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= 029737
(189 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 = 113 bits (282), Expect = 8e-26, Method: Compositional matrix adjust.
Identities = 51/85 (60%), Positives = 65/85 (76%)
Query: 19 DTTYTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAM 78
DTT+TK+FVGGL + T ++ KYFE FG+I EAVVITD+ TG+S+GYGFVT + AA
Sbjct: 14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAE 73
Query: 79 KACVDAAPVIDGRRANCNLACLGVQ 103
+AC D P+IDGR+AN NLA LG +
Sbjct: 74 RACKDPNPIIDGRKANVNLAYLGAK 98
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 75.1 bits (183), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 34/87 (39%), Positives = 52/87 (59%), Gaps = 1/87 (1%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACVD 83
K+FVGGL W T +ET+ YF Q+GE+++ V++ DK T +S+G+GFV F++P
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 84 AAPVIDGRRANCN-LACLGVQRSKPST 109
+DGR + G+Q S PS+
Sbjct: 78 RPHTLDGRNIDPKPCTPRGMQPSGPSS 104
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 67.8 bits (164), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 34/88 (38%), Positives = 56/88 (63%), Gaps = 2/88 (2%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACVD 83
K+FVGGL+++T ++++E+ F ++G+I E VV+ D+ T RS+G+GFVTF + A A +
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 84 -AAPVIDGRRANCNLACLGV-QRSKPST 109
+DGR+ + A RS PS+
Sbjct: 74 MNGKSVDGRQIRVDQAGKSSDNRSGPSS 101
>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
pdb|3S7R|B Chain B, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
Length = 87
Score = 67.0 bits (162), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 27/68 (39%), Positives = 44/68 (64%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACVD 83
K FVGGL+W+T K+ ++ YF +FGE+++ + D TGRS+G+GF+ F++ + K
Sbjct: 13 KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQ 72
Query: 84 AAPVIDGR 91
+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 = 66.2 bits (160), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 30/74 (40%), Positives = 47/74 (63%), Gaps = 5/74 (6%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACVDA 84
+F+GGL+W+T K+ ++ YF +FGE+++ + D TGRS+G+GFV F+E E+ K
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 85 -----APVIDGRRA 93
VID +RA
Sbjct: 62 EHKLNGKVIDPKRA 75
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 65.9 bits (159), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 29/75 (38%), Positives = 47/75 (62%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACVD 83
K+F+GGL+W+T +E + +YF QFGE+ E +V+ D T RS+G+GFVTF + K
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 86
Query: 84 AAPVIDGRRANCNLA 98
+ +D + + +A
Sbjct: 87 SRHELDSKTIDPKVA 101
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleaoproteins A2B1
Length = 116
Score = 65.5 bits (158), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 32/71 (45%), Positives = 51/71 (71%), Gaps = 2/71 (2%)
Query: 22 YTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKAC 81
+ K+F+GGL++ET +E++ Y+EQ+G++ + VV+ D A+ RS+G+GFVTF A + A
Sbjct: 27 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTF-SSMAEVDAA 85
Query: 82 VDAAP-VIDGR 91
+ A P IDGR
Sbjct: 86 MAARPHSIDGR 96
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 65.5 bits (158), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 29/75 (38%), Positives = 47/75 (62%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACVD 83
K+F+GGL+W+T +E + +YF QFGE+ E +V+ D T RS+G+GFVTF + K
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 84 AAPVIDGRRANCNLA 98
+ +D + + +A
Sbjct: 62 SRHELDSKTIDPKVA 76
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 63.5 bits (153), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 29/74 (39%), Positives = 44/74 (59%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACVDA 84
+FVGGL+ T E ++ YFEQFG++ +A+++ DK T R +G+GFVTF + K C
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 85 APVIDGRRANCNLA 98
I+ + C A
Sbjct: 62 FHEINNKMVECKKA 75
>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 = 1e-10, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 48/68 (70%), Gaps = 1/68 (1%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACVD 83
K+F+GGL W+T ++ + +YF ++G + + ++ D ATGRS+G+GF++F +P +++ V
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKP-SSVDEVVK 63
Query: 84 AAPVIDGR 91
++DG+
Sbjct: 64 TQHILDGK 71
Score = 57.4 bits (137), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 41/58 (70%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKAC 81
K+FVGG+ + + + E++F Q+G I++A ++ DK TG+S+G+GFVT+ +A + C
Sbjct: 89 KIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVC 146
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 61.6 bits (148), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 31/75 (41%), Positives = 45/75 (60%), Gaps = 1/75 (1%)
Query: 23 TKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACV 82
+ + V GL W+T ++ +++YF FGE+L V D TG SKG+GFV F E E +K +
Sbjct: 16 SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKV-M 74
Query: 83 DAAPVIDGRRANCNL 97
+IDGR +C L
Sbjct: 75 SQRHMIDGRWCDCKL 89
>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
pdb|1U1K|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt 7da
Ggg); A Human Telomeric Repeat Containing
7-Deaza-Adenine
pdb|1U1L|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt Prn
Ggg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1M|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 7gu
Gg); A Human Telomeric Repeat Containing
7-Deaza-Guanine
pdb|1U1N|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta
(Prn) Gg); A Human Telomeric Repeat Containing
Nebularine
pdb|1U1O|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggttag(Di)g); A Human Telomeric Repeat Containing
Inosine
pdb|1U1P|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 2pr
Gg); A Human Telomeric Repeat Containing 2-Aminopurine
pdb|1U1Q|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggtta(Di)gg); A Human Telomeric Repeat Containing
Inosine
pdb|1U1R|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggttag(2pr) G); A Human Telomeric Repeat
Containing 2-Aminopurine
Length = 196
Score = 60.8 bits (146), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 30/69 (43%), Positives = 48/69 (69%), Gaps = 2/69 (2%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACVD 83
K+F+GGL++ET E++ +FEQ+G + + VV+ D T RS+G+GFVT+ E + A ++
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE-EVDAAMN 73
Query: 84 AAP-VIDGR 91
A P +DGR
Sbjct: 74 ARPHKVDGR 82
Score = 60.5 bits (145), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 47/77 (61%), Gaps = 2/77 (2%)
Query: 21 TYTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKA 80
T K+FVGG+ +T++ + YFEQ+G+I ++TD+ +G+ +G+ FVTF + ++ K
Sbjct: 103 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 162
Query: 81 CVDAAPVIDGRRANCNL 97
+ ++G NC +
Sbjct: 163 VIQKYHTVNGH--NCEV 177
>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat
Containing 6-Methyl-8-(2-
Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi)
Length = 195
Score = 60.8 bits (146), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 30/69 (43%), Positives = 48/69 (69%), Gaps = 2/69 (2%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACVD 83
K+F+GGL++ET E++ +FEQ+G + + VV+ D T RS+G+GFVT+ E + A ++
Sbjct: 14 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE-EVDAAMN 72
Query: 84 AAP-VIDGR 91
A P +DGR
Sbjct: 73 ARPHKVDGR 81
Score = 60.5 bits (145), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 47/77 (61%), Gaps = 2/77 (2%)
Query: 21 TYTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKA 80
T K+FVGG+ +T++ + YFEQ+G+I ++TD+ +G+ +G+ FVTF + ++ K
Sbjct: 102 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 161
Query: 81 CVDAAPVIDGRRANCNL 97
+ ++G NC +
Sbjct: 162 VIQKYHTVNGH--NCEV 176
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 60.5 bits (145), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 30/69 (43%), Positives = 48/69 (69%), Gaps = 2/69 (2%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACVD 83
K+F+GGL++ET E++ +FEQ+G + + VV+ D T RS+G+GFVT+ E + A ++
Sbjct: 16 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE-EVDAAMN 74
Query: 84 AAP-VIDGR 91
A P +DGR
Sbjct: 75 ARPHKVDGR 83
Score = 60.5 bits (145), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 47/77 (61%), Gaps = 2/77 (2%)
Query: 21 TYTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKA 80
T K+FVGG+ +T++ + YFEQ+G+I ++TD+ +G+ +G+ FVTF + ++ K
Sbjct: 104 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 163
Query: 81 CVDAAPVIDGRRANCNL 97
+ ++G NC +
Sbjct: 164 VIQKYHTVNGH--NCEV 178
>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 = 60.5 bits (145), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 47/77 (61%), Gaps = 2/77 (2%)
Query: 21 TYTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKA 80
T K+FVGG+ +T++ + YFEQ+G+I ++TD+ +G+ +G+ FVTF + ++ K
Sbjct: 96 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 155
Query: 81 CVDAAPVIDGRRANCNL 97
+ ++G NC +
Sbjct: 156 VIQKYHTVNGH--NCEV 170
Score = 60.5 bits (145), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 30/69 (43%), Positives = 48/69 (69%), Gaps = 2/69 (2%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACVD 83
K+F+GGL++ET E++ +FEQ+G + + VV+ D T RS+G+GFVT+ E + A ++
Sbjct: 8 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE-EVDAAMN 66
Query: 84 AAP-VIDGR 91
A P +DGR
Sbjct: 67 ARPHKVDGR 75
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 60.5 bits (145), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 30/69 (43%), Positives = 48/69 (69%), Gaps = 2/69 (2%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACVD 83
K+F+GGL++ET E++ +FEQ+G + + VV+ D T RS+G+GFVT+ E + A ++
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE-EVDAAMN 73
Query: 84 AAP-VIDGR 91
A P +DGR
Sbjct: 74 ARPHKVDGR 82
Score = 60.5 bits (145), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 47/77 (61%), Gaps = 2/77 (2%)
Query: 21 TYTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKA 80
T K+FVGG+ +T++ + YFEQ+G+I ++TD+ +G+ +G+ FVTF + ++ K
Sbjct: 103 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 162
Query: 81 CVDAAPVIDGRRANCNL 97
+ ++G NC +
Sbjct: 163 VIQKYHTVNGH--NCEV 177
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 60.1 bits (144), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 30/69 (43%), Positives = 48/69 (69%), Gaps = 2/69 (2%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACVD 83
K+F+GGL++ET E++ +FEQ+G + + VV+ D T RS+G+GFVT+ E + A ++
Sbjct: 13 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE-EVDAAMN 71
Query: 84 AAP-VIDGR 91
A P +DGR
Sbjct: 72 ARPHKVDGR 80
Score = 60.1 bits (144), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 47/77 (61%), Gaps = 2/77 (2%)
Query: 21 TYTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKA 80
T K+FVGG+ +T++ + YFEQ+G+I ++TD+ +G+ +G+ FVTF + ++ K
Sbjct: 101 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 160
Query: 81 CVDAAPVIDGRRANCNL 97
+ ++G NC +
Sbjct: 161 VIQKYHTVNGH--NCEV 175
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 55.8 bits (133), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 39/63 (61%)
Query: 18 GDTTYTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAA 77
G + + ++VG L + ++ + FE FG+I V++ D TGRSKGYGF+TF + E A
Sbjct: 1 GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60
Query: 78 MKA 80
+A
Sbjct: 61 RRA 63
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 55.8 bits (133), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 35/92 (38%), Positives = 47/92 (51%), Gaps = 6/92 (6%)
Query: 20 TTYTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMK 79
+ + VFVG L+ E E ++ F FG+I +A V+ D ATG+SKGYGFV+F A
Sbjct: 13 SNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAEN 72
Query: 80 ACVD-AAPVIDGRRANCNLACLGVQRSKPSTP 110
A V + GR+ N A KP P
Sbjct: 73 AIVHMGGQWLGGRQIRTNWATR-----KPPAP 99
>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 = 53.9 bits (128), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 35/93 (37%), Positives = 46/93 (49%), Gaps = 6/93 (6%)
Query: 20 TTYTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMK 79
+ + VFVG L+ E E ++ F FG I +A V+ D ATG+SKGYGFV+F A
Sbjct: 13 SNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAEN 72
Query: 80 ACVD-AAPVIDGRRANCNLACLGVQRSKPSTPK 111
A + GR+ N A KP PK
Sbjct: 73 AIQQMGGQWLGGRQIRTNWATR-----KPPAPK 100
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 52.8 bits (125), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 24/57 (42%), Positives = 35/57 (61%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKA 80
+++VG L + ++ + FE FG I ++ D TGRSKGYGF+TF + E A KA
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKA 84
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 50.8 bits (120), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 37/60 (61%), Gaps = 1/60 (1%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACVD 83
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|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 50.1 bits (118), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 38/62 (61%)
Query: 19 DTTYTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAM 78
D K+F+G + ++ ++ FE+FG+I E V+ D+ TG KG F+T+ E E+A+
Sbjct: 10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESAL 69
Query: 79 KA 80
KA
Sbjct: 70 KA 71
>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 = 50.1 bits (118), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 28/82 (34%), Positives = 45/82 (54%), Gaps = 5/82 (6%)
Query: 23 TKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTF---REPEAAMK 79
T + V L + T +T+ + FE++G + + + D+ T S+G+ FV F R+ E AM
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 80 ACVDAAPVIDGRRANCNLACLG 101
A +D A V+DGR +A G
Sbjct: 108 A-MDGA-VLDGRELRVQMARYG 127
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 37/62 (59%)
Query: 19 DTTYTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAM 78
D + VFVG + +E +E ++ F + G ++ ++ D+ TG+ KGYGF +++ E A+
Sbjct: 5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETAL 64
Query: 79 KA 80
A
Sbjct: 65 SA 66
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 30/93 (32%), Positives = 48/93 (51%), Gaps = 9/93 (9%)
Query: 23 TKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTF---REPEAAMK 79
T + V L + T +T+ + FE++G + + + D+ T S+G+ FV F R+ E AM
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 80 ACVDAAPVIDGRRANCNLACLGVQRSKPSTPKH 112
A +D A V+DGR +A G +P H
Sbjct: 131 A-MDGA-VLDGRELRVQMARYG----RPPDSHH 157
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 36/59 (61%)
Query: 23 TKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKAC 81
K+FVGG+ + + +YF++FG + E V+I D R +G+GF+TF + ++ +A
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV 69
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 48.1 bits (113), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 35/63 (55%)
Query: 18 GDTTYTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAA 77
G + + +++ GL T + + K + +G+I+ I DK T + KGYGFV F P AA
Sbjct: 1 GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60
Query: 78 MKA 80
KA
Sbjct: 61 QKA 63
>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 = 48.1 bits (113), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 22/56 (39%), Positives = 35/56 (62%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMK 79
K+FVGGL+ +T +E + +YF FGE+ + D T + +G+ F+TF+E E K
Sbjct: 3 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKK 58
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 47.8 bits (112), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 39/68 (57%), Gaps = 4/68 (5%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACVD 83
++FV L++ + +E +EK F +G + E D T + KG+ FVTF PE A+KA +
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 84 AAPVIDGR 91
+DG+
Sbjct: 70 ----VDGQ 73
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 47.4 bits (111), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 38/66 (57%), Gaps = 3/66 (4%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFR---EPEAAMKAC 81
++V GL ++ ME+ F Q+G I+ + ++ D+ATG S+G GF+ F E E A+K
Sbjct: 93 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 152
Query: 82 VDAAPV 87
P+
Sbjct: 153 NGQKPL 158
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 30/59 (50%)
Query: 23 TKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKAC 81
T + V L ++ + F G+I ++ DK TG+S GYGFV + +P A KA
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI 63
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 47.4 bits (111), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 30/77 (38%), Positives = 44/77 (57%), Gaps = 8/77 (10%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPE---AAMKAC 81
+FV GL+ +T +ET++ E F + A ++TD+ TG SKG+GFV F E AA +A
Sbjct: 18 LFVKGLSEDTTEETLK---ESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAM 74
Query: 82 VDAAPVIDGRRANCNLA 98
D IDG + + A
Sbjct: 75 EDGE--IDGNKVTLDWA 89
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 46.6 bits (109), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 38/66 (57%), Gaps = 3/66 (4%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFR---EPEAAMKAC 81
++V GL ++ ME+ F Q+G I+ + ++ D+ATG S+G GF+ F E E A+K
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 82 VDAAPV 87
P+
Sbjct: 64 NGQKPL 69
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 46.6 bits (109), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 34/55 (61%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMK 79
+FVGGL+ +T +E + +YF FGE+ + D T + +G+ F+TF+E E K
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKK 56
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 46.2 bits (108), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 36/62 (58%)
Query: 19 DTTYTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAM 78
D K+FVG + ++ ++ FE+FG I E V+ D+ TG KG F+T+ ++A+
Sbjct: 12 DHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSAL 71
Query: 79 KA 80
KA
Sbjct: 72 KA 73
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 46.2 bits (108), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/62 (38%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 19 DTTYTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAM 78
D T+ +FVG L ET+ F+ F L V+ D TG S+GYGFV+F + A
Sbjct: 85 DDTFN-LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQ 143
Query: 79 KA 80
A
Sbjct: 144 NA 145
>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 = 46.2 bits (108), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 30/80 (37%), Positives = 40/80 (50%), Gaps = 1/80 (1%)
Query: 21 TYTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKA 80
++ VFVG L+ E + F FG I +A V+ D ATG+SKGYGFV+F A A
Sbjct: 5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENA 64
Query: 81 CVD-AAPVIDGRRANCNLAC 99
+ GR+ N A
Sbjct: 65 IQQMGGQWLGGRQIRTNWAT 84
>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 = 2e-05, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 29/57 (50%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKA 80
+FVG L ET+ F+ F L V+ D TG S+GYGFV+F + A A
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNA 59
>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 = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/47 (44%), Positives = 31/47 (65%), Gaps = 1/47 (2%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTF 71
VFVGG+ + + +F ++G + E +ITD+ TG SKGYGFV+F
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 57
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 21/47 (44%), Positives = 31/47 (65%), Gaps = 1/47 (2%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTF 71
VFVGG+ + + +F ++G + E +ITD+ TG SKGYGFV+F
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 58
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 21/47 (44%), Positives = 31/47 (65%), Gaps = 1/47 (2%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTF 71
VFVGG+ + + +F ++G + E +ITD+ TG SKGYGFV+F
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 57
>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
pdb|2QFJ|B Chain B, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
Length = 216
Score = 44.3 bits (103), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 34/60 (56%)
Query: 22 YTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKAC 81
+ +++V + + + ++ FE FG+I A + D TG+ KGYGF+ + + +++ A
Sbjct: 125 FNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAV 184
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 37/70 (52%)
Query: 23 TKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACV 82
++V+VG + +E ++T+ + F FG I + D T + KG+ FV + PEAA A
Sbjct: 29 SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 88
Query: 83 DAAPVIDGRR 92
V+ G R
Sbjct: 89 QMNSVMLGGR 98
>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 = 43.5 bits (101), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 36/65 (55%), Gaps = 3/65 (4%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFR---EPEAAMKAC 81
++V GL ++ +E+ F Q+G I+ + ++ D+ TG S+G GF+ F E E A+K
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 82 VDAAP 86
P
Sbjct: 151 NGQKP 155
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 30/59 (50%)
Query: 23 TKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKAC 81
T + V L +E F GEI ++ DK TG+S GYGFV + +P+ A KA
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61
>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 = 6e-05, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 43/85 (50%), Gaps = 6/85 (7%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACVDA 84
+ V L+ +T++ +++ F FG I + DK TG+SKG+ F++F E A +A
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV 77
Query: 85 APVIDGRRANCNLACLGVQRSKPST 109
+ + L V+ +KPST
Sbjct: 78 SGF------GYDHLILNVEWAKPST 96
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 43.5 bits (101), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 32/99 (32%), Positives = 46/99 (46%), Gaps = 16/99 (16%)
Query: 20 TTYTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMK 79
TT ++VGGLA E + + F FG+I + + D T + +G+ FV F E
Sbjct: 10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE---- 65
Query: 80 ACVDAAPVID--------GRRANCNLA-CLGVQRSKPST 109
DAA ID GR NLA + ++ S PS+
Sbjct: 66 ---DAAAAIDNMNESELFGRTIRVNLAKPMRIKESGPSS 101
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 43.1 bits (100), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 30/49 (61%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFRE 73
++VG L + E +++ F QFG++ +I D+ T + KG+GFV +E
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE 52
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
28
Length = 111
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 29/89 (32%), Positives = 47/89 (52%), Gaps = 10/89 (11%)
Query: 19 DTTYTK-VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAA 77
D T K VF+ L++++++E + + +QFG++ V+ T SKG F F EAA
Sbjct: 11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAA 70
Query: 78 MKACVDAAPV--------IDGRRANCNLA 98
K C+ AA + +DGR+ +LA
Sbjct: 71 QK-CLAAASLEAEGGGLKLDGRQLKVDLA 98
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 30/89 (33%), Positives = 40/89 (44%), Gaps = 15/89 (16%)
Query: 18 GDTTYTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAA 77
G TT ++VGGLA E + + F FG+I + + D T + +G+ FV F E
Sbjct: 1 GSTTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE-- 58
Query: 78 MKACVDAAPVID--------GRRANCNLA 98
DAA ID GR NLA
Sbjct: 59 -----DAAAAIDNMNESELFGRTIRVNLA 82
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 30/58 (51%)
Query: 23 TKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKA 80
T + V L ++ + F G+I ++ DK TG+S GYGFV + +P A KA
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
>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 = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 33/60 (55%)
Query: 22 YTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKAC 81
+ +++V + + + ++ FE FG+I + D TG+ KGYGF+ + + +++ A
Sbjct: 110 FNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAV 169
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 36/69 (52%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACVD 83
+V+VG + +E ++T+ + F FG I + D T + KG+ FV + PEAA A
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 84 AAPVIDGRR 92
V+ G R
Sbjct: 75 MNSVMLGGR 83
>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 = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 5/65 (7%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACVDA 84
V+VG + + + + +E +F G I ++ DK +G KGY ++ F E + VDA
Sbjct: 39 VYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAE-----RNSVDA 93
Query: 85 APVID 89
A +D
Sbjct: 94 AVAMD 98
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/59 (40%), Positives = 31/59 (52%), Gaps = 2/59 (3%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACVD 83
++V L E + K F FG I A V+ + GRSKG+GFV F PE A KA +
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTE 74
>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 = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 32/56 (57%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKA 80
V++G + ++ +E + G ++ ++ D TGRSKGY F+ FR+ E++ A
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 62
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 29/87 (33%), Positives = 39/87 (44%), Gaps = 15/87 (17%)
Query: 20 TTYTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMK 79
TT ++VGGLA E + + F FG+I + + D T + +G+ FV F E
Sbjct: 61 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE---- 116
Query: 80 ACVDAAPVID--------GRRANCNLA 98
DAA ID GR NLA
Sbjct: 117 ---DAAAAIDNMNESELFGRTIRVNLA 140
>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 = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 33/60 (55%)
Query: 22 YTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKAC 81
+ +++V + + + ++ FE FG+I + D TG+ KGYGF+ + + +++ A
Sbjct: 109 FNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAV 168
Score = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 34/69 (49%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACVD 83
+V+VG + +E ++T+ + F FG I D T + KG+ FV + PEAA A
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 84 AAPVIDGRR 92
V G R
Sbjct: 74 XNSVXLGGR 82
>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 = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 29/87 (33%), Positives = 39/87 (44%), Gaps = 15/87 (17%)
Query: 20 TTYTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMK 79
TT ++VGGLA E + + F FG+I + + D T + +G+ FV F E
Sbjct: 5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE---- 60
Query: 80 ACVDAAPVID--------GRRANCNLA 98
DAA ID GR NLA
Sbjct: 61 ---DAAAAIDNMNESELFGRTIRVNLA 84
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 32/56 (57%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKA 80
V++G + ++ +E + G ++ ++ D TGRSKGY F+ FR+ E++ A
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60
>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 = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 32/56 (57%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKA 80
V++G + ++ +E + G ++ ++ D TGRSKGY F+ FR+ E++ A
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 61
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 43/76 (56%), Gaps = 7/76 (9%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRS----KGYGFVTFREPEAAMK 79
KVFVGGL + ++ + F +FG ++ V KA +S KGY F+ F+E E++++
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLV--VDWPHKAESKSYFPPKGYAFLLFQE-ESSVQ 66
Query: 80 ACVDAAPVIDGRRANC 95
A +DA DG+ C
Sbjct: 67 ALIDACLEEDGKLYLC 82
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 14/53 (26%), Positives = 31/53 (58%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAA 77
V+V L + + + F ++G++++ ++ DK T +SKG F+ F + ++A
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSA 71
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 40.4 bits (93), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 29 GLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACVDAAPV- 87
GL+ T + + + F ++G I + ++ D+ + RS+G+ FV F + A +A A +
Sbjct: 53 GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME 112
Query: 88 IDGRRANCNLA 98
+DGRR + +
Sbjct: 113 LDGRRIRVDFS 123
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 40.0 bits (92), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 27 VGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACVDAAP 86
V GL+ T + + + F ++G I + ++ D+ + RS+G+ FV F + A +A A
Sbjct: 17 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 76
Query: 87 V-IDGRRANCNLA 98
+ +DGRR + +
Sbjct: 77 MELDGRRIRVDFS 89
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 40.0 bits (92), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 32/58 (55%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKAC 81
+++ GL ++ +E F +FG I+ + V+ D+ TG S+G F+ F + A +A
Sbjct: 90 NLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 28/59 (47%)
Query: 23 TKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKAC 81
T + V L ++ + F GE+ A +I DK G S GYGFV + + A +A
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
>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 = 40.0 bits (92), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 22/89 (24%), Positives = 45/89 (50%), Gaps = 5/89 (5%)
Query: 18 GDTTYTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAA 77
GD + +FV + ++T + + + FE +G I ++ K +G+ +GY F+ + E E
Sbjct: 99 GDA-FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEY-EHERD 156
Query: 78 MKACVDAAPVIDGRRANCNLACLGVQRSK 106
M + A DG++ + + V+R +
Sbjct: 157 MHSAYKHA---DGKKIDGRRVLVDVERGR 182
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 40.0 bits (92), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 37/64 (57%), Gaps = 2/64 (3%)
Query: 19 DTTYTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATG--RSKGYGFVTFREPEA 76
D K+FVG + ++ + + FEQ+G + E V+ D++ +SKG FVTF +A
Sbjct: 12 DLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKA 71
Query: 77 AMKA 80
A++A
Sbjct: 72 ALEA 75
Score = 29.6 bits (65), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTF 71
K+F+G ++ + + + F FG+I E ++ G S+G FVTF
Sbjct: 109 KLFIGMISKKCTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAFVTF 155
>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 = 40.0 bits (92), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 32/58 (55%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKAC 81
+++ GL ++ +E F +FG I+ + V+ D+ TG S+G F+ F + A +A
Sbjct: 90 NLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 28/59 (47%)
Query: 23 TKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKAC 81
T + V L ++ + F GE+ A +I DK G S GYGFV + + A +A
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 40.0 bits (92), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 1/64 (1%)
Query: 18 GDTTYTKVFVGGLAWETQKETMEKYFEQFGEILEAV-VITDKATGRSKGYGFVTFREPEA 76
G + + +F+G L E ++ + F FG IL+ ++ D TG SKGY F+ F +A
Sbjct: 1 GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60
Query: 77 AMKA 80
+ A
Sbjct: 61 SDAA 64
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 40.0 bits (92), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 8/63 (12%)
Query: 18 GDTTYTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAA 77
G + K+F+G L E ++ + FEQ+G++LE +I K YGFV + AA
Sbjct: 4 GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAA 55
Query: 78 MKA 80
A
Sbjct: 56 EDA 58
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 40.0 bits (92), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 27 VGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACVDAAP 86
V GL+ T + + + F ++G I + ++ D+ + RS+G+ FV F + A +A A
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 87 V-IDGRRANCNLA 98
+ +DGRR + +
Sbjct: 80 MELDGRRIRVDFS 92
>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 = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/82 (32%), Positives = 37/82 (45%), Gaps = 15/82 (18%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACVDA 84
++VGGLA E + + F FG+I + + D T + +G+ FV F E DA
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE-------DA 57
Query: 85 APVID--------GRRANCNLA 98
A ID GR NLA
Sbjct: 58 AAAIDNMNESELFGRTIRVNLA 79
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 29/57 (50%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKA 80
+F+ L E + F FG ++ A V DK T SK +GFV+F P++A A
Sbjct: 42 NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVA 98
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 39/68 (57%), Gaps = 3/68 (4%)
Query: 39 MEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKAC--VDAAPVIDGRRANCN 96
+ + FE++G I ++ D+ T +S+GYGFV F+ +A +A ++ +++ +R
Sbjct: 59 LRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILN-KRLKVA 117
Query: 97 LACLGVQR 104
LA G QR
Sbjct: 118 LAASGHQR 125
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 28/91 (30%), Positives = 46/91 (50%), Gaps = 4/91 (4%)
Query: 21 TYTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKA 80
T ++ V + + + + + F QFG+IL+ +I ++ SKG+GFVTF A +A
Sbjct: 14 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRA 71
Query: 81 CVD-AAPVIDGRRANCNLACLGV-QRSKPST 109
V++GR+ N A V S PS+
Sbjct: 72 REKLHGTVVEGRKIEVNNATARVMTNSGPSS 102
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 31/57 (54%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKAC 81
V+VGGL + + + + F Q G ++ + D+ TG+ +GYGFV F E A A
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 74
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 36/59 (61%), Gaps = 2/59 (3%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATG--RSKGYGFVTFREPEAAMKA 80
K+FVG + ++ + + FEQ+G + E V+ D++ +SKG FVTF +AA++A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Score = 29.3 bits (64), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTF 71
K+F+G ++ + + + F FG+I E ++ G S+G FVTF
Sbjct: 97 KLFIGMISKKCTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAFVTF 143
>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 = 0.002, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 37/65 (56%), Gaps = 1/65 (1%)
Query: 29 GLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACVDAAPV- 87
GL+ T + + + F ++G I + ++ D+ + RS+G+ FV F + A +A A +
Sbjct: 22 GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME 81
Query: 88 IDGRR 92
+DGRR
Sbjct: 82 LDGRR 86
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 42/88 (47%), Gaps = 11/88 (12%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACVD 83
K+FVG ++ + + FE+ G ++E V+ D Y FV E EA KA +
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHM-EKEADAKAAIA 61
Query: 84 A--APVIDGRRANCNLACLGVQRSKPST 109
+ G+R N L+ G ++S PS+
Sbjct: 62 QLNGKEVKGKRINVELSTKGQKKSGPSS 89
>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 = 0.002, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 36/59 (61%), Gaps = 2/59 (3%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATG--RSKGYGFVTFREPEAAMKA 80
K+FVG + ++ + + FEQ+G + E V+ D++ +SKG FVTF +AA++A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
>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 = 0.002, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 28/59 (47%)
Query: 23 TKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKAC 81
T + V L ++ + F GE+ A +I DK G S GYGFV + + A +A
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 63
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 40/77 (51%), Gaps = 3/77 (3%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACVD 83
++ V + + + + + F QFG+IL+ +I ++ SKG+GFVTF A +A
Sbjct: 31 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREK 88
Query: 84 -AAPVIDGRRANCNLAC 99
V++GR+ N A
Sbjct: 89 LHGTVVEGRKIEVNNAT 105
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKA 80
VFVG L ++E + + F Q G + + + D+ G+ K +GFV F+ PE+ A
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYA 73
>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 = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 28/59 (47%)
Query: 23 TKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKAC 81
T + V L ++ + F GE+ A +I DK G S GYGFV + + A +A
Sbjct: 20 TNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 78
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/87 (22%), Positives = 43/87 (49%), Gaps = 4/87 (4%)
Query: 20 TTYTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMK 79
+ +FV + ++T + + + FE +G I ++ K +G+ +GY F+ + E E M
Sbjct: 100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEY-EHERDMH 158
Query: 80 ACVDAAPVIDGRRANCNLACLGVQRSK 106
+ A DG++ + + V+R +
Sbjct: 159 SAYKHA---DGKKIDGRRVLVDVERGR 182
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 42/87 (48%), Gaps = 12/87 (13%)
Query: 18 GDTTYT---KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTF--R 72
G+ T+T ++FVG L + +E M K FE++G+ E + D KG+GF+ R
Sbjct: 15 GEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETR 68
Query: 73 EPEAAMKACVDAAPVIDGRRANCNLAC 99
K +D P + G++ AC
Sbjct: 69 TLAEIAKVELDNMP-LRGKQLRVRFAC 94
Score = 33.5 bits (75), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 26/55 (47%), Gaps = 1/55 (1%)
Query: 27 VGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKAC 81
V L E +E+ F FG++ AVVI D GR G G V F AA KA
Sbjct: 101 VRNLPQYVSNELLEEAFSVFGQVERAVVIVDD-RGRPSGKGIVEFSGKPAARKAL 154
>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 = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 35/59 (59%), Gaps = 2/59 (3%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATG--RSKGYGFVTFREPEAAMKA 80
K FVG + ++ + + FEQ+G + E V+ D++ +SKG FVTF +AA++A
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Score = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTF 71
K+F+G ++ + + + F FG+I E ++ G S+G FVTF
Sbjct: 97 KLFIGXISKKCTENDIRVXFSSFGQIEECRILRG-PDGLSRGCAFVTF 143
>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 = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 28/57 (49%), Gaps = 2/57 (3%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKA 80
+F+ L + + F FG IL V+ D+ SKGYGFV F EAA +A
Sbjct: 105 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERA 159
Score = 35.4 bits (80), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 29/56 (51%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKA 80
++VG L + + + + F G IL V D T RS GY +V F++P A +A
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERA 73
>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 = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKA 80
+F+ L + + F FG IL V+ D+ SKGYGFV F EAA +A
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERA 154
Score = 35.0 bits (79), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 29/56 (51%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKA 80
++VG L + + + + F G IL V D T RS GY +V F++P A +A
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERA 68
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 18 GDTTYTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAA 77
G + ++FV L ++ + ++ F + G +L A + + G+SKG G V F PE A
Sbjct: 4 GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVA 61
Query: 78 MKAC 81
+AC
Sbjct: 62 ERAC 65
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 33/72 (45%), Gaps = 7/72 (9%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACVDA 84
V+ GG+A + M + F FG+I+E V + KGY FV F E+A A V
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSV 81
Query: 85 -APVIDGRRANC 95
I+G C
Sbjct: 82 NGTTIEGHVVKC 93
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKA 80
+F+ L + + F FG IL V+ D+ SKGYGFV F EAA +A
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERA 67
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain
In Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 37.4 bits (85), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 18 GDTTYTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAA 77
G + + +FV L ++ + ++ F + G +L A + + G+SKG G V F PE A
Sbjct: 1 GSSGSSGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVA 58
Query: 78 MKAC 81
+AC
Sbjct: 59 ERAC 62
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 37.4 bits (85), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 25/62 (40%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 27 VGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKA---CVD 83
V L+ E +E+ F QFG + +AVV+ D GR+ G GFV F A KA C D
Sbjct: 101 VKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD-RGRATGKGFVEFAAKPPARKALERCGD 159
Query: 84 AA 85
A
Sbjct: 160 GA 161
Score = 36.2 bits (82), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 31/55 (56%), Gaps = 9/55 (16%)
Query: 18 GDTTYT---KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFV 69
G+ TYT ++FVG L + +E ++ FE++GE E + R +G+GF+
Sbjct: 15 GEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFI------NRDRGFGFI 63
>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 = 37.4 bits (85), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 9/82 (10%)
Query: 20 TTYTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTF--REPEAA 77
T +++FVG L + +E M K FE++G+ E + D KG+GF+ R
Sbjct: 13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEI 66
Query: 78 MKACVDAAPVIDGRRANCNLAC 99
K +D P + G++ AC
Sbjct: 67 AKVELDNMP-LRGKQLRVRFAC 87
>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 = 37.4 bits (85), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKA 80
+F+ L + + F FG IL V+ D+ SKGYGFV F EAA +A
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERA 61
>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 = 0.006, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 4/85 (4%)
Query: 18 GDTTYTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGR---SKGYGFVTFREP 74
G + + +F+ L + T +ET++ F + G I + K S G+GFV +++P
Sbjct: 1 GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60
Query: 75 EAAMKACVD-AAPVIDGRRANCNLA 98
E A KA +DG + ++
Sbjct: 61 EQAQKALKQLQGHTVDGHKLEVRIS 85
>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 = 37.0 bits (84), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 30/57 (52%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKA 80
+F+ L E + + + F FG ++ A V DK T SK +GFV++ P +A A
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 83
>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 = 37.0 bits (84), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 15/68 (22%), Positives = 33/68 (48%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACVDA 84
++VG + + E +E +F G + ++ DK +G KG+ ++ F + E+ +
Sbjct: 8 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALD 67
Query: 85 APVIDGRR 92
+ GR+
Sbjct: 68 ESLFRGRQ 75
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 37.0 bits (84), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 26/47 (55%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTF 71
VF LA + +E +F G++ + +I+D+ + RSKG +V F
Sbjct: 28 VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEF 74
>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 = 36.6 bits (83), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 15/68 (22%), Positives = 33/68 (48%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACVDA 84
++VG + + E +E +F G + ++ DK +G KG+ ++ F + E+ +
Sbjct: 9 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALD 68
Query: 85 APVIDGRR 92
+ GR+
Sbjct: 69 ESLFRGRQ 76
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 36.6 bits (83), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 43/86 (50%), Gaps = 4/86 (4%)
Query: 27 VGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAM--KACVDA 84
V L + T +++ + FE++G + + + + T +G+ FV F + A +A +D
Sbjct: 18 VDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDG 77
Query: 85 APVIDGRRANCNLACLGVQR-SKPST 109
A +DGR +A G + S PS+
Sbjct: 78 AE-LDGRELRVQVARYGRRDLSGPSS 102
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 36.6 bits (83), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 34/63 (53%), Gaps = 4/63 (6%)
Query: 21 TYTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFR---EPEAA 77
++ K+FVG L + ++ + + FE FG I E ++ G SKG FV + E +AA
Sbjct: 14 SHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRG-PDGNSKGCAFVKYSSHAEAQAA 72
Query: 78 MKA 80
+ A
Sbjct: 73 INA 75
>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 = 36.6 bits (83), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 33/59 (55%), Gaps = 3/59 (5%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFV---TFREPEAAMKA 80
+FV G+ E +E + F ++GEI + D+ TG KGY V T++E +AAM+
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 68
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 36.6 bits (83), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 33/59 (55%), Gaps = 3/59 (5%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFV---TFREPEAAMKA 80
+FV G+ E +E + F ++GEI + D+ TG KGY V T++E +AAM+
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 68
>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 = 36.2 bits (82), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 33/59 (55%), Gaps = 3/59 (5%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFV---TFREPEAAMKA 80
+FV G+ E +E + F ++GEI + D+ TG KGY V T++E +AAM+
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 68
>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 = 36.2 bits (82), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 33/59 (55%), Gaps = 3/59 (5%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFV---TFREPEAAMKA 80
+FV G+ E +E + F ++GEI + D+ TG KGY V T++E +AAM+
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 70
>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 = 36.2 bits (82), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 33/59 (55%), Gaps = 3/59 (5%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFV---TFREPEAAMKA 80
+FV G+ E +E + F ++GEI + D+ TG KGY V T++E +AAM+
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 84
>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 = 0.011, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 25/45 (55%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGF 68
K+F+GGL + +++ FG + ++ D ATG SKGY F
Sbjct: 116 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAF 160
>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 = 36.2 bits (82), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 3/64 (4%)
Query: 25 VFVGGLAWETQKETMEKYFEQFG--EILEAVVITDKATGRSKGYGFVTFREPEAAMKACV 82
+++G L W T E + + G +ILE ++A G+SKG+ V EA+ K +
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGS-EASSKKLM 62
Query: 83 DAAP 86
D P
Sbjct: 63 DLLP 66
>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 = 36.2 bits (82), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 33/59 (55%), Gaps = 3/59 (5%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFV---TFREPEAAMKA 80
+FV G+ E +E + F ++GEI + D+ TG KGY V T++E +AAM+
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 83
>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 = 0.013, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 26/48 (54%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTF 71
K+F+GGL + +++ FG + ++ D ATG SKGY F +
Sbjct: 98 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEY 145
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 35.8 bits (81), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 26/48 (54%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTF 71
K+F+GGL + +++ FG + ++ D ATG SKGY F +
Sbjct: 96 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEY 143
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 35.8 bits (81), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 27/50 (54%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFRE 73
K+F+GGL + +++ FG + ++ D ATG SKGY F + +
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVD 52
>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 = 35.0 bits (79), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 39/80 (48%), Gaps = 12/80 (15%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAV--------VITDKATGRSKGYGFVTFREPEA 76
+FV GL E++ YF+Q G I + TD+ TG+ KG V+F +P +
Sbjct: 16 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 75
Query: 77 AMKACVDAAPVIDGRRANCN 96
A KA +D DG+ + N
Sbjct: 76 A-KAAIDW---FDGKEFSGN 91
>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 = 35.0 bits (79), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 35/72 (48%), Gaps = 7/72 (9%)
Query: 21 TYT----KVFVGGLAWETQKETMEKYFEQFG--EILEAVVITDKATGRSKGYGFVTFREP 74
TYT +++G L W T E + + G +ILE ++A G+SKG+ V
Sbjct: 63 TYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGS- 121
Query: 75 EAAMKACVDAAP 86
EA+ K +D P
Sbjct: 122 EASSKKLMDLLP 133
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In
Trinucleotide Repeat Containing 4 Variant
Length = 102
Score = 34.7 bits (78), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 24/58 (41%), Positives = 31/58 (53%), Gaps = 4/58 (6%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFR---EPEAAM 78
K+FVG L + E + K FE FG I E V+ G SKG FV F+ E +AA+
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLR-GPDGTSKGCAFVKFQTHAEAQAAI 70
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14
Complex
Length = 110
Score = 34.7 bits (78), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 31/56 (55%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKA 80
+FV + E Q++ +++ F +GEI + D+ TG SKGY V + + A+ A
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 84
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 34.7 bits (78), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 39/80 (48%), Gaps = 12/80 (15%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAV--------VITDKATGRSKGYGFVTFREPEA 76
+FV GL E++ YF+Q G I + TD+ TG+ KG V+F +P +
Sbjct: 10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 69
Query: 77 AMKACVDAAPVIDGRRANCN 96
A KA +D DG+ + N
Sbjct: 70 A-KAAIDW---FDGKEFSGN 85
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 34.3 bits (77), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 29/57 (50%)
Query: 27 VGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACVD 83
V L ++ E+ FG + ++ + TG+SKGYGF + + ++A +A D
Sbjct: 100 VANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 156
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 34.3 bits (77), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 29/57 (50%)
Query: 27 VGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACVD 83
V L ++ E+ FG + ++ + TG+SKGYGF + + ++A +A D
Sbjct: 100 VANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 156
>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 = 33.9 bits (76), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 29/57 (50%)
Query: 27 VGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACVD 83
V L ++ E+ FG + ++ + TG+SKGYGF + + ++A +A D
Sbjct: 98 VANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 154
>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1HL6|C Chain C, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1RK8|A Chain A, Structure Of The Cytosolic Protein Pym Bound To The Mago-
Y14 Core Of The Exon Junction Complex
pdb|2X1G|A Chain A, Crystal Structure Of Importin13 - Mago-Y14 Complex
pdb|2X1G|C Chain C, Crystal Structure Of Importin13 - Mago-Y14 Complex
Length = 165
Score = 33.9 bits (76), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 31/56 (55%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKA 80
+FV + E Q++ +++ F +GEI + D+ TG SKGY V + + A+ A
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 130
>pdb|1WEL|A Chain A, Solution Structure Of Rna Binding Domain In Np_006038
Length = 124
Score = 33.9 bits (76), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACV 82
V++ GL +E + + + +F++ + +++ I G++ G GFV FR EA KA +
Sbjct: 28 VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRN-EADYKAAL 84
>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 = 0.077, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 36/79 (45%), Gaps = 8/79 (10%)
Query: 19 DTTYTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAM 78
D T T ++VGGL + + +F QFGEI V+ + F+ F +AA
Sbjct: 9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQC------AFIQFATRQAAE 62
Query: 79 KACVDA--APVIDGRRANC 95
A + +++GRR N
Sbjct: 63 VAAEKSFNKLIVNGRRLNV 81
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 33.1 bits (74), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 31/59 (52%), Gaps = 5/59 (8%)
Query: 23 TKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKAC 81
+KVFVG + E ++++F Q+GE+++ + + + FVTF + + A C
Sbjct: 12 SKVFVGRCTEDMTAEELQQFFCQYGEVVDVFI-----PKPFRAFAFVTFADDKVAQSLC 65
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 33.1 bits (74), Expect = 0.099, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 32/60 (53%), Gaps = 4/60 (6%)
Query: 24 KVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFR---EPEAAMKA 80
K+FVG L + +E + + F+ FG I E V+ G SKG FV F E +AA+ A
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLR-GPDGSSKGCAFVKFSSHTEAQAAIHA 75
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 33.1 bits (74), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 31/64 (48%), Gaps = 8/64 (12%)
Query: 18 GDTTYTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAA 77
G+ + T++FV + Q+ + + F FG + E ++ G+ FV F E E+A
Sbjct: 27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESA 78
Query: 78 MKAC 81
KA
Sbjct: 79 AKAI 82
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 33.1 bits (74), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 21 TYTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDK--ATGRSKGYGFVTFREPEAAM 78
T +K+ V + ++ + + + F FGE L+ V + K TG +G+GFV F + A
Sbjct: 14 TTSKILVRNIPFQANQREIRELFSTFGE-LKTVRLPKKMTGTGAHRGFGFVDFITKQDAK 72
Query: 79 KA 80
KA
Sbjct: 73 KA 74
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 32.7 bits (73), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 34/59 (57%), Gaps = 1/59 (1%)
Query: 23 TKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKAC 81
+ VFV L ++ + +++ F G ++ A ++ DK G+S+G G VTF + A++A
Sbjct: 16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAI 73
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 32.7 bits (73), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 8/56 (14%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKA 80
+FV LA +E +EK F QFG++ + D Y F+ F E + A+KA
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKA 61
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 32.7 bits (73), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 23 TKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGR-SKGYGFVTFREPEAAMKAC 81
TKV +G L K+ + + F +G+I + ++ SKGY +V F P+ A KA
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 32.3 bits (72), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 33/61 (54%), Gaps = 7/61 (11%)
Query: 25 VFVGGLAWETQKETMEK----YFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKA 80
+++ L + +K+ ++K F QFG+IL+ +V + + +G FV F+E +A A
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILV---SRSLKMRGQAFVIFKEVSSATNA 68
Query: 81 C 81
Sbjct: 69 L 69
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 31.6 bits (70), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 14/64 (21%), Positives = 32/64 (50%), Gaps = 5/64 (7%)
Query: 18 GDTTYTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAA 77
G + + VFVG + ++ + ++F Q+G++++ + + + FVTF + + A
Sbjct: 1 GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIA 55
Query: 78 MKAC 81
C
Sbjct: 56 QSLC 59
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein
U1a117, Nmr, 43 Structures
Length = 116
Score = 31.6 bits (70), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 33/61 (54%), Gaps = 7/61 (11%)
Query: 25 VFVGGLAWETQKETMEK----YFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKA 80
+++ L + +K+ ++K F QFG+IL+ +V + + +G FV F+E +A A
Sbjct: 11 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILV---SRSLKMRGQAFVIFKEVSSATNA 67
Query: 81 C 81
Sbjct: 68 L 68
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 31.2 bits (69), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 8/56 (14%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKA 80
+FV LA +E +EK F +FG++ + D Y FV F + AA+KA
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD--------YAFVHFEDRGAAVKA 65
>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 31.2 bits (69), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 33/61 (54%), Gaps = 7/61 (11%)
Query: 25 VFVGGLAWETQKETMEK----YFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKA 80
+++ L + +K+ ++K F QFG+IL+ +V + + +G FV F+E +A A
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILV---SRSLKMRGQAFVIFKEVSSATNA 68
Query: 81 C 81
Sbjct: 69 L 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 = 30.4 bits (67), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 38/78 (48%), Gaps = 5/78 (6%)
Query: 25 VFVGGLAWETQKETMEKYFEQFG--EILEAVVITDKATGRSKGYGFVTFREPEAAMKACV 82
V+VG +W T + + + G +++E ++A G+SKGY V E ++ +
Sbjct: 58 VYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVAS-ENSVHKLL 116
Query: 83 DAAP--VIDGRRANCNLA 98
+ P V++G + + A
Sbjct: 117 ELLPGKVLNGEKVDVRPA 134
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 30.0 bits (66), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 6/60 (10%)
Query: 23 TKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKACV 82
T+++VGGL T + + F++FG I D G S + ++ + +AA AC
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIR----TIDHVKGDS--FAYIQYESLDAAQAACA 71
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 30.0 bits (66), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 8/63 (12%)
Query: 19 DTTYTKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAM 78
+ + T++FV + Q+ + + F FG + E ++ G+ FV F E E+A
Sbjct: 1 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAA 52
Query: 79 KAC 81
KA
Sbjct: 53 KAI 55
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 29.6 bits (65), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 36/70 (51%), Gaps = 9/70 (12%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFV---TFREPEAAMKAC 81
+ + L++ +ET+++ FE+ + + G+SKGY F+ +F + + A+ +C
Sbjct: 18 LVLSNLSYSATEETLQEVFEK----ATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSC 73
Query: 82 VDAAPVIDGR 91
I+GR
Sbjct: 74 NKRE--IEGR 81
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 29.6 bits (65), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/58 (25%), Positives = 28/58 (48%), Gaps = 8/58 (13%)
Query: 23 TKVFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKA 80
TK+ VG ++ + + FE++G ++E ++ D Y FV E A++A
Sbjct: 11 TKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEA 60
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 28.5 bits (62), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 22/39 (56%), Gaps = 3/39 (7%)
Query: 43 FEQFGEILEAVVITDKATGRSKGYGFVTFREPEAAMKAC 81
F QFG+IL+ V + T + +G FV F+E +A A
Sbjct: 31 FSQFGQILDIVALK---TLKMRGQAFVIFKEIGSASNAL 66
>pdb|2M4M|A Chain A, Solution Structure Of The Rrm Domain Of The Hypothetical
Protein Cagl0m09691g From Candida Glabrata
Length = 124
Score = 27.3 bits (59), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 15/29 (51%), Positives = 18/29 (62%), Gaps = 2/29 (6%)
Query: 42 YFEQFGEILEAV--VITDKATGRSKGYGF 68
YF QFGEILE + + D T R+ GY F
Sbjct: 29 YFAQFGEILEDLESELGDTETMRTPGYFF 57
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif In Trna Selenocysteine Associated Protein
Length = 104
Score = 26.9 bits (58), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 23/49 (46%)
Query: 25 VFVGGLAWETQKETMEKYFEQFGEILEAVVITDKATGRSKGYGFVTFRE 73
+FVG L + + ++F + + TG SKGYGFV F +
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTD 60
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 26.6 bits (57), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 21/34 (61%)
Query: 36 KETMEKYFEQFGEILEAVVITDKATGRSKGYGFV 69
K+ + F + G+++ D+ATG++KG+ FV
Sbjct: 26 KKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFV 59
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 0.131 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,740,406
Number of Sequences: 62578
Number of extensions: 115289
Number of successful extensions: 434
Number of sequences better than 100.0: 146
Number of HSP's better than 100.0 without gapping: 120
Number of HSP's successfully gapped in prelim test: 26
Number of HSP's that attempted gapping in prelim test: 273
Number of HSP's gapped (non-prelim): 168
length of query: 189
length of database: 14,973,337
effective HSP length: 93
effective length of query: 96
effective length of database: 9,153,583
effective search space: 878743968
effective search space used: 878743968
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 bits)