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= 025858
(247 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 138 bits (347), Expect = 3e-33, Method: Compositional matrix adjust.
Identities = 72/166 (43%), Positives = 105/166 (63%), Gaps = 5/166 (3%)
Query: 20 KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIED 79
K+FIGGL DTT ++FGKYG +TD IMKD TG+ RGFGF+++ PS VD+V++
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 80 THIINGKQVEIKRTIPKGSGQSKDFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQII 139
HI++GK ++ KR IP+ KT KIFVGGI V E + FFS++G +++ Q++
Sbjct: 65 QHILDGKVIDPKRAIPRDEQD----KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLM 120
Query: 140 RDHETNRSRGFGFVIFDSEEVVDEMLSKGNMIDMAGTQVSLIGWSP 185
D +T +SRGFGFV +DS + VD + + ID ++ + P
Sbjct: 121 LDKDTGQSRGFGFVTYDSADAVDR-VCQNKFIDFKDRKIEIKRAEP 165
Score = 67.8 bits (164), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 33/79 (41%), Positives = 49/79 (62%), Gaps = 1/79 (1%)
Query: 19 GKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIE 78
GKIF+GG+ D F + F ++G I D+ +M D+ TGQ RGFGF+TY VD+V +
Sbjct: 88 GKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ 147
Query: 79 DTHI-INGKQVEIKRTIPK 96
+ I +++EIKR P+
Sbjct: 148 NKFIDFKDRKIEIKRAEPR 166
>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 = 114 bits (284), Expect = 7e-26, Method: Compositional matrix adjust.
Identities = 63/164 (38%), Positives = 95/164 (57%), Gaps = 5/164 (3%)
Query: 5 SKSDNPHTGDGASPGKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGF 64
SKS++P + K+FIGGL +TT + HF ++G +TD V+M+D T + RGFGF
Sbjct: 2 SKSESPKEPEQLR--KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF 59
Query: 65 ITYADPSVVDKVIEDT-HIINGKQVEIKRTIPKGSGQS--KDFKTKKIFVGGIPSSVSED 121
+TYA VD + H ++G+ VE KR + + Q KKIFVGGI E
Sbjct: 60 VTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEH 119
Query: 122 ELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEML 165
L+++F +YGK+ +I+ D + + RGF FV FD + VD+++
Sbjct: 120 HLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
Score = 50.8 bits (120), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 40/60 (66%)
Query: 107 KKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLS 166
+K+F+GG+ +++ L++ F ++G + + ++RD T RSRGFGFV + + E VD ++
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi)
G); A Human Telomeric Repeat Containing 6-Methyl-8-(2-
Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi)
Length = 195
Score = 113 bits (283), Expect = 8e-26, Method: Compositional matrix adjust.
Identities = 63/164 (38%), Positives = 95/164 (57%), Gaps = 5/164 (3%)
Query: 5 SKSDNPHTGDGASPGKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGF 64
SKS++P + K+FIGGL +TT + HF ++G +TD V+M+D T + RGFGF
Sbjct: 1 SKSESPKEPEQLR--KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF 58
Query: 65 ITYADPSVVDKVIEDT-HIINGKQVEIKRTIPKGSGQS--KDFKTKKIFVGGIPSSVSED 121
+TYA VD + H ++G+ VE KR + + Q KKIFVGGI E
Sbjct: 59 VTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEH 118
Query: 122 ELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEML 165
L+++F +YGK+ +I+ D + + RGF FV FD + VD+++
Sbjct: 119 HLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 162
Score = 50.8 bits (120), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 40/60 (66%)
Query: 107 KKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLS 166
+K+F+GG+ +++ L++ F ++G + + ++RD T RSRGFGFV + + E VD ++
Sbjct: 13 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 72
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 113 bits (283), Expect = 9e-26, Method: Compositional matrix adjust.
Identities = 63/164 (38%), Positives = 95/164 (57%), Gaps = 5/164 (3%)
Query: 5 SKSDNPHTGDGASPGKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGF 64
SKS++P + K+FIGGL +TT + HF ++G +TD V+M+D T + RGFGF
Sbjct: 2 SKSESPKEPEQLR--KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF 59
Query: 65 ITYADPSVVDKVIEDT-HIINGKQVEIKRTIPKGSGQS--KDFKTKKIFVGGIPSSVSED 121
+TYA VD + H ++G+ VE KR + + Q KKIFVGGI E
Sbjct: 60 VTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEH 119
Query: 122 ELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEML 165
L+++F +YGK+ +I+ D + + RGF FV FD + VD+++
Sbjct: 120 HLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
Score = 50.8 bits (120), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 40/60 (66%)
Query: 107 KKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLS 166
+K+F+GG+ +++ L++ F ++G + + ++RD T RSRGFGFV + + E VD ++
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 113 bits (283), Expect = 9e-26, Method: Compositional matrix adjust.
Identities = 63/164 (38%), Positives = 95/164 (57%), Gaps = 5/164 (3%)
Query: 5 SKSDNPHTGDGASPGKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGF 64
SKS++P + K+FIGGL +TT + HF ++G +TD V+M+D T + RGFGF
Sbjct: 3 SKSESPKEPEQLR--KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF 60
Query: 65 ITYADPSVVDKVIEDT-HIINGKQVEIKRTIPKGSGQS--KDFKTKKIFVGGIPSSVSED 121
+TYA VD + H ++G+ VE KR + + Q KKIFVGGI E
Sbjct: 61 VTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEH 120
Query: 122 ELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEML 165
L+++F +YGK+ +I+ D + + RGF FV FD + VD+++
Sbjct: 121 HLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 164
Score = 50.8 bits (120), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 40/60 (66%)
Query: 107 KKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLS 166
+K+F+GG+ +++ L++ F ++G + + ++RD T RSRGFGFV + + E VD ++
Sbjct: 15 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 74
>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 = 112 bits (281), Expect = 2e-25, Method: Compositional matrix adjust.
Identities = 59/149 (39%), Positives = 88/149 (59%), Gaps = 3/149 (2%)
Query: 20 KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIED 79
K+FIGGL +TT + HF ++G +TD V+M+D T + RGFGF+TYA VD +
Sbjct: 8 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67
Query: 80 T-HIINGKQVEIKRTIPKGSGQS--KDFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEH 136
H ++G+ VE KR + + Q KKIFVGGI E L+++F +YGK+
Sbjct: 68 RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI 127
Query: 137 QIIRDHETNRSRGFGFVIFDSEEVVDEML 165
+I+ D + + RGF FV FD + VD+++
Sbjct: 128 EIMTDRGSGKKRGFAFVTFDDHDSVDKIV 156
Score = 67.8 bits (164), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 35/93 (37%), Positives = 53/93 (56%), Gaps = 1/93 (1%)
Query: 5 SKSDNPHTGDGASPGKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGF 64
S+ D+ G + KIF+GG+ +DT +F +YG I IM DR +G+ RGF F
Sbjct: 84 SREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAF 143
Query: 65 ITYADPSVVDK-VIEDTHIINGKQVEIKRTIPK 96
+T+ D VDK VI+ H +NG E+++ + K
Sbjct: 144 VTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSK 176
Score = 50.8 bits (120), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 40/60 (66%)
Query: 107 KKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLS 166
+K+F+GG+ +++ L++ F ++G + + ++RD T RSRGFGFV + + E VD ++
Sbjct: 7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 112 bits (280), Expect = 2e-25, Method: Compositional matrix adjust.
Identities = 59/149 (39%), Positives = 88/149 (59%), Gaps = 3/149 (2%)
Query: 20 KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIED 79
K+FIGGL +TT + HF ++G +TD V+M+D T + RGFGF+TYA VD +
Sbjct: 13 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 72
Query: 80 T-HIINGKQVEIKRTIPKGSGQS--KDFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEH 136
H ++G+ VE KR + + Q KKIFVGGI E L+++F +YGK+
Sbjct: 73 RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI 132
Query: 137 QIIRDHETNRSRGFGFVIFDSEEVVDEML 165
+I+ D + + RGF FV FD + VD+++
Sbjct: 133 EIMTDRGSGKKRGFAFVTFDDHDSVDKIV 161
Score = 67.4 bits (163), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 35/93 (37%), Positives = 53/93 (56%), Gaps = 1/93 (1%)
Query: 5 SKSDNPHTGDGASPGKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGF 64
S+ D+ G + KIF+GG+ +DT +F +YG I IM DR +G+ RGF F
Sbjct: 89 SREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAF 148
Query: 65 ITYADPSVVDK-VIEDTHIINGKQVEIKRTIPK 96
+T+ D VDK VI+ H +NG E+++ + K
Sbjct: 149 VTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSK 181
Score = 50.8 bits (120), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 40/60 (66%)
Query: 107 KKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLS 166
+K+F+GG+ +++ L++ F ++G + + ++RD T RSRGFGFV + + E VD ++
Sbjct: 12 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 71
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 95.9 bits (237), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 47/150 (31%), Positives = 83/150 (55%), Gaps = 4/150 (2%)
Query: 17 SPGKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKV 76
S + + LP++ T F FG GDI +++D+ TGQ G+GF+ Y+DP+ DK
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 77 IEDTHIINGKQVEIKR-TIPKGSGQSKDFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLE 135
I + +NG +++ K + S + ++V G+P ++S+ E++ FS+YG+++
Sbjct: 63 I---NTLNGLKLQTKTIKVSYARPSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIIT 119
Query: 136 HQIIRDHETNRSRGFGFVIFDSEEVVDEML 165
+I+ D T SRG GF+ FD +E +
Sbjct: 120 SRILLDQATGVSRGVGFIRFDKRIEAEEAI 149
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 103 DFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVD 162
D KT + V +P ++++DE K+ F G + +++RD T +S G+GFV + D
Sbjct: 2 DSKTN-LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDAD 60
Query: 163 EMLSKGNMIDM 173
+ ++ N + +
Sbjct: 61 KAINTLNGLKL 71
>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 = 90.1 bits (222), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 45/150 (30%), Positives = 81/150 (54%), Gaps = 4/150 (2%)
Query: 17 SPGKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKV 76
S + + LP++ T F FG G+I +++D+ TGQ G+GF+ Y DP +K
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 77 IEDTHIINGKQVEIKR-TIPKGSGQSKDFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLE 135
I + +NG +++ K + S + ++V G+P ++++ EL+ FS+YG+++
Sbjct: 61 I---NTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIIT 117
Query: 136 HQIIRDHETNRSRGFGFVIFDSEEVVDEML 165
+I+ D T SRG GF+ FD +E +
Sbjct: 118 SRILVDQVTGVSRGVGFIRFDKRIEAEEAI 147
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 76.6 bits (187), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 46/163 (28%), Positives = 78/163 (47%), Gaps = 3/163 (1%)
Query: 16 ASPGKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDK 75
AS + + LP+D T F G I IM+D TG G+ F+ + +
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 76 VIEDTHIINGKQVEIKRTIPKGSGQSKDFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLE 135
I+ + I + +K + + G+S K ++V +P ++++D+L F KYG +++
Sbjct: 61 AIKVLNGITVRNKRLKVSYARPGGES--IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQ 118
Query: 136 HQIIRDHETNRSRGFGFVIFDSEEVVDEMLSK-GNMIDMAGTQ 177
I+RD T R RG FV ++ E E +S N+I G+Q
Sbjct: 119 KNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQ 161
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 41/88 (46%), Gaps = 10/88 (11%)
Query: 13 GDGASPGKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSV 72
G+ +++ LP+ T + FGKYG I I++D+ TG+PRG F+ Y
Sbjct: 84 GESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRY----- 138
Query: 73 VDKVIEDTHIINGKQVEIKRTIPKGSGQ 100
+K E I+ + IP+G Q
Sbjct: 139 -NKREEAQEAISA----LNNVIPEGGSQ 161
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 76.6 bits (187), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 34/80 (42%), Positives = 51/80 (63%), Gaps = 1/80 (1%)
Query: 19 GKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIE 78
GK+F+GGL TT T +F +YG++ D VIMKD+ T Q RGFGF+ + DP+ V V+
Sbjct: 17 GKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLA 76
Query: 79 D-THIINGKQVEIKRTIPKG 97
H ++G+ ++ K P+G
Sbjct: 77 SRPHTLDGRNIDPKPCTPRG 96
Score = 59.7 bits (143), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 26/59 (44%), Positives = 43/59 (72%)
Query: 108 KIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLS 166
K+FVGG+ S +++ L+++FS+YG+V++ I++D TN+SRGFGFV F V +L+
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLA 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 = 73.9 bits (180), Expect = 8e-14, Method: Compositional matrix adjust.
Identities = 47/173 (27%), Positives = 81/173 (46%), Gaps = 3/173 (1%)
Query: 6 KSDNPHTGDGASPGKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFI 65
+SD+ AS + + LP+D T F G I I +D TG G+ F+
Sbjct: 2 ESDDLMNDPRASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFV 61
Query: 66 TYADPSVVDKVIEDTHIINGKQVEIKRTIPKGSGQSKDFKTKKIFVGGIPSSVSEDELKN 125
+ + I+ + I + +K + + G+S K ++V +P ++++D+L
Sbjct: 62 DFTSEXDSQRAIKVLNGITVRNKRLKVSYARPGGES--IKDTNLYVTNLPRTITDDQLDT 119
Query: 126 FFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSK-GNMIDMAGTQ 177
F KYG +++ I+RD T R RG FV ++ E E +S N+I G+Q
Sbjct: 120 IFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQ 172
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 70.9 bits (172), Expect = 6e-13, Method: Compositional matrix adjust.
Identities = 32/150 (21%), Positives = 78/150 (52%), Gaps = 4/150 (2%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIEDT 80
+ + LP++ T F G++ + +++D+ G G+GF+ Y ++ I
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI--- 61
Query: 81 HIINGKQVEIKR-TIPKGSGQSKDFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQII 139
+ +NG +++ K + S+ K +++ G+P ++++ ++++ FS++G+++ +++
Sbjct: 62 NTLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVL 121
Query: 140 RDHETNRSRGFGFVIFDSEEVVDEMLSKGN 169
D T SRG F+ FD +E ++ N
Sbjct: 122 VDQTTGLSRGVAFIRFDKRSEAEEAITSFN 151
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 46/83 (55%)
Query: 109 IFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSKG 168
+ V +P ++++DEL++ FS G+V ++IRD S G+GFV + + + + ++
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 169 NMIDMAGTQVSLIGWSPVNQLLK 191
N + + + + P ++++K
Sbjct: 65 NGLRLQSKTIKVSYARPSSEVIK 87
>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 = 70.9 bits (172), Expect = 6e-13, Method: Compositional matrix adjust.
Identities = 32/150 (21%), Positives = 78/150 (52%), Gaps = 4/150 (2%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIEDT 80
+ + LP++ T F G++ + +++D+ G G+GF+ Y ++ I
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI--- 61
Query: 81 HIINGKQVEIKR-TIPKGSGQSKDFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQII 139
+ +NG +++ K + S+ K +++ G+P ++++ ++++ FS++G+++ +++
Sbjct: 62 NTLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVL 121
Query: 140 RDHETNRSRGFGFVIFDSEEVVDEMLSKGN 169
D T SRG F+ FD +E ++ N
Sbjct: 122 VDQTTGLSRGVAFIRFDKRSEAEEAITSFN 151
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 46/83 (55%)
Query: 109 IFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSKG 168
+ V +P ++++DEL++ FS G+V ++IRD S G+GFV + + + + ++
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 169 NMIDMAGTQVSLIGWSPVNQLLK 191
N + + + + P ++++K
Sbjct: 65 NGLRLQSKTIKVSYARPSSEVIK 87
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 69.7 bits (169), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 31/72 (43%), Positives = 51/72 (70%), Gaps = 1/72 (1%)
Query: 20 KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIED 79
KIF+GGLP TT A+ K+F +GDI ++V++ DR TG+ RG+GF+T AD + ++ +D
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 80 TH-IINGKQVEI 90
+ II+G++ +
Sbjct: 79 PNPIIDGRKANV 90
Score = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/87 (31%), Positives = 42/87 (48%), Gaps = 3/87 (3%)
Query: 102 KDFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVV 161
KD KIFVGG+P ++ L+ +F +G + E +I D +T +SRG+GFV
Sbjct: 13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAA 72
Query: 162 DEMLSKGNMI---DMAGTQVSLIGWSP 185
+ N I A ++ +G P
Sbjct: 73 ERACKDPNPIIDGRKANVNLAYLGAKP 99
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 67.8 bits (164), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 31/83 (37%), Positives = 54/83 (65%), Gaps = 1/83 (1%)
Query: 15 GASPGKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVD 74
G+S K+FIGGL TT ++FG++G++ + ++M+D T + RGFGF+T+ D + VD
Sbjct: 22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVD 81
Query: 75 KVI-EDTHIINGKQVEIKRTIPK 96
KV+ + H ++ K ++ K P+
Sbjct: 82 KVLAQSRHELDSKTIDPKVAFPR 104
Score = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 47/74 (63%), Gaps = 2/74 (2%)
Query: 94 IPKGSGQSKDFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFV 153
+P+GS K+F+GG+ +++ L+ +F ++G+V E ++RD T RSRGFGFV
Sbjct: 15 VPRGSHMGSS--GCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFV 72
Query: 154 IFDSEEVVDEMLSK 167
F + VD++L++
Sbjct: 73 TFMDQAGVDKVLAQ 86
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 67.8 bits (164), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 34/83 (40%), Positives = 51/83 (61%), Gaps = 1/83 (1%)
Query: 20 KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIE- 78
KIF+GG+P + ++F K+G +T+ V++ D +PRGFGFIT+ D VD+ +
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
Query: 79 DTHIINGKQVEIKRTIPKGSGQS 101
H I GK+VE+KR P+ S S
Sbjct: 72 HFHDIMGKKVEVKRAEPRDSKSS 94
Score = 63.9 bits (154), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 33/78 (42%), Positives = 48/78 (61%), Gaps = 1/78 (1%)
Query: 108 KIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSK 167
KIFVGGIP + E EL+ +F K+G V E +I D E R RGFGF+ F+ E+ VD+ ++
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
Query: 168 GNMIDMAGTQVSLIGWSP 185
+ D+ G +V + P
Sbjct: 72 -HFHDIMGKKVEVKRAEP 88
>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 = 65.9 bits (159), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 36/167 (21%), Positives = 81/167 (48%), Gaps = 13/167 (7%)
Query: 20 KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIED 79
++++G + + T + F +G I + D T + +GF F+ Y P +E
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 80 TH--IINGKQVEIKRTIPKGSGQSKDFKTK---------KIFVGGIPSSVSEDELKNFFS 128
+ ++ G+ +++ R P GQ++ + +I+V + +S+D++K+ F
Sbjct: 75 MNSVMLGGRNIKVGR--PSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFE 132
Query: 129 KYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSKGNMIDMAG 175
+GK+ + RD T + +G+GF+ ++ + + +S N+ D+ G
Sbjct: 133 AFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGG 179
Score = 36.6 bits (83), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 36/73 (49%)
Query: 108 KIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSK 167
+++VG I + ED ++ F+ +G + + D T + +GF FV ++ E L +
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 168 GNMIDMAGTQVSL 180
N + + G + +
Sbjct: 75 MNSVMLGGRNIKV 87
>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 = 65.5 bits (158), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 36/167 (21%), Positives = 81/167 (48%), Gaps = 13/167 (7%)
Query: 20 KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIED 79
++++G + + T + F +G I + D T + +GF F+ Y P +E
Sbjct: 30 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 89
Query: 80 TH--IINGKQVEIKRTIPKGSGQSKDFKTK---------KIFVGGIPSSVSEDELKNFFS 128
+ ++ G+ +++ R P GQ++ + +I+V + +S+D++K+ F
Sbjct: 90 MNSVMLGGRNIKVGR--PSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFE 147
Query: 129 KYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSKGNMIDMAG 175
+GK+ + RD T + +G+GF+ ++ + + +S N+ D+ G
Sbjct: 148 AFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGG 194
Score = 36.2 bits (82), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 36/73 (49%)
Query: 108 KIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSK 167
+++VG I + ED ++ F+ +G + + D T + +GF FV ++ E L +
Sbjct: 30 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 89
Query: 168 GNMIDMAGTQVSL 180
N + + G + +
Sbjct: 90 MNSVMLGGRNIKV 102
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 65.5 bits (158), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 33/86 (38%), Positives = 54/86 (62%), Gaps = 4/86 (4%)
Query: 20 KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIED 79
K+FIGGL +TT + ++ ++G +TD V+M+D + + RGFGF+T++ + VD +
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 88
Query: 80 T-HIINGKQVEIKRTIPK---GSGQS 101
H I+G+ VE KR + + GSG S
Sbjct: 89 RPHSIDGRVVEPKRAVAREESGSGPS 114
Score = 58.5 bits (140), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 28/81 (34%), Positives = 51/81 (62%), Gaps = 1/81 (1%)
Query: 93 TIPKGSGQSKDFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGF 152
T+P + + + +K+F+GG+ +E+ L+N++ ++GK+ + ++RD + RSRGFGF
Sbjct: 14 TVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGF 73
Query: 153 VIFDSEEVVD-EMLSKGNMID 172
V F S VD M ++ + ID
Sbjct: 74 VTFSSMAEVDAAMAARPHSID 94
>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 = 64.7 bits (156), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 36/167 (21%), Positives = 79/167 (47%), Gaps = 13/167 (7%)
Query: 20 KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIED 79
++++G + + T + F +G I D T + +GF F+ Y P +E
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 80 TH--IINGKQVEIKRTIPKGSGQSKDFKTK---------KIFVGGIPSSVSEDELKNFFS 128
+ + G+ +++ R P GQ++ + +I+V + +S+D++K+ F
Sbjct: 74 XNSVXLGGRNIKVGR--PSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFE 131
Query: 129 KYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSKGNMIDMAG 175
+GK+ + RD T + +G+GF+ ++ + + +S N+ D+ G
Sbjct: 132 AFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGG 178
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 35/73 (47%)
Query: 108 KIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSK 167
+++VG I + ED ++ F+ +G + D T + +GF FV ++ E L +
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 168 GNMIDMAGTQVSL 180
N + + G + +
Sbjct: 74 XNSVXLGGRNIKV 86
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 63.9 bits (154), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 32/91 (35%), Positives = 55/91 (60%), Gaps = 3/91 (3%)
Query: 16 ASPGKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDK 75
+ GK+F+GGL DT + + F KYG I++ V++KDR T + RGFGF+T+ + +D
Sbjct: 10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFEN---IDD 66
Query: 76 VIEDTHIINGKQVEIKRTIPKGSGQSKDFKT 106
+ +NGK V+ ++ +G+S D ++
Sbjct: 67 AKDAMMAMNGKSVDGRQIRVDQAGKSSDNRS 97
Score = 60.8 bits (146), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 33/83 (39%), Positives = 51/83 (61%), Gaps = 2/83 (2%)
Query: 108 KIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDS-EEVVDEMLS 166
K+FVGG+ +E L+ FSKYG++ E +++D ET RSRGFGFV F++ ++ D M++
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 167 -KGNMIDMAGTQVSLIGWSPVNQ 188
G +D +V G S N+
Sbjct: 74 MNGKSVDGRQIRVDQAGKSSDNR 96
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 62.4 bits (150), Expect = 2e-10, Method: Composition-based stats.
Identities = 28/73 (38%), Positives = 49/73 (67%), Gaps = 1/73 (1%)
Query: 20 KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVI-E 78
K+FIGGL TT ++FG++G++ + ++M+D T + RGFGF+T+ D + VDKV+ +
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 79 DTHIINGKQVEIK 91
H ++ K ++ K
Sbjct: 62 SRHELDSKTIDPK 74
Score = 55.8 bits (133), Expect = 2e-08, Method: Composition-based stats.
Identities = 24/60 (40%), Positives = 42/60 (70%)
Query: 108 KIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSK 167
K+F+GG+ +++ L+ +F ++G+V E ++RD T RSRGFGFV F + VD++L++
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
>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 = 62.0 bits (149), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 30/74 (40%), Positives = 45/74 (60%), Gaps = 1/74 (1%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIED- 79
+FIGGL DTT +F K+G++ D + D TG+ RGFGF+ + + VDKV++
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 80 THIINGKQVEIKRT 93
H +NGK ++ KR
Sbjct: 62 EHKLNGKVIDPKRA 75
Score = 55.1 bits (131), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 24/59 (40%), Positives = 42/59 (71%)
Query: 109 IFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSK 167
+F+GG+ ++ +LK++FSK+G+V++ + D T RSRGFGFV+F E VD+++ +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60
>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 = 60.8 bits (146), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 29/77 (37%), Positives = 47/77 (61%), Gaps = 1/77 (1%)
Query: 18 PGKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVI 77
GK F+GGL DT+ +F K+G++ D I D TG+ RGFGFI + D + V+KV+
Sbjct: 11 AGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVL 70
Query: 78 ED-THIINGKQVEIKRT 93
+ H ++G+ ++ K+
Sbjct: 71 DQKEHRLDGRVIDPKKA 87
Score = 54.7 bits (130), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 25/60 (41%), Positives = 41/60 (68%)
Query: 108 KIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSK 167
K FVGG+ S+ +LK++F+K+G+V++ I D T RSRGFGF++F V+++L +
Sbjct: 13 KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQ 72
>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 = 60.8 bits (146), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 38/158 (24%), Positives = 75/158 (47%), Gaps = 16/158 (10%)
Query: 19 GKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIE 78
+++G L D T A + F G I + +D T + G+ ++ + P+ ++ ++
Sbjct: 11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 70
Query: 79 DTH--IINGKQVEIKRTIPKGSGQSKDFKTKK-----IFVGGIPSSVSEDELKNFFSKYG 131
+ +I GK V I + +D +K IF+ + S+ L + FS +G
Sbjct: 71 TMNFDVIKGKPVRIMWS-------QRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFG 123
Query: 132 KVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSKGN 169
+L +++ D N S+G+GFV F+++E + + K N
Sbjct: 124 NILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMN 159
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 4/76 (5%)
Query: 19 GKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIE 78
G IFI L K F +G+I ++ D +G+GF+ + ++ IE
Sbjct: 99 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIE 156
Query: 79 DTH--IINGKQVEIKR 92
+ ++N ++V + R
Sbjct: 157 KMNGMLLNDRKVFVGR 172
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 60.5 bits (145), Expect = 8e-10, Method: Composition-based stats.
Identities = 30/73 (41%), Positives = 46/73 (63%), Gaps = 1/73 (1%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIE-D 79
IF+GGL +TT +F ++G + D+++M D+ T + RGFGF+T+ +V+KV E
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 80 THIINGKQVEIKR 92
H IN K VE K+
Sbjct: 62 FHEINNKMVECKK 74
Score = 57.8 bits (138), Expect = 5e-09, Method: Composition-based stats.
Identities = 24/56 (42%), Positives = 43/56 (76%)
Query: 109 IFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEM 164
IFVGG+ + + +++K++F ++GKV + ++ D TNR RGFGFV F+SE++V+++
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKV 57
>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 = 60.5 bits (145), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 38/158 (24%), Positives = 75/158 (47%), Gaps = 16/158 (10%)
Query: 19 GKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIE 78
+++G L D T A + F G I + +D T + G+ ++ + P+ ++ ++
Sbjct: 16 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 75
Query: 79 DTH--IINGKQVEIKRTIPKGSGQSKDFKTKK-----IFVGGIPSSVSEDELKNFFSKYG 131
+ +I GK V I + +D +K IF+ + S+ L + FS +G
Sbjct: 76 TMNFDVIKGKPVRIMWS-------QRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFG 128
Query: 132 KVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSKGN 169
+L +++ D N S+G+GFV F+++E + + K N
Sbjct: 129 NILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMN 164
Score = 28.9 bits (63), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 4/76 (5%)
Query: 19 GKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIE 78
G IFI L K F +G+I ++ D +G+GF+ + ++ IE
Sbjct: 104 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIE 161
Query: 79 DTH--IINGKQVEIKR 92
+ ++N ++V + R
Sbjct: 162 KMNGMLLNDRKVFVGR 177
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 59.3 bits (142), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 30/74 (40%), Positives = 46/74 (62%), Gaps = 4/74 (5%)
Query: 18 PGKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVI 77
PGK+FIGGL ++T FGK+G I++ +++KDR T + RGF FIT+ +P+
Sbjct: 7 PGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAA 65
Query: 78 EDTHIINGKQVEIK 91
+D +NGK + K
Sbjct: 66 KD---MNGKSLHGK 76
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 33/50 (66%), Gaps = 1/50 (2%)
Query: 108 KIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDS 157
K+F+GG+ +E LK F K+G + E +I+D T++SRGF F+ F++
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFEN 57
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 59.3 bits (142), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 44/168 (26%), Positives = 77/168 (45%), Gaps = 8/168 (4%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIEDT 80
+++G L K T ++F G I + IM D+ + + F+ Y + ++
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQ-- 59
Query: 81 HIINGKQVE---IKRTIPKGSGQSKDFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQ 137
+NGKQ+E +K S QS T +FVG + +V ++ L+N F + L
Sbjct: 60 -TLNGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGH 118
Query: 138 IIRDHETNRSRGFGFVIFDSEEVVDEMLSKGNMIDMAGTQVSLIGWSP 185
++ D +T SRG+GFV F S++ + D+ G + I W+
Sbjct: 119 VMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLR-INWAA 165
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 57.8 bits (138), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 35/147 (23%), Positives = 76/147 (51%), Gaps = 7/147 (4%)
Query: 20 KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQP--RGFGFIT-YADPSVVD-- 74
K+F+G +P+ + + F +YG + + +++DR P +G F+T Y + ++
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 75 KVIEDTHIINGKQVEIKRTIPKGSGQSKDFKTKKIFVGGIPSSVSEDELKNFFSKYGKVL 134
+ + ++ G I+ P S ++ + +K+F+G I +E++++ FS +G++
Sbjct: 65 NALHNMKVLPGMHHPIQMK-PADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIE 123
Query: 135 EHQIIRDHETNRSRGFGFVIFDSEEVV 161
E +I+R + SRG FV F + +
Sbjct: 124 ECRILRGPD-GLSRGCAFVTFTTRAMA 149
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 57.8 bits (138), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 35/147 (23%), Positives = 76/147 (51%), Gaps = 7/147 (4%)
Query: 20 KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQP--RGFGFIT-YADPSVVD-- 74
K+F+G +P+ + + F +YG + + +++DR P +G F+T Y + ++
Sbjct: 17 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 76
Query: 75 KVIEDTHIINGKQVEIKRTIPKGSGQSKDFKTKKIFVGGIPSSVSEDELKNFFSKYGKVL 134
+ + ++ G I+ P S ++ + +K+F+G I +E++++ FS +G++
Sbjct: 77 NALHNMKVLPGMHHPIQMK-PADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIE 135
Query: 135 EHQIIRDHETNRSRGFGFVIFDSEEVV 161
E +I+R + SRG FV F + +
Sbjct: 136 ECRILRGPD-GLSRGCAFVTFTTRAMA 161
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 32/55 (58%), Gaps = 2/55 (3%)
Query: 103 DFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETN--RSRGFGFVIF 155
D K+FVG +P + SE +L+ F +YG V E ++RD N +S+G FV F
Sbjct: 12 DLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTF 66
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 28/68 (41%), Positives = 44/68 (64%)
Query: 105 KTKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEM 164
KT + V G+P +E +LK +FS +G+VL Q+ +D +T S+GFGFV F E ++
Sbjct: 14 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKV 73
Query: 165 LSKGNMID 172
+S+ +MID
Sbjct: 74 MSQRHMID 81
Score = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 45/83 (54%), Gaps = 3/83 (3%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIEDT 80
+ + GLP TT ++F +G++ + KD TG +GFGF+ + + KV+
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 77
Query: 81 HIINGKQVEIKRTIPKGSGQSKD 103
H+I+G+ + K +P S QS+D
Sbjct: 78 HMIDGRWCDCK--LPN-SKQSQD 97
>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 = 55.5 bits (132), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 35/141 (24%), Positives = 73/141 (51%), Gaps = 7/141 (4%)
Query: 20 KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQP--RGFGFIT-YADPSVVD-- 74
K F+G +P+ + + F +YG + + +++DR P +G F+T Y + ++
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 75 KVIEDTHIINGKQVEIKRTIPKGSGQSKDFKTKKIFVGGIPSSVSEDELKNFFSKYGKVL 134
+ + ++ G I+ P S ++ + +K+F+G I +E++++ FS +G++
Sbjct: 65 NALHNXKVLPGXHHPIQXK-PADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQIE 123
Query: 135 EHQIIRDHETNRSRGFGFVIF 155
E +I+R + SRG FV F
Sbjct: 124 ECRILRGPD-GLSRGCAFVTF 143
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 55.1 bits (131), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 43/75 (57%), Gaps = 3/75 (4%)
Query: 17 SPGKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKV 76
S + + LP++ T F FG GDI +++D+ TGQ G+GF+ Y+DP+ DK
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 77 IEDTHIINGKQVEIK 91
I + +NG +++ K
Sbjct: 63 I---NTLNGLKLQTK 74
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 37/67 (55%), Gaps = 1/67 (1%)
Query: 103 DFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVD 162
D KT + V +P ++++DE K+ F G + +++RD T +S G+GFV + D
Sbjct: 2 DSKTN-LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDAD 60
Query: 163 EMLSKGN 169
+ ++ N
Sbjct: 61 KAINTLN 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 = 54.7 bits (130), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 43/77 (55%), Gaps = 1/77 (1%)
Query: 102 KDFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVV 161
+ K ++V +P ++++D+L F KYG +++ I+RD T R RG FV ++ E
Sbjct: 9 ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 68
Query: 162 DEMLSK-GNMIDMAGTQ 177
E +S N+I G+Q
Sbjct: 69 QEAISALNNVIPEGGSQ 85
Score = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 28/47 (59%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITY 67
+++ LP+ T + FGKYG I I++D+ TG+PRG F+ Y
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRY 62
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 53.5 bits (127), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 28/83 (33%), Positives = 47/83 (56%), Gaps = 1/83 (1%)
Query: 107 KKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLS 166
+ I+VG + S + +++K FS++GKV ++I D ET + +GFGFV EE V E ++
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIA 60
Query: 167 KGNMIDMAGTQVSLIGWSPVNQL 189
K + D G + + +P L
Sbjct: 61 KLDNTDFMGRTIRVTEANPKKSL 83
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 40/79 (50%), Gaps = 1/79 (1%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIE-D 79
I++G L T + F ++G + + ++ DR T +P+GFGF+ + SV + + + D
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAKLD 63
Query: 80 THIINGKQVEIKRTIPKGS 98
G+ + + PK S
Sbjct: 64 NTDFMGRTIRVTEANPKKS 82
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 53.5 bits (127), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 42/68 (61%)
Query: 108 KIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSK 167
+++VG + +++ED L+ F +G++ Q++ D ET RS+G+GF+ F E + L +
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 168 GNMIDMAG 175
N ++AG
Sbjct: 88 LNGFELAG 95
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 33/63 (52%)
Query: 16 ASPGKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDK 75
A P ++++G L + T F +G I +M D TG+ +G+GFIT++D K
Sbjct: 24 AGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKK 83
Query: 76 VIE 78
+E
Sbjct: 84 ALE 86
>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 = 52.0 bits (123), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 40/62 (64%)
Query: 106 TKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEML 165
KKIFVGG+ E++++ +F +G+V ++ D++TN+ RGF F+ F EE V +++
Sbjct: 1 VKKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 60
Query: 166 SK 167
K
Sbjct: 61 EK 62
Score = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 20 KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIED 79
KIF+GGL DT ++FG +G++ + D T + RGF FIT+ + V K++E
Sbjct: 3 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 62
Query: 80 T-HIINGKQVEIK 91
H + + EIK
Sbjct: 63 KYHNVGLSKCEIK 75
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 52.0 bits (123), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 43/151 (28%), Positives = 66/151 (43%), Gaps = 19/151 (12%)
Query: 19 GKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVD--KV 76
++F+G LP D T K F KYG + I KD +GFGFI ++ + KV
Sbjct: 23 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKV 76
Query: 77 IEDTHIINGKQVEIKRTIPKGSGQSKDFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEH 136
D + GKQ+ ++ S + V +P VS + L+ FS +G+V
Sbjct: 77 ELDNMPLRGKQLRVRFACHSAS----------LTVRNLPQYVSNELLEEAFSVFGQVERA 126
Query: 137 QIIRDHETNRSRGFGFVIFDSEEVVDEMLSK 167
+I D + R G G V F + + L +
Sbjct: 127 VVIVD-DRGRPSGKGIVEFSGKPAARKALDR 156
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 52.0 bits (123), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 37/57 (64%)
Query: 109 IFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEML 165
++V G+P ++S+ E++ FS+YG+++ +I+ D T SRG GF+ FD +E +
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
Score = 43.9 bits (102), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 33/65 (50%), Gaps = 6/65 (9%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIEDT 80
+++ GLPK + + F +YG I S I+ D+ TG RG GFI + DK IE
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRF------DKRIEAE 57
Query: 81 HIING 85
I G
Sbjct: 58 EAIKG 62
>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 = 50.4 bits (119), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 39/168 (23%), Positives = 80/168 (47%), Gaps = 9/168 (5%)
Query: 14 DGASPGKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVV 73
+ +P +FIG L + + A + D ++ D TG R FG++ + +
Sbjct: 9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDL 67
Query: 74 DKVIEDTHI-INGKQVEIKRTIPKGSGQSKDFKTKKIFVGGIPSSVSEDELKNFFSKYGK 132
+K +E T + + G ++++++ PKG K + + + +++EDELK F
Sbjct: 68 EKALELTGLKVFGNEIKLEK--PKGRDSKKVRAARTLLAKNLSFNITEDELKEVFE---D 122
Query: 133 VLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSKGNMIDMAGTQVSL 180
LE +++ + +S+G ++ F SE ++ L + ++ G VSL
Sbjct: 123 ALEIRLV--SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSL 168
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 50.4 bits (119), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 41/73 (56%)
Query: 103 DFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVD 162
D + +FVG IP +E++LK+ FS+ G V+ +++ D ET + +G+GF + +E
Sbjct: 5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETAL 64
Query: 163 EMLSKGNMIDMAG 175
+ N + +G
Sbjct: 65 SAMRNLNGREFSG 77
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 34/67 (50%), Gaps = 3/67 (4%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIEDT 80
+F+G +P + T F + G + ++ DR TG+P+G+GF Y D + +
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN- 69
Query: 81 HIINGKQ 87
+NG++
Sbjct: 70 --LNGRE 74
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 42/72 (58%)
Query: 113 GIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSKGNMID 172
G+ +E +L+ FSKYG + + I+ D ++ RSRGF FV F++ + E + N ++
Sbjct: 22 GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME 81
Query: 173 MAGTQVSLIGWS 184
+ G ++ + G S
Sbjct: 82 LDGRRIRVSGPS 93
Score = 35.8 bits (81), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 34/68 (50%), Gaps = 3/68 (4%)
Query: 25 GLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIEDTHIIN 84
GL TT + F KYG I D I+ D+ + + RGF F+ + + VD E N
Sbjct: 22 GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN---VDDAKEAKERAN 78
Query: 85 GKQVEIKR 92
G +++ +R
Sbjct: 79 GMELDGRR 86
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 37/63 (58%)
Query: 107 KKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLS 166
+ + V IP++V E +L+ F +YG + +I+ D ET +SRG+GFV F S + ++
Sbjct: 43 RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA 102
Query: 167 KGN 169
N
Sbjct: 103 GLN 105
Score = 33.1 bits (74), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 3/72 (4%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIEDT 80
+ + +P + F +YG I I+ DR T Q RG+GF+ + S + I
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG- 103
Query: 81 HIINGKQVEIKR 92
+NG + KR
Sbjct: 104 --LNGFNILNKR 113
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 41/150 (27%), Positives = 69/150 (46%), Gaps = 19/150 (12%)
Query: 20 KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIED 79
++F+G LP D T F + F +YG+ ++ I +D RGFGFI +E
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIR----------LES 67
Query: 80 THIINGKQVEIKRTIPKGSGQSKDFKT--KKIFVGGIPSSVSEDELKNFFSKYGKVLEHQ 137
+ + E+ TI K F T + V + VS + L+ FS++G V +
Sbjct: 68 RTLAEIAKAELDGTILKSRPLRIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAV 127
Query: 138 IIRDHETNRSRGFGFVIFDSEEVVDEMLSK 167
++ D + R+ G GFV F ++ + L +
Sbjct: 128 VVVD-DRGRATGKGFVEFAAKPPARKALER 156
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 48.9 bits (115), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 38/59 (64%)
Query: 109 IFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSK 167
IFVGG+ E++++ +F +G+V ++ D++TN+ RGF F+ F EE V +++ K
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Score = 47.4 bits (111), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIEDT 80
IF+GGL DT ++FG +G++ + D T + RGF FIT+ + V K++E
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Query: 81 -HIINGKQVEIK 91
H + + EIK
Sbjct: 62 YHNVGLSKCEIK 73
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 48.9 bits (115), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 41/70 (58%)
Query: 106 TKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEML 165
+ ++VG + +++ED L+ F +GK+ +++D +T RS+G+GF+ F E L
Sbjct: 5 SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
Query: 166 SKGNMIDMAG 175
+ N ++AG
Sbjct: 65 EQLNGFELAG 74
Score = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 33/58 (56%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIE 78
+++G L + T F +G I + V+MKD TG+ +G+GFIT++D + +E
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 48.5 bits (114), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 41/70 (58%)
Query: 111 VGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSKGNM 170
V G+ +E +L+ FSKYG + + I+ D ++ RSRGF FV F++ + E + N
Sbjct: 17 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 76
Query: 171 IDMAGTQVSL 180
+++ G ++ +
Sbjct: 77 MELDGRRIRV 86
Score = 35.4 bits (80), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 34/68 (50%), Gaps = 3/68 (4%)
Query: 25 GLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIEDTHIIN 84
GL TT + F KYG I D I+ D+ + + RGF F+ + + VD E N
Sbjct: 19 GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN---VDDAKEAKERAN 75
Query: 85 GKQVEIKR 92
G +++ +R
Sbjct: 76 GMELDGRR 83
>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 = 48.1 bits (113), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 44/72 (61%), Gaps = 5/72 (6%)
Query: 98 SGQSKDFKTK-KIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIF- 155
SGQ KD +FVG + ++ +++K F+ +G++ + ++++D T +S+G+GFV F
Sbjct: 6 SGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFF 65
Query: 156 ---DSEEVVDEM 164
D+E + +M
Sbjct: 66 NKWDAENAIQQM 77
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 38/72 (52%), Gaps = 2/72 (2%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIEDT 80
+F+G L + T F +G I+D+ ++KD TG+ +G+GF+++ + + I+
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 81 --HIINGKQVEI 90
+ G+Q+
Sbjct: 78 GGQWLGGRQIRT 89
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 48.1 bits (113), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 34/47 (72%)
Query: 109 IFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIF 155
++V +P S++ ++L FSKYGKV++ I++D +T +S+G F++F
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILF 65
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 33/74 (44%), Gaps = 3/74 (4%)
Query: 15 GASPGKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVD 74
S +++ LP T + F KYG + IMKD+ T + +G FI + D D
Sbjct: 13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDK---D 69
Query: 75 KVIEDTHIINGKQV 88
T IN KQ+
Sbjct: 70 SAQNCTRAINNKQL 83
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 47.8 bits (112), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 41/70 (58%)
Query: 111 VGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSKGNM 170
V G+ +E +L+ FSKYG + + I+ D ++ RSRGF FV F++ + E + N
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 171 IDMAGTQVSL 180
+++ G ++ +
Sbjct: 80 MELDGRRIRV 89
Score = 35.4 bits (80), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 28/91 (30%), Positives = 41/91 (45%), Gaps = 5/91 (5%)
Query: 2 GSKSKSDNPHTGDGASPGKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRG 61
GS S N D +F GL TT + F KYG I D I+ D+ + + RG
Sbjct: 1 GSSGSSGNRANPDPNCCLGVF--GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRG 58
Query: 62 FGFITYADPSVVDKVIEDTHIINGKQVEIKR 92
F F+ + + VD E NG +++ +R
Sbjct: 59 FAFVYFEN---VDDAKEAKERANGMELDGRR 86
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 47.8 bits (112), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 44/72 (61%), Gaps = 5/72 (6%)
Query: 98 SGQSKDFKTK-KIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIF- 155
SGQ KD +FVG + ++ +++K+ F+ +GK+ + ++++D T +S+G+GFV F
Sbjct: 6 SGQKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFY 65
Query: 156 ---DSEEVVDEM 164
D+E + M
Sbjct: 66 NKLDAENAIVHM 77
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 42/86 (48%), Gaps = 5/86 (5%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVI--E 78
+F+G L + T F +G I+D+ ++KD TG+ +G+GF+++ + + I
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 79 DTHIINGKQVEIK---RTIPKGSGQS 101
+ G+Q+ R P SG S
Sbjct: 78 GGQWLGGRQIRTNWATRKPPAPSGPS 103
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 47.8 bits (112), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 40/68 (58%)
Query: 113 GIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSKGNMID 172
G+ +E +L+ FSKYG + + I+ D ++ RSRGF FV F++ + E + N ++
Sbjct: 53 GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME 112
Query: 173 MAGTQVSL 180
+ G ++ +
Sbjct: 113 LDGRRIRV 120
Score = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 29/95 (30%), Positives = 46/95 (48%), Gaps = 10/95 (10%)
Query: 1 MGSKSKSDNPHTGDGASPGK---IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTG 57
MG S+ H G+ A+P + + GL TT + F KYG I D I+ D+ +
Sbjct: 30 MGRGSR----HVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSR 85
Query: 58 QPRGFGFITYADPSVVDKVIEDTHIINGKQVEIKR 92
+ RGF F+ + + VD E NG +++ +R
Sbjct: 86 RSRGFAFVYFEN---VDDAKEAKERANGMELDGRR 117
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 47.4 bits (111), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 29/76 (38%), Positives = 46/76 (60%), Gaps = 8/76 (10%)
Query: 95 PKGSGQSKDFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVI 154
P GSG+ +FVGGI + E E+++FF++YG V E +II D T S+G+GFV
Sbjct: 2 PLGSGK---IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVS 57
Query: 155 F----DSEEVVDEMLS 166
F D +++V+ ++
Sbjct: 58 FYNDVDVQKIVESQIN 73
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 42/79 (53%), Gaps = 1/79 (1%)
Query: 18 PGKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVI 77
P +F+GG+ F +YG + + I+ DR TG +G+GF+++ + V K++
Sbjct: 10 PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIV 68
Query: 78 EDTHIINGKQVEIKRTIPK 96
E +GK++++ I K
Sbjct: 69 ESQINFHGKKLKLGPAIRK 87
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 28/84 (33%), Positives = 44/84 (52%)
Query: 109 IFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSKG 168
++VGG+ VSE L F + G V+ + +D T + +G+GFV F SEE D +
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 169 NMIDMAGTQVSLIGWSPVNQLLKG 192
+MI + G + + S N+ L G
Sbjct: 78 DMIKLYGKPIRVNKASAHNKNLSG 101
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIEDT 80
+++GGL + + + F + G + ++ + KDR TGQ +G+GF+ + D I+
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 81 HIIN--GKQVEIKRT 93
+I GK + + +
Sbjct: 78 DMIKLYGKPIRVNKA 92
>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 = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/62 (40%), Positives = 41/62 (66%), Gaps = 5/62 (8%)
Query: 109 IFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIF----DSEEVVDEM 164
+FVGGI + E E+++FF++YG V E +II D T S+G+GFV F D +++V+
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 165 LS 166
++
Sbjct: 71 IN 72
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 42/79 (53%), Gaps = 1/79 (1%)
Query: 18 PGKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVI 77
P +F+GG+ F +YG + + I+ DR TG +G+GF+++ + V K++
Sbjct: 9 PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIV 67
Query: 78 EDTHIINGKQVEIKRTIPK 96
E +GK++++ I K
Sbjct: 68 ESQINFHGKKLKLGPAIRK 86
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 35/63 (55%)
Query: 97 GSGQSKDFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFD 156
GS KD K+F+G IP ++ E +LK F ++GK+ E +++D T +G F+ +
Sbjct: 4 GSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYC 63
Query: 157 SEE 159
E
Sbjct: 64 ERE 66
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 32/62 (51%)
Query: 20 KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIED 79
K+FIG +P++ F ++G I + ++KDR+TG +G F+TY + K
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74
Query: 80 TH 81
H
Sbjct: 75 LH 76
>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 = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/62 (40%), Positives = 41/62 (66%), Gaps = 5/62 (8%)
Query: 109 IFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIF----DSEEVVDEM 164
+FVGGI + E E+++FF++YG V E +II D T S+G+GFV F D +++V+
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 165 LS 166
++
Sbjct: 71 IN 72
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 42/79 (53%), Gaps = 1/79 (1%)
Query: 18 PGKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVI 77
P +F+GG+ F +YG + + I+ DR TG +G+GF+++ + V K++
Sbjct: 9 PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIV 67
Query: 78 EDTHIINGKQVEIKRTIPK 96
E +GK++++ I K
Sbjct: 68 ESQINFHGKKLKLGPAIRK 86
>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 = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/50 (42%), Positives = 31/50 (62%), Gaps = 2/50 (4%)
Query: 108 KIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETN--RSRGFGFVIF 155
K+FVG +P + SE +L+ F +YG V E ++RD N +S+G FV F
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTF 54
Score = 32.3 bits (72), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 13/50 (26%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 20 KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQP--RGFGFITY 67
K+F+G +P+ + + F +YG + + +++DR P +G F+T+
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTF 54
>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 = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 42/85 (49%), Gaps = 4/85 (4%)
Query: 13 GDGASPGKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYAD-PS 71
G A I++G + T HF G + I+ D+++G P+GF +I ++D S
Sbjct: 1 GXEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKES 60
Query: 72 VVDKVIEDTHIINGKQVEIKRTIPK 96
V + D + G+Q+++ IPK
Sbjct: 61 VRTSLALDESLFRGRQIKV---IPK 82
Score = 32.0 bits (71), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 6/74 (8%)
Query: 106 TKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVV---- 161
+ I+VG + + +EL+ F G V I+ D + +GF ++ F +E V
Sbjct: 6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 65
Query: 162 --DEMLSKGNMIDM 173
DE L +G I +
Sbjct: 66 ALDESLFRGRQIKV 79
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 36/77 (46%), Gaps = 5/77 (6%)
Query: 20 KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIED 79
K+F+G +D T + F +YG++ D I K R F F+T+AD V + +
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF-----RAFAFVTFADDKVAQSLCGE 67
Query: 80 THIINGKQVEIKRTIPK 96
II G V I PK
Sbjct: 68 DLIIKGISVHISNAEPK 84
Score = 35.4 bits (80), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 5/72 (6%)
Query: 108 KIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSK 167
K+FVG ++ +EL+ FF +YG+V++ I + R F FV F ++V + +
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF-----RAFAFVTFADDKVAQSLCGE 67
Query: 168 GNMIDMAGTQVS 179
+I +S
Sbjct: 68 DLIIKGISVHIS 79
>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 = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 41/82 (50%), Gaps = 4/82 (4%)
Query: 16 ASPGKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYAD-PSVVD 74
A I++G + T HF G + I+ D+++G P+GF +I ++D SV
Sbjct: 3 ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRT 62
Query: 75 KVIEDTHIINGKQVEIKRTIPK 96
+ D + G+Q+++ IPK
Sbjct: 63 SLALDESLFRGRQIKV---IPK 81
Score = 31.6 bits (70), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 33/72 (45%), Gaps = 6/72 (8%)
Query: 106 TKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVV---- 161
+ I+VG + + +EL+ F G V I+ D + +GF ++ F +E V
Sbjct: 5 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 64
Query: 162 --DEMLSKGNMI 171
DE L +G I
Sbjct: 65 ALDESLFRGRQI 76
>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 = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 25/121 (20%), Positives = 59/121 (48%), Gaps = 13/121 (10%)
Query: 58 QPRGFGFITYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGSGQSKDFK----TKKIFVG 112
Q + F F+ + + + D I G+ ++I+R D++ K+F+G
Sbjct: 51 QDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRR--------PHDYQPLPGAHKLFIG 102
Query: 113 GIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSKGNMID 172
G+P+ +++D++K + +G + +++D T S+G+ F + V D+ ++ N +
Sbjct: 103 GLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQ 162
Query: 173 M 173
+
Sbjct: 163 L 163
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 39/79 (49%), Gaps = 5/79 (6%)
Query: 18 PG--KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDK 75
PG K+FIGGLP + +G + ++KD TG +G+ F Y D +V D+
Sbjct: 94 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 153
Query: 76 VIEDTHIINGKQVEIKRTI 94
I +NG Q+ K+ +
Sbjct: 154 AIAG---LNGMQLGDKKLL 169
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 25/121 (20%), Positives = 59/121 (48%), Gaps = 13/121 (10%)
Query: 58 QPRGFGFITYADPSVVDKVIE-DTHIINGKQVEIKRTIPKGSGQSKDFK----TKKIFVG 112
Q + F F+ + + + D I G+ ++I+R D++ K+F+G
Sbjct: 49 QDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRR--------PHDYQPLPGAHKLFIG 100
Query: 113 GIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSKGNMID 172
G+P+ +++D++K + +G + +++D T S+G+ F + V D+ ++ N +
Sbjct: 101 GLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQ 160
Query: 173 M 173
+
Sbjct: 161 L 161
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 39/79 (49%), Gaps = 5/79 (6%)
Query: 18 PG--KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDK 75
PG K+FIGGLP + +G + ++KD TG +G+ F Y D +V D+
Sbjct: 92 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 151
Query: 76 VIEDTHIINGKQVEIKRTI 94
I +NG Q+ K+ +
Sbjct: 152 AIAG---LNGMQLGDKKLL 167
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 44.3 bits (103), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 28/129 (21%), Positives = 63/129 (48%), Gaps = 8/129 (6%)
Query: 53 DRYTGQPRGFGFITYADPSVVDKVIEDTHI-INGKQVEIKRTIPKGSGQSKDFKTKKIFV 111
D G R FG++ + ++K +E T + + G ++++++ PKG K+ + +
Sbjct: 41 DVRIGMTRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEK--PKGKDSKKERDARTLLA 98
Query: 112 GGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSKGNMI 171
+P V++DELK F ++ + +D +S+G ++ F +E ++ +
Sbjct: 99 KNLPYKVTQDELKEVFEDAAEI--RLVSKD---GKSKGIAYIEFKTEADAEKTFEEKQGT 153
Query: 172 DMAGTQVSL 180
++ G +SL
Sbjct: 154 EIDGRSISL 162
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 43.9 bits (102), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 16/66 (24%), Positives = 39/66 (59%)
Query: 108 KIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSK 167
K+F+GG+P+ +++D++K + +G + +++D T S+G+ F + V D+ ++
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 168 GNMIDM 173
N + +
Sbjct: 63 LNGMQL 68
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 3/75 (4%)
Query: 20 KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIED 79
K+FIGGLP + +G + ++KD TG +G+ F Y D +V D+ I
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 80 THIINGKQVEIKRTI 94
+NG Q+ K+ +
Sbjct: 63 ---LNGMQLGDKKLL 74
>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 = 43.9 bits (102), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 41/76 (53%), Gaps = 3/76 (3%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIE-D 79
+++G + +T HF G I I+ D+++G P+G+ +I +A+ + VD + D
Sbjct: 39 VYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMD 98
Query: 80 THIINGKQVEI--KRT 93
+ G+ +++ KRT
Sbjct: 99 ETVFRGRTIKVLPKRT 114
Score = 33.1 bits (74), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 19/100 (19%), Positives = 46/100 (46%), Gaps = 6/100 (6%)
Query: 95 PKGSGQSKDFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVI 154
P + + K+ + ++VG + + +L+ FS G + I+ D + +G+ ++
Sbjct: 25 PLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIE 84
Query: 155 F------DSEEVVDEMLSKGNMIDMAGTQVSLIGWSPVNQ 188
F D+ +DE + +G I + + ++ G S ++
Sbjct: 85 FAERNSVDAAVAMDETVFRGRTIKVLPKRTNMPGISSTDR 124
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 16/66 (24%), Positives = 39/66 (59%)
Query: 108 KIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSK 167
K+F+GG+P+ +++D++K + +G + +++D T S+G+ F + V D+ ++
Sbjct: 116 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 175
Query: 168 GNMIDM 173
N + +
Sbjct: 176 LNGMQL 181
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 38/78 (48%), Gaps = 3/78 (3%)
Query: 17 SPGKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKV 76
S K+FIGGLP + +G + ++KD TG +G+ F Y D +V D+
Sbjct: 113 SAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 172
Query: 77 IEDTHIINGKQVEIKRTI 94
I +NG Q+ K+ +
Sbjct: 173 IAG---LNGMQLGDKKLL 187
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 37/70 (52%), Gaps = 4/70 (5%)
Query: 109 IFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDS----EEVVDEM 164
+++ G+ ++ +L YGK++ + I D TN+ +G+GFV FDS ++ V +
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
Query: 165 LSKGNMIDMA 174
+ G MA
Sbjct: 68 KASGVQAQMA 77
Score = 33.9 bits (76), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 28/57 (49%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVI 77
++I GL TT K YG I + + D+ T + +G+GF+ + PS K +
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 64
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 29/77 (37%), Positives = 43/77 (55%), Gaps = 7/77 (9%)
Query: 106 TKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEML 165
+K +FV G+ +E+ LK F + +I+ D ET S+GFGFV F+SEE D
Sbjct: 15 SKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEE--DAKA 69
Query: 166 SKGNMID--MAGTQVSL 180
+K M D + G +V+L
Sbjct: 70 AKEAMEDGEIDGNKVTL 86
Score = 40.8 bits (94), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 41/79 (51%), Gaps = 7/79 (8%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITY---ADPSVVDKVI 77
+F+ GL +DTT T + F G + + I+ DR TG +GFGF+ + D + +
Sbjct: 18 LFVKGLSEDTTEETLKESF--DGSVR-ARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAM 74
Query: 78 EDTHIINGKQVEIKRTIPK 96
ED I+G +V + PK
Sbjct: 75 EDGE-IDGNKVTLDWAKPK 92
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 31/54 (57%)
Query: 102 KDFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIF 155
KD K+FVG IP + E +LK F ++G++ E +++D T +G F+ +
Sbjct: 11 KDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTY 64
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 44/87 (50%), Gaps = 5/87 (5%)
Query: 20 KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYA--DPSV-VDKV 76
K+F+G +P+ F ++G I + ++KDR TG +G F+TY D ++
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSA 76
Query: 77 IEDTHIING--KQVEIKRTIPKGSGQS 101
+ + + G + +++K +G G+S
Sbjct: 77 LHEQKTLPGMNRPIQVKPAASEGRGES 103
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 43/76 (56%), Gaps = 4/76 (5%)
Query: 94 IPKGSGQSKDFKT--KKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFG 151
+P+GS + + K+ K++ V IP + +L+ F ++GK+L+ +II + S+GFG
Sbjct: 15 VPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFG 72
Query: 152 FVIFDSEEVVDEMLSK 167
FV F++ D K
Sbjct: 73 FVTFENSADADRAREK 88
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/89 (22%), Positives = 46/89 (51%), Gaps = 6/89 (6%)
Query: 11 HTGDGASPGKIFIGGLPKDTTYATFNKHFGKYGDITD-SVIMKDRYTGQPRGFGFITYAD 69
+T + + P ++ + +P + FG++G I D +I +R + +GFGF+T+ +
Sbjct: 22 NTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS---KGFGFVTFEN 78
Query: 70 PSVVDKVIEDTH--IINGKQVEIKRTIPK 96
+ D+ E H ++ G+++E+ +
Sbjct: 79 SADADRAREKLHGTVVEGRKIEVNNATAR 107
>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 = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 37/65 (56%), Gaps = 4/65 (6%)
Query: 104 FKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIF----DSEE 159
F+ + V +P + ++DEL++ FS G+V ++IRD S G+GFV + D+E
Sbjct: 17 FQGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 76
Query: 160 VVDEM 164
++ +
Sbjct: 77 AINTL 81
Score = 35.0 bits (79), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 15/71 (21%), Positives = 35/71 (49%), Gaps = 3/71 (4%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIEDT 80
+ + LP++ T F G++ + +++D+ G G+GF+ Y ++ I
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI--- 78
Query: 81 HIINGKQVEIK 91
+ +NG +++ K
Sbjct: 79 NTLNGLRLQSK 89
>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 = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/51 (45%), Positives = 29/51 (56%), Gaps = 4/51 (7%)
Query: 118 VSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIF----DSEEVVDEM 164
S D L+ F KYG+V + I RD T SRGF FV F D+E+ +D M
Sbjct: 59 TSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 37/64 (57%), Gaps = 2/64 (3%)
Query: 30 TTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIE--DTHIINGKQ 87
T+ T + F KYG + D I +DRYT + RGF F+ + D + ++ D +++G++
Sbjct: 59 TSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRE 118
Query: 88 VEIK 91
+ ++
Sbjct: 119 LRVQ 122
>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 = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 40/80 (50%), Gaps = 1/80 (1%)
Query: 106 TKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEML 165
T +FVG + +V ++ L+N F + L ++ D +T SRG+GFV F S++ +
Sbjct: 1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60
Query: 166 SKGNMIDMAGTQVSLIGWSP 185
D+ G + I W+
Sbjct: 61 DSMQGQDLNGRPLR-INWAA 79
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 16/74 (21%), Positives = 30/74 (40%), Gaps = 2/74 (2%)
Query: 20 KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIED 79
+F+G L + T F + +M D TG RG+GF+++ ++
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 80 T--HIINGKQVEIK 91
+NG+ + I
Sbjct: 63 MQGQDLNGRPLRIN 76
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 40/73 (54%), Gaps = 8/73 (10%)
Query: 108 KIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSK 167
K+F+G +P +E E+++ F +YGKVLE II++ +GFV + + ++ +
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFVHIEDKTAAEDAIRN 61
Query: 168 GNMIDMAGTQVSL 180
+ + G +++
Sbjct: 62 LHHYKLHGVNINV 74
Score = 36.2 bits (82), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 10/71 (14%)
Query: 13 GDGASPG--KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADP 70
G S G K+FIG LP++ T F +YG + + I+K+ +GF+ D
Sbjct: 1 GSSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFVHIEDK 52
Query: 71 SVVDKVIEDTH 81
+ + I + H
Sbjct: 53 TAAEDAIRNLH 63
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 36/81 (44%), Gaps = 5/81 (6%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIEDT 80
+F+G D T + F +YGD+ D I K R F F+T+AD + + +
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFADDQIAQSLCGED 62
Query: 81 HIINGKQVEIKRTIPKGSGQS 101
II G V I PK + S
Sbjct: 63 LIIKGISVHISNAEPKHNSNS 83
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 5/62 (8%)
Query: 106 TKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEML 165
+ +FVG ++EDEL+ FFS+YG V++ I + R F FV F +++ +
Sbjct: 5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFADDQIAQSLC 59
Query: 166 SK 167
+
Sbjct: 60 GE 61
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 34/57 (59%), Gaps = 1/57 (1%)
Query: 109 IFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEML 165
+++ +P S+ E EL+N +G+V+ +I+RD + SRG GF +S E + ++
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVI 83
>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition
Motif Of Nono
pdb|2RS8|A Chain A, Solution Structure Of The N-Terminal Rna Recognition
Motif Of Nono
Length = 99
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 37/74 (50%), Gaps = 8/74 (10%)
Query: 20 KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVD--KVI 77
++F+G LP D T K F KYG + I KD +GFGFI ++ + KV
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 70
Query: 78 EDTHIINGKQVEIK 91
D + GKQ+ ++
Sbjct: 71 LDNMPLRGKQLRVR 84
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 41/73 (56%), Gaps = 6/73 (8%)
Query: 108 KIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSK 167
++FVG +P ++E+E++ F KYGK E I +D +GFGF+ ++ + + +
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 70
Query: 168 GNMIDMAGTQVSL 180
+ + + G Q+ +
Sbjct: 71 LDNMPLRGKQLRV 83
>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|B Chain B, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|C Chain C, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|D Chain D, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
Length = 84
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 36/60 (60%), Gaps = 4/60 (6%)
Query: 109 IFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIF----DSEEVVDEM 164
+ V +P ++++DEL++ FS G+V ++IRD S G+GFV + D+E ++ +
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Score = 36.2 bits (82), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 17/76 (22%), Positives = 38/76 (50%), Gaps = 5/76 (6%)
Query: 18 PGK--IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDK 75
PG+ + + LP++ T F G++ + +++D+ G G+GF+ Y ++
Sbjct: 2 PGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 61
Query: 76 VIEDTHIINGKQVEIK 91
I + +NG +++ K
Sbjct: 62 AI---NTLNGLRLQSK 74
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 38/72 (52%), Gaps = 5/72 (6%)
Query: 98 SGQSKDFKTKKI-FVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIF- 155
SG S TK++ +VGG+ V + L F +G + + QI D+ET + RGF FV F
Sbjct: 3 SGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE 62
Query: 156 ---DSEEVVDEM 164
D+ +D M
Sbjct: 63 LAEDAAAAIDNM 74
Score = 34.3 bits (77), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 26/47 (55%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITY 67
+++GGL ++ + F +GDITD I D T + RGF F+ +
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 61
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/58 (41%), Positives = 31/58 (53%), Gaps = 4/58 (6%)
Query: 111 VGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIF----DSEEVVDEM 164
V + S D L+ F KYG+V + I RD T SRGF FV F D+E+ +D M
Sbjct: 75 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 39/71 (54%), Gaps = 2/71 (2%)
Query: 23 IGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIE--DT 80
+ L T+ T + F KYG + D I +DRYT + RGF F+ + D + ++ D
Sbjct: 75 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 134
Query: 81 HIINGKQVEIK 91
+++G+++ ++
Sbjct: 135 AVLDGRELRVQ 145
>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 = 40.8 bits (94), Expect = 6e-04, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 4/60 (6%)
Query: 109 IFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIF----DSEEVVDEM 164
++VGG+ V + L F +G + + QI D+ET + RGF FV F D+ +D M
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Score = 35.0 bits (79), Expect = 0.043, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 26/47 (55%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITY 67
+++GGL ++ + F +GDITD I D T + RGF F+ +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 51
>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 = 40.4 bits (93), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 10/75 (13%)
Query: 95 PKGSGQSKDFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVI 154
P GSG IF+ + S+ L + FS +G +L +++ D N S+G+GFV
Sbjct: 2 PLGSGN--------IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVH 51
Query: 155 FDSEEVVDEMLSKGN 169
F+++E + + K N
Sbjct: 52 FETQEAAERAIEKMN 66
Score = 29.3 bits (64), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 4/76 (5%)
Query: 19 GKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIE 78
G IFI L K F +G+I ++ D +G+GF+ + ++ IE
Sbjct: 6 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIE 63
Query: 79 DTH--IINGKQVEIKR 92
+ ++N ++V + R
Sbjct: 64 KMNGMLLNDRKVFVGR 79
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 35/64 (54%), Gaps = 5/64 (7%)
Query: 106 TKKI-FVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIF----DSEEV 160
TK++ +VGG+ V + L F +G + + QI D+ET + RGF FV F D+
Sbjct: 62 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 121
Query: 161 VDEM 164
+D M
Sbjct: 122 IDNM 125
Score = 35.8 bits (81), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 26/47 (55%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITY 67
+++GGL ++ + F +GDITD I D T + RGF F+ +
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 112
>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 = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 35/64 (54%), Gaps = 5/64 (7%)
Query: 106 TKKI-FVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIF----DSEEV 160
TK++ +VGG+ V + L F +G + + QI D+ET + RGF FV F D+
Sbjct: 6 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 65
Query: 161 VDEM 164
+D M
Sbjct: 66 IDNM 69
Score = 34.7 bits (78), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 26/47 (55%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITY 67
+++GGL ++ + F +GDITD I D T + RGF F+ +
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 56
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 106 TKKI-FVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEM 164
TK++ +VGG+ V + L F +G + + QI D+ET + RGF FV F+ E
Sbjct: 4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 63
Query: 165 LSKGNMIDMAGTQVSL 180
+ N ++ G + +
Sbjct: 64 IDNMNESELFGRTIRV 79
Score = 34.7 bits (78), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 26/47 (55%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITY 67
+++GGL ++ + F +GDITD I D T + RGF F+ +
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 54
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 35/61 (57%), Gaps = 2/61 (3%)
Query: 109 IFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSKG 168
IF+ + S+ L + FS +G +L +++ D N S+G+GFV F+++E + + K
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 71
Query: 169 N 169
N
Sbjct: 72 N 72
Score = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 21/87 (24%), Positives = 37/87 (42%), Gaps = 11/87 (12%)
Query: 15 GASP-------GKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITY 67
GA P G IFI L K F +G+I ++ D +G+GF+ +
Sbjct: 1 GADPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHF 58
Query: 68 ADPSVVDKVIEDTH--IINGKQVEIKR 92
++ IE + ++N ++V + R
Sbjct: 59 ETQEAAERAIEKMNGMLLNDRKVFVGR 85
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 109 IFVGGIPSSVSEDELKNFFSKYGKVLEH-QIIRDHETNRSRGFGFVIFDSEEVVDEMLSK 167
IF+G + + E L + FS +G +L+ +I+RD +T S+G+ F+ F S + D +
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 168 GN 169
N
Sbjct: 68 MN 69
Score = 31.2 bits (69), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 27/59 (45%), Gaps = 1/59 (1%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSV-IMKDRYTGQPRGFGFITYADPSVVDKVIE 78
IFIG L + F +G I + IM+D TG +G+ FI +A D IE
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 34/58 (58%), Gaps = 2/58 (3%)
Query: 98 SGQSKDFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIF 155
S + +D +T +F + + + +L++FFS GKV + +II D + RS+G +V F
Sbjct: 19 SPEERDART--VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEF 74
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 1/78 (1%)
Query: 107 KKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLS 166
+ +FVG + + V E+ L F + G + + I +D E + + FGFV F E V ++
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIA 75
Query: 167 KGNMIDMAGTQVSLIGWS 184
N I + G +++ G S
Sbjct: 76 LLNGIRLYGRPINVSGPS 93
Score = 35.8 bits (81), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 4/65 (6%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIEDT 80
+F+G L + F + G +T I KDR G+P+ FGF+ + P V I
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYAI--- 74
Query: 81 HIING 85
++NG
Sbjct: 75 ALLNG 79
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/75 (24%), Positives = 41/75 (54%), Gaps = 8/75 (10%)
Query: 106 TKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEML 165
T KIFVG + ++ + EL++ F + G+V+E +++D + FV + E +
Sbjct: 9 TWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAI 60
Query: 166 SKGNMIDMAGTQVSL 180
++ N ++ G ++++
Sbjct: 61 AQLNGKEVKGKRINV 75
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 2/61 (3%)
Query: 107 KKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLS 166
K++ V IP + +L+ F ++GK+L+ +II + S+GFGFV F++ D
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRARE 73
Query: 167 K 167
K
Sbjct: 74 K 74
Score = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/83 (22%), Positives = 43/83 (51%), Gaps = 6/83 (7%)
Query: 17 SPGKIFIGGLPKDTTYATFNKHFGKYGDITD-SVIMKDRYTGQPRGFGFITYADPSVVDK 75
+P ++ + +P + FG++G I D +I +R + +GFGF+T+ + + D+
Sbjct: 14 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS---KGFGFVTFENSADADR 70
Query: 76 VIEDTH--IINGKQVEIKRTIPK 96
E H ++ G+++E+ +
Sbjct: 71 AREKLHGTVVEGRKIEVNNATAR 93
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 38/71 (53%), Gaps = 11/71 (15%)
Query: 36 NKHFGKYGDITDSV-IMKDRYTGQPRGFGFITYADPSVVDKVIEDTHIINGKQVEIKRTI 94
++ F G+ SV I+++R TG P G+ F+ +AD + +K + H INGK +
Sbjct: 27 SRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCL---HKINGKPL------ 77
Query: 95 PKGSGQSKDFK 105
G+ +K FK
Sbjct: 78 -PGATPAKRFK 87
>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 84
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 33/54 (61%)
Query: 106 TKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEE 159
++ +++G IP +E+++ + S G V+ +++ D +T RS+G+ F+ F E
Sbjct: 4 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLE 57
Score = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 31/68 (45%), Gaps = 3/68 (4%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIEDT 80
+++G +P D T G + + +M D TG+ +G+ FI + D ++
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRD---LESSASAV 63
Query: 81 HIINGKQV 88
+NG Q+
Sbjct: 64 RNLNGYQL 71
>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 = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 33/54 (61%)
Query: 106 TKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEE 159
++ +++G IP +E+++ + S G V+ +++ D +T RS+G+ F+ F E
Sbjct: 3 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLE 56
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 31/68 (45%), Gaps = 3/68 (4%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIEDT 80
+++G +P D T G + + +M D TG+ +G+ FI + D ++
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRD---LESSASAV 62
Query: 81 HIINGKQV 88
+NG Q+
Sbjct: 63 RNLNGYQL 70
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 32/50 (64%)
Query: 106 TKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIF 155
++ +++G IP +E+++ + S G V+ +++ D +T RS+G+ F+ F
Sbjct: 2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEF 51
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 31/68 (45%), Gaps = 3/68 (4%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIEDT 80
+++G +P D T G + + +M D TG+ +G+ FI + D ++
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRD---LESSASAV 61
Query: 81 HIINGKQV 88
+NG Q+
Sbjct: 62 RNLNGYQL 69
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 37.0 bits (84), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 33/61 (54%), Gaps = 2/61 (3%)
Query: 107 KKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETN--RSRGFGFVIFDSEEVVDEM 164
+K+FVGG+P + EDE+ F ++G ++ + + +G+ F++F E V +
Sbjct: 9 RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQAL 68
Query: 165 L 165
+
Sbjct: 69 I 69
Score = 32.3 bits (72), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 31/69 (44%), Gaps = 2/69 (2%)
Query: 20 KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTG--QPRGFGFITYADPSVVDKVI 77
K+F+GGLP D F ++G + K P+G+ F+ + + S V +I
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALI 69
Query: 78 EDTHIINGK 86
+ +GK
Sbjct: 70 DACLEEDGK 78
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 37.0 bits (84), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 40/76 (52%), Gaps = 6/76 (7%)
Query: 98 SGQSKDFKTK----KIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFV 153
SG S D T+ ++V + + ++ L+ FS +G + +++ E RS+GFGFV
Sbjct: 3 SGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVM--MEGGRSKGFGFV 60
Query: 154 IFDSEEVVDEMLSKGN 169
F S E + +++ N
Sbjct: 61 CFSSPEEATKAVTEMN 76
Score = 33.5 bits (75), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 5/57 (8%)
Query: 35 FNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIEDTHIINGKQVEIK 91
K F +G IT + +M + G+ +GFGF+ ++ P K + + +NG+ V K
Sbjct: 32 LRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTE---MNGRIVATK 83
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 37.0 bits (84), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 24/94 (25%), Positives = 48/94 (51%), Gaps = 8/94 (8%)
Query: 98 SGQSKDFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDS 157
SG S K K +FV + ++V+E+ L+ FS++GK+ + ++D + F+ FD
Sbjct: 3 SGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDE 54
Query: 158 EEVVDEMLSKGNMIDMAGTQVSLIGWSPVNQLLK 191
+ + + + N D+ G + ++ P +Q K
Sbjct: 55 RDGAVKAMEEMNGKDLEGENIEIVFAKPPDQKRK 88
>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 = 37.0 bits (84), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 39/79 (49%), Gaps = 3/79 (3%)
Query: 14 DGASPGKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVV 73
+G +FI LP++ + F +G++ + + D+ T + FGF++Y +P
Sbjct: 21 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSA 80
Query: 74 DKVIEDTHIINGKQVEIKR 92
I+ +NG Q+ +KR
Sbjct: 81 QAAIQS---MNGFQIGMKR 96
Score = 36.2 bits (82), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 35/67 (52%)
Query: 91 KRTIPKGSGQSKDFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGF 150
+++I Q + + +F+ +P + +L F +G V+ ++ D +TN S+ F
Sbjct: 10 QQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCF 69
Query: 151 GFVIFDS 157
GFV +D+
Sbjct: 70 GFVSYDN 76
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 36.6 bits (83), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 31/51 (60%)
Query: 109 IFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEE 159
+F+ +P ++ +L + F +G V+ ++ D +T+ S+ FGFV FD+ +
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPD 93
Score = 36.2 bits (82), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 3/79 (3%)
Query: 14 DGASPGKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVV 73
+G +FI LP++ T F +G++ + + D+ T + FGF+++ +P
Sbjct: 36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSA 95
Query: 74 DKVIEDTHIINGKQVEIKR 92
I+ +NG QV KR
Sbjct: 96 QVAIK---AMNGFQVGTKR 111
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 36.2 bits (82), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 4/77 (5%)
Query: 107 KKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLS 166
+K+FVG + SED+++ F +G + E I+R + N S+G FV + S ++
Sbjct: 16 RKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGN-SKGCAFVKYSSHAEAQAAIN 74
Query: 167 K--GNMIDMAGTQVSLI 181
G+ M G SL+
Sbjct: 75 ALHGSQT-MPGASSSLV 90
Score = 28.9 bits (63), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 15/62 (24%), Positives = 28/62 (45%), Gaps = 1/62 (1%)
Query: 20 KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIED 79
K+F+G L K + + F +G+I + I++ G +G F+ Y+ + I
Sbjct: 17 KLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRG-PDGNSKGCAFVKYSSHAEAQAAINA 75
Query: 80 TH 81
H
Sbjct: 76 LH 77
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 35.8 bits (81), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 39/85 (45%), Gaps = 3/85 (3%)
Query: 20 KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIE- 78
++F+ L ++ K F YG +++ D T +P+GF F+T+ P K
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 79 -DTHIINGKQVEI-KRTIPKGSGQS 101
D + G+ + + TI K + QS
Sbjct: 70 VDGQVFQGRMLHVLPSTIKKEASQS 94
Score = 35.8 bits (81), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 27/48 (56%)
Query: 108 KIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIF 155
++FV + + SE++L+ FS YG + E D T + +GF FV F
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTF 57
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 35.8 bits (81), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 36/84 (42%), Gaps = 6/84 (7%)
Query: 13 GDGASPGKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQ---PRGFGFITYAD 69
G S G +FI L TT T F K G I I K + GFGF+ Y
Sbjct: 1 GSSGSSG-LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKK 59
Query: 70 PSVVDKVIEDT--HIINGKQVEIK 91
P K ++ H ++G ++E++
Sbjct: 60 PEQAQKALKQLQGHTVDGHKLEVR 83
Score = 28.5 bits (62), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 32/69 (46%), Gaps = 5/69 (7%)
Query: 109 IFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETN---RSRGFGFVIFDSEEVVDEML 165
+F+ + S +E+ LK FSK G + I + S GFGFV + E + L
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 166 S--KGNMID 172
+G+ +D
Sbjct: 68 KQLQGHTVD 76
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 35.8 bits (81), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 33/176 (18%), Positives = 70/176 (39%), Gaps = 18/176 (10%)
Query: 20 KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIED 79
KI I GLP D T + D+ +K + + +G F+T + + I
Sbjct: 24 KILIRGLPGDVTNQEVH-------DLLSDYELKYCFVDKYKGTAFVTLLNGEQAEAAINA 76
Query: 80 THIINGKQVEIKRTIPKGSGQSKDFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQII 139
H ++ E+ + Q D + V +P S+++ + + +G + ++
Sbjct: 77 FHQSRLRERELSVQL-----QPTD---ALLCVANLPPSLTQQQFEELVRPFGSLERCFLV 128
Query: 140 RDHETNRSRGFGFVIFDSEEVVDEMLSKGNMIDMA-GTQVSLIGWSPVNQLLKGYL 194
T +S+G+GF + ++ +K +++ G + + W+ QL L
Sbjct: 129 YSERTGQSKGYGFAEYMKKDSAAR--AKSDLLGKPLGPRTLYVHWTDAGQLTPALL 182
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 35.8 bits (81), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 33/176 (18%), Positives = 70/176 (39%), Gaps = 18/176 (10%)
Query: 20 KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIED 79
KI I GLP D T + D+ +K + + +G F+T + + I
Sbjct: 24 KILIRGLPGDVTNQEVH-------DLLSDYELKYCFVDKYKGTAFVTLLNGEQAEAAINA 76
Query: 80 THIINGKQVEIKRTIPKGSGQSKDFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQII 139
H ++ E+ + Q D + V +P S+++ + + +G + ++
Sbjct: 77 FHQSRLRERELSVQL-----QPTD---ALLCVANLPPSLTQQQFEELVRPFGSLERCFLV 128
Query: 140 RDHETNRSRGFGFVIFDSEEVVDEMLSKGNMIDMA-GTQVSLIGWSPVNQLLKGYL 194
T +S+G+GF + ++ +K +++ G + + W+ QL L
Sbjct: 129 YSERTGQSKGYGFAEYMKKDSAAR--AKSDLLGKPLGPRTLYVHWTDAGQLTPALL 182
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 35.8 bits (81), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 2/82 (2%)
Query: 99 GQSKDFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSE 158
G S +IFV +P + LK+ F++ G VL I E +S+G G V F+S
Sbjct: 1 GSSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVKFESP 58
Query: 159 EVVDEMLSKGNMIDMAGTQVSL 180
EV + N + ++G ++ +
Sbjct: 59 EVAERACRMMNGMKLSGREIDV 80
>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 = 35.8 bits (81), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 33/176 (18%), Positives = 70/176 (39%), Gaps = 18/176 (10%)
Query: 20 KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIED 79
KI I GLP D T + D+ +K + + +G F+T + + I
Sbjct: 22 KILIRGLPGDVTNQEVH-------DLLSDYELKYCFVDKYKGTAFVTLLNGEQAEAAINA 74
Query: 80 THIINGKQVEIKRTIPKGSGQSKDFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQII 139
H ++ E+ + Q D + V +P S+++ + + +G + ++
Sbjct: 75 FHQSRLRERELSVQL-----QPTD---ALLCVANLPPSLTQQQFEELVRPFGSLERCFLV 126
Query: 140 RDHETNRSRGFGFVIFDSEEVVDEMLSKGNMIDMA-GTQVSLIGWSPVNQLLKGYL 194
T +S+G+GF + ++ +K +++ G + + W+ QL L
Sbjct: 127 YSERTGQSKGYGFAEYMKKDSAAR--AKSDLLGKPLGPRTLYVHWTDAGQLTPALL 180
>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 = 35.0 bits (79), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIEDT 80
+F+G L + T A F +G I+D+ ++KD TG+ +G+GF+++ + + I+
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 81 --HIINGKQVEIKRTIPK 96
+ G+Q+ K
Sbjct: 69 GGQWLGGRQIRTNWATRK 86
Score = 34.3 bits (77), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 36/60 (60%), Gaps = 4/60 (6%)
Query: 109 IFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIF----DSEEVVDEM 164
+FVG + ++ + F+ +G++ + ++++D T +S+G+GFV F D+E + +M
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 34.7 bits (78), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 15/58 (25%), Positives = 29/58 (50%), Gaps = 1/58 (1%)
Query: 20 KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVI 77
K+FI GLP T + +G + D ++ +R G+P+G ++ Y + S + +
Sbjct: 19 KLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAV 75
Score = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 44/84 (52%), Gaps = 14/84 (16%)
Query: 101 SKDFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRS---RGFGFVIFDS 157
S + K+F+ G+P S +++EL+ +G V + +++ TNR+ +G +V +++
Sbjct: 12 STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLV----TNRAGKPKGLAYVEYEN 67
Query: 158 EEV-------VDEMLSKGNMIDMA 174
E +D M K N+I +A
Sbjct: 68 ESQASQAVMKMDGMTIKENIIKVA 91
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 34.7 bits (78), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 26/52 (50%), Gaps = 7/52 (13%)
Query: 118 VSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIF-------DSEEVVD 162
S D L+ F KYG+V + I R+ T RGF FV F D+E +D
Sbjct: 25 TSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMD 76
Score = 32.3 bits (72), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 16/64 (25%), Positives = 33/64 (51%), Gaps = 2/64 (3%)
Query: 30 TTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVD--KVIEDTHIINGKQ 87
T+ + + F KYG + D I ++ +T PRGF F+ + D + D ++G++
Sbjct: 25 TSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRE 84
Query: 88 VEIK 91
+ ++
Sbjct: 85 LRVQ 88
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 34.7 bits (78), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 2/72 (2%)
Query: 109 IFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSKG 168
IFV +P + LK+ F++ G VL I E +S+G G V F+S EV +
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVKFESPEVAERACRMM 65
Query: 169 NMIDMAGTQVSL 180
N + ++G ++ +
Sbjct: 66 NGMKLSGREIDV 77
>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 = 34.7 bits (78), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 42/74 (56%), Gaps = 2/74 (2%)
Query: 109 IFVGGIPSSVSEDELKNFFSKYG-KVLEHQIIRDHETNRSRGFGFVIFDS-EEVVDEMLS 166
+ + +P + +ED+++ +G + E +++R+ + +SRGF FV F ++ M +
Sbjct: 4 VMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEA 63
Query: 167 KGNMIDMAGTQVSL 180
+ +++ G +VS+
Sbjct: 64 NQHSLNILGQKVSM 77
>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 = 34.3 bits (77), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 26/47 (55%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITY 67
+F+ + DTT + + F YG I ++ + +G+PRG+ FI Y
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEY 151
Score = 32.0 bits (71), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 15/72 (20%), Positives = 33/72 (45%)
Query: 87 QVEIKRTIPKGSGQSKDFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNR 146
+ E+K P ++ K +FV + +E +L+ F YG + ++ + +
Sbjct: 83 ETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGK 142
Query: 147 SRGFGFVIFDSE 158
RG+ F+ ++ E
Sbjct: 143 PRGYAFIEYEHE 154
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 34.3 bits (77), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 5/74 (6%)
Query: 20 KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVI-- 77
+I++G LP D F KYG I D + +K+R G P F F+ + DP + +
Sbjct: 24 RIYVGNLPPDIRTKDIEDVFYKYGAIRD-IDLKNRRGGPP--FAFVEFEDPRDAEDAVYG 80
Query: 78 EDTHIINGKQVEIK 91
D + +G ++ ++
Sbjct: 81 RDGYDYDGYRLRVE 94
Score = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 9/76 (11%)
Query: 108 KIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRG---FGFVIFDSEEVVDEM 164
+I+VG +P + ++++ F KYG IRD + RG F FV F+ ++
Sbjct: 24 RIYVGNLPPDIRTKDIEDVFYKYG------AIRDIDLKNRRGGPPFAFVEFEDPRDAEDA 77
Query: 165 LSKGNMIDMAGTQVSL 180
+ + D G ++ +
Sbjct: 78 VYGRDGYDYDGYRLRV 93
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 33.9 bits (76), Expect = 0.076, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 26/47 (55%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITY 67
I + L +DT + F +G I+ + KD+ TGQ +GF FI++
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISF 64
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 24/51 (47%)
Query: 109 IFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEE 159
I V + E +L+ F +G + + +D T +S+GF F+ F E
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRE 68
>pdb|2VOD|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auauuuu
pdb|2VOD|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auauuuu
pdb|2VON|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auaauuu
pdb|2VON|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auaauuu
pdb|2VOO|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Uuuuuuuu
pdb|2VOO|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Uuuuuuuu
pdb|2VOP|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auuuu
Length = 193
Score = 33.9 bits (76), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 47/83 (56%), Gaps = 8/83 (9%)
Query: 83 INGKQVEIKRT----IPKGSGQSK-DFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQ 137
I+ + +I+R+ +P+ + + K D K + +++ G P+ + D++K + G+VL Q
Sbjct: 81 ISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQ 140
Query: 138 IIRD-HETNRSRGFGFVIFDSEE 159
+ R H+ +G FV+FDS E
Sbjct: 141 MRRTLHKA--FKGSIFVVFDSIE 161
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 33.9 bits (76), Expect = 0.093, Method: Compositional matrix adjust.
Identities = 15/62 (24%), Positives = 28/62 (45%), Gaps = 8/62 (12%)
Query: 20 KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIED 79
++F+ P D + N+ FG +G + + I+ GF F+ + + K IE+
Sbjct: 33 RLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAKAIEE 84
Query: 80 TH 81
H
Sbjct: 85 VH 86
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 33/60 (55%), Gaps = 7/60 (11%)
Query: 109 IFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFV----IFDSEEVVDEM 164
+++ +P ++ +E+ + F KYG + + IR T +RG +V IFD++ VD +
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDAKNAVDHL 67
>pdb|1S79|A Chain A, Solution Structure Of The Central Rrm Of Human La Protein
Length = 103
Score = 32.7 bits (73), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 33/58 (56%), Gaps = 3/58 (5%)
Query: 103 DFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRD-HETNRSRGFGFVIFDSEE 159
D K + +++ G P+ + D++K + G+VL Q+ R H+ +G FV+FDS E
Sbjct: 8 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKA--FKGSIFVVFDSIE 63
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 32.7 bits (73), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 32/60 (53%), Gaps = 7/60 (11%)
Query: 109 IFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFV----IFDSEEVVDEM 164
+++ +P ++ +E+ + F KYG + + IR T +RG +V IFD++ D +
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDAKNACDHL 77
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 32.7 bits (73), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 33/77 (42%), Gaps = 3/77 (3%)
Query: 16 ASPGKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDK 75
AS + + LP+D T F G I IM+D TG G+ F+ + +
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 76 VIEDTHIINGKQVEIKR 92
I+ ++NG V KR
Sbjct: 61 AIK---VLNGITVRNKR 74
>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 = 32.7 bits (73), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 30/62 (48%), Gaps = 8/62 (12%)
Query: 14 DGASPGK--------IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFI 65
DG PG +F+ G+ ++ T + F +YG+I + + DR TG +G+ +
Sbjct: 10 DGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLV 69
Query: 66 TY 67
Y
Sbjct: 70 EY 71
Score = 31.6 bits (70), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 17/78 (21%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 109 IFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSKG 168
+FV G+ +E+++ + F++YG++ + D T +G+ V +++ + +
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 169 NMIDMAGTQVSLIGWSPV 186
N D+ G +S + W V
Sbjct: 85 NGQDLMGQPIS-VDWCFV 101
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 32.7 bits (73), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 33/63 (52%), Gaps = 7/63 (11%)
Query: 106 TKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFV----IFDSEEVV 161
+ +++ +P ++ +E+ + F KYG + + IR T +RG +V IFD++
Sbjct: 12 NRILYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDAKNAC 68
Query: 162 DEM 164
D +
Sbjct: 69 DHL 71
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 32.7 bits (73), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 7/74 (9%)
Query: 20 KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADP-SVVDKVIE 78
K+++G L + + FG YG + + ++ P GF F+ + DP D V E
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRE 129
Query: 79 -DTHIINGKQVEIK 91
D + G +V ++
Sbjct: 130 LDGRTLCGCRVRVE 143
>pdb|1YTY|A Chain A, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
pdb|1YTY|B Chain B, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
Length = 194
Score = 32.7 bits (73), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 46/83 (55%), Gaps = 8/83 (9%)
Query: 83 INGKQVEIKRT----IPKGSGQSK-DFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQ 137
I+ + +I+R+ +P+ + + K D K + +++ G P+ + D++K + G+VL Q
Sbjct: 82 ISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQ 141
Query: 138 IIRD-HETNRSRGFGFVIFDSEE 159
R H+ +G FV+FDS E
Sbjct: 142 XRRTLHKA--FKGSIFVVFDSIE 162
>pdb|1ZH5|A Chain A, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
pdb|1ZH5|B Chain B, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
Length = 195
Score = 32.3 bits (72), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 46/83 (55%), Gaps = 8/83 (9%)
Query: 83 INGKQVEIKRT----IPKGSGQSK-DFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQ 137
I+ + +I+R+ +P+ + + K D K + +++ G P+ + D++K + G+VL Q
Sbjct: 83 ISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQ 142
Query: 138 IIRD-HETNRSRGFGFVIFDSEE 159
R H+ +G FV+FDS E
Sbjct: 143 XRRTLHKA--FKGSIFVVFDSIE 163
>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 = 32.3 bits (72), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 15/72 (20%), Positives = 37/72 (51%)
Query: 109 IFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSKG 168
+FV G+ +E+++ + F++YG++ + D T +G+ V +++ + +
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 169 NMIDMAGTQVSL 180
N D+ G +S+
Sbjct: 72 NGQDLMGQPISV 83
Score = 30.8 bits (68), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 26/47 (55%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITY 67
+F+ G+ ++ T + F +YG+I + + DR TG +G+ + Y
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 58
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 32.3 bits (72), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 26/47 (55%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITY 67
+F+ + DTT + + F YG I ++ + +G+PRG+ FI Y
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEY 151
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 15/72 (20%), Positives = 33/72 (45%)
Query: 87 QVEIKRTIPKGSGQSKDFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNR 146
+ E+K P ++ K +FV + +E +L+ F YG + ++ + +
Sbjct: 83 ETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGK 142
Query: 147 SRGFGFVIFDSE 158
RG+ F+ ++ E
Sbjct: 143 PRGYAFIEYEHE 154
>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 = 32.3 bits (72), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 15/72 (20%), Positives = 37/72 (51%)
Query: 109 IFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSKG 168
+FV G+ +E+++ + F++YG++ + D T +G+ V +++ + +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 169 NMIDMAGTQVSL 180
N D+ G +S+
Sbjct: 70 NGQDLMGQPISV 81
Score = 30.8 bits (68), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 26/47 (55%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITY 67
+F+ G+ ++ T + F +YG+I + + DR TG +G+ + Y
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 56
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 32.0 bits (71), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 15/72 (20%), Positives = 37/72 (51%)
Query: 109 IFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSKG 168
+FV G+ +E+++ + F++YG++ + D T +G+ V +++ + +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 169 NMIDMAGTQVSL 180
N D+ G +S+
Sbjct: 70 NGQDLMGQPISV 81
Score = 31.2 bits (69), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 26/47 (55%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITY 67
+F+ G+ ++ T + F +YG+I + + DR TG +G+ + Y
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 56
>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 = 32.0 bits (71), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 30/62 (48%), Gaps = 8/62 (12%)
Query: 14 DGASPGK--------IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFI 65
DG PG +F+ G+ ++ T + F +YG+I + + DR TG +G+ +
Sbjct: 11 DGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLV 70
Query: 66 TY 67
Y
Sbjct: 71 EY 72
Score = 32.0 bits (71), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 16/76 (21%), Positives = 38/76 (50%), Gaps = 1/76 (1%)
Query: 109 IFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSKG 168
+FV G+ +E+++ + F++YG++ + D T +G+ V +++ + +
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 169 NMIDMAGTQVSLIGWS 184
N D+ G +S + W
Sbjct: 86 NGQDLMGQPIS-VDWC 100
>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 = 32.0 bits (71), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 17/78 (21%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 109 IFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSKG 168
+FV G+ +E+++ + F++YG++ + D T +G+ V +++ + +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 169 NMIDMAGTQVSLIGWSPV 186
N D+ G +S + W V
Sbjct: 70 NGQDLMGQPIS-VDWCFV 86
Score = 31.2 bits (69), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 26/47 (55%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITY 67
+F+ G+ ++ T + F +YG+I + + DR TG +G+ + Y
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 56
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 32.0 bits (71), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 23/37 (62%)
Query: 106 TKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDH 142
+ K+ VG I + + EL+ F +YG V+E I++D+
Sbjct: 10 STKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKDY 46
>pdb|1ZXO|A Chain A, X-Ray Crystal Structure Of Protein Q8a1p1 From Bacteroides
Thetaiotaomicron. Northeast Structural Genomics
Consortium Target Btr25.
pdb|1ZXO|F Chain F, X-Ray Crystal Structure Of Protein Q8a1p1 From Bacteroides
Thetaiotaomicron. Northeast Structural Genomics
Consortium Target Btr25.
pdb|1ZXO|B Chain B, X-Ray Crystal Structure Of Protein Q8a1p1 From Bacteroides
Thetaiotaomicron. Northeast Structural Genomics
Consortium Target Btr25.
pdb|1ZXO|D Chain D, X-Ray Crystal Structure Of Protein Q8a1p1 From Bacteroides
Thetaiotaomicron. Northeast Structural Genomics
Consortium Target Btr25.
pdb|1ZXO|C Chain C, X-Ray Crystal Structure Of Protein Q8a1p1 From Bacteroides
Thetaiotaomicron. Northeast Structural Genomics
Consortium Target Btr25.
pdb|1ZXO|E Chain E, X-Ray Crystal Structure Of Protein Q8a1p1 From Bacteroides
Thetaiotaomicron. Northeast Structural Genomics
Consortium Target Btr25
Length = 291
Score = 31.6 bits (70), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 31/66 (46%), Gaps = 1/66 (1%)
Query: 13 GDGASPGKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSV 72
G GA GK+ +G + K+ AT + F K D+T I+ DR QP F+ P +
Sbjct: 143 GSGAVLGKLLVGDILKNQLPATLKEEFLKQFDLTPPEII-DRVYRQPFPNRFLASLSPFI 201
Query: 73 VDKVIE 78
+ E
Sbjct: 202 AQHLEE 207
>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
pdb|2F9J|B Chain B, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
Length = 125
Score = 31.6 bits (70), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 31/60 (51%), Gaps = 7/60 (11%)
Query: 109 IFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFV----IFDSEEVVDEM 164
+ + +P ++ +E+ + F KYG + + IR T +RG +V IFD++ D +
Sbjct: 21 LMIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDAKNACDHL 77
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 31.2 bits (69), Expect = 0.52, Method: Composition-based stats.
Identities = 16/65 (24%), Positives = 29/65 (44%), Gaps = 8/65 (12%)
Query: 17 SPGKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKV 76
S ++F+ P D + N+ FG +G + + I+ GF F+ + + K
Sbjct: 3 SNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAKA 54
Query: 77 IEDTH 81
IE+ H
Sbjct: 55 IEEVH 59
>pdb|1RJ5|A Chain A, Crystal Structure Of The Extracellular Domain Of Murine
Carbonic Anhydrase Xiv
pdb|1RJ5|B Chain B, Crystal Structure Of The Extracellular Domain Of Murine
Carbonic Anhydrase Xiv
pdb|1RJ6|A Chain A, Crystal Structure Of The Extracellular Domain Of Murine
Carbonic Anhydrase Xiv In Complex With Acetazolamide
pdb|1RJ6|B Chain B, Crystal Structure Of The Extracellular Domain Of Murine
Carbonic Anhydrase Xiv In Complex With Acetazolamide
Length = 261
Score = 31.2 bits (69), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 23/41 (56%)
Query: 8 DNPHTGDGASPGKIFIGGLPKDTTYATFNKHFGKYGDITDS 48
+N HT + P + +GGLP+ T A + H+G+ G + S
Sbjct: 64 NNGHTVQLSLPPTLHLGGLPRKYTAAQLHLHWGQRGSLEGS 104
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 31.2 bits (69), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 25/49 (51%)
Query: 109 IFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDS 157
+FV I EDE++ F YG++ + D T S+G+ V +++
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYET 77
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 30.8 bits (68), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 14/60 (23%), Positives = 26/60 (43%), Gaps = 5/60 (8%)
Query: 20 KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIED 79
K+++G L + + FG YG + + ++ P GF F+ + DP + D
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRD 129
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 30.4 bits (67), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 25/43 (58%), Gaps = 3/43 (6%)
Query: 114 IPSS---VSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFV 153
IPS+ V + L + FSK GKV+ + D T +++GF FV
Sbjct: 17 IPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFV 59
Score = 26.9 bits (58), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 28/56 (50%), Gaps = 3/56 (5%)
Query: 39 FGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIEDTHIINGKQVEIKRTI 94
F K G + + D TG+ +GF F+ + K+I+ H GK++++K +
Sbjct: 33 FSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH---GKRLDLKHRL 85
>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 = 30.4 bits (67), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 25/49 (51%)
Query: 109 IFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDS 157
+FV I EDE++ F YG++ + D T S+G+ V +++
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYET 123
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 30.4 bits (67), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 18/83 (21%), Positives = 38/83 (45%), Gaps = 9/83 (10%)
Query: 12 TGDGASPGKIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPS 71
+G+ + +++GGL T HF ++G+I ++ Q + FI +A
Sbjct: 6 SGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVV------QRQQCAFIQFATRQ 59
Query: 72 VVDKVIEDTH---IINGKQVEIK 91
+ E + I+NG+++ +K
Sbjct: 60 AAEVAAEKSFNKLIVNGRRLNVK 82
Score = 29.6 bits (65), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 15/70 (21%), Positives = 36/70 (51%), Gaps = 8/70 (11%)
Query: 98 SGQSKDFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDS 157
SG+ K T ++VGG+ +++E +L+N F ++G++ +++ + F+ F +
Sbjct: 6 SGEDKTITT--LYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQC------AFIQFAT 57
Query: 158 EEVVDEMLSK 167
+ + K
Sbjct: 58 RQAAEVAAEK 67
>pdb|2DNN|A Chain A, Solution Structure Of Rna Binding Domain In Rna-Binding
Protein 12
Length = 109
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 2/63 (3%)
Query: 109 IFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSKG 168
+ V G+P S E+++++FF +V +++DH R+ G G V F S + E L +
Sbjct: 19 VSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGLVKFLSPQDTFEALKRN 76
Query: 169 NMI 171
M+
Sbjct: 77 RML 79
>pdb|3S8S|A Chain A, Crystal Structure Of The Rrm Domain Of Human Setd1a
Length = 110
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 32/69 (46%)
Query: 107 KKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLS 166
K++ + +V E LK+ KYG+V E +I+ T + G V+F S E +
Sbjct: 7 KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 66
Query: 167 KGNMIDMAG 175
++ + G
Sbjct: 67 NLHLTSVMG 75
>pdb|3NS6|A Chain A, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
pdb|3NS6|B Chain B, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
Length = 100
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 25/43 (58%), Gaps = 3/43 (6%)
Query: 114 IPSS---VSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFV 153
IPS+ V + L + FSK GKV+ + D T +++GF FV
Sbjct: 17 IPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFV 59
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 29.6 bits (65), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 110 FVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLS 166
+VG +P + + ++ F + +++RD +T++ +GF +V FD + + E L+
Sbjct: 19 YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT 74
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 107 KKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDS 157
+K+FVG + SE+++ F +G + E ++R + S+G FV F S
Sbjct: 16 RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPD-GSSKGCAFVKFSS 65
>pdb|2E5G|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 21
Length = 94
Score = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 14/72 (19%), Positives = 33/72 (45%), Gaps = 6/72 (8%)
Query: 21 IFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITYADPSVVDKVI-ED 79
+F+ G P+ A +++F +G + V+ KD+ F + D + V+ +
Sbjct: 11 VFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGV-----FAIVEMGDVGAREAVLSQS 65
Query: 80 THIINGKQVEIK 91
H + G ++ ++
Sbjct: 66 QHSLGGHRLRVR 77
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 28.9 bits (63), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 27/54 (50%), Gaps = 5/54 (9%)
Query: 53 DRYTGQPRGFGFITYADPSVVDKVIE--DTHIINGKQVEI---KRTIPKGSGQS 101
D+ TG+P+G ++Y DP +E D G ++++ ++ P SG S
Sbjct: 58 DKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSGPS 111
Score = 27.3 bits (59), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 8/63 (12%)
Query: 102 KDFKTKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQ--------IIRDHETNRSRGFGFV 153
+D I+V G+ SV+ D+L +FF + G V ++ I D ET + +G V
Sbjct: 11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATV 70
Query: 154 IFD 156
++
Sbjct: 71 SYE 73
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 28.5 bits (62), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 18/75 (24%), Positives = 37/75 (49%), Gaps = 5/75 (6%)
Query: 106 TKKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEML 165
+ + + +++EDELK F LE +++ + +S+G ++ F SE ++ L
Sbjct: 16 ARTLLAKNLSFNITEDELKEVFED---ALEIRLV--SQDGKSKGIAYIEFKSEADAEKNL 70
Query: 166 SKGNMIDMAGTQVSL 180
+ ++ G VSL
Sbjct: 71 EEKQGAEIDGRSVSL 85
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 28.1 bits (61), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 9/58 (15%)
Query: 108 KIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIF----DSEEVV 161
K++VG + + + EL+ FS YG + I R+ GF FV F D+E+ V
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPP-----GFAFVEFEDPRDAEDAV 54
>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 = 28.1 bits (61), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 12/50 (24%), Positives = 29/50 (58%), Gaps = 2/50 (4%)
Query: 44 DITDSVIMKDRYTGQPRGFGFITYADPSVVDKVIE--DTHIINGKQVEIK 91
D+ + ++R GQ +G+ + A + V K++E ++NG++V+++
Sbjct: 83 DVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVR 132
>pdb|3T0E|E Chain E, Crystal Structure Of A Complete Ternary Complex Of T Cell
Receptor, Peptide-Mhc And Cd4
Length = 373
Score = 28.1 bits (61), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 79 DTHIINGKQVEIKRTIPKGSGQSKDFKTK--KIFVGGIPSSVSEDELKNFFSKYGKVLEH 136
DTH++ G+ + + P GS S ++ K GG SVS+ EL++ + VL++
Sbjct: 105 DTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQN 164
Query: 137 Q 137
Q
Sbjct: 165 Q 165
>pdb|3S4S|G Chain G, Crystal Structure Of Cd4 Mutant Bound To Hla-Dr1
pdb|3S4S|H Chain H, Crystal Structure Of Cd4 Mutant Bound To Hla-Dr1
Length = 191
Score = 28.1 bits (61), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 79 DTHIINGKQVEIKRTIPKGSGQSKDFKTK--KIFVGGIPSSVSEDELKNFFSKYGKVLEH 136
DTH++ G+ + + P GS S ++ K GG SVS+ EL++ + VL++
Sbjct: 109 DTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQN 168
Query: 137 Q 137
Q
Sbjct: 169 Q 169
>pdb|1WIO|A Chain A, Structure Of T-Cell Surface Glycoprotein Cd4, Tetragonal
Crystal Form
pdb|1WIO|B Chain B, Structure Of T-Cell Surface Glycoprotein Cd4, Tetragonal
Crystal Form
pdb|1WIP|A Chain A, Structure Of T-Cell Surface Glycoprotein Cd4, Monoclinic
Crystal Form
pdb|1WIP|B Chain B, Structure Of T-Cell Surface Glycoprotein Cd4, Monoclinic
Crystal Form
pdb|1WIQ|A Chain A, Structure Of T-Cell Surface Glycoprotein Cd4, Trigonal
Crystal Form
pdb|1WIQ|B Chain B, Structure Of T-Cell Surface Glycoprotein Cd4, Trigonal
Crystal Form
Length = 363
Score = 28.1 bits (61), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 79 DTHIINGKQVEIKRTIPKGSGQSKDFKTK--KIFVGGIPSSVSEDELKNFFSKYGKVLEH 136
DTH++ G+ + + P GS S ++ K GG SVS+ EL++ + VL++
Sbjct: 105 DTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQN 164
Query: 137 Q 137
Q
Sbjct: 165 Q 165
>pdb|3S5L|G Chain G, Crystal Structure Of Cd4 Mutant Bound To Hla-Dr1
pdb|3S5L|H Chain H, Crystal Structure Of Cd4 Mutant Bound To Hla-Dr1
Length = 191
Score = 27.7 bits (60), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 79 DTHIINGKQVEIKRTIPKGSGQSKDFKTK--KIFVGGIPSSVSEDELKNFFSKYGKVLEH 136
DTH++ G+ + + P GS S ++ K GG SVS+ EL++ + VL++
Sbjct: 109 DTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQN 168
Query: 137 Q 137
Q
Sbjct: 169 Q 169
>pdb|1CDI|A Chain A, Structures Of An Hiv And Mhc Binding Fragment From Human
Cd4 As Refined In Two Crystal Lattices
Length = 179
Score = 27.7 bits (60), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 79 DTHIINGKQVEIKRTIPKGSGQSKDFKTK--KIFVGGIPSSVSEDELKNFFSKYGKVLEH 136
DTH++ G+ + + P GS S ++ K GG SVS+ EL++ + VL++
Sbjct: 106 DTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQN 165
Query: 137 Q 137
Q
Sbjct: 166 Q 166
>pdb|1JL4|D Chain D, Crystal Structure Of The Human Cd4 N-Terminal Two Domain
Fragment Complexed To A Class Ii Mhc Molecule
pdb|1CDH|A Chain A, Structures Of An Hiv And Mhc Binding Fragment From Human
Cd4 As Refined In Two Crystal Lattices
pdb|1CDJ|A Chain A, Structure Of T-Cell Surface Glycoprotein Cd4
Length = 178
Score = 27.7 bits (60), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 79 DTHIINGKQVEIKRTIPKGSGQSKDFKTK--KIFVGGIPSSVSEDELKNFFSKYGKVLEH 136
DTH++ G+ + + P GS S ++ K GG SVS+ EL++ + VL++
Sbjct: 105 DTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQN 164
Query: 137 Q 137
Q
Sbjct: 165 Q 165
>pdb|1CDU|A Chain A, Structure Of T-Cell Surface Glycoprotein Cd4 Mutant With
Phe 43 Replaced By Val
Length = 178
Score = 27.7 bits (60), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 79 DTHIINGKQVEIKRTIPKGSGQSKDFKTK--KIFVGGIPSSVSEDELKNFFSKYGKVLEH 136
DTH++ G+ + + P GS S ++ K GG SVS+ EL++ + VL++
Sbjct: 105 DTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQN 164
Query: 137 Q 137
Q
Sbjct: 165 Q 165
>pdb|2LXU|A Chain A, Solution Nmr Structure Of The Eukaryotic Rna Recognition
Motif, Rrm1, From The Heterogeneous Nuclear
Ribonucleoprotein H From Homo Sapiens, Northeast
Structural Genomics Consortium (Nesg) Target Hr8614a
Length = 108
Score = 27.7 bits (60), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 29/61 (47%), Gaps = 2/61 (3%)
Query: 109 IFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSR--GFGFVIFDSEEVVDEMLS 166
+ V G+P S S DE++ FFS Q IR T R G FV +SE+ V L
Sbjct: 10 VKVRGLPWSCSADEVQRFFSDCKIQNGAQGIRFIYTREGRPSGEAFVELESEDEVKLALK 69
Query: 167 K 167
K
Sbjct: 70 K 70
>pdb|1CDY|A Chain A, Structure Of T-Cell Surface Glycoprotein Cd4 Mutant With
Gly 47 Replaced By Ser
Length = 178
Score = 27.7 bits (60), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 79 DTHIINGKQVEIKRTIPKGSGQSKDFKTK--KIFVGGIPSSVSEDELKNFFSKYGKVLEH 136
DTH++ G+ + + P GS S ++ K GG SVS+ EL++ + VL++
Sbjct: 105 DTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQN 164
Query: 137 Q 137
Q
Sbjct: 165 Q 165
>pdb|2NXY|B Chain B, Hiv-1 Gp120 Envelope Glycoprotein(S334a) Complexed With
Cd4 And Antibody 17b
pdb|2NXZ|B Chain B, Hiv-1 Gp120 Envelope Glycoprotein (t257s, S334a, S375w)
Complexed With Cd4 And Antibody 17b
pdb|2NY0|B Chain B, Hiv-1 Gp120 Envelope Glycoprotein (M95w, W96c, T257s,
V275c, S334a, S375w, A433m) Complexed With Cd4 And
Antibody 17b
pdb|2NY1|B Chain B, Hiv-1 Gp120 Envelope Glycoprotein (I109c, T257s, S334a,
S375w, Q428c) Complexed With Cd4 And Antibody 17b
pdb|2NY2|B Chain B, Hiv-1 Gp120 Envelope Glycoprotein (T123c, T257s, S334a,
S375w, G431c) Complexed With Cd4 And Antibody 17b
pdb|2NY3|B Chain B, Hiv-1 Gp120 Envelope Glycoprotein (K231c, T257s, E267c,
S334a, S375w) Complexed With Cd4 And Antibody 17b
pdb|2NY4|B Chain B, Hiv-1 Gp120 Envelope Glycoprotein (K231c, T257s, E268c,
S334a, S375w) Complexed With Cd4 And Antibody 17b
pdb|2NY5|C Chain C, Hiv-1 Gp120 Envelope Glycoprotein (m95w, W96c, I109c,
T257s, V275c, S334a, S375w, Q428c, A433m) Complexed With
Cd4 And Antibody 17b
pdb|2NY6|B Chain B, Hiv-1 Gp120 Envelope Glycoprotein (m95w, W96c, I109c,
T123c, T257s, V275c,s334a, S375w, Q428c, G431c)
Complexed With Cd4 And Antibody 17b
pdb|3JWD|C Chain C, Structure Of Hiv-1 Gp120 With Gp41-Interactive Region:
Layered Architecture And Basis Of Conformational
Mobility
pdb|3JWD|D Chain D, Structure Of Hiv-1 Gp120 With Gp41-Interactive Region:
Layered Architecture And Basis Of Conformational
Mobility
pdb|3JWO|C Chain C, Structure Of Hiv-1 Gp120 With Gp41-Interactive Region:
Layered Architecture And Basis Of Conformational
Mobility
Length = 184
Score = 27.7 bits (60), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 79 DTHIINGKQVEIKRTIPKGSGQSKDFKTK--KIFVGGIPSSVSEDELKNFFSKYGKVLEH 136
DTH++ G+ + + P GS S ++ K GG SVS+ EL++ + VL++
Sbjct: 106 DTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQN 165
Query: 137 Q 137
Q
Sbjct: 166 Q 166
>pdb|3LQA|C Chain C, Crystal Structure Of Clade C Gp120 In Complex With Scd4
And
Length = 192
Score = 27.7 bits (60), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 79 DTHIINGKQVEIKRTIPKGSGQSKDFKTK--KIFVGGIPSSVSEDELKNFFSKYGKVLEH 136
DTH++ G+ + + P GS S ++ K GG SVS+ EL++ + VL++
Sbjct: 105 DTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQN 164
Query: 137 Q 137
Q
Sbjct: 165 Q 165
>pdb|1GC1|C Chain C, Hiv-1 Gp120 Core Complexed With Cd4 And A Neutralizing
Human Antibody
pdb|1G9M|C Chain C, Hiv-1 Hxbc2 Gp120 Envelope Glycoprotein Complexed With Cd4
And Induced Neutralizing Antibody 17b
pdb|1G9N|C Chain C, Hiv-1 Yu2 Gp120 Envelope Glycoprotein Complexed With Cd4
And Induced Neutralizing Antibody 17b
pdb|1RZJ|C Chain C, Hiv-1 Hxbc2 Gp120 Envelope Glycoprotein Complexed With Cd4
And Induced Neutralizing Antibody 17b
pdb|1RZK|C Chain C, Hiv-1 Yu2 Gp120 Envelope Glycoprotein Complexed With Cd4
And Induced Neutralizing Antibody 17b
Length = 185
Score = 27.7 bits (60), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 79 DTHIINGKQVEIKRTIPKGSGQSKDFKTK--KIFVGGIPSSVSEDELKNFFSKYGKVLEH 136
DTH++ G+ + + P GS S ++ K GG SVS+ EL++ + VL++
Sbjct: 105 DTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQN 164
Query: 137 Q 137
Q
Sbjct: 165 Q 165
>pdb|2B4C|C Chain C, Crystal Structure Of Hiv-1 Jr-fl Gp120 Core Protein
Containing The Third Variable Region (v3) Complexed With
Cd4 And The X5 Antibody
pdb|2QAD|B Chain B, Structure Of Tyrosine-Sulfated 412d Antibody Complexed
With Hiv-1 Yu2 Gp120 And Cd4
pdb|2QAD|F Chain F, Structure Of Tyrosine-Sulfated 412d Antibody Complexed
With Hiv-1 Yu2 Gp120 And Cd4
Length = 181
Score = 27.7 bits (60), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 79 DTHIINGKQVEIKRTIPKGSGQSKDFKTK--KIFVGGIPSSVSEDELKNFFSKYGKVLEH 136
DTH++ G+ + + P GS S ++ K GG SVS+ EL++ + VL++
Sbjct: 105 DTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQN 164
Query: 137 Q 137
Q
Sbjct: 165 Q 165
>pdb|3O2D|A Chain A, Crystal Structure Of Hiv-1 Primary Receptor Cd4 In Complex
With A Potent Antiviral Antibody
Length = 188
Score = 27.7 bits (60), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 79 DTHIINGKQVEIKRTIPKGSGQSKDFKTK--KIFVGGIPSSVSEDELKNFFSKYGKVLEH 136
DTH++ G+ + + P GS S ++ K GG SVS+ EL++ + VL++
Sbjct: 105 DTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQN 164
Query: 137 Q 137
Q
Sbjct: 165 Q 165
>pdb|3CD4|A Chain A, Refinement And Analysis Of The First Two Domains Of Human
Cd4
Length = 182
Score = 27.7 bits (60), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 79 DTHIINGKQVEIKRTIPKGSGQSKDFKTK--KIFVGGIPSSVSEDELKNFFSKYGKVLEH 136
DTH++ G+ + + P GS S ++ K GG SVS+ EL++ + VL++
Sbjct: 105 DTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQN 164
Query: 137 Q 137
Q
Sbjct: 165 Q 165
>pdb|2E4U|A Chain A, Crystal Structure Of The Extracellular Region Of The Group
Ii Metabotropic Glutamate Receptor Complexed With
L-glutamate
pdb|2E4U|B Chain B, Crystal Structure Of The Extracellular Region Of The Group
Ii Metabotropic Glutamate Receptor Complexed With
L-glutamate
pdb|2E4V|A Chain A, Crystal Structure Of The Extracellular Region Of The Group
Ii Metabotropic Glutamate Receptor Complexed With Dcg-Iv
pdb|2E4V|B Chain B, Crystal Structure Of The Extracellular Region Of The Group
Ii Metabotropic Glutamate Receptor Complexed With Dcg-Iv
pdb|2E4W|A Chain A, Crystal Structure Of The Extracellular Region Of The Group
Ii Metabotropic Glutamate Receptor Complexed With
1s,3s-Acpd
pdb|2E4W|B Chain B, Crystal Structure Of The Extracellular Region Of The Group
Ii Metabotropic Glutamate Receptor Complexed With
1s,3s-Acpd
pdb|2E4X|A Chain A, Crystal Structure Of The Extracellular Region Of The Group
Ii Metabotropic Glutamate Receptor Complexed With
1s,3r-Acpd
pdb|2E4X|B Chain B, Crystal Structure Of The Extracellular Region Of The Group
Ii Metabotropic Glutamate Receptor Complexed With
1s,3r-Acpd
pdb|2E4Y|A Chain A, Crystal Structure Of The Extracellular Region Of The Group
Ii Metabotropic Glutamate Receptor Complexed With
2r,4r-Apdc
pdb|2E4Y|B Chain B, Crystal Structure Of The Extracellular Region Of The Group
Ii Metabotropic Glutamate Receptor Complexed With
2r,4r-Apdc
Length = 555
Score = 27.7 bits (60), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 14/60 (23%), Positives = 29/60 (48%)
Query: 153 VIFDSEEVVDEMLSKGNMIDMAGTQVSLIGWSPVNQLLKGYLFIVYNVLLLFLFALRIYQ 212
V+F + E+++ N ++ + T V+ GW ++KG + Y + L L + + Q
Sbjct: 249 VLFMRSDDSRELIAAANRVNASFTWVASDGWGAQESIVKGSEHVAYGAITLELASHPVRQ 308
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 27.3 bits (59), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 7/69 (10%)
Query: 109 IFVGGIPSSVSEDELKNFFSK-YGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLSK 167
+FVG + V + L FF K Y +++ D +T S+G+GFV F DE+ K
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFVKF-----TDELEQK 65
Query: 168 GNMIDMAGT 176
+ + G
Sbjct: 66 RALTECQGA 74
>pdb|1WG4|A Chain A, Solution Structure Of Rrm Domain In Protein Bab31986
Length = 98
Score = 27.3 bits (59), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 11/48 (22%), Positives = 21/48 (43%), Gaps = 7/48 (14%)
Query: 20 KIFIGGLPKDTTYATFNKHFGKYGDITDSVIMKDRYTGQPRGFGFITY 67
++ + GLP ++ H + GD+ + + KD G G + Y
Sbjct: 17 RVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKD-------GMGMVEY 57
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 26.9 bits (58), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 12/64 (18%), Positives = 30/64 (46%)
Query: 107 KKIFVGGIPSSVSEDELKNFFSKYGKVLEHQIIRDHETNRSRGFGFVIFDSEEVVDEMLS 166
K +F+ + E+ L ++G + +++ +T S+G F F ++E + L+
Sbjct: 16 KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 75
Query: 167 KGNM 170
++
Sbjct: 76 AASL 79
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.320 0.140 0.412
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,403,686
Number of Sequences: 62578
Number of extensions: 329739
Number of successful extensions: 1155
Number of sequences better than 100.0: 185
Number of HSP's better than 100.0 without gapping: 135
Number of HSP's successfully gapped in prelim test: 50
Number of HSP's that attempted gapping in prelim test: 828
Number of HSP's gapped (non-prelim): 326
length of query: 247
length of database: 14,973,337
effective HSP length: 96
effective length of query: 151
effective length of database: 8,965,849
effective search space: 1353843199
effective search space used: 1353843199
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)