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= 024889
(261 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 = 103 bits (258), Expect = 6e-23, Method: Compositional matrix adjust.
Identities = 47/79 (59%), Positives = 58/79 (73%)
Query: 28 DTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAAR 87
DTT+TK+FVGGL + T ++R+YFE FG+I EAVVITD+ TG+S+GYGFVT + AA
Sbjct: 14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAE 73
Query: 88 RACADPTPFIDGRLRPATL 106
RAC DP P IDGR L
Sbjct: 74 RACKDPNPIIDGRKANVNL 92
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 74.7 bits (182), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 31/68 (45%), Positives = 45/68 (66%)
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 PTPFIDGR 100
+DGR
Sbjct: 78 RPHTLDGR 85
>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 = 70.1 bits (170), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 49/80 (61%)
Query: 22 LNSPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFR 81
+N+ + K FVGGL+W+T + ++ YF +FGE+++ + D NTGRS+G+GF+ F+
Sbjct: 2 INASKNEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFK 61
Query: 82 EPEAARRACADPTPFIDGRL 101
+ + + +DGR+
Sbjct: 62 DAASVEKVLDQKEHRLDGRV 81
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 67.0 bits (162), Expect = 1e-11, Method: Composition-based stats.
Identities = 29/68 (42%), Positives = 43/68 (63%)
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 PTPFIDGR 100
+D +
Sbjct: 62 SRHELDSK 69
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 66.6 bits (161), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 29/69 (42%), Positives = 43/69 (62%)
Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
K+F+GGL+W+T E +R YF QFGE+ E +V+ D T RS+G+GFVTF + + A
Sbjct: 26 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 85
Query: 92 DPTPFIDGR 100
+D +
Sbjct: 86 QSRHELDSK 94
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 64.7 bits (156), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 30/69 (43%), Positives = 46/69 (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 PTPFIDGRL 101
+DGR+
Sbjct: 76 RPHKVDGRV 84
Score = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 39/57 (68%)
Query: 30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
T K+FVGG+ +T+ +R YFEQ+G+I ++TD+ +G+ +G+ FVTF + ++
Sbjct: 104 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 160
>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 = 64.7 bits (156), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 30/69 (43%), Positives = 46/69 (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 PTPFIDGRL 101
+DGR+
Sbjct: 75 RPHKVDGRV 83
Score = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 39/57 (68%)
Query: 30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
T K+FVGG+ +T+ +R YFEQ+G+I ++TD+ +G+ +G+ FVTF + ++
Sbjct: 103 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 159
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 64.7 bits (156), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 30/69 (43%), Positives = 46/69 (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 PTPFIDGRL 101
+DGR+
Sbjct: 75 RPHKVDGRV 83
Score = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 40/59 (67%)
Query: 30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
T K+FVGG+ +T+ +R YFEQ+G+I ++TD+ +G+ +G+ FVTF + ++ +
Sbjct: 103 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK 161
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 64.7 bits (156), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 30/69 (43%), Positives = 46/69 (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 PTPFIDGRL 101
+DGR+
Sbjct: 73 RPHKVDGRV 81
Score = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 40/59 (67%)
Query: 30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
T K+FVGG+ +T+ +R YFEQ+G+I ++TD+ +G+ +G+ FVTF + ++ +
Sbjct: 101 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK 159
>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 = 64.7 bits (156), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 30/69 (43%), Positives = 46/69 (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 PTPFIDGRL 101
+DGR+
Sbjct: 74 RPHKVDGRV 82
Score = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 39/57 (68%)
Query: 30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
T K+FVGG+ +T+ +R YFEQ+G+I ++TD+ +G+ +G+ FVTF + ++
Sbjct: 102 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 158
>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 = 64.3 bits (155), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 30/69 (43%), Positives = 46/69 (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 PTPFIDGRL 101
+DGR+
Sbjct: 68 RPHKVDGRV 76
Score = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 40/59 (67%)
Query: 30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
T K+FVGG+ +T+ +R YFEQ+G+I ++TD+ +G+ +G+ FVTF + ++ +
Sbjct: 96 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK 154
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 64.3 bits (155), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 30/71 (42%), Positives = 47/71 (66%)
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 ADPTPFIDGRL 101
A IDGR+
Sbjct: 87 AARPHSIDGRV 97
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 63.5 bits (153), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 29/69 (42%), Positives = 47/69 (68%), Gaps = 1/69 (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 DPTPFIDGR 100
+DGR
Sbjct: 74 MNGKSVDGR 82
>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 = 63.5 bits (153), Expect = 1e-10, Method: Composition-based stats.
Identities = 24/68 (35%), Positives = 45/68 (66%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP 93
+F+GGL+W+T + ++ YF +FGE+++ + D TGRS+G+GFV F+E E+ +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 94 TPFIDGRL 101
++G++
Sbjct: 62 EHKLNGKV 69
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 62.8 bits (151), Expect = 2e-10, Method: Composition-based stats.
Identities = 25/57 (43%), Positives = 39/57 (68%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
+FVGGL+ T E ++ YFEQFG++ +A+++ DK T R +G+GFVTF + + C
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC 58
>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|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 = 58.5 bits (140), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 46/74 (62%), Gaps = 2/74 (2%)
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 PTPFIDGRLRPATL 106
FID + R +
Sbjct: 148 -NKFIDFKDRKIEI 160
Score = 57.4 bits (137), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 38/55 (69%)
Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
K+F+GGL W+T + +R YF ++G + + ++ D TGRS+G+GF++F +P +
Sbjct: 4 CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSV 58
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 55.8 bits (133), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 32/89 (35%), Positives = 43/89 (48%), Gaps = 1/89 (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 DPTPFIDGRLRPATLFSGSTQATRGPYIG 120
IDGR L + GP G
Sbjct: 76 -QRHMIDGRWCDCKLPNSKQSQDSGPSSG 103
>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|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 = 52.8 bits (125), 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|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 51.2 bits (121), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 26/62 (41%), Positives = 37/62 (59%)
Query: 29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
+ + VFVG L+ E +E ++ F FG+I +A V+ D TG+SKGYGFV+F A
Sbjct: 13 SNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAEN 72
Query: 89 AC 90
A
Sbjct: 73 AI 74
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 50.1 bits (118), Expect = 1e-06, 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|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In
Cytotoxic Granule-Associated Rna Binding Protein 1
pdb|2RNE|A Chain A, Solution Structure Of The Second Rna Recognition Motif
(Rrm) Of Tia-1
Length = 115
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/57 (45%), Positives = 34/57 (59%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
VFVG L+ E +E ++ F FG I +A V+ D TG+SKGYGFV+F A A
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAI 74
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 48.9 bits (115), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 35/58 (60%)
Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
K+FVGG+ +R YF++FG + E V+I D R +G+GF+TF + ++ +A
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQA 68
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 48.9 bits (115), 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|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 47.8 bits (112), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 24/56 (42%), Positives = 35/56 (62%), Gaps = 3/56 (5%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
+FV GL+ +T ET++ E F + A ++TD+ TG SKG+GFV F E A+ A
Sbjct: 18 LFVKGLSEDTTEETLK---ESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAA 70
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 47.4 bits (111), Expect = 7e-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 = 29.3 bits (64), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
++VG L + +++YF+ G I ++ DKN ++ Y FV + + A A
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNN-KNVNYAFVEYHQSHDANIAL 58
>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 = 7e-06, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 25 PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPE 84
P G VFVGG+ +R +F ++G + E +ITD+ TG SKGYGFV+F
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDV 61
Query: 85 AARRACADPTPFIDGRLR 102
++ F +L+
Sbjct: 62 DVQKIVESQINFHGKKLK 79
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 1/69 (1%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP 93
VFVGG+ +R +F ++G + E +ITD+ TG SKGYGFV+F ++
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 71
Query: 94 TPFIDGRLR 102
F +L+
Sbjct: 72 INFHGKKLK 80
>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 = 25/71 (35%), Positives = 40/71 (56%), Gaps = 3/71 (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 DPTPFIDGRLR 102
D T F+ +R
Sbjct: 63 DNTDFMGRTIR 73
>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 = 24/69 (34%), Positives = 37/69 (53%), Gaps = 1/69 (1%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP 93
VFVGG+ +R +F ++G + E +ITD+ TG SKGYGFV+F ++
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 94 TPFIDGRLR 102
F +L+
Sbjct: 71 INFHGKKLK 79
>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 = 2e-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|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
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|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 39/64 (60%), Gaps = 2/64 (3%)
Query: 48 MRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPF--IDGRLRPAT 105
+R+ FE++G I ++ D+ T +S+GYGFV F+ +A++A A F ++ RL+ A
Sbjct: 59 LRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL 118
Query: 106 LFSG 109
SG
Sbjct: 119 AASG 122
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 45.8 bits (107), Expect = 2e-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|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 = 45.8 bits (107), 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 = 40.4 bits (93), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 34/59 (57%)
Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRAC 90
++V+VG + +E +T+R+ F FG I + D T + KG+ FV + PEAA+ A
Sbjct: 29 SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLAL 87
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 44.7 bits (104), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 44/76 (57%), Gaps = 5/76 (6%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAAR---RAC 90
V+V L + + + R F ++G++++ ++ DK+T +SKG F+ F + ++A+ RA
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 91 ADPTPFIDGRLRPATL 106
+ F GR+ A++
Sbjct: 79 NNKQLF--GRVIKASI 92
>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 = 7e-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 = 33.5 bits (75), Expect = 0.12, 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|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 = 44.3 bits (103), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 37/70 (52%), Gaps = 1/70 (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 ADPTPFIDGR 100
A +DGR
Sbjct: 108 AMDGAVLDGR 117
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 44.3 bits (103), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 35/62 (56%)
Query: 25 PFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPE 84
P D + VFVG + +E E ++ F + G ++ ++ D+ TG+ KGYGF +++ E
Sbjct: 2 PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61
Query: 85 AA 86
A
Sbjct: 62 TA 63
>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 = 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: 108 AFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDA 167
Query: 90 CADPTPF 96
+ F
Sbjct: 168 VSSXNLF 174
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 32/58 (55%)
Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
+V+VG + +E +T+R+ F FG I D T + KG+ FV + PEAA+ A
Sbjct: 13 CRVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLA 70
>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 = 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: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERA 154
Score = 32.3 bits (72), Expect = 0.30, 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|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 = 1e-04, 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 = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 33/58 (56%)
Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
+V+VG + +E +T+R+ F FG I + D T + KG+ FV + PEAA+ A
Sbjct: 14 CRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLA 71
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 43.5 bits (101), Expect = 1e-04, 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|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 43.1 bits (100), Expect = 2e-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|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 37/70 (52%), Gaps = 1/70 (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 ADPTPFIDGR 100
A +DGR
Sbjct: 131 AMDGAVLDGR 140
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 25/68 (36%), Positives = 37/68 (54%), Gaps = 6/68 (8%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP 93
++V L E +R+ F FG I A V+ + GRSKG+GFV F PE A +A +
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTE- 74
Query: 94 TPFIDGRL 101
++GR+
Sbjct: 75 ---MNGRI 79
>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 = 22/63 (34%), Positives = 32/63 (50%)
Query: 27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
G TT ++VGGLA E + + F FG+I + + D T + +G+ FV F E A
Sbjct: 1 GSTTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60
Query: 87 RRA 89
A
Sbjct: 61 AAA 63
>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 = 29/101 (28%), Positives = 46/101 (45%), Gaps = 8/101 (7%)
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-------PFIDGRLRPATLFSGSTQATRGPYIG 120
++ A + +DGR L +A GP G
Sbjct: 71 QKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASGPSSG 111
>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 = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 25/61 (40%), Positives = 34/61 (55%)
Query: 30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
++ VFVG L+ E + + F FG I +A V+ D TG+SKGYGFV+F A A
Sbjct: 5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENA 64
Query: 90 C 90
Sbjct: 65 I 65
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 38/69 (55%), Gaps = 4/69 (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 PTPFIDGRL 101
+DG++
Sbjct: 70 ----VDGQV 74
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 40.8 bits (94), Expect = 8e-04, 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|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 = 40.4 bits (93), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 31/60 (51%)
Query: 30 TYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
+ T + V L E R F GEI ++ DK TG+S GYGFV + +P+ A +A
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Score = 37.0 bits (84), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 31/56 (55%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
++V GL + + + F Q+G I+ + ++ D+ TG S+G GF+ F + A A
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 146
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/98 (26%), Positives = 45/98 (45%), Gaps = 4/98 (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 EAARRACADPTPF-IDGRLRPATLFSGSTQATRGPYIG 120
E A++A +DG + +T+ GP G
Sbjct: 61 EQAQKALKQLQGHTVDGHKLEVRISERATKPASGPSSG 98
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 40.4 bits (93), Expect = 0.001, 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|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 40.0 bits (92), 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|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 30/58 (51%)
Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
+F+ L E + F FG ++ A V DK T SK +GFV+F P++A+ A
Sbjct: 41 CNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVA 98
>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 = 39.7 bits (91), Expect = 0.002, 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|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition
In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 84
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: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 62
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
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: 93 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEA 148
Score = 37.7 bits (86), Expect = 0.006, 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|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 = 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: 5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 64
Query: 89 A 89
A
Sbjct: 65 A 65
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 39.3 bits (90), Expect = 0.002, 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 = 0.14, 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|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain
In Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 39.3 bits (90), 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|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
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: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 61
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 38.9 bits (89), Expect = 0.003, 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|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 38.9 bits (89), Expect = 0.003, 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: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 38.9 bits (89), Expect = 0.003, 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|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 38.5 bits (88), Expect = 0.004, 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|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs
Of Human Antigen R
Length = 177
Score = 38.5 bits (88), Expect = 0.004, 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 = 0.014, 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|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|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 = 38.5 bits (88), Expect = 0.004, 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
>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 = 38.5 bits (88), Expect = 0.004, 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 = 0.015, 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|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet
Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 40/88 (45%), Gaps = 1/88 (1%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP 93
+F+ L E + + + F FG ++ A V DK T SK +GFV++ P +A+ A
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 94 TPFIDGRLRPATLFSGSTQATR-GPYIG 120
F G R S ++ GP G
Sbjct: 88 NGFQIGMKRLKVQLKRSKNDSKSGPSSG 115
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 38.1 bits (87), Expect = 0.004, 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|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 = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 16/67 (23%), Positives = 33/67 (49%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP 93
++VG + + +E + +F G + ++ DK +G KG+ ++ F + E+ R + A
Sbjct: 9 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALD 68
Query: 94 TPFIDGR 100
GR
Sbjct: 69 ESLFRGR 75
>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 = 19/56 (33%), Positives = 29/56 (51%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
++VGGLA E + + F FG+I + + D T + +G+ FV F E A A
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 60
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 31/62 (50%)
Query: 29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARR 88
TT ++VGGLA E + + F FG+I + + D T + +G+ FV F E A
Sbjct: 10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 69
Query: 89 AC 90
A
Sbjct: 70 AI 71
>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 = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 16/67 (23%), Positives = 33/67 (49%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP 93
++VG + + +E + +F G + ++ DK +G KG+ ++ F + E+ R + A
Sbjct: 8 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALD 67
Query: 94 TPFIDGR 100
GR
Sbjct: 68 ESLFRGR 74
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 37.4 bits (85), Expect = 0.009, 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|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In
Trinucleotide Repeat Containing 4 Variant
Length = 102
Score = 37.4 bits (85), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 24/57 (42%), Positives = 32/57 (56%), Gaps = 4/57 (7%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFR---EPEAA 86
K+FVG L + E +R+ FE FG I E V+ + G SKG FV F+ E +AA
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPD-GTSKGCAFVKFQTHAEAQAA 69
>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 = 37.0 bits (84), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 28/52 (53%)
Query: 29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTF 80
+ +FV + ++T +RR FE +G I ++ K +G+ +GY F+ +
Sbjct: 100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEY 151
>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 = 37.0 bits (84), Expect = 0.010, 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|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 = 37.0 bits (84), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 28/52 (53%)
Query: 29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTF 80
+ +FV + ++T +RR FE +G I ++ K +G+ +GY F+ +
Sbjct: 100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEY 151
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 37.0 bits (84), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 1/66 (1%)
Query: 36 VGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTP 95
V GL+ T +R F ++G I + ++ D+ + RS+G+ FV F + A+ A
Sbjct: 51 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 110
Query: 96 F-IDGR 100
+DGR
Sbjct: 111 MELDGR 116
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 37.0 bits (84), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 30/54 (55%)
Query: 36 VGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
V GL+ T +R F ++G I + ++ D+ + RS+G+ FV F + A+ A
Sbjct: 17 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 70
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 37.0 bits (84), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 32/57 (56%), Gaps = 2/57 (3%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
++ V + + + +R+ F QFG+IL+ +I N SKG+GFVTF A RA
Sbjct: 17 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIF--NERGSKGFGFVTFENSADADRA 71
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1
In Complex With Ugcaugu
Length = 109
Score = 36.6 bits (83), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 33/57 (57%), Gaps = 2/57 (3%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
++ V + + + +R+ F QFG+IL+ +I ++ SKG+GFVTF A RA
Sbjct: 31 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRA 85
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 36.6 bits (83), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 30/54 (55%)
Query: 36 VGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
V GL+ T +R F ++G I + ++ D+ + RS+G+ FV F + A+ A
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 73
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 36.6 bits (83), Expect = 0.016, 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|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 36.6 bits (83), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 1/64 (1%)
Query: 38 GLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTPF- 96
GL+ T +R F ++G I + ++ D+ + RS+G+ FV F + A+ A
Sbjct: 22 GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME 81
Query: 97 IDGR 100
+DGR
Sbjct: 82 LDGR 85
>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 = 36.2 bits (82), Expect = 0.018, 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 = 0.16, 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|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 35.8 bits (81), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 31/111 (27%), Positives = 49/111 (44%), Gaps = 21/111 (18%)
Query: 27 GDTTYT---KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREP 83
G+ TYT ++FVG L + E +R FE++GE E + R +G+GF+
Sbjct: 15 GEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFI------NRDRGFGFIRLESR 68
Query: 84 EAARRACADPTPFIDG--------RLRPATLFSGSTQATRGPYIGSFGYQQ 126
A A A+ +DG R+R AT + T P + + +Q
Sbjct: 69 TLAEIAKAE----LDGTILKSRPLRIRFATHGAALTVKNLSPVVSNELLEQ 115
Score = 35.8 bits (81), Expect = 0.024, 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
>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 = 35.4 bits (80), Expect = 0.029, 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|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 35.4 bits (80), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 29/56 (51%), Gaps = 6/56 (10%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA 89
V+ GG+A + MR+ F FG+I+E V + KGY FV F E+A A
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHA 77
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 35.4 bits (80), Expect = 0.031, 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|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 = 0.035, 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|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 35.0 bits (79), Expect = 0.036, 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|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 35.0 bits (79), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 33/64 (51%), Gaps = 4/64 (6%)
Query: 36 VGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPTP 95
V L + T +++RR FE++G + + + + +T +G+ FV F + RR D
Sbjct: 18 VDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHD----RRDAQDAEA 73
Query: 96 FIDG 99
+DG
Sbjct: 74 AMDG 77
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 35.0 bits (79), Expect = 0.043, 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|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 = 0.047, 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|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Rna-Binding Protein 14
Length = 90
Score = 34.3 bits (77), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 8/59 (13%)
Query: 33 KVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
K+FVG ++ S+ +R FE+ G ++E V+ D Y FV + A+ A A
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIA 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 = 0.065, 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|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 34.3 bits (77), Expect = 0.069, 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|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 34.3 bits (77), Expect = 0.071, 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 = 0.26, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 34/65 (52%), Gaps = 4/65 (6%)
Query: 45 SETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRA---CADPTPFIDGRL 101
+E + F FG++ AVVI D + GR G G V F AAR+A C++ + +
Sbjct: 110 NELLEEAFSVFGQVERAVVIVD-DRGRPSGKGIVEFSGKPAARKALDRCSEGSFLLTTFP 168
Query: 102 RPATL 106
RP T+
Sbjct: 169 RPVTV 173
>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 = 0.074, 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|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 34.3 bits (77), Expect = 0.074, 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|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 33.9 bits (76), Expect = 0.084, 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 = 0.092, 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|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 = 33.9 bits (76), Expect = 0.10, 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|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 = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 12/75 (16%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAV--------VITDKNTGRSKGYGFVTFREPEA 85
+FV GL E++ YF+Q G I + TD+ TG+ KG V+F +P +
Sbjct: 16 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 75
Query: 86 ARRACADPTPFIDGR 100
A+ A + DG+
Sbjct: 76 AKAAI----DWFDGK 86
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 33.5 bits (75), Expect = 0.11, 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|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 12/75 (16%)
Query: 55 FGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD--------PTPFID----GRLR 102
FG + ++ + TG+SKGYGF + + ++A RA +D T ++ G+L
Sbjct: 119 FGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLT 178
Query: 103 PATLFSGSTQATRGP 117
PA L S R P
Sbjct: 179 PALLHSRCLCVDRLP 193
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 12/75 (16%)
Query: 55 FGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD--------PTPFID----GRLR 102
FG + ++ + TG+SKGYGF + + ++A RA +D T ++ G+L
Sbjct: 119 FGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLT 178
Query: 103 PATLFSGSTQATRGP 117
PA L S R P
Sbjct: 179 PALLHSRCLCVDRLP 193
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14
Complex
Length = 110
Score = 33.5 bits (75), Expect = 0.12, 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|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 = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 12/75 (16%)
Query: 55 FGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACAD--------PTPFID----GRLR 102
FG + ++ + TG+SKGYGF + + ++A RA +D T ++ G+L
Sbjct: 117 FGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLT 176
Query: 103 PATLFSGSTQATRGP 117
PA L S R P
Sbjct: 177 PALLHSRCLCVDRLP 191
>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 = 0.12, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 6/52 (11%)
Query: 29 TTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTF 80
T +++FVG L + E MR+ FE++G+ E + D KG+GF+
Sbjct: 13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRL 58
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 33.5 bits (75), Expect = 0.14, Method: Composition-based stats.
Identities = 23/63 (36%), Positives = 33/63 (52%), Gaps = 8/63 (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 RRA 89
A
Sbjct: 62 EVA 64
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 33.1 bits (74), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 15/66 (22%), Positives = 33/66 (50%), Gaps = 5/66 (7%)
Query: 27 GDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAA 86
G + + VFVG + + +R +F Q+G++++ + + + FVTF + + A
Sbjct: 1 GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFI-----PKPFRAFAFVTFADDQIA 55
Query: 87 RRACAD 92
+ C +
Sbjct: 56 QSLCGE 61
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 32.7 bits (73), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 38/73 (52%), Gaps = 7/73 (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 ACADPTPFIDGRL 101
A D DG+L
Sbjct: 67 ALIDACLEEDGKL 79
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 32.3 bits (72), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 12/75 (16%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAV--------VITDKNTGRSKGYGFVTFREPEA 85
+FV GL E++ YF+Q G I + TD+ TG+ KG V+F +P +
Sbjct: 10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 69
Query: 86 ARRACADPTPFIDGR 100
A+ A + DG+
Sbjct: 70 AKAAI----DWFDGK 80
>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 = 32.0 bits (71), Expect = 0.40, 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|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 31.6 bits (70), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 21/86 (24%), Positives = 36/86 (41%), Gaps = 1/86 (1%)
Query: 35 FVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADPT 94
+VG L + T + F+ I ++ DK+T + KG+ +V F E ++ + A
Sbjct: 19 YVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDG 77
Query: 95 PFIDGRLRPATLFSGSTQATRGPYIG 120
+ R + G Q GP G
Sbjct: 78 ALLGDRSLRVDIAEGRKQDKSGPSSG 103
>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 = 0.48, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 36/75 (48%), Gaps = 10/75 (13%)
Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
T+++VGGL T + R F++FG I D G S + ++ + +AA+ ACA
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIR----TIDHVKGDS--FAYIQYESLDAAQAACA 71
Query: 92 DPTPF----IDGRLR 102
F D RLR
Sbjct: 72 KMRGFPLGGPDRRLR 86
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 30.8 bits (68), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 24/91 (26%), Positives = 39/91 (42%), Gaps = 11/91 (12%)
Query: 32 TKVFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACA 91
TK+ VG ++ ++ +R FE++G ++E ++ D Y FV E A A
Sbjct: 11 TKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIR 62
Query: 92 --DPTPFIDGRLRPATLFSGSTQATRGPYIG 120
D T F G+ L + + GP G
Sbjct: 63 GLDNTEF-QGKRMHVQLSTSRLRTASGPSSG 92
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 30.8 bits (68), Expect = 0.81, 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|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 30.0 bits (66), Expect = 1.5, 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|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 29.6 bits (65), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 34/82 (41%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP 93
+FVG L + + +F + + TG SKGYGFV F + +RA +
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTEC 71
Query: 94 TPFIDGRLRPATLFSGSTQATR 115
+ +P L +A+R
Sbjct: 72 QGAVGLGSKPVRLSVAIPKASR 93
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 29.6 bits (65), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 8/74 (10%)
Query: 24 SPFGDTTYTKVFVGGLAWETQSETMRRYFEQFGEILEAV--------VITDKNTGRSKGY 75
P D+ + ++V GL + + +F+Q G + + DK TG+ KG
Sbjct: 8 DPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGD 67
Query: 76 GFVTFREPEAARRA 89
V++ +P A+ A
Sbjct: 68 ATVSYEDPPTAKAA 81
>pdb|1WEL|A Chain A, Solution Structure Of Rna Binding Domain In Np_006038
Length = 124
Score = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 15/68 (22%), Positives = 34/68 (50%)
Query: 34 VFVGGLAWETQSETMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFREPEAARRACADP 93
V++ GL +E +++ + +F++ + +++ I G++ G GFV FR + A
Sbjct: 28 VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRH 87
Query: 94 TPFIDGRL 101
++ R
Sbjct: 88 KQYMGNRF 95
>pdb|2DRQ|A Chain A, Crystal Structure Of Reducing-End-Xylose Releasing
Exo-Oligoxylanase D263g Mutant
Length = 396
Score = 28.9 bits (63), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 21/47 (44%), Gaps = 4/47 (8%)
Query: 76 GFVTFREPEAARRACADPTPFIDGRLRPATLFS----GSTQATRGPY 118
F +EPE RR D PF + L P L + GS + GPY
Sbjct: 293 AFFADKEPEDYRRYKIDGEPFEEKSLHPVGLIATNAMGSLASVDGPY 339
>pdb|2DRR|A Chain A, Crystal Structure Of Reducing-End-Xylose Releasing
Exo-Oligoxylanase D263n Mutant
Length = 396
Score = 28.9 bits (63), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 21/47 (44%), Gaps = 4/47 (8%)
Query: 76 GFVTFREPEAARRACADPTPFIDGRLRPATLFS----GSTQATRGPY 118
F +EPE RR D PF + L P L + GS + GPY
Sbjct: 293 AFFADKEPEDYRRYKIDGEPFEEKSLHPVGLIATNAMGSLASVDGPY 339
>pdb|2DRS|A Chain A, Crystal Structure Of Reducing-End-Xylose Releasing
Exo-Oligoxylanase D263s Mutant
Length = 396
Score = 28.9 bits (63), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 21/47 (44%), Gaps = 4/47 (8%)
Query: 76 GFVTFREPEAARRACADPTPFIDGRLRPATLFS----GSTQATRGPY 118
F +EPE RR D PF + L P L + GS + GPY
Sbjct: 293 AFFADKEPEDYRRYKIDGEPFEEKSLHPVGLIATNAMGSLASVDGPY 339
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 28.9 bits (63), Expect = 3.4, 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 TPF-IDGR 100
I+GR
Sbjct: 74 NKREIEGR 81
>pdb|1WU4|A Chain A, Crystal Structure Of Reducing-End-Xylose Releasing
Exo-Oligoxylanase
pdb|1WU5|A Chain A, Crystal Structure Of Reducing-End-Xylose Releasing
Exo-Oligoxylanase Complexed With Xylose
Length = 396
Score = 28.5 bits (62), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 21/47 (44%), Gaps = 4/47 (8%)
Query: 76 GFVTFREPEAARRACADPTPFIDGRLRPATLFS----GSTQATRGPY 118
F +EPE RR D PF + L P L + GS + GPY
Sbjct: 293 AFFADKEPEDYRRYKIDGEPFEEKSLHPVGLIATNAMGSLASVDGPY 339
>pdb|1WU6|A Chain A, Crystal Structure Of Reducing-End-Xylose Releasing
Exo-Oligoxylanase E70a Mutant Complexed With Xylobiose
Length = 396
Score = 28.5 bits (62), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 21/47 (44%), Gaps = 4/47 (8%)
Query: 76 GFVTFREPEAARRACADPTPFIDGRLRPATLFS----GSTQATRGPY 118
F +EPE RR D PF + L P L + GS + GPY
Sbjct: 293 AFFADKEPEDYRRYKIDGEPFEEKSLHPVGLIATNAMGSLASVDGPY 339
>pdb|3A3V|A Chain A, Crystal Structure Of Reducing-End-Xylose Releasing
Exo-Oligoxylanase Y198f Mutant
Length = 396
Score = 28.5 bits (62), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 21/47 (44%), Gaps = 4/47 (8%)
Query: 76 GFVTFREPEAARRACADPTPFIDGRLRPATLFS----GSTQATRGPY 118
F +EPE RR D PF + L P L + GS + GPY
Sbjct: 293 AFFADKEPEDYRRYKIDGEPFEEKSLHPVGLIATNAMGSLASVDGPY 339
>pdb|2DRO|A Chain A, Crystal Structure Of Reducing-End-Xylose Releasing
Exo-Oligoxylanase D263c Mutant
Length = 396
Score = 28.5 bits (62), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 21/47 (44%), Gaps = 4/47 (8%)
Query: 76 GFVTFREPEAARRACADPTPFIDGRLRPATLFS----GSTQATRGPY 118
F +EPE RR D PF + L P L + GS + GPY
Sbjct: 293 AFFADKEPEDYRRYKIDGEPFEEKSLHPVGLIATNAMGSLASVDGPY 339
>pdb|1QUS|A Chain A, 1.7 A Resolution Structure Of The Soluble Lytic
Transglycosylase Slt35 From Escherichia Coli
pdb|1QUT|A Chain A, The Soluble Lytic Transglycosylase Slt35 From Escherichia
Coli In Complex With N-Acetylglucosamine
pdb|1QDR|A Chain A, 2.1 A Resolution Structure Of Escherichia Coli Lytic
Transglycosylase Slt35
pdb|1QDT|A Chain A, 2.1 A Resolution Structure Of Escherichia Coli Lytic
Transglycoyslase Slt35 In Complex With Calcium
pdb|1D0K|A Chain A, The Escherichia Coli Lytic Transglycosylase Slt35 In
Complex With Two Murodipeptides
(Glcnac-Murnac-L-Ala-D-Glu)
pdb|1D0L|A Chain A, The Escherichia Coli Lytic Transglycosylase Slt35 In
Complex With Bulgecin A
pdb|1D0M|A Chain A, The Escherichia Coli Lytic Transglycosylase Slt35 In
Complex With Bulgecin A And (Glcnac)2
Length = 322
Score = 27.3 bits (59), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 29/125 (23%), Positives = 50/125 (40%), Gaps = 29/125 (23%)
Query: 31 YTKVFV-------GGLAWETQSETMRRYFEQFG---EILEAVVITDKNTGRSKG------ 74
Y K F+ G + W + + R ++ +G EI+ ++ + GR G
Sbjct: 78 YRKKFITPDNVQNGVVFWNQYEDALNRAWQVYGVPPEIIVGIIGVETRWGRVMGKTRILD 137
Query: 75 -YGFVTFREPEAARRACADPTPFIDGRLRPATLFSGSTQAT----RGPYIGSFGYQQPLP 129
++F P RRA + G L L + Q +G + G+ GY Q +P
Sbjct: 138 ALATLSFNYP---RRA-----EYFSGELETFLLMARDEQDDPLNLKGSFAGAMGYGQFMP 189
Query: 130 YNYQQ 134
+Y+Q
Sbjct: 190 SSYKQ 194
>pdb|1LTM|A Chain A, Accelerated X-ray Structure Elucidation Of A 36 Kda
Muramidase/transglycosylase Using Warp
Length = 320
Score = 27.3 bits (59), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 29/125 (23%), Positives = 50/125 (40%), Gaps = 29/125 (23%)
Query: 31 YTKVFV-------GGLAWETQSETMRRYFEQFG---EILEAVVITDKNTGRSKG------ 74
Y K F+ G + W + + R ++ +G EI+ ++ + GR G
Sbjct: 76 YRKKFITPDNVQNGVVFWNQYEDALNRAWQVYGVPPEIIVGIIGVETRWGRVMGKTRILD 135
Query: 75 -YGFVTFREPEAARRACADPTPFIDGRLRPATLFSGSTQAT----RGPYIGSFGYQQPLP 129
++F P RRA + G L L + Q +G + G+ GY Q +P
Sbjct: 136 ALATLSFNYP---RRA-----EYFSGELETFLLMARDEQDDPLNLKGSFAGAMGYGQFMP 187
Query: 130 YNYQQ 134
+Y+Q
Sbjct: 188 SSYKQ 192
>pdb|4HA3|A Chain A, Structure Of Beta-Glycosidase From Acidilobus
Saccharovorans In Complex With Tris
pdb|4HA4|A Chain A, Structure Of Beta-Glycosidase From Acidilobus
Saccharovorans In Complex With Glycerol
Length = 489
Score = 27.3 bits (59), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 42/160 (26%), Positives = 64/160 (40%), Gaps = 26/160 (16%)
Query: 37 GGLAWETQSETMRRYFEQFGEILEAV-VITDKNTG---RSKGYGFVTFREPEAARRACAD 92
G L E M+ + +AV IT K G + + +T + EAA RA D
Sbjct: 226 GYLCLECAGRAMKNLVQAHARAYDAVKAITKKPVGVIYANSDFTPLTDADREAAERAKFD 285
Query: 93 PT-PFIDGRLRPATLFSGSTQAT---RGPYIGSFGYQQPLPYNYQQG-MVYPSYGY---- 143
F D +R GST+ R +IG Y + + G + P YG+
Sbjct: 286 NRWAFFDAVVRGQ--LGGSTRDDLKGRLDWIGVNYYTRQVVRARGSGYEIVPGYGHGCEP 343
Query: 144 ----------ATYGPEYVYPQGIYNPYQQYVPIYGVPGTV 173
+ +G E+ YP+G+YN ++Y Y +P V
Sbjct: 344 NGVSPAGRPCSDFGWEF-YPEGLYNVLKEYWDRYHLPLLV 382
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
0.318 0.138 0.431
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,846,826
Number of Sequences: 62578
Number of extensions: 402672
Number of successful extensions: 1080
Number of sequences better than 100.0: 152
Number of HSP's better than 100.0 without gapping: 124
Number of HSP's successfully gapped in prelim test: 28
Number of HSP's that attempted gapping in prelim test: 912
Number of HSP's gapped (non-prelim): 175
length of query: 261
length of database: 14,973,337
effective HSP length: 97
effective length of query: 164
effective length of database: 8,903,271
effective search space: 1460136444
effective search space used: 1460136444
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)