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= psy40
(168 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 82.4 bits (202), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 43/97 (44%), Positives = 62/97 (63%), Gaps = 13/97 (13%)
Query: 60 EEVDMEIPGPPH------------MDKLEIGKPEANATVKKMFVGGLK-DQEEDDLREYF 106
EEVD + PH + + + +P A+ TVKK+FVGG+K D EE LR+YF
Sbjct: 65 EEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYF 124
Query: 107 SQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKI 143
Q+G IE + ++T++ +G KRGFAF+ F+D+D VDKI
Sbjct: 125 EQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 161
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 80 PEANATVKKMFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
P+ ++K+F+GGL + D+ LR +F Q+GT+ ++ + T RGF F+ + +
Sbjct: 6 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 65
Query: 139 VVD 141
VD
Sbjct: 66 EVD 68
>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
pdb|1U1K|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt 7da
Ggg); A Human Telomeric Repeat Containing
7-Deaza-Adenine
pdb|1U1L|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt Prn
Ggg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1M|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 7gu
Gg); A Human Telomeric Repeat Containing 7-Deaza-Guanine
pdb|1U1N|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta (Prn)
Gg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1O|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggttag(Di)g); A Human Telomeric Repeat Containing
Inosine
pdb|1U1P|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 2pr
Gg); A Human Telomeric Repeat Containing 2-Aminopurine
pdb|1U1Q|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggtta(Di)gg); A Human Telomeric Repeat Containing
Inosine
pdb|1U1R|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(2pr)
G); A Human Telomeric Repeat Containing 2-Aminopurine
Length = 196
Score = 82.4 bits (202), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 43/97 (44%), Positives = 62/97 (63%), Gaps = 13/97 (13%)
Query: 60 EEVDMEIPGPPH------------MDKLEIGKPEANATVKKMFVGGLK-DQEEDDLREYF 106
EEVD + PH + + + +P A+ TVKK+FVGG+K D EE LR+YF
Sbjct: 66 EEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYF 125
Query: 107 SQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKI 143
Q+G IE + ++T++ +G KRGFAF+ F+D+D VDKI
Sbjct: 126 EQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 162
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 80 PEANATVKKMFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
P+ ++K+F+GGL + D+ LR +F Q+GT+ ++ + T RGF F+ + +
Sbjct: 7 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 66
Query: 139 VVD 141
VD
Sbjct: 67 EVD 69
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 82.4 bits (202), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 43/97 (44%), Positives = 62/97 (63%), Gaps = 13/97 (13%)
Query: 60 EEVDMEIPGPPH------------MDKLEIGKPEANATVKKMFVGGLK-DQEEDDLREYF 106
EEVD + PH + + + +P A+ TVKK+FVGG+K D EE LR+YF
Sbjct: 67 EEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYF 126
Query: 107 SQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKI 143
Q+G IE + ++T++ +G KRGFAF+ F+D+D VDKI
Sbjct: 127 EQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 163
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 80 PEANATVKKMFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
P+ ++K+F+GGL + D+ LR +F Q+GT+ ++ + T RGF F+ + +
Sbjct: 8 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 67
Query: 139 VVD 141
VD
Sbjct: 68 EVD 70
>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 = 82.0 bits (201), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 43/97 (44%), Positives = 62/97 (63%), Gaps = 13/97 (13%)
Query: 60 EEVDMEIPGPPH------------MDKLEIGKPEANATVKKMFVGGLK-DQEEDDLREYF 106
EEVD + PH + + + +P A+ TVKK+FVGG+K D EE LR+YF
Sbjct: 59 EEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYF 118
Query: 107 SQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKI 143
Q+G IE + ++T++ +G KRGFAF+ F+D+D VDKI
Sbjct: 119 EQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 155
Score = 40.0 bits (92), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 34/57 (59%), Gaps = 1/57 (1%)
Query: 86 VKKMFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVD 141
++K+F+GGL + D+ LR +F Q+GT+ ++ + T RGF F+ + + VD
Sbjct: 6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 62
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 82.0 bits (201), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 43/97 (44%), Positives = 62/97 (63%), Gaps = 13/97 (13%)
Query: 60 EEVDMEIPGPPH------------MDKLEIGKPEANATVKKMFVGGLK-DQEEDDLREYF 106
EEVD + PH + + + +P A+ TVKK+FVGG+K D EE LR+YF
Sbjct: 66 EEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYF 125
Query: 107 SQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKI 143
Q+G IE + ++T++ +G KRGFAF+ F+D+D VDKI
Sbjct: 126 EQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 162
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 80 PEANATVKKMFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
P+ ++K+F+GGL + D+ LR +F Q+GT+ ++ + T RGF F+ + +
Sbjct: 7 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 66
Query: 139 VVD 141
VD
Sbjct: 67 EVD 69
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 82.0 bits (201), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 43/97 (44%), Positives = 62/97 (63%), Gaps = 13/97 (13%)
Query: 60 EEVDMEIPGPPH------------MDKLEIGKPEANATVKKMFVGGLK-DQEEDDLREYF 106
EEVD + PH + + + +P A+ TVKK+FVGG+K D EE LR+YF
Sbjct: 64 EEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYF 123
Query: 107 SQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKI 143
Q+G IE + ++T++ +G KRGFAF+ F+D+D VDKI
Sbjct: 124 EQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 160
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 80 PEANATVKKMFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
P+ ++K+F+GGL + D+ LR +F Q+GT+ ++ + T RGF F+ + +
Sbjct: 5 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 64
Query: 139 VVD 141
VD
Sbjct: 65 EVD 67
>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 = 56.6 bits (135), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 28/59 (47%), Positives = 39/59 (66%), Gaps = 1/59 (1%)
Query: 86 VKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKI 143
VKK+FVGGL D E+ +REYF FG +ES+ + + +T +RGF FI F + + V KI
Sbjct: 1 VKKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKI 59
>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 = 55.8 bits (133), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 31/84 (36%), Positives = 49/84 (58%), Gaps = 2/84 (2%)
Query: 74 KLEIGKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFI 132
K I + E + T K+FVGG+ D + E+FSQ+GTI ++ +K+TG RGF F+
Sbjct: 76 KRAIPRDEQDKT-GKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFV 134
Query: 133 EFNDYDVVDKIRGFAFIEFNDYDV 156
++ D VD++ FI+F D +
Sbjct: 135 TYDSADAVDRVCQNKFIDFKDRKI 158
Score = 54.3 bits (129), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 25/57 (43%), Positives = 37/57 (64%), Gaps = 1/57 (1%)
Query: 88 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKI 143
KMF+GGL D ED+LREYF ++GT+ + ++ + TG RGF F+ F VD++
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 51.6 bits (122), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 25/56 (44%), Positives = 36/56 (64%), Gaps = 1/56 (1%)
Query: 89 MFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKI 143
+FVGGL D E+ +REYF FG +ES+ + + +T +RGF FI F + + V KI
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKI 57
>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 = 50.4 bits (119), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 43/71 (60%), Gaps = 2/71 (2%)
Query: 85 TVKKMFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK- 142
+ K+F+GGL + DD ++E + FG +++ N+V + TG +G+AF E+ D +V D+
Sbjct: 113 SAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 172
Query: 143 IRGFAFIEFND 153
I G ++ D
Sbjct: 173 IAGLNGMQLGD 183
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 50.1 bits (118), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 42/68 (61%), Gaps = 2/68 (2%)
Query: 88 KMFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK-IRG 145
K+F+GGL + DD ++E + FG +++ N+V + TG +G+AF E+ D +V D+ I G
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 146 FAFIEFND 153
++ D
Sbjct: 63 LNGMQLGD 70
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 50.1 bits (118), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 88 KMFVGGLKDQE-EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIRGF 146
KMF+GGL Q ++ LREYF QFG ++ ++ + T RGF F+ F D VDK+
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 86
Query: 147 AFIEFNDYDVVDKIV 161
+ E + + K+
Sbjct: 87 SRHELDSKTIDPKVA 101
>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 = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 44/72 (61%), Gaps = 2/72 (2%)
Query: 88 KMFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK-IRG 145
K+F+GGL + DD ++E + FG +++ N+V + TG +G+AF E+ D +V D+ I G
Sbjct: 98 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 157
Query: 146 FAFIEFNDYDVV 157
++ D ++
Sbjct: 158 LNGMQLGDKKLL 169
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 44/72 (61%), Gaps = 2/72 (2%)
Query: 88 KMFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK-IRG 145
K+F+GGL + DD ++E + FG +++ N+V + TG +G+AF E+ D +V D+ I G
Sbjct: 96 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 155
Query: 146 FAFIEFNDYDVV 157
++ D ++
Sbjct: 156 LNGMQLGDKKLL 167
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 48.9 bits (115), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 25/57 (43%), Positives = 35/57 (61%), Gaps = 1/57 (1%)
Query: 88 KMFVGGLKDQE-EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKI 143
KMF+GGL Q ++ LREYF QFG ++ ++ + T RGF F+ F D VDK+
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV 58
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 48.9 bits (115), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 39/66 (59%), Gaps = 1/66 (1%)
Query: 89 MFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIRGFA 147
+FVGGL + +D++ YF QFG ++ ++ +K T RGF F+ F D+V+K+
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 148 FIEFND 153
F E N+
Sbjct: 62 FHEINN 67
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 48.9 bits (115), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 81 EANATVKKMFVGGLKDQEED-DLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDV 139
+ + T K+FVGGL D LR+YF FG IE ++T+++TG RG+ F+ D
Sbjct: 12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAA 71
Query: 140 VDK 142
++
Sbjct: 72 AER 74
>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 = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/56 (41%), Positives = 35/56 (62%), Gaps = 1/56 (1%)
Query: 89 MFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKI 143
MF+GGL D + DL++YFS+FG + + + TG RGF F+ F + + VDK+
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKV 57
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 35/59 (59%), Gaps = 1/59 (1%)
Query: 86 VKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKI 143
+ K+FVGGL ++ LR YFSQ+G + ++ +K T RGF F++F D + V +
Sbjct: 16 IGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTV 74
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 47.8 bits (112), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 29/75 (38%), Positives = 41/75 (54%), Gaps = 6/75 (8%)
Query: 88 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIRGF 146
K+FVGG+ + E +LREYF +FG + V M+ + E RGF FI F D VD+
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
Query: 147 AFIEFNDYDVVDKIV 161
F +D++ K V
Sbjct: 72 HF-----HDIMGKKV 81
>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 = 47.0 bits (110), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 24/57 (42%), Positives = 34/57 (59%), Gaps = 1/57 (1%)
Query: 88 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKI 143
K FVGGL D + DL++YF++FG + + + TG RGF FI F D V+K+
Sbjct: 13 KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKV 69
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 47.0 bits (110), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 44/80 (55%), Gaps = 5/80 (6%)
Query: 81 EANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDV 139
+ +A +++VG L + ED LR F FG IES+ ++ + ETG +G+ FI F+D +
Sbjct: 21 KGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSEC 80
Query: 140 VDKIRGFAFIEFNDYDVVDK 159
K A + N +++ +
Sbjct: 81 AKK----ALEQLNGFELAGR 96
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/52 (44%), Positives = 32/52 (61%), Gaps = 1/52 (1%)
Query: 88 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
K+FVGGL D E L + FS++G I V +V ++ET RGF F+ F + D
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENID 65
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 41/77 (53%), Gaps = 4/77 (5%)
Query: 79 KPEANATVKKMFVGGLKDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
+ + NAT++ + +D E DL+E F FG+I + + +K TG +GFAFI F+ +
Sbjct: 11 RADDNATIRVTNLS--EDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRE 68
Query: 139 VVDKIRGFAFIEFNDYD 155
D R A + YD
Sbjct: 69 --DAARAIAGVSGFGYD 83
>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 = 44.3 bits (103), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 40/62 (64%), Gaps = 3/62 (4%)
Query: 80 PEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF-NDY 137
PE +FVGG+ +E ++R +F+++G+++ V ++T++ TG +G+ F+ F ND
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDV 61
Query: 138 DV 139
DV
Sbjct: 62 DV 63
>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 = 43.9 bits (102), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 40/62 (64%), Gaps = 3/62 (4%)
Query: 80 PEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF-NDY 137
PE +FVGG+ +E ++R +F+++G+++ V ++T++ TG +G+ F+ F ND
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDV 61
Query: 138 DV 139
DV
Sbjct: 62 DV 63
>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 = 43.5 bits (101), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 30/87 (34%), Positives = 44/87 (50%), Gaps = 4/87 (4%)
Query: 51 KAMEEAQSEEEVDMEIPGPPHMDKLEIGKPEANATV--KKMFVGGL-KDQEEDDLREYFS 107
KA EAQ+ +PG H + + E N V +K+F+G + K E+D+R FS
Sbjct: 58 KAALEAQNALHNXKVLPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFS 117
Query: 108 QFGTIESVNMVTNKETGAKRGFAFIEF 134
FG IE ++ + G RG AF+ F
Sbjct: 118 SFGQIEECRILRGPD-GLSRGCAFVTF 143
Score = 31.6 bits (70), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 3/50 (6%)
Query: 88 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGA--KRGFAFIEF 134
K FVG + + E DLRE F Q+G + +N++ ++ +G F+ F
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTF 54
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 43.1 bits (100), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 30/88 (34%), Positives = 45/88 (51%), Gaps = 4/88 (4%)
Query: 50 NKAMEEAQSEEEVDMEIPGPPHMDKLEIGKPEANATV--KKMFVGGL-KDQEEDDLREYF 106
KA EAQ+ +PG H +++ E N V +K+F+G + K E+D+R F
Sbjct: 57 RKAALEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMF 116
Query: 107 SQFGTIESVNMVTNKETGAKRGFAFIEF 134
S FG IE ++ + G RG AF+ F
Sbjct: 117 SSFGQIEECRILRGPD-GLSRGCAFVTF 143
Score = 34.3 bits (77), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 28/50 (56%), Gaps = 3/50 (6%)
Query: 88 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGA--KRGFAFIEF 134
KMFVG + + E DLRE F Q+G + +N++ ++ +G F+ F
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTF 54
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 28/45 (62%)
Query: 99 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKI 143
E DL+EYFS FG + V + + +TG +GF F+ F +Y+ K+
Sbjct: 29 EQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKV 73
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 30/87 (34%), Positives = 45/87 (51%), Gaps = 4/87 (4%)
Query: 51 KAMEEAQSEEEVDMEIPGPPHMDKLEIGKPEANATV--KKMFVGGL-KDQEEDDLREYFS 107
KA EAQ+ +PG H +++ E N V +K+F+G + K E+D+R FS
Sbjct: 70 KAALEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFS 129
Query: 108 QFGTIESVNMVTNKETGAKRGFAFIEF 134
FG IE ++ + G RG AF+ F
Sbjct: 130 SFGQIEECRILRGPD-GLSRGCAFVTF 155
Score = 34.3 bits (77), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 33/59 (55%), Gaps = 5/59 (8%)
Query: 79 KPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGA--KRGFAFIEF 134
+P+ +A KMFVG + + E DLRE F Q+G + +N++ ++ +G F+ F
Sbjct: 10 QPDLDAI--KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTF 66
>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|6 Chain 6, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|7 Chain 7, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|8 Chain 8, Crystal Structure Of Human Spliceosomal U1 Snrnp
Length = 216
Score = 42.4 bits (98), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 30/49 (61%), Gaps = 1/49 (2%)
Query: 87 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 134
K +FV + D E LR F +G I+ ++MV +K +G RG+AFIE+
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEY 151
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 42.4 bits (98), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 35/62 (56%), Gaps = 4/62 (6%)
Query: 98 EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIRGFAFIEFNDYDVV 157
+E LR+ F ++G IESV +V ++ET RG+ F++F + A N ++++
Sbjct: 55 DEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQ----AIAGLNGFNIL 110
Query: 158 DK 159
+K
Sbjct: 111 NK 112
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 43/75 (57%), Gaps = 2/75 (2%)
Query: 80 PEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
P + +++ +FVG + + E+ L++ FS+ G + S +V ++ETG +G+ F E+ D +
Sbjct: 2 PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61
Query: 139 -VVDKIRGFAFIEFN 152
+ +R EF+
Sbjct: 62 TALSAMRNLNGREFS 76
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 38/53 (71%), Gaps = 3/53 (5%)
Query: 89 MFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF-NDYDV 139
+FVGG+ +E ++R +F+++G+++ V ++T++ TG +G+ F+ F ND DV
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDV 64
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 30/49 (61%), Gaps = 1/49 (2%)
Query: 87 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 134
K +FV + D E LR F +G I+ ++MV +K +G RG+AFIE+
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEY 151
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 28/40 (70%)
Query: 99 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
E DLRE FS++G I V++V ++++ RGFAF+ F + D
Sbjct: 60 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 99
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 28/40 (70%)
Query: 99 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
E DLRE FS++G I V++V ++++ RGFAF+ F + D
Sbjct: 26 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 65
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 32/52 (61%), Gaps = 2/52 (3%)
Query: 87 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 137
+K+FVG L K Q EDD+R F FG IE ++ + G +G AF++++ +
Sbjct: 16 RKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPD-GNSKGCAFVKYSSH 66
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 28/40 (70%)
Query: 99 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
E DLRE FS++G I V++V ++++ RGFAF+ F + D
Sbjct: 29 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 68
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 40.4 bits (93), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 28/40 (70%)
Query: 99 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
E DLRE FS++G I V++V ++++ RGFAF+ F + D
Sbjct: 29 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 68
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 40.0 bits (92), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 32/56 (57%), Gaps = 1/56 (1%)
Query: 87 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVD 141
+K+F+GGL + E+ LR Y+ Q+G + ++ + + RGF F+ F+ VD
Sbjct: 28 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVD 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 = 39.7 bits (91), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 45/95 (47%), Gaps = 12/95 (12%)
Query: 52 AMEEAQSEEEVDMEIPGPPHM----DKLEIGKPEANATVKKMFVGGLK-DQEEDDLREYF 106
M+ S+ GPP +K EI K + ++VG + DL +F
Sbjct: 5 CMQTTHSKMTAGAYTEGPPQPLSAEEKKEIDK-------RSVYVGNVDYGSTAQDLEAHF 57
Query: 107 SQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVD 141
S G+I + ++ +K +G +G+A+IEF + + VD
Sbjct: 58 SSCGSINRITILCDKFSGHPKGYAYIEFAERNSVD 92
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 32/53 (60%), Gaps = 2/53 (3%)
Query: 84 ATVKK-MFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 134
AT K+ ++VGGL ++ +D L F FG I + + + ET RGFAF+EF
Sbjct: 60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 112
>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 = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 35/54 (64%), Gaps = 1/54 (1%)
Query: 82 ANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 134
A A + +++VG + + ED +R+ F+ FG I+S++M + T +GFAF+E+
Sbjct: 24 ALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEY 77
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 24/40 (60%)
Query: 95 KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 134
+D +DD++ F FG I+S + + TG +G+ FIE+
Sbjct: 135 QDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEY 174
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 7/58 (12%)
Query: 78 GKPEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 134
G + T+ ++VGGL D E DLR +F QFG I ++ +V ++ AFI+F
Sbjct: 4 GSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQC------AFIQF 55
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 40/72 (55%), Gaps = 5/72 (6%)
Query: 89 MFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIRGFA 147
++VG L + ED LR F FG I+++ ++ + +TG +G+ FI F+D + + A
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR----A 63
Query: 148 FIEFNDYDVVDK 159
+ N +++ +
Sbjct: 64 LEQLNGFELAGR 75
>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 = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 36/57 (63%), Gaps = 1/57 (1%)
Query: 79 KPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 134
+ A A + +++VG + + ED +R+ F+ FG I+S++M + T +GFAF+E+
Sbjct: 6 RQRALAIMCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEY 62
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 5/66 (7%)
Query: 70 PHMDKLEIGKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRG 128
P +D+L E +++V + +D +DD++ F FG I+S + + TG +G
Sbjct: 98 PIIDQLA----EEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKG 153
Query: 129 FAFIEF 134
+ FIE+
Sbjct: 154 YGFIEY 159
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 32/53 (60%), Gaps = 2/53 (3%)
Query: 84 ATVKK-MFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 134
AT K+ ++VGGL ++ +D L F FG I + + + ET RGFAF+EF
Sbjct: 9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 61
>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 = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 32/53 (60%), Gaps = 2/53 (3%)
Query: 84 ATVKK-MFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 134
AT K+ ++VGGL ++ +D L F FG I + + + ET RGFAF+EF
Sbjct: 4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 56
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 33/52 (63%), Gaps = 2/52 (3%)
Query: 87 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 137
+K+FVG L K Q ++D+R+ F FGTI+ ++ + G +G AF++F +
Sbjct: 13 RKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPD-GTSKGCAFVKFQTH 63
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/50 (42%), Positives = 34/50 (68%), Gaps = 4/50 (8%)
Query: 87 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFN 135
K +FV GL +D E+ L+E F G++ +VT++ETG+ +GF F++FN
Sbjct: 16 KTLFVKGLSEDTTEETLKESFD--GSVR-ARIVTDRETGSSKGFGFVDFN 62
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 31/53 (58%), Gaps = 1/53 (1%)
Query: 83 NATVKKMFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 134
+ T + ++VGGL ++ +D L F FG I + + + ET RGFAF+EF
Sbjct: 2 STTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 54
>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 = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 5/66 (7%)
Query: 70 PHMDKLEIGKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRG 128
P +D+L E +++V + +D +DD++ F FG I+S + + TG +G
Sbjct: 97 PIIDQLA----EEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKG 152
Query: 129 FAFIEF 134
+ FIE+
Sbjct: 153 YGFIEY 158
Score = 35.8 bits (81), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 34/57 (59%), Gaps = 1/57 (1%)
Query: 79 KPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 134
+ A A +++VG + + ED +R+ F+ FG I+S++ + T +GFAF+E+
Sbjct: 5 RQRALAIXCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEY 61
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 35/59 (59%), Gaps = 1/59 (1%)
Query: 86 VKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKI 143
++ ++VG L + ++E FSQFG + +V ++ ++ET +GF F+E + V + I
Sbjct: 1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAI 59
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 42/66 (63%), Gaps = 2/66 (3%)
Query: 73 DKLEIGKPEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAF 131
D+LE G P+ + +FV + ++ +ED+++E F +G I+++++ ++ TG +G+A
Sbjct: 14 DELEPG-PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYAL 72
Query: 132 IEFNDY 137
+E+ +
Sbjct: 73 VEYETH 78
>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 = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 39/65 (60%), Gaps = 4/65 (6%)
Query: 74 KLEIGKPEANATVK--KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFA 130
K+ +P ++A+++ ++V GL K + +L + FSQ+G I + ++ ++ TG RG
Sbjct: 75 KVSYARP-SSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVG 133
Query: 131 FIEFN 135
FI F+
Sbjct: 134 FIRFD 138
>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 84
Score = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 33/55 (60%), Gaps = 1/55 (1%)
Query: 83 NATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
N + +++G + DQ E+ + + S G + ++ M+ + +TG +G+AFIEF D
Sbjct: 1 NPPSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRD 55
>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 = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 29/49 (59%), Gaps = 1/49 (2%)
Query: 87 KKMFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 134
+ ++VGGL ++ +D L F FG I + + + ET RGFAF+EF
Sbjct: 3 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 51
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 39/65 (60%), Gaps = 4/65 (6%)
Query: 74 KLEIGKPEANATVK--KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFA 130
K+ +P ++A+++ ++V GL K + ++ + FSQ+G I + ++ ++ TG RG
Sbjct: 77 KVSYARP-SSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVG 135
Query: 131 FIEFN 135
FI F+
Sbjct: 136 FIRFD 140
Score = 36.2 bits (82), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 27/48 (56%)
Query: 95 KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 142
++ +D+ + F G IES +V +K TG G+ F+ ++D + DK
Sbjct: 14 QNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 37.0 bits (84), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 36/68 (52%), Gaps = 1/68 (1%)
Query: 78 GKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
G P + K+FVG + + +E DL+ F +FG I + ++ ++ TG +G AF+ +
Sbjct: 7 GVPMKDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCA 66
Query: 137 YDVVDKIR 144
D K +
Sbjct: 67 RDSALKAQ 74
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 36.6 bits (83), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 32/52 (61%), Gaps = 2/52 (3%)
Query: 87 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 137
+K+FVG L K Q E+D+ F FG I+ ++ + G+ +G AF++F+ +
Sbjct: 16 RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPD-GSSKGCAFVKFSSH 66
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 36.6 bits (83), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 30/48 (62%), Gaps = 1/48 (2%)
Query: 89 MFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFN 135
+++ GL + + D+ + FS+FG I + ++ ++ TG RG AFI F+
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFD 138
Score = 33.9 bits (76), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 23/40 (57%)
Query: 95 KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 134
++ +D+LR FS G +ES ++ +K G G+ F+ +
Sbjct: 12 QNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNY 51
>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 = 36.6 bits (83), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 42/66 (63%), Gaps = 2/66 (3%)
Query: 73 DKLEIGKPEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAF 131
D+LE G P+ + +FV + ++ +ED+++E F +G I+++++ ++ TG +G+A
Sbjct: 60 DELEPG-PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYAL 118
Query: 132 IEFNDY 137
+E+ +
Sbjct: 119 VEYETH 124
>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 = 36.6 bits (83), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 30/48 (62%), Gaps = 1/48 (2%)
Query: 89 MFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFN 135
+++ GL + + D+ + FS+FG I + ++ ++ TG RG AFI F+
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFD 138
Score = 33.9 bits (76), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 23/40 (57%)
Query: 95 KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 134
++ +D+LR FS G +ES ++ +K G G+ F+ +
Sbjct: 12 QNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNY 51
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 36.6 bits (83), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 89 MFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFN 135
++V GL K + ++ + FSQ+G I + ++ ++ TG RG FI F+
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFD 51
>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 90
Score = 36.2 bits (82), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 13/50 (26%), Positives = 34/50 (68%), Gaps = 1/50 (2%)
Query: 89 MFVGGLKDQE-EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 137
+FV G+ ++ E+D+ + F+++G I+++++ ++ TG +G+ +E+ Y
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 59
>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 = 36.2 bits (82), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 13/50 (26%), Positives = 34/50 (68%), Gaps = 1/50 (2%)
Query: 89 MFVGGLKDQE-EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 137
+FV G+ ++ E+D+ + F+++G I+++++ ++ TG +G+ +E+ Y
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 59
>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 = 36.2 bits (82), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 13/50 (26%), Positives = 34/50 (68%), Gaps = 1/50 (2%)
Query: 89 MFVGGLKDQE-EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 137
+FV G+ ++ E+D+ + F+++G I+++++ ++ TG +G+ +E+ Y
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 61
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 36.2 bits (82), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 13/50 (26%), Positives = 34/50 (68%), Gaps = 1/50 (2%)
Query: 89 MFVGGLKDQE-EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 137
+FV G+ ++ E+D+ + F+++G I+++++ ++ TG +G+ +E+ Y
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 59
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 36.2 bits (82), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 26/41 (63%)
Query: 96 DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
DQ E+ + + S G + ++ M+ + +TG +G+AFIEF D
Sbjct: 13 DQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRD 53
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 35.8 bits (81), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 27/48 (56%)
Query: 95 KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 142
++ +D+ + F G IES +V +K TG G+ F+ ++D + DK
Sbjct: 14 QNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
>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 = 0.012, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 26/41 (63%)
Query: 96 DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
DQ E+ + + S G + ++ M+ + +TG +G+AFIEF D
Sbjct: 14 DQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRD 54
>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 = 35.8 bits (81), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 13/50 (26%), Positives = 34/50 (68%), Gaps = 1/50 (2%)
Query: 89 MFVGGLKDQE-EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 137
+FV G+ ++ E+D+ + F+++G I+++++ ++ TG +G+ +E+ Y
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 75
>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 = 35.8 bits (81), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 13/50 (26%), Positives = 34/50 (68%), Gaps = 1/50 (2%)
Query: 89 MFVGGLKDQE-EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 137
+FV G+ ++ E+D+ + F+++G I+++++ ++ TG +G+ +E+ Y
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 74
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 35.4 bits (80), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 40/80 (50%), Gaps = 9/80 (11%)
Query: 66 IPGPPHMDKLEIGKPEANATVKKMFVGGLKDQEED-DLREYFSQFGTIESVNMVTNKETG 124
+P HM+ +P K++ V + + D DLR+ F QFG I V ++ N E G
Sbjct: 15 VPRGSHMNTENKSQP------KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERG 67
Query: 125 AKRGFAFIEFNDYDVVDKIR 144
+K GF F+ F + D+ R
Sbjct: 68 SK-GFGFVTFENSADADRAR 86
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 35.4 bits (80), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 99 EDDLREYFSQFGT-IESVNMVTNKETGAKRGFAFIEFN 135
EDD+R G V ++ NK +G RGFAF+EF+
Sbjct: 15 EDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFS 52
>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 = 35.4 bits (80), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 34/58 (58%), Gaps = 1/58 (1%)
Query: 84 ATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVV 140
A + ++VG + ++L +F G++ V ++ +K +G +GFA+IEF+D + V
Sbjct: 4 ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESV 61
>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 = 35.4 bits (80), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 34/58 (58%), Gaps = 1/58 (1%)
Query: 84 ATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVV 140
A + ++VG + ++L +F G++ V ++ +K +G +GFA+IEF+D + V
Sbjct: 3 ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESV 60
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 35.4 bits (80), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 1/65 (1%)
Query: 87 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIRG 145
K +F+ L D EE+ L E QFG ++ V +V + +T +G AF +F + K
Sbjct: 16 KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 75
Query: 146 FAFIE 150
A +E
Sbjct: 76 AASLE 80
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 35.4 bits (80), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 33/55 (60%), Gaps = 2/55 (3%)
Query: 89 MFVGGLKDQ-EEDDLREYFSQFGTI-ESVNMVTNKETGAKRGFAFIEFNDYDVVD 141
+F+G L + +E L + FS FG I ++ ++ + +TG +G+AFI F +D D
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASD 62
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 35.4 bits (80), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 21/37 (56%)
Query: 100 DDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
D LR F ++G + V + T A RGFAF+ F+D
Sbjct: 28 DSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHD 64
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 35.0 bits (79), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 31/48 (64%), Gaps = 1/48 (2%)
Query: 88 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 134
K+F+G + ++ +E DL+ F +FG I + ++ ++ TG +G AF+ +
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTY 62
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 35.0 bits (79), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 34/61 (55%), Gaps = 3/61 (4%)
Query: 85 TVKKMFVGGLKDQEED-DLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKI 143
T K++ V + + D DLR+ F QFG I V ++ N E G+K GF F+ F + D+
Sbjct: 14 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERGSK-GFGFVTFENSADADRA 71
Query: 144 R 144
R
Sbjct: 72 R 72
>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 = 34.7 bits (78), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 32/58 (55%), Gaps = 2/58 (3%)
Query: 89 MFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIE-FNDYDVVDKIR 144
+FVG L + +D++ F+ FG I +V + TG +G+ F+ FN +D + I+
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 75
>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 = 34.7 bits (78), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 28/50 (56%), Gaps = 3/50 (6%)
Query: 88 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGA--KRGFAFIEF 134
KMFVG + + E DLRE F Q+G + +N++ ++ +G F+ F
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTF 54
>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 = 34.7 bits (78), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 23/40 (57%)
Query: 95 KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 134
++ +D+LR FS G +ES ++ +K G G+ F+ +
Sbjct: 14 QNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNY 53
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 34.7 bits (78), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 32/59 (54%), Gaps = 2/59 (3%)
Query: 78 GKPEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKE-TGAKRGFAFIEF 134
G+ T K+ V + Q + ++RE FS FG +++V + TGA RGF F++F
Sbjct: 7 GQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDF 65
>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 = 34.3 bits (77), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 23/37 (62%)
Query: 99 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFN 135
+D L F ++G+I N++ +K TG RG AF+ +N
Sbjct: 27 DDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYN 63
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 34.3 bits (77), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 23/37 (62%)
Query: 99 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFN 135
+D L F ++G+I N++ +K TG RG AF+ +N
Sbjct: 103 DDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYN 139
Score = 27.7 bits (60), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 11/40 (27%), Positives = 22/40 (55%)
Query: 95 KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 134
+D + +L F G I + ++ + +TG G+AF++F
Sbjct: 13 QDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDF 52
>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 = 34.3 bits (77), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 22/37 (59%)
Query: 100 DDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
D LR F ++G + V + ++ T RGFAF+ F+D
Sbjct: 62 DTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHD 98
>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 = 33.9 bits (76), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 23/37 (62%)
Query: 99 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFN 135
+D L F ++G+I N++ +K TG RG AF+ +N
Sbjct: 114 DDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYN 150
>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 = 33.9 bits (76), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 23/40 (57%)
Query: 95 KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 134
++ +D+LR FS G +ES ++ +K G G+ F+ +
Sbjct: 29 QNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNY 68
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 33.5 bits (75), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 30/58 (51%), Gaps = 6/58 (10%)
Query: 89 MFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIRG 145
+FVG D ED+LRE+FSQ+G + V + R FAF+ F D + + G
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCG 60
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 33.5 bits (75), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 30/54 (55%), Gaps = 3/54 (5%)
Query: 89 MFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVD 141
+FVG L + +D++ F+ FG I +V + TG +G+ F+ F Y+ +D
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSF--YNKLD 69
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 33.5 bits (75), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 24/40 (60%)
Query: 99 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
+DL FS++G + V ++ +K+T +G AFI F D D
Sbjct: 30 NNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKD 69
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 33.5 bits (75), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 22/37 (59%)
Query: 100 DDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
D LR F ++G + V + ++ T RGFAF+ F+D
Sbjct: 85 DTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHD 121
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 32.7 bits (73), Expect = 0.098, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 37/75 (49%), Gaps = 7/75 (9%)
Query: 86 VKKMFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIR 144
V ++V L D +D+ LR+ FS FGTI S ++ E G +GF F+ F+ + K
Sbjct: 15 VVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMM--EGGRSKGFGFVCFSSPEEATK-- 70
Query: 145 GFAFIEFNDYDVVDK 159
A E N V K
Sbjct: 71 --AVTEMNGRIVATK 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 = 32.7 bits (73), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 5/63 (7%)
Query: 88 KMFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD----VVDK 142
+FVG L +D+ LR F F + S +++ + +TG+ RG+ F+ F D +D
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 143 IRG 145
++G
Sbjct: 63 MQG 65
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 32.3 bits (72), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 5/63 (7%)
Query: 88 KMFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD----VVDK 142
+FVG L +D+ LR F F + S +++ + +TG+ RG+ F+ F D +D
Sbjct: 89 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 148
Query: 143 IRG 145
++G
Sbjct: 149 MQG 151
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 32.3 bits (72), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 33/57 (57%), Gaps = 2/57 (3%)
Query: 88 KMFVGGL-KDQEEDDLREYFSQFGTIESVNM-VTNKETGAKRGFAFIEFNDYDVVDK 142
K+ +G L ++ +D + E FS +G I+ ++M V +G+A++EF + D +K
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEK 62
>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 = 32.3 bits (72), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 30/50 (60%), Gaps = 2/50 (4%)
Query: 88 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
K+F+ GL +++L E GT++ + +VTN+ G +G A++E+ +
Sbjct: 19 KLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYEN 67
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 32.0 bits (71), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 11/40 (27%), Positives = 24/40 (60%)
Query: 101 DLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVV 140
DL ++FS G + V +++++ + +G A++EF + V
Sbjct: 41 DLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSV 80
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 31.6 bits (70), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 31/61 (50%), Gaps = 7/61 (11%)
Query: 88 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND-YDVVDKIRG 145
K++VG L + +L FS +G + +V + N GFAF+EF D D D +RG
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPP-----GFAFVEFEDPRDAEDAVRG 56
Query: 146 F 146
Sbjct: 57 L 57
>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 = 0.24, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 88 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 134
++FV L E+DL + FS +G + ++ + T +GFAF+ F
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTF 57
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 30.4 bits (67), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 29/67 (43%), Gaps = 19/67 (28%)
Query: 88 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIRGF 146
K+F+GGL ++ E L+ F + G I V ++ D K RGF
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIK------------------DRTSKSRGF 50
Query: 147 AFIEFND 153
AFI F +
Sbjct: 51 AFITFEN 57
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 30.4 bits (67), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 9/63 (14%)
Query: 83 NATVKKMFVGGLKDQEE-DDLREYFSQFGTIES--------VNMVTNKETGAKRGFAFIE 133
N+ +FV GL + + + +YF Q G I++ +N+ T++ETG +G A +
Sbjct: 4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVS 63
Query: 134 FND 136
F+D
Sbjct: 64 FDD 66
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 30.4 bits (67), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 30/59 (50%), Gaps = 7/59 (11%)
Query: 88 KMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND-YDVVDKIR 144
K++VG L + + +L F +G + SV + N GFAF+EF D D D +R
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPP-----GFAFVEFEDPRDAADAVR 128
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 30.0 bits (66), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 9/57 (15%)
Query: 89 MFVGGLKDQEE-DDLREYFSQFGTIES--------VNMVTNKETGAKRGFAFIEFND 136
+FV GL + + + +YF Q G I++ +N+ T++ETG +G A + F+D
Sbjct: 16 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDD 72
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 30.0 bits (66), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 9/56 (16%)
Query: 84 ATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
A VK +FV L + E+ L + FSQFG +E V + + +AFI F++ D
Sbjct: 9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERD 56
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 30.0 bits (66), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 30/59 (50%), Gaps = 7/59 (11%)
Query: 88 KMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND-YDVVDKIR 144
K++VG L + + +L F +G + SV + N GFAF+EF D D D +R
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPP-----GFAFVEFEDPRDAADAVR 128
>pdb|1JI8|A Chain A, Solution Structure Of Pyrobaculum Aerophilum DsrcGAMMA
Subunit Of Dissimilatory Sulfite Reductase
Length = 111
Score = 29.6 bits (65), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 14/23 (60%), Positives = 16/23 (69%), Gaps = 1/23 (4%)
Query: 102 LREYFSQFGTIESVNMVTNKETG 124
LREY+ FGT + MVT KETG
Sbjct: 59 LREYWETFGTCPPIKMVT-KETG 80
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 29.3 bits (64), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 14/55 (25%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 89 MFVGGLKDQEED-DLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 142
+++ GL+ D DL + +G I S + +K T +G+ F++F+ K
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQK 62
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 28.9 bits (63), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 32/59 (54%), Gaps = 6/59 (10%)
Query: 88 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIRG 145
K+FVG +D ++L+++F Q+G E V++ K R FAF+ F D V + G
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYG--EVVDVFIPKPF---RAFAFVTFADDKVAQSLCG 66
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 28.9 bits (63), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 89 MFVGGLKDQEED-DLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
+F+ L + D DL F FG + S + +K+T + F F+ F++ D
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPD 93
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 28.9 bits (63), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 11/30 (36%), Positives = 21/30 (70%)
Query: 111 TIESVNMVTNKETGAKRGFAFIEFNDYDVV 140
+I SV +V +K+T +GF ++EF++ D +
Sbjct: 40 SIRSVRLVRDKDTDKFKGFCYVEFDEVDSL 69
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 28.5 bits (62), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 35/78 (44%), Gaps = 13/78 (16%)
Query: 66 IPGPPHMDKLEIGKPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETG 124
+P HM + E + ++FV D +E +L E F FG ++ V ++
Sbjct: 15 VPRGSHMHH----RQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN----- 65
Query: 125 AKRGFAFIEFNDYDVVDK 142
GFAF+EF + + K
Sbjct: 66 ---GFAFVEFEEAESAAK 80
>pdb|2JBR|A Chain A, Structure Of The Monooxygenase Component Of P-
Hydroxyphenylacetate Hydroxylase From Acinetobacter
Baumanni
pdb|2JBR|B Chain B, Structure Of The Monooxygenase Component Of P-
Hydroxyphenylacetate Hydroxylase From Acinetobacter
Baumanni
pdb|2JBR|C Chain C, Structure Of The Monooxygenase Component Of P-
Hydroxyphenylacetate Hydroxylase From Acinetobacter
Baumanni
pdb|2JBR|D Chain D, Structure Of The Monooxygenase Component Of P-
Hydroxyphenylacetate Hydroxylase From Acinetobacter
Baumanni
pdb|2JBS|A Chain A, Structure Of The Monooxygenase Component Of P-
Hydroxyphenylacetate Hydroxylase From Acinetobacter
Baumannii
pdb|2JBS|B Chain B, Structure Of The Monooxygenase Component Of P-
Hydroxyphenylacetate Hydroxylase From Acinetobacter
Baumannii
pdb|2JBS|C Chain C, Structure Of The Monooxygenase Component Of P-
Hydroxyphenylacetate Hydroxylase From Acinetobacter
Baumannii
pdb|2JBS|D Chain D, Structure Of The Monooxygenase Component Of P-
Hydroxyphenylacetate Hydroxylase From Acinetobacter
Baumannii
pdb|2JBT|A Chain A, Structure Of The Monooxygenase Component Of P-
Hydroxyphenylacetate Hydroxylase From Acinetobacter
Baumannii
pdb|2JBT|B Chain B, Structure Of The Monooxygenase Component Of P-
Hydroxyphenylacetate Hydroxylase From Acinetobacter
Baumannii
pdb|2JBT|C Chain C, Structure Of The Monooxygenase Component Of P-
Hydroxyphenylacetate Hydroxylase From Acinetobacter
Baumannii
pdb|2JBT|D Chain D, Structure Of The Monooxygenase Component Of P-
Hydroxyphenylacetate Hydroxylase From Acinetobacter
Baumannii
Length = 422
Score = 28.5 bits (62), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 30/58 (51%), Gaps = 8/58 (13%)
Query: 109 FGTIESV--NMVTNKETGAKRG-----FAFIEFNDYDV-VDKIRGFAFIEFNDYDVVD 158
FG +E V ++ N + G G +A + FN +D +KI F I +DY++VD
Sbjct: 151 FGKVEEVEGGIILNGDYGWSSGCDHAEYAIVGFNRFDADGNKIYSFGVIPRSDYEIVD 208
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 28.1 bits (61), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 11/46 (23%), Positives = 22/46 (47%)
Query: 99 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIR 144
+ E FG++E +V ++ TG +G+ F E+ D + +
Sbjct: 109 QQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAK 154
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 28.1 bits (61), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 11/46 (23%), Positives = 22/46 (47%)
Query: 99 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIR 144
+ E FG++E +V ++ TG +G+ F E+ D + +
Sbjct: 109 QQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAK 154
>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
pdb|3H2U|D Chain D, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
Length = 283
Score = 28.1 bits (61), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 11/46 (23%), Positives = 22/46 (47%)
Query: 99 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIR 144
+ E FG++E +V ++ TG +G+ F E+ D + +
Sbjct: 107 QQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAK 152
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 28.1 bits (61), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 11/40 (27%), Positives = 22/40 (55%)
Query: 95 KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 134
+D + +L F G I + ++ + +TG G+AF++F
Sbjct: 13 QDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDF 52
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 27.7 bits (60), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 35/89 (39%), Gaps = 26/89 (29%)
Query: 78 GKPEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
G PE A VK +FV L E+ L + FS+FG +E V
Sbjct: 7 GDPEVMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVK-------------------- 46
Query: 137 YDVVDKIRGFAFIEFNDYDVVDKIVCKYN 165
K++ +AF+ F D K + + N
Sbjct: 47 -----KLKDYAFVHFEDRGAAVKAMDEMN 70
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 27.7 bits (60), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 30/57 (52%), Gaps = 12/57 (21%)
Query: 96 DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD----VVDKIRGFAF 148
D +E +L E F FG ++ V ++ GFAF+EF + + ++++ G +F
Sbjct: 15 DVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAKAIEEVHGKSF 63
>pdb|2E5G|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 21
Length = 94
Score = 26.9 bits (58), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 27/52 (51%), Gaps = 6/52 (11%)
Query: 86 VKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
++ +FV G + + L EYF FG + SV V +K+ G FA +E D
Sbjct: 8 LRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGD 54
>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 = 26.9 bits (58), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 109 FGTIESVNMVTNKETGAKRGFAFIE-FNDYDVVDKIR 144
FG I +V + TG +G+ F+ FN +D + I+
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 66
>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 = 26.9 bits (58), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 10/38 (26%), Positives = 21/38 (55%)
Query: 99 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
+ DL + F FG + S + +K+T + F F+ +++
Sbjct: 39 DQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDN 76
>pdb|2GHP|A Chain A, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|B Chain B, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|C Chain C, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|D Chain D, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|E Chain E, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|F Chain F, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|G Chain G, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|H Chain H, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
Length = 292
Score = 26.9 bits (58), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 98 EEDDLREYFSQFGTIESVNM-VTNKETGAKRGFAFIEFNDYDVVDK 142
+E+ LRE F FG+IE +N+ KE AF F + D ++
Sbjct: 224 DENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFXVFENKDSAER 269
>pdb|2DIS|A Chain A, Solution Structure Of The Rrm Domain Of Unnamed Protein
Product
Length = 109
Score = 26.2 bits (56), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 13/60 (21%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 88 KMFVGGL-KDQEEDDLREYFSQF--GTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIR 144
++F+GG+ K ++ +++ E ++ G ++ + + + RGFAF+E+ + R
Sbjct: 10 RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 69
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
0.316 0.135 0.395
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,107,002
Number of Sequences: 62578
Number of extensions: 204305
Number of successful extensions: 786
Number of sequences better than 100.0: 155
Number of HSP's better than 100.0 without gapping: 111
Number of HSP's successfully gapped in prelim test: 44
Number of HSP's that attempted gapping in prelim test: 598
Number of HSP's gapped (non-prelim): 218
length of query: 168
length of database: 14,973,337
effective HSP length: 92
effective length of query: 76
effective length of database: 9,216,161
effective search space: 700428236
effective search space used: 700428236
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: 48 (23.1 bits)