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= psy14139
(327 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 132 bits (331), Expect = 3e-31, Method: Composition-based stats.
Identities = 56/78 (71%), Positives = 68/78 (87%)
Query: 209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEH 268
EDKTITTLYVG LGD +TE DLR+HFYQFGEIR++T++ +QQCAFIQ+ +R AAE A E
Sbjct: 8 EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEK 67
Query: 269 SFNKVILGGRRLNIKWGR 286
SFNK+I+ GRRLN+KWGR
Sbjct: 68 SFNKLIVNGRRLNVKWGR 85
>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 = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 29/80 (36%), Positives = 46/80 (57%), Gaps = 9/80 (11%)
Query: 213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTI------LSKQQCAFIQYTSRPAAEAAV 266
++ +YVG++ +L E +R F FG I+S+ + + + AF++Y AA+ A+
Sbjct: 28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLAL 87
Query: 267 EHSFNKVILGGRRLNIKWGR 286
E N V+LGGR NIK GR
Sbjct: 88 EQ-MNSVMLGGR--NIKVGR 104
Score = 35.0 bits (79), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 40/80 (50%), Gaps = 7/80 (8%)
Query: 209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL------SKQQCAFIQYTSRPAA 262
E + +YV ++ L++ D++ F FG+I+S T+ + FI+Y ++
Sbjct: 121 EARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSS 180
Query: 263 EAAVEHSFNKVILGGRRLNI 282
+ AV S N LGG+ L +
Sbjct: 181 QDAVS-SMNLFDLGGQYLRV 199
>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 = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 29/77 (37%), Positives = 44/77 (57%), Gaps = 9/77 (11%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTI------LSKQQCAFIQYTSRPAAEAAVEHS 269
+YVG++ +L E +R F FG I+S+ + + + AF++Y AA+ A+E
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ- 74
Query: 270 FNKVILGGRRLNIKWGR 286
N V+LGGR NIK GR
Sbjct: 75 MNSVMLGGR--NIKVGR 89
Score = 34.7 bits (78), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 40/80 (50%), Gaps = 7/80 (8%)
Query: 209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL------SKQQCAFIQYTSRPAA 262
E + +YV ++ L++ D++ F FG+I+S T+ + FI+Y ++
Sbjct: 106 EARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSS 165
Query: 263 EAAVEHSFNKVILGGRRLNI 282
+ AV S N LGG+ L +
Sbjct: 166 QDAVS-SMNLFDLGGQYLRV 184
>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 = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 30/77 (38%), Positives = 44/77 (57%), Gaps = 9/77 (11%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSV-----TILSKQQ-CAFIQYTSRPAAEAAVEHS 269
+YVG++ +L E +R F FG I+S+ ++ K + AF++Y AA+ A+E
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 270 FNKVILGGRRLNIKWGR 286
N V LGGR NIK GR
Sbjct: 75 -NSVXLGGR--NIKVGR 88
Score = 33.9 bits (76), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 40/80 (50%), Gaps = 7/80 (8%)
Query: 209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL------SKQQCAFIQYTSRPAA 262
E + +YV ++ L++ D++ F FG+I+S T+ + FI+Y ++
Sbjct: 105 EARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSS 164
Query: 263 EAAVEHSFNKVILGGRRLNI 282
+ AV S N LGG+ L +
Sbjct: 165 QDAVS-SXNLFDLGGQYLRV 183
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 43.1 bits (100), Expect = 2e-04, Method: Composition-based stats.
Identities = 24/65 (36%), Positives = 36/65 (55%), Gaps = 8/65 (12%)
Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL-----SKQQCAFIQYTSRPA 261
PP + L+VG L + +E D+R F FG I TIL + + CAF++Y+S
Sbjct: 12 PPSHRK---LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAE 68
Query: 262 AEAAV 266
A+AA+
Sbjct: 69 AQAAI 73
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVI 274
T+Y G + LT+Q +R F FG+I + + ++ +F+++++ +A A+ S N
Sbjct: 27 TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIV-SVNGTT 85
Query: 275 LGGRRLNIKWGR 286
+ G + WG+
Sbjct: 86 IEGHVVKCYWGK 97
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 5/57 (8%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS-----KQQCAFIQYTSRPAAEAAVE 267
L++G + K TE D+R F FG+I IL + CAF+ +T+R A+ A++
Sbjct: 98 LFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAIK 154
Score = 34.3 bits (77), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 8/75 (10%)
Query: 217 YVGNLGDKLTEQDLRDHFYQFGEIRSVTIL--------SKQQCAFIQYTSRPAAEAAVEH 268
+VG + +E+DLR+ F Q+G + + +L + C F+ + +R AA A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 269 SFNKVILGGRRLNIK 283
N +L G I+
Sbjct: 67 LHNXKVLPGXHHPIQ 81
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 29/81 (35%), Positives = 42/81 (51%), Gaps = 4/81 (4%)
Query: 208 PEDKTITT---LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEA 264
P +KT T L+VGNL +TE+D + F ++GE V I + FI+ SR AE
Sbjct: 14 PGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEI 73
Query: 265 AVEHSFNKVILGGRRLNIKWG 285
A + + IL R L I++
Sbjct: 74 A-KAELDGTILKSRPLRIRFA 93
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 5/57 (8%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS-----KQQCAFIQYTSRPAAEAAVE 267
L++G + K TE D+R F FG+I IL + CAF+ +T+R A+ A++
Sbjct: 98 LFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIK 154
Score = 35.8 bits (81), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 22/93 (23%), Positives = 42/93 (45%), Gaps = 8/93 (8%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL--------SKQQCAFIQYTSRPAAEAAVE 267
++VG + +E+DLR+ F Q+G + + +L + C F+ + +R AA A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 268 HSFNKVILGGRRLNIKWGRAQANRGEDTAELKV 300
N +L G I+ A + + + K+
Sbjct: 66 ALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKL 98
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 5/57 (8%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS-----KQQCAFIQYTSRPAAEAAVE 267
L++G + K TE D+R F FG+I IL + CAF+ +T+R A+ A++
Sbjct: 110 LFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIK 166
Score = 37.7 bits (86), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 26/106 (24%), Positives = 47/106 (44%), Gaps = 10/106 (9%)
Query: 205 LDPPE--DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL--------SKQQCAFI 254
LD P+ D ++VG + +E+DLR+ F Q+G + + +L + C F+
Sbjct: 5 LDHPDQPDLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFV 64
Query: 255 QYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDTAELKV 300
+ +R AA A N +L G I+ A + + + K+
Sbjct: 65 TFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKL 110
>pdb|3TP2|A Chain A, Crystal Structure Of The Splicing Factor Cwc2 From Yeast
pdb|3TP2|B Chain B, Crystal Structure Of The Splicing Factor Cwc2 From Yeast
Length = 229
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 37/140 (26%), Positives = 56/140 (40%), Gaps = 16/140 (11%)
Query: 146 ICSFWVKGECRRGEECPYRHEKPTDPD-DPLADQNIKDRYYGVNDPVAEKLMARASTMPK 204
C F+ KG C G +C Y H P + D LA + +G EK M
Sbjct: 74 FCLFFAKGMCCLGPKCEYLHHIPDEEDIGKLALRTEVLDCFG-----REKFADYREDMGG 128
Query: 205 LDPPEDKTITTLYVGNLGDKLT---------EQDLRDHFYQFGEIRSVTILSKQQCAFIQ 255
+ K TLYVG + L E +R F + G+I + + + C F++
Sbjct: 129 IGSFRKKN-KTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVK 187
Query: 256 YTSRPAAEAAVEHSFNKVIL 275
+ + AE A E N+ +L
Sbjct: 188 FKYQANAEFAKEAMSNQTLL 207
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 41.6 bits (96), Expect = 5e-04, Method: Composition-based stats.
Identities = 25/88 (28%), Positives = 44/88 (50%), Gaps = 7/88 (7%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL-----SKQQCAFIQYTSRPAAEAAVE--H 268
L+VG LG + T++D+R F FG I T+L + + CAF+++ + A+AA+ H
Sbjct: 15 LFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTLH 74
Query: 269 SFNKVILGGRRLNIKWGRAQANRGEDTA 296
S + L +K+ + G +
Sbjct: 75 SSRTLPGASSSLVVKFADTEKESGPSSG 102
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 41.6 bits (96), Expect = 7e-04, Method: Composition-based stats.
Identities = 28/81 (34%), Positives = 41/81 (50%), Gaps = 3/81 (3%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKV 273
T L+VG LG + L F +FG IR++ + A+IQY S AA+AA
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACA-KMRGF 76
Query: 274 ILGG--RRLNIKWGRAQANRG 292
LGG RRL + + ++ + G
Sbjct: 77 PLGGPDRRLRVDFAKSGPSSG 97
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 41.2 bits (95), Expect = 7e-04, Method: Composition-based stats.
Identities = 31/95 (32%), Positives = 45/95 (47%), Gaps = 9/95 (9%)
Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS------KQQCAFIQYTSRP 260
P +D L+VG + L EQDL+ F +FG I +T+L + CAF+ Y +R
Sbjct: 9 PMKDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARD 68
Query: 261 AAEAAVEHSFNKVILGG--RRLNIKWGRAQANRGE 293
+A A + L G R + +K A RGE
Sbjct: 69 SALKAQSALHEQKTLPGMNRPIQVKPA-ASEGRGE 102
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 41.2 bits (95), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 45/81 (55%), Gaps = 4/81 (4%)
Query: 208 PEDKTITT---LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEA 264
P +KT T L+VGNL +TE+++R F ++G+ V I + FI+ +R AE
Sbjct: 14 PGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEI 73
Query: 265 AVEHSFNKVILGGRRLNIKWG 285
A + + + L G++L +++
Sbjct: 74 A-KVELDNMPLRGKQLRVRFA 93
>pdb|3U1L|A Chain A, Structure Of The Mrna Splicing Complex Component Cwc2
pdb|3U1M|A Chain A, Structure Of The Mrna Splicing Complex Component Cwc2
Length = 240
Score = 41.2 bits (95), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 37/140 (26%), Positives = 56/140 (40%), Gaps = 16/140 (11%)
Query: 146 ICSFWVKGECRRGEECPYRHEKPTDPD-DPLADQNIKDRYYGVNDPVAEKLMARASTMPK 204
C F+ KG C G +C Y H P + D LA + +G EK M
Sbjct: 72 FCLFFAKGMCCLGPKCEYLHHIPDEEDIGKLALRTEVLDCFG-----REKFADYREDMGG 126
Query: 205 LDPPEDKTITTLYVGNLGDKLT---------EQDLRDHFYQFGEIRSVTILSKQQCAFIQ 255
+ K TLYVG + L E +R F + G+I + + + C F++
Sbjct: 127 IGSFRKKN-KTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVK 185
Query: 256 YTSRPAAEAAVEHSFNKVIL 275
+ + AE A E N+ +L
Sbjct: 186 FKYQANAEFAKEAMSNQTLL 205
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
Length = 124
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 39/74 (52%), Gaps = 8/74 (10%)
Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL------SKQQCAFIQYTSRPAAEAAVEH 268
++YVGN+ T QDL HF G I +TIL + A+I++ R + +AAV
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-- 95
Query: 269 SFNKVILGGRRLNI 282
+ ++ + GR + +
Sbjct: 96 AMDETVFRGRTIKV 109
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 25/82 (30%), Positives = 36/82 (43%), Gaps = 4/82 (4%)
Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAV 266
PP +TT Y+GN+ TE DL F FG I ++ C FI+Y + A +
Sbjct: 24 PPR---VTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCI 80
Query: 267 EHSFNKVILGGRRLNIKWGRAQ 288
+ GR L WG+ +
Sbjct: 81 V-ALANFPFQGRNLRTGWGKER 101
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 8/80 (10%)
Query: 209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAA 262
+D T T ++VG L T+ LR +F FG+I +++ +Q F+ R AA
Sbjct: 13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAA 72
Query: 263 EAAVEHSFNKVILGGRRLNI 282
E A + I+ GR+ N+
Sbjct: 73 ERACKDP--NPIIDGRKANV 90
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 43/80 (53%), Gaps = 4/80 (5%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC---AFIQYTSRPAAEAAVEHSFNK 272
+YVGNL + +D+ D FY++G IR + + +++ AF+++ AE AV + +
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAV-YGRDG 83
Query: 273 VILGGRRLNIKWGRAQANRG 292
G RL +++ R+ G
Sbjct: 84 YDYDGYRLRVEFPRSGRGTG 103
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 38.5 bits (88), Expect = 0.005, Method: Composition-based stats.
Identities = 20/56 (35%), Positives = 33/56 (58%), Gaps = 5/56 (8%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL-----SKQQCAFIQYTSRPAAEAAV 266
L+VG L + +E+D+ F FG I T+L S + CAF++++S A+AA+
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAI 73
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 40/75 (53%), Gaps = 6/75 (8%)
Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTI-LSKQQCA----FIQYTSRPAAEAAVEHS 269
TLYVGNL TE+ + + F + G+I+ + + L K + A F++Y SR AE A+ +
Sbjct: 20 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMRY- 78
Query: 270 FNKVILGGRRLNIKW 284
N L R + W
Sbjct: 79 INGTRLDDRIIRTDW 93
>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 = 37.7 bits (86), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 39/76 (51%), Gaps = 7/76 (9%)
Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTI----LSKQQCA--FIQYTSRPAAEAAVEH 268
TLYVGNL TE+ + + F + G+I+ + + + K C F++Y SR AE A+ +
Sbjct: 41 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100
Query: 269 SFNKVILGGRRLNIKW 284
N L R + W
Sbjct: 101 -INGTRLDDRIIRTDW 115
>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 = 0.011, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 6/63 (9%)
Query: 209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS------KQQCAFIQYTSRPAA 262
+D L++G + L E+DL+ F +FG+I +T+L + CAF+ Y R +A
Sbjct: 9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESA 68
Query: 263 EAA 265
A
Sbjct: 69 LKA 71
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 37.4 bits (85), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 43/75 (57%), Gaps = 7/75 (9%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAF------IQYTSRPAAEAAVEHS 269
L+V + ++ TE+D+ D F ++GEI+++ + ++ + ++Y + A+AA+E
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME-G 83
Query: 270 FNKVILGGRRLNIKW 284
N L G+ +++ W
Sbjct: 84 LNGQDLMGQPISVDW 98
>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 = 37.4 bits (85), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 7/62 (11%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVEHS 269
LY+ L +T++D+ D F +FG I + +L Q AFI++ R AE A+ S
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAIT-S 149
Query: 270 FN 271
FN
Sbjct: 150 FN 151
Score = 30.8 bits (68), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 36/79 (45%), Gaps = 7/79 (8%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVE 267
T L V L +T+ +LR F GE+ S ++ + F+ Y + AE A+
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI- 61
Query: 268 HSFNKVILGGRRLNIKWGR 286
++ N + L + + + + R
Sbjct: 62 NTLNGLRLQSKTIKVSYAR 80
>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
pdb|2RS8|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
Length = 99
Score = 37.0 bits (84), Expect = 0.013, Method: Composition-based stats.
Identities = 24/79 (30%), Positives = 44/79 (55%), Gaps = 4/79 (5%)
Query: 210 DKTITT---LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAV 266
+KT T L+VGNL +TE+++R F ++G+ V I + FI+ +R AE A
Sbjct: 9 EKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIA- 67
Query: 267 EHSFNKVILGGRRLNIKWG 285
+ + + L G++L +++
Sbjct: 68 KVELDNMPLRGKQLRVRFA 86
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 37.0 bits (84), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 7/62 (11%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVEHS 269
LY+ L +T++D+ D F +FG I + +L Q AFI++ R AE A+ S
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAIT-S 149
Query: 270 FN 271
FN
Sbjct: 150 FN 151
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 36/79 (45%), Gaps = 7/79 (8%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVE 267
T L V L +T+ +LR F GE+ S ++ + F+ Y + AE A+
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI- 61
Query: 268 HSFNKVILGGRRLNIKWGR 286
++ N + L + + + + R
Sbjct: 62 NTLNGLRLQSKTIKVSYAR 80
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 37.0 bits (84), Expect = 0.017, Method: Composition-based stats.
Identities = 20/88 (22%), Positives = 46/88 (52%), Gaps = 7/88 (7%)
Query: 208 PEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK-------QQCAFIQYTSRP 260
P+ +T + + V N+ + ++++R+ F FGE+++V + K + F+ + ++
Sbjct: 10 PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQ 69
Query: 261 AAEAAVEHSFNKVILGGRRLNIKWGRAQ 288
A+ A + L GRRL ++W ++
Sbjct: 70 DAKKAFNALCHSTHLYGRRLVLEWADSE 97
>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 = 36.6 bits (83), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 43/75 (57%), Gaps = 7/75 (9%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAF------IQYTSRPAAEAAVEHS 269
L+V + ++ TE+D+ D F ++GEI+++ + ++ + ++Y + A+AA+E
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME-G 68
Query: 270 FNKVILGGRRLNIKW 284
N L G+ +++ W
Sbjct: 69 LNGQDLMGQPISVDW 83
>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 = 36.6 bits (83), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 6/73 (8%)
Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS------KQQCAFIQYTSRP 260
P T+ ++VG + + E LRD+F Q+G+I + I++ K+ AF+ +
Sbjct: 91 PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD 150
Query: 261 AAEAAVEHSFNKV 273
+ + V ++ V
Sbjct: 151 SVDKIVIQKYHTV 163
Score = 30.0 bits (66), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 34/71 (47%), Gaps = 6/71 (8%)
Query: 209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL------SKQQCAFIQYTSRPAA 262
E + + L++G L + T++ LR HF Q+G + ++ + F+ Y +
Sbjct: 2 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 61
Query: 263 EAAVEHSFNKV 273
+AA+ +KV
Sbjct: 62 DAAMNARPHKV 72
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 36.6 bits (83), Expect = 0.019, Method: Composition-based stats.
Identities = 19/75 (25%), Positives = 43/75 (57%), Gaps = 7/75 (9%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAF------IQYTSRPAAEAAVEHS 269
L+V + ++ TE+D+ D F ++GEI+++ + ++ + ++Y + A+AA+E
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME-G 68
Query: 270 FNKVILGGRRLNIKW 284
N L G+ +++ W
Sbjct: 69 LNGQDLMGQPISVDW 83
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 36.6 bits (83), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 6/73 (8%)
Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS------KQQCAFIQYTSRP 260
P T+ ++VG + + E LRD+F Q+G+I + I++ K+ AF+ +
Sbjct: 98 PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD 157
Query: 261 AAEAAVEHSFNKV 273
+ + V ++ V
Sbjct: 158 SVDKIVIQKYHTV 170
Score = 32.7 bits (73), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 35/73 (47%), Gaps = 6/73 (8%)
Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL------SKQQCAFIQYTSRP 260
P E + + L++G L + T++ LR HF Q+G + ++ + F+ Y +
Sbjct: 7 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 66
Query: 261 AAEAAVEHSFNKV 273
+AA+ +KV
Sbjct: 67 EVDAAMNARPHKV 79
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 36.6 bits (83), Expect = 0.020, Method: Composition-based stats.
Identities = 20/77 (25%), Positives = 42/77 (54%), Gaps = 3/77 (3%)
Query: 213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNK 272
+ L++GNL + TEQ++R F Q+G++ I+ + F+ + AAE A+ + +
Sbjct: 8 MVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--KNYGFVHIEDKTAAEDAIR-NLHH 64
Query: 273 VILGGRRLNIKWGRAQA 289
L G +N++ + ++
Sbjct: 65 YKLHGVNINVEASKNKS 81
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 36.6 bits (83), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 6/73 (8%)
Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS------KQQCAFIQYTSRP 260
P T+ ++VG + + E LRD+F Q+G+I + I++ K+ AF+ +
Sbjct: 96 PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD 155
Query: 261 AAEAAVEHSFNKV 273
+ + V ++ V
Sbjct: 156 SVDKIVIQKYHTV 168
Score = 32.7 bits (73), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 35/73 (47%), Gaps = 6/73 (8%)
Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL------SKQQCAFIQYTSRP 260
P E + + L++G L + T++ LR HF Q+G + ++ + F+ Y +
Sbjct: 5 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 64
Query: 261 AAEAAVEHSFNKV 273
+AA+ +KV
Sbjct: 65 EVDAAMNARPHKV 77
>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 = 36.6 bits (83), Expect = 0.021, Method: Composition-based stats.
Identities = 19/75 (25%), Positives = 43/75 (57%), Gaps = 7/75 (9%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAF------IQYTSRPAAEAAVEHS 269
L+V + ++ TE+D+ D F ++GEI+++ + ++ + ++Y + A+AA+E
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME-G 70
Query: 270 FNKVILGGRRLNIKW 284
N L G+ +++ W
Sbjct: 71 LNGQDLMGQPISVDW 85
>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 = 36.6 bits (83), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 6/73 (8%)
Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS------KQQCAFIQYTSRP 260
P T+ ++VG + + E LRD+F Q+G+I + I++ K+ AF+ +
Sbjct: 98 PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD 157
Query: 261 AAEAAVEHSFNKV 273
+ + V ++ V
Sbjct: 158 SVDKIVIQKYHTV 170
Score = 32.7 bits (73), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 35/73 (47%), Gaps = 6/73 (8%)
Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL------SKQQCAFIQYTSRP 260
P E + + L++G L + T++ LR HF Q+G + ++ + F+ Y +
Sbjct: 7 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 66
Query: 261 AAEAAVEHSFNKV 273
+AA+ +KV
Sbjct: 67 EVDAAMNARPHKV 79
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 36.6 bits (83), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 6/73 (8%)
Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS------KQQCAFIQYTSRP 260
P T+ ++VG + + E LRD+F Q+G+I + I++ K+ AF+ +
Sbjct: 99 PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD 158
Query: 261 AAEAAVEHSFNKV 273
+ + V ++ V
Sbjct: 159 SVDKIVIQKYHTV 171
Score = 32.7 bits (73), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 35/73 (47%), Gaps = 6/73 (8%)
Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL------SKQQCAFIQYTSRP 260
P E + + L++G L + T++ LR HF Q+G + ++ + F+ Y +
Sbjct: 8 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 67
Query: 261 AAEAAVEHSFNKV 273
+AA+ +KV
Sbjct: 68 EVDAAMNARPHKV 80
>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 = 36.6 bits (83), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 6/73 (8%)
Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS------KQQCAFIQYTSRP 260
P T+ ++VG + + E LRD+F Q+G+I + I++ K+ AF+ +
Sbjct: 97 PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD 156
Query: 261 AAEAAVEHSFNKV 273
+ + V ++ V
Sbjct: 157 SVDKIVIQKYHTV 169
Score = 32.7 bits (73), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 35/73 (47%), Gaps = 6/73 (8%)
Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL------SKQQCAFIQYTSRP 260
P E + + L++G L + T++ LR HF Q+G + ++ + F+ Y +
Sbjct: 6 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 65
Query: 261 AAEAAVEHSFNKV 273
+AA+ +KV
Sbjct: 66 EVDAAMNARPHKV 78
>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 = 36.2 bits (82), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 43/75 (57%), Gaps = 7/75 (9%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAF------IQYTSRPAAEAAVEHS 269
L+V + ++ TE+D+ D F ++GEI+++ + ++ + ++Y + A+AA+E
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME-G 68
Query: 270 FNKVILGGRRLNIKW 284
N L G+ +++ W
Sbjct: 69 LNGQDLMGQPISVDW 83
>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 = 35.8 bits (81), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 8/76 (10%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL--------SKQQCAFIQYTSRPAAEAAVE 267
++VG + +E+DLR+ F Q+G + + +L + C F+ + +R AA A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 268 HSFNKVILGGRRLNIK 283
N +L G I+
Sbjct: 66 ALHNMKVLPGMHHPIQ 81
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 35.8 bits (81), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 28/95 (29%), Positives = 41/95 (43%), Gaps = 15/95 (15%)
Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIR--------SVTILSKQQC------ 251
DP ED + +YV L D +T DL D F Q G ++ + I ++
Sbjct: 8 DPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGD 67
Query: 252 AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGR 286
A + Y P A+AAVE F+ G +L + R
Sbjct: 68 ATVSYEDPPTAKAAVEW-FDGKDFQGSKLKVSLAR 101
>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 = 35.8 bits (81), Expect = 0.035, Method: Composition-based stats.
Identities = 19/75 (25%), Positives = 43/75 (57%), Gaps = 7/75 (9%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAF------IQYTSRPAAEAAVEHS 269
L+V + ++ TE+D+ D F ++GEI+++ + ++ + ++Y + A+AA+E
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME-G 84
Query: 270 FNKVILGGRRLNIKW 284
N L G+ +++ W
Sbjct: 85 LNGQDLMGQPISVDW 99
>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 = 35.8 bits (81), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 41/81 (50%), Gaps = 7/81 (8%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVE 267
L++ +L + +QDL F FG + S + +Q F+ Y + +A+AA++
Sbjct: 26 ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 85
Query: 268 HSFNKVILGGRRLNIKWGRAQ 288
S N +G +RL ++ R++
Sbjct: 86 -SMNGFQIGMKRLKVQLKRSK 105
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 35.4 bits (80), Expect = 0.040, Method: Composition-based stats.
Identities = 19/76 (25%), Positives = 38/76 (50%), Gaps = 7/76 (9%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEHS 269
++VG+L ++T +D++ F FG+I ++ F+ + ++ AE A+ H
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 270 FNKVILGGRRLNIKWG 285
+ LGGR++ W
Sbjct: 78 GGQ-WLGGRQIRTNWA 92
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 35.4 bits (80), Expect = 0.042, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 35/73 (47%), Gaps = 7/73 (9%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEHS 269
LYVG+L +TE LR F FG I S+ ++ + FI ++ A+ A+E
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ- 87
Query: 270 FNKVILGGRRLNI 282
N L GR + +
Sbjct: 88 LNGFELAGRPMKV 100
>pdb|2GHP|A Chain A, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|B Chain B, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|C Chain C, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|D Chain D, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|E Chain E, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|F Chain F, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|G Chain G, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|H Chain H, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
Length = 292
Score = 35.4 bits (80), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 42/78 (53%), Gaps = 10/78 (12%)
Query: 216 LYVGNLGDKLTEQDL-RDHFYQFGEIRSVTILSKQQ-------CAFIQYTSRPAAEAAVE 267
+ + NL +L +++L R+ F FG I + I + Q+ CAF + ++ +AE A++
Sbjct: 213 IXIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFXVFENKDSAERALQ 272
Query: 268 HSFNKVILGGRRLNIKWG 285
N+ +LG R +++
Sbjct: 273 X--NRSLLGNREISVSLA 288
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 35.4 bits (80), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 40/75 (53%), Gaps = 7/75 (9%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEHS 269
L V L TE+DLR+ F ++G I V+I+ QQ AF+ + + A+ A E +
Sbjct: 15 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 74
Query: 270 FNKVILGGRRLNIKW 284
N + L GRR+ + +
Sbjct: 75 -NGMELDGRRIRVDF 88
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 35.4 bits (80), Expect = 0.049, Method: Composition-based stats.
Identities = 22/93 (23%), Positives = 47/93 (50%), Gaps = 7/93 (7%)
Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRP 260
P D+++ +++VGN+ + TE+ L+D F + G + S ++ ++ F +Y +
Sbjct: 2 PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61
Query: 261 AAEAAVEHSFNKVILGGRRLNIKWGRAQANRGE 293
A +A+ + N GR L + ++ N+ E
Sbjct: 62 TALSAMR-NLNGREFSGRALRVDNAASEKNKEE 93
>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 = 35.0 bits (79), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 18/75 (24%), Positives = 37/75 (49%), Gaps = 7/75 (9%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL------SKQQCAFIQYTSRPAAEAAVEHS 269
++VG+L ++T +D++ F FG I ++ + F+ + ++ AE A++
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ- 76
Query: 270 FNKVILGGRRLNIKW 284
LGGR++ W
Sbjct: 77 MGGQWLGGRQIRTNW 91
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 35.0 bits (79), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 31/110 (28%), Positives = 51/110 (46%), Gaps = 21/110 (19%)
Query: 195 LMARASTMPKLDPPEDKTITTLYVGN------------LGDKL--TEQDLRDHFYQFGEI 240
L+ R S M + + + +VGN G L TE+DLR+ F ++G I
Sbjct: 14 LVPRGSHMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPI 73
Query: 241 RSVTILSKQQC------AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW 284
V+I+ QQ AF+ + + A+ A E + N + L GRR+ + +
Sbjct: 74 ADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA-NGMELDGRRIRVDF 122
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 35.0 bits (79), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 3/74 (4%)
Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVI 274
TLYV G+ +T LR F FG I +++ + CAF+ Y +A+ AV N
Sbjct: 41 TLYV--YGEDMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAE-LNGTQ 97
Query: 275 LGGRRLNIKWGRAQ 288
+ +L + R Q
Sbjct: 98 VESVQLKVNIARKQ 111
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 34.7 bits (78), Expect = 0.078, Method: Composition-based stats.
Identities = 22/64 (34%), Positives = 33/64 (51%), Gaps = 2/64 (3%)
Query: 213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNK 272
+ L+V NL + +TE+ L F QFG++ V L + AFI + R A A+E K
Sbjct: 11 VKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--KDYAFIHFDERDGAVKAMEEMNGK 68
Query: 273 VILG 276
+ G
Sbjct: 69 DLEG 72
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 34.7 bits (78), Expect = 0.085, Method: Composition-based stats.
Identities = 26/78 (33%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL-SKQQCAFIQYTSRPAAEAAVEHSFNKVI 274
+YVGNLG + +L F +G +R+V I + AF+++ AE AV KVI
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 62
Query: 275 LGGR-RLNIKWGRAQANR 291
G R R+ + G + +R
Sbjct: 63 CGSRVRVELSTGMPRRSR 80
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 34.3 bits (77), Expect = 0.094, Method: Compositional matrix adjust.
Identities = 26/92 (28%), Positives = 44/92 (47%), Gaps = 7/92 (7%)
Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQ-----QCAFIQYTSRPAAEAAVEHS 269
LYVGNL +TE L+ +F G I ++ I+ + AF++Y A A++ +
Sbjct: 2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQ-T 60
Query: 270 FNKVILGGRRLNIKWG-RAQANRGEDTAELKV 300
N + + I W ++Q + +DT L V
Sbjct: 61 LNGKQIENNIVKINWAFQSQQSSSDDTFNLFV 92
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 33.9 bits (76), Expect = 0.11, Method: Composition-based stats.
Identities = 23/79 (29%), Positives = 37/79 (46%)
Query: 213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNK 272
+ LY+GNL +T DLR F + +L K AF+ Y + A A+E K
Sbjct: 8 MNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGK 67
Query: 273 VILGGRRLNIKWGRAQANR 291
V L G+ + + + ++ R
Sbjct: 68 VELHGKIMEVDYSVSKKLR 86
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 33.9 bits (76), Expect = 0.11, Method: Composition-based stats.
Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 6/69 (8%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVE 267
+T+YV NL LT DL F ++G++ VTI+ + AFI + + +A+
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
Query: 268 HSFNKVILG 276
NK + G
Sbjct: 77 AINNKQLFG 85
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 36/65 (55%), Gaps = 5/65 (7%)
Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ---CAFIQYTSRPAAE 263
PPE I LY+ NL K+T +++ D F ++G IR + + + + A++ Y A+
Sbjct: 4 PPEVNRI--LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAK 61
Query: 264 AAVEH 268
AV+H
Sbjct: 62 NAVDH 66
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 33.9 bits (76), Expect = 0.12, Method: Composition-based stats.
Identities = 20/62 (32%), Positives = 32/62 (51%), Gaps = 2/62 (3%)
Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAA 265
DP + L+V NL +TE+ L F +FG++ V L + AF+ + R AA A
Sbjct: 8 DPEVMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVKKL--KDYAFVHFEDRGAAVKA 65
Query: 266 VE 267
++
Sbjct: 66 MD 67
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 33.9 bits (76), Expect = 0.13, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 36/63 (57%), Gaps = 7/63 (11%)
Query: 226 TEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEHSFNKVILGGRR 279
TE+DLR+ F ++G I V+I+ QQ AF+ + + A+ A E + N + L GRR
Sbjct: 28 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA-NGMELDGRR 86
Query: 280 LNI 282
+ +
Sbjct: 87 IRV 89
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 33.5 bits (75), Expect = 0.15, Method: Composition-based stats.
Identities = 22/65 (33%), Positives = 37/65 (56%), Gaps = 7/65 (10%)
Query: 226 TEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEHSFNKVILGGRR 279
TE+DLR+ F ++G I V+I+ QQ AF+ + + A+ A E + N + L GRR
Sbjct: 28 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA-NGMELDGRR 86
Query: 280 LNIKW 284
+ + +
Sbjct: 87 IRVDF 91
>pdb|3R27|A Chain A, Crystal Structure Of The First Rrm Domain Of Heterogeneous
Nuclear Ribonucleoprotein L (Hnrnp L)
pdb|3R27|B Chain B, Crystal Structure Of The First Rrm Domain Of Heterogeneous
Nuclear Ribonucleoprotein L (Hnrnp L)
Length = 100
Score = 33.1 bits (74), Expect = 0.19, Method: Composition-based stats.
Identities = 19/84 (22%), Positives = 41/84 (48%), Gaps = 1/84 (1%)
Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAA 265
DP + +++ L D + E DL + +FG I V ++ K++ A +++ A A
Sbjct: 14 DPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNA 73
Query: 266 VEHSF-NKVILGGRRLNIKWGRAQ 288
V ++ N++ + G + + +Q
Sbjct: 74 VNYAADNQIYIAGHPAFVNYSTSQ 97
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 33.1 bits (74), Expect = 0.23, Method: Composition-based stats.
Identities = 23/84 (27%), Positives = 42/84 (50%), Gaps = 8/84 (9%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEI-------RSVTILSKQQCAFIQYTSRPAAEAAVEH 268
+++GNL ++ E+ L D F FG I R + + AFI + S A++AA+E
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE- 66
Query: 269 SFNKVILGGRRLNIKWGRAQANRG 292
+ N L R + + + + ++G
Sbjct: 67 AMNGQYLCNRPITVSYAFKKDSKG 90
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 33.1 bits (74), Expect = 0.24, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 34/73 (46%), Gaps = 7/73 (9%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEHS 269
LYVG+L +TE LR F FG+I ++ ++ FI ++ A A+E
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ- 66
Query: 270 FNKVILGGRRLNI 282
N L GR + +
Sbjct: 67 LNGFELAGRPMRV 79
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 33.1 bits (74), Expect = 0.24, Method: Composition-based stats.
Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 2/52 (3%)
Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAV 266
TLYV G+ +T LR F FG I +++ + CAF+ Y +A+ AV
Sbjct: 17 TLYV--YGEDMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAV 66
>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 = 32.7 bits (73), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 6/70 (8%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQ------QCAFIQYTSRPAAEAAVE 267
T LYV NL +T+ L F ++G I IL + AF++Y R A+ A+
Sbjct: 101 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 160
Query: 268 HSFNKVILGG 277
N + GG
Sbjct: 161 ALNNVIPEGG 170
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 32.7 bits (73), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 30/66 (45%), Gaps = 5/66 (7%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL-----SKQQCAFIQYTSRPAAEAAVEH 268
T LY+ NL + EQ+L + FG++ S IL + + F + S EA + H
Sbjct: 26 TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGH 85
Query: 269 SFNKVI 274
K I
Sbjct: 86 FNGKFI 91
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 32.7 bits (73), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 26/92 (28%), Positives = 49/92 (53%), Gaps = 7/92 (7%)
Query: 195 LMARASTMPKLDPPEDKTITT-LYVGNLGDKLTEQ-DLRDHFYQFGEIRSVTILSKQQCA 252
L +AS + + P K+I + +++GNL L ++ D+ F ++G + ++ + A
Sbjct: 10 LKLQASNVTNKNDP--KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--HKGYA 65
Query: 253 FIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW 284
F+QY++ A AAV N +L G+ L+I
Sbjct: 66 FVQYSNERHARAAVLGE-NGRVLAGQTLDINM 96
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 32.7 bits (73), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 40/74 (54%), Gaps = 8/74 (10%)
Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL------SKQQCAFIQYTSRPAAEAAVEH 268
++YVGN+ T ++L HF+ G + VTIL + A+I+++ + + ++
Sbjct: 7 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-- 64
Query: 269 SFNKVILGGRRLNI 282
+ ++ + GR++ +
Sbjct: 65 ALDESLFRGRQIKV 78
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 32.7 bits (73), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 6/70 (8%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQ------QCAFIQYTSRPAAEAAVE 267
T LYV NL +T+ L F ++G I IL + AF++Y R A+ A+
Sbjct: 90 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 149
Query: 268 HSFNKVILGG 277
N + GG
Sbjct: 150 ALNNVIPEGG 159
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 32.3 bits (72), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 41/83 (49%), Gaps = 7/83 (8%)
Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEH 268
LY+ NL ++TE+DL F +F E + I + AFI + ++ A A+ H
Sbjct: 27 VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL-H 85
Query: 269 SFNKVILGGRRLNIKWGRAQANR 291
N L G+ L I++G+ + R
Sbjct: 86 LVNGYKLYGKILVIEFGKNKKQR 108
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 32.3 bits (72), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 19/90 (21%), Positives = 45/90 (50%), Gaps = 8/90 (8%)
Query: 208 PEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPA 261
PE++ T++ L ++ +DL D F G++R V I+S + A++++ +
Sbjct: 20 PEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQS 79
Query: 262 AEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
A+ + +++ G + ++ +A+ NR
Sbjct: 80 VPLAIGLTGQRLL--GVPIIVQASQAEKNR 107
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of Hypothetical
Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens
At 1.95 A Resolution
Length = 89
Score = 32.0 bits (71), Expect = 0.44, Method: Composition-based stats.
Identities = 17/74 (22%), Positives = 40/74 (54%), Gaps = 8/74 (10%)
Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEH 268
++YVGN+ T ++L HF+ G + VTIL + A+I+++ + + ++
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-- 65
Query: 269 SFNKVILGGRRLNI 282
+ ++ + GR++ +
Sbjct: 66 ALDESLFRGRQIKV 79
>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 = 32.0 bits (71), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 6/58 (10%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQ------QCAFIQYTSRPAAEAAVE 267
LYV L +T+++L F Q+G I + IL Q FI++ R AE A++
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 148
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 32.0 bits (71), Expect = 0.46, Method: Composition-based stats.
Identities = 23/86 (26%), Positives = 40/86 (46%), Gaps = 5/86 (5%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCA----FIQYTSRPAAEAAVEHSFN 271
L+V N+ + + DLR F QFG+I V I+ ++ + F+ + + A+ A E
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHG 77
Query: 272 KVILGGR-RLNIKWGRAQANRGEDTA 296
V+ G + +N R N G +
Sbjct: 78 TVVEGRKIEVNNATARVMTNSGPSSG 103
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 31.6 bits (70), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 25/99 (25%), Positives = 48/99 (48%), Gaps = 8/99 (8%)
Query: 195 LMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCA-- 252
L+ R S M + + K L+V N+ + + DLR F QFG+I V I+ ++ +
Sbjct: 14 LVPRGSHMNTENKSQPKR---LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKG 70
Query: 253 --FIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQA 289
F+ + + A+ A E + ++ GR++ + A+
Sbjct: 71 FGFVTFENSADADRARE-KLHGTVVEGRKIEVNNATARV 108
>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 = 31.6 bits (70), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 5/65 (7%)
Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ---CAFIQYTSRPAAE 263
PPE I LY+ NL K+T +++ D F ++G IR + + + + A++ Y A+
Sbjct: 14 PPEVNRI--LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAK 71
Query: 264 AAVEH 268
A +H
Sbjct: 72 NACDH 76
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 31.6 bits (70), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 10/31 (32%), Positives = 22/31 (70%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL 246
+++G L + T++ LR++F QFGE++ ++
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVM 58
>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 = 31.6 bits (70), Expect = 0.60, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 33/72 (45%), Gaps = 6/72 (8%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQ------QCAFIQYTSRPAAEAAVE 267
T LYV NL +T+ L F ++G I IL + AF++Y R A+ A+
Sbjct: 14 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 73
Query: 268 HSFNKVILGGRR 279
N + GG +
Sbjct: 74 ALNNVIPEGGSQ 85
>pdb|2CQE|A Chain A, Solution Structure Of The Zinc-Finger Domain In Kiaa1064
Protein
Length = 98
Score = 31.6 bits (70), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 146 ICSFWVKGECRRGEECPYRH 165
+C F++ G C R E CPY H
Sbjct: 15 LCKFYITGFCARAENCPYMH 34
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 31.6 bits (70), Expect = 0.61, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 5/65 (7%)
Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ---CAFIQYTSRPAAE 263
PPE I LY+ NL K+T +++ D F ++G IR + + + + A++ Y A+
Sbjct: 8 PPEVNRI--LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAK 65
Query: 264 AAVEH 268
A +H
Sbjct: 66 NACDH 70
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 31.6 bits (70), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 34/66 (51%), Gaps = 7/66 (10%)
Query: 208 PEDKTITTLYVGNLGDKLTEQDLRDHFY----QFGEIRSVTI---LSKQQCAFIQYTSRP 260
PE + T+Y+ NL +K+ + +L+ Y QFG+I + + L + AF+ +
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVS 62
Query: 261 AAEAAV 266
+A A+
Sbjct: 63 SATNAL 68
>pdb|2D9N|A Chain A, Solution Structure Of Ccch Type Zinc-Finger Domain 2 In
Cleavage And Polyadenylation Specificity Factor
Length = 77
Score = 31.6 bits (70), Expect = 0.69, Method: Composition-based stats.
Identities = 8/21 (38%), Positives = 16/21 (76%)
Query: 146 ICSFWVKGECRRGEECPYRHE 166
+C W++G C++G++C + HE
Sbjct: 12 VCKHWLRGLCKKGDQCEFLHE 32
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 31.6 bits (70), Expect = 0.71, Method: Composition-based stats.
Identities = 23/92 (25%), Positives = 39/92 (42%), Gaps = 15/92 (16%)
Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVE- 267
T+ V NL + E DL++ F FG I + + + AFI + R A A+
Sbjct: 17 TIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAG 76
Query: 268 ---HSFNKVILGGRRLNIKWGRAQANRGEDTA 296
++ +I LN++W + N G +
Sbjct: 77 VSGFGYDHLI-----LNVEWAKPSTNSGPSSG 103
>pdb|2RHK|C Chain C, Crystal Structure Of Influenza A Ns1a Protein In Complex
With F2f3 Fragment Of Human Cellular Factor Cpsf30,
Northeast Structural Genomics Targets Or8c And Hr6309a
pdb|2RHK|D Chain D, Crystal Structure Of Influenza A Ns1a Protein In Complex
With F2f3 Fragment Of Human Cellular Factor Cpsf30,
Northeast Structural Genomics Targets Or8c And Hr6309a
Length = 72
Score = 31.6 bits (70), Expect = 0.71, Method: Composition-based stats.
Identities = 8/21 (38%), Positives = 16/21 (76%)
Query: 146 ICSFWVKGECRRGEECPYRHE 166
+C W++G C++G++C + HE
Sbjct: 18 VCKHWLRGLCKKGDQCEFLHE 38
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 31.2 bits (69), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL-SKQQCAFIQYTS-RPAAEAAVE 267
+YVGNLG+ + +L F +G +RSV + + AF+++ R AA+A E
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRE 129
>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 = 31.2 bits (69), Expect = 0.86, Method: Composition-based stats.
Identities = 19/79 (24%), Positives = 36/79 (45%), Gaps = 7/79 (8%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVE 267
T L V L +T+ +LR F GE+ S ++ + F+ Y + AE A+
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI- 63
Query: 268 HSFNKVILGGRRLNIKWGR 286
++ N + L + + + + R
Sbjct: 64 NTLNGLRLQSKTIKVSYAR 82
>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 = 31.2 bits (69), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 23/116 (19%), Positives = 56/116 (48%), Gaps = 13/116 (11%)
Query: 181 KDRYYGVNDPVAEKLMA----RASTMPKLDPPEDKTIT--TLYVGNLGDKLTEQDLRDHF 234
K R +G + E + + R +L+P +++ L+V ++ ++ E ++++ F
Sbjct: 34 KGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKF 93
Query: 235 YQFGEIRSVTILSKQQCAF------IQYTSRPAAEAAVEHSFNKVILGGRRLNIKW 284
+GEI+++ + ++ F ++Y + A AA E + N + G+ + + W
Sbjct: 94 CDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE-ALNGAEIMGQTIQVDW 148
>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 = 31.2 bits (69), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 34/66 (51%), Gaps = 7/66 (10%)
Query: 208 PEDKTITTLYVGNLGDKLTEQDLRDHFY----QFGEIRSVTI---LSKQQCAFIQYTSRP 260
PE + T+Y+ NL +K+ + +L+ Y QFG+I + + L + AF+ +
Sbjct: 4 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVS 63
Query: 261 AAEAAV 266
+A A+
Sbjct: 64 SATNAL 69
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 31.2 bits (69), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 40/76 (52%), Gaps = 9/76 (11%)
Query: 209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL----SKQQ--CAFIQYTSRP-- 260
E + L++G L + TE+ LR+++ Q+G++ ++ SK+ F+ ++S
Sbjct: 23 EKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEV 82
Query: 261 -AAEAAVEHSFNKVIL 275
AA AA HS + ++
Sbjct: 83 DAAMAARPHSIDGRVV 98
>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 = 1.0, Method: Composition-based stats.
Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 4/66 (6%)
Query: 213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK----QQCAFIQYTSRPAAEAAVEH 268
+ LYV NL D + ++ LR F FG I S ++ + + F+ ++S A AV
Sbjct: 15 VVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTE 74
Query: 269 SFNKVI 274
+++
Sbjct: 75 MNGRIV 80
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 30.8 bits (68), Expect = 1.1, Method: Composition-based stats.
Identities = 10/31 (32%), Positives = 22/31 (70%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL 246
+++G L + T++ LR++F QFGE++ ++
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVM 33
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 7/77 (9%)
Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTI------LSKQQCAFIQYTSRPAAEAAVEH 268
LYVG L +++ ++ L F FG+I + I + AF+++ A AA++
Sbjct: 65 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID- 123
Query: 269 SFNKVILGGRRLNIKWG 285
+ N+ L GR + +
Sbjct: 124 NMNESELFGRTIRVNLA 140
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 7/76 (9%)
Query: 211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVE--H 268
K T L+VGN+ T Q+LR F ++G + I+ + AF+ AE AVE
Sbjct: 8 KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--KDYAFVHMER---AEDAVEAIR 62
Query: 269 SFNKVILGGRRLNIKW 284
+ G+R++++
Sbjct: 63 GLDNTEFQGKRMHVQL 78
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL 246
I L+VG L T++ LR +F Q+GE+ I+
Sbjct: 16 IGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIM 49
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 30.4 bits (67), Expect = 1.2, Method: Composition-based stats.
Identities = 18/66 (27%), Positives = 34/66 (51%), Gaps = 7/66 (10%)
Query: 208 PEDKTITTLYVGNLGDKLTEQDLRDHFY----QFGEIRSVTI---LSKQQCAFIQYTSRP 260
PE + T+Y+ NL +K+ + +L+ Y QFG+I + + L + AF+ +
Sbjct: 4 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVS 63
Query: 261 AAEAAV 266
+A A+
Sbjct: 64 SATNAL 69
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 30.4 bits (67), Expect = 1.3, Method: Composition-based stats.
Identities = 21/81 (25%), Positives = 40/81 (49%), Gaps = 6/81 (7%)
Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-----CAFIQYTSRPA 261
P +++ T++VGNL ++ E+ L + F Q G + VTI ++ F+ + +
Sbjct: 10 PAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPES 69
Query: 262 AEAAVEHSFNKVILGGRRLNI 282
A+ N + L GR +N+
Sbjct: 70 VSYAIA-LLNGIRLYGRPINV 89
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/89 (20%), Positives = 47/89 (52%), Gaps = 9/89 (10%)
Query: 204 KLDPPEDKTIT--TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAF------IQ 255
+L+P +++ L+V ++ ++ E ++++ F +GEI+++ + ++ F ++
Sbjct: 15 ELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVE 74
Query: 256 YTSRPAAEAAVEHSFNKVILGGRRLNIKW 284
Y + A AA E + N + G+ + + W
Sbjct: 75 YETHKQALAAKE-ALNGAEIMGQTIQVDW 102
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 30/51 (58%), Gaps = 2/51 (3%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL-SKQQCAFIQYTS-RPAAEA 264
+YVGNLG+ + +L F +G +RSV + + AF+++ R AA+A
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADA 126
>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
pdb|1HD1|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
Length = 75
Score = 30.4 bits (67), Expect = 1.6, Method: Composition-based stats.
Identities = 11/30 (36%), Positives = 21/30 (70%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTI 245
+++G L T++DL+D+F +FGE+ T+
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTL 31
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 30.0 bits (66), Expect = 1.8, Method: Composition-based stats.
Identities = 18/74 (24%), Positives = 39/74 (52%), Gaps = 8/74 (10%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL---SKQQ---CAFIQYTSRPAAEAAVEHS 269
++VG + E +LR++F +FG + V ++ KQ+ FI + + + AV
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMH 72
Query: 270 FNKVILGGRRLNIK 283
F+ ++ G+++ +K
Sbjct: 73 FHDIM--GKKVEVK 84
>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 = 30.0 bits (66), Expect = 2.0, Method: Composition-based stats.
Identities = 19/79 (24%), Positives = 35/79 (44%), Gaps = 7/79 (8%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVE 267
T L V L T+ +LR F GE+ S ++ + F+ Y + AE A+
Sbjct: 20 TNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI- 78
Query: 268 HSFNKVILGGRRLNIKWGR 286
++ N + L + + + + R
Sbjct: 79 NTLNGLRLQSKTIKVSYAR 97
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 29.6 bits (65), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 29/58 (50%), Gaps = 6/58 (10%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVE 267
LYV L ++++++ F Q+G I + IL Q FI++ R AE A++
Sbjct: 93 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 150
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 29.6 bits (65), Expect = 2.1, Method: Composition-based stats.
Identities = 18/68 (26%), Positives = 35/68 (51%), Gaps = 3/68 (4%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVIL 275
++VGN+ T Q+LR F + G + ++ + AF+ A+AA+ N +
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVV--KDYAFVHMEKEADAKAAIAQ-LNGKEV 68
Query: 276 GGRRLNIK 283
G+R+N++
Sbjct: 69 KGKRINVE 76
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 29.6 bits (65), Expect = 2.3, Method: Composition-based stats.
Identities = 21/81 (25%), Positives = 39/81 (48%), Gaps = 7/81 (8%)
Query: 212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAA 265
T LYVG L +++ ++ L F FG+I + I + AF+++ A AA
Sbjct: 11 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 70
Query: 266 VEHSFNKVILGGRRLNIKWGR 286
++ + N+ L GR + + +
Sbjct: 71 ID-NMNESELFGRTIRVNLAK 90
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 29.6 bits (65), Expect = 2.3, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 29/58 (50%), Gaps = 6/58 (10%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVE 267
LYV L ++++++ F Q+G I + IL Q FI++ R AE A++
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 61
>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 = 29.6 bits (65), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 41/78 (52%), Gaps = 7/78 (8%)
Query: 213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTI----LSKQQC--AFIQYTSRPAAEAAV 266
+ +LYVG+L +TE L + F G I S+ + ++++ A++ + AE A+
Sbjct: 15 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL 74
Query: 267 EHSFNKVILGGRRLNIKW 284
+ + N ++ G+ + I W
Sbjct: 75 D-TMNFDVIKGKPVRIMW 91
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 29.6 bits (65), Expect = 2.3, Method: Composition-based stats.
Identities = 21/81 (25%), Positives = 39/81 (48%), Gaps = 7/81 (8%)
Query: 212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAA 265
T LYVG L +++ ++ L F FG+I + I + AF+++ A AA
Sbjct: 4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 63
Query: 266 VEHSFNKVILGGRRLNIKWGR 286
++ + N+ L GR + + +
Sbjct: 64 ID-NMNESELFGRTIRVNLAK 83
>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 = 29.6 bits (65), Expect = 2.3, Method: Composition-based stats.
Identities = 21/81 (25%), Positives = 39/81 (48%), Gaps = 7/81 (8%)
Query: 212 TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAA 265
T LYVG L +++ ++ L F FG+I + I + AF+++ A AA
Sbjct: 6 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 65
Query: 266 VEHSFNKVILGGRRLNIKWGR 286
++ + N+ L GR + + +
Sbjct: 66 ID-NMNESELFGRTIRVNLAK 85
>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 = 29.3 bits (64), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 42/80 (52%), Gaps = 7/80 (8%)
Query: 213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTI----LSKQQC--AFIQYTSRPAAEAAV 266
+ +LYVG+L +TE L + F G I S+ + ++++ A++ + AE A+
Sbjct: 10 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL 69
Query: 267 EHSFNKVILGGRRLNIKWGR 286
+ + N ++ G+ + I W +
Sbjct: 70 D-TMNFDVIKGKPVRIMWSQ 88
>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
pdb|3S7R|B Chain B, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
Length = 87
Score = 29.3 bits (64), Expect = 2.9, Method: Composition-based stats.
Identities = 12/29 (41%), Positives = 20/29 (68%)
Query: 217 YVGNLGDKLTEQDLRDHFYQFGEIRSVTI 245
+VG L +++DL+D+F +FGE+ TI
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTI 43
>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 = 29.3 bits (64), Expect = 3.3, Method: Composition-based stats.
Identities = 20/73 (27%), Positives = 37/73 (50%), Gaps = 7/73 (9%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEHS 269
LYVG L +++ ++ L F FG+I + I + AF+++ A AA++ +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID-N 63
Query: 270 FNKVILGGRRLNI 282
N+ L GR + +
Sbjct: 64 MNESELFGRTIRV 76
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 28.9 bits (63), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 1/64 (1%)
Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-CAFIQYTSRPAAEA 264
D +++ TL NL K+T+ +L++ F EIR V+ K + A+I++ + AE
Sbjct: 86 DSKKERDARTLLAKNLPYKVTQDELKEVFEDAAEIRLVSKDGKSKGIAYIEFKTEADAEK 145
Query: 265 AVEH 268
E
Sbjct: 146 TFEE 149
>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 = 28.9 bits (63), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-CAFIQYTSRPAAEAAVEH 268
TL NL +TE +L++ F EIR V+ K + A+I++ S AE +E
Sbjct: 101 TLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEE 155
>pdb|1F89|A Chain A, Crystal Structure Of Saccharomyces Cerevisiae Nit3, A
Member Of Branch 10 Of The Nitrilase Superfamily
pdb|1F89|B Chain B, Crystal Structure Of Saccharomyces Cerevisiae Nit3, A
Member Of Branch 10 Of The Nitrilase Superfamily
Length = 291
Score = 28.5 bits (62), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 22/42 (52%)
Query: 194 KLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFY 235
K++ T+P+LDP DK T + N KL ++ + H +
Sbjct: 91 KIILVGGTIPELDPKTDKIYNTSIIFNEDGKLIDKHRKVHLF 132
>pdb|4II1|A Chain A, Crystal Structure Of The Zinc Finger Of Zgpat
pdb|4II1|B Chain B, Crystal Structure Of The Zinc Finger Of Zgpat
pdb|4II1|C Chain C, Crystal Structure Of The Zinc Finger Of Zgpat
pdb|4II1|D Chain D, Crystal Structure Of The Zinc Finger Of Zgpat
Length = 167
Score = 28.5 bits (62), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 137 PYYKRNRPHICSFWVKGECRRGEECPYRHEKPTDPDD--PLADQNIK 181
P +K +P C F+++G+CR E C + H + D+ P D ++
Sbjct: 71 PTHKSLKP--CPFFLEGKCRFKENCRFSHGQVVSLDELRPFQDPDLS 115
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 28.5 bits (62), Expect = 5.8, Method: Composition-based stats.
Identities = 14/64 (21%), Positives = 30/64 (46%), Gaps = 6/64 (9%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEHS 269
++VG L T +D++ +F QFG++ ++ + F+ + S E E
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 270 FNKV 273
F+++
Sbjct: 62 FHEI 65
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 28.1 bits (61), Expect = 6.2, Method: Composition-based stats.
Identities = 11/30 (36%), Positives = 19/30 (63%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTI 245
++VG +TE +LR+ F Q+G++ V I
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFI 37
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 28.1 bits (61), Expect = 7.1, Method: Composition-based stats.
Identities = 14/32 (43%), Positives = 20/32 (62%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTI 245
+ L V L K TEQDL+++F FGE+ V +
Sbjct: 16 SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQV 47
>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 = 28.1 bits (61), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 27/124 (21%), Positives = 54/124 (43%), Gaps = 21/124 (16%)
Query: 166 EKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLGDKL 225
EKP+ D+ + Q+I D K++ +P+ +DKT ++VG +G +
Sbjct: 53 EKPSSVDEVVKTQHILD----------GKVIDPKRAIPR--DEQDKT-GKIFVGGIGPDV 99
Query: 226 TEQDLRDHFYQFGEIRSVTIL------SKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRR 279
++ + F Q+G I ++ + F+ Y S A + ++ F + R+
Sbjct: 100 RPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKF--IDFKDRK 157
Query: 280 LNIK 283
+ IK
Sbjct: 158 IEIK 161
>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 = 27.7 bits (60), Expect = 8.7, Method: Composition-based stats.
Identities = 17/66 (25%), Positives = 34/66 (51%), Gaps = 7/66 (10%)
Query: 208 PEDKTITTLYVGNLGDKLTEQDLRDH----FYQFGEIRSVTI---LSKQQCAFIQYTSRP 260
PE + T+Y+ NL +K+ + +L+ F +FG+I + + L + AF+ +
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVS 62
Query: 261 AAEAAV 266
+A A+
Sbjct: 63 SATNAL 68
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 27.7 bits (60), Expect = 8.9, Method: Composition-based stats.
Identities = 22/66 (33%), Positives = 33/66 (50%), Gaps = 4/66 (6%)
Query: 206 DPPEDKTIT---TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-CAFIQYTSRPA 261
DP K + TL NL +TE +L++ F EIR V+ K + A+I++ S
Sbjct: 6 DPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEAD 65
Query: 262 AEAAVE 267
AE +E
Sbjct: 66 AEKNLE 71
>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 = 27.7 bits (60), Expect = 9.3, Method: Composition-based stats.
Identities = 11/36 (30%), Positives = 21/36 (58%), Gaps = 4/36 (11%)
Query: 215 TLYVGNLGDKLTEQDLRDHFY----QFGEIRSVTIL 246
T+Y+ N+ DK+ +++L+ Y QFG + + L
Sbjct: 8 TIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVAL 43
>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 = 27.7 bits (60), Expect = 9.8, Method: Composition-based stats.
Identities = 17/66 (25%), Positives = 34/66 (51%), Gaps = 7/66 (10%)
Query: 208 PEDKTITTLYVGNLGDKLTEQDLRDH----FYQFGEIRSVTI---LSKQQCAFIQYTSRP 260
PE + T+Y+ NL +K+ + +L+ F +FG+I + + L + AF+ +
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVS 62
Query: 261 AAEAAV 266
+A A+
Sbjct: 63 SATNAL 68
>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 = 27.7 bits (60), Expect = 9.9, Method: Composition-based stats.
Identities = 17/66 (25%), Positives = 34/66 (51%), Gaps = 7/66 (10%)
Query: 208 PEDKTITTLYVGNLGDKLTEQDLRDH----FYQFGEIRSVTI---LSKQQCAFIQYTSRP 260
PE + T+Y+ NL +K+ + +L+ F +FG+I + + L + AF+ +
Sbjct: 4 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVS 63
Query: 261 AAEAAV 266
+A A+
Sbjct: 64 SATNAL 69
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.318 0.134 0.409
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,703,548
Number of Sequences: 62578
Number of extensions: 395180
Number of successful extensions: 921
Number of sequences better than 100.0: 139
Number of HSP's better than 100.0 without gapping: 76
Number of HSP's successfully gapped in prelim test: 63
Number of HSP's that attempted gapping in prelim test: 818
Number of HSP's gapped (non-prelim): 155
length of query: 327
length of database: 14,973,337
effective HSP length: 99
effective length of query: 228
effective length of database: 8,778,115
effective search space: 2001410220
effective search space used: 2001410220
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)