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= psy11978
(91 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 74.7 bits (182), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 38/77 (49%), Positives = 51/77 (66%), Gaps = 4/77 (5%)
Query: 16 SMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTG--QSKGKIF 73
++ P+QPD D IKMFVGQ+PR+ E DL ++F +YG VY INVLRD+ QSKG F
Sbjct: 4 TLDHPDQPDLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCF 63
Query: 74 EAAFLKIARAAIEPQKA 90
+ + +AA+E Q A
Sbjct: 64 VTFYTR--KAALEAQNA 78
Score = 33.1 bits (74), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
K+F+G I + E D+ MFS +G++ +LR G S+G F
Sbjct: 109 KLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAF 152
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 67.0 bits (162), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 28/50 (56%), Positives = 37/50 (74%)
Query: 24 DPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
D D IK+FVGQIPR +DE DL +F E+GR+Y + VL+D++TG KG F
Sbjct: 12 DHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAF 61
>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 = 65.1 bits (157), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 34/67 (50%), Positives = 44/67 (65%), Gaps = 4/67 (5%)
Query: 26 DFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTG--QSKGKIFEAAFLKIARA 83
D IKMFVGQ+PR+ E DL ++F +YG VY INVLRD+ QSKG F + + +A
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTR--KA 59
Query: 84 AIEPQKA 90
A+E Q A
Sbjct: 60 ALEAQNA 66
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 65.1 bits (157), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 34/67 (50%), Positives = 44/67 (65%), Gaps = 4/67 (5%)
Query: 26 DFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTG--QSKGKIFEAAFLKIARA 83
D IKMFVGQ+PR+ E DL ++F +YG VY INVLRD+ QSKG F + + +A
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTR--KA 59
Query: 84 AIEPQKA 90
A+E Q A
Sbjct: 60 ALEAQNA 66
Score = 33.1 bits (74), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
K+F+G I + E D+ MFS +G++ +LR G S+G F
Sbjct: 97 KLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAF 140
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 65.1 bits (157), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 26/50 (52%), Positives = 37/50 (74%)
Query: 24 DPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
D D IK+F+GQIPR++DE DL +F E+G++Y + VL+D+ TG KG F
Sbjct: 10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAF 59
>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 = 62.8 bits (151), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 33/67 (49%), Positives = 43/67 (64%), Gaps = 4/67 (5%)
Query: 26 DFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTG--QSKGKIFEAAFLKIARA 83
D IK FVGQ+PR+ E DL ++F +YG VY INVLRD+ QSKG F + + +A
Sbjct: 2 DAIKXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTR--KA 59
Query: 84 AIEPQKA 90
A+E Q A
Sbjct: 60 ALEAQNA 66
Score = 31.2 bits (69), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
K+F+G I + E D+ FS +G++ +LR G S+G F
Sbjct: 97 KLFIGXISKKCTENDIRVXFSSFGQIEECRILRGP-DGLSRGCAF 140
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 46.6 bits (109), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 34/55 (61%), Gaps = 3/55 (5%)
Query: 22 QPDPDFIK---MFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
+P + IK +++ +PR+M + D+ MFS +GR+ N VL D+ TG S+G F
Sbjct: 80 RPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAF 134
Score = 35.8 bits (81), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 26/45 (57%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
+ V +P++M + +L +FS G V + ++RDKV G S G F
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGF 48
>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 = 46.2 bits (108), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 34/55 (61%), Gaps = 3/55 (5%)
Query: 22 QPDPDFIK---MFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
+P + IK +++ +PR+M + D+ MFS +GR+ N VL D+ TG S+G F
Sbjct: 80 RPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAF 134
Score = 35.4 bits (80), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 26/45 (57%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
+ V +P++M + +L +FS G V + ++RDKV G S G F
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGF 48
>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 = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 31/45 (68%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
++V +P++M + +L ++FS+YGR+ +L D+VTG S+G F
Sbjct: 90 NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGF 134
Score = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 26/45 (57%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
+ V +P++M + + +F G + + ++RDK+TGQS G F
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGF 48
>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 = 42.4 bits (98), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 29/45 (64%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
++V +PR++ + L +F +YG + N+LRDK+TG+ +G F
Sbjct: 15 NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAF 59
>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 = 42.0 bits (97), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 29/45 (64%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
++V +PR++ + L +F +YG + N+LRDK+TG+ +G F
Sbjct: 102 NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAF 146
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 42.0 bits (97), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 29/45 (64%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
++V +PR++ + L +F +YG + N+LRDK+TG+ +G F
Sbjct: 91 NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAF 135
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 42.0 bits (97), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 30/44 (68%)
Query: 30 MFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
++V +P S+ DL ++FS+YG+V + +++DK T +SKG F
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAF 62
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 41.2 bits (95), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 30/45 (66%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
++V +P++M + ++ ++FS+YGR+ +L D+ TG S+G F
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGF 47
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 29/52 (55%)
Query: 22 QPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
Q D F K+FVG +P +A L K F +G + V+ D+ TG+S+G F
Sbjct: 12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGF 63
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 30/45 (66%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
++V +P++M + ++ ++FS+YGR+ +L D+ TG S+G F
Sbjct: 92 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGF 136
Score = 34.3 bits (77), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 26/45 (57%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
+ V +P++M + + +F G + + ++RDK+TGQS G F
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGF 50
>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 = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 31/52 (59%)
Query: 22 QPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
QP P K+F+G +P +++ + ++ + +G + N+++D TG SKG F
Sbjct: 91 QPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAF 142
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 31/52 (59%)
Query: 22 QPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
QP P K+F+G +P +++ + ++ + +G + N+++D TG SKG F
Sbjct: 89 QPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAF 140
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 39.7 bits (91), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 33/52 (63%), Gaps = 1/52 (1%)
Query: 23 PDPDFIK-MFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
P+PD ++ + V IP ++DE L ++F YG + ++ ++ D+ T QS+G F
Sbjct: 37 PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGF 88
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 38.9 bits (89), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 27/45 (60%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
K+FVG + S + L FS+YG V + +++DK T QS+G F
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGF 62
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 38.5 bits (88), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 19 LPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
+ +Q + D +++ +P SMDE +L M +G+V + +LRD +G S+G F
Sbjct: 17 MAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGF 70
>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 = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 27/42 (64%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
KMF+G + E +L + F +YG V ++ +++D TG+S+G
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRG 46
Score = 33.5 bits (75), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 26/42 (61%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
K+FVG I + + + FS++G + + ++ DK TGQS+G
Sbjct: 89 KIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRG 130
>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 = 36.6 bits (83), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 27/49 (55%)
Query: 25 PDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
P + V +P++M + +L +FS G V + ++RDKV G S G F
Sbjct: 2 PGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGF 50
>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 = 36.6 bits (83), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 26 DFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIFEAAFLKI-ARAA 84
+ +FVG + + D+ F+ +GR+ + V++D TG+SKG F + F K A A
Sbjct: 14 NHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENA 73
Query: 85 IE 86
I+
Sbjct: 74 IQ 75
>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 = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 13/45 (28%), Positives = 28/45 (62%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
K+F+G +P +++ + ++ + +G + N+++D TG SKG F
Sbjct: 116 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAF 160
>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 = 36.2 bits (82), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 30 MFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG-KIFEAAFLKIARAAIE 86
+FV + E D+ F+EYG + NI++ D+ TG KG + E K A+AA+E
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 82
>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 = 36.2 bits (82), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 30 MFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG-KIFEAAFLKIARAAIE 86
+FV + E D+ F+EYG + NI++ D+ TG KG + E K A+AA+E
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 83
>pdb|2XB2|D Chain D, Crystal Structure Of The Core
Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How
The Ejc Is Bridged To The Nmd Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core
Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How
The Ejc Is Bridged To The Nmd Machinery
Length = 90
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 30 MFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG-KIFEAAFLKIARAAIE 86
+FV + E D+ F+EYG + NI++ D+ TG KG + E K A+AA+E
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 67
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 13/45 (28%), Positives = 28/45 (62%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
K+F+G +P +++ + ++ + +G + N+++D TG SKG F
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAF 47
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 35.8 bits (81), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 30 MFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG-KIFEAAFLKIARAAIE 86
+FV + E D+ F+EYG + NI++ D+ TG KG + E K A+AA+E
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 67
>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 = 35.8 bits (81), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 30 MFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG-KIFEAAFLKIARAAIE 86
+FV + E D+ F+EYG + NI++ D+ TG KG + E K A+AA+E
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 69
>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 = 35.8 bits (81), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 30 MFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG-KIFEAAFLKIARAAIE 86
+FV + E D+ F+EYG + NI++ D+ TG KG + E K A+AA+E
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 67
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 26/50 (52%)
Query: 24 DPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
D +FVG IP E L +FSE G V + ++ D+ TG+ KG F
Sbjct: 5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGF 54
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 10/36 (27%), Positives = 24/36 (66%)
Query: 27 FIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRD 62
+K+F+G +PR E ++ +F +YG+V +++++
Sbjct: 8 MVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN 43
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 35.0 bits (79), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 29/42 (69%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
K+FVG + +E L ++FS+YG++ + V++D+ T +S+G
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRG 55
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 35.0 bits (79), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 28/56 (50%)
Query: 18 SLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
S P + D + V + E DL ++F +G + I + +DK TGQSKG F
Sbjct: 6 SGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAF 61
>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 = 35.0 bits (79), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 26/45 (57%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
K+FVG I +E L F +YG++ I ++ D+ +G+ +G F
Sbjct: 105 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAF 149
Score = 28.9 bits (63), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 20 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
P++P+ K+F+G + + L F ++G + + V+RD T +S+G
Sbjct: 6 PKEPEQ-LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRG 55
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 35.0 bits (79), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 34/63 (53%), Gaps = 8/63 (12%)
Query: 18 SLPE---QPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIFE 74
SLPE P+ +FVG I MDE ++ F+ YG V + ++ D+ TG SKG F
Sbjct: 1 SLPEGKIMPNT----VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFV 55
Query: 75 AAF 77
+ +
Sbjct: 56 SFY 58
>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 = 35.0 bits (79), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 26/45 (57%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
K+FVG I +E L F +YG++ I ++ D+ +G+ +G F
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAF 150
Score = 29.3 bits (64), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 17 MSLPEQP-DPDFI-KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
MS E P +P+ + K+F+G + + L F ++G + + V+RD T +S+G
Sbjct: 1 MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRG 56
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 35.0 bits (79), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 26/45 (57%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
K+FVG I +E L F +YG++ I ++ D+ +G+ +G F
Sbjct: 107 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAF 151
Score = 28.9 bits (63), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 20 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
P++P+ K+F+G + + L F ++G + + V+RD T +S+G
Sbjct: 8 PKEPEQ-LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRG 57
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 35.0 bits (79), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 26/45 (57%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
K+FVG I +E L F +YG++ I ++ D+ +G+ +G F
Sbjct: 104 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAF 148
Score = 28.5 bits (62), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 20 PEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
P++P+ K+F+G + + L F ++G + + V+RD T +S+G
Sbjct: 5 PKEPEQ-LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRG 54
>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 = 35.0 bits (79), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 26/45 (57%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
K+FVG I +E L F +YG++ I ++ D+ +G+ +G F
Sbjct: 99 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAF 143
Score = 27.7 bits (60), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 12/42 (28%), Positives = 23/42 (54%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
K+F+G + + L F ++G + + V+RD T +S+G
Sbjct: 8 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRG 49
>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Rna, Uuguucuu
Length = 102
Score = 35.0 bits (79), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 34/63 (53%), Gaps = 8/63 (12%)
Query: 18 SLPE---QPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIFE 74
SLPE P+ +FVG I MDE ++ F+ YG V + ++ D+ TG SKG F
Sbjct: 1 SLPEGKIMPN----TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFV 55
Query: 75 AAF 77
+ +
Sbjct: 56 SFY 58
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 26/45 (57%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
K+FVG I +E L F +YG++ I ++ D+ +G+ +G F
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAF 150
Score = 29.3 bits (64), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 17 MSLPEQP-DPDFI-KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
MS E P +P+ + K+F+G + + L F ++G + + V+RD T +S+G
Sbjct: 1 MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRG 56
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 31/55 (56%)
Query: 26 DFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIFEAAFLKI 80
+ +FVG + + D+ F+ +G++ + V++D TG+SKG F + + K+
Sbjct: 14 NHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKL 68
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 34.7 bits (78), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 30 MFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIFEAAF 77
+FVG I MDE ++ F+ YG V + ++ D+ TG SKG F + +
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFY 59
>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 = 34.3 bits (77), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 35/66 (53%), Gaps = 5/66 (7%)
Query: 10 TYEYVRSMSLPE-QPDP----DFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKV 64
+YE VR+ E +P P + +FV I E ++ + F +YG + NI++ D+
Sbjct: 50 SYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRR 109
Query: 65 TGQSKG 70
TG SKG
Sbjct: 110 TGFSKG 115
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 34.3 bits (77), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 26/45 (57%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
+ V +P++M + + +F G + + ++RDK+TGQS G F
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGF 50
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 33.9 bits (76), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 35/69 (50%), Gaps = 7/69 (10%)
Query: 22 QPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIFEAAFLKIA 81
QP P K+FVG + + E D+ ++F +G + +LR G SKG AF+K +
Sbjct: 11 QP-PSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGP-DGNSKG----CAFVKYS 64
Query: 82 RAAIEPQKA 90
A E Q A
Sbjct: 65 SHA-EAQAA 72
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14
Complex
Length = 110
Score = 33.9 bits (76), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 35/66 (53%), Gaps = 5/66 (7%)
Query: 10 TYEYVRSMSLPE-QPDP----DFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKV 64
+YE VR+ E +P P + +FV I E ++ + F +YG + NI++ D+
Sbjct: 4 SYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRR 63
Query: 65 TGQSKG 70
TG SKG
Sbjct: 64 TGFSKG 69
>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 = 33.9 bits (76), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 12/47 (25%), Positives = 27/47 (57%)
Query: 27 FIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
F +++V + + + + D+ +F +G++ + + RD TG+ KG F
Sbjct: 109 FNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGF 155
>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 = 0.031, Method: Compositional matrix adjust.
Identities = 12/47 (25%), Positives = 27/47 (57%)
Query: 27 FIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
F +++V + + + + D+ +F +G++ + + RD TG+ KG F
Sbjct: 110 FNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGF 156
>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 = 33.5 bits (75), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 24/41 (58%)
Query: 30 MFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
MF+G + + DL FS++G V + + D +TG+S+G
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRG 42
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 33.1 bits (74), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 29/46 (63%)
Query: 28 IKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
++++VG + ++ E L +F +GR+ +I ++ D TG+SKG F
Sbjct: 27 MRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGF 72
>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 = 33.1 bits (74), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 12/47 (25%), Positives = 27/47 (57%)
Query: 27 FIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
F +++V + + + + D+ +F +G++ + + RD TG+ KG F
Sbjct: 125 FNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGF 171
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 32.7 bits (73), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 27/41 (65%)
Query: 30 MFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
++VG + S + ++FS++G+V+N+ ++ D+ T + KG
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKG 44
>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 = 32.7 bits (73), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 25/45 (55%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
+ V +P++ + +L +FS G V + ++RDKV G S G F
Sbjct: 21 NLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGF 65
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 32.7 bits (73), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 12/38 (31%), Positives = 24/38 (63%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTG 66
++FVG +P + E ++ K+F +YG+ + + +DK G
Sbjct: 24 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFG 61
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In
Trinucleotide Repeat Containing 4 Variant
Length = 102
Score = 32.3 bits (72), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 32/62 (51%), Gaps = 10/62 (16%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIFEAAFLKI-----ARA 83
K+FVG + + + D+ KMF +G + VLR G SKG AF+K A+A
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGP-DGTSKG----CAFVKFQTHAEAQA 68
Query: 84 AI 85
AI
Sbjct: 69 AI 70
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 32.3 bits (72), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 28/44 (63%)
Query: 30 MFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
++VG + ++ E L +F +G++ NI +++D TG+SKG F
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGF 51
>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 = 32.3 bits (72), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 12/38 (31%), Positives = 24/38 (63%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTG 66
++FVG +P + E ++ K+F +YG+ + + +DK G
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFG 54
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 32.3 bits (72), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 27/44 (61%)
Query: 30 MFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
++VG + + E L ++F + G V N ++ +D+VTGQ +G F
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGF 61
>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 = 32.3 bits (72), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 24/45 (53%)
Query: 25 PDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSK 69
P+ +F+ +P+ + DL +MF +G V + V DK T SK
Sbjct: 23 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSK 67
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 32.3 bits (72), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 22/41 (53%)
Query: 30 MFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
+ V +P E DL + FS +G V + V +D TG SKG
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKG 58
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 32.3 bits (72), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 30/59 (50%), Gaps = 2/59 (3%)
Query: 30 MFVGQIPRSMDEADLTKMFSEYGRVYNI-NVLRDKVTGQSKGKIF-EAAFLKIARAAIE 86
+F+G + +DE L FS +G + ++RD TG SKG F A + AAIE
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 32.0 bits (71), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 12/38 (31%), Positives = 21/38 (55%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTG 66
++FVG +P + E D ++F YG + + RD+ G
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFG 61
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 32.0 bits (71), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 32/63 (50%), Gaps = 10/63 (15%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIFEAAFLKI-----ARA 83
K+FVG + + E D+ ++F +G + VLR G SKG AF+K A+A
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKG----CAFVKFSSHTEAQA 71
Query: 84 AIE 86
AI
Sbjct: 72 AIH 74
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 31.6 bits (70), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 25/46 (54%)
Query: 28 IKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
KMF+G + + L + F ++G V V+RD +T +S+G F
Sbjct: 26 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGF 71
>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 = 31.6 bits (70), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 24/44 (54%)
Query: 30 MFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
+++G IP E + + S G V N+ ++ D TG+SKG F
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAF 50
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 31.6 bits (70), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
KMF+G + + L + F ++G V V+RD +T +S+G
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRG 43
>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
pdb|3S7R|B Chain B, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
Length = 87
Score = 31.2 bits (69), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 23/42 (54%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
K FVG + + DL F+++G V + + D TG+S+G
Sbjct: 13 KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRG 54
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 31.2 bits (69), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 24/44 (54%)
Query: 30 MFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
+++G IP E + + S G V N+ ++ D TG+SKG F
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAF 48
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 31.2 bits (69), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 23/32 (71%), Gaps = 1/32 (3%)
Query: 29 KMFVGQIP-RSMDEADLTKMFSEYGRVYNINV 59
++F+G +P +++ + DL ++FS YG + IN+
Sbjct: 4 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI 35
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 31.2 bits (69), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 25/45 (55%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
++FV + + E DL K+FS YG + ++ D +T + KG F
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAF 54
>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 = 31.2 bits (69), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 24/44 (54%)
Query: 30 MFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
+++G IP E + + S G V N+ ++ D TG+SKG F
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAF 49
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 30.8 bits (68), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 23/32 (71%), Gaps = 1/32 (3%)
Query: 29 KMFVGQIP-RSMDEADLTKMFSEYGRVYNINV 59
++F+G +P +++ + DL ++FS YG + IN+
Sbjct: 12 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI 43
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 30.8 bits (68), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 23/32 (71%), Gaps = 1/32 (3%)
Query: 29 KMFVGQIP-RSMDEADLTKMFSEYGRVYNINV 59
++F+G +P +++ + DL ++FS YG + IN+
Sbjct: 24 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI 55
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 30.8 bits (68), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 23/32 (71%), Gaps = 1/32 (3%)
Query: 29 KMFVGQIP-RSMDEADLTKMFSEYGRVYNINV 59
++F+G +P +++ + DL ++FS YG + IN+
Sbjct: 24 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI 55
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleaoproteins A2B1
Length = 116
Score = 30.4 bits (67), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 26/47 (55%)
Query: 27 FIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
F K+F+G + E L + ++G++ + V+RD + +S+G F
Sbjct: 27 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGF 73
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 30.0 bits (66), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 21/30 (70%)
Query: 44 LTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
LT +FS+ G+V N+ D+ TG++KG +F
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLF 58
>pdb|3NS6|A Chain A, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
pdb|3NS6|B Chain B, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
Length = 100
Score = 30.0 bits (66), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 21/30 (70%)
Query: 44 LTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
LT +FS+ G+V N+ D+ TG++KG +F
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLF 58
>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 = 29.3 bits (64), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 21/30 (70%)
Query: 44 LTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
L ++F +YGRV ++ + RD+ T +S+G F
Sbjct: 64 LRRVFEKYGRVGDVYIPRDRYTKESRGFAF 93
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 28.9 bits (63), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 22 QPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
PDP+ G + E DL ++FS+YG + +++++ D+ + +S+G F
Sbjct: 8 NPDPNCCLGVFG-LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAF 58
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 28.9 bits (63), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 34/74 (45%), Gaps = 13/74 (17%)
Query: 30 MFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG-------------KIFEAA 76
+FVG + + D+ F ++G+V + ++ DK T + +G K+ E
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 77 FLKIARAAIEPQKA 90
F +I +E +KA
Sbjct: 62 FHEINNKMVECKKA 75
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 28.9 bits (63), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 22 QPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
PDP+ G + E DL ++FS+YG + +++++ D+ + +S+G F
Sbjct: 11 NPDPNCCLGVFG-LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAF 61
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 28.9 bits (63), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 22 QPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
PDP+ G + E DL ++FS+YG + +++++ D+ + +S+G F
Sbjct: 11 NPDPNCCLGVFG-LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAF 61
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 28.9 bits (63), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 21/34 (61%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRD 62
K+FVG IP + E +L + F ++G V + ++ D
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYD 45
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 28.5 bits (62), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 22 QPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
PDP+ G + E DL ++FS+YG + +++++ D+ + +S+G F
Sbjct: 42 NPDPNCCLGVFG-LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAF 92
>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 = 28.5 bits (62), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 25/47 (53%)
Query: 27 FIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
F +FV ++ E+ L + F YG + I+++ K +G+ +G F
Sbjct: 102 FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAF 148
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 28.5 bits (62), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 21/30 (70%)
Query: 44 LTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
L ++F +YGRV ++ + RD+ T +S+G F
Sbjct: 87 LRRVFEKYGRVGDVYIPRDRYTKESRGFAF 116
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Rna-Binding Protein 14
Length = 90
Score = 28.5 bits (62), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 19/34 (55%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRD 62
K+FVG + + +L +F GRV +V++D
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVVKD 44
>pdb|2E5G|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 21
Length = 94
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 21/34 (61%)
Query: 30 MFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDK 63
+FV PR +D A L++ F +G V ++ + +DK
Sbjct: 11 VFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDK 44
>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 = 28.1 bits (61), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 23 PDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIFEAAFLKI-A 81
P +FVG + + A + F+ +GR+ + V++D TG+SKG F + F K A
Sbjct: 2 PLGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDA 61
Query: 82 RAAIE 86
AI+
Sbjct: 62 ENAIQ 66
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 28.1 bits (61), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 36 PRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
P + D+ DL K+ YG++ + + DK T + KG F
Sbjct: 15 PGTTDQ-DLVKLCQPYGKIVSTKAILDKTTNKCKGYGF 51
>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 = 27.7 bits (60), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 25/47 (53%)
Query: 27 FIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
F +FV ++ E+ L + F YG + I+++ K +G+ +G F
Sbjct: 102 FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAF 148
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 10/30 (33%), Positives = 15/30 (50%)
Query: 25 PDFIKMFVGQIPRSMDEADLTKMFSEYGRV 54
P ++G IP EADL +F +G +
Sbjct: 25 PRVTTAYIGNIPHFATEADLIPLFQNFGFI 54
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 27.3 bits (59), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 25/48 (52%)
Query: 26 DFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
D +FVG + ++D+ L F ++ + +V+ D TG S+G F
Sbjct: 86 DTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGF 133
>pdb|2ZCW|A Chain A, Crystal Structure Of Ttha1359, A Transcriptional
Regulator, CrpFNR FAMILY FROM THERMUS THERMOPHILUS HB8
Length = 202
Score = 27.3 bits (59), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 14 VRSMSLPEQPDPDFIKMFVGQIPRSMDEA 42
VR LPE PDP+ +K + + + EA
Sbjct: 79 VRLEPLPENPDPELLKDLAQHLSQGLAEA 107
>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 = 27.3 bits (59), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 13/46 (28%), Positives = 24/46 (52%)
Query: 28 IKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
+FVG + ++D+ L F ++ + +V+ D TG S+G F
Sbjct: 2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGF 47
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 26.9 bits (58), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 13/45 (28%), Positives = 24/45 (53%)
Query: 26 DFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKG 70
D +F Q+ + DL FS G+V ++ ++ D+ + +SKG
Sbjct: 24 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKG 68
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 26.9 bits (58), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 10/29 (34%), Positives = 17/29 (58%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNI 57
K+FVG+ M +L + F +YG V ++
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYGEVVDV 41
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 26.9 bits (58), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 8/32 (25%), Positives = 20/32 (62%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVL 60
++ V IP + DL +MF ++G++ ++ ++
Sbjct: 17 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEII 48
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 26.9 bits (58), Expect = 3.3, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 33/71 (46%), Gaps = 1/71 (1%)
Query: 14 VRSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
+R L Q P + V +P S+ + ++ +G + ++ + TGQSKG F
Sbjct: 82 LRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGF 141
Query: 74 EAAFLKIARAA 84
A ++K AA
Sbjct: 142 -AEYMKKDSAA 151
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 26.6 bits (57), Expect = 3.4, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 33/71 (46%), Gaps = 1/71 (1%)
Query: 14 VRSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
+R L Q P + V +P S+ + ++ +G + ++ + TGQSKG F
Sbjct: 82 LRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGF 141
Query: 74 EAAFLKIARAA 84
A ++K AA
Sbjct: 142 -AEYMKKDSAA 151
>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
pdb|3H2U|D Chain D, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
Length = 283
Score = 26.6 bits (57), Expect = 3.4, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 33/71 (46%), Gaps = 1/71 (1%)
Query: 14 VRSMSLPEQPDPDFIKMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRDKVTGQSKGKIF 73
+R L Q P + V +P S+ + ++ +G + ++ + TGQSKG F
Sbjct: 80 LRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGF 139
Query: 74 EAAFLKIARAA 84
A ++K AA
Sbjct: 140 -AEYMKKDSAA 149
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1
In Complex With Ugcaugu
Length = 109
Score = 26.6 bits (57), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 8/32 (25%), Positives = 20/32 (62%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVL 60
++ V IP + DL +MF ++G++ ++ ++
Sbjct: 31 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEII 62
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 26.6 bits (57), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 11/28 (39%), Positives = 18/28 (64%)
Query: 30 MFVGQIPRSMDEADLTKMFSEYGRVYNI 57
+FVG+ M E +L + FS+YG V ++
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDV 35
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 26.2 bits (56), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 10/24 (41%), Positives = 16/24 (66%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYG 52
K+FVG +P +DE ++T F +G
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFG 33
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 26.2 bits (56), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 11/33 (33%), Positives = 20/33 (60%)
Query: 30 MFVGQIPRSMDEADLTKMFSEYGRVYNINVLRD 62
+FV + ++ E L K FSE+G++ + L+D
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD 50
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 26.2 bits (56), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 18/34 (52%)
Query: 29 KMFVGQIPRSMDEADLTKMFSEYGRVYNINVLRD 62
K+ VG I + +L F EYG V ++++D
Sbjct: 12 KLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD 45
>pdb|3A62|A Chain A, Crystal Structure Of Phosphorylated P70s6k1
Length = 327
Score = 25.8 bits (55), Expect = 5.7, Method: Composition-based stats.
Identities = 14/31 (45%), Positives = 18/31 (58%), Gaps = 4/31 (12%)
Query: 51 YGRVYNINVLRDKVTGQSKGKIFEAAFLKIA 81
YG+V+ + KVTG + GKIF LK A
Sbjct: 30 YGKVFQVR----KVTGANTGKIFAMKVLKKA 56
>pdb|3A60|A Chain A, Crystal Structure Of Unphosphorylated P70s6k1 (Form I)
pdb|3A60|B Chain B, Crystal Structure Of Unphosphorylated P70s6k1 (Form I)
pdb|3A61|A Chain A, Crystal Structure Of Unphosphorylated P70s6k1 (Form Ii)
Length = 327
Score = 25.8 bits (55), Expect = 5.7, Method: Composition-based stats.
Identities = 14/31 (45%), Positives = 18/31 (58%), Gaps = 4/31 (12%)
Query: 51 YGRVYNINVLRDKVTGQSKGKIFEAAFLKIA 81
YG+V+ + KVTG + GKIF LK A
Sbjct: 30 YGKVFQVR----KVTGANTGKIFAMKVLKKA 56
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 25.8 bits (55), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 10/33 (30%), Positives = 20/33 (60%)
Query: 30 MFVGQIPRSMDEADLTKMFSEYGRVYNINVLRD 62
+FV + ++ E L K FS++G++ + L+D
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD 46
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
0.320 0.136 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,540,248
Number of Sequences: 62578
Number of extensions: 85700
Number of successful extensions: 376
Number of sequences better than 100.0: 113
Number of HSP's better than 100.0 without gapping: 106
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 256
Number of HSP's gapped (non-prelim): 127
length of query: 91
length of database: 14,973,337
effective HSP length: 58
effective length of query: 33
effective length of database: 11,343,813
effective search space: 374345829
effective search space used: 374345829
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)