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= 025249
(255 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 34/55 (61%)
Query: 11 LKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE 65
+++ +R++G+P+G+GF Y D+ A+R ++GREF R + V+ A + E
Sbjct: 38 FRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEKNKE 92
>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 = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 34/52 (65%), Gaps = 1/52 (1%)
Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
D ++ML++D+G+ RGFGF+TY A+D + +F DR I + +A+P+
Sbjct: 116 DAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKF-IDFKDRKIEIKRAEPR 166
Score = 36.2 bits (82), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 24/36 (66%)
Query: 9 NDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMH 44
DLKIM + +GR RGFGF+++ ++D+ ++ H
Sbjct: 31 TDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQH 66
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 34/53 (64%), Gaps = 1/53 (1%)
Query: 9 NDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
++ ++ + + RPRGFGFIT+ D +++D A+ MH + + + V +A+P+
Sbjct: 38 TEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKRAEPR 89
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 30/45 (66%)
Query: 11 LKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISV 55
+++M++ ++GR +G+GFIT++D A+ +++G E R + V
Sbjct: 56 IQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKV 100
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 30/50 (60%)
Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
KIM + D+G +G+ FI +A A D AI M+G+ +R I+V+ A K
Sbjct: 37 KIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKK 86
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 35/56 (62%), Gaps = 1/56 (1%)
Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE 65
++K++ +R++ +P+GFGF+ + ++ +AI ++ +F R I V +A PK E
Sbjct: 30 NVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAKLDNTDFMGRTIRVTEANPKKSLE 84
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 27/44 (61%)
Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVI 53
+LK+M + +GR +G+ FI + D + A+R ++G + G R +
Sbjct: 32 NLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFL 75
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 33/56 (58%)
Query: 9 NDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG 64
+++ +M + D+GR +G+GFIT++D A+ +++G E R + V ++ G
Sbjct: 33 DNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVTERLDG 88
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 27/44 (61%)
Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVI 53
+LK+M + +GR +G+ FI + D + A+R ++G + G R +
Sbjct: 31 NLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFL 74
>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In
Cytotoxic Granule-Associated Rna Binding Protein 1
pdb|2RNE|A Chain A, Solution Structure Of The Second Rna Recognition Motif
(Rrm) Of Tia-1
Length = 115
Score = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 34/53 (64%)
Query: 9 NDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
+D +++ + +G+ +G+GF+++ ++ ++AI++M G+ G R I N A K
Sbjct: 43 SDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK 95
>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2
pdb|3BS9|B Chain B, X-Ray Structure Of Human Tia-1 Rrm2
Length = 87
Score = 37.0 bits (84), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 34/53 (64%)
Query: 9 NDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
+D +++ + +G+ +G+GF+++ ++ ++AI++M G+ G R I N A K
Sbjct: 34 SDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK 86
>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition
In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 84
Score = 36.6 bits (83), Expect = 0.016, Method: Composition-based stats.
Identities = 14/44 (31%), Positives = 27/44 (61%)
Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVI 53
+LK+M + +GR +G+ FI + D + A+R ++G + G R +
Sbjct: 33 NLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFL 76
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 36.2 bits (82), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 30/49 (61%)
Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP 60
K++ ++ +G+ G+GF+ Y+D D AI ++G + + I V+ A+P
Sbjct: 35 KLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYARP 83
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 36.2 bits (82), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
K+M+E GR +GFGF+ ++ A+ EM+GR + + V AQ K
Sbjct: 46 KVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRK 93
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With
The Au-Rich Element
Length = 174
Score = 35.8 bits (81), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 30/49 (61%)
Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP 60
K++ ++ +G+ G+GF+ Y+D D AI ++G + + I V+ A+P
Sbjct: 35 KLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYARP 83
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 35.4 bits (80), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 32/50 (64%)
Query: 9 NDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
+++ ++ +R++ R RGFGF+T+ + DA+ M+G+ R I V++A
Sbjct: 40 SEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA 89
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 35.0 bits (79), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 32/53 (60%)
Query: 9 NDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
+D +++ + +G+ +G+GF+++ ++ ++AI M G+ G R I N A K
Sbjct: 43 SDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMGGQWLGGRQIRTNWATRK 95
>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 = 35.0 bits (79), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 9 NDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG 64
N + I+ ++ SG P+G+ +I +A+R ++D A+ M F R I V + M G
Sbjct: 64 NRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRTNMPG 118
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 34.7 bits (78), Expect = 0.056, Method: Composition-based stats.
Identities = 14/50 (28%), Positives = 30/50 (60%), Gaps = 1/50 (2%)
Query: 9 NDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
+D +M ++ + R RGFGF+T+ + + + + E+H E ++++ KA
Sbjct: 27 DDAMLMFDKTTNRHRGFGFVTF-ESEDIVEKVCEIHFHEINNKMVECKKA 75
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 33.9 bits (76), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 3/61 (4%)
Query: 1 MQQCLTHNNDLKIM-LERDS--GRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNK 57
+++ LT LK L +DS G +G+ F Y D D AI ++G + GD+ + V +
Sbjct: 18 VKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR 77
Query: 58 A 58
A
Sbjct: 78 A 78
>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 = 33.9 bits (76), Expect = 0.096, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 3/61 (4%)
Query: 1 MQQCLTHNNDLKIM-LERDS--GRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNK 57
+++ LT LK L +DS G +G+ F Y D D AI ++G + GD+ + V +
Sbjct: 131 VKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR 190
Query: 58 A 58
A
Sbjct: 191 A 191
>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 = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 3/61 (4%)
Query: 1 MQQCLTHNNDLKIM-LERDS--GRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNK 57
+++ LT LK L +DS G +G+ F Y D D AI ++G + GD+ + V +
Sbjct: 113 VKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR 172
Query: 58 A 58
A
Sbjct: 173 A 173
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 3/61 (4%)
Query: 1 MQQCLTHNNDLKIM-LERDS--GRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNK 57
+++ LT LK L +DS G +G+ F Y D D AI ++G + GD+ + V +
Sbjct: 111 VKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR 170
Query: 58 A 58
A
Sbjct: 171 A 171
>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The
C-Fos Rna
pdb|1G2E|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The
Tumor Necrosis Factor Alpha Rna
Length = 167
Score = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 29/49 (59%)
Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP 60
K++ ++ +G+ G+GF+ Y D + + AI ++G + I V+ A+P
Sbjct: 33 KLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP 81
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 21/30 (70%)
Query: 11 LKIMLERDSGRPRGFGFITYADRRAMDDAI 40
++IM +R SG+ RGF F+T+ D ++D +
Sbjct: 135 IEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 164
Score = 30.8 bits (68), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 9 NDLKIMLERDSGRPRGFGFITYADRRAMDDAI 40
D +M + ++ R RGFGF+TYA +D A+
Sbjct: 42 TDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 73
>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 = 33.1 bits (74), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 21/30 (70%)
Query: 11 LKIMLERDSGRPRGFGFITYADRRAMDDAI 40
++IM +R SG+ RGF F+T+ D ++D +
Sbjct: 133 IEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 162
Score = 30.8 bits (68), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 9 NDLKIMLERDSGRPRGFGFITYADRRAMDDAI 40
D +M + ++ R RGFGF+TYA +D A+
Sbjct: 40 TDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 71
>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 = 32.7 bits (73), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 21/30 (70%)
Query: 11 LKIMLERDSGRPRGFGFITYADRRAMDDAI 40
++IM +R SG+ RGF F+T+ D ++D +
Sbjct: 134 IEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
Score = 30.8 bits (68), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 9 NDLKIMLERDSGRPRGFGFITYADRRAMDDAI 40
D +M + ++ R RGFGF+TYA +D A+
Sbjct: 41 TDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 72
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 32.7 bits (73), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 30/49 (61%), Gaps = 1/49 (2%)
Query: 12 KIMLERD-SGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ 59
+++L +D + + RGF FIT+ + +A ++M+G+ + I V +A+
Sbjct: 36 EVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAK 84
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 32.7 bits (73), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 21/30 (70%)
Query: 11 LKIMLERDSGRPRGFGFITYADRRAMDDAI 40
++IM +R SG+ RGF F+T+ D ++D +
Sbjct: 132 IEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 161
Score = 30.8 bits (68), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 9 NDLKIMLERDSGRPRGFGFITYADRRAMDDAI 40
D +M + ++ R RGFGF+TYA +D A+
Sbjct: 39 TDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 70
>pdb|2YSA|A Chain A, Solution Structure Of The Zinc Finger Cchc Domain From The
Human Retinoblastoma-Binding Protein 6 (Retinoblastoma-
Binding Q Protein 1, Rbq-1)
Length = 55
Score = 32.7 bits (73), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 9/15 (60%), Positives = 14/15 (93%)
Query: 95 CFKCGRPGHWARDCP 109
CF+CG+PGH+ ++CP
Sbjct: 10 CFRCGKPGHYIKNCP 24
>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 = 32.7 bits (73), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 21/30 (70%)
Query: 11 LKIMLERDSGRPRGFGFITYADRRAMDDAI 40
++IM +R SG+ RGF F+T+ D ++D +
Sbjct: 127 IEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 156
Score = 30.8 bits (68), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 9 NDLKIMLERDSGRPRGFGFITYADRRAMDDAI 40
D +M + ++ R RGFGF+TYA +D A+
Sbjct: 34 TDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 65
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 32.7 bits (73), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 21/30 (70%)
Query: 11 LKIMLERDSGRPRGFGFITYADRRAMDDAI 40
++IM +R SG+ RGF F+T+ D ++D +
Sbjct: 134 IEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
Score = 30.8 bits (68), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 9 NDLKIMLERDSGRPRGFGFITYADRRAMDDAI 40
D +M + ++ R RGFGF+TYA +D A+
Sbjct: 41 TDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 72
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 32.7 bits (73), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 27/52 (51%)
Query: 9 NDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP 60
D++I L+ ++ + RGF F+ + AI M+ E R I VN A+P
Sbjct: 40 TDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKP 91
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 32.3 bits (72), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 25/46 (54%)
Query: 11 LKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVN 56
+ ++ + SG+PRG+ FI Y R M A + G++ R + V+
Sbjct: 132 IHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD 177
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 32.0 bits (71), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 25/50 (50%)
Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ 59
D+ I E + PRGF F+ + DRR DA M G E R + V A+
Sbjct: 42 DVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVAR 91
>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
pdb|3MD1|B Chain B, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
Length = 83
Score = 32.0 bits (71), Expect = 0.38, Method: Composition-based stats.
Identities = 12/46 (26%), Positives = 26/46 (56%)
Query: 13 IMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
+M + +G RG+GF+++ + +A+ M G++ R + +N A
Sbjct: 33 VMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 78
>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 = 31.6 bits (70), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 13/49 (26%), Positives = 27/49 (55%)
Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP 60
K++ ++ +G G+GF+ Y + + AI ++G + I V+ A+P
Sbjct: 50 KLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARP 98
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 31.6 bits (70), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 22/30 (73%)
Query: 13 IMLERDSGRPRGFGFITYADRRAMDDAIRE 42
++ +R +G+ RG+GF+T ADR A + A ++
Sbjct: 49 VITDRQTGKSRGYGFVTMADRAAAERACKD 78
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 31.2 bits (69), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 32/65 (49%), Gaps = 11/65 (16%)
Query: 1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAI----REMHGREFGDRVISVN 56
+++CL + L + R RGFGF+T+ D+ +D + E+ + +V
Sbjct: 52 VKECLVMRDPL-------TKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVAFPR 104
Query: 57 KAQPK 61
+AQPK
Sbjct: 105 RAQPK 109
>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|B Chain B, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|C Chain C, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|D Chain D, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
Length = 84
Score = 31.2 bits (69), Expect = 0.58, Method: Composition-based stats.
Identities = 13/49 (26%), Positives = 27/49 (55%)
Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP 60
K++ ++ +G G+GF+ Y + + AI ++G + I V+ A+P
Sbjct: 35 KLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARP 83
>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|6 Chain 6, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|7 Chain 7, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|8 Chain 8, Crystal Structure Of Human Spliceosomal U1 Snrnp
Length = 216
Score = 31.2 bits (69), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 25/46 (54%)
Query: 11 LKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVN 56
+ ++ + SG+PRG+ FI Y R M A + G++ R + V+
Sbjct: 132 IHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD 177
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 31.2 bits (69), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 2/43 (4%)
Query: 22 PRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA--QPKM 62
PR F+TY + D A+ E++G + + VN A QP +
Sbjct: 48 PRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPML 90
>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 = 30.8 bits (68), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 13/49 (26%), Positives = 27/49 (55%)
Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP 60
K++ ++ +G G+GF+ Y + + AI ++G + I V+ A+P
Sbjct: 33 KLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARP 81
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs
Of Human Antigen R
Length = 177
Score = 30.8 bits (68), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 13/49 (26%), Positives = 27/49 (55%)
Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP 60
K++ ++ +G G+GF+ Y + + AI ++G + I V+ A+P
Sbjct: 33 KLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARP 81
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 30.8 bits (68), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 12/46 (26%), Positives = 26/46 (56%)
Query: 13 IMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
+M + +G RG+GF+++ + +A+ M G++ R + +N A
Sbjct: 119 VMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 164
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug
Triplet Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 30.8 bits (68), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 11/44 (25%), Positives = 26/44 (59%)
Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISV 55
K+ +++ + + FGF++Y + + AI+ M+G + G + + V
Sbjct: 56 KVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKV 99
>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 = 0.95, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 2/46 (4%)
Query: 15 LERD--SGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
L RD +G+ +G+GFI Y ++ DA+ M+ + G + + V KA
Sbjct: 157 LARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 202
>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 = 30.4 bits (67), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 2/43 (4%)
Query: 22 PRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA--QPKM 62
PR F+TY + D A+ E++G + + VN A QP +
Sbjct: 72 PRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPML 114
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 30/54 (55%), Gaps = 4/54 (7%)
Query: 10 DLKIML-ERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM 62
D++I+ ER S +GFGF+T+ + D A ++HG R I VN A ++
Sbjct: 44 DVEIIFNERGS---KGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARV 94
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 14/54 (25%), Positives = 32/54 (59%), Gaps = 2/54 (3%)
Query: 11 LKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREF-GDRV-ISVNKAQPKM 62
+ I L++++G+P+G ++Y D A+ G++F G ++ +S+ + +P M
Sbjct: 53 IHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPM 106
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 24 GFGFITYADRRAMDDAIREMHGREFGDRVISV 55
GF F+ + + + AI E+HG+ F ++ + V
Sbjct: 66 GFAFVEFEEAESAAKAIEEVHGKSFANQPLEV 97
>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 = 1.3, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 2/46 (4%)
Query: 15 LERD--SGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
L RD +G+ +G+GFI Y ++ DA+ M+ + G + + V KA
Sbjct: 142 LARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 187
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 23/53 (43%), Gaps = 12/53 (22%)
Query: 8 NNDLKIMLERDSG------------RPRGFGFITYADRRAMDDAIREMHGREF 48
NN K LER G P GF F+ + D R DA+RE+ GR
Sbjct: 83 NNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTL 135
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 30/54 (55%), Gaps = 4/54 (7%)
Query: 10 DLKIML-ERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM 62
D++I+ ER S +GFGF+T+ + D A ++HG R I VN A ++
Sbjct: 58 DVEIIFNERGS---KGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARV 108
>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
pdb|4F02|D Chain D, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
Length = 213
Score = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 24/47 (51%)
Query: 9 NDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISV 55
N L + D +G+GF+ + + A + AI +M+G DR + V
Sbjct: 129 NILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 175
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 29.3 bits (64), Expect = 2.0, Method: Composition-based stats.
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 24 GFGFITYADRRAMDDAIREMHGREFGDRVISV 55
GF F+ + + + AI E+HG+ F ++ + V
Sbjct: 39 GFAFVEFEEAESAAKAIEEVHGKSFANQPLEV 70
>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 = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 24/47 (51%)
Query: 9 NDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISV 55
N L + D +G+GF+ + + A + AI +M+G DR + V
Sbjct: 31 NILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 77
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 29.3 bits (64), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 13/50 (26%), Positives = 26/50 (52%)
Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
+I+ +R++G +GFGF+ + A M E ++++ A+PK
Sbjct: 43 RIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPK 92
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of
Hypothetical Polyadenylate-Binding Protein (Pabpn1)
From Homo Sapiens At 1.95 A Resolution
Length = 89
Score = 29.3 bits (64), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 9/32 (28%), Positives = 22/32 (68%)
Query: 9 NDLKIMLERDSGRPRGFGFITYADRRAMDDAI 40
N + I+ ++ SG P+GF +I ++D+ ++ ++
Sbjct: 34 NRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 65
>pdb|1U6P|A Chain A, Nmr Structure Of The Mlv Encapsidation Signal Bound To The
Nucleocapsid Protein
pdb|1WWD|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
Sequence Aacagu
pdb|1WWE|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
Sequence Uuuugcu
pdb|1WWF|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
Sequence Ccuccgu
pdb|1WWG|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
Sequence Uaucug
Length = 56
Score = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 10/17 (58%), Positives = 11/17 (64%)
Query: 93 DDCFKCGRPGHWARDCP 109
D C C GHWA+DCP
Sbjct: 24 DQCAYCKEKGHWAKDCP 40
>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|B Chain B, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|C Chain C, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|D Chain D, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|E Chain E, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|F Chain F, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|G Chain G, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|H Chain H, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
Length = 190
Score = 29.3 bits (64), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 24/47 (51%)
Query: 9 NDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISV 55
N L + D +G+GF+ + + A + AI +M+G DR + V
Sbjct: 124 NILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 170
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 28.9 bits (63), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 9/32 (28%), Positives = 22/32 (68%)
Query: 9 NDLKIMLERDSGRPRGFGFITYADRRAMDDAI 40
N + I+ ++ SG P+GF +I ++D+ ++ ++
Sbjct: 33 NRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 64
>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 = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
D I + ++GR RGFGFI + D +++ + + R G RVI KA
Sbjct: 40 DCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDG-RVIDPKKA 87
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 24/47 (51%)
Query: 9 NDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISV 55
N L + D +G+GF+ + + A + AI +M+G DR + V
Sbjct: 37 NILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 83
>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 = 28.9 bits (63), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 2/49 (4%)
Query: 13 IMLERDSGRPRGFGFITYADRRAMDDAIREMHGR--EFGDRVISVNKAQ 59
I+ ++ +GRPRG F+ Y R +AI ++ E G + +SV A+
Sbjct: 45 ILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLAE 93
>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 = 28.5 bits (62), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 2/49 (4%)
Query: 13 IMLERDSGRPRGFGFITYADRRAMDDAIREMHGR--EFGDRVISVNKAQ 59
I+ ++ +GRPRG F+ Y R +AI ++ E G + +SV A+
Sbjct: 132 ILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLAE 180
>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm
pdb|2LEB|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uccagu-3'
pdb|2LEC|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uggagu-3'
Length = 135
Score = 28.1 bits (61), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 26/50 (52%)
Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ 59
D+ I +R + RGF F+ + D+R +DA+ M G R + V A+
Sbjct: 76 DVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMAR 125
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleaoproteins A2B1
Length = 116
Score = 28.1 bits (61), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 9 NDLKIMLERDSGRPRGFGFITYADRRAMDDAI 40
D +M + S R RGFGF+T++ +D A+
Sbjct: 55 TDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 86
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 28.1 bits (61), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 16/64 (25%), Positives = 33/64 (51%), Gaps = 5/64 (7%)
Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA-----QPKMGG 64
+KI+ +R++ + RG+GF+ + + AI ++G ++ + V A +P + G
Sbjct: 71 SVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAG 130
Query: 65 EVSD 68
V D
Sbjct: 131 AVGD 134
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 28.1 bits (61), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 11/44 (25%), Positives = 24/44 (54%), Gaps = 3/44 (6%)
Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVI 53
++++M + SG+ RGF F+ ++ + DA R M + ++
Sbjct: 31 EVRLMRNKSSGQSRGFAFVEFSH---LQDATRWMEANQHSLNIL 71
>pdb|2A51|A Chain A, Structure Of The (13-51) Domain Of The Nucleocapsid
Protein Ncp8 From Sivlhoest
Length = 39
Score = 28.1 bits (61), Expect = 4.8, Method: Composition-based stats.
Identities = 10/14 (71%), Positives = 11/14 (78%)
Query: 95 CFKCGRPGHWARDC 108
CF CG+PGH AR C
Sbjct: 3 CFNCGKPGHTARMC 16
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 28.1 bits (61), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 23/53 (43%), Gaps = 12/53 (22%)
Query: 8 NNDLKIMLERDSG------------RPRGFGFITYADRRAMDDAIREMHGREF 48
NN K LER G P GF F+ + D R DA+R++ GR
Sbjct: 83 NNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRDLDGRTL 135
>pdb|1A6B|B Chain B, Nmr Structure Of The Complex Between The Zinc Finger
Protein Ncp10 Of Moloney Murine Leukemia Virus And A
Sequence Of The Psi-Packaging Domain Of Hiv-1, 20
Structures
Length = 40
Score = 28.1 bits (61), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 10/17 (58%), Positives = 11/17 (64%)
Query: 93 DDCFKCGRPGHWARDCP 109
D C C GHWA+DCP
Sbjct: 11 DQCAYCKEKGHWAKDCP 27
>pdb|1CL4|A Chain A, Nucleocapsid Protein From Mason-Pfizer Monkey Virus (Mpmv)
Length = 60
Score = 28.1 bits (61), Expect = 5.4, Method: Composition-based stats.
Identities = 9/14 (64%), Positives = 13/14 (92%)
Query: 95 CFKCGRPGHWARDC 108
CFKCG+ GH+A++C
Sbjct: 4 CFKCGKKGHFAKNC 17
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 27.7 bits (60), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 11/33 (33%), Positives = 19/33 (57%)
Query: 13 IMLERDSGRPRGFGFITYADRRAMDDAIREMHG 45
I+ ++ +GRPRG F+ Y R +AI ++
Sbjct: 121 ILRDKLTGRPRGVAFVRYNKREEAQEAISALNN 153
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 27.7 bits (60), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 24/43 (55%)
Query: 16 ERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
+R +G+ +G+GF+ + D AI+ M + + I VNKA
Sbjct: 50 DRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA 92
>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 = 27.7 bits (60), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 26/46 (56%), Gaps = 2/46 (4%)
Query: 15 LERD--SGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
L RD +G+ +G+GFI Y ++ DA+ + + G + + V KA
Sbjct: 141 LARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVGKA 186
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 27.3 bits (59), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 25/49 (51%)
Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
D+ I +R + RGF F+ + D+R +DA+ M G R + V A
Sbjct: 99 DVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA 147
>pdb|1HVN|E Chain E, Zinc-And Sequence-Dependent Binding To Nucleic Acids By
The N-Terminal Zinc Finger Domain Of The Hiv-1
Nucleocapsid Protein: Nmr Structure Of The Complex With
The Psi-Site Analog, DACGCC
pdb|1HVO|E Chain E, Zinc-And Sequence-Dependent Binding To Nucleic Acids By
The N-Terminal Zinc Finger Domain Of The Hiv-1
Nucleocapsid Protein: Nmr Structure Of The Complex With
The Psi-Site Analog, DACGCC
pdb|2ZNF|A Chain A, High-Resolution Structure Of An Hiv Zinc Fingerlike Domain
Via A New Nmr-Based Distance Geometry Approach
Length = 18
Score = 27.3 bits (59), Expect = 8.4, Method: Composition-based stats.
Identities = 9/14 (64%), Positives = 11/14 (78%)
Query: 95 CFKCGRPGHWARDC 108
CF CG+ GH AR+C
Sbjct: 3 CFNCGKEGHIARNC 16
>pdb|2BL6|A Chain A, Solution Structure Of The Zn Complex Of Eiav Ncp11(22-58)
Peptide, Including Two Cchc Zn-Binding Motifs
Length = 37
Score = 27.3 bits (59), Expect = 8.7, Method: Composition-based stats.
Identities = 8/14 (57%), Positives = 12/14 (85%)
Query: 95 CFKCGRPGHWARDC 108
CFKC +PGH+++ C
Sbjct: 22 CFKCKQPGHFSKQC 35
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 27.3 bits (59), Expect = 8.7, Method: Composition-based stats.
Identities = 10/30 (33%), Positives = 19/30 (63%)
Query: 13 IMLERDSGRPRGFGFITYADRRAMDDAIRE 42
+M + + R RGFGF+T+ D+ +D + +
Sbjct: 32 VMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
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 0.140 0.446
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,903,128
Number of Sequences: 62578
Number of extensions: 266224
Number of successful extensions: 608
Number of sequences better than 100.0: 107
Number of HSP's better than 100.0 without gapping: 96
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 493
Number of HSP's gapped (non-prelim): 127
length of query: 255
length of database: 14,973,337
effective HSP length: 97
effective length of query: 158
effective length of database: 8,903,271
effective search space: 1406716818
effective search space used: 1406716818
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: 50 (23.9 bits)