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= 043937
(123 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 77.4 bits (189), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 32/64 (50%), Positives = 50/64 (78%)
Query: 52 KLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQA 111
KLFVGG+S++ ++ SL + F+KYG ++E ++ DRET RSRGFGFVTF +++A A+ A
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 112 LDGQ 115
++G+
Sbjct: 74 MNGK 77
>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 = 68.2 bits (165), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 32/71 (45%), Positives = 49/71 (69%), Gaps = 3/71 (4%)
Query: 49 SSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTF---STVEEA 105
S K+F+GG++++ +++LRE F KYG V + +I+ D TGRSRGFGF++F S+V+E
Sbjct: 2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61
Query: 106 SSAIQALDGQV 116
LDG+V
Sbjct: 62 VKTQHILDGKV 72
Score = 56.2 bits (134), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 41/62 (66%)
Query: 49 SSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSA 108
+ K+FVGGI ++ E F+++G + +A+++LD++TG+SRGFGFVT+ + +
Sbjct: 86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRV 145
Query: 109 IQ 110
Q
Sbjct: 146 CQ 147
>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 = 67.0 bits (162), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 32/69 (46%), Positives = 47/69 (68%), Gaps = 4/69 (5%)
Query: 52 KLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQA 111
KLF+GG+S+ D SLR F ++G + + ++ D T RSRGFGFVT++TVEE +A+ A
Sbjct: 14 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 73
Query: 112 ----LDGQV 116
+DG+V
Sbjct: 74 RPHKVDGRV 82
Score = 53.9 bits (128), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 43/74 (58%)
Query: 27 GKRISCESSISNPSIYQAIRCMSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDR 86
G+ + + ++S + ++ K+FVGGI + +++ LR+ F +YG + I+ DR
Sbjct: 80 GRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR 139
Query: 87 ETGRSRGFGFVTFS 100
+G+ RGF FVTF
Sbjct: 140 GSGKKRGFAFVTFD 153
>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 = 67.0 bits (162), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 32/69 (46%), Positives = 47/69 (68%), Gaps = 4/69 (5%)
Query: 52 KLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQA 111
KLF+GG+S+ D SLR F ++G + + ++ D T RSRGFGFVT++TVEE +A+ A
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 112 ----LDGQV 116
+DG+V
Sbjct: 75 RPHKVDGRV 83
Score = 53.9 bits (128), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 43/74 (58%)
Query: 27 GKRISCESSISNPSIYQAIRCMSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDR 86
G+ + + ++S + ++ K+FVGGI + +++ LR+ F +YG + I+ DR
Sbjct: 81 GRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR 140
Query: 87 ETGRSRGFGFVTFS 100
+G+ RGF FVTF
Sbjct: 141 GSGKKRGFAFVTFD 154
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 67.0 bits (162), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 32/69 (46%), Positives = 47/69 (68%), Gaps = 4/69 (5%)
Query: 52 KLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQA 111
KLF+GG+S+ D SLR F ++G + + ++ D T RSRGFGFVT++TVEE +A+ A
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 112 ----LDGQV 116
+DG+V
Sbjct: 75 RPHKVDGRV 83
Score = 53.9 bits (128), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 43/74 (58%)
Query: 27 GKRISCESSISNPSIYQAIRCMSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDR 86
G+ + + ++S + ++ K+FVGGI + +++ LR+ F +YG + I+ DR
Sbjct: 81 GRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR 140
Query: 87 ETGRSRGFGFVTFS 100
+G+ RGF FVTF
Sbjct: 141 GSGKKRGFAFVTFD 154
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 67.0 bits (162), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 32/69 (46%), Positives = 47/69 (68%), Gaps = 4/69 (5%)
Query: 52 KLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQA 111
KLF+GG+S+ D SLR F ++G + + ++ D T RSRGFGFVT++TVEE +A+ A
Sbjct: 13 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 72
Query: 112 ----LDGQV 116
+DG+V
Sbjct: 73 RPHKVDGRV 81
Score = 54.3 bits (129), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 43/74 (58%)
Query: 27 GKRISCESSISNPSIYQAIRCMSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDR 86
G+ + + ++S + ++ K+FVGGI + +++ LR+ F +YG + I+ DR
Sbjct: 79 GRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR 138
Query: 87 ETGRSRGFGFVTFS 100
+G+ RGF FVTF
Sbjct: 139 GSGKKRGFAFVTFD 152
>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 = 67.0 bits (162), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 32/69 (46%), Positives = 47/69 (68%), Gaps = 4/69 (5%)
Query: 52 KLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQA 111
KLF+GG+S+ D SLR F ++G + + ++ D T RSRGFGFVT++TVEE +A+ A
Sbjct: 8 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67
Query: 112 ----LDGQV 116
+DG+V
Sbjct: 68 RPHKVDGRV 76
Score = 54.3 bits (129), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 43/74 (58%)
Query: 27 GKRISCESSISNPSIYQAIRCMSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDR 86
G+ + + ++S + ++ K+FVGGI + +++ LR+ F +YG + I+ DR
Sbjct: 74 GRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR 133
Query: 87 ETGRSRGFGFVTFS 100
+G+ RGF FVTF
Sbjct: 134 GSGKKRGFAFVTFD 147
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 67.0 bits (162), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 32/69 (46%), Positives = 47/69 (68%), Gaps = 4/69 (5%)
Query: 52 KLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQA 111
KLF+GG+S+ D SLR F ++G + + ++ D T RSRGFGFVT++TVEE +A+ A
Sbjct: 16 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 75
Query: 112 ----LDGQV 116
+DG+V
Sbjct: 76 RPHKVDGRV 84
Score = 53.9 bits (128), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 43/74 (58%)
Query: 27 GKRISCESSISNPSIYQAIRCMSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDR 86
G+ + + ++S + ++ K+FVGGI + +++ LR+ F +YG + I+ DR
Sbjct: 82 GRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR 141
Query: 87 ETGRSRGFGFVTFS 100
+G+ RGF FVTF
Sbjct: 142 GSGKKRGFAFVTFD 155
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 61.6 bits (148), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 34/75 (45%), Positives = 50/75 (66%), Gaps = 4/75 (5%)
Query: 46 RCMSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEA 105
R S LFV G+S + + +L+E+F G V ARI+ DRETG S+GFGFV F++ E+A
Sbjct: 11 RSQPSKTLFVKGLSEDTTEETLKESF--DGSVR-ARIVTDRETGSSKGFGFVDFNSEEDA 67
Query: 106 SSAIQAL-DGQVTFN 119
+A +A+ DG++ N
Sbjct: 68 KAAKEAMEDGEIDGN 82
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 61.6 bits (148), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 28/58 (48%), Positives = 40/58 (68%)
Query: 51 SKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSA 108
+K+FVGG+ Y+ D SLR+ F +G + EA +I DR+TG+SRG+GFVT + A A
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA 75
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 61.2 bits (147), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 44/63 (69%)
Query: 52 KLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQA 111
+L+VG + +N+ ++ LR F +G + ++++D ETGRS+G+GF+TFS E A A++
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 112 LDG 114
L+G
Sbjct: 88 LNG 90
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 61.2 bits (147), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 39/106 (36%), Positives = 61/106 (57%), Gaps = 10/106 (9%)
Query: 16 SKVGNILRQTA-GKRISCESSISNPSIYQAIRCMSSS-----KLFVGGISYNMDDNSLRE 69
S NI QT GK+I E++I I A + SS LFVG ++ N+DD +LR
Sbjct: 51 SHDANIALQTLNGKQI--ENNIV--KINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRN 106
Query: 70 AFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQALDGQ 115
AF + ++ D +TG SRG+GFV+F++ ++A +A+ ++ GQ
Sbjct: 107 AFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQ 152
Score = 32.0 bits (71), Expect = 0.093, Method: Compositional matrix adjust.
Identities = 15/63 (23%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
L+VG + + ++ L++ F G + +I++D+ ++ + FV + +A+ A+Q L
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNN-KNVNYAFVEYHQSHDANIALQTL 61
Query: 113 DGQ 115
+G+
Sbjct: 62 NGK 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 = 60.5 bits (145), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 25/64 (39%), Positives = 43/64 (67%)
Query: 52 KLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQA 111
LFVG ++ N+DD +LR AF + ++ D +TG SRG+GFV+F++ ++A +A+ +
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 112 LDGQ 115
+ GQ
Sbjct: 63 MQGQ 66
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 60.1 bits (144), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 30/63 (47%), Positives = 40/63 (63%), Gaps = 3/63 (4%)
Query: 51 SKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQ 110
+K+FVGGI +N + LRE F K+G V E +I D E R RGFGF+TF E+ S Q
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITF---EDEQSVDQ 67
Query: 111 ALD 113
A++
Sbjct: 68 AVN 70
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 59.7 bits (143), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 26/64 (40%), Positives = 45/64 (70%), Gaps = 2/64 (3%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
L+V + +DD LR+AF+ +G + A++++ E GRS+GFGFV FS+ EEA+ A+ +
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMM--EGGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 113 DGQV 116
+G++
Sbjct: 76 NGRI 79
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 58.5 bits (140), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 42/71 (59%)
Query: 51 SKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQ 110
+ L+V G+ M + + F++YG + +RI+LD+ TG SRG GF+ F EA AI+
Sbjct: 2 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 61
Query: 111 ALDGQVTFNAS 121
L+GQ A+
Sbjct: 62 GLNGQKPLGAA 72
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 58.5 bits (140), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 28/69 (40%), Positives = 46/69 (66%), Gaps = 4/69 (5%)
Query: 52 KLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQA 111
KLF+GG+S+ + SLR + ++G + + ++ D + RSRGFGFVTFS++ E +A+ A
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 88
Query: 112 ----LDGQV 116
+DG+V
Sbjct: 89 RPHSIDGRV 97
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 58.2 bits (139), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 42/71 (59%)
Query: 51 SKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQ 110
+ L+V G+ M + + F++YG + +RI+LD+ TG SRG GF+ F EA AI+
Sbjct: 91 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 150
Query: 111 ALDGQVTFNAS 121
L+GQ A+
Sbjct: 151 GLNGQKPLGAA 161
Score = 46.2 bits (108), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 35/66 (53%)
Query: 49 SSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSA 108
S + L V + NM + + F G + +++ D+ TG+S G+GFV +S +A A
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 109 IQALDG 114
I L+G
Sbjct: 63 INTLNG 68
>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 = 58.2 bits (139), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 43/63 (68%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
+FVG +S + ++ AFA +G +++AR++ D TG+S+G+GFV+F +A +AIQ +
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 113 DGQ 115
GQ
Sbjct: 78 GGQ 80
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 57.8 bits (138), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 26/66 (39%), Positives = 40/66 (60%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
L+VGG++ +DD L AF +G + + +I LD ET + RGF FV F E+A++AI +
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 113 DGQVTF 118
+ F
Sbjct: 126 NESELF 131
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 57.8 bits (138), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 27/68 (39%), Positives = 44/68 (64%), Gaps = 2/68 (2%)
Query: 48 MSSSK--LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEA 105
M+++K L+VGG++ +DD L AF +G + + +I LD ET + RGF FV F E+A
Sbjct: 3 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 62
Query: 106 SSAIQALD 113
++AI ++
Sbjct: 63 AAAIDNMN 70
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 57.4 bits (137), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 27/68 (39%), Positives = 44/68 (64%), Gaps = 2/68 (2%)
Query: 48 MSSSK--LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEA 105
M+++K L+VGG++ +DD L AF +G + + +I LD ET + RGF FV F E+A
Sbjct: 8 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 67
Query: 106 SSAIQALD 113
++AI ++
Sbjct: 68 AAAIDNMN 75
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 57.0 bits (136), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 26/65 (40%), Positives = 44/65 (67%)
Query: 50 SSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAI 109
SS L+VG + +N+ ++ LR F +G ++ ++ D +TGRS+G+GF+TFS E A A+
Sbjct: 5 SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
Query: 110 QALDG 114
+ L+G
Sbjct: 65 EQLNG 69
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 56.6 bits (135), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 27/70 (38%), Positives = 41/70 (58%)
Query: 49 SSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSA 108
S L+VGG++ +DD L AF +G + + +I LD ET + RGF FV F E+A++A
Sbjct: 1 SKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 60
Query: 109 IQALDGQVTF 118
I ++ F
Sbjct: 61 IDNMNESELF 70
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 56.6 bits (135), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 25/61 (40%), Positives = 39/61 (63%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
L+VGG++ +DD L AF +G + + +I LD ET + RGF FV F E+A++AI +
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 113 D 113
+
Sbjct: 68 N 68
>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 = 56.2 bits (134), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 26/65 (40%), Positives = 40/65 (61%)
Query: 51 SKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQ 110
+ L+V G+ M L + F++YG + +RI++D+ TG SRG GF+ F EA AI+
Sbjct: 89 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 148
Query: 111 ALDGQ 115
L+GQ
Sbjct: 149 GLNGQ 153
Score = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 34/66 (51%)
Query: 49 SSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSA 108
S + L V + NM R F G + +++ D+ TG+S G+GFV + ++A A
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 109 IQALDG 114
I L+G
Sbjct: 61 INTLNG 66
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 55.8 bits (133), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 25/51 (49%), Positives = 33/51 (64%)
Query: 49 SSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTF 99
S K+F+GG+S+ LRE F ++G V E ++ D T RSRGFGFVTF
Sbjct: 24 SGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 74
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 55.5 bits (132), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 43/71 (60%), Gaps = 1/71 (1%)
Query: 45 IRCMSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEE 104
+ KLF+GG++ ++ L+ F K+G ++E +I DR T +SRGF F+TF +
Sbjct: 2 VEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPAD 60
Query: 105 ASSAIQALDGQ 115
A +A + ++G+
Sbjct: 61 AKNAAKDMNGK 71
>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 = 55.5 bits (132), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 28/68 (41%), Positives = 42/68 (61%), Gaps = 4/68 (5%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
+FVGGI MD+ +R FA+YG V E +II DR TG S+G+GFV+F + +++
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVES- 69
Query: 113 DGQVTFNA 120
Q+ F+
Sbjct: 70 --QINFHG 75
>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 = 55.1 bits (131), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 28/68 (41%), Positives = 42/68 (61%), Gaps = 4/68 (5%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
+FVGGI MD+ +R FA+YG V E +II DR TG S+G+GFV+F + +++
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVES- 69
Query: 113 DGQVTFNA 120
Q+ F+
Sbjct: 70 --QINFHG 75
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 55.1 bits (131), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 26/62 (41%), Positives = 37/62 (59%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
L V I +D+ LR+ F +YG + +I+ DRET +SRG+GFV F + A AI L
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 113 DG 114
+G
Sbjct: 105 NG 106
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 55.1 bits (131), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 42/63 (66%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
+FVG +S + ++ AFA +G +++AR++ D TG+S+G+GFV+F +A +AI +
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 113 DGQ 115
GQ
Sbjct: 78 GGQ 80
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 54.7 bits (130), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 28/68 (41%), Positives = 42/68 (61%), Gaps = 4/68 (5%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
+FVGGI MD+ +R FA+YG V E +II DR TG S+G+GFV+F + +++
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVES- 70
Query: 113 DGQVTFNA 120
Q+ F+
Sbjct: 71 --QINFHG 76
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 54.7 bits (130), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 47/77 (61%), Gaps = 5/77 (6%)
Query: 39 PSIYQAIRCMSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVT 98
P++ +++R +FVG I Y + L++ F++ G V R++ DRETG+ +G+GF
Sbjct: 2 PAVDRSLRS-----VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCE 56
Query: 99 FSTVEEASSAIQALDGQ 115
+ E A SA++ L+G+
Sbjct: 57 YQDQETALSAMRNLNGR 73
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 54.7 bits (130), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 24/48 (50%), Positives = 32/48 (66%)
Query: 52 KLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTF 99
K+F+GG+S+ LRE F ++G V E ++ D T RSRGFGFVTF
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49
>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 = 53.5 bits (127), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 26/68 (38%), Positives = 40/68 (58%), Gaps = 4/68 (5%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAI--- 109
+F+GG+S++ L++ F+K+G V + + LD TGRSRGFGFV F E +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 110 -QALDGQV 116
L+G+V
Sbjct: 62 EHKLNGKV 69
>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 = 53.1 bits (126), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 27/66 (40%), Positives = 36/66 (54%)
Query: 51 SKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQ 110
+ L V ++Y ++LR F KYG V + I DR T SRGF FV F +A A+
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 111 ALDGQV 116
A+DG V
Sbjct: 108 AMDGAV 113
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 53.1 bits (126), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 27/66 (40%), Positives = 36/66 (54%)
Query: 51 SKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQ 110
+ L V ++Y ++LR F KYG V + I DR T SRGF FV F +A A+
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 111 ALDGQV 116
A+DG V
Sbjct: 131 AMDGAV 136
>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 = 53.1 bits (126), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 27/65 (41%), Positives = 40/65 (61%), Gaps = 3/65 (4%)
Query: 49 SSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSA 108
+ K FVGG+S++ L++ F K+G V + I D TGRSRGFGF+ F ++A+S
Sbjct: 10 DAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILF---KDAASV 66
Query: 109 IQALD 113
+ LD
Sbjct: 67 EKVLD 71
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 52.4 bits (124), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 25/65 (38%), Positives = 36/65 (55%)
Query: 52 KLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQA 111
+LFV +SY + L + F+ YG ++E +D T + +GF FVTF E A A
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 112 LDGQV 116
+DGQV
Sbjct: 70 VDGQV 74
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 52.0 bits (123), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 40/76 (52%), Gaps = 4/76 (5%)
Query: 52 KLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAI-- 109
KLFVGG+ ++ +LR F++YG V + I+ D+ T +SRGFGFV F + +
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 110 --QALDGQVTFNASCV 123
LDG+ C
Sbjct: 78 RPHTLDGRNIDPKPCT 93
>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 = 52.0 bits (123), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 39/70 (55%)
Query: 46 RCMSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEA 105
R + LFV G+ + + + FA+YG + + LDR TG +G+ V + T +EA
Sbjct: 3 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEA 62
Query: 106 SSAIQALDGQ 115
+A++ L+GQ
Sbjct: 63 QAAMEGLNGQ 72
>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 = 51.6 bits (122), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 39/70 (55%)
Query: 46 RCMSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEA 105
R + LFV G+ + + + FA+YG + + LDR TG +G+ V + T +EA
Sbjct: 3 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEA 62
Query: 106 SSAIQALDGQ 115
+A++ L+GQ
Sbjct: 63 QAAMEGLNGQ 72
>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 = 51.6 bits (122), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 39/70 (55%)
Query: 46 RCMSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEA 105
R + LFV G+ + + + FA+YG + + LDR TG +G+ V + T +EA
Sbjct: 5 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEA 64
Query: 106 SSAIQALDGQ 115
+A++ L+GQ
Sbjct: 65 QAAMEGLNGQ 74
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 51.6 bits (122), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 37/67 (55%)
Query: 52 KLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQA 111
KLF+G I N+D+ L+ F ++G + E ++ DR TG +G F+T+ E A A A
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74
Query: 112 LDGQVTF 118
L Q T
Sbjct: 75 LHEQKTL 81
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 51.6 bits (122), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 39/70 (55%)
Query: 46 RCMSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEA 105
R + LFV G+ + + + FA+YG + + LDR TG +G+ V + T +EA
Sbjct: 3 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEA 62
Query: 106 SSAIQALDGQ 115
+A++ L+GQ
Sbjct: 63 QAAMEGLNGQ 72
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 51.2 bits (121), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 21/49 (42%), Positives = 33/49 (67%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFST 101
+FVGG+S N ++ F ++G V++A ++ D+ T R RGFGFVTF +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFES 50
>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 = 51.2 bits (121), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 39/70 (55%)
Query: 46 RCMSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEA 105
R + LFV G+ + + + FA+YG + + LDR TG +G+ V + T +EA
Sbjct: 18 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEA 77
Query: 106 SSAIQALDGQ 115
+A++ L+GQ
Sbjct: 78 QAAMEGLNGQ 87
>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 = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 39/70 (55%)
Query: 46 RCMSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEA 105
R + LFV G+ + + + FA+YG + + LDR TG +G+ V + T +EA
Sbjct: 19 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEA 78
Query: 106 SSAIQALDGQ 115
+A++ L+GQ
Sbjct: 79 QAAMEGLNGQ 88
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 45/71 (63%), Gaps = 1/71 (1%)
Query: 50 SSKLFVGGISYNMDDNSLREAFAKYGYV-NEARIILDRETGRSRGFGFVTFSTVEEASSA 108
SS +F+G + +D+ L + F+ +G + +I+ D +TG S+G+ F+ F++ + + +A
Sbjct: 5 SSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAA 64
Query: 109 IQALDGQVTFN 119
I+A++GQ N
Sbjct: 65 IEAMNGQYLCN 75
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 50.8 bits (120), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 37/66 (56%)
Query: 48 MSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASS 107
+ + L+V + + D+ L F KYG + + I+ D+ TGR RG FV ++ EEA
Sbjct: 87 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQE 146
Query: 108 AIQALD 113
AI AL+
Sbjct: 147 AISALN 152
Score = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 37/66 (56%)
Query: 49 SSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSA 108
S++ L V + +M D L F G +N RI+ D +TG S G+ FV F++ ++ A
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 109 IQALDG 114
I+ L+G
Sbjct: 62 IKVLNG 67
>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 = 50.8 bits (120), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 37/67 (55%)
Query: 47 CMSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEAS 106
+ + L+V + + D+ L F KYG + + I+ D+ TGR RG FV ++ EEA
Sbjct: 10 SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQ 69
Query: 107 SAIQALD 113
AI AL+
Sbjct: 70 EAISALN 76
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 50.8 bits (120), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 25/62 (40%), Positives = 38/62 (61%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
L V G+S + LRE F+KYG + + I+ D+++ RSRGF FV F V++A A +
Sbjct: 15 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 74
Query: 113 DG 114
+G
Sbjct: 75 NG 76
>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 = 50.8 bits (120), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 37/66 (56%)
Query: 48 MSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASS 107
+ + L+V + + D+ L F KYG + + I+ D+ TGR RG FV ++ EEA
Sbjct: 98 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQE 157
Query: 108 AIQALD 113
AI AL+
Sbjct: 158 AISALN 163
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 35/66 (53%)
Query: 49 SSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSA 108
S++ L V + + D L F G +N RI D +TG S G+ FV F++ ++ A
Sbjct: 13 SNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRA 72
Query: 109 IQALDG 114
I+ L+G
Sbjct: 73 IKVLNG 78
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 50.4 bits (119), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 25/62 (40%), Positives = 38/62 (61%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
L V G+S + LRE F+KYG + + I+ D+++ RSRGF FV F V++A A +
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 113 DG 114
+G
Sbjct: 78 NG 79
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 50.4 bits (119), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 25/62 (40%), Positives = 38/62 (61%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
L V G+S + LRE F+KYG + + I+ D+++ RSRGF FV F V++A A +
Sbjct: 49 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 108
Query: 113 DG 114
+G
Sbjct: 109 NG 110
>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 = 50.1 bits (118), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 36/64 (56%)
Query: 51 SKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQ 110
+ L V + NM + LR F+ G V A++I D+ G S G+GFV + T ++A AI
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 64
Query: 111 ALDG 114
L+G
Sbjct: 65 TLNG 68
>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 = 50.1 bits (118), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 36/64 (56%)
Query: 51 SKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQ 110
+ L V + NM + LR F+ G V A++I D+ G S G+GFV + T ++A AI
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 111 ALDG 114
L+G
Sbjct: 63 TLNG 66
Score = 48.1 bits (113), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 38/69 (55%)
Query: 47 CMSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEAS 106
+ + L++ G+ M + + F+++G + +R+++D+ TG SRG F+ F EA
Sbjct: 85 VIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAE 144
Query: 107 SAIQALDGQ 115
AI + +G
Sbjct: 145 EAITSFNGH 153
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 50.1 bits (118), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 25/62 (40%), Positives = 38/62 (61%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
L V G+S + LRE F+KYG + + I+ D+++ RSRGF FV F V++A A +
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 113 DG 114
+G
Sbjct: 78 NG 79
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 49.7 bits (117), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 36/64 (56%)
Query: 51 SKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQ 110
+ L V + NM + LR F+ G V A++I D+ G S G+GFV + T ++A AI
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 111 ALDG 114
L+G
Sbjct: 63 TLNG 66
Score = 48.1 bits (113), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 38/69 (55%)
Query: 47 CMSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEAS 106
+ + L++ G+ M + + F+++G + +R+++D+ TG SRG F+ F EA
Sbjct: 85 VIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAE 144
Query: 107 SAIQALDGQ 115
AI + +G
Sbjct: 145 EAITSFNGH 153
>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 = 49.3 bits (116), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 43/85 (50%)
Query: 30 ISCESSISNPSIYQAIRCMSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETG 89
+S S+ P + + S+ KLF+GG+ ++D+ ++E +G + ++ D TG
Sbjct: 94 MSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATG 153
Query: 90 RSRGFGFVTFSTVEEASSAIQALDG 114
S+G+ F + + AI L+G
Sbjct: 154 LSKGYAFCEYVDINVTDQAIAGLNG 178
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 37/68 (54%), Gaps = 6/68 (8%)
Query: 52 KLFVGGISYNMDDNSLREAF---AKYGYVNEA--RIILDRETGRSRGFGFVTFSTVEEAS 106
+L+VG I + + + ++ + F + G + +A +L + + + F F+ F +V+E +
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 107 SAIQALDG 114
A+ A DG
Sbjct: 66 QAM-AFDG 72
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 49.3 bits (116), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 27/61 (44%), Positives = 37/61 (60%), Gaps = 1/61 (1%)
Query: 52 KLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQA 111
KLF+G IS +N +R F+ +G + E R IL G SRG FVTF+T A +AI+A
Sbjct: 97 KLFIGMISKKCTENDIRVMFSSFGQIEECR-ILRGPDGLSRGCAFVTFTTRAMAQTAIKA 155
Query: 112 L 112
+
Sbjct: 156 M 156
Score = 43.9 bits (102), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 34/63 (53%), Gaps = 2/63 (3%)
Query: 52 KLFVGGISYNMDDNSLREAFAKYGYVNEARIILDR--ETGRSRGFGFVTFSTVEEASSAI 109
K+FVG + + LRE F +YG V E ++ DR +S+G FVTF T + A A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 110 QAL 112
AL
Sbjct: 65 NAL 67
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 48.9 bits (115), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 26/61 (42%), Positives = 38/61 (62%), Gaps = 1/61 (1%)
Query: 52 KLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQA 111
KLF+G IS +N +R F+ +G + E RI+ + G SRG FVTF+T A +AI+A
Sbjct: 109 KLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRAMAQTAIKA 167
Query: 112 L 112
+
Sbjct: 168 M 168
Score = 43.9 bits (102), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 36/67 (53%), Gaps = 2/67 (2%)
Query: 48 MSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDR--ETGRSRGFGFVTFSTVEEA 105
+ + K+FVG + + LRE F +YG V E ++ DR +S+G FVTF T + A
Sbjct: 13 LDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 72
Query: 106 SSAIQAL 112
A AL
Sbjct: 73 LEAQNAL 79
>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 = 48.9 bits (115), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 26/60 (43%), Positives = 37/60 (61%), Gaps = 1/60 (1%)
Query: 52 KLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQA 111
KLF+G IS +N +R F+ +G + E RI+ + G SRG FVTF+T A +AI+A
Sbjct: 97 KLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRAXAQTAIKA 155
Score = 42.4 bits (98), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 33/63 (52%), Gaps = 2/63 (3%)
Query: 52 KLFVGGISYNMDDNSLREAFAKYGYVNEARIILDR--ETGRSRGFGFVTFSTVEEASSAI 109
K FVG + + LRE F +YG V E ++ DR +S+G FVTF T + A A
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 110 QAL 112
AL
Sbjct: 65 NAL 67
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 48.5 bits (114), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 36/61 (59%), Gaps = 1/61 (1%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
++VG + Y+ ++E F+++G V ++I DRET + +GFGFV E S AI L
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAKL 62
Query: 113 D 113
D
Sbjct: 63 D 63
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 47.8 bits (112), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 36/62 (58%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
LFV I ++ ++E F YG + + LDR TG S+G+ V + T ++A +A +AL
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 113 DG 114
+G
Sbjct: 89 NG 90
>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 = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/67 (38%), Positives = 44/67 (65%)
Query: 49 SSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSA 108
S +FVG +S + ++ AFA +G +++AR++ D TG+S+G+GFV+F +A +A
Sbjct: 5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENA 64
Query: 109 IQALDGQ 115
IQ + GQ
Sbjct: 65 IQQMGGQ 71
>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 = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 33/60 (55%)
Query: 51 SKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQ 110
K+FVGG+S + + +RE F +G V + +D +T + RGF F+TF E ++
Sbjct: 2 KKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 61
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 2/79 (2%)
Query: 36 ISNPSIYQAIRCMSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFG 95
I P YQ + + KLF+GG+ ++D+ ++E +G + ++ D TG S+G+
Sbjct: 82 IRRPHDYQPLP--GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYA 139
Query: 96 FVTFSTVEEASSAIQALDG 114
F + + AI L+G
Sbjct: 140 FCEYVDINVTDQAIAGLNG 158
Score = 29.6 bits (65), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 39/71 (54%), Gaps = 6/71 (8%)
Query: 49 SSSKLFVGGISYNMDDNSLREAF---AKYGYVNEA--RIILDRETGRSRGFGFVTFSTVE 103
S+ +L+VG I + + + ++ + F + G + +A +L + + + F F+ F +V+
Sbjct: 3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62
Query: 104 EASSAIQALDG 114
E + A+ A DG
Sbjct: 63 ETTQAM-AFDG 72
>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 = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 2/79 (2%)
Query: 36 ISNPSIYQAIRCMSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFG 95
I P YQ + + KLF+GG+ ++D+ ++E +G + ++ D TG S+G+
Sbjct: 84 IRRPHDYQPLP--GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYA 141
Query: 96 FVTFSTVEEASSAIQALDG 114
F + + AI L+G
Sbjct: 142 FCEYVDINVTDQAIAGLNG 160
Score = 29.3 bits (64), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 39/71 (54%), Gaps = 6/71 (8%)
Query: 49 SSSKLFVGGISYNMDDNSLREAF---AKYGYVNEA--RIILDRETGRSRGFGFVTFSTVE 103
S+ +L+VG I + + + ++ + F + G + +A +L + + + F F+ F +V+
Sbjct: 5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 64
Query: 104 EASSAIQALDG 114
E + A+ A DG
Sbjct: 65 ETTQAM-AFDG 74
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 47.4 bits (111), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 35/62 (56%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
LF+ + D L F +G V A++ +D++T S+ FGFV+F + A AI+A+
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 113 DG 114
+G
Sbjct: 103 NG 104
>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 = 47.0 bits (110), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 35/64 (54%)
Query: 51 SKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQ 110
+ L V + N + LR F+ G V A++I D+ G S G+GFV + T ++A AI
Sbjct: 20 TNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 79
Query: 111 ALDG 114
L+G
Sbjct: 80 TLNG 83
>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 = 47.0 bits (110), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 36/62 (58%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
LFV I ++ ++E F YG + + LDR TG S+G+ V + T ++A +A +AL
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 113 DG 114
+G
Sbjct: 135 NG 136
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 47.0 bits (110), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 27/69 (39%), Positives = 39/69 (56%), Gaps = 1/69 (1%)
Query: 51 SKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQ 110
S +FV + Y + L+E F+ G V A I+ D++ G+SRG G VTF EA AI
Sbjct: 16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTFEQSIEAVQAIS 74
Query: 111 ALDGQVTFN 119
+GQ+ F+
Sbjct: 75 MFNGQLLFD 83
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 46.6 bits (109), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 35/66 (53%)
Query: 49 SSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSA 108
S + L V + NM + + F G + +++ D+ TG+S G+GFV +S +A A
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 109 IQALDG 114
I L+G
Sbjct: 63 INTLNG 68
>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 = 46.2 bits (108), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 39/62 (62%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
+++G I Y+ + + + + G V +++ D +TGRS+G+ F+ F +E ++SA++ L
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 113 DG 114
+G
Sbjct: 67 NG 68
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 46.2 bits (108), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 41/70 (58%)
Query: 49 SSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSA 108
S S ++V + +++ +N L F+KYG V + I+ D++T +S+G F+ F + A +
Sbjct: 15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNC 74
Query: 109 IQALDGQVTF 118
+A++ + F
Sbjct: 75 TRAINNKQLF 84
>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 = 45.8 bits (107), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 38/63 (60%)
Query: 51 SKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQ 110
S+++VG I Y + ++++R+AFA +G + + D T + +GF FV + E A A++
Sbjct: 29 SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 88
Query: 111 ALD 113
++
Sbjct: 89 QMN 91
Score = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 12/63 (19%), Positives = 36/63 (57%)
Query: 51 SKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQ 110
++++V + ++ D+ ++ F +G + A + D TG+ +G+GF+ + + + A+
Sbjct: 126 NRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVS 185
Query: 111 ALD 113
+++
Sbjct: 186 SMN 188
>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 = 45.8 bits (107), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 40/70 (57%), Gaps = 4/70 (5%)
Query: 44 AIRCMSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVE 103
AI C +++VG I Y + ++++R+AFA +G + + D T + +GF FV + E
Sbjct: 11 AIMC----RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPE 66
Query: 104 EASSAIQALD 113
A A++ ++
Sbjct: 67 AAQLALEQMN 76
Score = 39.7 bits (91), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 11/63 (17%), Positives = 35/63 (55%)
Query: 51 SKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQ 110
++++V + ++ D+ ++ F +G + + D TG+ +G+GF+ + + + A+
Sbjct: 111 NRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVS 170
Query: 111 ALD 113
+++
Sbjct: 171 SMN 173
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 45.8 bits (107), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 39/62 (62%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
+++G I Y+ + + + + G V +++ D +TGRS+G+ F+ F +E ++SA++ L
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 113 DG 114
+G
Sbjct: 65 NG 66
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 45.8 bits (107), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 32/58 (55%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQ 110
+FVGG+S + + +RE F +G V + +D +T + RGF F+TF E ++
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 59
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 45.4 bits (106), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 36/61 (59%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
++VGG+ + + L E F + G V + DR TG+ +G+GFV F + E+A AI+ +
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 113 D 113
D
Sbjct: 78 D 78
>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 = 45.4 bits (106), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 39/62 (62%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
+++G I Y+ + + + + G V +++ D +TGRS+G+ F+ F +E ++SA++ L
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 113 DG 114
+G
Sbjct: 66 NG 67
>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 = 45.4 bits (106), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 36/62 (58%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
LF+ + D L + F +G V A++ +D++T S+ FGFV++ A +AIQ++
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 113 DG 114
+G
Sbjct: 88 NG 89
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 45.1 bits (105), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 33/63 (52%)
Query: 50 SSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAI 109
SS L++ G+ D L + YG + + ILD+ T + +G+GFV F + A A+
Sbjct: 5 SSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 64
Query: 110 QAL 112
AL
Sbjct: 65 TAL 67
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 37/66 (56%)
Query: 49 SSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSA 108
S++ L V + +M D L F G +N RI+ D +TG S G+ FV F++ ++ A
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 109 IQALDG 114
I+ L+G
Sbjct: 62 IKVLNG 67
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/68 (36%), Positives = 37/68 (54%), Gaps = 2/68 (2%)
Query: 49 SSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSA 108
+ +L V I + D LR+ F ++G + + II + E G S+GFGFVTF +A A
Sbjct: 14 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERG-SKGFGFVTFENSADADRA 71
Query: 109 IQALDGQV 116
+ L G V
Sbjct: 72 REKLHGTV 79
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 37/71 (52%), Gaps = 1/71 (1%)
Query: 43 QAIRCMSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRE-TGRSRGFGFVTFST 101
Q + ++SK+ V I + + +RE F+ +G + R+ TG RGFGFV F T
Sbjct: 8 QVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFIT 67
Query: 102 VEEASSAIQAL 112
++A A AL
Sbjct: 68 KQDAKKAFNAL 78
>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 = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 34/63 (53%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
LFV ++Y+ ++ LR F YG + ++ + +G+ RG+ F+ + + SA +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 113 DGQ 115
DG+
Sbjct: 165 DGK 167
>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 = 1e-05, Method: Compositional matrix adjust.
Identities = 25/68 (36%), Positives = 36/68 (52%), Gaps = 2/68 (2%)
Query: 49 SSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSA 108
+L V I + D LR+ F ++G + + II + E G S+GFGFVTF +A A
Sbjct: 28 QPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERG-SKGFGFVTFENSADADRA 85
Query: 109 IQALDGQV 116
+ L G V
Sbjct: 86 REKLHGTV 93
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/62 (38%), Positives = 31/62 (50%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
L V ++Y +SLR F KYG V + I + T RGF FV F +A A A+
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75
Query: 113 DG 114
DG
Sbjct: 76 DG 77
>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 = 1e-05, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 39/72 (54%), Gaps = 2/72 (2%)
Query: 53 LFVGGISYNMDDNSLREAFAK-YGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQA 111
LFVG ++ ++DD L E F K Y +++LD +TG S+G+GFV F+ E A+
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFVKFTDELEQKRALTE 70
Query: 112 LDGQVTFNASCV 123
G V + V
Sbjct: 71 CQGAVGLGSKPV 82
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 35/65 (53%)
Query: 50 SSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAI 109
+ KLF+GG+ ++D+ ++E +G + ++ D TG S+G+ F + + AI
Sbjct: 1 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 60
Query: 110 QALDG 114
L+G
Sbjct: 61 AGLNG 65
>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 = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 37/67 (55%), Gaps = 4/67 (5%)
Query: 44 AIRCMSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVE 103
AI C +++VG I Y + ++++R+AFA +G + D T + +GF FV + E
Sbjct: 10 AIXC----RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPE 65
Query: 104 EASSAIQ 110
A A++
Sbjct: 66 AAQLALE 72
Score = 38.5 bits (88), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 11/59 (18%), Positives = 32/59 (54%)
Query: 51 SKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAI 109
++++V + ++ D+ ++ F +G + + D TG+ +G+GF+ + + + A+
Sbjct: 110 NRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAV 168
>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 = 43.9 bits (102), Expect = 2e-05, Method: Composition-based stats.
Identities = 17/63 (26%), Positives = 34/63 (53%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
LFV ++Y+ ++ LR F YG + ++ + +G+ RG+ F+ + + SA +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 113 DGQ 115
DG+
Sbjct: 165 DGK 167
>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 = 43.9 bits (102), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 34/63 (53%), Gaps = 2/63 (3%)
Query: 52 KLFVGGISYNMDDNSLREAFAKYGYVNEARIILDR--ETGRSRGFGFVTFSTVEEASSAI 109
K+FVG + + LRE F +YG V E ++ DR +S+G FVTF T + A A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 110 QAL 112
AL
Sbjct: 65 NAL 67
>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 = 43.9 bits (102), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 42/69 (60%), Gaps = 2/69 (2%)
Query: 48 MSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASS 107
+ S +F+ + ++D+ +L + F+ +G + +++ D E G S+G+GFV F T E A
Sbjct: 3 LGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENG-SKGYGFVHFETQEAAER 60
Query: 108 AIQALDGQV 116
AI+ ++G +
Sbjct: 61 AIEKMNGML 69
>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 = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 26/90 (28%), Positives = 49/90 (54%), Gaps = 6/90 (6%)
Query: 27 GKRISCESSISNPSIYQAIRCMSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDR 86
GK + S +PS+ R +F+ + ++D+ +L + F+ +G + +++ D
Sbjct: 79 GKPVRIMWSQRDPSL----RKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD- 133
Query: 87 ETGRSRGFGFVTFSTVEEASSAIQALDGQV 116
E G S+G+GFV F T E A AI+ ++G +
Sbjct: 134 ENG-SKGYGFVHFETQEAAERAIEKMNGML 162
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 32/54 (59%)
Query: 50 SSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVE 103
+S L V G+ + + L+E F+ +G V ++ D +TG S+GFGFV F+ E
Sbjct: 15 TSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYE 68
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 43.1 bits (100), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 38/69 (55%), Gaps = 1/69 (1%)
Query: 47 CMSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDR-ETGRSRGFGFVTFSTVEEA 105
M +K+ +G ++ N+ + + E F+ YG + + ++R S+G+ +V F +EA
Sbjct: 1 SMKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEA 60
Query: 106 SSAIQALDG 114
A++ +DG
Sbjct: 61 EKALKHMDG 69
>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 = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 26/90 (28%), Positives = 49/90 (54%), Gaps = 6/90 (6%)
Query: 27 GKRISCESSISNPSIYQAIRCMSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDR 86
GK + S +PS+ R +F+ + ++D+ +L + F+ +G + +++ D
Sbjct: 84 GKPVRIMWSQRDPSL----RKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD- 138
Query: 87 ETGRSRGFGFVTFSTVEEASSAIQALDGQV 116
E G S+G+GFV F T E A AI+ ++G +
Sbjct: 139 ENG-SKGYGFVHFETQEAAERAIEKMNGML 167
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 37/62 (59%), Gaps = 6/62 (9%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
++ GGI+ + D +R+ F+ +G + E R+ ++ G+ FV FST E A+ AI ++
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFSTHESAAHAIVSV 81
Query: 113 DG 114
+G
Sbjct: 82 NG 83
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 42.7 bits (99), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 36/70 (51%), Gaps = 1/70 (1%)
Query: 52 KLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQA 111
KLFVG ++ + + F +G ++E +L G S+G FV FS+ EA +AI A
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDEC-TVLRGPDGSSKGCAFVKFSSHTEAQAAIHA 75
Query: 112 LDGQVTFNAS 121
L G T +
Sbjct: 76 LHGSQTMPGA 85
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 42.7 bits (99), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 52 KLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQA 111
KLFVG + D +R+ F +G ++E +L G S+G FV F T EA +AI
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDEC-TVLRGPDGTSKGCAFVKFQTHAEAQAAINT 72
Query: 112 L 112
L
Sbjct: 73 L 73
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 42.4 bits (98), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 43/73 (58%), Gaps = 2/73 (2%)
Query: 44 AIRCMSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVE 103
++R +F+ + ++D+ +L + F+ +G + +++ D E G S+G+GFV F T E
Sbjct: 5 SLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENG-SKGYGFVHFETQE 62
Query: 104 EASSAIQALDGQV 116
A AI+ ++G +
Sbjct: 63 AAERAIEKMNGML 75
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 41.2 bits (95), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 39/69 (56%)
Query: 46 RCMSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEA 105
R ++ + V +S + + L+E F +G ++ + D+ TG+S+GF F++F E+A
Sbjct: 11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDA 70
Query: 106 SSAIQALDG 114
+ AI + G
Sbjct: 71 ARAIAGVSG 79
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
+FVG + + + L E F + G + + I DRE G+ + FGFV F E S AI L
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALL 77
Query: 113 DG 114
+G
Sbjct: 78 NG 79
>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 30/50 (60%), Gaps = 2/50 (4%)
Query: 65 NSLREAFAKYG--YVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
+S+ A + Y VN R+I D++T ++RGF FV S+ +AS +Q L
Sbjct: 24 DSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQIL 73
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 50 SSKLFVGGISYNMDDNSLREAFAKYG-YVNEARIILDRETGRSRGFGFVTFSTVEEASSA 108
++ L++G + MD+N + AFA G V +II +R TG G+ FV F+ + A
Sbjct: 9 AASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKC 68
Query: 109 IQALDGQVTFNAS 121
+ ++G+ A+
Sbjct: 69 LHKINGKPLPGAT 81
>pdb|2M2B|A Chain A, Nmr Structure Of The Rrm2 Domain Of The Protein Rbm10 From
Homo Sapiens
Length = 131
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 35/63 (55%), Gaps = 4/63 (6%)
Query: 65 NSLREAFAKYGYVNEA--RIILDRETGRSRGFGFVTFSTVEEAS--SAIQALDGQVTFNA 120
+S+ A A Y ++ + R+I D++T +RGF F+ ST+E A +QAL +T +
Sbjct: 38 DSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIEAAQLLQILQALHPPLTIDG 97
Query: 121 SCV 123
+
Sbjct: 98 KTI 100
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 15/76 (19%)
Query: 50 SSKLFVGGISYNMDDNSLREAFAKYGYV---------NEARIILDRETGRSRGFGFVTFS 100
SS LF+ ++++ + +L+ F+K G + N+A ++L S GFGFV +
Sbjct: 5 SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLL------SMGFGFVEYK 58
Query: 101 TVEEASSAIQALDGQV 116
E+A A++ L G
Sbjct: 59 KPEQAQKALKQLQGHT 74
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 31/63 (49%), Gaps = 6/63 (9%)
Query: 51 SKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQ 110
S+LFVG + ++ + +R+ F KYG E I D +GFGF+ T A A
Sbjct: 23 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKV 76
Query: 111 ALD 113
LD
Sbjct: 77 ELD 79
Score = 33.1 bits (74), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 36/67 (53%), Gaps = 5/67 (7%)
Query: 47 CMSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEAS 106
C S+S L V + + + L EAF+ +G V A +I+D + GR G G V FS
Sbjct: 94 CHSAS-LTVRNLPQYVSNELLEEAFSVFGQVERAVVIVD-DRGRPSGKGIVEFSG---KP 148
Query: 107 SAIQALD 113
+A +ALD
Sbjct: 149 AARKALD 155
>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 = 37.7 bits (86), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 31/63 (49%), Gaps = 6/63 (9%)
Query: 51 SKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQ 110
S+LFVG + ++ + +R+ F KYG E I D +GFGF+ T A A
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKV 69
Query: 111 ALD 113
LD
Sbjct: 70 ELD 72
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 32/70 (45%), Gaps = 5/70 (7%)
Query: 47 CMSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEAS 106
C K++VG + N + L AF YG + + + GF FV F +A+
Sbjct: 70 CPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAA 124
Query: 107 SAIQALDGQV 116
A++ LDG+
Sbjct: 125 DAVRELDGRT 134
>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 = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 1/61 (1%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
++VG + Y L F G VN I+ D+ +G +GF ++ FS E +++ AL
Sbjct: 8 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-AL 66
Query: 113 D 113
D
Sbjct: 67 D 67
>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 = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 1/61 (1%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
++VG + Y L F G VN I+ D+ +G +GF ++ FS E +++ AL
Sbjct: 9 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-AL 67
Query: 113 D 113
D
Sbjct: 68 D 68
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 1/66 (1%)
Query: 50 SSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAI 109
+ L++ + +MD+ L +G V RI+ D +G SRG GF + E+ + I
Sbjct: 25 PTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVI 83
Query: 110 QALDGQ 115
+G+
Sbjct: 84 GHFNGK 89
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 32/70 (45%), Gaps = 5/70 (7%)
Query: 47 CMSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEAS 106
C K++VG + N + L AF YG + + + GF FV F +A+
Sbjct: 70 CPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAA 124
Query: 107 SAIQALDGQV 116
A++ LDG+
Sbjct: 125 DAVRDLDGRT 134
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/64 (25%), Positives = 36/64 (56%), Gaps = 4/64 (6%)
Query: 50 SSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAI 109
S L + +SY+ + +L+E F K ++ + + G+S+G+ F+ F++ E+A A+
Sbjct: 15 SKTLVLSNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGYAFIEFASFEDAKEAL 70
Query: 110 QALD 113
+ +
Sbjct: 71 NSCN 74
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 33/71 (46%), Gaps = 10/71 (14%)
Query: 46 RCMSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEA 105
RC +LFVG + ++ + + F +YG +E I R RGFGF+ + A
Sbjct: 22 RC----RLFVGNLPTDITEEDFKRLFERYGEPSEVFI------NRDRGFGFIRLESRTLA 71
Query: 106 SSAIQALDGQV 116
A LDG +
Sbjct: 72 EIAKAELDGTI 82
Score = 35.4 bits (80), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 35/58 (60%), Gaps = 1/58 (1%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQ 110
L V +S + + L +AF+++G V +A +++D + GR+ G GFV F+ A A++
Sbjct: 99 LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALE 155
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 32/59 (54%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQA 111
+F+ +S++ ++ +L E ++G + R++L +T S+G F F T E A + A
Sbjct: 18 VFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 76
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 52 KLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQA 111
KL V + + + D ++E FA++G + +A + DR +GRS G V F +A A++
Sbjct: 30 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQ 88
Query: 112 LDG 114
+G
Sbjct: 89 YNG 91
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 35.8 bits (81), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 30/65 (46%), Gaps = 5/65 (7%)
Query: 52 KLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQA 111
K++VG + L AF+ YG + I + GF FV F +A A++
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRG 56
Query: 112 LDGQV 116
LDG+V
Sbjct: 57 LDGKV 61
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 35.4 bits (80), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 1/63 (1%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
+F ++ + L + F+ G V + RII DR + RS+G +V F ++ AI L
Sbjct: 28 VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GL 86
Query: 113 DGQ 115
GQ
Sbjct: 87 TGQ 89
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 31/49 (63%), Gaps = 1/49 (2%)
Query: 64 DNSLREAFAKYG-YVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQA 111
++ +R +G E R++ ++ +G+SRGF FV FS +++A+ ++A
Sbjct: 15 EDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEA 63
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 35.0 bits (79), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 36/65 (55%), Gaps = 2/65 (3%)
Query: 50 SSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAI 109
SS +FV + ++ L++ F + G+V A I + E G+S+G G V F + E A A
Sbjct: 5 SSGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKM--ENGKSKGCGVVKFESPEVAERAC 62
Query: 110 QALDG 114
+ ++G
Sbjct: 63 RMMNG 67
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 35.0 bits (79), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 6/72 (8%)
Query: 49 SSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSA 108
+ +KL V + + + D ++E FA++G + +A + DR +GRS G V F +A A
Sbjct: 87 TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKA 145
Query: 109 IQ-----ALDGQ 115
++ LDG+
Sbjct: 146 MKQYKGVPLDGR 157
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 35.0 bits (79), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 36/66 (54%), Gaps = 1/66 (1%)
Query: 49 SSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSA 108
+ +KL V + + + D ++E FA++G + +A + DR +GRS G V F +A A
Sbjct: 34 TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKA 92
Query: 109 IQALDG 114
++ G
Sbjct: 93 MKQYKG 98
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 35.0 bits (79), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 36/66 (54%), Gaps = 1/66 (1%)
Query: 49 SSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSA 108
+ +KL V + + + D ++E FA++G + +A + DR +GRS G V F +A A
Sbjct: 34 TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKA 92
Query: 109 IQALDG 114
++ G
Sbjct: 93 MKQYKG 98
>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 = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 1/63 (1%)
Query: 52 KLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQA 111
KL V + + + D ++E FA++G + +A + DR +GRS G V F +A A +
Sbjct: 31 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAXKQ 89
Query: 112 LDG 114
+G
Sbjct: 90 YNG 92
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
Length = 124
Score = 34.7 bits (78), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 16/64 (25%), Positives = 32/64 (50%), Gaps = 1/64 (1%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
++VG + Y L F+ G +N I+ D+ +G +G+ ++ F+ +A+ A+
Sbjct: 39 VYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AM 97
Query: 113 DGQV 116
D V
Sbjct: 98 DETV 101
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 33.9 bits (76), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 35/63 (55%), Gaps = 2/63 (3%)
Query: 52 KLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQA 111
++FV + ++ L++ F + G+V A I + E G+S+G G V F + E A A +
Sbjct: 10 QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKM--ENGKSKGCGVVKFESPEVAERACRM 67
Query: 112 LDG 114
++G
Sbjct: 68 MNG 70
>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 = 33.5 bits (75), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 8/75 (10%)
Query: 49 SSSKLFVGGISYNMDDNSLREAFAKYGYVNEAR--------IILDRETGRSRGFGFVTFS 100
++ +FV G+ N+ S+ + F + G + + + DRETG+ +G V+F
Sbjct: 12 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 71
Query: 101 TVEEASSAIQALDGQ 115
A +AI DG+
Sbjct: 72 DPPSAKAAIDWFDGK 86
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 33.1 bits (74), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 32/58 (55%), Gaps = 5/58 (8%)
Query: 50 SSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASS 107
SS +FVG + +M ++ LRE F++YG V + I R F FVTF+ + A S
Sbjct: 5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFI-----PKPFRAFAFVTFADDQIAQS 57
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 32.7 bits (73), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 8/75 (10%)
Query: 49 SSSKLFVGGISYNMDDNSLREAFAKYGYVNEAR--------IILDRETGRSRGFGFVTFS 100
++ +FV G+ N+ S+ + F + G + + + DRETG+ +G V+F
Sbjct: 6 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 65
Query: 101 TVEEASSAIQALDGQ 115
A +AI DG+
Sbjct: 66 DPPSAKAAIDWFDGK 80
>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 = 32.7 bits (73), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 27/51 (52%)
Query: 65 NSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQALDGQ 115
+L F+K G V +D TG+++GF FV ++ +A I++ G+
Sbjct: 27 KALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGK 77
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 32.3 bits (72), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 39/74 (52%), Gaps = 8/74 (10%)
Query: 50 SSKLFVGGISYNMDDNSLREAFAKYGYVNEAR--------IILDRETGRSRGFGFVTFST 101
+S ++V G++ ++ + L + F + G V + I LD+ETG+ +G V++
Sbjct: 15 NSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYED 74
Query: 102 VEEASSAIQALDGQ 115
A +A++ DG+
Sbjct: 75 PPTAKAAVEWFDGK 88
>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 = 32.0 bits (71), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 27/50 (54%)
Query: 66 SLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQALDGQ 115
+L F+K G V +D TG+++GF FV ++ +A I++ G+
Sbjct: 28 ALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGK 77
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 32.0 bits (71), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQ 110
LF+G ++ N L+ A ++ N+ ++ D TG +R FG+V F + E+ A++
Sbjct: 20 LFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDLEKALE 76
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 31.6 bits (70), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 29/62 (46%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
L++ +S + + L FA++ I TGR RG F+TF E A A+ +
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87
Query: 113 DG 114
+G
Sbjct: 88 NG 89
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 31.6 bits (70), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQ 110
LF+G ++ N L+ A ++ N+ ++ D TG +R FG+V F + E+ A++
Sbjct: 16 LFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDLEKALE 72
Score = 30.0 bits (66), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 19/93 (20%), Positives = 40/93 (43%), Gaps = 5/93 (5%)
Query: 22 LRQTAGKRISCESSISNPSIYQAIRCMSSSKLFVGGISYNMDDNSLREAFAKYGYVNEAR 81
L T K E + P + + ++ L +S+N+ ++ L+E F +
Sbjct: 71 LELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFE-----DALE 125
Query: 82 IILDRETGRSRGFGFVTFSTVEEASSAIQALDG 114
I L + G+S+G ++ F + +A ++ G
Sbjct: 126 IRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQG 158
>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 = 31.2 bits (69), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 37/66 (56%)
Query: 49 SSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSA 108
S L+VG +S+ + + E F+K G + + + LD+ + GF FV + + +A +A
Sbjct: 38 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENA 97
Query: 109 IQALDG 114
++ ++G
Sbjct: 98 MRYING 103
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 31.2 bits (69), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 27/61 (44%), Gaps = 8/61 (13%)
Query: 52 KLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQA 111
KLF+G + + +R F +YG V E II + +GFV A AI+
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRN 61
Query: 112 L 112
L
Sbjct: 62 L 62
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 30.8 bits (68), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 29/57 (50%), Gaps = 5/57 (8%)
Query: 51 SKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASS 107
SK+FVG + +M L++ F +YG V + I R F FVTF+ + A S
Sbjct: 12 SKVFVGRCTEDMTAEELQQFFCQYGEVVDVFI-----PKPFRAFAFVTFADDKVAQS 63
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 30.8 bits (68), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 34/63 (53%), Gaps = 6/63 (9%)
Query: 52 KLFVGGISYNMDDNSLREAFAKYG--YVNEARIILDRETGRSRGFGFVTFSTVEEASSAI 109
K+FVGG+ ++D++ + +F ++G V+ + +G+ F+ F + S++
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLF----QEESSV 65
Query: 110 QAL 112
QAL
Sbjct: 66 QAL 68
>pdb|2HZC|A Chain A, Crystal Structure Of The N-terminal Rrm Of The U2af Large
Subunit
Length = 87
Score = 29.6 bits (65), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 39/71 (54%), Gaps = 6/71 (8%)
Query: 49 SSSKLFVGGISYNMDDNSLREAF---AKYGYVNEA--RIILDRETGRSRGFGFVTFSTVE 103
S+ +L+VG I + + + ++ + F + G + +A +L + + + F F+ F +V+
Sbjct: 5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 64
Query: 104 EASSAIQALDG 114
E + A+ A DG
Sbjct: 65 ETTQAM-AFDG 74
>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 = 29.6 bits (65), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 37/66 (56%), Gaps = 1/66 (1%)
Query: 49 SSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSA 108
S L+VG +S+ + + E F+K G + + + LD+ + GF FV + + +A +A
Sbjct: 17 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDK-MKTACGFCFVEYYSRADAENA 75
Query: 109 IQALDG 114
++ ++G
Sbjct: 76 MRYING 81
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 28.9 bits (63), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 20/93 (21%), Positives = 36/93 (38%), Gaps = 5/93 (5%)
Query: 22 LRQTAGKRISCESSISNPSIYQAIRCMSSSKLFVGGISYNMDDNSLREAFAKYGYVNEAR 81
L T K E + P + + + L + Y + + L+E F + A
Sbjct: 65 LELTGLKVFGNEIKLEKPKGKDSKKERDARTLLAKNLPYKVTQDELKEVFE-----DAAE 119
Query: 82 IILDRETGRSRGFGFVTFSTVEEASSAIQALDG 114
I L + G+S+G ++ F T +A + G
Sbjct: 120 IRLVSKDGKSKGIAYIEFKTEADAEKTFEEKQG 152
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 28.9 bits (63), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 25/54 (46%), Gaps = 6/54 (11%)
Query: 61 NMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQALDG 114
+M LR AF+ +G I+D R FVT+ +E A A+ L+G
Sbjct: 48 DMTPTLLRGAFSPFGN------IIDLSMDPPRNCAFVTYEKMESADQAVAELNG 95
>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 = 28.9 bits (63), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 4/57 (7%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGY--VNEARIILDRETGRSRGFGFVTFSTVEEASS 107
L++G +++ D L EA G + E + +R G+S+GF V + EASS
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGS--EASS 58
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 28.9 bits (63), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 25/54 (46%), Gaps = 6/54 (11%)
Query: 61 NMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQALDG 114
+M LR AF+ +G I+D R FVT+ +E A A+ L+G
Sbjct: 24 DMTPTLLRGAFSPFGN------IIDLSMDPPRNCAFVTYEKMESADQAVAELNG 71
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 28.5 bits (62), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 12/25 (48%), Positives = 18/25 (72%)
Query: 92 RGFGFVTFSTVEEASSAIQALDGQV 116
R + FV FS E+A A++AL+G+V
Sbjct: 51 RDYAFVHFSNREDAVEAMKALNGKV 75
>pdb|1U2F|A Chain A, Solution Structure Of The First Rna-Binding Domain Of
Hu2af65
Length = 90
Score = 28.5 bits (62), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 38/70 (54%), Gaps = 6/70 (8%)
Query: 50 SSKLFVGGISYNMDDNSLREAF---AKYGYVNEA--RIILDRETGRSRGFGFVTFSTVEE 104
+ +L+VG I + + + ++ + F + G + +A +L + + + F F+ F +V+E
Sbjct: 1 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 60
Query: 105 ASSAIQALDG 114
+ A+ A DG
Sbjct: 61 TTQAM-AFDG 69
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 28.5 bits (62), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 14/63 (22%), Positives = 28/63 (44%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
L V + ++ E +G + ++ TG+S+G+GF + + A+ A L
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 113 DGQ 115
G+
Sbjct: 158 LGK 160
>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 = 28.5 bits (62), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 14/63 (22%), Positives = 28/63 (44%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
L V + ++ E +G + ++ TG+S+G+GF + + A+ A L
Sbjct: 96 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Query: 113 DGQ 115
G+
Sbjct: 156 LGK 158
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 28.5 bits (62), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 30/63 (47%), Gaps = 3/63 (4%)
Query: 52 KLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQA 111
+++VG + ++ + + F KYG + + + +R G F FV F +A A+
Sbjct: 24 RIYVGNLPPDIRTKDIEDVFYKYGAIRDID-LKNRRGGPP--FAFVEFEDPRDAEDAVYG 80
Query: 112 LDG 114
DG
Sbjct: 81 RDG 83
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 28.5 bits (62), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 14/63 (22%), Positives = 28/63 (44%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
L V + ++ E +G + ++ TG+S+G+GF + + A+ A L
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 113 DGQ 115
G+
Sbjct: 158 LGK 160
>pdb|2KRB|A Chain A, Solution Structure Of Eif3b-Rrm Bound To Eif3j Peptide
Length = 81
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 12/50 (24%), Positives = 27/50 (54%), Gaps = 2/50 (4%)
Query: 65 NSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQALDG 114
N + + F+K+G + E G+++G+ F+ +++ A A++ DG
Sbjct: 22 NVIHKIFSKFGKITND--FYPEEDGKTKGYIFLEYASPAHAVDAVKNADG 69
>pdb|1U6M|A Chain A, The Crystal Structure Of Acetyltransferase
pdb|1U6M|B Chain B, The Crystal Structure Of Acetyltransferase
pdb|1U6M|C Chain C, The Crystal Structure Of Acetyltransferase
pdb|1U6M|D Chain D, The Crystal Structure Of Acetyltransferase
Length = 199
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 64 DNSLREAFAKYGYVNEARIILDRET 88
D LRE F K+G + R+ ++ ET
Sbjct: 84 DEPLREVFKKHGLAEDVRLFIEEET 108
>pdb|2NLW|A Chain A, Solution Structure Of The Rrm Domain Of Human Eukaryotic
Initiation Factor 3b
Length = 105
Score = 27.7 bits (60), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 12/50 (24%), Positives = 27/50 (54%), Gaps = 2/50 (4%)
Query: 65 NSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQALDG 114
N + + F+K+G + E G+++G+ F+ +++ A A++ DG
Sbjct: 36 NVIHKIFSKFGKITND--FYPEEDGKTKGYIFLEYASPAHAVDAVKNADG 83
>pdb|2DIT|A Chain A, Solution Structure Of The Rrm_1 Domain Of Hiv Tat Specific
Factor 1 Variant
Length = 112
Score = 27.7 bits (60), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 4/51 (7%)
Query: 65 NSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQALDGQ 115
LR +K+G + + ++ DR G V+F EEA IQ LDG+
Sbjct: 41 EDLRVECSKFGQIRKL-LLFDRHPD---GVASVSFRDPEEADYCIQTLDGR 87
>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 = 26.9 bits (58), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 4/57 (7%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVN--EARIILDRETGRSRGFGFVTFSTVEEASS 107
L++G +++ D L EA G + E + +R G+S+GF V + EASS
Sbjct: 71 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGS--EASS 125
>pdb|2YWE|A Chain A, Crystal Structure Of Lepa From Aquifex Aeolicus
pdb|2YWF|A Chain A, Crystal Structure Of Gmppnp-Bound Lepa From Aquifex
Aeolicus
pdb|2YWH|A Chain A, Crystal Structure Of Gdp-Bound Lepa From Aquifex Aeolicus
Length = 600
Score = 26.2 bits (56), Expect = 4.4, Method: Composition-based stats.
Identities = 12/30 (40%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 67 LREAFAKYGYVNEARIILDRETGRSRGFGF 96
LR+A KY +N+A I+ + E+ + G GF
Sbjct: 312 LRDALEKYA-INDAAIVYEPESSPALGMGF 340
>pdb|2VZ8|A Chain A, Crystal Structure Of Mammalian Fatty Acid Synthase
pdb|2VZ8|B Chain B, Crystal Structure Of Mammalian Fatty Acid Synthase
pdb|2VZ9|A Chain A, Crystal Structure Of Mammalian Fatty Acid Synthase In
Complex With Nadp
pdb|2VZ9|B Chain B, Crystal Structure Of Mammalian Fatty Acid Synthase In
Complex With Nadp
Length = 2512
Score = 26.2 bits (56), Expect = 4.9, Method: Composition-based stats.
Identities = 18/50 (36%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 31 SCESSI-SNPSIYQAIRCMSSSKLFVGGISYNMDDNSLREAFAKYGYVNE 79
+C SS+ + S YQAIR S VGG++ + NS + F K G +++
Sbjct: 160 ACSSSLLALQSAYQAIRGGECSAAVVGGLNVLLKPNSSLQ-FMKLGMLSQ 208
>pdb|3DXB|A Chain A, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|B Chain B, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|C Chain C, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|D Chain D, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|E Chain E, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|F Chain F, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|G Chain G, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|H Chain H, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
Length = 222
Score = 26.2 bits (56), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 29/63 (46%), Gaps = 9/63 (14%)
Query: 61 NMDDN---SLREAFAKYGYVNEARIILDRETGRSRGFG-----FVTFSTVEEASSAIQAL 112
++DD+ + E K+G VN II + G FV FS E AIQAL
Sbjct: 137 DIDDDLEGEVTEECGKFGAVNRV-IIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQAL 195
Query: 113 DGQ 115
+G+
Sbjct: 196 NGR 198
>pdb|3UE2|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 1.23 A Resolution
pdb|3US5|A Chain A, Crystal Structure Of A Rna-Binding Domain Of A Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 1.38 A Resolution
Length = 118
Score = 26.2 bits (56), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 29/63 (46%), Gaps = 9/63 (14%)
Query: 61 NMDDN---SLREAFAKYGYVNEARIILDRETGRSRGFG-----FVTFSTVEEASSAIQAL 112
++DD+ + E K+G VN II + G FV FS E AIQAL
Sbjct: 33 DIDDDLEGEVTEECGKFGAVNRV-IIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQAL 91
Query: 113 DGQ 115
+G+
Sbjct: 92 NGR 94
>pdb|2DNY|A Chain A, Solution Structure Of The Third Rna Binding Domain Of Fbp-
Interacting Repressor, Siahbp1
Length = 119
Score = 26.2 bits (56), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 29/63 (46%), Gaps = 9/63 (14%)
Query: 61 NMDDN---SLREAFAKYGYVNEARIILDRETGRSRGFG-----FVTFSTVEEASSAIQAL 112
++DD+ + E K+G VN II + G FV FS E AIQAL
Sbjct: 28 DIDDDLEGEVTEECGKFGAVNRV-IIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQAL 86
Query: 113 DGQ 115
+G+
Sbjct: 87 NGR 89
>pdb|4E51|A Chain A, Crystal Structure Of A Histidyl-Trna Synthetase Hisrs From
Burkholderia Thailandensis Bound To Histidine
pdb|4E51|B Chain B, Crystal Structure Of A Histidyl-Trna Synthetase Hisrs From
Burkholderia Thailandensis Bound To Histidine
Length = 467
Score = 25.8 bits (55), Expect = 6.4, Method: Composition-based stats.
Identities = 15/50 (30%), Positives = 25/50 (50%)
Query: 66 SLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQALDGQ 115
+++ YGY N I++ +RG G VT +E S + AL+G+
Sbjct: 55 TVKSLLRAYGYQNIRTPIVEHTPLFTRGIGEVTDIVEKEMYSFVDALNGE 104
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 25.8 bits (55), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 15/69 (21%), Positives = 34/69 (49%), Gaps = 6/69 (8%)
Query: 46 RCMSSSKLFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEA 105
+ +++L+VGG+ N +L F ++G + +D G S F ++ + +++ A
Sbjct: 13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIR----TIDHVKGDS--FAYIQYESLDAA 66
Query: 106 SSAIQALDG 114
+A + G
Sbjct: 67 QAACAKMRG 75
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 25.4 bits (54), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 13/63 (20%), Positives = 32/63 (50%), Gaps = 8/63 (12%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSAIQAL 112
LFV ++ + + L +AF+++G + + + D + F+ F + A A++ +
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEM 65
Query: 113 DGQ 115
+G+
Sbjct: 66 NGK 68
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 25.4 bits (54), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 34/68 (50%), Gaps = 9/68 (13%)
Query: 50 SSKLFVGGISYNMDDNSLREA-FAKYGYVNEARIILDRETGRSRGFGFVTFSTVEEASSA 108
+S++F+G ++ + S E F+KYG V + +G+ FV +S A +A
Sbjct: 27 NSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAA 78
Query: 109 IQALDGQV 116
+ +G+V
Sbjct: 79 VLGENGRV 86
>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 = 25.4 bits (54), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 16/66 (24%), Positives = 30/66 (45%), Gaps = 2/66 (3%)
Query: 53 LFVGGISYNMDDNSLREAFAKYGY--VNEARIILDRETGRSRGFGFVTFSTVEEASSAIQ 110
++VG S+ D L + G V E + +R G+S+G+ V ++ ++
Sbjct: 58 VYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLE 117
Query: 111 ALDGQV 116
L G+V
Sbjct: 118 LLPGKV 123
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
0.321 0.133 0.378
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,113,986
Number of Sequences: 62578
Number of extensions: 104549
Number of successful extensions: 420
Number of sequences better than 100.0: 178
Number of HSP's better than 100.0 without gapping: 151
Number of HSP's successfully gapped in prelim test: 27
Number of HSP's that attempted gapping in prelim test: 219
Number of HSP's gapped (non-prelim): 207
length of query: 123
length of database: 14,973,337
effective HSP length: 85
effective length of query: 38
effective length of database: 9,654,207
effective search space: 366859866
effective search space used: 366859866
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)