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= psy10283
(59 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In
Trinucleotide Repeat Containing 4 Variant
Length = 102
Score = 75.5 bits (184), Expect = 8e-15, Method: Compositional matrix adjust.
Identities = 33/42 (78%), Positives = 39/42 (92%)
Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
D+KLFVGML KQQ ++DVRK+F PFGTI+ECTVL+GPDGTSK
Sbjct: 12 DRKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSK 53
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 74.3 bits (181), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 31/44 (70%), Positives = 38/44 (86%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
P +KLFVGML+KQQ+EDDVR++F FG IEECT+L+GPDG SK
Sbjct: 13 PSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSK 56
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 70.9 bits (172), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 30/42 (71%), Positives = 39/42 (92%)
Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
D+KLFVGML+KQQ+E+DV ++F PFG I+ECTVL+GPDG+SK
Sbjct: 15 DRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSK 56
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 61.2 bits (147), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 24/42 (57%), Positives = 35/42 (83%)
Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
D+KLF+GM+SK+ E+D+R +F+ FG IEEC +L+GPDG S+
Sbjct: 95 DRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSR 136
Score = 31.6 bits (70), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 22/33 (66%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
K+FVG + + +E D+R++F +G + E VL+
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLR 37
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 60.5 bits (145), Expect = 2e-10, Method: Composition-based stats.
Identities = 24/42 (57%), Positives = 35/42 (83%)
Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
D+KLF+GM+SK+ E+D+R +F+ FG IEEC +L+GPDG S+
Sbjct: 107 DRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSR 148
Score = 31.2 bits (69), Expect = 0.15, Method: Composition-based stats.
Identities = 12/33 (36%), Positives = 22/33 (66%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
K+FVG + + +E D+R++F +G + E VL+
Sbjct: 17 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLR 49
>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 = 57.4 bits (137), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 23/42 (54%), Positives = 33/42 (78%)
Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 57
D+KLF+G +SK+ E+D+R F+ FG IEEC +L+GPDG S+
Sbjct: 95 DRKLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDGLSR 136
Score = 30.0 bits (66), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 21/33 (63%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
K FVG + + +E D+R++F +G + E VL+
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLR 37
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 24/35 (68%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP 52
K+F+G LS Q ++ +R+ F FG ++EC V++ P
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDP 61
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 37.0 bits (84), Expect = 0.003, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 32/51 (62%), Gaps = 3/51 (5%)
Query: 11 TPLPPD--KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
+P P+ +KLF+G LS + ++ +R F +GT+ +C V++ P+ T + R
Sbjct: 7 SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPN-TKRSR 56
Score = 27.3 bits (59), Expect = 2.0, Method: Composition-based stats.
Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
KK+FVG + + E +R F +G IE ++ G+ K+R
Sbjct: 106 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD-RGSGKKR 147
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 24/35 (68%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP 52
K+F+G LS Q ++ +R+ F FG ++EC V++ P
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDP 36
>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 = 37.0 bits (84), Expect = 0.003, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 32/51 (62%), Gaps = 3/51 (5%)
Query: 11 TPLPPD--KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
+P P+ +KLF+G LS + ++ +R F +GT+ +C V++ P+ T + R
Sbjct: 5 SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPN-TKRSR 54
Score = 27.3 bits (59), Expect = 2.1, Method: Composition-based stats.
Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
KK+FVG + + E +R F +G IE ++ G+ K+R
Sbjct: 104 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD-RGSGKKR 145
>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 = 37.0 bits (84), Expect = 0.003, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 32/51 (62%), Gaps = 3/51 (5%)
Query: 11 TPLPPD--KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
+P P+ +KLF+G LS + ++ +R F +GT+ +C V++ P+ T + R
Sbjct: 6 SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPN-TKRSR 55
Score = 27.3 bits (59), Expect = 2.1, Method: Composition-based stats.
Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
KK+FVG + + E +R F +G IE ++ G+ K+R
Sbjct: 105 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD-RGSGKKR 146
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 36.6 bits (83), Expect = 0.004, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 32/51 (62%), Gaps = 3/51 (5%)
Query: 11 TPLPPD--KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
+P P+ +KLF+G LS + ++ +R F +GT+ +C V++ P+ T + R
Sbjct: 6 SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPN-TKRSR 55
Score = 27.3 bits (59), Expect = 2.4, Method: Composition-based stats.
Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
KK+FVG + + E +R F +G IE ++ G+ K+R
Sbjct: 105 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD-RGSGKKR 146
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 36.6 bits (83), Expect = 0.004, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 32/51 (62%), Gaps = 3/51 (5%)
Query: 11 TPLPPD--KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
+P P+ +KLF+G LS + ++ +R F +GT+ +C V++ P+ T + R
Sbjct: 4 SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPN-TKRSR 53
Score = 27.3 bits (59), Expect = 2.5, Method: Composition-based stats.
Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
KK+FVG + + E +R F +G IE ++ G+ K+R
Sbjct: 103 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD-RGSGKKR 144
>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex
pdb|1PO6|A Chain A, Crystal Structure Of Up1 Complexed With
D(Tagg(6mi)ttaggg): A Human Telomeric Repeat Containing
6-Methyl-8-(2-Deoxy-
Beta-Ribofuranosyl)isoxanthopteridine (6mi)
Length = 183
Score = 36.2 bits (82), Expect = 0.005, Method: Composition-based stats.
Identities = 15/43 (34%), Positives = 28/43 (65%), Gaps = 1/43 (2%)
Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
+KLF+G LS + ++ +R F +GT+ +C V++ P+ T + R
Sbjct: 7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPN-TKRSR 48
Score = 27.3 bits (59), Expect = 2.0, Method: Composition-based stats.
Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
KK+FVG + + E +R F +G IE ++ G+ K+R
Sbjct: 98 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD-RGSGKKR 139
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 34.7 bits (78), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 22/33 (66%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
KLF+G L ++ E ++R +F +G + EC ++K
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDIIK 42
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 34.3 bits (77), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 21/33 (63%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
KLFVG LS NE + ++F+ +G I E V+K
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVK 46
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 34.3 bits (77), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 16/33 (48%), Positives = 22/33 (66%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
KLFVG + + +E D++ +F FG I E TVLK
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLK 49
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 33.5 bits (75), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 22/33 (66%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
KLF+G + + +E D++ +F FG I E TVLK
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLK 47
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 33.5 bits (75), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 21/33 (63%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
+FVG LS + +D++ FAPFG I + V+K
Sbjct: 17 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVK 49
>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 = 33.5 bits (75), Expect = 0.033, Method: Composition-based stats.
Identities = 10/35 (28%), Positives = 23/35 (65%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP 52
+++V + + ++DD++ +F FG I+ CT+ + P
Sbjct: 112 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDP 146
Score = 30.0 bits (66), Expect = 0.31, Method: Composition-based stats.
Identities = 11/27 (40%), Positives = 19/27 (70%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIE 44
+++VG + + ED +R+ FAPFG I+
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGPIK 41
>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 = 33.5 bits (75), Expect = 0.035, Method: Composition-based stats.
Identities = 10/35 (28%), Positives = 23/35 (65%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP 52
+++V + + ++DD++ +F FG I+ CT+ + P
Sbjct: 111 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDP 145
Score = 30.0 bits (66), Expect = 0.33, Method: Composition-based stats.
Identities = 11/27 (40%), Positives = 19/27 (70%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIE 44
+++VG + + ED +R+ FAPFG I+
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIK 40
>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In
Cytotoxic Granule-Associated Rna Binding Protein 1
pdb|2RNE|A Chain A, Solution Structure Of The Second Rna Recognition Motif
(Rrm) Of Tia-1
Length = 115
Score = 33.1 bits (74), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 21/32 (65%)
Query: 19 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
+FVG LS + +D++ FAPFG I + V+K
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVK 49
>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex
With Rna
pdb|2KM8|C Chain C, Interdomain Rrm Packing Contributes To Rna Recognition
In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 167
Score = 32.7 bits (73), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 26/42 (61%), Gaps = 1/42 (2%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
K+F+G L+ ED++R+ F +GT+ + ++K P T + R
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDP-ATGRSR 45
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleaoproteins A2B1
Length = 116
Score = 32.3 bits (72), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 23/36 (63%)
Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP 52
+KLF+G LS + E+ +R + +G + +C V++ P
Sbjct: 28 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDP 63
>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAF|B Chain B, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAG|A Chain A, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAG|B Chain B, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAH|A Chain A, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAH|B Chain B, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAI|A Chain A, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAI|B Chain B, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAJ|A Chain A, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAJ|B Chain B, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAK|A Chain A, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAK|B Chain B, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAL|A Chain A, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|B Chain B, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|D Chain D, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|I Chain I, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAM|A Chain A, Structure Of U2af65 Variant With Bru5c2 Dna
pdb|3VAM|B Chain B, Structure Of U2af65 Variant With Bru5c2 Dna
Length = 174
Score = 32.3 bits (72), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 23/39 (58%)
Query: 12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
PLP KLF+G L N+D V+++ FG ++ ++K
Sbjct: 92 PLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVK 130
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 32.3 bits (72), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 23/39 (58%)
Query: 12 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
PLP KLF+G L N+D V+++ FG ++ ++K
Sbjct: 90 PLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVK 128
>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 = 32.3 bits (72), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 22/33 (66%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
K+FVG + + +E D+R++F +G + E VL+
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLR 37
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 32.0 bits (71), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 19 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 57
L+VG L ED +R IF PFG I+ ++K D G SK
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSK 47
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 31.2 bits (69), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 25/37 (67%), Gaps = 1/37 (2%)
Query: 13 LPPDKKLFVGMLS-KQQNEDDVRKIFAPFGTIEECTV 48
+PP +LF+G L K +++D+ +IF+P+G I + +
Sbjct: 7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI 43
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 31.2 bits (69), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 18/32 (56%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVL 49
K+FVG L + +RK F FG IEE V+
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVI 50
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 31.2 bits (69), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 19/32 (59%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVL 49
+L+VG L ED +R IF PFG IE ++
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLM 59
>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 = 30.4 bits (67), Expect = 0.28, Method: Composition-based stats.
Identities = 11/27 (40%), Positives = 19/27 (70%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIE 44
+++VG + + ED +R+ FAPFG I+
Sbjct: 30 RVYVGSIYYELGEDTIRQAFAPFGPIK 56
Score = 30.0 bits (66), Expect = 0.39, Method: Composition-based stats.
Identities = 9/35 (25%), Positives = 22/35 (62%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP 52
+++V + + ++DD++ +F FG I+ T+ + P
Sbjct: 127 RIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDP 161
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 30.0 bits (66), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 11/33 (33%), Positives = 20/33 (60%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
KLFVG L ++ +R F+ +G + +C ++K
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMK 50
>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
pdb|3S7R|B Chain B, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
Length = 87
Score = 29.6 bits (65), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
K FVG LS ++ D++ F FG + +CT+ P+ T + R
Sbjct: 13 KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPN-TGRSR 53
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 29.3 bits (64), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 12 PLPPDKKLFVGMLSKQ-QNEDDVRKIFAPFGTIEECTVLKG 51
P + ++F+G L+ + DV IF+ +G + C+V KG
Sbjct: 23 PKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKG 63
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 28.9 bits (63), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 12 PLPPDKKLFVGMLSK-QQNEDDVRKIFAPFGTIEECTVLKG 51
P + ++F+G L+ + DV IF+ +G I C+V KG
Sbjct: 11 PRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKG 51
>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 = 28.9 bits (63), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 18/28 (64%)
Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIE 44
KK+FVG LS E+ +R+ F FG +E
Sbjct: 2 KKIFVGGLSPDTPEEKIREYFGGFGEVE 29
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 27.7 bits (60), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 23/35 (65%), Gaps = 1/35 (2%)
Query: 15 PDKKLFVGMLS-KQQNEDDVRKIFAPFGTIEECTV 48
P +LF+G L K +++D+ +IF+P+G I + +
Sbjct: 1 PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI 35
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 27.7 bits (60), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 19/29 (65%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEEC 46
+LFV LS +E+D+ K+F+ +G + E
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSEL 38
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 21/41 (51%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG 54
P D K++VG L N+ ++ + F +G + V + P G
Sbjct: 71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG 111
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 21/41 (51%)
Query: 14 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG 54
P D K++VG L N+ ++ + F +G + V + P G
Sbjct: 71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG 111
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 27.7 bits (60), Expect = 1.9, Method: Composition-based stats.
Identities = 13/38 (34%), Positives = 22/38 (57%), Gaps = 2/38 (5%)
Query: 15 PDK--KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
PD KLF+G L N+D V+++ FG ++ ++K
Sbjct: 111 PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVK 148
>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 = 27.3 bits (59), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 10/30 (33%), Positives = 19/30 (63%)
Query: 19 LFVGMLSKQQNEDDVRKIFAPFGTIEECTV 48
+F+G LS + D++ F+ FG + +CT+
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTL 31
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 27.3 bits (59), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 19/31 (61%)
Query: 19 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVL 49
L+V L +++ +RK F+PFGTI V+
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVM 48
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Rna-Binding Protein 14
Length = 90
Score = 27.3 bits (59), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
K+FVG +S ++R +F G + EC V+K
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVVK 43
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 26.9 bits (58), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 20/36 (55%)
Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
+ +LFV E ++ +IF PFG ++E +L G
Sbjct: 31 NTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG 66
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 26.9 bits (58), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 22/39 (56%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTS 56
KL V L ++ D++++FA FGT+++ V G S
Sbjct: 30 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRS 68
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 26.6 bits (57), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 20/36 (55%)
Query: 16 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 51
+ +LFV E ++ +IF PFG ++E +L G
Sbjct: 4 NTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG 39
>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 = 26.6 bits (57), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 22/39 (56%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTS 56
KL V L ++ D++++FA FGT+++ V G S
Sbjct: 31 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRS 69
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 26.2 bits (56), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 20/34 (58%)
Query: 17 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
KLF+G L N+D V+++ FG ++ ++K
Sbjct: 2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVK 35
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 26.2 bits (56), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 19 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
LF+ L+ E+ ++ +F+ G I+ CT+ K
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISK 39
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 25.8 bits (55), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 22/32 (68%), Gaps = 1/32 (3%)
Query: 18 KLFVGMLS-KQQNEDDVRKIFAPFGTIEECTV 48
+LF+G L K +++D+ +IF+P+G I + +
Sbjct: 24 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI 55
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 25.8 bits (55), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 22/32 (68%), Gaps = 1/32 (3%)
Query: 18 KLFVGMLS-KQQNEDDVRKIFAPFGTIEECTV 48
+LF+G L K +++D+ +IF+P+G I + +
Sbjct: 24 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI 55
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 25.8 bits (55), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 19 LFVGMLSKQQNEDDVRKIFAPFGTIE 44
+FVG LS E+ +R+ F FG +E
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVE 27
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 25.8 bits (55), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 20/31 (64%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTV 48
KL V L ++ D++++FA FGT+++ V
Sbjct: 90 KLLVSNLDFGVSDADIQELFAEFGTLKKAAV 120
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 25.8 bits (55), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 12/42 (28%), Positives = 23/42 (54%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSKER 59
K+ V + Q N+ ++R++F+ FG ++ + K GT R
Sbjct: 17 KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHR 58
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 25.8 bits (55), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
+LFVG L E+++RK+F +G E + K
Sbjct: 24 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK 56
>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 = 25.4 bits (54), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
+LFVG L E+++RK+F +G E + K
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK 49
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 25.4 bits (54), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 20/31 (64%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTV 48
KL V L ++ D++++FA FGT+++ V
Sbjct: 37 KLLVSNLDFGVSDADIQELFAEFGTLKKAAV 67
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 25.4 bits (54), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 20/31 (64%)
Query: 18 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTV 48
KL V L ++ D++++FA FGT+++ V
Sbjct: 37 KLLVSNLDFGVSDADIQELFAEFGTLKKAAV 67
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 25.4 bits (54), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 21 VGMLSKQQNEDDVRKIFAPFGTIEECTVLK 50
V LS+ E D++++F PFG+I + K
Sbjct: 20 VTNLSEDTRETDLQELFRPFGSISRIYLAK 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
0.319 0.141 0.442
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,967,965
Number of Sequences: 62578
Number of extensions: 58066
Number of successful extensions: 230
Number of sequences better than 100.0: 65
Number of HSP's better than 100.0 without gapping: 59
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 158
Number of HSP's gapped (non-prelim): 78
length of query: 59
length of database: 14,973,337
effective HSP length: 30
effective length of query: 29
effective length of database: 13,095,997
effective search space: 379783913
effective search space used: 379783913
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)