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= 014397
(425 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 104 bits (260), Expect = 7e-23, Method: Compositional matrix adjust.
Identities = 60/178 (33%), Positives = 95/178 (53%), Gaps = 3/178 (1%)
Query: 67 DPTQ-RKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGA 125
+P Q RKLFI GL ++TT E LRS F +G L + VV+ D T +S+G+GF+T+ ++
Sbjct: 9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 68
Query: 126 MLALKEPSKKIDGRVTVTNLAVAGNSGNSTNNPVDVSLRKIFVGNVPNDMSADKLLAHFA 185
A+ K+DGRV AV+ +S ++++KIFVG + D L +F
Sbjct: 69 DAAMNARPHKVDGRVVEPKRAVSRE--DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFE 126
Query: 186 CYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALVDPIKTVDGKQLNCRLADNKK 243
YG+IE + D+ +GK +GFA + + ++ TV+G R A +K+
Sbjct: 127 QYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQ 184
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 104 bits (260), Expect = 8e-23, Method: Compositional matrix adjust.
Identities = 60/178 (33%), Positives = 95/178 (53%), Gaps = 3/178 (1%)
Query: 67 DPTQ-RKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGA 125
+P Q RKLFI GL ++TT E LRS F +G L + VV+ D T +S+G+GF+T+ ++
Sbjct: 10 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 69
Query: 126 MLALKEPSKKIDGRVTVTNLAVAGNSGNSTNNPVDVSLRKIFVGNVPNDMSADKLLAHFA 185
A+ K+DGRV AV+ +S ++++KIFVG + D L +F
Sbjct: 70 DAAMNARPHKVDGRVVEPKRAVSRE--DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFE 127
Query: 186 CYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALVDPIKTVDGKQLNCRLADNKK 243
YG+IE + D+ +GK +GFA + + ++ TV+G R A +K+
Sbjct: 128 QYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQ 185
>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 = 104 bits (260), Expect = 8e-23, Method: Compositional matrix adjust.
Identities = 60/178 (33%), Positives = 95/178 (53%), Gaps = 3/178 (1%)
Query: 67 DPTQ-RKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGA 125
+P Q RKLFI GL ++TT E LRS F +G L + VV+ D T +S+G+GF+T+ ++
Sbjct: 8 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 67
Query: 126 MLALKEPSKKIDGRVTVTNLAVAGNSGNSTNNPVDVSLRKIFVGNVPNDMSADKLLAHFA 185
A+ K+DGRV AV+ +S ++++KIFVG + D L +F
Sbjct: 68 DAAMNARPHKVDGRVVEPKRAVSRE--DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFE 125
Query: 186 CYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALVDPIKTVDGKQLNCRLADNKK 243
YG+IE + D+ +GK +GFA + + ++ TV+G R A +K+
Sbjct: 126 QYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQ 183
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 103 bits (258), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 60/178 (33%), Positives = 95/178 (53%), Gaps = 3/178 (1%)
Query: 67 DPTQ-RKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGA 125
+P Q RKLFI GL ++TT E LRS F +G L + VV+ D T +S+G+GF+T+ ++
Sbjct: 9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 68
Query: 126 MLALKEPSKKIDGRVTVTNLAVAGNSGNSTNNPVDVSLRKIFVGNVPNDMSADKLLAHFA 185
A+ K+DGRV AV+ +S ++++KIFVG + D L +F
Sbjct: 69 DAAMNARPHKVDGRVVEPKRAVSRE--DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFE 126
Query: 186 CYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALVDPIKTVDGKQLNCRLADNKK 243
YG+IE + D+ +GK +GFA + + ++ TV+G R A +K+
Sbjct: 127 QYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQ 184
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 103 bits (258), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 60/178 (33%), Positives = 95/178 (53%), Gaps = 3/178 (1%)
Query: 67 DPTQ-RKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGA 125
+P Q RKLFI GL ++TT E LRS F +G L + VV+ D T +S+G+GF+T+ ++
Sbjct: 7 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 66
Query: 126 MLALKEPSKKIDGRVTVTNLAVAGNSGNSTNNPVDVSLRKIFVGNVPNDMSADKLLAHFA 185
A+ K+DGRV AV+ +S ++++KIFVG + D L +F
Sbjct: 67 DAAMNARPHKVDGRVVEPKRAVSRE--DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFE 124
Query: 186 CYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALVDPIKTVDGKQLNCRLADNKK 243
YG+IE + D+ +GK +GFA + + ++ TV+G R A +K+
Sbjct: 125 QYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQ 182
>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 = 103 bits (257), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 60/178 (33%), Positives = 95/178 (53%), Gaps = 3/178 (1%)
Query: 67 DPTQ-RKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGA 125
+P Q RKLFI GL ++TT E LRS F +G L + VV+ D T +S+G+GF+T+ ++
Sbjct: 2 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 61
Query: 126 MLALKEPSKKIDGRVTVTNLAVAGNSGNSTNNPVDVSLRKIFVGNVPNDMSADKLLAHFA 185
A+ K+DGRV AV+ +S ++++KIFVG + D L +F
Sbjct: 62 DAAMNARPHKVDGRVVEPKRAVSRE--DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFE 119
Query: 186 CYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALVDPIKTVDGKQLNCRLADNKK 243
YG+IE + D+ +GK +GFA + + ++ TV+G R A +K+
Sbjct: 120 QYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQ 177
>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 = 82.8 bits (203), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 54/175 (30%), Positives = 87/175 (49%), Gaps = 14/175 (8%)
Query: 72 KLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALKE 131
K+FI GL WDTT + LR F YG + + ++ D ATG+S+G+GF++F+ +K
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK- 63
Query: 132 PSKKIDGRVTVTNLAVAGNSGNSTNNPVDVSLRKIFVGNVPNDMSADKLLAHFACYGEIE 191
+DG+V A+ + + T KIFVG + D+ + F+ +G I
Sbjct: 64 TQHILDGKVIDPKRAIPRDEQDKTG--------KIFVGGIGPDVRPKEFEEFFSQWGTII 115
Query: 192 EGPLGFDKQTGKPKGFALFVYKTAEGAQAALVDPIKTVDGKQLNCRLADNKKAKP 246
+ L DK TG+ +GF Y +A+ + K +D K R + K+A+P
Sbjct: 116 DAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQN--KFIDFKD---RKIEIKRAEP 165
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 77.0 bits (188), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 40/83 (48%), Positives = 51/83 (61%)
Query: 67 DPTQRKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAM 126
D T K+F+ GL + TT LR F +G++EEAVVI D+ TGKS+GYGF+T A
Sbjct: 14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAE 73
Query: 127 LALKEPSKKIDGRVTVTNLAVAG 149
A K+P+ IDGR NLA G
Sbjct: 74 RACKDPNPIIDGRKANVNLAYLG 96
Score = 56.6 bits (135), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 28/80 (35%), Positives = 42/80 (52%)
Query: 160 DVSLRKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQ 219
D + KIFVG +P + L +F +G+IEE + D+QTGK +G+ A+
Sbjct: 14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAE 73
Query: 220 AALVDPIKTVDGKQLNCRLA 239
A DP +DG++ N LA
Sbjct: 74 RACKDPNPIIDGRKANVNLA 93
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 70.9 bits (172), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 32/71 (45%), Positives = 49/71 (69%), Gaps = 5/71 (7%)
Query: 72 KLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHID---GAMLA 128
KLF+ GL +DT + L +FS YG++ E VV+ D+ T +S+G+GF+TF++ID AM+A
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 129 LKEPSKKIDGR 139
+ K +DGR
Sbjct: 74 MN--GKSVDGR 82
Score = 44.7 bits (104), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 45/89 (50%), Gaps = 1/89 (1%)
Query: 165 KIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALVD 224
K+FVG + D + L F+ YG+I E + D++T + +GF ++ + A+ A++
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 225 PI-KTVDGKQLNCRLADNKKAKPMGPDGG 252
K+VDG+Q+ A GP G
Sbjct: 74 MNGKSVDGRQIRVDQAGKSSDNRSGPSSG 102
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 67.8 bits (164), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 31/68 (45%), Positives = 42/68 (61%)
Query: 72 KLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALKE 131
KLF+ GL W TT E LRS FS YGE+ + V++ DK T +S+G+GF+ FK + L
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 132 PSKKIDGR 139
+DGR
Sbjct: 78 RPHTLDGR 85
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 43/88 (48%)
Query: 165 KIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALVD 224
K+FVG + + + L ++F+ YGE+ + + DK T + +GF +K L
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 225 PIKTVDGKQLNCRLADNKKAKPMGPDGG 252
T+DG+ ++ + + +P GP G
Sbjct: 78 RPHTLDGRNIDPKPCTPRGMQPSGPSSG 105
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 65.5 bits (158), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 36/81 (44%), Positives = 50/81 (61%), Gaps = 6/81 (7%)
Query: 71 RKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFK---HIDGAML 127
RKLFI GL ++TT E LR+ + +G+L + VV+ D A+ +S+G+GF+TF +D AM
Sbjct: 28 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA 87
Query: 128 ALKEPSKKIDGRVTVTNLAVA 148
A IDGRV AVA
Sbjct: 88 ARPHS---IDGRVVEPKRAVA 105
Score = 36.2 bits (82), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 17/90 (18%), Positives = 43/90 (47%)
Query: 163 LRKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAAL 222
RK+F+G + + + + L ++ +G++ + + D + + +GF + + AA+
Sbjct: 27 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 86
Query: 223 VDPIKTVDGKQLNCRLADNKKAKPMGPDGG 252
++DG+ + + A ++ GP G
Sbjct: 87 AARPHSIDGRVVEPKRAVAREESGSGPSSG 116
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 63.9 bits (154), Expect = 2e-10, Method: Composition-based stats.
Identities = 28/68 (41%), Positives = 42/68 (61%)
Query: 72 KLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALKE 131
K+FI GL W TT EGLR F +GE++E +V+ D T +S+G+GF+TF G L +
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 132 PSKKIDGR 139
++D +
Sbjct: 62 SRHELDSK 69
Score = 34.3 bits (77), Expect = 0.12, Method: Composition-based stats.
Identities = 17/75 (22%), Positives = 35/75 (46%)
Query: 165 KIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALVD 224
K+F+G + + + L +F +GE++E + D T + +GF + G L
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 225 PIKTVDGKQLNCRLA 239
+D K ++ ++A
Sbjct: 62 SRHELDSKTIDPKVA 76
>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 = 62.8 bits (151), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 41/159 (25%), Positives = 79/159 (49%), Gaps = 12/159 (7%)
Query: 72 KLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALKE 131
++++ + ++ + +R F+ +G ++ + D T K KG+ F+ ++ + A LAL++
Sbjct: 30 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 89
Query: 132 -PSKKIDGRVTVTNLAVAGNSGNSTNNPVDVSL-------RKIFVGNVPNDMSADKLLAH 183
S + GR N+ V S P+ L +I+V +V D+S D + +
Sbjct: 90 MNSVMLGGR----NIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSV 145
Query: 184 FACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAAL 222
F +G+I+ L D TGK KG+ Y+ A+ +Q A+
Sbjct: 146 FEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAV 184
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 37/61 (60%)
Query: 60 VRSIADADPTQRKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITF 119
+ +A+ ++++ + D + + ++S+F A+G+++ A + D TGK KGYGFI +
Sbjct: 115 IDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEY 174
Query: 120 K 120
+
Sbjct: 175 E 175
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 34/60 (56%)
Query: 163 LRKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAAL 222
+ +++VG++ ++ D + FA +G I+ + +D T K KGFA Y+ E AQ AL
Sbjct: 28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLAL 87
>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 = 62.0 bits (149), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 41/159 (25%), Positives = 78/159 (49%), Gaps = 12/159 (7%)
Query: 72 KLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALKE 131
++++ + ++ + +R F+ +G ++ D T K KG+ F+ ++ + A LAL++
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 132 P-SKKIDGRVTVTNLAVAGNSGNSTNNPVDVSL-------RKIFVGNVPNDMSADKLLAH 183
S + GR N+ V S P+ L +I+V +V D+S D + +
Sbjct: 74 XNSVXLGGR----NIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSV 129
Query: 184 FACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAAL 222
F +G+I+ L D TGK KG+ Y+ A+ +Q A+
Sbjct: 130 FEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAV 168
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 62.0 bits (149), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 45/152 (29%), Positives = 69/152 (45%), Gaps = 11/152 (7%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALKEP 132
L + L D T L ++F A G + ++ D TG S GY F+ F + A+K
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 133 S--KKIDGRVTVTNLAVAGNSGNSTNNPVDVSLRKIFVGNVPNDMSADKLLAHFACYGEI 190
+ + R+ V+ G S TN ++V N+P ++ D+L F YG I
Sbjct: 66 NGITVRNKRLKVSYARPGGESIKDTN---------LYVTNLPRTITDDQLDTIFGKYGSI 116
Query: 191 EEGPLGFDKQTGKPKGFALFVYKTAEGAQAAL 222
+ + DK TG+P+G A Y E AQ A+
Sbjct: 117 VQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 148
>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 = 61.6 bits (148), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 45/152 (29%), Positives = 68/152 (44%), Gaps = 11/152 (7%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALKEP 132
L + L D T L ++F A G + + D TG S GY F+ F + A+K
Sbjct: 17 LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 133 S--KKIDGRVTVTNLAVAGNSGNSTNNPVDVSLRKIFVGNVPNDMSADKLLAHFACYGEI 190
+ + R+ V+ G S TN ++V N+P ++ D+L F YG I
Sbjct: 77 NGITVRNKRLKVSYARPGGESIKDTN---------LYVTNLPRTITDDQLDTIFGKYGSI 127
Query: 191 EEGPLGFDKQTGKPKGFALFVYKTAEGAQAAL 222
+ + DK TG+P+G A Y E AQ A+
Sbjct: 128 VQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 159
>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 = 61.6 bits (148), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 41/159 (25%), Positives = 79/159 (49%), Gaps = 12/159 (7%)
Query: 72 KLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALKE 131
++++ + ++ + +R F+ +G ++ + D T K KG+ F+ ++ + A LAL++
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 132 P-SKKIDGRVTVTNLAVAGNSGNSTNNPVDVSL-------RKIFVGNVPNDMSADKLLAH 183
S + GR N+ V S P+ L +I+V +V D+S D + +
Sbjct: 75 MNSVMLGGR----NIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSV 130
Query: 184 FACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAAL 222
F +G+I+ L D TGK KG+ Y+ A+ +Q A+
Sbjct: 131 FEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAV 169
>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 = 61.2 bits (147), Expect = 1e-09, Method: Composition-based stats.
Identities = 26/68 (38%), Positives = 43/68 (63%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALKEP 132
+FI GL WDTT + L+ FS +GE+ + + LD TG+S+G+GF+ FK + + +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 133 SKKIDGRV 140
K++G+V
Sbjct: 62 EHKLNGKV 69
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 22/79 (27%), Positives = 41/79 (51%), Gaps = 5/79 (6%)
Query: 166 IFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALVDP 225
+F+G + D + L +F+ +GE+ + L D TG+ +GF ++K +E VD
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESES-----VDK 56
Query: 226 IKTVDGKQLNCRLADNKKA 244
+ +LN ++ D K+A
Sbjct: 57 VMDQKEHKLNGKVIDPKRA 75
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 60.8 bits (146), Expect = 1e-09, Method: Composition-based stats.
Identities = 28/68 (41%), Positives = 42/68 (61%)
Query: 72 KLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALKE 131
K+FI GL W TT EGLR F +GE++E +V+ D T +S+G+GF+TF G L +
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 86
Query: 132 PSKKIDGR 139
++D +
Sbjct: 87 SRHELDSK 94
Score = 37.4 bits (85), Expect = 0.016, Method: Composition-based stats.
Identities = 19/82 (23%), Positives = 40/82 (48%)
Query: 165 KIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALVD 224
K+F+G + + + L +F +GE++E + D T + +GF + G L
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 86
Query: 225 PIKTVDGKQLNCRLADNKKAKP 246
+D K ++ ++A ++A+P
Sbjct: 87 SRHELDSKTIDPKVAFPRRAQP 108
>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 = 58.5 bits (140), Expect = 7e-09, Method: Composition-based stats.
Identities = 26/69 (37%), Positives = 41/69 (59%)
Query: 72 KLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALKE 131
K F+ GL WDT+ + L+ F+ +GE+ + + D TG+S+G+GFI FK L +
Sbjct: 13 KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQ 72
Query: 132 PSKKIDGRV 140
++DGRV
Sbjct: 73 KEHRLDGRV 81
Score = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 28/92 (30%), Positives = 43/92 (46%), Gaps = 7/92 (7%)
Query: 153 NSTNNPVDVSLRKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVY 212
N++ N D K FVG + D S L +F +GE+ + + D TG+ +GF ++
Sbjct: 3 NASKNEEDAG--KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILF 60
Query: 213 KTAEGAQAALVDPIKTVDGKQLNCRLADNKKA 244
K A + L +DG R+ D KKA
Sbjct: 61 KDAASVEKVLDQKEHRLDG-----RVIDPKKA 87
>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 = 55.8 bits (133), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 44/153 (28%), Positives = 72/153 (47%), Gaps = 13/153 (8%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALKEP 132
L + L + T E RS+F + GE+E ++ DK TG+S GYGF+ + ID K+
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNY--IDP-----KDA 57
Query: 133 SKKIDGRVTVTNLAVAGNSGN-STNNPVDVSLR--KIFVGNVPNDMSADKLLAHFACYGE 189
K I+ T+ L + + S P S+R ++V +P M+ +L F+ YG
Sbjct: 58 EKAIN---TLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGR 114
Query: 190 IEEGPLGFDKQTGKPKGFALFVYKTAEGAQAAL 222
I + D+ TG +G + A+ A+
Sbjct: 115 IITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 147
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 48/79 (60%), Gaps = 4/79 (5%)
Query: 159 VDVSLRKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGA 218
VD SLR +FVGN+P + + ++L F+ G + L +D++TGKPKG+ Y+ E A
Sbjct: 4 VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETA 63
Query: 219 QAALVDPIKTVDGKQLNCR 237
+A+ + ++G++ + R
Sbjct: 64 LSAM----RNLNGREFSGR 78
Score = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/86 (31%), Positives = 48/86 (55%), Gaps = 2/86 (2%)
Query: 67 DPTQRKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAM 126
D + R +F+ + ++ T E L+ IFS G + ++ D+ TGK KGYGF ++ + A+
Sbjct: 5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETAL 64
Query: 127 LALKEPS-KKIDGR-VTVTNLAVAGN 150
A++ + ++ GR + V N A N
Sbjct: 65 SAMRNLNGREFSGRALRVDNAASEKN 90
>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 = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 71 RKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALK 130
+ LF+ + +DTT LR F YG ++ ++ K +GK +GY FI ++H A K
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 131 EPS-KKIDGRVTVTNL 145
KKIDGR + ++
Sbjct: 163 HADGKKIDGRRVLVDV 178
Score = 45.8 bits (107), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 4/76 (5%)
Query: 162 SLRKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAA 221
+ + +FV V D + KL F YG I+ + + K++GKP+G+A Y+ +A
Sbjct: 101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSA 160
Query: 222 LVDPIKTVDGKQLNCR 237
K DGK+++ R
Sbjct: 161 Y----KHADGKKIDGR 172
>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 = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 71 RKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALK 130
+ LF+ + +DTT LR F YG ++ ++ K +GK +GY FI ++H A K
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 131 EPS-KKIDGRVTVTNL 145
KKIDGR + ++
Sbjct: 163 HADGKKIDGRRVLVDV 178
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 4/76 (5%)
Query: 162 SLRKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAA 221
+ + +FV V D + KL F YG I+ + + K++GKP+G+A Y+ +A
Sbjct: 101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSA 160
Query: 222 LVDPIKTVDGKQLNCR 237
K DGK+++ R
Sbjct: 161 Y----KHADGKKIDGR 172
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 52.8 bits (125), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 28/76 (36%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITF-KHIDGAMLALKE 131
+F+ L + TTE ++S F+ +G++ +A V+ D ATGKSKGYGF++F +D +
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 132 PSKKIDGRVTVTNLAV 147
+ + GR TN A
Sbjct: 78 GGQWLGGRQIRTNWAT 93
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 28/105 (26%), Positives = 52/105 (49%), Gaps = 1/105 (0%)
Query: 149 GNSGNSTNNPVDVSLRKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFA 208
G+SG+S + +FVG++ +++ + + + FA +G+I + + D TGK KG+
Sbjct: 1 GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYG 60
Query: 209 LFVYKTAEGAQAALVD-PIKTVDGKQLNCRLADNKKAKPMGPDGG 252
+ A+ A+V + + G+Q+ A K P GP G
Sbjct: 61 FVSFYNKLDAENAIVHMGGQWLGGRQIRTNWATRKPPAPSGPSSG 105
>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 = 52.4 bits (124), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 39/153 (25%), Positives = 71/153 (46%), Gaps = 13/153 (8%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALKEP 132
L + L + T + LRS+FS+ GE+E A +I DK G S GYGF+ + + K+
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNY-------VTAKDA 57
Query: 133 SKKIDGRVTVTNLAVAGNSGN-STNNPVDVSLR--KIFVGNVPNDMSADKLLAHFACYGE 189
+ I+ T+ L + + S P ++ +++ +P M+ + F+ +G
Sbjct: 58 ERAIN---TLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGR 114
Query: 190 IEEGPLGFDKQTGKPKGFALFVYKTAEGAQAAL 222
I + D+ TG +G A + A+ A+
Sbjct: 115 IINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 52.4 bits (124), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 39/153 (25%), Positives = 71/153 (46%), Gaps = 13/153 (8%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALKEP 132
L + L + T + LRS+FS+ GE+E A +I DK G S GYGF+ + + K+
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNY-------VTAKDA 57
Query: 133 SKKIDGRVTVTNLAVAGNSGN-STNNPVDVSLR--KIFVGNVPNDMSADKLLAHFACYGE 189
+ I+ T+ L + + S P ++ +++ +P M+ + F+ +G
Sbjct: 58 ERAIN---TLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGR 114
Query: 190 IEEGPLGFDKQTGKPKGFALFVYKTAEGAQAAL 222
I + D+ TG +G A + A+ A+
Sbjct: 115 IINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 52.4 bits (124), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 27/69 (39%), Positives = 40/69 (57%), Gaps = 4/69 (5%)
Query: 72 KLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALKE 131
+LF+R L + ++ E L +FSAYG L E +D T K KG+ F+TF + A+ A E
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 132 PSKKIDGRV 140
+DG+V
Sbjct: 70 ----VDGQV 74
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 29/94 (30%), Positives = 40/94 (42%), Gaps = 10/94 (10%)
Query: 165 KIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALVD 224
++FV N+ S + L F+ YG + E D T KPKGFA + E A A +
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 225 PIKTVDGKQLNCRLAD------NKKAKPMGPDGG 252
VDG+ R+ K+A GP G
Sbjct: 70 ----VDGQVFQGRMLHVLPSTIKKEASQSGPSSG 99
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 52.0 bits (123), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 38/153 (24%), Positives = 69/153 (45%), Gaps = 13/153 (8%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALKEP 132
L + L + T + +S+F + G++E ++ DK TG+S GYGF+ + + A A+
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN-- 64
Query: 133 SKKIDGRVTVTNLAVAGNSGN-STNNPVDVSLR--KIFVGNVPNDMSADKLLAHFACYGE 189
T+ L + + S P S+R ++V +P MS ++ F+ YG
Sbjct: 65 --------TLNGLKLQTKTIKVSYARPSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGR 116
Query: 190 IEEGPLGFDKQTGKPKGFALFVYKTAEGAQAAL 222
I + D+ TG +G + A+ A+
Sbjct: 117 IITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 149
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 34/105 (32%), Positives = 52/105 (49%), Gaps = 11/105 (10%)
Query: 27 PQDARKIVERLTSDQL-LDVLSSAVARHDDVLESVRSIADADPTQRKLFIRGLGWDTTTE 85
P DA K + L +L + + AR S SI DA+ L++ GL + +
Sbjct: 56 PNDADKAINTLNGLKLQTKTIKVSYAR-----PSSASIRDAN-----LYVSGLPKTMSQK 105
Query: 86 GLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALK 130
+ +FS YG + + ++LD+ATG S+G GFI F A A+K
Sbjct: 106 EMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 150
>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 = 51.6 bits (122), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 28/76 (36%), Positives = 47/76 (61%), Gaps = 1/76 (1%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALKE- 131
+F+ L + TTE +++ F+ +G + +A V+ D ATGKSKGYGF++F + A A+++
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 132 PSKKIDGRVTVTNLAV 147
+ + GR TN A
Sbjct: 78 GGQWLGGRQIRTNWAT 93
Score = 36.2 bits (82), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 25/99 (25%), Positives = 47/99 (47%), Gaps = 1/99 (1%)
Query: 149 GNSGNSTNNPVDVSLRKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFA 208
G+SG+S + +FVG++ +++ + + A FA +G I + + D TGK KG+
Sbjct: 1 GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYG 60
Query: 209 LFVYKTAEGAQAALVD-PIKTVDGKQLNCRLADNKKAKP 246
+ A+ A+ + + G+Q+ A K P
Sbjct: 61 FVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAP 99
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 51.6 bits (122), Expect = 8e-07, Method: Composition-based stats.
Identities = 24/60 (40%), Positives = 39/60 (65%)
Query: 72 KLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALKE 131
+L++ L ++ T + LR IF +G +E +++D TG+SKGYGFITF + A AL++
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Score = 38.1 bits (87), Expect = 0.010, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 33/58 (56%)
Query: 165 KIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAAL 222
+++VG++ +++ D L F +G IE L D +TG+ KG+ + +E A+ AL
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKAL 85
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 24/59 (40%), Positives = 39/59 (66%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALKE 131
L++ L ++ T + LR IF +G+++ V++ D TG+SKGYGFITF + A AL++
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66
Score = 35.0 bits (79), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 32/57 (56%)
Query: 166 IFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAAL 222
++VG++ +++ D L F +G+I+ L D TG+ KG+ + +E A+ AL
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D (Auf1) With Telomere Dna
pdb|1X0F|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D(Auf1) With Telomeric Dna
Length = 79
Score = 50.4 bits (119), Expect = 2e-06, Method: Composition-based stats.
Identities = 26/66 (39%), Positives = 37/66 (56%), Gaps = 8/66 (12%)
Query: 71 RKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALK 130
+K+F+ GL DT E +R F +GE+E + +D T K +G+ FITFK +
Sbjct: 2 KKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKE--------E 53
Query: 131 EPSKKI 136
EP KKI
Sbjct: 54 EPVKKI 59
Score = 42.7 bits (99), Expect = 3e-04, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 30/54 (55%)
Query: 163 LRKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAE 216
++KIFVG + D +K+ +F +GE+E L D +T K +GF +K E
Sbjct: 1 VKKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEE 54
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 49.7 bits (117), Expect = 3e-06, Method: Composition-based stats.
Identities = 18/51 (35%), Positives = 36/51 (70%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHID 123
+F+ GL +TT E ++ F +G++++A+++ DK T + +G+GF+TF+ D
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESED 52
Score = 38.9 bits (89), Expect = 0.006, Method: Composition-based stats.
Identities = 18/79 (22%), Positives = 44/79 (55%), Gaps = 5/79 (6%)
Query: 166 IFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALVDP 225
IFVG + + + + + +F +G++++ L FDK T + +GF +++ + +V+
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESED-----IVEK 56
Query: 226 IKTVDGKQLNCRLADNKKA 244
+ + ++N ++ + KKA
Sbjct: 57 VCEIHFHEINNKMVECKKA 75
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 48.5 bits (114), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 44/77 (57%), Gaps = 1/77 (1%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALKEP 132
L + GL TT LR +FS YG + + ++ D+ + +S+G+ F+ F+++D A A +
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 133 S-KKIDGRVTVTNLAVA 148
+ ++DGR + ++
Sbjct: 78 NGMELDGRRIRVDFSIT 94
Score = 29.3 bits (64), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 11/38 (28%), Positives = 23/38 (60%)
Query: 184 FACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAA 221
F+ YG I + + +D+Q+ + +GFA ++ + A+ A
Sbjct: 36 FSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 73
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 48.5 bits (114), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 48/86 (55%), Gaps = 2/86 (2%)
Query: 64 ADADPTQRKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHID 123
A+ DP L + GL TT LR +FS YG + + ++ D+ + +S+G+ F+ F+++D
Sbjct: 41 ANPDPNC-CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 99
Query: 124 GAMLALKEPS-KKIDGRVTVTNLAVA 148
A A + + ++DGR + ++
Sbjct: 100 DAKEAKERANGMELDGRRIRVDFSIT 125
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 47.8 bits (112), Expect = 1e-05, Method: Composition-based stats.
Identities = 25/64 (39%), Positives = 35/64 (54%), Gaps = 8/64 (12%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALKEP 132
+F+ GL DT E +R F +GE+E + +D T K +G+ FITFK +EP
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKE--------EEP 53
Query: 133 SKKI 136
KKI
Sbjct: 54 VKKI 57
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 18/51 (35%), Positives = 27/51 (52%)
Query: 166 IFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAE 216
IFVG + D +K+ +F +GE+E L D +T K +GF +K E
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEE 52
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 45/77 (58%), Gaps = 2/77 (2%)
Query: 64 ADADPTQRKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHID 123
A+ DP L + GL TT LR +FS YG + + ++ D+ + +S+G+ F+ F+++D
Sbjct: 10 ANPDPNC-CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 68
Query: 124 GAMLALKEPS-KKIDGR 139
A A + + ++DGR
Sbjct: 69 DAKEAKERANGMELDGR 85
Score = 29.6 bits (65), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 9/73 (12%)
Query: 180 LLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALVDPIKTVDGKQLNCRLA 239
L F+ YG I + + +D+Q+ + +GFA ++ + A+ A + +G +L
Sbjct: 32 LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK----ERANGMEL----- 82
Query: 240 DNKKAKPMGPDGG 252
D ++ + GP G
Sbjct: 83 DGRRIRVSGPSSG 95
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 47.4 bits (111), Expect = 1e-05, Method: Composition-based stats.
Identities = 22/88 (25%), Positives = 45/88 (51%)
Query: 165 KIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALVD 224
KIFVG +P++ +L +F +G + E + +D + +P+GF ++ + A+
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
Query: 225 PIKTVDGKQLNCRLADNKKAKPMGPDGG 252
+ GK++ + A+ + +K GP G
Sbjct: 72 HFHDIMGKKVEVKRAEPRDSKSSGPSSG 99
Score = 37.4 bits (85), Expect = 0.016, Method: Composition-based stats.
Identities = 17/49 (34%), Positives = 28/49 (57%)
Query: 72 KLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFK 120
K+F+ G+ + LR F +G + E V+I D + +G+GFITF+
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFE 60
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 38/168 (22%), Positives = 75/168 (44%), Gaps = 12/168 (7%)
Query: 71 RKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALK 130
R L++ L T + L+ F G + +++DK K+ Y F+ + A +AL+
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQ 59
Query: 131 EPS-KKIDGRVTVTNLAVAGNSGNSTNNPVDVSLRKIFVGNVPNDMSADKLLAHFACYGE 189
+ K+I+ + N A +S + +FVG++ ++ + L F +
Sbjct: 60 TLNGKQIENNIVKINWAFQSQQSSSDDTF------NLFVGDLNVNVDDETLRNAFKDFPS 113
Query: 190 IEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALVDPIKTVDGKQLNCR 237
G + +D QTG +G+ + + + AQ A+ ++ G+ LN R
Sbjct: 114 YLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM----DSMQGQDLNGR 157
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 36/75 (48%), Gaps = 1/75 (1%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALKEP 132
LF+ L + E LR+ F + V+ D TG S+GYGF++F D A A+
Sbjct: 90 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 149
Query: 133 S-KKIDGRVTVTNLA 146
+ ++GR N A
Sbjct: 150 QGQDLNGRPLRINWA 164
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/60 (40%), Positives = 39/60 (65%), Gaps = 1/60 (1%)
Query: 72 KLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALKE 131
KLFI GL +T + L+++F +G + E ++I D+ T KS+G+ FITF++ A A K+
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKD 67
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 39/155 (25%), Positives = 69/155 (44%), Gaps = 10/155 (6%)
Query: 72 KLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATG--KSKGYGFITFKHIDGAMLAL 129
K+F+ + + + LR +F YG + E V+ D++ +SKG F+TF A+ A
Sbjct: 17 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 76
Query: 130 K--EPSKKIDGRVTVTNLAVAGNSGNSTNNPVDVSLRKIFVGNVPNDMSADKLLAHFACY 187
K + G + A + N+ V RK+F+G + + + + F+ +
Sbjct: 77 NALHNMKVLPGMHHPIQMKPADSEKNNA-----VEDRKLFIGMISKKCTENDIRVMFSSF 131
Query: 188 GEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAAL 222
G+IEE + G +G A + T AQ A+
Sbjct: 132 GQIEECRI-LRGPDGLSRGCAFVTFTTRAMAQTAI 165
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 33/60 (55%), Gaps = 1/60 (1%)
Query: 71 RKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALK 130
RKLFI + T +R +FS++G++EE IL G S+G F+TF A A+K
Sbjct: 108 RKLFIGMISKKCTENDIRVMFSSFGQIEEC-RILRGPDGLSRGCAFVTFTTRAMAQTAIK 166
>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 = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 48/178 (26%), Positives = 73/178 (41%), Gaps = 18/178 (10%)
Query: 51 ARHDDVLESVRSIADADPTQRKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGK 110
A H L PT L + L T + + +G LE ++ + TG+
Sbjct: 74 AFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQ 133
Query: 111 SKGYGFITFKHIDGAMLALKE-PSKKIDGRVTVTNLAVAGNSGNSTNNPVDVSLRKIFVG 169
SKGYGF + D A A + K + R + AG P + R + V
Sbjct: 134 SKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQL-----TPALLHSRCLCVD 188
Query: 170 NVP---NDMSA-DKLLA--HFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAA 221
+P ND+ A + L+ H + ++ G Q G+ KGFA+ Y+TAE A+ A
Sbjct: 189 RLPPGFNDVDALCRALSAVHSPTFCQLACG------QDGQLKGFAVLEYETAEMAEEA 240
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 40/155 (25%), Positives = 65/155 (41%), Gaps = 20/155 (12%)
Query: 70 QRKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLAL 129
+RK+ IRGL D T + + + S Y EL+ V K KG F+T + + A A+
Sbjct: 20 RRKILIRGLPGDVTNQEVHDLLSDY-ELKYCFV------DKYKGTAFVTLLNGEQAEAAI 72
Query: 130 KEPSKKIDGRVTVTNLAVAGNSGNSTNNPVDVSLRKIFVGNVPNDMSADKLLAHFACYGE 189
+ R+ L+V P D L V N+P ++ + +G
Sbjct: 73 NAFHQ---SRLRERELSV-------QLQPTDALL---CVANLPPSLTQQQFEELVRPFGS 119
Query: 190 IEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALVD 224
+E L + ++TG+ KG+ Y + A A D
Sbjct: 120 LERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 154
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 48/178 (26%), Positives = 73/178 (41%), Gaps = 18/178 (10%)
Query: 51 ARHDDVLESVRSIADADPTQRKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGK 110
A H L PT L + L T + + +G LE ++ + TG+
Sbjct: 76 AFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQ 135
Query: 111 SKGYGFITFKHIDGAMLALKE-PSKKIDGRVTVTNLAVAGNSGNSTNNPVDVSLRKIFVG 169
SKGYGF + D A A + K + R + AG P + R + V
Sbjct: 136 SKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQL-----TPALLHSRCLCVD 190
Query: 170 NVP---NDMSA-DKLLA--HFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAA 221
+P ND+ A + L+ H + ++ G Q G+ KGFA+ Y+TAE A+ A
Sbjct: 191 RLPPGFNDVDALCRALSAVHSPTFCQLACG------QDGQLKGFAVLEYETAEMAEEA 242
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 40/155 (25%), Positives = 65/155 (41%), Gaps = 20/155 (12%)
Query: 70 QRKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLAL 129
+RK+ IRGL D T + + + S Y EL+ V K KG F+T + + A A+
Sbjct: 22 RRKILIRGLPGDVTNQEVHDLLSDY-ELKYCFV------DKYKGTAFVTLLNGEQAEAAI 74
Query: 130 KEPSKKIDGRVTVTNLAVAGNSGNSTNNPVDVSLRKIFVGNVPNDMSADKLLAHFACYGE 189
+ R+ L+V P D L V N+P ++ + +G
Sbjct: 75 NAFHQ---SRLRERELSV-------QLQPTDALL---CVANLPPSLTQQQFEELVRPFGS 121
Query: 190 IEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALVD 224
+E L + ++TG+ KG+ Y + A A D
Sbjct: 122 LERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 156
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 48/178 (26%), Positives = 73/178 (41%), Gaps = 18/178 (10%)
Query: 51 ARHDDVLESVRSIADADPTQRKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGK 110
A H L PT L + L T + + +G LE ++ + TG+
Sbjct: 76 AFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQ 135
Query: 111 SKGYGFITFKHIDGAMLALKE-PSKKIDGRVTVTNLAVAGNSGNSTNNPVDVSLRKIFVG 169
SKGYGF + D A A + K + R + AG P + R + V
Sbjct: 136 SKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQL-----TPALLHSRCLCVD 190
Query: 170 NVP---NDMSA-DKLLA--HFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAA 221
+P ND+ A + L+ H + ++ G Q G+ KGFA+ Y+TAE A+ A
Sbjct: 191 RLPPGFNDVDALCRALSAVHSPTFCQLACG------QDGQLKGFAVLEYETAEMAEEA 242
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 40/155 (25%), Positives = 65/155 (41%), Gaps = 20/155 (12%)
Query: 70 QRKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLAL 129
+RK+ IRGL D T + + + S Y EL+ V K KG F+T + + A A+
Sbjct: 22 RRKILIRGLPGDVTNQEVHDLLSDY-ELKYCFV------DKYKGTAFVTLLNGEQAEAAI 74
Query: 130 KEPSKKIDGRVTVTNLAVAGNSGNSTNNPVDVSLRKIFVGNVPNDMSADKLLAHFACYGE 189
+ R+ L+V P D L V N+P ++ + +G
Sbjct: 75 NAFHQ---SRLRERELSV-------QLQPTDALL---CVANLPPSLTQQQFEELVRPFGS 121
Query: 190 IEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALVD 224
+E L + ++TG+ KG+ Y + A A D
Sbjct: 122 LERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 156
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 46.6 bits (109), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 24/57 (42%), Positives = 31/57 (54%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLAL 129
L+IRGL TT + L + YG++ ILDK T K KGYGF+ F A A+
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 64
>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 = 46.6 bits (109), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/52 (42%), Positives = 32/52 (61%)
Query: 68 PTQRKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITF 119
P + L + L + T + LRS+FS+ GE+E A +I DK G S GYGF+ +
Sbjct: 2 PGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNY 53
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 41/81 (50%), Gaps = 4/81 (4%)
Query: 166 IFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALVDP 225
+ V +P +M+ D+L + F+ GE+E L DK G G+ Y TA+ A+ A
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA---- 62
Query: 226 IKTVDGKQLNCRLADNKKAKP 246
I T++G +L + A+P
Sbjct: 63 INTLNGLRLQSKTIKVSYARP 83
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 46.2 bits (108), Expect = 3e-05, Method: Composition-based stats.
Identities = 26/81 (32%), Positives = 44/81 (54%), Gaps = 1/81 (1%)
Query: 68 PTQRKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAML 127
P++ +++ L + T L IFS YG++ + ++ DK T KSKG FI F D A
Sbjct: 14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQN 73
Query: 128 ALKE-PSKKIDGRVTVTNLAV 147
+ +K++ GRV ++A+
Sbjct: 74 CTRAINNKQLFGRVIKASIAI 94
Score = 35.0 bits (79), Expect = 0.074, Method: Composition-based stats.
Identities = 21/77 (27%), Positives = 40/77 (51%), Gaps = 4/77 (5%)
Query: 162 SLRKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAA 221
S ++V N+P ++ + L F+ YG++ + + DK T K KG A ++ + AQ
Sbjct: 15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQ-- 72
Query: 222 LVDPIKTVDGKQLNCRL 238
+ + ++ KQL R+
Sbjct: 73 --NCTRAINNKQLFGRV 87
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 46.2 bits (108), Expect = 4e-05, Method: Composition-based stats.
Identities = 25/67 (37%), Positives = 36/67 (53%), Gaps = 1/67 (1%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALKEP 132
L + GL W TT + L+ FS +GE+ V D TG SKG+GF+ F + + + +
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ- 76
Query: 133 SKKIDGR 139
IDGR
Sbjct: 77 RHMIDGR 83
Score = 43.1 bits (100), Expect = 3e-04, Method: Composition-based stats.
Identities = 28/104 (26%), Positives = 50/104 (48%), Gaps = 1/104 (0%)
Query: 149 GNSGNSTNNPVDVSLRKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFA 208
G+SG+S + V +P + L +F+ +GE+ + D +TG KGF
Sbjct: 1 GSSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFG 60
Query: 209 LFVYKTAEGAQAALVDPIKTVDGKQLNCRLADNKKAKPMGPDGG 252
FV T Q ++ +DG+ +C+L ++K+++ GP G
Sbjct: 61 -FVRFTEYETQVKVMSQRHMIDGRWCDCKLPNSKQSQDSGPSSG 103
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 45.8 bits (107), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 41/157 (26%), Positives = 71/157 (45%), Gaps = 14/157 (8%)
Query: 72 KLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATG--KSKGYGFITFKHIDGAMLAL 129
K+F+ + + + LR +F YG + E V+ D++ +SKG F+TF A+ A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 130 K--EPSKKIDGRVTVTNLAVAGNSGNSTNNPVDVSLRKIFVGNVPNDMSADKLLAHFACY 187
K + G + A + N+ V RK+F+G + + + + F+ +
Sbjct: 65 NALHNMKVLPGMHHPIQMKPADSEKNNA-----VEDRKLFIGMISKKCTENDIRVMFSSF 119
Query: 188 GEIEEGPL--GFDKQTGKPKGFALFVYKTAEGAQAAL 222
G+IEE + G D G +G A + T AQ A+
Sbjct: 120 GQIEECRILRGPD---GLSRGCAFVTFTTRAMAQTAI 153
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 33/60 (55%), Gaps = 1/60 (1%)
Query: 71 RKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALK 130
RKLFI + T +R +FS++G++EE IL G S+G F+TF A A+K
Sbjct: 96 RKLFIGMISKKCTENDIRVMFSSFGQIEEC-RILRGPDGLSRGCAFVTFTTRAMAQTAIK 154
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 45.8 bits (107), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 44/167 (26%), Positives = 73/167 (43%), Gaps = 21/167 (12%)
Query: 57 LESVRSIADADPTQR-KLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYG 115
L++ R + TQR +LF+ L D T E +R +F YG+ E + K KG+G
Sbjct: 8 LKNFRKPGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI------HKDKGFG 61
Query: 116 FITFKHIDGAMLALKEPSKKIDGRVTVTNLAVAGNSGNSTNNPVDVSLRKIFVGNVPNDM 175
FI + A +A +V + N+ + G SL V N+P +
Sbjct: 62 FIRLETRTLAEIA----------KVELDNMPLRGKQLRVRFACHSASLT---VRNLPQYV 108
Query: 176 SADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAAL 222
S + L F+ +G++E + D + G+P G + + A+ AL
Sbjct: 109 SNELLEEAFSVFGQVERAVVIVDDR-GRPSGKGIVEFSGKPAARKAL 154
>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1HL6|C Chain C, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1RK8|A Chain A, Structure Of The Cytosolic Protein Pym Bound To The Mago-
Y14 Core Of The Exon Junction Complex
pdb|2X1G|A Chain A, Crystal Structure Of Importin13 - Mago-Y14 Complex
pdb|2X1G|C Chain C, Crystal Structure Of Importin13 - Mago-Y14 Complex
Length = 165
Score = 45.4 bits (106), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 34/111 (30%), Positives = 52/111 (46%), Gaps = 12/111 (10%)
Query: 123 DGAMLALKEPSKKIDGRV--TVTNLAVAGNSGNSTNNPVDVSLR----------KIFVGN 170
D ++ LKE +K GR + +N A +S N D L +FV +
Sbjct: 20 DQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTS 79
Query: 171 VPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAA 221
+ + D++ F YGEI+ L D++TG KG+AL Y+T + A AA
Sbjct: 80 IHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 130
Score = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 30/56 (53%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLA 128
LF+ + + + ++ F YGE++ + LD+ TG SKGY + ++ A+ A
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 130
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 45.1 bits (105), Expect = 8e-05, Method: Composition-based stats.
Identities = 26/79 (32%), Positives = 46/79 (58%), Gaps = 2/79 (2%)
Query: 62 SIADADPTQRKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKH 121
S A+ DP L + GL TT LR +FS YG + + ++ D+ + +S+G+ F+ F++
Sbjct: 5 SRANPDPNC-CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 63
Query: 122 IDGAMLALKEPS-KKIDGR 139
+D A A + + ++DGR
Sbjct: 64 VDDAKEAKERANGMELDGR 82
>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 = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 42/78 (53%), Gaps = 3/78 (3%)
Query: 166 IFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQ---AAL 222
++V N+P ++ D+L F YG I + + DK TG+P+G A Y E AQ +AL
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 223 VDPIKTVDGKQLNCRLAD 240
+ I + L+ RLA+
Sbjct: 76 NNVIPEGGSQPLSVRLAE 93
Score = 35.8 bits (81), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 30/57 (52%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLAL 129
L++ L T + L +IF YG + + ++ DK TG+ +G F+ + + A A+
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 72
>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 = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 41/160 (25%), Positives = 68/160 (42%), Gaps = 20/160 (12%)
Query: 72 KLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATG--KSKGYGFITFKHIDGAMLAL 129
K F+ + + + LR +F YG + E V+ D++ +SKG F+TF A+ A
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 130 K--EPSKKIDGRVTVTNLAVAGNSGNSTNNPVDVSLRKIFVGNVPNDMSADKLLAHFACY 187
K + G A + N+ V RK+F+G + + + + F+ +
Sbjct: 65 NALHNXKVLPGXHHPIQXKPADSEKNNA-----VEDRKLFIGXISKKCTENDIRVXFSSF 119
Query: 188 GEIEE-----GPLGFDKQTGKPKGFALFVYKTAEGAQAAL 222
G+IEE GP G +G A + T AQ A+
Sbjct: 120 GQIEECRILRGPDGLS------RGCAFVTFTTRAXAQTAI 153
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 32/60 (53%), Gaps = 1/60 (1%)
Query: 71 RKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALK 130
RKLFI + T +R FS++G++EE IL G S+G F+TF A A+K
Sbjct: 96 RKLFIGXISKKCTENDIRVXFSSFGQIEEC-RILRGPDGLSRGCAFVTFTTRAXAQTAIK 154
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 30/91 (32%), Positives = 43/91 (47%), Gaps = 13/91 (14%)
Query: 164 RKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFD-------KQTGKPKGFALFVYKTAE 216
RK+FVG +P D+ D++ A F + GPL D K PKG+A +++
Sbjct: 9 RKVFVGGLPPDIDEDEITASFRRF-----GPLVVDWPHKAESKSYFPPKGYAFLLFQEES 63
Query: 217 GAQAALVDPIKTVDGKQLNCRLADNKKAKPM 247
Q AL+D DGK C + K KP+
Sbjct: 64 SVQ-ALIDACLEEDGKLYLCVSSPTIKDKPV 93
>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 = 43.9 bits (102), Expect = 2e-04, Method: Composition-based stats.
Identities = 21/47 (44%), Positives = 30/47 (63%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITF 119
L + L + T + LRS+FS+ GE+E A +I DK G S GYGF+ +
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNY 68
Score = 38.9 bits (89), Expect = 0.006, Method: Composition-based stats.
Identities = 24/81 (29%), Positives = 40/81 (49%), Gaps = 4/81 (4%)
Query: 166 IFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALVDP 225
+ V +P + + D+L + F+ GE+E L DK G G+ Y TA+ A+ A
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA---- 77
Query: 226 IKTVDGKQLNCRLADNKKAKP 246
I T++G +L + A+P
Sbjct: 78 INTLNGLRLQSKTIKVSYARP 98
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 43/78 (55%), Gaps = 6/78 (7%)
Query: 71 RKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALK 130
+ LF++GL DTT E L+ F G + A ++ D+ TG SKG+GF+ F + A A K
Sbjct: 16 KTLFVKGLSEDTTEETLKESFD--GSVR-ARIVTDRETGSSKGFGFVDFNSEEDAK-AAK 71
Query: 131 EPSK--KIDGRVTVTNLA 146
E + +IDG + A
Sbjct: 72 EAMEDGEIDGNKVTLDWA 89
Score = 28.9 bits (63), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 3/73 (4%)
Query: 149 GNSGNSTNNPVDVSLRKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFA 208
G+SG+S N + +FV + D + + L F G + + D++TG KGF
Sbjct: 1 GSSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFD--GSVR-ARIVTDRETGSSKGFG 57
Query: 209 LFVYKTAEGAQAA 221
+ + E A+AA
Sbjct: 58 FVDFNSEEDAKAA 70
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 43.5 bits (101), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 34/63 (53%)
Query: 68 PTQRKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAML 127
P LFI L + T L S F +G + A V +DK T SK +GF++F + D A +
Sbjct: 38 PEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQV 97
Query: 128 ALK 130
A+K
Sbjct: 98 AIK 100
Score = 32.0 bits (71), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 34/72 (47%), Gaps = 4/72 (5%)
Query: 166 IFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALVDP 225
+F+ ++P + + L + F +G + + DKQT K F + + AQ A
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVA---- 98
Query: 226 IKTVDGKQLNCR 237
IK ++G Q+ +
Sbjct: 99 IKAMNGFQVGTK 110
>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 = 43.1 bits (100), Expect = 3e-04, Method: Composition-based stats.
Identities = 24/76 (31%), Positives = 38/76 (50%)
Query: 159 VDVSLRKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGA 218
++ R I+VGNV +A++L AHF G + + DK +G PKGFA + E
Sbjct: 1 MEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESV 60
Query: 219 QAALVDPIKTVDGKQL 234
+ +L G+Q+
Sbjct: 61 RTSLALDESLFRGRQI 76
>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 = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 42/75 (56%), Gaps = 4/75 (5%)
Query: 164 RKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALV 223
R +++G++P D + +++L + G + + FD QTG+ KG+A ++ E + +A
Sbjct: 4 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA-- 61
Query: 224 DPIKTVDGKQLNCRL 238
++ ++G QL R
Sbjct: 62 --VRNLNGYQLGSRF 74
Score = 38.1 bits (87), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 42/84 (50%), Gaps = 4/84 (4%)
Query: 71 RKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALK 130
R +++ + +D T E + + S G + ++ D TG+SKGY FI F+ ++ + A+
Sbjct: 4 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV- 62
Query: 131 EPSKKIDGRVTVTNLAVAGNSGNS 154
+ ++G + G S NS
Sbjct: 63 ---RNLNGYQLGSRFLKCGYSSNS 83
>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 = 20/75 (26%), Positives = 42/75 (56%), Gaps = 4/75 (5%)
Query: 164 RKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALV 223
R +++G++P D + +++L + G + + FD QTG+ KG+A ++ E + +A
Sbjct: 5 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA-- 62
Query: 224 DPIKTVDGKQLNCRL 238
++ ++G QL R
Sbjct: 63 --VRNLNGYQLGSRF 75
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 44/88 (50%), Gaps = 4/88 (4%)
Query: 67 DPTQRKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAM 126
+P R +++ + +D T E + + S G + ++ D TG+SKGY FI F+ ++ +
Sbjct: 1 NPPSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSA 60
Query: 127 LALKEPSKKIDGRVTVTNLAVAGNSGNS 154
A+ + ++G + G S NS
Sbjct: 61 SAV----RNLNGYQLGSRFLKCGYSSNS 84
>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 = 42.7 bits (99), Expect = 4e-04, Method: Composition-based stats.
Identities = 24/71 (33%), Positives = 36/71 (50%)
Query: 164 RKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALV 223
R I+VGNV +A++L AHF G + + DK +G PKGFA + E + +L
Sbjct: 7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 66
Query: 224 DPIKTVDGKQL 234
G+Q+
Sbjct: 67 LDESLFRGRQI 77
>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 = 42.7 bits (99), Expect = 4e-04, Method: Composition-based stats.
Identities = 22/57 (38%), Positives = 34/57 (59%)
Query: 166 IFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAAL 222
+FV V + + + + FA YGEI+ L D++TG KG+ L Y+T + AQAA+
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Score = 38.5 bits (88), Expect = 0.007, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFI---TFKHIDGAMLAL 129
LF+ G+ + T E + F+ YGE++ + LD+ TG KGY + T+K AM L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 28/102 (27%), Positives = 54/102 (52%), Gaps = 1/102 (0%)
Query: 152 GNSTNNPVDVSLRKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFV 211
G+S ++ + + R ++VG + ++ L A F +G+I + + D +T K +GFA
Sbjct: 1 GSSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 60
Query: 212 YKTAEGAQAALVDPIKT-VDGKQLNCRLADNKKAKPMGPDGG 252
++ AE A AA+ + ++ + G+ + LA + K GP G
Sbjct: 61 FELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIKESGPSSG 102
Score = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 69 TQRKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLA 128
T+R L++ GL + + L + F +G++ + + LD T K +G+ F+ F+ + A A
Sbjct: 11 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 70
Query: 129 LKEPSK-KIDGRVTVTNLA 146
+ ++ ++ GR NLA
Sbjct: 71 IDNMNESELFGRTIRVNLA 89
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 42.4 bits (98), Expect = 5e-04, Method: Composition-based stats.
Identities = 22/57 (38%), Positives = 34/57 (59%)
Query: 166 IFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAAL 222
+FV V + + + + FA YGEI+ L D++TG KG+ L Y+T + AQAA+
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Score = 38.1 bits (87), Expect = 0.009, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFI---TFKHIDGAMLAL 129
LF+ G+ + T E + F+ YGE++ + LD+ TG KGY + T+K AM L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
>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 = 42.0 bits (97), Expect = 6e-04, Method: Composition-based stats.
Identities = 22/57 (38%), Positives = 34/57 (59%)
Query: 166 IFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAAL 222
+FV V + + + + FA YGEI+ L D++TG KG+ L Y+T + AQAA+
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 81
Score = 38.5 bits (88), Expect = 0.006, Method: Composition-based stats.
Identities = 26/80 (32%), Positives = 38/80 (47%), Gaps = 8/80 (10%)
Query: 58 ESVRSIADADPTQRK-----LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSK 112
+SV D QR LF+ G+ + T E + F+ YGE++ + LD+ TG K
Sbjct: 5 DSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK 64
Query: 113 GYGFI---TFKHIDGAMLAL 129
GY + T+K AM L
Sbjct: 65 GYTLVEYETYKEAQAAMEGL 84
>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 = 42.0 bits (97), Expect = 7e-04, Method: Composition-based stats.
Identities = 22/57 (38%), Positives = 34/57 (59%)
Query: 166 IFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAAL 222
+FV V + + + + FA YGEI+ L D++TG KG+ L Y+T + AQAA+
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Score = 37.7 bits (86), Expect = 0.012, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFI---TFKHIDGAMLAL 129
LF+ G+ + T E + F+ YGE++ + LD+ TG KGY + T+K AM L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 42.0 bits (97), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 30/59 (50%)
Query: 71 RKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLAL 129
R L + + LR +F YG +E ++ D+ T +S+GYGF+ F+ A A+
Sbjct: 43 RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAI 101
Score = 36.6 bits (83), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 32/66 (48%)
Query: 157 NPVDVSLRKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAE 216
NP LR + V +P + +L F YG IE + D++T + +G+ +++
Sbjct: 36 NPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGS 95
Query: 217 GAQAAL 222
AQ A+
Sbjct: 96 SAQQAI 101
>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 = 41.6 bits (96), Expect = 8e-04, Method: Composition-based stats.
Identities = 22/57 (38%), Positives = 34/57 (59%)
Query: 166 IFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAAL 222
+FV V + + + + FA YGEI+ L D++TG KG+ L Y+T + AQAA+
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 68
Score = 37.7 bits (86), Expect = 0.014, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFI---TFKHIDGAMLAL 129
LF+ G+ + T E + F+ YGE++ + LD+ TG KGY + T+K AM L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
Length = 124
Score = 41.6 bits (96), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 32/63 (50%)
Query: 160 DVSLRKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQ 219
++ R ++VGNV +A L AHF+ G I + DK +G PKG+A +
Sbjct: 33 EIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVD 92
Query: 220 AAL 222
AA+
Sbjct: 93 AAV 95
Score = 38.1 bits (87), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 29/50 (58%)
Query: 70 QRKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITF 119
+R +++ + + +T + L + FS+ G + ++ DK +G KGY +I F
Sbjct: 36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEF 85
>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
pdb|4F02|D Chain D, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
Length = 213
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 46/170 (27%), Positives = 68/170 (40%), Gaps = 21/170 (12%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALKEP 132
L++ L D T L FS G + V D T +S GY ++ F+ A AL
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD-- 75
Query: 133 SKKIDGRVTVTNLAVAGNSGNSTNNPVDVSLRK-----IFVGNVPNDMSADKLLAHFACY 187
T+ + G + D SLRK IF+ N+ + L F+ +
Sbjct: 76 --------TMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAF 127
Query: 188 GEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALVDPIKTVDGKQLNCR 237
G I + D+ K GF F +T E A+ A I+ ++G LN R
Sbjct: 128 GNILSCKVVCDENGSKGYGFVHF--ETQEAAERA----IEKMNGMLLNDR 171
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 41.6 bits (96), Expect = 0.001, Method: Composition-based stats.
Identities = 21/56 (37%), Positives = 33/56 (58%)
Query: 166 IFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAA 221
+FV ++ + D++ F YGEI+ L D++TG KG+AL Y+T + A AA
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 84
Score = 33.1 bits (74), Expect = 0.34, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALKE 131
LF+ + + + ++ F YGE++ + LD+ TG SKGY + ++ A LA KE
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQA-LAAKE 86
>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 = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 22/57 (38%), Positives = 34/57 (59%)
Query: 166 IFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAAL 222
+FV V + + + + FA YGEI+ L D++TG KG+ L Y+T + AQAA+
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 82
Score = 37.7 bits (86), Expect = 0.013, Method: Composition-based stats.
Identities = 26/80 (32%), Positives = 38/80 (47%), Gaps = 8/80 (10%)
Query: 58 ESVRSIADADPTQRK-----LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSK 112
+SV D QR LF+ G+ + T E + F+ YGE++ + LD+ TG K
Sbjct: 6 DSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK 65
Query: 113 GYGFI---TFKHIDGAMLAL 129
GY + T+K AM L
Sbjct: 66 GYTLVEYETYKEAQAAMEGL 85
>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 = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 34/55 (61%), Gaps = 1/55 (1%)
Query: 94 YGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALKEP-SKKIDGRVTVTNLAV 147
+G + +A V+ D ATGKSKGYGF++F + A A+++ + + GR TN A
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWAT 84
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 20/75 (26%), Positives = 42/75 (56%), Gaps = 4/75 (5%)
Query: 164 RKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALV 223
R +++G++P D + +++L + G + + FD QTG+ KG+A ++ E + +A
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA-- 60
Query: 224 DPIKTVDGKQLNCRL 238
++ ++G QL R
Sbjct: 61 --VRNLNGYQLGSRF 73
Score = 36.6 bits (83), Expect = 0.031, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 34/60 (56%)
Query: 71 RKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALK 130
R +++ + +D T E + + S G + ++ D TG+SKGY FI F+ ++ + A++
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 68 PTQRKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAML 127
P+ RKLF+ L + + +R +F A+G +EE IL G SKG F+ + A
Sbjct: 13 PSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEE-CTILRGPDGNSKGCAFVKYSSHAEAQA 71
Query: 128 AL 129
A+
Sbjct: 72 AI 73
Score = 35.0 bits (79), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 35/74 (47%), Gaps = 1/74 (1%)
Query: 149 GNSGNSTNNPVDVSLRKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFA 208
G+SG+S S RK+FVG + S D + F +G IEE + G KG A
Sbjct: 1 GSSGSSGCLRQPPSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTI-LRGPDGNSKGCA 59
Query: 209 LFVYKTAEGAQAAL 222
Y + AQAA+
Sbjct: 60 FVKYSSHAEAQAAI 73
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 30/47 (63%), Gaps = 1/47 (2%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITF 119
+F+ G+ +RS F+ YG ++E +I D+ TG SKGYGF++F
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 58
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 31/51 (60%)
Query: 69 TQRKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITF 119
++ L + L + T + +S+F + G++E ++ DK TG+S GYGF+ +
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNY 53
Score = 36.6 bits (83), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 37/81 (45%), Gaps = 4/81 (4%)
Query: 166 IFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALVDP 225
+ V +P +M+ D+ + F G+IE L DK TG+ G+ Y A A
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA---- 62
Query: 226 IKTVDGKQLNCRLADNKKAKP 246
I T++G +L + A+P
Sbjct: 63 INTLNGLKLQTKTIKVSYARP 83
>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|B Chain B, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|C Chain C, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|D Chain D, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|E Chain E, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|F Chain F, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|G Chain G, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|H Chain H, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
Length = 190
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 46/170 (27%), Positives = 68/170 (40%), Gaps = 21/170 (12%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALKEP 132
L++ L D T L FS G + V D T +S GY ++ F+ A AL
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD-- 70
Query: 133 SKKIDGRVTVTNLAVAGNSGNSTNNPVDVSLRK-----IFVGNVPNDMSADKLLAHFACY 187
T+ + G + D SLRK IF+ N+ + L F+ +
Sbjct: 71 --------TMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAF 122
Query: 188 GEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALVDPIKTVDGKQLNCR 237
G I + D+ K GF F +T E A+ A I+ ++G LN R
Sbjct: 123 GNILSCKVVCDENGSKGYGFVHF--ETQEAAERA----IEKMNGMLLNDR 166
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 31/97 (31%), Positives = 45/97 (46%), Gaps = 8/97 (8%)
Query: 66 ADPTQRK-LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDG 124
+D T+ K +FIR L +D+ E L + +G+L+ V+L T SKG F F +
Sbjct: 10 SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEA 69
Query: 125 AMLALKEPS-------KKIDGRVTVTNLAVAGNSGNS 154
A L S K+DGR +LAV + S
Sbjct: 70 AQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAAS 106
Score = 28.5 bits (62), Expect = 7.5, Method: Composition-based stats.
Identities = 27/103 (26%), Positives = 41/103 (39%), Gaps = 8/103 (7%)
Query: 158 PVDVSLRK-IFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAE 216
P DV+ K +F+ N+ D + L +G+++ + T KG A + T E
Sbjct: 9 PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQE 68
Query: 217 GAQAALVDPI-------KTVDGKQLNCRLADNKKAKPMGPDGG 252
AQ L +DG+QL LA + GP G
Sbjct: 69 AAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASGPSSG 111
>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 = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 19/47 (40%), Positives = 30/47 (63%), Gaps = 1/47 (2%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITF 119
+F+ G+ +RS F+ YG ++E +I D+ TG SKGYGF++F
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 57
>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 = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 19/47 (40%), Positives = 30/47 (63%), Gaps = 1/47 (2%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITF 119
+F+ G+ +RS F+ YG ++E +I D+ TG SKGYGF++F
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 57
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/59 (38%), Positives = 29/59 (49%), Gaps = 8/59 (13%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALKE 131
LF+R L T E L FS +G+LE K K Y FI F DGA+ A++E
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLER--------VKKLKDYAFIHFDERDGAVKAMEE 64
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 18/47 (38%), Positives = 30/47 (63%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITF 119
L++ GL + + + +FS YG + + ++LD+ATG S+G GFI F
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRF 50
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 15/50 (30%), Positives = 31/50 (62%)
Query: 71 RKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFK 120
R +++ L + T+E ++ +FS +G++ +I D+ T K KG+GF+ +
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ 51
Score = 38.1 bits (87), Expect = 0.011, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 35/60 (58%), Gaps = 1/60 (1%)
Query: 163 LRKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAAL 222
+R I+VGN+ +++++ F+ +G++ L +D++T KPKGF FV E A+
Sbjct: 1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFG-FVEMQEESVSEAI 59
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 34/66 (51%), Gaps = 3/66 (4%)
Query: 64 ADADPTQRKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHID 123
AD + T R + L DT L+ +F +G + + DK TG+SKG+ FI+F +
Sbjct: 12 ADDNATIR---VTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRE 68
Query: 124 GAMLAL 129
A A+
Sbjct: 69 DAARAI 74
Score = 34.7 bits (78), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 32/75 (42%)
Query: 149 GNSGNSTNNPVDVSLRKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFA 208
G+SG+S N I V N+ D L F +G I L DK TG+ KGFA
Sbjct: 1 GSSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFA 60
Query: 209 LFVYKTAEGAQAALV 223
+ E A A+
Sbjct: 61 FISFHRREDAARAIA 75
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 22/79 (27%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 69 TQRKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLA 128
T+R L++ GL + + L + F +G++ + + LD T K +G+ F+ F+ + A A
Sbjct: 62 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 121
Query: 129 LKEPSK-KIDGRVTVTNLA 146
+ ++ ++ GR NLA
Sbjct: 122 IDNMNESELFGRTIRVNLA 140
Score = 36.6 bits (83), Expect = 0.027, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 33/59 (55%)
Query: 164 RKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAAL 222
R ++VG + ++ L A F +G+I + + D +T K +GFA ++ AE A AA+
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 122
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 6/71 (8%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALKEP 132
L+++ L E LR FS +G + A V+++ G+SKG+GF+ F + A A+ E
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTE- 74
Query: 133 SKKIDGRVTVT 143
++GR+ T
Sbjct: 75 ---MNGRIVAT 82
Score = 35.8 bits (81), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 26/105 (24%), Positives = 49/105 (46%), Gaps = 3/105 (2%)
Query: 149 GNSGNSTNNPVDVSLRKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFA 208
G+SG+S + + ++V N+ + + ++L F+ +G I + + G+ KGF
Sbjct: 1 GSSGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMM--EGGRSKGFG 58
Query: 209 LFVYKTAEGAQAALVDPI-KTVDGKQLNCRLADNKKAKPMGPDGG 252
+ + E A A+ + + V K L LA K+ + GP G
Sbjct: 59 FVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQSGPSSG 103
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGK---SKGYGFITFKHIDGAMLAL 129
LFI+ L + TT E L+ +FS G ++ + K S G+GF+ +K + A AL
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 130 KE 131
K+
Sbjct: 68 KQ 69
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 25/91 (27%), Positives = 37/91 (40%), Gaps = 4/91 (4%)
Query: 166 IFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGK---PKGFALFVYKTAEGAQAAL 222
+F+ N+ + + L F+ G I+ + K GF YK E AQ AL
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 223 VDPI-KTVDGKQLNCRLADNKKAKPMGPDGG 252
TVDG +L R+++ GP G
Sbjct: 68 KQLQGHTVDGHKLEVRISERATKPASGPSSG 98
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 22/79 (27%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 69 TQRKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLA 128
T+R L++ GL + + L + F +G++ + + LD T K +G+ F+ F+ + A A
Sbjct: 4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 63
Query: 129 LKEPSK-KIDGRVTVTNLA 146
+ ++ ++ GR NLA
Sbjct: 64 IDNMNESELFGRTIRVNLA 82
Score = 36.2 bits (82), Expect = 0.032, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 33/59 (55%)
Query: 164 RKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAAL 222
R ++VG + ++ L A F +G+I + + D +T K +GFA ++ AE A AA+
Sbjct: 6 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 64
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 24/71 (33%), Positives = 38/71 (53%), Gaps = 7/71 (9%)
Query: 66 ADPTQRK-----LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFK 120
ADP+ RK +FI+ L + L FSA+G + V+ D+ SKGYGF+ F+
Sbjct: 2 ADPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFE 59
Query: 121 HIDGAMLALKE 131
+ A A+++
Sbjct: 60 TQEAAERAIEK 70
>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 = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 22/79 (27%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 69 TQRKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLA 128
T+R L++ GL + + L + F +G++ + + LD T K +G+ F+ F+ + A A
Sbjct: 6 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 65
Query: 129 LKEPSK-KIDGRVTVTNLA 146
+ ++ ++ GR NLA
Sbjct: 66 IDNMNESELFGRTIRVNLA 84
Score = 36.2 bits (82), Expect = 0.033, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 33/59 (55%)
Query: 164 RKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAAL 222
R ++VG + ++ L A F +G+I + + D +T K +GFA ++ AE A AA+
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 66
>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 = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 44/88 (50%), Gaps = 5/88 (5%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITF---KHIDGAMLAL 129
L + L + T+ + LR +F YG + + + D+ T +S+G+ F+ F + + AM A+
Sbjct: 50 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109
Query: 130 KEPSKKIDGRVTVTNLAVAGNSGNSTNN 157
+DGR +A G +S ++
Sbjct: 110 D--GAVLDGRELRVQMARYGRPPDSHHS 135
Score = 32.0 bits (71), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 41/85 (48%), Gaps = 4/85 (4%)
Query: 158 PVDVS-LRKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAE 216
P DV + + V N+ S D L F YG + + + D+ T + +GFA +
Sbjct: 41 PPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKR 100
Query: 217 GAQAALVDPIK--TVDGKQLNCRLA 239
A+ A+ D + +DG++L ++A
Sbjct: 101 DAEDAM-DAMDGAVLDGRELRVQMA 124
>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 = 38.1 bits (87), Expect = 0.009, Method: Composition-based stats.
Identities = 24/75 (32%), Positives = 36/75 (48%), Gaps = 1/75 (1%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALKE- 131
LF+ L + E LR+ F + V+ D TG S+GYGF++F D A A+
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 132 PSKKIDGRVTVTNLA 146
+ ++GR N A
Sbjct: 64 QGQDLNGRPLRINWA 78
Score = 30.4 bits (67), Expect = 1.7, Method: Composition-based stats.
Identities = 18/72 (25%), Positives = 36/72 (50%), Gaps = 4/72 (5%)
Query: 166 IFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALVDP 225
+FVG++ ++ + L F + G + +D QTG +G+ + + + AQ A+
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM--- 60
Query: 226 IKTVDGKQLNCR 237
++ G+ LN R
Sbjct: 61 -DSMQGQDLNGR 71
>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 = 38.1 bits (87), Expect = 0.010, Method: Composition-based stats.
Identities = 21/79 (26%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 69 TQRKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLA 128
++R L++ GL + + L + F +G++ + + LD T K +G+ F+ F+ + A A
Sbjct: 1 SKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 60
Query: 129 LKEPSK-KIDGRVTVTNLA 146
+ ++ ++ GR NLA
Sbjct: 61 IDNMNESELFGRTIRVNLA 79
Score = 37.4 bits (85), Expect = 0.018, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 34/61 (55%)
Query: 162 SLRKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAA 221
S R ++VG + ++ L A F +G+I + + D +T K +GFA ++ AE A AA
Sbjct: 1 SKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 60
Query: 222 L 222
+
Sbjct: 61 I 61
>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 = 37.7 bits (86), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 33/111 (29%), Positives = 53/111 (47%), Gaps = 18/111 (16%)
Query: 47 SSAVARHDDVLESVRSIADADPTQRKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDK 106
SS V R+ LE + KLFI GL + T E L I A+G +++ ++ ++
Sbjct: 5 SSGVFRYSTSLE-----------KHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR 53
Query: 107 ATGKSKGYGFITFKHIDGAMLALKEPSKKIDGRVTVTNL--AVAGNSGNST 155
A GK KG ++ +++ A A+ K+DG N+ NSG S+
Sbjct: 54 A-GKPKGLAYVEYENESQASQAV----MKMDGMTIKENIIKVAISNSGPSS 99
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet
Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 37.7 bits (86), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 26/92 (28%), Positives = 41/92 (44%), Gaps = 9/92 (9%)
Query: 166 IFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALVDP 225
+F+ ++P + LL F +G + + DKQT K F Y AQAA
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA---- 83
Query: 226 IKTVDG-----KQLNCRLADNKKAKPMGPDGG 252
I++++G K+L +L +K GP G
Sbjct: 84 IQSMNGFQIGMKRLKVQLKRSKNDSKSGPSSG 115
Score = 34.7 bits (78), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 32/63 (50%)
Query: 68 PTQRKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAML 127
P LFI L + + L +F +G + A V +DK T SK +GF+++ + A
Sbjct: 23 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQA 82
Query: 128 ALK 130
A++
Sbjct: 83 AIQ 85
>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 = 37.0 bits (84), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 31/56 (55%)
Query: 68 PTQRKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHID 123
P KLFI GL + ++ + +++G L+ ++ D ATG SKGY F + I+
Sbjct: 94 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDIN 149
Score = 35.4 bits (80), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 36/151 (23%), Positives = 63/151 (41%), Gaps = 21/151 (13%)
Query: 71 RKLFIRGLGWDTTTEGLRSIFSA---YGELEEA--VVILDKATGKSKGYGFITFKHIDGA 125
R+L++ + + T E + F+A G L +A +L + K + F+ F+ +D
Sbjct: 7 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 66
Query: 126 MLALKEPSKKIDGRVTVTNLAVAGNSGNSTNNPVDVS----LRKIFVGNVPNDMSADKLL 181
A+ DG + G S P D K+F+G +PN ++ D++
Sbjct: 67 TQAMA-----FDG------IIFQGQS-LKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVK 114
Query: 182 AHFACYGEIEEGPLGFDKQTGKPKGFALFVY 212
+G ++ L D TG KG+A Y
Sbjct: 115 ELLTSFGPLKAFNLVKDSATGLSKGYAFCEY 145
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 36.6 bits (83), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 31/56 (55%)
Query: 68 PTQRKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHID 123
P KLFI GL + ++ + +++G L+ ++ D ATG SKGY F + I+
Sbjct: 92 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDIN 147
Score = 35.0 bits (79), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 36/151 (23%), Positives = 63/151 (41%), Gaps = 21/151 (13%)
Query: 71 RKLFIRGLGWDTTTEGLRSIFSA---YGELEEA--VVILDKATGKSKGYGFITFKHIDGA 125
R+L++ + + T E + F+A G L +A +L + K + F+ F+ +D
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 126 MLALKEPSKKIDGRVTVTNLAVAGNSGNSTNNPVDVS----LRKIFVGNVPNDMSADKLL 181
A+ DG + G S P D K+F+G +PN ++ D++
Sbjct: 65 TQAMA-----FDG------IIFQGQS-LKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVK 112
Query: 182 AHFACYGEIEEGPLGFDKQTGKPKGFALFVY 212
+G ++ L D TG KG+A Y
Sbjct: 113 ELLTSFGPLKAFNLVKDSATGLSKGYAFCEY 143
>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 = 36.6 bits (83), Expect = 0.026, Method: Composition-based stats.
Identities = 28/92 (30%), Positives = 45/92 (48%), Gaps = 13/92 (14%)
Query: 165 KIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALVD 224
++FVGN+P D++ +++ F YG+ E + K KGF +T A+ A V+
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFI------HKDKGFGFIRLETRTLAEIAKVE 70
Query: 225 ----PIKTVDGKQLNCRLADNKKAKPMGPDGG 252
P++ GKQL R A + + GP G
Sbjct: 71 LDNMPLR---GKQLRVRFACHSASLTSGPSSG 99
Score = 33.1 bits (74), Expect = 0.30, Method: Composition-based stats.
Identities = 20/53 (37%), Positives = 28/53 (52%), Gaps = 7/53 (13%)
Query: 69 TQR-KLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFK 120
TQR +LF+ L D T E +R +F YG+ E + K KG+GFI +
Sbjct: 13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI------HKDKGFGFIRLE 59
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 36.6 bits (83), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 30/52 (57%)
Query: 72 KLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHID 123
KLFI GL + ++ + +++G L+ ++ D ATG SKGY F + I+
Sbjct: 116 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDIN 167
Score = 35.4 bits (80), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 37/163 (22%), Positives = 69/163 (42%), Gaps = 25/163 (15%)
Query: 71 RKLFIRGLGWDTTTEGLRSIFSA---YGELEEA--VVILDKATGKSKGYGFITFKHID-- 123
R+L++ + + T E + F+A G L +A +L + K + F+ F+ +D
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 124 ------------GAMLALKEPS--KKIDGRVTVTNLAVAGNSGNSTNNPVDVSLRKIFVG 169
G L ++ P + + G ++ V G + V S K+F+G
Sbjct: 65 TQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPG----VVSTVVPDSAHKLFIG 120
Query: 170 NVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVY 212
+PN ++ D++ +G ++ L D TG KG+A Y
Sbjct: 121 GLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEY 163
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 36.2 bits (82), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 41/78 (52%), Gaps = 8/78 (10%)
Query: 148 AGNSGNSTNNPVDVSLRKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGF 207
+G+SG ++ + K+F+G +P ++ L F +G+I E + D+ TG KG
Sbjct: 3 SGSSGMKDHDAI-----KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGC 57
Query: 208 ALFVY---KTAEGAQAAL 222
A Y ++A AQ+AL
Sbjct: 58 AFLTYCERESALKAQSAL 75
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 36.2 bits (82), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 37/77 (48%), Gaps = 3/77 (3%)
Query: 149 GNSGNSTNNPVDVSLRKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFA 208
G+SG+S D K+FVG +P + L F +G I E + D+ TG KG A
Sbjct: 1 GSSGSSGVPMKDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCA 60
Query: 209 LFVY---KTAEGAQAAL 222
Y +A AQ+AL
Sbjct: 61 FLTYCARDSALKAQSAL 77
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 35.4 bits (80), Expect = 0.058, Method: Composition-based stats.
Identities = 27/89 (30%), Positives = 41/89 (46%), Gaps = 7/89 (7%)
Query: 71 RKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALK 130
+ L + L + T E L+ +F E + + GKSKGY FI F + A AL
Sbjct: 16 KTLVLSNLSYSATEETLQEVF----EKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALN 71
Query: 131 EPSKK-IDGRVTVTNLAVAGNSGNSTNNP 158
+K+ I+GR L + G G+ + P
Sbjct: 72 SCNKREIEGR--AIRLELQGPRGSPNSGP 98
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 35.4 bits (80), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 40/80 (50%), Gaps = 5/80 (6%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITF---KHIDGAMLAL 129
L + L + T+ + LR +F YG + + + D+ T +S+G+ F+ F + + AM A+
Sbjct: 73 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132
Query: 130 KEPSKKIDGRVTVTNLAVAG 149
+DGR +A G
Sbjct: 133 --DGAVLDGRELRVQMARYG 150
Score = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 3/74 (4%)
Query: 168 VGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALVDPIK 227
V N+ S D L F YG + + + D+ T + +GFA + A+ A+ D +
Sbjct: 75 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAM-DAMD 133
Query: 228 --TVDGKQLNCRLA 239
+DG++L ++A
Sbjct: 134 GAVLDGRELRVQMA 147
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 35.0 bits (79), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 30/53 (56%)
Query: 71 RKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHID 123
KLFI GL + ++ + +++G L+ ++ D ATG SKGY F + I+
Sbjct: 2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDIN 54
Score = 30.4 bits (67), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 26/49 (53%)
Query: 164 RKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVY 212
K+F+G +PN ++ D++ +G ++ L D TG KG+A Y
Sbjct: 2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEY 50
>pdb|2M2B|A Chain A, Nmr Structure Of The Rrm2 Domain Of The Protein Rbm10 From
Homo Sapiens
Length = 131
Score = 35.0 bits (79), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 29/95 (30%), Positives = 41/95 (43%), Gaps = 9/95 (9%)
Query: 166 IFVGNVPNDMSADKLLAHFACYGEIEEGPLGF--DKQTGKPKGFALFVYKTAEGAQ---- 219
I + N+ + D +L A Y + + DKQT +GFA T E AQ
Sbjct: 26 IILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIEAAQLLQI 85
Query: 220 -AALVDPIKTVDGKQLNCRLADNKKAKPMGPDGGG 253
AL P+ T+DGK +N A K + M + G
Sbjct: 86 LQALHPPL-TIDGKTINVEFAKGSK-RDMASNEGS 118
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 35.0 bits (79), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGE-LEEAVVILDKATGKSKGYGFITFKHIDGAMLALK 130
+FI L + + L FSA+G L+ ++ D TG SKGY FI F D + A++
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66
Score = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 27/93 (29%), Positives = 45/93 (48%), Gaps = 10/93 (10%)
Query: 166 IFVGNVPNDMSADKLLAHFACYGEIEEGP-LGFDKQTGKPKGFALFVYKTAEGAQAALVD 224
IF+GN+ ++ L F+ +G I + P + D TG KG+A + + + + AA
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAA--- 64
Query: 225 PIKTVDGKQLNCR-----LADNKKAKPMGPDGG 252
I+ ++G+ L R A K +K GP G
Sbjct: 65 -IEAMNGQYLCNRPITVSYAFKKDSKGSGPSSG 96
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 34.3 bits (77), Expect = 0.13, Method: Composition-based stats.
Identities = 21/83 (25%), Positives = 39/83 (46%)
Query: 56 VLESVRSIADADPTQRKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYG 115
V E V +++ + R +F L L FSA G++ + +I D+ + +SKG
Sbjct: 11 VREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIA 70
Query: 116 FITFKHIDGAMLALKEPSKKIDG 138
++ F I LA+ +++ G
Sbjct: 71 YVEFCEIQSVPLAIGLTGQRLLG 93
>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 = 33.9 bits (76), Expect = 0.18, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 2/59 (3%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALKE 131
+FI+ L + L FSA+G + V+ D+ SKGYGF+ F+ + A A+++
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEK 64
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 33.5 bits (75), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 40/152 (26%), Positives = 64/152 (42%), Gaps = 31/152 (20%)
Query: 69 TQR-KLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAML 127
TQR +LF+ L D T E + +F YGE E + + +G+GFI + A +
Sbjct: 20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFI------NRDRGFGFIRLESRTLAEI 73
Query: 128 ALKEPSKKIDGRVTVT---NLAVAGNSGNSTNNPVDVSLRKIFVGNVPNDMSADKLLAHF 184
A E +DG + + + A + T V N+ +S + L F
Sbjct: 74 AKAE----LDGTILKSRPLRIRFATHGAALT------------VKNLSPVVSNELLEQAF 117
Query: 185 ACYGEIEEGPLGFD---KQTGKPKGFALFVYK 213
+ +G +E+ + D + TG KGF F K
Sbjct: 118 SQFGPVEKAVVVVDDRGRATG--KGFVEFAAK 147
>pdb|2EK6|A Chain A, Crystal Structure Of Human Rna-Binding Protein 12
pdb|2EK6|B Chain B, Crystal Structure Of Human Rna-Binding Protein 12
pdb|2EK6|C Chain C, Crystal Structure Of Human Rna-Binding Protein 12
pdb|2EK6|D Chain D, Crystal Structure Of Human Rna-Binding Protein 12
Length = 95
Score = 33.5 bits (75), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 40/87 (45%), Gaps = 9/87 (10%)
Query: 166 IFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALVDP 225
I V N+P +S D++L F Y I + G P G A+ +++ + A AA++D
Sbjct: 18 IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID- 76
Query: 226 IKTVDGKQLNCRLADNKKAKPMGPDGG 252
LN R ++K K GP G
Sbjct: 77 --------LNDRPIGSRKVKLSGPSSG 95
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 33.5 bits (75), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 27/59 (45%), Gaps = 8/59 (13%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALKE 131
LF+R L T E L FS +G+LE K K Y F+ F+ A+ A+ E
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLER--------VKKLKDYAFVHFEDRGAAVKAMDE 68
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 33.5 bits (75), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 34/117 (29%), Positives = 51/117 (43%), Gaps = 17/117 (14%)
Query: 149 GNSGNSTNNPVDVSLRKIFVGNVPNDMSADKLLAHFACYGEIEEGP--------LGFDKQ 200
G+SG+S + D I+V + + ++ D L F G ++ + DK+
Sbjct: 1 GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE 60
Query: 201 TGKPKGFALFVYKTAEGAQAALVDPIKTVDGK-----QLNCRLADNKKAKPMGPDGG 252
TGKPKG A Y+ A+AA ++ DGK +L LA K GP G
Sbjct: 61 TGKPKGDATVSYEDPPTAKAA----VEWFDGKDFQGSKLKVSLARKKPPMNSGPSSG 113
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 33.1 bits (74), Expect = 0.32, Method: Composition-based stats.
Identities = 28/107 (26%), Positives = 48/107 (44%), Gaps = 3/107 (2%)
Query: 149 GNSGNSTNNPVDVSLRKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQ-TGKPKGF 207
G+SG+S P + KI V N+P + ++ F+ +GE++ L TG +GF
Sbjct: 1 GSSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGF 60
Query: 208 ALFVYKTAEGAQAALVDPIKTVD--GKQLNCRLADNKKAKPMGPDGG 252
+ T + A+ A + G++L AD++ GP G
Sbjct: 61 GFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSGPSSG 107
Score = 32.7 bits (73), Expect = 0.42, Method: Composition-based stats.
Identities = 18/54 (33%), Positives = 29/54 (53%), Gaps = 5/54 (9%)
Query: 69 TQRKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDK---ATGKSKGYGFITF 119
T K+ +R + + +R +FS +GEL+ V L K TG +G+GF+ F
Sbjct: 14 TTSKILVRNIPFQANQREIRELFSTFGELK--TVRLPKKMTGTGAHRGFGFVDF 65
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 32.7 bits (73), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 11/52 (21%)
Query: 72 KLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHID 123
KLFI L + T + +RS+F YG++ E +I K YGF+ HI+
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFV---HIE 50
Score = 30.0 bits (66), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 41/89 (46%), Gaps = 9/89 (10%)
Query: 165 KIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALVD 224
K+F+GN+P + + ++ + F YG++ E + K GF KTA A+ A+ +
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDI------IKNYGFVHIEDKTA--AEDAIRN 61
Query: 225 PIK-TVDGKQLNCRLADNKKAKPMGPDGG 252
+ G +N + NK GP G
Sbjct: 62 LHHYKLHGVNINVEASKNKSKASSGPSSG 90
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 32.7 bits (73), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 41/88 (46%), Gaps = 5/88 (5%)
Query: 168 VGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVY---KTAEGAQAALVD 224
V N+ S D L F YG + + + + T P+GFA + + A+ A+AA+
Sbjct: 18 VDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM-- 75
Query: 225 PIKTVDGKQLNCRLADNKKAKPMGPDGG 252
+DG++L ++A + GP G
Sbjct: 76 DGAELDGRELRVQVARYGRRDLSGPSSG 103
Score = 30.0 bits (66), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 12/47 (25%), Positives = 24/47 (51%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITF 119
L + L + T+ + LR +F YG + + + + T +G+ F+ F
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRF 62
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 31.6 bits (70), Expect = 0.88, Method: Composition-based stats.
Identities = 14/54 (25%), Positives = 31/54 (57%), Gaps = 1/54 (1%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYG-ELEEAVVILDKATGKSKGYGFITFKHIDGA 125
+ +R L T + +R ++G + E ++ +K++G+S+G+ F+ F H+ A
Sbjct: 4 VMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDA 57
>pdb|2EK1|A Chain A, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|B Chain B, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|C Chain C, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|D Chain D, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|E Chain E, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|F Chain F, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|G Chain G, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|H Chain H, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
Length = 95
Score = 31.2 bits (69), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 38/87 (43%), Gaps = 9/87 (10%)
Query: 166 IFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALVDP 225
I V N P +S D++L F Y I + G P G A +++ + A AA++D
Sbjct: 18 IKVQNXPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGXPTGEAXVAFESRDEATAAVID- 76
Query: 226 IKTVDGKQLNCRLADNKKAKPMGPDGG 252
LN R ++K K GP G
Sbjct: 77 --------LNDRPIGSRKVKLSGPSSG 95
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 31.2 bits (69), Expect = 1.1, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 24/51 (47%)
Query: 69 TQRKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITF 119
+ L + L D T L ++F A G + ++ D TG S GY F+ F
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDF 52
Score = 29.3 bits (64), Expect = 3.8, Method: Composition-based stats.
Identities = 22/83 (26%), Positives = 37/83 (44%), Gaps = 4/83 (4%)
Query: 166 IFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAALVDP 225
+ V +P DM+ +L A F G I + D +TG G+A + + +Q A
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA---- 61
Query: 226 IKTVDGKQLNCRLADNKKAKPMG 248
IK ++G + + A+P G
Sbjct: 62 IKVLNGITVRNKRLKVSYARPGG 84
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 43/78 (55%), Gaps = 3/78 (3%)
Query: 72 KLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGK-SKGYGFITFKHIDGAMLALK 130
K+ I L + T + + IFS YG+++ + +++ SKGY ++ F++ D A ALK
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65
Query: 131 EPS-KKIDGRVTVTNLAV 147
+IDG+ +T AV
Sbjct: 66 HMDGGQIDGQ-EITATAV 82
>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 = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 40/74 (54%), Gaps = 1/74 (1%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALKEP 132
L++ L + TT E + +FS G++++ ++ LDK + G+ F+ + A A++
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 133 S-KKIDGRVTVTNL 145
+ ++D R+ T+
Sbjct: 102 NGTRLDDRIIRTDW 115
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLAL 129
+F+ L + + L+ +FS G + A ++ DK GKS+G G +TF+ A+ A+
Sbjct: 18 VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAI 73
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 30.8 bits (68), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 29/57 (50%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLAL 129
L+++ L T L S+F+ + E + + TG+ +G FITF + + A AL
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 84
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 30.8 bits (68), Expect = 1.7, Method: Composition-based stats.
Identities = 25/91 (27%), Positives = 45/91 (49%), Gaps = 6/91 (6%)
Query: 69 TQRKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKH-IDGAML 127
T ++L + + + LR +F +G++ + +I ++ SKG+GF+TF++ D
Sbjct: 14 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRA 71
Query: 128 ALKEPSKKIDGRVTVTNLAVA---GNSGNST 155
K ++GR N A A NSG S+
Sbjct: 72 REKLHGTVVEGRKIEVNNATARVMTNSGPSS 102
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 30.4 bits (67), Expect = 1.8, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 29/63 (46%), Gaps = 1/63 (1%)
Query: 67 DPTQRKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAM 126
+ R +F+ L E L +F G L + + D+ GK K +GF+ FKH +
Sbjct: 13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVS 71
Query: 127 LAL 129
A+
Sbjct: 72 YAI 74
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 30.4 bits (67), Expect = 1.8, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 7/57 (12%)
Query: 165 KIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKP-KGFALFVYKTAEGAQA 220
K+FVG DM+A++L F YGE+ D KP + FA + + AQ+
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYGEV------VDVFIPKPFRAFAFVTFADDKVAQS 63
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 29.3 bits (64), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 37/89 (41%), Gaps = 10/89 (11%)
Query: 166 IFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAA--LV 223
+FVG DM+ D+L F+ YG++ + + PK F F + T Q A L
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFI--------PKPFRAFAFVTFADDQIAQSLC 59
Query: 224 DPIKTVDGKQLNCRLADNKKAKPMGPDGG 252
+ G ++ A+ K GP G
Sbjct: 60 GEDLIIKGISVHISNAEPKHNSNSGPSSG 88
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 29.3 bits (64), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 164 RKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAAL 222
RK+FVG + S + +L F +G I+E + G KG A + + AQAA+
Sbjct: 16 RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTV-LRGPDGSSKGCAFVKFSSHTEAQAAI 73
>pdb|4AF5|A Chain A, Structure Of The C. Glutamicum Acnr Crystal Form I
Length = 190
Score = 29.3 bits (64), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 24/45 (53%)
Query: 85 EGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLAL 129
EG R F+ +G V L++ATGKS+G F F + LAL
Sbjct: 20 EGARRCFAEHGYEGATVRRLEEATGKSRGAIFHHFGDKENLFLAL 64
>pdb|3NS6|A Chain A, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
pdb|3NS6|B Chain B, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
Length = 100
Score = 29.3 bits (64), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 22/33 (66%)
Query: 85 EGLRSIFSAYGELEEAVVILDKATGKSKGYGFI 117
+ L S+FS G++ +D+ATGK+KG+ F+
Sbjct: 27 KALTSLFSKAGKVVNMEFPIDEATGKTKGFLFV 59
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 29.3 bits (64), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 22/33 (66%)
Query: 85 EGLRSIFSAYGELEEAVVILDKATGKSKGYGFI 117
+ L S+FS G++ +D+ATGK+KG+ F+
Sbjct: 27 KALTSLFSKAGKVVNMEFPIDEATGKTKGFLFV 59
>pdb|4AC6|A Chain A, Corynebacterium Glutamicum Acnr Au Derivative Structure
pdb|4ACI|A Chain A, Structure Of The C. Glutamicum Acnr Crystal Form Ii
pdb|4ACI|B Chain B, Structure Of The C. Glutamicum Acnr Crystal Form Ii
Length = 191
Score = 28.9 bits (63), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 24/45 (53%)
Query: 85 EGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLAL 129
EG R F+ +G V L++ATGKS+G F F + LAL
Sbjct: 21 EGARRCFAEHGYEGATVRRLEEATGKSRGAIFHHFGDKENLFLAL 65
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 28.9 bits (63), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 29/58 (50%)
Query: 73 LFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKHIDGAMLALK 130
+++ GL + L +F G + + D+ TG+ +GYGF+ F + A A+K
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIK 75
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 28.9 bits (63), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 38/82 (46%), Gaps = 13/82 (15%)
Query: 158 PVDVSLRKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEG 217
P+D K++VGN+ N+ + +L F Y GPL P GFA ++
Sbjct: 71 PLDC---KVYVGNLGNNGNKTELERAFGYY-----GPLRSVWVARNPPGFAFVEFEDPRD 122
Query: 218 AQAALVDPIKTVDGKQL-NCRL 238
A D ++ +DG+ L CR+
Sbjct: 123 A----ADAVRELDGRTLCGCRV 140
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 28.9 bits (63), Expect = 6.0, Method: Composition-based stats.
Identities = 33/106 (31%), Positives = 48/106 (45%), Gaps = 18/106 (16%)
Query: 149 GNSGNSTNNPVDVSLRKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFA 208
G+SG+S N KIFVGNV ++ +L + F G + E + K +A
Sbjct: 1 GSSGSSGNT------WKIFVGNVSAACTSQELRSLFERRGRVIECDV--------VKDYA 46
Query: 209 LFVYKTAEGAQAALVDPI--KTVDGKQLNCRLADNKKAKPMGPDGG 252
FV+ E A + + K V GK++N L+ K K GP G
Sbjct: 47 -FVHMEKEADAKAAIAQLNGKEVKGKRINVELS-TKGQKKSGPSSG 90
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 28.9 bits (63), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 27/93 (29%), Positives = 43/93 (46%), Gaps = 7/93 (7%)
Query: 164 RKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEGAQAAL- 222
RK+FVG + + + + F +G I+E + G KG A ++T AQAA+
Sbjct: 13 RKLFVGMLGKQQTDEDVRKMFEPFGTIDECTV-LRGPDGTSKGCAFVKFQTHAEAQAAIN 71
Query: 223 -VDPIKTVDG--KQLNCRLADNKKAKPMGPDGG 252
+ +T+ G L + AD +K GP G
Sbjct: 72 TLHSSRTLPGASSSLVVKFADTEKES--GPSSG 102
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 28.5 bits (62), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 38/82 (46%), Gaps = 13/82 (15%)
Query: 158 PVDVSLRKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFALFVYKTAEG 217
P+D K++VGN+ N+ + +L F Y GPL P GFA ++
Sbjct: 71 PLDC---KVYVGNLGNNGNKTELERAFGYY-----GPLRSVWVARNPPGFAFVEFEDPRD 122
Query: 218 AQAALVDPIKTVDGKQL-NCRL 238
A D ++ +DG+ L CR+
Sbjct: 123 A----ADAVRDLDGRTLCGCRV 140
>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 = 28.5 bits (62), Expect = 7.1, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 72 KLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATG--KSKGYGFITF 119
K+F+ + + + LR +F YG + E V+ D++ +SKG F+TF
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTF 54
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 28.5 bits (62), Expect = 7.8, Method: Composition-based stats.
Identities = 20/79 (25%), Positives = 39/79 (49%), Gaps = 3/79 (3%)
Query: 71 RKLFIRGLGWDTTTEGLRSIFSAYGELEEAVVILDKATGKSKGYGFITFKH-IDGAMLAL 129
++L + + + LR +F +G++ + +I ++ SKG+GF+TF++ D
Sbjct: 30 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRARE 87
Query: 130 KEPSKKIDGRVTVTNLAVA 148
K ++GR N A A
Sbjct: 88 KLHGTVVEGRKIEVNNATA 106
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 28.1 bits (61), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 25/104 (24%), Positives = 46/104 (44%), Gaps = 1/104 (0%)
Query: 149 GNSGNSTNNPVDVSLRKIFVGNVPNDMSADKLLAHFACYGEIEEGPLGFDKQTGKPKGFA 208
G+SG+S D R ++VGN+ D++ +L F+ G + + + + P F
Sbjct: 1 GSSGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFV 60
Query: 209 LFVYKTAEGAQAALVDPIKTVDGKQLNCRLADNKKAKPMGPDGG 252
F Y+ + A A + + GK++ A ++ GP G
Sbjct: 61 EF-YEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQKSGPSSG 103
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
0.313 0.134 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,832,126
Number of Sequences: 62578
Number of extensions: 461220
Number of successful extensions: 1204
Number of sequences better than 100.0: 153
Number of HSP's better than 100.0 without gapping: 118
Number of HSP's successfully gapped in prelim test: 35
Number of HSP's that attempted gapping in prelim test: 909
Number of HSP's gapped (non-prelim): 263
length of query: 425
length of database: 14,973,337
effective HSP length: 102
effective length of query: 323
effective length of database: 8,590,381
effective search space: 2774693063
effective search space used: 2774693063
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (25.0 bits)