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= 032483
(139 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 29/35 (82%)
Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
G K+FVGR ++ TAE+L+++F ++G ++DV++PK
Sbjct: 11 GSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPK 45
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 25/32 (78%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
+FVGR + T ++LR +FS++G ++DV++PK
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPK 39
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 40.0 bits (92), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 25/33 (75%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
K+F+G LP+EAT +++R F ++G++L+ + K
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDIIK 42
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 39.7 bits (91), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 32/127 (25%), Positives = 51/127 (40%), Gaps = 43/127 (33%)
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 FSRFGRI 128
F ++G+I
Sbjct: 126 FEQYGKI 132
Score = 32.3 bits (72), Expect = 0.076, 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|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 = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 32/127 (25%), Positives = 51/127 (40%), Gaps = 43/127 (33%)
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 FSRFGRI 128
F ++G+I
Sbjct: 125 FEQYGKI 131
Score = 32.7 bits (73), Expect = 0.075, 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|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 = 39.3 bits (90), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 32/127 (25%), Positives = 51/127 (40%), Gaps = 43/127 (33%)
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 FSRFGRI 128
F ++G+I
Sbjct: 124 FEQYGKI 130
Score = 32.7 bits (73), Expect = 0.074, 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|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 39.3 bits (90), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 32/127 (25%), Positives = 51/127 (40%), Gaps = 43/127 (33%)
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 FSRFGRI 128
F ++G+I
Sbjct: 125 FEQYGKI 131
Score = 32.0 bits (71), Expect = 0.12, 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|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 39.3 bits (90), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 32/127 (25%), Positives = 51/127 (40%), Gaps = 43/127 (33%)
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 FSRFGRI 128
F ++G+I
Sbjct: 123 FEQYGKI 129
Score = 32.0 bits (71), Expect = 0.11, 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|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 = 39.3 bits (90), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 32/127 (25%), Positives = 51/127 (40%), Gaps = 43/127 (33%)
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 FSRFGRI 128
F ++G+I
Sbjct: 118 FEQYGKI 124
Score = 32.3 bits (72), Expect = 0.079, 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|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 28/49 (57%)
Query: 89 SFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKVR 137
SF GE + ++FVG LP + T ED +R F R+G +V++ + R
Sbjct: 10 SFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR 58
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 35.8 bits (81), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 21/33 (63%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
K+FVG L T E LR YFS++G ++D + K
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMK 50
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 35.0 bits (79), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 17/38 (44%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
Q+ I +G LP + T +DL+ YFS FG +L V V K
Sbjct: 13 QKTSDLIVLG-LPWKTTEQDLKEYFSTFGEVLMVQVKK 49
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 34.7 bits (78), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 21/33 (63%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
KIFVG + T+++LR F R GR+++ V K
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVVK 43
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 34.7 bits (78), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 29/47 (61%)
Query: 89 SFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
+F GE + ++FVG LP + T E++R+ F ++G+ +V++ K
Sbjct: 10 NFRKPGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK 56
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 34.7 bits (78), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 23/35 (65%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKVR 137
K+FVG++P+ +DL+ F FGRI ++ V K R
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDR 51
>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic
Granule-Associated Rna Binding Protein 1
pdb|2RNE|A Chain A, Solution Structure Of The Second Rna Recognition Motif
(Rrm) Of Tia-1
Length = 115
Score = 34.7 bits (78), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 16/32 (50%), Positives = 20/32 (62%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
+FVG L E T ED++ F+ FGRI D V K
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVK 49
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 34.3 bits (77), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 18/36 (50%), Positives = 20/36 (55%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKVRQ 138
KIFVG LP T LR+YF FG I + V RQ
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQ 54
>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 = 34.3 bits (77), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 24/33 (72%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
++FVG LP + T E++R+ F ++G+ +V++ K
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK 49
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 34.3 bits (77), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 22/41 (53%)
Query: 93 RGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
RG G K+F+G L + T E LR YF +FG + + V
Sbjct: 17 RGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLV 57
Score = 28.1 bits (61), Expect = 1.6, 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 = 34.3 bits (77), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 21/32 (65%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
+K+F+G L E T E LR Y+ ++G++ D V
Sbjct: 28 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVV 59
Score = 32.0 bits (71), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 3 KDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKED 49
+D SK RG GF+TF+S V+ M H + G V RA +E+
Sbjct: 61 RDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAREE 108
>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 = 34.3 bits (77), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 1/61 (1%)
Query: 3 KDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGY 62
KD + RG GF++F SV+ ++ H L G + RA P+ D+ G++ GG
Sbjct: 37 KDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDGKVIDPKRAIPR-DEQDKTGKIFVGGI 95
Query: 63 G 63
G
Sbjct: 96 G 96
Score = 32.3 bits (72), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 22/33 (66%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
K+F+G L + T ++LR YF ++G + D+ + K
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMK 37
Score = 27.7 bits (60), Expect = 2.4, 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|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 = 34.3 bits (77), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 20/28 (71%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDV 131
+F+G L + T +DL+ YFS+FG ++D
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDC 29
Score = 26.6 bits (57), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 11 RGIGFITFASADSVENLM-VDTHELGGSTVVVDRA 44
RG GF+ F ++SV+ +M H+L G + RA
Sbjct: 41 RGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKRA 75
>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 = 33.9 bits (76), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 21/31 (67%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
K FVG L + + +DL+ YF++FG ++D +
Sbjct: 13 KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTI 43
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 33.9 bits (76), Expect = 0.030, Method: Compositional matrix adjust.
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
Score = 33.1 bits (74), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 18/27 (66%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILD 130
IFVG L T ED++ YF +FG++ D
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDD 28
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 33.9 bits (76), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 20/32 (62%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
+FVG L E T ED++ F+ FG+I D V K
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVK 49
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 33.5 bits (75), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 23/35 (65%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKVR 137
K+F+G++P+ +DL+ F FG+I ++ V K R
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDR 49
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 33.5 bits (75), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 21/32 (65%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
+K+FVG L ++ + +D+RR F FG I + +
Sbjct: 16 RKLFVGMLNKQQSEDDVRRLFEAFGNIEECTI 47
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 32.7 bits (73), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 19/31 (61%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
KIFVG +P +LR YF +FG + +V +
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVM 42
Score = 30.8 bits (68), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 11 RGIGFITFASADSVEN-LMVDTHELGGSTVVVDRATPKE 48
RG GFITF SV+ + + H++ G V V RA P++
Sbjct: 52 RGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVKRAEPRD 90
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 32.7 bits (73), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 21/32 (65%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
+K+FVG L ++ T ED+R+ F FG I + V
Sbjct: 13 RKLFVGMLGKQQTDEDVRKMFEPFGTIDECTV 44
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 32.0 bits (71), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 19/31 (61%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
K+F+G L + T E LR YF +FG + + V
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLV 32
Score = 27.3 bits (59), Expect = 2.9, Method: Compositional matrix adjust.
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|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 32.0 bits (71), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 21/30 (70%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDV 131
+ I+VG L AT+E ++ FS+FG++ +V
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNV 31
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 32.0 bits (71), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 24/37 (64%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKVRQH 139
K+FVG++P+ + +DLR F ++G + ++ V + R
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQ 41
Score = 31.6 bits (70), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 21/32 (65%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
+K+F+G + ++ T D+R FS FG+I + +
Sbjct: 96 RKLFIGMISKKCTENDIRVMFSSFGQIEECRI 127
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 32.0 bits (71), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 24/35 (68%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKVR 137
K+FVG++P+ + +DLR F ++G + ++ V + R
Sbjct: 17 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDR 51
Score = 31.6 bits (70), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 21/32 (65%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
+K+F+G + ++ T D+R FS FG+I + +
Sbjct: 108 RKLFIGMISKKCTENDIRVMFSSFGQIEECRI 139
>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 = 32.0 bits (71), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 24/47 (51%)
Query: 91 YGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKVR 137
YGR + V L + + LRR F ++GR+ DVY+P+ R
Sbjct: 37 YGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDR 83
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 31.6 bits (70), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 106 VGRLPQEATAEDLRRYFSRFGRILDVYVPKVR 137
V L + + LRR F ++GR+ DVY+P+ R
Sbjct: 75 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDR 106
>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 = 31.6 bits (70), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 22/31 (70%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
K+FVG++P+ + +DLR F ++G + ++ V
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINV 35
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 31.6 bits (70), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 20/32 (62%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
++V LP T DL R FS++G+++ V + K
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMK 50
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 31.6 bits (70), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 23/36 (63%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKVRQ 138
K+FVG L + + L + FS++G+I +V V K R+
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRE 49
Score = 28.9 bits (63), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 3 KDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKEDD 50
KD+ ++ RG GF+TF + D ++ M ++ + G + VD+A D+
Sbjct: 46 KDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDN 95
>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 = 31.2 bits (69), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 21/32 (65%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
+K+F+G + ++ T D+R FS FG+I + +
Sbjct: 96 RKLFIGXISKKCTENDIRVXFSSFGQIEECRI 127
Score = 30.8 bits (68), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 23/35 (65%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKVR 137
K FVG++P+ + +DLR F ++G + ++ V + R
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDR 39
>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 = 31.2 bits (69), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 19/33 (57%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP 134
KKIFVG L + E +R YF FG + + +P
Sbjct: 2 KKIFVGGLSPDTPEEKIREYFGGFGEVESIELP 34
>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 = 31.2 bits (69), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 23/43 (53%)
Query: 91 YGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
Y R S +++ LP+ T +D+ FSRFGRI++ V
Sbjct: 78 YARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRV 120
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 31.2 bits (69), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 23/43 (53%)
Query: 91 YGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
Y R S +++ LP+ T +D+ FSRFGRI++ V
Sbjct: 78 YARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRV 120
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 30.8 bits (68), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 19/33 (57%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
KI V +P +A ++R FS FG + V +PK
Sbjct: 17 KILVRNIPFQANQREIRELFSTFGELKTVRLPK 49
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 30.4 bits (67), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 20/32 (62%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
+ V L + + LRR F ++GR+ DVY+P+
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPR 47
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 30.4 bits (67), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
+K+FVG L ++ + ED+ R F FG I + V
Sbjct: 16 RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTV 47
>pdb|2B6N|A Chain A, The 1.8 A Crystal Structure Of A Proteinase K Like Enzyme
From A Psychrotroph Serratia Species
Length = 278
Score = 30.0 bits (66), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 18/39 (46%), Gaps = 4/39 (10%)
Query: 96 SSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP 134
S R I VG T+ D R FS +G LD+Y P
Sbjct: 168 SPARAADAITVG----STTSNDSRSSFSNYGTCLDIYAP 202
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 30.0 bits (66), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRIL 129
+ +FVG +P EAT E L+ FS G ++
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVV 36
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 30.0 bits (66), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
K++ V +P DLR+ F +FG+ILDV +
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEI 47
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 30.0 bits (66), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
K++ V +P DLR+ F +FG+ILDV +
Sbjct: 30 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEI 61
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 29.3 bits (64), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKVRQH 139
K+ +GRL + T + + FS +G+I + +P R H
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMH 42
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 29.3 bits (64), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 28/47 (59%), Gaps = 2/47 (4%)
Query: 1 MPKDQGSKAHRGIGFITFASADSVENL--MVDTHELGGSTVVVDRAT 45
MPKD+ + H+G GF+ F S + + ++D +L G + V++A+
Sbjct: 47 MPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKAS 93
>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 = 29.3 bits (64), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 23/39 (58%)
Query: 91 YGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRIL 129
Y R S+ ++V LP+ T ++L + FS++GRI+
Sbjct: 78 YARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRII 116
>pdb|3F7M|A Chain A, Crystal Structure Of Apo Cuticle-Degrading Protease
(Ver112) From Verticillium Psalliotae
Length = 279
Score = 28.9 bits (63), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 8/20 (40%), Positives = 15/20 (75%)
Query: 115 AEDLRRYFSRFGRILDVYVP 134
+ D+R FS +GR++D++ P
Sbjct: 186 SNDVRSTFSNYGRVVDIFAP 205
>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 = 28.9 bits (63), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 23/36 (63%), Gaps = 4/36 (11%)
Query: 104 IFVGRLPQEATAEDLRR----YFSRFGRILDVYVPK 135
I++ L ++ ++L++ FSRFG+ILD+ V +
Sbjct: 8 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR 43
>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 = 28.9 bits (63), Expect = 1.00, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 23/36 (63%), Gaps = 4/36 (11%)
Query: 104 IFVGRLPQEATAEDLRR----YFSRFGRILDVYVPK 135
I++ L ++ ++L++ FSRFG+ILD+ V +
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR 47
>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 = 28.9 bits (63), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 23/36 (63%), Gaps = 4/36 (11%)
Query: 104 IFVGRLPQEATAEDLRR----YFSRFGRILDVYVPK 135
I++ L ++ ++L++ FSRFG+ILD+ V +
Sbjct: 7 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR 42
>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 = 28.9 bits (63), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 23/36 (63%), Gaps = 4/36 (11%)
Query: 104 IFVGRLPQEATAEDLRR----YFSRFGRILDVYVPK 135
I++ L ++ ++L++ FSRFG+ILD+ V +
Sbjct: 6 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR 41
>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 = 28.9 bits (63), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 23/36 (63%), Gaps = 4/36 (11%)
Query: 104 IFVGRLPQEATAEDLRR----YFSRFGRILDVYVPK 135
I++ L ++ ++L++ FSRFG+ILD+ V +
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR 47
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 28.9 bits (63), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 17/33 (51%)
Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
G +F+ LPQE T DL F FG ++ V
Sbjct: 40 GCNLFIYHLPQEFTDTDLASTFLPFGNVISAKV 72
>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 = 28.9 bits (63), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 23/36 (63%), Gaps = 4/36 (11%)
Query: 104 IFVGRLPQEATAEDLRR----YFSRFGRILDVYVPK 135
I++ L ++ ++L++ FSRFG+ILD+ V +
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR 46
>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 = 28.9 bits (63), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 23/36 (63%), Gaps = 4/36 (11%)
Query: 104 IFVGRLPQEATAEDLRR----YFSRFGRILDVYVPK 135
I++ L ++ ++L++ FSRFG+ILD+ V +
Sbjct: 9 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR 44
>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 = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 23/36 (63%), Gaps = 4/36 (11%)
Query: 104 IFVGRLPQEATAEDLRR----YFSRFGRILDVYVPK 135
I++ L ++ ++L++ FSRFG+ILD+ V +
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR 46
>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 = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 23/36 (63%), Gaps = 4/36 (11%)
Query: 104 IFVGRLPQEATAEDLRR----YFSRFGRILDVYVPK 135
I++ L ++ ++L++ FSRFG+ILD+ V +
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR 46
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 28.5 bits (62), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 23/36 (63%), Gaps = 4/36 (11%)
Query: 104 IFVGRLPQEATAEDLRR----YFSRFGRILDVYVPK 135
I++ L ++ ++L++ FSRFG+ILD+ V +
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR 46
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 28.5 bits (62), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 23/36 (63%), Gaps = 4/36 (11%)
Query: 104 IFVGRLPQEATAEDLRR----YFSRFGRILDVYVPK 135
I++ L ++ ++L++ FSRFG+ILD+ V +
Sbjct: 9 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR 44
>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 = 28.5 bits (62), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 23/36 (63%), Gaps = 4/36 (11%)
Query: 104 IFVGRLPQEATAEDLRR----YFSRFGRILDVYVPK 135
I++ L ++ ++L++ FSRFG+ILD+ V +
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR 47
>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 = 28.5 bits (62), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
G +F+ LPQE +DL + F FG ++ V
Sbjct: 25 GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKV 57
>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 = 28.5 bits (62), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 11/28 (39%), Positives = 15/28 (53%)
Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRI 128
G + V LPQ T ++LR FS G +
Sbjct: 19 GTNLIVNYLPQNXTQDELRSLFSSIGEV 46
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 28.1 bits (61), Expect = 1.4, 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|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 = 1.5, 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|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 28.1 bits (61), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVP 134
IFVG L + E +R YF FG + + +P
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELP 32
>pdb|3Q9V|A Chain A, Crystal Structure Of Rra C-Terminal Domain(123-221) From
Deinococcus Radiodurans
pdb|3Q9V|B Chain B, Crystal Structure Of Rra C-Terminal Domain(123-221) From
Deinococcus Radiodurans
Length = 133
Score = 27.7 bits (60), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 20/36 (55%), Gaps = 4/36 (11%)
Query: 83 LYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDL 118
L PG Y R Q IG++I+ GRLP+ + D+
Sbjct: 72 LIRQPGRVYSR----QEIGQEIWQGRLPEGSNVVDV 103
>pdb|3Q9S|A Chain A, Crystal Structure Of Rra(1-215) From Deinococcus
Radiodurans
Length = 249
Score = 27.7 bits (60), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 20/36 (55%), Gaps = 4/36 (11%)
Query: 83 LYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDL 118
L PG Y R Q IG++I+ GRLP+ + D+
Sbjct: 194 LIRQPGRVYSR----QEIGQEIWQGRLPEGSNVVDV 225
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 27.7 bits (60), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 11/39 (28%), Positives = 23/39 (58%)
Query: 91 YGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRIL 129
Y R S+ ++V LP+ + +++ + FS++GRI+
Sbjct: 80 YARPSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRII 118
>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 = 27.3 bits (59), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 11/33 (33%), Positives = 21/33 (63%)
Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
G +FV + +EAT ED+ F+ +G I ++++
Sbjct: 22 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHL 54
>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 = 27.3 bits (59), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 11/33 (33%), Positives = 21/33 (63%)
Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
G +FV + +EAT ED+ F+ +G I ++++
Sbjct: 7 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHL 39
>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 = 27.3 bits (59), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 11/33 (33%), Positives = 21/33 (63%)
Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
G +FV + +EAT ED+ F+ +G I ++++
Sbjct: 9 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHL 41
>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 = 27.3 bits (59), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 11/33 (33%), Positives = 21/33 (63%)
Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
G +FV + +EAT ED+ F+ +G I ++++
Sbjct: 23 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHL 55
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 27.3 bits (59), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 11/33 (33%), Positives = 21/33 (63%)
Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
G +FV + +EAT ED+ F+ +G I ++++
Sbjct: 7 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHL 39
>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 = 27.3 bits (59), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 11/33 (33%), Positives = 21/33 (63%)
Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
G +FV + +EAT ED+ F+ +G I ++++
Sbjct: 7 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHL 39
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 26.9 bits (58), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKVRQ 138
++VG L T DLR +F +FG I + V + +Q
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQ 49
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 26.6 bits (57), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 10/29 (34%), Positives = 18/29 (62%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDV 131
+I+VG LP + +D+ F ++G I D+
Sbjct: 24 RIYVGNLPPDIRTKDIEDVFYKYGAIRDI 52
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 26.2 bits (56), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 10/28 (35%), Positives = 18/28 (64%)
Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRIL 129
+K+FVG LP + +++ F RFG ++
Sbjct: 9 RKVFVGGLPPDIDEDEITASFRRFGPLV 36
>pdb|2E5J|A Chain A, Solution Structure Of Rna Binding Domain In
Methenyltetrahydrofolate Synthetase Domain Containing
Length = 97
Score = 26.2 bits (56), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 9/29 (31%), Positives = 16/29 (55%)
Query: 100 IGKKIFVGRLPQEATAEDLRRYFSRFGRI 128
+ ++VG LP++A DL+R G +
Sbjct: 18 LAADVYVGNLPRDARVSDLKRALRELGSV 46
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 26.2 bits (56), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 10/32 (31%), Positives = 20/32 (62%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVP 134
++FV L ++ EDL + FS +G + +++ P
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYP 41
>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 = 25.8 bits (55), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 94 GESSQRIGKK-IFVGRLPQEATAEDLRRYFSRFGRI 128
E + I K+ ++VG + +TA+DL +FS G I
Sbjct: 28 AEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSI 63
>pdb|1X74|A Chain A, Alpha-Methylacyl-Coa Racemase From Mycobacterium
Tuberculosis- Mutational And Structural Characterization
Of The Fold And Active Site
pdb|1X74|B Chain B, Alpha-Methylacyl-Coa Racemase From Mycobacterium
Tuberculosis- Mutational And Structural Characterization
Of The Fold And Active Site
pdb|1X74|C Chain C, Alpha-Methylacyl-Coa Racemase From Mycobacterium
Tuberculosis- Mutational And Structural Characterization
Of The Fold And Active Site
pdb|1X74|D Chain D, Alpha-Methylacyl-Coa Racemase From Mycobacterium
Tuberculosis- Mutational And Structural Characterization
Of The Fold And Active Site
pdb|2GCE|A Chain A, The 1,1-Proton Transfer Reaction Mechanism By Alpha-
Methylacyl-Coa Racemase Is Catalyzed By An
AspartateHISTIDINE PAIR AND INVOLVES A SMOOTH,
METHIONINE- Rich Surface For Binding The Fatty Acyl
Moiety
pdb|2GCE|B Chain B, The 1,1-Proton Transfer Reaction Mechanism By Alpha-
Methylacyl-Coa Racemase Is Catalyzed By An
AspartateHISTIDINE PAIR AND INVOLVES A SMOOTH,
METHIONINE- Rich Surface For Binding The Fatty Acyl
Moiety
pdb|2GCE|C Chain C, The 1,1-Proton Transfer Reaction Mechanism By Alpha-
Methylacyl-Coa Racemase Is Catalyzed By An
AspartateHISTIDINE PAIR AND INVOLVES A SMOOTH,
METHIONINE- Rich Surface For Binding The Fatty Acyl
Moiety
pdb|2GCE|D Chain D, The 1,1-Proton Transfer Reaction Mechanism By Alpha-
Methylacyl-Coa Racemase Is Catalyzed By An
AspartateHISTIDINE PAIR AND INVOLVES A SMOOTH,
METHIONINE- Rich Surface For Binding The Fatty Acyl
Moiety
pdb|2GCI|A Chain A, The 1,1-Proton Transfer Reaction Mechanism By
Alpha-Methylacyl-Coa Racemase Is Catalyzed By An
AsparteHISTIDINE PAIR AND INVOLVES A Smooth,
Methionine-Rich Surface For Binding The Fatty Acyl
Moiety
pdb|2GCI|B Chain B, The 1,1-Proton Transfer Reaction Mechanism By
Alpha-Methylacyl-Coa Racemase Is Catalyzed By An
AsparteHISTIDINE PAIR AND INVOLVES A Smooth,
Methionine-Rich Surface For Binding The Fatty Acyl
Moiety
pdb|2GCI|C Chain C, The 1,1-Proton Transfer Reaction Mechanism By
Alpha-Methylacyl-Coa Racemase Is Catalyzed By An
AsparteHISTIDINE PAIR AND INVOLVES A Smooth,
Methionine-Rich Surface For Binding The Fatty Acyl
Moiety
pdb|2GCI|D Chain D, The 1,1-Proton Transfer Reaction Mechanism By
Alpha-Methylacyl-Coa Racemase Is Catalyzed By An
AsparteHISTIDINE PAIR AND INVOLVES A Smooth,
Methionine-Rich Surface For Binding The Fatty Acyl
Moiety
pdb|2GD0|A Chain A, The 1,1-Proton Transfer Reaction Mechanism By
Alpha-Methylacyl-Coa Racemase Is Catalyzed By An
AspartateHISTIDINE PAIR AND INVOLVES A Smooth,
Methionine-Rich Surface For Binding The Fatty Acyl
Moiety
pdb|2GD0|B Chain B, The 1,1-Proton Transfer Reaction Mechanism By
Alpha-Methylacyl-Coa Racemase Is Catalyzed By An
AspartateHISTIDINE PAIR AND INVOLVES A Smooth,
Methionine-Rich Surface For Binding The Fatty Acyl
Moiety
pdb|2GD0|C Chain C, The 1,1-Proton Transfer Reaction Mechanism By
Alpha-Methylacyl-Coa Racemase Is Catalyzed By An
AspartateHISTIDINE PAIR AND INVOLVES A Smooth,
Methionine-Rich Surface For Binding The Fatty Acyl
Moiety
pdb|2GD0|D Chain D, The 1,1-Proton Transfer Reaction Mechanism By
Alpha-Methylacyl-Coa Racemase Is Catalyzed By An
AspartateHISTIDINE PAIR AND INVOLVES A Smooth,
Methionine-Rich Surface For Binding The Fatty Acyl
Moiety
pdb|2GD2|A Chain A, The 1,1-Proton Transfer Reaction Mechanism By
Alpha-Methylacyl-Coa Racemase Is Catalyzed By An
AspartateHISTIDINE PAIR AND INVOLVES A Smooth,
Methionine-Rich Surface For Binding The Fatty Acyl
Moiety
pdb|2GD2|B Chain B, The 1,1-Proton Transfer Reaction Mechanism By
Alpha-Methylacyl-Coa Racemase Is Catalyzed By An
AspartateHISTIDINE PAIR AND INVOLVES A Smooth,
Methionine-Rich Surface For Binding The Fatty Acyl
Moiety
pdb|2GD2|C Chain C, The 1,1-Proton Transfer Reaction Mechanism By
Alpha-Methylacyl-Coa Racemase Is Catalyzed By An
AspartateHISTIDINE PAIR AND INVOLVES A Smooth,
Methionine-Rich Surface For Binding The Fatty Acyl
Moiety
pdb|2GD2|D Chain D, The 1,1-Proton Transfer Reaction Mechanism By
Alpha-Methylacyl-Coa Racemase Is Catalyzed By An
AspartateHISTIDINE PAIR AND INVOLVES A Smooth,
Methionine-Rich Surface For Binding The Fatty Acyl
Moiety
pdb|2GD6|A Chain A, The 1,1-Proton Transfer Reaction Mechanism By
Alpha-Methylacyl-Coa Racemase Is Catalyzed By An
AspartateHISTIDINE PAIR AND INVOLVES A Smooth,
Methionine-Rich Surface For Binding The Fatty Acyl
Moiety
pdb|2GD6|B Chain B, The 1,1-Proton Transfer Reaction Mechanism By
Alpha-Methylacyl-Coa Racemase Is Catalyzed By An
AspartateHISTIDINE PAIR AND INVOLVES A Smooth,
Methionine-Rich Surface For Binding The Fatty Acyl
Moiety
pdb|2GD6|C Chain C, The 1,1-Proton Transfer Reaction Mechanism By
Alpha-Methylacyl-Coa Racemase Is Catalyzed By An
AspartateHISTIDINE PAIR AND INVOLVES A Smooth,
Methionine-Rich Surface For Binding The Fatty Acyl
Moiety
pdb|2GD6|D Chain D, The 1,1-Proton Transfer Reaction Mechanism By
Alpha-Methylacyl-Coa Racemase Is Catalyzed By An
AspartateHISTIDINE PAIR AND INVOLVES A Smooth,
Methionine-Rich Surface For Binding The Fatty Acyl
Moiety
pdb|2YIM|A Chain A, The Enolisation Chemistry Of A Thioester-Dependent
Racemase: The 1.4 A Crystal Structure Of A Complex With
A Planar Reaction Intermediate Analogue
pdb|2YIM|B Chain B, The Enolisation Chemistry Of A Thioester-Dependent
Racemase: The 1.4 A Crystal Structure Of A Complex With
A Planar Reaction Intermediate Analogue
pdb|2YIM|C Chain C, The Enolisation Chemistry Of A Thioester-Dependent
Racemase: The 1.4 A Crystal Structure Of A Complex With
A Planar Reaction Intermediate Analogue
pdb|2YIM|D Chain D, The Enolisation Chemistry Of A Thioester-Dependent
Racemase: The 1.4 A Crystal Structure Of A Complex With
A Planar Reaction Intermediate Analogue
Length = 360
Score = 25.8 bits (55), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 30/64 (46%), Gaps = 8/64 (12%)
Query: 28 MVDTHELGGSTVVVD-----RATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGA-- 80
+VD + GS+V++ RAT D R M GG Y+ Y A RY A+GA
Sbjct: 183 VVDAAMVDGSSVLIQMMWAMRATGMWTDTRGA-NMLDGGAPYYDTYECADGRYVAVGAIE 241
Query: 81 PTLY 84
P Y
Sbjct: 242 PQFY 245
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 0.138 0.408
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,418,470
Number of Sequences: 62578
Number of extensions: 183037
Number of successful extensions: 620
Number of sequences better than 100.0: 103
Number of HSP's better than 100.0 without gapping: 90
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 482
Number of HSP's gapped (non-prelim): 153
length of query: 139
length of database: 14,973,337
effective HSP length: 89
effective length of query: 50
effective length of database: 9,403,895
effective search space: 470194750
effective search space used: 470194750
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: 46 (22.3 bits)