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= 025070
(258 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 77.8 bits (190), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 51/180 (28%), Positives = 87/180 (48%), Gaps = 11/180 (6%)
Query: 83 RVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEK 142
RVY+G+I + D + + G ++ ++ +D T + + FAFV + E A +E+
Sbjct: 30 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 89
Query: 143 LNGTEIGGREIKV----NITEKPLVQVDLSLLQAEDSNFVDSPYKVYVGNLAKTVTSEML 198
+N +GGR IKV NI + Q + L E F ++YV ++ + ++ + +
Sbjct: 90 MNSVMLGGRNIKVGRPSNIGQ---AQPIIDQLAEEARAF----NRIYVASVHQDLSDDDI 142
Query: 199 KKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXLNNSLLEGQRIRVNKA 258
K F G++ SA + R P T K G+GF+ + +N L GQ +RV KA
Sbjct: 143 KSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 202
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/91 (19%), Positives = 49/91 (53%), Gaps = 3/91 (3%)
Query: 74 VDTPSEFAR---RVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMM 130
+D +E AR R+Y+ ++ +++ +D++ + + G ++ A + D TG+ + + F+
Sbjct: 115 IDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEY 174
Query: 131 KTVEDANAVIEKLNGTEIGGREIKVNITEKP 161
+ + + + +N ++GG+ ++V P
Sbjct: 175 EKAQSSQDAVSSMNLFDLGGQYLRVGKAVTP 205
>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 = 76.6 bits (187), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 50/180 (27%), Positives = 86/180 (47%), Gaps = 11/180 (6%)
Query: 83 RVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEK 142
RVY+G+I + D + + G ++ ++ +D T + + FAFV + E A +E+
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 143 LNGTEIGGREIKV----NITEKPLVQVDLSLLQAEDSNFVDSPYKVYVGNLAKTVTSEML 198
+N +GGR IKV NI + Q + L E F ++YV ++ + ++ + +
Sbjct: 75 MNSVMLGGRNIKVGRPSNIGQ---AQPIIDQLAEEARAF----NRIYVASVHQDLSDDDI 127
Query: 199 KKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXLNNSLLEGQRIRVNKA 258
K F G++ S + R P T K G+GF+ + +N L GQ +RV KA
Sbjct: 128 KSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 187
Score = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 17/91 (18%), Positives = 48/91 (52%), Gaps = 3/91 (3%)
Query: 74 VDTPSEFAR---RVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMM 130
+D +E AR R+Y+ ++ +++ +D++ + + G ++ + D TG+ + + F+
Sbjct: 100 IDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEY 159
Query: 131 KTVEDANAVIEKLNGTEIGGREIKVNITEKP 161
+ + + + +N ++GG+ ++V P
Sbjct: 160 EKAQSSQDAVSSMNLFDLGGQYLRVGKAVTP 190
>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 = 74.3 bits (181), Expect = 6e-14, Method: Compositional matrix adjust.
Identities = 50/180 (27%), Positives = 83/180 (46%), Gaps = 11/180 (6%)
Query: 83 RVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEK 142
RVY+G+I + D + + G ++ + +D T + + FAFV + E A +E+
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 143 LNGTEIGGREIKV----NITEKPLVQVDLSLLQAEDSNFVDSPYKVYVGNLAKTVTSEML 198
N +GGR IKV NI + Q + L E F ++YV ++ + ++ + +
Sbjct: 74 XNSVXLGGRNIKVGRPSNIGQ---AQPIIDQLAEEARAF----NRIYVASVHQDLSDDDI 126
Query: 199 KKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXLNNSLLEGQRIRVNKA 258
K F G++ S + R P T K G+GF+ + N L GQ +RV KA
Sbjct: 127 KSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVGKA 186
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/91 (18%), Positives = 47/91 (51%), Gaps = 3/91 (3%)
Query: 74 VDTPSEFAR---RVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMM 130
+D +E AR R+Y+ ++ +++ +D++ + + G ++ + D TG+ + + F+
Sbjct: 99 IDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEY 158
Query: 131 KTVEDANAVIEKLNGTEIGGREIKVNITEKP 161
+ + + + N ++GG+ ++V P
Sbjct: 159 EKAQSSQDAVSSXNLFDLGGQYLRVGKAVTP 189
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 73.2 bits (178), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 48/177 (27%), Positives = 81/177 (45%), Gaps = 13/177 (7%)
Query: 82 RRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIE 141
R +Y+GN+ + I D L + Q G + +++ DK ++ +AFV DAN ++
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQ 59
Query: 142 KLNGTEIGGREIKVNITEKPLVQVDLSLLQAEDSNFVDSPYKVYVGNLAKTVTSEMLKKC 201
LNG +I +K+N Q++ S+ D + ++VG+L V E L+
Sbjct: 60 TLNGKQIENNIVKINWA-----------FQSQQSS-SDDTFNLFVGDLNVNVDDETLRNA 107
Query: 202 FSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXLNNSLLEGQRIRVNKA 258
F + LS V+ T S G+GFV+F + L G+ +R+N A
Sbjct: 108 FKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 164
Score = 48.9 bits (115), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 20/85 (23%), Positives = 46/85 (54%)
Query: 76 TPSEFARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVED 135
+ S+ +++G++ N+D++ L ++ + V++D TG SR + FV + +D
Sbjct: 82 SSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDD 141
Query: 136 ANAVIEKLNGTEIGGREIKVNITEK 160
A ++ + G ++ GR +++N K
Sbjct: 142 AQNAMDSMQGQDLNGRPLRINWAAK 166
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 67.4 bits (163), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 39/142 (27%), Positives = 72/142 (50%), Gaps = 14/142 (9%)
Query: 89 IPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKLNGTEI 148
+P+N+ DE + G +E +++ DK TG+S + FV DA+ I LNG ++
Sbjct: 12 LPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKL 71
Query: 149 GGREIKVNITEKPLVQVDLSLLQAEDSNFVDSPYKVYVGNLAKTVTSEMLKKCFSEKGQV 208
+ IKV+ + D+N +YV L KT++ + +++ FS+ G++
Sbjct: 72 QTKTIKVSYARPSSASI-------RDAN-------LYVSGLPKTMSQKEMEQLFSQYGRI 117
Query: 209 LSAKVLRVPGTSKSSGFGFVTF 230
+++++L T S G GF+ F
Sbjct: 118 ITSRILLDQATGVSRGVGFIRF 139
Score = 37.0 bits (84), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 40/80 (50%), Gaps = 2/80 (2%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKL 143
+Y+ +P+ + E+ ++ ++G + + ++ D+ TG SR F+ +A I+ L
Sbjct: 93 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 152
Query: 144 NGTE-IGGRE-IKVNITEKP 161
NG + +G E I V P
Sbjct: 153 NGQKPLGAAEPITVKFANNP 172
>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 = 1e-11, Method: Compositional matrix adjust.
Identities = 44/142 (30%), Positives = 73/142 (51%), Gaps = 14/142 (9%)
Query: 89 IPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKLNGTEI 148
+P+N+ DEL + G VE A++I DK G S + FV T +DA I LNG +
Sbjct: 10 LPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRL 69
Query: 149 GGREIKVNITEKPLVQVDLSLLQAEDSNFVDSPYKVYVGNLAKTVTSEMLKKCFSEKGQV 208
+ IKV+ +P +V +D+N +Y+ L +T+T + ++ FS G++
Sbjct: 70 QSKTIKVSYA-RPSSEV------IKDAN-------LYISGLPRTMTQKDVEDMFSRFGRI 115
Query: 209 LSAKVLRVPGTSKSSGFGFVTF 230
++++VL T S G F+ F
Sbjct: 116 INSRVLVDQTTGLSRGVAFIRF 137
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 36/73 (49%)
Query: 186 VGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXLNN 245
V L + +T + L+ FS G+V SAK++R S G+GFV + LN
Sbjct: 7 VNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNG 66
Query: 246 SLLEGQRIRVNKA 258
L+ + I+V+ A
Sbjct: 67 LRLQSKTIKVSYA 79
Score = 35.4 bits (80), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 31/67 (46%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKL 143
+YI +PR + ++ + G + + V+ D+ TG SR AF+ +A I
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 144 NGTEIGG 150
NG + G
Sbjct: 151 NGHKPPG 157
>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 = 66.2 bits (160), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 44/142 (30%), Positives = 73/142 (51%), Gaps = 14/142 (9%)
Query: 89 IPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKLNGTEI 148
+P+N+ DEL + G VE A++I DK G S + FV T +DA I LNG +
Sbjct: 10 LPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRL 69
Query: 149 GGREIKVNITEKPLVQVDLSLLQAEDSNFVDSPYKVYVGNLAKTVTSEMLKKCFSEKGQV 208
+ IKV+ +P +V +D+N +Y+ L +T+T + ++ FS G++
Sbjct: 70 QSKTIKVSYA-RPSSEV------IKDAN-------LYISGLPRTMTQKDVEDMFSRFGRI 115
Query: 209 LSAKVLRVPGTSKSSGFGFVTF 230
++++VL T S G F+ F
Sbjct: 116 INSRVLVDQTTGLSRGVAFIRF 137
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 36/73 (49%)
Query: 186 VGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXLNN 245
V L + +T + L+ FS G+V SAK++R S G+GFV + LN
Sbjct: 7 VNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNG 66
Query: 246 SLLEGQRIRVNKA 258
L+ + I+V+ A
Sbjct: 67 LRLQSKTIKVSYA 79
Score = 35.4 bits (80), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 31/67 (46%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKL 143
+YI +PR + ++ + G + + V+ D+ TG SR AF+ +A I
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 144 NGTEIGG 150
NG + G
Sbjct: 151 NGHKPPG 157
>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 = 63.9 bits (154), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 42/142 (29%), Positives = 73/142 (51%), Gaps = 14/142 (9%)
Query: 89 IPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKLNGTEI 148
+P+N+ +E + G +E +++ DK TG+S + FV +DA I LNG +
Sbjct: 10 LPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRL 69
Query: 149 GGREIKVNITEKPLVQVDLSLLQAEDSNFVDSPYKVYVGNLAKTVTSEMLKKCFSEKGQV 208
+ IKV+ +P S D+N +YV L KT+T + L++ FS+ G++
Sbjct: 70 QTKTIKVSYA-RP------SSASIRDAN-------LYVSGLPKTMTQKELEQLFSQYGRI 115
Query: 209 LSAKVLRVPGTSKSSGFGFVTF 230
+++++L T S G GF+ F
Sbjct: 116 ITSRILVDQVTGVSRGVGFIRF 137
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 35/67 (52%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKL 143
+Y+ +P+ + EL ++ ++G + + ++ D+ TG SR F+ +A I+ L
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 144 NGTEIGG 150
NG + G
Sbjct: 151 NGQKPSG 157
Score = 34.3 bits (77), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 35/73 (47%)
Query: 186 VGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXLNN 245
V L + +T E + F G++ S K++R T +S G+GFV + LN
Sbjct: 7 VNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNG 66
Query: 246 SLLEGQRIRVNKA 258
L+ + I+V+ A
Sbjct: 67 LRLQTKTIKVSYA 79
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 59.7 bits (143), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 29/79 (36%), Positives = 48/79 (60%), Gaps = 1/79 (1%)
Query: 83 RVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEK 142
R+Y+G++ NI D L I + G +E +++ D TGRS+ + F+ E A +E+
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 143 LNGTEIGGREIKV-NITEK 160
LNG E+ GR +KV ++TE+
Sbjct: 88 LNGFELAGRPMKVGHVTER 106
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 40/77 (51%)
Query: 180 SPYKVYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXX 239
P ++YVG+L +T +ML+ F G++ S +++ T +S G+GF+TF
Sbjct: 25 GPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKA 84
Query: 240 XXXLNNSLLEGQRIRVN 256
LN L G+ ++V
Sbjct: 85 LEQLNGFELAGRPMKVG 101
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 58.9 bits (141), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 40/162 (24%), Positives = 72/162 (44%), Gaps = 14/162 (8%)
Query: 89 IPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKLNGTEI 148
+P+++ + EL + + G + ++ D TG S +AFV + D+ I+ LNG +
Sbjct: 11 LPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITV 70
Query: 149 GGREIKVNITEKPLVQVDLSLLQAEDSNFVDSPYKVYVGNLAKTVTSEMLKKCFSEKGQV 208
+ +KV+ + +D+N +YV NL +T+T + L F + G +
Sbjct: 71 RNKRLKVSYARPGGESI-------KDTN-------LYVTNLPRTITDDQLDTIFGKYGSI 116
Query: 209 LSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXLNNSLLEG 250
+ +LR T + G FV + LNN + EG
Sbjct: 117 VQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEG 158
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 36/61 (59%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKL 143
+Y+ N+PR I +D+L I ++G++ + ++ DK TGR R AFV E+A I L
Sbjct: 92 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151
Query: 144 N 144
N
Sbjct: 152 N 152
>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 = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 40/162 (24%), Positives = 70/162 (43%), Gaps = 14/162 (8%)
Query: 89 IPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKLNGTEI 148
+P++ + EL + + G + + D TG S +AFV + D+ I+ LNG +
Sbjct: 22 LPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVLNGITV 81
Query: 149 GGREIKVNITEKPLVQVDLSLLQAEDSNFVDSPYKVYVGNLAKTVTSEMLKKCFSEKGQV 208
+ +KV+ + +D+N +YV NL +T+T + L F + G +
Sbjct: 82 RNKRLKVSYARPGGESI-------KDTN-------LYVTNLPRTITDDQLDTIFGKYGSI 127
Query: 209 LSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXLNNSLLEG 250
+ +LR T + G FV + LNN + EG
Sbjct: 128 VQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEG 169
Score = 50.8 bits (120), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 44/79 (55%), Gaps = 2/79 (2%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKL 143
+Y+ N+PR I +D+L I ++G++ + ++ DK TGR R AFV E+A I L
Sbjct: 103 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 162
Query: 144 NGT--EIGGREIKVNITEK 160
N E G + + V + E+
Sbjct: 163 NNVIPEGGSQPLSVRLAEE 181
>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 = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 44/182 (24%), Positives = 82/182 (45%), Gaps = 14/182 (7%)
Query: 76 TPSEFARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVED 135
PS +Y+G++ ++ L + G + V D T RS +A+V + D
Sbjct: 10 APSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPAD 69
Query: 136 ANAVIEKLNGTEIGGREIKVNITEKPLVQVDLSLLQAEDSNFVDSPYKVYVGNLAKTVTS 195
A ++ +N I G+ +++ +++ D SL ++ N +++ NL K++ +
Sbjct: 70 AERALDTMNFDVIKGKPVRIMWSQR-----DPSLRKSGVGN-------IFIKNLDKSIDN 117
Query: 196 EMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXLNNSLLEGQRIRV 255
+ L FS G +LS KV V + S G+GFV F +N LL +++ V
Sbjct: 118 KALYDTFSAFGNILSCKV--VCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 175
Query: 256 NK 257
+
Sbjct: 176 GR 177
>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 = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 44/182 (24%), Positives = 82/182 (45%), Gaps = 14/182 (7%)
Query: 76 TPSEFARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVED 135
PS +Y+G++ ++ L + G + V D T RS +A+V + D
Sbjct: 5 APSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPAD 64
Query: 136 ANAVIEKLNGTEIGGREIKVNITEKPLVQVDLSLLQAEDSNFVDSPYKVYVGNLAKTVTS 195
A ++ +N I G+ +++ +++ D SL ++ N +++ NL K++ +
Sbjct: 65 AERALDTMNFDVIKGKPVRIMWSQR-----DPSLRKSGVGN-------IFIKNLDKSIDN 112
Query: 196 EMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXLNNSLLEGQRIRV 255
+ L FS G +LS KV V + S G+GFV F +N LL +++ V
Sbjct: 113 KALYDTFSAFGNILSCKV--VCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 170
Query: 256 NK 257
+
Sbjct: 171 GR 172
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 55.8 bits (133), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 43/67 (64%), Gaps = 2/67 (2%)
Query: 97 ELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKLNGTEIGGREIKVN 156
+L ++ ++G + ++YD+ + RSR FAFV + V+DA E+ NG E+ GR I+V+
Sbjct: 31 DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD 90
Query: 157 --ITEKP 161
IT++P
Sbjct: 91 FSITKRP 97
Score = 32.7 bits (73), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 31/68 (45%)
Query: 189 LAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXLNNSLL 248
L+ T L++ FS+ G + ++ + +S GF FV F N L
Sbjct: 23 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 82
Query: 249 EGQRIRVN 256
+G+RIRV+
Sbjct: 83 DGRRIRVD 90
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 55.8 bits (133), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 43/67 (64%), Gaps = 2/67 (2%)
Query: 97 ELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKLNGTEIGGREIKVN 156
+L ++ ++G + ++YD+ + RSR FAFV + V+DA E+ NG E+ GR I+V+
Sbjct: 28 DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD 87
Query: 157 --ITEKP 161
IT++P
Sbjct: 88 FSITKRP 94
Score = 33.1 bits (74), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 32/71 (45%)
Query: 186 VGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXLNN 245
V L+ T L++ FS+ G + ++ + +S GF FV F N
Sbjct: 17 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 76
Query: 246 SLLEGQRIRVN 256
L+G+RIRV+
Sbjct: 77 MELDGRRIRVD 87
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 55.1 bits (131), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 43/67 (64%), Gaps = 2/67 (2%)
Query: 97 ELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKLNGTEIGGREIKVN 156
+L ++ ++G + ++YD+ + RSR FAFV + V+DA E+ NG E+ GR I+V+
Sbjct: 62 DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD 121
Query: 157 --ITEKP 161
IT++P
Sbjct: 122 FSITKRP 128
Score = 32.3 bits (72), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 31/69 (44%)
Query: 188 NLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXLNNSL 247
L+ T L++ FS+ G + ++ + +S GF FV F N
Sbjct: 53 GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME 112
Query: 248 LEGQRIRVN 256
L+G+RIRV+
Sbjct: 113 LDGRRIRVD 121
>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 = 53.5 bits (127), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 34/148 (22%), Positives = 71/148 (47%), Gaps = 16/148 (10%)
Query: 83 RVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEK 142
+++IG + + D L + ++G V +++ D TGRSR F F+ + + V++
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 143 LNGTEIGGREIKVNITEKPLVQVDLSLLQAEDSNFVDSPYKVYVGNLAKTVTSEMLKKCF 202
+ I + ++ ++ + E D K++VG + V + ++ F
Sbjct: 65 QH------------ILDGKVIDPKRAIPRDEQ----DKTGKIFVGGIGPDVRPKEFEEFF 108
Query: 203 SEKGQVLSAKVLRVPGTSKSSGFGFVTF 230
S+ G ++ A+++ T +S GFGFVT+
Sbjct: 109 SQWGTIIDAQLMLDKDTGQSRGFGFVTY 136
Score = 36.2 bits (82), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 33/57 (57%), Gaps = 3/57 (5%)
Query: 83 RVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAV 139
++++G I ++ E + + G + A+++ DK TG+SR F FV T + A+AV
Sbjct: 89 KIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFV---TYDSADAV 142
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 53.1 bits (126), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 46/78 (58%)
Query: 81 ARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVI 140
+R VY+G+IP + +++ + G V ++++D TGRS+ +AF+ + +E + + +
Sbjct: 2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61
Query: 141 EKLNGTEIGGREIKVNIT 158
LNG ++G R +K +
Sbjct: 62 RNLNGYQLGSRFLKCGYS 79
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 53.1 bits (126), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 41/75 (54%)
Query: 82 RRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIE 141
R V++GNIP ++L I E G V ++YD+ TG+ + + F + E A + +
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68
Query: 142 KLNGTEIGGREIKVN 156
LNG E GR ++V+
Sbjct: 69 NLNGREFSGRALRVD 83
Score = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 36/75 (48%)
Query: 184 VYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXL 243
V+VGN+ T E LK FSE G V+S +++ T K G+GF + L
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 244 NNSLLEGQRIRVNKA 258
N G+ +RV+ A
Sbjct: 71 NGREFSGRALRVDNA 85
>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 = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 46/78 (58%)
Query: 81 ARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVI 140
+R VY+G+IP + +++ + G V ++++D TGRS+ +AF+ + +E + + +
Sbjct: 3 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 62
Query: 141 EKLNGTEIGGREIKVNIT 158
LNG ++G R +K +
Sbjct: 63 RNLNGYQLGSRFLKCGYS 80
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 52.4 bits (124), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 38/60 (63%)
Query: 97 ELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKLNGTEIGGREIKVN 156
+L ++ ++G + ++YD+ + RSR FAFV + V+DA E+ NG E+ GR I+V+
Sbjct: 31 DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVS 90
Score = 31.2 bits (69), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 31/69 (44%)
Query: 188 NLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXLNNSL 247
L+ T L++ FS+ G + ++ + +S GF FV F N
Sbjct: 22 GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME 81
Query: 248 LEGQRIRVN 256
L+G+RIRV+
Sbjct: 82 LDGRRIRVS 90
>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 = 52.4 bits (124), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 43/77 (55%)
Query: 182 YKVYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXX 241
+ V+VG+L+ +T+E +K F+ G++ A+V++ T KS G+GFV+F
Sbjct: 16 FHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 75
Query: 242 XLNNSLLEGQRIRVNKA 258
+ L G++IR N A
Sbjct: 76 QMGGQWLGGRQIRTNWA 92
Score = 51.2 bits (121), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 27/88 (30%), Positives = 46/88 (52%), Gaps = 3/88 (3%)
Query: 75 DTPSEFARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVE 134
DT + F V++G++ I +++ G + A V+ D TG+S+ + FV
Sbjct: 11 DTSNHF--HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKW 68
Query: 135 DANAVIEKLNGTEIGGREIKVNI-TEKP 161
DA I+++ G +GGR+I+ N T KP
Sbjct: 69 DAENAIQQMGGQWLGGRQIRTNWATRKP 96
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 52.4 bits (124), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 43/77 (55%)
Query: 182 YKVYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXX 241
+ V+VG+L+ +T+E +K F+ G++ A+V++ T KS G+GFV+F
Sbjct: 16 FHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIV 75
Query: 242 XLNNSLLEGQRIRVNKA 258
+ L G++IR N A
Sbjct: 76 HMGGQWLGGRQIRTNWA 92
Score = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 27/88 (30%), Positives = 44/88 (50%), Gaps = 3/88 (3%)
Query: 75 DTPSEFARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVE 134
DT + F V++G++ I +++ G + A V+ D TG+S+ + FV
Sbjct: 11 DTSNHF--HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKL 68
Query: 135 DANAVIEKLNGTEIGGREIKVNI-TEKP 161
DA I + G +GGR+I+ N T KP
Sbjct: 69 DAENAIVHMGGQWLGGRQIRTNWATRKP 96
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 52.4 bits (124), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 46/78 (58%), Gaps = 1/78 (1%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKL 143
+Y+G++ NI D L I + G ++ ++ D TGRS+ + F+ E A +E+L
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 144 NGTEIGGREIKV-NITEK 160
NG E+ GR ++V ++TE+
Sbjct: 68 NGFELAGRPMRVGHVTER 85
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 38/73 (52%)
Query: 184 VYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXL 243
+YVG+L +T +ML+ F G++ + +++ T +S G+GF+TF L
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 244 NNSLLEGQRIRVN 256
N L G+ +RV
Sbjct: 68 NGFELAGRPMRVG 80
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 51.6 bits (122), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 36/154 (23%), Positives = 70/154 (45%), Gaps = 19/154 (12%)
Query: 82 RRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVI- 140
R+++IG + ++ L ++ G + V+ D T RSR F FV TVE+ +A +
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 141 ---EKLNGTEI-GGREIKVNITEKPLVQVDLSLLQAEDSNFVDSPYKVYVGNLAKTVTSE 196
K++G + R + +++P + + K++VG + +
Sbjct: 74 ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVK--------------KIFVGGIKEDTEEH 119
Query: 197 MLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTF 230
L+ F + G++ +++ G+ K GF FVTF
Sbjct: 120 HLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
>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 = 51.6 bits (122), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 36/154 (23%), Positives = 70/154 (45%), Gaps = 19/154 (12%)
Query: 82 RRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVI- 140
R+++IG + ++ L ++ G + V+ D T RSR F FV TVE+ +A +
Sbjct: 7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66
Query: 141 ---EKLNGTEI-GGREIKVNITEKPLVQVDLSLLQAEDSNFVDSPYKVYVGNLAKTVTSE 196
K++G + R + +++P + + K++VG + +
Sbjct: 67 ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVK--------------KIFVGGIKEDTEEH 112
Query: 197 MLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTF 230
L+ F + G++ +++ G+ K GF FVTF
Sbjct: 113 HLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 146
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 51.6 bits (122), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 36/154 (23%), Positives = 70/154 (45%), Gaps = 19/154 (12%)
Query: 82 RRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVI- 140
R+++IG + ++ L ++ G + V+ D T RSR F FV TVE+ +A +
Sbjct: 12 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 71
Query: 141 ---EKLNGTEI-GGREIKVNITEKPLVQVDLSLLQAEDSNFVDSPYKVYVGNLAKTVTSE 196
K++G + R + +++P + + K++VG + +
Sbjct: 72 ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVK--------------KIFVGGIKEDTEEH 117
Query: 197 MLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTF 230
L+ F + G++ +++ G+ K GF FVTF
Sbjct: 118 HLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 151
>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 = 51.6 bits (122), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 36/154 (23%), Positives = 70/154 (45%), Gaps = 19/154 (12%)
Query: 82 RRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVI- 140
R+++IG + ++ L ++ G + V+ D T RSR F FV TVE+ +A +
Sbjct: 13 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 72
Query: 141 ---EKLNGTEI-GGREIKVNITEKPLVQVDLSLLQAEDSNFVDSPYKVYVGNLAKTVTSE 196
K++G + R + +++P + + K++VG + +
Sbjct: 73 ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVK--------------KIFVGGIKEDTEEH 118
Query: 197 MLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTF 230
L+ F + G++ +++ G+ K GF FVTF
Sbjct: 119 HLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 152
>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 = 51.6 bits (122), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 36/154 (23%), Positives = 70/154 (45%), Gaps = 19/154 (12%)
Query: 82 RRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVI- 140
R+++IG + ++ L ++ G + V+ D T RSR F FV TVE+ +A +
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 141 ---EKLNGTEI-GGREIKVNITEKPLVQVDLSLLQAEDSNFVDSPYKVYVGNLAKTVTSE 196
K++G + R + +++P + + K++VG + +
Sbjct: 74 ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVK--------------KIFVGGIKEDTEEH 119
Query: 197 MLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTF 230
L+ F + G++ +++ G+ K GF FVTF
Sbjct: 120 HLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
>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 = 51.2 bits (121), Expect = 5e-07, Method: Composition-based stats.
Identities = 22/74 (29%), Positives = 45/74 (60%)
Query: 81 ARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVI 140
+R VY+G+IP + +++ + G V ++++D TGRS+ +AF+ + +E + + +
Sbjct: 4 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 63
Query: 141 EKLNGTEIGGREIK 154
LNG ++G R +K
Sbjct: 64 RNLNGYQLGSRFLK 77
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 51.2 bits (121), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 36/154 (23%), Positives = 70/154 (45%), Gaps = 19/154 (12%)
Query: 82 RRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVI- 140
R+++IG + ++ L ++ G + V+ D T RSR F FV TVE+ +A +
Sbjct: 15 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 74
Query: 141 ---EKLNGTEI-GGREIKVNITEKPLVQVDLSLLQAEDSNFVDSPYKVYVGNLAKTVTSE 196
K++G + R + +++P + + K++VG + +
Sbjct: 75 ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVK--------------KIFVGGIKEDTEEH 120
Query: 197 MLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTF 230
L+ F + G++ +++ G+ K GF FVTF
Sbjct: 121 HLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 154
>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 = 50.8 bits (120), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 44/79 (55%), Gaps = 2/79 (2%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKL 143
+Y+ N+PR I +D+L I ++G++ + ++ DK TGR R AFV E+A I L
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 144 NGT--EIGGREIKVNITEK 160
N E G + + V + E+
Sbjct: 76 NNVIPEGGSQPLSVRLAEE 94
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 31/67 (46%)
Query: 184 VYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXL 243
+YV NL +T+T + L F + G ++ +LR T + G FV + L
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 244 NNSLLEG 250
NN + EG
Sbjct: 76 NNVIPEG 82
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 50.4 bits (119), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 37/148 (25%), Positives = 72/148 (48%), Gaps = 27/148 (18%)
Query: 83 RVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEK 142
R+++GN+P +I ++ ++ + +G E +EV + R R F F+ +++ A +
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYG--EPSEV----FINRDRGFGFIRLESRTLAEIAKAE 77
Query: 143 LNGTEIGGREIKVNITEKPLVQVDLSLLQAEDSNFVDSPYKVYVGNLAKTVTSEMLKKCF 202
L+GT + R +++ F + V NL+ V++E+L++ F
Sbjct: 78 LDGTILKSRPLRI--------------------RFATHGAALTVKNLSPVVSNELLEQAF 117
Query: 203 SEKGQVLSAKVLRVPGTSKSSGFGFVTF 230
S+ G V A V+ V +++G GFV F
Sbjct: 118 SQFGPVEKAVVV-VDDRGRATGKGFVEF 144
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 45/78 (57%)
Query: 83 RVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEK 142
++++G + + + L ++ ++G + + V+ D+ T RSR F FV + ++DA +
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 143 LNGTEIGGREIKVNITEK 160
+NG + GR+I+V+ K
Sbjct: 74 MNGKSVDGRQIRVDQAGK 91
Score = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 43/76 (56%)
Query: 183 KVYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXX 242
K++VG L+ + L++ FS+ GQ+ V++ T +S GFGFVTF
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 243 LNNSLLEGQRIRVNKA 258
+N ++G++IRV++A
Sbjct: 74 MNGKSVDGRQIRVDQA 89
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 44/81 (54%), Gaps = 1/81 (1%)
Query: 82 RRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIE 141
R +Y+G + +D+ L G + ++ D T + R FAFV + EDA A I+
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
Query: 142 KLNGTEIGGREIKVNITEKPL 162
+N +E+ GR I+VN+ KP+
Sbjct: 73 NMNESELFGRTIRVNLA-KPM 92
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 34/75 (45%)
Query: 184 VYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXL 243
+YVG LA+ V ++L F G + ++ T K GF FV F +
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 244 NNSLLEGQRIRVNKA 258
N S L G+ IRVN A
Sbjct: 75 NESELFGRTIRVNLA 89
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 41/160 (25%), Positives = 76/160 (47%), Gaps = 17/160 (10%)
Query: 75 DTPSEFARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTG--RSRRFAFVMMKT 132
D P A ++++G +PR +L ++ +++GAV + V+ D+ +S+ FV T
Sbjct: 9 DQPDLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYT 68
Query: 133 VEDANAVIEKLNGTEIGGREIKVNITEKPLVQ--VDLSLLQAEDSNFVDSPYKVYVGNLA 190
+ A +E N N+ P + + + +E +N V+ K+++G ++
Sbjct: 69 RK---AALEAQNALH--------NMKVLPGMHHPIQMKPADSEKNNAVED-RKLFIGMIS 116
Query: 191 KTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTF 230
K T ++ FS GQ+ ++LR P S G FVTF
Sbjct: 117 KKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTF 155
>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 = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/68 (38%), Positives = 37/68 (54%)
Query: 89 IPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKLNGTEI 148
+P+N+ DEL + G VE A++I DK G S + FV T +DA I LNG +
Sbjct: 12 LPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRL 71
Query: 149 GGREIKVN 156
+ IKV+
Sbjct: 72 QSKTIKVS 79
Score = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 36/73 (49%)
Query: 186 VGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXLNN 245
V L + +T + L+ FS G+V SAK++R S G+GFV + LN
Sbjct: 9 VNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNG 68
Query: 246 SLLEGQRIRVNKA 258
L+ + I+V+ A
Sbjct: 69 LRLQSKTIKVSYA 81
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 44/82 (53%), Gaps = 1/82 (1%)
Query: 83 RVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEK 142
+++IG + R + L + +HG + + +I D+ T +SR FAF+ + DA +
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKD 67
Query: 143 LNGTEIGGREIKVNITEKPLVQ 164
+NG + G+ IKV +KP Q
Sbjct: 68 MNGKSLHGKAIKVEQAKKPSFQ 89
Score = 47.4 bits (111), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 27/82 (32%), Positives = 42/82 (51%), Gaps = 3/82 (3%)
Query: 178 VDSPYKVYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPG-TSKSSGFGFVTFXXXXXX 236
D P K+++G L + +MLK F + G + ++VL + TSKS GF F+TF
Sbjct: 4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPI--SEVLLIKDRTSKSRGFAFITFENPADA 61
Query: 237 XXXXXXLNNSLLEGQRIRVNKA 258
+N L G+ I+V +A
Sbjct: 62 KNAAKDMNGKSLHGKAIKVEQA 83
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 43/74 (58%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKL 143
VY+ N+P ++ N++L +I ++G V K ++ DK T +S+ AF++ + A +
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 144 NGTEIGGREIKVNI 157
N ++ GR IK +I
Sbjct: 79 NNKQLFGRVIKASI 92
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 38/75 (50%)
Query: 184 VYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXL 243
VYV NL ++T+ L + FS+ G+V+ +++ T KS G F+ F +
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 244 NNSLLEGQRIRVNKA 258
NN L G+ I+ + A
Sbjct: 79 NNKQLFGRVIKASIA 93
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 41/76 (53%)
Query: 82 RRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIE 141
R +Y+G + +D+ L G + ++ D T + R FAFV + EDA A I+
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
Query: 142 KLNGTEIGGREIKVNI 157
+N +E+ GR I+VN+
Sbjct: 124 NMNESELFGRTIRVNL 139
Score = 40.4 bits (93), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 34/75 (45%)
Query: 184 VYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXL 243
+YVG LA+ V ++L F G + ++ T K GF FV F +
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 244 NNSLLEGQRIRVNKA 258
N S L G+ IRVN A
Sbjct: 126 NESELFGRTIRVNLA 140
>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 = 48.9 bits (115), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 41/77 (53%)
Query: 82 RRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIE 141
R +Y+G + +D+ L G + ++ D T + R FAFV + EDA A I+
Sbjct: 3 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 62
Query: 142 KLNGTEIGGREIKVNIT 158
+N +E+ GR I+VN+
Sbjct: 63 NMNESELFGRTIRVNLA 79
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 34/75 (45%)
Query: 184 VYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXL 243
+YVG LA+ V ++L F G + ++ T K GF FV F +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 244 NNSLLEGQRIRVNKA 258
N S L G+ IRVN A
Sbjct: 65 NESELFGRTIRVNLA 79
>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 = 48.9 bits (115), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 41/77 (53%)
Query: 82 RRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIE 141
R +Y+G + +D+ L G + ++ D T + R FAFV + EDA A I+
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
Query: 142 KLNGTEIGGREIKVNIT 158
+N +E+ GR I+VN+
Sbjct: 68 NMNESELFGRTIRVNLA 84
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 34/75 (45%)
Query: 184 VYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXL 243
+YVG LA+ V ++L F G + ++ T K GF FV F +
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 244 NNSLLEGQRIRVNKA 258
N S L G+ IRVN A
Sbjct: 70 NESELFGRTIRVNLA 84
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 41/77 (53%)
Query: 82 RRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIE 141
R +Y+G + +D+ L G + ++ D T + R FAFV + EDA A I+
Sbjct: 6 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65
Query: 142 KLNGTEIGGREIKVNIT 158
+N +E+ GR I+VN+
Sbjct: 66 NMNESELFGRTIRVNLA 82
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 34/75 (45%)
Query: 184 VYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXL 243
+YVG LA+ V ++L F G + ++ T K GF FV F +
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 244 NNSLLEGQRIRVNKA 258
N S L G+ IRVN A
Sbjct: 68 NESELFGRTIRVNLA 82
>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 = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 26/67 (38%), Positives = 35/67 (52%)
Query: 89 IPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKLNGTEI 148
+P+N DEL + G VE A++I DK G S + FV T +DA I LNG +
Sbjct: 27 LPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRL 86
Query: 149 GGREIKV 155
+ IKV
Sbjct: 87 QSKTIKV 93
Score = 37.0 bits (84), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 35/73 (47%)
Query: 186 VGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXLNN 245
V L + T + L+ FS G+V SAK++R S G+GFV + LN
Sbjct: 24 VNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNG 83
Query: 246 SLLEGQRIRVNKA 258
L+ + I+V+ A
Sbjct: 84 LRLQSKTIKVSYA 96
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 48.1 bits (113), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 28/75 (37%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 184 VYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXL 243
+YVGNL + TSE +K+ FS+ G+V + K++ T K GFGFV L
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEM-QEESVSEAIAKL 62
Query: 244 NNSLLEGQRIRVNKA 258
+N+ G+ IRV +A
Sbjct: 63 DNTDFMGRTIRVTEA 77
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 44/74 (59%), Gaps = 1/74 (1%)
Query: 82 RRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIE 141
R +Y+GN+ + ++++ ++ + G V ++IYD+ T + + F FV M+ E + I
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIA 60
Query: 142 KLNGTEIGGREIKV 155
KL+ T+ GR I+V
Sbjct: 61 KLDNTDFMGRTIRV 74
>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
pdb|3MD1|B Chain B, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
Length = 83
Score = 47.8 bits (112), Expect = 6e-06, Method: Composition-based stats.
Identities = 19/77 (24%), Positives = 43/77 (55%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKL 143
+++G++ N+D++ L ++ + V++D TG SR + FV + +DA ++ +
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 144 NGTEIGGREIKVNITEK 160
G ++ GR +++N K
Sbjct: 64 QGQDLNGRPLRINWAAK 80
Score = 40.0 bits (92), Expect = 0.001, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 35/77 (45%)
Query: 182 YKVYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXX 241
+ ++VG+L V E L+ F + LS V+ T S G+GFV+F
Sbjct: 2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 242 XLNNSLLEGQRIRVNKA 258
+ L G+ +R+N A
Sbjct: 62 SMQGQDLNGRPLRINWA 78
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 47.8 bits (112), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 39/148 (26%), Positives = 69/148 (46%), Gaps = 27/148 (18%)
Query: 83 RVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEK 142
R+++GN+P +I +E+ K+ +++G EV K G F F+ ++T A +
Sbjct: 24 RLFVGNLPPDITEEEMRKLFEKYGKA--GEVFIHKDKG----FGFIRLETRTLAEIAKVE 77
Query: 143 LNGTEIGGREIKVNITEKPLVQVDLSLLQAEDSNFVDSPYKVYVGNLAKTVTSEMLKKCF 202
L+ + G++++V F + V NL + V++E+L++ F
Sbjct: 78 LDNMPLRGKQLRV--------------------RFACHSASLTVRNLPQYVSNELLEEAF 117
Query: 203 SEKGQVLSAKVLRVPGTSKSSGFGFVTF 230
S GQV A V+ V + SG G V F
Sbjct: 118 SVFGQVERAVVI-VDDRGRPSGKGIVEF 144
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 6/76 (7%)
Query: 183 KVYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXX 242
+++VGNL +T E ++K F + G+ + +V K GFGF+
Sbjct: 24 RLFVGNLPPDITEEEMRKLFEKYGK--AGEVF----IHKDKGFGFIRLETRTLAEIAKVE 77
Query: 243 LNNSLLEGQRIRVNKA 258
L+N L G+++RV A
Sbjct: 78 LDNMPLRGKQLRVRFA 93
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 47.4 bits (111), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 39/154 (25%), Positives = 74/154 (48%), Gaps = 17/154 (11%)
Query: 81 ARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTG--RSRRFAFVMMKTVEDANA 138
A ++++G +PR +L ++ +++GAV + V+ D+ +S+ FV T + A
Sbjct: 3 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRK---A 59
Query: 139 VIEKLNGTEIGGREIKVNITEKPLVQ--VDLSLLQAEDSNFVDSPYKVYVGNLAKTVTSE 196
+E N N+ P + + + +E +N V+ K+++G ++K T
Sbjct: 60 ALEAQNALH--------NMKVLPGMHHPIQMKPADSEKNNAVED-RKLFIGMISKKCTEN 110
Query: 197 MLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTF 230
++ FS GQ+ ++LR P S G FVTF
Sbjct: 111 DIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTF 143
>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 = 1e-05, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 42/78 (53%), Gaps = 8/78 (10%)
Query: 83 RVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEK 142
++++GN+ + EL + + G V + +V+ D +AFV M+ DA A I +
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQ 62
Query: 143 LNGTEIGGREIKVNITEK 160
LNG E+ G+ I V ++ K
Sbjct: 63 LNGKEVKGKRINVELSTK 80
Score = 35.8 bits (81), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 35/74 (47%), Gaps = 8/74 (10%)
Query: 182 YKVYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXX 241
+K++VGN++ TS+ L+ F +G+V+ V++ + FV
Sbjct: 10 WKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIA 61
Query: 242 XLNNSLLEGQRIRV 255
LN ++G+RI V
Sbjct: 62 QLNGKEVKGKRINV 75
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 45/75 (60%), Gaps = 2/75 (2%)
Query: 82 RRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIE 141
+R+++ NIP + +L ++ + G + E+I+++ S+ F FV + DA+ E
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRARE 73
Query: 142 KLNGTEIGGREIKVN 156
KL+GT + GR+I+VN
Sbjct: 74 KLHGTVVEGRKIEVN 88
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 42/79 (53%), Gaps = 2/79 (2%)
Query: 180 SPYKVYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXX 239
+P +++V N+ L++ F + G++L +++ SK GFGFVTF
Sbjct: 14 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSK--GFGFVTFENSADADRA 71
Query: 240 XXXLNNSLLEGQRIRVNKA 258
L+ +++EG++I VN A
Sbjct: 72 REKLHGTVVEGRKIEVNNA 90
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 45/75 (60%), Gaps = 2/75 (2%)
Query: 82 RRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIE 141
+R+++ NIP + +L ++ + G + E+I+++ S+ F FV + DA+ E
Sbjct: 30 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRARE 87
Query: 142 KLNGTEIGGREIKVN 156
KL+GT + GR+I+VN
Sbjct: 88 KLHGTVVEGRKIEVN 102
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
Query: 181 PYKVYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXX 240
P +++V N+ L++ F + G++L ++ + S GFGFVTF
Sbjct: 29 PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEI--IFNERGSKGFGFVTFENSADADRAR 86
Query: 241 XXLNNSLLEGQRIRVNKA 258
L+ +++EG++I VN A
Sbjct: 87 EKLHGTVVEGRKIEVNNA 104
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 36/67 (53%)
Query: 89 IPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKLNGTEI 148
+P+N+ DE + G +E +++ DK TG+S + FV DA+ I LNG ++
Sbjct: 12 LPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKL 71
Query: 149 GGREIKV 155
+ IKV
Sbjct: 72 QTKTIKV 78
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 35/61 (57%)
Query: 170 LQAEDSNFVDSPYKVYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVT 229
L S+ S K+++G L+ T E L++ F + G+V V+R P T +S GFGFVT
Sbjct: 14 LVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVT 73
Query: 230 F 230
F
Sbjct: 74 F 74
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 24/46 (52%)
Query: 83 RVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFV 128
+++IG + + L + + G V++ V+ D T RSR F FV
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFV 72
>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 = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 40/74 (54%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKL 143
++I ++P+ + +L ++ G V A+V DK T S+ F FV A A I+ +
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 144 NGTEIGGREIKVNI 157
NG +IG + +KV +
Sbjct: 88 NGFQIGMKRLKVQL 101
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 44/79 (55%)
Query: 77 PSEFARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDA 136
P A +++IG +P +++D++ +++ G ++ ++ D TG S+ +AF +
Sbjct: 90 PLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVT 149
Query: 137 NAVIEKLNGTEIGGREIKV 155
+ I LNG ++G +++ V
Sbjct: 150 DQAIAGLNGMQLGDKKLLV 168
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 34/183 (18%), Positives = 75/183 (40%), Gaps = 20/183 (10%)
Query: 81 ARRVYIGNIPRNIDNDELTKIVQEH---GAVEKA--EVIYDKYTGRSRRFAFVMMKTVED 135
ARR+Y+GNIP I + + G + +A + + + FAF+ ++V++
Sbjct: 4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63
Query: 136 ANAVIEKLNGTEIGGREIKVNITEKPLVQVDLSLLQAEDSNFVDSPYKVYVGNLAKTVTS 195
+ +G G+ +K+ +P D + +K+++G L +
Sbjct: 64 TTQAM-AFDGIIFQGQSLKI---RRP-----------HDYQPLPGAHKLFIGGLPNYLND 108
Query: 196 EMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXLNNSLLEGQRIRV 255
+ +K+ + G + + +++ T S G+ F + LN L +++ V
Sbjct: 109 DQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLV 168
Query: 256 NKA 258
+A
Sbjct: 169 QRA 171
>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 = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 40/154 (25%), Positives = 72/154 (46%), Gaps = 17/154 (11%)
Query: 81 ARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTG--RSRRFAFVMMKTVEDANA 138
A + ++G +PR +L ++ +++GAV + V+ D+ +S+ FV T + A
Sbjct: 3 AIKXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALE 62
Query: 139 VIEKLNGTEI--GGREIKVNITEKPLVQVDLSLLQAEDSNFVDSPYKVYVGNLAKTVTSE 196
L+ ++ G I KP +E +N V+ K+++G ++K T
Sbjct: 63 AQNALHNXKVLPGXHH---PIQXKP--------ADSEKNNAVED-RKLFIGXISKKCTEN 110
Query: 197 MLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTF 230
++ FS GQ+ ++LR P S G FVTF
Sbjct: 111 DIRVXFSSFGQIEECRILRGP-DGLSRGCAFVTF 143
>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 = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 44/79 (55%)
Query: 77 PSEFARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDA 136
P A +++IG +P +++D++ +++ G ++ ++ D TG S+ +AF +
Sbjct: 92 PLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVT 151
Query: 137 NAVIEKLNGTEIGGREIKV 155
+ I LNG ++G +++ V
Sbjct: 152 DQAIAGLNGMQLGDKKLLV 170
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 34/187 (18%), Positives = 75/187 (40%), Gaps = 20/187 (10%)
Query: 77 PSEFARRVYIGNIPRNIDNDELTKIVQEH---GAVEKA--EVIYDKYTGRSRRFAFVMMK 131
P ARR+Y+GNIP I + + G + +A + + + FAF+ +
Sbjct: 2 PLGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFR 61
Query: 132 TVEDANAVIEKLNGTEIGGREIKVNITEKPLVQVDLSLLQAEDSNFVDSPYKVYVGNLAK 191
+V++ + +G G+ +K+ + D + +K+++G L
Sbjct: 62 SVDETTQAM-AFDGIIFQGQSLKIR--------------RPHDYQPLPGAHKLFIGGLPN 106
Query: 192 TVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXLNNSLLEGQ 251
+ + +K+ + G + + +++ T S G+ F + LN L +
Sbjct: 107 YLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDK 166
Query: 252 RIRVNKA 258
++ V +A
Sbjct: 167 KLLVQRA 173
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 43/82 (52%), Gaps = 15/82 (18%)
Query: 83 RVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMM-------KTVED 135
++++G +P + + L K + G +E+A VI D+ TG+SR + FV M + +D
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 136 ANAVIEKLNGTEIGGREIKVNI 157
N +I+ GR+ VN+
Sbjct: 79 PNPIID--------GRKANVNL 92
Score = 36.2 bits (82), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 35/76 (46%), Gaps = 1/76 (1%)
Query: 183 KVYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXX 242
K++VG L T L+K F G + A V+ T KS G+GFVT
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 243 LNNSLLEGQRIRVNKA 258
N +++G++ VN A
Sbjct: 79 -PNPIIDGRKANVNLA 93
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 45.1 bits (105), Expect = 4e-05, Method: Composition-based stats.
Identities = 21/48 (43%), Positives = 31/48 (64%)
Query: 183 KVYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTF 230
K+++G L+ T E L++ F + G+V V+R P T +S GFGFVTF
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49
Score = 27.7 bits (60), Expect = 6.4, Method: Composition-based stats.
Identities = 14/46 (30%), Positives = 24/46 (52%)
Query: 83 RVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFV 128
+++IG + + L + + G V++ V+ D T RSR F FV
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFV 47
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 41/77 (53%)
Query: 82 RRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIE 141
R + + IP +D +L ++ + +G +E +++ D+ T +SR + FV ++ A I
Sbjct: 43 RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA 102
Query: 142 KLNGTEIGGREIKVNIT 158
LNG I + +KV +
Sbjct: 103 GLNGFNILNKRLKVALA 119
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 44.7 bits (104), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 38/74 (51%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKL 143
++I ++P+ + +L G V A+V DK T S+ F FV + A I+ +
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 144 NGTEIGGREIKVNI 157
NG ++G + +KV +
Sbjct: 103 NGFQVGTKRLKVQL 116
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 33/72 (45%)
Query: 184 VYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXL 243
+++ +L + T L F G V+SAKV TS S FGFV+F +
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 244 NNSLLEGQRIRV 255
N + +R++V
Sbjct: 103 NGFQVGTKRLKV 114
>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 = 44.7 bits (104), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 18/75 (24%), Positives = 43/75 (57%)
Query: 81 ARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVI 140
A +++IG +P +++D++ +++ G ++ ++ D TG S+ +AF + + I
Sbjct: 114 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 173
Query: 141 EKLNGTEIGGREIKV 155
LNG ++G +++ V
Sbjct: 174 AGLNGMQLGDKKLLV 188
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 38/193 (19%), Positives = 81/193 (41%), Gaps = 20/193 (10%)
Query: 81 ARRVYIGNIPRNIDNDELTKIVQEH---GAVEKA--EVIYDKYTGRSRRFAFVMMKTVED 135
ARR+Y+GNIP I + + G + +A + + + FAF+ ++V++
Sbjct: 4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63
Query: 136 ANAVIEKLNGTEIGGREIKV----------NITEKPLVQVDLSLLQAEDSNFVDSPYKVY 185
+ +G G+ +K+ ++E P V V + + DS +K++
Sbjct: 64 TTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVV----STVVPDSAHKLF 118
Query: 186 VGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXLNN 245
+G L + + +K+ + G + + +++ T S G+ F + LN
Sbjct: 119 IGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNG 178
Query: 246 SLLEGQRIRVNKA 258
L +++ V +A
Sbjct: 179 MQLGDKKLLVQRA 191
>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 = 44.7 bits (104), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 40/79 (50%), Gaps = 1/79 (1%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKL 143
V++G++ I + G + A V+ D TG+S+ + FV DA I+++
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 144 NGTEIGGREIKVNI-TEKP 161
G +GGR+I+ N T KP
Sbjct: 69 GGQWLGGRQIRTNWATRKP 87
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 43/81 (53%)
Query: 178 VDSPYKVYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXX 237
+ S + V+VG+L+ +T+ + F+ G++ A+V++ T KS G+GFV+F
Sbjct: 3 LGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAE 62
Query: 238 XXXXXLNNSLLEGQRIRVNKA 258
+ L G++IR N A
Sbjct: 63 NAIQQMGGQWLGGRQIRTNWA 83
>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 = 44.7 bits (104), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 38/73 (52%)
Query: 86 IGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKLNG 145
+ N+ D L ++ +++G V + D+YT SR FAFV DA ++ ++G
Sbjct: 52 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 111
Query: 146 TEIGGREIKVNIT 158
+ GRE++V +
Sbjct: 112 AVLDGRELRVQMA 124
Score = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 35/73 (47%)
Query: 186 VGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXLNN 245
V NL + + L++ F + G+V + R T +S GF FV F ++
Sbjct: 52 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 111
Query: 246 SLLEGQRIRVNKA 258
++L+G+ +RV A
Sbjct: 112 AVLDGRELRVQMA 124
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 44.3 bits (103), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 38/72 (52%)
Query: 86 IGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKLNG 145
+ N+ D L ++ +++G V + D+YT SR FAFV DA ++ ++G
Sbjct: 75 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 134
Query: 146 TEIGGREIKVNI 157
+ GRE++V +
Sbjct: 135 AVLDGRELRVQM 146
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 35/73 (47%)
Query: 186 VGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXLNN 245
V NL + + L++ F + G+V + R T +S GF FV F ++
Sbjct: 75 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 134
Query: 246 SLLEGQRIRVNKA 258
++L+G+ +RV A
Sbjct: 135 AVLDGRELRVQMA 147
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 43.9 bits (102), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 4/72 (5%)
Query: 159 EKPLVQVDLSLLQAEDSNFVDSPYKVYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPG 218
EK L V L + E F K+++G L+ T E L+ + + G++ V+R P
Sbjct: 9 EKTLETVPLERKKREKEQF----RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPA 64
Query: 219 TSKSSGFGFVTF 230
+ +S GFGFVTF
Sbjct: 65 SKRSRGFGFVTF 76
Score = 30.8 bits (68), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 14/59 (23%), Positives = 29/59 (49%)
Query: 82 RRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVI 140
R+++IG + + L ++ G + V+ D + RSR F FV ++ + +A +
Sbjct: 28 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 86
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 43.9 bits (102), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 41/81 (50%), Gaps = 5/81 (6%)
Query: 81 ARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVI 140
AR + N+P + DEL ++ ++ AE+ G+S+ A++ KT DA
Sbjct: 93 ARTLLAKNLPYKVTQDELKEVFEDA-----AEIRLVSKDGKSKGIAYIEFKTEADAEKTF 147
Query: 141 EKLNGTEIGGREIKVNITEKP 161
E+ GTEI GR I + T +P
Sbjct: 148 EEKQGTEIDGRSISLYYTGEP 168
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 40/150 (26%), Positives = 67/150 (44%), Gaps = 19/150 (12%)
Query: 81 ARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVI 140
A +++GN+ N EL + + A V+ D G +R+F +V ++ ED +
Sbjct: 7 AFNLFVGNLNFNKSAPELKTGISDVFAKNDLAVV-DVRIGMTRKFGYVDFESAEDLEKAL 65
Query: 141 EKLNGTEIGGREIKVNITEKPLVQVDLSLLQAEDSNFVDSPYKVYVGNLAKTVTSEMLKK 200
E L G ++ G EIK+ EKP + +DS + NL VT + LK+
Sbjct: 66 E-LTGLKVFGNEIKL---EKP---------KGKDSKKERDARTLLAKNLPYKVTQDELKE 112
Query: 201 CFSEKGQVLSAKVLRVPGTSKSSGFGFVTF 230
F + +A++ V KS G ++ F
Sbjct: 113 VFED-----AAEIRLVSKDGKSKGIAYIEF 137
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 43.9 bits (102), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 40/76 (52%), Gaps = 8/76 (10%)
Query: 83 RVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEK 142
++++GNI N EL +E+G V + +++ D +AFV M+ EDA I
Sbjct: 12 KLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRG 63
Query: 143 LNGTEIGGREIKVNIT 158
L+ TE G+ + V ++
Sbjct: 64 LDNTEFQGKRMHVQLS 79
Score = 33.9 bits (76), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 35/73 (47%), Gaps = 8/73 (10%)
Query: 183 KVYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXX 242
K++VGN++ T T++ L+ F E G V+ +++ + FV
Sbjct: 12 KLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRG 63
Query: 243 LNNSLLEGQRIRV 255
L+N+ +G+R+ V
Sbjct: 64 LDNTEFQGKRMHV 76
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKL 143
+YI N+P ++D EL +++ G V ++ D +G SR F M++ E AVI
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHF 86
Query: 144 NG 145
NG
Sbjct: 87 NG 88
Score = 31.2 bits (69), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 7/64 (10%)
Query: 163 VQVDLSLLQAEDSNFVDSPYKVYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLR-VPGTSK 221
VQ ++ Q +D P +Y+ NL ++ + L+ GQV+S ++LR GTS+
Sbjct: 13 VQAQMAKQQEQD------PTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSR 66
Query: 222 SSGF 225
GF
Sbjct: 67 GVGF 70
>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 = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 41/147 (27%), Positives = 68/147 (46%), Gaps = 19/147 (12%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKL 143
++IGN+ N EL + E A V+ D TG +R+F +V ++ ED +E L
Sbjct: 16 LFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDLEKALE-L 73
Query: 144 NGTEIGGREIKVNITEKPLVQVDLSLLQAEDSNFVDSPYKVYVGNLAKTVTSEMLKKCFS 203
G ++ G EIK+ EKP + DS V + + NL+ +T + LK+ F
Sbjct: 74 TGLKVFGNEIKL---EKP---------KGRDSKKVRAARTLLAKNLSFNITEDELKEVFE 121
Query: 204 EKGQVLSAKVLRVPGTSKSSGFGFVTF 230
+ + ++ V KS G ++ F
Sbjct: 122 D-----ALEIRLVSQDGKSKGIAYIEF 143
Score = 35.0 bits (79), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 41/78 (52%), Gaps = 5/78 (6%)
Query: 81 ARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVI 140
AR + N+ NI DEL ++ ++ A+E V D G+S+ A++ K+ DA +
Sbjct: 99 ARTLLAKNLSFNITEDELKEVFED--ALEIRLVSQD---GKSKGIAYIEFKSEADAEKNL 153
Query: 141 EKLNGTEIGGREIKVNIT 158
E+ G EI GR + + T
Sbjct: 154 EEKQGAEIDGRSVSLYYT 171
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 33/56 (58%)
Query: 81 ARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDA 136
A +++IG IPRN+D +L + +E G + + V+ D++TG + AF+ E A
Sbjct: 13 AIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESA 68
Score = 28.1 bits (61), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 13/48 (27%), Positives = 25/48 (52%)
Query: 183 KVYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTF 230
K+++G + + + + LK F E G++ VL+ T G F+T+
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTY 62
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 42.7 bits (99), Expect = 2e-04, Method: Composition-based stats.
Identities = 18/75 (24%), Positives = 43/75 (57%)
Query: 81 ARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVI 140
A +++IG +P +++D++ +++ G ++ ++ D TG S+ +AF + + I
Sbjct: 1 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 60
Query: 141 EKLNGTEIGGREIKV 155
LNG ++G +++ V
Sbjct: 61 AGLNGMQLGDKKLLV 75
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 38/75 (50%)
Query: 184 VYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXL 243
VYVG L + V+ +L + F + G V++ + + T + G+GFV F +
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 244 NNSLLEGQRIRVNKA 258
+ L G+ IRVNKA
Sbjct: 78 DMIKLYGKPIRVNKA 92
Score = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 39/73 (53%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKL 143
VY+G + + L ++ + G V + D+ TG+ + + FV + EDA+ I+ +
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 144 NGTEIGGREIKVN 156
+ ++ G+ I+VN
Sbjct: 78 DMIKLYGKPIRVN 90
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 82 RRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIE 141
R V++GN+ + + L ++ + G + K + D+ G+ + F FV K E + I
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYAIA 75
Query: 142 KLNGTEIGGREIKVN 156
LNG + GR I V+
Sbjct: 76 LLNGIRLYGRPINVS 90
Score = 31.6 bits (70), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 31/73 (42%), Gaps = 1/73 (1%)
Query: 184 VYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXL 243
V+VGNL V E+L + F + G + + + K FGFV F L
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICK-DREGKPKSFGFVCFKHPESVSYAIALL 77
Query: 244 NNSLLEGQRIRVN 256
N L G+ I V+
Sbjct: 78 NGIRLYGRPINVS 90
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 42/84 (50%), Gaps = 1/84 (1%)
Query: 78 SEFARRVYIGNIPRNIDNDELTKIVQEHGAV-EKAEVIYDKYTGRSRRFAFVMMKTVEDA 136
S + ++IGN+ ID L G + + +++ D TG S+ +AF+ + + +
Sbjct: 2 SSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDAS 61
Query: 137 NAVIEKLNGTEIGGREIKVNITEK 160
+A IE +NG + R I V+ K
Sbjct: 62 DAAIEAMNGQYLCNRPITVSYAFK 85
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 40.8 bits (94), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 184 VYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXL 243
+YV NL + E L+K FS G + SAKV+ G SK GFGFV F +
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSK--GFGFVCFSSPEEATKAVTEM 75
Query: 244 NNSLL 248
N ++
Sbjct: 76 NGRIV 80
Score = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 41/77 (53%), Gaps = 2/77 (2%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKL 143
+Y+ N+ ID++ L K G + A+V+ + GRS+ F FV + E+A + ++
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 144 NGTEIGGREIKVNITEK 160
NG + + + V + ++
Sbjct: 76 NGRIVATKPLYVALAQR 92
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 40.8 bits (94), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 31/48 (64%)
Query: 183 KVYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTF 230
K++VG L + T E L+ FS+ G+V+ +++ T++S GFGFV F
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF 65
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 42/79 (53%), Gaps = 5/79 (6%)
Query: 83 RVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEK 142
++++G IP N EL + ++ G V + +IYD R R F F+ T ED +V +
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFI---TFEDEQSVDQA 68
Query: 143 LNG--TEIGGREIKVNITE 159
+N +I G++++V E
Sbjct: 69 VNMHFHDIMGKKVEVKRAE 87
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 17/76 (22%), Positives = 40/76 (52%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKL 143
+ + N+P ++ + ++V+ G++E+ ++Y + TG+S+ + F + A L
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 144 NGTEIGGREIKVNITE 159
G +G R + V+ T+
Sbjct: 158 LGKPLGPRTLYVHWTD 173
Score = 36.6 bits (83), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 33/149 (22%), Positives = 60/149 (40%), Gaps = 27/149 (18%)
Query: 82 RRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIE 141
R++ I +P ++ N E+ ++ ++ E DKY G AFV + E A A I
Sbjct: 23 RKILIRGLPGDVTNQEVHDLLSDY---ELKYCFVDKYKGT----AFVTLLNGEQAEAAIN 75
Query: 142 KLNGTEIGGREIKVNITEKPLVQVDLSLLQAEDSNFVDSPYKVYVGNLAKTVTSEMLKKC 201
+ + + RE+ V LQ D+ V NL ++T + ++
Sbjct: 76 AFHQSRLRERELSVQ-------------LQPTDALLC-------VANLPPSLTQQQFEEL 115
Query: 202 FSEKGQVLSAKVLRVPGTSKSSGFGFVTF 230
G + ++ T +S G+GF +
Sbjct: 116 VRPFGSLERCFLVYSERTGQSKGYGFAEY 144
>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 = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/76 (22%), Positives = 40/76 (52%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKL 143
+ + N+P ++ + ++V+ G++E+ ++Y + TG+S+ + F + A L
Sbjct: 96 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Query: 144 NGTEIGGREIKVNITE 159
G +G R + V+ T+
Sbjct: 156 LGKPLGPRTLYVHWTD 171
Score = 36.2 bits (82), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 33/149 (22%), Positives = 60/149 (40%), Gaps = 27/149 (18%)
Query: 82 RRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIE 141
R++ I +P ++ N E+ ++ ++ E DKY G AFV + E A A I
Sbjct: 21 RKILIRGLPGDVTNQEVHDLLSDY---ELKYCFVDKYKGT----AFVTLLNGEQAEAAIN 73
Query: 142 KLNGTEIGGREIKVNITEKPLVQVDLSLLQAEDSNFVDSPYKVYVGNLAKTVTSEMLKKC 201
+ + + RE+ V LQ D+ V NL ++T + ++
Sbjct: 74 AFHQSRLRERELSVQ-------------LQPTDALLC-------VANLPPSLTQQQFEEL 113
Query: 202 FSEKGQVLSAKVLRVPGTSKSSGFGFVTF 230
G + ++ T +S G+GF +
Sbjct: 114 VRPFGSLERCFLVYSERTGQSKGYGFAEY 142
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/76 (22%), Positives = 40/76 (52%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKL 143
+ + N+P ++ + ++V+ G++E+ ++Y + TG+S+ + F + A L
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 144 NGTEIGGREIKVNITE 159
G +G R + V+ T+
Sbjct: 158 LGKPLGPRTLYVHWTD 173
Score = 36.2 bits (82), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 33/149 (22%), Positives = 60/149 (40%), Gaps = 27/149 (18%)
Query: 82 RRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIE 141
R++ I +P ++ N E+ ++ ++ E DKY G AFV + E A A I
Sbjct: 23 RKILIRGLPGDVTNQEVHDLLSDY---ELKYCFVDKYKGT----AFVTLLNGEQAEAAIN 75
Query: 142 KLNGTEIGGREIKVNITEKPLVQVDLSLLQAEDSNFVDSPYKVYVGNLAKTVTSEMLKKC 201
+ + + RE+ V LQ D+ V NL ++T + ++
Sbjct: 76 AFHQSRLRERELSVQ-------------LQPTDALLC-------VANLPPSLTQQQFEEL 115
Query: 202 FSEKGQVLSAKVLRVPGTSKSSGFGFVTF 230
G + ++ T +S G+GF +
Sbjct: 116 VRPFGSLERCFLVYSERTGQSKGYGFAEY 144
>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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 81 ARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVI 140
AR +Y+GN+ +EL G+V + ++ DK++G + FA++ E +
Sbjct: 5 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 64
Query: 141 EKLNGTEIGGREIKV 155
L+ + GR+IKV
Sbjct: 65 -ALDESLFRGRQIKV 78
Score = 31.2 bits (69), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 1/72 (1%)
Query: 184 VYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXL 243
+YVGN+ T+E L+ F G V +L + GF ++ F L
Sbjct: 8 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEF-SDKESVRTSLAL 66
Query: 244 NNSLLEGQRIRV 255
+ SL G++I+V
Sbjct: 67 DESLFRGRQIKV 78
>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 = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 81 ARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVI 140
AR +Y+GN+ +EL G+V + ++ DK++G + FA++ E +
Sbjct: 6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 65
Query: 141 EKLNGTEIGGREIKV 155
L+ + GR+IKV
Sbjct: 66 -ALDESLFRGRQIKV 79
Score = 31.2 bits (69), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 1/72 (1%)
Query: 184 VYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXL 243
+YVGN+ T+E L+ F G V +L + GF ++ F L
Sbjct: 9 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEF-SDKESVRTSLAL 67
Query: 244 NNSLLEGQRIRV 255
+ SL G++I+V
Sbjct: 68 DESLFRGRQIKV 79
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 36/81 (44%)
Query: 178 VDSPYKVYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXX 237
VD + V NL + + L++ F + G+V + R P T GF FV F
Sbjct: 10 VDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQ 69
Query: 238 XXXXXLNNSLLEGQRIRVNKA 258
++ + L+G+ +RV A
Sbjct: 70 DAEAAMDGAELDGRELRVQVA 90
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 32/63 (50%)
Query: 96 DELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKLNGTEIGGREIKV 155
D L ++ +++G V + + +T R FAFV DA ++G E+ GRE++V
Sbjct: 28 DSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRV 87
Query: 156 NIT 158
+
Sbjct: 88 QVA 90
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 30/73 (41%), Gaps = 5/73 (6%)
Query: 183 KVYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXX 242
KVYVGNL L++ F G + S V R P GF FV F
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAVRD 129
Query: 243 LNNSLLEGQRIRV 255
L+ L G R+RV
Sbjct: 130 LDGRTLCGCRVRV 142
Score = 33.9 bits (76), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 24/105 (22%), Positives = 42/105 (40%), Gaps = 5/105 (4%)
Query: 54 DSTTRLFAVAEETAXXXXXXVDTPSEFARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEV 113
D T+ F V E + +VY+GN+ N + EL + +G + V
Sbjct: 46 DDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWV 105
Query: 114 IYDKYTGRSRRFAFVMMKTVEDANAVIEKLNGTEIGGREIKVNIT 158
+ FAFV + DA + L+G + G ++V ++
Sbjct: 106 ARN-----PPGFAFVEFEDPRDAADAVRDLDGRTLCGCRVRVELS 145
>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 = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 2/72 (2%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKL 143
++I N+ ++IDN L G + +V+ D+ S+ + FV +T E A IEK+
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKM 65
Query: 144 NGTEIGGREIKV 155
NG + R++ V
Sbjct: 66 NGMLLNDRKVFV 77
>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 = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 28/48 (58%)
Query: 183 KVYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTF 230
K +VG L+ + + LK F++ G+V+ + P T +S GFGF+ F
Sbjct: 13 KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILF 60
Score = 32.3 bits (72), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 16/64 (25%), Positives = 29/64 (45%)
Query: 79 EFARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANA 138
E A + ++G + + +L + G V + D TGRSR F F++ K
Sbjct: 9 EDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEK 68
Query: 139 VIEK 142
V+++
Sbjct: 69 VLDQ 72
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 30/73 (41%), Gaps = 5/73 (6%)
Query: 183 KVYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXX 242
KVYVGNL L++ F G + S V R P GF FV F
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAVRE 129
Query: 243 LNNSLLEGQRIRV 255
L+ L G R+RV
Sbjct: 130 LDGRTLCGCRVRV 142
Score = 34.3 bits (77), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 24/105 (22%), Positives = 43/105 (40%), Gaps = 5/105 (4%)
Query: 54 DSTTRLFAVAEETAXXXXXXVDTPSEFARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEV 113
D T+ F V E + +VY+GN+ N + EL + +G + V
Sbjct: 46 DDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWV 105
Query: 114 IYDKYTGRSRRFAFVMMKTVEDANAVIEKLNGTEIGGREIKVNIT 158
+ FAFV + DA + +L+G + G ++V ++
Sbjct: 106 ARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELS 145
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 32/73 (43%), Gaps = 5/73 (6%)
Query: 183 KVYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXX 242
KVYVGNL L++ FS G + + + R P GF FV F
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVRG 56
Query: 243 LNNSLLEGQRIRV 255
L+ ++ G R+RV
Sbjct: 57 LDGKVICGSRVRV 69
Score = 31.6 bits (70), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 18/76 (23%), Positives = 33/76 (43%), Gaps = 5/76 (6%)
Query: 83 RVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEK 142
+VY+GN+ EL + +G + + + FAFV + DA +
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPG-----FAFVEFEDPRDAEDAVRG 56
Query: 143 LNGTEIGGREIKVNIT 158
L+G I G ++V ++
Sbjct: 57 LDGKVICGSRVRVELS 72
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 43/72 (59%), Gaps = 1/72 (1%)
Query: 83 RVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDK-YTGRSRRFAFVMMKTVEDANAVIE 141
+V+IG + RN+ D + +I +G ++ ++ ++ + S+ +A+V + ++A ++
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65
Query: 142 KLNGTEIGGREI 153
++G +I G+EI
Sbjct: 66 HMDGGQIDGQEI 77
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 2/72 (2%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKL 143
++I N+ ++IDN L G + +V+ D+ S+ + FV +T E A IEK+
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKM 71
Query: 144 NGTEIGGREIKV 155
NG + R++ V
Sbjct: 72 NGMLLNDRKVFV 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 = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 38/68 (55%), Gaps = 2/68 (2%)
Query: 92 NIDNDE--LTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKLNGTEIG 149
N D E L + + +G +++ ++Y K +G+ R +AF+ + D ++ + +G +I
Sbjct: 111 NYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKID 170
Query: 150 GREIKVNI 157
GR + V++
Sbjct: 171 GRRVLVDV 178
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 29/48 (60%)
Query: 81 ARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFV 128
A ++++G IPR +D +L + +E G + + V+ D+ TG + AF+
Sbjct: 15 AIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFL 62
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 15/62 (24%), Positives = 33/62 (53%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKL 143
+Y+ +P+ + E+ ++ ++G + + ++ D+ TG SR F+ +A I+ L
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 144 NG 145
NG
Sbjct: 64 NG 65
Score = 37.4 bits (85), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 31/47 (65%)
Query: 184 VYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTF 230
+YV L KT++ + +++ FS+ G+++++++L T S G GF+ F
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRF 50
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 36.6 bits (83), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 83 RVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEK 142
++ + N+ + + ++ ++ E G ++KA V YD+ +GRS A V + DA +++
Sbjct: 30 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQ 88
Query: 143 LNGTEIGGREIKVNI 157
NG + GR + + +
Sbjct: 89 YNGVPLDGRPMNIQL 103
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 36.6 bits (83), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 8/72 (11%)
Query: 184 VYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXL 243
++V NLA TVT E+L+K FS+ G++ K L+ + F+ F +
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLK--------DYAFIHFDERDGAVKAMEEM 65
Query: 244 NNSLLEGQRIRV 255
N LEG+ I +
Sbjct: 66 NGKDLEGENIEI 77
Score = 27.3 bits (59), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 15/78 (19%), Positives = 37/78 (47%), Gaps = 8/78 (10%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKL 143
+++ N+ + + L K + G +E+ + + D +AF+ + A +E++
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEM 65
Query: 144 NGTEIGGREIKVNITEKP 161
NG ++ G I++ + P
Sbjct: 66 NGKDLEGENIEIVFAKPP 83
>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 = 36.6 bits (83), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 6/76 (7%)
Query: 183 KVYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXX 242
+++VGNL +T E ++K F + G+ + K GFGF+
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFI------HKDKGFGFIRLETRTLAEIAKVE 70
Query: 243 LNNSLLEGQRIRVNKA 258
L+N L G+++RV A
Sbjct: 71 LDNMPLRGKQLRVRFA 86
Score = 35.4 bits (80), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 40/75 (53%), Gaps = 6/75 (8%)
Query: 83 RVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEK 142
R+++GN+P +I +E+ K+ +++G EV K G F F+ ++T A +
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKA--GEVFIHKDKG----FGFIRLETRTLAEIAKVE 70
Query: 143 LNGTEIGGREIKVNI 157
L+ + G++++V
Sbjct: 71 LDNMPLRGKQLRVRF 85
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 36.6 bits (83), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 3/79 (3%)
Query: 77 PSEFARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDA 136
P E R +YI N+P I +E+ I ++G + + V T +R A+V+ + + DA
Sbjct: 4 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDIFDA 60
Query: 137 NAVIEKLNGTEIGGREIKV 155
++ L+G + R + V
Sbjct: 61 KNAVDHLSGFNVSNRYLVV 79
>pdb|2KH9|A Chain A, Solution Structure Of Yeast Prp24-Rrm2 Bound To A Fragment
Of U6 Rna
Length = 92
Score = 36.2 bits (82), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 35/67 (52%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKL 143
+++ N P + + ++Q+ V + + SRRFA++ + + EDA +EKL
Sbjct: 6 LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 65
Query: 144 NGTEIGG 150
NG +I G
Sbjct: 66 NGLKIEG 72
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 36.2 bits (82), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 43/83 (51%), Gaps = 2/83 (2%)
Query: 82 RRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIE 141
R +Y+GN+ R++ + ++ + G + ++I + + + + FV DA A +
Sbjct: 16 RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALA 73
Query: 142 KLNGTEIGGREIKVNITEKPLVQ 164
+NG +I G+E+KVN P Q
Sbjct: 74 AMNGRKILGKEVKVNWATTPSSQ 96
Score = 33.9 bits (76), Expect = 0.099, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 2/78 (2%)
Query: 181 PYKVYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXX 240
P +YVGNL++ VT ++ + FS+ G S K++ + + + FV F
Sbjct: 15 PRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITE--HTSNDPYCFVEFYEHRDAAAAL 72
Query: 241 XXLNNSLLEGQRIRVNKA 258
+N + G+ ++VN A
Sbjct: 73 AAMNGRKILGKEVKVNWA 90
>pdb|1X4F|A Chain A, Solution Structure Of The Second Rrm Domain In Matrin 3
Length = 112
Score = 36.2 bits (82), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 23/89 (25%), Positives = 47/89 (52%), Gaps = 9/89 (10%)
Query: 75 DTPSEFARRVYIGNIPRNIDNDE-LTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTV 133
D E R +++ N+P + +D + K+ + +G ++ ++ R + AF+ M+T
Sbjct: 19 DQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM------RMKSQAFIEMETR 72
Query: 134 EDANAVIEKL--NGTEIGGREIKVNITEK 160
EDA A+++ GR +KV+++EK
Sbjct: 73 EDAMAMVDHCLKKALWFQGRCVKVDLSEK 101
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 36.2 bits (82), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 110 KAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKLNGTEIGGREIKVNITEKP 161
+A ++ D+ TG S+ F FV + EDA A E + EI G ++ ++ KP
Sbjct: 41 RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWA-KP 91
Score = 32.3 bits (72), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 4/79 (5%)
Query: 181 PYK-VYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXX 239
P K ++V L++ T E LK+ F G V A+++ T S GFGFV F
Sbjct: 14 PSKTLFVKGLSEDTTEETLKESFD--GSVR-ARIVTDRETGSSKGFGFVDFNSEEDAKAA 70
Query: 240 XXXLNNSLLEGQRIRVNKA 258
+ + ++G ++ ++ A
Sbjct: 71 KEAMEDGEIDGNKVTLDWA 89
>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 = 36.2 bits (82), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 14/60 (23%), Positives = 35/60 (58%)
Query: 98 LTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKLNGTEIGGREIKVNI 157
L + + +G +++ ++Y K +G+ R +AF+ + D ++ + +G +I GR + V++
Sbjct: 119 LRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV 178
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 35.8 bits (81), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
Query: 82 RRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIE 141
+++I +P + +EL +I + HG V+ ++ ++ G+ + A+V + A+ +
Sbjct: 18 HKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVM 76
Query: 142 KLNGTEIGGREIKVNIT 158
K++G I IKV I+
Sbjct: 77 KMDGMTIKENIIKVAIS 93
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 35.8 bits (81), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 33/72 (45%), Gaps = 6/72 (8%)
Query: 184 VYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXL 243
VY G +A +T +++++ FS GQ++ +V G+ FV F +
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVF------PEKGYSFVRFSTHESAAHAIVSV 81
Query: 244 NNSLLEGQRIRV 255
N + +EG ++
Sbjct: 82 NGTTIEGHVVKC 93
Score = 28.5 bits (62), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 30/72 (41%), Gaps = 6/72 (8%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKL 143
VY G I + + + + G + + V +K ++FV T E A I +
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFSTHESAAHAIVSV 81
Query: 144 NGTEIGGREIKV 155
NGT I G +K
Sbjct: 82 NGTTIEGHVVKC 93
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 35.4 bits (80), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 36/68 (52%)
Query: 89 IPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKLNGTEI 148
+P+++ + EL + + G + ++ D TG S +AFV + D+ I+ LNG +
Sbjct: 11 LPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITV 70
Query: 149 GGREIKVN 156
+ +KV+
Sbjct: 71 RNKRLKVS 78
>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
pdb|1HD1|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
Length = 75
Score = 35.4 bits (80), Expect = 0.028, Method: Composition-based stats.
Identities = 18/47 (38%), Positives = 28/47 (59%)
Query: 184 VYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTF 230
+++G L+ T + LK FS+ G+V+ + P T +S GFGFV F
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLF 48
Score = 35.4 bits (80), Expect = 0.029, Method: Composition-based stats.
Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 4/69 (5%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIE-- 141
++IG + + +L + G V + D TGRSR F FV+ K E + V++
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 142 --KLNGTEI 148
KLNG I
Sbjct: 62 EHKLNGKVI 70
>pdb|2GO9|A Chain A, Rrm Domains 1 And 2 Of Prp24 From S. Cerevisiae
Length = 161
Score = 35.4 bits (80), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 35/67 (52%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKL 143
+++ N P + + ++Q+ V + + SRRFA++ + + EDA +EKL
Sbjct: 83 LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 142
Query: 144 NGTEIGG 150
NG +I G
Sbjct: 143 NGLKIEG 149
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 35.4 bits (80), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 3/79 (3%)
Query: 77 PSEFARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDA 136
P E R +YI N+P I +E+ I ++G + + V T +R A+V+ + + DA
Sbjct: 8 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDIFDA 64
Query: 137 NAVIEKLNGTEIGGREIKV 155
+ L+G + R + V
Sbjct: 65 KNACDHLSGFNVCNRYLVV 83
>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 = 35.4 bits (80), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 15/29 (51%), Positives = 21/29 (72%)
Query: 122 SRRFAFVMMKTVEDANAVIEKLNGTEIGG 150
SRRFA++ + + EDA +EKLNG +I G
Sbjct: 158 SRRFAYIDVTSKEDARYCVEKLNGLKIEG 186
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 35.4 bits (80), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 41/78 (52%), Gaps = 5/78 (6%)
Query: 81 ARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVI 140
AR + N+ NI DEL ++ ++ A+E V D G+S+ A++ K+ DA +
Sbjct: 16 ARTLLAKNLSFNITEDELKEVFED--ALEIRLVSQD---GKSKGIAYIEFKSEADAEKNL 70
Query: 141 EKLNGTEIGGREIKVNIT 158
E+ G EI GR + + T
Sbjct: 71 EEKQGAEIDGRSVSLYYT 88
>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 = 35.0 bits (79), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 3/79 (3%)
Query: 77 PSEFARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDA 136
P E R +YI N+P I +E+ I ++G + + V T +R A+V+ + + DA
Sbjct: 14 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDIFDA 70
Query: 137 NAVIEKLNGTEIGGREIKV 155
+ L+G + R + V
Sbjct: 71 KNACDHLSGFNVCNRYLVV 89
>pdb|2E5J|A Chain A, Solution Structure Of Rna Binding Domain In
Methenyltetrahydrofolate Synthetase Domain Containing
Length = 97
Score = 35.0 bits (79), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 39/83 (46%), Gaps = 5/83 (6%)
Query: 78 SEFARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDAN 137
+ A VY+GN+PR+ +L + ++E G+V + + G RR AF+ A
Sbjct: 16 APLAADVYVGNLPRDARVSDLKRALRELGSVP----LRLTWQG-PRRRAFLHYPDSAAAQ 70
Query: 138 AVIEKLNGTEIGGREIKVNITEK 160
+ L G +G ++V + +
Sbjct: 71 QAVSCLQGLRLGTDTLRVALARQ 93
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 34.7 bits (78), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 41/83 (49%), Gaps = 2/83 (2%)
Query: 77 PSEFARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDA 136
P+E Y+GN+P N ++ I ++ ++ ++ DK T + + F +V V+
Sbjct: 11 PTEPPYTAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSL 69
Query: 137 NAVIEKLNGTEIGGREIKVNITE 159
+ +G +G R ++V+I E
Sbjct: 70 KEAL-TYDGALLGDRSLRVDIAE 91
Score = 27.3 bits (59), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 33/78 (42%), Gaps = 2/78 (2%)
Query: 181 PYKVYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXX 240
PY YVGNL + F + + S +++R T K GF +V F
Sbjct: 15 PYTAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEF-DEVDSLKEA 72
Query: 241 XXLNNSLLEGQRIRVNKA 258
+ +LL + +RV+ A
Sbjct: 73 LTYDGALLGDRSLRVDIA 90
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 34.7 bits (78), Expect = 0.049, Method: Composition-based stats.
Identities = 18/47 (38%), Positives = 28/47 (59%)
Query: 184 VYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTF 230
++VG L+ T E +K F + G+V A ++ T++ GFGFVTF
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF 48
Score = 33.5 bits (75), Expect = 0.12, Method: Composition-based stats.
Identities = 22/76 (28%), Positives = 41/76 (53%), Gaps = 6/76 (7%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKL 143
+++G + N +++ ++ G V+ A +++DK T R R F FV ++ ED ++EK+
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFES-ED---IVEKV 57
Query: 144 NGTEIGGREIKVNITE 159
EI EI + E
Sbjct: 58 --CEIHFHEINNKMVE 71
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 34.7 bits (78), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 41/78 (52%), Gaps = 5/78 (6%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKL 143
++IGN+ N EL + E A V+ D TG +R+F +V ++ ED +E L
Sbjct: 20 LFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDLEKALE-L 77
Query: 144 NGTEIGGREIKVNITEKP 161
G ++ G EIK+ EKP
Sbjct: 78 TGLKVFGNEIKL---EKP 92
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 34.7 bits (78), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 39/77 (50%), Gaps = 11/77 (14%)
Query: 83 RVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRR----FAFVMMKTVEDANA 138
R+Y+GN+P +I ++ + ++GA+ ++ ++RR FAFV + DA
Sbjct: 24 RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL-------KNRRGGPPFAFVEFEDPRDAED 76
Query: 139 VIEKLNGTEIGGREIKV 155
+ +G + G ++V
Sbjct: 77 AVYGRDGYDYDGYRLRV 93
>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 = 34.7 bits (78), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 36/74 (48%), Gaps = 1/74 (1%)
Query: 82 RRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIE 141
R VY+GN+ +L G++ + ++ DK++G + +A++ +A +
Sbjct: 37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV- 95
Query: 142 KLNGTEIGGREIKV 155
++ T GR IKV
Sbjct: 96 AMDETVFRGRTIKV 109
>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 = 34.3 bits (77), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 39/75 (52%), Gaps = 1/75 (1%)
Query: 83 RVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEK 142
++ + N+ + + ++ ++ E G ++KA V YD+ +GRS A V + DA ++
Sbjct: 31 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAXKQ 89
Query: 143 LNGTEIGGREIKVNI 157
NG + GR + +
Sbjct: 90 YNGVPLDGRPXNIQL 104
>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 = 33.9 bits (76), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 46/87 (52%), Gaps = 3/87 (3%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGA-VEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIE- 141
V + +P+ D++ +Q HG + ++ +K +G+SR FAFV ++DA +E
Sbjct: 4 VMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEA 63
Query: 142 KLNGTEIGGREIKVNITE-KPLVQVDL 167
+ I G+++ ++ ++ KP + D
Sbjct: 64 NQHSLNILGQKVSMHYSDPKPKINEDW 90
>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 90
Score = 33.9 bits (76), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 31/53 (58%)
Query: 104 EHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKLNGTEIGGREIKVN 156
E+G ++ + D+ TG + + V +T ++A A +E LNG ++ G+ I V+
Sbjct: 30 EYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 82
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 33.9 bits (76), Expect = 0.094, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 28/56 (50%)
Query: 105 HGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKLNGTEIGGREIKVNITEK 160
GA I D R AFV + +E A+ + +LNGT++ ++KVNI K
Sbjct: 55 RGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARK 110
>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 = 33.9 bits (76), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 31/53 (58%)
Query: 104 EHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKLNGTEIGGREIKVN 156
E+G ++ + D+ TG + + V +T ++A A +E LNG ++ G+ I V+
Sbjct: 32 EYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 84
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 33.9 bits (76), Expect = 0.098, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 28/56 (50%)
Query: 105 HGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKLNGTEIGGREIKVNITEK 160
GA I D R AFV + +E A+ + +LNGT++ ++KVNI K
Sbjct: 31 RGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARK 86
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 33.9 bits (76), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 31/53 (58%)
Query: 104 EHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKLNGTEIGGREIKVN 156
E+G ++ + D+ TG + + V +T ++A A +E LNG ++ G+ I V+
Sbjct: 30 EYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 82
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 33/62 (53%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKL 143
+ + N+ + +L ++ + G++ + + DK TG+S+ FAF+ EDA I +
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV 77
Query: 144 NG 145
+G
Sbjct: 78 SG 79
>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 = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 31/53 (58%)
Query: 104 EHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKLNGTEIGGREIKVN 156
E+G ++ + D+ TG + + V +T ++A A +E LNG ++ G+ I V+
Sbjct: 30 EYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 82
>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX
pdb|1P27|D Chain D, Crystal Structure Of The Human Y14MAGOH COMPLEX
Length = 106
Score = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 31/55 (56%)
Query: 104 EHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKLNGTEIGGREIKVNIT 158
E+G ++ + D+ TG + + V +T ++A A +E LNG ++ G+ I V+
Sbjct: 46 EYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC 100
>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 = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 31/55 (56%)
Query: 104 EHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKLNGTEIGGREIKVNIT 158
E+G ++ + D+ TG + + V +T ++A A +E LNG ++ G+ I V+
Sbjct: 45 EYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC 99
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 33.5 bits (75), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 31/65 (47%), Gaps = 3/65 (4%)
Query: 183 KVYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVP-GTSKSSGFGFVTFXXXXXXXXXXX 241
K++VG L K T E ++K F G + VLR P GTSK G FV F
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSK--GCAFVKFQTHAEAQAAIN 71
Query: 242 XLNNS 246
L++S
Sbjct: 72 TLHSS 76
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 33/73 (45%), Gaps = 2/73 (2%)
Query: 183 KVYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXX 242
+++V NL T +MLK F+E G VL A + G SK G G V F
Sbjct: 10 QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSK--GCGVVKFESPEVAERACRM 67
Query: 243 LNNSLLEGQRIRV 255
+N L G+ I V
Sbjct: 68 MNGMKLSGREIDV 80
Score = 31.6 bits (70), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 39/82 (47%), Gaps = 2/82 (2%)
Query: 76 TPSEFARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVED 135
+ S A ++++ N+P + L E G V A++ + G+S+ V ++ E
Sbjct: 3 SGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEV 60
Query: 136 ANAVIEKLNGTEIGGREIKVNI 157
A +NG ++ GREI V I
Sbjct: 61 AERACRMMNGMKLSGREIDVRI 82
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 33.1 bits (74), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 29/48 (60%), Gaps = 6/48 (12%)
Query: 183 KVYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTF 230
K+Y+GNL+ VT++ L++ F ++ L+ +VL SG+ FV +
Sbjct: 10 KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDY 51
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 32.7 bits (73), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 15/66 (22%), Positives = 36/66 (54%), Gaps = 1/66 (1%)
Query: 82 RRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIE 141
R++++G + + +++ ++ Q G +++ V+ G S+ AFV + +A A I
Sbjct: 16 RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIH 74
Query: 142 KLNGTE 147
L+G++
Sbjct: 75 ALHGSQ 80
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 32.7 bits (73), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 32/72 (44%), Gaps = 2/72 (2%)
Query: 184 VYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXL 243
++V NL T +MLK F+E G VL A + G SK G G V F +
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSK--GCGVVKFESPEVAERACRMM 65
Query: 244 NNSLLEGQRIRV 255
N L G+ I V
Sbjct: 66 NGMKLSGREIDV 77
Score = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 2/74 (2%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKL 143
+++ N+P + L E G V A++ + G+S+ V ++ E A +
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMM 65
Query: 144 NGTEIGGREIKVNI 157
NG ++ GREI V I
Sbjct: 66 NGMKLSGREIDVRI 79
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation Initiation
Factor 4b
Length = 100
Score = 32.7 bits (73), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 39/80 (48%), Gaps = 5/80 (6%)
Query: 181 PYKVYVGNLAKTVTSEMLKKCFSEKGQVLSA-KVLRVPGTSKS-SGFGFVTFXXXXXXXX 238
PY ++GNL VT E +K+ F +G +SA ++ R P + GFG+ F
Sbjct: 19 PYTAFLGNLPYDVTEESIKEFF--RGLNISAVRLPREPSNPERLKGFGYAEF-EDLDSLL 75
Query: 239 XXXXLNNSLLEGQRIRVNKA 258
LN L +RIRV+ A
Sbjct: 76 SALSLNEESLGNRRIRVDVA 95
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of Eukaryotic
Initiation Factor 4b
Length = 104
Score = 32.7 bits (73), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 39/80 (48%), Gaps = 5/80 (6%)
Query: 181 PYKVYVGNLAKTVTSEMLKKCFSEKGQVLSA-KVLRVPGTSKS-SGFGFVTFXXXXXXXX 238
PY ++GNL VT E +K+ F +G +SA ++ R P + GFG+ F
Sbjct: 15 PYTAFLGNLPYDVTEESIKEFF--RGLNISAVRLPREPSNPERLKGFGYAEF-EDLDSLL 71
Query: 239 XXXXLNNSLLEGQRIRVNKA 258
LN L +RIRV+ A
Sbjct: 72 SALSLNEESLGNKRIRVDVA 91
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 32.7 bits (73), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 15/66 (22%), Positives = 36/66 (54%), Gaps = 1/66 (1%)
Query: 82 RRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIE 141
R++++G + + D++ ++ + G +E+ ++ G S+ AFV + +A A I
Sbjct: 16 RKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGP-DGNSKGCAFVKYSSHAEAQAAIN 74
Query: 142 KLNGTE 147
L+G++
Sbjct: 75 ALHGSQ 80
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 32.3 bits (72), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 33/73 (45%)
Query: 183 KVYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXX 242
+++V NL+ T + E L+K FS G + T K GF FVTF
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 243 LNNSLLEGQRIRV 255
++ + +G+ + V
Sbjct: 70 VDGQVFQGRMLHV 82
>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 = 32.0 bits (71), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIE 141
V++G I +D E+ +G+V++ ++I D+ TG S+ + FV D ++E
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE 68
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 32.0 bits (71), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 22/38 (57%)
Query: 120 GRSRRFAFVMMKTVEDANAVIEKLNGTEIGGREIKVNI 157
G+S+ +AF+ + EDA + N EI GR I++ +
Sbjct: 50 GKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLEL 87
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 32.0 bits (71), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 40/84 (47%), Gaps = 1/84 (1%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKL 143
V++ N+ + +L ++ G V +A+++ DK G+SR V + +A I
Sbjct: 18 VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMF 76
Query: 144 NGTEIGGREIKVNITEKPLVQVDL 167
NG + R + V + E+ L + D
Sbjct: 77 NGQLLFDRPMHVKMDERALPKGDF 100
>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 = 32.0 bits (71), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 27/51 (52%)
Query: 98 LTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKLNGTEI 148
LT + + G V E D+ TG+++ F FV ++ DA +I+ +G +
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRL 79
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 32.0 bits (71), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIE 141
V++G I +D E+ +G+V++ ++I D+ TG S+ + FV D ++E
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE 68
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 32.0 bits (71), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 27/102 (26%), Positives = 47/102 (46%), Gaps = 9/102 (8%)
Query: 82 RRVYIGNIPRNIDNDELTKIVQEHGA--VEKAEVIYDKYTGRSRRFAFVMMKTVEDANAV 139
R+V++G +P +ID DE+T + G V+ K + +AF++ + A+
Sbjct: 9 RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQAL 68
Query: 140 IEKLNGTEIGGREIKVN---ITEKPLVQVDLSLLQAEDSNFV 178
I+ E G + V+ I +KP V + DS+FV
Sbjct: 69 IDACL-EEDGKLYLCVSSPTIKDKP---VQIRPWNLSDSDFV 106
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 32.0 bits (71), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIE 141
V++G I +D E+ +G+V++ ++I D+ TG S+ + FV D ++E
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE 69
>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 = 31.6 bits (70), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 27/51 (52%)
Query: 98 LTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKLNGTEI 148
LT + + G V E D+ TG+++ F FV ++ DA +I+ +G +
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRL 79
>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D (Auf1) With Telomere Dna
pdb|1X0F|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D(Auf1) With Telomeric Dna
Length = 79
Score = 31.6 bits (70), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 14/62 (22%), Positives = 30/62 (48%)
Query: 81 ARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVI 140
+++++G + + +++ + G VE E+ D T + R F F+ K E ++
Sbjct: 1 VKKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 60
Query: 141 EK 142
EK
Sbjct: 61 EK 62
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 27/48 (56%)
Query: 183 KVYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTF 230
K++VG L+ E +++ F G+V S ++ T+K GF F+TF
Sbjct: 3 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITF 50
>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 = 31.6 bits (70), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 3/79 (3%)
Query: 77 PSEFARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDA 136
P E R + I N+P I +E+ I ++G + + V T +R A+V+ + + DA
Sbjct: 14 PPEVNRILMIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDIFDA 70
Query: 137 NAVIEKLNGTEIGGREIKV 155
+ L+G + R + V
Sbjct: 71 KNACDHLSGFNVCNRYLVV 89
>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 = 31.6 bits (70), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 1/73 (1%)
Query: 184 VYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXL 243
+YVGNL+ T E + + FS+ G + ++ + + GF FV + +
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKI-IMGLDKMKTACGFCFVEYYSRADAENAMRYI 79
Query: 244 NNSLLEGQRIRVN 256
N + L+ + IR +
Sbjct: 80 NGTRLDDRIIRTD 92
>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 31.6 bits (70), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 30/54 (55%), Gaps = 4/54 (7%)
Query: 107 AVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKLNG----TEIGGREIKVN 156
AV +I DK T ++R FAFV + + DA+ +++ L +I G+ I V+
Sbjct: 37 AVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVD 90
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 31.6 bits (70), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 26/90 (28%), Positives = 38/90 (42%), Gaps = 11/90 (12%)
Query: 77 PSEFARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRS--RRFAFVMMKTVE 134
P RV+IGN L +V + VE Y K G S + FAFV
Sbjct: 11 PRSMNSRVFIGN---------LNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNER 61
Query: 135 DANAVIEKLNGTEIGGREIKVNITEKPLVQ 164
+A A + +G I G+ + +N+ +P V
Sbjct: 62 NARAAVAGEDGRMIAGQVLDINLAAEPKVN 91
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 31.6 bits (70), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 16/32 (50%), Positives = 23/32 (71%)
Query: 184 VYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLR 215
++V NLA TVT E+L+K FSE G++ K L+
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLK 49
>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|C Chain C, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|B Chain B, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|D Chain D, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
Length = 88
Score = 31.2 bits (69), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 30/65 (46%), Gaps = 2/65 (3%)
Query: 183 KVYVGNLAKTVTSEMLKKCFSEKGQVLSAKVL--RVPGTSKSSGFGFVTFXXXXXXXXXX 240
K++VG + +T + + L++ F + G V VL R +S G FVTF
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 241 XXLNN 245
L+N
Sbjct: 65 NALHN 69
Score = 29.3 bits (64), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 10/37 (27%), Positives = 24/37 (64%)
Query: 81 ARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDK 117
A ++++G +PR +L ++ +++GAV + V+ D+
Sbjct: 3 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDR 39
>pdb|3H2V|E Chain E, Human Raver1 Rrm1 Domain In Complex With Human Vinculin
Tail Domain Vt
pdb|3H2V|F Chain F, Human Raver1 Rrm1 Domain In Complex With Human Vinculin
Tail Domain Vt
pdb|3H2V|G Chain G, Human Raver1 Rrm1 Domain In Complex With Human Vinculin
Tail Domain Vt
pdb|3H2V|H Chain H, Human Raver1 Rrm1 Domain In Complex With Human Vinculin
Tail Domain Vt
Length = 74
Score = 30.8 bits (68), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 7/76 (9%)
Query: 82 RRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIE 141
R++ I +P ++ N E+ ++ ++ E DKY G AFV + E A A I
Sbjct: 3 RKILIRGLPGDVTNQEVHDLLSDY---ELKYCFVDKYKGT----AFVTLLNGEQAEAAIN 55
Query: 142 KLNGTEIGGREIKVNI 157
+ + + RE+ V +
Sbjct: 56 AFHQSRLRERELSVQL 71
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 30.8 bits (68), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 36/73 (49%), Gaps = 8/73 (10%)
Query: 83 RVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEK 142
+++IGN+PR E+ + +++G V + ++I + + FV ++ A I
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRN 61
Query: 143 LNGTEIGGREIKV 155
L+ ++ G I V
Sbjct: 62 LHHYKLHGVNINV 74
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 32/73 (43%), Gaps = 8/73 (10%)
Query: 183 KVYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXX 242
K+++GNL + T + ++ F + G+VL +++ +GFV
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDIIK--------NYGFVHIEDKTAAEDAIRN 61
Query: 243 LNNSLLEGQRIRV 255
L++ L G I V
Sbjct: 62 LHHYKLHGVNINV 74
>pdb|2DGX|A Chain A, Solution Structure Of The Rna Recognition Motif In
Kiaa0430 Protein
Length = 96
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 41/79 (51%), Gaps = 7/79 (8%)
Query: 84 VYIGNIPRNIDNDELTKIVQE----HGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAV 139
V + NI + EL +++QE HG V+ E+ +T + A V M+ ++DA
Sbjct: 12 VQVSNIDYRLSRKELQQLLQEAFARHGKVKSVEL--SPHTDYQLK-AVVQMENLQDAIGA 68
Query: 140 IEKLNGTEIGGREIKVNIT 158
+ L+ +IG ++I V++
Sbjct: 69 VNSLHRYKIGSKKILVSLA 87
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 30.0 bits (66), Expect = 1.2, Method: Composition-based stats.
Identities = 18/68 (26%), Positives = 29/68 (42%)
Query: 184 VYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXXXL 243
+Y+ L T + L K G+++S K + T+K G+GFV F L
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
Query: 244 NNSLLEGQ 251
S ++ Q
Sbjct: 68 KASGVQAQ 75
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 30.0 bits (66), Expect = 1.5, Method: Composition-based stats.
Identities = 14/59 (23%), Positives = 28/59 (47%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEK 142
+++G + + +++ + G VE E+ D T + R F F+ K E ++EK
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Score = 28.9 bits (63), Expect = 3.3, Method: Composition-based stats.
Identities = 15/47 (31%), Positives = 26/47 (55%)
Query: 184 VYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTF 230
++VG L+ E +++ F G+V S ++ T+K GF F+TF
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITF 48
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 29.6 bits (65), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/85 (22%), Positives = 40/85 (47%), Gaps = 8/85 (9%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAE--------VIYDKYTGRSRRFAFVMMKTVED 135
+Y+ + ++ D+L ++ G V+ + + DK TG+ + A V +
Sbjct: 18 IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPT 77
Query: 136 ANAVIEKLNGTEIGGREIKVNITEK 160
A A +E +G + G ++KV++ K
Sbjct: 78 AKAAVEWFDGKDFQGSKLKVSLARK 102
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 29.6 bits (65), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 23/43 (53%)
Query: 188 NLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTF 230
L T + LK+ FS G+VL +V + T S GFGFV F
Sbjct: 22 GLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF 64
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 29.3 bits (64), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 38/93 (40%), Gaps = 19/93 (20%)
Query: 75 DTPSEFARRVYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGR------SRRFAFV 128
+ P RV+IGN+ N L K E I+ KY GR + +AFV
Sbjct: 21 NDPKSINSRVFIGNL-----NTALVK-------KSDVETIFSKY-GRVAGCSVHKGYAFV 67
Query: 129 MMKTVEDANAVIEKLNGTEIGGREIKVNITEKP 161
A A + NG + G+ + +N+ +P
Sbjct: 68 QYSNERHARAAVLGENGRVLAGQTLDINMAGEP 100
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 28.9 bits (63), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 33/75 (44%), Gaps = 3/75 (4%)
Query: 184 VYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRV---PGTSKSSGFGFVTFXXXXXXXXXX 240
+++ NL + T E LK FS+ G + S + + G S GFGFV +
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 241 XXLNNSLLEGQRIRV 255
L ++G ++ V
Sbjct: 68 KQLQGHTVDGHKLEV 82
>pdb|3MKV|A Chain A, Crystal Structure Of Amidohydrolase Eaj56179
pdb|3MKV|B Chain B, Crystal Structure Of Amidohydrolase Eaj56179
pdb|3MKV|C Chain C, Crystal Structure Of Amidohydrolase Eaj56179
pdb|3MKV|D Chain D, Crystal Structure Of Amidohydrolase Eaj56179
pdb|3MKV|E Chain E, Crystal Structure Of Amidohydrolase Eaj56179
pdb|3MKV|F Chain F, Crystal Structure Of Amidohydrolase Eaj56179
pdb|3MKV|G Chain G, Crystal Structure Of Amidohydrolase Eaj56179
pdb|3MKV|H Chain H, Crystal Structure Of Amidohydrolase Eaj56179
Length = 426
Score = 28.5 bits (62), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 32/79 (40%), Gaps = 4/79 (5%)
Query: 53 EDSTTRLFAVAEETAXXXXXXVDTPSEFARRVYIG--NIPR-NIDNDELTKIVQEHGA-V 108
ED + A A+ TP+ AR V G I N+ +DE ++V EHGA V
Sbjct: 214 EDEIRAIVAEAQGRGTYVLAHAYTPAAIARAVRCGVRTIEHGNLIDDETARLVAEHGAYV 273
Query: 109 EKAEVIYDKYTGRSRRFAF 127
V YD ++
Sbjct: 274 VPTLVTYDALASEGEKYGL 292
>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO3|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO4|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3IIN|A Chain A, Plasticity Of The Kink Turn Structural Motif
Length = 95
Score = 28.5 bits (62), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 32/75 (42%), Gaps = 5/75 (6%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRF---AFVMMKTVEDANAVI 140
+YI N+ I DEL K + H + I D RS + AFV+ K V A +
Sbjct: 9 IYINNLNEKIKKDELKKSL--HAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 66
Query: 141 EKLNGTEIGGREIKV 155
+ G + +++
Sbjct: 67 RSMQGFPFYDKPMRI 81
>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 = 28.5 bits (62), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 36/73 (49%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKL 143
+Y+GN+ +++ ++ + G ++K + DK + F FV + DA + +
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 144 NGTEIGGREIKVN 156
NGT + R I+ +
Sbjct: 102 NGTRLDDRIIRTD 114
Score = 27.7 bits (60), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 36/74 (48%), Gaps = 2/74 (2%)
Query: 184 VYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSS-GFGFVTFXXXXXXXXXXXX 242
+YVGNL+ T E + + FS+ G + ++ + K++ GF FV +
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKI-IMGLDKMKKTACGFCFVEYYSRADAENAMRY 100
Query: 243 LNNSLLEGQRIRVN 256
+N + L+ + IR +
Sbjct: 101 INGTRLDDRIIRTD 114
>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|B Chain B, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|C Chain C, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|D Chain D, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
Length = 96
Score = 28.5 bits (62), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 32/75 (42%), Gaps = 5/75 (6%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRF---AFVMMKTVEDANAVI 140
+YI N+ I DEL K + H + I D RS + AFV+ K V A +
Sbjct: 11 IYINNLNEKIKKDELKKSL--HAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 68
Query: 141 EKLNGTEIGGREIKV 155
+ G + +++
Sbjct: 69 RSMQGFPFYDKPMRI 83
>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
pdb|3IWN|D Chain D, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
Length = 91
Score = 28.5 bits (62), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 32/75 (42%), Gaps = 5/75 (6%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRF---AFVMMKTVEDANAVI 140
+YI N+ I DEL K + H + I D RS + AFV+ K V A +
Sbjct: 7 IYINNLNEKIKKDELKKSL--HAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 64
Query: 141 EKLNGTEIGGREIKV 155
+ G + +++
Sbjct: 65 RSMQGFPFYDKPMRI 79
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 28.5 bits (62), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 29/57 (50%), Gaps = 9/57 (15%)
Query: 106 GAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKLNGTEIGGREIKVNITEKPL 162
GAVE+ + I R +AFV EDA ++ LNG + G I+V + KP+
Sbjct: 42 GAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA-KPV 89
Score = 27.3 bits (59), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 33/77 (42%), Gaps = 10/77 (12%)
Query: 184 VYVGNLAKTVTSEMLKKCFS--EKGQVLSAKVLRVPGTSKSSGFGFVTFXXXXXXXXXXX 241
+YV NL + + EM++K F+ + G V K +R + FV F
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIR--------DYAFVHFSNREDAVEAMK 69
Query: 242 XLNNSLLEGQRIRVNKA 258
LN +L+G I V A
Sbjct: 70 ALNGKVLDGSPIEVTLA 86
>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|B Chain B, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|C Chain C, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1NU4|A Chain A, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|1NU4|B Chain B, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|3HHN|B Chain B, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
pdb|3HHN|D Chain D, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
Length = 97
Score = 28.5 bits (62), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 32/75 (42%), Gaps = 5/75 (6%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRF---AFVMMKTVEDANAVI 140
+YI N+ I DEL K + H + I D RS + AFV+ K V A +
Sbjct: 11 IYINNLNEKIKKDELKKSL--HAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 68
Query: 141 EKLNGTEIGGREIKV 155
+ G + +++
Sbjct: 69 RSMQGFPFYDKPMRI 83
>pdb|1U6B|A Chain A, Crystal Structure Of A Self-Splicing Group I Intron With
Both Exons
pdb|1ZZN|A Chain A, Crystal Structure Of A Group I IntronTWO EXON COMPLEX THAT
Includes All Catalytic Metal Ion Ligands.
pdb|3G8S|A Chain A, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|B Chain B, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|C Chain C, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|D Chain D, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8T|A Chain A, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|B Chain B, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|C Chain C, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|D Chain D, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G96|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G9C|A Chain A, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|B Chain B, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|C Chain C, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|D Chain D, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3IRW|P Chain P, Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3MUM|P Chain P, Crystal Structure Of The G20a Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUR|P Chain P, Crystal Structure Of The C92u Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUT|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Gmp
pdb|3MUV|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Amp
pdb|3MXH|P Chain P, Native Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3P49|B Chain B, Crystal Structure Of A Glycine Riboswitch From
Fusobacterium Nucleatum
pdb|3R1H|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1H|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1L|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3R1L|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3UCU|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Pgpg
pdb|3UCZ|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Gpg
pdb|3UD3|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Pgpa
pdb|3UD4|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Gpa
Length = 98
Score = 28.5 bits (62), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 32/75 (42%), Gaps = 5/75 (6%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRF---AFVMMKTVEDANAVI 140
+YI N+ I DEL K + H + I D RS + AFV+ K V A +
Sbjct: 12 IYINNLNEKIKKDELKKSL--HAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 69
Query: 141 EKLNGTEIGGREIKV 155
+ G + +++
Sbjct: 70 RSMQGFPFYDKPMRI 84
>pdb|3L3C|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
Length = 90
Score = 28.5 bits (62), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 32/75 (42%), Gaps = 5/75 (6%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRF---AFVMMKTVEDANAVI 140
+YI N+ I DEL K + H + I D RS + AFV+ K V A +
Sbjct: 6 IYINNLNEKIKKDELKKSL--HAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 63
Query: 141 EKLNGTEIGGREIKV 155
+ G + +++
Sbjct: 64 RSMQGFPFYDKPMRI 78
>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 = 28.5 bits (62), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 38/70 (54%), Gaps = 2/70 (2%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIY--DKYTGRSRRFAFVMMKTVEDANAVIE 141
+YIGN+ +++LT+ V G + E+ + ++ G+S+ FA V + + + +++
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63
Query: 142 KLNGTEIGGR 151
L E+ G+
Sbjct: 64 LLPKRELHGQ 73
>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures
pdb|1DZ5|A Chain A, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
pdb|1DZ5|B Chain B, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
Length = 101
Score = 28.5 bits (62), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 32/75 (42%), Gaps = 5/75 (6%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRF---AFVMMKTVEDANAVI 140
+YI N+ I DEL K + H + I D RS + AFV+ K V A +
Sbjct: 11 IYINNLNEKIKKDELKKSL--HAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 68
Query: 141 EKLNGTEIGGREIKV 155
+ G + +++
Sbjct: 69 RSMQGFPFYDKPMRI 83
>pdb|1WI6|A Chain A, Solution Structure Of The Rna Binding Domain From Mouse
Hypothetical Protein Bab23670
Length = 88
Score = 28.5 bits (62), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 7/74 (9%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRFAFVMMKTVEDANAVIEKL 143
+ I +P ++ N E+ ++ ++ E DKY G AFV + E A A I
Sbjct: 8 ILIRGLPGDVTNQEVHDLLSDY---ELKYCFVDKYKGT----AFVTLLNGEQAEAAINTF 60
Query: 144 NGTEIGGREIKVNI 157
+ + + RE+ V +
Sbjct: 61 HQSRLRERELSVQL 74
>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|B Chain B, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|C Chain C, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|D Chain D, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
Length = 94
Score = 28.5 bits (62), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 32/75 (42%), Gaps = 5/75 (6%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRF---AFVMMKTVEDANAVI 140
+YI N+ I DEL K + H + I D RS + AFV+ K V A +
Sbjct: 8 IYINNLNEKIKKDELKKSL--HAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 65
Query: 141 EKLNGTEIGGREIKV 155
+ G + +++
Sbjct: 66 RSMQGFPFYDKPMRI 80
>pdb|1M5K|C Chain C, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5K|F Chain F, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5O|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5O|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1SJ3|P Chain P, Hepatitis Delta Virus Gemonic Ribozyme Precursor, With
Mg2+ Bound
pdb|1SJ4|P Chain P, Crystal Structure Of A C75u Mutant Hepatitis Delta Virus
Ribozyme Precursor, In Cu2+ Solution
pdb|1SJF|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Cobalt
Hexammine Solution
pdb|1VBX|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Edta Solution
pdb|1VBY|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, And Mn2+ Bound
pdb|1VBZ|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Ba2+ Solution
pdb|1VC0|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Imidazole And
Sr2+ Solution
pdb|1VC5|A Chain A, Crystal Structure Of The Wild Type Hepatitis Delta Virus
Gemonic Ribozyme Precursor, In Edta Solution
pdb|1VC6|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Product With C75u Mutaion, Cleaved In Imidazole
And Mg2+ Solutions
pdb|1VC7|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Sr2+ Solution
pdb|2OIH|A Chain A, Hepatitis Delta Virus Gemonic Ribozyme Precursor With C75u
Mutation And Bound To Monovalent Cation Tl+
pdb|2OJ3|A Chain A, Hepatitis Delta Virus Ribozyme Precursor Structure, With
C75u Mutation, Bound To Tl+ And Cobalt Hexammine
(Co(Nh3) 63+)
Length = 100
Score = 28.1 bits (61), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 32/75 (42%), Gaps = 5/75 (6%)
Query: 84 VYIGNIPRNIDNDELTKIVQEHGAVEKAEVIYDKYTGRSRRF---AFVMMKTVEDANAVI 140
+YI N+ I DEL K + H + I D RS + AFV+ K V A +
Sbjct: 12 IYINNLNEKIKKDELKKSL--HAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 69
Query: 141 EKLNGTEIGGREIKV 155
+ G + +++
Sbjct: 70 RSMQGFPFYDKPMRI 84
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 28.1 bits (61), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 29/48 (60%), Gaps = 5/48 (10%)
Query: 183 KVYVGNLAKTVTSEMLKKCFSEKGQVLSAKVLRVPGTSKSSGFGFVTF 230
KV+VG + +T+E L++ F + G+V+ + +P ++ F FVTF
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYGEVVD---VFIPKPFRA--FAFVTF 55
>pdb|2HZC|A Chain A, Crystal Structure Of The N-terminal Rrm Of The U2af Large
Subunit
Length = 87
Score = 27.7 bits (60), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 19/84 (22%), Positives = 38/84 (45%), Gaps = 6/84 (7%)
Query: 77 PSEFARRVYIGNIPRNIDNDELTKIVQEH---GAVEKA--EVIYDKYTGRSRRFAFVMMK 131
P ARR+Y+GNIP I + + G + +A + + + FAF+ +
Sbjct: 2 PLGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFR 61
Query: 132 TVEDANAVIEKLNGTEIGGREIKV 155
+V++ + +G G+ +K+
Sbjct: 62 SVDETTQAM-AFDGIIFQGQSLKI 84
>pdb|1U2F|A Chain A, Solution Structure Of The First Rna-Binding Domain Of
Hu2af65
Length = 90
Score = 27.7 bits (60), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 18/80 (22%), Positives = 37/80 (46%), Gaps = 6/80 (7%)
Query: 81 ARRVYIGNIPRNIDNDELTKIVQEH---GAVEKA--EVIYDKYTGRSRRFAFVMMKTVED 135
ARR+Y+GNIP I + + G + +A + + + FAF+ ++V++
Sbjct: 1 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 60
Query: 136 ANAVIEKLNGTEIGGREIKV 155
+ +G G+ +K+
Sbjct: 61 TTQAM-AFDGIIFQGQSLKI 79
>pdb|3DXB|A Chain A, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|B Chain B, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|C Chain C, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|D Chain D, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|E Chain E, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|F Chain F, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|G Chain G, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|H Chain H, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
Length = 222
Score = 27.7 bits (60), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 37/79 (46%), Gaps = 9/79 (11%)
Query: 90 PRNIDND---ELTKIVQEHGAVEKAEVIYDKYTGRSRRFA-----FVMMKTVEDANAVIE 141
P++ID+D E+T+ + GAV + +IY + G FV + + I+
Sbjct: 135 PKDIDDDLEGEVTEECGKFGAVNRV-IIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQ 193
Query: 142 KLNGTEIGGREIKVNITEK 160
LNG GR++ + ++
Sbjct: 194 ALNGRWFAGRKVVAEVYDQ 212
>pdb|2DNY|A Chain A, Solution Structure Of The Third Rna Binding Domain Of Fbp-
Interacting Repressor, Siahbp1
Length = 119
Score = 27.3 bits (59), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 9/72 (12%)
Query: 90 PRNIDND---ELTKIVQEHGAVEKAEVIYDKYTGRSRRFA-----FVMMKTVEDANAVIE 141
P++ID+D E+T+ + GAV + +IY + G FV + + I+
Sbjct: 26 PKDIDDDLEGEVTEECGKFGAVNRV-IIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQ 84
Query: 142 KLNGTEIGGREI 153
LNG GR++
Sbjct: 85 ALNGRWFAGRKV 96
>pdb|3UE2|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 1.23 A Resolution
pdb|3US5|A Chain A, Crystal Structure Of A Rna-Binding Domain Of A Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 1.38 A Resolution
Length = 118
Score = 27.3 bits (59), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 9/72 (12%)
Query: 90 PRNIDND---ELTKIVQEHGAVEKAEVIYDKYTGRSRRFA-----FVMMKTVEDANAVIE 141
P++ID+D E+T+ + GAV + +IY + G FV + + I+
Sbjct: 31 PKDIDDDLEGEVTEECGKFGAVNRV-IIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQ 89
Query: 142 KLNGTEIGGREI 153
LNG GR++
Sbjct: 90 ALNGRWFAGRKV 101
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.317 0.132 0.359
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,665,025
Number of Sequences: 62578
Number of extensions: 198660
Number of successful extensions: 843
Number of sequences better than 100.0: 188
Number of HSP's better than 100.0 without gapping: 131
Number of HSP's successfully gapped in prelim test: 57
Number of HSP's that attempted gapping in prelim test: 546
Number of HSP's gapped (non-prelim): 308
length of query: 258
length of database: 14,973,337
effective HSP length: 97
effective length of query: 161
effective length of database: 8,903,271
effective search space: 1433426631
effective search space used: 1433426631
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: 50 (23.9 bits)