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= psy2136
(166 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 187 bits (474), Expect = 3e-48, Method: Compositional matrix adjust.
Identities = 87/122 (71%), Positives = 103/122 (84%), Gaps = 7/122 (5%)
Query: 45 LRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLE 104
RVYVGSI +EL EDTIRQAF PFGPIKSI+MSWD +T KHKGFAFVEY++PEAAQL+LE
Sbjct: 14 CRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 73
Query: 105 QMNGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEED 164
QMN VMLGGRNIK VGRPSN+ QAQ +ID++ EEA+ +NRIYVAS+H DL+++D
Sbjct: 74 QMNSVMLGGRNIK-------VGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDD 126
Query: 165 IK 166
IK
Sbjct: 127 IK 128
Score = 68.9 bits (167), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 30/73 (41%), Positives = 48/73 (65%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
R+YV S+ +L +D I+ F FG IKS ++ DP T KHKG+ F+EY+ +++Q ++
Sbjct: 112 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 171
Query: 106 MNGVMLGGRNIKV 118
MN LGG+ ++V
Sbjct: 172 MNLFDLGGQYLRV 184
>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 = 187 bits (474), Expect = 3e-48, Method: Compositional matrix adjust.
Identities = 87/121 (71%), Positives = 103/121 (85%), Gaps = 7/121 (5%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
RVYVGSI +EL EDTIRQAF PFGPIKSI+MSWD +T KHKGFAFVEY++PEAAQL+LEQ
Sbjct: 30 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 89
Query: 106 MNGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDI 165
MN VMLGGRNIK VGRPSN+ QAQ +ID++ EEA+ +NRIYVAS+H DL+++DI
Sbjct: 90 MNSVMLGGRNIK-------VGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDI 142
Query: 166 K 166
K
Sbjct: 143 K 143
Score = 68.2 bits (165), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 30/73 (41%), Positives = 48/73 (65%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
R+YV S+ +L +D I+ F FG IKS ++ DP T KHKG+ F+EY+ +++Q ++
Sbjct: 127 RIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 186
Query: 106 MNGVMLGGRNIKV 118
MN LGG+ ++V
Sbjct: 187 MNLFDLGGQYLRV 199
>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 = 179 bits (453), Expect = 9e-46, Method: Compositional matrix adjust.
Identities = 84/122 (68%), Positives = 100/122 (81%), Gaps = 7/122 (5%)
Query: 45 LRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLE 104
RVYVGSI +EL EDTIRQAF PFGPIKSI+ SWD +T KHKGFAFVEY++PEAAQL+LE
Sbjct: 13 CRVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALE 72
Query: 105 QMNGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEED 164
Q N V LGGRNIK VGRPSN+ QAQ +ID++ EEA+ +NRIYVAS+H DL+++D
Sbjct: 73 QXNSVXLGGRNIK-------VGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDD 125
Query: 165 IK 166
IK
Sbjct: 126 IK 127
Score = 66.6 bits (161), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 29/73 (39%), Positives = 47/73 (64%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
R+YV S+ +L +D I+ F FG IKS ++ DP T KHKG+ F+EY+ +++Q ++
Sbjct: 111 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 170
Query: 106 MNGVMLGGRNIKV 118
N LGG+ ++V
Sbjct: 171 XNLFDLGGQYLRV 183
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 76.3 bits (186), Expect = 7e-15, Method: Compositional matrix adjust.
Identities = 35/79 (44%), Positives = 50/79 (63%)
Query: 40 NSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAA 99
S P+R+YVGS+ F + ED +R F PFG I+SI + D T + KG+ F+ + E A
Sbjct: 22 GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECA 81
Query: 100 QLSLEQMNGVMLGGRNIKV 118
+ +LEQ+NG L GR +KV
Sbjct: 82 KKALEQLNGFELAGRPMKV 100
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 67.8 bits (164), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 30/75 (40%), Positives = 48/75 (64%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
+YVG ++ E+ + + AF+PFG I I + D T+KH+GFAFVE+++ E A +++ M
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 107 NGVMLGGRNIKVHFP 121
N L GR I+V+
Sbjct: 126 NESELFGRTIRVNLA 140
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 67.8 bits (164), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 31/82 (37%), Positives = 50/82 (60%)
Query: 40 NSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAA 99
S + +YVG ++ E+ + + AF+PFG I I + D T+KH+GFAFVE+++ E A
Sbjct: 1 GSTTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60
Query: 100 QLSLEQMNGVMLGGRNIKVHFP 121
+++ MN L GR I+V+
Sbjct: 61 AAAIDNMNESELFGRTIRVNLA 82
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 67.4 bits (163), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 30/75 (40%), Positives = 48/75 (64%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
+YVG ++ E+ + + AF+PFG I I + D T+KH+GFAFVE+++ E A +++ M
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 107 NGVMLGGRNIKVHFP 121
N L GR I+V+
Sbjct: 65 NESELFGRTIRVNLA 79
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 67.4 bits (163), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 30/75 (40%), Positives = 48/75 (64%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
+YVG ++ E+ + + AF+PFG I I + D T+KH+GFAFVE+++ E A +++ M
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 107 NGVMLGGRNIKVHFP 121
N L GR I+V+
Sbjct: 70 NESELFGRTIRVNLA 84
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 66.6 bits (161), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 30/74 (40%), Positives = 48/74 (64%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
+YVG ++ E+ + + AF+PFG I I + D T+KH+GFAFVE+++ E A +++ M
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 107 NGVMLGGRNIKVHF 120
N L GR I+V+
Sbjct: 75 NESELFGRTIRVNL 88
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 65.5 bits (158), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 31/79 (39%), Positives = 47/79 (59%)
Query: 40 NSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAA 99
S+ +YVGS+ F + ED +R F PFG I +I + D T + KG+ F+ + E A
Sbjct: 1 GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60
Query: 100 QLSLEQMNGVMLGGRNIKV 118
+ +LEQ+NG L GR ++V
Sbjct: 61 RRALEQLNGFELAGRPMRV 79
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 56.6 bits (135), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 27/88 (30%), Positives = 50/88 (56%)
Query: 33 GPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVE 92
GP+ N + + V +S E +R+ F +GPI +++ +D +++ +GFAFV
Sbjct: 1 GPLGSRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVY 60
Query: 93 YDIPEAAQLSLEQMNGVMLGGRNIKVHF 120
++ + A+ + E+ NG+ L GR I+V F
Sbjct: 61 FENVDDAKEAKERANGMELDGRRIRVDF 88
>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 = 56.6 bits (135), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 28/76 (36%), Positives = 43/76 (56%)
Query: 45 LRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLE 104
V+VG +S E+ + I+ AF PFG I + D T K KG+ FV + A+ +++
Sbjct: 16 FHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 75
Query: 105 QMNGVMLGGRNIKVHF 120
QM G LGGR I+ ++
Sbjct: 76 QMGGQWLGGRQIRTNW 91
>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 = 55.8 bits (133), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 28/80 (35%), Positives = 47/80 (58%), Gaps = 1/80 (1%)
Query: 42 NSPLRV-YVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQ 100
N P RV Y+GSI ++ E+ I GP+ ++ M +DP T + KG+AF+E+ E++
Sbjct: 1 NPPSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSA 60
Query: 101 LSLEQMNGVMLGGRNIKVHF 120
++ +NG LG R +K +
Sbjct: 61 SAVRNLNGYQLGSRFLKCGY 80
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 55.5 bits (132), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 49/85 (57%), Gaps = 4/85 (4%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
+++VG +SF+ E ++ Q F +G I + + D TQ+ +GF FV ++ + A+ ++
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 106 MNGVMLGGRNIKVHFPHVQVGRPSN 130
MNG + GR I+V Q G+ S+
Sbjct: 74 MNGKSVDGRQIRVD----QAGKSSD 94
>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 = 55.5 bits (132), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 48/78 (61%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
++V SI E +ED I++ F +G IK+I+++ D T KG+A VEY+ + A + E +
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 107 NGVMLGGRNIKVHFPHVQ 124
NG + G+ I+V + V+
Sbjct: 135 NGAEIMGQTIQVDWCFVK 152
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 55.5 bits (132), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 48/78 (61%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
++V SI E +ED I++ F +G IK+I+++ D T KG+A VEY+ + A + E +
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 107 NGVMLGGRNIKVHFPHVQ 124
NG + G+ I+V + V+
Sbjct: 89 NGAEIMGQTIQVDWCFVK 106
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 55.1 bits (131), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 44/74 (59%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
VY+GSI ++ E+ I GP+ ++ M +DP T + KG+AF+E+ E++ ++ +
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 107 NGVMLGGRNIKVHF 120
NG LG R +K +
Sbjct: 65 NGYQLGSRFLKCGY 78
>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 = 55.1 bits (131), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 44/74 (59%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
VY+GSI ++ E+ I GP+ ++ M +DP T + KG+AF+E+ E++ ++ +
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 107 NGVMLGGRNIKVHF 120
NG LG R +K +
Sbjct: 66 NGYQLGSRFLKCGY 79
>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 = 54.3 bits (129), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 27/92 (29%), Positives = 52/92 (56%), Gaps = 4/92 (4%)
Query: 37 PDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIP 96
PDV + L+V ++++ DT+R+ F +G + + + D T++ +GFAFV +
Sbjct: 42 PDVEGMTSLKV--DNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDK 99
Query: 97 EAAQLSLEQMNGVMLGGRNIKVHFPHVQVGRP 128
A+ +++ M+G +L GR ++V + GRP
Sbjct: 100 RDAEDAMDAMDGAVLDGRELRVQM--ARYGRP 129
>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 = 4e-08, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 40/72 (55%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
V+VG+I +E E+ ++ F GP+ S + +D T K KG+ F EY E A ++ +
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 107 NGVMLGGRNIKV 118
NG GR ++V
Sbjct: 71 NGREFSGRALRV 82
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 53.9 bits (128), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 47/79 (59%), Gaps = 2/79 (2%)
Query: 42 NSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQL 101
N L V+ +S E +R+ F +GPI +++ +D +++ +GFAFV ++ + A+
Sbjct: 15 NCCLGVF--GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 72
Query: 102 SLEQMNGVMLGGRNIKVHF 120
+ E+ NG+ L GR I+V F
Sbjct: 73 AKERANGMELDGRRIRVDF 91
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 53.1 bits (126), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 47/79 (59%), Gaps = 2/79 (2%)
Query: 42 NSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQL 101
N L V+ +S E +R+ F +GPI +++ +D +++ +GFAFV ++ + A+
Sbjct: 46 NCCLGVF--GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 103
Query: 102 SLEQMNGVMLGGRNIKVHF 120
+ E+ NG+ L GR I+V F
Sbjct: 104 AKERANGMELDGRRIRVDF 122
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 53.1 bits (126), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 26/91 (28%), Positives = 51/91 (56%), Gaps = 4/91 (4%)
Query: 38 DVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPE 97
DV + L+V ++++ DT+R+ F +G + + + D T++ +GFAFV +
Sbjct: 66 DVEGMTSLKV--DNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKR 123
Query: 98 AAQLSLEQMNGVMLGGRNIKVHFPHVQVGRP 128
A+ +++ M+G +L GR ++V + GRP
Sbjct: 124 DAEDAMDAMDGAVLDGRELRVQM--ARYGRP 152
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 52.8 bits (125), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 45/81 (55%)
Query: 40 NSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAA 99
++++ V+VG +S E+ + I+ AF PFG I + D T K KG+ FV + A
Sbjct: 11 DTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDA 70
Query: 100 QLSLEQMNGVMLGGRNIKVHF 120
+ ++ M G LGGR I+ ++
Sbjct: 71 ENAIVHMGGQWLGGRQIRTNW 91
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 52.8 bits (125), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 47/80 (58%), Gaps = 2/80 (2%)
Query: 42 NSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQL 101
N L V+ +S E +R+ F +GPI +++ +D +++ +GFAFV ++ + A+
Sbjct: 15 NCCLGVF--GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 72
Query: 102 SLEQMNGVMLGGRNIKVHFP 121
+ E+ NG+ L GR I+V P
Sbjct: 73 AKERANGMELDGRRIRVSGP 92
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 51.6 bits (122), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 49/80 (61%), Gaps = 7/80 (8%)
Query: 41 SNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKH----KGFAFVEYDIP 96
S P +V++G ++ + +D I + F +G IK I+M P+ + H KG+A+VE++ P
Sbjct: 1 SMKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDM---PVERMHPHLSKGYAYVEFENP 57
Query: 97 EAAQLSLEQMNGVMLGGRNI 116
+ A+ +L+ M+G + G+ I
Sbjct: 58 DEAEKALKHMDGGQIDGQEI 77
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 51.2 bits (121), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 29/91 (31%), Positives = 50/91 (54%), Gaps = 5/91 (5%)
Query: 39 VNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEA 98
V ++ P ++++G ++ E E ++ F GPI + + D T K +GFAF+ ++ P
Sbjct: 2 VEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPAD 60
Query: 99 AQLSLEQMNGVMLGGRNIKVHFPHVQVGRPS 129
A+ + + MNG L G+ IKV Q +PS
Sbjct: 61 AKNAAKDMNGKSLHGKAIKVE----QAKKPS 87
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 51.2 bits (121), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 37/65 (56%)
Query: 55 ELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQMNGVMLGGR 114
E + + FLPFG + S + D T K F FV +D P++AQ++++ MNG +G +
Sbjct: 51 EFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTK 110
Query: 115 NIKVH 119
+KV
Sbjct: 111 RLKVQ 115
>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
pdb|4F02|D Chain D, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
Length = 213
Score = 50.8 bits (120), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 50/89 (56%)
Query: 32 VGPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFV 91
+G + P S +YVG + ++ E + + F P GPI SI + D IT++ G+A+V
Sbjct: 3 LGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYV 62
Query: 92 EYDIPEAAQLSLEQMNGVMLGGRNIKVHF 120
+ P A+ +L+ MN ++ G+ +++ +
Sbjct: 63 NFQQPADAERALDTMNFDVIKGKPVRIMW 91
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 41/82 (50%), Gaps = 2/82 (2%)
Query: 37 PDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIP 96
P + + +++ ++ + + F FG I S + D KG+ FV ++
Sbjct: 96 PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQ 153
Query: 97 EAAQLSLEQMNGVMLGGRNIKV 118
EAA+ ++E+MNG++L R + V
Sbjct: 154 EAAERAIEKMNGMLLNDRKVFV 175
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 50.8 bits (120), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 44/73 (60%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
R++V ++S+ E+ + + F +GP+ ++ D +T+K KGFAFV + PE A + +
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 106 MNGVMLGGRNIKV 118
++G + GR + V
Sbjct: 70 VDGQVFQGRMLHV 82
>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 = 50.4 bits (119), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 36/66 (54%)
Query: 55 ELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQMNGVMLGGR 114
E + + Q F+PFG + S + D T K F FV YD P +AQ +++ MNG +G +
Sbjct: 36 EFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMK 95
Query: 115 NIKVHF 120
+KV
Sbjct: 96 RLKVQL 101
>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 = 50.1 bits (118), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 26/92 (28%), Positives = 46/92 (50%), Gaps = 4/92 (4%)
Query: 32 VGPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFV 91
V + PD S ++++G + L +D +++ FGP+K+ N+ D T KG+AF
Sbjct: 106 VSTVVPD----SAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 161
Query: 92 EYDIPEAAQLSLEQMNGVMLGGRNIKVHFPHV 123
EY ++ +NG+ LG + + V V
Sbjct: 162 EYVDINVTDQAIAGLNGMQLGDKKLLVQRASV 193
Score = 32.7 bits (73), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 23/89 (25%), Positives = 43/89 (48%), Gaps = 20/89 (22%)
Query: 46 RVYVGSISFELKEDTIRQAF-----------LPFGPIKSINMSWDPITQKHKGFAFVEY- 93
R+YVG+I F + E+ + F P P+ ++ ++ D K FAF+E+
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFR 59
Query: 94 DIPEAAQLSLEQMNGVMLGGRNIKVHFPH 122
+ E Q +G++ G+++K+ PH
Sbjct: 60 SVDETTQAM--AFDGIIFQGQSLKIRRPH 86
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 49.7 bits (117), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 45/81 (55%)
Query: 41 SNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQ 100
S+ ++VG ++ + ++T+R AF F S ++ WD T +G+ FV + + AQ
Sbjct: 84 SDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQ 143
Query: 101 LSLEQMNGVMLGGRNIKVHFP 121
+++ M G L GR +++++
Sbjct: 144 NAMDSMQGQDLNGRPLRINWA 164
Score = 43.9 bits (102), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
+YVG++ + ED ++Q F GPI +I + D K+ +AFVEY A ++L+ +
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTL 61
Query: 107 NGVMLGGRNIKVHFP 121
NG + +K+++
Sbjct: 62 NGKQIENNIVKINWA 76
>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 = 49.7 bits (117), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 24/91 (26%), Positives = 49/91 (53%), Gaps = 3/91 (3%)
Query: 37 PDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIP 96
P+ ++ ++V ++++ E +R+ F +GPIK I+M + + K +G+AF+EY+
Sbjct: 95 PNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHE 154
Query: 97 EAAQLSLEQMNGVMLGGRNIKVHFPHVQVGR 127
+ + +G + GR + V V+ GR
Sbjct: 155 RDMHSAYKHADGKKIDGRRVLV---DVERGR 182
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 49.7 bits (117), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 41/78 (52%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
++++G + L +D +++ FGP+K+ N+ D T KG+AF EY ++
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 106 MNGVMLGGRNIKVHFPHV 123
+NG+ LG + + V V
Sbjct: 63 LNGMQLGDKKLLVQRASV 80
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 46/78 (58%)
Query: 42 NSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQL 101
N VYVG + ++ E + + FL GP+ + +M D +T +H+G+ FVE+ E A
Sbjct: 13 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 72
Query: 102 SLEQMNGVMLGGRNIKVH 119
+++ M+ + L G+ I+V+
Sbjct: 73 AIKIMDMIKLYGKPIRVN 90
>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 = 48.9 bits (115), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 40/74 (54%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
++++G + L +D +++ FGP+K+ N+ D T KG+AF EY ++
Sbjct: 98 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 157
Query: 106 MNGVMLGGRNIKVH 119
+NG+ LG + + V
Sbjct: 158 LNGMQLGDKKLLVQ 171
Score = 33.5 bits (75), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 24/93 (25%), Positives = 44/93 (47%), Gaps = 20/93 (21%)
Query: 42 NSPLRVYVGSISFELKEDTIRQAF-----------LPFGPIKSINMSWDPITQKHKGFAF 90
S R+YVG+I F + E+ + F P P+ ++ ++ D K FAF
Sbjct: 4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAF 57
Query: 91 VEY-DIPEAAQLSLEQMNGVMLGGRNIKVHFPH 122
+E+ + E Q +G++ G+++K+ PH
Sbjct: 58 LEFRSVDETTQAM--AFDGIIFQGQSLKIRRPH 88
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 48.9 bits (115), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 40/74 (54%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
++++G + L +D +++ FGP+K+ N+ D T KG+AF EY ++
Sbjct: 96 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 155
Query: 106 MNGVMLGGRNIKVH 119
+NG+ LG + + V
Sbjct: 156 LNGMQLGDKKLLVQ 169
Score = 33.5 bits (75), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 24/92 (26%), Positives = 44/92 (47%), Gaps = 20/92 (21%)
Query: 43 SPLRVYVGSISFELKEDTIRQAF-----------LPFGPIKSINMSWDPITQKHKGFAFV 91
S R+YVG+I F + E+ + F P P+ ++ ++ D K FAF+
Sbjct: 3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFL 56
Query: 92 EY-DIPEAAQLSLEQMNGVMLGGRNIKVHFPH 122
E+ + E Q +G++ G+++K+ PH
Sbjct: 57 EFRSVDETTQAM--AFDGIIFQGQSLKIRRPH 86
>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|B Chain B, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|C Chain C, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|D Chain D, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|E Chain E, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|F Chain F, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|G Chain G, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|H Chain H, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
Length = 190
Score = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 45/76 (59%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
+YVG + ++ E + + F P GPI SI + D IT++ G+A+V + P A+ +L+ M
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 72
Query: 107 NGVMLGGRNIKVHFPH 122
N ++ G+ +++ +
Sbjct: 73 NFDVIKGKPVRIMWSQ 88
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 41/82 (50%), Gaps = 2/82 (2%)
Query: 37 PDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIP 96
P + + +++ ++ + + F FG I S + D KG+ FV ++
Sbjct: 91 PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQ 148
Query: 97 EAAQLSLEQMNGVMLGGRNIKV 118
EAA+ ++E+MNG++L R + V
Sbjct: 149 EAAERAIEKMNGMLLNDRKVFV 170
>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 = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 44/78 (56%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
++V + E E+ I F +G IK+I+++ D T KG+ VEY+ + AQ ++E +
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 107 NGVMLGGRNIKVHFPHVQ 124
NG L G+ I V + V+
Sbjct: 86 NGQDLMGQPISVDWCFVR 103
>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 = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 33/103 (32%), Positives = 49/103 (47%), Gaps = 8/103 (7%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
+YVG++SF E+ I + F G IK I M D + + GF FVEY A+ ++ +
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 107 NGVMLGGRNIKVHF-----PHVQVGRPSNMPQAQSVIDEITEE 144
NG L R I+ + Q GR + Q V DE ++
Sbjct: 102 NGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQ---VRDEYRQD 141
>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 = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 43/77 (55%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
++V + E E+ I F +G IK+I+++ D T KG+ VEY+ + AQ ++E +
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 107 NGVMLGGRNIKVHFPHV 123
NG L G+ I V + V
Sbjct: 85 NGQDLMGQPISVDWCFV 101
>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 = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 44/78 (56%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
++V + E E+ I F +G IK+I+++ D T KG+ VEY+ + AQ ++E +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 107 NGVMLGGRNIKVHFPHVQ 124
NG L G+ I V + V+
Sbjct: 70 NGQDLMGQPISVDWCFVR 87
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 44/78 (56%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
++V + E E+ I F +G IK+I+++ D T KG+ VEY+ + AQ ++E +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 107 NGVMLGGRNIKVHFPHVQ 124
NG L G+ I V + V+
Sbjct: 70 NGQDLMGQPISVDWCFVR 87
>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 = 47.8 bits (112), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 24/91 (26%), Positives = 49/91 (53%), Gaps = 3/91 (3%)
Query: 37 PDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIP 96
P+ ++ ++V ++++ E +R+ F +GPIK I+M + + K +G+AF+EY+
Sbjct: 95 PNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHE 154
Query: 97 EAAQLSLEQMNGVMLGGRNIKVHFPHVQVGR 127
+ + +G + GR + V V+ GR
Sbjct: 155 RDMHSAYKHADGKKIDGRRVLV---DVERGR 182
>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 = 47.8 bits (112), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 43/77 (55%)
Query: 45 LRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLE 104
++VG ++ + ++T+R AF F S ++ WD T +G+ FV + + AQ +++
Sbjct: 2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 105 QMNGVMLGGRNIKVHFP 121
M G L GR +++++
Sbjct: 62 SMQGQDLNGRPLRINWA 78
>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 = 47.8 bits (112), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 44/78 (56%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
++V + E E+ I F +G IK+I+++ D T KG+ VEY+ + AQ ++E +
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 107 NGVMLGGRNIKVHFPHVQ 124
NG L G+ I V + V+
Sbjct: 72 NGQDLMGQPISVDWCFVR 89
>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 = 47.8 bits (112), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 43/77 (55%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
++V + E E+ I F +G IK+I+++ D T KG+ VEY+ + AQ ++E +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 107 NGVMLGGRNIKVHFPHV 123
NG L G+ I V + V
Sbjct: 70 NGQDLMGQPISVDWCFV 86
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 47.4 bits (111), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 29/102 (28%), Positives = 53/102 (51%), Gaps = 12/102 (11%)
Query: 40 NSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHK-------GFAFVE 92
S+ +++ +++F E+T++ F G IKS +S +K+K GF FVE
Sbjct: 1 GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTIS----KKKNKAGVLLSMGFGFVE 56
Query: 93 YDIPEAAQLSLEQMNGVMLGGRNIKVHFPHVQVGRPSNMPQA 134
Y PE AQ +L+Q+ G + G ++V + +P++ P +
Sbjct: 57 YKKPEQAQKALKQLQGHTVDGHKLEVRISE-RATKPASGPSS 97
>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 = 47.4 bits (111), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 29/115 (25%), Positives = 55/115 (47%), Gaps = 12/115 (10%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
+++ ++ + + F FG I S + D KG+ FV ++ EAA+ ++E+M
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 65
Query: 107 NGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLT 161
NG++L R V VGR + + ++ E+ AK + +Y+ + P T
Sbjct: 66 NGMLLNDR-------KVFVGRFKSRKEREA---ELGARAKEFTNVYIKNFGPGST 110
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 47.0 bits (110), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 48/86 (55%), Gaps = 2/86 (2%)
Query: 40 NSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAA 99
N + P R++V +I F ++ +RQ F FG I + + ++ + KGF FV ++ A
Sbjct: 25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADA 82
Query: 100 QLSLEQMNGVMLGGRNIKVHFPHVQV 125
+ E+++G ++ GR I+V+ +V
Sbjct: 83 DRAREKLHGTVVEGRKIEVNNATARV 108
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 46.6 bits (109), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 46/87 (52%), Gaps = 2/87 (2%)
Query: 33 GPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVE 92
G PDV+ L+V ++++ D++R+ F +G + + + +P T+ +GFAFV
Sbjct: 4 GSSGPDVDGMITLKV--DNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVR 61
Query: 93 YDIPEAAQLSLEQMNGVMLGGRNIKVH 119
+ AQ + M+G L GR ++V
Sbjct: 62 FHDRRDAQDAEAAMDGAELDGRELRVQ 88
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 46.2 bits (108), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 45/78 (57%), Gaps = 5/78 (6%)
Query: 45 LRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLE 104
+VYVG++ + + +AF +GP++S+ ++ +P GFAFVE++ P A ++
Sbjct: 74 CKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAVR 128
Query: 105 QMNGVMLGGRNIKVHFPH 122
+++G L G ++V +
Sbjct: 129 ELDGRTLCGCRVRVELSN 146
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 46.2 bits (108), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 43/84 (51%), Gaps = 8/84 (9%)
Query: 39 VNSNSP--LRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIP 96
VN +SP VY G I+ L + +RQ F PFG I I + KG++FV +
Sbjct: 18 VNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF------PEKGYSFVRFSTH 71
Query: 97 EAAQLSLEQMNGVMLGGRNIKVHF 120
E+A ++ +NG + G +K ++
Sbjct: 72 ESAAHAIVSVNGTTIEGHVVKCYW 95
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 46.2 bits (108), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
V+VG++ ++E+ + + FL GP+ + + D K K F FV + PE+ ++ +
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYAIALL 77
Query: 107 NGVMLGGRNIKVHFP 121
NG+ L GR I V P
Sbjct: 78 NGIRLYGRPINVSGP 92
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 45.8 bits (107), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 47/83 (56%), Gaps = 2/83 (2%)
Query: 43 SPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLS 102
+P R++V +I F ++ +RQ F FG I + + ++ + KGF FV ++ A +
Sbjct: 14 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRA 71
Query: 103 LEQMNGVMLGGRNIKVHFPHVQV 125
E+++G ++ GR I+V+ +V
Sbjct: 72 REKLHGTVVEGRKIEVNNATARV 94
>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 = 45.8 bits (107), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 29/79 (36%), Positives = 42/79 (53%)
Query: 42 NSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQL 101
S V+VG +S E+ I AF PFG I + D T K KG+ FV + A+
Sbjct: 4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAEN 63
Query: 102 SLEQMNGVMLGGRNIKVHF 120
+++QM G LGGR I+ ++
Sbjct: 64 AIQQMGGQWLGGRQIRTNW 82
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 45.4 bits (106), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 44/78 (56%), Gaps = 5/78 (6%)
Query: 45 LRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLE 104
+VYVG++ + + +AF +GP++S+ ++ +P GFAFVE++ P A ++
Sbjct: 74 CKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAVR 128
Query: 105 QMNGVMLGGRNIKVHFPH 122
++G L G ++V +
Sbjct: 129 DLDGRTLCGCRVRVELSN 146
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/93 (29%), Positives = 47/93 (50%), Gaps = 4/93 (4%)
Query: 37 PDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIP 96
PDV N + V I + E +RQ F +GPI+S+ + D T++ +G+ FV++
Sbjct: 39 PDVLRN----LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSG 94
Query: 97 EAAQLSLEQMNGVMLGGRNIKVHFPHVQVGRPS 129
+AQ ++ +NG + + +KV RP
Sbjct: 95 SSAQQAIAGLNGFNILNKRLKVALAASGHQRPG 127
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 44/81 (54%), Gaps = 6/81 (7%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQ-----L 101
V++ ++SF+ +E+ + + FG +K + + P T+ KG AF ++ EAAQ
Sbjct: 18 VFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAA 77
Query: 102 SLE-QMNGVMLGGRNIKVHFP 121
SLE + G+ L GR +KV
Sbjct: 78 SLEAEGGGLKLDGRQLKVDLA 98
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 46/93 (49%), Gaps = 9/93 (9%)
Query: 41 SNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKG---FAFVEYDIPE 97
N+ R+YVG++ +++ I F +G I+ I++ + +G FAFVE++ P
Sbjct: 19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL------KNRRGGPPFAFVEFEDPR 72
Query: 98 AAQLSLEQMNGVMLGGRNIKVHFPHVQVGRPSN 130
A+ ++ +G G ++V FP G S
Sbjct: 73 DAEDAVYGRDGYDYDGYRLRVEFPRSGRGTGSG 105
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 46/76 (60%), Gaps = 5/76 (6%)
Query: 45 LRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLE 104
++VYVG++ + + +AF +GP++++ ++ +P GFAFVE++ P A+ ++
Sbjct: 1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVR 55
Query: 105 QMNGVMLGGRNIKVHF 120
++G ++ G ++V
Sbjct: 56 GLDGKVICGSRVRVEL 71
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 44.3 bits (103), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 34/53 (64%)
Query: 41 SNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEY 93
+S ++++G +S++ ++ +R+ F FG +K + DP+T++ +GF FV +
Sbjct: 22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 74
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 44.3 bits (103), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 32/122 (26%), Positives = 58/122 (47%), Gaps = 15/122 (12%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
++++G +SFE ++++R F +G + + DP T++ +GF FV Y ++E+
Sbjct: 16 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY-------ATVEE 68
Query: 106 MNGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVIDEITEEAKL-YNRIYVASIHPDLTEED 164
++ M N + PH GR +A S D A L +I+V I D E
Sbjct: 69 VDAAM----NAR---PHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHH 121
Query: 165 IK 166
++
Sbjct: 122 LR 123
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 29/49 (59%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYD 94
+++VG I + +E +R F +G I+ I + D + K +GFAFV +D
Sbjct: 107 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFD 155
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 44.3 bits (103), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 32/122 (26%), Positives = 58/122 (47%), Gaps = 15/122 (12%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
++++G +SFE ++++R F +G + + DP T++ +GF FV Y ++E+
Sbjct: 13 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY-------ATVEE 65
Query: 106 MNGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVIDEITEEAKL-YNRIYVASIHPDLTEED 164
++ M N + PH GR +A S D A L +I+V I D E
Sbjct: 66 VDAAM----NAR---PHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHH 118
Query: 165 IK 166
++
Sbjct: 119 LR 120
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 29/49 (59%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYD 94
+++VG I + +E +R F +G I+ I + D + K +GFAFV +D
Sbjct: 104 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFD 152
>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 = 44.3 bits (103), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 32/122 (26%), Positives = 58/122 (47%), Gaps = 15/122 (12%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
++++G +SFE ++++R F +G + + DP T++ +GF FV Y ++E+
Sbjct: 8 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY-------ATVEE 60
Query: 106 MNGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVIDEITEEAKL-YNRIYVASIHPDLTEED 164
++ M N + PH GR +A S D A L +I+V I D E
Sbjct: 61 VDAAM----NAR---PHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHH 113
Query: 165 IK 166
++
Sbjct: 114 LR 115
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 29/49 (59%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYD 94
+++VG I + +E +R F +G I+ I + D + K +GFAFV +D
Sbjct: 99 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFD 147
>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 = 44.3 bits (103), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 32/122 (26%), Positives = 58/122 (47%), Gaps = 15/122 (12%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
++++G +SFE ++++R F +G + + DP T++ +GF FV Y ++E+
Sbjct: 14 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY-------ATVEE 66
Query: 106 MNGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVIDEITEEAKL-YNRIYVASIHPDLTEED 164
++ M N + PH GR +A S D A L +I+V I D E
Sbjct: 67 VDAAM----NAR---PHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHH 119
Query: 165 IK 166
++
Sbjct: 120 LR 121
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 29/49 (59%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYD 94
+++VG I + +E +R F +G I+ I + D + K +GFAFV +D
Sbjct: 105 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFD 153
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 43.9 bits (102), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 32/122 (26%), Positives = 58/122 (47%), Gaps = 15/122 (12%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
++++G +SFE ++++R F +G + + DP T++ +GF FV Y ++E+
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY-------ATVEE 67
Query: 106 MNGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVIDEITEEAKL-YNRIYVASIHPDLTEED 164
++ M N + PH GR +A S D A L +I+V I D E
Sbjct: 68 VDAAM----NAR---PHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHH 120
Query: 165 IK 166
++
Sbjct: 121 LR 122
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 29/49 (59%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYD 94
+++VG I + +E +R F +G I+ I + D + K +GFAFV +D
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFD 154
>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 = 43.9 bits (102), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 32/122 (26%), Positives = 58/122 (47%), Gaps = 15/122 (12%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
++++G +SFE ++++R F +G + + DP T++ +GF FV Y ++E+
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY-------ATVEE 67
Query: 106 MNGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVIDEITEEAKL-YNRIYVASIHPDLTEED 164
++ M N + PH GR +A S D A L +I+V I D E
Sbjct: 68 VDAAM----NAR---PHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHH 120
Query: 165 IK 166
++
Sbjct: 121 LR 122
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 29/49 (59%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYD 94
+++VG I + +E +R F +G I+ I + D + K +GFAFV +D
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFD 154
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 43.9 bits (102), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 39/75 (52%), Gaps = 1/75 (1%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
+YVG++SF E+ I + F G IK I M D + + GF FVEY A+ ++ +
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKM-KTACGFCFVEYYSRADAENAMRYI 79
Query: 107 NGVMLGGRNIKVHFP 121
NG L R I+ +
Sbjct: 80 NGTRLDDRIIRTDWD 94
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 43.9 bits (102), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 5/75 (6%)
Query: 55 ELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQMNGVMLGGR 114
+ +D + F G I+S + D IT + G+ FV Y P A ++ +NG+ L +
Sbjct: 15 NMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTK 74
Query: 115 NIKVHFPHVQVGRPS 129
IKV + RPS
Sbjct: 75 TIKVSY-----ARPS 84
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 43.5 bits (101), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 26/111 (23%), Positives = 54/111 (48%), Gaps = 18/111 (16%)
Query: 56 LKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQMNGVMLGGRN 115
+ +D +R F G ++S + D + G+ FV Y + A+ ++ +NG+ L +
Sbjct: 14 MTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKT 73
Query: 116 IKVHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIK 166
IKV + RPS+ E+ ++A L Y++ + +T++D++
Sbjct: 74 IKVSY-----ARPSS---------EVIKDANL----YISGLPRTMTQKDVE 106
Score = 29.3 bits (64), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 14/62 (22%), Positives = 28/62 (45%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
+Y+ + + + + F FG I + + D T +G AF+ +D A+ ++
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 107 NG 108
NG
Sbjct: 151 NG 152
>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 = 43.5 bits (101), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 26/111 (23%), Positives = 54/111 (48%), Gaps = 18/111 (16%)
Query: 56 LKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQMNGVMLGGRN 115
+ +D +R F G ++S + D + G+ FV Y + A+ ++ +NG+ L +
Sbjct: 14 MTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKT 73
Query: 116 IKVHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIK 166
IKV + RPS+ E+ ++A L Y++ + +T++D++
Sbjct: 74 IKVSY-----ARPSS---------EVIKDANL----YISGLPRTMTQKDVE 106
Score = 29.3 bits (64), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 14/62 (22%), Positives = 28/62 (45%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
+Y+ + + + + F FG I + + D T +G AF+ +D A+ ++
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 107 NG 108
NG
Sbjct: 151 NG 152
>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos
Rna
pdb|1G2E|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The Tumor
Necrosis Factor Alpha Rna
Length = 167
Score = 43.1 bits (100), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 5/75 (6%)
Query: 56 LKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQMNGVMLGGRN 115
+ ++ R F G I+S + D IT + G+ FV Y P+ A+ ++ +NG+ L +
Sbjct: 14 MTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKT 73
Query: 116 IKVHFPHVQVGRPSN 130
IKV + RPS+
Sbjct: 74 IKVSYA-----RPSS 83
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 43.1 bits (100), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 5/75 (6%)
Query: 56 LKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQMNGVMLGGRN 115
+ +D + F G I+S + D IT + G+ FV Y P A ++ +NG+ L +
Sbjct: 16 MTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKT 75
Query: 116 IKVHFPHVQVGRPSN 130
IKV + RPS+
Sbjct: 76 IKVSYA-----RPSS 85
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 43.1 bits (100), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
+YVG++ + + +++ F FG + ++ + +D T+K KGF FVE E+ ++ ++
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAKL 62
Query: 107 NGVMLGGRNIKV 118
+ GR I+V
Sbjct: 63 DNTDFMGRTIRV 74
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 43.1 bits (100), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 41/76 (53%)
Query: 33 GPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVE 92
G P+ ++ + V ++S + +E +++ F PFG I I ++ D T + KGFAF+
Sbjct: 4 GSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFIS 63
Query: 93 YDIPEAAQLSLEQMNG 108
+ E A ++ ++G
Sbjct: 64 FHRREDAARAIAGVSG 79
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 42.7 bits (99), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 38/65 (58%), Gaps = 2/65 (3%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
+YV ++ + ++ +R+AF PFG I S + + + KGF FV + PE A ++ +M
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG--GRSKGFGFVCFSSPEEATKAVTEM 75
Query: 107 NGVML 111
NG ++
Sbjct: 76 NGRIV 80
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 42.4 bits (98), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 2/76 (2%)
Query: 44 PLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSL 103
P YVG++ F + I F I+S+ + D T K KGF +VE+D ++ + +L
Sbjct: 15 PYTAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL 73
Query: 104 EQMNGVMLGGRNIKVH 119
+G +LG R+++V
Sbjct: 74 -TYDGALLGDRSLRVD 88
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 42.4 bits (98), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 32/49 (65%)
Query: 45 LRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEY 93
++++G +S++ ++ +R+ F FG +K + DP+T++ +GF FV +
Sbjct: 1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49
>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 = 42.4 bits (98), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 35/60 (58%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
+++VG +S + E+ IR+ F FG ++SI + D T K +GF F+ + E + +E+
Sbjct: 3 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 62
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 43/82 (52%), Gaps = 1/82 (1%)
Query: 40 NSNSPLRVYVGSISFELKEDTIRQAFLPFGPI-KSINMSWDPITQKHKGFAFVEYDIPEA 98
S+ +++G++ E+ E + F FG I ++ + DP T KG+AF+ + +A
Sbjct: 1 GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60
Query: 99 AQLSLEQMNGVMLGGRNIKVHF 120
+ ++E MNG L R I V +
Sbjct: 61 SDAAIEAMNGQYLCNRPITVSY 82
>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 = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 13/54 (24%), Positives = 33/54 (61%)
Query: 45 LRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEA 98
++++G ++++ ED +R+ F +G + + + DP T + +GF F+ ++ P +
Sbjct: 4 CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSS 57
Score = 32.0 bits (71), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 27/53 (50%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEA 98
+++VG I +++ + F +G I + D T + +GF FV YD +A
Sbjct: 89 KIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADA 141
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 37/71 (52%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
VYV ++ F L + + + F +G + + + D T+K KG AF+ + ++AQ +
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 107 NGVMLGGRNIK 117
N L GR IK
Sbjct: 79 NNKQLFGRVIK 89
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 40/80 (50%), Gaps = 2/80 (2%)
Query: 37 PDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIP 96
P + + +++ ++ + + F FG I S + D KG+ FV ++
Sbjct: 4 PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQ 61
Query: 97 EAAQLSLEQMNGVMLGGRNI 116
EAA+ ++E+MNG++L R +
Sbjct: 62 EAAERAIEKMNGMLLNDRKV 81
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLE-Q 105
++VG +S + E+ IR+ F FG ++SI + D T K +GF F+ + E + +E +
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Query: 106 MNGVMLGGRNIKV 118
+ V L IKV
Sbjct: 62 YHNVGLSKCEIKV 74
>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|B Chain B, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|C Chain C, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|D Chain D, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
Length = 84
Score = 40.4 bits (93), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 5/74 (6%)
Query: 56 LKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQMNGVMLGGRN 115
+ +D +R F G ++S + D + G+ FV Y + A+ ++ +NG+ L +
Sbjct: 16 MTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKT 75
Query: 116 IKVHFPHVQVGRPS 129
IKV + RPS
Sbjct: 76 IKVSYA-----RPS 84
>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 = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 35/72 (48%), Gaps = 5/72 (6%)
Query: 58 EDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQMNGVMLGGRNIK 117
+D +R F G ++S + D + G+ FV Y + A+ ++ +NG+ L + IK
Sbjct: 33 QDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIK 92
Query: 118 VHFPHVQVGRPS 129
V + RPS
Sbjct: 93 VSYA-----RPS 99
>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 = 6e-04, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 43/75 (57%), Gaps = 8/75 (10%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
++V +++ + E+ + +AF FG ++ + +K K +AF+ +D + A ++E+M
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERV--------KKLKDYAFIHFDERDGAVKAMEEM 65
Query: 107 NGVMLGGRNIKVHFP 121
NG L G NI++ F
Sbjct: 66 NGKDLEGENIEIVFA 80
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 40.0 bits (92), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 42/76 (55%), Gaps = 8/76 (10%)
Query: 43 SPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLS 102
S R++V +++E + + F PFGP+K + + GFAFVE++ E+A +
Sbjct: 3 SNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI--------LNGFAFVEFEEAESAAKA 54
Query: 103 LEQMNGVMLGGRNIKV 118
+E+++G + ++V
Sbjct: 55 IEEVHGKSFANQPLEV 70
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 39.7 bits (91), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 42/83 (50%), Gaps = 8/83 (9%)
Query: 40 NSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAA 99
+N R++VG + + + F FG I++I+ K FA+++Y+ +AA
Sbjct: 13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV------KGDSFAYIQYESLDAA 66
Query: 100 QLSLEQMNGVMLGG--RNIKVHF 120
Q + +M G LGG R ++V F
Sbjct: 67 QAACAKMRGFPLGGPDRRLRVDF 89
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 39.7 bits (91), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 42/76 (55%), Gaps = 8/76 (10%)
Query: 43 SPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLS 102
S R++V +++E + + F PFGP+K + + GFAFVE++ E+A +
Sbjct: 30 SNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKA 81
Query: 103 LEQMNGVMLGGRNIKV 118
+E+++G + ++V
Sbjct: 82 IEEVHGKSFANQPLEV 97
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 39.7 bits (91), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 15/69 (21%), Positives = 35/69 (50%), Gaps = 4/69 (5%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYD----IPEAAQLS 102
++VG +S + ++ F FG + + +D T +H+GF FV ++ + + ++
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 103 LEQMNGVML 111
++N M+
Sbjct: 62 FHEINNKMV 70
>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 = 39.7 bits (91), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 15/59 (25%), Positives = 32/59 (54%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
+++G +S++ + ++ F FG + + DPIT + +GF FV + E+ ++Q
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 39.7 bits (91), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
+YVG++ + + + F G + + + D + KGFA++E+ E+ + SL +
Sbjct: 8 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-AL 66
Query: 107 NGVMLGGRNIKV 118
+ + GR IKV
Sbjct: 67 DESLFRGRQIKV 78
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of Hypothetical
Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens
At 1.95 A Resolution
Length = 89
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
+YVG++ + + + F G + + + D + KGFA++E+ E+ + SL +
Sbjct: 9 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-AL 67
Query: 107 NGVMLGGRNIKV 118
+ + GR IKV
Sbjct: 68 DESLFRGRQIKV 79
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleaoproteins A2B1
Length = 116
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 13/48 (27%), Positives = 30/48 (62%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEY 93
++++G +SFE E+++R + +G + + DP +++ +GF FV +
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTF 76
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 32/95 (33%), Positives = 46/95 (48%), Gaps = 15/95 (15%)
Query: 44 PLRVYVGSISFELKEDTIRQAFLPFGPIKSINM-----SWDPITQKHKGFAFVEYDIPEA 98
P +YVG++S ++ E I Q F GP KS M S DP + FVE+
Sbjct: 15 PRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP-------YCFVEFYEHRD 67
Query: 99 AQLSLEQMNGVMLGGRNIKVHF---PHVQVGRPSN 130
A +L MNG + G+ +KV++ P Q PS+
Sbjct: 68 AAAALAAMNGRKILGKEVKVNWATTPSSQKSGPSS 102
>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 = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/71 (22%), Positives = 33/71 (46%)
Query: 35 ITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYD 94
I N + +VG +S++ + ++ F FG + + DP T + +GF F+ +
Sbjct: 2 INASKNEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFK 61
Query: 95 IPEAAQLSLEQ 105
+ + L+Q
Sbjct: 62 DAASVEKVLDQ 72
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 23/41 (56%)
Query: 67 PFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQMN 107
P+G I S D T K KG+ FV++D P AAQ ++ +
Sbjct: 28 PYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALK 68
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 42/77 (54%), Gaps = 7/77 (9%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ- 105
+YVG + + E +R F FG I++I + Q+ + AF+++ +AA+++ E+
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTI-----TVVQRQQ-CAFIQFATRQAAEVAAEKS 68
Query: 106 MNGVMLGGRNIKVHFPH 122
N +++ GR + V +
Sbjct: 69 FNKLIVNGRRLNVKWGR 85
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/86 (24%), Positives = 40/86 (46%), Gaps = 2/86 (2%)
Query: 41 SNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQ 100
S+ +++V ++ F+ ++ F G + ++ + K KG V+++ PE A+
Sbjct: 5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAE 62
Query: 101 LSLEQMNGVMLGGRNIKVHFPHVQVG 126
+ MNG+ L GR I V G
Sbjct: 63 RACRMMNGMKLSGREIDVRIDRNASG 88
>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 = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 25/35 (71%)
Query: 86 KGFAFVEYDIPEAAQLSLEQMNGVMLGGRNIKVHF 120
KGFA +EY+ E A+ + +Q +G+ LGG +++V F
Sbjct: 224 KGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSF 258
Score = 33.9 bits (76), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 28/54 (51%)
Query: 67 PFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQMNGVMLGGRNIKVHF 120
PFG ++ + + T + KG+ F EY ++A + + G LG R + VH+
Sbjct: 116 PFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHW 169
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 25/35 (71%)
Query: 86 KGFAFVEYDIPEAAQLSLEQMNGVMLGGRNIKVHF 120
KGFA +EY+ E A+ + +Q +G+ LGG +++V F
Sbjct: 226 KGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSF 260
Score = 33.9 bits (76), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 28/54 (51%)
Query: 67 PFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQMNGVMLGGRNIKVHF 120
PFG ++ + + T + KG+ F EY ++A + + G LG R + VH+
Sbjct: 118 PFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHW 171
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 25/35 (71%)
Query: 86 KGFAFVEYDIPEAAQLSLEQMNGVMLGGRNIKVHF 120
KGFA +EY+ E A+ + +Q +G+ LGG +++V F
Sbjct: 226 KGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSF 260
Score = 33.9 bits (76), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 28/54 (51%)
Query: 67 PFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQMNGVMLGGRNIKVHF 120
PFG ++ + + T + KG+ F EY ++A + + G LG R + VH+
Sbjct: 118 PFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHW 171
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 1/71 (1%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
+++VG + + ++T+R F +G + + D T + +GF FV++ P L
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 106 MNGVMLGGRNI 116
L GRNI
Sbjct: 78 RPHT-LDGRNI 87
>pdb|2GHP|A Chain A, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|B Chain B, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|C Chain C, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|D Chain D, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|E Chain E, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|F Chain F, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|G Chain G, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|H Chain H, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
Length = 292
Score = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 43/77 (55%), Gaps = 9/77 (11%)
Query: 47 VYVGSISFEL-KEDTIRQAFLPFGPIKSINMSWDPITQKHKGF----AFVEYDIPEAAQL 101
+ + ++S EL E+ +R++F FG I+ IN+ P QK F AF ++ ++A+
Sbjct: 213 IXIRNLSTELLDENLLRESFEGFGSIEKINI---PAGQKEHSFNNCCAFXVFENKDSAER 269
Query: 102 SLEQMNGVMLGGRNIKV 118
+L Q N +LG R I V
Sbjct: 270 AL-QXNRSLLGNREISV 285
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 36.6 bits (83), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 37/135 (27%), Positives = 61/135 (45%), Gaps = 19/135 (14%)
Query: 34 PITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQ--KHKGFAFV 91
P PD+++ ++++VG + E +R+ F +G + IN+ D + KG FV
Sbjct: 8 PDQPDLDA---IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFV 64
Query: 92 EYDIPEAAQLSLEQMNGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRI 151
+ +AA LE N + N+KV P + P M A S + E+ KL
Sbjct: 65 TFYTRKAA---LEAQNAL----HNMKV-LPGMH--HPIQMKPADSEKNNAVEDRKL---- 110
Query: 152 YVASIHPDLTEEDIK 166
++ I TE DI+
Sbjct: 111 FIGMISKKCTENDIR 125
Score = 32.7 bits (73), Expect = 0.091, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 1/68 (1%)
Query: 40 NSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAA 99
N+ ++++G IS + E+ IR F FG I+ + P +G AFV + A
Sbjct: 103 NAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMA 161
Query: 100 QLSLEQMN 107
Q +++ M+
Sbjct: 162 QTAIKAMH 169
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 36.6 bits (83), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 35/64 (54%), Gaps = 6/64 (9%)
Query: 61 IRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQMNGVMLGGRNIKVHF 120
+R AF PFG I I++S DP + AFV Y+ E+A ++ ++NG + +KV+
Sbjct: 30 LRGAFSPFGNI--IDLSMDP----PRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI 83
Query: 121 PHVQ 124
Q
Sbjct: 84 ARKQ 87
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 36.6 bits (83), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 1/63 (1%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
+++VG ++ + ED +R+ F FG I+ + P KG AFV+Y AQ ++
Sbjct: 17 KLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGP-DGNSKGCAFVKYSSHAEAQAAINA 75
Query: 106 MNG 108
++G
Sbjct: 76 LHG 78
>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 = 0.008, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 31/61 (50%)
Query: 39 VNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEA 98
+ + +++++G I L E ++ F FG I + + D T HKG AF+ Y E+
Sbjct: 8 MKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERES 67
Query: 99 A 99
A
Sbjct: 68 A 68
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 36.2 bits (82), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 18/76 (23%), Positives = 40/76 (52%), Gaps = 5/76 (6%)
Query: 51 SISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQMNGVM 110
++SF + ED +++ F I+ ++ K KG A++E+ A+ +LE+ G
Sbjct: 23 NLSFNITEDELKEVFEDALEIRLVSQDG-----KSKGIAYIEFKSEADAEKNLEEKQGAE 77
Query: 111 LGGRNIKVHFPHVQVG 126
+ GR++ +++ + G
Sbjct: 78 IDGRSVSLYYTGEKGG 93
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 36.2 bits (82), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 27/49 (55%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYD 94
+++VG I E +R+ F FG + + M +D Q+ +GF F+ ++
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFE 60
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 36.2 bits (82), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 28/99 (28%), Positives = 46/99 (46%), Gaps = 4/99 (4%)
Query: 39 VNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEY---DI 95
+ + ++++VG I L E ++ F FG I + + D +T HKG AF+ Y D
Sbjct: 10 MKDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDS 69
Query: 96 PEAAQLSLEQMNGVMLGGRNIKVHFPHVQVGRPSNMPQA 134
AQ +L + + R I+V P GR + P +
Sbjct: 70 ALKAQSALHEQKTLPGMNRPIQVK-PAASEGRGESGPSS 107
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 36.2 bits (82), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 40/76 (52%), Gaps = 9/76 (11%)
Query: 46 RVYVGSISFEL-KEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLE 104
RV++G+++ L K+ + F +G + ++ HKG+AFV+Y A+ ++
Sbjct: 29 RVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVL 80
Query: 105 QMNGVMLGGRNIKVHF 120
NG +L G+ + ++
Sbjct: 81 GENGRVLAGQTLDINM 96
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 35.8 bits (81), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 35/64 (54%), Gaps = 6/64 (9%)
Query: 61 IRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQMNGVMLGGRNIKVHF 120
+R AF PFG I I++S DP + AFV Y+ E+A ++ ++NG + +KV+
Sbjct: 54 LRGAFSPFGNI--IDLSMDP----PRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI 107
Query: 121 PHVQ 124
Q
Sbjct: 108 ARKQ 111
>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 = 35.4 bits (80), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 15/58 (25%), Positives = 30/58 (51%)
Query: 65 FLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQMNGVMLGGRNIKVHFPH 122
F GPI + + D T G+AFV++ +Q +++ +NG+ + + +KV +
Sbjct: 35 FRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVLNGITVRNKRLKVSYAR 92
>pdb|2M2B|A Chain A, Nmr Structure Of The Rrm2 Domain Of The Protein Rbm10 From
Homo Sapiens
Length = 131
Score = 35.4 bits (80), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 36/69 (52%), Gaps = 7/69 (10%)
Query: 59 DTIRQAFLPFGPIKSINMSW--DPITQKHKGFAFVEYDIPEAAQLSLEQMNG----VMLG 112
D+I A P+ + S N+ D TQ ++GFAF++ EAAQL L+ + + +
Sbjct: 38 DSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIEAAQL-LQILQALHPPLTID 96
Query: 113 GRNIKVHFP 121
G+ I V F
Sbjct: 97 GKTINVEFA 105
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 35.0 bits (79), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 37/80 (46%), Gaps = 2/80 (2%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
++V ++ F+ ++ F G + ++ + K KG V+++ PE A+ + M
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMM 65
Query: 107 NGVMLGGRNIKVHFPHVQVG 126
NG+ L GR I V G
Sbjct: 66 NGMKLSGREIDVRIDRNASG 85
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 35.0 bits (79), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 15/58 (25%), Positives = 30/58 (51%)
Query: 65 FLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQMNGVMLGGRNIKVHFPH 122
F GPI + + D T G+AFV++ +Q +++ +NG+ + + +KV +
Sbjct: 24 FRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR 81
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 35.0 bits (79), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 15/58 (25%), Positives = 30/58 (51%)
Query: 65 FLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQMNGVMLGGRNIKVHFPH 122
F GPI + + D T G+AFV++ +Q +++ +NG+ + + +KV +
Sbjct: 24 FRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR 81
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
Length = 124
Score = 35.0 bits (79), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 23/91 (25%), Positives = 41/91 (45%), Gaps = 7/91 (7%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
VYVG++ + + F G I I + D + KG+A++E+ + ++ M
Sbjct: 39 VYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AM 97
Query: 107 NGVMLGGRNIKVHFPHVQVGRPSNMPQAQSV 137
+ + GR IKV + + +NMP S
Sbjct: 98 DETVFRGRTIKV------LPKRTNMPGISST 122
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 35.0 bits (79), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 38/71 (53%), Gaps = 5/71 (7%)
Query: 51 SISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQMNGVM 110
++SF + ED +++ F I+ ++ K KG A++E+ A+ +LE+ G
Sbjct: 106 NLSFNITEDELKEVFEDALEIRLVSQDG-----KSKGIAYIEFKSEADAEKNLEEKQGAE 160
Query: 111 LGGRNIKVHFP 121
+ GR++ +++
Sbjct: 161 IDGRSVSLYYT 171
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 34.7 bits (78), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 34/124 (27%), Positives = 55/124 (44%), Gaps = 16/124 (12%)
Query: 45 LRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQ--KHKGFAFVEYDIPEAAQLS 102
++++VG + E +R+ F +G + IN+ D + KG FV + +AA
Sbjct: 4 IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA--- 60
Query: 103 LEQMNGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTE 162
LE N + N+KV P + P M A S + E+ KL ++ I TE
Sbjct: 61 LEAQNAL----HNMKV-LPGMH--HPIQMKPADSEKNNAVEDRKL----FIGMISKKCTE 109
Query: 163 EDIK 166
DI+
Sbjct: 110 NDIR 113
Score = 32.7 bits (73), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 1/68 (1%)
Query: 40 NSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAA 99
N+ ++++G IS + E+ IR F FG I+ + P +G AFV + A
Sbjct: 91 NAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMA 149
Query: 100 QLSLEQMN 107
Q +++ M+
Sbjct: 150 QTAIKAMH 157
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 34.3 bits (77), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 40/78 (51%), Gaps = 1/78 (1%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
+++VG + + + ++R+ F FG I+ + D T K +G+ FV AA+ + +
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 106 MNGVMLGGRNIKVHFPHV 123
N ++ GR V+ ++
Sbjct: 79 PN-PIIDGRKANVNLAYL 95
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 34.3 bits (77), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 23/89 (25%), Positives = 45/89 (50%), Gaps = 12/89 (13%)
Query: 46 RVYVGSI-SFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLE 104
RV++G++ + +K+ + F +G I ++ HKGFAFV+Y A+ ++
Sbjct: 17 RVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVA 68
Query: 105 QMNGVMLGGRNIKVHF---PHVQVGRPSN 130
+G M+ G+ + ++ P V PS+
Sbjct: 69 GEDGRMIAGQVLDINLAAEPKVNRSGPSS 97
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 33.9 bits (76), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 21/90 (23%), Positives = 45/90 (50%), Gaps = 3/90 (3%)
Query: 33 GPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVE 92
G P+ S ++V +S + E+T++++F G +++ ++ D T KGF FV+
Sbjct: 4 GSSGPNARSQPSKTLFVKGLSEDTTEETLKESFD--GSVRARIVT-DRETGSSKGFGFVD 60
Query: 93 YDIPEAAQLSLEQMNGVMLGGRNIKVHFPH 122
++ E A+ + E M + G + + +
Sbjct: 61 FNSEEDAKAAKEAMEDGEIDGNKVTLDWAK 90
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 33.5 bits (75), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 42/82 (51%), Gaps = 2/82 (2%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPI-TQKHKGFAFVEYDIPEAAQLSLE 104
++ V +I F+ + IR+ F FG +K++ + T H+GF FV++ + A+ +
Sbjct: 17 KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 76
Query: 105 QM-NGVMLGGRNIKVHFPHVQV 125
+ + L GR + + + +V
Sbjct: 77 ALCHSTHLYGRRLVLEWADSEV 98
>pdb|2E5J|A Chain A, Solution Structure Of Rna Binding Domain In
Methenyltetrahydrofolate Synthetase Domain Containing
Length = 97
Score = 33.1 bits (74), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 38/78 (48%), Gaps = 5/78 (6%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
VYVG++ + + +++A G + + ++W Q + AF+ Y AAQ ++ +
Sbjct: 22 VYVGNLPRDARVSDLKRALRELGSV-PLRLTW----QGPRRRAFLHYPDSAAAQQAVSCL 76
Query: 107 NGVMLGGRNIKVHFPHVQ 124
G+ LG ++V Q
Sbjct: 77 QGLRLGTDTLRVALARQQ 94
>pdb|1U2F|A Chain A, Solution Structure Of The First Rna-Binding Domain Of
Hu2af65
Length = 90
Score = 32.7 bits (73), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 23/89 (25%), Positives = 43/89 (48%), Gaps = 20/89 (22%)
Query: 46 RVYVGSISFELKEDTIRQAF-----------LPFGPIKSINMSWDPITQKHKGFAFVEY- 93
R+YVG+I F + E+ + F P P+ ++ ++ D K FAF+E+
Sbjct: 3 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFR 56
Query: 94 DIPEAAQLSLEQMNGVMLGGRNIKVHFPH 122
+ E Q +G++ G+++K+ PH
Sbjct: 57 SVDETTQAM--AFDGIIFQGQSLKIRRPH 83
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 32.3 bits (72), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
+++VG + + ++ +R+ F PFG I + P KG AFV++ AQ ++
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGP-DGTSKGCAFVKFQTHAEAQAAINT 72
Query: 106 MN 107
++
Sbjct: 73 LH 74
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 31.6 bits (70), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
+++VG ++ + E+ + + F PFG I + P KG AFV++ AQ ++
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHA 75
Query: 106 MNG 108
++G
Sbjct: 76 LHG 78
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 31.6 bits (70), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 14/67 (20%), Positives = 35/67 (52%), Gaps = 5/67 (7%)
Query: 54 FELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQMNGVMLGG 113
+++ +D +++ F I+ ++ K KG A++E+ A+ + E+ G + G
Sbjct: 103 YKVTQDELKEVFEDAAEIRLVSKDG-----KSKGIAYIEFKTEADAEKTFEEKQGTEIDG 157
Query: 114 RNIKVHF 120
R+I +++
Sbjct: 158 RSISLYY 164
>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 = 31.6 bits (70), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 32/65 (49%), Gaps = 1/65 (1%)
Query: 40 NSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAA 99
N+ ++++G IS + E+ IR F FG I+ + P +G AFV + A
Sbjct: 91 NAVEDRKLFIGXISKKCTENDIRVXFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAXA 149
Query: 100 QLSLE 104
Q +++
Sbjct: 150 QTAIK 154
Score = 31.2 bits (69), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 32/128 (25%), Positives = 56/128 (43%), Gaps = 24/128 (18%)
Query: 45 LRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQ--KHKGFAFVEYDIPEAAQLS 102
++ +VG + E +R+ F +G + IN+ D + KG FV + +AA
Sbjct: 4 IKXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA--- 60
Query: 103 LEQMNGVMLGGRNIKV----HFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHP 158
LE N + N KV H P +Q +P++ + +V D ++++ I
Sbjct: 61 LEAQNAL----HNXKVLPGXHHP-IQX-KPADSEKNNAVEDR---------KLFIGXISK 105
Query: 159 DLTEEDIK 166
TE DI+
Sbjct: 106 KCTENDIR 113
>pdb|3S8S|A Chain A, Crystal Structure Of The Rrm Domain Of Human Setd1a
Length = 110
Score = 30.8 bits (68), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 14/61 (22%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 52 ISFELKEDTIRQAFLP-----FGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
++F D +R+ FL +G ++ + + P T+KH G A V + A+ +++ +
Sbjct: 9 VTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNL 68
Query: 107 N 107
+
Sbjct: 69 H 69
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 30.4 bits (67), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 19/82 (23%), Positives = 38/82 (46%), Gaps = 8/82 (9%)
Query: 40 NSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAA 99
+S + +++VG++S +R F G + + D + K +AFV + A
Sbjct: 5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRV----IECDVV----KDYAFVHMEKEADA 56
Query: 100 QLSLEQMNGVMLGGRNIKVHFP 121
+ ++ Q+NG + G+ I V
Sbjct: 57 KAAIAQLNGKEVKGKRINVELS 78
>pdb|1WYT|B Chain B, Crystal Structure Of Glycine Decarboxylase (P-Protein) Of
The Glycine Cleavage System, In Apo Form
pdb|1WYT|D Chain D, Crystal Structure Of Glycine Decarboxylase (P-Protein) Of
The Glycine Cleavage System, In Apo Form
pdb|1WYU|B Chain B, Crystal Structure Of Glycine Decarboxylase (P-Protein) Of
The Glycine Cleavage System, In Holo Form
pdb|1WYU|D Chain D, Crystal Structure Of Glycine Decarboxylase (P-Protein) Of
The Glycine Cleavage System, In Holo Form
pdb|1WYU|F Chain F, Crystal Structure Of Glycine Decarboxylase (P-Protein) Of
The Glycine Cleavage System, In Holo Form
pdb|1WYU|H Chain H, Crystal Structure Of Glycine Decarboxylase (P-Protein) Of
The Glycine Cleavage System, In Holo Form
pdb|1WYV|B Chain B, Crystal Structure Of Glycine Decarboxylase (P-Protein) Of
The Glycine Cleavage System, In Inhibitor-Bound Form
pdb|1WYV|D Chain D, Crystal Structure Of Glycine Decarboxylase (P-Protein) Of
The Glycine Cleavage System, In Inhibitor-Bound Form
pdb|1WYV|F Chain F, Crystal Structure Of Glycine Decarboxylase (P-Protein) Of
The Glycine Cleavage System, In Inhibitor-Bound Form
pdb|1WYV|H Chain H, Crystal Structure Of Glycine Decarboxylase (P-Protein) Of
The Glycine Cleavage System, In Inhibitor-Bound Form
Length = 474
Score = 30.4 bits (67), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 37/85 (43%), Gaps = 9/85 (10%)
Query: 25 PLYDLKQVGPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQK 84
P L++V P P+V+ + +R Y G ++ DT F P+ S M ++P +
Sbjct: 31 PKEHLREVPPRLPEVDELTLVRHYTGLSRRQVGVDTT------FYPLGSCTMKYNPKLHE 84
Query: 85 HKGFAFVE---YDIPEAAQLSLEQM 106
F + Y P AQ +L M
Sbjct: 85 EAARLFADLHPYQDPRTAQGALRLM 109
>pdb|2DIS|A Chain A, Solution Structure Of The Rrm Domain Of Unnamed Protein
Product
Length = 109
Score = 30.4 bits (67), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 22/90 (24%), Positives = 45/90 (50%), Gaps = 4/90 (4%)
Query: 40 NSNSPLRVYVGSI-SFELKEDTIRQ-AFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPE 97
S+ R+++G I + +E+ + + A + G + I + K++GFAFVEY+
Sbjct: 4 GSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHR 63
Query: 98 AAQLSLEQM--NGVMLGGRNIKVHFPHVQV 125
AA ++ ++ + L G I V + ++
Sbjct: 64 AAAMARRKLMPGRIQLWGHQIAVDWAEPEI 93
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 30.0 bits (66), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 28/104 (26%), Positives = 50/104 (48%), Gaps = 15/104 (14%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPI------KSINMSWDPITQKHKGFAFVEYDIPEAA 99
+V+VG + ++ ED I +F FGP+ K+ + S+ P KG+AF+ + +
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFP----PKGYAFLLFQEESSV 65
Query: 100 Q----LSLEQMNGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVID 139
Q LE+ + L + + VQ+ RP N+ + V+D
Sbjct: 66 QALIDACLEEDGKLYLCVSSPTIKDKPVQI-RPWNLSDSDFVMD 108
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 30.0 bits (66), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 24/90 (26%), Positives = 45/90 (50%), Gaps = 9/90 (10%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQ--KHKGFAFVEYDIPEAAQLSLE 104
+ + ++S+ E+T+++ F IK P Q K KG+AF+E+ E A+ +L
Sbjct: 18 LVLSNLSYSATEETLQEVFEKATFIKV------PQNQNGKSKGYAFIEFASFEDAKEALN 71
Query: 105 QMNGVMLGGRNIKVHFPHVQVGRPSNMPQA 134
N + GR I++ + G P++ P +
Sbjct: 72 SCNKREIEGRAIRLELQGPR-GSPNSGPSS 100
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 30.0 bits (66), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 15/62 (24%), Positives = 36/62 (58%), Gaps = 8/62 (12%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
++V +++ + E+ + ++F FG ++ + +K K +AFV ++ AA ++++M
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERV--------KKLKDYAFVHFEDRGAAVKAMDEM 69
Query: 107 NG 108
NG
Sbjct: 70 NG 71
>pdb|2HZC|A Chain A, Crystal Structure Of The N-terminal Rrm Of The U2af Large
Subunit
Length = 87
Score = 29.6 bits (65), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 23/92 (25%), Positives = 43/92 (46%), Gaps = 20/92 (21%)
Query: 42 NSPLRVYVGSISFELKEDTIRQAF-----------LPFGPIKSINMSWDPITQKHKGFAF 90
S R+YVG+I F + E+ + F P P+ ++ ++ D K FAF
Sbjct: 4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAF 57
Query: 91 VEY-DIPEAAQLSLEQMNGVMLGGRNIKVHFP 121
+E+ + E Q +G++ G+++K+ P
Sbjct: 58 LEFRSVDETTQAM--AFDGIIFQGQSLKIRRP 87
>pdb|2DIT|A Chain A, Solution Structure Of The Rrm_1 Domain Of Hiv Tat Specific
Factor 1 Variant
Length = 112
Score = 29.6 bits (65), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 5/62 (8%)
Query: 55 ELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQMNGVMLGGR 114
E++ED +R FG I+ + + + G A V + PE A ++ ++G GGR
Sbjct: 38 EIRED-LRVECSKFGQIRKLLL----FDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGR 92
Query: 115 NI 116
I
Sbjct: 93 QI 94
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 29.3 bits (64), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 16/74 (21%), Positives = 40/74 (54%), Gaps = 3/74 (4%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
+Y+ ++ +++ + + F +GPI+ I + P T +G A+V Y+ A+ +++ +
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIFDAKNAVDHL 67
Query: 107 NGVMLGGRNIKVHF 120
+G + R + V +
Sbjct: 68 SGFNVSNRYLVVLY 81
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 29.3 bits (64), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 24/92 (26%), Positives = 41/92 (44%), Gaps = 9/92 (9%)
Query: 37 PDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPI--------TQKHKGF 88
PD +S++ +YV ++ + D + F G +K + P+ T K KG
Sbjct: 9 PDEDSDNSA-IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGD 67
Query: 89 AFVEYDIPEAAQLSLEQMNGVMLGGRNIKVHF 120
A V Y+ P A+ ++E +G G +KV
Sbjct: 68 ATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSL 99
>pdb|1R9J|A Chain A, Transketolase From Leishmania Mexicana
pdb|1R9J|B Chain B, Transketolase From Leishmania Mexicana
Length = 673
Score = 28.9 bits (63), Expect = 1.3, Method: Composition-based stats.
Identities = 26/91 (28%), Positives = 41/91 (45%), Gaps = 17/91 (18%)
Query: 45 LRVYVGSIS----FELKEDTIRQAFLPFG-PIKS----INMSWDPITQKHKGFAFVEYDI 95
LRV V S+ F+ + DT RQA LP G P+ S ++ W+ + H G +
Sbjct: 572 LRVRVVSMPCQELFDAQPDTYRQAVLPAGVPVVSVEAYVSFGWEKYSHAHVGMSGFGASA 631
Query: 96 PEAA-----QLSLEQMNGVMLGGRNIKVHFP 121
P +++E+ V+ GR + FP
Sbjct: 632 PAGVLYKKFGITVEE---VVRTGRELAKRFP 659
>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 = 28.9 bits (63), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 16/73 (21%), Positives = 37/73 (50%), Gaps = 1/73 (1%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
++++ + F ++ + + G +K + + + K KG A+VEY+ A ++ +
Sbjct: 19 KLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMK 77
Query: 106 MNGVMLGGRNIKV 118
M+G+ + IKV
Sbjct: 78 MDGMTIKENIIKV 90
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 28.9 bits (63), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 16/74 (21%), Positives = 39/74 (52%), Gaps = 3/74 (4%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
+Y+ ++ +++ + + F +GPI+ I + P T +G A+V Y+ A+ + + +
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIFDAKNACDHL 77
Query: 107 NGVMLGGRNIKVHF 120
+G + R + V +
Sbjct: 78 SGFNVCNRYLVVLY 91
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 28.5 bits (62), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 16/74 (21%), Positives = 39/74 (52%), Gaps = 3/74 (4%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
+Y+ ++ +++ + + F +GPI+ I + P T +G A+V Y+ A+ + + +
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIFDAKNACDHL 71
Query: 107 NGVMLGGRNIKVHF 120
+G + R + V +
Sbjct: 72 SGFNVCNRYLVVLY 85
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 28.5 bits (62), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 33/61 (54%), Gaps = 11/61 (18%)
Query: 46 RVYVGSISFE--LKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSL 103
R+++G++ + KED R F P+G I IN+ F F+++D P++ + ++
Sbjct: 24 RLFIGNLPLKNVSKEDLFR-IFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAI 74
Query: 104 E 104
E
Sbjct: 75 E 75
>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 28.5 bits (62), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 3/46 (6%)
Query: 59 DTIRQAFLPFG--PIKSINMSWDPITQKHKGFAFVEYDIP-EAAQL 101
D+I A P+ + +I + D TQ+++GFAFV+ +A+QL
Sbjct: 24 DSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQL 69
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 28.1 bits (61), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 47 VYVGSISFELKEDTIRQAFLPFG-PIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
+++G + + E+ I +AF G + S+ + + +T G+ FVE+ A+ L +
Sbjct: 12 LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71
Query: 106 MNG 108
+NG
Sbjct: 72 ING 74
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 28.1 bits (61), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 18/77 (23%), Positives = 33/77 (42%), Gaps = 2/77 (2%)
Query: 54 FELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQMNGVMLGG 113
++ E +++ F FG + + + D T KGF FV + E + Q + M+ G
Sbjct: 25 WKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRH--MIDG 82
Query: 114 RNIKVHFPHVQVGRPSN 130
R P+ + + S
Sbjct: 83 RWCDCKLPNSKQSQDSG 99
>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 = 28.1 bits (61), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 9/76 (11%)
Query: 45 LRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQ--KHKGFAFVEYDIPEAAQLS 102
++++VG + E +R+ F +G + IN+ D + KG FV + +AA
Sbjct: 4 IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA--- 60
Query: 103 LEQMNGVMLGGRNIKV 118
LE N + N+KV
Sbjct: 61 LEAQNAL----HNMKV 72
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 27.7 bits (60), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 24/98 (24%), Positives = 44/98 (44%), Gaps = 1/98 (1%)
Query: 34 PITPDVNSNSPLRV-YVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVE 92
P+ N P +V Y+ ++S + E + F F K + + +T + +G AF+
Sbjct: 14 PMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFIT 73
Query: 93 YDIPEAAQLSLEQMNGVMLGGRNIKVHFPHVQVGRPSN 130
+ E A +L +NG L G+ + + F + R S
Sbjct: 74 FPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQRSSG 111
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 27.7 bits (60), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 14/67 (20%), Positives = 34/67 (50%), Gaps = 4/67 (5%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEY----DIPEAAQLS 102
V+ ++ ++ + F G ++ + + D +++ KG A+VE+ +P A L+
Sbjct: 28 VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLT 87
Query: 103 LEQMNGV 109
+++ GV
Sbjct: 88 GQRLLGV 94
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 27.7 bits (60), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 27/95 (28%), Positives = 40/95 (42%), Gaps = 16/95 (16%)
Query: 31 QVGPITPD-VNSNSPLRV---YVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKH- 85
QV P D + ++P RV Y+G+I E + F FG I KH
Sbjct: 10 QVNPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDF---------KHY 60
Query: 86 --KGFAFVEYDIPEAAQLSLEQMNGVMLGGRNIKV 118
KG F++YD E A + + + GRN++
Sbjct: 61 PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRT 95
>pdb|2UWX|A Chain A, Active Site Restructuring Regulates Ligand Recognition
In Class A Penicillin-Binding Proteins
Length = 494
Score = 27.3 bits (59), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 12/38 (31%), Positives = 22/38 (57%)
Query: 38 DVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSIN 75
D++S S + G++ ++ D +RQ FLP G + I+
Sbjct: 1 DISSISEITYSDGTVIASIESDMLRQDFLPSGTVTGIS 38
>pdb|2BG1|A Chain A, Active Site Restructuring Regulates Ligand Recognition
In Classa Penicillin-Binding Proteins (Pbps)
pdb|2XD5|A Chain A, Structural Insights Into The Catalytic Mechanism And The
Role Of Streptococcus Pneumoniae Pbp1b
pdb|2XD5|B Chain B, Structural Insights Into The Catalytic Mechanism And The
Role Of Streptococcus Pneumoniae Pbp1b
Length = 494
Score = 27.3 bits (59), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 12/38 (31%), Positives = 22/38 (57%)
Query: 38 DVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSIN 75
D++S S + G++ ++ D +RQ FLP G + I+
Sbjct: 1 DISSISEITYSDGTVIASIESDMLRQDFLPSGTVTGIS 38
>pdb|2Y2G|A Chain A, Penicillin-Binding Protein 1b (Pbp-1b) In Complex With
An Alkyl Boronate (A01)
pdb|2Y2G|B Chain B, Penicillin-Binding Protein 1b (Pbp-1b) In Complex With
An Alkyl Boronate (A01)
pdb|2Y2H|A Chain A, Penicillin-Binding Protein 1b (Pbp-1b) In Complex With
An Alkyl Boronate (Za2)
pdb|2Y2H|B Chain B, Penicillin-Binding Protein 1b (Pbp-1b) In Complex With
An Alkyl Boronate (Za2)
pdb|2Y2I|A Chain A, Penicillin-Binding Protein 1b (Pbp-1b) In Complex With
An Alkyl Boronate (Za3)
pdb|2Y2J|A Chain A, Penicillin-Binding Protein 1b (Pbp-1b) In Complex With
An Alkyl Boronate (Za4)
pdb|2Y2K|A Chain A, Penicillin-Binding Protein 1b (Pbp-1b) In Complex With
An Alkyl Boronate (Za5)
pdb|2Y2L|A Chain A, Penicillin-Binding Protein 1b (Pbp-1b) In Complex With
An Alkyl Boronate (E06)
pdb|2Y2L|B Chain B, Penicillin-Binding Protein 1b (Pbp-1b) In Complex With
An Alkyl Boronate (E06)
pdb|2Y2M|A Chain A, Penicillin-Binding Protein 1b (Pbp-1b) In Complex With
An Alkyl Boronate (E08)
pdb|2Y2N|A Chain A, Penicillin-Binding Protein 1b (Pbp-1b) In Complex With
An Alkyl Boronate (E07)
pdb|2Y2O|A Chain A, Penicillin-Binding Protein 1b (Pbp-1b) In Complex With
An Alkyl Boronate (Eo9)
pdb|2Y2P|A Chain A, Penicillin-Binding Protein 1b (Pbp-1b) In Complex With
An Alkyl Boronate (Z10)
pdb|2Y2Q|A Chain A, Penicillin-Binding Protein 1b (Pbp-1b) In Complex With
An Alkyl Boronate (Z06)
pdb|2Y2Q|B Chain B, Penicillin-Binding Protein 1b (Pbp-1b) In Complex With
An Alkyl Boronate (Z06)
Length = 494
Score = 27.3 bits (59), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 12/38 (31%), Positives = 22/38 (57%)
Query: 38 DVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSIN 75
D++S S + G++ ++ D +RQ FLP G + I+
Sbjct: 1 DISSISEITYSDGTVIASIESDLLRQDFLPSGTVTGIS 38
>pdb|2XD1|A Chain A, Active Site Restructuring Regulates Ligand Recognition
In Class A Penicillin-Binding Proteins
pdb|2XD1|B Chain B, Active Site Restructuring Regulates Ligand Recognition
In Class A Penicillin-Binding Proteins
Length = 494
Score = 27.3 bits (59), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 12/38 (31%), Positives = 22/38 (57%)
Query: 38 DVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSIN 75
D++S S + G++ ++ D +RQ FLP G + I+
Sbjct: 1 DISSISEITYSDGTVIASIESDLLRQDFLPSGTVTGIS 38
>pdb|2E5G|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 21
Length = 94
Score = 26.2 bits (56), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 32/74 (43%), Gaps = 8/74 (10%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKG-FAFVEYDIPEAAQLSLEQ 105
V+V + + + FL FGP+ S+ M D KG FA VE A + L Q
Sbjct: 11 VFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKD------KGVFAIVEMGDVGAREAVLSQ 64
Query: 106 MNGVMLGGRNIKVH 119
LGG ++V
Sbjct: 65 SQH-SLGGHRLRVR 77
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
0.318 0.137 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,473,288
Number of Sequences: 62578
Number of extensions: 166569
Number of successful extensions: 651
Number of sequences better than 100.0: 174
Number of HSP's better than 100.0 without gapping: 129
Number of HSP's successfully gapped in prelim test: 45
Number of HSP's that attempted gapping in prelim test: 464
Number of HSP's gapped (non-prelim): 211
length of query: 166
length of database: 14,973,337
effective HSP length: 92
effective length of query: 74
effective length of database: 9,216,161
effective search space: 681995914
effective search space used: 681995914
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)