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= 029987
(184 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 72.8 bits (177), Expect = 9e-14, Method: Compositional matrix adjust.
Identities = 50/139 (35%), Positives = 66/139 (47%), Gaps = 28/139 (20%)
Query: 1 MATHVDMSLDDIIKSRKKSEXXXXXXXXXXXXXXXXXXXXXXXXXXMTGAARRGPLSNAR 60
MA +DMSLDDIIK + G RR + AR
Sbjct: 15 MADKMDMSLDDIIKLNRNQRRVNR-----------------------GGGPRRNRPAIAR 51
Query: 61 PSSYTIAKSFRRTRNFP--WQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIREL 118
A + R + P WQHDLF+ G G+E G KL VSNL GV++ DI+EL
Sbjct: 52 GGRNRPA-PYSRPKPLPDKWQHDLFDSG--CGGGEGVETGAKLLVSNLDFGVSDADIQEL 108
Query: 119 FSEIGELKRYAIHFDKNGR 137
F+E G LK+ A+ +D++GR
Sbjct: 109 FAEFGTLKKAAVDYDRSGR 127
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 67.8 bits (164), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 31/60 (51%), Positives = 42/60 (70%), Gaps = 2/60 (3%)
Query: 78 WQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGR 137
WQHDLF+ G G+E G KL VSNL GV++ DI+ELF+E G LK+ A+ +D++GR
Sbjct: 17 WQHDLFDSG--CGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGR 74
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 67.8 bits (164), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 31/60 (51%), Positives = 42/60 (70%), Gaps = 2/60 (3%)
Query: 78 WQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGR 137
WQHDLF+ G G+E G KL VSNL GV++ DI+ELF+E G LK+ A+ +D++GR
Sbjct: 17 WQHDLFDSG--CGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGR 74
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 58.2 bits (139), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 32/68 (47%), Positives = 43/68 (63%), Gaps = 4/68 (5%)
Query: 72 RTRNFP--WQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYA 129
R + P WQHDLF+ E G KL VSNL GV++ DI+ELF+E G LK+ A
Sbjct: 2 RPKQLPDKWQHDLFDSGFGGGAGV--ETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAA 59
Query: 130 IHFDKNGR 137
+H+D++GR
Sbjct: 60 VHYDRSGR 67
>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex
Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A
Resolution
Length = 107
Score = 57.8 bits (138), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 32/68 (47%), Positives = 43/68 (63%), Gaps = 4/68 (5%)
Query: 72 RTRNFP--WQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYA 129
R + P WQHDLF+ E G KL VSNL GV++ DI+ELF+E G LK+ A
Sbjct: 3 RPKQLPDKWQHDLFDSGFGGGAGV--ETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAA 60
Query: 130 IHFDKNGR 137
+H+D++GR
Sbjct: 61 VHYDRSGR 68
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 36.2 bits (82), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 16/31 (51%), Positives = 20/31 (64%)
Query: 91 GISGIEVGTKLYVSNLHPGVTNDDIRELFSE 121
G SG KLY+ NL P VT DD+R+LF +
Sbjct: 1 GSSGSSGMNKLYIGNLSPAVTADDLRQLFGD 31
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 35.8 bits (81), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 27/54 (50%)
Query: 98 GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSVSSVACFATFSP 151
G L V NL P V+N+ + + FS+ G +++ + D GR + FA P
Sbjct: 96 GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPP 149
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 35.4 bits (80), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 27/50 (54%)
Query: 86 SLRAAGISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKN 135
+ R G ++L+V NL P +T +++R+LF + G+ IH DK
Sbjct: 10 NFRKPGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG 59
Score = 34.7 bits (78), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 26/47 (55%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSVSSVACFA 147
L V NL V+N+ + E FS G+++R + D GRPS + F+
Sbjct: 99 LTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFS 145
>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 = 35.0 bits (79), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 24/37 (64%)
Query: 99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKN 135
++L+V NL P +T +++R+LF + G+ IH DK
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG 52
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 34.7 bits (78), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 26/39 (66%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPS 139
+YVSNL +TN+D+ +FS+ G++ + I DK+ R S
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKS 57
>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 = 32.7 bits (73), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 25/52 (48%)
Query: 98 GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSVSSVACFATF 149
K++V + + D+RELF + G + + D++ P S CF TF
Sbjct: 3 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTF 54
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 32.3 bits (72), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 24/51 (47%)
Query: 96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSVSSVACF 146
E ++V NL V + + ELF + G L + I D+ G+P CF
Sbjct: 14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCF 64
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 32.3 bits (72), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 25/50 (50%)
Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSVSSVACFATF 149
K++V + + D+RELF + G + + D++ P S CF TF
Sbjct: 17 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTF 66
Score = 27.3 bits (59), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 3/51 (5%)
Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSVSSVACFATFS 150
KL++ + T +DIR +FS G+++ I +G +S F TF+
Sbjct: 109 KLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDG---LSRGCAFVTFT 156
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 32.3 bits (72), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 25/50 (50%)
Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSVSSVACFATF 149
K++V + + D+RELF + G + + D++ P S CF TF
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTF 54
Score = 27.7 bits (60), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 3/51 (5%)
Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSVSSVACFATFS 150
KL++ + T +DIR +FS G+++ I +G +S F TF+
Sbjct: 97 KLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDG---LSRGCAFVTFT 144
>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 = 31.6 bits (70), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 5/53 (9%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSVSSVACFATFSPLF 153
LYV NL T + I ELFS+ G++K+ + DK + AC F +
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDK-----MKKTACGFCFVEYY 89
>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 = 31.6 bits (70), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 39/81 (48%), Gaps = 11/81 (13%)
Query: 54 GPLSNARPSSYTIAKSFRRTRNFPWQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTND 113
G SN R + + S+ R RN +D L +E G L+V+++H D
Sbjct: 39 GSDSNTREAIH----SYERVRNED------DDELEPGPQRSVE-GWILFVTSIHEEAQED 87
Query: 114 DIRELFSEIGELKRYAIHFDK 134
+I+E F + GE+K ++ D+
Sbjct: 88 EIQEKFCDYGEIKNIHLNLDR 108
>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 = 31.6 bits (70), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 23/37 (62%)
Query: 98 GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK 134
G L+V+ +H T +DI + F+E GE+K ++ D+
Sbjct: 7 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDR 43
>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 = 31.6 bits (70), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 22/34 (64%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK 134
L+V+ +H T +DI + F+E GE+K ++ D+
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDR 43
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 31.6 bits (70), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 22/34 (64%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK 134
L+V+ +H T +DI + F+E GE+K ++ D+
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDR 43
>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 = 31.2 bits (69), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 22/34 (64%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK 134
L+V+ +H T +DI + F+E GE+K ++ D+
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDR 45
>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 = 31.2 bits (69), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 22/34 (64%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK 134
L+V+ +H T +DI + F+E GE+K ++ D+
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDR 59
>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 = 31.2 bits (69), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 22/34 (64%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK 134
L+V+ +H T +DI + F+E GE+K ++ D+
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDR 58
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 31.2 bits (69), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 33/66 (50%), Gaps = 7/66 (10%)
Query: 69 SFRRTRNFPWQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRY 128
S+ R RN +D L +E G L+V+++H D+I+E F + GE+K
Sbjct: 4 SYERVRNED------DDELEPGPQRSVE-GWILFVTSIHEEAQEDEIQEKFCDYGEIKNI 56
Query: 129 AIHFDK 134
++ D+
Sbjct: 57 HLNLDR 62
>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 = 31.2 bits (69), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 16/37 (43%), Positives = 22/37 (59%)
Query: 98 GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK 134
GT L V+ L T D++R LFS IGE++ + DK
Sbjct: 19 GTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDK 55
>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 = 30.8 bits (68), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 15/34 (44%), Positives = 21/34 (61%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK 134
LYV NL T + I ELFS+ G++K+ + DK
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDK 54
>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 = 30.4 bits (67), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 24/50 (48%)
Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSVSSVACFATF 149
K +V + + D+RELF + G + + D++ P S CF TF
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTF 54
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 30.4 bits (67), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 31/53 (58%), Gaps = 7/53 (13%)
Query: 89 AAGISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKR------YA-IHFDK 134
++G SG+ L+V NL VT + + + FS+ G+L+R YA IHFD+
Sbjct: 2 SSGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKDYAFIHFDE 54
>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 = 30.0 bits (66), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 10/34 (29%), Positives = 23/34 (67%)
Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFD 133
++YV+++H +++DDI+ +F G++K + D
Sbjct: 127 RIYVASVHQDLSDDDIKSVFEAFGKIKSATLARD 160
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 30.0 bits (66), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
Query: 99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRP 138
T LYV+NL +T+D + +F + G + + I DK GRP
Sbjct: 90 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRP 130
>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 = 30.0 bits (66), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 9/27 (33%), Positives = 21/27 (77%)
Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELK 126
++YV+++H +++DDI+ +F G++K
Sbjct: 112 RIYVASVHQDLSDDDIKSVFEAFGKIK 138
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 30.0 bits (66), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 12/25 (48%), Positives = 16/25 (64%)
Query: 99 TKLYVSNLHPGVTNDDIRELFSEIG 123
TKL+V N+ P TN ++R F E G
Sbjct: 11 TKLHVGNISPTCTNQELRAKFEEYG 35
>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 = 29.6 bits (65), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 9/28 (32%), Positives = 21/28 (75%)
Query: 99 TKLYVSNLHPGVTNDDIRELFSEIGELK 126
++YV+++H +++DDI+ +F G++K
Sbjct: 110 NRIYVASVHQDLSDDDIKSVFEAFGKIK 137
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 29.6 bits (65), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 22/36 (61%)
Query: 99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK 134
T L V+ L +T D++R LFS IGE++ + DK
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDK 38
>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 = 29.6 bits (65), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 22/36 (61%)
Query: 99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK 134
T L V+ L +T D++R LFS IGE++ + DK
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDK 38
>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 = 29.6 bits (65), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 22/36 (61%)
Query: 99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK 134
T L V+ L +T D++R LFS IGE++ + DK
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDK 40
>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 = 29.6 bits (65), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
Query: 99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRP 138
T LYV+NL +T+D + +F + G + + I DK GRP
Sbjct: 101 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRP 141
>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 = 29.6 bits (65), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
Query: 99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRP 138
T LYV+NL +T+D + +F + G + + I DK GRP
Sbjct: 14 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRP 54
>pdb|2H39|A Chain A, Crystal Structure Of An Adp-Glucose Phosphorylase From
Arabidopsis Thaliana With Bound Adp-Glucose
pdb|2H39|B Chain B, Crystal Structure Of An Adp-Glucose Phosphorylase From
Arabidopsis Thaliana With Bound Adp-Glucose
Length = 351
Score = 28.9 bits (63), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 16/67 (23%), Positives = 32/67 (47%), Gaps = 6/67 (8%)
Query: 58 NARPSSYTIAKSFRRT--RNFPWQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDI 115
N P +Y I S + P+ H + + +G+ G E+GT Y++ + P +D+
Sbjct: 286 NDPPYNYMIHTSPLKVTESQLPYTHWFLQIVPQLSGVGGFEIGTGCYINPVFP----EDV 341
Query: 116 RELFSEI 122
++ E+
Sbjct: 342 AKVMREV 348
>pdb|1Z84|A Chain A, X-Ray Structure Of Galt-Like Protein From Arabidopsis
Thaliana At5g18200
pdb|1Z84|B Chain B, X-Ray Structure Of Galt-Like Protein From Arabidopsis
Thaliana At5g18200
pdb|1ZWJ|A Chain A, X-Ray Structure Of Galt-Like Protein From Arabidopsis
Thaliana At5g18200
pdb|1ZWJ|B Chain B, X-Ray Structure Of Galt-Like Protein From Arabidopsis
Thaliana At5g18200
pdb|2Q4H|A Chain A, Ensemble Refinement Of The Crystal Structure Of Galt-Like
Protein From Arabidopsis Thaliana At5g18200
pdb|2Q4H|B Chain B, Ensemble Refinement Of The Crystal Structure Of Galt-Like
Protein From Arabidopsis Thaliana At5g18200
pdb|2Q4L|A Chain A, Ensemble Refinement Of The Crystal Structure Of Galt-Like
Protein From Arabidopsis Thaliana At5g18200
pdb|2Q4L|B Chain B, Ensemble Refinement Of The Crystal Structure Of Galt-Like
Protein From Arabidopsis Thaliana At5g18200
Length = 351
Score = 28.9 bits (63), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 16/67 (23%), Positives = 32/67 (47%), Gaps = 6/67 (8%)
Query: 58 NARPSSYTIAKSFRRT--RNFPWQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDI 115
N P +Y I S + P+ H + + +G+ G E+GT Y++ + P +D+
Sbjct: 286 NDPPYNYMIHTSPLKVTESQLPYTHWFLQIVPQLSGVGGFEIGTGCYINPVFP----EDV 341
Query: 116 RELFSEI 122
++ E+
Sbjct: 342 AKVMREV 348
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 28.9 bits (63), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 19/37 (51%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGR 137
LYV NL +T D +++ F G + I DKN +
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNK 39
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 28.9 bits (63), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 27/52 (51%), Gaps = 4/52 (7%)
Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFD-KNGRPSVSSVACFATFS 150
+LYV +LH +T D +R +F G ++ + D + GR S F TFS
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGR---SKGYGFITFS 76
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 28.5 bits (62), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 25/43 (58%), Gaps = 7/43 (16%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKR------YA-IHFDKNG 136
L+V NL VT + + + FSE G+L+R YA +HF+ G
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKDYAFVHFEDRG 60
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 28.5 bits (62), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 22/34 (64%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK 134
+YV NL T++ ++ELFS+ G++ + +D+
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDR 37
>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 = 28.5 bits (62), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 2/51 (3%)
Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSVSSVACFATFS 150
K++V L P + IRE F GE++ +I + + + CF TF
Sbjct: 3 KIFVGGLSPDTPEEKIREYFGGFGEVE--SIELPMDNKTNKRRGFCFITFK 51
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 28.5 bits (62), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 17/32 (53%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHF 132
LY+ NL P VT D+ LF+ E K I F
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQF 59
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 28.1 bits (61), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 11/35 (31%), Positives = 21/35 (60%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKN 135
L++ NL+ T + ++ +FS++G +K I KN
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKN 42
>pdb|1UZ5|A Chain A, The Crystal Structure Of Molybdopterin Biosynthesis Moea
Protein From Pyrococcus Horikosii
Length = 402
Score = 28.1 bits (61), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 1/60 (1%)
Query: 84 EDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSVSSV 143
++SL+A + VG + +S G T D + E+GE+K + I + G+P++ V
Sbjct: 233 KESLKALIEKAVNVGDVVVISGGASGGTKDLTASVIEELGEVKVHGIAI-QPGKPTIIGV 291
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 27.7 bits (60), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 11/36 (30%), Positives = 19/36 (52%)
Query: 98 GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFD 133
G K+++ L T + +RE F + GE+K + D
Sbjct: 25 GCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRD 60
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 27.7 bits (60), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 31/71 (43%), Gaps = 9/71 (12%)
Query: 99 TKLYVSNLHPGVTNDDIRELFSEIGELK------RYAIHFDKNGRPSVSSVACFATFSPL 152
T LYV L +T D+R F + GE++ R F + + VA +F+ L
Sbjct: 13 TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKL 72
Query: 153 FL---WVQLKW 160
+ + +KW
Sbjct: 73 IVNGRRLNVKW 83
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 27.3 bits (59), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 17/28 (60%)
Query: 99 TKLYVSNLHPGVTNDDIRELFSEIGELK 126
+K+ V N+ +IRELFS GELK
Sbjct: 16 SKILVRNIPFQANQREIRELFSTFGELK 43
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 26.9 bits (58), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 99 TKLYVSNLHPGVTNDDIRELFSEIGELK 126
TK+++ L VT D I E+FS G++K
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIK 32
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 26.9 bits (58), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 2/50 (4%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSVSSVACFATFS 150
++V L P + IRE F GE++ +I + + + CF TF
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVE--SIELPMDNKTNKRRGFCFITFK 49
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 26.6 bits (57), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 11/39 (28%), Positives = 21/39 (53%)
Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRP 138
++YV NL P + DI ++F + G ++ + + G P
Sbjct: 24 RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPP 62
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 26.6 bits (57), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 4/53 (7%)
Query: 99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKN-GRPSVSSVACFATFS 150
+ LYV +LH +T D +R +F G++ + D + GR S F TFS
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGR---SKGYGFITFS 55
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 26.6 bits (57), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 10/39 (25%), Positives = 25/39 (64%), Gaps = 1/39 (2%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRP 138
++V N+ T + ++++FSE+G + + + +D+ G+P
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKP 49
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
0.322 0.134 0.415
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,670,833
Number of Sequences: 62578
Number of extensions: 171192
Number of successful extensions: 511
Number of sequences better than 100.0: 63
Number of HSP's better than 100.0 without gapping: 55
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 441
Number of HSP's gapped (non-prelim): 73
length of query: 184
length of database: 14,973,337
effective HSP length: 93
effective length of query: 91
effective length of database: 9,153,583
effective search space: 832976053
effective search space used: 832976053
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 bits)