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= 012289
(466 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 147 bits (372), Expect = 1e-35, Method: Compositional matrix adjust.
Identities = 71/161 (44%), Positives = 107/161 (66%), Gaps = 16/161 (9%)
Query: 3 SDNGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEI 62
++ K+FIGG++WDT E+ L+EYF YG V + IMKD TGR+RGFGF+ F P+ +
Sbjct: 1 KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDE 60
Query: 63 VIQEKHNIDGRMVEAKKAVPRDDQIVLNRXXXXXXXXXXXXRTRKIFVGGLASTVTESDF 122
V++ +H +DG++++ K+A+PRD+Q +T KIFVGG+ V +F
Sbjct: 61 VVKTQHILDGKVIDPKRAIPRDEQ----------------DKTGKIFVGGIGPDVRPKEF 104
Query: 123 KKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKV 163
+++F Q+GTI D +M D +T + RGFGF+TYDS +AVD+V
Sbjct: 105 EEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRV 145
Score = 67.4 bits (163), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 32/83 (38%), Positives = 51/83 (61%), Gaps = 1/83 (1%)
Query: 2 QSDNGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAE 61
Q GK+F+GGI D + +E+FS +G +++A +M D++TG++RGFGFV + +
Sbjct: 84 QDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVD 143
Query: 62 IVIQEKH-NIDGRMVEAKKAVPR 83
V Q K + R +E K+A PR
Sbjct: 144 RVCQNKFIDFKDRKIEIKRAEPR 166
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 121 bits (303), Expect = 1e-27, Method: Compositional matrix adjust.
Identities = 59/158 (37%), Positives = 93/158 (58%), Gaps = 11/158 (6%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQE 66
KLFIGG+S++T +E L+ +F +G + + V+M+D NT R+RGFGFV +A + +
Sbjct: 16 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 75
Query: 67 K-HNIDGRMVEAKKAVPRDDQIVLNRXXXXXXXXXXXXRTRKIFVGGLASTVTESDFKKY 125
+ H +DGR+VE K+AV R+D +KIFVGG+ E + Y
Sbjct: 76 RPHKVDGRVVEPKRAVSRED----------SQRPGAHLTVKKIFVGGIKEDTEEHHLRDY 125
Query: 126 FDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKV 163
F+Q+G I + +M D + + RGF F+T+D ++VDK+
Sbjct: 126 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 163
Score = 75.1 bits (183), Expect = 7e-14, Method: Compositional matrix adjust.
Identities = 35/80 (43%), Positives = 52/80 (65%), Gaps = 1/80 (1%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFAD-PAVAEIVIQ 65
K+F+GGI DT E L++YF YG++ IM DR +G+ RGF FV F D +V +IVIQ
Sbjct: 107 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 166
Query: 66 EKHNIDGRMVEAKKAVPRDD 85
+ H ++G E +KA+ + +
Sbjct: 167 KYHTVNGHNCEVRKALSKQE 186
Score = 72.0 bits (175), Expect = 6e-13, Method: Compositional matrix adjust.
Identities = 32/66 (48%), Positives = 46/66 (69%)
Query: 106 RKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVKR 165
RK+F+GGL+ T+ + +F+Q+GT+TD VVM D NT+R RGFGF+TY + E VD
Sbjct: 15 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 74
Query: 166 AVPKEL 171
A P ++
Sbjct: 75 ARPHKV 80
>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 = 120 bits (302), Expect = 1e-27, Method: Compositional matrix adjust.
Identities = 59/158 (37%), Positives = 93/158 (58%), Gaps = 11/158 (6%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQE 66
KLFIGG+S++T +E L+ +F +G + + V+M+D NT R+RGFGFV +A + +
Sbjct: 14 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 73
Query: 67 K-HNIDGRMVEAKKAVPRDDQIVLNRXXXXXXXXXXXXRTRKIFVGGLASTVTESDFKKY 125
+ H +DGR+VE K+AV R+D +KIFVGG+ E + Y
Sbjct: 74 RPHKVDGRVVEPKRAVSRED----------SQRPGAHLTVKKIFVGGIKEDTEEHHLRDY 123
Query: 126 FDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKV 163
F+Q+G I + +M D + + RGF F+T+D ++VDK+
Sbjct: 124 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 161
Score = 75.1 bits (183), Expect = 8e-14, Method: Compositional matrix adjust.
Identities = 35/80 (43%), Positives = 52/80 (65%), Gaps = 1/80 (1%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFAD-PAVAEIVIQ 65
K+F+GGI DT E L++YF YG++ IM DR +G+ RGF FV F D +V +IVIQ
Sbjct: 105 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 164
Query: 66 EKHNIDGRMVEAKKAVPRDD 85
+ H ++G E +KA+ + +
Sbjct: 165 KYHTVNGHNCEVRKALSKQE 184
Score = 72.0 bits (175), Expect = 7e-13, Method: Compositional matrix adjust.
Identities = 32/66 (48%), Positives = 46/66 (69%)
Query: 106 RKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVKR 165
RK+F+GGL+ T+ + +F+Q+GT+TD VVM D NT+R RGFGF+TY + E VD
Sbjct: 13 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 72
Query: 166 AVPKEL 171
A P ++
Sbjct: 73 ARPHKV 78
>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
pdb|1U1K|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt 7da
Ggg); A Human Telomeric Repeat Containing
7-Deaza-Adenine
pdb|1U1L|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt Prn
Ggg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1M|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 7gu
Gg); A Human Telomeric Repeat Containing 7-Deaza-Guanine
pdb|1U1N|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta (Prn)
Gg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1O|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggttag(Di)g); A Human Telomeric Repeat Containing
Inosine
pdb|1U1P|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 2pr
Gg); A Human Telomeric Repeat Containing 2-Aminopurine
pdb|1U1Q|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggtta(Di)gg); A Human Telomeric Repeat Containing
Inosine
pdb|1U1R|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(2pr)
G); A Human Telomeric Repeat Containing 2-Aminopurine
Length = 196
Score = 120 bits (302), Expect = 1e-27, Method: Compositional matrix adjust.
Identities = 59/158 (37%), Positives = 93/158 (58%), Gaps = 11/158 (6%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQE 66
KLFIGG+S++T +E L+ +F +G + + V+M+D NT R+RGFGFV +A + +
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 67 K-HNIDGRMVEAKKAVPRDDQIVLNRXXXXXXXXXXXXRTRKIFVGGLASTVTESDFKKY 125
+ H +DGR+VE K+AV R+D +KIFVGG+ E + Y
Sbjct: 75 RPHKVDGRVVEPKRAVSRED----------SQRPGAHLTVKKIFVGGIKEDTEEHHLRDY 124
Query: 126 FDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKV 163
F+Q+G I + +M D + + RGF F+T+D ++VDK+
Sbjct: 125 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 162
Score = 75.1 bits (183), Expect = 8e-14, Method: Compositional matrix adjust.
Identities = 35/80 (43%), Positives = 52/80 (65%), Gaps = 1/80 (1%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFAD-PAVAEIVIQ 65
K+F+GGI DT E L++YF YG++ IM DR +G+ RGF FV F D +V +IVIQ
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 165
Query: 66 EKHNIDGRMVEAKKAVPRDD 85
+ H ++G E +KA+ + +
Sbjct: 166 KYHTVNGHNCEVRKALSKQE 185
Score = 72.0 bits (175), Expect = 6e-13, Method: Compositional matrix adjust.
Identities = 32/66 (48%), Positives = 46/66 (69%)
Query: 106 RKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVKR 165
RK+F+GGL+ T+ + +F+Q+GT+TD VVM D NT+R RGFGF+TY + E VD
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 166 AVPKEL 171
A P ++
Sbjct: 74 ARPHKV 79
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 120 bits (300), Expect = 2e-27, Method: Compositional matrix adjust.
Identities = 59/158 (37%), Positives = 93/158 (58%), Gaps = 11/158 (6%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQE 66
KLFIGG+S++T +E L+ +F +G + + V+M+D NT R+RGFGFV +A + +
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 67 K-HNIDGRMVEAKKAVPRDDQIVLNRXXXXXXXXXXXXRTRKIFVGGLASTVTESDFKKY 125
+ H +DGR+VE K+AV R+D +KIFVGG+ E + Y
Sbjct: 75 RPHKVDGRVVEPKRAVSRED----------SQRPGAHLTVKKIFVGGIKEDTEEHHLRDY 124
Query: 126 FDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKV 163
F+Q+G I + +M D + + RGF F+T+D ++VDK+
Sbjct: 125 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 162
Score = 74.3 bits (181), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 35/78 (44%), Positives = 51/78 (65%), Gaps = 1/78 (1%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFAD-PAVAEIVIQ 65
K+F+GGI DT E L++YF YG++ IM DR +G+ RGF FV F D +V +IVIQ
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 165
Query: 66 EKHNIDGRMVEAKKAVPR 83
+ H ++G E +KA+ +
Sbjct: 166 KYHTVNGHNCEVRKALSK 183
Score = 71.2 bits (173), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 32/66 (48%), Positives = 46/66 (69%)
Query: 106 RKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVKR 165
RK+F+GGL+ T+ + +F+Q+GT+TD VVM D NT+R RGFGF+TY + E VD
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 166 AVPKEL 171
A P ++
Sbjct: 74 ARPHKV 79
>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 = 119 bits (299), Expect = 2e-27, Method: Compositional matrix adjust.
Identities = 59/158 (37%), Positives = 93/158 (58%), Gaps = 11/158 (6%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQE 66
KLFIGG+S++T +E L+ +F +G + + V+M+D NT R+RGFGFV +A + +
Sbjct: 8 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67
Query: 67 K-HNIDGRMVEAKKAVPRDDQIVLNRXXXXXXXXXXXXRTRKIFVGGLASTVTESDFKKY 125
+ H +DGR+VE K+AV R+D +KIFVGG+ E + Y
Sbjct: 68 RPHKVDGRVVEPKRAVSRED----------SQRPGAHLTVKKIFVGGIKEDTEEHHLRDY 117
Query: 126 FDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKV 163
F+Q+G I + +M D + + RGF F+T+D ++VDK+
Sbjct: 118 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 155
Score = 74.7 bits (182), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 35/80 (43%), Positives = 52/80 (65%), Gaps = 1/80 (1%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFAD-PAVAEIVIQ 65
K+F+GGI DT E L++YF YG++ IM DR +G+ RGF FV F D +V +IVIQ
Sbjct: 99 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 158
Query: 66 EKHNIDGRMVEAKKAVPRDD 85
+ H ++G E +KA+ + +
Sbjct: 159 KYHTVNGHNCEVRKALSKQE 178
Score = 71.6 bits (174), Expect = 9e-13, Method: Compositional matrix adjust.
Identities = 32/66 (48%), Positives = 46/66 (69%)
Query: 106 RKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVKR 165
RK+F+GGL+ T+ + +F+Q+GT+TD VVM D NT+R RGFGF+TY + E VD
Sbjct: 7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66
Query: 166 AVPKEL 171
A P ++
Sbjct: 67 ARPHKV 72
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 119 bits (299), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 59/158 (37%), Positives = 93/158 (58%), Gaps = 11/158 (6%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQE 66
KLFIGG+S++T +E L+ +F +G + + V+M+D NT R+RGFGFV +A + +
Sbjct: 13 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 72
Query: 67 K-HNIDGRMVEAKKAVPRDDQIVLNRXXXXXXXXXXXXRTRKIFVGGLASTVTESDFKKY 125
+ H +DGR+VE K+AV R+D +KIFVGG+ E + Y
Sbjct: 73 RPHKVDGRVVEPKRAVSRED----------SQRPGAHLTVKKIFVGGIKEDTEEHHLRDY 122
Query: 126 FDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKV 163
F+Q+G I + +M D + + RGF F+T+D ++VDK+
Sbjct: 123 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 160
Score = 74.3 bits (181), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 35/78 (44%), Positives = 51/78 (65%), Gaps = 1/78 (1%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFAD-PAVAEIVIQ 65
K+F+GGI DT E L++YF YG++ IM DR +G+ RGF FV F D +V +IVIQ
Sbjct: 104 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 163
Query: 66 EKHNIDGRMVEAKKAVPR 83
+ H ++G E +KA+ +
Sbjct: 164 KYHTVNGHNCEVRKALSK 181
Score = 71.2 bits (173), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 32/66 (48%), Positives = 46/66 (69%)
Query: 106 RKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVKR 165
RK+F+GGL+ T+ + +F+Q+GT+TD VVM D NT+R RGFGF+TY + E VD
Sbjct: 12 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 71
Query: 166 AVPKEL 171
A P ++
Sbjct: 72 ARPHKV 77
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 95.9 bits (237), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 41/79 (51%), Positives = 54/79 (68%), Gaps = 1/79 (1%)
Query: 6 GKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADP-AVAEIVI 64
GKLF+GG+ W T +E L+ YFS YGEVV+ VIMKD+ T ++RGFGFV F DP V ++
Sbjct: 17 GKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLA 76
Query: 65 QEKHNIDGRMVEAKKAVPR 83
H +DGR ++ K PR
Sbjct: 77 SRPHTLDGRNIDPKPCTPR 95
Score = 57.0 bits (136), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 25/65 (38%), Positives = 36/65 (55%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVKRA 166
K+FVGGL + T+ + YF Q+G + D V+M D T + RGFGF+ + V V +
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 167 VPKEL 171
P L
Sbjct: 78 RPHTL 82
>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 = 92.4 bits (228), Expect = 5e-19, Method: Composition-based stats.
Identities = 42/80 (52%), Positives = 62/80 (77%), Gaps = 1/80 (1%)
Query: 2 QSDNGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAE 61
+ D GK F+GG+SWDT+++ LK+YF+ +GEVV+ I D NTGR+RGFGF++F D A E
Sbjct: 8 EEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVE 67
Query: 62 IVI-QEKHNIDGRMVEAKKA 80
V+ Q++H +DGR+++ KKA
Sbjct: 68 KVLDQKEHRLDGRVIDPKKA 87
Score = 55.8 bits (133), Expect = 5e-08, Method: Composition-based stats.
Identities = 26/57 (45%), Positives = 35/57 (61%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKV 163
K FVGGL+ ++ D K YF +FG + D + D NT R RGFGFI + +V+KV
Sbjct: 13 KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKV 69
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 85.5 bits (210), Expect = 6e-17, Method: Composition-based stats.
Identities = 41/87 (47%), Positives = 58/87 (66%), Gaps = 1/87 (1%)
Query: 1 MQSDNGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPA-V 59
M S K+FIGG+SW T +E L+EYF +GEV E ++M+D T R+RGFGFV F D A V
Sbjct: 21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGV 80
Query: 60 AEIVIQEKHNIDGRMVEAKKAVPRDDQ 86
+++ Q +H +D + ++ K A PR Q
Sbjct: 81 DKVLAQSRHELDSKTIDPKVAFPRRAQ 107
Score = 59.3 bits (142), Expect = 4e-09, Method: Composition-based stats.
Identities = 26/57 (45%), Positives = 39/57 (68%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKV 163
K+F+GGL+ T+ ++YF QFG + + +VM D T+R RGFGF+T+ + VDKV
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV 83
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 84.0 bits (206), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 39/82 (47%), Positives = 56/82 (68%), Gaps = 2/82 (2%)
Query: 1 MQSDNGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFA--DPA 58
M SD GKLF+GG+S+DTNE+ L++ FS YG++ E V++KDR T R+RGFGFV F D A
Sbjct: 8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDA 67
Query: 59 VAEIVIQEKHNIDGRMVEAKKA 80
++ ++DGR + +A
Sbjct: 68 KDAMMAMNGKSVDGRQIRVDQA 89
Score = 58.2 bits (139), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 27/61 (44%), Positives = 40/61 (65%), Gaps = 3/61 (4%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVKRA 166
K+FVGGL+ E ++ F ++G I++VVV+ D TQR RGFGF+T+ E +D K A
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTF---ENIDDAKDA 70
Query: 167 V 167
+
Sbjct: 71 M 71
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 81.3 bits (199), Expect = 1e-15, Method: Composition-based stats.
Identities = 36/75 (48%), Positives = 53/75 (70%), Gaps = 1/75 (1%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPA-VAEIVIQ 65
K+FIGG+SW T +E L+EYF +GEV E ++M+D T R+RGFGFV F D A V +++ Q
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 66 EKHNIDGRMVEAKKA 80
+H +D + ++ K A
Sbjct: 62 SRHELDSKTIDPKVA 76
Score = 61.2 bits (147), Expect = 1e-09, Method: Composition-based stats.
Identities = 26/57 (45%), Positives = 39/57 (68%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKV 163
K+F+GGL+ T+ ++YF QFG + + +VM D T+R RGFGF+T+ + VDKV
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV 58
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 81.3 bits (199), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 36/80 (45%), Positives = 58/80 (72%), Gaps = 1/80 (1%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQE 66
KLFIGG+S++T EE L+ Y+ +G++ + V+M+D + R+RGFGFV F+ A + +
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 88
Query: 67 K-HNIDGRMVEAKKAVPRDD 85
+ H+IDGR+VE K+AV R++
Sbjct: 89 RPHSIDGRVVEPKRAVAREE 108
Score = 67.0 bits (162), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 29/66 (43%), Positives = 42/66 (63%)
Query: 106 RKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVKR 165
RK+F+GGL+ TE + Y++Q+G +TD VVM D ++R RGFGF+T+ S VD
Sbjct: 28 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA 87
Query: 166 AVPKEL 171
A P +
Sbjct: 88 ARPHSI 93
>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 = 79.0 bits (193), Expect = 6e-15, Method: Composition-based stats.
Identities = 34/74 (45%), Positives = 58/74 (78%), Gaps = 1/74 (1%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADP-AVAEIVIQE 66
+FIGG+SWDT ++ LK+YFS +GEVV+ + D TGR+RGFGFV+F + +V +++ Q+
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 67 KHNIDGRMVEAKKA 80
+H ++G++++ K+A
Sbjct: 62 EHKLNGKVIDPKRA 75
Score = 57.8 bits (138), Expect = 1e-08, Method: Composition-based stats.
Identities = 25/56 (44%), Positives = 35/56 (62%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKV 163
+F+GGL+ T+ D K YF +FG + D + D T R RGFGF+ + E+VDKV
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKV 57
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 73.9 bits (180), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 37/86 (43%), Positives = 55/86 (63%), Gaps = 16/86 (18%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDK---- 162
KIFVGG+ E++ ++YF +FG +T+VV++YD QRPRGFGFIT++ E++VD+
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
Query: 163 -----------VKRAVPKE-LSPGPT 176
VKRA P++ S GP+
Sbjct: 72 HFHDIMGKKVEVKRAEPRDSKSSGPS 97
Score = 69.7 bits (169), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 35/81 (43%), Positives = 49/81 (60%), Gaps = 1/81 (1%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADP-AVAEIVIQ 65
K+F+GGI + E L+EYF +G V E V++ D R RGFGF+ F D +V + V
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
Query: 66 EKHNIDGRMVEAKKAVPRDDQ 86
H+I G+ VE K+A PRD +
Sbjct: 72 HFHDIMGKKVEVKRAEPRDSK 92
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 72.8 bits (177), Expect = 4e-13, Method: Composition-based stats.
Identities = 30/56 (53%), Positives = 41/56 (73%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKV 163
IFVGGL+ T D K YF+QFG + D ++M+D T R RGFGF+T++SE+ V+KV
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKV 57
Score = 68.9 bits (167), Expect = 5e-12, Method: Composition-based stats.
Identities = 33/74 (44%), Positives = 48/74 (64%), Gaps = 1/74 (1%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQ-E 66
+F+GG+S +T E +K YF +G+V +A++M D+ T R RGFGFV F + E V +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 67 KHNIDGRMVEAKKA 80
H I+ +MVE KKA
Sbjct: 62 FHEINNKMVECKKA 75
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 67.8 bits (164), Expect = 1e-11, Method: Composition-based stats.
Identities = 32/71 (45%), Positives = 45/71 (63%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQEK 67
L + G+ W T E+ LKEYFST+GEV+ + KD TG ++GFGFV F + V+ ++
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 77
Query: 68 HNIDGRMVEAK 78
H IDGR + K
Sbjct: 78 HMIDGRWCDCK 88
Score = 42.0 bits (97), Expect = 6e-04, Method: Composition-based stats.
Identities = 23/60 (38%), Positives = 30/60 (50%)
Query: 104 RTRKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKV 163
+T + V GL TE D K+YF FG + V V D T +GFGF+ + E KV
Sbjct: 14 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKV 73
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 67.8 bits (164), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 30/68 (44%), Positives = 48/68 (70%), Gaps = 1/68 (1%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQE 66
K+F+GG+ + T + L++YF +G++ EAV++ DR TG++RG+GFV AD A AE ++
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 67 KHN-IDGR 73
+ IDGR
Sbjct: 79 PNPIIDGR 86
Score = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 24/59 (40%), Positives = 36/59 (61%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVKR 165
KIFVGGL T++ +KYF+ FG I + VV+ D T + RG+GF+T A ++ +
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 77
>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 = 65.1 bits (157), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 41/159 (25%), Positives = 74/159 (46%), Gaps = 22/159 (13%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQEK 67
L + + + +E + F + GE+ +++D+ TG++ G+GFV + DP AE I
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 68 H--NIDGRMVEAKKAVPRDDQIVLNRXXXXXXXXXXXXRTRKIFVGGLASTVTESDFKKY 125
+ + + ++ A P I R ++V GL T+T+ + ++
Sbjct: 65 NGLRLQTKTIKVSYARPSSASI----------------RDANLYVSGLPKTMTQKELEQL 108
Query: 126 FDQFGTITDVVVMYDHNTQRPRGFGFITYD----SEEAV 160
F Q+G I ++ D T RG GFI +D +EEA+
Sbjct: 109 FSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 147
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 35/61 (57%)
Query: 5 NGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVI 64
+ L++ G+ ++ L++ FS YG ++ + I+ D+ TG +RG GF+ F AE I
Sbjct: 88 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 147
Query: 65 Q 65
+
Sbjct: 148 K 148
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 62.4 bits (150), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 38/159 (23%), Positives = 75/159 (47%), Gaps = 22/159 (13%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQEK 67
L + + + ++ K F + G++ +++D+ TG++ G+GFV ++DP A+ I
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 68 H--NIDGRMVEAKKAVPRDDQIVLNRXXXXXXXXXXXXRTRKIFVGGLASTVTESDFKKY 125
+ + + ++ A P I R ++V GL T+++ + ++
Sbjct: 67 NGLKLQTKTIKVSYARPSSASI----------------RDANLYVSGLPKTMSQKEMEQL 110
Query: 126 FDQFGTITDVVVMYDHNTQRPRGFGFITYD----SEEAV 160
F Q+G I ++ D T RG GFI +D +EEA+
Sbjct: 111 FSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 149
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 36/61 (59%)
Query: 5 NGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVI 64
+ L++ G+ +++ +++ FS YG ++ + I+ D+ TG +RG GF+ F AE I
Sbjct: 90 DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 149
Query: 65 Q 65
+
Sbjct: 150 K 150
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 61.6 bits (148), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 29/77 (37%), Positives = 53/77 (68%), Gaps = 3/77 (3%)
Query: 6 GKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQ 65
GKLFIGG++ +TNE+ LK F +G + E +++KDR T ++RGF F+ F +PA A+ +
Sbjct: 8 GKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAK 66
Query: 66 EKH--NIDGRMVEAKKA 80
+ + ++ G+ ++ ++A
Sbjct: 67 DMNGKSLHGKAIKVEQA 83
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 30/49 (61%), Gaps = 1/49 (2%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYD 155
K+F+GGL E K F + G I++V+++ D T + RGF FIT++
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFE 56
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 60.8 bits (146), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 40/159 (25%), Positives = 73/159 (45%), Gaps = 22/159 (13%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQEK 67
L + + + ++ L+ FS+ GEV A +++D+ G + G+GFV + AE I
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 68 H--NIDGRMVEAKKAVPRDDQIVLNRXXXXXXXXXXXXRTRKIFVGGLASTVTESDFKKY 125
+ + + ++ A P + I + +++ GL T+T+ D +
Sbjct: 65 NGLRLQSKTIKVSYARPSSEVI----------------KDANLYISGLPRTMTQKDVEDM 108
Query: 126 FDQFGTITDVVVMYDHNTQRPRGFGFITYD----SEEAV 160
F +FG I + V+ D T RG FI +D +EEA+
Sbjct: 109 FSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147
Score = 38.1 bits (87), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 34/60 (56%)
Query: 5 NGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVI 64
+ L+I G+ ++ +++ FS +G ++ + ++ D+ TG +RG F+ F + AE I
Sbjct: 88 DANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147
>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 = 60.8 bits (146), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 40/159 (25%), Positives = 73/159 (45%), Gaps = 22/159 (13%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQEK 67
L + + + ++ L+ FS+ GEV A +++D+ G + G+GFV + AE I
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 68 H--NIDGRMVEAKKAVPRDDQIVLNRXXXXXXXXXXXXRTRKIFVGGLASTVTESDFKKY 125
+ + + ++ A P + I + +++ GL T+T+ D +
Sbjct: 65 NGLRLQSKTIKVSYARPSSEVI----------------KDANLYISGLPRTMTQKDVEDM 108
Query: 126 FDQFGTITDVVVMYDHNTQRPRGFGFITYD----SEEAV 160
F +FG I + V+ D T RG FI +D +EEA+
Sbjct: 109 FSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147
Score = 38.1 bits (87), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 34/60 (56%)
Query: 5 NGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVI 64
+ L+I G+ ++ +++ FS +G ++ + ++ D+ TG +RG F+ F + AE I
Sbjct: 88 DANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147
>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 = 58.9 bits (141), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 34/161 (21%), Positives = 75/161 (46%), Gaps = 19/161 (11%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQE 66
++++G I ++ E+ +++ F+ +G + + D T + +GF FV + P A++ +++
Sbjct: 30 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 89
Query: 67 KHNID--------GRMVEAKKAVPRDDQIVLNRXXXXXXXXXXXXRTRKIFVGGLASTVT 118
+++ GR +A P DQ+ +I+V + ++
Sbjct: 90 MNSVMLGGRNIKVGRPSNIGQAQPIIDQLA-----------EEARAFNRIYVASVHQDLS 138
Query: 119 ESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEA 159
+ D K F+ FG I + D T + +G+GFI Y+ ++
Sbjct: 139 DDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQS 179
>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 = 58.5 bits (140), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 34/161 (21%), Positives = 74/161 (45%), Gaps = 19/161 (11%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQE 66
++++G I ++ E+ +++ F+ +G + D T + +GF FV + P A++ +++
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 67 KHNID--------GRMVEAKKAVPRDDQIVLNRXXXXXXXXXXXXRTRKIFVGGLASTVT 118
+++ GR +A P DQ+ +I+V + ++
Sbjct: 74 XNSVXLGGRNIKVGRPSNIGQAQPIIDQLA-----------EEARAFNRIYVASVHQDLS 122
Query: 119 ESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEA 159
+ D K F+ FG I + D T + +G+GFI Y+ ++
Sbjct: 123 DDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQS 163
>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 = 57.8 bits (138), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 34/161 (21%), Positives = 75/161 (46%), Gaps = 19/161 (11%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQE 66
++++G I ++ E+ +++ F+ +G + + D T + +GF FV + P A++ +++
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 67 KHNID--------GRMVEAKKAVPRDDQIVLNRXXXXXXXXXXXXRTRKIFVGGLASTVT 118
+++ GR +A P DQ+ +I+V + ++
Sbjct: 75 MNSVMLGGRNIKVGRPSNIGQAQPIIDQLA-----------EEARAFNRIYVASVHQDLS 123
Query: 119 ESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEA 159
+ D K F+ FG I + D T + +G+GFI Y+ ++
Sbjct: 124 DDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQS 164
>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 = 57.0 bits (136), Expect = 2e-08, Method: Composition-based stats.
Identities = 28/76 (36%), Positives = 46/76 (60%), Gaps = 1/76 (1%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQE 66
K+F+GG+S DT EE+++EYF +GEV + D T + RGF F+ F + + ++++
Sbjct: 3 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 62
Query: 67 K-HNIDGRMVEAKKAV 81
K HN+ E K A+
Sbjct: 63 KYHNVGLSKCEIKVAM 78
Score = 54.3 bits (129), Expect = 1e-07, Method: Composition-based stats.
Identities = 24/58 (41%), Positives = 35/58 (60%)
Query: 106 RKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKV 163
+KIFVGGL+ E ++YF FG + + + D+ T + RGF FIT+ EE V K+
Sbjct: 2 KKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKI 59
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 55.1 bits (131), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 44/182 (24%), Positives = 77/182 (42%), Gaps = 17/182 (9%)
Query: 3 SDNGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDR--NTGRARGFGFVVFADPAVA 60
SD K+F+G + +E+ L+E F YG V E +++DR N +++G FV F A
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 61 EIVIQEKHNIDGR--MVEAKKAVPRDDQIVLNRXXXXXXXXXXXXRTRKIFVGGLASTVT 118
HN+ M + P D + RK+F+G ++ T
Sbjct: 61 LEAQNALHNMKVLPGMHHPIQMKPADSE------------KNNAVEDRKLFIGMISKKCT 108
Query: 119 ESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVKRAVPKELSPGPTRS 178
E+D + F FG I + ++ + RG F+T+ + +A+ + + S
Sbjct: 109 ENDIRVMFSSFGQIEECRILRGPDG-LSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSS 167
Query: 179 PL 180
P+
Sbjct: 168 PM 169
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 54.7 bits (130), Expect = 1e-07, Method: Composition-based stats.
Identities = 27/74 (36%), Positives = 44/74 (59%), Gaps = 1/74 (1%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQEK 67
+F+GG+S DT EE+++EYF +GEV + D T + RGF F+ F + + ++++K
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Query: 68 -HNIDGRMVEAKKA 80
HN+ E K A
Sbjct: 62 YHNVGLSKCEIKVA 75
Score = 51.2 bits (121), Expect = 1e-06, Method: Composition-based stats.
Identities = 23/56 (41%), Positives = 33/56 (58%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKV 163
IFVGGL+ E ++YF FG + + + D+ T + RGF FIT+ EE V K+
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKI 57
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 43/181 (23%), Positives = 76/181 (41%), Gaps = 17/181 (9%)
Query: 4 DNGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDR--NTGRARGFGFVVFADPAVAE 61
D K+F+G + +E+ L+E F YG V E +++DR N +++G FV F A
Sbjct: 14 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 73
Query: 62 IVIQEKHNIDGR--MVEAKKAVPRDDQIVLNRXXXXXXXXXXXXRTRKIFVGGLASTVTE 119
HN+ M + P D + RK+F+G ++ TE
Sbjct: 74 EAQNALHNMKVLPGMHHPIQMKPADSE------------KNNAVEDRKLFIGMISKKCTE 121
Query: 120 SDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVKRAVPKELSPGPTRSP 179
+D + F FG I + ++ + RG F+T+ + +A+ + + SP
Sbjct: 122 NDIRVMFSSFGQIEECRILRGPDG-LSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSP 180
Query: 180 L 180
+
Sbjct: 181 M 181
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 53.1 bits (126), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 46/80 (57%), Gaps = 2/80 (2%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQEK 67
L++G + ++ E+ L+ F +G++ V+MKD +TGR++G+GF+ F+D A +++
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 68 H--NIDGRMVEAKKAVPRDD 85
+ + GR + R D
Sbjct: 68 NGFELAGRPMRVGHVTERLD 87
Score = 48.9 bits (115), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 32/112 (28%), Positives = 49/112 (43%), Gaps = 27/112 (24%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVKRAV 167
++VG L +TE + F+ FG I ++V+M D +T R +G+GFIT+ E +RA+
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA---RRAL 64
Query: 168 PKELSPGPTRSPLGGYHYGLSRVNSFLNGYTQGYTPSTVGGYGLRMDGRFSP 219
+ LNG+ P VG R+DG P
Sbjct: 65 EQ------------------------LNGFELAGRPMRVGHVTERLDGGSGP 92
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 52.8 bits (125), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 38/171 (22%), Positives = 69/171 (40%), Gaps = 18/171 (10%)
Query: 3 SDNGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEI 62
+ N L + + D + L F G + IM+D TG + G+ FV F ++
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 63 VIQEKHNIDGRMVEAKKAVPRDDQIVLNRXXXXXXXXXXXXRTRKIFVGGLASTVTESDF 122
I+ + I R K + R + ++V L T+T+
Sbjct: 61 AIKVLNGITVRNKRLKVSYAR--------------PGGESIKDTNLYVTNLPRTITDDQL 106
Query: 123 KKYFDQFGTITDVVVMYDHNTQRPRGFGFITY----DSEEAVDKVKRAVPK 169
F ++G+I ++ D T RPRG F+ Y +++EA+ + +P+
Sbjct: 107 DTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPE 157
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 52.8 bits (125), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 37/61 (60%), Gaps = 3/61 (4%)
Query: 106 RKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSE---EAVDK 162
R I+VG L + T K+ F QFG + +V ++YD T++P+GFGF+ E EA+ K
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAK 61
Query: 163 V 163
+
Sbjct: 62 L 62
Score = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 45/78 (57%), Gaps = 3/78 (3%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQEK 67
+++G + + E++KE FS +G+V ++ DR T + +GFGFV + +V+E I +
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSE-AIAKL 62
Query: 68 HNID--GRMVEAKKAVPR 83
N D GR + +A P+
Sbjct: 63 DNTDFMGRTIRVTEANPK 80
>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 = 52.0 bits (123), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 40/154 (25%), Positives = 66/154 (42%), Gaps = 13/154 (8%)
Query: 3 SDNGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDR--NTGRARGFGFVVFADPAVA 60
SD K F+G + +E+ L+E F YG V E +++DR N +++G FV F A
Sbjct: 1 SDAIKXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 61 EIVIQEKHNIDGRMVEAKKAVPRDDQIVLNRXXXXXXXXXXXXRTRKIFVGGLASTVTES 120
HN K +P + + RK+F+G ++ TE+
Sbjct: 61 LEAQNALHN--------XKVLPGXHHPIQXK--PADSEKNNAVEDRKLFIGXISKKCTEN 110
Query: 121 DFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY 154
D + F FG I + ++ + RG F+T+
Sbjct: 111 DIRVXFSSFGQIEECRILRGPDG-LSRGCAFVTF 143
Score = 38.9 bits (89), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 37/63 (58%), Gaps = 2/63 (3%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRP--RGFGFITYDSEEAVDKVK 164
K FVG + T +E D ++ F+Q+G + ++ V+ D + P +G F+T+ + +A + +
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 165 RAV 167
A+
Sbjct: 65 NAL 67
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 34/78 (43%), Positives = 41/78 (52%), Gaps = 5/78 (6%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVF--ADPAVAEIVIQ 65
LF+ G+S DT EE LKE F V A I+ DR TG ++GFGFV F + A A
Sbjct: 18 LFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAM 74
Query: 66 EKHNIDGRMVEAKKAVPR 83
E IDG V A P+
Sbjct: 75 EDGEIDGNKVTLDWAKPK 92
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 35/63 (55%), Gaps = 3/63 (4%)
Query: 105 TRKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVK 164
++ +FV GL+ TE K+ FD G++ +V D T +GFGF+ ++SEE K
Sbjct: 15 SKTLFVKGLSEDTTEETLKESFD--GSVRARIVT-DRETGSSKGFGFVDFNSEEDAKAAK 71
Query: 165 RAV 167
A+
Sbjct: 72 EAM 74
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 41/174 (23%), Positives = 74/174 (42%), Gaps = 20/174 (11%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQEK 67
L++G + E+ LK+YF G + IM D+N + FV + A I +Q
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNV-NYAFVEYHQSHDANIALQT- 60
Query: 68 HNIDGRMVEAKKAVPRDDQIVLNRXXXXXXXXXXXXRTRKIFVGGLASTVTESDFKKYFD 127
++G+ +E ++ T +FVG L V + + F
Sbjct: 61 --LNGKQIENN---------IVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFK 109
Query: 128 QFGTITDVVVMYDHNTQRPRGFGFITY----DSEEAVDKVKRAVPKELSPGPTR 177
F + VM+D T RG+GF+++ D++ A+D ++ ++L+ P R
Sbjct: 110 DFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQ---GQDLNGRPLR 160
Score = 37.7 bits (86), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 2/72 (2%)
Query: 4 DNGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFA--DPAVAE 61
D LF+G ++ + ++E L+ F + + +M D TG +RG+GFV F D A
Sbjct: 86 DTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNA 145
Query: 62 IVIQEKHNIDGR 73
+ + +++GR
Sbjct: 146 MDSMQGQDLNGR 157
Score = 34.3 bits (77), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 106 RKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY 154
R ++VG L +TE K+YF G I ++ +M D N + + F+ Y
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNN-KNVNYAFVEY 48
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 50.4 bits (119), Expect = 2e-06, Method: Composition-based stats.
Identities = 29/81 (35%), Positives = 42/81 (51%), Gaps = 5/81 (6%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQE 66
K+F+G + D E L+++F YGEVV+ I K R F FV FAD VA+ + E
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSLCGE 67
Query: 67 KHNIDGRMVEAKKAVPRDDQI 87
I G V A P+ +++
Sbjct: 68 DLIIKGISVHISNAEPKHNKL 88
Score = 34.7 bits (78), Expect = 0.11, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 11/65 (16%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRP-RGFGFITYDSEEAVDKVKR 165
K+FVG +T + +++F Q+G + DV + +P R F F+T+ A DKV +
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYGEVVDVFI------PKPFRAFAFVTF----ADDKVAQ 62
Query: 166 AVPKE 170
++ E
Sbjct: 63 SLCGE 67
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 39/66 (59%), Gaps = 3/66 (4%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQEK 67
+F+G I ++ EE+LK+ FS G VV ++ DR TG+ +G+GF + D E +
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQD---QETALSAM 67
Query: 68 HNIDGR 73
N++GR
Sbjct: 68 RNLNGR 73
Score = 45.8 bits (107), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 28/53 (52%)
Query: 106 RKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEE 158
R +FVG + TE K F + G + ++YD T +P+G+GF Y +E
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61
>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 = 50.1 bits (118), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 41/162 (25%), Positives = 73/162 (45%), Gaps = 17/162 (10%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQEK 67
L++G + D E L E FS G ++ + +D T R+ G+ +V F PA AE + +
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL-DT 76
Query: 68 HNIDGRMVEAKKAVPRDDQIVLNRXXXXXXXXXXXXRTRKIFVGGLASTVTESDFKKYFD 127
N D +++ K +I+ ++ IF+ L ++ F
Sbjct: 77 MNFD--VIKGKPV-----RIMWSQRDPSLRKSGVG----NIFIKNLDKSIDNKALYDTFS 125
Query: 128 QFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVKRAVPK 169
FG I V+ D N +G+GF+ ++++EA + RA+ K
Sbjct: 126 AFGNILSCKVVCDENGS--KGYGFVHFETQEAAE---RAIEK 162
Score = 33.5 bits (75), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 39/75 (52%), Gaps = 5/75 (6%)
Query: 6 GKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQ 65
G +FI + + + L + FS +G ++ ++ D N ++G+GFV F AE I+
Sbjct: 104 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIE 161
Query: 66 EKHNIDGRMVEAKKA 80
+ ++G ++ +K
Sbjct: 162 K---MNGMLLNDRKV 173
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 50.1 bits (118), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 40/76 (52%), Gaps = 5/76 (6%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQEK 67
+F+G + D E+ L+E+FS YG+V++ I K R F FV FAD +A+ + E
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCGED 62
Query: 68 HNIDGRMVEAKKAVPR 83
I G V A P+
Sbjct: 63 LIIKGISVHISNAEPK 78
Score = 34.3 bits (77), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 35/64 (54%), Gaps = 11/64 (17%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRP-RGFGFITYDSEEAVDKVKRA 166
+FVG +TE + +++F Q+G + DV + +P R F F+T+ A D++ ++
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFI------PKPFRAFAFVTF----ADDQIAQS 57
Query: 167 VPKE 170
+ E
Sbjct: 58 LCGE 61
>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|B Chain B, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|C Chain C, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
Length = 184
Score = 49.3 bits (116), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 37/172 (21%), Positives = 69/172 (40%), Gaps = 18/172 (10%)
Query: 2 QSDNGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAE 61
++ N L + + D + L F G + I +D TG + G+ FV F ++
Sbjct: 11 RASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQ 70
Query: 62 IVIQEKHNIDGRMVEAKKAVPRDDQIVLNRXXXXXXXXXXXXRTRKIFVGGLASTVTESD 121
I+ + I R K + R + ++V L T+T+
Sbjct: 71 RAIKVLNGITVRNKRLKVSYAR--------------PGGESIKDTNLYVTNLPRTITDDQ 116
Query: 122 FKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY----DSEEAVDKVKRAVPK 169
F ++G+I ++ D T RPRG F+ Y +++EA+ + +P+
Sbjct: 117 LDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPE 168
>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 = 48.5 bits (114), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 41/162 (25%), Positives = 73/162 (45%), Gaps = 17/162 (10%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQEK 67
L++G + D E L E FS G ++ + +D T R+ G+ +V F PA AE + +
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL-DT 71
Query: 68 HNIDGRMVEAKKAVPRDDQIVLNRXXXXXXXXXXXXRTRKIFVGGLASTVTESDFKKYFD 127
N D +++ K +I+ ++ IF+ L ++ F
Sbjct: 72 MNFD--VIKGKPV-----RIMWSQRDPSLRKSGVG----NIFIKNLDKSIDNKALYDTFS 120
Query: 128 QFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVKRAVPK 169
FG I V+ D N +G+GF+ ++++EA + RA+ K
Sbjct: 121 AFGNILSCKVVCDENGS--KGYGFVHFETQEAAE---RAIEK 157
Score = 32.7 bits (73), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 39/75 (52%), Gaps = 5/75 (6%)
Query: 6 GKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQ 65
G +FI + + + L + FS +G ++ ++ D N ++G+GFV F AE I+
Sbjct: 99 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIE 156
Query: 66 EKHNIDGRMVEAKKA 80
+ ++G ++ +K
Sbjct: 157 K---MNGMLLNDRKV 168
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 48.1 bits (113), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 34/57 (59%), Gaps = 3/57 (5%)
Query: 110 VGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVKRA 166
V GL+ TE D ++ F ++G I DV ++YD ++R RGF F+ + E VD K A
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF---ENVDDAKEA 73
Score = 45.1 bits (105), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 4/74 (5%)
Query: 5 NGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVI 64
N L + G+S T E L+E FS YG + + I+ D+ + R+RGF FV F + A+
Sbjct: 15 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA- 73
Query: 65 QEKHN---IDGRMV 75
+E+ N +DGR +
Sbjct: 74 KERANGMELDGRRI 87
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 40/152 (26%), Positives = 63/152 (41%), Gaps = 27/152 (17%)
Query: 3 SDNGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEI 62
+ +LF+G + D EE K F YGE E I +D RGFGF+ +AEI
Sbjct: 20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEI 73
Query: 63 VIQEKHNIDGRMVEAKKAVPRDDQIVLNRXXXXXXXXXXXXRTRKIFVGGLASTVTESDF 122
K +DG +++++ R + V L+ V+
Sbjct: 74 A---KAELDGTILKSRPLRIR-----------------FATHGAALTVKNLSPVVSNELL 113
Query: 123 KKYFDQFGTITDVVVMYDHNTQRPRGFGFITY 154
++ F QFG + VV+ D + R G GF+ +
Sbjct: 114 EQAFSQFGPVEKAVVVVD-DRGRATGKGFVEF 144
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 32/50 (64%), Gaps = 6/50 (12%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS 156
++FVG L + +TE DFK+ F+++G ++V + D RGFGFI +S
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLES 67
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 46/78 (58%), Gaps = 1/78 (1%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQEK 67
+F+GGI +E ++ +F+ YG V E I+ DR TG ++G+GFV F + + +++ +
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 71
Query: 68 HNIDGRMVEAKKAVPRDD 85
N G+ ++ A+ + +
Sbjct: 72 INFHGKKLKLGPAIRKQN 89
Score = 36.6 bits (83), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 43/72 (59%), Gaps = 5/72 (6%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVKRAV 167
+FVGG+ + E++ + +F ++G++ +V ++ D T +G+GF+++ ++ V K+ +
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 71
Query: 168 P----KELSPGP 175
K+L GP
Sbjct: 72 INFHGKKLKLGP 83
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 34/57 (59%), Gaps = 3/57 (5%)
Query: 110 VGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVKRA 166
V GL+ TE D ++ F ++G I DV ++YD ++R RGF F+ + E VD K A
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF---ENVDDAKEA 73
Score = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/82 (32%), Positives = 45/82 (54%), Gaps = 4/82 (4%)
Query: 5 NGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVI 64
N L + G+S T E L+E FS YG + + I+ D+ + R+RGF FV F + A+
Sbjct: 15 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA- 73
Query: 65 QEKHN---IDGRMVEAKKAVPR 83
+E+ N +DGR + ++ +
Sbjct: 74 KERANGMELDGRRIRVDFSITK 95
>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 = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 41/64 (64%)
Query: 3 SDNGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEI 62
S++ +F+G +S + E +K F+ +G + +A ++KD TG+++G+GFV F + AE
Sbjct: 13 SNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAEN 72
Query: 63 VIQE 66
IQ+
Sbjct: 73 AIQQ 76
Score = 45.4 bits (106), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 4/60 (6%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFIT----YDSEEAVDKV 163
+FVG L+ +T D K F FG I+D V+ D T + +G+GF++ +D+E A+ ++
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Rna, Uuguucuu
Length = 102
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 46/78 (58%), Gaps = 1/78 (1%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQEK 67
+F+GGI +E ++ +F+ YG V E I+ DR TG ++G+GFV F + + +++ +
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 68 HNIDGRMVEAKKAVPRDD 85
N G+ ++ A+ + +
Sbjct: 71 INFHGKKLKLGPAIRKQN 88
Score = 37.4 bits (85), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 47/83 (56%), Gaps = 7/83 (8%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVKRAV 167
+FVGG+ + E++ + +F ++G++ +V ++ D T +G+GF+++ ++ V K+ +
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 168 P----KELSPGPT--RSPLGGYH 184
K+L GP + L YH
Sbjct: 71 INFHGKKLKLGPAIRKQNLSTYH 93
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 34/57 (59%), Gaps = 3/57 (5%)
Query: 110 VGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVKRA 166
V GL+ TE D ++ F ++G I DV ++YD ++R RGF F+ + E VD K A
Sbjct: 51 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF---ENVDDAKEA 104
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 42/76 (55%), Gaps = 4/76 (5%)
Query: 5 NGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVI 64
N L + G+S T E L+E FS YG + + I+ D+ + R+RGF FV F + A+
Sbjct: 46 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA- 104
Query: 65 QEKHN---IDGRMVEA 77
+E+ N +DGR +
Sbjct: 105 KERANGMELDGRRIRV 120
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 34/57 (59%), Gaps = 3/57 (5%)
Query: 110 VGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVKRA 166
V GL+ TE D ++ F ++G I DV ++YD ++R RGF F+ + E VD K A
Sbjct: 17 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF---ENVDDAKEA 70
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 4/74 (5%)
Query: 5 NGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVI 64
N L + G+S T E L+E FS YG + + I+ D+ + R+RGF FV F + A+
Sbjct: 12 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA- 70
Query: 65 QEKHN---IDGRMV 75
+E+ N +DGR +
Sbjct: 71 KERANGMELDGRRI 84
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 47.0 bits (110), Expect = 2e-05, Method: Composition-based stats.
Identities = 21/81 (25%), Positives = 45/81 (55%), Gaps = 2/81 (2%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQE 66
+L++G + ++ E+ L+ F +G + +M D TGR++G+GF+ F+D A+ +++
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 67 KHNID--GRMVEAKKAVPRDD 85
+ + GR ++ R D
Sbjct: 88 LNGFELAGRPMKVGHVTERTD 108
Score = 44.7 bits (104), Expect = 1e-04, Method: Composition-based stats.
Identities = 20/56 (35%), Positives = 31/56 (55%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDK 162
+++VG L +TE + F+ FG I + +M D T R +G+GFIT+ E K
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKK 83
>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 = 47.0 bits (110), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQEK 67
+F+GGI +E ++ +F+ YG V E I+ DR TG ++G+GFV F + + +++ +
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 68 HNIDGRMVEAKKAVPR 83
N G+ ++ A+ +
Sbjct: 71 INFHGKKLKLGPAIRK 86
Score = 35.8 bits (81), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 43/72 (59%), Gaps = 5/72 (6%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVKRAV 167
+FVGG+ + E++ + +F ++G++ +V ++ D T +G+GF+++ ++ V K+ +
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 168 P----KELSPGP 175
K+L GP
Sbjct: 71 INFHGKKLKLGP 82
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 46.6 bits (109), Expect = 3e-05, Method: Composition-based stats.
Identities = 22/65 (33%), Positives = 36/65 (55%), Gaps = 4/65 (6%)
Query: 106 RKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY----DSEEAVD 161
R ++VGGLA V + F FG ITD+ + D+ T++ RGF F+ + D+ A+D
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
Query: 162 KVKRA 166
+ +
Sbjct: 124 NMNES 128
Score = 38.5 bits (88), Expect = 0.009, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVF--ADPAVAEIVIQ 65
L++GG++ + +++ L F +G++ + I D T + RGF FV F A+ A A I
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 66 EKHNIDGRMVEAKKA 80
+ + GR + A
Sbjct: 126 NESELFGRTIRVNLA 140
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 46.2 bits (108), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 42/71 (59%), Gaps = 5/71 (7%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQEK 67
L++ + ++ERL++ FS +G + A +M + GR++GFGFV F+ P A + E
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTE- 74
Query: 68 HNIDGRMVEAK 78
++GR+V K
Sbjct: 75 --MNGRIVATK 83
Score = 36.6 bits (83), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 2/55 (3%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDK 162
++V L + + +K F FGTIT VM + R +GFGF+ + S E K
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGG--RSKGFGFVCFSSPEEATK 70
>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 = 45.8 bits (107), Expect = 4e-05, Method: Composition-based stats.
Identities = 22/65 (33%), Positives = 36/65 (55%), Gaps = 4/65 (6%)
Query: 106 RKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY----DSEEAVD 161
R ++VGGLA V + F FG ITD+ + D+ T++ RGF F+ + D+ A+D
Sbjct: 3 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 62
Query: 162 KVKRA 166
+ +
Sbjct: 63 NMNES 67
Score = 38.1 bits (87), Expect = 0.012, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVF--ADPAVAEIVIQ 65
L++GG++ + +++ L F +G++ + I D T + RGF FV F A+ A A I
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 66 EKHNIDGRMVEAKKA 80
+ + GR + A
Sbjct: 65 NESELFGRTIRVNLA 79
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 45.8 bits (107), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 40/62 (64%)
Query: 3 SDNGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEI 62
S++ +F+G +S + E +K F+ +G++ +A ++KD TG+++G+GFV F + AE
Sbjct: 13 SNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAEN 72
Query: 63 VI 64
I
Sbjct: 73 AI 74
Score = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 34/57 (59%), Gaps = 4/57 (7%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY----DSEEAV 160
+FVG L+ +T D K F FG I+D V+ D T + +G+GF+++ D+E A+
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAI 74
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 45.8 bits (107), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 37/67 (55%), Gaps = 1/67 (1%)
Query: 106 RKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYD-SEEAVDKVK 164
R ++VGGLA V + F FG ITD+ + D+ T++ RGF F+ ++ +E+A +
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
Query: 165 RAVPKEL 171
EL
Sbjct: 73 NMNESEL 79
Score = 39.3 bits (90), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 42/84 (50%), Gaps = 2/84 (2%)
Query: 1 MQSDNGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVF--ADPA 58
M + L++GG++ + +++ L F +G++ + I D T + RGF FV F A+ A
Sbjct: 8 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 67
Query: 59 VAEIVIQEKHNIDGRMVEAKKAVP 82
A I + + GR + A P
Sbjct: 68 AAAIDNMNESELFGRTIRVNLAKP 91
>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 = 45.8 bits (107), Expect = 6e-05, Method: Composition-based stats.
Identities = 22/65 (33%), Positives = 36/65 (55%), Gaps = 4/65 (6%)
Query: 106 RKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY----DSEEAVD 161
R ++VGGLA V + F FG ITD+ + D+ T++ RGF F+ + D+ A+D
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
Query: 162 KVKRA 166
+ +
Sbjct: 68 NMNES 72
Score = 37.7 bits (86), Expect = 0.014, Method: Composition-based stats.
Identities = 23/82 (28%), Positives = 41/82 (50%), Gaps = 2/82 (2%)
Query: 1 MQSDNGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVF--ADPA 58
M + L++GG++ + +++ L F +G++ + I D T + RGF FV F A+ A
Sbjct: 3 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 62
Query: 59 VAEIVIQEKHNIDGRMVEAKKA 80
A I + + GR + A
Sbjct: 63 AAAIDNMNESELFGRTIRVNLA 84
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 45.4 bits (106), Expect = 6e-05, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 40/72 (55%), Gaps = 1/72 (1%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVKRA 166
K+F+G + + E D K F++FG I ++ V+ D T +G F+TY E+ K + A
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74
Query: 167 VPKELS-PGPTR 177
+ ++ + PG R
Sbjct: 75 LHEQKTLPGMNR 86
Score = 44.7 bits (104), Expect = 1e-04, Method: Composition-based stats.
Identities = 26/82 (31%), Positives = 44/82 (53%), Gaps = 5/82 (6%)
Query: 4 DNGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFAD---PAVA 60
D KLFIG I + +E+ LK F +G++ E ++KDR TG +G F+ + + A
Sbjct: 12 DAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKA 71
Query: 61 EIVIQEKHNIDG--RMVEAKKA 80
+ + E+ + G R ++ K A
Sbjct: 72 QSALHEQKTLPGMNRPIQVKPA 93
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 45.4 bits (106), Expect = 6e-05, Method: Composition-based stats.
Identities = 22/65 (33%), Positives = 36/65 (55%), Gaps = 4/65 (6%)
Query: 106 RKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY----DSEEAVD 161
R ++VGGLA V + F FG ITD+ + D+ T++ RGF F+ + D+ A+D
Sbjct: 6 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65
Query: 162 KVKRA 166
+ +
Sbjct: 66 NMNES 70
Score = 37.4 bits (85), Expect = 0.016, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVF--ADPAVAEIVIQ 65
L++GG++ + +++ L F +G++ + I D T + RGF FV F A+ A A I
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 66 EKHNIDGRMVEAKKA 80
+ + GR + A
Sbjct: 68 NESELFGRTIRVNLA 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 = 45.1 bits (105), Expect = 8e-05, Method: Composition-based stats.
Identities = 22/76 (28%), Positives = 44/76 (57%), Gaps = 2/76 (2%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQEK 67
+++ + + L FS YG+VV+ IMKD++T +++G F++F D A+ +
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 68 HN--IDGRMVEAKKAV 81
+N + GR+++A A+
Sbjct: 79 NNKQLFGRVIKASIAI 94
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 30/51 (58%)
Query: 4 DNGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVF 54
DN + + +S DT E L+E F +G + + KD+ TG+++GF F+ F
Sbjct: 14 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISF 64
Score = 37.0 bits (84), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 28/51 (54%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEE 158
I V L+ E+D ++ F FG+I+ + + D T + +GF FI++ E
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRE 68
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 3/72 (4%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQE 66
+LF+ +S+ ++EE L++ FS YG + E D T + +GF FV F P E ++
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFP---EHAVKA 66
Query: 67 KHNIDGRMVEAK 78
+DG++ + +
Sbjct: 67 YAEVDGQVFQGR 78
Score = 41.6 bits (96), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 31/48 (64%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY 154
++FV L+ T +E D +K F +G ++++ D T++P+GF F+T+
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTF 57
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 39/162 (24%), Positives = 65/162 (40%), Gaps = 31/162 (19%)
Query: 3 SDNGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEI 62
+ +LF+G + D EE +++ F YG+ E I KD +GFGF+ +AEI
Sbjct: 20 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEI 73
Query: 63 VIQEKHN--IDGRMVEAKKAVPRDDQIVLNRXXXXXXXXXXXXRTRKIFVGGLASTVTES 120
E N + G+ + + A + + V L V+
Sbjct: 74 AKVELDNMPLRGKQLRVRFAC----------------------HSASLTVRNLPQYVSNE 111
Query: 121 DFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDK 162
++ F FG + VV+ D + RP G G + + + A K
Sbjct: 112 LLEEAFSVFGQVERAVVIVD-DRGRPSGKGIVEFSGKPAARK 152
>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 = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 30/49 (61%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFAD 56
+++G I +D EE++ + S G V+ +M D TGR++G+ F+ F D
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRD 55
Score = 32.7 bits (73), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 30/61 (49%), Gaps = 1/61 (1%)
Query: 105 TRKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY-DSEEAVDKV 163
+R +++G + TE G + ++ +M+D T R +G+ FI + D E + V
Sbjct: 4 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 63
Query: 164 K 164
+
Sbjct: 64 R 64
>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 = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 30/49 (61%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFAD 56
+++G I +D EE++ + S G V+ +M D TGR++G+ F+ F D
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRD 54
Score = 32.3 bits (72), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 30/61 (49%), Gaps = 1/61 (1%)
Query: 105 TRKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY-DSEEAVDKV 163
+R +++G + TE G + ++ +M+D T R +G+ FI + D E + V
Sbjct: 3 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 62
Query: 164 K 164
+
Sbjct: 63 R 63
>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 = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 2/75 (2%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQEK 67
L + +++ T+ + L+ F YG V + I +DR T +RGF FV F D AE +
Sbjct: 50 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109
Query: 68 HN--IDGRMVEAKKA 80
+DGR + + A
Sbjct: 110 DGAVLDGRELRVQMA 124
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 42.7 bits (99), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 30/49 (61%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFAD 56
+++G I +D EE++ + S G V+ +M D TGR++G+ F+ F D
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRD 53
Score = 32.3 bits (72), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 30/61 (49%), Gaps = 1/61 (1%)
Query: 105 TRKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY-DSEEAVDKV 163
+R +++G + TE G + ++ +M+D T R +G+ FI + D E + V
Sbjct: 2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61
Query: 164 K 164
+
Sbjct: 62 R 62
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 42.7 bits (99), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 31/51 (60%)
Query: 106 RKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS 156
R + V + +TV E ++ F+++G I V ++ D T++ RG+GF+ + S
Sbjct: 43 RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQS 93
Score = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 31/57 (54%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVI 64
L + I +E +L++ F YG + I+ DR T ++RG+GFV F + A+ I
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAI 101
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 42.4 bits (98), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 36/61 (59%)
Query: 5 NGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVI 64
+ L++ G+ +++ +++ FS YG ++ + I+ D+ TG +RG GF+ F AE I
Sbjct: 1 DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
Query: 65 Q 65
+
Sbjct: 61 K 61
Score = 42.0 bits (97), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 33/57 (57%), Gaps = 4/57 (7%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYD----SEEAV 160
++V GL T+++ + ++ F Q+G I ++ D T RG GFI +D +EEA+
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 42.0 bits (97), Expect = 7e-04, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVKRA 166
K+FVG + + E D K F++FG I ++ V+ D T +G F+TY + ++ K + A
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSA 76
Query: 167 VPKELS-PGPTR 177
+ ++ + PG R
Sbjct: 77 LHEQKTLPGMNR 88
Score = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 27/82 (32%), Positives = 44/82 (53%), Gaps = 5/82 (6%)
Query: 4 DNGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFA--DPAV-A 60
D KLF+G I +E+ LK F +G + E ++KDR TG +G F+ + D A+ A
Sbjct: 14 DAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKA 73
Query: 61 EIVIQEKHNIDG--RMVEAKKA 80
+ + E+ + G R ++ K A
Sbjct: 74 QSALHEQKTLPGMNRPIQVKPA 95
>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second
Rna-Binding Domain Of Sex-Lethal Determined By
Multidimensional Heteronuclear Magnetic Resonance
Spectroscopy
Length = 97
Score = 41.6 bits (96), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 35/66 (53%), Gaps = 4/66 (6%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY----DSEEAVDKV 163
++V L T+T+ F ++G+I ++ D T RPRG F+ Y +++EA+ +
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 164 KRAVPK 169
+P+
Sbjct: 76 NNVIPE 81
Score = 38.9 bits (89), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 33/63 (52%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQEK 67
L++ + +++L F YG +V+ I++D+ TGR RG FV + A+ I
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 68 HNI 70
+N+
Sbjct: 76 NNV 78
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 44/82 (53%), Gaps = 3/82 (3%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEA-VIMKDRNTGRARGFGFVVFA--DPAVAEIVI 64
+FIG + + +E+ L + FS +G +++ IM+D +TG ++G+ F+ FA D + A I
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 65 QEKHNIDGRMVEAKKAVPRDDQ 86
+ R + A +D +
Sbjct: 68 MNGQYLCNRPITVSYAFKKDSK 89
>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 = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 35/58 (60%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVI 64
KLFIGG+ N++++KE +++G + ++KD TG ++G+ F + D V + I
Sbjct: 98 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 155
Score = 30.0 bits (66), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 14/58 (24%), Positives = 26/58 (44%)
Query: 105 TRKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDK 162
K+F+GGL + + + K+ FG + ++ D T +G+ F Y D+
Sbjct: 96 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 153
>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 = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 35/58 (60%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVI 64
KLFIGG+ N++++KE +++G + ++KD TG ++G+ F + D V + I
Sbjct: 116 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 173
Score = 30.4 bits (67), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 14/58 (24%), Positives = 26/58 (44%)
Query: 105 TRKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDK 162
K+F+GGL + + + K+ FG + ++ D T +G+ F Y D+
Sbjct: 114 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 171
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 35/58 (60%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVI 64
KLFIGG+ N++++KE +++G + ++KD TG ++G+ F + D V + I
Sbjct: 96 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 153
Score = 30.0 bits (66), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 14/58 (24%), Positives = 26/58 (44%)
Query: 105 TRKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDK 162
K+F+GGL + + + K+ FG + ++ D T +G+ F Y D+
Sbjct: 94 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 151
>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 = 0.001, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 30/52 (57%)
Query: 106 RKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSE 157
+ +FV + TES ++ F+ +G I + ++Y + +PRG+ FI Y+ E
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHE 154
Score = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 6/72 (8%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQEK 67
LF+ +++DT E +L+ F YG + ++ + +G+ RG+ F+ + ++ K
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYE--HERDMHSAYK 162
Query: 68 H----NIDGRMV 75
H IDGR V
Sbjct: 163 HADGKKIDGRRV 174
>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 = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 6/71 (8%)
Query: 3 SDNGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEI 62
+ +LF+G + D EE +++ F YG+ E I KD +GFGF+ +AEI
Sbjct: 13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEI 66
Query: 63 VIQEKHNIDGR 73
E N+ R
Sbjct: 67 AKVELDNMPLR 77
Score = 35.8 bits (81), Expect = 0.059, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 31/58 (53%), Gaps = 6/58 (10%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVK 164
++FVG L +TE + +K F+++G +V + D +GFGFI ++ + K
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAK 68
>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 = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 30/52 (57%)
Query: 106 RKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSE 157
+ +FV + TES ++ F+ +G I + ++Y + +PRG+ FI Y+ E
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHE 154
Score = 39.3 bits (90), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 28/47 (59%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVF 54
LF+ +++DT E +L+ F YG + ++ + +G+ RG+ F+ +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEY 151
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 2/75 (2%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQEK 67
L + +++ T+ + L+ F YG V + I +DR T +RGF FV F D AE +
Sbjct: 73 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132
Query: 68 HN--IDGRMVEAKKA 80
+DGR + + A
Sbjct: 133 DGAVLDGRELRVQMA 147
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 42/81 (51%), Gaps = 2/81 (2%)
Query: 2 QSDNGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAE 61
++ + +++GG+ +E L E F G VV + KDR TG+ +G+GFV F A+
Sbjct: 12 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDAD 71
Query: 62 --IVIQEKHNIDGRMVEAKKA 80
I I + + G+ + KA
Sbjct: 72 YAIKIMDMIKLYGKPIRVNKA 92
Score = 36.2 bits (82), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 30/54 (55%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVD 161
++VGGL V+E + F Q G + + + D T + +G+GF+ + SEE D
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDAD 71
>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|C Chain C, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|B Chain B, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|D Chain D, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
Length = 88
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 38/63 (60%), Gaps = 2/63 (3%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFG--FITYDSEEAVDKVK 164
K+FVG + T +E D ++ F+Q+G + ++ V+ D + P+ G F+T+ + +A + +
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 165 RAV 167
A+
Sbjct: 65 NAL 67
Score = 39.3 bits (90), Expect = 0.005, Method: Composition-based stats.
Identities = 20/54 (37%), Positives = 32/54 (59%), Gaps = 2/54 (3%)
Query: 3 SDNGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDR--NTGRARGFGFVVF 54
SD K+F+G + +E+ L+E F YG V E +++DR N +++G FV F
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTF 54
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 39.7 bits (91), Expect = 0.004, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 35/58 (60%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVI 64
KLFIGG+ N++++KE +++G + ++KD TG ++G+ F + D V + I
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 60
Score = 29.6 bits (65), Expect = 4.1, Method: Composition-based stats.
Identities = 13/48 (27%), Positives = 24/48 (50%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY 154
K+F+GGL + + + K+ FG + ++ D T +G+ F Y
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEY 50
>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 = 39.3 bits (90), Expect = 0.005, Method: Composition-based stats.
Identities = 15/56 (26%), Positives = 31/56 (55%)
Query: 1 MQSDNGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFAD 56
M++D +++G + + E L+ +F G V I+ D+ +G +GF ++ F+D
Sbjct: 1 MEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSD 56
Score = 37.0 bits (84), Expect = 0.024, Method: Composition-based stats.
Identities = 15/55 (27%), Positives = 30/55 (54%)
Query: 106 RKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAV 160
R I+VG + T + + +F G++ V ++ D + P+GF +I + +E+V
Sbjct: 6 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESV 60
>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 = 38.9 bits (89), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 37/68 (54%), Gaps = 2/68 (2%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFA--DPAVAEIVIQ 65
LF+G ++ + ++E L+ F + + +M D TG +RG+GFV F D A +
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 66 EKHNIDGR 73
+ +++GR
Sbjct: 64 QGQDLNGR 71
Score = 35.4 bits (80), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 1/74 (1%)
Query: 105 TRKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVK 164
T +FVG L V + + F F + VM+D T RG+GF+++ S++
Sbjct: 1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60
Query: 165 RAVP-KELSPGPTR 177
++ ++L+ P R
Sbjct: 61 DSMQGQDLNGRPLR 74
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 38.1 bits (87), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 35/62 (56%), Gaps = 2/62 (3%)
Query: 106 RKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVKR 165
+++ V + + D ++ F QFG I DV +++ N + +GFGF+T+++ D+ +
Sbjct: 30 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIF--NERGSKGFGFVTFENSADADRARE 87
Query: 166 AV 167
+
Sbjct: 88 KL 89
Score = 35.8 bits (81), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 45/85 (52%), Gaps = 6/85 (7%)
Query: 2 QSDNGKLFIGGISWDTNEERLKEYFSTYGEVVEA-VIMKDRNTGRARGFGFVVFADPAVA 60
+S +L + I + + L++ F +G++++ +I +R + +GFGFV F + A A
Sbjct: 26 KSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS---KGFGFVTFENSADA 82
Query: 61 EIVIQEKHN--IDGRMVEAKKAVPR 83
+ ++ H ++GR +E A R
Sbjct: 83 DRAREKLHGTVVEGRKIEVNNATAR 107
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 38.1 bits (87), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 35/62 (56%), Gaps = 2/62 (3%)
Query: 106 RKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVKR 165
+++ V + + D ++ F QFG I DV +++ N + +GFGF+T+++ D+ +
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIF--NERGSKGFGFVTFENSADADRARE 73
Query: 166 AV 167
+
Sbjct: 74 KL 75
Score = 35.8 bits (81), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 43/80 (53%), Gaps = 6/80 (7%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEA-VIMKDRNTGRARGFGFVVFADPAVAEIVIQ 65
+L + I + + L++ F +G++++ +I +R + +GFGFV F + A A+ +
Sbjct: 17 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS---KGFGFVTFENSADADRARE 73
Query: 66 EKHN--IDGRMVEAKKAVPR 83
+ H ++GR +E A R
Sbjct: 74 KLHGTVVEGRKIEVNNATAR 93
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 38.1 bits (87), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRN-TGRARGFGFVVF 54
K+ + I + N+ ++E FST+GE+ + K TG RGFGFV F
Sbjct: 17 KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDF 65
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 37.7 bits (86), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 40/71 (56%), Gaps = 3/71 (4%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQEK 67
L + + + ++ K F + G++ +++D+ TG++ G+GFV ++DP A+ I
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI--- 63
Query: 68 HNIDGRMVEAK 78
+ ++G ++ K
Sbjct: 64 NTLNGLKLQTK 74
Score = 32.0 bits (71), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 25/55 (45%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDK 162
+ V L +T+ +FK F G I ++ D T + G+GF+ Y DK
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 37.4 bits (85), Expect = 0.017, Method: Composition-based stats.
Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 8/63 (12%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQE 66
KLFIG + + E+ ++ F YG+V+E I+K+ +GFV D AE I+
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFVHIEDKTAAEDAIRN 61
Query: 67 KHN 69
H+
Sbjct: 62 LHH 64
Score = 28.9 bits (63), Expect = 6.5, Method: Composition-based stats.
Identities = 13/59 (22%), Positives = 29/59 (49%), Gaps = 8/59 (13%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVKR 165
K+F+G L TE + + F+Q+G + + ++ + +GF+ + + A + R
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIR 60
>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 = 37.4 bits (85), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 32/54 (59%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAE 61
L++G +S+ T EE++ E FS G++ + ++ D+ A GF FV + A AE
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAE 95
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of
Hypothetical Polyadenylate-Binding Protein (Pabpn1)
From Homo Sapiens At 1.95 A Resolution
Length = 89
Score = 37.0 bits (84), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 14/55 (25%), Positives = 30/55 (54%)
Query: 2 QSDNGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFAD 56
++D +++G + + E L+ +F G V I+ D+ +G +GF ++ F+D
Sbjct: 3 EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSD 57
Score = 36.6 bits (83), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 30/55 (54%)
Query: 106 RKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAV 160
R I+VG + T + + +F G++ V ++ D + P+GF +I + +E+V
Sbjct: 7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESV 61
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 37.0 bits (84), Expect = 0.024, Method: Composition-based stats.
Identities = 21/70 (30%), Positives = 35/70 (50%), Gaps = 8/70 (11%)
Query: 106 RKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQR-----PRGFGFITYDSEEAV 160
RK+FVGGL + E + F +FG + VV + H + P+G+ F+ + E +V
Sbjct: 9 RKVFVGGLPPDIDEDEITASFRRFGPL---VVDWPHKAESKSYFPPKGYAFLLFQEESSV 65
Query: 161 DKVKRAVPKE 170
+ A +E
Sbjct: 66 QALIDACLEE 75
Score = 28.5 bits (62), Expect = 8.1, Method: Composition-based stats.
Identities = 16/70 (22%), Positives = 35/70 (50%), Gaps = 2/70 (2%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGR--ARGFGFVVFADPAVAEIVI 64
K+F+GG+ D +E+ + F +G +V K + +G+ F++F + + + +I
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALI 69
Query: 65 QEKHNIDGRM 74
DG++
Sbjct: 70 DACLEEDGKL 79
>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 = 36.6 bits (83), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 39/71 (54%), Gaps = 3/71 (4%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQEK 67
L + + + ++ L+ FS+ GEV A +++D+ G + G+GFV + AE I
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI--- 63
Query: 68 HNIDGRMVEAK 78
+ ++G +++K
Sbjct: 64 NTLNGLRLQSK 74
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 36.6 bits (83), Expect = 0.030, Method: Composition-based stats.
Identities = 18/59 (30%), Positives = 33/59 (55%)
Query: 3 SDNGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAE 61
S + L+I G+ T ++ L + YG++V + D+ T + +G+GFV F P+ A+
Sbjct: 3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQ 61
Score = 35.8 bits (81), Expect = 0.056, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 29/60 (48%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVKRAV 167
+++ GL T+ D K +G I + D T + +G+GF+ +DS A K A+
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
>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 = 36.6 bits (83), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 36/59 (61%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQE 66
+F+G +S + + F+ +G + +A ++KD TG+++G+GFV F + AE IQ+
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Score = 32.7 bits (73), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 35/60 (58%), Gaps = 4/60 (6%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFIT----YDSEEAVDKV 163
+FVG L+ +T + F FG I+D V+ D T + +G+GF++ +D+E A+ ++
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
>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 = 36.6 bits (83), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 39/71 (54%), Gaps = 3/71 (4%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQEK 67
L + + + ++ L+ FS+ GEV A +++D+ G + G+GFV + AE I
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI--- 78
Query: 68 HNIDGRMVEAK 78
+ ++G +++K
Sbjct: 79 NTLNGLRLQSK 89
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 36.6 bits (83), Expect = 0.034, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 106 RKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAV 160
R +FVG L + V E + F Q G +T V + D +P+ FGF+ + E+V
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREG-KPKSFGFVCFKHPESV 70
Score = 36.2 bits (82), Expect = 0.043, Method: Composition-based stats.
Identities = 19/50 (38%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADP 57
+F+G + EE L E F G + + I KDR G+ + FGFV F P
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHP 67
>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 = 36.6 bits (83), Expect = 0.034, Method: Composition-based stats.
Identities = 14/56 (25%), Positives = 29/56 (51%)
Query: 106 RKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVD 161
R ++VG + T D + +F G+I + ++ D + P+G+ +I + +VD
Sbjct: 37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVD 92
Score = 34.7 bits (78), Expect = 0.11, Method: Composition-based stats.
Identities = 12/53 (22%), Positives = 31/53 (58%)
Query: 4 DNGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFAD 56
D +++G + + + + L+ +FS+ G + I+ D+ +G +G+ ++ FA+
Sbjct: 35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAE 87
>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
pdb|3H2U|D Chain D, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
Length = 283
Score = 35.4 bits (80), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 30/158 (18%), Positives = 58/158 (36%), Gaps = 27/158 (17%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQE 66
K+ I G+ D + + + S Y +K + +G FV + AE I
Sbjct: 22 KILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFVTLLNGEQAEAAINA 74
Query: 67 KHNIDGRMVEAKKAVPRDDQIVLNRXXXXXXXXXXXXRTRKIFVGGLASTVTESDFKKYF 126
H R E + D + + V L ++T+ F++
Sbjct: 75 FHQSRLRERELSVQLQPTDAL--------------------LCVANLPPSLTQQQFEELV 114
Query: 127 DQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVK 164
FG++ ++Y T + +G+GF Y +++ + K
Sbjct: 115 RPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAK 152
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 35.4 bits (80), Expect = 0.066, Method: Composition-based stats.
Identities = 14/31 (45%), Positives = 22/31 (70%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVM 138
++VGGL T+TE+D + +F QFG I + V+
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVV 45
Score = 28.5 bits (62), Expect = 9.1, Method: Composition-based stats.
Identities = 17/74 (22%), Positives = 35/74 (47%), Gaps = 9/74 (12%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQEK 67
L++GG+ E L+ +F +GE+ +++ + F+ FA AE+ ++
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQC------AFIQFATRQAAEVAAEKS 68
Query: 68 HN---IDGRMVEAK 78
N ++GR + K
Sbjct: 69 FNKLIVNGRRLNVK 82
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 35.4 bits (80), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 30/158 (18%), Positives = 58/158 (36%), Gaps = 27/158 (17%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQE 66
K+ I G+ D + + + S Y +K + +G FV + AE I
Sbjct: 24 KILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFVTLLNGEQAEAAINA 76
Query: 67 KHNIDGRMVEAKKAVPRDDQIVLNRXXXXXXXXXXXXRTRKIFVGGLASTVTESDFKKYF 126
H R E + D + + V L ++T+ F++
Sbjct: 77 FHQSRLRERELSVQLQPTDAL--------------------LCVANLPPSLTQQQFEELV 116
Query: 127 DQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVK 164
FG++ ++Y T + +G+GF Y +++ + K
Sbjct: 117 RPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAK 154
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 35.4 bits (80), Expect = 0.076, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 2/75 (2%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAE--IVIQ 65
L + +++ T+ + L+ F YG V + I ++ +T RGF FV F D A+
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75
Query: 66 EKHNIDGRMVEAKKA 80
+ +DGR + + A
Sbjct: 76 DGAELDGRELRVQVA 90
Score = 34.3 bits (77), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 32/61 (52%), Gaps = 7/61 (11%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY-------DSEEAV 160
+ V L + ++ F+++G + DV + + +T+ PRGF F+ + D+E A+
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75
Query: 161 D 161
D
Sbjct: 76 D 76
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14
Complex
Length = 110
Score = 35.4 bits (80), Expect = 0.077, Method: Composition-based stats.
Identities = 15/47 (31%), Positives = 26/47 (55%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVF 54
LF+ I + E+ ++E F YGE+ + DR TG ++G+ V +
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEY 75
>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1HL6|C Chain C, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1RK8|A Chain A, Structure Of The Cytosolic Protein Pym Bound To The Mago-
Y14 Core Of The Exon Junction Complex
pdb|2X1G|A Chain A, Crystal Structure Of Importin13 - Mago-Y14 Complex
pdb|2X1G|C Chain C, Crystal Structure Of Importin13 - Mago-Y14 Complex
Length = 165
Score = 35.0 bits (79), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 26/47 (55%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVF 54
LF+ I + E+ ++E F YGE+ + DR TG ++G+ V +
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEY 121
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 35.0 bits (79), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 30/158 (18%), Positives = 58/158 (36%), Gaps = 27/158 (17%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQE 66
K+ I G+ D + + + S Y +K + +G FV + AE I
Sbjct: 24 KILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFVTLLNGEQAEAAINA 76
Query: 67 KHNIDGRMVEAKKAVPRDDQIVLNRXXXXXXXXXXXXRTRKIFVGGLASTVTESDFKKYF 126
H R E + D + + V L ++T+ F++
Sbjct: 77 FHQSRLRERELSVQLQPTDAL--------------------LCVANLPPSLTQQQFEELV 116
Query: 127 DQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVK 164
FG++ ++Y T + +G+GF Y +++ + K
Sbjct: 117 RPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAK 154
>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 = 34.7 bits (78), Expect = 0.11, Method: Composition-based stats.
Identities = 15/47 (31%), Positives = 26/47 (55%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVF 54
LF+ G+ + EE + + F+ YGE+ + DR TG +G+ V +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 56
Score = 31.2 bits (69), Expect = 1.2, Method: Composition-based stats.
Identities = 13/49 (26%), Positives = 25/49 (51%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS 156
+FV G+ TE D F ++G I ++ + D T +G+ + Y++
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 58
>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 = 34.7 bits (78), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 28/47 (59%), Gaps = 2/47 (4%)
Query: 8 LFIGGISWDTNEERLKEYFSTYG--EVVEAVIMKDRNTGRARGFGFV 52
L+IG ++W T +E L E + G +++E ++R G+++GF V
Sbjct: 71 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALV 117
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 34.3 bits (77), Expect = 0.14, Method: Composition-based stats.
Identities = 15/47 (31%), Positives = 26/47 (55%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVF 54
LF+ G+ + EE + + F+ YGE+ + DR TG +G+ V +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 56
Score = 30.8 bits (68), Expect = 1.5, Method: Composition-based stats.
Identities = 13/49 (26%), Positives = 25/49 (51%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS 156
+FV G+ TE D F ++G I ++ + D T +G+ + Y++
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 58
>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 = 34.3 bits (77), Expect = 0.14, Method: Composition-based stats.
Identities = 15/47 (31%), Positives = 26/47 (55%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVF 54
LF+ G+ + EE + + F+ YGE+ + DR TG +G+ V +
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 71
Score = 30.8 bits (68), Expect = 1.6, Method: Composition-based stats.
Identities = 13/49 (26%), Positives = 25/49 (51%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS 156
+FV G+ TE D F ++G I ++ + D T +G+ + Y++
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 73
>pdb|2XB2|D Chain D, Crystal Structure Of The Core
Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How
The Ejc Is Bridged To The Nmd Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core
Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How
The Ejc Is Bridged To The Nmd Machinery
Length = 90
Score = 34.3 bits (77), Expect = 0.15, Method: Composition-based stats.
Identities = 15/47 (31%), Positives = 26/47 (55%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVF 54
LF+ G+ + EE + + F+ YGE+ + DR TG +G+ V +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 56
Score = 30.8 bits (68), Expect = 1.6, Method: Composition-based stats.
Identities = 13/49 (26%), Positives = 25/49 (51%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS 156
+FV G+ TE D F ++G I ++ + D T +G+ + Y++
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 58
>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
At Ph 6.0
pdb|4F26|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
A Ph 9.0
Length = 115
Score = 34.3 bits (77), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 5/62 (8%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVKRAV 167
IF+ L ++ F FG I V+ D N +G+GF+ ++++EA + RA+
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS--KGYGFVHFETQEAAE---RAI 62
Query: 168 PK 169
K
Sbjct: 63 EK 64
Score = 33.5 bits (75), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 39/74 (52%), Gaps = 5/74 (6%)
Query: 6 GKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQ 65
G +FI + + + L + FS +G ++ ++ D N ++G+GFV F AE I+
Sbjct: 6 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIE 63
Query: 66 EKHNIDGRMVEAKK 79
+ ++G ++ +K
Sbjct: 64 K---MNGMLLNDRK 74
>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 = 0.17, Method: Composition-based stats.
Identities = 15/47 (31%), Positives = 26/47 (55%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVF 54
LF+ G+ + EE + + F+ YGE+ + DR TG +G+ V +
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 58
Score = 30.8 bits (68), Expect = 1.9, Method: Composition-based stats.
Identities = 13/49 (26%), Positives = 25/49 (51%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS 156
+FV G+ TE D F ++G I ++ + D T +G+ + Y++
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 60
>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 = 33.9 bits (76), Expect = 0.20, Method: Composition-based stats.
Identities = 15/47 (31%), Positives = 26/47 (55%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVF 54
LF+ G+ + EE + + F+ YGE+ + DR TG +G+ V +
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 72
Score = 30.4 bits (67), Expect = 2.1, Method: Composition-based stats.
Identities = 13/49 (26%), Positives = 25/49 (51%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS 156
+FV G+ TE D F ++G I ++ + D T +G+ + Y++
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 74
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 33.9 bits (76), Expect = 0.23, Method: Composition-based stats.
Identities = 13/35 (37%), Positives = 24/35 (68%)
Query: 22 LKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFAD 56
L+++FS G+V + I+ DRN+ R++G +V F +
Sbjct: 42 LEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCE 76
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 33.5 bits (75), Expect = 0.24, Method: Composition-based stats.
Identities = 21/91 (23%), Positives = 41/91 (45%), Gaps = 8/91 (8%)
Query: 3 SDNGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEI 62
++ +FI +S+D+ EE L E +G++ ++ +T ++G F F A+
Sbjct: 13 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQK 72
Query: 63 VIQEKH--------NIDGRMVEAKKAVPRDD 85
+ +DGR ++ AV RD+
Sbjct: 73 CLAAASLEAEGGGLKLDGRQLKVDLAVTRDE 103
Score = 29.3 bits (64), Expect = 5.0, Method: Composition-based stats.
Identities = 17/69 (24%), Positives = 30/69 (43%)
Query: 106 RKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVKR 165
+ +F+ L+ E + QFG + V V+ +T+ +G F + ++EA K
Sbjct: 16 KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 75
Query: 166 AVPKELSPG 174
A E G
Sbjct: 76 AASLEAEGG 84
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 33.5 bits (75), Expect = 0.26, Method: Composition-based stats.
Identities = 15/33 (45%), Positives = 21/33 (63%)
Query: 106 RKIFVGGLASTVTESDFKKYFDQFGTITDVVVM 138
RK+FVG L T+ D +K F+ FGTI + V+
Sbjct: 13 RKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVL 45
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 33.5 bits (75), Expect = 0.27, Method: Composition-based stats.
Identities = 20/54 (37%), Positives = 31/54 (57%), Gaps = 1/54 (1%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAE 61
L++G +S+ T EE++ E FS G+ ++ +IM A GF FV + A AE
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGD-IKKIIMGLDKMKTACGFCFVEYYSRADAE 73
>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 = 33.5 bits (75), Expect = 0.28, Method: Composition-based stats.
Identities = 15/47 (31%), Positives = 28/47 (59%), Gaps = 2/47 (4%)
Query: 8 LFIGGISWDTNEERLKEYFSTYG--EVVEAVIMKDRNTGRARGFGFV 52
L+IG ++W T +E L E + G +++E ++R G+++GF V
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALV 50
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 33.1 bits (74), Expect = 0.33, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDR-NTGRARGFGFVVFADPAVAEIVIQ 65
K+ IG ++ + ++ + E FSTYG++ + +R + ++G+ +V F +P AE ++
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65
Query: 66 --EKHNIDGRMVEA 77
+ IDG+ + A
Sbjct: 66 HMDGGQIDGQEITA 79
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 33.1 bits (74), Expect = 0.36, Method: Composition-based stats.
Identities = 15/60 (25%), Positives = 29/60 (48%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVKRAV 167
+F+ L T++D F FG + V D T + FGF+++D+ ++ +A+
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
>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 = 33.1 bits (74), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 22/48 (45%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYD 155
+F+ L + D + F FG + V D T + FGF++YD
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYD 75
>pdb|2E5G|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 21
Length = 94
Score = 32.7 bits (73), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 36/80 (45%), Gaps = 9/80 (11%)
Query: 8 LFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVI-QE 66
+F+ G + +L EYF +G V V+ KD+ F V D E V+ Q
Sbjct: 11 VFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGV-----FAIVEMGDVGAREAVLSQS 65
Query: 67 KHNIDGRMVEAKKAVPRDDQ 86
+H++ G + + PR+ +
Sbjct: 66 QHSLGGHRLRVR---PREQK 82
>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 = 32.7 bits (73), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 33/57 (57%), Gaps = 2/57 (3%)
Query: 1 MQSDNGKLFIGGISWDTNEERLKEYFSTYG--EVVEAVIMKDRNTGRARGFGFVVFA 55
+++ +++G SW T +++L + + G +VVE ++R G+++G+ VV A
Sbjct: 51 LRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVA 107
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 32.7 bits (73), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 18/75 (24%), Positives = 39/75 (52%), Gaps = 8/75 (10%)
Query: 5 NGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFA--DPAVAEI 62
N ++ GGI+ ++ +++ FS +G+++E + + +G+ FV F+ + A I
Sbjct: 25 NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAI 78
Query: 63 VIQEKHNIDGRMVEA 77
V I+G +V+
Sbjct: 79 VSVNGTTIEGHVVKC 93
Score = 30.4 bits (67), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 13/52 (25%), Positives = 29/52 (55%), Gaps = 6/52 (11%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEA 159
++ GG+AS +T+ ++ F FG I ++ V + +G+ F+ + + E+
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHES 73
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 32.3 bits (72), Expect = 0.57, Method: Composition-based stats.
Identities = 20/78 (25%), Positives = 41/78 (52%), Gaps = 5/78 (6%)
Query: 2 QSDNGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAE 61
+S G +FI + + + L + FS +G ++ ++ D N ++G+GFV F AE
Sbjct: 8 KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAE 65
Query: 62 IVIQEKHNIDGRMVEAKK 79
I++ ++G ++ +K
Sbjct: 66 RAIEK---MNGMLLNDRK 80
Score = 31.2 bits (69), Expect = 1.1, Method: Composition-based stats.
Identities = 15/55 (27%), Positives = 28/55 (50%), Gaps = 2/55 (3%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDK 162
IF+ L ++ F FG I V+ D N +G+GF+ ++++EA ++
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS--KGYGFVHFETQEAAER 66
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 32.3 bits (72), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 23/38 (60%)
Query: 104 RTRKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDH 141
+ + +FV LA+TVTE +K F +FG + V + D+
Sbjct: 14 KVKVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKDY 51
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 32.3 bits (72), Expect = 0.64, Method: Composition-based stats.
Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 6/76 (7%)
Query: 106 RKIFVGGLASTVTESDFKKYFDQFGTITDVVVMY--DHNTQRPRGFGFITYDSE-EAVDK 162
RK+FVG L +E D ++ F+ FG I + ++ D N+ +G F+ Y S EA
Sbjct: 16 RKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNS---KGCAFVKYSSHAEAQAA 72
Query: 163 VKRAVPKELSPGPTRS 178
+ + PG + S
Sbjct: 73 INALHGSQTMPGASSS 88
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 32.0 bits (71), Expect = 0.76, Method: Composition-based stats.
Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 1/63 (1%)
Query: 2 QSDNGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAE 61
+ D L+I + +E+ L+ +G+V+ I++D ++G +RG GF E
Sbjct: 22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCE 80
Query: 62 IVI 64
VI
Sbjct: 81 AVI 83
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of
Eukaryotic Initiation Factor 4b
Length = 104
Score = 32.0 bits (71), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 23/46 (50%)
Query: 9 FIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVF 54
F+G + +D EE +KE+F + + N R +GFG+ F
Sbjct: 19 FLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEF 64
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 31.6 bits (70), Expect = 0.92, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 8/59 (13%)
Query: 104 RTRKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDK 162
+ + +FV LA+TVTE +K F QFG + V + D + FI +D + K
Sbjct: 10 KVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVK 60
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif In Trna Selenocysteine Associated Protein
Length = 104
Score = 31.6 bits (70), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 41/84 (48%), Gaps = 5/84 (5%)
Query: 8 LFIGGISWDTNEERLKEYF-STYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQE 66
LF+G ++ D ++ L E+F Y ++ D+ TG ++G+GFV F D + + E
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTE 70
Query: 67 KHNIDG---RMVEAKKAVPRDDQI 87
G + V A+P+ ++
Sbjct: 71 CQGAVGLGSKPVRLSVAIPKASRV 94
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 31.6 bits (70), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 31/70 (44%), Gaps = 8/70 (11%)
Query: 3 SDNGKLFIGGISWDTNEERLKEYFSTYGEVVEAV--------IMKDRNTGRARGFGFVVF 54
SDN +F+ G+ + E + +YF G + + DR TG+ +G V F
Sbjct: 5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSF 64
Query: 55 ADPAVAEIVI 64
DP A+ I
Sbjct: 65 DDPPSAKAAI 74
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation
Initiation Factor 4b
Length = 100
Score = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 23/46 (50%)
Query: 9 FIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVF 54
F+G + +D EE +KE+F + + N R +GFG+ F
Sbjct: 23 FLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEF 68
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 30.8 bits (68), Expect = 1.6, Method: Composition-based stats.
Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQE 66
KLF+G ++ +EE + F +G + E +++ + G ++G FV F+ A+ I
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPD-GSSKGCAFVKFSSHTEAQAAIHA 75
Query: 67 KH 68
H
Sbjct: 76 LH 77
Score = 29.3 bits (64), Expect = 4.3, Method: Composition-based stats.
Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 2/74 (2%)
Query: 106 RKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSE-EAVDKVK 164
RK+FVG L +E D + F FG I + V+ + +G F+ + S EA +
Sbjct: 16 RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSS-KGCAFVKFSSHTEAQAAIH 74
Query: 165 RAVPKELSPGPTRS 178
+ PG + S
Sbjct: 75 ALHGSQTMPGASSS 88
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 30.8 bits (68), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 33/81 (40%)
Query: 3 SDNGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEI 62
+ N L + + D + L F G + IM+D TG + G+ FV F ++
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 63 VIQEKHNIDGRMVEAKKAVPR 83
I+ + I R K + R
Sbjct: 61 AIKVLNGITVRNKRLKVSYAR 81
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 30.4 bits (67), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 3/58 (5%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVK 164
K+ V L V+++D ++ F +FGT+ V YD + R G E D +K
Sbjct: 90 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSG---RSLGTADVHFERRADALK 144
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 30.4 bits (67), Expect = 2.2, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 31/55 (56%), Gaps = 2/55 (3%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAE 61
++F+ + +D + LK+ F+ G V+ A I + G+++G G V F P VAE
Sbjct: 10 QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAE 62
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 30.4 bits (67), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 30/56 (53%), Gaps = 6/56 (10%)
Query: 105 TRKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAV 160
T +++VGGL + + + FD+FG+I + DH + F +I Y+S +A
Sbjct: 17 TTRLWVGGLGPNTSLAALAREFDRFGSIRTI----DH--VKGDSFAYIQYESLDAA 66
>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 = 30.0 bits (66), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 30/69 (43%), Gaps = 8/69 (11%)
Query: 4 DNGKLFIGGISWDTNEERLKEYFSTYGEVVEAV--------IMKDRNTGRARGFGFVVFA 55
DN +F+ G+ + E + +YF G + + DR TG+ +G V F
Sbjct: 12 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 71
Query: 56 DPAVAEIVI 64
DP A+ I
Sbjct: 72 DPPSAKAAI 80
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 30.0 bits (66), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 8/71 (11%)
Query: 3 SDNGKLFIGGISWDTNEERLKEYFSTYGEVVE--------AVIMKDRNTGRARGFGFVVF 54
SDN +++ G++ + L ++F G V I D+ TG+ +G V +
Sbjct: 13 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSY 72
Query: 55 ADPAVAEIVIQ 65
DP A+ ++
Sbjct: 73 EDPPTAKAAVE 83
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain
In Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 30.0 bits (66), Expect = 2.8, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 2/59 (3%)
Query: 3 SDNGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAE 61
S + +F+ + +D + LK+ F+ G V+ A I + G+++G G V F P VAE
Sbjct: 3 SGSSGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAE 59
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 29.6 bits (65), Expect = 3.8, Method: Composition-based stats.
Identities = 12/51 (23%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSE 157
K+F+ GL + T+ + ++ GT+ D+ ++ + +P+G ++ Y++E
Sbjct: 19 KLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENE 68
>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 = 3.9, Method: Composition-based stats.
Identities = 14/34 (41%), Positives = 19/34 (55%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKD 40
KL +G IS + L+ F YG V+E I+KD
Sbjct: 12 KLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD 45
>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex
Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A
Resolution
Length = 107
Score = 29.6 bits (65), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 3/58 (5%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVK 164
K+ V L V+++D ++ F +FGT+ V YD + R G E D +K
Sbjct: 31 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSG---RSLGTADVHFERKADALK 85
>pdb|1WG5|A Chain A, Solution Structure Of The First Rrm Domain In
Heterogeneous Nuclear Ribonucleoprotein H
Length = 104
Score = 29.6 bits (65), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 41/79 (51%), Gaps = 1/79 (1%)
Query: 3 SDNGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEI 62
+++G + + G+ + ++E + ++FS V + + GR+ G FV FA +AE
Sbjct: 13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEK 72
Query: 63 VIQE-KHNIDGRMVEAKKA 80
+++ K I R +E K+
Sbjct: 73 ALKKHKERIGHRYIEIFKS 91
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 29.3 bits (64), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 8/71 (11%)
Query: 5 NGKLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVI 64
+ K+++G + + N+ L+ F YG + + ++ GF FV F DP A +
Sbjct: 73 DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAV 127
Query: 65 QEKHNIDGRMV 75
+E +DGR +
Sbjct: 128 RE---LDGRTL 135
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 29.3 bits (64), Expect = 5.5, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 3/58 (5%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVK 164
K+ V L V+++D ++ F +FGT+ V YD + R G E D +K
Sbjct: 30 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSG---RSLGTADVHFERKADALK 84
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Rna-Binding Protein 14
Length = 90
Score = 28.5 bits (62), Expect = 9.1, Method: Composition-based stats.
Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 11/73 (15%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQE 66
K+F+G +S + L+ F G V+E ++KD + FV A A+ I +
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQ 62
Query: 67 KHNIDGRMVEAKK 79
++G+ V+ K+
Sbjct: 63 ---LNGKEVKGKR 72
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor
9g8
Length = 101
Score = 28.5 bits (62), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 34/69 (49%), Gaps = 8/69 (11%)
Query: 7 KLFIGGISWDTNEERLKEYFSTYGEVVEAVIMKDRNTGRARGFGFVVFADPAVAEIVIQE 66
K+++G + + L+ FS YG + I ++ GF FV F DP AE ++
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVR- 55
Query: 67 KHNIDGRMV 75
+DG+++
Sbjct: 56 --GLDGKVI 62
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
0.316 0.137 0.409
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,794,751
Number of Sequences: 62578
Number of extensions: 427516
Number of successful extensions: 1312
Number of sequences better than 100.0: 154
Number of HSP's better than 100.0 without gapping: 126
Number of HSP's successfully gapped in prelim test: 28
Number of HSP's that attempted gapping in prelim test: 982
Number of HSP's gapped (non-prelim): 283
length of query: 466
length of database: 14,973,337
effective HSP length: 102
effective length of query: 364
effective length of database: 8,590,381
effective search space: 3126898684
effective search space used: 3126898684
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)