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= 025068
(258 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 118 bits (295), Expect = 4e-27, Method: Compositional matrix adjust.
Identities = 55/87 (63%), Positives = 68/87 (78%), Gaps = 1/87 (1%)
Query: 28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAAR 87
DTT+TK+FVGGL + T ++R+YFE FG+I EAVVITD+ TG+S+GYGFVT + AA
Sbjct: 14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAE 73
Query: 88 RACADPTPFIDGRRANCNLASLG-RPR 113
RAC DP P IDGR+AN NLA LG +PR
Sbjct: 74 RACKDPNPIIDGRKANVNLAYLGAKPR 100
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 75.1 bits (183), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 31/71 (43%), Positives = 46/71 (64%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
K+FVGGL W T ET+R YF Q+GE+++ V++ DK T +S+G+GFV F++P A
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 93 PTPFIDGRRAN 103
+DGR +
Sbjct: 78 RPHTLDGRNID 88
>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 = 69.3 bits (168), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 48/79 (60%)
Query: 22 LNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFR 81
+N+ + K FVGGL+W+T + ++ YF +FGE+++ + D NTGRS+G+GF+ F+
Sbjct: 2 INASKNEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFK 61
Query: 82 EPEAARRACADPTPFIDGR 100
+ + + +DGR
Sbjct: 62 DAASVEKVLDQKEHRLDGR 80
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 67.8 bits (164), Expect = 5e-12, Method: Composition-based stats.
Identities = 30/75 (40%), Positives = 46/75 (61%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
K+F+GGL+W+T E +R YF QFGE+ E +V+ D T RS+G+GFVTF + + A
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 93 PTPFIDGRRANCNLA 107
+D + + +A
Sbjct: 62 SRHELDSKTIDPKVA 76
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 67.8 bits (164), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 32/87 (36%), Positives = 52/87 (59%)
Query: 29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
++ K+F+GGL+W+T E +R YF QFGE+ E +V+ D T RS+G+GFVTF + +
Sbjct: 23 SSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDK 82
Query: 89 ACADPTPFIDGRRANCNLASLGRPRPQ 115
A +D + + +A R +P+
Sbjct: 83 VLAQSRHELDSKTIDPKVAFPRRAQPK 109
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 64.7 bits (156), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 30/76 (39%), Positives = 50/76 (65%), Gaps = 1/76 (1%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA-CA 91
K+FVGGL+++T +++ + F ++G+I E VV+ D+ T RS+G+GFVTF + A+ A A
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 92 DPTPFIDGRRANCNLA 107
+DGR+ + A
Sbjct: 74 MNGKSVDGRQIRVDQA 89
>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 = 63.9 bits (154), Expect = 9e-11, Method: Compositional matrix adjust.
Identities = 30/68 (44%), Positives = 45/68 (66%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
K+F+GGL++ET E++R +FEQ+G + + VV+ D NT RS+G+GFVT+ E A
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 93 PTPFIDGR 100
+DGR
Sbjct: 75 RPHKVDGR 82
Score = 58.2 bits (139), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 46/77 (59%), Gaps = 2/77 (2%)
Query: 30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
T K+FVGG+ +T+ +R YFEQ+G+I ++TD+ +G+ +G+ FVTF + ++ +
Sbjct: 103 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 162
Query: 90 CADPTPFIDGRRANCNL 106
++G NC +
Sbjct: 163 VIQKYHTVNGH--NCEV 177
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 63.9 bits (154), Expect = 9e-11, Method: Compositional matrix adjust.
Identities = 30/68 (44%), Positives = 45/68 (66%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
K+F+GGL++ET E++R +FEQ+G + + VV+ D NT RS+G+GFVT+ E A
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 93 PTPFIDGR 100
+DGR
Sbjct: 75 RPHKVDGR 82
Score = 58.2 bits (139), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 46/77 (59%), Gaps = 2/77 (2%)
Query: 30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
T K+FVGG+ +T+ +R YFEQ+G+I ++TD+ +G+ +G+ FVTF + ++ +
Sbjct: 103 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 162
Query: 90 CADPTPFIDGRRANCNL 106
++G NC +
Sbjct: 163 VIQKYHTVNGH--NCEV 177
>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 = 63.9 bits (154), Expect = 9e-11, Method: Compositional matrix adjust.
Identities = 30/68 (44%), Positives = 45/68 (66%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
K+F+GGL++ET E++R +FEQ+G + + VV+ D NT RS+G+GFVT+ E A
Sbjct: 14 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 73
Query: 93 PTPFIDGR 100
+DGR
Sbjct: 74 RPHKVDGR 81
Score = 58.2 bits (139), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 46/77 (59%), Gaps = 2/77 (2%)
Query: 30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
T K+FVGG+ +T+ +R YFEQ+G+I ++TD+ +G+ +G+ FVTF + ++ +
Sbjct: 102 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 161
Query: 90 CADPTPFIDGRRANCNL 106
++G NC +
Sbjct: 162 VIQKYHTVNGH--NCEV 176
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 63.9 bits (154), Expect = 9e-11, Method: Compositional matrix adjust.
Identities = 30/68 (44%), Positives = 45/68 (66%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
K+F+GGL++ET E++R +FEQ+G + + VV+ D NT RS+G+GFVT+ E A
Sbjct: 16 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 75
Query: 93 PTPFIDGR 100
+DGR
Sbjct: 76 RPHKVDGR 83
Score = 58.2 bits (139), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 46/77 (59%), Gaps = 2/77 (2%)
Query: 30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
T K+FVGG+ +T+ +R YFEQ+G+I ++TD+ +G+ +G+ FVTF + ++ +
Sbjct: 104 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 163
Query: 90 CADPTPFIDGRRANCNL 106
++G NC +
Sbjct: 164 VIQKYHTVNGH--NCEV 178
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 63.5 bits (153), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 30/68 (44%), Positives = 45/68 (66%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
K+F+GGL++ET E++R +FEQ+G + + VV+ D NT RS+G+GFVT+ E A
Sbjct: 13 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 72
Query: 93 PTPFIDGR 100
+DGR
Sbjct: 73 RPHKVDGR 80
Score = 58.2 bits (139), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 46/77 (59%), Gaps = 2/77 (2%)
Query: 30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
T K+FVGG+ +T+ +R YFEQ+G+I ++TD+ +G+ +G+ FVTF + ++ +
Sbjct: 101 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 160
Query: 90 CADPTPFIDGRRANCNL 106
++G NC +
Sbjct: 161 VIQKYHTVNGH--NCEV 175
>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 = 63.5 bits (153), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 30/68 (44%), Positives = 45/68 (66%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
K+F+GGL++ET E++R +FEQ+G + + VV+ D NT RS+G+GFVT+ E A
Sbjct: 8 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67
Query: 93 PTPFIDGR 100
+DGR
Sbjct: 68 RPHKVDGR 75
Score = 58.2 bits (139), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 46/77 (59%), Gaps = 2/77 (2%)
Query: 30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
T K+FVGG+ +T+ +R YFEQ+G+I ++TD+ +G+ +G+ FVTF + ++ +
Sbjct: 96 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 155
Query: 90 CADPTPFIDGRRANCNL 106
++G NC +
Sbjct: 156 VIQKYHTVNGH--NCEV 170
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 63.5 bits (153), Expect = 1e-10, Method: Composition-based stats.
Identities = 28/74 (37%), Positives = 44/74 (59%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP 93
+FVGGL+ T E ++ YFEQFG++ +A+++ DK T R +G+GFVTF + + C
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 94 TPFIDGRRANCNLA 107
I+ + C A
Sbjct: 62 FHEINNKMVECKKA 75
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 63.2 bits (152), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 30/70 (42%), Positives = 46/70 (65%)
Query: 31 YTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
+ K+F+GGL++ET E++R Y+EQ+G++ + VV+ D + RS+G+GFVTF A
Sbjct: 27 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 86
Query: 91 ADPTPFIDGR 100
A IDGR
Sbjct: 87 AARPHSIDGR 96
>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 = 63.2 bits (152), Expect = 1e-10, Method: Composition-based stats.
Identities = 23/55 (41%), Positives = 40/55 (72%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
+F+GGL+W+T + ++ YF +FGE+++ + D TGRS+G+GFV F+E E+ +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDK 56
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 62.4 bits (150), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 29/70 (41%), Positives = 42/70 (60%)
Query: 27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
G + + ++VG L + + +R FE FG+I V++ D +TGRSKGYGF+TF + E A
Sbjct: 1 GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60
Query: 87 RRACADPTPF 96
RRA F
Sbjct: 61 RRALEQLNGF 70
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 60.5 bits (145), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 30/75 (40%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
+ + V GL W+T + ++ YF FGE+L V D TG SKG+GFV F E E + +
Sbjct: 16 SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 75
Query: 92 DPTPFIDGRRANCNL 106
IDGR +C L
Sbjct: 76 -QRHMIDGRWCDCKL 89
>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 = 58.2 bits (139), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 26/66 (39%), Positives = 43/66 (65%), Gaps = 2/66 (3%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
K+FVGG+ + + + +F Q+G I++A ++ DK+TG+S+G+GFVT+ +A R C
Sbjct: 89 KIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ- 147
Query: 93 PTPFID 98
FID
Sbjct: 148 -NKFID 152
Score = 57.4 bits (137), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 38/54 (70%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
K+F+GGL W+T + +R YF ++G + + ++ D TGRS+G+GF++F +P +
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSV 58
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 55.5 bits (132), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 25/64 (39%), Positives = 37/64 (57%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
+++VG L + + +R FE FG I ++ D TGRSKGYGF+TF + E A++A
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 93 PTPF 96
F
Sbjct: 88 LNGF 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 = 54.3 bits (129), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 33/86 (38%), Positives = 46/86 (53%), Gaps = 1/86 (1%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD- 92
VFVG L+ E +E ++ F FG I +A V+ D TG+SKGYGFV+F A A
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 93 PTPFIDGRRANCNLASLGRPRPQVLY 118
++ GR+ N A+ P P+ Y
Sbjct: 78 GGQWLGGRQIRTNWATRKPPAPKSTY 103
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 53.5 bits (127), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 32/88 (36%), Positives = 47/88 (53%), Gaps = 1/88 (1%)
Query: 29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
+ + VFVG L+ E +E ++ F FG+I +A V+ D TG+SKGYGFV+F A
Sbjct: 13 SNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAEN 72
Query: 89 ACAD-PTPFIDGRRANCNLASLGRPRPQ 115
A ++ GR+ N A+ P P
Sbjct: 73 AIVHMGGQWLGGRQIRTNWATRKPPAPS 100
>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain
Of Hnrnp D (Auf1) With Telomere Dna
pdb|1X0F|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain
Of Hnrnp D(Auf1) With Telomeric Dna
Length = 79
Score = 53.1 bits (126), Expect = 2e-07, Method: Composition-based stats.
Identities = 22/56 (39%), Positives = 35/56 (62%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
K+FVGGL+ +T E +R YF FGE+ + D T + +G+ F+TF+E E ++
Sbjct: 3 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKK 58
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 52.0 bits (123), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 37/60 (61%), Gaps = 1/60 (1%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
K+F+GGL ET + ++ F + G I E ++I D+ T +S+G+ F+TF P A+ A D
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKD 67
>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 = 51.2 bits (121), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 27/82 (32%), Positives = 42/82 (51%), Gaps = 1/82 (1%)
Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC- 90
T + V L + T +T+RR FE++G + + + D+ T S+G+ FV F + A A
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 91 ADPTPFIDGRRANCNLASLGRP 112
A +DGR +A GRP
Sbjct: 108 AMDGAVLDGRELRVQMARYGRP 129
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 50.4 bits (119), Expect = 9e-07, Method: Composition-based stats.
Identities = 21/55 (38%), Positives = 34/55 (61%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
+FVGGL+ +T E +R YF FGE+ + D T + +G+ F+TF+E E ++
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKK 56
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 30/77 (38%), Positives = 43/77 (55%), Gaps = 8/77 (10%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPE---AARRAC 90
+FV GL+ +T ET++ E F + A ++TD+ TG SKG+GFV F E AA+ A
Sbjct: 18 LFVKGLSEDTTEETLK---ESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAM 74
Query: 91 ADPTPFIDGRRANCNLA 107
D IDG + + A
Sbjct: 75 EDGE--IDGNKVTLDWA 89
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 49.7 bits (117), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 40/77 (51%)
Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
K+FVGG+ +R YF++FG + E V+I D R +G+GF+TF + ++ +A
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN 70
Query: 92 DPTPFIDGRRANCNLAS 108
I G++ A
Sbjct: 71 MHFHDIMGKKVEVKRAE 87
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/82 (32%), Positives = 42/82 (51%), Gaps = 1/82 (1%)
Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC- 90
T + V L + T +T+RR FE++G + + + D+ T S+G+ FV F + A A
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 91 ADPTPFIDGRRANCNLASLGRP 112
A +DGR +A GRP
Sbjct: 131 AMDGAVLDGRELRVQMARYGRP 152
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 25/70 (35%), Positives = 41/70 (58%), Gaps = 1/70 (1%)
Query: 48 MRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPF-IDGRRANCNL 106
+R+ FE++G I ++ D+ T +S+GYGFV F+ +A++A A F I +R L
Sbjct: 59 LRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL 118
Query: 107 ASLGRPRPQV 116
A+ G RP +
Sbjct: 119 AASGHQRPGI 128
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 38/67 (56%)
Query: 23 NSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFRE 82
+S D K+F+G + + ++ FE+FG+I E V+ D+ TG KG F+T+ E
Sbjct: 5 SSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCE 64
Query: 83 PEAARRA 89
E+A +A
Sbjct: 65 RESALKA 71
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 48.1 bits (113), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 34/63 (53%), Gaps = 1/63 (1%)
Query: 28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAAR 87
D T+ +FVG L ET+R F+ F L V+ D TG S+GYGFV+F + A+
Sbjct: 85 DDTFN-LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQ 143
Query: 88 RAC 90
A
Sbjct: 144 NAM 146
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/77 (22%), Positives = 36/77 (46%), Gaps = 5/77 (6%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP 93
++VG L + +++YF+ G I ++ DKN ++ Y FV + + A A
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNN-KNVNYAFVEYHQSHDANIAL--- 58
Query: 94 TPFIDGRRANCNLASLG 110
++G++ N+ +
Sbjct: 59 -QTLNGKQIENNIVKIN 74
>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 = 47.4 bits (111), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 24/56 (42%), Positives = 33/56 (58%), Gaps = 1/56 (1%)
Query: 25 PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTF 80
P G VFVGG+ +R +F ++G + E +ITD+ TG SKGYGFV+F
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 57
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 38/66 (57%), Gaps = 3/66 (4%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA-- 91
++VG L + SE ++ F QFG++ +I D+ T + KG+GFV +E E+ A A
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAKL 62
Query: 92 DPTPFI 97
D T F+
Sbjct: 63 DNTDFM 68
>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 = 46.6 bits (109), Expect = 1e-05, Method: Composition-based stats.
Identities = 23/56 (41%), Positives = 31/56 (55%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
+FVG L ET+R F+ F L V+ D TG S+GYGFV+F + A+ A
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNA 59
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 22/47 (46%), Positives = 31/47 (65%), Gaps = 1/47 (2%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTF 80
VFVGG+ +R +F ++G + E +ITD+ TG SKGYGFV+F
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 58
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/56 (42%), Positives = 33/56 (58%), Gaps = 1/56 (1%)
Query: 25 PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTF 80
P G VFVGG+ +R +F ++G + E +ITD+ TG SKGYGFV+F
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 57
>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 = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 37/67 (55%)
Query: 30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
+ +++V + + + ++ FE FG+I A + D TG+ KGYGF+ + + ++++ A
Sbjct: 124 AFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDA 183
Query: 90 CADPTPF 96
+ F
Sbjct: 184 VSSMNLF 190
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 43/81 (53%), Gaps = 4/81 (4%)
Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
++V+VG + +E +T+R+ F FG I + D T + KG+ FV + PEAA+ A
Sbjct: 29 SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 88
Query: 92 DPTPFIDGRRANCNLASLGRP 112
+ G R N+ +GRP
Sbjct: 89 QMNSVMLGGR---NI-KVGRP 105
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 35/65 (53%)
Query: 25 PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPE 84
P D K+FVG + + ++ FE+FG I E V+ D+ TG KG F+T+ +
Sbjct: 9 PMKDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARD 68
Query: 85 AARRA 89
+A +A
Sbjct: 69 SALKA 73
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 36/65 (55%)
Query: 25 PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPE 84
P D + VFVG + +E E ++ F + G ++ ++ D+ TG+ KGYGF +++ E
Sbjct: 2 PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61
Query: 85 AARRA 89
A A
Sbjct: 62 TALSA 66
>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 = 44.3 bits (103), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 23/56 (41%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
+F+ L ++ + F FG IL V+ D+N SKGYGFV F EAA RA
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERA 159
Score = 33.9 bits (76), Expect = 0.100, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 27/56 (48%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
++VG L + + F G IL V D T RS GY +V F++P A RA
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERA 73
>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 = 44.3 bits (103), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 16/67 (23%), Positives = 36/67 (53%)
Query: 30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
+ +++V + + + ++ FE FG+I + D TG+ KGYGF+ + + ++++ A
Sbjct: 108 AFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDA 167
Query: 90 CADPTPF 96
+ F
Sbjct: 168 VSSXNLF 174
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 40/81 (49%), Gaps = 4/81 (4%)
Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
+V+VG + +E +T+R+ F FG I D T + KG+ FV + PEAA+ A
Sbjct: 13 CRVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALE 72
Query: 92 DPTPFIDGRRANCNLASLGRP 112
G R N+ +GRP
Sbjct: 73 QXNSVXLGGR---NI-KVGRP 89
>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 = 43.9 bits (102), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 16/67 (23%), Positives = 36/67 (53%)
Query: 30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
+ +++V + + + ++ FE FG+I + D TG+ KGYGF+ + + ++++ A
Sbjct: 109 AFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDA 168
Query: 90 CADPTPF 96
+ F
Sbjct: 169 VSSMNLF 175
Score = 40.8 bits (94), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 42/81 (51%), Gaps = 4/81 (4%)
Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
+V+VG + +E +T+R+ F FG I + D T + KG+ FV + PEAA+ A
Sbjct: 14 CRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 73
Query: 92 DPTPFIDGRRANCNLASLGRP 112
+ G R N+ +GRP
Sbjct: 74 QMNSVMLGGR---NI-KVGRP 90
>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 = 43.9 bits (102), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 23/56 (41%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
+F+ L ++ + F FG IL V+ D+N SKGYGFV F EAA RA
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERA 154
Score = 32.7 bits (73), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 27/56 (48%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
++VG L + + F G IL V D T RS GY +V F++P A RA
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERA 68
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 43.9 bits (102), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 34/63 (53%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP 93
+ V L+ +T+ ++ F FG I + DK TG+SKG+ F++F E A RA A
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV 77
Query: 94 TPF 96
+ F
Sbjct: 78 SGF 80
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 32/63 (50%), Gaps = 8/63 (12%)
Query: 27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
G + K+F+G L E + +R FEQ+G++LE +I K YGFV + AA
Sbjct: 4 GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAA 55
Query: 87 RRA 89
A
Sbjct: 56 EDA 58
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/56 (41%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
+F+ L ++ + F FG IL V+ D+N SKGYGFV F EAA RA
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERA 61
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 34/54 (62%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAAR 87
V+V L + + + R F ++G++++ ++ DK+T +SKG F+ F + ++A+
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQ 72
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/56 (41%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
+F+ L ++ + F FG IL V+ D+N SKGYGFV F EAA RA
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERA 67
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 43.1 bits (100), Expect = 2e-04, Method: Composition-based stats.
Identities = 21/63 (33%), Positives = 36/63 (57%)
Query: 27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
G + + +++ GL T + + + + +G+I+ I DK T + KGYGFV F P AA
Sbjct: 1 GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60
Query: 87 RRA 89
++A
Sbjct: 61 QKA 63
>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 = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 29/80 (36%), Positives = 42/80 (52%), Gaps = 1/80 (1%)
Query: 30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
++ VFVG L+ E + + F FG I +A V+ D TG+SKGYGFV+F A A
Sbjct: 5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENA 64
Query: 90 CAD-PTPFIDGRRANCNLAS 108
++ GR+ N A+
Sbjct: 65 IQQMGGQWLGGRQIRTNWAT 84
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 1/76 (1%)
Query: 38 GLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPF- 96
GL+ T +R F ++G I + ++ D+ + RS+G+ FV F + A+ A
Sbjct: 53 GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME 112
Query: 97 IDGRRANCNLASLGRP 112
+DGRR + + RP
Sbjct: 113 LDGRRIRVDFSITKRP 128
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 36 VGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTP 95
V GL+ T +R F ++G I + ++ D+ + RS+G+ FV F + A+ A
Sbjct: 17 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 76
Query: 96 F-IDGRRANCNLASLGRP 112
+DGRR + + RP
Sbjct: 77 MELDGRRIRVDFSITKRP 94
>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 = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 29/98 (29%), Positives = 43/98 (43%), Gaps = 6/98 (6%)
Query: 30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
+ T + V L E R F GEI ++ DK TG+S GYGFV + +P+ A +A
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 90 CADPTPFIDGRRANCNLASLGRPRPQVLYGRLRPATLF 127
++G R + RP +R A L+
Sbjct: 61 INT----LNGLRLQTKTIKVSYARPS--SASIRDANLY 92
Score = 37.4 bits (85), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 31/57 (54%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
++V GL + + + F Q+G I+ + ++ D+ TG S+G GF+ F + A A
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 147
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/59 (38%), Positives = 32/59 (54%), Gaps = 2/59 (3%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
++V L E +R+ F FG I A V+ + GRSKG+GFV F PE A +A +
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTE 74
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 41.6 bits (96), Expect = 4e-04, Method: Composition-based stats.
Identities = 27/82 (32%), Positives = 39/82 (47%), Gaps = 1/82 (1%)
Query: 27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
G TT ++VGGLA E + + F FG+I + + D T + +G+ FV F E A
Sbjct: 1 GSTTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60
Query: 87 RRACADPTPF-IDGRRANCNLA 107
A + + GR NLA
Sbjct: 61 AAAIDNMNESELFGRTIRVNLA 82
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 36 VGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTP 95
V GL+ T +R F ++G I + ++ D+ + RS+G+ FV F + A+ A
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 96 F-IDGRRANCNLASLGRP 112
+DGRR + + RP
Sbjct: 80 MELDGRRIRVDFSITKRP 97
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 44/88 (50%), Gaps = 8/88 (9%)
Query: 28 DTTYTK-VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
D T K VF+ L+++++ E + +QFG++ V+ +T SKG F F EAA
Sbjct: 11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAA 70
Query: 87 RRACADPT-------PFIDGRRANCNLA 107
++ A + +DGR+ +LA
Sbjct: 71 QKCLAAASLEAEGGGLKLDGRQLKVDLA 98
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 40.8 bits (94), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 37/68 (54%), Gaps = 4/68 (5%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
++FV L++ + E + + F +G + E D T + KG+ FVTF PE A +A A+
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 93 PTPFIDGR 100
+DG+
Sbjct: 70 ----VDGQ 73
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 1/64 (1%)
Query: 27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEA-VVITDKNTGRSKGYGFVTFREPEA 85
G + + +F+G L E + + F FG IL+ ++ D +TG SKGY F+ F +A
Sbjct: 1 GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60
Query: 86 ARRA 89
+ A
Sbjct: 61 SDAA 64
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 40.4 bits (93), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 40/83 (48%), Gaps = 9/83 (10%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
K+FVG ++ S+ +R FE+ G ++E V+ D Y FV + A+ A A
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQ 62
Query: 93 PT-PFIDGRRANCNLASLGRPRP 114
+ G+R N L++ G+ +
Sbjct: 63 LNGKEVKGKRINVELSTKGQKKS 85
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
G + ++FV L ++ + ++ F + G +L A + + G+SKG G V F PE A
Sbjct: 4 GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVA 61
Query: 87 RRAC 90
RAC
Sbjct: 62 ERAC 65
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 1/60 (1%)
Query: 30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
++ K+FVG L + + +RR FE FG I E ++ + G SKG FV + A+ A
Sbjct: 14 SHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPD-GNSKGCAFVKYSSHAEAQAA 72
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 35/66 (53%), Gaps = 3/66 (4%)
Query: 27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTG---RSKGYGFVTFREP 83
G + + +F+ L + T ET++ F + G I + KN S G+GFV +++P
Sbjct: 1 GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60
Query: 84 EAARRA 89
E A++A
Sbjct: 61 EQAQKA 66
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 30/56 (53%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
+F+ L E + F FG ++ A V DK T SK +GFV+F P++A+ A
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVA 98
>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 = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 31/56 (55%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
V++G + ++ E + G ++ ++ D TGRSKGY F+ FR+ E++ A
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 62
>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 = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 28/59 (47%)
Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
T + V L + +R F GE+ A +I DK G S GYGFV + + A RA
Sbjct: 20 TNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 78
>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 = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 35/68 (51%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP 93
V++G + ++ E + G ++ ++ D TGRSKGY F+ FR+ E++ A +
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 94 TPFIDGRR 101
+ G R
Sbjct: 66 NGYQLGSR 73
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain
In Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
G + + +FV L ++ + ++ F + G +L A + + G+SKG G V F PE A
Sbjct: 1 GSSGSSGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVA 58
Query: 87 RRAC 90
RAC
Sbjct: 59 ERAC 62
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 38/80 (47%), Gaps = 1/80 (1%)
Query: 29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
TT ++VGGLA E + + F FG+I + + D T + +G+ FV F E A
Sbjct: 10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 69
Query: 89 ACADPTPF-IDGRRANCNLA 107
A + + GR NLA
Sbjct: 70 AIDNMNESELFGRTIRVNLA 89
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 31/57 (54%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
++V GL + M + F Q+G I+ + ++ D+ TG S+G GF+ F + A A
Sbjct: 93 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 149
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 30/61 (49%)
Query: 30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
+ T + V L + + F G+I ++ DK TG+S GYGFV + +P A +A
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 90 C 90
Sbjct: 63 I 63
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 39.3 bits (90), Expect = 0.002, Method: Composition-based stats.
Identities = 26/80 (32%), Positives = 38/80 (47%), Gaps = 1/80 (1%)
Query: 29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
TT ++VGGLA E + + F FG+I + + D T + +G+ FV F E A
Sbjct: 5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 64
Query: 89 ACADPTPF-IDGRRANCNLA 107
A + + GR NLA
Sbjct: 65 AIDNMNESELFGRTIRVNLA 84
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 31/56 (55%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
V++G + ++ E + G ++ ++ D TGRSKGY F+ FR+ E++ A
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
VFVG L + E + F Q G + + + D+ G+ K +GFV F+ PE+ A A
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIA 75
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 30/60 (50%)
Query: 30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
+ T + V L + + F G+I ++ DK TG+S GYGFV + +P A +A
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 3/77 (3%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
++ V + + + +R+ F QFG+IL+ +I N SKG+GFVTF A RA
Sbjct: 31 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIF--NERGSKGFGFVTFENSADADRAREK 88
Query: 93 PT-PFIDGRRANCNLAS 108
++GR+ N A+
Sbjct: 89 LHGTVVEGRKIEVNNAT 105
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs
Of Human Antigen R
Length = 177
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 28/59 (47%)
Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
T + V L + +R F GE+ A +I DK G S GYGFV + + A RA
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Score = 36.6 bits (83), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 29/57 (50%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
+++ GL + + F +FG I+ + V+ D+ TG S+G F+ F + A A
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTG--RSKGYGFVTFREPEA 85
D K+FVG + + +R FEQ+G + E V+ D++ +SKG FVTF +A
Sbjct: 12 DLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKA 71
Query: 86 ARRA 89
A A
Sbjct: 72 ALEA 75
Score = 33.1 bits (74), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTF 80
K+F+G ++ + +R F FG+I E ++ + G S+G FVTF
Sbjct: 109 KLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPD-GLSRGCAFVTF 155
>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 = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 38/80 (47%), Gaps = 3/80 (3%)
Query: 29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
+ +FV + ++T +RR FE +G I ++ K +G+ +GY F+ +
Sbjct: 100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHS 159
Query: 89 A--CADPTPFIDGRRANCNL 106
A AD IDGRR ++
Sbjct: 160 AYKHADGKK-IDGRRVLVDV 178
>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 = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 28/59 (47%)
Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
T + V L + +R F GE+ A +I DK G S GYGFV + + A RA
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Score = 36.6 bits (83), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 29/57 (50%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
+++ GL + + F +FG I+ + V+ D+ TG S+G F+ F + A A
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 3/77 (3%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD 92
++ V + + + +R+ F QFG+IL+ +I N SKG+GFVTF A RA
Sbjct: 17 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIF--NERGSKGFGFVTFENSADADRAREK 74
Query: 93 PT-PFIDGRRANCNLAS 108
++GR+ N A+
Sbjct: 75 LHGTVVEGRKIEVNNAT 91
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 38 GLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPF- 96
GL+ T +R F ++G I + ++ D+ + RS+G+ FV F + A+ A
Sbjct: 22 GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME 81
Query: 97 IDGRR 101
+DGRR
Sbjct: 82 LDGRR 86
>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 = 38.5 bits (88), Expect = 0.004, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 28/58 (48%)
Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
T + V L + +R F GE+ A +I DK G S GYGFV + + A RA
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 62
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 38.5 bits (88), Expect = 0.004, Method: Composition-based stats.
Identities = 18/56 (32%), Positives = 31/56 (55%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
++V GL + M + F Q+G I+ + ++ D+ TG S+G GF+ F + A A
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEA 59
>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 = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 34/68 (50%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP 93
++VG + + +E + +F G + ++ DK +G KG+ ++ F + E+ R + A
Sbjct: 9 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALD 68
Query: 94 TPFIDGRR 101
GR+
Sbjct: 69 ESLFRGRQ 76
>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 = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 23/59 (38%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDK--NTGRSKGYGFVTFREPEAARRA 89
K+FVG + + +R FEQ+G + E V+ D+ N +SKG FVTF +AA A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
>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 = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 38/80 (47%), Gaps = 3/80 (3%)
Query: 29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
+ +FV + ++T +RR FE +G I ++ K +G+ +GY F+ +
Sbjct: 100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHS 159
Query: 89 A--CADPTPFIDGRRANCNL 106
A AD IDGRR ++
Sbjct: 160 AYKHAD-GKKIDGRRVLVDV 178
>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 = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 34/68 (50%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP 93
++VG + + +E + +F G + ++ DK +G KG+ ++ F + E+ R + A
Sbjct: 8 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALD 67
Query: 94 TPFIDGRR 101
GR+
Sbjct: 68 ESLFRGRQ 75
>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 = 0.006, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
K+FVG L + E +R+ FE FG I E V+ + G SKG FV F+ A+ A
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPD-GTSKGCAFVKFQTHAEAQAA 69
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 37.7 bits (86), Expect = 0.006, Method: Composition-based stats.
Identities = 24/75 (32%), Positives = 36/75 (48%), Gaps = 1/75 (1%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP 93
++VGGLA E + + F FG+I + + D T + +G+ FV F E A A +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 94 TPF-IDGRRANCNLA 107
+ GR NLA
Sbjct: 65 NESELFGRTIRVNLA 79
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 27/49 (55%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFRE 82
VF LA + + +F G++ + +I+D+N+ RSKG +V F E
Sbjct: 28 VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCE 76
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 31/61 (50%)
Query: 29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
TT ++VGGLA E + + F FG+I + + D T + +G+ FV F E A
Sbjct: 61 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 120
Query: 89 A 89
A
Sbjct: 121 A 121
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet
Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 34/68 (50%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP 93
+F+ L E + + + F FG ++ A V DK T SK +GFV++ P +A+ A
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 94 TPFIDGRR 101
F G +
Sbjct: 88 NGFQIGMK 95
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 36 VGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA-CADPT 94
V L + T +++RR FE++G + + + + +T +G+ FV F + A+ A A
Sbjct: 18 VDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDG 77
Query: 95 PFIDGRRANCNLASLGR 111
+DGR +A GR
Sbjct: 78 AELDGRELRVQVARYGR 94
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
Length = 124
Score = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 1/64 (1%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA-D 92
V+VG + + + ++ + +F G I ++ DK +G KGY ++ F E + A A D
Sbjct: 39 VYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMD 98
Query: 93 PTPF 96
T F
Sbjct: 99 ETVF 102
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 37.0 bits (84), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTG--RSKGYGFVTFREPEAARRA 89
K+FVG + + +R FEQ+G + E V+ D++ +SKG FVTF +AA A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Score = 32.7 bits (73), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTF 80
K+F+G ++ + +R F FG+I E ++ + G S+G FVTF
Sbjct: 97 KLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPD-GLSRGCAFVTF 143
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 36.6 bits (83), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 33/60 (55%), Gaps = 4/60 (6%)
Query: 36 VGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA---CAD 92
V L+ +E + + F QFG + +AVV+ D + GR+ G GFV F AR+A C D
Sbjct: 101 VKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGD 159
Score = 35.4 bits (80), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 34/69 (49%), Gaps = 9/69 (13%)
Query: 27 GDTTYT---KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREP 83
G+ TYT ++FVG L + E +R FE++GE E + R +G+GF+
Sbjct: 15 GEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFI------NRDRGFGFIRLESR 68
Query: 84 EAARRACAD 92
A A A+
Sbjct: 69 TLAEIAKAE 77
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 36.2 bits (82), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 29/57 (50%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
V+VGGL + + F Q G ++ + D+ TG+ +GYGFV F E A A
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 74
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 36.2 bits (82), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 33/72 (45%), Gaps = 7/72 (9%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP 93
V+ GG+A + MR+ F FG+I+E V + KGY FV F E+A A
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSV 81
Query: 94 T-PFIDGRRANC 104
I+G C
Sbjct: 82 NGTTIEGHVVKC 93
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 35.8 bits (81), Expect = 0.022, Method: Composition-based stats.
Identities = 27/79 (34%), Positives = 39/79 (49%), Gaps = 10/79 (12%)
Query: 28 DTTYTKVFVGGLAWETQSET-MRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
D T T ++VGGL +T +ET +R +F QFGEI V+ + F+ F +AA
Sbjct: 9 DKTITTLYVGGLG-DTITETDLRNHFYQFGEIRTITVVQRQQC------AFIQFATRQAA 61
Query: 87 RRACADP--TPFIDGRRAN 103
A ++GRR N
Sbjct: 62 EVAAEKSFNKLIVNGRRLN 80
>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 = 35.8 bits (81), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 28/59 (47%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
K+F+GGL + ++ FG + ++ D TG SKGY F + + +A A
Sbjct: 116 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 174
>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 = 35.8 bits (81), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 32/59 (54%), Gaps = 2/59 (3%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTG--RSKGYGFVTFREPEAARRA 89
K FVG + + +R FEQ+G + E V+ D++ +SKG FVTF +AA A
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Score = 33.1 bits (74), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTF 80
K+F+G ++ + +R F FG+I E ++ + G S+G FVTF
Sbjct: 97 KLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPD-GLSRGCAFVTF 143
>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 = 35.4 bits (80), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 28/59 (47%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
K+F+GGL + ++ FG + ++ D TG SKGY F + + +A A
Sbjct: 98 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 156
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 35.4 bits (80), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 28/90 (31%), Positives = 41/90 (45%), Gaps = 22/90 (24%)
Query: 55 FGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLASLGRPR- 113
FG + ++ + TG+SKGYGF + + ++A RA +D LG+P
Sbjct: 119 FGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD---------------LLGKPLG 163
Query: 114 PQVLY------GRLRPATLFSGSTQATRGP 137
P+ LY G+L PA L S R P
Sbjct: 164 PRTLYVHWTDAGQLTPALLHSRCLCVDRLP 193
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 35.4 bits (80), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 28/90 (31%), Positives = 41/90 (45%), Gaps = 22/90 (24%)
Query: 55 FGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLASLGRPR- 113
FG + ++ + TG+SKGYGF + + ++A RA +D LG+P
Sbjct: 119 FGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD---------------LLGKPLG 163
Query: 114 PQVLY------GRLRPATLFSGSTQATRGP 137
P+ LY G+L PA L S R P
Sbjct: 164 PRTLYVHWTDAGQLTPALLHSRCLCVDRLP 193
>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
pdb|3H2U|D Chain D, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
Length = 283
Score = 35.4 bits (80), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 28/90 (31%), Positives = 41/90 (45%), Gaps = 22/90 (24%)
Query: 55 FGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPFIDGRRANCNLASLGRPR- 113
FG + ++ + TG+SKGYGF + + ++A RA +D LG+P
Sbjct: 117 FGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD---------------LLGKPLG 161
Query: 114 PQVLY------GRLRPATLFSGSTQATRGP 137
P+ LY G+L PA L S R P
Sbjct: 162 PRTLYVHWTDAGQLTPALLHSRCLCVDRLP 191
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 35.4 bits (80), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 34/60 (56%), Gaps = 1/60 (1%)
Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
+ VFV L ++ + ++ F G ++ A ++ DK+ G+S+G G VTF + A +A +
Sbjct: 16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTFEQSIEAVQAIS 74
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 35.4 bits (80), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 28/59 (47%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
K+F+GGL + ++ FG + ++ D TG SKGY F + + +A A
Sbjct: 96 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 154
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 35.0 bits (79), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 32/112 (28%), Positives = 50/112 (44%), Gaps = 11/112 (9%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRS----KGYGFVTFREPEAARR 88
KVFVGGL + + + F +FG ++ V K +S KGY F+ F+E E++ +
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLV--VDWPHKAESKSYFPPKGYAFLLFQE-ESSVQ 66
Query: 89 ACADPTPFIDGRRANCNLASLGRPRPQVLYGRLRPATLFSGSTQATRGPYIG 140
A D DG+ C + + +P ++RP L GP G
Sbjct: 67 ALIDACLEEDGKLYLCVSSPTIKDKPV----QIRPWNLSDSDFVMDSGPSSG 114
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 35.0 bits (79), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
K+FVG L + E + R F+ FG I E V+ + G SKG FV F A+ A
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPD-GSSKGCAFVKFSSHTEAQAA 72
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 34.7 bits (78), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 34/62 (54%), Gaps = 5/62 (8%)
Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
+KVFVG + +E ++++F Q+GE+++ + + + FVTF + + A+ C
Sbjct: 12 SKVFVGRCTEDMTAEELQQFFCQYGEVVDVFI-----PKPFRAFAFVTFADDKVAQSLCG 66
Query: 92 DP 93
+
Sbjct: 67 ED 68
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 34.7 bits (78), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 12/80 (15%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAV--------VITDKNTGRSKGYGFVTFREPEA 85
+FV GL E++ YF+Q G I + TD+ TG+ KG V+F +P +
Sbjct: 16 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 75
Query: 86 ARRACADPTPFIDGRRANCN 105
A+ A + DG+ + N
Sbjct: 76 AKAAI----DWFDGKEFSGN 91
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 34.7 bits (78), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 9/57 (15%)
Query: 27 GDTTYT---KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTF 80
G+ T+T ++FVG L + E MR+ FE++G+ E + D KG+GF+
Sbjct: 15 GEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRL 65
Score = 32.3 bits (72), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 28/51 (54%), Gaps = 4/51 (7%)
Query: 45 SETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA---CAD 92
+E + F FG++ AVVI D + GR G G V F AAR+A C++
Sbjct: 110 NELLEEAFSVFGQVERAVVIVD-DRGRPSGKGIVEFSGKPAARKALDRCSE 159
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 34.3 bits (77), Expect = 0.063, Method: Composition-based stats.
Identities = 17/59 (28%), Positives = 28/59 (47%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
K+F+GGL + ++ FG + ++ D TG SKGY F + + +A A
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 61
>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 = 34.3 bits (77), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 3/56 (5%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFV---TFREPEAA 86
+FV G+ E E + F ++GEI + D+ TG KGY V T++E +AA
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 65
>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 = 34.3 bits (77), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 3/56 (5%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFV---TFREPEAA 86
+FV G+ E E + F ++GEI + D+ TG KGY V T++E +AA
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 67
>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 = 34.3 bits (77), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 3/56 (5%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFV---TFREPEAA 86
+FV G+ E E + F ++GEI + D+ TG KGY V T++E +AA
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 81
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 34.3 bits (77), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 3/56 (5%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFV---TFREPEAA 86
+FV G+ E E + F ++GEI + D+ TG KGY V T++E +AA
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 65
>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At
3.2 A Resolution
pdb|2J0Q|G Chain G, The Crystal Structure Of The Exon Junction Complex At
3.2 A Resolution
Length = 109
Score = 33.9 bits (76), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 3/56 (5%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFV---TFREPEAA 86
+FV G+ E E + F ++GEI + D+ TG KGY V T++E +AA
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 65
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 33.9 bits (76), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDK--NTGRSKGYGFVTFREPEAAR 87
T +K+ V + ++ +R F FGE L+ V + K TG +G+GFV F + A+
Sbjct: 14 TTSKILVRNIPFQANQREIRELFSTFGE-LKTVRLPKKMTGTGAHRGFGFVDFITKQDAK 72
Query: 88 RA 89
+A
Sbjct: 73 KA 74
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14
Complex
Length = 110
Score = 33.9 bits (76), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 3/59 (5%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFV---TFREPEAARRA 89
+FV + E Q + ++ F +GEI + D+ TG SKGY V T ++ AA+ A
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87
>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 = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 28/50 (56%), Gaps = 6/50 (12%)
Query: 29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFV 78
T +++FVG L + E MR+ FE++G+ E + D KG+GF+
Sbjct: 13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFI 56
>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 = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 3/56 (5%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFV---TFREPEAA 86
+FV G+ E E + F ++GEI + D+ TG KGY V T++E +AA
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 80
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 33.5 bits (75), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 15/67 (22%), Positives = 33/67 (49%), Gaps = 5/67 (7%)
Query: 27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
G + + VFVG + + +R +F Q+G++++ + + + FVTF + + A
Sbjct: 1 GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFI-----PKPFRAFAFVTFADDQIA 55
Query: 87 RRACADP 93
+ C +
Sbjct: 56 QSLCGED 62
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 33.5 bits (75), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 12/80 (15%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAV--------VITDKNTGRSKGYGFVTFREPEA 85
+FV GL E++ YF+Q G I + TD+ TG+ KG V+F +P +
Sbjct: 10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 69
Query: 86 ARRACADPTPFIDGRRANCN 105
A+ A + DG+ + N
Sbjct: 70 AKAAI----DWFDGKEFSGN 85
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 32.3 bits (72), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 26/96 (27%), Positives = 43/96 (44%), Gaps = 21/96 (21%)
Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC- 90
TK+ VG ++ ++ +R FE++G ++E ++ D Y FV E A A
Sbjct: 11 TKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIR 62
Query: 91 -ADPTPFIDGRRANCNLASLGRPRPQVLYGRLRPAT 125
D T F G+R + L++ RLR A+
Sbjct: 63 GLDNTEF-QGKRMHVQLST----------SRLRTAS 87
>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 = 32.3 bits (72), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 3/59 (5%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFV---TFREPEAARRA 89
+FV + E Q + ++ F +GEI + D+ TG SKGY V T ++ AA+ A
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 133
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 31.6 bits (70), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 38/82 (46%), Gaps = 9/82 (10%)
Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
T+++VGGL T + R F++FG I D G S + ++ + +AA+ ACA
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIR----TIDHVKGDS--FAYIQYESLDAAQAACA 71
Query: 92 DPTPFIDG---RRANCNLASLG 110
F G RR + A G
Sbjct: 72 KMRGFPLGGPDRRLRVDFAKSG 93
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 31.6 bits (70), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 30/66 (45%), Gaps = 8/66 (12%)
Query: 27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
G+ + T++FV + Q + F FG + E ++ G+ FV F E E+A
Sbjct: 27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESA 78
Query: 87 RRACAD 92
+A +
Sbjct: 79 AKAIEE 84
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 30.8 bits (68), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 24/101 (23%), Positives = 44/101 (43%), Gaps = 14/101 (13%)
Query: 24 SPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAV--------VITDKNTGRSKGY 75
P D+ + ++V GL + + +F+Q G + + DK TG+ KG
Sbjct: 8 DPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGD 67
Query: 76 GFVTFREPEAARRACADPTPFIDGR--RANCNLASLGRPRP 114
V++ +P A+ A + DG+ + + SL R +P
Sbjct: 68 ATVSYEDPPTAKAAVE----WFDGKDFQGSKLKVSLARKKP 104
>pdb|2WQK|A Chain A, Crystal Structure Of Sure Protein From Aquifex Aeolicus
pdb|2WQK|B Chain B, Crystal Structure Of Sure Protein From Aquifex Aeolicus
Length = 251
Score = 30.8 bits (68), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 34/132 (25%), Positives = 55/132 (41%), Gaps = 16/132 (12%)
Query: 48 MRRYFEQFGEILEAVVITDKNTGRSKGYGF-VTFREPEAARRACADPTPFIDGRRANCNL 106
+R + G ++ VV D+N G G +TF EP R+ D IDG A+C
Sbjct: 20 LREALKSLGRVV--VVAPDRNLS---GVGHSLTFTEPLKMRKIDTDFYTVIDGTPADC-- 72
Query: 107 ASLGRPRPQVLYGRLRPATLFSGSTQATRGPYIGSFGYQQPLPYNYQQGMVY--PSYGYA 164
LG +V+ +P + SG + GP +G +G + PS ++
Sbjct: 73 VHLGY---RVILEEKKPDLVLSGINE---GPNLGEDITYSGTVSGAMEGRILGIPSIAFS 126
Query: 165 TYGPEYVYPQGI 176
+G E + + I
Sbjct: 127 AFGRENIMFEEI 138
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 22/39 (56%), Gaps = 3/39 (7%)
Query: 52 FEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
F QFG+IL+ V + T + +G FV F+E +A A
Sbjct: 31 FSQFGQILDIVAL---KTLKMRGQAFVIFKEIGSASNAL 66
>pdb|1WEL|A Chain A, Solution Structure Of Rna Binding Domain In Np_006038
Length = 124
Score = 29.6 bits (65), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 13/48 (27%), Positives = 29/48 (60%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFR 81
V++ GL +E +++ + +F++ + +++ I G++ G GFV FR
Sbjct: 28 VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFR 75
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif In Trna Selenocysteine Associated Protein
Length = 104
Score = 29.3 bits (64), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 25/56 (44%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
+FVG L + + +F + + TG SKGYGFV F + +RA
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRA 67
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 29.3 bits (64), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 37/81 (45%), Gaps = 2/81 (2%)
Query: 35 FVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT 94
+VG L + T + F+ I ++ DK+T + KG+ +V F E ++ + A
Sbjct: 19 YVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDG 77
Query: 95 PFIDGRRANCNLASLGRPRPQ 115
+ R ++A GR + +
Sbjct: 78 ALLGDRSLRVDIAE-GRKQDK 97
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 28.9 bits (63), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 5/68 (7%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP 93
+ + L++ ET++ FE+ + + G+SKGY F+ F E A+ A
Sbjct: 18 LVLSNLSYSATEETLQEVFEK----ATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSC 73
Query: 94 TP-FIDGR 100
I+GR
Sbjct: 74 NKREIEGR 81
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 0.441
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,717,079
Number of Sequences: 62578
Number of extensions: 390411
Number of successful extensions: 1077
Number of sequences better than 100.0: 142
Number of HSP's better than 100.0 without gapping: 122
Number of HSP's successfully gapped in prelim test: 20
Number of HSP's that attempted gapping in prelim test: 911
Number of HSP's gapped (non-prelim): 165
length of query: 258
length of database: 14,973,337
effective HSP length: 97
effective length of query: 161
effective length of database: 8,903,271
effective search space: 1433426631
effective search space used: 1433426631
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)