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= 023688
(278 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 = 122 bits (305), Expect = 3e-28, Method: Compositional matrix adjust.
Identities = 59/96 (61%), Positives = 74/96 (77%), Gaps = 3/96 (3%)
Query: 19 NDTTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAA 78
DTTFTKIFVGGL + T ++R+YFE FG+I EAVVITD+ TG+S+GYGFVT D AA
Sbjct: 13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAA 72
Query: 79 MRACQNPSPVIDGRRANCNLASLGAHKTRPPTPQHG 114
RAC++P+P+IDGR+AN NLA LGA +P + Q G
Sbjct: 73 ERACKDPNPIIDGRKANVNLAYLGA---KPRSLQTG 105
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 75.9 bits (185), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 31/71 (43%), Positives = 47/71 (66%)
Query: 25 KIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQN 84
K+FVGGL W T ++T+R YF Q+GE+++ V++ DK T +S+G+GFV FKDP +
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 85 PSPVIDGRRAN 95
+DGR +
Sbjct: 78 RPHTLDGRNID 88
>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
pdb|3S7R|B Chain B, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
Length = 87
Score = 73.2 bits (178), Expect = 2e-13, Method: Composition-based stats.
Identities = 29/74 (39%), Positives = 46/74 (62%)
Query: 19 NDTTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAA 78
N+ K FVGGL+W+T + ++ YF +FGE+++ + D NTGRS+G+GF+ FKD +
Sbjct: 7 NEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASV 66
Query: 79 MRACQNPSPVIDGR 92
+ +DGR
Sbjct: 67 EKVLDQKEHRLDGR 80
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 67.4 bits (163), Expect = 9e-12, Method: Composition-based stats.
Identities = 27/50 (54%), Positives = 39/50 (78%)
Query: 25 KIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKD 74
K+F+GGL+W+T ++ +R YF QFGE+ E +V+ D T RS+G+GFVTF D
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMD 51
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 66.6 bits (161), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 30/84 (35%), Positives = 50/84 (59%)
Query: 16 GDYNDTTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDP 75
G + ++ K+F+GGL+W+T ++ +R YF QFGE+ E +V+ D T RS+G+GFVTF D
Sbjct: 18 GSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 77
Query: 76 EAAMRACQNPSPVIDGRRANCNLA 99
+ +D + + +A
Sbjct: 78 AGVDKVLAQSRHELDSKTIDPKVA 101
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 66.6 bits (161), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 33/90 (36%), Positives = 54/90 (60%), Gaps = 5/90 (5%)
Query: 25 KIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFK---DPEAAMRA 81
K+FVGGL+++T ++ + F ++G+I E VV+ D+ T RS+G+GFVTF+ D + AM A
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 82 CQNPSPVIDGRRANCNLASLGAHKTRPPTP 111
S +DGR+ + A + P+
Sbjct: 74 MNGKS--VDGRQIRVDQAGKSSDNRSGPSS 101
>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 = 64.3 bits (155), Expect = 6e-11, Method: Composition-based stats.
Identities = 28/74 (37%), Positives = 46/74 (62%), Gaps = 5/74 (6%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQNP 85
+F+GGL+W+T + ++ YF +FGE+++ + D TGRS+G+GFV FK+ E+ +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 86 S-----PVIDGRRA 94
VID +RA
Sbjct: 62 EHKLNGKVIDPKRA 75
>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
pdb|1U1K|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt 7da
Ggg); A Human Telomeric Repeat Containing
7-Deaza-Adenine
pdb|1U1L|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt Prn
Ggg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1M|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 7gu
Gg); A Human Telomeric Repeat Containing
7-Deaza-Guanine
pdb|1U1N|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta
(Prn) Gg); A Human Telomeric Repeat Containing
Nebularine
pdb|1U1O|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggttag(Di)g); A Human Telomeric Repeat Containing
Inosine
pdb|1U1P|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 2pr
Gg); A Human Telomeric Repeat Containing 2-Aminopurine
pdb|1U1Q|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggtta(Di)gg); A Human Telomeric Repeat Containing
Inosine
pdb|1U1R|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggttag(2pr) G); A Human Telomeric Repeat
Containing 2-Aminopurine
Length = 196
Score = 63.5 bits (153), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 31/71 (43%), Positives = 48/71 (67%), Gaps = 2/71 (2%)
Query: 23 FTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRAC 82
K+F+GGL++ET +++R +FEQ+G + + VV+ D NT RS+G+GFVT+ E + A
Sbjct: 13 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE-EVDAA 71
Query: 83 QNPSP-VIDGR 92
N P +DGR
Sbjct: 72 MNARPHKVDGR 82
Score = 60.5 bits (145), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 30/95 (31%), Positives = 52/95 (54%), Gaps = 4/95 (4%)
Query: 4 QRPLQMVGGNHPGDYNDTTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGR 63
+R + PG + T KIFVGG+ +T+ +R YFEQ+G+I ++TD+ +G+
Sbjct: 87 KRAVSREDSQRPGAH--LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGK 144
Query: 64 SKGYGFVTFKDPEAAMRACQNPSPVIDGRRANCNL 98
+G+ FVTF D ++ + ++G NC +
Sbjct: 145 KRGFAFVTFDDHDSVDKIVIQKYHTVNGH--NCEV 177
>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat
Containing 6-Methyl-8-(2-
Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi)
Length = 195
Score = 63.5 bits (153), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 31/71 (43%), Positives = 48/71 (67%), Gaps = 2/71 (2%)
Query: 23 FTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRAC 82
K+F+GGL++ET +++R +FEQ+G + + VV+ D NT RS+G+GFVT+ E + A
Sbjct: 12 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE-EVDAA 70
Query: 83 QNPSP-VIDGR 92
N P +DGR
Sbjct: 71 MNARPHKVDGR 81
Score = 60.1 bits (144), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 30/95 (31%), Positives = 52/95 (54%), Gaps = 4/95 (4%)
Query: 4 QRPLQMVGGNHPGDYNDTTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGR 63
+R + PG + T KIFVGG+ +T+ +R YFEQ+G+I ++TD+ +G+
Sbjct: 86 KRAVSREDSQRPGAH--LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGK 143
Query: 64 SKGYGFVTFKDPEAAMRACQNPSPVIDGRRANCNL 98
+G+ FVTF D ++ + ++G NC +
Sbjct: 144 KRGFAFVTFDDHDSVDKIVIQKYHTVNGH--NCEV 176
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 63.5 bits (153), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 31/71 (43%), Positives = 48/71 (67%), Gaps = 2/71 (2%)
Query: 23 FTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRAC 82
K+F+GGL++ET +++R +FEQ+G + + VV+ D NT RS+G+GFVT+ E + A
Sbjct: 14 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE-EVDAA 72
Query: 83 QNPSP-VIDGR 92
N P +DGR
Sbjct: 73 MNARPHKVDGR 83
Score = 60.1 bits (144), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 30/95 (31%), Positives = 52/95 (54%), Gaps = 4/95 (4%)
Query: 4 QRPLQMVGGNHPGDYNDTTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGR 63
+R + PG + T KIFVGG+ +T+ +R YFEQ+G+I ++TD+ +G+
Sbjct: 88 KRAVSREDSQRPGAH--LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGK 145
Query: 64 SKGYGFVTFKDPEAAMRACQNPSPVIDGRRANCNL 98
+G+ FVTF D ++ + ++G NC +
Sbjct: 146 KRGFAFVTFDDHDSVDKIVIQKYHTVNGH--NCEV 178
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 63.2 bits (152), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 31/71 (43%), Positives = 48/71 (67%), Gaps = 2/71 (2%)
Query: 23 FTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRAC 82
K+F+GGL++ET +++R +FEQ+G + + VV+ D NT RS+G+GFVT+ E + A
Sbjct: 13 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE-EVDAA 71
Query: 83 QNPSP-VIDGR 92
N P +DGR
Sbjct: 72 MNARPHKVDGR 82
Score = 60.1 bits (144), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 30/95 (31%), Positives = 52/95 (54%), Gaps = 4/95 (4%)
Query: 4 QRPLQMVGGNHPGDYNDTTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGR 63
+R + PG + T KIFVGG+ +T+ +R YFEQ+G+I ++TD+ +G+
Sbjct: 87 KRAVSREDSQRPGAH--LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGK 144
Query: 64 SKGYGFVTFKDPEAAMRACQNPSPVIDGRRANCNL 98
+G+ FVTF D ++ + ++G NC +
Sbjct: 145 KRGFAFVTFDDHDSVDKIVIQKYHTVNGH--NCEV 177
>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex
pdb|1PO6|A Chain A, Crystal Structure Of Up1 Complexed With
D(Tagg(6mi)ttaggg): A Human Telomeric Repeat Containing
6-Methyl-8-(2-Deoxy-
Beta-Ribofuranosyl)isoxanthopteridine (6mi)
Length = 183
Score = 63.2 bits (152), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 31/71 (43%), Positives = 48/71 (67%), Gaps = 2/71 (2%)
Query: 23 FTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRAC 82
K+F+GGL++ET +++R +FEQ+G + + VV+ D NT RS+G+GFVT+ E + A
Sbjct: 6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE-EVDAA 64
Query: 83 QNPSP-VIDGR 92
N P +DGR
Sbjct: 65 MNARPHKVDGR 75
Score = 60.1 bits (144), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 30/95 (31%), Positives = 52/95 (54%), Gaps = 4/95 (4%)
Query: 4 QRPLQMVGGNHPGDYNDTTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGR 63
+R + PG + T KIFVGG+ +T+ +R YFEQ+G+I ++TD+ +G+
Sbjct: 80 KRAVSREDSQRPGAH--LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGK 137
Query: 64 SKGYGFVTFKDPEAAMRACQNPSPVIDGRRANCNL 98
+G+ FVTF D ++ + ++G NC +
Sbjct: 138 KRGFAFVTFDDHDSVDKIVIQKYHTVNGH--NCEV 170
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 63.2 bits (152), Expect = 2e-10, Method: Composition-based stats.
Identities = 28/74 (37%), Positives = 46/74 (62%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQNP 85
IFVGGL+ T + ++ YFEQFG++ +A+++ DK T R +G+GFVTF+ + + C+
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 86 SPVIDGRRANCNLA 99
I+ + C A
Sbjct: 62 FHEINNKMVECKKA 75
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleaoproteins A2B1
Length = 116
Score = 63.2 bits (152), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 32/73 (43%), Positives = 51/73 (69%), Gaps = 6/73 (8%)
Query: 23 FTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFK---DPEAAM 79
F K+F+GGL++ET +++R Y+EQ+G++ + VV+ D + RS+G+GFVTF + +AAM
Sbjct: 27 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 86
Query: 80 RACQNPSPVIDGR 92
A + IDGR
Sbjct: 87 AARPHS---IDGR 96
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 63.2 bits (152), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 31/71 (43%), Positives = 48/71 (67%), Gaps = 2/71 (2%)
Query: 23 FTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRAC 82
K+F+GGL++ET +++R +FEQ+G + + VV+ D NT RS+G+GFVT+ E + A
Sbjct: 11 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE-EVDAA 69
Query: 83 QNPSP-VIDGR 92
N P +DGR
Sbjct: 70 MNARPHKVDGR 80
Score = 60.1 bits (144), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 30/95 (31%), Positives = 52/95 (54%), Gaps = 4/95 (4%)
Query: 4 QRPLQMVGGNHPGDYNDTTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGR 63
+R + PG + T KIFVGG+ +T+ +R YFEQ+G+I ++TD+ +G+
Sbjct: 85 KRAVSREDSQRPGAH--LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGK 142
Query: 64 SKGYGFVTFKDPEAAMRACQNPSPVIDGRRANCNL 98
+G+ FVTF D ++ + ++G NC +
Sbjct: 143 KRGFAFVTFDDHDSVDKIVIQKYHTVNGH--NCEV 175
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 62.8 bits (151), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 28/58 (48%), Positives = 38/58 (65%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQ 83
++VG L + D +R FE FG+I V++ D +TGRSKGYGF+TF D E A RA +
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
>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 = 62.0 bits (149), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 32/86 (37%), Positives = 48/86 (55%), Gaps = 1/86 (1%)
Query: 15 PGDYNDTTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKD 74
P D D T KIFVGG+ + + +F Q+G I++A ++ DK+TG+S+G+GFVT+
Sbjct: 80 PRDEQDKT-GKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDS 138
Query: 75 PEAAMRACQNPSPVIDGRRANCNLAS 100
+A R CQN R+ A
Sbjct: 139 ADAVDRVCQNKFIDFKDRKIEIKRAE 164
Score = 60.5 bits (145), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 45/74 (60%), Gaps = 4/74 (5%)
Query: 25 KIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQN 84
K+F+GGL W+T D +R YF ++G + + ++ D TGRS+G+GF++F+ P + +
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 85 ----PSPVIDGRRA 94
VID +RA
Sbjct: 65 QHILDGKVIDPKRA 78
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 60.5 bits (145), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 29/75 (38%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 24 TKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQ 83
+ + V GL W+T ++ YF FGE+L V D TG SKG+GFV F + E ++
Sbjct: 16 SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKV-M 74
Query: 84 NPSPVIDGRRANCNL 98
+ +IDGR +C L
Sbjct: 75 SQRHMIDGRWCDCKL 89
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 58.2 bits (139), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 26/59 (44%), Positives = 36/59 (61%)
Query: 25 KIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQ 83
+++VG L + D +R FE FG I ++ D TGRSKGYGF+TF D E A +A +
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALE 86
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 57.0 bits (136), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 35/113 (30%), Positives = 62/113 (54%), Gaps = 15/113 (13%)
Query: 9 MVGGNHPGDYNDTTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYG 68
MV +HPG K+F+GGL ET ++ F + G I E ++I D+ T +S+G+
Sbjct: 1 MVEADHPG--------KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFA 51
Query: 69 FVTFKDPEAAMRACQNPSPVIDGRRANCNLASLGAHKTRPPTPQHGGGRFRPA 121
F+TF++P A A ++ ++G+ + + ++ + + P+ Q GG R PA
Sbjct: 52 FITFENPADAKNAAKD----MNGK--SLHGKAIKVEQAKKPSFQSGGRRRPPA 98
>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 = 57.0 bits (136), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 33/94 (35%), Positives = 47/94 (50%), Gaps = 9/94 (9%)
Query: 23 FTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTF---KDPEAAM 79
T + V L + T DT+RR FE++G + + + D+ T S+G+ FV F +D E AM
Sbjct: 47 MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAM 106
Query: 80 RACQNPSPVIDGRRANCNLASLGAHKTRPPTPQH 113
A V+DGR +A G RPP H
Sbjct: 107 DAMDG--AVLDGRELRVQMARYG----RPPDSHH 134
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 55.5 bits (132), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 33/94 (35%), Positives = 47/94 (50%), Gaps = 9/94 (9%)
Query: 23 FTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTF---KDPEAAM 79
T + V L + T DT+RR FE++G + + + D+ T S+G+ FV F +D E AM
Sbjct: 70 MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAM 129
Query: 80 RACQNPSPVIDGRRANCNLASLGAHKTRPPTPQH 113
A V+DGR +A G RPP H
Sbjct: 130 DAMD--GAVLDGRELRVQMARYG----RPPDSHH 157
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 53.9 bits (128), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 28/87 (32%), Positives = 45/87 (51%)
Query: 24 TKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQ 83
KIFVGG+ +R YF++FG + E V+I D R +G+GF+TF+D ++ +A
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN 70
Query: 84 NPSPVIDGRRANCNLASLGAHKTRPPT 110
I G++ A K+ P+
Sbjct: 71 MHFHDIMGKKVEVKRAEPRDSKSSGPS 97
>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 = 52.4 bits (124), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 32/88 (36%), Positives = 47/88 (53%), Gaps = 6/88 (6%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQN- 84
+FVG L+ E + ++ F FG I +A V+ D TG+SKGYGFV+F + A A Q
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 85 PSPVIDGRRANCNLASLGAHKTRPPTPQ 112
+ GR+ N A+ +PP P+
Sbjct: 78 GGQWLGGRQIRTNWATR-----KPPAPK 100
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 50.8 bits (120), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 38/65 (58%)
Query: 20 DTTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAM 79
D + +FVG + +E + ++ F + G ++ ++ D+ TG+ KGYGF ++D E A+
Sbjct: 5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETAL 64
Query: 80 RACQN 84
A +N
Sbjct: 65 SAMRN 69
>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 = 50.4 bits (119), Expect = 1e-06, Method: Composition-based stats.
Identities = 22/52 (42%), Positives = 33/52 (63%)
Query: 25 KIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPE 76
KIFVGGL+ +T + +R YF FGE+ + D T + +G+ F+TFK+ E
Sbjct: 3 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEE 54
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 31/87 (35%), Positives = 47/87 (54%), Gaps = 6/87 (6%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQN- 84
+FVG L+ E + ++ F FG+I +A V+ D TG+SKGYGFV+F + A A +
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 85 PSPVIDGRRANCNLASLGAHKTRPPTP 111
+ GR+ N A+ +PP P
Sbjct: 78 GGQWLGGRQIRTNWAT-----RKPPAP 99
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 48.9 bits (115), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 45/77 (58%), Gaps = 8/77 (10%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTF---KDPEAAMRAC 82
+FV GL+ +T +T++ E F + A ++TD+ TG SKG+GFV F +D +AA A
Sbjct: 18 LFVKGLSEDTTEETLK---ESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAM 74
Query: 83 QNPSPVIDGRRANCNLA 99
++ IDG + + A
Sbjct: 75 EDGE--IDGNKVTLDWA 89
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 48.5 bits (114), Expect = 4e-06, Method: Composition-based stats.
Identities = 21/51 (41%), Positives = 32/51 (62%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPE 76
IFVGGL+ +T + +R YF FGE+ + D T + +G+ F+TFK+ E
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEE 52
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 47.4 bits (111), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 36/63 (57%)
Query: 19 NDTTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAA 78
D K+F+G + ++ FE+FG+I E V+ D+ TG KG F+T+ + E+A
Sbjct: 9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESA 68
Query: 79 MRA 81
++A
Sbjct: 69 LKA 71
>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 = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 27/95 (28%), Positives = 44/95 (46%), Gaps = 17/95 (17%)
Query: 23 FTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRAC 82
F +I+V + + D ++ FE FG+I A + D TG+ KGYGF+ ++ +++ A
Sbjct: 125 FNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAV 184
Query: 83 QNPSPVIDGRRANCNLASLGAHKTR------PPTP 111
++ NL LG R PP P
Sbjct: 185 -----------SSMNLFDLGGQYLRVGKAVTPPMP 208
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 40/72 (55%)
Query: 22 TFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRA 81
++++VG + +E DT+R+ F FG I + D T + KG+ FV ++ PEAA A
Sbjct: 27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLA 86
Query: 82 CQNPSPVIDGRR 93
+ + V+ G R
Sbjct: 87 LEQMNSVMLGGR 98
>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 = 1e-05, Method: Composition-based stats.
Identities = 21/47 (44%), Positives = 31/47 (65%), Gaps = 1/47 (2%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTF 72
+FVGG+ +R +F ++G + E +ITD+ TG SKGYGFV+F
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 57
>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 = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 32/113 (28%), Positives = 48/113 (42%), Gaps = 6/113 (5%)
Query: 5 RPLQMVGGNHPGDYNDTTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRS 64
+P++++ + IF+ L + F FG IL V+ D+N S
Sbjct: 85 KPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--S 142
Query: 65 KGYGFVTFKDPEAAMRACQNPSPVIDGRRANCNLASLGAHKTRPPTPQHGGGR 117
KGYGFV F+ EAA RA + ++G N +G K+R G R
Sbjct: 143 KGYGFVHFETQEAAERAIEK----MNGMLLNDRKVFVGRFKSRKEREAELGAR 191
Score = 33.1 bits (74), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 31/68 (45%), Gaps = 1/68 (1%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQNP 85
++VG L + + F G IL V D T RS GY +V F+ P A RA
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77
Query: 86 S-PVIDGR 92
+ VI G+
Sbjct: 78 NFDVIKGK 85
>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 = 2e-05, Method: Compositional matrix adjust.
Identities = 31/84 (36%), Positives = 43/84 (51%), Gaps = 6/84 (7%)
Query: 20 DTTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTF---KDPE 76
D TF +FVG L +T+R F+ F L V+ D TG S+GYGFV+F D +
Sbjct: 85 DDTFN-LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQ 143
Query: 77 AAMRACQNPSPVIDGRRANCNLAS 100
AM + Q ++GR N A+
Sbjct: 144 NAMDSMQGQD--LNGRPLRINWAA 165
Score = 32.3 bits (72), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 36/77 (46%), Gaps = 5/77 (6%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQNP 85
++VG L D +++YF+ G I ++ DKN ++ Y FV + A A Q
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNN-KNVNYAFVEYHQSHDANIALQ-- 59
Query: 86 SPVIDGRRANCNLASLG 102
++G++ N+ +
Sbjct: 60 --TLNGKQIENNIVKIN 74
>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Rna, Uuguucuu
Length = 102
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 35/59 (59%), Gaps = 1/59 (1%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQN 84
+FVGG+ +R +F ++G + E +ITD+ TG SKGYGFV+F + + ++
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVES 69
>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 = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 32/113 (28%), Positives = 48/113 (42%), Gaps = 6/113 (5%)
Query: 5 RPLQMVGGNHPGDYNDTTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRS 64
+P++++ + IF+ L + F FG IL V+ D+N S
Sbjct: 80 KPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--S 137
Query: 65 KGYGFVTFKDPEAAMRACQNPSPVIDGRRANCNLASLGAHKTRPPTPQHGGGR 117
KGYGFV F+ EAA RA + ++G N +G K+R G R
Sbjct: 138 KGYGFVHFETQEAAERAIEK----MNGMLLNDRKVFVGRFKSRKEREAELGAR 186
Score = 32.3 bits (72), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 31/68 (45%), Gaps = 1/68 (1%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQNP 85
++VG L + + F G IL V D T RS GY +V F+ P A RA
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 72
Query: 86 S-PVIDGR 92
+ VI G+
Sbjct: 73 NFDVIKGK 80
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 46.2 bits (108), Expect = 2e-05, Method: Composition-based stats.
Identities = 21/47 (44%), Positives = 31/47 (65%), Gaps = 1/47 (2%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTF 72
+FVGG+ +R +F ++G + E +ITD+ TG SKGYGFV+F
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 58
>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 = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 29/83 (34%), Positives = 41/83 (49%), Gaps = 5/83 (6%)
Query: 25 KIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTF---KDPEAAMRA 81
+FVG L +T+R F+ F L V+ D TG S+GYGFV+F D + AM +
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 82 CQNPSPVIDGRRANCNLASLGAH 104
Q ++GR N A+ H
Sbjct: 63 MQGQD--LNGRPLRINWAAKLEH 83
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 28/90 (31%), Positives = 50/90 (55%), Gaps = 3/90 (3%)
Query: 12 GNHPGDYNDTTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVT 71
G+H N + ++ V + + + +R+ F QFG+IL+ +I ++ SKG+GFVT
Sbjct: 18 GSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVT 75
Query: 72 FKDPEAAMRACQNP-SPVIDGRRANCNLAS 100
F++ A RA + V++GR+ N A+
Sbjct: 76 FENSADADRAREKLHGTVVEGRKIEVNNAT 105
>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 = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 39/72 (54%)
Query: 22 TFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRA 81
+++VG + +E DT+R+ F FG I + D T + KG+ FV ++ PEAA A
Sbjct: 12 IMCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLA 71
Query: 82 CQNPSPVIDGRR 93
+ + V+ G R
Sbjct: 72 LEQMNSVMLGGR 83
Score = 44.3 bits (103), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 43/95 (45%), Gaps = 17/95 (17%)
Query: 23 FTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRAC 82
F +I+V + + D ++ FE FG+I + D TG+ KGYGF+ ++ +++ A
Sbjct: 110 FNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAV 169
Query: 83 QNPSPVIDGRRANCNLASLGAHKTR------PPTP 111
++ NL LG R PP P
Sbjct: 170 -----------SSMNLFDLGGQYLRVGKAVTPPMP 193
>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 = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 31/92 (33%), Positives = 41/92 (44%), Gaps = 6/92 (6%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQNP 85
IF+ L + F FG IL V+ D+N SKGYGFV F+ EAA RA +
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEK- 64
Query: 86 SPVIDGRRANCNLASLGAHKTRPPTPQHGGGR 117
++G N +G K+R G R
Sbjct: 65 ---MNGMLLNDRKVFVGRFKSRKEREAELGAR 93
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 44.7 bits (104), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 40/68 (58%), Gaps = 4/68 (5%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQNP 85
++V L + + + R F ++G++++ ++ DK+T +SKG F+ F D ++A QN
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSA----QNC 74
Query: 86 SPVIDGRR 93
+ I+ ++
Sbjct: 75 TRAINNKQ 82
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 44.3 bits (103), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 34/63 (53%)
Query: 19 NDTTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAA 78
D K+FVG + ++ FE+FG I E V+ D+ TG KG F+T+ ++A
Sbjct: 11 KDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSA 70
Query: 79 MRA 81
++A
Sbjct: 71 LKA 73
>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 2.50 A Resolution
Length = 200
Score = 44.3 bits (103), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 43/95 (45%), Gaps = 17/95 (17%)
Query: 23 FTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRAC 82
F +I+V + + D ++ FE FG+I + D TG+ KGYGF+ ++ +++ A
Sbjct: 109 FNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAV 168
Query: 83 QNPSPVIDGRRANCNLASLGAHKTR------PPTP 111
++ NL LG R PP P
Sbjct: 169 -----------SSXNLFDLGGQYLRVGKAVTPPXP 192
Score = 43.9 bits (102), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 37/70 (52%)
Query: 24 TKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQ 83
+++VG + +E DT+R+ F FG I D T + KG+ FV ++ PEAA A +
Sbjct: 13 CRVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALE 72
Query: 84 NPSPVIDGRR 93
+ V G R
Sbjct: 73 QXNSVXLGGR 82
>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2
pdb|3BS9|B Chain B, X-Ray Structure Of Human Tia-1 Rrm2
Length = 87
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 29/76 (38%), Positives = 40/76 (52%), Gaps = 1/76 (1%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQN- 84
+FVG L+ E + F FG I +A V+ D TG+SKGYGFV+F + A A Q
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 85 PSPVIDGRRANCNLAS 100
+ GR+ N A+
Sbjct: 69 GGQWLGGRQIRTNWAT 84
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 43.5 bits (101), Expect = 1e-04, Method: Composition-based stats.
Identities = 24/69 (34%), Positives = 34/69 (49%), Gaps = 8/69 (11%)
Query: 16 GDYNDTTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDP 75
G + K+F+G L E +R FEQ+G++LE +I K YGFV +D
Sbjct: 1 GSSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDK 52
Query: 76 EAAMRACQN 84
AA A +N
Sbjct: 53 TAAEDAIRN 61
>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 = 2e-04, Method: Composition-based stats.
Identities = 16/49 (32%), Positives = 29/49 (59%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKD 74
I+VG L + + ++ F QFG++ +I D+ T + KG+GFV ++
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE 52
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 36/72 (50%), Gaps = 4/72 (5%)
Query: 11 GGNHPGDYNDTTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFV 70
G N D N T I V L+ +T+ ++ F FG I + DK TG+SKG+ F+
Sbjct: 7 GPNRRADDNAT----IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFI 62
Query: 71 TFKDPEAAMRAC 82
+F E A RA
Sbjct: 63 SFHRREDAARAI 74
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 38/71 (53%), Gaps = 3/71 (4%)
Query: 13 NHPGDYNDTTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDK--NTGRSKGYGFV 70
+HP D D K+FVG + +R FEQ+G + E V+ D+ N +SKG FV
Sbjct: 6 DHP-DQPDLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFV 64
Query: 71 TFKDPEAAMRA 81
TF +AA+ A
Sbjct: 65 TFYTRKAALEA 75
Score = 35.4 bits (80), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 35/67 (52%), Gaps = 2/67 (2%)
Query: 6 PLQMVGGNHPGDYNDTTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSK 65
P+QM + + N K+F+G ++ + + +R F FG+I E ++ + G S+
Sbjct: 91 PIQMKPADSEKN-NAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPD-GLSR 148
Query: 66 GYGFVTF 72
G FVTF
Sbjct: 149 GCAFVTF 155
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 45/77 (58%), Gaps = 3/77 (3%)
Query: 25 KIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQN 84
++ V + + + +R+ F QFG+IL+ +I ++ SKG+GFVTF++ A RA +
Sbjct: 17 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREK 74
Query: 85 P-SPVIDGRRANCNLAS 100
V++GR+ N A+
Sbjct: 75 LHGTVVEGRKIEVNNAT 91
>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 = 3e-04, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 30/58 (51%)
Query: 24 TKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRA 81
T + V L +D + F G+I ++ DK TG+S GYGFV + DP A +A
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/58 (41%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQ 83
IF+ L + F FG IL V+ D+N SKGYGFV F+ EAA RA +
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIE 69
>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 = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 23 FTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRAC 82
F +FV + ++T +RR FE +G I ++ K +G+ +GY F+ ++ A
Sbjct: 102 FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAY 161
Query: 83 QNPS-PVIDGRRANCNL 98
++ IDGRR ++
Sbjct: 162 KHADGKKIDGRRVLVDV 178
>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 = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 29/59 (49%)
Query: 24 TKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRAC 82
T + V L +D +R F GE+ A +I DK G S GYGFV + + A RA
Sbjct: 20 TNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 78
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 33/60 (55%), Gaps = 4/60 (6%)
Query: 25 KIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFK---DPEAAMRA 81
K+FVG L + D +RR FE FG I E ++ + G SKG FV + + +AA+ A
Sbjct: 17 KLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPD-GNSKGCAFVKYSSHAEAQAAINA 75
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 39/80 (48%), Gaps = 1/80 (1%)
Query: 21 TTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMR 80
TT ++VGGLA E + F FG+I + + D T + +G+ FV F+ E A
Sbjct: 10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 69
Query: 81 ACQNPSPV-IDGRRANCNLA 99
A N + + GR NLA
Sbjct: 70 AIDNMNESELFGRTIRVNLA 89
>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 = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 31/59 (52%)
Query: 24 TKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRAC 82
T + V L ++ R F GEI ++ DK TG+S GYGFV + DP+ A +A
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 34/65 (52%), Gaps = 3/65 (4%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFK---DPEAAMRAC 82
++V GL + + + F Q+G I+ + ++ D+ TG S+G GF+ F + E A++
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 83 QNPSP 87
P
Sbjct: 151 NGQKP 155
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With
The Au-Rich Element
Length = 174
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 30/59 (50%)
Query: 24 TKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRAC 82
T + V L +D + F G+I ++ DK TG+S GYGFV + DP A +A
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI 63
Score = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 3/66 (4%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFK---DPEAAMRAC 82
++V GL + M + F Q+G I+ + ++ D+ TG S+G GF+ F + E A++
Sbjct: 93 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 152
Query: 83 QNPSPV 88
P+
Sbjct: 153 NGQKPL 158
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 28 VGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQNPSP 87
V GL+ T +R F ++G I + ++ D+ + RS+G+ FV F++ + A A + +
Sbjct: 51 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 110
Query: 88 V-IDGRRANCNLA 99
+ +DGRR + +
Sbjct: 111 MELDGRRIRVDFS 123
>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 = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 40/81 (49%), Gaps = 5/81 (6%)
Query: 21 TTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTF---KDPEA 77
F +FV + ++T +RR FE +G I ++ K +G+ +GY F+ + +D +
Sbjct: 100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHS 159
Query: 78 AMRACQNPSPVIDGRRANCNL 98
A + IDGRR ++
Sbjct: 160 AYKHADGKK--IDGRRVLVDV 178
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 41.2 bits (95), Expect = 6e-04, Method: Composition-based stats.
Identities = 27/80 (33%), Positives = 39/80 (48%), Gaps = 1/80 (1%)
Query: 21 TTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMR 80
TT ++VGGLA E + F FG+I + + D T + +G+ FV F+ E A
Sbjct: 3 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 62
Query: 81 ACQNPSPV-IDGRRANCNLA 99
A N + + GR NLA
Sbjct: 63 AIDNMNESELFGRTIRVNLA 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 = 6e-04, Method: Composition-based stats.
Identities = 27/80 (33%), Positives = 39/80 (48%), Gaps = 1/80 (1%)
Query: 21 TTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMR 80
TT ++VGGLA E + F FG+I + + D T + +G+ FV F+ E A
Sbjct: 5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 64
Query: 81 ACQNPSPV-IDGRRANCNLA 99
A N + + GR NLA
Sbjct: 65 AIDNMNESELFGRTIRVNLA 84
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 28 VGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQNPSP 87
V GL+ T +R F ++G I + ++ D+ + RS+G+ FV F++ + A A + +
Sbjct: 17 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 76
Query: 88 V-IDGRRANCNLA 99
+ +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 = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 33/59 (55%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQN 84
+++G + ++ + + G ++ ++ D TGRSKGY F+ F+D E++ A +N
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 64
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 28 VGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQNPSP 87
V GL+ T +R F ++G I + ++ D+ + RS+G+ FV F++ + A A + +
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 88 V-IDGRRANCNLA 99
+ +DGRR + +
Sbjct: 80 MELDGRRIRVDFS 92
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs
Of Human Antigen R
Length = 177
Score = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 29/59 (49%)
Query: 24 TKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRAC 82
T + V L +D +R F GE+ A +I DK G S GYGFV + + A RA
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Score = 36.6 bits (83), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 28/57 (49%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRAC 82
+++ GL + + F +FG I+ + V+ D+ TG S+G F+ F A A
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 25/91 (27%), Positives = 43/91 (47%), Gaps = 11/91 (12%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTF------KDPEAAM 79
+ V L + T D++RR FE++G + + + + +T +G+ FV F +D EAAM
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75
Query: 80 RACQNPSPVIDGRRANCNLASLGAHKTRPPT 110
+ +DGR +A G P+
Sbjct: 76 DGAE-----LDGRELRVQVARYGRRDLSGPS 101
>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 = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 24/59 (40%), Positives = 30/59 (50%), Gaps = 3/59 (5%)
Query: 24 TKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGF---VTFKDPEAAM 79
T + V L +D +R F GE+ A +I DK G S GYGF VT KD E A+
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Score = 36.2 bits (82), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 28/57 (49%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRAC 82
+++ GL + + F +FG I+ + V+ D+ TG S+G F+ F A A
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 40.8 bits (94), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 33/59 (55%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQN 84
+++G + ++ + + G ++ ++ D TGRSKGY F+ F+D E++ A +N
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63
>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 = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 33/60 (55%), Gaps = 2/60 (3%)
Query: 24 TKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDK--NTGRSKGYGFVTFKDPEAAMRA 81
K+FVG + +R FEQ+G + E V+ D+ N +SKG FVTF +AA+ A
Sbjct: 4 IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 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 = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 22/58 (37%), Positives = 29/58 (50%)
Query: 24 TKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRA 81
T + V L +D +R F GE+ A +I DK G S GYGFV + + A RA
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 62
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 39/67 (58%), Gaps = 1/67 (1%)
Query: 28 VGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQNPSP 87
V GL+ T +R F ++G I + ++ D+ + RS+G+ FV F++ + A A + +
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 88 V-IDGRR 93
+ +DGRR
Sbjct: 80 MELDGRR 86
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 37/78 (47%), Gaps = 4/78 (5%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTG---RSKGYGFVTFKDPEAAMRAC 82
+F+ L + T +T++ F + G I + KN S G+GFV +K PE A +A
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 83 -QNPSPVIDGRRANCNLA 99
Q +DG + ++
Sbjct: 68 KQLQGHTVDGHKLEVRIS 85
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 28/43 (65%)
Query: 40 MRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRAC 82
+R+ FE++G I ++ D+ T +S+GYGFV F+ +A +A
Sbjct: 59 LRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAI 101
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 40.0 bits (92), Expect = 0.001, Method: Composition-based stats.
Identities = 20/56 (35%), Positives = 31/56 (55%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRA 81
+++ GL T + + + +G+I+ I DK T + KGYGFV F P AA +A
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA 63
>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 = 40.0 bits (92), Expect = 0.001, Method: Composition-based stats.
Identities = 25/75 (33%), Positives = 37/75 (49%), Gaps = 1/75 (1%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQNP 85
++VGGLA E + F FG+I + + D T + +G+ FV F+ E A A N
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 86 SPV-IDGRRANCNLA 99
+ + GR NLA
Sbjct: 65 NESELFGRTIRVNLA 79
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 31/58 (53%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQ 83
+F+ L E + F FG ++ A V DK T SK +GFV+F +P++A A +
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIK 100
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEA-VVITDKNTGRSKGYGFVTFKDPEAAMRACQ 83
IF+G L E + F FG IL+ ++ D +TG SKGY F+ F +A+ A +
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 31/57 (54%), Gaps = 2/57 (3%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRAC 82
++V L + +R+ F FG I A V+ + GRSKG+GFV F PE A +A
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAV 72
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 3/66 (4%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFK---DPEAAMRAC 82
++V GL + M + F Q+G I+ + ++ D+ TG S+G GF+ F + E A++
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 83 QNPSPV 88
P+
Sbjct: 64 NGQKPL 69
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 39.3 bits (90), Expect = 0.002, Method: Composition-based stats.
Identities = 21/59 (35%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 25 KIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQ 83
+IFV L ++ ++ F + G +L A + + G+SKG G V F+ PE A RAC+
Sbjct: 10 QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACR 66
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 32/57 (56%)
Query: 25 KIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRA 81
++FV L++ + + + + F +G + E D T + KG+ FVTF PE A++A
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKA 66
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/59 (38%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 25 KIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDK--NTGRSKGYGFVTFKDPEAAMRA 81
K+FVG + +R FEQ+G + E V+ D+ N +SKG FVTF +AA+ A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Score = 35.4 bits (80), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 35/67 (52%), Gaps = 2/67 (2%)
Query: 6 PLQMVGGNHPGDYNDTTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSK 65
P+QM + + N K+F+G ++ + + +R F FG+I E ++ + G S+
Sbjct: 79 PIQMKPADSEKN-NAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPD-GLSR 136
Query: 66 GYGFVTF 72
G FVTF
Sbjct: 137 GCAFVTF 143
>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 = 0.003, Method: Composition-based stats.
Identities = 25/87 (28%), Positives = 40/87 (45%), Gaps = 9/87 (10%)
Query: 25 KIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTF-KDPEAAMRACQ 83
KIFVG ++ +R FE+ G ++E V+ D Y FV K+ +A Q
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQ 62
Query: 84 NPSPVIDGRRANCNLASLGAHKTRPPT 110
+ G+R N L++ G K+ P +
Sbjct: 63 LNGKEVKGKRINVELSTKGQKKSGPSS 89
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain
In Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 38.9 bits (89), Expect = 0.003, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 2/58 (3%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQ 83
IFV L ++ ++ F + G +L A + + G+SKG G V F+ PE A RAC+
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACR 63
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 39/80 (48%), Gaps = 1/80 (1%)
Query: 21 TTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMR 80
TT ++VGGLA E + F FG+I + + D T + +G+ FV F+ E A
Sbjct: 61 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 120
Query: 81 ACQNPSPV-IDGRRANCNLA 99
A N + + GR NLA
Sbjct: 121 AIDNMNESELFGRTIRVNLA 140
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 38.9 bits (89), Expect = 0.003, Method: Composition-based stats.
Identities = 24/78 (30%), Positives = 36/78 (46%), Gaps = 8/78 (10%)
Query: 20 DTTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAM 79
D T T ++VGGL +R +F QFGEI V+ + F+ F +AA
Sbjct: 9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQC------AFIQFATRQAAE 62
Query: 80 RACQNP--SPVIDGRRAN 95
A + +++GRR N
Sbjct: 63 VAAEKSFNKLIVNGRRLN 80
>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 = 38.5 bits (88), Expect = 0.004, Method: Composition-based stats.
Identities = 16/59 (27%), Positives = 33/59 (55%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQN 84
+++G + ++ + + G ++ ++ D TGRSKGY F+ F+D E++ 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 = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 32/59 (54%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQN 84
+F+ L E + + F FG ++ A V DK T SK +GFV++ +P +A A Q+
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86
>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 = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 23/59 (38%), Positives = 32/59 (54%), Gaps = 2/59 (3%)
Query: 25 KIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDK--NTGRSKGYGFVTFKDPEAAMRA 81
K FVG + +R FEQ+G + E V+ D+ N +SKG FVTF +AA+ A
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Score = 33.9 bits (76), Expect = 0.096, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 25 KIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTF 72
K+F+G ++ + + +R F FG+I E ++ + G S+G FVTF
Sbjct: 97 KLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPD-GLSRGCAFVTF 143
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
28
Length = 111
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 43/89 (48%), Gaps = 8/89 (8%)
Query: 19 NDTTFTK-IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEA 77
+D T K +F+ L+++++ + + +QFG++ V+ +T SKG F F EA
Sbjct: 10 SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEA 69
Query: 78 AMRACQNPS-------PVIDGRRANCNLA 99
A + S +DGR+ +LA
Sbjct: 70 AQKCLAAASLEAEGGGLKLDGRQLKVDLA 98
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAA 78
+FVG L + + + F Q G + + + D+ G+ K +GFV FK PE+
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESV 70
>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 = 36.6 bits (83), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 27/58 (46%)
Query: 25 KIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRAC 82
K+F+GGL D ++ FG + ++ D TG SKGY F + D +A
Sbjct: 116 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 173
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 36.2 bits (82), Expect = 0.018, Method: Composition-based stats.
Identities = 17/50 (34%), Positives = 25/50 (50%)
Query: 25 KIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKD 74
K+F+GGL D ++ FG + ++ D TG SKGY F + D
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVD 52
>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 = 36.2 bits (82), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 27/58 (46%)
Query: 25 KIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRAC 82
K+F+GGL D ++ FG + ++ D TG SKGY F + D +A
Sbjct: 98 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 155
>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 = 0.019, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 35/72 (48%), Gaps = 3/72 (4%)
Query: 12 GNHPGDYNDTTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFV- 70
G+ PG +FV G+ E + + F ++GEI + D+ TG KGY V
Sbjct: 12 GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVE 71
Query: 71 --TFKDPEAAMR 80
T+K+ +AAM
Sbjct: 72 YETYKEAQAAME 83
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In
Trinucleotide Repeat Containing 4 Variant
Length = 102
Score = 36.2 bits (82), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 25 KIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFK 73
K+FVG L + + +R+ FE FG I E V+ + G SKG FV F+
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPD-GTSKGCAFVKFQ 61
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14
Complex
Length = 110
Score = 36.2 bits (82), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 30/56 (53%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRA 81
+FV + E Q D ++ F +GEI + D+ TG SKGY V ++ + A+ A
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 84
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 36.2 bits (82), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 27/58 (46%)
Query: 25 KIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRAC 82
K+F+GGL D ++ FG + ++ D TG SKGY F + D +A
Sbjct: 96 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 153
>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 = 35.8 bits (81), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 35/72 (48%), Gaps = 3/72 (4%)
Query: 12 GNHPGDYNDTTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFV- 70
G+ PG +FV G+ E + + F ++GEI + D+ TG KGY V
Sbjct: 11 GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVE 70
Query: 71 --TFKDPEAAMR 80
T+K+ +AAM
Sbjct: 71 YETYKEAQAAME 82
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 35.4 bits (80), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 30/58 (51%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQ 83
++VGGL + + F Q G ++ + D+ TG+ +GYGFV F E A A +
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIK 75
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 35.4 bits (80), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 34/72 (47%), Gaps = 7/72 (9%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQNP 85
++ GG+A MR+ F FG+I+E V + KGY FV F E+A A +
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSV 81
Query: 86 S-PVIDGRRANC 96
+ I+G C
Sbjct: 82 NGTTIEGHVVKC 93
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 35.4 bits (80), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 6/61 (9%)
Query: 13 NHPGDYNDTTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTF 72
PG+ T +++FVG L + + MR+ FE++G+ E + D KG+GF+
Sbjct: 12 RKPGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRL 65
Query: 73 K 73
+
Sbjct: 66 E 66
Score = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 24/49 (48%), Gaps = 1/49 (2%)
Query: 38 DTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQNPS 86
+ + F FG++ AVVI D + GR G G V F AA +A S
Sbjct: 111 ELLEEAFSVFGQVERAVVIVD-DRGRPSGKGIVEFSGKPAARKALDRCS 158
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 35.4 bits (80), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 33/59 (55%), Gaps = 1/59 (1%)
Query: 24 TKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRAC 82
+ +FV L ++ ++ F G ++ A ++ DK+ G+S+G G VTF+ A++A
Sbjct: 16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTFEQSIEAVQAI 73
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 35.0 bits (79), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 26/47 (55%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTF 72
+F LA + + +F G++ + +I+D+N+ RSKG +V F
Sbjct: 28 VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEF 74
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 35.0 bits (79), Expect = 0.049, Method: Composition-based stats.
Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 3/59 (5%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFV---TFKDPEAAMRA 81
+FV G+ E + + F ++GEI + D+ TG KGY V T+K+ +AAM
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 68
>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 = 34.7 bits (78), Expect = 0.057, Method: Composition-based stats.
Identities = 15/68 (22%), Positives = 32/68 (47%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQNP 85
I+VG + + + + +F G + ++ DK +G KG+ ++ F D E+ +
Sbjct: 9 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALD 68
Query: 86 SPVIDGRR 93
+ GR+
Sbjct: 69 ESLFRGRQ 76
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 34.7 bits (78), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 6/60 (10%)
Query: 14 HPGDYNDTTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFK 73
PG+ T ++FVG L + + +R FE++GE E + R +G+GF+ +
Sbjct: 13 KPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFI------NRDRGFGFIRLE 66
Score = 33.1 bits (74), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 34/73 (46%), Gaps = 12/73 (16%)
Query: 28 VGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQN--- 84
V L+ + + + F QFG + +AVV+ D + GR+ G GFV F A +A +
Sbjct: 101 VKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGD 159
Query: 85 --------PSPVI 89
P PVI
Sbjct: 160 GAFLLTTTPRPVI 172
>pdb|2XB2|D Chain D, Crystal Structure Of The Core
Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How
The Ejc Is Bridged To The Nmd Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core
Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How
The Ejc Is Bridged To The Nmd Machinery
Length = 90
Score = 34.7 bits (78), Expect = 0.066, Method: Composition-based stats.
Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 3/59 (5%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFV---TFKDPEAAMRA 81
+FV G+ E + + F ++GEI + D+ TG KGY V T+K+ +AAM
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 68
>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 = 34.3 bits (77), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 30/56 (53%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRA 81
+FV + E Q D ++ F +GEI + D+ TG SKGY V ++ + A+ A
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 130
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 34.3 bits (77), Expect = 0.068, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 33/70 (47%), Gaps = 3/70 (4%)
Query: 15 PGDYNDTTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFV---T 71
PG +FV G+ E + + F ++GEI + D+ TG KGY V T
Sbjct: 1 PGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 60
Query: 72 FKDPEAAMRA 81
+K+ +AAM
Sbjct: 61 YKEAQAAMEG 70
>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 = 34.3 bits (77), Expect = 0.076, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 3/58 (5%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFV---TFKDPEAAMR 80
+FV G+ E + + F ++GEI + D+ TG KGY V T+K+ +AAM
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 67
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 34.3 bits (77), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 32/60 (53%), Gaps = 4/60 (6%)
Query: 25 KIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFK---DPEAAMRA 81
K+FVG L + + + R F+ FG I E V+ + G SKG FV F + +AA+ A
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPD-GSSKGCAFVKFSSHTEAQAAIHA 75
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 33.5 bits (75), Expect = 0.12, Method: Composition-based stats.
Identities = 15/59 (25%), Positives = 31/59 (52%), Gaps = 5/59 (8%)
Query: 24 TKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRAC 82
+K+FVG + + ++++F Q+GE+++ + + + FVTF D + A C
Sbjct: 12 SKVFVGRCTEDMTAEELQQFFCQYGEVVDVFI-----PKPFRAFAFVTFADDKVAQSLC 65
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 33.5 bits (75), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 31/66 (46%), Gaps = 8/66 (12%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAV--------VITDKNTGRSKGYGFVTFKDPEA 77
IFV GL +++ YF+Q G I + TD+ TG+ KG V+F DP +
Sbjct: 16 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 75
Query: 78 AMRACQ 83
A A
Sbjct: 76 AKAAID 81
>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 = 33.5 bits (75), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 15/68 (22%), Positives = 32/68 (47%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQNP 85
I+VG + + + + +F G + ++ DK +G KG+ ++ F D E+ +
Sbjct: 8 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALD 67
Query: 86 SPVIDGRR 93
+ GR+
Sbjct: 68 ESLFRGRQ 75
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 33.1 bits (74), Expect = 0.15, Method: Composition-based stats.
Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 5/57 (8%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRAC 82
+FVG + D +R +F Q+G++++ + + + FVTF D + A C
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFI-----PKPFRAFAFVTFADDQIAQSLC 59
>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 = 0.18, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 22 TFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDK--NTGRSKGYGFVTFKDPEAAM 79
T +KI V + ++ + +R F FGE L+ V + K TG +G+GFV F + A
Sbjct: 14 TTSKILVRNIPFQANQREIRELFSTFGE-LKTVRLPKKMTGTGAHRGFGFVDFITKQDAK 72
Query: 80 RA 81
+A
Sbjct: 73 KA 74
>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 = 33.1 bits (74), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 16/67 (23%), Positives = 30/67 (44%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQNP 85
++VG + + + + +F G I ++ DK +G KGY ++ F + + A
Sbjct: 39 VYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMD 98
Query: 86 SPVIDGR 92
V GR
Sbjct: 99 ETVFRGR 105
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 33.1 bits (74), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 31/66 (46%), Gaps = 8/66 (12%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAV--------VITDKNTGRSKGYGFVTFKDPEA 77
IFV GL +++ YF+Q G I + TD+ TG+ KG V+F DP +
Sbjct: 10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 69
Query: 78 AMRACQ 83
A A
Sbjct: 70 AKAAID 75
>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 = 0.20, Method: Compositional matrix adjust.
Identities = 24/98 (24%), Positives = 42/98 (42%), Gaps = 12/98 (12%)
Query: 20 DTTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAV--------VITDKNTGRSKGYGFVT 71
D+ + I+V GL D + +F+Q G + + DK TG+ KG V+
Sbjct: 12 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVS 71
Query: 72 FKDPEAAMRACQNPSPVIDGRRANCNLASLGAHKTRPP 109
++DP A A + DG+ + + + +PP
Sbjct: 72 YEDPPTAKAAVE----WFDGKDFQGSKLKVSLARKKPP 105
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 32.3 bits (72), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 18/76 (23%), Positives = 36/76 (47%), Gaps = 9/76 (11%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFV---TFKDPEAAMRAC 82
+ + L++ +T++ FE+ + + G+SKGY F+ +F+D + A+ +C
Sbjct: 18 LVLSNLSYSATEETLQEVFEK----ATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSC 73
Query: 83 QNPSPVIDGRRANCNL 98
I+GR L
Sbjct: 74 NKRE--IEGRAIRLEL 87
>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition
Motif Of Nono
pdb|2RS8|A Chain A, Solution Structure Of The N-Terminal Rna Recognition
Motif Of Nono
Length = 99
Score = 32.3 bits (72), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 31/57 (54%), Gaps = 9/57 (15%)
Query: 20 DTTFT---KIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFK 73
+ TFT ++FVG L + + MR+ FE++G+ E + D KG+GF+ +
Sbjct: 9 EKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLE 59
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 32.0 bits (71), Expect = 0.43, Method: Composition-based stats.
Identities = 17/62 (27%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 24 TKIFVGGLAWETQRDTMRRYFEQFGEI-LEAVVITDKNTGRSKGYGFVTFKDPEAAMRAC 82
TK+ +G L +D + F +G+I + + + + SKGY +V F++P+ A +A
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
Query: 83 QN 84
++
Sbjct: 65 KH 66
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 31.6 bits (70), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 7/76 (9%)
Query: 25 KIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRS----KGYGFVTFKDPEAAMR 80
K+FVGGL + D + F +FG ++ V K +S KGY F+ F++ E++++
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLV--VDWPHKAESKSYFPPKGYAFLLFQE-ESSVQ 66
Query: 81 ACQNPSPVIDGRRANC 96
A + DG+ C
Sbjct: 67 ALIDACLEEDGKLYLC 82
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 31.6 bits (70), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 21/35 (60%)
Query: 47 FGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRA 81
FG + ++ + TG+SKGYGF + ++A RA
Sbjct: 119 FGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA 153
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 31.6 bits (70), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 21/35 (60%)
Query: 47 FGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRA 81
FG + ++ + TG+SKGYGF + ++A 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 = 31.6 bits (70), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 21/35 (60%)
Query: 47 FGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRA 81
FG + ++ + TG+SKGYGF + ++A RA
Sbjct: 117 FGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA 151
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif In Trna Selenocysteine Associated Protein
Length = 104
Score = 30.8 bits (68), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 27/61 (44%), Gaps = 3/61 (4%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDP---EAAMRAC 82
+FVG L + + +F + + TG SKGYGFV F D + A+ C
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTEC 71
Query: 83 Q 83
Q
Sbjct: 72 Q 72
>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 = 0.92, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 38/83 (45%), Gaps = 3/83 (3%)
Query: 1 MSQQRPLQMVGGNHPGDYNDTTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKN 60
+SQ R G N + ++VG L++ T + + F + G+I + ++ DK
Sbjct: 17 LSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKM 76
Query: 61 TGRSKGYGFVTF---KDPEAAMR 80
+ G+ FV + D E AMR
Sbjct: 77 KKTACGFCFVEYYSRADAENAMR 99
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 30.0 bits (66), Expect = 1.5, Method: Composition-based stats.
Identities = 19/78 (24%), Positives = 37/78 (47%), Gaps = 9/78 (11%)
Query: 24 TKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQ 83
TK+ VG ++ +R FE++G ++E ++ D Y FV + E A+ A +
Sbjct: 11 TKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIR 62
Query: 84 N-PSPVIDGRRANCNLAS 100
+ G+R + L++
Sbjct: 63 GLDNTEFQGKRMHVQLST 80
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 30.0 bits (66), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 8/59 (13%)
Query: 26 IFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQN 84
+FV LA + + + F +FG++ + + K Y FV F+D AA++A
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKL--------ERVKKLKDYAFVHFEDRGAAVKAMDE 68
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 29.6 bits (65), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 15/65 (23%), Positives = 30/65 (46%), Gaps = 8/65 (12%)
Query: 20 DTTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAM 79
+ + T++FV + Q + F FG + E ++ G+ FV F++ E+A
Sbjct: 28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAA 79
Query: 80 RACQN 84
+A +
Sbjct: 80 KAIEE 84
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 6/59 (10%)
Query: 24 TKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRAC 82
T+++VGGL T + R F++FG I D G S + ++ ++ +AA AC
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIR----TIDHVKGDS--FAYIQYESLDAAQAAC 70
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 28.9 bits (63), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 23/40 (57%), Gaps = 3/40 (7%)
Query: 44 FEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQ 83
F QFG+IL+ V + T + +G FV FK+ +A A +
Sbjct: 31 FSQFGQILDIVAL---KTLKMRGQAFVIFKEIGSASNALR 67
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 28.1 bits (61), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 16/73 (21%), Positives = 34/73 (46%), Gaps = 1/73 (1%)
Query: 27 FVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRSKGYGFVTFKDPEAAMRACQNPS 86
+VG L + T + + F+ I ++ DK+T + KG+ +V F + ++ A
Sbjct: 19 YVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDG 77
Query: 87 PVIDGRRANCNLA 99
++ R ++A
Sbjct: 78 ALLGDRSLRVDIA 90
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 27.7 bits (60), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 35/78 (44%), Gaps = 4/78 (5%)
Query: 5 RPLQMVGGNHPGDYNDTTFTKIFVGGLAWETQRDTMRRYFEQFGEILEAVVITDKNTGRS 64
R + M +PG+ N + K + T+RD + F +F E + TGR
Sbjct: 11 RKIPMFSSYNPGEPNKVLYLKNLSPRV---TERDLVS-LFARFQEKKGPPIQFRMMTGRM 66
Query: 65 KGYGFVTFKDPEAAMRAC 82
+G F+TF + E A +A
Sbjct: 67 RGQAFITFPNKEIAWQAL 84
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
0.319 0.136 0.431
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,286,457
Number of Sequences: 62578
Number of extensions: 334480
Number of successful extensions: 743
Number of sequences better than 100.0: 143
Number of HSP's better than 100.0 without gapping: 118
Number of HSP's successfully gapped in prelim test: 25
Number of HSP's that attempted gapping in prelim test: 580
Number of HSP's gapped (non-prelim): 165
length of query: 278
length of database: 14,973,337
effective HSP length: 98
effective length of query: 180
effective length of database: 8,840,693
effective search space: 1591324740
effective search space used: 1591324740
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)