2W75|B Chain B, Structures Of P. Aeruginosa Fpva Bound To Heterologous
Pyoverdines: Apo-Fpva
pdb|2W76|A Chain A, Structures Of P. Aeruginosa Fpva Bound To Heterologous
Pyoverdines: Fpva-Pvd(Pa6)-Fe Complex
pdb|2W76|B Chain B, Structures Of P. Aeruginosa Fpva Bound To Heterologous
Pyoverdines: Fpva-Pvd(Pa6)-Fe Complex
pdb|2W77|A Chain A, Structures Of P. Aeruginosa Fpva Bound To Heterologous
Pyoverdines: Fpva-Pvd(Pfl18.1)-Fe Complex
pdb|2W77|B Chain B, Structures Of P. Aeruginosa Fpva Bound To Heterologous
Pyoverdines: Fpva-Pvd(Pfl18.1)-Fe Complex
pdb|2W78|A Chain A, Structures Of P. Aeruginosa Fpva Bound To Heterologous
Pyoverdines: Fpva-Pvd(Atcc13535)-Fe Complex
pdb|2W78|B Chain B, Structures Of P. Aeruginosa Fpva Bound To Heterologous
Pyoverdines: Fpva-Pvd(Atcc13535)-Fe Complex
Length = 772
Score = 26.6 bits (57), Expect = 5.9, Method: Composition-based stats.
Identities = 20/80 (25%), Positives = 37/80 (46%), Gaps = 7/80 (8%)
Query: 74 LSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL----- 128
+ + + ++L A QE+G +VLY E R++ + K E A+ L
Sbjct: 3 VEFDIPPQALGSALQEFGRQADIQVLYRPEEVRNKRSSAI--KGKLEPNQAITELLRGTG 60
Query: 129 NGVELEGRAMRVSLAQGRRS 148
V+ +G A+ +S+A+ S
Sbjct: 61 ASVDFQGNAITISVAEAADS 80
>pdb|2OMY|A Chain A, Crystal Structure Of Inla S192n/hec1 Complex
Length = 461
Score = 25.8 bits (55), Expect = 8.9, Method: Composition-based stats.
Identities = 9/20 (45%), Positives = 16/20 (80%)
Query: 34 IENLDGREYLGRILRVNFSD 53
I+++DG EYL + ++NFS+
Sbjct: 53 IKSIDGVEYLNNLTQINFSN 72
>pdb|2OMV|A Chain A, Crystal Structure Of Inla S192n Y369s/hec1 Complex
pdb|2OMW|A Chain A, Crystal Structure Of Inla S192n Y369s/mec1 Complex
Length = 461
Score = 25.8 bits (55), Expect = 8.9, Method: Composition-based stats.
Identities = 9/20 (45%), Positives = 16/20 (80%)
Query: 34 IENLDGREYLGRILRVNFSD 53
I+++DG EYL + ++NFS+
Sbjct: 53 IKSIDGVEYLNNLTQINFSN 72
>pdb|2OMX|A Chain A, Crystal Structure Of Inla S192n G194s+sHEC1 COMPLEX
Length = 462
Score = 25.8 bits (55), Expect = 9.1, Method: Composition-based stats.
Identities = 9/20 (45%), Positives = 16/20 (80%)
Query: 34 IENLDGREYLGRILRVNFSD 53
I+++DG EYL + ++NFS+
Sbjct: 53 IKSIDGVEYLNNLTQINFSN 72
>pdb|2OMT|A Chain A, Crystal Structure Of Inla G194s+sHEC1 COMPLEX
Length = 462
Score = 25.8 bits (55), Expect = 9.1, Method: Composition-based stats.
Identities = 9/20 (45%), Positives = 16/20 (80%)
Query: 34 IENLDGREYLGRILRVNFSD 53
I+++DG EYL + ++NFS+
Sbjct: 53 IKSIDGVEYLNNLTQINFSN 72
>pdb|1O6S|A Chain A, Internalin (Listeria Monocytogenes) E-Cadherin (Human)
Recognition Complex
pdb|1O6T|A Chain A, Internalin (Inla,Listeria Monocytogenes) - Functional
Domain, Uncomplexed
pdb|1O6V|A Chain A, Internalin (Inla,Listeria Monocytogenes) - Functional
Domain, Uncomplexed
pdb|1O6V|B Chain B, Internalin (Inla,Listeria Monocytogenes) - Functional
Domain, Uncomplexed
Length = 466
Score = 25.8 bits (55), Expect = 9.2, Method: Composition-based stats.
Identities = 9/20 (45%), Positives = 16/20 (80%)
Query: 34 IENLDGREYLGRILRVNFSD 53
I+++DG EYL + ++NFS+
Sbjct: 58 IKSIDGVEYLNNLTQINFSN 77
>pdb|2OMZ|A Chain A, Crystal Structure Of Inla Y369a/hec1 Complex
Length = 466
Score = 25.8 bits (55), Expect = 9.2, Method: Composition-based stats.
Identities = 9/20 (45%), Positives = 16/20 (80%)
Query: 34 IENLDGREYLGRILRVNFSD 53
I+++DG EYL + ++NFS+
Sbjct: 57 IKSIDGVEYLNNLTQINFSN 76
>pdb|2OMU|A Chain A, Crystal Structure Of Inla G194s+s Y369s/hec1 Complex
Length = 462
Score = 25.8 bits (55), Expect = 9.2, Method: Composition-based stats.
Identities = 9/20 (45%), Positives = 16/20 (80%)
Query: 34 IENLDGREYLGRILRVNFSD 53
I+++DG EYL + ++NFS+
Sbjct: 53 IKSIDGVEYLNNLTQINFSN 72
>pdb|4FM9|A Chain A, Human Topoisomerase Ii Alpha Bound To Dna
Length = 763
Score = 25.8 bits (55), Expect = 9.4, Method: Composition-based stats.
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 34 IENLDGREYLGRILRVNFSDKPKPKLPLY 62
I N D RE + I R+ ++P P LP Y
Sbjct: 434 IPNFDVREIVNNIRRLMDGEEPLPMLPSY 462
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 25.8 bits (55), Expect = 10.0, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 7/73 (9%)
Query: 69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE-S 127
L+VG L ++T L F ++G + V+ + + F+ ++T+ E A E S
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVV------QRQQCAFIQFATRQAAEVAAEKS 68
Query: 128 LNGVELEGRAMRV 140
N + + GR + V
Sbjct: 69 FNKLIVNGRRLNV 81
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
0.318 0.134 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,058,183
Number of Sequences: 62578
Number of extensions: 156873
Number of successful extensions: 790
Number of sequences better than 100.0: 202
Number of HSP's better than 100.0 without gapping: 176
Number of HSP's successfully gapped in prelim test: 26
Number of HSP's that attempted gapping in prelim test: 393
Number of HSP's gapped (non-prelim): 361
length of query: 148
length of database: 14,973,337
effective HSP length: 90
effective length of query: 58
effective length of database: 9,341,317
effective search space: 541796386
effective search space used: 541796386
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)