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= psy15515
(242 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 79.0 bits (193), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 37/88 (42%), Positives = 58/88 (65%), Gaps = 2/88 (2%)
Query: 39 GTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAK 98
G ++P VFVGGI E E+ F++YG VK+VKI+ DR G+SKGYGF++F ++ + +
Sbjct: 5 GKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQ 64
Query: 99 RLQKDSDNIMFKEKRLNIAPAIKKQGFT 126
++ + N F K+L + PAI+KQ +
Sbjct: 65 KIVESQIN--FHGKKLKLGPAIRKQNLS 90
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 78.2 bits (191), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 37/85 (43%), Positives = 57/85 (67%), Gaps = 2/85 (2%)
Query: 39 GTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAK 98
G ++P VFVGGI E E+ F++YG VK+VKI+ DR G+SKGYGF++F ++ + +
Sbjct: 6 GKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQ 65
Query: 99 RLQKDSDNIMFKEKRLNIAPAIKKQ 123
++ + N F K+L + PAI+KQ
Sbjct: 66 KIVESQIN--FHGKKLKLGPAIRKQ 88
>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 = 77.8 bits (190), Expect = 6e-15, Method: Compositional matrix adjust.
Identities = 37/85 (43%), Positives = 57/85 (67%), Gaps = 2/85 (2%)
Query: 39 GTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAK 98
G ++P VFVGGI E E+ F++YG VK+VKI+ DR G+SKGYGF++F ++ + +
Sbjct: 5 GKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQ 64
Query: 99 RLQKDSDNIMFKEKRLNIAPAIKKQ 123
++ + N F K+L + PAI+KQ
Sbjct: 65 KIVESQIN--FHGKKLKLGPAIRKQ 87
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 53.5 bits (127), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 44/79 (55%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQK 102
P ++F+GG+ T E L +F ++G + +V ++ DR S+G+ FITF++ +AK K
Sbjct: 7 PGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAK 66
Query: 103 DSDNIMFKEKRLNIAPAIK 121
D + K + + A K
Sbjct: 67 DMNGKSLHGKAIKVEQAKK 85
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 41/65 (63%), Gaps = 2/65 (3%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR--AGISKGYGFITFDSEEEAKRL 100
P +V +G +T T+D + E+FS YG +K + + V+R +SKGY ++ F++ +EA++
Sbjct: 4 PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKA 63
Query: 101 QKDSD 105
K D
Sbjct: 64 LKHMD 68
>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 = 52.4 bits (124), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 37/58 (63%), Gaps = 1/58 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRL 100
K++FVGGI T E L + F QYG ++ ++I+ DR +G +G+ F+TFD + ++
Sbjct: 105 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 162
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 34/54 (62%), Gaps = 1/54 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEE 96
+++F+GG++ TT++ L F Q+G + ++ D S+G+GF+T+ + EE
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 67
>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 = 52.0 bits (123), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 26/64 (40%), Positives = 40/64 (62%), Gaps = 1/64 (1%)
Query: 36 PKYGTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSE 94
P ++ ++V G+ T T+ EL +LFSQYG + +I+VD+ G+S+G GFI FD
Sbjct: 81 PSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKR 140
Query: 95 EEAK 98
EA+
Sbjct: 141 IEAE 144
Score = 30.8 bits (68), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 56 TEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRL 114
T++E LF G ++ K+V D+ G S GYGF+ + ++A++ + + + K +
Sbjct: 15 TQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTI 74
Query: 115 NIAPA 119
++ A
Sbjct: 75 KVSYA 79
>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 = 52.0 bits (123), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 37/58 (63%), Gaps = 1/58 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRL 100
K++FVGGI T E L + F QYG ++ ++I+ DR +G +G+ F+TFD + ++
Sbjct: 104 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 161
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 34/54 (62%), Gaps = 1/54 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEE 96
+++F+GG++ TT++ L F Q+G + ++ D S+G+GF+T+ + EE
Sbjct: 13 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 66
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 52.0 bits (123), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 37/58 (63%), Gaps = 1/58 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRL 100
K++FVGGI T E L + F QYG ++ ++I+ DR +G +G+ F+TFD + ++
Sbjct: 105 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 162
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 34/55 (61%), Gaps = 1/55 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEA 97
+++F+GG++ TT++ L F Q+G + ++ D S+G+GF+T+ + EE
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 68
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 52.0 bits (123), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 37/58 (63%), Gaps = 1/58 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRL 100
K++FVGGI T E L + F QYG ++ ++I+ DR +G +G+ F+TFD + ++
Sbjct: 106 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 163
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 34/54 (62%), Gaps = 1/54 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEE 96
+++F+GG++ TT++ L F Q+G + ++ D S+G+GF+T+ + EE
Sbjct: 15 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 68
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 52.0 bits (123), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 37/58 (63%), Gaps = 1/58 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRL 100
K++FVGGI T E L + F QYG ++ ++I+ DR +G +G+ F+TFD + ++
Sbjct: 103 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 160
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 34/55 (61%), Gaps = 1/55 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEA 97
+++F+GG++ TT++ L F Q+G + ++ D S+G+GF+T+ + EE
Sbjct: 12 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 66
>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 = 52.0 bits (123), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 37/58 (63%), Gaps = 1/58 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRL 100
K++FVGGI T E L + F QYG ++ ++I+ DR +G +G+ F+TFD + ++
Sbjct: 98 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 155
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 34/54 (62%), Gaps = 1/54 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEE 96
+++F+GG++ TT++ L F Q+G + ++ D S+G+GF+T+ + EE
Sbjct: 7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 51.6 bits (122), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 41/65 (63%), Gaps = 1/65 (1%)
Query: 36 PKYGTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSE 94
P ++ ++V G+ T ++ E+ +LFSQYG + +I++D+A G+S+G GFI FD
Sbjct: 83 PSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKR 142
Query: 95 EEAKR 99
EA+
Sbjct: 143 IEAEE 147
Score = 33.1 bits (74), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 56 TEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKR 99
T+DE LF G ++ K+V D+ G S GYGF+ + +A +
Sbjct: 17 TQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 51.2 bits (121), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 28/68 (41%), Positives = 42/68 (61%), Gaps = 2/68 (2%)
Query: 33 NNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITF 91
NN K G+ P R++VG + TED L +F +G ++ +++++D G SKGYGFITF
Sbjct: 17 NNLQK-GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITF 75
Query: 92 DSEEEAKR 99
E AK+
Sbjct: 76 SDSECAKK 83
>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 = 51.2 bits (121), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 47/76 (61%), Gaps = 2/76 (2%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQKD 103
++FVGGI E E FSQ+G + ++++D+ G S+G+GF+T+DS + R+ ++
Sbjct: 89 KIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQN 148
Query: 104 SDNIMFKEKRLNIAPA 119
I FK++++ I A
Sbjct: 149 K-FIDFKDRKIEIKRA 163
Score = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 23/49 (46%), Positives = 35/49 (71%), Gaps = 1/49 (2%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFD 92
++F+GG+ TTED L E F +YG V +KI+ D A G S+G+GF++F+
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFE 53
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 49/82 (59%), Gaps = 1/82 (1%)
Query: 37 KYGTVVPK-RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEE 95
+Y T + K ++F+ G+ + T++EL E+ +G VK +++V +RAG KG ++ +++E
Sbjct: 10 RYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENES 69
Query: 96 EAKRLQKDSDNIMFKEKRLNIA 117
+A + D + KE + +A
Sbjct: 70 QASQAVMKMDGMTIKENIIKVA 91
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/54 (42%), Positives = 38/54 (70%), Gaps = 1/54 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAK 98
++V G+ T ++ E+ +LFSQYG + +I++D+A G+S+G GFI FD EA+
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAE 57
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 48.9 bits (115), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 23/55 (41%), Positives = 40/55 (72%), Gaps = 1/55 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAK 98
++FVGG++ T E L ++FS+YG + +V +V DR S+G+GF+TF++ ++AK
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAK 68
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 47.8 bits (112), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 49/82 (59%), Gaps = 2/82 (2%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQKD 103
R+FV ++ T++E++L +LFS YG + ++ +D KG+ F+TF E A + +
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 104 SDNIMFKEKRLNIAPA-IKKQG 124
D +F+ + L++ P+ IKK+
Sbjct: 70 VDGQVFQGRMLHVLPSTIKKEA 91
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 47.8 bits (112), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 44/75 (58%), Gaps = 2/75 (2%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQKD 103
++FVGG+ TT+ L + F +G +++ ++ DR G S+GYGF+T A+R KD
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 104 SDNIMFKEK-RLNIA 117
+ I+ K +N+A
Sbjct: 79 PNPIIDGRKANVNLA 93
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 47.4 bits (111), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 28/56 (50%), Positives = 38/56 (67%), Gaps = 4/56 (7%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAK 98
K +FV G++ TTE+ L E F G V+ +IV DR G SKG+GF+ F+SEE+AK
Sbjct: 16 KTLFVKGLSEDTTEETLKESFD--GSVR-ARIVTDRETGSSKGFGFVDFNSEEDAK 68
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 47.4 bits (111), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 29/79 (36%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 42 VPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAG-ISKGYGFITFDSEEEAKRL 100
V + + V I +T E +L +LF +YG ++ VKIV DR S+GYGF+ F S A++
Sbjct: 41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQA 100
Query: 101 QKDSDNIMFKEKRLNIAPA 119
+ KRL +A A
Sbjct: 101 IAGLNGFNILNKRLKVALA 119
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 50/80 (62%), Gaps = 1/80 (1%)
Query: 48 VGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAKRLQKDSDN 106
V G++ TTE +L E+FS+YG + V IV D ++ S+G+ F+ F++ ++AK ++ ++
Sbjct: 17 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 76
Query: 107 IMFKEKRLNIAPAIKKQGFT 126
+ +R+ + +I K+ T
Sbjct: 77 MELDGRRIRVDFSITKRPHT 96
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 48/75 (64%), Gaps = 1/75 (1%)
Query: 50 GITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAKRLQKDSDNIM 108
G++ TTE +L E+FS+YG + V IV D ++ S+G+ F+ F++ ++AK ++ ++ +
Sbjct: 53 GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME 112
Query: 109 FKEKRLNIAPAIKKQ 123
+R+ + +I K+
Sbjct: 113 LDGRRIRVDFSITKR 127
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 50/80 (62%), Gaps = 1/80 (1%)
Query: 48 VGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAKRLQKDSDN 106
V G++ TTE +L E+FS+YG + V IV D ++ S+G+ F+ F++ ++AK ++ ++
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 107 IMFKEKRLNIAPAIKKQGFT 126
+ +R+ + +I K+ T
Sbjct: 80 MELDGRRIRVDFSITKRPHT 99
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 33/80 (41%), Positives = 41/80 (51%), Gaps = 3/80 (3%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQKDS 104
V+VGG+ +E L ELF Q G V + DR G +GYGF+ F SEE+A K
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 105 DNIMF--KEKRLNIAPAIKK 122
D I K R+N A A K
Sbjct: 78 DMIKLYGKPIRVNKASAHNK 97
>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D (Auf1) With Telomere Dna
pdb|1X0F|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D(Auf1) With Telomeric Dna
Length = 79
Score = 45.8 bits (107), Expect = 2e-05, Method: Composition-based stats.
Identities = 23/76 (30%), Positives = 46/76 (60%), Gaps = 2/76 (2%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAKR-LQ 101
K++FVGG++ T E+++ E F +G V+ +++ +D + +G+ FITF EE K+ ++
Sbjct: 2 KKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 61
Query: 102 KDSDNIMFKEKRLNIA 117
K N+ + + +A
Sbjct: 62 KKYHNVGLSKCEIKVA 77
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 44.7 bits (104), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 46/80 (57%), Gaps = 1/80 (1%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQK 102
PKR+ V I + +L ++F Q+G + V+I+ + G SKG+GF+TF++ +A R ++
Sbjct: 29 PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRARE 87
Query: 103 DSDNIMFKEKRLNIAPAIKK 122
+ + +++ + A +
Sbjct: 88 KLHGTVVEGRKIEVNNATAR 107
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 44.7 bits (104), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 45/69 (65%), Gaps = 1/69 (1%)
Query: 50 GITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAKRLQKDSDNIM 108
G++ TTE +L E+FS+YG + V IV D ++ S+G+ F+ F++ ++AK ++ ++ +
Sbjct: 22 GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME 81
Query: 109 FKEKRLNIA 117
+R+ ++
Sbjct: 82 LDGRRIRVS 90
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 44.7 bits (104), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 46/80 (57%), Gaps = 1/80 (1%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQK 102
PKR+ V I + +L ++F Q+G + V+I+ + G SKG+GF+TF++ +A R ++
Sbjct: 15 PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRARE 73
Query: 103 DSDNIMFKEKRLNIAPAIKK 122
+ + +++ + A +
Sbjct: 74 KLHGTVVEGRKIEVNNATAR 93
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 44.7 bits (104), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 30/93 (32%), Positives = 48/93 (51%), Gaps = 8/93 (8%)
Query: 32 NNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQ-YGIVKQVKIVVDRAGISKGYGFIT 90
++ P+Y +FVG +T + L E F + Y + K+V+D+ G+SKGYGF+
Sbjct: 4 GSSGPEY------SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVK 57
Query: 91 FDSEEEAKR-LQKDSDNIMFKEKRLNIAPAIKK 122
F E E KR L + + K + ++ AI K
Sbjct: 58 FTDELEQKRALTECQGAVGLGSKPVRLSVAIPK 90
>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 = 44.3 bits (103), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 38/66 (57%), Gaps = 3/66 (4%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAG---ISKGYGFITFDSEEEAKRLQ 101
++FVG + T +E +L ELF QYG V ++ ++ DR+ SKG F+TF + + A Q
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 102 KDSDNI 107
N+
Sbjct: 65 NALHNM 70
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 44.3 bits (103), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 43/81 (53%), Gaps = 1/81 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQK 102
+ VFVG I TE++L ++FS+ G V ++V DR G KGYGF + +E A +
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68
Query: 103 DSDNIMFKEKRLNIAPAIKKQ 123
+ + F + L + A ++
Sbjct: 69 NLNGREFSGRALRVDNAASEK 89
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 44.3 bits (103), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 33/52 (63%), Gaps = 1/52 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEE 95
++FVGGI E EL E F ++G+V +V ++ D +G+GFITF+ E+
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQ 63
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 38/66 (57%), Gaps = 3/66 (4%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAG---ISKGYGFITFDSEEEAKRLQ 101
++FVG + T +E +L ELF QYG V ++ ++ DR+ SKG F+TF + + A Q
Sbjct: 17 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 76
Query: 102 KDSDNI 107
N+
Sbjct: 77 NALHNM 82
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 40/65 (61%)
Query: 34 NAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDS 93
++ K V +++F+G I+ TE+++ +FS +G +++ +I+ G+S+G F+TF +
Sbjct: 98 DSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTT 157
Query: 94 EEEAK 98
A+
Sbjct: 158 RAMAQ 162
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 38/66 (57%), Gaps = 3/66 (4%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAG---ISKGYGFITFDSEEEAKRLQ 101
++FVG + T +E +L ELF QYG V ++ ++ DR+ SKG F+TF + + A Q
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 102 KDSDNI 107
N+
Sbjct: 65 NALHNM 70
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 40/65 (61%)
Query: 34 NAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDS 93
++ K V +++F+G I+ TE+++ +FS +G +++ +I+ G+S+G F+TF +
Sbjct: 86 DSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTT 145
Query: 94 EEEAK 98
A+
Sbjct: 146 RAMAQ 150
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 43.1 bits (100), Expect = 1e-04, Method: Composition-based stats.
Identities = 22/74 (29%), Positives = 44/74 (59%), Gaps = 2/74 (2%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAKR-LQKD 103
+FVGG++ T E+++ E F +G V+ +++ +D + +G+ FITF EE K+ ++K
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Query: 104 SDNIMFKEKRLNIA 117
N+ + + +A
Sbjct: 62 YHNVGLSKCEIKVA 75
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 40/69 (57%), Gaps = 1/69 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSD 105
+F+ + + L + FS +G + K+V D G SKGYGF+ F+++E A+R + +
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMN 164
Query: 106 NIMFKEKRL 114
++ ++++
Sbjct: 165 GMLLNDRKV 173
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 38/64 (59%), Gaps = 1/64 (1%)
Query: 36 PKYGTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSE 94
P + +++ G+ T T+ ++ ++FS++G + +++VD+ G+S+G FI FD
Sbjct: 81 PSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKR 140
Query: 95 EEAK 98
EA+
Sbjct: 141 SEAE 144
Score = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 39/65 (60%), Gaps = 1/65 (1%)
Query: 56 TEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRL 114
T+DEL LFS G V+ K++ D+ AG S GYGF+ + + ++A+R + + + K +
Sbjct: 15 TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTI 74
Query: 115 NIAPA 119
++ A
Sbjct: 75 KVSYA 79
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 42.7 bits (99), Expect = 2e-04, Method: Composition-based stats.
Identities = 18/56 (32%), Positives = 36/56 (64%), Gaps = 1/56 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRL 100
+FVGG++ TT +++ F Q+G V ++ D+ +G+GF+TF+SE+ +++
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKV 57
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 40/69 (57%), Gaps = 1/69 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSD 105
+F+ + + L + FS +G + K+V D G SKGYGF+ F+++E A+R + +
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMN 159
Query: 106 NIMFKEKRL 114
++ ++++
Sbjct: 160 GMLLNDRKV 168
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 38/64 (59%), Gaps = 1/64 (1%)
Query: 36 PKYGTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSE 94
P + +++ G+ T T+ ++ ++FS++G + +++VD+ G+S+G FI FD
Sbjct: 81 PSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKR 140
Query: 95 EEAK 98
EA+
Sbjct: 141 SEAE 144
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 39/65 (60%), Gaps = 1/65 (1%)
Query: 56 TEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRL 114
T+DEL LFS G V+ K++ D+ AG S GYGF+ + + ++A+R + + + K +
Sbjct: 15 TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTI 74
Query: 115 NIAPA 119
++ A
Sbjct: 75 KVSYA 79
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 43/77 (55%), Gaps = 2/77 (2%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGIS-KGYGFITFDSEEEAKRLQK 102
+ ++VG + + T +++ ELFSQ+G V VK++ DR KG+GF+ E ++ + K
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAK 61
Query: 103 DSDNIMFKEKRLNIAPA 119
DN F + + + A
Sbjct: 62 -LDNTDFMGRTIRVTEA 77
>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 = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 41/72 (56%), Gaps = 5/72 (6%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
R+FVG + TE+E+ +LF +YG +V I D KG+GFI ++ A+ + +
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVEL 71
Query: 105 DNIMFKEKRLNI 116
DN+ + K+L +
Sbjct: 72 DNMPLRGKQLRV 83
>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 = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 39/65 (60%), Gaps = 1/65 (1%)
Query: 56 TEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRL 114
T+DEL LFS G V+ K++ D+ AG S GYGF+ + + ++A+R + + + K +
Sbjct: 17 TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTI 76
Query: 115 NIAPA 119
++ A
Sbjct: 77 KVSYA 81
>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 = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAKRLQK 102
K +FV + TTE +L F YG +K++ +V R+G +GY FI ++ E + K
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 103 DSDNIMFKEKRL 114
+D +R+
Sbjct: 163 HADGKKIDGRRV 174
>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 = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 40/69 (57%), Gaps = 1/69 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSD 105
+F+ + + L + FS +G + K+V D G SKGYGF+ F+++E A+R + +
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMN 66
Query: 106 NIMFKEKRL 114
++ ++++
Sbjct: 67 GMLLNDRKV 75
>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 = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 39/65 (60%)
Query: 34 NAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDS 93
++ K V +++F+G I+ TE+++ FS +G +++ +I+ G+S+G F+TF +
Sbjct: 86 DSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDGLSRGCAFVTFTT 145
Query: 94 EEEAK 98
A+
Sbjct: 146 RAXAQ 150
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 35/60 (58%), Gaps = 3/60 (5%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAG---ISKGYGFITFDSEEEAKRLQ 101
+ FVG + T +E +L ELF QYG V ++ ++ DR+ SKG F+TF + + A Q
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 41/72 (56%), Gaps = 5/72 (6%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
R+FVG + TE+E+ +LF +YG +V I D KG+GFI ++ A+ + +
Sbjct: 24 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVEL 78
Query: 105 DNIMFKEKRLNI 116
DN+ + K+L +
Sbjct: 79 DNMPLRGKQLRV 90
>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 = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 39/65 (60%), Gaps = 1/65 (1%)
Query: 56 TEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRL 114
T+DEL LFS G V+ K++ D+ AG S GYGF+ + + ++A+R + + + K +
Sbjct: 32 TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTI 91
Query: 115 NIAPA 119
++ A
Sbjct: 92 KVSYA 96
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 41.6 bits (96), Expect = 4e-04, Method: Composition-based stats.
Identities = 19/48 (39%), Positives = 33/48 (68%), Gaps = 1/48 (2%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITF 91
++F+GG++ TT++ L E F Q+G VK+ ++ D S+G+GF+TF
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 29/52 (55%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEE 95
+ VFVG + + E+ L ELF Q G + +V I DR G K +GF+ F E
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPE 68
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 33/48 (68%), Gaps = 1/48 (2%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITF 91
++F+GG++ TT++ L E F Q+G VK+ ++ D S+G+GF+TF
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 74
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14
Complex
Length = 110
Score = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 31/53 (58%), Gaps = 1/53 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEA 97
+FV I EDE+ E F YG +K + + +D R G SKGY + +++ ++A
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQA 81
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 40/69 (57%), Gaps = 1/69 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSD 105
+F+ + + L + FS +G + K+V D G SKGYGF+ F+++E A+R + +
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMN 72
Query: 106 NIMFKEKRL 114
++ ++++
Sbjct: 73 GMLLNDRKV 81
>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 = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAKRLQK 102
K +FV + TTE +L F YG +K++ +V R+G +GY FI ++ E + K
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 103 DSDNIMFKEKRL 114
+D +R+
Sbjct: 163 HADGKKIDGRRV 174
>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 = 40.8 bits (94), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 31/53 (58%), Gaps = 1/53 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEA 97
+FV I EDE+ E F YG +K + + +D R G SKGY + +++ ++A
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQA 127
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 1/65 (1%)
Query: 56 TEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRL 114
T+ EL LF G + +I+ D + G S GY F+ F SE +++R K + I + KRL
Sbjct: 16 TDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRL 75
Query: 115 NIAPA 119
++ A
Sbjct: 76 KVSYA 80
>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 = 40.4 bits (93), Expect = 8e-04, Method: Composition-based stats.
Identities = 22/71 (30%), Positives = 39/71 (54%), Gaps = 7/71 (9%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQKDS 104
+F+GG++ TT+ +L + FS++G V + +D G S+G+GF+ F E ++
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ- 60
Query: 105 DNIMFKEKRLN 115
KE +LN
Sbjct: 61 -----KEHKLN 66
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 40.4 bits (93), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKR 99
++VG + TED L +F +G + + ++ D G SKGYGFITF E A+R
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62
>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 = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 35/54 (64%), Gaps = 1/54 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAK 98
VFVG ++ T +++ F+ +G + ++V D A G SKGYGF++F ++ +A+
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAE 71
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 35/55 (63%), Gaps = 1/55 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAK 98
VFVG ++ T +++ F+ +G + ++V D A G SKGYGF++F ++ +A+
Sbjct: 17 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAE 71
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 5/72 (6%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
R+FVG + + TE++ LF +YG +V I DR G+GFI +S A+ + +
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR-----GFGFIRLESRTLAEIAKAEL 78
Query: 105 DNIMFKEKRLNI 116
D + K + L I
Sbjct: 79 DGTILKSRPLRI 90
Score = 33.9 bits (76), Expect = 0.076, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 31/52 (59%)
Query: 48 VGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
V ++ + + L + FSQ+G V++ +VVD G + G GF+ F ++ A++
Sbjct: 101 VKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARK 152
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 1/65 (1%)
Query: 56 TEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRL 114
T+ EL LF G + +I+ D + G S GY F+ F SE +++R K + I + KRL
Sbjct: 16 TDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRL 75
Query: 115 NIAPA 119
++ A
Sbjct: 76 KVSYA 80
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 36/64 (56%), Gaps = 1/64 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQKDS 104
++V + T T+D+L +F +YG + Q I+ D+ G +G F+ ++ EEA+
Sbjct: 92 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151
Query: 105 DNIM 108
+N++
Sbjct: 152 NNVI 155
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/48 (41%), Positives = 31/48 (64%), Gaps = 1/48 (2%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITF 91
++FVGG+ +TT++ L FSQYG V I+ D+ S+G+GF+ F
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF 65
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleaoproteins A2B1
Length = 116
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 33/51 (64%), Gaps = 1/51 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAG-ISKGYGFITFDS 93
+++F+GG++ TTE+ L + Q+G + ++ D A S+G+GF+TF S
Sbjct: 28 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSS 78
>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 = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 35/54 (64%), Gaps = 1/54 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAK 98
+FV G+ TE+++ + F++YG +K + + +D R G KGY + +++ +EA+
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 63
>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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 35/54 (64%), Gaps = 1/54 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAK 98
+FV G+ TE+++ + F++YG +K + + +D R G KGY + +++ +EA+
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 65
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 35/54 (64%), Gaps = 1/54 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAK 98
+FV G+ TE+++ + F++YG +K + + +D R G KGY + +++ +EA+
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 63
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 43/78 (55%), Gaps = 1/78 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSD 105
++V + ++ L + FS +G + K++++ G SKG+GF+ F S EEA + + +
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMN 76
Query: 106 NIMFKEKRLNIAPAIKKQ 123
+ K L +A A +K+
Sbjct: 77 GRIVATKPLYVALAQRKE 94
>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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 35/54 (64%), Gaps = 1/54 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAK 98
+FV G+ TE+++ + F++YG +K + + +D R G KGY + +++ +EA+
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 63
>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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 35/54 (64%), Gaps = 1/54 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAK 98
+FV G+ TE+++ + F++YG +K + + +D R G KGY + +++ +EA+
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 79
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 7/72 (9%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
++ VG I+ T T EL F +YG V + IV D Y F+ + E+A +
Sbjct: 12 KLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD-------YAFVHMERAEDAVEAIRGL 64
Query: 105 DNIMFKEKRLNI 116
DN F+ KR+++
Sbjct: 65 DNTEFQGKRMHV 76
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 32/55 (58%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAK 98
+++FVG + +E+++ LF +G++ + ++ G SKG F+ F S EA+
Sbjct: 16 RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQ 70
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 41/78 (52%), Gaps = 6/78 (7%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSD 105
VFVG T TEDEL E FSQYG V V I + + F+TF ++ A+ L +
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFI----PKPFRAFAFVTFADDQIAQSLC--GE 61
Query: 106 NIMFKEKRLNIAPAIKKQ 123
+++ K ++I+ A K
Sbjct: 62 DLIIKGISVHISNAEPKH 79
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 40/83 (48%), Gaps = 7/83 (8%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
++FVG +++ T EL LF + G V + +V D Y F+ + E +AK
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVVKD-------YAFVHMEKEADAKAAIAQL 63
Query: 105 DNIMFKEKRLNIAPAIKKQGFTG 127
+ K KR+N+ + K Q +G
Sbjct: 64 NGKEVKGKRINVELSTKGQKKSG 86
>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 = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 35/54 (64%), Gaps = 1/54 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAK 98
+FV G+ TE+++ + F++YG +K + + +D R G KGY + +++ +EA+
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 78
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKR 99
+ V ++ T E +L ELF +G + ++ + D+ G SKG+ FI+F E+A R
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAAR 72
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 32/55 (58%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAK 98
+++FVG + +ED++ LF +G +++ I+ G SKG F+ + S EA+
Sbjct: 16 RKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQ 70
>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 = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAKRLQKDS 104
+ V + T+ EL LF G + +I D + G S GY F+ F SE +++R K
Sbjct: 17 LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 105 DNIMFKEKRLNIAPA 119
+ I + KRL ++ A
Sbjct: 77 NGITVRNKRLKVSYA 91
Score = 37.0 bits (84), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 32/54 (59%), Gaps = 1/54 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAK 98
++V + T T+D+L +F +YG + Q I+ D+ G +G F+ ++ EEA+
Sbjct: 103 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQ 156
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKR 99
+++ G+ TT+ +L +L YG + K ++D+ KGYGF+ FDS A++
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQK 62
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQ 101
++F+G I E +L LF ++G + ++ ++ DR G+ KG F+T+ E A + Q
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQ 72
>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 = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 42/76 (55%), Gaps = 2/76 (2%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQK 102
+ ++VG + T +EL F G V +V I+ D+ +G KG+ +I F S++E+ R
Sbjct: 7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEF-SDKESVRTSL 65
Query: 103 DSDNIMFKEKRLNIAP 118
D +F+ +++ + P
Sbjct: 66 ALDESLFRGRQIKVIP 81
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 10/77 (12%)
Query: 21 NNAFFNYQAAVNNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA 80
N ++ VN ++PK TV + GGI S T+ + + FS +G + ++++ +
Sbjct: 8 NTKQLRFEDVVNQSSPKNCTV-----YCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-- 60
Query: 81 GISKGYGFITFDSEEEA 97
KGY F+ F + E A
Sbjct: 61 ---KGYSFVRFSTHESA 74
>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 = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 42/76 (55%), Gaps = 2/76 (2%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQK 102
+ ++VG + T +EL F G V +V I+ D+ +G KG+ +I F S++E+ R
Sbjct: 6 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEF-SDKESVRTSL 64
Query: 103 DSDNIMFKEKRLNIAP 118
D +F+ +++ + P
Sbjct: 65 ALDESLFRGRQIKVIP 80
>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 = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 33/57 (57%), Gaps = 2/57 (3%)
Query: 43 PKRV-FVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEA 97
P RV ++G I TE+++ +L S G V +K++ D + G SKGY FI F E +
Sbjct: 3 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESS 59
>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 = 37.0 bits (84), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 36/64 (56%), Gaps = 1/64 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQKDS 104
++V + T T+D+L +F +YG + Q I+ D+ G +G F+ ++ EEA+
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 105 DNIM 108
+N++
Sbjct: 76 NNVI 79
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 36.6 bits (83), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 34/58 (58%), Gaps = 1/58 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQ 101
++FVG I E +L LF ++G + ++ ++ DR G+ KG F+T+ + + A + Q
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQ 74
>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 = 36.6 bits (83), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 24/62 (38%), Positives = 36/62 (58%), Gaps = 3/62 (4%)
Query: 43 PKRV-FVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITF-DSEEEAKR 99
P RV ++G I TE+++ +L S G V +K++ D + G SKGY FI F D E A
Sbjct: 2 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 61
Query: 100 LQ 101
++
Sbjct: 62 VR 63
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 36.6 bits (83), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 29/52 (55%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
VFV + +L E+FS G+V + I+ D+ G S+G G +TF+ EA
Sbjct: 18 VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEA 69
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 36.6 bits (83), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 36/53 (67%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAK 98
++VG ++ TTE+++ ELFS+ G +K++ + +D+ + G+ F+ + S +A+
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAE 73
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 36.6 bits (83), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 33/57 (57%), Gaps = 2/57 (3%)
Query: 43 PKRV-FVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEA 97
P RV ++G I TE+++ +L S G V +K++ D + G SKGY FI F E +
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESS 57
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 36.2 bits (82), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEE 95
+ V G+ TTE +L E FS +G V V++ D + G SKG+GF+ F E
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYE 68
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 35.8 bits (81), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQKDS 104
+F+ + T+ +L F +G V K+ +D+ +SK +GF++FD+ + A+ K
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 105 DNIMFKEKRLNI 116
+ KRL +
Sbjct: 103 NGFQVGTKRLKV 114
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 35.0 bits (79), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 16/72 (22%), Positives = 39/72 (54%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
++ V + ++ ++ ELF+++G +K+ + DR+G S G + F+ + +A + K
Sbjct: 30 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 89
Query: 105 DNIMFKEKRLNI 116
+ + + +NI
Sbjct: 90 NGVPLDGRPMNI 101
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In
Trinucleotide Repeat Containing 4 Variant
Length = 102
Score = 35.0 bits (79), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 14/55 (25%), Positives = 32/55 (58%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAK 98
+++FVG + T++++ ++F +G + + ++ G SKG F+ F + EA+
Sbjct: 13 RKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQ 67
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 35.0 bits (79), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 36/78 (46%), Gaps = 7/78 (8%)
Query: 39 GTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAK 98
G + R+FV E EL E+F +G +K+VKI+ G+ F+ F+ E A
Sbjct: 27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAA 79
Query: 99 RLQKDSDNIMFKEKRLNI 116
+ ++ F + L +
Sbjct: 80 KAIEEVHGKSFANQPLEV 97
>pdb|3N9U|C Chain C, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
pdb|3N9U|I Chain I, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
Length = 156
Score = 34.7 bits (78), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 42/80 (52%), Gaps = 3/80 (3%)
Query: 46 VFVGGITSTTTEDELCELFSQYGI--VKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQK 102
V+VG + TT+ +L ++ G+ V ++K +RA G SKGY + SE +L +
Sbjct: 58 VYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLE 117
Query: 103 DSDNIMFKEKRLNIAPAIKK 122
+ +++++ PA ++
Sbjct: 118 LLPGKVLNGEKVDVRPATRQ 137
>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 = 34.7 bits (78), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 14/55 (25%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAK 98
R++V + ++D++ +F +G +K + D G KGYGFI ++ + ++
Sbjct: 127 RIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQ 181
>pdb|3P5T|L Chain L, Cfim25-Cfim68 Complex
pdb|3P5T|M Chain M, Cfim25-Cfim68 Complex
pdb|3P5T|N Chain N, Cfim25-Cfim68 Complex
pdb|3P5T|O Chain O, Cfim25-Cfim68 Complex
pdb|3P5T|P Chain P, Cfim25-Cfim68 Complex
pdb|3P5T|Q Chain Q, Cfim25-Cfim68 Complex
pdb|3P6Y|C Chain C, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|D Chain D, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|G Chain G, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|H Chain H, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|K Chain K, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|L Chain L, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|O Chain O, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|P Chain P, Cf Im25-Cf Im68-Uguaa Complex
Length = 90
Score = 34.7 bits (78), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 34/58 (58%), Gaps = 3/58 (5%)
Query: 46 VFVGGITSTTTEDELCELFSQYGI--VKQVKIVVDRA-GISKGYGFITFDSEEEAKRL 100
+++G +T TT+++L E G+ + ++K +RA G SKG+ + SE +K+L
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKL 61
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 34.7 bits (78), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 37/65 (56%), Gaps = 7/65 (10%)
Query: 42 VPKR-----VFVGGITSTTTEDELCELFSQYGIVKQVKI--VVDRAGISKGYGFITFDSE 94
VPK+ + V I + E+ ELFS +G +K V++ + G +G+GF+ F ++
Sbjct: 9 VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITK 68
Query: 95 EEAKR 99
++AK+
Sbjct: 69 QDAKK 73
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 34.7 bits (78), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 32/59 (54%), Gaps = 7/59 (11%)
Query: 39 GTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
G K +FV + +T TE+ L + FSQ+G +++VK + D Y FI FD + A
Sbjct: 7 GMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD-------YAFIHFDERDGA 58
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 34.3 bits (77), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQKDS 104
V+V + + T ++L +FS+YG V +V I+ D+ SKG FI F ++ A+ +
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 105 DN 106
+N
Sbjct: 79 NN 80
>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 = 34.3 bits (77), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 14/55 (25%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAK 98
R++V + ++D++ +F +G +K + D G KGYGFI ++ + ++
Sbjct: 112 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQ 166
>pdb|3Q2S|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2S|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2T|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
pdb|3Q2T|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
Length = 229
Score = 34.3 bits (77), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 37/66 (56%), Gaps = 5/66 (7%)
Query: 40 TVVPKRV--FVGGITSTTTEDELCELFSQYGI--VKQVKIVVDRA-GISKGYGFITFDSE 94
T KR+ ++G +T TT+++L E G+ + ++K +RA G SKG+ + SE
Sbjct: 63 TYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSE 122
Query: 95 EEAKRL 100
+K+L
Sbjct: 123 ASSKKL 128
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 33.9 bits (76), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 29/56 (51%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAK 98
P +++ + + E EL + +G V +I+ D +G S+G GF +S E+ +
Sbjct: 25 PTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCE 80
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 33.9 bits (76), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 28/54 (51%), Gaps = 7/54 (12%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAK 98
++F+G + TE E+ LF QYG V + I+ K YGF+ + + A+
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAE 56
>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 = 0.083, Method: Compositional matrix adjust.
Identities = 14/55 (25%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAK 98
R++V + ++D++ +F +G +K + D G KGYGFI ++ + ++
Sbjct: 111 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQ 165
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 33.9 bits (76), Expect = 0.089, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 1/65 (1%)
Query: 56 TEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRL 114
T+DE LF G ++ K+V D+ G S GYGF+ + +A + + + + K +
Sbjct: 17 TQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTI 76
Query: 115 NIAPA 119
++ A
Sbjct: 77 KVSYA 81
>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex
Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A
Resolution
Length = 107
Score = 33.9 bits (76), Expect = 0.091, Method: Compositional matrix adjust.
Identities = 16/72 (22%), Positives = 38/72 (52%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
++ V + ++ ++ ELF+++G +K+ + DR+G S G + F+ + +A + K
Sbjct: 31 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQY 90
Query: 105 DNIMFKEKRLNI 116
+ + + NI
Sbjct: 91 NGVPLDGRPXNI 102
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 33.5 bits (75), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQV-KIVVD-RAGISKGYGFITFDS 93
+F+G + E L + FS +G++ Q KI+ D G SKGY FI F S
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFAS 57
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 33.5 bits (75), Expect = 0.10, Method: Composition-based stats.
Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 7/72 (9%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
R+FV E EL E+F +G +K+VKI+ G+ F+ F+ E A + ++
Sbjct: 6 RLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEEV 58
Query: 105 DNIMFKEKRLNI 116
F + L +
Sbjct: 59 HGKSFANQPLEV 70
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 40/76 (52%), Gaps = 9/76 (11%)
Query: 39 GTVVPKRVFVGGI-TSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
G+ + R+F+G + ++++L +FS YG + Q+ I +GFI FD+ +
Sbjct: 18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQIN-------IKNAFGFIQFDNPQSV 70
Query: 98 KR-LQKDSDNIMFKEK 112
+ ++ +S + F +K
Sbjct: 71 RDAIEXESQEMNFGKK 86
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 33.1 bits (74), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 27/52 (51%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
++VG + TED L + F G + +KI++D+ + Y F+ + +A
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDA 54
Score = 32.0 bits (71), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAK 98
+FVG + ++ L F + ++ D + G S+GYGF++F S+++A+
Sbjct: 90 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQ 143
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 33.1 bits (74), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 32/56 (57%), Gaps = 3/56 (5%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
K + + ++ + TE+ L E+F + +K + ++ G SKGY FI F S E+AK
Sbjct: 16 KTLVLSNLSYSATEETLQEVFEKATFIK---VPQNQNGKSKGYAFIEFASFEDAKE 68
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 33.1 bits (74), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 5/86 (5%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQK 102
P+ ++VG ++ TE + +LFSQ G K K++ + + Y F+ F +A
Sbjct: 15 PRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALA 73
Query: 103 --DSDNIMFKEKRLNIA--PAIKKQG 124
+ I+ KE ++N A P+ +K G
Sbjct: 74 AMNGRKILGKEVKVNWATTPSSQKSG 99
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 33.1 bits (74), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 42/86 (48%), Gaps = 9/86 (10%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVK--------QVKIVVDR-AGISKGYGFITFDSEEE 96
++V G+ + T D+L + F Q G+VK + I +D+ G KG ++++
Sbjct: 18 IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPT 77
Query: 97 AKRLQKDSDNIMFKEKRLNIAPAIKK 122
AK + D F+ +L ++ A KK
Sbjct: 78 AKAAVEWFDGKDFQGSKLKVSLARKK 103
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 30/65 (46%), Gaps = 13/65 (20%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGIS--------KGYGFITFDSEE 95
++VFVGG+ EDE+ F ++G +VVD + KGY F+ F E
Sbjct: 9 RKVFVGGLPPDIDEDEITASFRRFG-----PLVVDWPHKAESKSYFPPKGYAFLLFQEES 63
Query: 96 EAKRL 100
+ L
Sbjct: 64 SVQAL 68
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 32.7 bits (73), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 16/78 (20%), Positives = 38/78 (48%)
Query: 39 GTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAK 98
G ++ V + ++ ++ ELF+++G +K+ + DR+G S G + F+ +A
Sbjct: 84 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADAL 143
Query: 99 RLQKDSDNIMFKEKRLNI 116
+ K + + ++I
Sbjct: 144 KAMKQYKGVPLDGRPMDI 161
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 32.7 bits (73), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 36/62 (58%), Gaps = 4/62 (6%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIV--VDRAGI--SKGYGFITFDSEEEAKRLQ 101
+F+ + +TTE+ L +FS+ G +K I ++AG+ S G+GF+ + E+A++
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 102 KD 103
K
Sbjct: 68 KQ 69
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 32.7 bits (73), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 32/61 (52%), Gaps = 8/61 (13%)
Query: 39 GTVVPKRVFVGGI-TSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
G+ + R+F+G + ++++L +FS YG + Q+ I +GFI FD+ +
Sbjct: 18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQIN-------IKNAFGFIQFDNPQSV 70
Query: 98 K 98
+
Sbjct: 71 R 71
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 32.3 bits (72), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 29/56 (51%), Gaps = 4/56 (7%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRL 100
+VFVG T T +EL + F QYG V V I + + F+TF ++ A+ L
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYGEVVDVFI----PKPFRAFAFVTFADDKVAQSL 64
>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 = 32.3 bits (72), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAK 98
+FVG + ++ L F + ++ D + G S+GYGF++F S+++A+
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQ 57
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 32.0 bits (71), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 48 VGGITSTTTEDELCELFSQYGIVKQVKIVV-DRAGISKGYGFITFDSEEEAKRLQKD 103
V + + T+ + EL +G +++ +V +R G SKGYGF + ++ A R + D
Sbjct: 100 VANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 156
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 32.0 bits (71), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 48 VGGITSTTTEDELCELFSQYGIVKQVKIVV-DRAGISKGYGFITFDSEEEAKRLQKD 103
V + + T+ + EL +G +++ +V +R G SKGYGF + ++ A R + D
Sbjct: 100 VANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 156
>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 = 32.0 bits (71), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 48 VGGITSTTTEDELCELFSQYGIVKQVKIVV-DRAGISKGYGFITFDSEEEAKRLQKD 103
V + + T+ + EL +G +++ +V +R G SKGYGF + ++ A R + D
Sbjct: 98 VANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 154
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 32.0 bits (71), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 9/61 (14%)
Query: 40 TVVPK-RVFVGGIT-STTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
+ PK R+F+G + ++++L +FS YG + Q+ I +GFI FD+ +
Sbjct: 6 NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQI-------NIKNAFGFIQFDNPQSV 58
Query: 98 K 98
+
Sbjct: 59 R 59
>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 = 32.0 bits (71), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 33/54 (61%), Gaps = 1/54 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAK 98
VFVG ++ T + F+ +G + ++V D A G SKGYGF++F ++ +A+
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAE 62
>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|X Chain X, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|Y Chain Y, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2V|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
pdb|1N52|B Chain B, Cap Binding Complex
pdb|1N54|B Chain B, Cap Binding Complex M7gpppg Free
pdb|3FEX|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex.
pdb|3FEY|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex
Length = 156
Score = 31.6 bits (70), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 36/54 (66%), Gaps = 1/54 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISK-GYGFITFDSEEEAK 98
++VG ++ TTE+++ ELFS+ G +K++ + +D+ + G+ F+ + S +A+
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAE 95
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 31.6 bits (70), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 21/86 (24%), Positives = 44/86 (51%), Gaps = 7/86 (8%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAKR--- 99
K VF+ ++ + E+ L E+ Q+G +K V++V+ SKG F F ++E A++
Sbjct: 16 KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 75
Query: 100 ---LQKDSDNIMFKEKRLNIAPAIKK 122
L+ + + ++L + A+ +
Sbjct: 76 AASLEAEGGGLKLDGRQLKVDLAVTR 101
>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 = 31.6 bits (70), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 57 EDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRLN 115
+ +L ++F +G V K+ +D+ +SK +GF+++D+ A+ + + KRL
Sbjct: 39 DQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLK 98
Query: 116 I 116
+
Sbjct: 99 V 99
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 31.6 bits (70), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 29/55 (52%), Gaps = 8/55 (14%)
Query: 45 RVFVGGI-TSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAK 98
R+F+G + ++++L +FS YG + Q+ I +GFI FD+ + +
Sbjct: 4 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQI-------NIKNAFGFIQFDNPQSVR 51
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 31.2 bits (69), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 15/64 (23%), Positives = 33/64 (51%)
Query: 39 GTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAK 98
G ++ V + ++ ++ ELF+++G +K+ + DR+G S G + F+ +A
Sbjct: 31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADAL 90
Query: 99 RLQK 102
+ K
Sbjct: 91 KAMK 94
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 31.2 bits (69), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 15/64 (23%), Positives = 33/64 (51%)
Query: 39 GTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAK 98
G ++ V + ++ ++ ELF+++G +K+ + DR+G S G + F+ +A
Sbjct: 31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADAL 90
Query: 99 RLQK 102
+ K
Sbjct: 91 KAMK 94
>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 31.2 bits (69), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 4/52 (7%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
+F+ + T E L LF+Q+ K+V++V R I+ F+ FD+E +A
Sbjct: 210 LFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIA----FVEFDNEVQA 257
>pdb|2U1A|A Chain A, Rna Binding Domain 2 Of Human U1a Protein, Nmr, 20
Structures
Length = 88
Score = 31.2 bits (69), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 4/52 (7%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
+F+ + T E L LF+Q+ K+V++V R I+ F+ FD+E +A
Sbjct: 16 LFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIA----FVEFDNEVQA 63
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 38/72 (52%), Gaps = 6/72 (8%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAK-RLQKDS 104
++VGG+ T TE +L F Q+G ++ + +V + FI F + + A+ +K
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQ-----CAFIQFATRQAAEVAAEKSF 69
Query: 105 DNIMFKEKRLNI 116
+ ++ +RLN+
Sbjct: 70 NKLIVNGRRLNV 81
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 29.6 bits (65), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 14/72 (19%), Positives = 33/72 (45%), Gaps = 2/72 (2%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
R++VG + ++ ++F +YG ++ + + R G + F+ F+ +A+
Sbjct: 24 RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPP--FAFVEFEDPRDAEDAVYGR 81
Query: 105 DNIMFKEKRLNI 116
D + RL +
Sbjct: 82 DGYDYDGYRLRV 93
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 34/72 (47%), Gaps = 4/72 (5%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
+V+VG + + + EL FS YG ++ V I + G+ F+ F+ +A+ +
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGL 57
Query: 105 DNIMFKEKRLNI 116
D + R+ +
Sbjct: 58 DGKVICGSRVRV 69
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 29/49 (59%), Gaps = 7/49 (14%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFD 92
K +FV + +T TE+ L + FS++G +++VK + D Y F+ F+
Sbjct: 16 KVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKD-------YAFVHFE 57
>pdb|2VOD|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auauuuu
pdb|2VOD|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auauuuu
pdb|2VON|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auaauuu
pdb|2VON|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auaauuu
pdb|2VOO|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Uuuuuuuu
pdb|2VOO|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Uuuuuuuu
pdb|2VOP|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auuuu
Length = 193
Score = 28.1 bits (61), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 27/57 (47%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRL 100
+ V++ G + T D++ E G V +++ KG F+ FDS E AK+
Sbjct: 110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKF 166
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 27.3 bits (59), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 13/60 (21%), Positives = 30/60 (50%)
Query: 40 TVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
+ P +F+G + + EL S+ + +V R G ++ +G++ F+S E+ ++
Sbjct: 14 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEK 73
>pdb|1S79|A Chain A, Solution Structure Of The Central Rrm Of Human La Protein
Length = 103
Score = 27.3 bits (59), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 28/60 (46%)
Query: 41 VVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRL 100
V + V++ G + T D++ E G V +++ KG F+ FDS E AK+
Sbjct: 9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKF 68
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 26.9 bits (58), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 9/62 (14%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVK--------QVKIVVDR-AGISKGYGFITFDSEEE 96
+FV G+ T + + + F Q GI+K + + DR G KG ++FD
Sbjct: 16 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 75
Query: 97 AK 98
AK
Sbjct: 76 AK 77
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 26.9 bits (58), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 9/62 (14%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVK--------QVKIVVDR-AGISKGYGFITFDSEEE 96
+FV G+ T + + + F Q GI+K + + DR G KG ++FD
Sbjct: 10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 69
Query: 97 AK 98
AK
Sbjct: 70 AK 71
>pdb|1ZH5|A Chain A, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
pdb|1ZH5|B Chain B, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
Length = 195
Score = 26.9 bits (58), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 29/65 (44%), Gaps = 1/65 (1%)
Query: 37 KYGTVVPKR-VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEE 95
+Y V R V++ G + T D++ E G V ++ KG F+ FDS E
Sbjct: 104 EYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQXRRTLHKAFKGSIFVVFDSIE 163
Query: 96 EAKRL 100
AK+
Sbjct: 164 SAKKF 168
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.319 0.135 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,977,803
Number of Sequences: 62578
Number of extensions: 203466
Number of successful extensions: 679
Number of sequences better than 100.0: 156
Number of HSP's better than 100.0 without gapping: 99
Number of HSP's successfully gapped in prelim test: 57
Number of HSP's that attempted gapping in prelim test: 487
Number of HSP's gapped (non-prelim): 177
length of query: 242
length of database: 14,973,337
effective HSP length: 96
effective length of query: 146
effective length of database: 8,965,849
effective search space: 1309013954
effective search space used: 1309013954
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: 50 (23.9 bits)