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= 004002
(780 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 53.9 bits (128), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 36/111 (32%), Positives = 55/111 (49%), Gaps = 11/111 (9%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 254
LFV N+ ++ + E+R LFE+YG ++ K +GF I A A L N PL
Sbjct: 25 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIH-KDKGFGFIRLETRTLAEIAKVELDNMPL 83
Query: 255 RRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVK 305
R ++L + F+ + +L V NL VSNE L + F +G+V+
Sbjct: 84 RGKQLRVRFAC----------HSASLTVRNLPQYVSNELLEEAFSVFGQVE 124
>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 = 51.6 bits (122), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 37/169 (21%), Positives = 83/169 (49%), Gaps = 17/169 (10%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAMRAL 249
++V +I + + +R F +G I+++ KH+GF + Y AA+ A+ +
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 250 QNKPLRRRKLDIH--FSIPKDNPSDKDLNQGT-----LVVFNLDPSVSNEDLRQIFGAYG 302
+ L R + + +I + P L + + V ++ +S++D++ +F A+G
Sbjct: 91 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 150
Query: 303 EVKE--IRETPHKRHHK---FIEFYDVRAAEAALKSLNRSDIAGKRIKL 346
++K + P HK FIE+ ++++ A+ S+N D+ G+ +++
Sbjct: 151 KIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 199
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 49.3 bits (116), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 38/124 (30%), Positives = 57/124 (45%), Gaps = 13/124 (10%)
Query: 183 GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAA 242
GE Y + LFV N+ +++ + + + LFE+YG+ ++ + RGF I A
Sbjct: 15 GEKTYTQRCR--LFVGNLPTDITEEDFKRLFERYGEPSEVFIN-RDRGFGFIRLESRTLA 71
Query: 243 RTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYG 302
A L L+ R L I F+ + L V NL P VSNE L Q F +G
Sbjct: 72 EIAKAELDGTILKSRPLRIRFAT----------HGAALTVKNLSPVVSNELLEQAFSQFG 121
Query: 303 EVKE 306
V++
Sbjct: 122 PVEK 125
>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 = 49.3 bits (116), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 37/169 (21%), Positives = 83/169 (49%), Gaps = 17/169 (10%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAMRAL 249
++V +I + + +R F +G I+++ KH+GF + Y AA+ A+ +
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 250 QNKPLRRRKLDIH--FSIPKDNPSDKDLNQGT-----LVVFNLDPSVSNEDLRQIFGAYG 302
+ L R + + +I + P L + + V ++ +S++D++ +F A+G
Sbjct: 76 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 135
Query: 303 EVKE--IRETPHKRHHK---FIEFYDVRAAEAALKSLNRSDIAGKRIKL 346
++K + P HK FIE+ ++++ A+ S+N D+ G+ +++
Sbjct: 136 KIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 184
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 48.1 bits (113), Expect = 2e-05, Method: Composition-based stats.
Identities = 40/151 (26%), Positives = 70/151 (46%), Gaps = 14/151 (9%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAMRAL 249
L V + ++ D EL ALF G I T Y G+ + + ++ A++ L
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 250 QNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE--- 306
+R ++L + ++ P S KD N L V NL +++++ L IFG YG + +
Sbjct: 66 NGITVRNKRLKVSYARP-GGESIKDTN---LYVTNLPRTITDDQLDTIFGKYGSIVQKNI 121
Query: 307 IRE--TPHKRHHKFIEFYDVRAAEAALKSLN 335
+R+ T R F+ + A+ A+ +LN
Sbjct: 122 LRDKLTGRPRGVAFVRYNKREEAQEAISALN 152
Score = 36.6 bits (83), Expect = 0.051, Method: Composition-based stats.
Identities = 22/79 (27%), Positives = 41/79 (51%), Gaps = 5/79 (6%)
Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSL 334
L+V L +++ +L +F A G + R +T + + F++F ++ A+K L
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 335 NRSDIAGKRIKLEPSRPGG 353
N + KR+K+ +RPGG
Sbjct: 66 NGITVRNKRLKVSYARPGG 84
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 47.4 bits (111), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 38/157 (24%), Positives = 73/157 (46%), Gaps = 17/157 (10%)
Query: 195 LFVRNINSNVEDSELRALFEQYG---DIRTLYTACKH----RGFVMISYYDIRAARTAMR 247
+FV + + +LR LFEQYG +I L ++ +G +++Y +AA A
Sbjct: 18 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 77
Query: 248 ALQNKPLRRRKLDIHFSI---PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEV 304
AL N + +H I P D+ + + L + + + D+R +F ++G++
Sbjct: 78 ALHNMKVLP---GMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQI 134
Query: 305 KEIR--ETPH--KRHHKFIEFYDVRAAEAALKSLNRS 337
+E R P R F+ F A+ A+K+++++
Sbjct: 135 EECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQA 171
Score = 37.4 bits (85), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 7/75 (9%)
Query: 268 DNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-------RETPHKRHHKFIE 320
D+P DL+ + V + + S +DLR++F YG V EI + P + F+
Sbjct: 6 DHPDQPDLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVT 65
Query: 321 FYDVRAAEAALKSLN 335
FY +AA A +L+
Sbjct: 66 FYTRKAALEAQNALH 80
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 47.0 bits (110), Expect = 4e-05, Method: Composition-based stats.
Identities = 38/157 (24%), Positives = 73/157 (46%), Gaps = 17/157 (10%)
Query: 195 LFVRNINSNVEDSELRALFEQYG---DIRTLYTACKH----RGFVMISYYDIRAARTAMR 247
+FV + + +LR LFEQYG +I L ++ +G +++Y +AA A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 248 ALQNKPLRRRKLDIHFSI---PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEV 304
AL N + +H I P D+ + + L + + + D+R +F ++G++
Sbjct: 66 ALHNMKVLP---GMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQI 122
Query: 305 KEIR--ETPH--KRHHKFIEFYDVRAAEAALKSLNRS 337
+E R P R F+ F A+ A+K+++++
Sbjct: 123 EECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQA 159
>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 = 46.6 bits (109), Expect = 5e-05, Method: Composition-based stats.
Identities = 41/161 (25%), Positives = 67/161 (41%), Gaps = 22/161 (13%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACK---------HRGFVMISYYDIRAARTA 245
L V + N+ E R+LF G+I + CK G+ ++Y D + A A
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIES----CKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 246 MRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVK 305
+ L L+ + + + ++ PS + L V L +++ ++L Q+F YG +
Sbjct: 61 INTLNGLRLQTKTIKVSYA----RPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRII 116
Query: 306 EIR-----ETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG 341
R T R FI F AE A+K LN +G
Sbjct: 117 TSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSG 157
Score = 40.8 bits (94), Expect = 0.003, Method: Composition-based stats.
Identities = 25/84 (29%), Positives = 46/84 (54%), Gaps = 5/84 (5%)
Query: 276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEV---KEIRE--TPHKRHHKFIEFYDVRAAEAA 330
++ L+V L +++ E+ R +FG+ GE+ K +R+ T + F+ + D + AE A
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 331 LKSLNRSDIAGKRIKLEPSRPGGA 354
+ +LN + K IK+ +RP A
Sbjct: 61 INTLNGLRLQTKTIKVSYARPSSA 84
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 46.2 bits (108), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 40/155 (25%), Positives = 64/155 (41%), Gaps = 22/155 (14%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACK---------HRGFVMISYYDIRAARTA 245
L V + N+ E ++LF GDI + CK G+ ++Y D A A
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIES----CKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 246 MRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVK 305
+ L L+ + + + ++ PS + L V L ++S +++ Q+F YG +
Sbjct: 63 INTLNGLKLQTKTIKVSYA----RPSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRII 118
Query: 306 EIR-----ETPHKRHHKFIEFYDVRAAEAALKSLN 335
R T R FI F AE A+K LN
Sbjct: 119 TSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLN 153
Score = 34.7 bits (78), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 43/80 (53%), Gaps = 5/80 (6%)
Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEV---KEIRE--TPHKRHHKFIEFYDVRAAEAALKSL 334
L+V L +++ ++ + +FG+ G++ K +R+ T + F+ + D A+ A+ +L
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 335 NRSDIAGKRIKLEPSRPGGA 354
N + K IK+ +RP A
Sbjct: 67 NGLKLQTKTIKVSYARPSSA 86
>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 = 46.2 bits (108), Expect = 7e-05, Method: Composition-based stats.
Identities = 41/186 (22%), Positives = 85/186 (45%), Gaps = 28/186 (15%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAMRAL 249
++V +I + + +R F +G I+++ KH+GF + Y AA+ A+
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 250 QNKPLRRRKLDIH--FSIPKDNPSDKDLNQ-----GTLVVFNLDPSVSNEDLRQIFGAYG 302
+ L R + + +I + P L + + V ++ +S++D++ +F A+G
Sbjct: 75 NSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 134
Query: 303 EVKE--IRETPHKRHHK---FIEFYDVRAAEAALKSLNRSDIAGKRIK-----------L 346
++K + P HK FIE+ ++++ A+ S N D+ G+ ++ L
Sbjct: 135 KIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVGKAVTPPXPLL 194
Query: 347 EPSRPG 352
P+ PG
Sbjct: 195 TPATPG 200
>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 = 46.2 bits (108), Expect = 7e-05, Method: Composition-based stats.
Identities = 40/151 (26%), Positives = 69/151 (45%), Gaps = 14/151 (9%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAMRAL 249
L V + + D EL ALF G I T Y G+ + + ++ A++ L
Sbjct: 17 LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 250 QNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE--- 306
+R ++L + ++ P S KD N L V NL +++++ L IFG YG + +
Sbjct: 77 NGITVRNKRLKVSYARP-GGESIKDTN---LYVTNLPRTITDDQLDTIFGKYGSIVQKNI 132
Query: 307 IRE--TPHKRHHKFIEFYDVRAAEAALKSLN 335
+R+ T R F+ + A+ A+ +LN
Sbjct: 133 LRDKLTGRPRGVAFVRYNKREEAQEAISALN 163
Score = 35.8 bits (81), Expect = 0.090, Method: Composition-based stats.
Identities = 23/88 (26%), Positives = 43/88 (48%), Gaps = 5/88 (5%)
Query: 271 SDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVR 325
+D + L+V L ++ +L +F A G + R +T + + F++F
Sbjct: 8 NDPRASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEX 67
Query: 326 AAEAALKSLNRSDIAGKRIKLEPSRPGG 353
++ A+K LN + KR+K+ +RPGG
Sbjct: 68 DSQRAIKVLNGITVRNKRLKVSYARPGG 95
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 45.1 bits (105), Expect = 1e-04, Method: Composition-based stats.
Identities = 45/170 (26%), Positives = 74/170 (43%), Gaps = 19/170 (11%)
Query: 195 LFVRNINSNVEDSELRA----LFEQYG----DIRTLYTACKHRGFVMISYYDIRAARTAM 246
LFV N+N N EL+ +F + D+R T R F Y D +A
Sbjct: 10 LFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRIGMT----RKF---GYVDFESAEDLE 62
Query: 247 RALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE 306
+AL+ L+ +I PK S K+ + TL+ NL V+ ++L+++F E++
Sbjct: 63 KALELTGLKVFGNEIKLEKPKGKDSKKERDARTLLAKNLPYKVTQDELKEVFEDAAEIRL 122
Query: 307 IRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKL----EPSRPG 352
+ + + +IEF AE + ++I G+ I L EP G
Sbjct: 123 VSKDGKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSISLYYTGEPKGEG 172
Score = 34.7 bits (78), Expect = 0.22, Method: Composition-based stats.
Identities = 19/82 (23%), Positives = 35/82 (42%)
Query: 183 GEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAA 242
G+ E +RTL +N+ V EL+ +FE +IR + K +G I + A
Sbjct: 84 GKDSKKERDARTLLAKNLPYKVTQDELKEVFEDAAEIRLVSKDGKSKGIAYIEFKTEADA 143
Query: 243 RTAMRALQNKPLRRRKLDIHFS 264
Q + R + ++++
Sbjct: 144 EKTFEEKQGTEIDGRSISLYYT 165
>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 = 44.7 bits (104), Expect = 2e-04, Method: Composition-based stats.
Identities = 41/160 (25%), Positives = 74/160 (46%), Gaps = 15/160 (9%)
Query: 195 LFVRNINSNVEDSELR-ALFEQYG-------DIRTLYTACKHRGFVMISYYDIRAARTAM 246
LF+ N+N N +EL+ A+ E + D+RT +R F Y D +A
Sbjct: 16 LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRT----GTNRKF---GYVDFESAEDLE 68
Query: 247 RALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE 306
+AL+ L+ +I PK S K TL+ NL +++ ++L+++F E++
Sbjct: 69 KALELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRL 128
Query: 307 IRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKL 346
+ + + +IEF AE L+ ++I G+ + L
Sbjct: 129 VSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSL 168
Score = 35.0 bits (79), Expect = 0.17, Method: Composition-based stats.
Identities = 17/73 (23%), Positives = 36/73 (49%)
Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN 251
+RTL +N++ N+ + EL+ +FE +IR + K +G I + A + Q
Sbjct: 99 ARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQG 158
Query: 252 KPLRRRKLDIHFS 264
+ R + ++++
Sbjct: 159 AEIDGRSVSLYYT 171
>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 44/81 (54%), Gaps = 6/81 (7%)
Query: 190 HPSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAAR 243
P+ T+++ N+N ++ EL+ A+F Q+G I + + K RG + + ++ +A
Sbjct: 7 RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSAT 66
Query: 244 TAMRALQNKPLRRRKLDIHFS 264
A+R++Q P + + I ++
Sbjct: 67 NALRSMQGFPFYDKPMRIQYA 87
>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 = 43.5 bits (101), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 34/155 (21%), Positives = 74/155 (47%), Gaps = 12/155 (7%)
Query: 190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHR------GFVMISYYDIRAAR 243
+P +L+V +++ +V ++ L F G I ++ C+ G+ +++ A
Sbjct: 13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSI-RVCRDMITRRSLGYAYVNFQQPADAE 71
Query: 244 TAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGE 303
A+ + ++ + + I +S + +PS + G + + NLD S+ N+ L F A+G
Sbjct: 72 RALDTMNFDVIKGKPVRIMWS--QRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGN 129
Query: 304 V---KEIRETPHKRHHKFIEFYDVRAAEAALKSLN 335
+ K + + + + F+ F AAE A++ +N
Sbjct: 130 ILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 164
Score = 29.6 bits (65), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 36/83 (43%), Gaps = 5/83 (6%)
Query: 269 NPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYD 323
NPS +L V +L P V+ L + F G + IR T + ++ F
Sbjct: 7 NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ 66
Query: 324 VRAAEAALKSLNRSDIAGKRIKL 346
AE AL ++N I GK +++
Sbjct: 67 PADAERALDTMNFDVIKGKPVRI 89
>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
pdb|3NNA|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 43.5 bits (101), Expect = 5e-04, Method: Composition-based stats.
Identities = 36/153 (23%), Positives = 67/153 (43%), Gaps = 11/153 (7%)
Query: 196 FVRNINSNVEDSELRALFEQYG---DIRTLYTACKH----RGFVMISYYDIRAARTAMRA 248
FV + + +LR LFEQYG +I L ++ +G +++Y +AA A A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 249 LQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR 308
L N + P D+ + + L + + + D+R F ++G+++E R
Sbjct: 67 LHNXKVLPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQIEECR 126
Query: 309 --ETPH--KRHHKFIEFYDVRAAEAALKSLNRS 337
P R F+ F A+ A+K+ +++
Sbjct: 127 ILRGPDGLSRGCAFVTFTTRAXAQTAIKAXHQA 159
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 43.1 bits (100), Expect = 5e-04, Method: Composition-based stats.
Identities = 20/80 (25%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 191 PSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAART 244
P+ T+++ N+N ++ EL+ A+F Q+G I + + K RG + + ++ +A
Sbjct: 8 PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATN 67
Query: 245 AMRALQNKPLRRRKLDIHFS 264
A+R++Q P + + I ++
Sbjct: 68 ALRSMQGFPFYDKPMRIQYA 87
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 43.1 bits (100), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 42/77 (54%), Gaps = 1/77 (1%)
Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHK-RHHKFIEFYDVRAAEAALKSLNRS 337
TLV+ NL S + E L+++F +K + K + + FIEF A+ AL S N+
Sbjct: 17 TLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKR 76
Query: 338 DIAGKRIKLEPSRPGGA 354
+I G+ I+LE P G+
Sbjct: 77 EIEGRAIRLELQGPRGS 93
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 43.1 bits (100), Expect = 6e-04, Method: Composition-based stats.
Identities = 20/80 (25%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 191 PSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAART 244
P+ T+++ N+N ++ EL+ A+F Q+G I + + K RG + + ++ +A
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATN 66
Query: 245 AMRALQNKPLRRRKLDIHFS 264
A+R++Q P + + I ++
Sbjct: 67 ALRSMQGFPFYDKPMRIQYA 86
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 42.4 bits (98), Expect = 9e-04, Method: Composition-based stats.
Identities = 21/77 (27%), Positives = 42/77 (54%), Gaps = 5/77 (6%)
Query: 276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAA 330
++G L V L + + L Q+F YG++ E+ RET R F+ F ++ A+ A
Sbjct: 11 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 70
Query: 331 LKSLNRSDIAGKRIKLE 347
+ ++N + G++I+++
Sbjct: 71 MMAMNGKSVDGRQIRVD 87
Score = 32.3 bits (72), Expect = 1.1, Method: Composition-based stats.
Identities = 18/72 (25%), Positives = 36/72 (50%), Gaps = 5/72 (6%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRAL 249
LFV ++ + + L +F +YG I + + RGF +++ +I A+ AM A+
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 250 QNKPLRRRKLDI 261
K + R++ +
Sbjct: 75 NGKSVDGRQIRV 86
>pdb|2ADC|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd34 Complexed With Cucucu Rna
pdb|2EVZ|A Chain A, Structure Of Rna Binding Domains 3 And 4 Of Polypyrimidine
Tract Binding Protein
Length = 229
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 44/179 (24%), Positives = 68/179 (37%), Gaps = 33/179 (18%)
Query: 194 TLFVRNIN-SNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNK 252
L V N+N V L LF YGD++ + + ++ D A+ AM L
Sbjct: 36 VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGH 95
Query: 253 PLRRRKLDIHFS------IPKDNPSDKDLNQ-------------------------GTLV 281
L + + I S +P++ D+ L + TL
Sbjct: 96 KLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLH 155
Query: 282 VFNLDPSVSNEDLRQIFGAY-GEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 339
+ N+ PSVS EDL+ +F + G VK + R I+ V A AL L+ D+
Sbjct: 156 LSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDL 214
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 279 TLVVFNLDPS-VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRS 337
L+V NL+P V+ + L +FG YG+V+ ++ +K+ + ++ D A+ A+ LN
Sbjct: 36 VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGH 95
Query: 338 DIAGKRIKLEPSR 350
+ GK I++ S+
Sbjct: 96 KLHGKPIRITLSK 108
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 195 LFVRNINS-NVEDSELRALFEQYGDIRTLYTACK-HRGFVMISYYDIRAARTAMRALQNK 252
+F+ N+N+ V+ S++ A+F +YG I C H+GF + Y + R AR A+ +
Sbjct: 18 VFIGNLNTLVVKKSDVEAIFSKYGKI----VGCSVHKGFAFVQYVNERNARAAVAGEDGR 73
Query: 253 PLRRRKLDIHFSI-PKDNPS 271
+ + LDI+ + PK N S
Sbjct: 74 MIAGQVLDINLAAEPKVNRS 93
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 42/81 (51%), Gaps = 5/81 (6%)
Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSL 334
L+V + +V LRQ+F YG ++ + RET R + F++F +A+ A+ L
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 335 NRSDIAGKRIKLEPSRPGGAR 355
N +I KR+K+ + G R
Sbjct: 105 NGFNILNKRLKVALAASGHQR 125
Score = 38.9 bits (89), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 5/77 (6%)
Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTAMR 247
R L V I + V++ +LR LFE+YG I ++ C + RG+ + + +A+ A+
Sbjct: 43 RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA 102
Query: 248 ALQNKPLRRRKLDIHFS 264
L + ++L + +
Sbjct: 103 GLNGFNILNKRLKVALA 119
>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 = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 37/71 (52%), Gaps = 1/71 (1%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 254
LFV N+ ++ + E+R LFE+YG ++ K +GF I A A L N PL
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIH-KDKGFGFIRLETRTLAEIAKVELDNMPL 76
Query: 255 RRRKLDIHFSI 265
R ++L + F+
Sbjct: 77 RGKQLRVRFAC 87
>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 = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 35/154 (22%), Positives = 72/154 (46%), Gaps = 10/154 (6%)
Query: 190 HPSRTLFVRNINSNVEDSELRALFEQYG---DIRTLYTACKHR--GFVMISYYDIRAART 244
+P +L+V +++ +V ++ L F G IR R G+ +++ A
Sbjct: 8 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAER 67
Query: 245 AMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEV 304
A+ + ++ + + I +S + +PS + G + + NLD S+ N+ L F A+G +
Sbjct: 68 ALDTMNFDVIKGKPVRIMWS--QRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNI 125
Query: 305 ---KEIRETPHKRHHKFIEFYDVRAAEAALKSLN 335
K + + + + F+ F AAE A++ +N
Sbjct: 126 LSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 159
>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 = 41.6 bits (96), Expect = 0.002, Method: Composition-based stats.
Identities = 19/80 (23%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 191 PSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAART 244
P+ T+++ N+N ++ EL+ A+F ++G I + + K RG + + ++ +A
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 66
Query: 245 AMRALQNKPLRRRKLDIHFS 264
A+R++Q P + + I ++
Sbjct: 67 ALRSMQGFPFYDKPMRIQYA 86
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 41.6 bits (96), Expect = 0.002, Method: Composition-based stats.
Identities = 42/161 (26%), Positives = 61/161 (37%), Gaps = 31/161 (19%)
Query: 184 EHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------KHRGFVMI 234
E P R LF+ ++ D LR+ FEQ+G + T C + RGF +
Sbjct: 3 ESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTL----TDCVVMRDPNTKRSRGFGFV 58
Query: 235 SYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKD-------LNQGTLVVFNLDP 287
+Y + AM A R K+D PK S +D L + V +
Sbjct: 59 TYATVEEVDAAMNA------RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKE 112
Query: 288 SVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYD 323
LR F YG+++ I R + KR F+ F D
Sbjct: 113 DTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 153
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 42/161 (26%), Positives = 61/161 (37%), Gaps = 31/161 (19%)
Query: 184 EHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------KHRGFVMI 234
E P R LF+ ++ D LR+ FEQ+G + T C + RGF +
Sbjct: 5 ESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTL----TDCVVMRDPNTKRSRGFGFV 60
Query: 235 SYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKD-------LNQGTLVVFNLDP 287
+Y + AM A R K+D PK S +D L + V +
Sbjct: 61 TYATVEEVDAAMNA------RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKE 114
Query: 288 SVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYD 323
LR F YG+++ I R + KR F+ F D
Sbjct: 115 DTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 155
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 43/166 (25%), Positives = 62/166 (37%), Gaps = 31/166 (18%)
Query: 179 GTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------KHR 229
G E P R LF+ ++ D LR+ FEQ+G + T C + R
Sbjct: 1 GGSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTL----TDCVVMRDPNTKRSR 56
Query: 230 GFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKD-------LNQGTLVV 282
GF ++Y + AM A R K+D PK S +D L + V
Sbjct: 57 GFGFVTYATVEEVDAAMNA------RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFV 110
Query: 283 FNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYD 323
+ LR F YG+++ I R + KR F+ F D
Sbjct: 111 GGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 156
>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 = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 6/86 (6%)
Query: 268 DNPSDKDLNQG-TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEF 321
D P + +G L V + + ED+ F YGE+K I R T + + + +E+
Sbjct: 12 DEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 71
Query: 322 YDVRAAEAALKSLNRSDIAGKRIKLE 347
+ A+AA++ LN D+ G+ I ++
Sbjct: 72 ETYKEAQAAMEGLNGQDLMGQPISVD 97
Score = 32.3 bits (72), Expect = 0.93, Method: Composition-based stats.
Identities = 15/72 (20%), Positives = 34/72 (47%), Gaps = 5/72 (6%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHR-----GFVMISYYDIRAARTAMRAL 249
LFV ++ + ++ F +YG+I+ ++ R G+ ++ Y + A+ AM L
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 250 QNKPLRRRKLDI 261
+ L + + +
Sbjct: 85 NGQDLMGQPISV 96
>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 = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 5/73 (6%)
Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSL 334
L V + + ED+ F YGE+K I R T + + + +E+ + A+AA++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 335 NRSDIAGKRIKLE 347
N D+ G+ I ++
Sbjct: 70 NGQDLMGQPISVD 82
Score = 32.7 bits (73), Expect = 0.73, Method: Composition-based stats.
Identities = 15/72 (20%), Positives = 34/72 (47%), Gaps = 5/72 (6%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHR-----GFVMISYYDIRAARTAMRAL 249
LFV ++ + ++ F +YG+I+ ++ R G+ ++ Y + A+ AM L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 250 QNKPLRRRKLDI 261
+ L + + +
Sbjct: 70 NGQDLMGQPISV 81
>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 = 40.8 bits (94), Expect = 0.003, Method: Composition-based stats.
Identities = 42/161 (26%), Positives = 61/161 (37%), Gaps = 31/161 (19%)
Query: 184 EHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------KHRGFVMI 234
E P R LF+ ++ D LR+ FEQ+G + T C + RGF +
Sbjct: 5 ESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTL----TDCVVMRDPNTKRSRGFGFV 60
Query: 235 SYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKD-------LNQGTLVVFNLDP 287
+Y + AM A R K+D PK S +D L + V +
Sbjct: 61 TYATVEEVDAAMNA------RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKE 114
Query: 288 SVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYD 323
LR F YG+++ I R + KR F+ F D
Sbjct: 115 DTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 155
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 40.8 bits (94), Expect = 0.003, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 5/73 (6%)
Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSL 334
L V + + ED+ F YGE+K I R T + + + +E+ + A+AA++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 335 NRSDIAGKRIKLE 347
N D+ G+ I ++
Sbjct: 70 NGQDLMGQPISVD 82
Score = 32.7 bits (73), Expect = 0.89, Method: Composition-based stats.
Identities = 15/72 (20%), Positives = 34/72 (47%), Gaps = 5/72 (6%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHR-----GFVMISYYDIRAARTAMRAL 249
LFV ++ + ++ F +YG+I+ ++ R G+ ++ Y + A+ AM L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 250 QNKPLRRRKLDI 261
+ L + + +
Sbjct: 70 NGQDLMGQPISV 81
>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 = 40.8 bits (94), Expect = 0.003, Method: Composition-based stats.
Identities = 42/161 (26%), Positives = 61/161 (37%), Gaps = 31/161 (19%)
Query: 184 EHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------KHRGFVMI 234
E P R LF+ ++ D LR+ FEQ+G + T C + RGF +
Sbjct: 4 ESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTL----TDCVVMRDPNTKRSRGFGFV 59
Query: 235 SYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKD-------LNQGTLVVFNLDP 287
+Y + AM A R K+D PK S +D L + V +
Sbjct: 60 TYATVEEVDAAMNA------RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKE 113
Query: 288 SVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYD 323
LR F YG+++ I R + KR F+ F D
Sbjct: 114 DTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 154
>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 = 40.8 bits (94), Expect = 0.003, Method: Composition-based stats.
Identities = 40/152 (26%), Positives = 59/152 (38%), Gaps = 31/152 (20%)
Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC---------KHRGFVMISYYDIRAAR 243
R LF+ ++ D LR+ FEQ+G + T C + RGF ++Y +
Sbjct: 7 RKLFIGGLSFETTDESLRSHFEQWGTL----TDCVVMRDPNTKRSRGFGFVTYATVEEVD 62
Query: 244 TAMRALQNKPLRRRKLDIHFSIPKDNPSDKD-------LNQGTLVVFNLDPSVSNEDLRQ 296
AM A R K+D PK S +D L + V + LR
Sbjct: 63 AAMNA------RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRD 116
Query: 297 IFGAYGEVKEI-----RETPHKRHHKFIEFYD 323
F YG+++ I R + KR F+ F D
Sbjct: 117 YFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 148
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 40.8 bits (94), Expect = 0.003, Method: Composition-based stats.
Identities = 27/81 (33%), Positives = 44/81 (54%), Gaps = 2/81 (2%)
Query: 271 SDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAE-A 329
S +D TL V L +++ DLR F +GE++ I ++ FI+F +AAE A
Sbjct: 6 SGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTI-TVVQRQQCAFIQFATRQAAEVA 64
Query: 330 ALKSLNRSDIAGKRIKLEPSR 350
A KS N+ + G+R+ ++ R
Sbjct: 65 AEKSFNKLIVNGRRLNVKWGR 85
Score = 32.3 bits (72), Expect = 1.0, Method: Composition-based stats.
Identities = 20/71 (28%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKP 253
TL+V + + +++LR F Q+G+IRT+ T + + I + +AA A NK
Sbjct: 14 TLYVGGLGDTITETDLRNHFYQFGEIRTI-TVVQRQQCAFIQFATRQAAEVAAEKSFNKL 72
Query: 254 L-RRRKLDIHF 263
+ R+L++ +
Sbjct: 73 IVNGRRLNVKW 83
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 40.8 bits (94), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 279 TLVVFNLDPS-VSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRS 337
L+V NL+P V+ + L +FG YG+V+ ++ +K+ + ++ D A+ A+ LN
Sbjct: 5 VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGH 64
Query: 338 DIAGKRIKLEPSR 350
+ GK I++ S+
Sbjct: 65 KLHGKPIRITLSK 77
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 44/179 (24%), Positives = 68/179 (37%), Gaps = 33/179 (18%)
Query: 194 TLFVRNIN-SNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNK 252
L V N+N V L LF YGD++ + + ++ D A+ AM L
Sbjct: 5 VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGH 64
Query: 253 PLRRRKLDIHFS------IPKDNPSDKDLNQ-------------------------GTLV 281
L + + I S +P++ D+ L + TL
Sbjct: 65 KLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLH 124
Query: 282 VFNLDPSVSNEDLRQIFGAY-GEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 339
+ N+ PSVS EDL+ +F + G VK + R I+ V A AL L+ D+
Sbjct: 125 LSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDL 183
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 40.8 bits (94), Expect = 0.003, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 5/75 (6%)
Query: 276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAA 330
++ T+ V NL S++N DL +IF YG+V ++ ++T + FI F D +A+
Sbjct: 15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNC 74
Query: 331 LKSLNRSDIAGKRIK 345
+++N + G+ IK
Sbjct: 75 TRAINNKQLFGRVIK 89
Score = 32.3 bits (72), Expect = 0.91, Method: Composition-based stats.
Identities = 21/81 (25%), Positives = 41/81 (50%), Gaps = 6/81 (7%)
Query: 191 PSR-TLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAART 244
PS+ T++V N+ ++ +++L +F +YG + + K +G I + D +A+
Sbjct: 14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQN 73
Query: 245 AMRALQNKPLRRRKLDIHFSI 265
RA+ NK L R + +I
Sbjct: 74 CTRAINNKQLFGRVIKASIAI 94
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 5/72 (6%)
Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMR 247
+TLFV +N + +S+LR FE YG I+ ++ + K RG+ I Y R +A +
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 248 ALQNKPLRRRKL 259
K + R++
Sbjct: 163 HADGKKIDGRRV 174
Score = 33.5 bits (75), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 35/77 (45%), Gaps = 5/77 (6%)
Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIEFYDVRAAEAALKS 333
TL V ++ + LR+ F YG +K I KR K FIE+ R +A K
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 334 LNRSDIAGKRIKLEPSR 350
+ I G+R+ ++ R
Sbjct: 164 ADGKKIDGRRVLVDVER 180
>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 90
Score = 40.4 bits (93), Expect = 0.003, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 5/73 (6%)
Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSL 334
L V + + ED+ F YGE+K I R T + + + +E+ + A+AA++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 335 NRSDIAGKRIKLE 347
N D+ G+ I ++
Sbjct: 70 NGQDLMGQPISVD 82
Score = 33.1 bits (74), Expect = 0.56, Method: Composition-based stats.
Identities = 16/81 (19%), Positives = 37/81 (45%), Gaps = 5/81 (6%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHR-----GFVMISYYDIRAARTAMRAL 249
LFV ++ + ++ F +YG+I+ ++ R G+ ++ Y + A+ AM L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 250 QNKPLRRRKLDIHFSIPKDNP 270
+ L + + + + + P
Sbjct: 70 NGQDLMGQPISVDWCFVRGPP 90
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 40.4 bits (93), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 34/151 (22%), Positives = 63/151 (41%), Gaps = 14/151 (9%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAMRAL 249
L V + N+ ELR+LF G++ + A G+ ++Y + A A+ L
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 250 QNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR- 308
L+ + + + ++ PS + + L + L +++ +D+ +F +G + R
Sbjct: 65 NGLRLQSKTIKVSYA----RPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRV 120
Query: 309 ----ETPHKRHHKFIEFYDVRAAEAALKSLN 335
T R FI F AE A+ S N
Sbjct: 121 LVDQTTGLSRGVAFIRFDKRSEAEEAITSFN 151
Score = 37.4 bits (85), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 5/77 (6%)
Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEV---KEIRETP--HKRHHKFIEFYDVRAAEAALKSL 334
L+V L +++ ++LR +F + GEV K IR+ H + F+ + + AE A+ +L
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 335 NRSDIAGKRIKLEPSRP 351
N + K IK+ +RP
Sbjct: 65 NGLRLQSKTIKVSYARP 81
>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX
pdb|1P27|D Chain D, Crystal Structure Of The Human Y14MAGOH COMPLEX
Length = 106
Score = 40.4 bits (93), Expect = 0.004, Method: Composition-based stats.
Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 6/86 (6%)
Query: 268 DNPSDKDLNQG-TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEF 321
D P + +G L V + + ED+ F YGE+K I R T + + + +E+
Sbjct: 13 DEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 72
Query: 322 YDVRAAEAALKSLNRSDIAGKRIKLE 347
+ A+AA++ LN D+ G+ I ++
Sbjct: 73 ETYKEAQAAMEGLNGQDLMGQPISVD 98
Score = 33.1 bits (74), Expect = 0.69, Method: Composition-based stats.
Identities = 16/81 (19%), Positives = 37/81 (45%), Gaps = 5/81 (6%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHR-----GFVMISYYDIRAARTAMRAL 249
LFV ++ + ++ F +YG+I+ ++ R G+ ++ Y + A+ AM L
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 250 QNKPLRRRKLDIHFSIPKDNP 270
+ L + + + + + P
Sbjct: 86 NGQDLMGQPISVDWCFVRGPP 106
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 40.4 bits (93), Expect = 0.004, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 5/73 (6%)
Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSL 334
L V + + ED+ F YGE+K I R T + + + +E+ + A+AA++ L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 335 NRSDIAGKRIKLE 347
N D+ G+ I ++
Sbjct: 72 NGQDLMGQPISVD 84
Score = 32.3 bits (72), Expect = 1.2, Method: Composition-based stats.
Identities = 15/72 (20%), Positives = 34/72 (47%), Gaps = 5/72 (6%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHR-----GFVMISYYDIRAARTAMRAL 249
LFV ++ + ++ F +YG+I+ ++ R G+ ++ Y + A+ AM L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 250 QNKPLRRRKLDI 261
+ L + + +
Sbjct: 72 NGQDLMGQPISV 83
>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 = 40.4 bits (93), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 34/151 (22%), Positives = 63/151 (41%), Gaps = 14/151 (9%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAMRAL 249
L V + N+ ELR+LF G++ + A G+ ++Y + A A+ L
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 250 QNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIR- 308
L+ + + + ++ PS + + L + L +++ +D+ +F +G + R
Sbjct: 65 NGLRLQSKTIKVSYA----RPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRV 120
Query: 309 ----ETPHKRHHKFIEFYDVRAAEAALKSLN 335
T R FI F AE A+ S N
Sbjct: 121 LVDQTTGLSRGVAFIRFDKRSEAEEAITSFN 151
Score = 37.4 bits (85), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 5/77 (6%)
Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEV---KEIRETP--HKRHHKFIEFYDVRAAEAALKSL 334
L+V L +++ ++LR +F + GEV K IR+ H + F+ + + AE A+ +L
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 335 NRSDIAGKRIKLEPSRP 351
N + K IK+ +RP
Sbjct: 65 NGLRLQSKTIKVSYARP 81
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 40.0 bits (92), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 4/77 (5%)
Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR 247
G S +FV ++ + ELR F QYGD+ ++ R F +++ D + A++
Sbjct: 1 GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQS--- 57
Query: 248 ALQNKPLRRRKLDIHFS 264
L + L + + +H S
Sbjct: 58 -LCGEDLIIKGISVHIS 73
>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 = 39.7 bits (91), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 44/81 (54%), Gaps = 6/81 (7%)
Query: 190 HPSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAAR 243
P+ T+++ N+N ++ EL+ A+F ++G I + + K RG + + ++ +A
Sbjct: 7 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 66
Query: 244 TAMRALQNKPLRRRKLDIHFS 264
A+R++Q P + + I ++
Sbjct: 67 NALRSMQGFPFYDKPMRIQYA 87
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 39.3 bits (90), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 38/77 (49%), Gaps = 3/77 (3%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 254
LF+ N+ + E+R+LFEQYG + K+ GFV I D AA A+R L + L
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLEC-DIIKNYGFVHIE--DKTAAEDAIRNLHHYKL 67
Query: 255 RRRKLDIHFSIPKDNPS 271
+++ S K S
Sbjct: 68 HGVNINVEASKNKSKAS 84
>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 = 39.3 bits (90), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 191 PSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAART 244
P+ T+++ N+N ++ EL+ A+F ++G I + + K RG + + ++ +A
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 66
Query: 245 AMRALQNKPLRRRKLDIHFS 264
A+R++Q P + + I ++
Sbjct: 67 ALRSMQGFPFYDKPMRIQYA 86
>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 = 39.3 bits (90), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 191 PSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAART 244
P+ T+++ N+N ++ EL+ A+F ++G I + + K RG + + ++ +A
Sbjct: 5 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 64
Query: 245 AMRALQNKPLRRRKLDIHFS 264
A+R++Q P + + I ++
Sbjct: 65 ALRSMQGFPFYDKPMRIQYA 84
>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 = 39.3 bits (90), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 191 PSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAART 244
P+ T+++ N+N ++ EL+ A+F ++G I + + K RG + + ++ +A
Sbjct: 8 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 67
Query: 245 AMRALQNKPLRRRKLDIHFS 264
A+R++Q P + + I ++
Sbjct: 68 ALRSMQGFPFYDKPMRIQYA 87
>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 = 39.3 bits (90), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 191 PSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAART 244
P+ T+++ N+N ++ EL+ A+F ++G I + + K RG + + ++ +A
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 66
Query: 245 AMRALQNKPLRRRKLDIHFS 264
A+R++Q P + + I ++
Sbjct: 67 ALRSMQGFPFYDKPMRIQYA 86
>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 = 39.3 bits (90), Expect = 0.010, Method: Composition-based stats.
Identities = 27/81 (33%), Positives = 42/81 (51%), Gaps = 6/81 (7%)
Query: 277 QGTLVVFNLDPSVSNED-LRQIFGAYGEV---KEIRE--TPHKRHHKFIEFYDVRAAEAA 330
QGT ++ N P +D LR +F + GEV K IR+ H + F+ + + AE A
Sbjct: 18 QGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 77
Query: 331 LKSLNRSDIAGKRIKLEPSRP 351
+ +LN + K IK+ +RP
Sbjct: 78 INTLNGLRLQSKTIKVSYARP 98
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 38.9 bits (89), Expect = 0.010, Method: Composition-based stats.
Identities = 22/81 (27%), Positives = 41/81 (50%), Gaps = 2/81 (2%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 254
++V N+ + EL F YG +RT++ A GF + + D R A A+R L K +
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 62
Query: 255 --RRRKLDIHFSIPKDNPSDK 273
R ++++ +P+ + D+
Sbjct: 63 CGSRVRVELSTGMPRRSRFDR 83
Score = 35.8 bits (81), Expect = 0.085, Method: Composition-based stats.
Identities = 24/76 (31%), Positives = 38/76 (50%), Gaps = 1/76 (1%)
Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG 341
V NL +L + F YG ++ + + F+EF D R AE A++ L+ I G
Sbjct: 5 VGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICG 64
Query: 342 KRIKLEPSRPGGARRN 357
R+++E S G RR+
Sbjct: 65 SRVRVELS-TGMPRRS 79
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 38.9 bits (89), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 5/76 (6%)
Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
L VF L + DLR++F YG + ++ +++ R F+ F +V A+ A +
Sbjct: 48 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 107
Query: 334 LNRSDIAGKRIKLEPS 349
N ++ G+RI+++ S
Sbjct: 108 ANGMELDGRRIRVDFS 123
Score = 33.1 bits (74), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 5/82 (6%)
Query: 191 PSRTLFVRNINSNVEDSELRALFEQYG---DIRTLY--TACKHRGFVMISYYDIRAARTA 245
P+ L V ++ + +LR +F +YG D+ +Y + + RGF + + ++ A+ A
Sbjct: 45 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 104
Query: 246 MRALQNKPLRRRKLDIHFSIPK 267
L R++ + FSI K
Sbjct: 105 KERANGMELDGRRIRVDFSITK 126
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 38.9 bits (89), Expect = 0.012, Method: Composition-based stats.
Identities = 19/80 (23%), Positives = 42/80 (52%), Gaps = 6/80 (7%)
Query: 191 PSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAART 244
P+ T+++ N+N ++ EL+ A+F ++G I + + K RG + + ++ +A
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATN 66
Query: 245 AMRALQNKPLRRRKLDIHFS 264
A+R+ Q P + I ++
Sbjct: 67 ALRSXQGFPFYDKPXRIQYA 86
>pdb|3CUL|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUL|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3EGZ|A Chain A, Crystal Structure Of An In Vitro Evolved Tetracycline
Aptamer And Artificial Riboswitch
Length = 98
Score = 38.9 bits (89), Expect = 0.012, Method: Composition-based stats.
Identities = 19/80 (23%), Positives = 42/80 (52%), Gaps = 6/80 (7%)
Query: 191 PSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAART 244
P+ T+++ N+N ++ EL+ A+F ++G I + + K RG + + ++ +A
Sbjct: 8 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATN 67
Query: 245 AMRALQNKPLRRRKLDIHFS 264
A+R+ Q P + I ++
Sbjct: 68 ALRSXQGFPFYDKPXRIQYA 87
>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 = 38.9 bits (89), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 5/76 (6%)
Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRA 248
+L V N+ LR +FE+YG + +Y + RGF + ++D R A AM A
Sbjct: 49 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 108
Query: 249 LQNKPLRRRKLDIHFS 264
+ L R+L + +
Sbjct: 109 MDGAVLDGRELRVQMA 124
>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 = 38.9 bits (89), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 191 PSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAART 244
P+ T+++ N+N ++ EL+ A+F ++G I + + K RG + + ++ +A
Sbjct: 2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 61
Query: 245 AMRALQNKPLRRRKLDIHFS 264
A+R++Q P + + I ++
Sbjct: 62 ALRSMQGFPFYDKPMRIQYA 81
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 38.9 bits (89), Expect = 0.012, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 32/60 (53%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 254
++V N+ +N +EL F YG +R+++ A GF + + D R A A+R L + L
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTL 135
Score = 35.8 bits (81), Expect = 0.086, Method: Composition-based stats.
Identities = 20/68 (29%), Positives = 36/68 (52%)
Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG 341
V NL + + +L + FG YG ++ + + F+EF D R A A++ L+ + G
Sbjct: 78 VGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCG 137
Query: 342 KRIKLEPS 349
R+++E S
Sbjct: 138 CRVRVELS 145
>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 = 38.9 bits (89), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 191 PSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAART 244
P+ T+++ N+N ++ EL+ A+F ++G I + + K RG + + ++ +A
Sbjct: 4 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 63
Query: 245 AMRALQNKPLRRRKLDIHFS 264
A+R++Q P + + I ++
Sbjct: 64 ALRSMQGFPFYDKPMRIQYA 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 = 38.9 bits (89), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 191 PSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAART 244
P+ T+++ N+N ++ EL+ A+F ++G I + + K RG + + ++ +A
Sbjct: 3 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 62
Query: 245 AMRALQNKPLRRRKLDIHFS 264
A+R++Q P + + I ++
Sbjct: 63 ALRSMQGFPFYDKPMRIQYA 82
>pdb|1A9N|B Chain B, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
pdb|1A9N|D Chain D, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
Length = 96
Score = 38.9 bits (89), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 44/81 (54%), Gaps = 8/81 (9%)
Query: 191 PSRTLFVRNINSNVEDSELR----ALFEQYG---DIRTLYTACKHRGFVMISYYDIRAAR 243
P+ T+++ N+N ++ EL+ ALF Q+G DI L T K RG + + ++ ++
Sbjct: 5 PNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKT-MKMRGQAFVIFKELGSST 63
Query: 244 TAMRALQNKPLRRRKLDIHFS 264
A+R LQ P + + I ++
Sbjct: 64 NALRQLQGFPFYGKPMRIQYA 84
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 38.5 bits (88), Expect = 0.014, Method: Composition-based stats.
Identities = 19/80 (23%), Positives = 42/80 (52%), Gaps = 6/80 (7%)
Query: 191 PSRTLFVRNINSNVEDSELR----ALFEQYGDIRTLYT--ACKHRGFVMISYYDIRAART 244
P+ T+++ N+N ++ EL+ A+F ++G I + + K RG + + ++ +A
Sbjct: 5 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATN 64
Query: 245 AMRALQNKPLRRRKLDIHFS 264
A+R+ Q P + I ++
Sbjct: 65 ALRSXQGFPFYDKPXRIQYA 84
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 38.5 bits (88), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 5/73 (6%)
Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
L VF L + DLR++F YG + ++ +++ R F+ F +V A+ A +
Sbjct: 17 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76
Query: 334 LNRSDIAGKRIKL 346
N ++ G+RI++
Sbjct: 77 ANGMELDGRRIRV 89
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 38.5 bits (88), Expect = 0.016, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 32/60 (53%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 254
++V N+ +N +EL F YG +R+++ A GF + + D R A A+R L + L
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRDLDGRTL 135
Score = 35.8 bits (81), Expect = 0.089, Method: Composition-based stats.
Identities = 20/68 (29%), Positives = 36/68 (52%)
Query: 282 VFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAG 341
V NL + + +L + FG YG ++ + + F+EF D R A A++ L+ + G
Sbjct: 78 VGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRDLDGRTLCG 137
Query: 342 KRIKLEPS 349
R+++E S
Sbjct: 138 CRVRVELS 145
>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 = 38.5 bits (88), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 5/77 (6%)
Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEV---KEIRETP--HKRHHKFIEFYDVRAAEAALKSL 334
L+V L +++ ++LR +F + GEV K IR+ H + F+ + + AE A+ +L
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 335 NRSDIAGKRIKLEPSRP 351
N + K IK+ +RP
Sbjct: 67 NGLRLQSKTIKVSYARP 83
Score = 29.3 bits (64), Expect = 10.0, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 6/82 (7%)
Query: 191 PSRT-LFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAART 244
P RT L V + N+ ELR+LF G++ + A G+ ++Y + A
Sbjct: 2 PGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 61
Query: 245 AMRALQNKPLRRRKLDIHFSIP 266
A+ L L+ + + + ++ P
Sbjct: 62 AINTLNGLRLQSKTIKVSYARP 83
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 38.1 bits (87), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 35/79 (44%), Gaps = 5/79 (6%)
Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAMR 247
R L+V + V+D L A F +GDI + Y KHRGF + + A A+
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
Query: 248 ALQNKPLRRRKLDIHFSIP 266
+ L R + ++ + P
Sbjct: 73 NMNESELFGRTIRVNLAKP 91
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 38.1 bits (87), Expect = 0.017, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 37/77 (48%), Gaps = 7/77 (9%)
Query: 194 TLFVRNINSNVEDSELRALFEQYGDI------RTLYTACKHRGFVMISYYDIRAARTAMR 247
+L V N+ LR +FE+YG + R YT + RGF + ++D R A AM
Sbjct: 72 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTK-ESRGFAFVRFHDKRDAEDAMD 130
Query: 248 ALQNKPLRRRKLDIHFS 264
A+ L R+L + +
Sbjct: 131 AMDGAVLDGRELRVQMA 147
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 38.1 bits (87), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 5/76 (6%)
Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKS 333
L VF L + DLR++F YG + ++ +++ R F+ F +V A+ A +
Sbjct: 17 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76
Query: 334 LNRSDIAGKRIKLEPS 349
N ++ G+RI+++ S
Sbjct: 77 ANGMELDGRRIRVDFS 92
Score = 32.3 bits (72), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 5/82 (6%)
Query: 191 PSRTLFVRNINSNVEDSELRALFEQYG---DIRTLY--TACKHRGFVMISYYDIRAARTA 245
P+ L V ++ + +LR +F +YG D+ +Y + + RGF + + ++ A+ A
Sbjct: 14 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 73
Query: 246 MRALQNKPLRRRKLDIHFSIPK 267
L R++ + FSI K
Sbjct: 74 KERANGMELDGRRIRVDFSITK 95
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 37.7 bits (86), Expect = 0.024, Method: Composition-based stats.
Identities = 27/92 (29%), Positives = 45/92 (48%), Gaps = 13/92 (14%)
Query: 191 PSRTLFVRNIN----SNVEDSELRALFEQYG---DIRTLYTACKHRGFVMISYYDIRAAR 243
P++T+++ N+N L A+F Q+G DI L T K RG + + +I +A
Sbjct: 5 PNQTIYINNLNEKIKKEELKKSLYAIFSQFGQILDIVALKT-LKMRGQAFVIFKEIGSAS 63
Query: 244 TAMRALQNKPLRRRKLDIHFSIPKDNPSDKDL 275
A+R +Q P + + I +S SD D+
Sbjct: 64 NALRTMQGFPFYDKPMQIAYS-----KSDSDI 90
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 37.7 bits (86), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 36/68 (52%), Gaps = 1/68 (1%)
Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
T+ + ++++ +RQ F +G++ EIR P K + F+ F +A A+ S+N +
Sbjct: 27 TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK-GYSFVRFSTHESAAHAIVSVNGTT 85
Query: 339 IAGKRIKL 346
I G +K
Sbjct: 86 IEGHVVKC 93
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 37.7 bits (86), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 7/79 (8%)
Query: 177 GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK------HRG 230
G+ +G+ P + S+ L VRNI E+R LF +G+++T+ K HRG
Sbjct: 1 GSSGSSGQVPKKQTTSKIL-VRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRG 59
Query: 231 FVMISYYDIRAARTAMRAL 249
F + + + A+ A AL
Sbjct: 60 FGFVDFITKQDAKKAFNAL 78
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 37.7 bits (86), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 37/71 (52%), Gaps = 5/71 (7%)
Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSL 334
+ V +L P ++ ED++ F +G++ + R T + + F+ FY+ AE A+ +
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 335 NRSDIAGKRIK 345
+ G++I+
Sbjct: 78 GGQWLGGRQIR 88
>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 = 37.4 bits (85), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 16/71 (22%), Positives = 37/71 (52%), Gaps = 5/71 (7%)
Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSL 334
+ V +L P ++ ED++ F +G + + R T + + F+ F++ AE A++ +
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 335 NRSDIAGKRIK 345
+ G++I+
Sbjct: 78 GGQWLGGRQIR 88
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 37.4 bits (85), Expect = 0.035, Method: Composition-based stats.
Identities = 22/79 (27%), Positives = 41/79 (51%), Gaps = 5/79 (6%)
Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSL 334
L+V L +++ +L +F A G + R +T + + F++F ++ A+K L
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 335 NRSDIAGKRIKLEPSRPGG 353
N + KR+K+ +RPGG
Sbjct: 66 NGITVRNKRLKVSYARPGG 84
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 37.4 bits (85), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 39/72 (54%), Gaps = 6/72 (8%)
Query: 195 LFVRNINSN-VEDSELRALFEQYGDIRTLYTACK-HRGFVMISYYDIRAARTAMRALQNK 252
+F+ N+N+ V+ S++ +F +YG + C H+G+ + Y + R AR A+ +
Sbjct: 30 VFIGNLNTALVKKSDVETIFSKYGRV----AGCSVHKGYAFVQYSNERHARAAVLGENGR 85
Query: 253 PLRRRKLDIHFS 264
L + LDI+ +
Sbjct: 86 VLAGQTLDINMA 97
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 37.4 bits (85), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 7/70 (10%)
Query: 189 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK------HRGFVMISYYDIRAA 242
+H + LF+ I N+++ +L+ LFE++G I L T K H+G ++Y + +A
Sbjct: 10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYEL-TVLKDRFTGMHKGCAFLTYCERESA 68
Query: 243 RTAMRALQNK 252
A AL +
Sbjct: 69 LKAQSALHEQ 78
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 37.0 bits (84), Expect = 0.041, Method: Composition-based stats.
Identities = 21/75 (28%), Positives = 40/75 (53%), Gaps = 5/75 (6%)
Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAAEAALKSL 334
L VF L + DLR++F YG + ++ +++ R F+ F +V A+ A +
Sbjct: 15 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 74
Query: 335 NRSDIAGKRIKLEPS 349
N ++ G+RI+++ S
Sbjct: 75 NGMELDGRRIRVDFS 89
Score = 31.2 bits (69), Expect = 2.0, Method: Composition-based stats.
Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 5/82 (6%)
Query: 191 PSRTLFVRNINSNVEDSELRALFEQYG---DIRTLY--TACKHRGFVMISYYDIRAARTA 245
P+ L V ++ + +LR +F +YG D+ +Y + + RGF + + ++ A+ A
Sbjct: 11 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 70
Query: 246 MRALQNKPLRRRKLDIHFSIPK 267
L R++ + FSI K
Sbjct: 71 KERANGMELDGRRIRVDFSITK 92
>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 = 37.0 bits (84), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 5/75 (6%)
Query: 195 LFVRNINSNVEDSELRALFEQY-----GDIRTLYTACKHRGFVMISYYDIRAARTAMRAL 249
LFV ++N NV+D LR F+ + G + RG+ +S+ A+ AM ++
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 250 QNKPLRRRKLDIHFS 264
Q + L R L I+++
Sbjct: 64 QGQDLNGRPLRINWA 78
>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 = 36.6 bits (83), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 41/76 (53%), Gaps = 5/76 (6%)
Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSL 334
L +++L ++DL Q+F +G V + +T + F+ + + +A+AA++S+
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 335 NRSDIAGKRIKLEPSR 350
N I KR+K++ R
Sbjct: 88 NGFQIGMKRLKVQLKR 103
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 36.6 bits (83), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 35/76 (46%), Gaps = 5/76 (6%)
Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRA 248
TL V N+ LR +FE+YG + +Y RGF + ++D R A+ A A
Sbjct: 15 TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74
Query: 249 LQNKPLRRRKLDIHFS 264
+ L R+L + +
Sbjct: 75 MDGAELDGRELRVQVA 90
>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 = 36.6 bits (83), Expect = 0.060, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 5/72 (6%)
Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMR 247
+TLFV +N + +S+LR FE YG I+ ++ + K RG+ I Y R +A +
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 248 ALQNKPLRRRKL 259
K + R++
Sbjct: 163 HADGKKIDGRRV 174
Score = 34.3 bits (77), Expect = 0.27, Method: Composition-based stats.
Identities = 25/90 (27%), Positives = 41/90 (45%), Gaps = 5/90 (5%)
Query: 266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIE 320
P ++P+ + TL V ++ + LR+ F YG +K I KR K FIE
Sbjct: 91 PHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIE 150
Query: 321 FYDVRAAEAALKSLNRSDIAGKRIKLEPSR 350
+ R +A K + I G+R+ ++ R
Sbjct: 151 YEHERDMHSAYKHADGKKIDGRRVLVDVER 180
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 36.2 bits (82), Expect = 0.066, Method: Composition-based stats.
Identities = 18/65 (27%), Positives = 37/65 (56%), Gaps = 2/65 (3%)
Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR--ETPHKRHHKFIEFYDVRAAEAALKSLNRS 337
L + NL ++ E++ IFG YG +++IR TP R ++ + D+ A+ A+ L+
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGF 70
Query: 338 DIAGK 342
+++ +
Sbjct: 71 NVSNR 75
Score = 32.3 bits (72), Expect = 1.1, Method: Composition-based stats.
Identities = 20/70 (28%), Positives = 34/70 (48%), Gaps = 2/70 (2%)
Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC--KHRGFVMISYYDIRAARTAMRAL 249
+R L++RN+ + E+ +F +YG IR + + RG + Y DI A+ A+ L
Sbjct: 8 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHL 67
Query: 250 QNKPLRRRKL 259
+ R L
Sbjct: 68 SGFNVSNRYL 77
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 36.2 bits (82), Expect = 0.070, Method: Composition-based stats.
Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 3/70 (4%)
Query: 269 NPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEV---KEIRETPHKRHHKFIEFYDVR 325
+PS + G + + NLD S+ N+ L F A+G + K + + + + F+ F
Sbjct: 3 DPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQE 62
Query: 326 AAEAALKSLN 335
AAE A++ +N
Sbjct: 63 AAERAIEKMN 72
Score = 29.6 bits (65), Expect = 6.2, Method: Composition-based stats.
Identities = 14/68 (20%), Positives = 33/68 (48%), Gaps = 3/68 (4%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKH---RGFVMISYYDIRAARTAMRALQN 251
+F++N++ ++++ L F +G+I + C +G+ + + AA A+ +
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 73
Query: 252 KPLRRRKL 259
L RK+
Sbjct: 74 MLLNDRKV 81
>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 = 36.2 bits (82), Expect = 0.071, Method: Composition-based stats.
Identities = 18/65 (27%), Positives = 36/65 (55%), Gaps = 2/65 (3%)
Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR--ETPHKRHHKFIEFYDVRAAEAALKSLNRS 337
L++ NL ++ E++ IFG YG +++IR TP R ++ + D+ A+ A L+
Sbjct: 21 LMIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGF 80
Query: 338 DIAGK 342
++ +
Sbjct: 81 NVCNR 85
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 36.2 bits (82), Expect = 0.081, Method: Composition-based stats.
Identities = 22/82 (26%), Positives = 35/82 (42%), Gaps = 5/82 (6%)
Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAA 242
G R L+V + V+D L A F +GDI + Y KHRGF + + A
Sbjct: 1 GSTTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60
Query: 243 RTAMRALQNKPLRRRKLDIHFS 264
A+ + L R + ++ +
Sbjct: 61 AAAIDNMNESELFGRTIRVNLA 82
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 35.8 bits (81), Expect = 0.10, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 5/75 (6%)
Query: 195 LFVRNINSNVEDSELRALFEQY-----GDIRTLYTACKHRGFVMISYYDIRAARTAMRAL 249
LFV ++N NV+D LR F+ + G + RG+ +S+ A+ AM ++
Sbjct: 90 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 149
Query: 250 QNKPLRRRKLDIHFS 264
Q + L R L I+++
Sbjct: 150 QGQDLNGRPLRINWA 164
Score = 33.1 bits (74), Expect = 0.64, Method: Composition-based stats.
Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRH----HKFIEFYDVRAAEAALKSLN 335
L V NLD +++ + L+Q F G + I+ K + + F+E++ A AL++LN
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 336 RSDIAGKRIKL 346
I +K+
Sbjct: 63 GKQIENNIVKI 73
>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 = 35.4 bits (80), Expect = 0.13, Method: Composition-based stats.
Identities = 18/65 (27%), Positives = 35/65 (53%), Gaps = 2/65 (3%)
Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR--ETPHKRHHKFIEFYDVRAAEAALKSLNRS 337
L + NL ++ E++ IFG YG +++IR TP R ++ + D+ A+ A L+
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGF 80
Query: 338 DIAGK 342
++ +
Sbjct: 81 NVCNR 85
Score = 31.6 bits (70), Expect = 1.7, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC--KHRGFVMISYYDIRAARTA 245
+R L++RN+ + E+ +F +YG IR + + RG + Y DI A+ A
Sbjct: 18 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNA 73
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 35.4 bits (80), Expect = 0.13, Method: Composition-based stats.
Identities = 18/65 (27%), Positives = 35/65 (53%), Gaps = 2/65 (3%)
Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR--ETPHKRHHKFIEFYDVRAAEAALKSLNRS 337
L + NL ++ E++ IFG YG +++IR TP R ++ + D+ A+ A L+
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGF 74
Query: 338 DIAGK 342
++ +
Sbjct: 75 NVCNR 79
Score = 31.6 bits (70), Expect = 1.7, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTAC--KHRGFVMISYYDIRAARTA 245
+R L++RN+ + E+ +F +YG IR + + RG + Y DI A+ A
Sbjct: 12 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNA 67
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 35.4 bits (80), Expect = 0.13, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 34/73 (46%), Gaps = 10/73 (13%)
Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLY-------TACKHRGFVMISYYDIRAART 244
S TL+V N++ + ++ LF + GDI+ + TAC GF + YY A
Sbjct: 18 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTAC---GFCFVEYYSRADAEN 74
Query: 245 AMRALQNKPLRRR 257
AMR + L R
Sbjct: 75 AMRYINGTRLDDR 87
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 35.4 bits (80), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 7/73 (9%)
Query: 186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACK------HRGFVMISYYDI 239
P +H + LFV I +++ +L+ LFE++G I L T K H+G ++Y
Sbjct: 9 PMKDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYEL-TVLKDRLTGLHKGCAFLTYCAR 67
Query: 240 RAARTAMRALQNK 252
+A A AL +
Sbjct: 68 DSALKAQSALHEQ 80
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 35.4 bits (80), Expect = 0.14, Method: Composition-based stats.
Identities = 25/101 (24%), Positives = 48/101 (47%), Gaps = 13/101 (12%)
Query: 269 NPSDKDLNQG--------TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRH 315
N D +L G L V ++ +++++ F YGE+K I R T +
Sbjct: 10 NEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKG 69
Query: 316 HKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARR 356
+ +E+ + A AA ++LN ++I G+ I+++ G +R
Sbjct: 70 YALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKR 110
Score = 30.8 bits (68), Expect = 3.4, Method: Composition-based stats.
Identities = 17/78 (21%), Positives = 36/78 (46%), Gaps = 5/78 (6%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHR-----GFVMISYYDIRAARTAMRAL 249
LFV +I+ ++ E++ F YG+I+ ++ R G+ ++ Y + A A AL
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 250 QNKPLRRRKLDIHFSIPK 267
+ + + + + K
Sbjct: 89 NGAEIMGQTIQVDWCFVK 106
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 35.0 bits (79), Expect = 0.14, Method: Composition-based stats.
Identities = 17/73 (23%), Positives = 36/73 (49%)
Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN 251
+RTL +N++ N+ + EL+ +FE +IR + K +G I + A + Q
Sbjct: 16 ARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQG 75
Query: 252 KPLRRRKLDIHFS 264
+ R + ++++
Sbjct: 76 AEIDGRSVSLYYT 88
Score = 31.6 bits (70), Expect = 2.0, Method: Composition-based stats.
Identities = 18/78 (23%), Positives = 39/78 (50%)
Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSD 338
TL+ NL +++ ++L+++F E++ + + + +IEF AE L+ ++
Sbjct: 18 TLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAE 77
Query: 339 IAGKRIKLEPSRPGGARR 356
I G+ + L + G R
Sbjct: 78 IDGRSVSLYYTGEKGGTR 95
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 35.0 bits (79), Expect = 0.16, Method: Composition-based stats.
Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 3/76 (3%)
Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNK 252
+ LFVRN+ + V + L F Q+G + + K + + I + + A AM + K
Sbjct: 12 KVLFVRNLANTVTEEILEKAFSQFGKLERVK---KLKDYAFIHFDERDGAVKAMEEMNGK 68
Query: 253 PLRRRKLDIHFSIPKD 268
L ++I F+ P D
Sbjct: 69 DLEGENIEIVFAKPPD 84
>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 = 35.0 bits (79), Expect = 0.16, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 3/64 (4%)
Query: 275 LNQGTLVVFNLDPSVSNEDLRQIFGAYGEV---KEIRETPHKRHHKFIEFYDVRAAEAAL 331
L G + + NLD S+ N+ L F A+G + K + + + + F+ F AAE A+
Sbjct: 3 LGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAI 62
Query: 332 KSLN 335
+ +N
Sbjct: 63 EKMN 66
Score = 30.0 bits (66), Expect = 5.1, Method: Composition-based stats.
Identities = 15/71 (21%), Positives = 34/71 (47%), Gaps = 3/71 (4%)
Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH---RGFVMISYYDIRAARTAMRA 248
S +F++N++ ++++ L F +G+I + C +G+ + + AA A+
Sbjct: 5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEK 64
Query: 249 LQNKPLRRRKL 259
+ L RK+
Sbjct: 65 MNGMLLNDRKV 75
>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 = 35.0 bits (79), Expect = 0.16, Method: Composition-based stats.
Identities = 21/77 (27%), Positives = 34/77 (44%), Gaps = 5/77 (6%)
Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAMR 247
R L+V + V+D L A F +GDI + Y KHRGF + + A A+
Sbjct: 3 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 62
Query: 248 ALQNKPLRRRKLDIHFS 264
+ L R + ++ +
Sbjct: 63 NMNESELFGRTIRVNLA 79
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 35.0 bits (79), Expect = 0.16, Method: Composition-based stats.
Identities = 21/77 (27%), Positives = 34/77 (44%), Gaps = 5/77 (6%)
Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAMR 247
R L+V + V+D L A F +GDI + Y KHRGF + + A A+
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
Query: 248 ALQNKPLRRRKLDIHFS 264
+ L R + ++ +
Sbjct: 124 NMNESELFGRTIRVNLA 140
>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 = 35.0 bits (79), Expect = 0.16, Method: Composition-based stats.
Identities = 21/77 (27%), Positives = 34/77 (44%), Gaps = 5/77 (6%)
Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAMR 247
R L+V + V+D L A F +GDI + Y KHRGF + + A A+
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
Query: 248 ALQNKPLRRRKLDIHFS 264
+ L R + ++ +
Sbjct: 68 NMNESELFGRTIRVNLA 84
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 35.0 bits (79), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 37/79 (46%), Gaps = 5/79 (6%)
Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAA 242
G S L+V +++ N+ + LR +FE +G I + + +G+ I++ D A
Sbjct: 1 GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60
Query: 243 RTAMRALQNKPLRRRKLDI 261
R A+ L L R + +
Sbjct: 61 RRALEQLNGFELAGRPMRV 79
>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1HL6|C Chain C, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1RK8|A Chain A, Structure Of The Cytosolic Protein Pym Bound To The Mago-
Y14 Core Of The Exon Junction Complex
pdb|2X1G|A Chain A, Crystal Structure Of Importin13 - Mago-Y14 Complex
pdb|2X1G|C Chain C, Crystal Structure Of Importin13 - Mago-Y14 Complex
Length = 165
Score = 35.0 bits (79), Expect = 0.18, Method: Composition-based stats.
Identities = 25/101 (24%), Positives = 48/101 (47%), Gaps = 13/101 (12%)
Query: 269 NPSDKDLNQG--------TLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRH 315
N D +L G L V ++ +++++ F YGE+K I R T +
Sbjct: 56 NEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKG 115
Query: 316 HKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRPGGARR 356
+ +E+ + A AA ++LN ++I G+ I+++ G +R
Sbjct: 116 YALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKR 156
Score = 30.4 bits (67), Expect = 4.1, Method: Composition-based stats.
Identities = 17/78 (21%), Positives = 36/78 (46%), Gaps = 5/78 (6%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHR-----GFVMISYYDIRAARTAMRAL 249
LFV +I+ ++ E++ F YG+I+ ++ R G+ ++ Y + A A AL
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 250 QNKPLRRRKLDIHFSIPK 267
+ + + + + K
Sbjct: 135 NGAEIMGQTIQVDWCFVK 152
>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 = 34.7 bits (78), Expect = 0.18, Method: Composition-based stats.
Identities = 23/74 (31%), Positives = 34/74 (45%), Gaps = 11/74 (14%)
Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLY--------TACKHRGFVMISYYDIRAAR 243
S TL+V N++ + ++ LF + GDI+ + TAC GF + YY A
Sbjct: 39 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTAC---GFCFVEYYSRADAE 95
Query: 244 TAMRALQNKPLRRR 257
AMR + L R
Sbjct: 96 NAMRYINGTRLDDR 109
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 34.7 bits (78), Expect = 0.19, Method: Composition-based stats.
Identities = 22/92 (23%), Positives = 41/92 (44%), Gaps = 8/92 (8%)
Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHR--------GFVMISYYDI 239
G S LF++N+N + + L+ +F + G I++ + K GF + Y
Sbjct: 1 GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60
Query: 240 RAARTAMRALQNKPLRRRKLDIHFSIPKDNPS 271
A+ A++ LQ + KL++ S P+
Sbjct: 61 EQAQKALKQLQGHTVDGHKLEVRISERATKPA 92
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 34.7 bits (78), Expect = 0.22, Method: Composition-based stats.
Identities = 21/66 (31%), Positives = 36/66 (54%), Gaps = 6/66 (9%)
Query: 285 LDPSVSNEDLRQIFGAYGEVKEI-----RETPH-KRHHKFIEFYDVRAAEAALKSLNRSD 338
L +V+ + + +IF YG++K I R PH + + ++EF + AE ALK ++
Sbjct: 12 LTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQ 71
Query: 339 IAGKRI 344
I G+ I
Sbjct: 72 IDGQEI 77
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 34.3 bits (77), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 38/79 (48%), Gaps = 5/79 (6%)
Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLY----TACKHRGFVMISYYDIRAAR 243
+HP + LF+ +N + L+A+F ++G I + K RGF I++ + A+
Sbjct: 4 ADHPGK-LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAK 62
Query: 244 TAMRALQNKPLRRRKLDIH 262
A + + K L + + +
Sbjct: 63 NAAKDMNGKSLHGKAIKVE 81
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 34.3 bits (77), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 3/70 (4%)
Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 339
L V N+ P+ +N++LR F YG V E + + F+ A A++ L+ ++
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIV---KDYAFVHMERAEDAVEAIRGLDNTEF 69
Query: 340 AGKRIKLEPS 349
GKR+ ++ S
Sbjct: 70 QGKRMHVQLS 79
Score = 30.8 bits (68), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 33/76 (43%), Gaps = 3/76 (3%)
Query: 192 SRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN 251
S L V NI+ + ELRA FE+YG + + + + A A+R L N
Sbjct: 10 STKLHVGNISPTCTNQELRAKFEEYGPVIECDIV---KDYAFVHMERAEDAVEAIRGLDN 66
Query: 252 KPLRRRKLDIHFSIPK 267
+ +++ + S +
Sbjct: 67 TEFQGKRMHVQLSTSR 82
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 34.3 bits (77), Expect = 0.26, Method: Composition-based stats.
Identities = 27/103 (26%), Positives = 46/103 (44%), Gaps = 6/103 (5%)
Query: 186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDI---RTLY--TACKHRGFVMISYYDIR 240
P + R++FV NI + +L+ +F + G + R +Y K +G+ Y D
Sbjct: 2 PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61
Query: 241 AARTAMRALQNKPLRRRKLDIHFSIPKDNPSD-KDLNQGTLVV 282
A +AMR L + R L + + + N + K L G V+
Sbjct: 62 TALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGTGAPVI 104
Score = 33.1 bits (74), Expect = 0.54, Method: Composition-based stats.
Identities = 19/74 (25%), Positives = 38/74 (51%), Gaps = 5/74 (6%)
Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKS 333
++ V N+ + E L+ IF G V R ET + + F E+ D A +A+++
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 334 LNRSDIAGKRIKLE 347
LN + +G+ ++++
Sbjct: 70 LNGREFSGRALRVD 83
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 34.3 bits (77), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 38/71 (53%), Gaps = 3/71 (4%)
Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-TPHKRH--HKFIEFYDVRAAEAALKSLN 335
TL V NL V+ + Q+F G K + T H + + F+EFY+ R A AAL ++N
Sbjct: 17 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMN 76
Query: 336 RSDIAGKRIKL 346
I GK +K+
Sbjct: 77 GRKILGKEVKV 87
Score = 30.0 bits (66), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 16/75 (21%), Positives = 40/75 (53%), Gaps = 3/75 (4%)
Query: 193 RTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRG---FVMISYYDIRAARTAMRAL 249
RTL+V N++ +V + + LF Q G ++ +H + + +Y+ R A A+ A+
Sbjct: 16 RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAM 75
Query: 250 QNKPLRRRKLDIHFS 264
+ + +++ ++++
Sbjct: 76 NGRKILGKEVKVNWA 90
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 34.3 bits (77), Expect = 0.27, Method: Composition-based stats.
Identities = 21/84 (25%), Positives = 45/84 (53%), Gaps = 5/84 (5%)
Query: 276 NQGTLVVFNLDPSVSNEDLRQIFGAYGEV---KEIRE--TPHKRHHKFIEFYDVRAAEAA 330
++ L+V L +++ ++ + +FG+ G++ K +R+ T + F+ + D A+ A
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 331 LKSLNRSDIAGKRIKLEPSRPGGA 354
+ +LN + K IK+ +RP A
Sbjct: 63 INTLNGLKLQTKTIKVSYARPSSA 86
>pdb|2DGX|A Chain A, Solution Structure Of The Rna Recognition Motif In
Kiaa0430 Protein
Length = 96
Score = 34.3 bits (77), Expect = 0.28, Method: Composition-based stats.
Identities = 20/69 (28%), Positives = 39/69 (56%), Gaps = 6/69 (8%)
Query: 282 VFNLDPSVSNEDLRQI----FGAYGEVKEIRETPHKRHH--KFIEFYDVRAAEAALKSLN 335
V N+D +S ++L+Q+ F +G+VK + +PH + ++ +++ A A+ SL+
Sbjct: 14 VSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLH 73
Query: 336 RSDIAGKRI 344
R I K+I
Sbjct: 74 RYKIGSKKI 82
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 34.3 bits (77), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 35/62 (56%), Gaps = 6/62 (9%)
Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEV----KEIR--ETPHKRHHKFIEFYDVRAAEAALKS 333
+ + NLDP + + L F A+G + K +R +T + + + FI F A++AA+++
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 334 LN 335
+N
Sbjct: 68 MN 69
>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 = 33.9 bits (76), Expect = 0.36, Method: Composition-based stats.
Identities = 21/90 (23%), Positives = 47/90 (52%), Gaps = 6/90 (6%)
Query: 266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIE 320
P K++++ ++ V N+D + +DL F + G + I + + H + + +IE
Sbjct: 25 PLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIE 84
Query: 321 FYDVRAAEAALKSLNRSDIAGKRIKLEPSR 350
F + + +AA+ +++ + G+ IK+ P R
Sbjct: 85 FAERNSVDAAV-AMDETVFRGRTIKVLPKR 113
>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Rna, Uuguucuu
Length = 102
Score = 33.5 bits (75), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 6/75 (8%)
Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSL 334
T+ V +D + ++R F YG VKE++ T + + F+ FY+ + ++S
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVES- 69
Query: 335 NRSDIAGKRIKLEPS 349
+ + GK++KL P+
Sbjct: 70 -QINFHGKKLKLGPA 83
Score = 32.0 bits (71), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 32/57 (56%), Gaps = 4/57 (7%)
Query: 186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH----RGFVMISYYD 238
P G+ T+FV I+ ++++E+R+ F +YG ++ + +G+ +S+Y+
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYN 59
>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 = 33.5 bits (75), Expect = 0.45, Method: Composition-based stats.
Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 6/75 (8%)
Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSL 334
T+ V +D + ++R F YG VKE++ T + + F+ FY+ + ++S
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVES- 69
Query: 335 NRSDIAGKRIKLEPS 349
+ + GK++KL P+
Sbjct: 70 -QINFHGKKLKLGPA 83
Score = 32.0 bits (71), Expect = 1.5, Method: Composition-based stats.
Identities = 14/57 (24%), Positives = 32/57 (56%), Gaps = 4/57 (7%)
Query: 186 PYGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH----RGFVMISYYD 238
P G+ T+FV I+ ++++E+R+ F +YG ++ + +G+ +S+Y+
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYN 59
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 33.1 bits (74), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 3/77 (3%)
Query: 188 GEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR 247
GE + LFVR +V++SEL +F +G ++ + GF + + + +A A+
Sbjct: 27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL---NGFAFVEFEEAESAAKAIE 83
Query: 248 ALQNKPLRRRKLDIHFS 264
+ K + L++ +S
Sbjct: 84 EVHGKSFANQPLEVVYS 100
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 33.1 bits (74), Expect = 0.60, Method: Composition-based stats.
Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 6/75 (8%)
Query: 279 TLVVFNLDPSVSNEDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFYDVRAAEAALKSL 334
T+ V +D + ++R F YG VKE++ T + + F+ FY+ + ++S
Sbjct: 12 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVES- 70
Query: 335 NRSDIAGKRIKLEPS 349
+ + GK++KL P+
Sbjct: 71 -QINFHGKKLKLGPA 84
Score = 29.6 bits (65), Expect = 6.9, Method: Composition-based stats.
Identities = 12/49 (24%), Positives = 29/49 (59%), Gaps = 4/49 (8%)
Query: 194 TLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH----RGFVMISYYD 238
T+FV I+ ++++E+R+ F +YG ++ + +G+ +S+Y+
Sbjct: 12 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYN 60
>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 = 33.1 bits (74), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 7/64 (10%)
Query: 195 LFVRNINSNVEDSELRALFEQYG---DIRTLYTACKH----RGFVMISYYDIRAARTAMR 247
+FV + + +LR LFEQYG +I L ++ +G +++Y +AA A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 248 ALQN 251
AL N
Sbjct: 66 ALHN 69
Score = 30.8 bits (68), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 7/59 (11%)
Query: 288 SVSNEDLRQIFGAYGEVKEI-------RETPHKRHHKFIEFYDVRAAEAALKSLNRSDI 339
+ S +DLR++F YG V EI + P + F+ FY +AA A +L+ +
Sbjct: 14 TWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKV 72
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 32.7 bits (73), Expect = 0.73, Method: Composition-based stats.
Identities = 26/85 (30%), Positives = 42/85 (49%), Gaps = 6/85 (7%)
Query: 187 YGE-HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTA 245
YG+ +P+ L+V + N + L F+++G IRT+ K F I Y + AA+ A
Sbjct: 11 YGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTI-DHVKGDSFAYIQYESLDAAQAA 69
Query: 246 MRALQNKPL----RRRKLDIHFSIP 266
++ PL RR ++D S P
Sbjct: 70 CAKMRGFPLGGPDRRLRVDFAKSGP 94
>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 = 32.3 bits (72), Expect = 0.97, Method: Composition-based stats.
Identities = 32/167 (19%), Positives = 70/167 (41%), Gaps = 17/167 (10%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLY-----TACKHRGFVMISYYDIRAARTAMRAL 249
+F+ +N + + LR F +YG + L + RGF +S+ + ++
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT- 64
Query: 250 QNKPLRRRKLDIHFSIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-- 307
L + +D +IP+D DK G + V + P V ++ + F +G + +
Sbjct: 65 -QHILDGKVIDPKRAIPRDE-QDK---TGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQL 119
Query: 308 ---RETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEPSRP 351
++T R F+ + A + ++ D ++I+++ + P
Sbjct: 120 MLDKDTGQSRGFGFVTYDSADAVDRVCQN-KFIDFKDRKIEIKRAEP 165
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 32.3 bits (72), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 36/72 (50%), Gaps = 5/72 (6%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTAMRAL 249
L+V +++ N+ + LR +FE +G I ++ + +G+ I++ D A+ A+ L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 250 QNKPLRRRKLDI 261
L R + +
Sbjct: 89 NGFELAGRPMKV 100
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 32.0 bits (71), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 5/85 (5%)
Query: 183 GEHPYGEHPS--RTLFVRNINSNVEDSELRALFEQYG---DIRTLYTACKHRGFVMISYY 237
G H E+ S + L V NI D +LR +F Q+G D+ ++ +GF +++
Sbjct: 18 GSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFE 77
Query: 238 DIRAARTAMRALQNKPLRRRKLDIH 262
+ A A L + RK++++
Sbjct: 78 NSADADRAREKLHGTVVEGRKIEVN 102
Score = 31.6 bits (70), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 40/70 (57%), Gaps = 3/70 (4%)
Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK---FIEFYDVRAAEAALKSLNR 336
L V N+ + DLRQ+FG +G++ ++ ++R K F+ F + A+ A + L+
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHG 91
Query: 337 SDIAGKRIKL 346
+ + G++I++
Sbjct: 92 TVVEGRKIEV 101
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 32.0 bits (71), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 43/71 (60%), Gaps = 2/71 (2%)
Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLN-RSD 338
L + NL P+V+ +DLRQ+FG ++ + K + F+++ D A A+++L+ + +
Sbjct: 11 LYIGNLSPAVTADDLRQLFGDR-KLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVE 69
Query: 339 IAGKRIKLEPS 349
+ GK ++++ S
Sbjct: 70 LHGKIMEVDYS 80
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 40/70 (57%), Gaps = 3/70 (4%)
Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK---FIEFYDVRAAEAALKSLNR 336
L V N+ + DLRQ+FG +G++ ++ ++R K F+ F + A+ A + L+
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHG 77
Query: 337 SDIAGKRIKL 346
+ + G++I++
Sbjct: 78 TVVEGRKIEV 87
Score = 31.6 bits (70), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 35/73 (47%), Gaps = 3/73 (4%)
Query: 193 RTLFVRNINSNVEDSELRALFEQYG---DIRTLYTACKHRGFVMISYYDIRAARTAMRAL 249
+ L V NI D +LR +F Q+G D+ ++ +GF +++ + A A L
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKL 75
Query: 250 QNKPLRRRKLDIH 262
+ RK++++
Sbjct: 76 HGTVVEGRKIEVN 88
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 31.2 bits (69), Expect = 2.3, Method: Composition-based stats.
Identities = 22/82 (26%), Positives = 45/82 (54%), Gaps = 6/82 (7%)
Query: 195 LFVRNINSNVEDSELRALFEQYG---DIRTLYTACKH--RGFVMISYYDIRAARTAMRAL 249
+FV I N ++ELR F+++G ++ +Y A K RGF I++ D ++ A+ +
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-M 71
Query: 250 QNKPLRRRKLDIHFSIPKDNPS 271
+ +K+++ + P+D+ S
Sbjct: 72 HFHDIMGKKVEVKRAEPRDSKS 93
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 30.8 bits (68), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 22/92 (23%), Positives = 41/92 (44%), Gaps = 13/92 (14%)
Query: 272 DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIE----------- 320
D+D + + V L+ SV+ +DL F G VK + T H +++
Sbjct: 10 DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDAT 69
Query: 321 --FYDVRAAEAALKSLNRSDIAGKRIKLEPSR 350
+ D A+AA++ + D G ++K+ +R
Sbjct: 70 VSYEDPPTAKAAVEWFDGKDFQGSKLKVSLAR 101
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 30.8 bits (68), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 3/62 (4%)
Query: 288 SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE 347
+VS EDL +IF YG + +I K FI+F + ++ A++ ++ GK++ LE
Sbjct: 22 NVSKEDLFRIFSPYGHIMQINI---KNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILE 78
Query: 348 PS 349
S
Sbjct: 79 VS 80
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 30.8 bits (68), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 32/68 (47%), Gaps = 8/68 (11%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDI---RTLYTACKHRGFVMISYYDIRAARTAM----- 246
L+V+N++ ++D LR F +G I + + + +GF + + A A+
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNG 77
Query: 247 RALQNKPL 254
R + KPL
Sbjct: 78 RIVATKPL 85
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 30.8 bits (68), Expect = 3.1, Method: Composition-based stats.
Identities = 20/84 (23%), Positives = 40/84 (47%), Gaps = 2/84 (2%)
Query: 270 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI--RETPHKRHHKFIEFYDVRAA 327
P+ + TL V L + E L++ F + + RET + F++F A
Sbjct: 8 PNARSQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDA 67
Query: 328 EAALKSLNRSDIAGKRIKLEPSRP 351
+AA +++ +I G ++ L+ ++P
Sbjct: 68 KAAKEAMEDGEIDGNKVTLDWAKP 91
Score = 29.6 bits (65), Expect = 6.7, Method: Composition-based stats.
Identities = 18/82 (21%), Positives = 40/82 (48%), Gaps = 6/82 (7%)
Query: 190 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKH----RGFVMISYYDIRAARTA 245
PS+TLFV+ ++ + + L+ F+ G +R + +GF + + A+ A
Sbjct: 13 QPSKTLFVKGLSEDTTEETLKESFD--GSVRARIVTDRETGSSKGFGFVDFNSEEDAKAA 70
Query: 246 MRALQNKPLRRRKLDIHFSIPK 267
A+++ + K+ + ++ PK
Sbjct: 71 KEAMEDGEIDGNKVTLDWAKPK 92
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 30.4 bits (67), Expect = 3.7, Method: Composition-based stats.
Identities = 17/70 (24%), Positives = 35/70 (50%), Gaps = 3/70 (4%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 254
LFVR +V++SEL +F +G ++ + GF + + + +A A+ + K
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFGPMKEVKIL---NGFAFVEFEEAESAAKAIEEVHGKSF 63
Query: 255 RRRKLDIHFS 264
+ L++ +S
Sbjct: 64 ANQPLEVVYS 73
>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second
Rna-Binding Domain Of Sex-Lethal Determined By
Multidimensional Heteronuclear Magnetic Resonance
Spectroscopy
Length = 97
Score = 30.4 bits (67), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 5/71 (7%)
Query: 270 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKE---IRE--TPHKRHHKFIEFYDV 324
P + + L V NL +++++ L IFG YG + + +R+ T R F+ +
Sbjct: 6 PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKR 65
Query: 325 RAAEAALKSLN 335
A+ A+ +LN
Sbjct: 66 EEAQEAISALN 76
Score = 29.3 bits (64), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 33/74 (44%), Gaps = 8/74 (10%)
Query: 185 HPYGEHPSRT-LFVRNINSNVEDSELRALFEQYGDI------RTLYTACKHRGFVMISYY 237
P GE T L+V N+ + D +L +F +YG I R T + RG + Y
Sbjct: 5 RPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTG-RPRGVAFVRYN 63
Query: 238 DIRAARTAMRALQN 251
A+ A+ AL N
Sbjct: 64 KREEAQEAISALNN 77
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 30.4 bits (67), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 3/62 (4%)
Query: 288 SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE 347
+VS EDL +IF YG + +I K FI+F + ++ A++ ++ GK++ LE
Sbjct: 34 NVSKEDLFRIFSPYGHIMQIN---IKNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILE 90
Query: 348 PS 349
S
Sbjct: 91 VS 92
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 30.0 bits (66), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 32/72 (44%), Gaps = 5/72 (6%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTAMRAL 249
LFVRN++ + +L LF YG + L+ K +GF +++ A A +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 250 QNKPLRRRKLDI 261
+ + R L +
Sbjct: 71 DGQVFQGRMLHV 82
Score = 29.3 bits (64), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 33/75 (44%), Gaps = 5/75 (6%)
Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSL 334
L V NL + S EDL ++F AYG + E+ T + F+ F A A +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 335 NRSDIAGKRIKLEPS 349
+ G+ + + PS
Sbjct: 71 DGQVFQGRMLHVLPS 85
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 30.0 bits (66), Expect = 5.0, Method: Composition-based stats.
Identities = 19/77 (24%), Positives = 37/77 (48%), Gaps = 6/77 (7%)
Query: 195 LFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 254
+FV ++ EL+ F QYG++ ++ R F +++ D + A++ L + L
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQS----LCGEDL 69
Query: 255 RRRKLDIHFS--IPKDN 269
+ + +H S PK N
Sbjct: 70 IIKGISVHISNAEPKHN 86
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 30.0 bits (66), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 3/62 (4%)
Query: 288 SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE 347
+VS EDL +IF YG + +I K FI+F + ++ A++ ++ GK++ LE
Sbjct: 14 NVSKEDLFRIFSPYGHIMQIN---IKNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILE 70
Query: 348 PS 349
S
Sbjct: 71 VS 72
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 30.0 bits (66), Expect = 5.7, Method: Composition-based stats.
Identities = 25/91 (27%), Positives = 41/91 (45%), Gaps = 6/91 (6%)
Query: 273 KDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVRAA 327
KD + V L ++ LR+ F +G+++E R+T R + F+ D AA
Sbjct: 13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAA 72
Query: 328 EAALKSLNRSDIAGKRIKLEPSRPGGARRNL 358
E A K N I G++ + + G R+L
Sbjct: 73 ERACKDPN-PIIDGRKANVNLAYLGAKPRSL 102
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 30.0 bits (66), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 3/62 (4%)
Query: 288 SVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLE 347
+VS EDL +IF YG + +I K FI+F + ++ A++ ++ GK++ LE
Sbjct: 34 NVSKEDLFRIFSPYGHIMQIN---IKNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILE 90
Query: 348 PS 349
S
Sbjct: 91 VS 92
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 29.6 bits (65), Expect = 6.3, Method: Composition-based stats.
Identities = 17/73 (23%), Positives = 37/73 (50%), Gaps = 5/73 (6%)
Query: 280 LVVFNLDPSVSNEDLRQIFGAYGEVKEIR-----ETPHKRHHKFIEFYDVRAAEAALKSL 334
L +++L ++ DL F +G V + +T + F+ F + +A+ A+K++
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 335 NRSDIAGKRIKLE 347
N + KR+K++
Sbjct: 103 NGFQVGTKRLKVQ 115
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 29.6 bits (65), Expect = 7.6, Method: Composition-based stats.
Identities = 16/71 (22%), Positives = 34/71 (47%), Gaps = 5/71 (7%)
Query: 266 PKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHK-----FIE 320
P DN S ++ + T+ L + DL F A G+V+++R + + ++E
Sbjct: 14 PVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVE 73
Query: 321 FYDVRAAEAAL 331
F ++++ A+
Sbjct: 74 FCEIQSVPLAI 84
>pdb|2A3J|A Chain A, Structure Of Urndesign, A Complete Computational Redesign
Of Human U1a Protein
Length = 127
Score = 29.3 bits (64), Expect = 9.3, Method: Composition-based stats.
Identities = 27/104 (25%), Positives = 43/104 (41%), Gaps = 9/104 (8%)
Query: 183 GEHPYGEHPSRTLFVRNINSNVEDSELRALF----EQYGDIRTLYT--ACKHRGFVMISY 236
G P PS+ + + NIN V +L+AL GDI + + + G I +
Sbjct: 20 GSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVF 79
Query: 237 YDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSDKDLNQGTL 280
+A+ + A Q P + L I FS + P + G+L
Sbjct: 80 ATQESAQAFVEAFQGYPFQGNPLVITFS---ETPQSQVAEDGSL 120
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.316 0.136 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 23,032,919
Number of Sequences: 62578
Number of extensions: 968416
Number of successful extensions: 2524
Number of sequences better than 100.0: 143
Number of HSP's better than 100.0 without gapping: 30
Number of HSP's successfully gapped in prelim test: 113
Number of HSP's that attempted gapping in prelim test: 2361
Number of HSP's gapped (non-prelim): 227
length of query: 780
length of database: 14,973,337
effective HSP length: 106
effective length of query: 674
effective length of database: 8,340,069
effective search space: 5621206506
effective search space used: 5621206506
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)