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= 048750
(344 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 = 84.0 bits (206), Expect = 1e-16, Method: Composition-based stats.
Identities = 38/78 (48%), Positives = 55/78 (70%)
Query: 190 EDESIKTLYVGGVDARITEQDLRDNFYAHGEIESIKMHPQKAFAFVTYTTREGAEKAAEE 249
ED++I TLYVGG+ ITE DLR++FY GEI +I + ++ AF+ + TR+ AE AAE+
Sbjct: 8 EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEK 67
Query: 250 LSNKLVIKGLRLKLMWGK 267
NKL++ G RL + WG+
Sbjct: 68 SFNKLIVNGRRLNVKWGR 85
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 56.6 bits (135), Expect = 2e-08, Method: Composition-based stats.
Identities = 29/83 (34%), Positives = 46/83 (55%), Gaps = 1/83 (1%)
Query: 196 TLYVGGVDARITEQDLRDNFYAHGEIESIKMHPQKAFAFVTYTTREGAEKAAEELSNKLV 255
T+Y GG+ + +T+Q +R F G+I I++ P+K ++FV ++T E A A + N
Sbjct: 27 TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSV-NGTT 85
Query: 256 IKGLRLKLMWGKPQTQRPEGESS 278
I+G +K WGK G SS
Sbjct: 86 IEGHVVKCYWGKESPDMTSGPSS 108
>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 = 48.1 bits (113), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 36/138 (26%), Positives = 62/138 (44%), Gaps = 14/138 (10%)
Query: 129 VCSFYVRGECTRGAECPYRHEMPVTGELSQQNIKDRYYGVNDPVAL-KLLNKAGEMPSLE 187
C F+ +G C G +C Y H +P ++ + ++ V D K + +M +
Sbjct: 74 FCLFFAKGMCCLGPKCEYLHHIPDEEDIGKLALRTE---VLDCFGREKFADYREDMGGIG 130
Query: 188 PPEDESIKTLYVGGVDARIT---------EQDLRDNFYAHGEIESIKMHPQKAFAFVTYT 238
++ KTLYVGG+D + E +R F G+I+ I+ K FV +
Sbjct: 131 SFRKKN-KTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFK 189
Query: 239 TREGAEKAAEELSNKLVI 256
+ AE A E +SN+ ++
Sbjct: 190 YQANAEFAKEAMSNQTLL 207
>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 = 47.8 bits (112), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 36/138 (26%), Positives = 62/138 (44%), Gaps = 14/138 (10%)
Query: 129 VCSFYVRGECTRGAECPYRHEMPVTGELSQQNIKDRYYGVNDPVAL-KLLNKAGEMPSLE 187
C F+ +G C G +C Y H +P ++ + ++ V D K + +M +
Sbjct: 72 FCLFFAKGMCCLGPKCEYLHHIPDEEDIGKLALRTE---VLDCFGREKFADYREDMGGIG 128
Query: 188 PPEDESIKTLYVGGVDARIT---------EQDLRDNFYAHGEIESIKMHPQKAFAFVTYT 238
++ KTLYVGG+D + E +R F G+I+ I+ K FV +
Sbjct: 129 SFRKKN-KTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFK 187
Query: 239 TREGAEKAAEELSNKLVI 256
+ AE A E +SN+ ++
Sbjct: 188 YQANAEFAKEAMSNQTLL 205
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 30/98 (30%), Positives = 55/98 (56%), Gaps = 5/98 (5%)
Query: 194 IKTLYVGGVDARITEQDLRDNFYAHGEIESIKMHPQKAFAFVTYTTREGAEKAAEELSNK 253
+K L+V + +TE+ L F G++E +K K +AF+ + R+GA KA EE++ K
Sbjct: 11 VKVLFVRNLANTVTEEILEKAFSQFGKLERVK--KLKDYAFIHFDERDGAVKAMEEMNGK 68
Query: 254 LVIKGLRLKLMWGKPQTQRPEGESSDEVRQQAAIAHSG 291
++G +++++ KP Q+ + + RQ A+ SG
Sbjct: 69 -DLEGENIEIVFAKPPDQKRKERKAQ--RQAASGPSSG 103
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESIKMHPQKAFAFVTYTTREGAEKAAEELSNKLVI 256
L+VG + ITE+++R F +G+ + +H K F F+ TR AE A EL N + +
Sbjct: 25 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDN-MPL 83
Query: 257 KGLRLKLMWG 266
+G +L++ +
Sbjct: 84 RGKQLRVRFA 93
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 31/84 (36%), Positives = 42/84 (50%), Gaps = 3/84 (3%)
Query: 195 KTLYVGGVDARITEQDLRDNFYAHGEIESIKMHPQKAFAFVTYTTREGAEKAAEELSNKL 254
TLYV G D +T LR F G I + M P + AFVTY E A++A EL N
Sbjct: 16 NTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAEL-NGT 72
Query: 255 VIKGLRLKLMWGKPQTQRPEGESS 278
++ ++LK+ + Q G SS
Sbjct: 73 QVESVQLKVNIARKQPMLDSGPSS 96
>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 = 43.1 bits (100), Expect = 2e-04, Method: Composition-based stats.
Identities = 26/82 (31%), Positives = 43/82 (52%), Gaps = 1/82 (1%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESIKMHPQKAFAFVTYTTREGAEKAAEELSNKLVI 256
L+VG + ITE+++R F +G+ + +H K F F+ TR AE A EL N + +
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDN-MPL 76
Query: 257 KGLRLKLMWGKPQTQRPEGESS 278
+G +L++ + G SS
Sbjct: 77 RGKQLRVRFACHSASLTSGPSS 98
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 42.0 bits (97), Expect = 5e-04, Method: Composition-based stats.
Identities = 25/83 (30%), Positives = 45/83 (54%), Gaps = 4/83 (4%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESIKM-HPQKAFAFVTYTTREGAEKAAEELSNKLV 255
++VG +TE +LR+ F +G++ + + P +AFAFVT+ + A+ E L+
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGE---DLI 64
Query: 256 IKGLRLKLMWGKPQTQRPEGESS 278
IKG+ + + +P+ G SS
Sbjct: 65 IKGISVHISNAEPKHNSNSGPSS 87
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 41.6 bits (96), Expect = 6e-04, Method: Composition-based stats.
Identities = 24/98 (24%), Positives = 49/98 (50%), Gaps = 9/98 (9%)
Query: 189 PEDESIKTLYVGGVDARITEQDLRDNFYAHGEIESIKMHPQK--------AFAFVTYTTR 240
P+ ++ + V + + ++++R+ F GE++++++ P+K F FV + T+
Sbjct: 10 PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRL-PKKMTGTGAHRGFGFVDFITK 68
Query: 241 EGAEKAAEELSNKLVIKGLRLKLMWGKPQTQRPEGESS 278
+ A+KA L + + G RL L W + G SS
Sbjct: 69 QDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSGPSS 106
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 41.2 bits (95), Expect = 8e-04, Method: Composition-based stats.
Identities = 24/61 (39%), Positives = 34/61 (55%), Gaps = 6/61 (9%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESIKMH------PQKAFAFVTYTTREGAEKAAEEL 250
LYVG + ITE LR F G IESI++ K + F+T++ E A+KA E+L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 251 S 251
+
Sbjct: 89 N 89
>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 = 41.2 bits (95), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 28/75 (37%), Positives = 39/75 (52%), Gaps = 3/75 (4%)
Query: 195 KTLYVGGVDARITEQDLRDNFYAHGEIESIKMHPQKAFAFVTYTTREGAEKAAEELSNKL 254
TLYV G D +T LR F G I + M P + AFVTY E A++A EL N
Sbjct: 40 NTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAEL-NGT 96
Query: 255 VIKGLRLKLMWGKPQ 269
++ ++LK+ + Q
Sbjct: 97 QVESVQLKVNIARKQ 111
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 34/98 (34%), Positives = 49/98 (50%), Gaps = 17/98 (17%)
Query: 206 ITEQDLRDNFYAHGEIESIKMHPQK------AFAFVTYTTREGAEKAAEELSNKLVIKGL 259
+T+ +LR F + GE+ES K+ K + FV Y T + AE+A L+ GL
Sbjct: 14 MTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLN------GL 67
Query: 260 RLKLMWGKPQTQRPEGESSDEVRQQAAIAHSGMLPRSL 297
RL+ K RP S EV + A + SG LPR++
Sbjct: 68 RLQSKTIKVSYARP----SSEVIKDANLYISG-LPRTM 100
>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 = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 34/98 (34%), Positives = 49/98 (50%), Gaps = 17/98 (17%)
Query: 206 ITEQDLRDNFYAHGEIESIKMHPQK------AFAFVTYTTREGAEKAAEELSNKLVIKGL 259
+T+ +LR F + GE+ES K+ K + FV Y T + AE+A L+ GL
Sbjct: 14 MTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLN------GL 67
Query: 260 RLKLMWGKPQTQRPEGESSDEVRQQAAIAHSGMLPRSL 297
RL+ K RP S EV + A + SG LPR++
Sbjct: 68 RLQSKTIKVSYARP----SSEVIKDANLYISG-LPRTM 100
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 27/80 (33%), Positives = 36/80 (45%), Gaps = 4/80 (5%)
Query: 188 PPEDESIKTLYVGGVDARITEQDLRDNFYAHGEIESIKMHPQKAFAFVTYTTREGAEKAA 247
PP + T Y+G + TE DL F G I K +P+K F+ Y T E A
Sbjct: 24 PPR---VTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCI 80
Query: 248 EELSNKLVIKGLRLKLMWGK 267
L+N +G L+ WGK
Sbjct: 81 VALAN-FPFQGRNLRTGWGK 99
>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 = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 36/67 (53%), Gaps = 4/67 (5%)
Query: 193 SIKTLYVGGVDARITEQDLRDNFYAHGEIESIKM----HPQKAFAFVTYTTREGAEKAAE 248
+ +++ +D I + L D F A G I S K+ + K + FV + T+E AE+A E
Sbjct: 102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIE 161
Query: 249 ELSNKLV 255
+++ L+
Sbjct: 162 KMNGMLL 168
Score = 36.2 bits (82), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 41/80 (51%), Gaps = 7/80 (8%)
Query: 194 IKTLYVGGVDARITEQDLRDNFYAHGEIESIKM------HPQKAFAFVTYTTREGAEKAA 247
+ +LYVG + +TE L + F G I SI++ +A+V + AE+A
Sbjct: 15 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL 74
Query: 248 EELSNKLVIKGLRLKLMWGK 267
+ + N VIKG +++MW +
Sbjct: 75 DTM-NFDVIKGKPVRIMWSQ 93
>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 = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 36/66 (54%), Gaps = 4/66 (6%)
Query: 194 IKTLYVGGVDARITEQDLRDNFYAHGEIESIKM----HPQKAFAFVTYTTREGAEKAAEE 249
+ +++ +D I + L D F A G I S K+ + K + FV + T+E AE+A E+
Sbjct: 98 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEK 157
Query: 250 LSNKLV 255
++ L+
Sbjct: 158 MNGMLL 163
Score = 35.4 bits (80), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 41/80 (51%), Gaps = 7/80 (8%)
Query: 194 IKTLYVGGVDARITEQDLRDNFYAHGEIESIKM------HPQKAFAFVTYTTREGAEKAA 247
+ +LYVG + +TE L + F G I SI++ +A+V + AE+A
Sbjct: 10 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL 69
Query: 248 EELSNKLVIKGLRLKLMWGK 267
+ + N VIKG +++MW +
Sbjct: 70 DTM-NFDVIKGKPVRIMWSQ 88
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 37/69 (53%), Gaps = 5/69 (7%)
Query: 195 KTLYVGGVDARITEQDLRDNFYAHGEIESIKM-----HPQKAFAFVTYTTREGAEKAAEE 249
+ L++G + + TE D+R F + G+IE ++ + AFVT+TTR A+ A +
Sbjct: 96 RKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKA 155
Query: 250 LSNKLVIKG 258
+ ++G
Sbjct: 156 MHQAQTMEG 164
Score = 36.2 bits (82), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 37/71 (52%), Gaps = 8/71 (11%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESIKMH-------PQ-KAFAFVTYTTREGAEKAAE 248
++VG V +E+DLR+ F +G + I + PQ K FVT+ TR+ A +A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 249 ELSNKLVIKGL 259
L N V+ G+
Sbjct: 66 ALHNMKVLPGM 76
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 37/69 (53%), Gaps = 5/69 (7%)
Query: 195 KTLYVGGVDARITEQDLRDNFYAHGEIESIKM-----HPQKAFAFVTYTTREGAEKAAEE 249
+ L++G + + TE D+R F + G+IE ++ + AFVT+TTR A+ A +
Sbjct: 108 RKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKA 167
Query: 250 LSNKLVIKG 258
+ ++G
Sbjct: 168 MHQAQTMEG 176
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 28/87 (32%), Positives = 46/87 (52%), Gaps = 9/87 (10%)
Query: 181 GEMPSLEPPEDESIKTLYVGGVDARITEQDLRDNFYAHGEIESIKMH-------PQ-KAF 232
G + + P+ ++IK ++VG V +E+DLR+ F +G + I + PQ K
Sbjct: 3 GTLDHPDQPDLDAIK-MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGC 61
Query: 233 AFVTYTTREGAEKAAEELSNKLVIKGL 259
FVT+ TR+ A +A L N V+ G+
Sbjct: 62 CFVTFYTRKAALEAQNALHNMKVLPGM 88
>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 = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 40/78 (51%), Gaps = 9/78 (11%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESIKMH------PQKAFAFVTYTTREGAEKAAEEL 250
+YVG + + E +R F G I+SI M K FAFV Y E A+ A E++
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 251 SNKLVIKGLRLKLMWGKP 268
N +++ G +K+ G+P
Sbjct: 76 -NSVMLGGRNIKV--GRP 90
>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 = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 6/67 (8%)
Query: 185 SLEPPEDESIKTLYVGGVDARITEQDLRDNFYAHGEIESIKMHP------QKAFAFVTYT 238
S P ++K ++VGG+ E LRD F +G+IE I++ ++ FAFVT+
Sbjct: 95 SQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFD 154
Query: 239 TREGAEK 245
+ +K
Sbjct: 155 DHDSVDK 161
Score = 37.7 bits (86), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 45/95 (47%), Gaps = 6/95 (6%)
Query: 185 SLEPPEDESIKTLYVGGVDARITEQDLRDNFYAHGEI-ESIKMHP-----QKAFAFVTYT 238
S P E E ++ L++GG+ T++ LR +F G + + + M + F FVTY
Sbjct: 4 SESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA 63
Query: 239 TREGAEKAAEELSNKLVIKGLRLKLMWGKPQTQRP 273
T E + A +K+ + + K + +QRP
Sbjct: 64 TVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP 98
>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 = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 6/67 (8%)
Query: 185 SLEPPEDESIKTLYVGGVDARITEQDLRDNFYAHGEIESIKMHP------QKAFAFVTYT 238
S P ++K ++VGG+ E LRD F +G+IE I++ ++ FAFVT+
Sbjct: 88 SQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFD 147
Query: 239 TREGAEK 245
+ +K
Sbjct: 148 DHDSVDK 154
Score = 34.3 bits (77), Expect = 0.093, Method: Compositional matrix adjust.
Identities = 24/90 (26%), Positives = 43/90 (47%), Gaps = 6/90 (6%)
Query: 190 EDESIKTLYVGGVDARITEQDLRDNFYAHGEI-ESIKMHP-----QKAFAFVTYTTREGA 243
E E ++ L++GG+ T++ LR +F G + + + M + F FVTY T E
Sbjct: 2 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 61
Query: 244 EKAAEELSNKLVIKGLRLKLMWGKPQTQRP 273
+ A +K+ + + K + +QRP
Sbjct: 62 DAAMNARPHKVDGRVVEPKRAVSREDSQRP 91
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 6/67 (8%)
Query: 185 SLEPPEDESIKTLYVGGVDARITEQDLRDNFYAHGEIESIKMHP------QKAFAFVTYT 238
S P ++K ++VGG+ E LRD F +G+IE I++ ++ FAFVT+
Sbjct: 96 SQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFD 155
Query: 239 TREGAEK 245
+ +K
Sbjct: 156 DHDSVDK 162
Score = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 27/99 (27%), Positives = 46/99 (46%), Gaps = 6/99 (6%)
Query: 181 GEMPSLEPPEDESIKTLYVGGVDARITEQDLRDNFYAHGEI-ESIKMHP-----QKAFAF 234
G S P E E ++ L++GG+ T++ LR +F G + + + M + F F
Sbjct: 1 GGSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF 60
Query: 235 VTYTTREGAEKAAEELSNKLVIKGLRLKLMWGKPQTQRP 273
VTY T E + A +K+ + + K + +QRP
Sbjct: 61 VTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP 99
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 6/67 (8%)
Query: 185 SLEPPEDESIKTLYVGGVDARITEQDLRDNFYAHGEIESIKMHP------QKAFAFVTYT 238
S P ++K ++VGG+ E LRD F +G+IE I++ ++ FAFVT+
Sbjct: 93 SQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFD 152
Query: 239 TREGAEK 245
+ +K
Sbjct: 153 DHDSVDK 159
Score = 37.4 bits (85), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 45/95 (47%), Gaps = 6/95 (6%)
Query: 185 SLEPPEDESIKTLYVGGVDARITEQDLRDNFYAHGEI-ESIKMHP-----QKAFAFVTYT 238
S P E E ++ L++GG+ T++ LR +F G + + + M + F FVTY
Sbjct: 2 SESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA 61
Query: 239 TREGAEKAAEELSNKLVIKGLRLKLMWGKPQTQRP 273
T E + A +K+ + + K + +QRP
Sbjct: 62 TVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP 96
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 6/67 (8%)
Query: 185 SLEPPEDESIKTLYVGGVDARITEQDLRDNFYAHGEIESIKMHP------QKAFAFVTYT 238
S P ++K ++VGG+ E LRD F +G+IE I++ ++ FAFVT+
Sbjct: 95 SQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFD 154
Query: 239 TREGAEK 245
+ +K
Sbjct: 155 DHDSVDK 161
Score = 37.4 bits (85), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 45/95 (47%), Gaps = 6/95 (6%)
Query: 185 SLEPPEDESIKTLYVGGVDARITEQDLRDNFYAHGEI-ESIKMHP-----QKAFAFVTYT 238
S P E E ++ L++GG+ T++ LR +F G + + + M + F FVTY
Sbjct: 4 SESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA 63
Query: 239 TREGAEKAAEELSNKLVIKGLRLKLMWGKPQTQRP 273
T E + A +K+ + + K + +QRP
Sbjct: 64 TVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP 98
>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 = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 6/67 (8%)
Query: 185 SLEPPEDESIKTLYVGGVDARITEQDLRDNFYAHGEIESIKMHP------QKAFAFVTYT 238
S P ++K ++VGG+ E LRD F +G+IE I++ ++ FAFVT+
Sbjct: 94 SQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFD 153
Query: 239 TREGAEK 245
+ +K
Sbjct: 154 DHDSVDK 160
Score = 37.4 bits (85), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 45/95 (47%), Gaps = 6/95 (6%)
Query: 185 SLEPPEDESIKTLYVGGVDARITEQDLRDNFYAHGEI-ESIKMHP-----QKAFAFVTYT 238
S P E E ++ L++GG+ T++ LR +F G + + + M + F FVTY
Sbjct: 3 SESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA 62
Query: 239 TREGAEKAAEELSNKLVIKGLRLKLMWGKPQTQRP 273
T E + A +K+ + + K + +QRP
Sbjct: 63 TVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP 97
>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 = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 40/78 (51%), Gaps = 9/78 (11%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESIKMH------PQKAFAFVTYTTREGAEKAAEEL 250
+YVG + + E +R F G I+SI M K FAFV Y E A+ A E++
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 251 SNKLVIKGLRLKLMWGKP 268
N +++ G +K+ G+P
Sbjct: 91 -NSVMLGGRNIKV--GRP 105
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 38.9 bits (89), Expect = 0.004, Method: Composition-based stats.
Identities = 24/79 (30%), Positives = 40/79 (50%), Gaps = 7/79 (8%)
Query: 181 GEMPSLEPPEDESIKTLYVGGVDARITEQDLRDNFYAHGEIESIKM----HPQKAFAFVT 236
G PSL + +++ +D I + L D F A G I S K+ + K + FV
Sbjct: 1 GADPSLR---KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVH 57
Query: 237 YTTREGAEKAAEELSNKLV 255
+ T+E AE+A E+++ L+
Sbjct: 58 FETQEAAERAIEKMNGMLL 76
>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 = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 5/57 (8%)
Query: 195 KTLYVGGVDARITEQDLRDNFYAHGEIESIKM-----HPQKAFAFVTYTTREGAEKA 246
+ L++G + + TE D+R F + G+IE ++ + AFVT+TTR A+ A
Sbjct: 96 RKLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTA 152
Score = 34.3 bits (77), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 35/69 (50%), Gaps = 8/69 (11%)
Query: 198 YVGGVDARITEQDLRDNFYAHGEIESIKMH-------PQ-KAFAFVTYTTREGAEKAAEE 249
+VG V +E+DLR+ F +G + I + PQ K FVT+ TR+ A +A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 250 LSNKLVIKG 258
L N V+ G
Sbjct: 67 LHNXKVLPG 75
>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D (Auf1) With Telomere Dna
pdb|1X0F|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D(Auf1) With Telomeric Dna
Length = 79
Score = 38.1 bits (87), Expect = 0.007, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 6/62 (9%)
Query: 194 IKTLYVGGVDARITEQDLRDNFYAHGEIESI------KMHPQKAFAFVTYTTREGAEKAA 247
+K ++VGG+ E+ +R+ F GE+ESI K + ++ F F+T+ E +K
Sbjct: 1 VKKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 60
Query: 248 EE 249
E+
Sbjct: 61 EK 62
>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
At Ph 6.0
pdb|4F26|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
A Ph 9.0
Length = 115
Score = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 35/64 (54%), Gaps = 4/64 (6%)
Query: 196 TLYVGGVDARITEQDLRDNFYAHGEIESIKM----HPQKAFAFVTYTTREGAEKAAEELS 251
+++ +D I + L D F A G I S K+ + K + FV + T+E AE+A E+++
Sbjct: 7 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 66
Query: 252 NKLV 255
L+
Sbjct: 67 GMLL 70
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 27/96 (28%), Positives = 43/96 (44%), Gaps = 7/96 (7%)
Query: 184 PSLEPPEDESIKTLYVGGVDARITEQDLRDNFYAHGEIESIKM------HPQKAFAFVTY 237
P+ PE + ++ L V + + E LR F +G IES+K+ + + FV +
Sbjct: 32 PTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKF 91
Query: 238 TTREGAEKAAEELSNKLVIKGLRLKLMWGKPQTQRP 273
+ A++A L N I RLK+ QRP
Sbjct: 92 QSGSSAQQAIAGL-NGFNILNKRLKVALAASGHQRP 126
>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 = 38.1 bits (87), Expect = 0.007, Method: Composition-based stats.
Identities = 21/63 (33%), Positives = 34/63 (53%), Gaps = 6/63 (9%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESIKMHPQ------KAFAFVTYTTREGAEKAAEEL 250
L+V GV TE+D+ D F +GEI++I ++ K + V Y T + A+ A E L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 251 SNK 253
+ +
Sbjct: 70 NGQ 72
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 38.1 bits (87), Expect = 0.008, Method: Composition-based stats.
Identities = 27/94 (28%), Positives = 47/94 (50%), Gaps = 3/94 (3%)
Query: 185 SLEPPEDESIKTLYVGGVDARITEQDLRDNFYAHGEIESIKMHPQKAFAFVTYTTREGAE 244
S +P +K L+V + +TE+ L +F G++E +K K +AFV + R A
Sbjct: 6 SGDPEVMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVK--KLKDYAFVHFEDRGAAV 63
Query: 245 KAAEELSNKLVIKGLRLKLMWGKPQTQRPEGESS 278
KA +E++ K + ++ KP ++ G SS
Sbjct: 64 KAMDEMNGKEIEGEEIEIVL-AKPPDKKRSGPSS 96
>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 = 37.7 bits (86), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 34/63 (53%), Gaps = 6/63 (9%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESIKMHPQ------KAFAFVTYTTREGAEKAAEEL 250
L+V GV TE+D+ D F +GEI++I ++ K + V Y T + A+ A E L
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 251 SNK 253
+ +
Sbjct: 86 NGQ 88
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 37.4 bits (85), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 40/88 (45%), Gaps = 6/88 (6%)
Query: 195 KTLYVGGVDARITEQDLRDNFYAHGEIESIKMHPQK-----AFAFVTYTTREGAEKAAEE 249
+ LYVG +D ITE L+ F G I +IK+ K +AFV Y A A +
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQT 60
Query: 250 LSNKLVIKGLRLKLMWGKPQTQRPEGES 277
L+ K + + +K+ W Q ++
Sbjct: 61 LNGKQIENNI-VKINWAFQSQQSSSDDT 87
>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 = 37.4 bits (85), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 34/63 (53%), Gaps = 6/63 (9%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESIKMHPQ------KAFAFVTYTTREGAEKAAEEL 250
L+V GV TE+D+ D F +GEI++I ++ K + V Y T + A+ A E L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 251 SNK 253
+ +
Sbjct: 70 NGQ 72
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 37.4 bits (85), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 34/63 (53%), Gaps = 6/63 (9%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESIKMHPQ------KAFAFVTYTTREGAEKAAEEL 250
L+V GV TE+D+ D F +GEI++I ++ K + V Y T + A+ A E L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 251 SNK 253
+ +
Sbjct: 70 NGQ 72
>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 = 37.4 bits (85), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 34/63 (53%), Gaps = 6/63 (9%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESIKMHPQ------KAFAFVTYTTREGAEKAAEEL 250
L+V GV TE+D+ D F +GEI++I ++ K + V Y T + A+ A E L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 251 SNK 253
+ +
Sbjct: 72 NGQ 74
>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 = 21/63 (33%), Positives = 34/63 (53%), Gaps = 6/63 (9%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESIKMHPQ------KAFAFVTYTTREGAEKAAEEL 250
L+V GV TE+D+ D F +GEI++I ++ K + V Y T + A+ A E L
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 251 SNK 253
+ +
Sbjct: 85 NGQ 87
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 37.4 bits (85), Expect = 0.013, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 37/73 (50%), Gaps = 8/73 (10%)
Query: 196 TLYVGGVDARITEQDLRDNFYAHGEIESIKMHP-----QKAFAFVTYTTREGAEKAAEEL 250
T++VGG+D R+ E ++R F +G ++ +K+ K + FV++ +K E
Sbjct: 12 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQ 71
Query: 251 SNKLVIKGLRLKL 263
N G +LKL
Sbjct: 72 IN---FHGKKLKL 81
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 37.0 bits (84), Expect = 0.017, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 37/73 (50%), Gaps = 8/73 (10%)
Query: 196 TLYVGGVDARITEQDLRDNFYAHGEIESIKMHP-----QKAFAFVTYTTREGAEKAAEEL 250
T++VGG+D R+ E ++R F +G ++ +K+ K + FV++ +K E
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 251 SNKLVIKGLRLKL 263
N G +LKL
Sbjct: 71 IN---FHGKKLKL 80
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 37.0 bits (84), Expect = 0.017, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 33/61 (54%), Gaps = 6/61 (9%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESIKMHP------QKAFAFVTYTTREGAEKAAEEL 250
LYVG + ITE LR F G+I++I + K + F+T++ E A +A E+L
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 251 S 251
+
Sbjct: 68 N 68
>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 = 37.0 bits (84), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 37/72 (51%), Gaps = 8/72 (11%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESIKMH-------PQ-KAFAFVTYTTREGAEKAAE 248
++VG V +E+DLR+ F +G + I + PQ K FVT+ TR+ A +A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 249 ELSNKLVIKGLR 260
L N V+ G+
Sbjct: 66 ALHNMKVLPGMH 77
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 36.6 bits (83), Expect = 0.019, Method: Composition-based stats.
Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 4/78 (5%)
Query: 195 KTLYVGGVDARITEQDLRDNFYAHGEIESI---KMHPQKAFAFVTYTTREGAEKAAEELS 251
KTL+V G+ TE+ L+++F + + K F FV + + E A KAA+E
Sbjct: 16 KTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDA-KAAKEAM 74
Query: 252 NKLVIKGLRLKLMWGKPQ 269
I G ++ L W KP+
Sbjct: 75 EDGEIDGNKVTLDWAKPK 92
>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 = 36.6 bits (83), Expect = 0.021, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 37/73 (50%), Gaps = 8/73 (10%)
Query: 196 TLYVGGVDARITEQDLRDNFYAHGEIESIKMHP-----QKAFAFVTYTTREGAEKAAEEL 250
T++VGG+D R+ E ++R F +G ++ +K+ K + FV++ +K E
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 251 SNKLVIKGLRLKL 263
N G +LKL
Sbjct: 71 IN---FHGKKLKL 80
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 36.6 bits (83), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 31/59 (52%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESIKMHPQKAFAFVTYTTREGAEKAAEELSNKLV 255
L+VG + ITE+D + F +GE + ++ + F F+ +R AE A EL ++
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTIL 83
>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 = 36.2 bits (82), Expect = 0.027, Method: Composition-based stats.
Identities = 18/64 (28%), Positives = 35/64 (54%), Gaps = 6/64 (9%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIE--SIKMHP----QKAFAFVTYTTREGAEKAAEEL 250
+++GG+ T++DL+D F GE+ ++K+ P + F FV + E +K ++
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 251 SNKL 254
+KL
Sbjct: 62 EHKL 65
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 35.8 bits (81), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 33/62 (53%), Gaps = 5/62 (8%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESI-----KMHPQKAFAFVTYTTREGAEKAAEELS 251
L++GG++ E+ L+ F HG I + + + FAF+T+ A+ AA++++
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 252 NK 253
K
Sbjct: 70 GK 71
>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 = 35.8 bits (81), Expect = 0.035, Method: Composition-based stats.
Identities = 24/78 (30%), Positives = 40/78 (51%), Gaps = 7/78 (8%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESIKMHPQK------AFAFVTYTTREGAEKAAEEL 250
L V + +T+ +LR F + GE+ES K+ K + FV Y T + AE+A L
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 251 SNKLVIKGLRLKLMWGKP 268
N L ++ +K+ + +P
Sbjct: 67 -NGLRLQSKTIKVSYARP 83
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 35.8 bits (81), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 28/97 (28%), Positives = 41/97 (42%), Gaps = 7/97 (7%)
Query: 188 PPEDESIKTLYVGGVDARITEQDLRDNFYAHGEIESIKMHP------QKAFAFVTYTTRE 241
P +D L+VG + + EQDL+ F G I + + K AF+TY R+
Sbjct: 9 PMKDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARD 68
Query: 242 GAEKAAEELSNKLVIKGLRLKLMWGKPQTQRPEGESS 278
A KA L + + G+ + KP GES
Sbjct: 69 SALKAQSALHEQKTLPGMNRPIQV-KPAASEGRGESG 104
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 35.8 bits (81), Expect = 0.039, Method: Composition-based stats.
Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 6/59 (10%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESI------KMHPQKAFAFVTYTTREGAEKAAEE 249
++VGG+ E+ +R+ F GE+ESI K + ++ F F+T+ E +K E+
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
>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 = 35.8 bits (81), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 10/77 (12%)
Query: 195 KTLYVGGVDARITEQDLRDNFYAHGEIESIKM-------HPQKAFAFVTYTTREGAEKAA 247
+++YVG VD T QDL +F + G I I + HP K +A++ + R + A
Sbjct: 37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHP-KGYAYIEFAERNSVDAAV 95
Query: 248 EELSNKLVIKGLRLKLM 264
++ V +G +K++
Sbjct: 96 A--MDETVFRGRTIKVL 110
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 35.4 bits (80), Expect = 0.047, Method: Composition-based stats.
Identities = 24/90 (26%), Positives = 42/90 (46%), Gaps = 7/90 (7%)
Query: 195 KTLYVGGVDARITEQDLRDNFYAHGEIESIKM------HPQKAFAFVTYTTREGAEKAAE 248
+ LYVGG+ + ++ L F G+I I++ + FAFV + E A A +
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
Query: 249 ELSNKLVIKGLRLKLMWGKPQTQRPEGESS 278
+ N+ + G +++ KP + G SS
Sbjct: 73 NM-NESELFGRTIRVNLAKPMRIKESGPSS 101
>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 = 35.4 bits (80), Expect = 0.047, Method: Composition-based stats.
Identities = 22/68 (32%), Positives = 36/68 (52%), Gaps = 7/68 (10%)
Query: 207 TEQDLRDNFYAHGEIESIKMHPQK------AFAFVTYTTREGAEKAAEELSNKLVIKGLR 260
T+ +LR F + GE+ES K+ K + FV Y T + AE+A L N L ++
Sbjct: 32 TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL-NGLRLQSKT 90
Query: 261 LKLMWGKP 268
+K+ + +P
Sbjct: 91 IKVSYARP 98
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 35.4 bits (80), Expect = 0.048, Method: Composition-based stats.
Identities = 22/78 (28%), Positives = 44/78 (56%), Gaps = 6/78 (7%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESIKM-HPQKAFAFVTYTTREGAEKAAEELSNK-L 254
++VG +T ++L+ F +GE+ + + P +AFAFVT+ +K A+ L + L
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFAD----DKVAQSLCGEDL 69
Query: 255 VIKGLRLKLMWGKPQTQR 272
+IKG+ + + +P+ +
Sbjct: 70 IIKGISVHISNAEPKHNK 87
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 35.0 bits (79), Expect = 0.057, Method: Composition-based stats.
Identities = 23/85 (27%), Positives = 41/85 (48%)
Query: 194 IKTLYVGGVDARITEQDLRDNFYAHGEIESIKMHPQKAFAFVTYTTREGAEKAAEELSNK 253
+ LY+G + +T DLR F + ++ + +AFV Y + A +A E LS K
Sbjct: 8 MNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGK 67
Query: 254 LVIKGLRLKLMWGKPQTQRPEGESS 278
+ + G +++ + + R G SS
Sbjct: 68 VELHGKIMEVDYSVSKKLRSSGPSS 92
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 35.0 bits (79), Expect = 0.064, Method: Composition-based stats.
Identities = 30/97 (30%), Positives = 45/97 (46%), Gaps = 8/97 (8%)
Query: 187 EPPEDESIKTLYVGGVDARITEQDLRDNFYAHGEIE--SIKMHP---QKAFAFVTYTTRE 241
+PP S + L+VG ++ + +E D+R F A G IE +I P K AFV Y++
Sbjct: 11 QPP---SHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHA 67
Query: 242 GAEKAAEELSNKLVIKGLRLKLMWGKPQTQRPEGESS 278
A+ A L + G L+ T + G SS
Sbjct: 68 EAQAAINALHGSQTMPGASSSLVVKFADTDKESGPSS 104
>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 = 35.0 bits (79), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 31/111 (27%), Positives = 46/111 (41%), Gaps = 18/111 (16%)
Query: 196 TLYVGGVDARITEQDLRDNFYAHGEIESIKMHPQK------AFAFVTYTTREGAEKA--- 246
TLYVG + TE+ + + F G+I+ I M K F FV Y +R AE A
Sbjct: 41 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100
Query: 247 --AEELSNKLV----IKGLRLKLMWGKPQTQRPEGESSDEVRQQAAIAHSG 291
L ++++ G + +G+ R G+ DE RQ G
Sbjct: 101 INGTRLDDRIIRTDWDAGFKEGRQYGRG---RSGGQVRDEYRQDYDAGRGG 148
>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 = 34.7 bits (78), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 37/78 (47%), Gaps = 9/78 (11%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESIKMH------PQKAFAFVTYTTREGAEKAAEEL 250
+YVG + + E +R F G I+SI K FAFV Y E A+ A E+
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ- 73
Query: 251 SNKLVIKGLRLKLMWGKP 268
N + + G +K+ G+P
Sbjct: 74 XNSVXLGGRNIKV--GRP 89
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 34.7 bits (78), Expect = 0.080, Method: Composition-based stats.
Identities = 21/56 (37%), Positives = 28/56 (50%), Gaps = 5/56 (8%)
Query: 196 TLYVGGVDARITEQDLRDNFYAHGEIESI-----KMHPQKAFAFVTYTTREGAEKA 246
TLYVG + TE+ + + F G+I+ I KM F FV Y +R AE A
Sbjct: 20 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENA 75
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 34.7 bits (78), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 43/83 (51%), Gaps = 9/83 (10%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESIKM------HPQKAFAFVTYTTREGAEKAAEEL 250
L V G+ TE+DLR+ F +G I + + + FAFV + + A K A+E
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA-KEAKER 76
Query: 251 SNKLVIKGLRLKLMWGKPQTQRP 273
+N + + G R+++ + T+RP
Sbjct: 77 ANGMELDGRRIRVDF--SITKRP 97
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 34.7 bits (78), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 43/83 (51%), Gaps = 9/83 (10%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESIKM------HPQKAFAFVTYTTREGAEKAAEEL 250
L V G+ TE+DLR+ F +G I + + + FAFV + + A K A+E
Sbjct: 15 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA-KEAKER 73
Query: 251 SNKLVIKGLRLKLMWGKPQTQRP 273
+N + + G R+++ + T+RP
Sbjct: 74 ANGMELDGRRIRVDFS--ITKRP 94
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 34.3 bits (77), Expect = 0.10, Method: Composition-based stats.
Identities = 24/88 (27%), Positives = 42/88 (47%), Gaps = 5/88 (5%)
Query: 195 KTLYVGGVDARITEQDLRDNFYAHGEIESIKM----HPQKAFAFVTYTTREGAEKAAEEL 250
K L+V + R + DLR F G+I +++ K F FVT+ A++A E+L
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKL 75
Query: 251 SNKLVIKGLRLKLMWGKPQTQRPEGESS 278
V++G ++++ + G SS
Sbjct: 76 HGT-VVEGRKIEVNNATARVMTNSGPSS 102
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 33.9 bits (76), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 43/84 (51%), Gaps = 9/84 (10%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESIKM------HPQKAFAFVTYTTREGAEKAAEEL 250
L V G+ TE+DLR+ F +G I + + + FAFV + + A K A+E
Sbjct: 49 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA-KEAKER 107
Query: 251 SNKLVIKGLRLKLMWGKPQTQRPE 274
+N + + G R+++ + T+RP
Sbjct: 108 ANGMELDGRRIRVDF--SITKRPH 129
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 33.5 bits (75), Expect = 0.18, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 4/65 (6%)
Query: 195 KTLYVGGVDARITEQDLRDNFYAHGEIESIKM----HPQKAFAFVTYTTREGAEKAAEEL 250
K L+V + R + DLR F G+I +++ K F FVT+ A++A E+L
Sbjct: 30 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKL 89
Query: 251 SNKLV 255
+V
Sbjct: 90 HGTVV 94
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 33.1 bits (74), Expect = 0.23, Method: Composition-based stats.
Identities = 20/88 (22%), Positives = 40/88 (45%), Gaps = 7/88 (7%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESIKM------HPQKAFAFVTYTTREGAEKAAEEL 250
++VG + IT +D++ F G+I ++ K + FV++ + AE A +
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 251 SNKLVIKGLRLKLMWGKPQTQRPEGESS 278
+ + G +++ W + P G SS
Sbjct: 78 GGQW-LGGRQIRTNWATRKPPAPSGPSS 104
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 33.1 bits (74), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 6/66 (9%)
Query: 190 EDESIKTLYVGGVDARITEQDLRDNFYAHGEIESI------KMHPQKAFAFVTYTTREGA 243
+D + ++VGG+ T+ LR F G+IE + + + FVT R A
Sbjct: 13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAA 72
Query: 244 EKAAEE 249
E+A ++
Sbjct: 73 ERACKD 78
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 32.7 bits (73), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 44/88 (50%), Gaps = 9/88 (10%)
Query: 186 LEPPEDESIK--TLYVGGVDARITEQDLRDNFYAHGEIESIKMHP------QKAFAFVTY 237
LEP S++ L+V + E ++++ F +GEI++I ++ K +A V Y
Sbjct: 16 LEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEY 75
Query: 238 TTREGAEKAAEELSNKLVIKGLRLKLMW 265
T + A AA+E N I G +++ W
Sbjct: 76 ETHKQA-LAAKEALNGAEIMGQTIQVDW 102
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 32.7 bits (73), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 36/78 (46%), Gaps = 10/78 (12%)
Query: 190 EDESIKTLYVGGVDARITEQDLRDNFYAHGEIESIK--------MHPQKAFAFVTYTTRE 241
+D L++G + + E+DL+ F G+I + MH K AF+TY RE
Sbjct: 9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMH--KGCAFLTYCERE 66
Query: 242 GAEKAAEELSNKLVIKGL 259
A KA L + + G+
Sbjct: 67 SALKAQSALHEQKTLPGM 84
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 32.7 bits (73), Expect = 0.32, Method: Composition-based stats.
Identities = 22/86 (25%), Positives = 43/86 (50%), Gaps = 14/86 (16%)
Query: 188 PPEDESIKTLYVGGVDARITEQDLRDNFYAHGEIESIKM-----HPQKAFAFVTYTTREG 242
P ++E+ +T++VG ++AR+ E+ L + F G + + + K+F FV + E
Sbjct: 10 PAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPES 69
Query: 243 AEKAAEELSNKLVIKGLRLKLMWGKP 268
A ++ G+RL +G+P
Sbjct: 70 VSYAIA------LLNGIRL---YGRP 86
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 32.7 bits (73), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 7/76 (9%)
Query: 195 KTLYVGGVDARITEQDLRDNFYAHGEIESIKM------HPQKAFAFVTYTTREGAEKAAE 248
+ LYVGG+ + ++ L F G+I I++ + FAFV + E A A +
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
Query: 249 ELS-NKLVIKGLRLKL 263
++ ++L + +R+ L
Sbjct: 124 NMNESELFGRTIRVNL 139
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 32.3 bits (72), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 6/72 (8%)
Query: 188 PPEDESIKTLYVGGVDARITEQDLRDNFYAHGEIESIKM------HPQKAFAFVTYTTRE 241
P D S+++++VG + TE+ L+D F G + S ++ K + F Y +E
Sbjct: 2 PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61
Query: 242 GAEKAAEELSNK 253
A A L+ +
Sbjct: 62 TALSAMRNLNGR 73
>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 = 32.3 bits (72), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 44/88 (50%), Gaps = 9/88 (10%)
Query: 186 LEPPEDESIK--TLYVGGVDARITEQDLRDNFYAHGEIESIKMHPQ------KAFAFVTY 237
LEP S++ L+V + E ++++ F +GEI++I ++ K +A V Y
Sbjct: 62 LEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEY 121
Query: 238 TTREGAEKAAEELSNKLVIKGLRLKLMW 265
T + A AA+E N I G +++ W
Sbjct: 122 ETHKQA-LAAKEALNGAEIMGQTIQVDW 148
>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 = 32.3 bits (72), Expect = 0.43, Method: Composition-based stats.
Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 7/78 (8%)
Query: 193 SIKTLYVGGVDARITEQDLRDNFYAHGEIESIKM------HPQKAFAFVTYTTREGAEKA 246
S + LYVGG+ + ++ L F G+I I++ + FAFV + E A A
Sbjct: 1 SKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 60
Query: 247 AEELS-NKLVIKGLRLKL 263
+ ++ ++L + +R+ L
Sbjct: 61 IDNMNESELFGRTIRVNL 78
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 32.0 bits (71), Expect = 0.45, Method: Composition-based stats.
Identities = 27/82 (32%), Positives = 40/82 (48%), Gaps = 4/82 (4%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESIKMHPQKAFAFVTYTTREGAEKAAEELSNKLVI 256
++VG V A T Q+LR F G + I+ K +AFV A+ A +L+ K V
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRV--IECDVVKDYAFVHMEKEADAKAAIAQLNGKEV- 68
Query: 257 KGLRLKLMWGKPQTQRPEGESS 278
KG R+ + + Q+ G SS
Sbjct: 69 KGKRINVELST-KGQKKSGPSS 89
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 32.0 bits (71), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 29/94 (30%), Positives = 44/94 (46%), Gaps = 13/94 (13%)
Query: 195 KTLYVGGVDARITEQDLRDNFYAHGE---------IESIKMHPQKAFAFVTYTTREGAEK 245
K LY+ + R+TE+DL F E + + +M Q AF+T+ +E A +
Sbjct: 26 KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQ---AFITFPNKEIAWQ 82
Query: 246 AAEELSNKLVIKGLRLKLMWGKPQTQRPEGESSD 279
A L N + G L + +GK + QR G SS
Sbjct: 83 AL-HLVNGYKLYGKILVIEFGKNKKQRSSGPSSG 115
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 32.0 bits (71), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 15/79 (18%)
Query: 196 TLYVGGVDARITEQDLRDNFYAHGEIESIKM------HPQKAFAFVTYTTREGAEKAAEE 249
T+YVGG+D +++E L + F G + + M + + FV + + E A+ A
Sbjct: 17 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA--- 73
Query: 250 LSNKLVIKGLRLKLMWGKP 268
IK + + ++GKP
Sbjct: 74 ------IKIMDMIKLYGKP 86
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 32.0 bits (71), Expect = 0.57, Method: Composition-based stats.
Identities = 29/89 (32%), Positives = 43/89 (48%), Gaps = 12/89 (13%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGE-------IESIKMHPQKAFAFVTYTTREGAEKAAEE 249
L+V + +E+DL F A+G I+S+ P K FAFVT+ E A KA E
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKP-KGFAFVTFMFPEHAVKAYAE 69
Query: 250 LSNKLVIKGLRLKLMWGKPQTQRPEGESS 278
+ + V +G L ++ P T + E S
Sbjct: 70 VDGQ-VFQGRMLHVL---PSTIKKEASQS 94
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 31.6 bits (70), Expect = 0.62, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 7/76 (9%)
Query: 195 KTLYVGGVDARITEQDLRDNFYAHGEIESIKM------HPQKAFAFVTYTTREGAEKAAE 248
+ LYVGG+ + ++ L F G+I I++ + FAFV + E A A +
Sbjct: 6 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65
Query: 249 ELS-NKLVIKGLRLKL 263
++ ++L + +R+ L
Sbjct: 66 NMNESELFGRTIRVNL 81
>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 = 31.6 bits (70), Expect = 0.62, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 7/76 (9%)
Query: 195 KTLYVGGVDARITEQDLRDNFYAHGEIESIKM------HPQKAFAFVTYTTREGAEKAAE 248
+ LYVGG+ + ++ L F G+I I++ + FAFV + E A A +
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
Query: 249 ELS-NKLVIKGLRLKL 263
++ ++L + +R+ L
Sbjct: 68 NMNESELFGRTIRVNL 83
>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 = 0.63, Method: Composition-based stats.
Identities = 24/81 (29%), Positives = 35/81 (43%), Gaps = 7/81 (8%)
Query: 196 TLYVGGVDARITEQDLRDNFYAHGEIESIKMHP------QKAFAFVTYTTREGAEKAAEE 249
T+ V + E DL++ F G I I + K FAF+++ RE A +A
Sbjct: 17 TIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAG 76
Query: 250 LSNKLVIKGLRLKLMWGKPQT 270
+S L L + W KP T
Sbjct: 77 VSG-FGYDHLILNVEWAKPST 96
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 31.6 bits (70), Expect = 0.63, Method: Composition-based stats.
Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 3/53 (5%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESIKMHPQKA---FAFVTYTTREGAEKA 246
+YVG + I +D+ D FY +G I I + ++ FAFV + AE A
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDA 77
>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 = 0.63, Method: Composition-based stats.
Identities = 21/84 (25%), Positives = 44/84 (52%), Gaps = 8/84 (9%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEI-ESIKMHP-----QKAFAFVTYTTREGAEKAAEEL 250
+++GG+ + T++ LR+ F GE+ E + M + F FVT+ + G +K +
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 87
Query: 251 SNKLVIKGLRLKLMWGKPQTQRPE 274
++L K + K+ + P+ +P+
Sbjct: 88 RHELDSKTIDPKVAF--PRRAQPK 109
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 31.6 bits (70), Expect = 0.68, Method: Composition-based stats.
Identities = 25/91 (27%), Positives = 42/91 (46%), Gaps = 10/91 (10%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESIKMHPQK---------AFAFVTYTTREGAEKAA 247
L++ ++ TE+ L+ F G I+S + +K F FV Y E A+KA
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 248 EELSNKLVIKGLRLKLMWGKPQTQRPEGESS 278
++L V G +L++ + T+ G SS
Sbjct: 68 KQLQGHTV-DGHKLEVRISERATKPASGPSS 97
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 31.6 bits (70), Expect = 0.72, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 7/73 (9%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESIKM------HPQKAFAFVTYTTREGAEKAAEEL 250
L V G+ TE+DLR+ F +G I + + + FAFV + + A K A+E
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA-KEAKER 76
Query: 251 SNKLVIKGLRLKL 263
+N + + G R+++
Sbjct: 77 ANGMELDGRRIRV 89
>pdb|2CQE|A Chain A, Solution Structure Of The Zinc-Finger Domain In Kiaa1064
Protein
Length = 98
Score = 31.2 bits (69), Expect = 0.77, Method: Composition-based stats.
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 126 RAHVCSFYVRGECTRGAECPYRH 148
+ +C FY+ G C R CPY H
Sbjct: 12 KRELCKFYITGFCARAENCPYMH 34
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 31.2 bits (69), Expect = 0.83, Method: Composition-based stats.
Identities = 17/64 (26%), Positives = 34/64 (53%), Gaps = 6/64 (9%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEI-ESIKMHP-----QKAFAFVTYTTREGAEKAAEEL 250
+++GG+ + T++ LR+ F GE+ E + M + F FVT+ + G +K +
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62
Query: 251 SNKL 254
++L
Sbjct: 63 RHEL 66
>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 = 31.2 bits (69), Expect = 0.83, Method: Composition-based stats.
Identities = 18/70 (25%), Positives = 34/70 (48%), Gaps = 6/70 (8%)
Query: 191 DESIKTLYVGGVDARITEQDLRDNFYAHGEIE--SIKMHPQ----KAFAFVTYTTREGAE 244
+E +VGG+ +++DL+D F GE+ +IK P + F F+ + E
Sbjct: 8 EEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVE 67
Query: 245 KAAEELSNKL 254
K ++ ++L
Sbjct: 68 KVLDQKEHRL 77
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 31.2 bits (69), Expect = 0.98, Method: Composition-based stats.
Identities = 22/68 (32%), Positives = 33/68 (48%), Gaps = 9/68 (13%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEI------ESIKMHPQKAFAFVTYTTREGAEKAAEEL 250
L V G+ + TEQDL++ F GE+ + +K K F FV +T E K +
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKV---M 74
Query: 251 SNKLVIKG 258
S + +I G
Sbjct: 75 SQRHMIDG 82
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 35/75 (46%), Gaps = 10/75 (13%)
Query: 189 PEDESIK--TLYVGGVDARITEQDLRDNFYAHGEI-------ESIKMHPQKAFAFVTYTT 239
P ESIK LYV + IT+ L F +G I + + P + AFV Y
Sbjct: 82 PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRP-RGVAFVRYNK 140
Query: 240 REGAEKAAEELSNKL 254
RE A++A L+N +
Sbjct: 141 REEAQEAISALNNVI 155
>pdb|2WBR|A Chain A, The Rrm Domain In Gw182 Proteins Contributes To Mirna-
Mediated Gene Silencing
Length = 89
Score = 30.8 bits (68), Expect = 1.2, Method: Composition-based stats.
Identities = 19/56 (33%), Positives = 26/56 (46%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESIKMHPQKAFAFVTYTTREGAEKAAEELSN 252
L + + A+I LR HG + S + + A YTTRE A KA L+N
Sbjct: 10 LLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQGIALCKYTTREEANKAQMALNN 65
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 30.8 bits (68), Expect = 1.3, Method: Composition-based stats.
Identities = 18/65 (27%), Positives = 30/65 (46%), Gaps = 6/65 (9%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESI------KMHPQKAFAFVTYTTREGAEKAAEEL 250
L+VGG+ EQ L F +G+I + + + F FVT+ + A+ A +
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 251 SNKLV 255
+ K V
Sbjct: 75 NGKSV 79
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 30.4 bits (67), Expect = 1.3, Method: Composition-based stats.
Identities = 23/89 (25%), Positives = 39/89 (43%), Gaps = 5/89 (5%)
Query: 195 KTLYVGGVDARITEQDLRDNFYAHGEIESIKM-----HPQKAFAFVTYTTREGAEKAAEE 249
+ L+VG + + T++D+R F G I+ + K AFV + T A+ A
Sbjct: 13 RKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINT 72
Query: 250 LSNKLVIKGLRLKLMWGKPQTQRPEGESS 278
L + + G L+ T++ G SS
Sbjct: 73 LHSSRTLPGASSSLVVKFADTEKESGPSS 101
>pdb|2CQ2|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Loc91801
Length = 114
Score = 30.4 bits (67), Expect = 1.5, Method: Composition-based stats.
Identities = 17/64 (26%), Positives = 32/64 (50%)
Query: 200 GGVDARITEQDLRDNFYAHGEIESIKMHPQKAFAFVTYTTREGAEKAAEELSNKLVIKGL 259
GG+ ++ L G ++++ M P K ++F Y T E +++A L+ K V+ L
Sbjct: 33 GGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDDL 92
Query: 260 RLKL 263
K+
Sbjct: 93 GQKI 96
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 30/56 (53%), Gaps = 6/56 (10%)
Query: 190 EDESIKTLYVGGVDARITEQDLRDNFYAHGEI-ESIKMHP-----QKAFAFVTYTT 239
E E + L++GG+ TE+ LR+ + G++ + + M + F FVT+++
Sbjct: 23 EKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSS 78
>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 = 30.4 bits (67), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 35/75 (46%), Gaps = 10/75 (13%)
Query: 189 PEDESIK--TLYVGGVDARITEQDLRDNFYAHGEI-------ESIKMHPQKAFAFVTYTT 239
P ESIK LYV + IT+ L F +G I + + P + AFV Y
Sbjct: 93 PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRP-RGVAFVRYNK 151
Query: 240 REGAEKAAEELSNKL 254
RE A++A L+N +
Sbjct: 152 REEAQEAISALNNVI 166
>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 = 1.6, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 35/75 (46%), Gaps = 10/75 (13%)
Query: 189 PEDESIK--TLYVGGVDARITEQDLRDNFYAHGEI-------ESIKMHPQKAFAFVTYTT 239
P ESIK LYV + IT+ L F +G I + + P + AFV Y
Sbjct: 6 PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRP-RGVAFVRYNK 64
Query: 240 REGAEKAAEELSNKL 254
RE A++A L+N +
Sbjct: 65 REEAQEAISALNNVI 79
>pdb|3THT|A Chain A, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing Trna
Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
pdb|3THT|B Chain B, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing Trna
Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
pdb|3THT|C Chain C, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing Trna
Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
pdb|3THT|D Chain D, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing Trna
Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
Length = 345
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 32/64 (50%)
Query: 200 GGVDARITEQDLRDNFYAHGEIESIKMHPQKAFAFVTYTTREGAEKAAEELSNKLVIKGL 259
GG+ ++ L G ++++ M P K ++F Y T E +++A L+ K V+ L
Sbjct: 26 GGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDDL 85
Query: 260 RLKL 263
K+
Sbjct: 86 GQKI 89
>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 = 2.3, Method: Compositional matrix adjust.
Identities = 22/96 (22%), Positives = 43/96 (44%), Gaps = 8/96 (8%)
Query: 189 PEDESIKTLYVGGVDARITEQDLRDNFYAHGEIESIKM------HPQKAFAFVTYTTREG 242
PE+ +T++ + ARI +DL D F A G++ +++ K A+V + +
Sbjct: 20 PEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQS 79
Query: 243 AEKAAEELSNKLVIKGLRLKLMWGKPQTQRPEGESS 278
A +L+ G+ + + + + R G SS
Sbjct: 80 VPLAIGLTGQRLL--GVPIIVQASQAEKNRLSGPSS 113
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 29.6 bits (65), Expect = 2.8, Method: Composition-based stats.
Identities = 17/64 (26%), Positives = 32/64 (50%), Gaps = 7/64 (10%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEI---ESIKMHP----QKAFAFVTYTTREGAEKAAEE 249
+++G +D I E+ L D F A G I I P K +AF+ + + + ++ A E
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 250 LSNK 253
++ +
Sbjct: 68 MNGQ 71
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 29.3 bits (64), Expect = 3.2, Method: Composition-based stats.
Identities = 19/88 (21%), Positives = 40/88 (45%), Gaps = 8/88 (9%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESIKM------HPQKAFAFVTYTTREGAEKAAEEL 250
++VGG+ E +LR+ F G + + M + F F+T+ + ++A
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMH 72
Query: 251 SNKLVIKGLRLKLMWGKPQTQRPEGESS 278
+ I G ++++ +P+ + G SS
Sbjct: 73 FHD--IMGKKVEVKRAEPRDSKSSGPSS 98
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 29.3 bits (64), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 37/82 (45%), Gaps = 3/82 (3%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESIKMHPQKAFAFVTYTTREGAEKAAEELSNKLVI 256
L+VG + T Q+LR F +G + I+ K +AFV E A +A L N
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPV--IECDIVKDYAFVHMERAEDAVEAIRGLDNT-EF 69
Query: 257 KGLRLKLMWGKPQTQRPEGESS 278
+G R+ + + + G SS
Sbjct: 70 QGKRMHVQLSTSRLRTASGPSS 91
>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 = 29.3 bits (64), Expect = 3.7, Method: Composition-based stats.
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 129 VCSFYVRGECTRGAECPYRHEMPVT 153
VC ++RG C +G +C + HE +T
Sbjct: 18 VCKHWLRGLCKKGDQCEFLHEYDMT 42
>pdb|2D9N|A Chain A, Solution Structure Of Ccch Type Zinc-Finger Domain 2 In
Cleavage And Polyadenylation Specificity Factor
Length = 77
Score = 28.9 bits (63), Expect = 4.1, Method: Composition-based stats.
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 129 VCSFYVRGECTRGAECPYRHEMPVT 153
VC ++RG C +G +C + HE +T
Sbjct: 12 VCKHWLRGLCKKGDQCEFLHEYDMT 36
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 28.9 bits (63), Expect = 4.2, Method: Composition-based stats.
Identities = 20/82 (24%), Positives = 40/82 (48%), Gaps = 3/82 (3%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESIKMHPQKAFAFVTYTTREGAEKAAEELSNKLVI 256
L++G + TEQ++R F +G++ ++ K + FV + AE A L + +
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKV--LECDIIKNYGFVHIEDKTAAEDAIRNL-HHYKL 67
Query: 257 KGLRLKLMWGKPQTQRPEGESS 278
G+ + + K +++ G SS
Sbjct: 68 HGVNINVEASKNKSKASSGPSS 89
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 28.9 bits (63), Expect = 4.7, Method: Composition-based stats.
Identities = 16/61 (26%), Positives = 34/61 (55%), Gaps = 7/61 (11%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESI-----KMHPQ--KAFAFVTYTTREGAEKAAEE 249
+++G + +T+ + + F +G+I+ I +MHP K +A+V + + AEKA +
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 250 L 250
+
Sbjct: 67 M 67
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 28.9 bits (63), Expect = 4.9, Method: Composition-based stats.
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 192 ESIKTLYVGGVDARITEQDLRDNFYAHGEI 221
+ I L+VGG+D T++ LR F +GE+
Sbjct: 14 DEIGKLFVGGLDWSTTQETLRSYFSQYGEV 43
>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 = 28.5 bits (62), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 5/67 (7%)
Query: 188 PPEDESIKTLYVGGVDARITEQDLRDNFYAHGEIESIKM--HPQ-KAFAFVTYTTREGAE 244
PPE I LY+ + +IT +++ D F +G I I++ P+ + A+V Y A+
Sbjct: 14 PPEVNRI--LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAK 71
Query: 245 KAAEELS 251
A + LS
Sbjct: 72 NACDHLS 78
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 28.5 bits (62), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 5/67 (7%)
Query: 188 PPEDESIKTLYVGGVDARITEQDLRDNFYAHGEIESIKM--HPQ-KAFAFVTYTTREGAE 244
PPE I LY+ + +IT +++ D F +G I I++ P+ + A+V Y A+
Sbjct: 4 PPEVNRI--LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAK 61
Query: 245 KAAEELS 251
A + LS
Sbjct: 62 NAVDHLS 68
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 28.1 bits (61), Expect = 6.6, Method: Composition-based stats.
Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 5/67 (7%)
Query: 188 PPEDESIKTLYVGGVDARITEQDLRDNFYAHGEIESIKM--HPQ-KAFAFVTYTTREGAE 244
PPE I LY+ + +IT +++ D F +G I I++ P+ + A+V Y A+
Sbjct: 8 PPEVNRI--LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAK 65
Query: 245 KAAEELS 251
A + LS
Sbjct: 66 NACDHLS 72
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 28.1 bits (61), Expect = 6.7, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 2/57 (3%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESIKMHPQKAFAFVTYTTREGAEKAAEELSNK 253
L+V + E +L + F G ++ +K+ FAFV + E A KA EE+ K
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFGPMKEVKI--LNGFAFVEFEEAESAAKAIEEVHGK 61
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 27.7 bits (60), Expect = 8.7, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 2/57 (3%)
Query: 197 LYVGGVDARITEQDLRDNFYAHGEIESIKMHPQKAFAFVTYTTREGAEKAAEELSNK 253
L+V + E +L + F G ++ +K+ FAFV + E A KA EE+ K
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKI--LNGFAFVEFEEAESAAKAIEEVHGK 88
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 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,763,571
Number of Sequences: 62578
Number of extensions: 372895
Number of successful extensions: 997
Number of sequences better than 100.0: 132
Number of HSP's better than 100.0 without gapping: 44
Number of HSP's successfully gapped in prelim test: 88
Number of HSP's that attempted gapping in prelim test: 899
Number of HSP's gapped (non-prelim): 148
length of query: 344
length of database: 14,973,337
effective HSP length: 100
effective length of query: 244
effective length of database: 8,715,537
effective search space: 2126591028
effective search space used: 2126591028
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)