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= 023959
(274 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 = 115 bits (287), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 52/82 (63%), Positives = 65/82 (79%)
Query: 30 YSKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRAC 89
++KIFVGGL + T +++ YFE FGDI EAVVITDR TGKS+GYGFVT D +A RAC
Sbjct: 17 FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERAC 76
Query: 90 ENPYPVIDGRRANCNLAHLGAH 111
++P P+IDGR+AN NLA+LGA
Sbjct: 77 KDPNPIIDGRKANVNLAYLGAK 98
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 72.0 bits (175), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 29/74 (39%), Positives = 47/74 (63%)
Query: 29 KYSKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRA 88
+ K+FVGGL W T ET++ YF Q+G++++ V++ D+ T +S+G+GFV FKDP
Sbjct: 15 EIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTV 74
Query: 89 CENPYPVIDGRRAN 102
+ +DGR +
Sbjct: 75 LASRPHTLDGRNID 88
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 70.5 bits (171), Expect = 1e-12, Method: Composition-based stats.
Identities = 30/74 (40%), Positives = 47/74 (63%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACENP 92
IFVGGL+ T E +KHYFEQFG + +A+++ D+ T + +G+GFVTF+ + + CE
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 93 YPVIDGRRANCNLA 106
+ I+ + C A
Sbjct: 62 FHEINNKMVECKKA 75
>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
pdb|3S7R|B Chain B, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
Length = 87
Score = 67.8 bits (164), Expect = 6e-12, Method: Composition-based stats.
Identities = 27/68 (39%), Positives = 44/68 (64%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN 91
K FVGGL+W+T + +K YF +FG++++ + D TG+S+G+GF+ FKD S + +
Sbjct: 13 KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQ 72
Query: 92 PYPVIDGR 99
+DGR
Sbjct: 73 KEHRLDGR 80
>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 = 65.9 bits (159), Expect = 3e-11, Method: Composition-based stats.
Identities = 28/74 (37%), Positives = 48/74 (64%), Gaps = 5/74 (6%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACENP 92
+F+GGL+W+T + +K YF +FG++++ + D +TG+S+G+GFV FK+ ES + +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 93 Y-----PVIDGRRA 101
VID +RA
Sbjct: 62 EHKLNGKVIDPKRA 75
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 65.9 bits (159), Expect = 3e-11, Method: Composition-based stats.
Identities = 25/50 (50%), Positives = 39/50 (78%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKD 81
K+F+GGL+W+T E ++ YF QFG++ E +V+ D +T +S+G+GFVTF D
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMD 51
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 65.1 bits (157), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 32/88 (36%), Positives = 55/88 (62%), Gaps = 3/88 (3%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRA--C 89
K+FVGGL+++T ++++ F ++G I E VV+ DR T +S+G+GFVTF++ + A+ A
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 90 ENPYPVIDGRRANCNLAHLGAHHKKRPP 117
N V DGR+ + A + ++ P
Sbjct: 74 MNGKSV-DGRQIRVDQAGKSSDNRSGPS 100
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 64.3 bits (155), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 25/51 (49%), Positives = 39/51 (76%)
Query: 31 SKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKD 81
K+F+GGL+W+T E ++ YF QFG++ E +V+ D +T +S+G+GFVTF D
Sbjct: 26 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMD 76
>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 = 62.8 bits (151), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 47/79 (59%)
Query: 29 KYSKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRA 88
K KIFVGG+ + R + + +F Q+G I++A ++ D+ TG+S+G+GFVT+ ++ R
Sbjct: 86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRV 145
Query: 89 CENPYPVIDGRRANCNLAH 107
C+N + R+ A
Sbjct: 146 CQNKFIDFKDRKIEIKRAE 164
Score = 57.8 bits (138), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 46/74 (62%), Gaps = 4/74 (5%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN 91
K+F+GGL W+T + ++ YF ++G + + ++ D TG+S+G+GF++F+ P S +
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 92 PY----PVIDGRRA 101
+ VID +RA
Sbjct: 65 QHILDGKVIDPKRA 78
>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 = 61.6 bits (148), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 29/74 (39%), Positives = 44/74 (59%), Gaps = 2/74 (2%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN 91
KIFVGG+ +T ++ YFEQ+G I ++TDR +GK +G+ FVTF D +S +
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 165
Query: 92 PYPVIDGRRANCNL 105
Y ++G NC +
Sbjct: 166 KYHTVNGH--NCEV 177
Score = 57.8 bits (138), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 27/68 (39%), Positives = 44/68 (64%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN 91
K+F+GGL++ET E+++ +FEQ+G + + VV+ D T +S+G+GFVT+ E A
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 92 PYPVIDGR 99
+DGR
Sbjct: 75 RPHKVDGR 82
>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 = 61.6 bits (148), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 29/74 (39%), Positives = 44/74 (59%), Gaps = 2/74 (2%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN 91
KIFVGG+ +T ++ YFEQ+G I ++TDR +GK +G+ FVTF D +S +
Sbjct: 105 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 164
Query: 92 PYPVIDGRRANCNL 105
Y ++G NC +
Sbjct: 165 KYHTVNGH--NCEV 176
Score = 57.8 bits (138), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 27/68 (39%), Positives = 44/68 (64%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN 91
K+F+GGL++ET E+++ +FEQ+G + + VV+ D T +S+G+GFVT+ E A
Sbjct: 14 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 73
Query: 92 PYPVIDGR 99
+DGR
Sbjct: 74 RPHKVDGR 81
>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 = 61.2 bits (147), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 29/74 (39%), Positives = 44/74 (59%), Gaps = 2/74 (2%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN 91
KIFVGG+ +T ++ YFEQ+G I ++TDR +GK +G+ FVTF D +S +
Sbjct: 99 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 158
Query: 92 PYPVIDGRRANCNL 105
Y ++G NC +
Sbjct: 159 KYHTVNGH--NCEV 170
Score = 57.4 bits (137), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 45/71 (63%)
Query: 29 KYSKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRA 88
+ K+F+GGL++ET E+++ +FEQ+G + + VV+ D T +S+G+GFVT+ E A
Sbjct: 5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 64
Query: 89 CENPYPVIDGR 99
+DGR
Sbjct: 65 MNARPHKVDGR 75
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 61.2 bits (147), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 29/74 (39%), Positives = 44/74 (59%), Gaps = 2/74 (2%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN 91
KIFVGG+ +T ++ YFEQ+G I ++TDR +GK +G+ FVTF D +S +
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 165
Query: 92 PYPVIDGRRANCNL 105
Y ++G NC +
Sbjct: 166 KYHTVNGH--NCEV 177
Score = 57.4 bits (137), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 45/71 (63%)
Query: 29 KYSKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRA 88
+ K+F+GGL++ET E+++ +FEQ+G + + VV+ D T +S+G+GFVT+ E A
Sbjct: 12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 71
Query: 89 CENPYPVIDGR 99
+DGR
Sbjct: 72 MNARPHKVDGR 82
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 61.2 bits (147), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 29/74 (39%), Positives = 44/74 (59%), Gaps = 2/74 (2%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN 91
KIFVGG+ +T ++ YFEQ+G I ++TDR +GK +G+ FVTF D +S +
Sbjct: 107 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 166
Query: 92 PYPVIDGRRANCNL 105
Y ++G NC +
Sbjct: 167 KYHTVNGH--NCEV 178
Score = 57.4 bits (137), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 27/68 (39%), Positives = 44/68 (64%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN 91
K+F+GGL++ET E+++ +FEQ+G + + VV+ D T +S+G+GFVT+ E A
Sbjct: 16 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 75
Query: 92 PYPVIDGR 99
+DGR
Sbjct: 76 RPHKVDGR 83
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 61.2 bits (147), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 29/74 (39%), Positives = 44/74 (59%), Gaps = 2/74 (2%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN 91
KIFVGG+ +T ++ YFEQ+G I ++TDR +GK +G+ FVTF D +S +
Sbjct: 104 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 163
Query: 92 PYPVIDGRRANCNL 105
Y ++G NC +
Sbjct: 164 KYHTVNGH--NCEV 175
Score = 57.4 bits (137), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 27/68 (39%), Positives = 44/68 (64%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN 91
K+F+GGL++ET E+++ +FEQ+G + + VV+ D T +S+G+GFVT+ E A
Sbjct: 13 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 72
Query: 92 PYPVIDGR 99
+DGR
Sbjct: 73 RPHKVDGR 80
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 60.8 bits (146), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 31/77 (40%), Positives = 44/77 (57%), Gaps = 1/77 (1%)
Query: 29 KYSKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRA 88
K S + V GL W+T + +K YF FG++L V D TG SKG+GFV F + E+ +
Sbjct: 14 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKV 73
Query: 89 CENPYPVIDGRRANCNL 105
+ +IDGR +C L
Sbjct: 74 MSQRH-MIDGRWCDCKL 89
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleaoproteins A2B1
Length = 116
Score = 59.7 bits (143), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 46/71 (64%)
Query: 29 KYSKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRA 88
++ K+F+GGL++ET E++++Y+EQ+G + + VV+ D + +S+G+GFVTF A
Sbjct: 26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAA 85
Query: 89 CENPYPVIDGR 99
IDGR
Sbjct: 86 MAARPHSIDGR 96
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 59.3 bits (142), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 28/60 (46%), Positives = 38/60 (63%)
Query: 31 SKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACE 90
S ++VG L + + ++ FE FG I V++ D TG+SKGYGF+TF D E ARRA E
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
>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 = 55.1 bits (131), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 32/75 (42%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN- 91
+FVG L+ E TE +K F FG I +A V+ D TGKSKGYGFV+F + A A +
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 92 PYPVIDGRRANCNLA 106
+ GR+ N A
Sbjct: 78 GGQWLGGRQIRTNWA 92
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 54.7 bits (130), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 25/60 (41%), Positives = 40/60 (66%), Gaps = 1/60 (1%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN 91
K+F+GGL ET + +K F + G I E ++I DR T KS+G+ F+TF++P A+ A ++
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKD 67
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 54.3 bits (129), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 24/59 (40%), Positives = 37/59 (62%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACE 90
+++VG L + + ++ FE FG I ++ D TG+SKGYGF+TF D E A++A E
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALE 86
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 53.9 bits (128), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 32/75 (42%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN- 91
+FVG L+ E TE +K F FG I +A V+ D TGKSKGYGFV+F + A A +
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 92 PYPVIDGRRANCNLA 106
+ GR+ N A
Sbjct: 78 GGQWLGGRQIRTNWA 92
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 30/78 (38%), Positives = 46/78 (58%), Gaps = 8/78 (10%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTF---KDPESARRAC 89
+FV GL+ +T ET+K F+ + A ++TDR TG SKG+GFV F +D ++A+ A
Sbjct: 18 LFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAM 74
Query: 90 ENPYPVIDGRRANCNLAH 107
E+ IDG + + A
Sbjct: 75 EDGE--IDGNKVTLDWAK 90
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 52.0 bits (123), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 43/77 (55%)
Query: 31 SKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACE 90
+KIFVGG+ ++ YF++FG + E V+I D + +G+GF+TF+D +S +A
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN 70
Query: 91 NPYPVIDGRRANCNLAH 107
+ I G++ A
Sbjct: 71 MHFHDIMGKKVEVKRAE 87
>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain
Of Hnrnp D (Auf1) With Telomere Dna
pdb|1X0F|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain
Of Hnrnp D(Auf1) With Telomeric Dna
Length = 79
Score = 51.6 bits (122), Expect = 4e-07, Method: Composition-based stats.
Identities = 24/62 (38%), Positives = 37/62 (59%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN 91
KIFVGGL+ +T E ++ YF FG++ + D T K +G+ F+TFK+ E ++ E
Sbjct: 3 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 62
Query: 92 PY 93
Y
Sbjct: 63 KY 64
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 23/59 (38%), Positives = 35/59 (59%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN 91
+FVG + +E E +K F + G ++ ++ DR TGK KGYGF ++D E+A A N
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 49.7 bits (117), Expect = 2e-06, Method: Composition-based stats.
Identities = 23/61 (37%), Positives = 36/61 (59%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACENP 92
IFVGGL+ +T E ++ YF FG++ + D T K +G+ F+TFK+ E ++ E
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Query: 93 Y 93
Y
Sbjct: 62 Y 62
>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 = 48.9 bits (115), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 32/112 (28%), Positives = 50/112 (44%), Gaps = 21/112 (18%)
Query: 31 SKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACE 90
S+++VG + +E +T++ F FG I + D VT K KG+ FV ++ PE+A+ A E
Sbjct: 29 SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 88
Query: 91 NPYPVIDGRRANCNLAHLGAHHKKRPPLLHGNVTAAEPSTVDFGQPPVPQYA 142
V+ G R N+ PS + QP + Q A
Sbjct: 89 QMNSVMLGGR---------------------NIKVGRPSNIGQAQPIIDQLA 119
Score = 45.1 bits (105), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 36/62 (58%)
Query: 30 YSKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRAC 89
+++I+V + + + +K FE FG I A + D TGK KGYGF+ ++ +S++ A
Sbjct: 125 FNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAV 184
Query: 90 EN 91
+
Sbjct: 185 SS 186
>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 = 48.5 bits (114), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 28/91 (30%), Positives = 45/91 (49%), Gaps = 6/91 (6%)
Query: 31 SKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACE 90
+ + V L + T +T++ FE++G + + + DR T +S+G+ FV F D A A +
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 91 N-PYPVIDGRRANCNLAHLGAHHKKRPPLLH 120
V+DGR +A G RPP H
Sbjct: 108 AMDGAVLDGRELRVQMARYG-----RPPDSH 133
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 48.1 bits (113), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 34/57 (59%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRA 88
K+F+G + + +K FE+FG I E V+ DR TG KG F+T+ + ESA +A
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKA 71
>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 = 48.1 bits (113), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 36/59 (61%), Gaps = 1/59 (1%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN 91
+FVGG+ ++ +F ++G + E +ITDR TG SKGYGFV+F + ++ E+
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVES 69
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 47.8 bits (112), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 28/91 (30%), Positives = 45/91 (49%), Gaps = 6/91 (6%)
Query: 31 SKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACE 90
+ + V L + T +T++ FE++G + + + DR T +S+G+ FV F D A A +
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 91 N-PYPVIDGRRANCNLAHLGAHHKKRPPLLH 120
V+DGR +A G RPP H
Sbjct: 131 AMDGAVLDGRELRVQMARYG-----RPPDSH 156
>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 = 47.4 bits (111), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 31/111 (27%), Positives = 49/111 (44%), Gaps = 21/111 (18%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN 91
+++VG + +E +T++ F FG I + D VT K KG+ FV ++ PE+A+ A E
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 92 PYPVIDGRRANCNLAHLGAHHKKRPPLLHGNVTAAEPSTVDFGQPPVPQYA 142
V+ G R N+ PS + QP + Q A
Sbjct: 75 MNSVMLGGR---------------------NIKVGRPSNIGQAQPIIDQLA 104
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 35/62 (56%)
Query: 30 YSKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRAC 89
+++I+V + + + +K FE FG I + D TGK KGYGF+ ++ +S++ A
Sbjct: 110 FNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAV 169
Query: 90 EN 91
+
Sbjct: 170 SS 171
>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 = 2e-05, Method: Composition-based stats.
Identities = 22/59 (37%), Positives = 36/59 (61%), Gaps = 1/59 (1%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN 91
+FVGG+ ++ +F ++G + E +ITDR TG SKGYGFV+F + ++ E+
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVES 70
>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: Composition-based stats.
Identities = 22/59 (37%), Positives = 36/59 (61%), Gaps = 1/59 (1%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN 91
+FVGG+ ++ +F ++G + E +ITDR TG SKGYGFV+F + ++ E+
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVES 69
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 46.6 bits (109), Expect = 2e-05, Method: Composition-based stats.
Identities = 23/56 (41%), Positives = 32/56 (57%), Gaps = 1/56 (1%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRA 88
I+VG L + +E +K F QFG + +I DR T K KG+GFV ++ ES A
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEA 58
>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 = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 31/111 (27%), Positives = 47/111 (42%), Gaps = 21/111 (18%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN 91
+++VG + +E +T++ F FG I D VT K KG+ FV ++ PE+A+ A E
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 92 PYPVIDGRRANCNLAHLGAHHKKRPPLLHGNVTAAEPSTVDFGQPPVPQYA 142
V G R N+ PS + QP + Q A
Sbjct: 74 XNSVXLGGR---------------------NIKVGRPSNIGQAQPIIDQLA 103
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 35/62 (56%)
Query: 30 YSKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRAC 89
+++I+V + + + +K FE FG I + D TGK KGYGF+ ++ +S++ A
Sbjct: 109 FNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAV 168
Query: 90 EN 91
+
Sbjct: 169 SS 170
>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 = 3e-05, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 34/57 (59%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRA 88
K+FVG + + +K FE+FG I E V+ DR+TG KG F+T+ +SA +A
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKA 73
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 33/58 (56%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACE 90
+FVG L ET+++ F+ F L V+ D TG S+GYGFV+F + A+ A +
Sbjct: 90 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 147
Score = 28.1 bits (61), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 17/76 (22%), Positives = 34/76 (44%), Gaps = 5/76 (6%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACENP 92
++VG L + +K YF+ G I ++ D+ K+ Y FV + A A +
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQ-- 59
Query: 93 YPVIDGRRANCNLAHL 108
++G++ N+ +
Sbjct: 60 --TLNGKQIENNIVKI 73
>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 = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 33/59 (55%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACE 90
+FVG L ET+++ F+ F L V+ D TG S+GYGFV+F + A+ A +
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
>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 = 44.3 bits (103), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 30/75 (40%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN- 91
+FVG L+ E T + F FG I +A V+ D TGKSKGYGFV+F + A A +
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 92 PYPVIDGRRANCNLA 106
+ GR+ N A
Sbjct: 69 GGQWLGGRQIRTNWA 83
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 44.3 bits (103), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 42/76 (55%), Gaps = 3/76 (3%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN 91
++ V + + R ++ F QFG IL+ +I + SKG+GFVTF++ A RA E
Sbjct: 31 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREK 88
Query: 92 PY-PVIDGRRANCNLA 106
+ V++GR+ N A
Sbjct: 89 LHGTVVEGRKIEVNNA 104
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With
The Au-Rich Element
Length = 174
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 18/42 (42%), Positives = 25/42 (59%)
Query: 48 KHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRAC 89
K F GDI ++ D++TG+S GYGFV + DP A +A
Sbjct: 22 KSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI 63
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 29/107 (27%), Positives = 46/107 (42%), Gaps = 25/107 (23%)
Query: 31 SKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACE 90
+ ++V GL + M+ F Q+G I+ + ++ D+ TG S+G GF+ F R E
Sbjct: 91 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRF----DKRIEAE 146
Query: 91 NPYPVIDGRRANCNLAHLGAHHKKRPPLLHGNVTAAEPSTVDFGQPP 137
++G++ PL AAEP TV F P
Sbjct: 147 EAIKGLNGQK----------------PL-----GAAEPITVKFANNP 172
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 42/76 (55%), Gaps = 3/76 (3%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN 91
++ V + + R ++ F QFG IL+ +I + SKG+GFVTF++ A RA E
Sbjct: 17 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREK 74
Query: 92 PY-PVIDGRRANCNLA 106
+ V++GR+ N A
Sbjct: 75 LHGTVVEGRKIEVNNA 90
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 43.9 bits (102), Expect = 1e-04, Method: Composition-based stats.
Identities = 20/58 (34%), Positives = 30/58 (51%)
Query: 31 SKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRA 88
+ + V L + K F GDI ++ D++TG+S GYGFV + DP A +A
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESA 85
+FVG L R E + F Q G + + + DR GK K +GFV FK PES
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESV 70
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 4/77 (5%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN 91
++FV L++ + E ++ F +G + E D +T K KG+ FVTF PE A +A
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKA--- 66
Query: 92 PYPVIDGRRANCNLAHL 108
Y +DG+ + H+
Sbjct: 67 -YAEVDGQVFQGRMLHV 82
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 42.4 bits (98), Expect = 3e-04, Method: Composition-based stats.
Identities = 20/58 (34%), Positives = 32/58 (55%)
Query: 31 SKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRA 88
S +++ GL T + + + +G I+ I D+ T K KGYGFV F P +A++A
Sbjct: 6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA 63
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 31/57 (54%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRAC 89
I V L+ +TR ++ F FG I + D+ TG+SKG+ F++F E A RA
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 74
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 42.4 bits (98), Expect = 3e-04, Method: Composition-based stats.
Identities = 27/75 (36%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN- 91
++VGGLA E + + F FGDI + + D T K +G+ FV F+ E A A +N
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 92 PYPVIDGRRANCNLA 106
+ GR NLA
Sbjct: 68 NESELFGRTIRVNLA 82
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 42.4 bits (98), Expect = 3e-04, Method: Composition-based stats.
Identities = 27/75 (36%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN- 91
++VGGLA E + + F FGDI + + D T K +G+ FV F+ E A A +N
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 92 PYPVIDGRRANCNLA 106
+ GR NLA
Sbjct: 65 NESELFGRTIRVNLA 79
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 42.4 bits (98), Expect = 3e-04, Method: Composition-based stats.
Identities = 27/75 (36%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN- 91
++VGGLA E + + F FGDI + + D T K +G+ FV F+ E A A +N
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 92 PYPVIDGRRANCNLA 106
+ GR NLA
Sbjct: 70 NESELFGRTIRVNLA 84
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain
In Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 42.0 bits (97), Expect = 4e-04, Method: Composition-based stats.
Identities = 24/59 (40%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 31 SKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRAC 89
S IFV L ++ + +K F + G +L A + + GKSKG G V F+ PE A RAC
Sbjct: 6 SGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERAC 62
>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 = 17/45 (37%), Positives = 27/45 (60%)
Query: 45 ETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRAC 89
E + F G+I ++ D++TG+S GYGFV + DP+ A +A
Sbjct: 17 EEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 33/60 (55%)
Query: 31 SKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACE 90
+ ++V GL + ++ F Q+G I+ + ++ D+VTG S+G GF+ F A A +
Sbjct: 89 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 148
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN- 91
++VGGLA E + + F FGDI + + D T K +G+ FV F+ E A A +N
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 92 PYPVIDGRRANCNLA 106
+ GR NLA
Sbjct: 75 NESELFGRTIRVNLA 89
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 38/65 (58%), Gaps = 3/65 (4%)
Query: 47 MKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACE--NPYPVIDGRRANCN 104
++ FE++G I ++ DR T +S+GYGFV F+ SA++A N + +++ +R
Sbjct: 59 LRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILN-KRLKVA 117
Query: 105 LAHLG 109
LA G
Sbjct: 118 LAASG 122
>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 = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACE 90
IF+ L + + F FG+IL V+ D SKGYGFV F+ E+A RA E
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIE 161
Score = 37.4 bits (85), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 34/70 (48%), Gaps = 1/70 (1%)
Query: 31 SKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACE 90
+ ++VG L + + F G IL V D +T +S GY +V F+ P A RA +
Sbjct: 16 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 75
Query: 91 N-PYPVIDGR 99
+ VI G+
Sbjct: 76 TMNFDVIKGK 85
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 41.2 bits (95), Expect = 6e-04, Method: Composition-based stats.
Identities = 29/107 (27%), Positives = 47/107 (43%), Gaps = 25/107 (23%)
Query: 31 SKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACE 90
+ ++V GL + M+ F Q+G I+ + ++ D+ TG S+G GF+ F A A +
Sbjct: 2 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 61
Query: 91 NPYPVIDGRRANCNLAHLGAHHKKRPPLLHGNVTAAEPSTVDFGQPP 137
++G++ PL AAEP TV F P
Sbjct: 62 G----LNGQK----------------PL-----GAAEPITVKFANNP 83
>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 = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACE 90
IF+ L + + F FG+IL V+ D SKGYGFV F+ E+A RA E
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIE 156
Score = 37.0 bits (84), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 34/70 (48%), Gaps = 1/70 (1%)
Query: 31 SKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACE 90
+ ++VG L + + F G IL V D +T +S GY +V F+ P A RA +
Sbjct: 11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 70
Query: 91 N-PYPVIDGR 99
+ VI G+
Sbjct: 71 TMNFDVIKGK 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 = 40.8 bits (94), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 26/66 (39%), Positives = 33/66 (50%), Gaps = 8/66 (12%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILE--------AVVITDRVTGKSKGYGFVTFKDPES 84
IFV GL E++ YF+Q G I + TDR TGK KG V+F DP S
Sbjct: 16 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 75
Query: 85 ARRACE 90
A+ A +
Sbjct: 76 AKAAID 81
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 26/66 (39%), Positives = 33/66 (50%), Gaps = 8/66 (12%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAV--------VITDRVTGKSKGYGFVTFKDPES 84
IFV GL E++ YF+Q G I + TDR TGK KG V+F DP S
Sbjct: 10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 69
Query: 85 ARRACE 90
A+ A +
Sbjct: 70 AKAAID 75
>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 = 40.8 bits (94), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACE 90
IF+ L + + F FG+IL V+ D SKGYGFV F+ E+A RA E
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIE 63
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN- 91
++VGGLA E + + F FGDI + + D T K +G+ FV F+ E A A +N
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 92 PYPVIDGRRANCNLA 106
+ GR NLA
Sbjct: 126 NESELFGRTIRVNLA 140
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 32/60 (53%)
Query: 31 SKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACE 90
+ ++VGGL + + F Q G ++ + DRVTG+ +GYGFV F E A A +
Sbjct: 16 ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIK 75
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACE 90
IF+ L + + F FG+IL V+ D SKGYGFV F+ E+A RA E
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIE 69
>pdb|3N9U|C Chain C, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
pdb|3N9U|I Chain I, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
Length = 156
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/96 (25%), Positives = 42/96 (43%), Gaps = 9/96 (9%)
Query: 29 KYSKIFVGGLAWETRTETMKHYFEQFG--DILEAVVITDRVTGKSKGYGFVTFKDPESAR 86
+ + ++VG +W T + + G D++E +R G+SKGY V S
Sbjct: 54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVH 113
Query: 87 RACE-NPYPVIDGRRANC------NLAHLGAHHKKR 115
+ E P V++G + + NL+ A +KR
Sbjct: 114 KLLELLPGKVLNGEKVDVRPATRQNLSQFEAQARKR 149
>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 = 23/59 (38%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 31 SKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRAC 89
+IFV L ++ + +K F + G +L A + + GKSKG G V F+ PE A RAC
Sbjct: 9 CQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERAC 65
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 39.7 bits (91), Expect = 0.002, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 31/60 (51%), Gaps = 8/60 (13%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN 91
K+F+G L E + ++ FEQ+G +LE +I K YGFV +D +A A N
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRN 61
>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 = 39.7 bits (91), Expect = 0.002, Method: Composition-based stats.
Identities = 17/68 (25%), Positives = 34/68 (50%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACENP 92
I+VG + + E ++ +F G + ++ D+ +G KG+ ++ F D ES R +
Sbjct: 9 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALD 68
Query: 93 YPVIDGRR 100
+ GR+
Sbjct: 69 ESLFRGRQ 76
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 37 GLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACENPYPV- 95
GL+ T ++ F ++G I + ++ D+ + +S+G+ FV F++ + A+ A E +
Sbjct: 53 GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME 112
Query: 96 IDGRRANCNLA 106
+DGRR + +
Sbjct: 113 LDGRRIRVDFS 123
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 35 VGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACENPYP 94
V GL+ T ++ F ++G I + ++ D+ + +S+G+ FV F++ + A+ A E
Sbjct: 17 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 76
Query: 95 V-IDGRRANCNLA 106
+ +DGRR + +
Sbjct: 77 MELDGRRIRVDFS 89
>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 = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 32/59 (54%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN 91
+++G + ++ E + G ++ ++ D TG+SKGY F+ F+D ES+ A N
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 64
>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 = 17/59 (28%), Positives = 32/59 (54%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN 91
+++G + ++ E + G ++ ++ D TG+SKGY F+ F+D ES+ A N
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 37 GLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACENPYPV- 95
GL+ T ++ F ++G I + ++ D+ + +S+G+ FV F++ + A+ A E +
Sbjct: 22 GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME 81
Query: 96 IDGRRANCNLA 106
+DGRR + +
Sbjct: 82 LDGRRIRVDFS 92
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 33/58 (56%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACE 90
+F+ L E + F FG+++ A V D+ T SK +GFV+F +P+SA+ A +
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIK 100
>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 = 19/65 (29%), Positives = 38/65 (58%), Gaps = 1/65 (1%)
Query: 37 GLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACENPYPV- 95
GL+ T ++ F ++G I + ++ D+ + +S+G+ FV F++ + A+ A E +
Sbjct: 22 GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME 81
Query: 96 IDGRR 100
+DGRR
Sbjct: 82 LDGRR 86
>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 = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 34/68 (50%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACENP 92
I+VG + + E ++ +F G + ++ D+ +G KG+ ++ F D ES R +
Sbjct: 8 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALD 67
Query: 93 YPVIDGRR 100
+ GR+
Sbjct: 68 ESLFRGRQ 75
>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 = 20/78 (25%), Positives = 37/78 (47%)
Query: 12 RNKMVLVSDXXXXXXXXKYSKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKS 71
++K + VS K + +++ GL + ++ F +FG I+ + V+ D+ TG S
Sbjct: 70 QSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLS 129
Query: 72 KGYGFVTFKDPESARRAC 89
+G F+ F A A
Sbjct: 130 RGVAFIRFDKRSEAEEAI 147
Score = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 25/45 (55%)
Query: 45 ETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRAC 89
+ ++ F G++ A +I D+V G S GYGFV + + A RA
Sbjct: 17 DELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
pdb|4ED5|B Chain B, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
Length = 177
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 37/78 (47%)
Query: 12 RNKMVLVSDXXXXXXXXKYSKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKS 71
++K + VS K + +++ GL + ++ F +FG I+ + V+ D+ TG S
Sbjct: 70 QSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLS 129
Query: 72 KGYGFVTFKDPESARRAC 89
+G F+ F A A
Sbjct: 130 RGVAFIRFDKRSEAEEAI 147
Score = 37.4 bits (85), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 25/45 (55%)
Query: 45 ETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRAC 89
+ ++ F G++ A +I D+V G S GYGFV + + A RA
Sbjct: 17 DELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 31 SKIFVGGLAWETRTETMKHYFEQFGDILEA-VVITDRVTGKSKGYGFVTFKDPESARRAC 89
S IF+G L E + + F FG IL+ ++ D TG SKGY F+ F +++ A
Sbjct: 6 SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAI 65
Query: 90 E 90
E
Sbjct: 66 E 66
>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 = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 25/45 (55%)
Query: 45 ETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRAC 89
+ ++ F G++ A +I D+V G S GYGFV + + A RA
Sbjct: 34 DELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 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 = 37.7 bits (86), Expect = 0.006, Method: Composition-based stats.
Identities = 17/59 (28%), Positives = 32/59 (54%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN 91
+++G + ++ E + G ++ ++ D TG+SKGY F+ F+D ES+ A N
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 65
>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 = 0.009, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 34/59 (57%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN 91
+F+ L E + + F FG+++ A V D+ T SK +GFV++ +P SA+ A ++
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 37.4 bits (85), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 38/81 (46%), Gaps = 4/81 (4%)
Query: 31 SKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGK---SKGYGFVTFKDPESARR 87
S +F+ L + T ET+K F + G I + + S G+GFV +K PE A++
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 88 ACENPYP-VIDGRRANCNLAH 107
A + +DG + ++
Sbjct: 66 ALKQLQGHTVDGHKLEVRISE 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 = 37.0 bits (84), Expect = 0.011, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 29/58 (50%)
Query: 31 SKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRA 88
+ + V L + ++ F G++ A +I D+V G S GYGFV + + A RA
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 62
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 37.0 bits (84), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 19/44 (43%), Positives = 26/44 (59%), Gaps = 2/44 (4%)
Query: 45 ETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRA 88
E ++ F FG I A V+ + G+SKG+GFV F PE A +A
Sbjct: 30 ERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKA 71
>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 = 36.6 bits (83), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 32/59 (54%), Gaps = 2/59 (3%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTG--KSKGYGFVTFKDPESARRA 88
K+FVG + + ++ FEQ+G + E V+ DR +SKG FVTF ++A A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 36.6 bits (83), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 38/81 (46%), Gaps = 7/81 (8%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRA---- 88
+F+ L++++ E + +QFGD+ V+ T SKG F F E+A++
Sbjct: 18 VFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAA 77
Query: 89 ---CENPYPVIDGRRANCNLA 106
E +DGR+ +LA
Sbjct: 78 SLEAEGGGLKLDGRQLKVDLA 98
>pdb|3Q2S|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2S|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2T|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
pdb|3Q2T|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
Length = 229
Score = 36.2 bits (82), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 2/64 (3%)
Query: 29 KYSKIFVGGLAWETRTETMKHYFEQFG--DILEAVVITDRVTGKSKGYGFVTFKDPESAR 86
K +++G L W T E + G DILE +R G+SKG+ V S++
Sbjct: 67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSK 126
Query: 87 RACE 90
+ +
Sbjct: 127 KLMD 130
>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 = 36.2 bits (82), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 27/58 (46%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRAC 89
K+F+GGL + +K FG + ++ D TG SKGY F + D +A
Sbjct: 116 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 173
>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 = 35.8 bits (81), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 40/79 (50%), Gaps = 5/79 (6%)
Query: 30 YSKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTF---KDPESAR 86
+ +FV + ++T ++ FE +G I ++ + +GK +GY F+ + +D SA
Sbjct: 102 FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAY 161
Query: 87 RACENPYPVIDGRRANCNL 105
+ + IDGRR ++
Sbjct: 162 KHADGKK--IDGRRVLVDV 178
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 35.8 bits (81), Expect = 0.023, Method: Composition-based stats.
Identities = 17/50 (34%), Positives = 25/50 (50%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKD 81
K+F+GGL + +K FG + ++ D TG SKGY F + D
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVD 52
>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 = 23/63 (36%), Positives = 31/63 (49%), Gaps = 12/63 (19%)
Query: 45 ETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN-----------PY 93
E ++ F QFG + +AVV+ D G++ G GFV F AR+A E P
Sbjct: 111 ELLEQAFSQFGPVEKAVVVVDD-RGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPR 169
Query: 94 PVI 96
PVI
Sbjct: 170 PVI 172
Score = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 32/70 (45%), Gaps = 10/70 (14%)
Query: 29 KYSKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRA 88
+ ++FVG L + E K FE++G+ E + DR G+GF+ + +R
Sbjct: 21 QRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLE----SRTL 70
Query: 89 CENPYPVIDG 98
E +DG
Sbjct: 71 AEIAKAELDG 80
>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 = 0.028, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 10/75 (13%)
Query: 31 SKIFVGGLAWETRTET-MKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRAC 89
+ ++VGGL +T TET ++++F QFG+I V+ + + F+ F ++A A
Sbjct: 13 TTLYVGGLG-DTITETDLRNHFYQFGEIRTITVV------QRQQCAFIQFATRQAAEVAA 65
Query: 90 ENPYP--VIDGRRAN 102
E + +++GRR N
Sbjct: 66 EKSFNKLIVNGRRLN 80
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 35.8 bits (81), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 32/59 (54%), Gaps = 2/59 (3%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTG--KSKGYGFVTFKDPESARRA 88
K+FVG + + ++ FEQ+G + E V+ DR +SKG FVTF ++A A
Sbjct: 17 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 75
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRA 88
K+F+G ++ + ++ F FG I E ++ G S+G FVTF A+ A
Sbjct: 109 KLFIGMISKKCTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAFVTFTTRAMAQTA 164
>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 = 35.8 bits (81), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 27/58 (46%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRAC 89
K+F+GGL + +K FG + ++ D TG SKGY F + D +A
Sbjct: 98 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 155
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 35.4 bits (80), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 27/58 (46%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRAC 89
K+F+GGL + +K FG + ++ D TG SKGY F + D +A
Sbjct: 96 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 153
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
Length = 124
Score = 35.4 bits (80), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 16/67 (23%), Positives = 32/67 (47%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACENP 92
++VG + + + + ++ +F G I ++ D+ +G KGY ++ F + S A
Sbjct: 39 VYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMD 98
Query: 93 YPVIDGR 99
V GR
Sbjct: 99 ETVFRGR 105
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 35.4 bits (80), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 32/59 (54%), Gaps = 2/59 (3%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTG--KSKGYGFVTFKDPESARRA 88
K+FVG + + ++ FEQ+G + E V+ DR +SKG FVTF ++A A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Score = 29.6 bits (65), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRA 88
K+F+G ++ + ++ F FG I E ++ G S+G FVTF A+ A
Sbjct: 97 KLFIGMISKKCTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAFVTFTTRAMAQTA 152
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 35.4 bits (80), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 28/53 (52%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESA 85
+F LA R ++ +F G + + +I+DR + +SKG +V F + +S
Sbjct: 28 VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSV 80
>pdb|3P5T|L Chain L, Cfim25-Cfim68 Complex
pdb|3P5T|M Chain M, Cfim25-Cfim68 Complex
pdb|3P5T|N Chain N, Cfim25-Cfim68 Complex
pdb|3P5T|O Chain O, Cfim25-Cfim68 Complex
pdb|3P5T|P Chain P, Cfim25-Cfim68 Complex
pdb|3P5T|Q Chain Q, Cfim25-Cfim68 Complex
pdb|3P6Y|C Chain C, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|D Chain D, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|G Chain G, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|H Chain H, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|K Chain K, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|L Chain L, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|O Chain O, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|P Chain P, Cf Im25-Cf Im68-Uguaa Complex
Length = 90
Score = 35.4 bits (80), Expect = 0.039, Method: Composition-based stats.
Identities = 17/57 (29%), Positives = 27/57 (47%), Gaps = 2/57 (3%)
Query: 33 IFVGGLAWETRTETMKHYFEQFG--DILEAVVITDRVTGKSKGYGFVTFKDPESARR 87
+++G L W T E + G DILE +R G+SKG+ V S+++
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKK 60
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 35.0 bits (79), Expect = 0.046, Method: Composition-based stats.
Identities = 16/59 (27%), Positives = 31/59 (52%), Gaps = 5/59 (8%)
Query: 31 SKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRAC 89
SK+FVG + E ++ +F Q+G++++ + + + FVTF D + A+ C
Sbjct: 12 SKVFVGRCTEDMTAEELQQFFCQYGEVVDVF-----IPKPFRAFAFVTFADDKVAQSLC 65
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 34.7 bits (78), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 31 SKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRAC 89
S +FV L ++ + +K F G ++ A ++ D+ GKS+G G VTF+ A +A
Sbjct: 16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAI 73
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 34.3 bits (77), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 30 YSKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRA 88
+ K+FVG L + + ++ FE FG+I E ++ G SKG FV + A+ A
Sbjct: 15 HRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRG-PDGNSKGCAFVKYSSHAEAQAA 72
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 34.3 bits (77), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 28/60 (46%), Gaps = 6/60 (10%)
Query: 29 KYSKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRA 88
K ++ GG+A + M+ F FG I+E V + KGY FV F ESA A
Sbjct: 24 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHA 77
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In
Trinucleotide Repeat Containing 4 Variant
Length = 102
Score = 34.3 bits (77), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRA 88
K+FVG L + E ++ FE FG I E V+ G SKG FV F+ A+ A
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRG-PDGTSKGCAFVKFQTHAEAQAA 69
>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 = 34.3 bits (77), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 31/59 (52%), Gaps = 2/59 (3%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTG--KSKGYGFVTFKDPESARRA 88
K FVG + + ++ FEQ+G + E V+ DR +SKG FVTF ++A A
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Score = 30.0 bits (66), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRA 88
K+F+G ++ + ++ F FG I E ++ G S+G FVTF A+ A
Sbjct: 97 KLFIGXISKKCTENDIRVXFSSFGQIEECRILRG-PDGLSRGCAFVTFTTRAXAQTA 152
>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 = 33.9 bits (76), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 40/79 (50%), Gaps = 5/79 (6%)
Query: 30 YSKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTF---KDPESAR 86
+ +FV + ++T ++ FE +G I ++ + +GK +GY F+ + +D SA
Sbjct: 102 FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAY 161
Query: 87 RACENPYPVIDGRRANCNL 105
+ + IDGRR ++
Sbjct: 162 KHADGKK--IDGRRVLVDV 178
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 33.9 bits (76), Expect = 0.11, Method: Composition-based stats.
Identities = 15/59 (25%), Positives = 30/59 (50%), Gaps = 5/59 (8%)
Query: 31 SKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRAC 89
S +FVG + + ++ +F Q+GD+++ + + + FVTF D + A+ C
Sbjct: 6 SGVFVGRCTGDMTEDELREFFSQYGDVMDVF-----IPKPFRAFAFVTFADDQIAQSLC 59
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 33.5 bits (75), Expect = 0.11, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 30/58 (51%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACE 90
+FV G+ E E + F ++G+I + DR TG KGY V ++ + A+ A E
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 67
>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 = 33.1 bits (74), Expect = 0.15, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 30/58 (51%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACE 90
+FV G+ E E + F ++G+I + DR TG KGY V ++ + A+ A E
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 69
>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 = 33.1 bits (74), Expect = 0.16, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 30/58 (51%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACE 90
+FV G+ E E + F ++G+I + DR TG KGY V ++ + A+ A E
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 67
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 32.7 bits (73), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 26/99 (26%), Positives = 46/99 (46%), Gaps = 13/99 (13%)
Query: 31 SKIFVGGLAWETRTETMKHYFEQFGDILEAV--------VITDRVTGKSKGYGFVTFKDP 82
S I+V GL + + +F+Q G + + D+ TGK KG V+++DP
Sbjct: 16 SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 75
Query: 83 ESARRACENPYPVIDGRRANCNLAHLGAHHKKRPPLLHG 121
+A+ A E DG+ + + + +K+PP+ G
Sbjct: 76 PTAKAAVE----WFDGKDFQGSKLKV-SLARKKPPMNSG 109
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 32.0 bits (71), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 20/35 (57%)
Query: 54 FGDILEAVVITDRVTGKSKGYGFVTFKDPESARRA 88
FG + ++ TG+SKGYGF + +SA RA
Sbjct: 119 FGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA 153
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 32.0 bits (71), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 33/60 (55%), Gaps = 3/60 (5%)
Query: 31 SKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKS--KGYGFVTFKDPESARRA 88
SKI V + ++ ++ F FG+ L+ V + ++TG +G+GFV F + A++A
Sbjct: 16 SKILVRNIPFQANQREIRELFSTFGE-LKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKA 74
>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 = 32.0 bits (71), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 30/58 (51%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACE 90
+FV G+ E E + F ++G+I + DR TG KGY V ++ + A+ A E
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 83
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 32.0 bits (71), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 20/35 (57%)
Query: 54 FGDILEAVVITDRVTGKSKGYGFVTFKDPESARRA 88
FG + ++ TG+SKGYGF + +SA RA
Sbjct: 119 FGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA 153
>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 = 32.0 bits (71), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 20/35 (57%)
Query: 54 FGDILEAVVITDRVTGKSKGYGFVTFKDPESARRA 88
FG + ++ TG+SKGYGF + +SA RA
Sbjct: 117 FGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA 151
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 31.6 bits (70), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 6/52 (11%)
Query: 29 KYSKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFK 80
+ S++FVG L + E M+ FE++G E + K KG+GF+ +
Sbjct: 21 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI------HKDKGFGFIRLE 66
Score = 31.2 bits (69), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 1/47 (2%)
Query: 45 ETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACEN 91
E ++ F FG + AVVI D G+ G G V F +AR+A +
Sbjct: 111 ELLEEAFSVFGQVERAVVIVDD-RGRPSGKGIVEFSGKPAARKALDR 156
>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 = 31.6 bits (70), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 30/58 (51%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACE 90
+FV G+ E E + F ++G+I + DR TG KGY V ++ + A+ A E
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 67
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 31.2 bits (69), Expect = 0.58, Method: Composition-based stats.
Identities = 24/87 (27%), Positives = 40/87 (45%), Gaps = 11/87 (12%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRA-CE 90
KIFVG ++ ++ ++ FE+ G ++E V+ D Y FV + A+ A +
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQ 62
Query: 91 NPYPVIDGRRANCNLAHLGAHHKKRPP 117
+ G+R N L+ G KK P
Sbjct: 63 LNGKEVKGKRINVELSTKG--QKKSGP 87
>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 = 31.2 bits (69), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 30/58 (51%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACE 90
+FV G+ E E + F ++G+I + DR TG KGY V ++ + A+ A E
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 82
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 30.8 bits (68), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 27/57 (47%), Gaps = 1/57 (1%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRA 88
K+FVG L + E + F+ FG I E V+ G SKG FV F A+ A
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAA 72
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 30.8 bits (68), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 31/68 (45%), Gaps = 6/68 (8%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACENP 92
+ L++ + +K FE D LE +++ GKSKG ++ FK A + E
Sbjct: 102 LLAKNLSFNITEDELKEVFE---DALEIRLVSQ--DGKSKGIAYIEFKSEADAEKNLEEK 156
Query: 93 YPV-IDGR 99
IDGR
Sbjct: 157 QGAEIDGR 164
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 30.8 bits (68), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRA 88
K+F+ GL + E ++ + G + + ++T+R GK KG +V +++ A +A
Sbjct: 19 KLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRA-GKPKGLAYVEYENESQASQA 74
>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 = 30.8 bits (68), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 26/50 (52%), Gaps = 6/50 (12%)
Query: 31 SKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFK 80
S++FVG L + E M+ FE++G E + D KG+GF+ +
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLE 59
>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|X Chain X, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|Y Chain Y, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2V|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
pdb|1N52|B Chain B, Cap Binding Complex
pdb|1N54|B Chain B, Cap Binding Complex M7gpppg Free
pdb|3FEX|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex.
pdb|3FEY|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex
Length = 156
Score = 30.8 bits (68), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 4/74 (5%)
Query: 29 KYSKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRA 88
K ++VG L++ T E + F + GDI + ++ D++ + G+ FV + +R
Sbjct: 38 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEY----YSRAD 93
Query: 89 CENPYPVIDGRRAN 102
EN I+G R +
Sbjct: 94 AENAMRYINGTRLD 107
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 30.4 bits (67), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 30/61 (49%), Gaps = 9/61 (14%)
Query: 31 SKIFVGGLAWETRT-ETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRAC 89
S++F+G L + + E + F +G I++ + +GF+ F +P+S R A
Sbjct: 11 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAI 62
Query: 90 E 90
E
Sbjct: 63 E 63
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 30.4 bits (67), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 32/58 (55%), Gaps = 3/58 (5%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRAC 89
+I+VG L + RT+ ++ F ++G I + + + +R G + FV F+DP A A
Sbjct: 24 RIYVGNLPPDIRTKDIEDVFYKYGAIRD-IDLKNRRGGPP--FAFVEFEDPRDAEDAV 78
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 9/70 (12%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFV---TFKDPESARRAC 89
+ + L++ ET++ FE+ + + GKSKGY F+ +F+D + A +C
Sbjct: 18 LVLSNLSYSATEETLQEVFEK----ATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSC 73
Query: 90 ENPYPVIDGR 99
I+GR
Sbjct: 74 NKRE--IEGR 81
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 1/78 (1%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRA-CEN 91
+ V L + T ++++ FE++G + + + + T +G+ FV F D A+ A
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75
Query: 92 PYPVIDGRRANCNLAHLG 109
+DGR +A G
Sbjct: 76 DGAELDGRELRVQVARYG 93
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 31/68 (45%), Gaps = 6/68 (8%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACENP 92
+ L++ + +K FE D LE +++ GKSKG ++ FK A + E
Sbjct: 19 LLAKNLSFNITEDELKEVFE---DALEIRLVSQ--DGKSKGIAYIEFKSEADAEKNLEEK 73
Query: 93 YPV-IDGR 99
IDGR
Sbjct: 74 QGAEIDGR 81
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14
Complex
Length = 110
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 30/58 (51%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRACE 90
+FV + E + + ++ F +G+I + DR TG SKGY V ++ + A A E
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 86
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif In Trna Selenocysteine Associated Protein
Length = 104
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 29/57 (50%), Gaps = 2/57 (3%)
Query: 33 IFVGGLAWETRTETMKHYFEQ-FGDILEAVVITDRVTGKSKGYGFVTFKDPESARRA 88
+FVG L + + +F + + V+ D+ TG SKGYGFV F D +RA
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRA 67
>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 = 30.0 bits (66), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 5/50 (10%)
Query: 77 VTFKDPESARRACENPYPVIDGRRANCNLAHLG---AHHKKRPPLLHGNV 123
+TF +P R+ + Y VIDG A+C HLG +K+P L+ +
Sbjct: 46 LTFTEPLKMRKIDTDFYTVIDGTPADC--VHLGYRVILEEKKPDLVLSGI 93
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 30/61 (49%), Gaps = 9/61 (14%)
Query: 31 SKIFVGGLAWETRT-ETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRAC 89
S++F+G L + + E + F +G I++ + +GF+ F +P+S R A
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAI 74
Query: 90 E 90
E
Sbjct: 75 E 75
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 29.6 bits (65), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 31/59 (52%), Gaps = 6/59 (10%)
Query: 31 SKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRAC 89
++++VGGL T + F++FG I D V G S + ++ ++ ++A+ AC
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIR----TIDHVKGDS--FAYIQYESLDAAQAAC 70
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 30/61 (49%), Gaps = 9/61 (14%)
Query: 31 SKIFVGGLAWETRT-ETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRAC 89
S++F+G L + + E + F +G I++ + +GF+ F +P+S R A
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAI 74
Query: 90 E 90
E
Sbjct: 75 E 75
>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 = 28.9 bits (63), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 26/48 (54%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFK 80
+FV + E + + ++ F +G+I + DR TG SKGY V ++
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYE 122
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 28.9 bits (63), Expect = 3.7, Method: Composition-based stats.
Identities = 16/61 (26%), Positives = 30/61 (49%), Gaps = 9/61 (14%)
Query: 31 SKIFVGGLAWETRT-ETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRAC 89
S++F+G L + + E + F +G I++ + +GF+ F +P+S R A
Sbjct: 3 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAI 54
Query: 90 E 90
E
Sbjct: 55 E 55
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 28.5 bits (62), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 7/76 (9%)
Query: 32 KIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKS----KGYGFVTFKDPESARR 87
K+FVGGL + + + F +FG ++ V + KS KGY F+ F++ ES+ +
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLV--VDWPHKAESKSYFPPKGYAFLLFQE-ESSVQ 66
Query: 88 ACENPYPVIDGRRANC 103
A + DG+ C
Sbjct: 67 ALIDACLEEDGKLYLC 82
>pdb|1WEL|A Chain A, Solution Structure Of Rna Binding Domain In Np_006038
Length = 124
Score = 28.5 bits (62), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 12/49 (24%), Positives = 28/49 (57%)
Query: 33 IFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKD 81
+++ GL +E + + +F++ + +++ I GK+ G GFV F++
Sbjct: 28 VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRN 76
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 27.7 bits (60), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 5/74 (6%)
Query: 29 KYSKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRA 88
K ++VG L++ T E + F + GDI + ++ D++ + G+ FV + +R
Sbjct: 17 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMK-TACGFCFVEY----YSRAD 71
Query: 89 CENPYPVIDGRRAN 102
EN I+G R +
Sbjct: 72 AENAMRYINGTRLD 85
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 27.7 bits (60), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 29/62 (46%), Gaps = 8/62 (12%)
Query: 29 KYSKIFVGGLAWETRTETMKHYFEQFGDILEAVVITDRVTGKSKGYGFVTFKDPESARRA 88
K +FV LA E ++ F QFG + +RV K K Y F+ F + + A +A
Sbjct: 10 KVKVLFVRNLANTVTEEILEKAFSQFGKL-------ERVK-KLKDYAFIHFDERDGAVKA 61
Query: 89 CE 90
E
Sbjct: 62 ME 63
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 0.135 0.422
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,424,679
Number of Sequences: 62578
Number of extensions: 261638
Number of successful extensions: 659
Number of sequences better than 100.0: 149
Number of HSP's better than 100.0 without gapping: 107
Number of HSP's successfully gapped in prelim test: 42
Number of HSP's that attempted gapping in prelim test: 512
Number of HSP's gapped (non-prelim): 171
length of query: 274
length of database: 14,973,337
effective HSP length: 97
effective length of query: 177
effective length of database: 8,903,271
effective search space: 1575878967
effective search space used: 1575878967
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: 51 (24.3 bits)