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= 017735
(367 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 = 132 bits (331), Expect = 4e-31, Method: Compositional matrix adjust.
Identities = 67/150 (44%), Positives = 102/150 (68%), Gaps = 5/150 (3%)
Query: 40 KHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPK 99
++FGKYG +TD IMKD TG+ RGFGF+++ PS VD+V++ HI++GK ++ KR IP+
Sbjct: 22 EYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDGKVIDPKRAIPR 81
Query: 100 GAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFD 159
+ KT KIFVGGI V EF++FF Q+G + + Q+M D T +SRGFGF+T+D
Sbjct: 82 ----DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYD 137
Query: 160 TEQAVDDLLAKGNKLELAGAQVEVKKAEPK 189
+ AV D + + ++ ++E+K+AEP+
Sbjct: 138 SADAV-DRVCQNKFIDFKDRKIEIKRAEPR 166
Score = 60.1 bits (144), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 28/82 (34%), Positives = 55/82 (67%), Gaps = 2/82 (2%)
Query: 108 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDL 167
++ K+F+GG+ ED +++F ++G V + +IM+D +T RSRGFGF++F+ +VD++
Sbjct: 2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61
Query: 168 LAKGNKLELAGAQVEVKKAEPK 189
+ + L+ G ++ K+A P+
Sbjct: 62 VKTQHILD--GKVIDPKRAIPR 81
Score = 57.4 bits (137), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 32/87 (36%), Positives = 49/87 (56%), Gaps = 3/87 (3%)
Query: 14 NRQTTTQKMTGLSLTPVTEPALAQFIKHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADP 73
+ Q T K+ + P P +F + F ++G I D+ +M D+ TGQ RGFGFVTY
Sbjct: 82 DEQDKTGKIFVGGIGPDVRPK--EFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSA 139
Query: 74 SVVDKVIEDTHI-INGKQVEIKRTIPK 99
VD+V ++ I +++EIKR P+
Sbjct: 140 DAVDRVCQNKFIDFKDRKIEIKRAEPR 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 = 105 bits (262), Expect = 4e-23, Method: Compositional matrix adjust.
Identities = 66/185 (35%), Positives = 95/185 (51%), Gaps = 18/185 (9%)
Query: 24 GLSLTPVTEPALAQFIKHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDT 83
GLS E + HF ++G +TD V+M+D T + RGFGFVTYA VD +
Sbjct: 20 GLSFETTDESLRS----HFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 84 -HIINGKQVEIKRTIPKGAVGSKD-------FKTKKIFVGGIPSSVNEDEFKDFFMQFGD 135
H ++G+ VE PK AV +D KKIFVGGI E +D+F Q+G
Sbjct: 76 PHKVDGRVVE-----PKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 130
Query: 136 VQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPNLPQ 195
++ +IM D + + RGF F+TFD +VD ++ + + G EV+KA K+
Sbjct: 131 IEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHT-VNGHNCEVRKALSKQEMASA 189
Query: 196 PSYRR 200
S +R
Sbjct: 190 SSSQR 194
Score = 55.1 bits (131), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 50/78 (64%), Gaps = 3/78 (3%)
Query: 110 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL- 168
+K+F+GG+ ++ + F Q+G + + +MRD +T RSRGFGF+T+ T + VD +
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 169 AKGNKLELAGAQVEVKKA 186
A+ +K++ G VE K+A
Sbjct: 74 ARPHKVD--GRVVEPKRA 89
>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 = 105 bits (262), Expect = 4e-23, Method: Compositional matrix adjust.
Identities = 66/185 (35%), Positives = 95/185 (51%), Gaps = 18/185 (9%)
Query: 24 GLSLTPVTEPALAQFIKHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDT 83
GLS E + HF ++G +TD V+M+D T + RGFGFVTYA VD +
Sbjct: 19 GLSFETTDESLRS----HFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 74
Query: 84 -HIINGKQVEIKRTIPKGAVGSKD-------FKTKKIFVGGIPSSVNEDEFKDFFMQFGD 135
H ++G+ VE PK AV +D KKIFVGGI E +D+F Q+G
Sbjct: 75 PHKVDGRVVE-----PKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 129
Query: 136 VQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPNLPQ 195
++ +IM D + + RGF F+TFD +VD ++ + + G EV+KA K+
Sbjct: 130 IEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHT-VNGHNCEVRKALSKQEMASA 188
Query: 196 PSYRR 200
S +R
Sbjct: 189 SSSQR 193
Score = 55.1 bits (131), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 50/78 (64%), Gaps = 3/78 (3%)
Query: 110 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL- 168
+K+F+GG+ ++ + F Q+G + + +MRD +T RSRGFGF+T+ T + VD +
Sbjct: 13 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 72
Query: 169 AKGNKLELAGAQVEVKKA 186
A+ +K++ G VE K+A
Sbjct: 73 ARPHKVD--GRVVEPKRA 88
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 105 bits (261), Expect = 5e-23, Method: Compositional matrix adjust.
Identities = 66/185 (35%), Positives = 95/185 (51%), Gaps = 18/185 (9%)
Query: 24 GLSLTPVTEPALAQFIKHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDT 83
GLS E + HF ++G +TD V+M+D T + RGFGFVTYA VD +
Sbjct: 21 GLSFETTDESLRS----HFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 76
Query: 84 -HIINGKQVEIKRTIPKGAVGSKD-------FKTKKIFVGGIPSSVNEDEFKDFFMQFGD 135
H ++G+ VE PK AV +D KKIFVGGI E +D+F Q+G
Sbjct: 77 PHKVDGRVVE-----PKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 131
Query: 136 VQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPNLPQ 195
++ +IM D + + RGF F+TFD +VD ++ + + G EV+KA K+
Sbjct: 132 IEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHT-VNGHNCEVRKALSKQEMASA 190
Query: 196 PSYRR 200
S +R
Sbjct: 191 SSSQR 195
Score = 55.1 bits (131), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 50/78 (64%), Gaps = 3/78 (3%)
Query: 110 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL- 168
+K+F+GG+ ++ + F Q+G + + +MRD +T RSRGFGF+T+ T + VD +
Sbjct: 15 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 74
Query: 169 AKGNKLELAGAQVEVKKA 186
A+ +K++ G VE K+A
Sbjct: 75 ARPHKVD--GRVVEPKRA 90
>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 = 103 bits (258), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 64/175 (36%), Positives = 92/175 (52%), Gaps = 18/175 (10%)
Query: 24 GLSLTPVTEPALAQFIKHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDT 83
GLS E + HF ++G +TD V+M+D T + RGFGFVTYA VD +
Sbjct: 13 GLSFETTDESLRS----HFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68
Query: 84 -HIINGKQVEIKRTIPKGAVGSKD-------FKTKKIFVGGIPSSVNEDEFKDFFMQFGD 135
H ++G+ VE PK AV +D KKIFVGGI E +D+F Q+G
Sbjct: 69 PHKVDGRVVE-----PKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 123
Query: 136 VQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKK 190
++ +IM D + + RGF F+TFD +VD ++ + + G EV+KA K+
Sbjct: 124 IEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHT-VNGHNCEVRKALSKQ 177
Score = 55.1 bits (131), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 50/78 (64%), Gaps = 3/78 (3%)
Query: 110 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL- 168
+K+F+GG+ ++ + F Q+G + + +MRD +T RSRGFGF+T+ T + VD +
Sbjct: 7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66
Query: 169 AKGNKLELAGAQVEVKKA 186
A+ +K++ G VE K+A
Sbjct: 67 ARPHKVD--GRVVEPKRA 82
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 103 bits (258), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 64/175 (36%), Positives = 92/175 (52%), Gaps = 18/175 (10%)
Query: 24 GLSLTPVTEPALAQFIKHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDT 83
GLS E + HF ++G +TD V+M+D T + RGFGFVTYA VD +
Sbjct: 20 GLSFETTDESLRS----HFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 84 -HIINGKQVEIKRTIPKGAVGSKD-------FKTKKIFVGGIPSSVNEDEFKDFFMQFGD 135
H ++G+ VE PK AV +D KKIFVGGI E +D+F Q+G
Sbjct: 76 PHKVDGRVVE-----PKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 130
Query: 136 VQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKK 190
++ +IM D + + RGF F+TFD +VD ++ + + G EV+KA K+
Sbjct: 131 IEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHT-VNGHNCEVRKALSKQ 184
Score = 55.1 bits (131), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 50/78 (64%), Gaps = 3/78 (3%)
Query: 110 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL- 168
+K+F+GG+ ++ + F Q+G + + +MRD +T RSRGFGF+T+ T + VD +
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 169 AKGNKLELAGAQVEVKKA 186
A+ +K++ G VE K+A
Sbjct: 74 ARPHKVD--GRVVEPKRA 89
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 103 bits (257), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 64/175 (36%), Positives = 92/175 (52%), Gaps = 18/175 (10%)
Query: 24 GLSLTPVTEPALAQFIKHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDT 83
GLS E + HF ++G +TD V+M+D T + RGFGFVTYA VD +
Sbjct: 18 GLSFETTDESLRS----HFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 73
Query: 84 -HIINGKQVEIKRTIPKGAVGSKD-------FKTKKIFVGGIPSSVNEDEFKDFFMQFGD 135
H ++G+ VE PK AV +D KKIFVGGI E +D+F Q+G
Sbjct: 74 PHKVDGRVVE-----PKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 128
Query: 136 VQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKK 190
++ +IM D + + RGF F+TFD +VD ++ + + G EV+KA K+
Sbjct: 129 IEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHT-VNGHNCEVRKALSKQ 182
Score = 55.1 bits (131), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 50/78 (64%), Gaps = 3/78 (3%)
Query: 110 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL- 168
+K+F+GG+ ++ + F Q+G + + +MRD +T RSRGFGF+T+ T + VD +
Sbjct: 12 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 71
Query: 169 AKGNKLELAGAQVEVKKA 186
A+ +K++ G VE K+A
Sbjct: 72 ARPHKVD--GRVVEPKRA 87
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 83.2 bits (204), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 44/136 (32%), Positives = 75/136 (55%), Gaps = 8/136 (5%)
Query: 37 QFIKHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRT 96
+F FG G+I +++D+ TGQ G+GFV Y+DP+ DK I + +NG +++ K
Sbjct: 20 EFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI---NTLNGLKLQTKTI 76
Query: 97 -IPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGF 155
+ S + ++V G+P ++++ E + F Q+G + +I+ D +T SRG GF
Sbjct: 77 KVSYARPSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGF 136
Query: 156 ITFD----TEQAVDDL 167
I FD E+A+ L
Sbjct: 137 IRFDKRIEAEEAIKGL 152
Score = 52.4 bits (124), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 46/88 (52%), Gaps = 1/88 (1%)
Query: 106 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVD 165
D KT + V +P ++ +DEFK F GD++ +++RD T +S G+GF+ + D
Sbjct: 2 DSKTN-LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDAD 60
Query: 166 DLLAKGNKLELAGAQVEVKKAEPKKPNL 193
+ N L+L ++V A P ++
Sbjct: 61 KAINTLNGLKLQTKTIKVSYARPSSASI 88
>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 = 80.1 bits (196), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 44/136 (32%), Positives = 71/136 (52%), Gaps = 8/136 (5%)
Query: 37 QFIKHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRT 96
+F FG GEI +++D+ TGQ G+GFV Y DP +K I + +NG +++ K
Sbjct: 18 EFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI---NTLNGLRLQTKTI 74
Query: 97 -IPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGF 155
+ S + ++V G+P ++ + E + F Q+G + +I+ D T SRG GF
Sbjct: 75 KVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGF 134
Query: 156 ITFD----TEQAVDDL 167
I FD E+A+ L
Sbjct: 135 IRFDKRIEAEEAIKGL 150
Score = 48.5 bits (114), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 47/86 (54%), Gaps = 8/86 (9%)
Query: 112 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDL 167
+ V +P ++ ++EF+ F G+++ +++RD T +S G+GF+ + D E+A++ L
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 168 LAKGNKLELAGAQVEVKKAEPKKPNL 193
N L L ++V A P ++
Sbjct: 65 ----NGLRLQTKTIKVSYARPSSASI 86
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 73.2 bits (178), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 39/87 (44%), Positives = 55/87 (63%), Gaps = 1/87 (1%)
Query: 111 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 170
KIFVGGIP + E E +++F +FG V E ++ D R RGFGFITF+ EQ+VD +
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
Query: 171 GNKLELAGAQVEVKKAEPKKPNLPQPS 197
+ ++ G +VEVK+AEP+ PS
Sbjct: 72 -HFHDIMGKKVEVKRAEPRDSKSSGPS 97
Score = 52.8 bits (125), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 26/66 (39%), Positives = 43/66 (65%), Gaps = 1/66 (1%)
Query: 40 KHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIP 98
++F K+G +T+ V++ D + +PRGFGF+T+ D VD+ + H I GK+VE+KR P
Sbjct: 29 EYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVKRAEP 88
Query: 99 KGAVGS 104
+ + S
Sbjct: 89 RDSKSS 94
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 67.4 bits (163), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 36/95 (37%), Positives = 61/95 (64%), Gaps = 5/95 (5%)
Query: 97 IPKGA-VGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGF 155
+P+G+ +GS K +F+GG+ ++ +++F QFG+V+E +MRD T RSRGFGF
Sbjct: 15 VPRGSHMGSSGCK---MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGF 71
Query: 156 ITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKK 190
+TF + VD +LA+ ++ EL ++ K A P++
Sbjct: 72 VTFMDQAGVDKVLAQ-SRHELDSKTIDPKVAFPRR 105
Score = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 43/63 (68%), Gaps = 1/63 (1%)
Query: 40 KHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVI-EDTHIINGKQVEIKRTIP 98
++FG++GE+ + ++M+D T + RGFGFVT+ D + VDKV+ + H ++ K ++ K P
Sbjct: 44 EYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVAFP 103
Query: 99 KGA 101
+ A
Sbjct: 104 RRA 106
>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 = 64.7 bits (156), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 32/132 (24%), Positives = 66/132 (50%), Gaps = 4/132 (3%)
Query: 42 FGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRT-IPKG 100
F GE+ + +++D+ G G+GFV Y ++ I + +NG +++ K +
Sbjct: 23 FSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI---NTLNGLRLQSKTIKVSYA 79
Query: 101 AVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDT 160
S+ K +++ G+P ++ + + +D F +FG + +++ D +T SRG FI FD
Sbjct: 80 RPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDK 139
Query: 161 EQAVDDLLAKGN 172
++ + N
Sbjct: 140 RSEAEEAITSFN 151
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 8/81 (9%)
Query: 112 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDL 167
+ V +P ++ +DE + F G+V+ +++RD S G+GF+ + D E+A++ L
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 168 LAKGNKLELAGAQVEVKKAEP 188
N L L ++V A P
Sbjct: 65 ----NGLRLQSKTIKVSYARP 81
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 64.7 bits (156), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 32/132 (24%), Positives = 66/132 (50%), Gaps = 4/132 (3%)
Query: 42 FGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRT-IPKG 100
F GE+ + +++D+ G G+GFV Y ++ I + +NG +++ K +
Sbjct: 23 FSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI---NTLNGLRLQSKTIKVSYA 79
Query: 101 AVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDT 160
S+ K +++ G+P ++ + + +D F +FG + +++ D +T SRG FI FD
Sbjct: 80 RPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDK 139
Query: 161 EQAVDDLLAKGN 172
++ + N
Sbjct: 140 RSEAEEAITSFN 151
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 8/81 (9%)
Query: 112 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDL 167
+ V +P ++ +DE + F G+V+ +++RD S G+GF+ + D E+A++ L
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 168 LAKGNKLELAGAQVEVKKAEP 188
N L L ++V A P
Sbjct: 65 ----NGLRLQSKTIKVSYARP 81
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 64.3 bits (155), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 39/141 (27%), Positives = 68/141 (48%), Gaps = 5/141 (3%)
Query: 42 FGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRT-IPKG 100
F G I IM+D KTG G+ FV + + I+ ++NG V KR +
Sbjct: 24 FRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK---VLNGITVRNKRLKVSYA 80
Query: 101 AVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDT 160
G + K ++V +P ++ +D+ F ++G + + I+RD T R RG F+ ++
Sbjct: 81 RPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNK 140
Query: 161 -EQAVDDLLAKGNKLELAGAQ 180
E+A + + A N + G+Q
Sbjct: 141 REEAQEAISALNNVIPEGGSQ 161
>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 = 63.9 bits (154), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 42/166 (25%), Positives = 80/166 (48%), Gaps = 14/166 (8%)
Query: 40 KHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKR-- 95
+ F +G I + D T + +GF FV Y P +E ++ ++ G+ +++ R
Sbjct: 32 QAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPS 91
Query: 96 -------TIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTS 148
I + A ++ F +I+V + +++D+ K F FG ++ + RD +T
Sbjct: 92 NIGQAQPIIDQLAEEARAFN--RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTG 149
Query: 149 RSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA-EPKKPNL 193
+ +G+GFI ++ Q+ D ++ N +L G + V KA P P L
Sbjct: 150 KHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLL 195
Score = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 41/86 (47%), Gaps = 2/86 (2%)
Query: 111 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 170
+++VG I + ED + F FG ++ + D T + +GF F+ ++ +A L +
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 171 GNKLELAGAQVEVKKAEPKKPNLPQP 196
N + L G ++V + P QP
Sbjct: 75 MNSVMLGGRNIKVGR--PSNIGQAQP 98
>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 = 63.9 bits (154), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 42/166 (25%), Positives = 80/166 (48%), Gaps = 14/166 (8%)
Query: 40 KHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKR-- 95
+ F +G I + D T + +GF FV Y P +E ++ ++ G+ +++ R
Sbjct: 47 QAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPS 106
Query: 96 -------TIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTS 148
I + A ++ F +I+V + +++D+ K F FG ++ + RD +T
Sbjct: 107 NIGQAQPIIDQLAEEARAFN--RIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTG 164
Query: 149 RSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA-EPKKPNL 193
+ +G+GFI ++ Q+ D ++ N +L G + V KA P P L
Sbjct: 165 KHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLL 210
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 41/86 (47%), Gaps = 2/86 (2%)
Query: 111 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 170
+++VG I + ED + F FG ++ + D T + +GF F+ ++ +A L +
Sbjct: 30 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 89
Query: 171 GNKLELAGAQVEVKKAEPKKPNLPQP 196
N + L G ++V + P QP
Sbjct: 90 MNSVMLGGRNIKVGR--PSNIGQAQP 113
>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 = 63.2 bits (152), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 42/166 (25%), Positives = 78/166 (46%), Gaps = 14/166 (8%)
Query: 40 KHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEIKR-- 95
+ F +G I D T + +GF FV Y P +E ++ + G+ +++ R
Sbjct: 31 QAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQXNSVXLGGRNIKVGRPS 90
Query: 96 -------TIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTS 148
I + A ++ F +I+V + +++D+ K F FG ++ + RD +T
Sbjct: 91 NIGQAQPIIDQLAEEARAFN--RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTG 148
Query: 149 RSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA-EPKKPNL 193
+ +G+GFI ++ Q+ D ++ N +L G + V KA P P L
Sbjct: 149 KHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVGKAVTPPXPLL 194
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 37/75 (49%)
Query: 111 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 170
+++VG I + ED + F FG ++ D T + +GF F+ ++ +A L +
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 171 GNKLELAGAQVEVKK 185
N + L G ++V +
Sbjct: 74 XNSVXLGGRNIKVGR 88
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 62.8 bits (151), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 31/76 (40%), Positives = 50/76 (65%), Gaps = 1/76 (1%)
Query: 111 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 170
K+F+GG+ ++ +++F QFG+V+E +MRD T RSRGFGF+TF + VD +LA+
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 171 GNKLELAGAQVEVKKA 186
++ EL ++ K A
Sbjct: 62 -SRHELDSKTIDPKVA 76
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/56 (39%), Positives = 40/56 (71%), Gaps = 1/56 (1%)
Query: 40 KHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDT-HIINGKQVEIK 94
++FG++GE+ + ++M+D T + RGFGFVT+ D + VDKV+ + H ++ K ++ K
Sbjct: 19 EYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPK 74
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 62.4 bits (150), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 27/61 (44%), Positives = 40/61 (65%), Gaps = 1/61 (1%)
Query: 41 HFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIED-THIINGKQVEIKRTIPK 99
+F +YGE+ D VIMKD+ T Q RGFGFV + DP+ V V+ H ++G+ ++ K P+
Sbjct: 36 YFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRNIDPKPCTPR 95
Query: 100 G 100
G
Sbjct: 96 G 96
Score = 58.5 bits (140), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 28/79 (35%), Positives = 46/79 (58%), Gaps = 1/79 (1%)
Query: 111 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 170
K+FVGG+ S ++ + +F Q+G+V + IM+D +T++SRGFGF+ F V +LA
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 171 GNKLELAGAQVEVKKAEPK 189
L G ++ K P+
Sbjct: 78 -RPHTLDGRNIDPKPCTPR 95
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 60.8 bits (146), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 30/87 (34%), Positives = 45/87 (51%)
Query: 111 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 170
K+FVGG+ NE + F ++G + E +++D T RSRGFGF+TF+ D +
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 171 GNKLELAGAQVEVKKAEPKKPNLPQPS 197
N + G Q+ V +A N PS
Sbjct: 74 MNGKSVDGRQIRVDQAGKSSDNRSGPS 100
Score = 48.5 bits (114), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 28/69 (40%), Positives = 42/69 (60%), Gaps = 7/69 (10%)
Query: 24 GLSLTPVTEPALAQFIKHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDT 83
GLS E +L Q F KYG+I++ V++KDR+T + RGFGFVT+ + +D +
Sbjct: 19 GLSF-DTNEQSLEQV---FSKYGQISEVVVVKDRETQRSRGFGFVTFEN---IDDAKDAM 71
Query: 84 HIINGKQVE 92
+NGK V+
Sbjct: 72 MAMNGKSVD 80
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 60.1 bits (144), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 29/88 (32%), Positives = 52/88 (59%), Gaps = 1/88 (1%)
Query: 110 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 169
+K+F+GG+ E+ ++++ Q+G + + +MRD ++ RSRGFGF+TF + VD +A
Sbjct: 28 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA 87
Query: 170 KGNKLELAGAQVEVKKAEPKKPNLPQPS 197
+ G VE K+A ++ + PS
Sbjct: 88 -ARPHSIDGRVVEPKRAVAREESGSGPS 114
Score = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 31/82 (37%), Positives = 48/82 (58%), Gaps = 5/82 (6%)
Query: 24 GLSLTPVTEPALAQFIKHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDT 83
GLS TE +L + + +GK +TD V+M+D + + RGFGFVT++ + VD +
Sbjct: 34 GLSFE-TTEESLRNYYEQWGK---LTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAAR 89
Query: 84 -HIINGKQVEIKRTIPKGAVGS 104
H I+G+ VE KR + + GS
Sbjct: 90 PHSIDGRVVEPKRAVAREESGS 111
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 57.8 bits (138), Expect = 1e-08, Method: Composition-based stats.
Identities = 30/75 (40%), Positives = 47/75 (62%), Gaps = 1/75 (1%)
Query: 112 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 171
IFVGG+ + ++ K +F QFG V + +M D +T+R RGFGF+TF++E V+ + +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEK-VCEI 60
Query: 172 NKLELAGAQVEVKKA 186
+ E+ VE KKA
Sbjct: 61 HFHEINNKMVECKKA 75
Score = 51.6 bits (122), Expect = 7e-07, Method: Composition-based stats.
Identities = 30/74 (40%), Positives = 45/74 (60%), Gaps = 7/74 (9%)
Query: 24 GLSLTPVTEPALAQFIKH-FGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIE- 81
GLS+ E +KH F ++G++ D+++M D+ T + RGFGFVT+ +V+KV E
Sbjct: 6 GLSVNTTVED-----VKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60
Query: 82 DTHIINGKQVEIKR 95
H IN K VE K+
Sbjct: 61 HFHEINNKMVECKK 74
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 56.2 bits (134), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 42/73 (57%)
Query: 111 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 170
+++VG + ++ ED + F FG ++ Q+M D T RS+G+GFITF + L +
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 171 GNKLELAGAQVEV 183
N ELAG ++V
Sbjct: 88 LNGFELAGRPMKV 100
Score = 37.0 bits (84), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 3/52 (5%)
Query: 30 VTEPALAQFIKHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIE 81
+TE L + FG+ I +M D +TG+ +G+GF+T++D K +E
Sbjct: 38 ITEDMLRGIFEPFGRIESIQ---LMMDSETGRSKGYGFITFSDSECAKKALE 86
>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 = 55.5 bits (132), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 41/168 (24%), Positives = 81/168 (48%), Gaps = 19/168 (11%)
Query: 30 VTEPALAQFIKHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDTH--IIN 87
VTE A + F G I + +D T + G+ +V + P+ ++ ++ + +I
Sbjct: 27 VTE---AMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIK 83
Query: 88 GKQVEIKRT-----IPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIM 142
GK V I + + K VG+ IF+ + S++ D F FG++ +++
Sbjct: 84 GKPVRIMWSQRDPSLRKSGVGN-------IFIKNLDKSIDNKALYDTFSAFGNILSCKVV 136
Query: 143 RDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKK 190
D + S+ G+GF+ F+T++A + + K N + L +V V + + +K
Sbjct: 137 CDENGSK--GYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK 182
>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 = 55.1 bits (131), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 41/168 (24%), Positives = 81/168 (48%), Gaps = 19/168 (11%)
Query: 30 VTEPALAQFIKHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDTH--IIN 87
VTE A + F G I + +D T + G+ +V + P+ ++ ++ + +I
Sbjct: 22 VTE---AMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIK 78
Query: 88 GKQVEIKRT-----IPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIM 142
GK V I + + K VG+ IF+ + S++ D F FG++ +++
Sbjct: 79 GKPVRIMWSQRDPSLRKSGVGN-------IFIKNLDKSIDNKALYDTFSAFGNILSCKVV 131
Query: 143 RDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKK 190
D + S+ G+GF+ F+T++A + + K N + L +V V + + +K
Sbjct: 132 CDENGSK--GYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK 177
>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 = 54.7 bits (130), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 36/165 (21%), Positives = 78/165 (47%), Gaps = 15/165 (9%)
Query: 30 VTEPALAQFIKHFGKYGEITDS--VIMKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHII 86
+TE A+ F + G +T + + + Q + F F+ + + + D I
Sbjct: 18 ITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIF 77
Query: 87 NGKQVEIKRTIPKGAVGSKDFK----TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIM 142
G+ ++I+R D++ K+F+GG+P+ +N+D+ K+ FG ++ ++
Sbjct: 78 QGQSLKIRR--------PHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLV 129
Query: 143 RDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE 187
+D +T S+G+ F + D +A N ++L ++ V++A
Sbjct: 130 KDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS 174
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 37/167 (22%), Positives = 79/167 (47%), Gaps = 19/167 (11%)
Query: 30 VTEPALAQFIKHFGKYGEITDS----VIMKDRKTGQPRGFGFVTYADPSVVDKVIE-DTH 84
+TE A+ F + G +T + V+ + Q + F F+ + + + D
Sbjct: 16 ITEEAMMDFFNAQMRLGGLTQAPGNPVLAV--QINQDKNFAFLEFRSVDETTQAMAFDGI 73
Query: 85 IINGKQVEIKRTIPKGAVGSKDFK----TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQ 140
I G+ ++I+R D++ K+F+GG+P+ +N+D+ K+ FG ++
Sbjct: 74 IFQGQSLKIRR--------PHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFN 125
Query: 141 IMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE 187
+++D +T S+G+ F + D +A N ++L ++ V++A
Sbjct: 126 LVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS 172
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 34/104 (32%), Positives = 53/104 (50%), Gaps = 10/104 (9%)
Query: 100 GAVGSKDFKTKK--IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFIT 157
G+ GS T K ++VGG+ V++ F+ FGD+ + QI D+ T + RGF F+
Sbjct: 1 GSSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 60
Query: 158 F----DTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPNLPQPS 197
F D A+D++ N+ EL G + V A+P + PS
Sbjct: 61 FELAEDAAAAIDNM----NESELFGRTIRVNLAKPMRIKESGPS 100
>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
pdb|3S7R|B Chain B, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
Length = 87
Score = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 30/76 (39%), Positives = 46/76 (60%), Gaps = 1/76 (1%)
Query: 111 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 170
K FVGG+ ++ + KD+F +FG+V + I D +T RSRGFGFI F +V+ +L +
Sbjct: 13 KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQ 72
Query: 171 GNKLELAGAQVEVKKA 186
+ L G ++ KKA
Sbjct: 73 -KEHRLDGRVIDPKKA 87
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 37/57 (64%), Gaps = 1/57 (1%)
Query: 41 HFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDT-HIINGKQVEIKRT 96
+F K+GE+ D I D TG+ RGFGF+ + D + V+KV++ H ++G+ ++ K+
Sbjct: 31 YFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDGRVIDPKKA 87
>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 = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 48/76 (63%), Gaps = 1/76 (1%)
Query: 109 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL 168
KKIFVGG+ E++ +++F FG+V+ ++ D+ T++ RGF FITF E+ V ++
Sbjct: 1 VKKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 60
Query: 169 AKG-NKLELAGAQVEV 183
K + + L+ +++V
Sbjct: 61 EKKYHNVGLSKCEIKV 76
Score = 37.0 bits (84), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 32/56 (57%), Gaps = 1/56 (1%)
Query: 40 KHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDT-HIINGKQVEIK 94
++FG +GE+ + D KT + RGF F+T+ + V K++E H + + EIK
Sbjct: 20 EYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIK 75
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 35/61 (57%)
Query: 105 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAV 164
KD KIFVGG+P + + +F FGD++E ++ D T +SRG+GF+T A
Sbjct: 13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAA 72
Query: 165 D 165
+
Sbjct: 73 E 73
Score = 51.2 bits (121), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 41/59 (69%), Gaps = 1/59 (1%)
Query: 36 AQFIKHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDTH-IINGKQVEI 93
A K+F +G+I ++V++ DR+TG+ RG+GFVT AD + ++ +D + II+G++ +
Sbjct: 32 ASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANV 90
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 52.8 bits (125), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 46/88 (52%), Gaps = 1/88 (1%)
Query: 106 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVD 165
D KT + V +P ++ +DEFK F GD++ +++RD T +S G+GF+ + D
Sbjct: 2 DSKTN-LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDAD 60
Query: 166 DLLAKGNKLELAGAQVEVKKAEPKKPNL 193
+ N L+L ++V A P ++
Sbjct: 61 KAINTLNGLKLQTKTIKVSYARPSSASI 88
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 36/58 (62%), Gaps = 3/58 (5%)
Query: 37 QFIKHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIK 94
+F FG G+I +++D+ TGQ G+GFV Y+DP+ DK I + +NG +++ K
Sbjct: 20 EFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI---NTLNGLKLQTK 74
>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 = 52.8 bits (125), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 45/77 (58%)
Query: 111 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 170
K+F+GG+P+ +N+D+ K+ FG ++ +++D +T S+G+ F + D +A
Sbjct: 116 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 175
Query: 171 GNKLELAGAQVEVKKAE 187
N ++L ++ V++A
Sbjct: 176 LNGMQLGDKKLLVQRAS 192
Score = 34.7 bits (78), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 35/63 (55%), Gaps = 4/63 (6%)
Query: 45 YGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQV-EIKRTIPKGAVG 103
+G + ++KD TG +G+ F Y D +V D+ I +NG Q+ + K + + +VG
Sbjct: 138 FGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG---LNGMQLGDKKLLVQRASVG 194
Query: 104 SKD 106
+K+
Sbjct: 195 AKN 197
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 52.4 bits (124), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 27/89 (30%), Positives = 43/89 (48%)
Query: 109 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL 168
+ ++VG + ++ ED + F FG + +M+D T RS+G+GFITF + L
Sbjct: 5 SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
Query: 169 AKGNKLELAGAQVEVKKAEPKKPNLPQPS 197
+ N ELAG + V + PS
Sbjct: 65 EQLNGFELAGRPMRVGHVTERLDGGSGPS 93
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 31/52 (59%), Gaps = 3/52 (5%)
Query: 30 VTEPALAQFIKHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIE 81
+TE L + FGK I + V+MKD TG+ +G+GF+T++D + +E
Sbjct: 17 ITEDMLRGIFEPFGK---IDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 52.4 bits (124), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 46/81 (56%), Gaps = 1/81 (1%)
Query: 110 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 169
+ I+VG + S ++ K+ F QFG V +++ D T + +GFGF+ E++V + +A
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIA 60
Query: 170 KGNKLELAGAQVEVKKAEPKK 190
K + + G + V +A PKK
Sbjct: 61 KLDNTDFMGRTIRVTEANPKK 81
Score = 36.2 bits (82), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 36/62 (58%), Gaps = 1/62 (1%)
Query: 42 FGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEIKRTIPKG 100
F ++G++ + ++ DR+T +P+GFGFV + SV + + + D G+ + + PK
Sbjct: 22 FSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAKLDNTDFMGRTIRVTEANPKK 81
Query: 101 AV 102
++
Sbjct: 82 SL 83
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 52.0 bits (123), Expect = 5e-07, Method: Composition-based stats.
Identities = 21/76 (27%), Positives = 45/76 (59%)
Query: 111 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 170
K+F+GG+P+ +N+D+ K+ FG ++ +++D +T S+G+ F + D +A
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 171 GNKLELAGAQVEVKKA 186
N ++L ++ V++A
Sbjct: 63 LNGMQLGDKKLLVQRA 78
Score = 33.9 bits (76), Expect = 0.15, Method: Composition-based stats.
Identities = 19/63 (30%), Positives = 35/63 (55%), Gaps = 4/63 (6%)
Query: 45 YGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKR-TIPKGAVG 103
+G + ++KD TG +G+ F Y D +V D+ I +NG Q+ K+ + + +VG
Sbjct: 25 FGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG---LNGMQLGDKKLLVQRASVG 81
Query: 104 SKD 106
+K+
Sbjct: 82 AKN 84
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 45/86 (52%)
Query: 112 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 171
++VGG+ V+E + F+Q G V + +D T + +G+GF+ F +E+ D +
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 172 NKLELAGAQVEVKKAEPKKPNLPQPS 197
+ ++L G + V KA NL PS
Sbjct: 78 DMIKLYGKPIRVNKASAHNKNLSGPS 103
Score = 34.7 bits (78), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 5/69 (7%)
Query: 30 VTEPALAQFIKHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIIN-- 87
V+EP L + F + G + ++ + KDR TGQ +G+GFV + D I+ +I
Sbjct: 27 VSEPLLWEL---FLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLY 83
Query: 88 GKQVEIKRT 96
GK + + +
Sbjct: 84 GKPIRVNKA 92
>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 = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 46/75 (61%), Gaps = 1/75 (1%)
Query: 112 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 171
+F+GG+ + + KD+F +FG+V + + D T RSRGFGF+ F ++VD ++ +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ- 60
Query: 172 NKLELAGAQVEVKKA 186
+ +L G ++ K+A
Sbjct: 61 KEHKLNGKVIDPKRA 75
Score = 49.7 bits (117), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 24/57 (42%), Positives = 36/57 (63%), Gaps = 1/57 (1%)
Query: 41 HFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDT-HIINGKQVEIKRT 96
+F K+GE+ D + D TG+ RGFGFV + + VDKV++ H +NGK ++ KR
Sbjct: 19 YFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKRA 75
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 31/90 (34%), Positives = 47/90 (52%), Gaps = 3/90 (3%)
Query: 111 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 170
K+F+GG+ NE K F + G + E +++D TS+SRGF FITF+ +
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKD 67
Query: 171 GNKLELAGAQVEVKKAEPKKPNLPQPSYRR 200
N L G ++V++A KKP+ RR
Sbjct: 68 MNGKSLHGKAIKVEQA--KKPSFQSGGRRR 95
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 34/53 (64%), Gaps = 4/53 (7%)
Query: 42 FGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIK 94
FGK+G I++ +++KDR T + RGF F+T+ +P+ +D +NGK + K
Sbjct: 28 FGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKD---MNGKSLHGK 76
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 38/59 (64%)
Query: 112 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 170
IFVGG+ E++ +++F FG+V+ ++ D+ T++ RGF FITF E+ V ++ K
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Score = 37.0 bits (84), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 32/56 (57%), Gaps = 1/56 (1%)
Query: 40 KHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDT-HIINGKQVEIK 94
++FG +GE+ + D KT + RGF F+T+ + V K++E H + + EIK
Sbjct: 18 EYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIK 73
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 30/89 (33%), Positives = 43/89 (48%), Gaps = 7/89 (7%)
Query: 109 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL 168
+ +FVG + EDE ++FF Q+GDV + I + R F F+TF +Q L
Sbjct: 5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFADDQIAQSLC 59
Query: 169 AKGNKLELAGAQVEVKKAEPKKPNLPQPS 197
G L + G V + AEPK + PS
Sbjct: 60 --GEDLIIKGISVHISNAEPKHNSNSGPS 86
Score = 36.6 bits (83), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 33/70 (47%), Gaps = 8/70 (11%)
Query: 30 VTEPALAQFIKHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGK 89
+TE L +F F +YG++ D I K R F FVT+AD + + + II G
Sbjct: 17 MTEDELREF---FSQYGDVMDVFIPKPF-----RAFAFVTFADDQIAQSLCGEDLIIKGI 68
Query: 90 QVEIKRTIPK 99
V I PK
Sbjct: 69 SVHISNAEPK 78
>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 = 49.3 bits (116), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 48/87 (55%), Gaps = 1/87 (1%)
Query: 112 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 171
+FVG + + ++ K F FG + + ++++D +T +S+G+GF++F + ++ + +
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 172 NKLELAGAQVEVKKAEPKKPNLPQPSY 198
L G Q+ A +KP P+ +Y
Sbjct: 78 GGQWLGGRQIRTNWAT-RKPPAPKSTY 103
Score = 36.2 bits (82), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 31/52 (59%), Gaps = 2/52 (3%)
Query: 42 FGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDT--HIINGKQV 91
F +G I+D+ ++KD TG+ +G+GFV++ + + I+ + G+Q+
Sbjct: 36 FAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 87
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 40/146 (27%), Positives = 67/146 (45%), Gaps = 14/146 (9%)
Query: 29 PVTEPALAQFIKHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIING 88
+TE L Q+ F G I + IM D K + + FV Y + ++ +NG
Sbjct: 11 AITEDILKQY---FQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQ---TLNG 63
Query: 89 KQVE---IKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDH 145
KQ+E +K + S T +FVG + +V+++ ++ F F +M D
Sbjct: 64 KQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDM 123
Query: 146 STSRSRGFGFITF----DTEQAVDDL 167
T SRG+GF++F D + A+D +
Sbjct: 124 QTGSSRGYGFVSFTSQDDAQNAMDSM 149
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 41/85 (48%)
Query: 106 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVD 165
D + +FVG IP E++ KD F + G V +++ D T + +G+GF + ++
Sbjct: 5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETAL 64
Query: 166 DLLAKGNKLELAGAQVEVKKAEPKK 190
+ N E +G + V A +K
Sbjct: 65 SAMRNLNGREFSGRALRVDNAASEK 89
Score = 33.1 bits (74), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 36/82 (43%), Gaps = 3/82 (3%)
Query: 37 QFIKHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRT 96
Q F + G + ++ DR+TG+P+G+GF Y D + + +NG++ +
Sbjct: 24 QLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN---LNGREFSGRAL 80
Query: 97 IPKGAVGSKDFKTKKIFVGGIP 118
A K+ + K G P
Sbjct: 81 RVDNAASEKNKEELKSLGTGAP 102
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 30/85 (35%), Positives = 49/85 (57%), Gaps = 6/85 (7%)
Query: 100 GAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF- 158
G +GS +FVGGI ++E E + FF ++G V+E +I+ D T S+G+GF++F
Sbjct: 1 GPLGSGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFY 59
Query: 159 ---DTEQAVDDLLA-KGNKLELAGA 179
D ++ V+ + G KL+L A
Sbjct: 60 NDVDVQKIVESQINFHGKKLKLGPA 84
Score = 36.2 bits (82), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 35/58 (60%), Gaps = 1/58 (1%)
Query: 42 FGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPK 99
F +YG + + I+ DR TG +G+GFV++ + V K++E +GK++++ I K
Sbjct: 31 FARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQINFHGKKLKLGPAIRK 87
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 48.5 bits (114), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 32/124 (25%), Positives = 61/124 (49%), Gaps = 7/124 (5%)
Query: 42 FGKYGEITDSVIMKDRKTGQP--RGFGFVT-YADPSVVD--KVIEDTHIINGKQVEIKRT 96
F +YG + + +++DR P +G FVT Y + ++ + + ++ G I+
Sbjct: 36 FEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMK 95
Query: 97 IPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFI 156
P + + + +K+F+G I E++ + F FG ++E +I+R SRG F+
Sbjct: 96 -PADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAFV 153
Query: 157 TFDT 160
TF T
Sbjct: 154 TFTT 157
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 30/92 (32%), Positives = 52/92 (56%), Gaps = 5/92 (5%)
Query: 106 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTS--RSRGFGFITFDTEQ- 162
D K+FVG +P + +E + ++ F Q+G V E ++RD S + +S+G F+TF T +
Sbjct: 12 DLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKA 71
Query: 163 AVDDLLAKGNKLELAGAQ--VEVKKAEPKKPN 192
A++ A N L G +++K A+ +K N
Sbjct: 72 ALEAQNALHNMKVLPGMHHPIQMKPADSEKNN 103
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 48.5 bits (114), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 44/86 (51%)
Query: 112 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 171
+FVG + + ++ K F FG + + ++++D +T +S+G+GF++F + ++ +
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 172 NKLELAGAQVEVKKAEPKKPNLPQPS 197
L G Q+ A K P PS
Sbjct: 78 GGQWLGGRQIRTNWATRKPPAPSGPS 103
Score = 34.7 bits (78), Expect = 0.098, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 23/29 (79%)
Query: 42 FGKYGEITDSVIMKDRKTGQPRGFGFVTY 70
F +G+I+D+ ++KD TG+ +G+GFV++
Sbjct: 36 FAPFGKISDARVVKDMATGKSKGYGFVSF 64
>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 = 48.5 bits (114), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 8/86 (9%)
Query: 107 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQ 162
F+ + V +P + +DE + F G+V+ +++RD S G+GF+ + D E+
Sbjct: 17 FQGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 76
Query: 163 AVDDLLAKGNKLELAGAQVEVKKAEP 188
A++ L N L L ++V A P
Sbjct: 77 AINTL----NGLRLQSKTIKVSYARP 98
Score = 31.6 bits (70), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 14/53 (26%), Positives = 28/53 (52%), Gaps = 3/53 (5%)
Query: 42 FGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIK 94
F GE+ + +++D+ G G+GFV Y ++ I + +NG +++ K
Sbjct: 40 FSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI---NTLNGLRLQSK 89
>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 = 48.5 bits (114), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 8/81 (9%)
Query: 112 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDL 167
+ V +P ++ +DE + F G+V+ +++RD S G+GF+ + D E+A++ L
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 168 LAKGNKLELAGAQVEVKKAEP 188
N L L ++V A P
Sbjct: 67 ----NGLRLQSKTIKVSYARP 83
Score = 31.6 bits (70), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 14/53 (26%), Positives = 28/53 (52%), Gaps = 3/53 (5%)
Query: 42 FGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIK 94
F GE+ + +++D+ G G+GFV Y ++ I + +NG +++ K
Sbjct: 25 FSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI---NTLNGLRLQSK 74
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 48.5 bits (114), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 32/124 (25%), Positives = 61/124 (49%), Gaps = 7/124 (5%)
Query: 42 FGKYGEITDSVIMKDRKTGQP--RGFGFVT-YADPSVVD--KVIEDTHIINGKQVEIKRT 96
F +YG + + +++DR P +G FVT Y + ++ + + ++ G I+
Sbjct: 24 FEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMK 83
Query: 97 IPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFI 156
P + + + +K+F+G I E++ + F FG ++E +I+R SRG F+
Sbjct: 84 -PADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAFV 141
Query: 157 TFDT 160
TF T
Sbjct: 142 TFTT 145
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 29/87 (33%), Positives = 51/87 (58%), Gaps = 5/87 (5%)
Query: 111 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTS--RSRGFGFITFDTEQ-AVDDL 167
K+FVG +P + +E + ++ F Q+G V E ++RD S + +S+G F+TF T + A++
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 168 LAKGNKLELAGAQ--VEVKKAEPKKPN 192
A N L G +++K A+ +K N
Sbjct: 65 NALHNMKVLPGMHHPIQMKPADSEKNN 91
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 48.1 bits (113), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 37/65 (56%)
Query: 100 GAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFD 159
G+ G KD K+F+G IP +++E + K F +FG + E +++D T +G F+T+
Sbjct: 4 GSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYC 63
Query: 160 TEQAV 164
++
Sbjct: 64 ERESA 68
Score = 32.3 bits (72), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 21/31 (67%)
Query: 42 FGKYGEITDSVIMKDRKTGQPRGFGFVTYAD 72
F ++G+I + ++KDR TG +G F+TY +
Sbjct: 34 FEEFGKIYELTVLKDRFTGMHKGCAFLTYCE 64
>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
pdb|3NNA|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 48.1 bits (113), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 32/124 (25%), Positives = 61/124 (49%), Gaps = 7/124 (5%)
Query: 42 FGKYGEITDSVIMKDRKTGQP--RGFGFVT-YADPSVVD--KVIEDTHIINGKQVEIKRT 96
F +YG + + +++DR P +G FVT Y + ++ + + ++ G I+
Sbjct: 24 FEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNXKVLPGXHHPIQXK 83
Query: 97 IPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFI 156
P + + + +K+F+G I E++ + F FG ++E +I+R SRG F+
Sbjct: 84 -PADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQIEECRILRG-PDGLSRGCAFV 141
Query: 157 TFDT 160
TF T
Sbjct: 142 TFTT 145
Score = 45.1 bits (105), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 35/56 (62%), Gaps = 2/56 (3%)
Query: 111 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTS--RSRGFGFITFDTEQAV 164
K FVG +P + +E + ++ F Q+G V E ++RD S + +S+G F+TF T +A
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 43/77 (55%)
Query: 110 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 169
+ + V IP++V+E + + F ++G ++ +I+ D T +SRG+GF+ F + + +A
Sbjct: 43 RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA 102
Query: 170 KGNKLELAGAQVEVKKA 186
N + +++V A
Sbjct: 103 GLNGFNILNKRLKVALA 119
Score = 34.7 bits (78), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 30/60 (50%), Gaps = 3/60 (5%)
Query: 36 AQFIKHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKR 95
Q + F +YG I I+ DR+T Q RG+GFV + S + I +NG + KR
Sbjct: 57 VQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG---LNGFNILNKR 113
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 4/60 (6%)
Query: 112 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFD----TEQAVDDL 167
++V G+P ++++ E + F Q+G + +I+ D +T SRG GFI FD E+A+ L
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 24/47 (51%), Gaps = 6/47 (12%)
Query: 42 FGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIING 88
F +YG I S I+ D+ TG RG GF+ + DK IE I G
Sbjct: 22 FSQYGRIITSRILLDQATGVSRGVGFIRF------DKRIEAEEAIKG 62
>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 = 47.0 bits (110), Expect = 2e-05, Method: Composition-based stats.
Identities = 26/79 (32%), Positives = 42/79 (53%), Gaps = 8/79 (10%)
Query: 112 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDL 167
++VGG+ V++ F+ FGD+ + QI D+ T + RGF F+ F D A+D++
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 168 LAKGNKLELAGAQVEVKKA 186
N+ EL G + V A
Sbjct: 65 ----NESELFGRTIRVNLA 79
>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 = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 28/88 (31%), Positives = 45/88 (51%), Gaps = 8/88 (9%)
Query: 103 GSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF---- 158
GS + ++VGG+ V++ F+ FGD+ + QI D+ T + RGF F+ F
Sbjct: 1 GSMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 60
Query: 159 DTEQAVDDLLAKGNKLELAGAQVEVKKA 186
D A+D++ N+ EL G + V A
Sbjct: 61 DAAAAIDNM----NESELFGRTIRVNLA 84
>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 = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 45/73 (61%), Gaps = 6/73 (8%)
Query: 112 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDL 167
+FVGGI ++E E + FF ++G V+E +I+ D T S+G+GF++F D ++ V+
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 168 LA-KGNKLELAGA 179
+ G KL+L A
Sbjct: 71 INFHGKKLKLGPA 83
Score = 36.2 bits (82), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 35/58 (60%), Gaps = 1/58 (1%)
Query: 42 FGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPK 99
F +YG + + I+ DR TG +G+GFV++ + V K++E +GK++++ I K
Sbjct: 30 FARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQINFHGKKLKLGPAIRK 86
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 28/83 (33%), Positives = 45/83 (54%), Gaps = 9/83 (10%)
Query: 109 TKKI-FVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQA 163
TK++ +VGG+ V++ F+ FGD+ + QI D+ T + RGF F+ F D A
Sbjct: 62 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 121
Query: 164 VDDLLAKGNKLELAGAQVEVKKA 186
+D++ N+ EL G + V A
Sbjct: 122 IDNM----NESELFGRTIRVNLA 140
>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 = 46.6 bits (109), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 45/73 (61%), Gaps = 6/73 (8%)
Query: 112 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDL 167
+FVGGI ++E E + FF ++G V+E +I+ D T S+G+GF++F D ++ V+
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 168 LA-KGNKLELAGA 179
+ G KL+L A
Sbjct: 71 INFHGKKLKLGPA 83
Score = 35.8 bits (81), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 35/58 (60%), Gaps = 1/58 (1%)
Query: 42 FGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTIPK 99
F +YG + + I+ DR TG +G+GFV++ + V K++E +GK++++ I K
Sbjct: 30 FARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQINFHGKKLKLGPAIRK 86
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 43/81 (53%), Gaps = 8/81 (9%)
Query: 110 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVD 165
+ ++VGG+ V++ F+ FGD+ + QI D+ T + RGF F+ F D A+D
Sbjct: 6 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65
Query: 166 DLLAKGNKLELAGAQVEVKKA 186
++ N+ EL G + V A
Sbjct: 66 NM----NESELFGRTIRVNLA 82
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 45.1 bits (105), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 31/54 (57%)
Query: 105 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF 158
KD K+FVG IP ++E + K F +FG + E +++D T +G F+T+
Sbjct: 11 KDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTY 64
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 42 FGKYGEITDSVIMKDRKTGQPRGFGFVTYA 71
F ++G I + ++KDR TG +G F+TY
Sbjct: 36 FEEFGRIYELTVLKDRLTGLHKGCAFLTYC 65
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 45.1 bits (105), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 30/51 (58%)
Query: 108 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF 158
KT + V G+P E + K++F FG+V Q+ +D T S+GFGF+ F
Sbjct: 14 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF 64
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 32/55 (58%)
Query: 40 KHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIK 94
++F +GE+ + KD KTG +GFGFV + + KV+ H+I+G+ + K
Sbjct: 34 EYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCK 88
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 45.1 bits (105), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 24/95 (25%), Positives = 47/95 (49%), Gaps = 2/95 (2%)
Query: 100 GAVGSKDFKTKKIFVG--GIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFIT 157
G +GS+ +G G+ E + ++ F ++G + + I+ D + RSRGF F+
Sbjct: 1 GPLGSRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVY 60
Query: 158 FDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPN 192
F+ + + N +EL G ++ V + K+P+
Sbjct: 61 FENVDDAKEAKERANGMELDGRRIRVDFSITKRPH 95
Score = 35.0 bits (79), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 38/72 (52%), Gaps = 7/72 (9%)
Query: 24 GLSLTPVTEPALAQFIKHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDT 83
GLSL TE L + F KYG I D I+ D+++ + RGF FV + + VD E
Sbjct: 19 GLSLY-TTERDLREV---FSKYGPIADVSIVYDQQSRRSRGFAFVYFEN---VDDAKEAK 71
Query: 84 HIINGKQVEIKR 95
NG +++ +R
Sbjct: 72 ERANGMELDGRR 83
>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|C Chain C, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|B Chain B, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|D Chain D, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
Length = 88
Score = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 21/55 (38%), Positives = 36/55 (65%), Gaps = 2/55 (3%)
Query: 111 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTS--RSRGFGFITFDTEQA 163
K+FVG +P + +E + ++ F Q+G V E ++RD S + +S+G F+TF T +A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKA 59
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 41/79 (51%)
Query: 114 VGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK 173
V G+ E + ++ F ++G + + I+ D + RSRGF F+ F+ + + N
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 174 LELAGAQVEVKKAEPKKPN 192
+EL G ++ V + K+P+
Sbjct: 80 MELDGRRIRVDFSITKRPH 98
Score = 35.4 bits (80), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 38/72 (52%), Gaps = 7/72 (9%)
Query: 24 GLSLTPVTEPALAQFIKHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDT 83
GLSL TE L + F KYG I D I+ D+++ + RGF FV + + VD E
Sbjct: 22 GLSLY-TTERDLREV---FSKYGPIADVSIVYDQQSRRSRGFAFVYFEN---VDDAKEAK 74
Query: 84 HIINGKQVEIKR 95
NG +++ +R
Sbjct: 75 ERANGMELDGRR 86
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 41/79 (51%)
Query: 114 VGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK 173
V G+ E + ++ F ++G + + I+ D + RSRGF F+ F+ + + N
Sbjct: 51 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 110
Query: 174 LELAGAQVEVKKAEPKKPN 192
+EL G ++ V + K+P+
Sbjct: 111 MELDGRRIRVDFSITKRPH 129
Score = 35.0 bits (79), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 38/72 (52%), Gaps = 7/72 (9%)
Query: 24 GLSLTPVTEPALAQFIKHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDT 83
GLSL TE L + F KYG I D I+ D+++ + RGF FV + + VD E
Sbjct: 53 GLSLY-TTERDLREV---FSKYGPIADVSIVYDQQSRRSRGFAFVYFEN---VDDAKEAK 105
Query: 84 HIINGKQVEIKR 95
NG +++ +R
Sbjct: 106 ERANGMELDGRR 117
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 33/140 (23%), Positives = 66/140 (47%), Gaps = 9/140 (6%)
Query: 56 DRKTGQPRGFGFVTYADPSVVDKVIEDTHI-INGKQVEIKRTIPKGAVGSKDFKTKKIFV 114
D + G R FG+V + ++K +E T + + G ++++++ PKG K+ + +
Sbjct: 41 DVRIGMTRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEK--PKGKDSKKERDARTLLA 98
Query: 115 GGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKL 174
+P V +DE K+ F +++ + +D +S+G +I F TE + +
Sbjct: 99 KNLPYKVTQDELKEVFEDAAEIR--LVSKD---GKSKGIAYIEFKTEADAEKTFEEKQGT 153
Query: 175 ELAGAQVEV-KKAEPKKPNL 193
E+ G + + EPK L
Sbjct: 154 EIDGRSISLYYTGEPKGEGL 173
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 25/68 (36%), Positives = 38/68 (55%), Gaps = 11/68 (16%)
Query: 111 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 170
++FVG +P+ + E++FK F ++G+ E I RD RGFGFI ++ LA+
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESR-----TLAE 72
Query: 171 GNKLELAG 178
K EL G
Sbjct: 73 IAKAELDG 80
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 39/83 (46%), Gaps = 7/83 (8%)
Query: 111 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 170
K+FVG + +E + FF Q+G+V + I + R F F+TF ++ L
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF-----RAFAFVTFADDKVAQSLC-- 65
Query: 171 GNKLELAGAQVEVKKAEPKKPNL 193
G L + G V + AEPK L
Sbjct: 66 GEDLIIKGISVHISNAEPKHNKL 88
Score = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 35/81 (43%), Gaps = 8/81 (9%)
Query: 19 TQKMTGLSLTPVTEPALAQFIKHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDK 78
++ G +T L QF F +YGE+ D I K R F FVT+AD V
Sbjct: 12 SKVFVGRCTEDMTAEELQQF---FCQYGEVVDVFIPKPF-----RAFAFVTFADDKVAQS 63
Query: 79 VIEDTHIINGKQVEIKRTIPK 99
+ + II G V I PK
Sbjct: 64 LCGEDLIIKGISVHISNAEPK 84
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 29/98 (29%), Positives = 47/98 (47%), Gaps = 11/98 (11%)
Query: 103 GSKDFKTK-KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTE 161
G K F + ++FVG +P + E+E + F ++G E I +D +GFGFI +T
Sbjct: 15 GEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETR 68
Query: 162 QAVDDLLAKGNKLELAGAQVEVK----KAEPKKPNLPQ 195
+ + + + L G Q+ V+ A NLPQ
Sbjct: 69 TLAEIAKVELDNMPLRGKQLRVRFACHSASLTVRNLPQ 106
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 28/90 (31%), Positives = 40/90 (44%), Gaps = 1/90 (1%)
Query: 109 TKKIFVGGIPSSVNEDEFKDFFMQFGDV-QEHQIMRDHSTSRSRGFGFITFDTEQAVDDL 167
+ IF+G + ++E D F FG + Q +IMRD T S+G+ FI F + A D
Sbjct: 5 SSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAA 64
Query: 168 LAKGNKLELAGAQVEVKKAEPKKPNLPQPS 197
+ N L + V A K PS
Sbjct: 65 IEAMNGQYLCNRPITVSYAFKKDSKGSGPS 94
Score = 28.5 bits (62), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 53 IMKDRKTGQPRGFGFVTYADPSVVDKVIE 81
IM+D TG +G+ F+ +A D IE
Sbjct: 38 IMRDPDTGNSKGYAFINFASFDASDAAIE 66
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 41.6 bits (96), Expect = 7e-04, Method: Composition-based stats.
Identities = 22/87 (25%), Positives = 42/87 (48%), Gaps = 8/87 (9%)
Query: 111 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 170
K+F+G +P E E + F Q+G V E I+++ +GF+ + + A +D +
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFVHIEDKTAAEDAIRN 61
Query: 171 GNKLELAGAQVEVKKAEPKKPNLPQPS 197
+ +L G + V+ ++ K PS
Sbjct: 62 LHHYKLHGVNINVEASKNKSKASSGPS 88
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 19/70 (27%), Positives = 36/70 (51%)
Query: 114 VGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK 173
V G+ E + ++ F ++G + + I+ D + RSRGF F+ F+ + + N
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 174 LELAGAQVEV 183
+EL G ++ V
Sbjct: 80 MELDGRRIRV 89
Score = 34.3 bits (77), Expect = 0.12, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 30/54 (55%), Gaps = 3/54 (5%)
Query: 42 FGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKR 95
F KYG I D I+ D+++ + RGF FV + + VD E NG +++ +R
Sbjct: 36 FSKYGPIADVSIVYDQQSRRSRGFAFVYFEN---VDDAKEAKERANGMELDGRR 86
>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 = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 6/76 (7%)
Query: 111 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 170
++FVG +P + E+E + F ++G E I +D +GFGFI +T + +
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 70
Query: 171 GNKLELAGAQVEVKKA 186
+ + L G Q+ V+ A
Sbjct: 71 LDNMPLRGKQLRVRFA 86
>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 = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 31/129 (24%), Positives = 62/129 (48%), Gaps = 8/129 (6%)
Query: 56 DRKTGQPRGFGFVTYADPSVVDKVIEDTHI-INGKQVEIKRTIPKGAVGSKDFKTKKIFV 114
D +TG R FG+V + ++K +E T + + G ++++++ PKG K + +
Sbjct: 47 DVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEK--PKGRDSKKVRAARTLLA 104
Query: 115 GGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKL 174
+ ++ EDE K+ F D E +++ +S+G +I F +E + L +
Sbjct: 105 KNLSFNITEDELKEVFE---DALEIRLV--SQDGKSKGIAYIEFKSEADAEKNLEEKQGA 159
Query: 175 ELAGAQVEV 183
E+ G V +
Sbjct: 160 EIDGRSVSL 168
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 49/95 (51%), Gaps = 4/95 (4%)
Query: 97 IPKGAVGSKDFKT--KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFG 154
+P+G+ + + K+ K++ V IP + + + F QFG + + +I+ + S+ GFG
Sbjct: 15 VPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSK--GFG 72
Query: 155 FITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPK 189
F+TF+ D K + + G ++EV A +
Sbjct: 73 FVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107
Score = 37.7 bits (86), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 40/71 (56%), Gaps = 9/71 (12%)
Query: 32 EPALAQFIKHFGKYGEITD-SVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDTH--IING 88
+P L Q FG++G+I D +I +R + +GFGFVT+ + + D+ E H ++ G
Sbjct: 43 DPDLRQM---FGQFGKILDVEIIFNERGS---KGFGFVTFENSADADRAREKLHGTVVEG 96
Query: 89 KQVEIKRTIPK 99
+++E+ +
Sbjct: 97 RKIEVNNATAR 107
>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 = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/29 (55%), Positives = 20/29 (68%)
Query: 42 FGKYGEITDSVIMKDRKTGQPRGFGFVTY 70
FGKYG I I++D+ TG+PRG FV Y
Sbjct: 34 FGKYGSIVQKNILRDKLTGRPRGVAFVRY 62
>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 = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/29 (55%), Positives = 20/29 (68%)
Query: 42 FGKYGEITDSVIMKDRKTGQPRGFGFVTY 70
FGKYG I I++D+ TG+PRG FV Y
Sbjct: 121 FGKYGSIVQKNILRDKLTGRPRGVAFVRY 149
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 28/84 (33%), Positives = 42/84 (50%), Gaps = 9/84 (10%)
Query: 109 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHS-TSRSRGFGFITFDTEQ----A 163
T KI V IP N+ E ++ F FG+++ ++ + + T RGFGF+ F T+Q A
Sbjct: 15 TSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKA 74
Query: 164 VDDLLAK----GNKLELAGAQVEV 183
+ L G +L L A EV
Sbjct: 75 FNALCHSTHLYGRRLVLEWADSEV 98
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 21/79 (26%), Positives = 44/79 (55%), Gaps = 2/79 (2%)
Query: 112 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 171
IF+ + S++ D F FG++ +++ D + S+ G+GF+ F+T++A + + K
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSK--GYGFVHFETQEAAERAIEKM 71
Query: 172 NKLELAGAQVEVKKAEPKK 190
N + L +V V + + +K
Sbjct: 72 NGMLLNDRKVFVGRFKSRK 90
>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 = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 40/75 (53%), Gaps = 2/75 (2%)
Query: 117 IPSSVNEDEFKDFFMQFG-DVQEHQIMRDHSTSRSRGFGFITFDTEQ-AVDDLLAKGNKL 174
+P + ED+ + G +E ++MR+ S+ +SRGF F+ F Q A + A + L
Sbjct: 9 LPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSL 68
Query: 175 ELAGAQVEVKKAEPK 189
+ G +V + ++PK
Sbjct: 69 NILGQKVSMHYSDPK 83
>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 = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 4/63 (6%)
Query: 109 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAV 164
T +FVG + +V+++ ++ F F +M D T SRG+GF++F D + A+
Sbjct: 1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60
Query: 165 DDL 167
D +
Sbjct: 61 DSM 63
>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 = 38.9 bits (89), Expect = 0.004, Method: Composition-based stats.
Identities = 21/79 (26%), Positives = 44/79 (55%), Gaps = 2/79 (2%)
Query: 112 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 171
IF+ + S++ D F FG++ +++ D + S+ G+GF+ F+T++A + + K
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSK--GYGFVHFETQEAAERAIEKM 65
Query: 172 NKLELAGAQVEVKKAEPKK 190
N + L +V V + + +K
Sbjct: 66 NGMLLNDRKVFVGRFKSRK 84
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 42/88 (47%), Gaps = 2/88 (2%)
Query: 110 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 169
K++ V IP + + + F QFG + + +I+ + S+ GFGF+TF+ D
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSK--GFGFVTFENSADADRARE 73
Query: 170 KGNKLELAGAQVEVKKAEPKKPNLPQPS 197
K + + G ++EV A + PS
Sbjct: 74 KLHGTVVEGRKIEVNNATARVMTNSGPS 101
Score = 37.4 bits (85), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 40/71 (56%), Gaps = 9/71 (12%)
Query: 32 EPALAQFIKHFGKYGEITD-SVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDTH--IING 88
+P L Q FG++G+I D +I +R + +GFGFVT+ + + D+ E H ++ G
Sbjct: 29 DPDLRQM---FGQFGKILDVEIIFNERGS---KGFGFVTFENSADADRAREKLHGTVVEG 82
Query: 89 KQVEIKRTIPK 99
+++E+ +
Sbjct: 83 RKIEVNNATAR 93
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 37/73 (50%)
Query: 112 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 171
+F+ +P + + F+ FG+V ++ D TS S+ FGF++FD + +
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 172 NKLELAGAQVEVK 184
N ++ +++V+
Sbjct: 103 NGFQVGTKRLKVQ 115
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 46/84 (54%), Gaps = 9/84 (10%)
Query: 109 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQ---AVD 165
+K +FV G+ E+ K+ F G V+ +I+ D T S+GFGF+ F++E+ A
Sbjct: 15 SKTLFVKGLSEDTTEETLKESFD--GSVR-ARIVTDRETGSSKGFGFVDFNSEEDAKAAK 71
Query: 166 DLLAKGNKLELAGAQVEVKKAEPK 189
+ + G E+ G +V + A+PK
Sbjct: 72 EAMEDG---EIDGNKVTLDWAKPK 92
Score = 33.1 bits (74), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 27/50 (54%), Gaps = 4/50 (8%)
Query: 53 IMKDRKTGQPRGFGFVTY---ADPSVVDKVIEDTHIINGKQVEIKRTIPK 99
I+ DR+TG +GFGFV + D + +ED I+G +V + PK
Sbjct: 44 IVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGE-IDGNKVTLDWAKPK 92
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 42/78 (53%), Gaps = 7/78 (8%)
Query: 22 MTGL---SLTPVTEPALAQFIKHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDK 78
MT L +LT T P + + F KYG + D I +DR T + RGF FV + D +
Sbjct: 70 MTSLKVDNLTYRTSPDTLRRV--FEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 127
Query: 79 VIE--DTHIINGKQVEIK 94
++ D +++G+++ ++
Sbjct: 128 AMDAMDGAVLDGRELRVQ 145
Score = 36.6 bits (83), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 37/78 (47%)
Query: 114 VGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK 173
V + + D + F ++G V + I RD T SRGF F+ F ++ +D + +
Sbjct: 75 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 134
Query: 174 LELAGAQVEVKKAEPKKP 191
L G ++ V+ A +P
Sbjct: 135 AVLDGRELRVQMARYGRP 152
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 38.1 bits (87), Expect = 0.007, Method: Composition-based stats.
Identities = 25/101 (24%), Positives = 50/101 (49%), Gaps = 3/101 (2%)
Query: 98 PKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFIT 157
P + ++ + +F + + + + +DFF G V++ +I+ D ++ RS+G ++
Sbjct: 14 PVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVE 73
Query: 158 FDTEQAVDDLLAKG-NKLELAGAQVEVKKAEPKKPNLPQPS 197
F Q+V LA G L G + V+ ++ +K L PS
Sbjct: 74 FCEIQSVP--LAIGLTGQRLLGVPIIVQASQAEKNRLSGPS 112
>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 = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 43/81 (53%), Gaps = 7/81 (8%)
Query: 19 TQKMTGL---SLTPVTEPALAQFIKHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSV 75
+ MT L +LT T P + + F KYG + D I +DR T + RGF FV + D
Sbjct: 44 VEGMTSLKVDNLTYRTSPDTLRRV--FEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRD 101
Query: 76 VDKVIE--DTHIINGKQVEIK 94
+ ++ D +++G+++ ++
Sbjct: 102 AEDAMDAMDGAVLDGRELRVQ 122
Score = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 34/68 (50%)
Query: 124 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 183
D + F ++G V + I RD T SRGF F+ F ++ +D + + L G ++ V
Sbjct: 62 DTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV 121
Query: 184 KKAEPKKP 191
+ A +P
Sbjct: 122 QMARYGRP 129
>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 = 38.1 bits (87), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 23/100 (23%), Positives = 47/100 (47%), Gaps = 2/100 (2%)
Query: 100 GAVGSKDF--KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFIT 157
GA GS+ + +F+ +P + + FM FG+V ++ D T+ S+ FGF++
Sbjct: 14 GAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVS 73
Query: 158 FDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPNLPQPS 197
+D + + N ++ +++V+ K + PS
Sbjct: 74 YDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSKSGPS 113
Score = 35.8 bits (81), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 31/58 (53%), Gaps = 3/58 (5%)
Query: 38 FIKHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKR 95
++ F +G + + + D++T + FGFV+Y +P I+ +NG Q+ +KR
Sbjct: 42 LLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS---MNGFQIGMKR 96
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 38.1 bits (87), Expect = 0.008, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 2/61 (3%)
Query: 110 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSR--SRGFGFITFDTEQAVDDL 167
+K+FVGG+P ++EDE F +FG + + S S +G+ F+ F E +V L
Sbjct: 9 RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQAL 68
Query: 168 L 168
+
Sbjct: 69 I 69
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 38.1 bits (87), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 112 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 171
+++ +P S++E E ++ FG V +I+RD S+ SRG GF ++ + + ++
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHF 86
Query: 172 N 172
N
Sbjct: 87 N 87
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 38.1 bits (87), Expect = 0.008, Method: Composition-based stats.
Identities = 25/94 (26%), Positives = 43/94 (45%), Gaps = 6/94 (6%)
Query: 110 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL- 168
K +F+ + E+ + QFGD++ +++ T S+G F F T++A L
Sbjct: 16 KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 75
Query: 169 -----AKGNKLELAGAQVEVKKAEPKKPNLPQPS 197
A+G L+L G Q++V A + PS
Sbjct: 76 AASLEAEGGGLKLDGRQLKVDLAVTRDEAASGPS 109
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 38.1 bits (87), Expect = 0.009, Method: Composition-based stats.
Identities = 34/92 (36%), Positives = 47/92 (51%), Gaps = 14/92 (15%)
Query: 32 EPALAQ-FI-KHFGKYGEITDSV-IMKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIING 88
EP + + FI + F GE SV I+++R TG P G+ FV +AD + +K + H ING
Sbjct: 18 EPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCL---HKING 74
Query: 89 KQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSS 120
K + GA +K FK G PSS
Sbjct: 75 KPL-------PGATPAKRFKLNYATYSG-PSS 98
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 37.7 bits (86), Expect = 0.010, Method: Composition-based stats.
Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 1/63 (1%)
Query: 112 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF-DTEQAVDDLLAK 170
++V +P S+ ++ F ++G V + IM+D T +S+G FI F D + A + A
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 171 GNK 173
NK
Sbjct: 79 NNK 81
Score = 35.4 bits (80), Expect = 0.048, Method: Composition-based stats.
Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 3/50 (6%)
Query: 42 FGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQV 91
F KYG++ IMKD+ T + +G F+ + D D T IN KQ+
Sbjct: 37 FSKYGKVVKVTIMKDKDTRKSKGVAFILFLDK---DSAQNCTRAINNKQL 83
>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 = 37.7 bits (86), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 33/59 (55%), Gaps = 3/59 (5%)
Query: 41 HFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIE-DTHIINGKQVEI--KRT 96
HF G I I+ D+ +G P+G+ ++ +A+ + VD + D + G+ +++ KRT
Sbjct: 56 HFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRGRTIKVLPKRT 114
Score = 34.7 bits (78), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 21/97 (21%), Positives = 41/97 (42%), Gaps = 4/97 (4%)
Query: 98 PKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFIT 157
P A K+ + ++VG + + + F G + I+ D + +G+ +I
Sbjct: 25 PLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIE 84
Query: 158 FDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPNLP 194
F +VD +A + G ++V PK+ N+P
Sbjct: 85 FAERNSVDAAVAMDETV-FRGRTIKVL---PKRTNMP 117
>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 = 37.7 bits (86), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 24/91 (26%), Positives = 43/91 (47%), Gaps = 4/91 (4%)
Query: 112 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 171
+FV I EDE ++ F +G+++ + D T S+G+ + ++T + L AK
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQA--LAAKE 132
Query: 172 --NKLELAGAQVEVKKAEPKKPNLPQPSYRR 200
N E+ G ++V K P + S +R
Sbjct: 133 ALNGAEIMGQTIQVDWCFVKGPKRVKKSEKR 163
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 25 LSLTPVTEPALAQFIKH-FGKYGEITDSVIMKDRKTGQPRGFGFVTY 70
L +T + E A I+ F YGEI + + DR+TG +G+ V Y
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEY 121
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 37.0 bits (84), Expect = 0.016, Method: Composition-based stats.
Identities = 25/88 (28%), Positives = 46/88 (52%), Gaps = 9/88 (10%)
Query: 100 GAVGS--KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFIT 157
G+ GS +D ++VGG+ ++ E + ++ F QFG+++ +++ + FI
Sbjct: 1 GSSGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCA------FIQ 54
Query: 158 FDTEQAVDDLLAKG-NKLELAGAQVEVK 184
F T QA + K NKL + G ++ VK
Sbjct: 55 FATRQAAEVAAEKSFNKLIVNGRRLNVK 82
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 37.0 bits (84), Expect = 0.019, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 38/74 (51%), Gaps = 1/74 (1%)
Query: 110 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 169
+ +FVG + + V E+ + F+Q G + + I +D + + FGF+ F ++V +A
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIA 75
Query: 170 KGNKLELAGAQVEV 183
N + L G + V
Sbjct: 76 LLNGIRLYGRPINV 89
Score = 31.2 bits (69), Expect = 0.88, Method: Composition-based stats.
Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 42 FGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVI 80
F + G +T I KDR+ G+P+ FGFV + P V I
Sbjct: 37 FLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAI 74
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 36.2 bits (82), Expect = 0.033, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 27/50 (54%)
Query: 109 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF 158
++ +++G IP E++ D G V ++M D T RS+G+ FI F
Sbjct: 2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEF 51
>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 = 36.2 bits (82), Expect = 0.033, Method: Composition-based stats.
Identities = 24/85 (28%), Positives = 39/85 (45%), Gaps = 4/85 (4%)
Query: 110 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 169
+ I+VG + +E + F G V I+ D + +GF +I F +++V LA
Sbjct: 6 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 65
Query: 170 KGNKLELAGAQVEVKKAEPKKPNLP 194
L G Q++V PK+ N P
Sbjct: 66 LDESL-FRGRQIKVI---PKRTNRP 86
Score = 36.2 bits (82), Expect = 0.034, Method: Composition-based stats.
Identities = 18/60 (30%), Positives = 33/60 (55%), Gaps = 4/60 (6%)
Query: 41 HFGKYGEITDSVIMKDRKTGQPRGFGFVTYADP-SVVDKVIEDTHIINGKQVEIKRTIPK 99
HF G + I+ D+ +G P+GF ++ ++D SV + D + G+Q+++ IPK
Sbjct: 25 HFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKV---IPK 81
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 35.8 bits (81), Expect = 0.036, Method: Composition-based stats.
Identities = 19/80 (23%), Positives = 36/80 (45%)
Query: 112 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 171
+FV I EDE ++ F +G+++ + D T S+G+ + ++T +
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 172 NKLELAGAQVEVKKAEPKKP 191
N E+ G ++V K P
Sbjct: 89 NGAEIMGQTIQVDWCFVKGP 108
Score = 28.1 bits (61), Expect = 7.5, Method: Composition-based stats.
Identities = 17/47 (36%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 25 LSLTPVTEPALAQFIKH-FGKYGEITDSVIMKDRKTGQPRGFGFVTY 70
L +T + E A I+ F YGEI + + DR+TG +G+ V Y
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEY 75
>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 = 35.8 bits (81), Expect = 0.037, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 27/50 (54%)
Query: 109 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF 158
++ +++G IP E++ D G V ++M D T RS+G+ FI F
Sbjct: 3 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEF 52
>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 = 35.8 bits (81), Expect = 0.039, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 27/50 (54%)
Query: 109 TKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF 158
++ +++G IP E++ D G V ++M D T RS+G+ FI F
Sbjct: 4 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEF 53
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 35.8 bits (81), Expect = 0.040, Method: Composition-based stats.
Identities = 24/88 (27%), Positives = 44/88 (50%), Gaps = 4/88 (4%)
Query: 110 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTE---QAVDD 166
+K+FVG + +ED+ + F FG+++E I+R S+G F+ + + QA +
Sbjct: 16 RKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRG-PDGNSKGCAFVKYSSHAEAQAAIN 74
Query: 167 LLAKGNKLELAGAQVEVKKAEPKKPNLP 194
L + A + + VK A+ K + P
Sbjct: 75 ALHGSQTMPGASSSLVVKFADTDKESGP 102
>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 = 35.8 bits (81), Expect = 0.043, Method: Composition-based stats.
Identities = 24/85 (28%), Positives = 39/85 (45%), Gaps = 4/85 (4%)
Query: 110 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 169
+ I+VG + +E + F G V I+ D + +GF +I F +++V LA
Sbjct: 7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 66
Query: 170 KGNKLELAGAQVEVKKAEPKKPNLP 194
L G Q++V PK+ N P
Sbjct: 67 LDESL-FRGRQIKVI---PKRTNRP 87
Score = 35.8 bits (81), Expect = 0.044, Method: Composition-based stats.
Identities = 18/60 (30%), Positives = 33/60 (55%), Gaps = 4/60 (6%)
Query: 41 HFGKYGEITDSVIMKDRKTGQPRGFGFVTYADP-SVVDKVIEDTHIINGKQVEIKRTIPK 99
HF G + I+ D+ +G P+GF ++ ++D SV + D + G+Q+++ IPK
Sbjct: 26 HFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKV---IPK 82
>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 = 35.8 bits (81), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 18/78 (23%), Positives = 39/78 (50%)
Query: 112 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 171
+FVG + + F FG + + ++++D +T +S+G+GF++F + ++ + +
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 172 NKLELAGAQVEVKKAEPK 189
L G Q+ A K
Sbjct: 69 GGQWLGGRQIRTNWATRK 86
Score = 34.7 bits (78), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 31/57 (54%), Gaps = 2/57 (3%)
Query: 45 YGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDT--HIINGKQVEIKRTIPK 99
+G I+D+ ++KD TG+ +G+GFV++ + + I+ + G+Q+ K
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK 86
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 35.4 bits (80), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 25/113 (22%), Positives = 49/113 (43%), Gaps = 14/113 (12%)
Query: 63 RGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTI-PKGAVGSKDFKTKKIFVGGIPSSV 121
+G FVT + + I H ++ E+ + P A+ + V +P S+
Sbjct: 57 KGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDAL---------LCVANLPPSL 107
Query: 122 NEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDLLAK 170
+ +F++ FG ++ ++ T +S+G+GF + +A DLL K
Sbjct: 108 TQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGK 160
>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
pdb|3H2U|D Chain D, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
Length = 283
Score = 35.0 bits (79), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 25/113 (22%), Positives = 49/113 (43%), Gaps = 14/113 (12%)
Query: 63 RGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTI-PKGAVGSKDFKTKKIFVGGIPSSV 121
+G FVT + + I H ++ E+ + P A+ + V +P S+
Sbjct: 55 KGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDAL---------LCVANLPPSL 105
Query: 122 NEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDLLAK 170
+ +F++ FG ++ ++ T +S+G+GF + +A DLL K
Sbjct: 106 TQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGK 158
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 35.0 bits (79), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 25/113 (22%), Positives = 49/113 (43%), Gaps = 14/113 (12%)
Query: 63 RGFGFVTYADPSVVDKVIEDTHIINGKQVEIKRTI-PKGAVGSKDFKTKKIFVGGIPSSV 121
+G FVT + + I H ++ E+ + P A+ + V +P S+
Sbjct: 57 KGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDAL---------LCVANLPPSL 107
Query: 122 NEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDLLAK 170
+ +F++ FG ++ ++ T +S+G+GF + +A DLL K
Sbjct: 108 TQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGK 160
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 34.3 bits (77), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 19/91 (20%), Positives = 43/91 (47%), Gaps = 2/91 (2%)
Query: 107 FKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDD 166
++ ++V + ++++ + F FG + ++M + RS+GFGF+ F + +
Sbjct: 13 YQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGG--RSKGFGFVCFSSPEEATK 70
Query: 167 LLAKGNKLELAGAQVEVKKAEPKKPNLPQPS 197
+ + N +A + V A+ K+ PS
Sbjct: 71 AVTEMNGRIVATKPLYVALAQRKEERQSGPS 101
Score = 33.5 bits (75), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 5/55 (9%)
Query: 40 KHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIK 94
K F +G IT + +M + G+ +GFGFV ++ P K + + +NG+ V K
Sbjct: 34 KAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTE---MNGRIVATK 83
>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 = 33.9 bits (76), Expect = 0.14, Method: Composition-based stats.
Identities = 15/72 (20%), Positives = 34/72 (47%)
Query: 112 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 171
+FV G+ E++ D F ++G+++ + D T +G+ + ++T + +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 172 NKLELAGAQVEV 183
N +L G + V
Sbjct: 70 NGQDLMGQPISV 81
Score = 29.3 bits (64), Expect = 3.4, Method: Composition-based stats.
Identities = 18/47 (38%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 25 LSLTPVTEPALAQFI-KHFGKYGEITDSVIMKDRKTGQPRGFGFVTY 70
L +T V E A + I F +YGEI + + DR+TG +G+ V Y
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 56
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 43/88 (48%), Gaps = 4/88 (4%)
Query: 110 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTE---QAVDD 166
+K+FVG + +++ + F FG + E ++R + S+G F+ F T QA +
Sbjct: 13 RKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGT-SKGCAFVKFQTHAEAQAAIN 71
Query: 167 LLAKGNKLELAGAQVEVKKAEPKKPNLP 194
L L A + + VK A+ +K + P
Sbjct: 72 TLHSSRTLPGASSSLVVKFADTEKESGP 99
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 24/90 (26%), Positives = 43/90 (47%), Gaps = 9/90 (10%)
Query: 100 GAVGSKDF-KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF 158
G+ GS K K +FV + ++V E+ + F QFG ++ + ++D + FI F
Sbjct: 1 GSSGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHF 52
Query: 159 DTEQAVDDLLAKGNKLELAGAQVEVKKAEP 188
D + + N +L G +E+ A+P
Sbjct: 53 DERDGAVKAMEEMNGKDLEGENIEIVFAKP 82
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 33.9 bits (76), Expect = 0.17, Method: Composition-based stats.
Identities = 15/72 (20%), Positives = 34/72 (47%)
Query: 112 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 171
+FV G+ E++ D F ++G+++ + D T +G+ + ++T + +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 172 NKLELAGAQVEV 183
N +L G + V
Sbjct: 70 NGQDLMGQPISV 81
Score = 28.9 bits (63), Expect = 4.2, Method: Composition-based stats.
Identities = 18/47 (38%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 25 LSLTPVTEPALAQFIK-HFGKYGEITDSVIMKDRKTGQPRGFGFVTY 70
L +T V E A + I F +YGEI + + DR+TG +G+ V Y
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 56
>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 = 33.5 bits (75), Expect = 0.17, Method: Composition-based stats.
Identities = 15/72 (20%), Positives = 34/72 (47%)
Query: 112 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 171
+FV G+ E++ D F ++G+++ + D T +G+ + ++T + +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 172 NKLELAGAQVEV 183
N +L G + V
Sbjct: 70 NGQDLMGQPISV 81
Score = 28.9 bits (63), Expect = 4.5, Method: Composition-based stats.
Identities = 18/47 (38%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 25 LSLTPVTEPALAQFIK-HFGKYGEITDSVIMKDRKTGQPRGFGFVTY 70
L +T V E A + I F +YGEI + + DR+TG +G+ V Y
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 56
>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 = 33.5 bits (75), Expect = 0.20, Method: Composition-based stats.
Identities = 15/72 (20%), Positives = 34/72 (47%)
Query: 112 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 171
+FV G+ E++ D F ++G+++ + D T +G+ + ++T + +
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 172 NKLELAGAQVEV 183
N +L G + V
Sbjct: 72 NGQDLMGQPISV 83
Score = 28.9 bits (63), Expect = 4.9, Method: Composition-based stats.
Identities = 18/47 (38%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 25 LSLTPVTEPALAQFIK-HFGKYGEITDSVIMKDRKTGQPRGFGFVTY 70
L +T V E A + I F +YGEI + + DR+TG +G+ V Y
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 58
>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 = 33.5 bits (75), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 16/80 (20%), Positives = 36/80 (45%)
Query: 112 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 171
+FV G+ E++ D F ++G+++ + D T +G+ + ++T + +
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 172 NKLELAGAQVEVKKAEPKKP 191
N +L G + V + P
Sbjct: 86 NGQDLMGQPISVDWCFVRGP 105
Score = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 25 LSLTPVTEPALAQFIKH-FGKYGEITDSVIMKDRKTGQPRGFGFVTY 70
L +T V E A + I F +YGEI + + DR+TG +G+ V Y
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 72
>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 = 33.1 bits (74), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 37/66 (56%), Gaps = 3/66 (4%)
Query: 31 TEPALAQFIKHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIING 88
T+ L Q I+ G Y ++ + ++R GQ +G+ V A + V K++E ++NG
Sbjct: 68 TDQQLIQVIRSIGVY-DVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNG 126
Query: 89 KQVEIK 94
++V+++
Sbjct: 127 EKVDVR 132
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 33.1 bits (74), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 25/47 (53%)
Query: 112 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF 158
I V + E + ++ F FG + + +D +T +S+GF FI+F
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISF 64
Score = 30.0 bits (66), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 19/29 (65%)
Query: 42 FGKYGEITDSVIMKDRKTGQPRGFGFVTY 70
F +G I+ + KD+ TGQ +GF F+++
Sbjct: 36 FRPFGSISRIYLAKDKTTGQSKGFAFISF 64
>pdb|2DNN|A Chain A, Solution Structure Of Rna Binding Domain In Rna-Binding
Protein 12
Length = 109
Score = 32.0 bits (71), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 3/79 (3%)
Query: 112 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 171
+ V G+P S E++ +DFF V +++DH R+ G G + F + Q + L K
Sbjct: 19 VSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGLVKFLSPQDTFEAL-KR 75
Query: 172 NKLELAGAQVEVKKAEPKK 190
N++ + VEV A ++
Sbjct: 76 NRMLMIQRYVEVSPATERQ 94
>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 = 32.0 bits (71), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 15/72 (20%), Positives = 34/72 (47%)
Query: 112 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 171
+FV G+ E++ D F ++G+++ + D T +G+ + ++T + +
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 172 NKLELAGAQVEV 183
N +L G + V
Sbjct: 85 NGQDLMGQPISV 96
Score = 30.4 bits (67), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 25 LSLTPVTEPALAQFIKH-FGKYGEITDSVIMKDRKTGQPRGFGFVTY 70
L +T V E A + I F +YGEI + + DR+TG +G+ V Y
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 71
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 32.0 bits (71), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 16/76 (21%), Positives = 33/76 (43%), Gaps = 6/76 (7%)
Query: 108 KTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDL 167
K ++ GGI S + + + F FG + E ++ + +G+ F+ F T ++
Sbjct: 24 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHA 77
Query: 168 LAKGNKLELAGAQVEV 183
+ N + G V+
Sbjct: 78 IVSVNGTTIEGHVVKC 93
>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 = 32.0 bits (71), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 18/81 (22%), Positives = 43/81 (53%), Gaps = 8/81 (9%)
Query: 104 SKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTE-- 161
S + K+F+ G+P S ++E ++ G V++ +++ + + + +G ++ ++ E
Sbjct: 12 STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRA-GKPKGLAYVEYENESQ 70
Query: 162 --QAV---DDLLAKGNKLELA 177
QAV D + K N +++A
Sbjct: 71 ASQAVMKMDGMTIKENIIKVA 91
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 31.6 bits (70), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 13/48 (27%), Positives = 26/48 (54%)
Query: 111 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF 158
++FV + + +E++ + F +G + E D T + +GF F+TF
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTF 57
Score = 30.0 bits (66), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 31/68 (45%), Gaps = 3/68 (4%)
Query: 40 KHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIE--DTHIINGKQVEI-KRT 96
K F YG +++ D T +P+GF FVT+ P K D + G+ + + T
Sbjct: 27 KLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPST 86
Query: 97 IPKGAVGS 104
I K A S
Sbjct: 87 IKKEASQS 94
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 31.6 bits (70), Expect = 0.79, Method: Composition-based stats.
Identities = 15/70 (21%), Positives = 37/70 (52%), Gaps = 4/70 (5%)
Query: 112 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDT----EQAVDDL 167
+++ G+ + + +G + + + D +T++ +G+GF+ FD+ ++AV L
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
Query: 168 LAKGNKLELA 177
A G + ++A
Sbjct: 68 KASGVQAQMA 77
Score = 30.4 bits (67), Expect = 1.8, Method: Composition-based stats.
Identities = 12/36 (33%), Positives = 21/36 (58%)
Query: 45 YGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVI 80
YG+I + + D+ T + +G+GFV + PS K +
Sbjct: 29 YGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 64
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 31.2 bits (69), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 24/101 (23%), Positives = 44/101 (43%), Gaps = 8/101 (7%)
Query: 105 KDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQ--------IMRDHSTSRSRGFGFI 156
+D I+V G+ SV D+ DFF Q G V+ ++ I D T + +G +
Sbjct: 11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATV 70
Query: 157 TFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPNLPQPS 197
+++ + + + G++++V A K P PS
Sbjct: 71 SYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSGPS 111
Score = 28.5 bits (62), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 5/57 (8%)
Query: 30 VTEPALAQFIKHFG--KYGEITDSVIMK---DRKTGQPRGFGFVTYADPSVVDKVIE 81
VT LA F K G K + T ++ D++TG+P+G V+Y DP +E
Sbjct: 27 VTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVE 83
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 31.2 bits (69), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 20/89 (22%), Positives = 41/89 (46%), Gaps = 12/89 (13%)
Query: 99 KGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRG---FGF 155
+G G+ D + I+VG +P + + +D F ++G +RD RG F F
Sbjct: 15 RGPAGNNDCR---IYVGNLPPDIRTKDIEDVFYKYG------AIRDIDLKNRRGGPPFAF 65
Query: 156 ITFDTEQAVDDLLAKGNKLELAGAQVEVK 184
+ F+ + +D + + + G ++ V+
Sbjct: 66 VEFEDPRDAEDAVYGRDGYDYDGYRLRVE 94
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 20/85 (23%), Positives = 40/85 (47%), Gaps = 2/85 (2%)
Query: 113 FVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN 172
+VG +P + + + F ++ +++RD T + +GF ++ FD ++ + L
Sbjct: 19 YVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDG 77
Query: 173 KLELAGAQVEVKKAEPKKPNLPQPS 197
L L + V AE +K + PS
Sbjct: 78 AL-LGDRSLRVDIAEGRKQDKSGPS 101
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 22/94 (23%), Positives = 40/94 (42%), Gaps = 13/94 (13%)
Query: 106 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVD 165
+ ++FV P V E E + F FG ++E +I+ GF F+ F+ ++
Sbjct: 28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAA 79
Query: 166 DLLAKGNKLELAGAQVEVKKAEPKKPNLPQPSYR 199
+ + + A +EV ++ LP YR
Sbjct: 80 KAIEEVHGKSFANQPLEVVYSK-----LPAKRYR 108
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 28/58 (48%), Gaps = 5/58 (8%)
Query: 42 FGKYGEITDSVIMKDR-KTG--QPRGFGFVTYADPSVVDKVIEDT--HIINGKQVEIK 94
F K G I I K + K G GFGFV Y P K ++ H ++G ++E++
Sbjct: 26 FSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVR 83
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 30.8 bits (68), Expect = 1.2, Method: Composition-based stats.
Identities = 24/88 (27%), Positives = 41/88 (46%), Gaps = 4/88 (4%)
Query: 110 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTE---QAVDD 166
+K+FVG + +E++ F FG + E ++R S S+G F+ F + QA
Sbjct: 16 RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGS-SKGCAFVKFSSHTEAQAAIH 74
Query: 167 LLAKGNKLELAGAQVEVKKAEPKKPNLP 194
L + A + + VK A+ K + P
Sbjct: 75 ALHGSQTMPGASSSLVVKFADTDKESGP 102
>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 = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/94 (18%), Positives = 41/94 (43%)
Query: 90 QVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSR 149
+ E+K P ++ K +FV + E + + F +G ++ ++ + +
Sbjct: 83 ETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGK 142
Query: 150 SRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 183
RG+ FI ++ E+ + + ++ G +V V
Sbjct: 143 PRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV 176
Score = 28.1 bits (61), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 10/35 (28%), Positives = 21/35 (60%)
Query: 36 AQFIKHFGKYGEITDSVIMKDRKTGQPRGFGFVTY 70
++ + F YG I ++ +++G+PRG+ F+ Y
Sbjct: 117 SKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEY 151
>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 = 1.5, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 34/70 (48%), Gaps = 6/70 (8%)
Query: 28 TPVTEPALAQFIKHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIIN 87
PV + AL F K G++ + D TG+ +GF FV + K+I+ H
Sbjct: 22 VPVLKKALTSL---FSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH--- 75
Query: 88 GKQVEIKRTI 97
GK++++K +
Sbjct: 76 GKRLDLKHRL 85
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 18/31 (58%)
Query: 42 FGKYGEITDSVIMKDRKTGQPRGFGFVTYAD 72
F KYG + D I ++ T PRGF FV + D
Sbjct: 34 FEKYGRVGDVYIPREPHTKAPRGFAFVRFHD 64
>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 = 30.4 bits (67), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 34/70 (48%), Gaps = 6/70 (8%)
Query: 28 TPVTEPALAQFIKHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIIN 87
PV + AL F K G++ + D TG+ +GF FV + K+I+ H
Sbjct: 22 VPVLKKALTSL---FSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH--- 75
Query: 88 GKQVEIKRTI 97
GK++++K +
Sbjct: 76 GKRLDLKHRL 85
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 30.4 bits (67), Expect = 1.6, Method: Composition-based stats.
Identities = 18/74 (24%), Positives = 37/74 (50%), Gaps = 2/74 (2%)
Query: 111 KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 170
+IFV +P KD F + G V I ++ +S+G G + F++ + +
Sbjct: 10 QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENG--KSKGCGVVKFESPEVAERACRM 67
Query: 171 GNKLELAGAQVEVK 184
N ++L+G +++V+
Sbjct: 68 MNGMKLSGREIDVR 81
>pdb|3BEG|B Chain B, Crystal Structure Of Sr Protein Kinase 1 Complexed To Its
Substrate AsfSF2
Length = 115
Score = 30.0 bits (66), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 28/101 (27%), Positives = 43/101 (42%), Gaps = 13/101 (12%)
Query: 98 PKGAVGSKDFKTK-KIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFI 156
P+G G +++ ++ V G+P S + + KD + GDV + RD G G +
Sbjct: 4 PRGRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVV 56
Query: 157 TF----DTEQAVDDL-LAKGNKLELAGAQVEVKKAEPKKPN 192
F D AV L K E A + VK P+ P+
Sbjct: 57 EFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPS 97
>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 = 29.6 bits (65), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 17/94 (18%), Positives = 41/94 (43%)
Query: 90 QVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSR 149
+ E+K P ++ K +FV + E + + F +G ++ ++ + +
Sbjct: 83 ETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGK 142
Query: 150 SRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 183
RG+ FI ++ E+ + + ++ G +V V
Sbjct: 143 PRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV 176
Score = 27.7 bits (60), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 10/35 (28%), Positives = 21/35 (60%)
Query: 36 AQFIKHFGKYGEITDSVIMKDRKTGQPRGFGFVTY 70
++ + F YG I ++ +++G+PRG+ F+ Y
Sbjct: 117 SKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEY 151
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 29.6 bits (65), Expect = 2.9, Method: Composition-based stats.
Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 2/73 (2%)
Query: 112 IFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 171
IFV +P KD F + G V I ++ +S+G G + F++ + +
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENG--KSKGCGVVKFESPEVAERACRMM 65
Query: 172 NKLELAGAQVEVK 184
N ++L+G +++V+
Sbjct: 66 NGMKLSGREIDVR 78
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 29.3 bits (64), Expect = 3.2, Method: Composition-based stats.
Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 9/59 (15%)
Query: 111 KIFVGGIP-SSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL 168
++F+G +P +V++++ F +G + + I FGFI FD Q+V D +
Sbjct: 24 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAI 74
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 29.3 bits (64), Expect = 3.4, Method: Composition-based stats.
Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 9/59 (15%)
Query: 111 KIFVGGIP-SSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL 168
++F+G +P +V++++ F +G + + I FGFI FD Q+V D +
Sbjct: 4 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAI 54
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 29.3 bits (64), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 25/54 (46%), Gaps = 3/54 (5%)
Query: 42 FGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVDKVIEDTHIINGKQVEIKR 95
F G I IM+D KTG G+ FV + + I+ ++NG V KR
Sbjct: 24 FRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK---VLNGITVRNKR 74
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of Eukaryotic
Initiation Factor 4b
Length = 104
Score = 29.3 bits (64), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 113 FVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHST-SRSRGFGFITFD 159
F+G +P V E+ K+FF ++ ++ R+ S R +GFG+ F+
Sbjct: 19 FLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEFE 65
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation Initiation
Factor 4b
Length = 100
Score = 28.9 bits (63), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 113 FVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHST-SRSRGFGFITFD 159
F+G +P V E+ K+FF ++ ++ R+ S R +GFG+ F+
Sbjct: 23 FLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEFE 69
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 28.9 bits (63), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 18/78 (23%), Positives = 34/78 (43%), Gaps = 8/78 (10%)
Query: 106 DFKTKKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVD 165
+ ++FV P V E E + F FG ++E +I+ GF F+ F+ ++
Sbjct: 1 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAA 52
Query: 166 DLLAKGNKLELAGAQVEV 183
+ + + A +EV
Sbjct: 53 KAIEEVHGKSFANQPLEV 70
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 28.9 bits (63), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 9/59 (15%)
Query: 111 KIFVGGIP-SSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL 168
++F+G +P +V++++ F +G + + I FGFI FD Q+V D +
Sbjct: 24 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAI 74
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 28.9 bits (63), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 9/59 (15%)
Query: 111 KIFVGGIP-SSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL 168
++F+G +P +V++++ F +G + + I FGFI FD Q+V D +
Sbjct: 12 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAI 62
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 28.5 bits (62), Expect = 6.1, Method: Composition-based stats.
Identities = 19/88 (21%), Positives = 40/88 (45%), Gaps = 9/88 (10%)
Query: 111 KIFVGGIPSS-VNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 169
++F+G + ++ V + + + F ++G V S +G+ F+ + E+ +
Sbjct: 29 RVFIGNLNTALVKKSDVETIFSKYGRVA--------GCSVHKGYAFVQYSNERHARAAVL 80
Query: 170 KGNKLELAGAQVEVKKAEPKKPNLPQPS 197
N LAG +++ A KP+ PS
Sbjct: 81 GENGRVLAGQTLDINMAGEPKPDRSGPS 108
>pdb|2E5G|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 21
Length = 94
Score = 28.1 bits (61), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 19/85 (22%), Positives = 39/85 (45%), Gaps = 6/85 (7%)
Query: 110 KKIFVGGIPSSVNEDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 169
+ +FV G P V+ + ++F+ FG V + +D F + A + +L+
Sbjct: 9 RSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGV-----FAIVEMGDVGAREAVLS 63
Query: 170 KGNKLELAGAQVEVKKAEPKKPNLP 194
+ ++ L G ++ V+ E K+ P
Sbjct: 64 Q-SQHSLGGHRLRVRPREQKEFQSP 87
>pdb|1QU0|A Chain A, Crystal Structure Of The Fifth Laminin G-like Module Of
The Mouse Laminin Alpha2 Chain
pdb|1QU0|B Chain B, Crystal Structure Of The Fifth Laminin G-like Module Of
The Mouse Laminin Alpha2 Chain
pdb|1QU0|C Chain C, Crystal Structure Of The Fifth Laminin G-like Module Of
The Mouse Laminin Alpha2 Chain
pdb|1QU0|D Chain D, Crystal Structure Of The Fifth Laminin G-like Module Of
The Mouse Laminin Alpha2 Chain
Length = 191
Score = 28.1 bits (61), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 27/108 (25%), Positives = 46/108 (42%), Gaps = 15/108 (13%)
Query: 18 TTQKMTGLSLTPVTEPALAQFIKHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVD 77
++QKM G+ + + E + G++ I D+ I GQ V
Sbjct: 50 SSQKMDGMGIEMIDEKLMFHVDNGAGRFTAIYDAEIPGHMCNGQWH----------KVTA 99
Query: 78 KVIED--THIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNE 123
K I++ +++G QV+ + P A S D +FVGG P +N+
Sbjct: 100 KKIKNRLELVVDGNQVDAQS--PNSASTSAD-TNDPVFVGGFPGGLNQ 144
>pdb|1DYK|A Chain A, Laminin Alpha 2 Chain Lg4-5 Domain Pair
Length = 394
Score = 27.7 bits (60), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 27/108 (25%), Positives = 46/108 (42%), Gaps = 15/108 (13%)
Query: 18 TTQKMTGLSLTPVTEPALAQFIKHFGKYGEITDSVIMKDRKTGQPRGFGFVTYADPSVVD 77
++QKM G+ + + E + G++ I D+ I GQ V
Sbjct: 253 SSQKMDGMGIEMIDEKLMFHVDNGAGRFTAIYDAEIPGHMCNGQWH----------KVTA 302
Query: 78 KVIED--THIINGKQVEIKRTIPKGAVGSKDFKTKKIFVGGIPSSVNE 123
K I++ +++G QV+ + P A S D +FVGG P +N+
Sbjct: 303 KKIKNRLELVVDGNQVDAQS--PNSASTSAD-TNDPVFVGGFPGGLNQ 347
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
0.317 0.137 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,515,903
Number of Sequences: 62578
Number of extensions: 275542
Number of successful extensions: 1017
Number of sequences better than 100.0: 167
Number of HSP's better than 100.0 without gapping: 118
Number of HSP's successfully gapped in prelim test: 49
Number of HSP's that attempted gapping in prelim test: 734
Number of HSP's gapped (non-prelim): 280
length of query: 367
length of database: 14,973,337
effective HSP length: 100
effective length of query: 267
effective length of database: 8,715,537
effective search space: 2327048379
effective search space used: 2327048379
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)