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= 026534
(237 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 63.5 bits (153), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 34/86 (39%), Positives = 51/86 (59%), Gaps = 3/86 (3%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADR-VSR 161
KIFVG +P +LR YF +FG + +V + D ++ RGFGF+TF +E D+ V+
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
Query: 162 RSHEICGQQVAIDSATPLD--DAGPS 185
H+I G++V + A P D +GPS
Sbjct: 72 HFHDIMGKKVEVKRAEPRDSKSSGPS 97
Score = 30.8 bits (68), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 11 RGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKE 48
RG GFITF SV+ + + H++ G V V RA P++
Sbjct: 52 RGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVKRAEPRD 90
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 62.4 bits (150), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 31/78 (39%), Positives = 48/78 (61%), Gaps = 5/78 (6%)
Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRVS 160
G K+FVGR ++ TAE+L+++F ++G ++DV++PK R F FVTFA++ VA +
Sbjct: 11 GSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSLC 65
Query: 161 RRSHEICGQQVAIDSATP 178
I G V I +A P
Sbjct: 66 GEDLIIKGISVHISNAEP 83
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 58.5 bits (140), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 32/86 (37%), Positives = 46/86 (53%), Gaps = 3/86 (3%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAE-EVVADRVSR 161
K+FVG L T E LR YFS++G ++D + KD RGFGFV F + V ++
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 162 RSHEICGQQVAIDSATP--LDDAGPS 185
R H + G+ + TP + +GPS
Sbjct: 78 RPHTLDGRNIDPKPCTPRGMQPSGPS 103
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 58.2 bits (139), Expect = 4e-09, Method: Composition-based stats.
Identities = 30/74 (40%), Positives = 40/74 (54%), Gaps = 1/74 (1%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRVSR-R 162
IFVG L T ED++ YF +FG++ D + D HRGFGFVTF E + ++V
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 163 SHEICGQQVAIDSA 176
HEI + V A
Sbjct: 62 FHEINNKMVECKKA 75
Score = 33.1 bits (74), Expect = 0.12, Method: Composition-based stats.
Identities = 16/42 (38%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 4 DQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRA 44
D+ + HRG GF+TF S D VE + + HE+ V +A
Sbjct: 34 DKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA 75
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 58.2 bits (139), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 33/87 (37%), Positives = 47/87 (54%), Gaps = 1/87 (1%)
Query: 93 RGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAE 152
RG G K+F+G L + T E LR YF +FG + + V +DP RGFGFVTF +
Sbjct: 17 RGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMD 76
Query: 153 EVVADRVSRRS-HEICGQQVAIDSATP 178
+ D+V +S HE+ + + A P
Sbjct: 77 QAGVDKVLAQSRHELDSKTIDPKVAFP 103
Score = 28.1 bits (61), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 3 KDQGSKAHRGIGFITFASADSVENLMVDT-HELGGSTVVVDRATPK 47
+D +K RG GF+TF V+ ++ + HEL T+ A P+
Sbjct: 59 RDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVAFPR 104
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 57.8 bits (138), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 31/83 (37%), Positives = 47/83 (56%), Gaps = 1/83 (1%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVAD-RVS 160
+K+F+G L E T E LR Y+ ++G++ D V +DP RGFGFVTF+ D ++
Sbjct: 28 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA 87
Query: 161 RRSHEICGQQVAIDSATPLDDAG 183
R H I G+ V A +++G
Sbjct: 88 ARPHSIDGRVVEPKRAVAREESG 110
Score = 32.0 bits (71), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 3 KDQGSKAHRGIGFITFASADSVENLMVDT-HELGGSTVVVDRATPKED 49
+D SK RG GF+TF+S V+ M H + G V RA +E+
Sbjct: 61 RDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAREE 108
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 57.4 bits (137), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 31/84 (36%), Positives = 49/84 (58%), Gaps = 7/84 (8%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRVSRRS 163
+FVGR + T ++LR +FS++G ++DV++PK R F FVTFA++ +A +
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGED 62
Query: 164 HEICGQQVAIDSATPL--DDAGPS 185
I G V I +A P ++GPS
Sbjct: 63 LIIKGISVHISNAEPKHNSNSGPS 86
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 57.0 bits (136), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 37/91 (40%), Positives = 51/91 (56%), Gaps = 5/91 (5%)
Query: 98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGH-RGFGFVTFAEEVVA 156
Q+ I +G LP + T +DL+ YFS FG +L V V KD K TGH +GFGFV F E
Sbjct: 13 QKTSDLIVLG-LPWKTTEQDLKEYFSTFGEVLMVQVKKDLK-TGHSKGFGFVRFTEYETQ 70
Query: 157 DRVSRRSHEICGQ--QVAIDSATPLDDAGPS 185
+V + H I G+ + ++ D+GPS
Sbjct: 71 VKVMSQRHMIDGRWCDCKLPNSKQSQDSGPS 101
>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 = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 45/79 (56%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRVSRR 162
K+F+G L + T ++LR YF ++G + D+ + KDP RGFGF++F + D V +
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 163 SHEICGQQVAIDSATPLDD 181
H + G+ + A P D+
Sbjct: 65 QHILDGKVIDPKRAIPRDE 83
Score = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 41/177 (23%), Positives = 66/177 (37%), Gaps = 49/177 (27%)
Query: 3 KDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGY 62
KD + RG GF++F SV+ ++ H L G + RA P+++
Sbjct: 37 KDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDGKVIDPKRAIPRDE------------- 83
Query: 63 GAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYF 122
D G KIFVG + + ++ +F
Sbjct: 84 ---------------------QDKTG--------------KIFVGGIGPDVRPKEFEEFF 108
Query: 123 SRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRVSRRSH-EICGQQVAIDSATP 178
S++G I+D + D RGFGFVT+ DRV + + +++ I A P
Sbjct: 109 SQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAEP 165
Score = 27.3 bits (59), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 13/45 (28%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 4 DQGSKAHRGIGFITFASADSVENLMVDTH-ELGGSTVVVDRATPK 47
D+ + RG GF+T+ SAD+V+ + + + + + RA P+
Sbjct: 122 DKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAEPR 166
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 55.8 bits (133), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 42/132 (31%), Positives = 64/132 (48%), Gaps = 8/132 (6%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFA--EEVVADRV 159
+K+F+G L E T E LR +F ++G + D V +DP RGFGFVT+A EEV A +
Sbjct: 15 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA-AM 73
Query: 160 SRRSHEICGQQVAIDSATPLDDAGPSQNFMMNAAETFGGYGGP-----MRTYGRMYGSLD 214
+ R H++ G+ V A +D+ + GG +R Y YG ++
Sbjct: 74 NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 133
Query: 215 FDDWGYGMGSGR 226
+ GSG+
Sbjct: 134 VIEIMTDRGSGK 145
Score = 54.3 bits (129), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 45/176 (25%), Positives = 72/176 (40%), Gaps = 44/176 (25%)
Query: 3 KDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGG 61
+D +K RG GF+T+A+ + V+ M H++ G V RA +ED RP
Sbjct: 48 RDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP-------- 99
Query: 62 YGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRY 121
A+++ KKIFVG + ++ LR Y
Sbjct: 100 ----GAHLTV------------------------------KKIFVGGIKEDTEEHHLRDY 125
Query: 122 FSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADR-VSRRSHEICGQQVAIDSA 176
F ++G+I + + D RGF FVTF + D+ V ++ H + G + A
Sbjct: 126 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA 181
Score = 32.7 bits (73), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 4 DQGSKAHRGIGFITFASADSVENLMVDT-HELGGSTVVVDRATPKED 49
D+GS RG F+TF DSV+ +++ H + G V +A K++
Sbjct: 140 DRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQE 186
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 55.8 bits (133), Expect = 2e-08, Method: Composition-based stats.
Identities = 28/65 (43%), Positives = 40/65 (61%), Gaps = 1/65 (1%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRVSRR 162
K+F+G L + T E LR YF +FG + + V +DP RGFGFVTF ++ D+V +
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 163 S-HEI 166
S HE+
Sbjct: 62 SRHEL 66
Score = 27.3 bits (59), Expect = 6.7, Method: Composition-based stats.
Identities = 13/38 (34%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 3 KDQGSKAHRGIGFITFASADSVENLMVDT-HELGGSTV 39
+D +K RG GF+TF V+ ++ + HEL T+
Sbjct: 34 RDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTI 71
>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 = 55.8 bits (133), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 42/132 (31%), Positives = 64/132 (48%), Gaps = 8/132 (6%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFA--EEVVADRV 159
+K+F+G L E T E LR +F ++G + D V +DP RGFGFVT+A EEV A +
Sbjct: 13 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA-AM 71
Query: 160 SRRSHEICGQQVAIDSATPLDDAGPSQNFMMNAAETFGGYGGP-----MRTYGRMYGSLD 214
+ R H++ G+ V A +D+ + GG +R Y YG ++
Sbjct: 72 NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 131
Query: 215 FDDWGYGMGSGR 226
+ GSG+
Sbjct: 132 VIEIMTDRGSGK 143
Score = 53.9 bits (128), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 45/176 (25%), Positives = 72/176 (40%), Gaps = 44/176 (25%)
Query: 3 KDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGG 61
+D +K RG GF+T+A+ + V+ M H++ G V RA +ED RP
Sbjct: 46 RDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP-------- 97
Query: 62 YGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRY 121
A+++ KKIFVG + ++ LR Y
Sbjct: 98 ----GAHLTV------------------------------KKIFVGGIKEDTEEHHLRDY 123
Query: 122 FSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADR-VSRRSHEICGQQVAIDSA 176
F ++G+I + + D RGF FVTF + D+ V ++ H + G + A
Sbjct: 124 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA 179
Score = 32.7 bits (73), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 4 DQGSKAHRGIGFITFASADSVENLMVDT-HELGGSTVVVDRATPKED 49
D+GS RG F+TF DSV+ +++ H + G V +A K++
Sbjct: 138 DRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQE 184
>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 = 55.8 bits (133), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 42/132 (31%), Positives = 64/132 (48%), Gaps = 8/132 (6%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFA--EEVVADRV 159
+K+F+G L E T E LR +F ++G + D V +DP RGFGFVT+A EEV A +
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA-AM 72
Query: 160 SRRSHEICGQQVAIDSATPLDDAGPSQNFMMNAAETFGGYGGP-----MRTYGRMYGSLD 214
+ R H++ G+ V A +D+ + GG +R Y YG ++
Sbjct: 73 NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 132
Query: 215 FDDWGYGMGSGR 226
+ GSG+
Sbjct: 133 VIEIMTDRGSGK 144
Score = 53.9 bits (128), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 45/176 (25%), Positives = 72/176 (40%), Gaps = 44/176 (25%)
Query: 3 KDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGG 61
+D +K RG GF+T+A+ + V+ M H++ G V RA +ED RP
Sbjct: 47 RDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP-------- 98
Query: 62 YGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRY 121
A+++ KKIFVG + ++ LR Y
Sbjct: 99 ----GAHLTV------------------------------KKIFVGGIKEDTEEHHLRDY 124
Query: 122 FSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADR-VSRRSHEICGQQVAIDSA 176
F ++G+I + + D RGF FVTF + D+ V ++ H + G + A
Sbjct: 125 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA 180
Score = 32.7 bits (73), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 4 DQGSKAHRGIGFITFASADSVENLMVDT-HELGGSTVVVDRATPKED 49
D+GS RG F+TF DSV+ +++ H + G V +A K++
Sbjct: 139 DRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQE 185
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 55.8 bits (133), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 42/132 (31%), Positives = 64/132 (48%), Gaps = 8/132 (6%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFA--EEVVADRV 159
+K+F+G L E T E LR +F ++G + D V +DP RGFGFVT+A EEV A +
Sbjct: 12 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA-AM 70
Query: 160 SRRSHEICGQQVAIDSATPLDDAGPSQNFMMNAAETFGGYGGP-----MRTYGRMYGSLD 214
+ R H++ G+ V A +D+ + GG +R Y YG ++
Sbjct: 71 NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 130
Query: 215 FDDWGYGMGSGR 226
+ GSG+
Sbjct: 131 VIEIMTDRGSGK 142
Score = 53.5 bits (127), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 45/176 (25%), Positives = 72/176 (40%), Gaps = 44/176 (25%)
Query: 3 KDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGG 61
+D +K RG GF+T+A+ + V+ M H++ G V RA +ED RP
Sbjct: 45 RDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP-------- 96
Query: 62 YGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRY 121
A+++ KKIFVG + ++ LR Y
Sbjct: 97 ----GAHLTV------------------------------KKIFVGGIKEDTEEHHLRDY 122
Query: 122 FSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADR-VSRRSHEICGQQVAIDSA 176
F ++G+I + + D RGF FVTF + D+ V ++ H + G + A
Sbjct: 123 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA 178
Score = 32.0 bits (71), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 4 DQGSKAHRGIGFITFASADSVENLMVDT-HELGGSTVVVDRATPKE 48
D+GS RG F+TF DSV+ +++ H + G V +A K+
Sbjct: 137 DRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQ 182
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 55.8 bits (133), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 42/132 (31%), Positives = 64/132 (48%), Gaps = 8/132 (6%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFA--EEVVADRV 159
+K+F+G L E T E LR +F ++G + D V +DP RGFGFVT+A EEV A +
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA-AM 72
Query: 160 SRRSHEICGQQVAIDSATPLDDAGPSQNFMMNAAETFGGYGGP-----MRTYGRMYGSLD 214
+ R H++ G+ V A +D+ + GG +R Y YG ++
Sbjct: 73 NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 132
Query: 215 FDDWGYGMGSGR 226
+ GSG+
Sbjct: 133 VIEIMTDRGSGK 144
Score = 53.5 bits (127), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 45/176 (25%), Positives = 72/176 (40%), Gaps = 44/176 (25%)
Query: 3 KDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGG 61
+D +K RG GF+T+A+ + V+ M H++ G V RA +ED RP
Sbjct: 47 RDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP-------- 98
Query: 62 YGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRY 121
A+++ KKIFVG + ++ LR Y
Sbjct: 99 ----GAHLTV------------------------------KKIFVGGIKEDTEEHHLRDY 124
Query: 122 FSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADR-VSRRSHEICGQQVAIDSA 176
F ++G+I + + D RGF FVTF + D+ V ++ H + G + A
Sbjct: 125 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA 180
Score = 32.0 bits (71), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 4 DQGSKAHRGIGFITFASADSVENLMVDT-HELGGSTVVVDRATPKE 48
D+GS RG F+TF DSV+ +++ H + G V +A K+
Sbjct: 139 DRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQ 184
>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 = 55.5 bits (132), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 42/132 (31%), Positives = 64/132 (48%), Gaps = 8/132 (6%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFA--EEVVADRV 159
+K+F+G L E T E LR +F ++G + D V +DP RGFGFVT+A EEV A +
Sbjct: 7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA-AM 65
Query: 160 SRRSHEICGQQVAIDSATPLDDAGPSQNFMMNAAETFGGYGGP-----MRTYGRMYGSLD 214
+ R H++ G+ V A +D+ + GG +R Y YG ++
Sbjct: 66 NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 125
Query: 215 FDDWGYGMGSGR 226
+ GSG+
Sbjct: 126 VIEIMTDRGSGK 137
Score = 53.5 bits (127), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 45/176 (25%), Positives = 72/176 (40%), Gaps = 44/176 (25%)
Query: 3 KDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGG 61
+D +K RG GF+T+A+ + V+ M H++ G V RA +ED RP
Sbjct: 40 RDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP-------- 91
Query: 62 YGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRY 121
A+++ KKIFVG + ++ LR Y
Sbjct: 92 ----GAHLTV------------------------------KKIFVGGIKEDTEEHHLRDY 117
Query: 122 FSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADR-VSRRSHEICGQQVAIDSA 176
F ++G+I + + D RGF FVTF + D+ V ++ H + G + A
Sbjct: 118 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA 173
Score = 32.3 bits (72), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 4 DQGSKAHRGIGFITFASADSVENLMVDT-HELGGSTVVVDRATPKED 49
D+GS RG F+TF DSV+ +++ H + G V +A K++
Sbjct: 132 DRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQE 178
>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 = 54.7 bits (130), Expect = 5e-08, Method: Composition-based stats.
Identities = 26/69 (37%), Positives = 42/69 (60%), Gaps = 1/69 (1%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRV-SRR 162
+F+G L + T +DL+ YFS+FG ++D + DP RGFGFV F E D+V ++
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 163 SHEICGQQV 171
H++ G+ +
Sbjct: 62 EHKLNGKVI 70
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 53.1 bits (126), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 31/88 (35%), Positives = 52/88 (59%), Gaps = 6/88 (6%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRVSR 161
K++ V +P DLR+ F +FG+ILDV + + + G +GFGFVTF ADR
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRARE 73
Query: 162 RSH--EICGQQVAIDSATP--LDDAGPS 185
+ H + G+++ +++AT + ++GPS
Sbjct: 74 KLHGTVVEGRKIEVNNATARVMTNSGPS 101
>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 = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 41/70 (58%), Gaps = 1/70 (1%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRV-SR 161
K FVG L + + +DL+ YF++FG ++D + DP RGFGF+ F + ++V +
Sbjct: 13 KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQ 72
Query: 162 RSHEICGQQV 171
+ H + G+ +
Sbjct: 73 KEHRLDGRVI 82
>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 = 51.2 bits (121), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 41/77 (53%), Gaps = 5/77 (6%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRV-S 160
KKIFVG L + E +R YF FG + + +P D K RGF F+TF EE ++
Sbjct: 2 KKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 61
Query: 161 RRSHEI----CGQQVAI 173
++ H + C +VA+
Sbjct: 62 KKYHNVGLSKCEIKVAM 78
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 51.2 bits (121), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 27/64 (42%), Positives = 35/64 (54%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRVSRR 162
KIFVG LP T LR+YF FG I + V D + RG+GFVT A+ A+R +
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 163 SHEI 166
+ I
Sbjct: 79 PNPI 82
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 50.8 bits (120), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 46/78 (58%), Gaps = 4/78 (5%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRVSR 161
K++ V +P DLR+ F +FG+ILDV + + + G +GFGFVTF ADR
Sbjct: 30 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRARE 87
Query: 162 RSH--EICGQQVAIDSAT 177
+ H + G+++ +++AT
Sbjct: 88 KLHGTVVEGRKIEVNNAT 105
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 50.4 bits (119), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 46/78 (58%), Gaps = 1/78 (1%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRVSR 161
+ I+VG L AT+E ++ FS+FG++ +V + D + +GFGFV EE V++ +++
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAK 61
Query: 162 RSH-EICGQQVAIDSATP 178
+ + G+ + + A P
Sbjct: 62 LDNTDFMGRTIRVTEANP 79
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 32/89 (35%), Positives = 49/89 (55%), Gaps = 8/89 (8%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVAD----R 158
K+FVG L + + L + FS++G+I +V V KD + RGFGFVTF E + D
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTF--ENIDDAKDAM 71
Query: 159 VSRRSHEICGQQVAIDSATPLDD--AGPS 185
++ + G+Q+ +D A D +GPS
Sbjct: 72 MAMNGKSVDGRQIRVDQAGKSSDNRSGPS 100
Score = 28.1 bits (61), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 29/52 (55%), Gaps = 2/52 (3%)
Query: 1 MPKDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKEDD 50
+ KD+ ++ RG GF+TF + D ++ M ++ + G + VD+A D+
Sbjct: 44 VVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDN 95
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 31/86 (36%), Positives = 47/86 (54%), Gaps = 4/86 (4%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADR--VSR 161
+FVG L E T ED++ F+ FG+I D V KD +G+GFV+F ++ A+ V
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 162 RSHEICGQQVAIDSAT--PLDDAGPS 185
+ G+Q+ + AT P +GPS
Sbjct: 78 GGQWLGGRQIRTNWATRKPPAPSGPS 103
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 49.3 bits (116), Expect = 2e-06, Method: Composition-based stats.
Identities = 23/65 (35%), Positives = 33/65 (50%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRVSRRS 163
IFVG L + E +R YF FG + + +P D K RGF F+TF EE ++ +
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Query: 164 HEICG 168
+ G
Sbjct: 62 YHNVG 66
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 48.9 bits (115), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 29/86 (33%), Positives = 46/86 (53%), Gaps = 4/86 (4%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTF--AEEVVADRVSR 161
++VG L +E + L F FG I D+ +P D + HRGF FV F AE+ A +
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 162 RSHEICGQQVAIDSATPL--DDAGPS 185
E+ G+ + ++ A P+ ++GPS
Sbjct: 75 NESELFGRTIRVNLAKPMRIKESGPS 100
Score = 28.5 bits (62), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 6/50 (12%)
Query: 1 MPKDQGSKAHRGIGFITFASAD----SVENLMVDTHELGGSTVVVDRATP 46
+P D ++ HRG F+ F A+ +++N+ + EL G T+ V+ A P
Sbjct: 44 IPLDYETEKHRGFAFVEFELAEDAAAAIDNM--NESELFGRTIRVNLAKP 91
>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 = 47.8 bits (112), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 42/76 (55%), Gaps = 2/76 (2%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRVSRR- 162
+FVG L E T ED++ F+ FGRI D V KD +G+GFV+F + A+ ++
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 163 -SHEICGQQVAIDSAT 177
+ G+Q+ + AT
Sbjct: 78 GGQWLGGRQIRTNWAT 93
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 35/63 (55%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRVSRR 162
K+F+G++P+ +DL+ F FG+I ++ V KD H+G F+T+ E A +
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74
Query: 163 SHE 165
HE
Sbjct: 75 LHE 77
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 46.2 bits (108), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 6/69 (8%)
Query: 89 SFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFV 148
SF GE + ++FVG LP + T ED +R F R+G +V++ +D RGFGF+
Sbjct: 10 SFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFI 63
Query: 149 TFAEEVVAD 157
+A+
Sbjct: 64 RLESRTLAE 72
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 48/87 (55%), Gaps = 12/87 (13%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRVSRR 162
K+F+G LP+EAT +++R F ++G++L+ + K+ +GFV ++ A+ R
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFVHIEDKTAAEDAIRN 61
Query: 163 SH--EICGQQVAIDSATPLDDA--GPS 185
H ++ G + ++++ A GPS
Sbjct: 62 LHHYKLHGVNINVEASKNKSKASSGPS 88
>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 = 3e-05, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 34/63 (53%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRVSRR 162
K+FVG++P+ +DL+ F FGRI ++ V KD H+G F+T+ A +
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSA 76
Query: 163 SHE 165
HE
Sbjct: 77 LHE 79
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 44.7 bits (104), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/49 (46%), Positives = 29/49 (59%), Gaps = 1/49 (2%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTG-HRGFGFVTF 150
KI V +P +A ++R FS FG + V +PK TG HRGFGFV F
Sbjct: 17 KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDF 65
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 44.3 bits (103), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 28/47 (59%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTF 150
+ V L + + LRR F ++GR+ DVY+P++P RGF FV F
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRF 62
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 43.9 bits (102), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 45/85 (52%), Gaps = 5/85 (5%)
Query: 94 GESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTF--A 151
G +++R+ ++VG L +E + L F FG I D+ +P D + HRGF FV F A
Sbjct: 1 GSTTKRV---LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELA 57
Query: 152 EEVVADRVSRRSHEICGQQVAIDSA 176
E+ A + E+ G+ + ++ A
Sbjct: 58 EDAAAAIDNMNESELFGRTIRVNLA 82
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 48/87 (55%), Gaps = 8/87 (9%)
Query: 89 SFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFV 148
+F GE + ++FVG LP + T E++R+ F ++G+ +V++ KD +GFGF+
Sbjct: 10 NFRKPGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFI 63
Query: 149 TFAEEVVAD--RVSRRSHEICGQQVAI 173
+A+ +V + + G+Q+ +
Sbjct: 64 RLETRTLAEIAKVELDNMPLRGKQLRV 90
>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
pdb|2RS8|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
Length = 99
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 44/77 (57%), Gaps = 8/77 (10%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVAD--RVS 160
++FVG LP + T E++R+ F ++G+ +V++ KD +GFGF+ +A+ +V
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 70
Query: 161 RRSHEICGQQVAIDSAT 177
+ + G+Q+ + A
Sbjct: 71 LDNMPLRGKQLRVRFAC 87
>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 = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/87 (31%), Positives = 45/87 (51%), Gaps = 5/87 (5%)
Query: 92 GRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTF- 150
G +++R+ ++VG L +E + L F FG I D+ +P D + HRGF FV F
Sbjct: 1 GSMATTKRV---LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE 57
Query: 151 -AEEVVADRVSRRSHEICGQQVAIDSA 176
AE+ A + E+ G+ + ++ A
Sbjct: 58 LAEDAAAAIDNMNESELFGRTIRVNLA 84
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 31/58 (53%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRVSR 161
++V LP T DL R FS++G+++ V + KD +G F+ F ++ A +R
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
>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 = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 27/82 (32%), Positives = 43/82 (52%), Gaps = 5/82 (6%)
Query: 97 SQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTF--AEEV 154
S+R+ ++VG L +E + L F FG I D+ +P D + HRGF FV F AE+
Sbjct: 1 SKRV---LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 57
Query: 155 VADRVSRRSHEICGQQVAIDSA 176
A + E+ G+ + ++ A
Sbjct: 58 AAAIDNMNESELFGRTIRVNLA 79
>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm
pdb|2LEB|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uccagu-3'
pdb|2LEC|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uggagu-3'
Length = 135
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 34/67 (50%)
Query: 91 YGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTF 150
YGR + V L + + LRR F ++GR+ DVY+P+D RGF FV F
Sbjct: 37 YGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRF 96
Query: 151 AEEVVAD 157
++ A+
Sbjct: 97 HDKRDAE 103
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 29/50 (58%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEE 153
+ V L + + LRR F ++GR+ DVY+P+D RGF FV F ++
Sbjct: 73 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDK 122
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 34/64 (53%), Gaps = 1/64 (1%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRVSR 161
+K+F+G + ++ T D+R FS FG+I + + + P RG FVTF +A +
Sbjct: 108 RKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLS-RGCAFVTFTTRAMAQTAIK 166
Query: 162 RSHE 165
H+
Sbjct: 167 AMHQ 170
Score = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 31/50 (62%), Gaps = 2/50 (4%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRT--GHRGFGFVTF 150
K+FVG++P+ + +DLR F ++G + ++ V +D + +G FVTF
Sbjct: 17 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTF 66
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTF--AEEVVADRVSR 161
++VG L +E + L F FG I D+ +P D + HRGF FV F AE+ A +
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 162 RSHEICGQQVAIDSA 176
E+ G+ + ++ A
Sbjct: 126 NESELFGRTIRVNLA 140
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 34/64 (53%), Gaps = 1/64 (1%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRVSR 161
+K+F+G + ++ T D+R FS FG+I + + + P RG FVTF +A +
Sbjct: 96 RKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLS-RGCAFVTFTTRAMAQTAIK 154
Query: 162 RSHE 165
H+
Sbjct: 155 AMHQ 158
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 31/50 (62%), Gaps = 2/50 (4%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRT--GHRGFGFVTF 150
K+FVG++P+ + +DLR F ++G + ++ V +D + +G FVTF
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTF 54
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 40.4 bits (93), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 42/82 (51%), Gaps = 2/82 (2%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRVSRRS 163
++VG L T + LR F FG+I ++ + KD +G+GF+TF++ A R +
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 164 H--EICGQQVAIDSATPLDDAG 183
+ E+ G+ + + T D G
Sbjct: 68 NGFELAGRPMRVGHVTERLDGG 89
>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 = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 1/64 (1%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRVSR 161
+K+F+G + ++ T D+R FS FG+I + + + P RG FVTF A +
Sbjct: 96 RKLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDGLS-RGCAFVTFTTRAXAQTAIK 154
Query: 162 RSHE 165
H+
Sbjct: 155 AXHQ 158
Score = 35.8 bits (81), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 30/50 (60%), Gaps = 2/50 (4%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRT--GHRGFGFVTF 150
K FVG++P+ + +DLR F ++G + ++ V +D + +G FVTF
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTF 54
>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 = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 30/52 (57%)
Query: 99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTF 150
R +I+V + Q+ + +D++ F FG+I + +DP H+G+GF+ +
Sbjct: 123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEY 174
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 27/116 (23%), Positives = 51/116 (43%), Gaps = 7/116 (6%)
Query: 88 GSFYGRGESSQR-----IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGH 142
G GRG ++QR I +++VG + E + +R+ F+ FG I + + D H
Sbjct: 10 GQQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKH 69
Query: 143 RGFGFVTFAEEVVADRVSRRSHEIC--GQQVAIDSATPLDDAGPSQNFMMNAAETF 196
+GF FV + A + + + G+ + + + + A P + + A F
Sbjct: 70 KGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAF 125
>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 = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 30/52 (57%)
Query: 99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTF 150
R +I+V + Q+ + +D++ F FG+I + +DP H+G+GF+ +
Sbjct: 108 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEY 159
Score = 30.8 bits (68), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 27/51 (52%)
Query: 100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTF 150
I +++VG + E + +R+ F+ FG I + + D H+GF FV +
Sbjct: 12 IMCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEY 62
>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 = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 30/52 (57%)
Query: 99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTF 150
R +I+V + Q+ + +D++ F FG+I + +DP H+G+GF+ +
Sbjct: 107 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEY 158
Score = 30.8 bits (68), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 21/100 (21%), Positives = 42/100 (42%), Gaps = 2/100 (2%)
Query: 100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRV 159
I +++VG + E + +R+ F+ FG I + D H+GF FV + A
Sbjct: 11 IXCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLA 70
Query: 160 SRRSHEIC--GQQVAIDSATPLDDAGPSQNFMMNAAETFG 197
+ + + G+ + + + + A P + + A F
Sbjct: 71 LEQXNSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFN 110
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 27/50 (54%)
Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTF 150
G +F+ LPQE T DL F FG ++ V D + + + FGFV+F
Sbjct: 40 GCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSF 89
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 2/77 (2%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRVSR 161
+ +FVG +P EAT E L+ FS G ++ + D + +G+GF + ++ A R
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68
Query: 162 RSH--EICGQQVAIDSA 176
+ E G+ + +D+A
Sbjct: 69 NLNGREFSGRALRVDNA 85
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 41/81 (50%), Gaps = 2/81 (2%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRVSRR 162
+++VG L T + LR F FGRI + + D + +G+GF+TF++ A + +
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 163 SH--EICGQQVAIDSATPLDD 181
+ E+ G+ + + T D
Sbjct: 88 LNGFELAGRPMKVGHVTERTD 108
>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 = 0.004, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 29/56 (51%)
Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVA 156
G +F+ LPQE +DL + F FG ++ V D + + FGFV++ V A
Sbjct: 25 GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSA 80
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 33/71 (46%), Gaps = 5/71 (7%)
Query: 91 YGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTF 150
Y R S +++ LP+ T +D+ FSRFGRI++ V D RG F+ F
Sbjct: 78 YARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRF 137
Query: 151 -----AEEVVA 156
AEE +
Sbjct: 138 DKRSEAEEAIT 148
Score = 34.7 bits (78), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 34/133 (25%), Positives = 52/133 (39%), Gaps = 15/133 (11%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHR-GFGFVTFAEEVVADRVSR 161
+ V LPQ T ++LR FS G + + +D K GH G+GFV + V A R
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRD-KVAGHSLGYGFVNY---VTAKDAER 59
Query: 162 RSHEICGQQVAIDSATPLDDAGPSQNFMMNAAETFGGYGGPMRT---------YGRMYGS 212
+ + G ++ + A PS + +A G M +GR+ S
Sbjct: 60 AINTLNGLRLQ-SKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINS 118
Query: 213 LDFDDWGYGMGSG 225
D G+ G
Sbjct: 119 RVLVDQTTGLSRG 131
>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 = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 35/67 (52%)
Query: 91 YGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTF 150
Y R S+ ++V LP+ T ++L + FS++GRI+ + D RG GF+ F
Sbjct: 78 YARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRF 137
Query: 151 AEEVVAD 157
+ + A+
Sbjct: 138 DKRIEAE 144
Score = 31.2 bits (69), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 22/49 (44%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAE 152
+ V LPQ T E+ R F G I + +D G+GFV + +
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYID 53
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 44/86 (51%), Gaps = 11/86 (12%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRVSRR 162
KIFVG + T+++LR F R GR+++ V KD + FV +E A +
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQ 62
Query: 163 SH--EICGQQVAIDSATP-LDDAGPS 185
+ E+ G+++ ++ +T +GPS
Sbjct: 63 LNGKEVKGKRINVELSTKGQKKSGPS 88
>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 = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 33/71 (46%), Gaps = 5/71 (7%)
Query: 91 YGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTF 150
Y R S +++ LP+ T +D+ FSRFGRI++ V D RG F+ F
Sbjct: 78 YARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRF 137
Query: 151 -----AEEVVA 156
AEE +
Sbjct: 138 DKRSEAEEAIT 148
Score = 34.7 bits (78), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 34/132 (25%), Positives = 52/132 (39%), Gaps = 15/132 (11%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHR-GFGFVTFAEEVVADRVSRR 162
+ V LPQ T ++LR FS G + + +D K GH G+GFV + V A R
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRD-KVAGHSLGYGFVNY---VTAKDAERA 60
Query: 163 SHEICGQQVAIDSATPLDDAGPSQNFMMNAAETFGGYGGPMRT---------YGRMYGSL 213
+ + G ++ + A PS + +A G M +GR+ S
Sbjct: 61 INTLNGLRLQ-SKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSR 119
Query: 214 DFDDWGYGMGSG 225
D G+ G
Sbjct: 120 VLVDQTTGLSRG 131
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 28/48 (58%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTF 150
++FV L ++ EDL + FS +G + +++ P D +GF FVTF
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTF 57
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 37.7 bits (86), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 27/89 (30%), Positives = 43/89 (48%), Gaps = 6/89 (6%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTF-----AEEVVA 156
+K+FVG L ++ T ED+R+ F FG I + V + P T +G FV F A+ +
Sbjct: 13 RKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTS-KGCAFVKFQTHAEAQAAIN 71
Query: 157 DRVSRRSHEICGQQVAIDSATPLDDAGPS 185
S R+ + + A ++GPS
Sbjct: 72 TLHSSRTLPGASSSLVVKFADTEKESGPS 100
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 31/54 (57%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVAD 157
++VG L ++ + L F + G +++ ++PKD H+G+GFV F E AD
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDAD 71
Score = 28.9 bits (63), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 4/48 (8%)
Query: 1 MPKDQGSKAHRGIGFITFAS---ADSVENLMVDTHELGGSTVVVDRAT 45
MPKD+ + H+G GF+ F S AD +M D +L G + V++A+
Sbjct: 47 MPKDRVTGQHQGYGFVEFLSEEDADYAIKIM-DMIKLYGKPIRVNKAS 93
>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 = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 31/50 (62%), Gaps = 2/50 (4%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRT--GHRGFGFVTF 150
K+FVG++P+ + +DLR F ++G + ++ V +D + +G FVTF
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTF 54
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 37.0 bits (84), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 33/64 (51%), Gaps = 2/64 (3%)
Query: 113 ATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRVSRRSH--EICGQQ 170
T DLR FS++G I DV + D + RGF FV F A R++ E+ G++
Sbjct: 27 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR 86
Query: 171 VAID 174
+ +D
Sbjct: 87 IRVD 90
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 37.0 bits (84), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 33/64 (51%), Gaps = 2/64 (3%)
Query: 113 ATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRVSRRSH--EICGQQ 170
T DLR FS++G I DV + D + RGF FV F A R++ E+ G++
Sbjct: 58 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR 117
Query: 171 VAID 174
+ +D
Sbjct: 118 IRVD 121
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 37.0 bits (84), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 35/68 (51%)
Query: 91 YGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTF 150
Y R S+ ++V LP+ + +++ + FS++GRI+ + D RG GF+ F
Sbjct: 80 YARPSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRF 139
Query: 151 AEEVVADR 158
+ + A+
Sbjct: 140 DKRIEAEE 147
Score = 30.8 bits (68), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 26/55 (47%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADR 158
+ V LPQ T ++ + F G I + +D G+GFV +++ AD+
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 37.0 bits (84), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVA 156
+K+FVG L ++ + +D+RR F FG I + + + P +G FV ++ A
Sbjct: 16 RKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNS-KGCAFVKYSSHAEA 69
>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 = 36.6 bits (83), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 30/59 (50%), Gaps = 2/59 (3%)
Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHR-GFGFVTFAEEVVADR 158
G + V LPQ T ++LR FS G + + +D K GH G+GFV + A+R
Sbjct: 19 GTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRD-KVAGHSLGYGFVNYVTAKDAER 76
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 36.6 bits (83), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 33/64 (51%), Gaps = 2/64 (3%)
Query: 113 ATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRVSRRSH--EICGQQ 170
T DLR FS++G I DV + D + RGF FV F A R++ E+ G++
Sbjct: 24 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR 83
Query: 171 VAID 174
+ +D
Sbjct: 84 IRVD 87
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 36.6 bits (83), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 36/83 (43%), Gaps = 3/83 (3%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDV-YVPKDPKRTGHRGFGFVTFAEEVVADRV--S 160
IF+G L E + L FS FG IL + +DP +G+ F+ FA +D +
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 161 RRSHEICGQQVAIDSATPLDDAG 183
+C + + + A D G
Sbjct: 68 MNGQYLCNRPITVSYAFKKDSKG 90
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 36.2 bits (82), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 3/75 (4%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTG-HRGFGFVTFAEEVVADRVSRR 162
+FVG + ++R +F+R+G + +V + D RTG +G+GFV+F +V ++
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD--RTGVSKGYGFVSFYNDVDVQKIVES 70
Query: 163 SHEICGQQVAIDSAT 177
G+++ + A
Sbjct: 71 QINFHGKKLKLGPAI 85
>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 = 36.2 bits (82), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 37/80 (46%), Gaps = 2/80 (2%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRV--S 160
+FVG L E LR F F L +V D + RG+GFV+F + A S
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 161 RRSHEICGQQVAIDSATPLD 180
+ ++ G+ + I+ A L+
Sbjct: 63 MQGQDLNGRPLRINWAAKLE 82
>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|B Chain B, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|C Chain C, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|D Chain D, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
Length = 94
Score = 35.8 bits (81), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 7/53 (13%)
Query: 104 IFVGRLPQEATAEDLRR----YFSRFGRILDVYVPKDPKRTGHRGFGFVTFAE 152
I++ L ++ ++L++ FSRFG+ILD+ V + K RG FV F E
Sbjct: 8 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK---MRGQAFVIFKE 57
>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 = 0.019, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 43/77 (55%), Gaps = 4/77 (5%)
Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGH-RGFGFVTFA--EEVVAD 157
G +FV + +EAT ED+ F+ +G I ++++ D +RTG+ +G+ V + +E A
Sbjct: 23 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLD-RRTGYLKGYTLVEYETYKEAQAA 81
Query: 158 RVSRRSHEICGQQVAID 174
++ GQ +++D
Sbjct: 82 MEGLNGQDLMGQPISVD 98
>pdb|1M5K|C Chain C, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5K|F Chain F, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5O|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5O|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1SJ3|P Chain P, Hepatitis Delta Virus Gemonic Ribozyme Precursor, With
Mg2+ Bound
pdb|1SJ4|P Chain P, Crystal Structure Of A C75u Mutant Hepatitis Delta Virus
Ribozyme Precursor, In Cu2+ Solution
pdb|1SJF|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Cobalt
Hexammine Solution
pdb|1VBX|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Edta Solution
pdb|1VBY|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, And Mn2+ Bound
pdb|1VBZ|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Ba2+ Solution
pdb|1VC0|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Imidazole And
Sr2+ Solution
pdb|1VC5|A Chain A, Crystal Structure Of The Wild Type Hepatitis Delta Virus
Gemonic Ribozyme Precursor, In Edta Solution
pdb|1VC6|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Product With C75u Mutaion, Cleaved In Imidazole
And Mg2+ Solutions
pdb|1VC7|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Sr2+ Solution
pdb|2OIH|A Chain A, Hepatitis Delta Virus Gemonic Ribozyme Precursor With C75u
Mutation And Bound To Monovalent Cation Tl+
pdb|2OJ3|A Chain A, Hepatitis Delta Virus Ribozyme Precursor Structure, With
C75u Mutation, Bound To Tl+ And Cobalt Hexammine
(Co(Nh3) 63+)
Length = 100
Score = 35.8 bits (81), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 7/53 (13%)
Query: 104 IFVGRLPQEATAEDLRR----YFSRFGRILDVYVPKDPKRTGHRGFGFVTFAE 152
I++ L ++ ++L++ FSRFG+ILD+ V + K RG FV F E
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK---MRGQAFVIFKE 61
>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 = 35.8 bits (81), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 43/77 (55%), Gaps = 4/77 (5%)
Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGH-RGFGFVTFA--EEVVAD 157
G +FV + +EAT ED+ F+ +G I ++++ D +RTG+ +G+ V + +E A
Sbjct: 9 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLD-RRTGYLKGYTLVEYETYKEAQAA 67
Query: 158 RVSRRSHEICGQQVAID 174
++ GQ +++D
Sbjct: 68 MEGLNGQDLMGQPISVD 84
>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
pdb|3IWN|D Chain D, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
Length = 91
Score = 35.8 bits (81), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 7/53 (13%)
Query: 104 IFVGRLPQEATAEDLRR----YFSRFGRILDVYVPKDPKRTGHRGFGFVTFAE 152
I++ L ++ ++L++ FSRFG+ILD+ V + K RG FV F E
Sbjct: 7 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK---MRGQAFVIFKE 56
>pdb|1U6B|A Chain A, Crystal Structure Of A Self-Splicing Group I Intron With
Both Exons
pdb|1ZZN|A Chain A, Crystal Structure Of A Group I IntronTWO EXON COMPLEX THAT
Includes All Catalytic Metal Ion Ligands.
pdb|3G8S|A Chain A, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|B Chain B, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|C Chain C, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|D Chain D, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8T|A Chain A, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|B Chain B, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|C Chain C, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|D Chain D, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G96|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G9C|A Chain A, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|B Chain B, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|C Chain C, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|D Chain D, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3IRW|P Chain P, Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3MUM|P Chain P, Crystal Structure Of The G20a Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUR|P Chain P, Crystal Structure Of The C92u Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUT|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Gmp
pdb|3MUV|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Amp
pdb|3MXH|P Chain P, Native Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3P49|B Chain B, Crystal Structure Of A Glycine Riboswitch From
Fusobacterium Nucleatum
pdb|3R1H|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1H|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1L|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3R1L|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3UCU|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Pgpg
pdb|3UCZ|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Gpg
pdb|3UD3|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Pgpa
pdb|3UD4|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Gpa
Length = 98
Score = 35.8 bits (81), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 7/53 (13%)
Query: 104 IFVGRLPQEATAEDLRR----YFSRFGRILDVYVPKDPKRTGHRGFGFVTFAE 152
I++ L ++ ++L++ FSRFG+ILD+ V + K RG FV F E
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK---MRGQAFVIFKE 61
>pdb|3L3C|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
Length = 90
Score = 35.8 bits (81), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 7/53 (13%)
Query: 104 IFVGRLPQEATAEDLRR----YFSRFGRILDVYVPKDPKRTGHRGFGFVTFAE 152
I++ L ++ ++L++ FSRFG+ILD+ V + K RG FV F E
Sbjct: 6 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK---MRGQAFVIFKE 55
>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 = 0.022, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 43/77 (55%), Gaps = 4/77 (5%)
Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGH-RGFGFVTFA--EEVVAD 157
G +FV + +EAT ED+ F+ +G I ++++ D +RTG+ +G+ V + +E A
Sbjct: 22 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLD-RRTGYLKGYTLVEYETYKEAQAA 80
Query: 158 RVSRRSHEICGQQVAID 174
++ GQ +++D
Sbjct: 81 MEGLNGQDLMGQPISVD 97
>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|B Chain B, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|C Chain C, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|D Chain D, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
Length = 96
Score = 35.8 bits (81), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 7/53 (13%)
Query: 104 IFVGRLPQEATAEDLRR----YFSRFGRILDVYVPKDPKRTGHRGFGFVTFAE 152
I++ L ++ ++L++ FSRFG+ILD+ V + K RG FV F E
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK---MRGQAFVIFKE 60
>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 = 35.8 bits (81), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 37/66 (56%), Gaps = 3/66 (4%)
Query: 94 GESSQRIGKK-IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGH-RGFGFVTFA 151
E + I K+ ++VG + +TA+DL +FS G I + + D K +GH +G+ ++ FA
Sbjct: 28 AEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCD-KFSGHPKGYAYIEFA 86
Query: 152 EEVVAD 157
E D
Sbjct: 87 ERNSVD 92
>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|B Chain B, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|C Chain C, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1NU4|A Chain A, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|1NU4|B Chain B, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|3HHN|B Chain B, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
pdb|3HHN|D Chain D, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
Length = 97
Score = 35.8 bits (81), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 7/53 (13%)
Query: 104 IFVGRLPQEATAEDLRR----YFSRFGRILDVYVPKDPKRTGHRGFGFVTFAE 152
I++ L ++ ++L++ FSRFG+ILD+ V + K RG FV F E
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK---MRGQAFVIFKE 60
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 35.8 bits (81), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 43/77 (55%), Gaps = 4/77 (5%)
Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGH-RGFGFVTFA--EEVVAD 157
G +FV + +EAT ED+ F+ +G I ++++ D +RTG+ +G+ V + +E A
Sbjct: 7 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLD-RRTGYLKGYTLVEYETYKEAQAA 65
Query: 158 RVSRRSHEICGQQVAID 174
++ GQ +++D
Sbjct: 66 MEGLNGQDLMGQPISVD 82
>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 = 35.8 bits (81), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 3/75 (4%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTG-HRGFGFVTFAEEVVADRVSRR 162
+FVG + ++R +F+R+G + +V + D RTG +G+GFV+F +V ++
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD--RTGVSKGYGFVSFYNDVDVQKIVES 69
Query: 163 SHEICGQQVAIDSAT 177
G+++ + A
Sbjct: 70 QINFHGKKLKLGPAI 84
>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 = 35.4 bits (80), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 43/77 (55%), Gaps = 4/77 (5%)
Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGH-RGFGFVTFA--EEVVAD 157
G +FV + +EAT ED+ F+ +G I ++++ D +RTG+ +G+ V + +E A
Sbjct: 7 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLD-RRTGYLKGYTLVEYETYKEAQAA 65
Query: 158 RVSRRSHEICGQQVAID 174
++ GQ +++D
Sbjct: 66 MEGLNGQDLMGQPISVD 82
>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO3|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO4|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3IIN|A Chain A, Plasticity Of The Kink Turn Structural Motif
Length = 95
Score = 35.4 bits (80), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 7/53 (13%)
Query: 104 IFVGRLPQEATAEDLRR----YFSRFGRILDVYVPKDPKRTGHRGFGFVTFAE 152
I++ L ++ ++L++ FSRFG+ILD+ V + K RG FV F E
Sbjct: 9 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK---MRGQAFVIFKE 58
>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures
pdb|1DZ5|A Chain A, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
pdb|1DZ5|B Chain B, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
Length = 101
Score = 35.4 bits (80), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 7/53 (13%)
Query: 104 IFVGRLPQEATAEDLRR----YFSRFGRILDVYVPKDPKRTGHRGFGFVTFAE 152
I++ L ++ ++L++ FSRFG+ILD+ V + K RG FV F E
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK---MRGQAFVIFKE 60
>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 = 35.4 bits (80), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 3/75 (4%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTG-HRGFGFVTFAEEVVADRVSRR 162
+FVG + ++R +F+R+G + +V + D RTG +G+GFV+F +V ++
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD--RTGVSKGYGFVSFYNDVDVQKIVES 69
Query: 163 SHEICGQQVAIDSAT 177
G+++ + A
Sbjct: 70 QINFHGKKLKLGPAI 84
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 35.4 bits (80), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVA 156
+K+FVG L ++ + ED+ R F FG I + V + P + +G FV F+ A
Sbjct: 16 RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSS-KGCAFVKFSSHTEA 69
>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 = 35.4 bits (80), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 43/77 (55%), Gaps = 4/77 (5%)
Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGH-RGFGFVTFA--EEVVAD 157
G +FV + +EAT ED+ F+ +G I ++++ D +RTG+ +G+ V + +E A
Sbjct: 7 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLD-RRTGYLKGYTLVEYETYKEAQAA 65
Query: 158 RVSRRSHEICGQQVAID 174
++ GQ +++D
Sbjct: 66 MEGLNGQDLMGQPISVD 82
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 35.4 bits (80), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 7/53 (13%)
Query: 104 IFVGRLPQEATAEDLRR----YFSRFGRILDVYVPKDPKRTGHRGFGFVTFAE 152
I++ L ++ ++L++ FSRFG+ILD+ V + K RG FV F E
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK---XRGQAFVIFKE 60
>pdb|3CUL|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUL|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3EGZ|A Chain A, Crystal Structure Of An In Vitro Evolved Tetracycline
Aptamer And Artificial Riboswitch
Length = 98
Score = 35.4 bits (80), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 7/53 (13%)
Query: 104 IFVGRLPQEATAEDLRR----YFSRFGRILDVYVPKDPKRTGHRGFGFVTFAE 152
I++ L ++ ++L++ FSRFG+ILD+ V + K RG FV F E
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK---XRGQAFVIFKE 61
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 35.4 bits (80), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 32/62 (51%), Gaps = 2/62 (3%)
Query: 114 TAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRVSRRSH--EICGQQV 171
T DLR FS++G I DV + D + RGF FV F A R++ E+ G+++
Sbjct: 28 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 87
Query: 172 AI 173
+
Sbjct: 88 RV 89
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 35.4 bits (80), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 7/53 (13%)
Query: 104 IFVGRLPQEATAEDLRR----YFSRFGRILDVYVPKDPKRTGHRGFGFVTFAE 152
I++ L ++ ++L++ FSRFG+ILD+ V + K RG FV F E
Sbjct: 9 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK---XRGQAFVIFKE 58
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 35.0 bits (79), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 31/54 (57%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVAD 157
++V LP+ + +++ + FS++GRI+ + D RG GF+ F + + A+
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAE 57
>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 = 35.0 bits (79), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHR-GFGFVTFAEEVVADR 158
+ V LPQ T ++LR FS G + + +D K GH G+GFV + A+R
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRD-KVAGHSLGYGFVNYVTAKDAER 61
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 34.7 bits (78), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 24/47 (51%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTF 150
I V L ++ DL+ F FG I +Y+ KD +GF F++F
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISF 64
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 34.3 bits (77), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 42/74 (56%), Gaps = 4/74 (5%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTG-HRGFGFVTFA--EEVVADRVS 160
+FV + +EA ++++ F +G I ++++ D +RTG +G+ V + ++ +A + +
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLD-RRTGFSKGYALVEYETHKQALAAKEA 87
Query: 161 RRSHEICGQQVAID 174
EI GQ + +D
Sbjct: 88 LNGAEIMGQTIQVD 101
>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 = 34.3 bits (77), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 39/76 (51%), Gaps = 2/76 (2%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRVSRR- 162
+FVG L E T + F+ FGRI D V KD +G+GFV+F + A+ ++
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 163 -SHEICGQQVAIDSAT 177
+ G+Q+ + AT
Sbjct: 69 GGQWLGGRQIRTNWAT 84
>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 = 34.3 bits (77), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 27/55 (49%), Gaps = 2/55 (3%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADR 158
IF+ L + + L FS FG IL V D G +G+GFV F + A+R
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAER 60
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 34.3 bits (77), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 30/53 (56%), Gaps = 7/53 (13%)
Query: 104 IFVGRLPQEATAEDLRR----YFSRFGRILDVYVPKDPKRTGHRGFGFVTFAE 152
I++ L ++ ++L++ FS+FG+ILD+ V + K RG FV F E
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLK---MRGQAFVIFKE 61
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 33.9 bits (76), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 27/55 (49%), Gaps = 2/55 (3%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADR 158
IF+ L + + L FS FG IL V D G +G+GFV F + A+R
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAER 66
>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 = 33.9 bits (76), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 42/74 (56%), Gaps = 4/74 (5%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTG-HRGFGFVTFA--EEVVADRVS 160
+FV + +EA ++++ F +G I ++++ D +RTG +G+ V + ++ +A + +
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLD-RRTGFSKGYALVEYETHKQALAAKEA 133
Query: 161 RRSHEICGQQVAID 174
EI GQ + +D
Sbjct: 134 LNGAEIMGQTIQVD 147
>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 = 33.9 bits (76), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 2/61 (3%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRVSRRS 163
IF+ L + + L FS FG IL V D G +G+GFV F + A+R +
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 163
Query: 164 H 164
+
Sbjct: 164 N 164
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 33.5 bits (75), Expect = 0.093, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 30/53 (56%), Gaps = 7/53 (13%)
Query: 104 IFVGRLPQEATAEDLRR----YFSRFGRILDVYVPKDPKRTGHRGFGFVTFAE 152
I++ L ++ ++L++ FS+FG+ILD+ V + K RG FV F E
Sbjct: 11 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLK---MRGQAFVIFKE 60
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 33.5 bits (75), Expect = 0.094, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 25/51 (49%)
Query: 100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTF 150
+ + + V +P LR+ F R+G I V + D + RG+GFV F
Sbjct: 41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKF 91
>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 = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 27/55 (49%), Gaps = 2/55 (3%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADR 158
IF+ L + + L FS FG IL V D G +G+GFV F + A+R
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAER 153
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 33.1 bits (74), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 24/51 (47%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEE 153
+FVG L E LR F F L +V D + RG+GFV+F +
Sbjct: 89 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQ 139
>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 32.7 bits (73), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 31/58 (53%), Gaps = 7/58 (12%)
Query: 99 RIGKKIFVGRLPQEATAEDLRR----YFSRFGRILDVYVPKDPKRTGHRGFGFVTFAE 152
R I++ L ++ ++L++ FS+FG+ILD+ V + K RG FV F E
Sbjct: 7 RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLK---MRGQAFVIFKE 61
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 32.0 bits (71), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 34/75 (45%), Gaps = 5/75 (6%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTG---HRGFGFVTFAEEVVADRVS 160
+F+ L T E L+ FS+ G I + K + G GFGFV + + A +
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 161 R--RSHEICGQQVAI 173
+ + H + G ++ +
Sbjct: 68 KQLQGHTVDGHKLEV 82
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of Eukaryotic
Initiation Factor 4b
Length = 104
Score = 31.6 bits (70), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 41/85 (48%), Gaps = 5/85 (5%)
Query: 105 FVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGH-RGFGFVTFAEEVVADRVSRRS 163
F+G LP + T E ++ +F R I V +P++P +GFG+ F + +
Sbjct: 19 FLGNLPYDVTEESIKEFF-RGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLN 77
Query: 164 HEICG-QQVAIDSATPLD--DAGPS 185
E G +++ +D A D+GPS
Sbjct: 78 EESLGNKRIRVDVADQAQDKDSGPS 102
>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|X Chain X, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|Y Chain Y, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2V|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
pdb|1N52|B Chain B, Cap Binding Complex
pdb|1N54|B Chain B, Cap Binding Complex M7gpppg Free
pdb|3FEX|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex.
pdb|3FEY|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex
Length = 156
Score = 31.6 bits (70), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 33/75 (44%), Gaps = 3/75 (4%)
Query: 90 FYGRGESSQRIGKK---IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFG 146
F G E +++ KK ++VG L T E + FS+ G I + + D + GF
Sbjct: 25 FRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFC 84
Query: 147 FVTFAEEVVADRVSR 161
FV + A+ R
Sbjct: 85 FVEYYSRADAENAMR 99
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 31.6 bits (70), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 26/55 (47%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADR 158
+ V LPQ T ++ + F G I + +D G+GFV +++ AD+
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 31.2 bits (69), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 25/55 (45%)
Query: 98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAE 152
+R + +F +L DL +FS G++ DV + D +G +V F E
Sbjct: 22 ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCE 76
>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 = 31.2 bits (69), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 2/75 (2%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRVSR 161
K +FV R+ + T LRR F +G I +++ + RG+ F+ + E +
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 162 RS--HEICGQQVAID 174
+ +I G++V +D
Sbjct: 163 HADGKKIDGRRVLVD 177
>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 = 31.2 bits (69), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 11/49 (22%), Positives = 27/49 (55%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTF 150
+ +++G +P + T E + S G ++++ + DP+ +G+ F+ F
Sbjct: 4 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEF 52
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 31.2 bits (69), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 34/75 (45%), Gaps = 4/75 (5%)
Query: 90 FYGRGESSQRIGKK---IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFG 146
F G E +++ KK ++VG L T E + FS+ G I + + D +T GF
Sbjct: 4 FRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTAC-GFC 62
Query: 147 FVTFAEEVVADRVSR 161
FV + A+ R
Sbjct: 63 FVEYYSRADAENAMR 77
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 30.8 bits (68), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 11/49 (22%), Positives = 27/49 (55%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTF 150
+ +++G +P + T E + S G ++++ + DP+ +G+ F+ F
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEF 51
>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 = 30.8 bits (68), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 11/49 (22%), Positives = 27/49 (55%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTF 150
+ +++G +P + T E + S G ++++ + DP+ +G+ F+ F
Sbjct: 5 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEF 53
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 30.8 bits (68), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 37/83 (44%), Gaps = 2/83 (2%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRVSRR 162
+IFV LP + T + L+ F+ G +L Y + +G G V F VA+R R
Sbjct: 10 QIFVRNLPFDFTWKMLKDKFNECGHVL--YADIKMENGKSKGCGVVKFESPEVAERACRM 67
Query: 163 SHEICGQQVAIDSATPLDDAGPS 185
+ + ID + +GPS
Sbjct: 68 MNGMKLSGREIDVRIDRNASGPS 90
>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 = 0.72, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 6/77 (7%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRVSR 161
K +FV R+ + T LRR F +G I +++ + RG+ F+ + E D S
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHE--RDMHSA 160
Query: 162 RSH----EICGQQVAID 174
H +I G++V +D
Sbjct: 161 YKHADGKKIDGRRVLVD 177
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 30.8 bits (68), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 30/60 (50%), Gaps = 5/60 (8%)
Query: 99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRIL--DVYVPKDPKRTGHRGFGFVTFAEEVVA 156
R+G +FV L + + L+ FS G ++ D+ KD K RG G VTF + + A
Sbjct: 13 RLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGK---SRGIGTVTFEQSIEA 69
>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 = 30.8 bits (68), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 32/54 (59%), Gaps = 2/54 (3%)
Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGH-RGFGFVTFAEE 153
+ I+VG + ATAE+L +F G + V + D K +GH +GF ++ F+++
Sbjct: 6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCD-KFSGHPKGFAYIEFSDK 58
>pdb|1A9N|B Chain B, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
pdb|1A9N|D Chain D, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
Length = 96
Score = 30.8 bits (68), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 7/53 (13%)
Query: 104 IFVGRLPQEATAEDLRR----YFSRFGRILDVYVPKDPKRTGHRGFGFVTFAE 152
I++ + + E+L+R FS+FG ++D+ K K RG FV F E
Sbjct: 9 IYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMK---MRGQAFVIFKE 58
>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 = 30.4 bits (67), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 32/54 (59%), Gaps = 2/54 (3%)
Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGH-RGFGFVTFAEE 153
+ I+VG + ATAE+L +F G + V + D K +GH +GF ++ F+++
Sbjct: 5 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCD-KFSGHPKGFAYIEFSDK 57
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 30.4 bits (67), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 30/54 (55%), Gaps = 2/54 (3%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRT--GHRGFGFVTFAEE 153
+K+FVG LP + +++ F RFG ++ + K ++ +G+ F+ F EE
Sbjct: 9 RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEE 62
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 30.4 bits (67), Expect = 1.00, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 26/50 (52%), Gaps = 3/50 (6%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAE 152
+I+VG LP + +D+ F ++G I D+ + R G F FV F +
Sbjct: 24 RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL---KNRRGGPPFAFVEFED 70
>pdb|4A5W|A Chain A, Crystal Structure Of C5b6
Length = 1580
Score = 30.0 bits (66), Expect = 1.1, Method: Composition-based stats.
Identities = 22/87 (25%), Positives = 33/87 (37%), Gaps = 14/87 (16%)
Query: 153 EVVADRVSRRSHEICGQQVAIDSATPLDDAGPSQNFMMNAA--------------ETFGG 198
E+V+D V E CG Q+ + + D P Q +N A +G
Sbjct: 535 ELVSDSVWLNIEEKCGNQLQVHLSPDADAYSPGQTVSLNMATGMDSWVALAAVDSAVYGV 594
Query: 199 YGGPMRTYGRMYGSLDFDDWGYGMGSG 225
G + R++ L+ D G G G G
Sbjct: 595 QRGAKKPLERVFQFLEKSDLGCGAGGG 621
>pdb|3CU7|A Chain A, Human Complement Component 5
pdb|3CU7|B Chain B, Human Complement Component 5
pdb|3KLS|A Chain A, Structure Of Complement C5 In Complex With Ssl7
pdb|3KLS|B Chain B, Structure Of Complement C5 In Complex With Ssl7
pdb|3KM9|A Chain A, Structure Of Complement C5 In Complex With The C-Terminal
Beta-Grasp Domain Of Ssl7
pdb|3KM9|B Chain B, Structure Of Complement C5 In Complex With The C-Terminal
Beta-Grasp Domain Of Ssl7
pdb|4E0S|A Chain A, Crystal Structure Of C5b-6
Length = 1676
Score = 30.0 bits (66), Expect = 1.1, Method: Composition-based stats.
Identities = 22/87 (25%), Positives = 33/87 (37%), Gaps = 14/87 (16%)
Query: 153 EVVADRVSRRSHEICGQQVAIDSATPLDDAGPSQNFMMNAA--------------ETFGG 198
E+V+D V E CG Q+ + + D P Q +N A +G
Sbjct: 553 ELVSDSVWLNIEEKCGNQLQVHLSPDADAYSPGQTVSLNMATGMDSWVALAAVDSAVYGV 612
Query: 199 YGGPMRTYGRMYGSLDFDDWGYGMGSG 225
G + R++ L+ D G G G G
Sbjct: 613 QRGAKKPLERVFQFLEKSDLGCGAGGG 639
>pdb|3PRX|A Chain A, Structure Of Complement C5 In Complex With Cvf And Ssl7
pdb|3PRX|C Chain C, Structure Of Complement C5 In Complex With Cvf And Ssl7
pdb|3PVM|A Chain A, Structure Of Complement C5 In Complex With Cvf
pdb|3PVM|C Chain C, Structure Of Complement C5 In Complex With Cvf
Length = 1676
Score = 30.0 bits (66), Expect = 1.1, Method: Composition-based stats.
Identities = 22/87 (25%), Positives = 33/87 (37%), Gaps = 14/87 (16%)
Query: 153 EVVADRVSRRSHEICGQQVAIDSATPLDDAGPSQNFMMNAA--------------ETFGG 198
E+V+D V E CG Q+ + + D P Q +N A +G
Sbjct: 553 ELVSDSVWLNIEEKCGNQLQVHLSPDADAYSPGQTVSLNMATGMDSWVALAAVDSAVYGV 612
Query: 199 YGGPMRTYGRMYGSLDFDDWGYGMGSG 225
G + R++ L+ D G G G G
Sbjct: 613 QRGAKKPLERVFQFLEKSDLGCGAGGG 639
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 29.6 bits (65), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 39/83 (46%), Gaps = 9/83 (10%)
Query: 94 GESSQRIGK----KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVT 149
G S RI + ++V L E LR+ FS FG I V + R+ +GFGFV
Sbjct: 4 GSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRS--KGFGFVC 61
Query: 150 FAEEVVADRVSRRSHEICGQQVA 172
F+ + ++ E+ G+ VA
Sbjct: 62 FSS---PEEATKAVTEMNGRIVA 81
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 13/56 (23%), Positives = 26/56 (46%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADR 158
K+F+G LP + ++ + FG + + KD +G+ F + + V D+
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 58
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation Initiation
Factor 4b
Length = 100
Score = 29.3 bits (64), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 3/79 (3%)
Query: 105 FVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGH-RGFGFVTFAEEVVADRVSRRS 163
F+G LP + T E ++ +F R I V +P++P +GFG+ F + +
Sbjct: 23 FLGNLPYDVTEESIKEFF-RGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLN 81
Query: 164 HEICG-QQVAIDSATPLDD 181
E G +++ +D A D
Sbjct: 82 EESLGNRRIRVDVADQAQD 100
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 24/95 (25%), Positives = 40/95 (42%), Gaps = 10/95 (10%)
Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRVS 160
GK +F+ L ++ E L +FG + V V P +G F F + A +
Sbjct: 15 GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCL 74
Query: 161 RRSH--------EICGQQVAIDSATPLDDA--GPS 185
+ ++ G+Q+ +D A D+A GPS
Sbjct: 75 AAASLEAEGGGLKLDGRQLKVDLAVTRDEAASGPS 109
>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 = 29.3 bits (64), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 36/81 (44%), Gaps = 4/81 (4%)
Query: 81 PTLYDHPGSFYGRGESSQRI---GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDP 137
P + ++P S Y G S + K+F+G LP + ++ + FG + + KD
Sbjct: 92 PGMSENP-SVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDS 150
Query: 138 KRTGHRGFGFVTFAEEVVADR 158
+G+ F + + V D+
Sbjct: 151 ATGLSKGYAFCEYVDINVTDQ 171
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 28.9 bits (63), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 38/74 (51%), Gaps = 5/74 (6%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGH--RGFGFVTFAEEVVADRVS 160
K+ +GRL + T + + FS +G+I + +P + + H +G+ +V F A++
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVE-RMHPHLSKGYAYVEFENPDEAEKAL 64
Query: 161 RRSH--EICGQQVA 172
+ +I GQ++
Sbjct: 65 KHMDGGQIDGQEIT 78
>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 = 28.9 bits (63), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 13/56 (23%), Positives = 26/56 (46%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADR 158
K+F+G LP + ++ + FG + + KD +G+ F + + V D+
Sbjct: 98 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 153
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 28.5 bits (62), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 13/56 (23%), Positives = 26/56 (46%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADR 158
K+F+G LP + ++ + FG + + KD +G+ F + + V D+
Sbjct: 96 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 151
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 28.5 bits (62), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 34/81 (41%), Gaps = 10/81 (12%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEE--VVADRV 159
K +FV L T E L + FS+FG++ V KD + F+ F E V
Sbjct: 12 KVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAME 63
Query: 160 SRRSHEICGQQVAIDSATPLD 180
++ G+ + I A P D
Sbjct: 64 EMNGKDLEGENIEIVFAKPPD 84
>pdb|2NLW|A Chain A, Solution Structure Of The Rrm Domain Of Human Eukaryotic
Initiation Factor 3b
Length = 105
Score = 28.1 bits (61), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 33/65 (50%), Gaps = 8/65 (12%)
Query: 93 RGESSQRIGKKIFVGRLPQ------EATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFG 146
R + + I I V +PQ E + + FS+FG+I + + P++ +T +G+
Sbjct: 7 RPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKT--KGYI 64
Query: 147 FVTFA 151
F+ +A
Sbjct: 65 FLEYA 69
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 28.1 bits (61), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 19/35 (54%), Gaps = 3/35 (8%)
Query: 118 LRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAE 152
L FS+FG+ILD+ K K RG FV F E
Sbjct: 27 LYAIFSQFGQILDIVALKTLK---MRGQAFVIFKE 58
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 28.1 bits (61), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 105 FVGRLPQEATAEDLRRYFSRFGRILD 130
++G +P AT DL F FG ILD
Sbjct: 31 YIGNIPHFATEADLIPLFQNFGFILD 56
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 28.1 bits (61), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 6/60 (10%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAEEVVADRVSRRS 163
++VG L T DLR +F +FG I + V + + F+ FA A+ + +S
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQ------CAFIQFATRQAAEVAAEKS 68
>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 = 27.7 bits (60), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 27/95 (28%), Positives = 41/95 (43%), Gaps = 15/95 (15%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGH-RGFGFVTFAEEVVADRVSRR 162
++V LP+ T + L F ++G I+ + +D K TG RG FV R ++R
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRD-KLTGRPRGVAFV---------RYNKR 65
Query: 163 SHEICGQQVAIDSATPLDDAGPSQNFMMNAAETFG 197
Q AI + + G SQ + AE G
Sbjct: 66 EE----AQEAISALNNVIPEGGSQPLSVRLAEEHG 96
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 27.3 bits (59), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 33/68 (48%), Gaps = 9/68 (13%)
Query: 84 YDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGH- 142
Y PG GES + ++V LP+ T + L F ++G I+ + +D K TG
Sbjct: 79 YARPG-----GESIK--DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRD-KLTGRP 130
Query: 143 RGFGFVTF 150
RG FV +
Sbjct: 131 RGVAFVRY 138
>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 = 27.3 bits (59), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 2/49 (4%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGH-RGFGFVTF 150
++V LP+ T + L F ++G I+ + +D K TG RG FV +
Sbjct: 102 NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRD-KLTGRPRGVAFVRY 149
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 26.9 bits (58), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 13/53 (24%), Positives = 28/53 (52%), Gaps = 3/53 (5%)
Query: 100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKDPKRTGHRGFGFVTFAE 152
+ + +++ LP + TAE++ F ++G I + V P+ RG +V + +
Sbjct: 11 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYED 60
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.320 0.139 0.428
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,030,827
Number of Sequences: 62578
Number of extensions: 355685
Number of successful extensions: 966
Number of sequences better than 100.0: 158
Number of HSP's better than 100.0 without gapping: 123
Number of HSP's successfully gapped in prelim test: 35
Number of HSP's that attempted gapping in prelim test: 759
Number of HSP's gapped (non-prelim): 228
length of query: 237
length of database: 14,973,337
effective HSP length: 96
effective length of query: 141
effective length of database: 8,965,849
effective search space: 1264184709
effective search space used: 1264184709
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)