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= 030632
(174 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 115 bits (287), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 53/90 (58%), Positives = 66/90 (73%)
Query: 2 ANLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKE 61
+ +A K LYVGGLAEEV++ +LHAAFIPFGDI D++ PLD T+KHR F FV F E
Sbjct: 6 SGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 65
Query: 62 DAIQAMDNMDGAELYGRVLTVNYALPERIK 91
DA A+DNM+ +EL+GR + VN A P RIK
Sbjct: 66 DAAAAIDNMNESELFGRTIRVNLAKPMRIK 95
>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 = 107 bits (266), Expect = 4e-24, Method: Compositional matrix adjust.
Identities = 49/83 (59%), Positives = 62/83 (74%)
Query: 3 NLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKED 62
++A K LYVGGLAEEV++ +LHAAFIPFGDI D++ PLD T+KHR F FV F ED
Sbjct: 2 SMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 61
Query: 63 AIQAMDNMDGAELYGRVLTVNYA 85
A A+DNM+ +EL+GR + VN A
Sbjct: 62 AAAAIDNMNESELFGRTIRVNLA 84
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 106 bits (265), Expect = 6e-24, Method: Compositional matrix adjust.
Identities = 49/81 (60%), Positives = 60/81 (74%)
Query: 5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
A K LYVGGLAEEV++ +LHAAFIPFGDI D++ PLD T+KHR F FV F EDA
Sbjct: 60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 119
Query: 65 QAMDNMDGAELYGRVLTVNYA 85
A+DNM+ +EL+GR + VN A
Sbjct: 120 AAIDNMNESELFGRTIRVNLA 140
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 104 bits (260), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 48/81 (59%), Positives = 60/81 (74%)
Query: 5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
+ K LYVGGLAEEV++ +LHAAFIPFGDI D++ PLD T+KHR F FV F EDA
Sbjct: 2 STTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 61
Query: 65 QAMDNMDGAELYGRVLTVNYA 85
A+DNM+ +EL+GR + VN A
Sbjct: 62 AAIDNMNESELFGRTIRVNLA 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 = 104 bits (260), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 48/79 (60%), Positives = 59/79 (74%)
Query: 7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
K LYVGGLAEEV++ +LHAAFIPFGDI D++ PLD T+KHR F FV F EDA A
Sbjct: 1 SKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 60
Query: 67 MDNMDGAELYGRVLTVNYA 85
+DNM+ +EL+GR + VN A
Sbjct: 61 IDNMNESELFGRTIRVNLA 79
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 67.4 bits (163), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 34/79 (43%), Positives = 50/79 (63%)
Query: 7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
Q T+YVGGL E+V+E +L F+ G + + P D+ T +H+ +GFV FL +EDA A
Sbjct: 14 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA 73
Query: 67 MDNMDGAELYGRVLTVNYA 85
+ MD +LYG+ + VN A
Sbjct: 74 IKIMDMIKLYGKPIRVNKA 92
>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 = 63.2 bits (152), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 31/75 (41%), Positives = 43/75 (57%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
++VG L+ E+ + AAF PFG I D + D AT K + +GFV+F K DA A+ M
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 71 DGAELYGRVLTVNYA 85
G L GR + N+A
Sbjct: 78 GGQWLGGRQIRTNWA 92
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 62.4 bits (150), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 33/82 (40%), Positives = 47/82 (57%)
Query: 4 LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDA 63
+A + L+VGGL+ + NE L F +G I +V D+ TQ+ R FGFVTF +DA
Sbjct: 8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDA 67
Query: 64 IQAMDNMDGAELYGRVLTVNYA 85
AM M+G + GR + V+ A
Sbjct: 68 KDAMMAMNGKSVDGRQIRVDQA 89
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 60.5 bits (145), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 30/75 (40%), Positives = 44/75 (58%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
++VG L+ E+ + +AF PFG I D + D AT K + +GFV+F K DA A+ +M
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 71 DGAELYGRVLTVNYA 85
G L GR + N+A
Sbjct: 78 GGQWLGGRQIRTNWA 92
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 60.1 bits (144), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 31/84 (36%), Positives = 49/84 (58%), Gaps = 1/84 (1%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
LYVG L + E +L F PFG I ++ D T + + +GF+TF + E A +A++ +
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 71 DGAELYGRVLTVNYALPERIKGGE 94
+G EL GR + V + + ER+ GG
Sbjct: 68 NGFELAGRPMRVGH-VTERLDGGS 90
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 60.1 bits (144), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 45/75 (60%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
LYVG L + E +L F PFG I+ ++ +D T + + +GF+TF + E A +A++ +
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 71 DGAELYGRVLTVNYA 85
+G EL GR + V +
Sbjct: 89 NGFELAGRPMKVGHV 103
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 56.2 bits (134), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 32/77 (41%), Positives = 40/77 (51%)
Query: 9 NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
+L V L + L F +G + DV P D+ T++ R F FV F +K DA AMD
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 69 NMDGAELYGRVLTVNYA 85
MDGA L GR L V A
Sbjct: 131 AMDGAVLDGRELRVQMA 147
>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 = 56.2 bits (134), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 32/77 (41%), Positives = 40/77 (51%)
Query: 9 NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
+L V L + L F +G + DV P D+ T++ R F FV F +K DA AMD
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 69 NMDGAELYGRVLTVNYA 85
MDGA L GR L V A
Sbjct: 108 AMDGAVLDGRELRVQMA 124
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 55.8 bits (133), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 30/75 (40%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
L++GGL E NE +L A F G I +V D+ T K R F F+TF DA A +M
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDM 68
Query: 71 DGAELYGRVLTVNYA 85
+G L+G+ + V A
Sbjct: 69 NGKSLHGKAIKVEQA 83
>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 = 53.9 bits (128), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 32/75 (42%), Positives = 44/75 (58%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
++VG L+ E+ A + AAF PFG I D + D AT K + +GFV+F K DA A+ M
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 71 DGAELYGRVLTVNYA 85
G L GR + N+A
Sbjct: 69 GGQWLGGRQIRTNWA 83
>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 = 53.9 bits (128), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 29/75 (38%), Positives = 40/75 (53%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
L+VG L V++ L AF F D T R +GFV+F ++DA AMD+M
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 71 DGAELYGRVLTVNYA 85
G +L GR L +N+A
Sbjct: 64 QGQDLNGRPLRINWA 78
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 53.5 bits (127), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 29/76 (38%), Positives = 40/76 (52%)
Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
L+VG L V++ L AF F D T R +GFV+F ++DA AMD+
Sbjct: 89 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 148
Query: 70 MDGAELYGRVLTVNYA 85
M G +L GR L +N+A
Sbjct: 149 MQGQDLNGRPLRINWA 164
>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 = 52.8 bits (125), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 38/73 (52%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
+YVG + E+ E + AF PFG IK + D T KH+ F FV + E A A++ M
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 71 DGAELYGRVLTVN 83
+ L GR + V
Sbjct: 76 NSVMLGGRNIKVG 88
Score = 43.1 bits (100), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 43/78 (55%)
Query: 9 NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
N +YV + +++++ + + F FG IK D T KH+ +GF+ + + + + A+
Sbjct: 111 NRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVS 170
Query: 69 NMDGAELYGRVLTVNYAL 86
+M+ +L G+ L V A+
Sbjct: 171 SMNLFDLGGQYLRVGKAV 188
>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 = 52.8 bits (125), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 38/73 (52%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
+YVG + E+ E + AF PFG IK + D T KH+ F FV + E A A++ M
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 71 DGAELYGRVLTVN 83
+ L GR + V
Sbjct: 91 NSVMLGGRNIKVG 103
Score = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 43/78 (55%)
Query: 9 NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
N +YV + +++++ + + F FG IK D T KH+ +GF+ + + + + A+
Sbjct: 126 NRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVS 185
Query: 69 NMDGAELYGRVLTVNYAL 86
+M+ +L G+ L V A+
Sbjct: 186 SMNLFDLGGQYLRVGKAV 203
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 52.4 bits (124), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 29/81 (35%), Positives = 44/81 (54%), Gaps = 3/81 (3%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
L+V L+ +E L F +G + ++ P+D T+K + F FVTF+ E A++A +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 71 DGAELYGRVLTVNYALPERIK 91
DG GR+L V LP IK
Sbjct: 71 DGQVFQGRMLHV---LPSTIK 88
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 51.2 bits (121), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 28/80 (35%), Positives = 43/80 (53%)
Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
L V GL+ E L F +G I DV DQ +++ R F FV F +DA +A +
Sbjct: 17 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76
Query: 70 MDGAELYGRVLTVNYALPER 89
+G EL GR + V++++ +R
Sbjct: 77 ANGMELDGRRIRVDFSITKR 96
>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 = 50.8 bits (120), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 37/73 (50%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
+YVG + E+ E + AF PFG IK + D T KH+ F FV + E A A++
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 71 DGAELYGRVLTVN 83
+ L GR + V
Sbjct: 75 NSVXLGGRNIKVG 87
Score = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 42/78 (53%)
Query: 9 NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
N +YV + +++++ + + F FG IK D T KH+ +GF+ + + + + A+
Sbjct: 110 NRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVS 169
Query: 69 NMDGAELYGRVLTVNYAL 86
+ + +L G+ L V A+
Sbjct: 170 SXNLFDLGGQYLRVGKAV 187
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 50.8 bits (120), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 28/80 (35%), Positives = 43/80 (53%)
Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
L V GL+ E L F +G I DV DQ +++ R F FV F +DA +A +
Sbjct: 48 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 107
Query: 70 MDGAELYGRVLTVNYALPER 89
+G EL GR + V++++ +R
Sbjct: 108 ANGMELDGRRIRVDFSITKR 127
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 50.4 bits (119), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 28/80 (35%), Positives = 43/80 (53%)
Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
L V GL+ E L F +G I DV DQ +++ R F FV F +DA +A +
Sbjct: 14 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 73
Query: 70 MDGAELYGRVLTVNYALPER 89
+G EL GR + V++++ +R
Sbjct: 74 ANGMELDGRRIRVDFSITKR 93
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 49.7 bits (117), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 27/87 (31%), Positives = 42/87 (48%)
Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
T+ V L+E+ E L F PFG I + D+ T + + F F++F +EDA +A+
Sbjct: 17 TIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAG 76
Query: 70 MDGAELYGRVLTVNYALPERIKGGEQG 96
+ G +L V +A P G G
Sbjct: 77 VSGFGYDHLILNVEWAKPSTNSGPSSG 103
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 49.7 bits (117), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 43/82 (52%)
Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
+++VG + E E L F G + + D+ T K + +GF + ++E A+ AM N
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 70 MDGAELYGRVLTVNYALPERIK 91
++G E GR L V+ A E+ K
Sbjct: 70 LNGREFSGRALRVDNAASEKNK 91
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 43/78 (55%), Gaps = 8/78 (10%)
Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
L+V LA V E IL AF FG ++ VK K + + F+ F E++ A++AM+
Sbjct: 13 VLFVRNLANTVTEEILEKAFSQFGKLERVK--------KLKDYAFIHFDERDGAVKAMEE 64
Query: 70 MDGAELYGRVLTVNYALP 87
M+G +L G + + +A P
Sbjct: 65 MNGKDLEGENIEIVFAKP 82
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 48.9 bits (115), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 30/76 (39%), Positives = 37/76 (48%)
Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
TL V L + L F +G + DV P + T+ R F FV F ++ DA A
Sbjct: 15 TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74
Query: 70 MDGAELYGRVLTVNYA 85
MDGAEL GR L V A
Sbjct: 75 MDGAELDGRELRVQVA 90
>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 = 23/73 (31%), Positives = 41/73 (56%)
Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
+LYVG L +V EA+L+ F P G I ++ D T++ + +V F + DA +A+D
Sbjct: 12 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 71
Query: 70 MDGAELYGRVLTV 82
M+ + G+ + +
Sbjct: 72 MNFDVIKGKPVRI 84
Score = 35.0 bits (79), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 2/72 (2%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
+++ L + ++ L+ F FG+I K D+ K +GFV F +E A +A++ M
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSK--GYGFVHFETQEAAERAIEKM 158
Query: 71 DGAELYGRVLTV 82
+G L R + V
Sbjct: 159 NGMLLNDRKVFV 170
>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain
Of Hnrnp D (Auf1) With Telomere Dna
pdb|1X0F|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain
Of Hnrnp D(Auf1) With Telomeric Dna
Length = 79
Score = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 35/58 (60%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
++VGGL+ + E + F FG+++ ++ P+D T K R F F+TF E+E + M+
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 61
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 35/58 (60%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
++VGGL+ + E + F FG+++ ++ P+D T K R F F+TF E+E + M+
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 59
>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 = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 41/73 (56%)
Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
+LYVG L +V EA+L+ F P G I ++ D T++ + +V F + DA +A+D
Sbjct: 17 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 76
Query: 70 MDGAELYGRVLTV 82
M+ + G+ + +
Sbjct: 77 MNFDVIKGKPVRI 89
Score = 34.7 bits (78), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 2/72 (2%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
+++ L + ++ L+ F FG+I K D+ K +GFV F +E A +A++ M
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSK--GYGFVHFETQEAAERAIEKM 163
Query: 71 DGAELYGRVLTV 82
+G L R + V
Sbjct: 164 NGMLLNDRKVFV 175
>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 = 48.1 bits (113), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 48/88 (54%), Gaps = 3/88 (3%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
L+V + EE E + F +G+IK++ LD+ T + + V + + A+ A + +
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 71 DGAELYGRVLTVNYAL---PERIKGGEQ 95
+GAE+ G+ + V++ P+R+K E+
Sbjct: 135 NGAEIMGQTIQVDWCFVKGPKRVKKSEK 162
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 47.8 bits (112), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 45/79 (56%), Gaps = 3/79 (3%)
Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
TL+V GL+E+ E L +F G ++ + D+ T + FGFV F +EDA A +
Sbjct: 17 TLFVKGLSEDTTEETLKESFD--GSVR-ARIVTDRETGSSKGFGFVDFNSEEDAKAAKEA 73
Query: 70 MDGAELYGRVLTVNYALPE 88
M+ E+ G +T+++A P+
Sbjct: 74 MEDGEIDGNKVTLDWAKPK 92
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 47.8 bits (112), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 47/82 (57%)
Query: 5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
+V+ L+V G+ EE E +H F +G+IK++ LD+ T + + V + ++A
Sbjct: 4 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 63
Query: 65 QAMDNMDGAELYGRVLTVNYAL 86
AM+ ++G +L G+ ++V++
Sbjct: 64 AAMEGLNGQDLMGQPISVDWCF 85
>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 = 47.8 bits (112), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 47/82 (57%)
Query: 5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
+V+ L+V G+ EE E +H F +G+IK++ LD+ T + + V + ++A
Sbjct: 4 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 63
Query: 65 QAMDNMDGAELYGRVLTVNYAL 86
AM+ ++G +L G+ ++V++
Sbjct: 64 AAMEGLNGQDLMGQPISVDWCF 85
>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 = 47.4 bits (111), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 47/82 (57%)
Query: 5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
+V+ L+V G+ EE E +H F +G+IK++ LD+ T + + V + ++A
Sbjct: 6 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 65
Query: 65 QAMDNMDGAELYGRVLTVNYAL 86
AM+ ++G +L G+ ++V++
Sbjct: 66 AAMEGLNGQDLMGQPISVDWCF 87
>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 = 47.4 bits (111), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 47/82 (57%)
Query: 5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
+V+ L+V G+ EE E +H F +G+IK++ LD+ T + + V + ++A
Sbjct: 4 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 63
Query: 65 QAMDNMDGAELYGRVLTVNYAL 86
AM+ ++G +L G+ ++V++
Sbjct: 64 AAMEGLNGQDLMGQPISVDWCF 85
>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 = 47.4 bits (111), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 47/82 (57%)
Query: 5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
+V+ L+V G+ EE E +H F +G+IK++ LD+ T + + V + ++A
Sbjct: 20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 79
Query: 65 QAMDNMDGAELYGRVLTVNYAL 86
AM+ ++G +L G+ ++V++
Sbjct: 80 AAMEGLNGQDLMGQPISVDWCF 101
>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 = 47.4 bits (111), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 47/82 (57%)
Query: 5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
+V+ L+V G+ EE E +H F +G+IK++ LD+ T + + V + ++A
Sbjct: 19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 78
Query: 65 QAMDNMDGAELYGRVLTVNYAL 86
AM+ ++G +L G+ ++V++
Sbjct: 79 AAMEGLNGQDLMGQPISVDWCF 100
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 47.4 bits (111), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
T++VG L V E IL+ F+ G + V D+ K +SFGFV F E A+
Sbjct: 18 TVFVGNLEARVREEILYELFLQAGPLTKVTICKDREG-KPKSFGFVCFKHPESVSYAIAL 76
Query: 70 MDGAELYGRVLTVN 83
++G LYGR + V+
Sbjct: 77 LNGIRLYGRPINVS 90
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 47.0 bits (110), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 41/79 (51%), Gaps = 1/79 (1%)
Query: 9 NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
N ++VGG+ E L F FG + +V D Q+ R FGF+TF +++ QA+
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV- 69
Query: 69 NMDGAELYGRVLTVNYALP 87
NM ++ G+ + V A P
Sbjct: 70 NMHFHDIMGKKVEVKRAEP 88
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 46.6 bits (109), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 38/74 (51%)
Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
L V GL+ E L F +G I DV DQ +++ R F FV F +DA +A +
Sbjct: 17 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76
Query: 70 MDGAELYGRVLTVN 83
+G EL GR + V+
Sbjct: 77 ANGMELDGRRIRVS 90
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 46.6 bits (109), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 43/83 (51%)
Query: 4 LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDA 63
LA K+T+YV L + L+ F +G + V D+ T+K + F+ FL+K+ A
Sbjct: 12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSA 71
Query: 64 IQAMDNMDGAELYGRVLTVNYAL 86
++ +L+GRV+ + A+
Sbjct: 72 QNCTRAINNKQLFGRVIKASIAI 94
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 46.2 bits (108), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 38/69 (55%), Gaps = 2/69 (2%)
Query: 19 EVNEAILHAAFIPFGDIKDVKTPLDQ-ATQKHRSFGFVTFLEKEDAIQAMDNM-DGAELY 76
+ N+ + F FG++K V+ P T HR FGFV F+ K+DA +A + + LY
Sbjct: 26 QANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLY 85
Query: 77 GRVLTVNYA 85
GR L + +A
Sbjct: 86 GRRLVLEWA 94
>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 = 45.8 bits (107), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
+++GGL+ + + L F FG++ D LD T + R FGFV F E E + MD
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 71 DGAELYGRVL 80
+ +L G+V+
Sbjct: 62 E-HKLNGKVI 70
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 42/77 (54%), Gaps = 8/77 (10%)
Query: 9 NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
NTLYV G E++ +L AF PFG+I +D + R+ FVT+ + E A QA+
Sbjct: 16 NTLYVYG--EDMTPTLLRGAFSPFGNI------IDLSMDPPRNCAFVTYEKMESADQAVA 67
Query: 69 NMDGAELYGRVLTVNYA 85
++G ++ L VN A
Sbjct: 68 ELNGTQVESVQLKVNIA 84
>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 = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 42/77 (54%), Gaps = 8/77 (10%)
Query: 9 NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
NTLYV G E++ +L AF PFG+I +D + R+ FVT+ + E A QA+
Sbjct: 40 NTLYVYG--EDMTPTLLRGAFSPFGNI------IDLSMDPPRNCAFVTYEKMESADQAVA 91
Query: 69 NMDGAELYGRVLTVNYA 85
++G ++ L VN A
Sbjct: 92 ELNGTQVESVQLKVNIA 108
>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 = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 43/80 (53%)
Query: 8 KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
K L V L + + + + F G+I+ K D+ T + +GFV +++ +DA +A+
Sbjct: 2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61
Query: 68 DNMDGAELYGRVLTVNYALP 87
+ ++G L + + V+YA P
Sbjct: 62 NTLNGLRLQTKTIKVSYARP 81
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 43/83 (51%), Gaps = 2/83 (2%)
Query: 5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
+++ LYV GL + + + L F +G I + +DQ T R GF+ F ++ +A
Sbjct: 85 SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAE 144
Query: 65 QAMDNMDGAELYGRV--LTVNYA 85
+A+ ++G + G +TV +A
Sbjct: 145 EAIKGLNGQKPSGATEPITVKFA 167
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 41/79 (51%), Gaps = 1/79 (1%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
+YVG L + F FG + +VK D+ T+K + FGFV +++E +A+ +
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVE-MQEESVSEAIAKL 62
Query: 71 DGAELYGRVLTVNYALPER 89
D + GR + V A P++
Sbjct: 63 DNTDFMGRTIRVTEANPKK 81
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With
The Au-Rich Element
Length = 174
Score = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 42/81 (51%)
Query: 8 KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
K L V L + + + + F GDI+ K D+ T + +GFV + + DA +A+
Sbjct: 4 KTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI 63
Query: 68 DNMDGAELYGRVLTVNYALPE 88
+ ++G +L + + V+YA P
Sbjct: 64 NTLNGLKLQTKTIKVSYARPS 84
Score = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 45/83 (54%), Gaps = 2/83 (2%)
Query: 5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
+++ LYV GL + +++ + F +G I + LDQAT R GF+ F ++ +A
Sbjct: 87 SIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAE 146
Query: 65 QAMDNMDGAELYG--RVLTVNYA 85
+A+ ++G + G +TV +A
Sbjct: 147 EAIKGLNGQKPLGAAEPITVKFA 169
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 44.7 bits (104), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 42/81 (51%)
Query: 8 KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
K L V L + + + + F GDI+ K D+ T + +GFV + + DA +A+
Sbjct: 4 KTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI 63
Query: 68 DNMDGAELYGRVLTVNYALPE 88
+ ++G +L + + V+YA P
Sbjct: 64 NTLNGLKLQTKTIKVSYARPS 84
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 44.7 bits (104), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 40/72 (55%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
L++ L +E + L + F+PFG++ K +D+ T + FGFV+F + A A+ M
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 71 DGAELYGRVLTV 82
+G ++ + L V
Sbjct: 103 NGFQVGTKRLKV 114
>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 = 44.3 bits (103), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 39/80 (48%)
Query: 4 LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDA 63
L + TLYVG L+ E ++ F GDIK + LD+ + F FV + + DA
Sbjct: 35 LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADA 94
Query: 64 IQAMDNMDGAELYGRVLTVN 83
AM ++G L R++ +
Sbjct: 95 ENAMRYINGTRLDDRIIRTD 114
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 44.3 bits (103), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 29/88 (32%), Positives = 43/88 (48%), Gaps = 3/88 (3%)
Query: 7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
Q TLYVG L+ +V E ++ F G K K + + + FV F E DA A
Sbjct: 14 QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSND--PYCFVEFYEHRDAAAA 71
Query: 67 MDNMDGAELYGRVLTVNYA-LPERIKGG 93
+ M+G ++ G+ + VN+A P K G
Sbjct: 72 LAAMNGRKILGKEVKVNWATTPSSQKSG 99
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 44.3 bits (103), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 47/88 (53%), Gaps = 3/88 (3%)
Query: 5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
+V+ L+V + EE E + F +G+IK++ LD+ T + + V + + A+
Sbjct: 23 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQAL 82
Query: 65 QAMDNMDGAELYGRVLTVNYAL---PER 89
A + ++GAE+ G+ + V++ P+R
Sbjct: 83 AAKEALNGAEIMGQTIQVDWCFVKGPKR 110
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 44.3 bits (103), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 46/85 (54%), Gaps = 5/85 (5%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTP---LDQATQKHRSFGFVTFLEKEDAIQAM 67
+++G L E++E +L+ F FG I ++TP D T + + F+ F + + A+
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVI--LQTPKIMRDPDTGNSKGYAFINFASFDASDAAI 65
Query: 68 DNMDGAELYGRVLTVNYALPERIKG 92
+ M+G L R +TV+YA + KG
Sbjct: 66 EAMNGQYLCNRPITVSYAFKKDSKG 90
>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1)
From Homo Sapiens At 1.90 A Resolution
pdb|4FXV|B Chain B, Crystal Structure Of An Elav-Like Protein 1 (Elavl1)
From Homo Sapiens At 1.90 A Resolution
pdb|4FXV|C Chain C, Crystal Structure Of An Elav-Like Protein 1 (Elavl1)
From Homo Sapiens At 1.90 A Resolution
pdb|4FXV|D Chain D, Crystal Structure Of An Elav-Like Protein 1 (Elavl1)
From Homo Sapiens At 1.90 A Resolution
Length = 99
Score = 43.9 bits (102), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 42/85 (49%)
Query: 3 NLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKED 62
NL Q L V L + + L + F G+++ K D+ +GFV ++ +D
Sbjct: 14 NLYFQGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKD 73
Query: 63 AIQAMDNMDGAELYGRVLTVNYALP 87
A +A++ ++G L + + V+YA P
Sbjct: 74 AERAINTLNGLRLQSKTIKVSYARP 98
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 43.9 bits (102), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 38/76 (50%)
Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
LY+ L+ V E L + F F + K T + R F+TF KE A QA+
Sbjct: 27 VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86
Query: 70 MDGAELYGRVLTVNYA 85
++G +LYG++L + +
Sbjct: 87 VNGYKLYGKILVIEFG 102
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 43.5 bits (101), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 2/62 (3%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
LYV L + +++ L AF PFG I K ++ + + FGFV F E+A +A+ M
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGG--RSKGFGFVCFSSPEEATKAVTEM 75
Query: 71 DG 72
+G
Sbjct: 76 NG 77
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 43.1 bits (100), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
++VGGL+ + F FG + D D+ T +HR FGFVTF E ED ++ + +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF-ESEDIVEKVCEI 60
Query: 71 DGAELYGRVL 80
E+ +++
Sbjct: 61 HFHEINNKMV 70
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 42.7 bits (99), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 24/90 (26%), Positives = 44/90 (48%), Gaps = 5/90 (5%)
Query: 2 ANLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKE 61
+++ +++GGL+ + + L F FG++K+ D T++ R FGFVTF+++
Sbjct: 19 SHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQA 78
Query: 62 --DAIQAMDNMDGAELYGRVLTVNYALPER 89
D + A EL + + A P R
Sbjct: 79 GVDKVLAQSR---HELDSKTIDPKVAFPRR 105
>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|B Chain B, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|C Chain C, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1NU4|A Chain A, U1a Rna Binding Domain At 1.8 Angstrom Resolution
Reveals A Pre- Organized C-Terminal Helix
pdb|1NU4|B Chain B, U1a Rna Binding Domain At 1.8 Angstrom Resolution
Reveals A Pre- Organized C-Terminal Helix
pdb|3HHN|B Chain B, Crystal Structure Of Class I Ligase Ribozyme
Self-Ligation Product, In Complex With U1a Rbd
pdb|3HHN|D Chain D, Crystal Structure Of Class I Ligase Ribozyme
Self-Ligation Product, In Complex With U1a Rbd
Length = 97
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 39/81 (48%), Gaps = 7/81 (8%)
Query: 9 NTLYVGGLAEEVNE----AILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
+T+Y+ L E++ + LHA F FG I D+ L + K R FV F E A
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDI---LVSRSLKMRGQAFVIFKEVSSAT 65
Query: 65 QAMDNMDGAELYGRVLTVNYA 85
A+ +M G Y + + + YA
Sbjct: 66 NALRSMQGFPFYDKPMRIQYA 86
>pdb|1U6B|A Chain A, Crystal Structure Of A Self-Splicing Group I Intron With
Both Exons
pdb|1ZZN|A Chain A, Crystal Structure Of A Group I IntronTWO EXON COMPLEX
THAT Includes All Catalytic Metal Ion Ligands.
pdb|3G8S|A Chain A, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|B Chain B, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|C Chain C, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|D Chain D, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8T|A Chain A, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|B Chain B, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|C Chain C, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|D Chain D, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G96|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Man6p
pdb|3G96|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Man6p
pdb|3G96|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Man6p
pdb|3G96|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Man6p
pdb|3G9C|A Chain A, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|B Chain B, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|C Chain C, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|D Chain D, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3IRW|P Chain P, Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3MUM|P Chain P, Crystal Structure Of The G20a Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUR|P Chain P, Crystal Structure Of The C92u Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUT|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Gmp
pdb|3MUV|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Amp
pdb|3MXH|P Chain P, Native Structure Of A C-Di-Gmp Riboswitch From V.
Cholerae
pdb|3P49|B Chain B, Crystal Structure Of A Glycine Riboswitch From
Fusobacterium Nucleatum
pdb|3R1H|A Chain A, Crystal Structure Of The Class I Ligase
Ribozyme-Substrate Preligation Complex, C47u Mutant,
Ca2+ Bound
pdb|3R1H|D Chain D, Crystal Structure Of The Class I Ligase
Ribozyme-Substrate Preligation Complex, C47u Mutant,
Ca2+ Bound
pdb|3R1L|A Chain A, Crystal Structure Of The Class I Ligase
Ribozyme-Substrate Preligation Complex, C47u Mutant,
Mg2+ Bound
pdb|3R1L|D Chain D, Crystal Structure Of The Class I Ligase
Ribozyme-Substrate Preligation Complex, C47u Mutant,
Mg2+ Bound
pdb|3UCU|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Pgpg
pdb|3UCZ|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Gpg
pdb|3UD3|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Pgpa
pdb|3UD4|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Gpa
Length = 98
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 39/81 (48%), Gaps = 7/81 (8%)
Query: 9 NTLYVGGLAEEVNE----AILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
+T+Y+ L E++ + LHA F FG I D+ L + K R FV F E A
Sbjct: 10 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDI---LVSRSLKMRGQAFVIFKEVSSAT 66
Query: 65 QAMDNMDGAELYGRVLTVNYA 85
A+ +M G Y + + + YA
Sbjct: 67 NALRSMQGFPFYDKPMRIQYA 87
>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group
I Intron
pdb|3BO3|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group
I Intron
pdb|3BO4|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group
I Intron
pdb|3IIN|A Chain A, Plasticity Of The Kink Turn Structural Motif
Length = 95
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 39/81 (48%), Gaps = 7/81 (8%)
Query: 9 NTLYVGGLAEEVNE----AILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
+T+Y+ L E++ + LHA F FG I D+ L + K R FV F E A
Sbjct: 7 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDI---LVSRSLKMRGQAFVIFKEVSSAT 63
Query: 65 QAMDNMDGAELYGRVLTVNYA 85
A+ +M G Y + + + YA
Sbjct: 64 NALRSMQGFPFYDKPMRIQYA 84
>pdb|1M5K|C Chain C, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5K|F Chain F, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5O|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5O|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1SJ3|P Chain P, Hepatitis Delta Virus Gemonic Ribozyme Precursor, With
Mg2+ Bound
pdb|1SJ4|P Chain P, Crystal Structure Of A C75u Mutant Hepatitis Delta Virus
Ribozyme Precursor, In Cu2+ Solution
pdb|1SJF|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Cobalt
Hexammine Solution
pdb|1VBX|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Edta Solution
pdb|1VBY|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, And Mn2+ Bound
pdb|1VBZ|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Ba2+ Solution
pdb|1VC0|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Imidazole And
Sr2+ Solution
pdb|1VC5|A Chain A, Crystal Structure Of The Wild Type Hepatitis Delta Virus
Gemonic Ribozyme Precursor, In Edta Solution
pdb|1VC6|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Product With C75u Mutaion, Cleaved In
Imidazole And Mg2+ Solutions
pdb|1VC7|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Sr2+ Solution
pdb|2OIH|A Chain A, Hepatitis Delta Virus Gemonic Ribozyme Precursor With
C75u Mutation And Bound To Monovalent Cation Tl+
pdb|2OJ3|A Chain A, Hepatitis Delta Virus Ribozyme Precursor Structure, With
C75u Mutation, Bound To Tl+ And Cobalt Hexammine
(Co(Nh3) 63+)
Length = 100
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 39/81 (48%), Gaps = 7/81 (8%)
Query: 9 NTLYVGGLAEEVNE----AILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
+T+Y+ L E++ + LHA F FG I D+ L + K R FV F E A
Sbjct: 10 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDI---LVSRSLKMRGQAFVIFKEVSSAT 66
Query: 65 QAMDNMDGAELYGRVLTVNYA 85
A+ +M G Y + + + YA
Sbjct: 67 NALRSMQGFPFYDKPMRIQYA 87
>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|B Chain B, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|C Chain C, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|D Chain D, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
Length = 96
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 39/81 (48%), Gaps = 7/81 (8%)
Query: 9 NTLYVGGLAEEVNE----AILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
+T+Y+ L E++ + LHA F FG I D+ L + K R FV F E A
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDI---LVSRSLKMRGQAFVIFKEVSSAT 65
Query: 65 QAMDNMDGAELYGRVLTVNYA 85
A+ +M G Y + + + YA
Sbjct: 66 NALRSMQGFPFYDKPMRIQYA 86
>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To
Its Catalytic Cofactor
pdb|2NZ4|B Chain B, Structural Investigation Of The Glms Ribozyme Bound To
Its Catalytic Cofactor
pdb|2NZ4|C Chain C, Structural Investigation Of The Glms Ribozyme Bound To
Its Catalytic Cofactor
pdb|2NZ4|D Chain D, Structural Investigation Of The Glms Ribozyme Bound To
Its Catalytic Cofactor
Length = 94
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 39/81 (48%), Gaps = 7/81 (8%)
Query: 9 NTLYVGGLAEEVNE----AILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
+T+Y+ L E++ + LHA F FG I D+ L + K R FV F E A
Sbjct: 6 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDI---LVSRSLKMRGQAFVIFKEVSSAT 62
Query: 65 QAMDNMDGAELYGRVLTVNYA 85
A+ +M G Y + + + YA
Sbjct: 63 NALRSMQGFPFYDKPMRIQYA 83
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 29/83 (34%), Positives = 43/83 (51%), Gaps = 5/83 (6%)
Query: 7 QKNT----LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKED 62
QK+T ++VGGL +A L F FGDI++ D+ T K R +GFVT ++
Sbjct: 12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAA 71
Query: 63 AIQAMDNMDGAELYGRVLTVNYA 85
A +A + + + GR VN A
Sbjct: 72 AERACKDPN-PIIDGRKANVNLA 93
>pdb|3L3C|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Glc6p
pdb|3L3C|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Glc6p
pdb|3L3C|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Glc6p
pdb|3L3C|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Glc6p
Length = 90
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 39/81 (48%), Gaps = 7/81 (8%)
Query: 9 NTLYVGGLAEEVNE----AILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
+T+Y+ L E++ + LHA F FG I D+ L + K R FV F E A
Sbjct: 4 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDI---LVSRSLKMRGQAFVIFKEVSSAT 60
Query: 65 QAMDNMDGAELYGRVLTVNYA 85
A+ +M G Y + + + YA
Sbjct: 61 NALRSMQGFPFYDKPMRIQYA 81
>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures
pdb|1DZ5|A Chain A, The Nmr Structure Of The 38kda U1a Protein-Pie Rna
Complex Reveals The Basis Of Cooperativity In
Regulation Of Polyadenylation By Human U1a Protein
pdb|1DZ5|B Chain B, The Nmr Structure Of The 38kda U1a Protein-Pie Rna
Complex Reveals The Basis Of Cooperativity In
Regulation Of Polyadenylation By Human U1a Protein
Length = 101
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 39/81 (48%), Gaps = 7/81 (8%)
Query: 9 NTLYVGGLAEEVNE----AILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
+T+Y+ L E++ + LHA F FG I D+ L + K R FV F E A
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDI---LVSRSLKMRGQAFVIFKEVSSAT 65
Query: 65 QAMDNMDGAELYGRVLTVNYA 85
A+ +M G Y + + + YA
Sbjct: 66 NALRSMQGFPFYDKPMRIQYA 86
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 41/81 (50%), Gaps = 7/81 (8%)
Query: 1 MANLAVQKN-TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLE 59
+ N + KN T+Y GG+A + + ++ F PFG I +++ + + FV F
Sbjct: 17 VVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIR------VFPEKGYSFVRFST 70
Query: 60 KEDAIQAMDNMDGAELYGRVL 80
E A A+ +++G + G V+
Sbjct: 71 HESAAHAIVSVNGTTIEGHVV 91
>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
pdb|3IWN|D Chain D, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
Length = 91
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 39/81 (48%), Gaps = 7/81 (8%)
Query: 9 NTLYVGGLAEEVNE----AILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
+T+Y+ L E++ + LHA F FG I D+ L + K R FV F E A
Sbjct: 5 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDI---LVSRSLKMRGQAFVIFKEVSSAT 61
Query: 65 QAMDNMDGAELYGRVLTVNYA 85
A+ +M G Y + + + YA
Sbjct: 62 NALRSMQGFPFYDKPMRIQYA 82
>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 = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 1/80 (1%)
Query: 7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
Q L++GGL+ E + L + F +G + D D T++ R FGFVT+ E+ A
Sbjct: 11 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 70
Query: 67 MDNMDGAELYGRVLTVNYAL 86
M N ++ GRV+ A+
Sbjct: 71 M-NARPHKVDGRVVEPKRAV 89
Score = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 2 ANLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTF 57
A+L V+K ++VGG+ E+ E L F +G I+ ++ D+ + K R F FVTF
Sbjct: 99 AHLTVKK--IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 152
>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 = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 1/80 (1%)
Query: 7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
Q L++GGL+ E + L + F +G + D D T++ R FGFVT+ E+ A
Sbjct: 12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 71
Query: 67 MDNMDGAELYGRVLTVNYAL 86
M N ++ GRV+ A+
Sbjct: 72 M-NARPHKVDGRVVEPKRAV 90
Score = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 2 ANLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTF 57
A+L V+K ++VGG+ E+ E L F +G I+ ++ D+ + K R F FVTF
Sbjct: 100 AHLTVKK--IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 1/80 (1%)
Query: 7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
Q L++GGL+ E + L + F +G + D D T++ R FGFVT+ E+ A
Sbjct: 13 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 72
Query: 67 MDNMDGAELYGRVLTVNYAL 86
M N ++ GRV+ A+
Sbjct: 73 M-NARPHKVDGRVVEPKRAV 91
Score = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 2 ANLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTF 57
A+L V+K ++VGG+ E+ E L F +G I+ ++ D+ + K R F FVTF
Sbjct: 101 AHLTVKK--IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 154
>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 = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 41/81 (50%)
Query: 8 KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
+ L V L + + + L + F G+++ K D+ +GFV ++ +DA +A+
Sbjct: 4 RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 63
Query: 68 DNMDGAELYGRVLTVNYALPE 88
+ ++G L + + V+YA P
Sbjct: 64 NTLNGLRLQSKTIKVSYARPS 84
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 31/50 (62%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEK 60
+++GGL+ + + L F FG++K+ D T++ R FGFVTF+++
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 52
>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 = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 41/80 (51%)
Query: 8 KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
+ L V L + + + L + F G+++ K D+ +GFV ++ +DA +A+
Sbjct: 2 RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Query: 68 DNMDGAELYGRVLTVNYALP 87
+ ++G L + + V+YA P
Sbjct: 62 NTLNGLRLQSKTIKVSYARP 81
Score = 35.8 bits (81), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 41/83 (49%), Gaps = 2/83 (2%)
Query: 5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
++ LY+ GL + + + F FG I + + +DQ T R F+ F ++ +A
Sbjct: 85 VIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAE 144
Query: 65 QAMDNMDGAELYGRV--LTVNYA 85
+A+ + +G + G +TV +A
Sbjct: 145 EAITSFNGHKPPGSSEPITVKFA 167
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs
Of Human Antigen R
Length = 177
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 41/80 (51%)
Query: 8 KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
+ L V L + + + L + F G+++ K D+ +GFV ++ +DA +A+
Sbjct: 2 RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Query: 68 DNMDGAELYGRVLTVNYALP 87
+ ++G L + + V+YA P
Sbjct: 62 NTLNGLRLQSKTIKVSYARP 81
Score = 35.4 bits (80), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 41/83 (49%), Gaps = 2/83 (2%)
Query: 5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
++ LY+ GL + + + F FG I + + +DQ T R F+ F ++ +A
Sbjct: 85 VIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAE 144
Query: 65 QAMDNMDGAELYGRV--LTVNYA 85
+A+ + +G + G +TV +A
Sbjct: 145 EAITSFNGHKPPGSSEPITVXFA 167
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 1/80 (1%)
Query: 7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
Q L++GGL+ E + L + F +G + D D T++ R FGFVT+ E+ A
Sbjct: 10 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 69
Query: 67 MDNMDGAELYGRVLTVNYAL 86
M N ++ GRV+ A+
Sbjct: 70 M-NARPHKVDGRVVEPKRAV 88
Score = 40.0 bits (92), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 2 ANLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTF 57
A+L V+K ++VGG+ E+ E L F +G I+ ++ D+ + K R F FVTF
Sbjct: 98 AHLTVKK--IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 151
>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 = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 1/80 (1%)
Query: 7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
Q L++GGL+ E + L + F +G + D D T++ R FGFVT+ E+ A
Sbjct: 5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 64
Query: 67 MDNMDGAELYGRVLTVNYAL 86
M N ++ GRV+ A+
Sbjct: 65 M-NARPHKVDGRVVEPKRAV 83
Score = 40.0 bits (92), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 2 ANLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTF 57
A+L V+K ++VGG+ E+ E L F +G I+ ++ D+ + K R F FVTF
Sbjct: 93 AHLTVKK--IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 146
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 1/80 (1%)
Query: 7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
Q L++GGL+ E + L + F +G + D D T++ R FGFVT+ E+ A
Sbjct: 12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 71
Query: 67 MDNMDGAELYGRVLTVNYAL 86
M N ++ GRV+ A+
Sbjct: 72 M-NARPHKVDGRVVEPKRAV 90
Score = 40.0 bits (92), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 2 ANLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTF 57
A+L V+K ++VGG+ E+ E L F +G I+ ++ D+ + K R F FVTF
Sbjct: 100 AHLTVKK--IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 2/77 (2%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
LYV GL + +++ + F +G I + LDQAT R GF+ F ++ +A +A+ +
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 71 DGAELYG--RVLTVNYA 85
+G + G +TV +A
Sbjct: 64 NGQKPLGAAEPITVKFA 80
>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 = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 39/72 (54%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
L++ L +E + L F+PFG++ K +D+ T + FGFV++ A A+ +M
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 71 DGAELYGRVLTV 82
+G ++ + L V
Sbjct: 88 NGFQIGMKRLKV 99
>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 = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 40/81 (49%), Gaps = 1/81 (1%)
Query: 4 LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDA 63
L + TLYVG L+ E ++ F GDIK + LD+ + F FV + + DA
Sbjct: 14 LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKM-KTACGFCFVEYYSRADA 72
Query: 64 IQAMDNMDGAELYGRVLTVNY 84
AM ++G L R++ ++
Sbjct: 73 ENAMRYINGTRLDDRIIRTDW 93
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein
U1a117, Nmr, 43 Structures
Length = 116
Score = 40.0 bits (92), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 39/81 (48%), Gaps = 7/81 (8%)
Query: 9 NTLYVGGLAEEVNE----AILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
+T+Y+ L E++ + L+A F FG I D+ L + K R FV F E A
Sbjct: 9 HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDI---LVSRSLKMRGQAFVIFKEVSSAT 65
Query: 65 QAMDNMDGAELYGRVLTVNYA 85
A+ +M G Y + + + YA
Sbjct: 66 NALRSMQGFPFYDKPMRIQYA 86
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleaoproteins A2B1
Length = 116
Score = 40.0 bits (92), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 28/51 (54%)
Query: 7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTF 57
Q L++GGL+ E E L + +G + D D A+++ R FGFVTF
Sbjct: 26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTF 76
>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 40.0 bits (92), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 39/81 (48%), Gaps = 7/81 (8%)
Query: 9 NTLYVGGLAEEVNE----AILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
+T+Y+ L E++ + L+A F FG I D+ L + K R FV F E A
Sbjct: 10 HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDI---LVSRSLKMRGQAFVIFKEVSSAT 66
Query: 65 QAMDNMDGAELYGRVLTVNYA 85
A+ +M G Y + + + YA
Sbjct: 67 NALRSMQGFPFYDKPMRIQYA 87
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 39/81 (48%), Gaps = 7/81 (8%)
Query: 9 NTLYVGGLAEEVNE----AILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
+T+Y+ L E++ + L+A F FG I D+ L + K R FV F E A
Sbjct: 10 HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDI---LVSRSLKMRGQAFVIFKEVSSAT 66
Query: 65 QAMDNMDGAELYGRVLTVNYA 85
A+ +M G Y + + + YA
Sbjct: 67 NALRSMQGFPFYDKPMRIQYA 87
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 44/84 (52%), Gaps = 7/84 (8%)
Query: 9 NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
N LY+G L+ V L F D K PL + FV + ++ AI+A++
Sbjct: 9 NKLYIGNLSPAVTADDLRQLF------GDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIE 62
Query: 69 NMDG-AELYGRVLTVNYALPERIK 91
+ G EL+G+++ V+Y++ ++++
Sbjct: 63 TLSGKVELHGKIMEVDYSVSKKLR 86
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 34/64 (53%), Gaps = 8/64 (12%)
Query: 9 NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
L+V LA V E IL +F FG ++ VK K + + FV F ++ A++AMD
Sbjct: 16 KVLFVRNLATTVTEEILEKSFSEFGKLERVK--------KLKDYAFVHFEDRGAAVKAMD 67
Query: 69 NMDG 72
M+G
Sbjct: 68 EMNG 71
>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 = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 2/77 (2%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
+++GGL + E L F +G + D+K D AT + R FGF++F EK ++ +
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSF-EKPSSVDEVVKT 64
Query: 71 DGAELYGRVLTVNYALP 87
L G+V+ A+P
Sbjct: 65 QHI-LDGKVIDPKRAIP 80
Score = 36.2 bits (82), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 1/77 (1%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
++VGG+ +V F +G I D + LD+ T + R FGFVT+ + DA+ +
Sbjct: 90 IFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTY-DSADAVDRVCQN 148
Query: 71 DGAELYGRVLTVNYALP 87
+ R + + A P
Sbjct: 149 KFIDFKDRKIEIKRAEP 165
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 37/79 (46%), Gaps = 2/79 (2%)
Query: 7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
Q L+V + + L F FG I DV+ ++ K FGFVTF DA +A
Sbjct: 28 QPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSK--GFGFVTFENSADADRA 85
Query: 67 MDNMDGAELYGRVLTVNYA 85
+ + G + GR + VN A
Sbjct: 86 REKLHGTVVEGRKIEVNNA 104
>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 = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 1/69 (1%)
Query: 12 YVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMD 71
+VGGL+ + ++ L F FG++ D D T + R FGF+ F + + +D +
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQKE 74
Query: 72 GAELYGRVL 80
L GRV+
Sbjct: 75 -HRLDGRVI 82
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 4/73 (5%)
Query: 6 VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDA-- 63
+ NT++VGG+ ++E + + F +G +K+VK D+ T + +GFV+F D
Sbjct: 8 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQK 66
Query: 64 -IQAMDNMDGAEL 75
+++ N G +L
Sbjct: 67 IVESQINFHGKKL 79
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 4/73 (5%)
Query: 6 VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDA-- 63
+ NT++VGG+ ++E + + F +G +K+VK D+ T + +GFV+F D
Sbjct: 7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQK 65
Query: 64 -IQAMDNMDGAEL 75
+++ N G +L
Sbjct: 66 IVESQINFHGKKL 78
>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Rna, Uuguucuu
Length = 102
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 4/73 (5%)
Query: 6 VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDA-- 63
+ NT++VGG+ ++E + + F +G +K+VK D+ T + +GFV+F D
Sbjct: 7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQK 65
Query: 64 -IQAMDNMDGAEL 75
+++ N G +L
Sbjct: 66 IVESQINFHGKKL 78
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 36/75 (48%), Gaps = 2/75 (2%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
L+V + + L F FG I DV+ ++ K FGFVTF DA +A + +
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSK--GFGFVTFENSADADRAREKL 75
Query: 71 DGAELYGRVLTVNYA 85
G + GR + VN A
Sbjct: 76 HGTVVEGRKIEVNNA 90
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 32/64 (50%), Gaps = 1/64 (1%)
Query: 5 AVQKNT-LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDA 63
AVQK + L V GL + E L F FG++ V+ D T + FGFV F E E
Sbjct: 11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQ 70
Query: 64 IQAM 67
++ M
Sbjct: 71 VKVM 74
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 31/56 (55%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
L++G + ++E L F FG I ++ D+ T H+ F+T+ E+E A++A
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKA 71
>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 = 37.0 bits (84), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 39/83 (46%)
Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
TL+V + + E+ L F +G IK + + + K R + F+ + + D A +
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 70 MDGAELYGRVLTVNYALPERIKG 92
DG ++ GR + V+ +KG
Sbjct: 164 ADGKKIDGRRVLVDVERGRTVKG 186
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 37.0 bits (84), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 6/77 (7%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
LYV L +E ++ F ++K + +K R + FV F +EDA++AM +
Sbjct: 18 LYVRNLMLSTSEEMIEKEF------NNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKAL 71
Query: 71 DGAELYGRVLTVNYALP 87
+G L G + V A P
Sbjct: 72 NGKVLDGSPIEVTLAKP 88
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 36.6 bits (83), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 25/47 (53%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTF 57
L+VGGL + L + F +G++ D D+ T + R FGFV F
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF 65
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 35.8 bits (81), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 36/75 (48%), Gaps = 8/75 (10%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
L+V +V E+ L+ F PFG +K+VK F FV F E E A +A++ +
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFGPMKEVKI--------LNGFAFVEFEEAESAAKAIEEV 58
Query: 71 DGAELYGRVLTVNYA 85
G + L V Y+
Sbjct: 59 HGKSFANQPLEVVYS 73
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 35.8 bits (81), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 36/75 (48%), Gaps = 8/75 (10%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
L+V +V E+ L+ F PFG +K+VK F FV F E E A +A++ +
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKI--------LNGFAFVEFEEAESAAKAIEEV 85
Query: 71 DGAELYGRVLTVNYA 85
G + L V Y+
Sbjct: 86 HGKSFANQPLEVVYS 100
>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 = 35.8 bits (81), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 39/83 (46%)
Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
TL+V + + E+ L F +G IK + + + K R + F+ + + D A +
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 70 MDGAELYGRVLTVNYALPERIKG 92
DG ++ GR + V+ +KG
Sbjct: 164 ADGKKIDGRRVLVDVERGRTVKG 186
>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 = 35.4 bits (80), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 2/72 (2%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
+++ L + ++ L+ F FG+I K D+ K +GFV F +E A +A++ M
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSK--GYGFVHFETQEAAERAIEKM 65
Query: 71 DGAELYGRVLTV 82
+G L R + V
Sbjct: 66 NGMLLNDRKVFV 77
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 35.4 bits (80), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 37/73 (50%), Gaps = 2/73 (2%)
Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
+++ L + ++ L+ F FG+I K D+ K +GFV F +E A +A++
Sbjct: 13 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSK--GYGFVHFETQEAAERAIEK 70
Query: 70 MDGAELYGRVLTV 82
M+G L R + V
Sbjct: 71 MNGMLLNDRKVFV 83
>pdb|1A9N|B Chain B, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
pdb|1A9N|D Chain D, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
Length = 96
Score = 35.0 bits (79), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 39/81 (48%), Gaps = 7/81 (8%)
Query: 9 NTLYVGGLAEEVNE----AILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
+T+Y+ + +++ + L+A F FG + D+ + T K R FV F E +
Sbjct: 7 HTIYINNMNDKIKKEELKRSLYALFSQFGHVVDI---VALKTMKMRGQAFVIFKELGSST 63
Query: 65 QAMDNMDGAELYGRVLTVNYA 85
A+ + G YG+ + + YA
Sbjct: 64 NALRQLQGFPFYGKPMRIQYA 84
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 34.7 bits (78), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 23/47 (48%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTF 57
LY+ GL + L P+G I K LD+ T K + +GFV F
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDF 54
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 33.9 bits (76), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 31/67 (46%), Gaps = 5/67 (7%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
+YVG L N+ L AF +G ++ V + F FV F + DA A+ ++
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSV-----WVARNPPGFAFVEFEDPRDAADAVRDL 130
Query: 71 DGAELYG 77
DG L G
Sbjct: 131 DGRTLCG 137
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 33.1 bits (74), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 39/86 (45%), Gaps = 4/86 (4%)
Query: 3 NLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEK-- 60
N AV+ L++G ++++ E + F FG I++ + L R FVTF +
Sbjct: 90 NNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRI-LRGPDGLSRGCAFVTFTTRAM 148
Query: 61 -EDAIQAMDNMDGAELYGRVLTVNYA 85
+ AI+AM E + V +A
Sbjct: 149 AQTAIKAMHQAQTMEGCSSPMVVKFA 174
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 33.1 bits (74), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 34/80 (42%), Gaps = 6/80 (7%)
Query: 6 VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQ 65
Q+ L+VG L ++ E F +G+ P + + R FGF+ + A
Sbjct: 20 TQRCRLFVGNLPTDITEEDFKRLFERYGE------PSEVFINRDRGFGFIRLESRTLAEI 73
Query: 66 AMDNMDGAELYGRVLTVNYA 85
A +DG L R L + +A
Sbjct: 74 AKAELDGTILKSRPLRIRFA 93
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 33.1 bits (74), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 39/86 (45%), Gaps = 4/86 (4%)
Query: 3 NLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEK-- 60
N AV+ L++G ++++ E + F FG I++ + L R FVTF +
Sbjct: 102 NNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRI-LRGPDGLSRGCAFVTFTTRAM 160
Query: 61 -EDAIQAMDNMDGAELYGRVLTVNYA 85
+ AI+AM E + V +A
Sbjct: 161 AQTAIKAMHQAQTMEGCSSPMVVKFA 186
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 33.1 bits (74), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 35/78 (44%), Gaps = 7/78 (8%)
Query: 9 NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDA-IQAM 67
TLYVGGL + + E L F FG+I+ + Q F+ F ++ A + A
Sbjct: 13 TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQC------AFIQFATRQAAEVAAE 66
Query: 68 DNMDGAELYGRVLTVNYA 85
+ + + GR L V +
Sbjct: 67 KSFNKLIVNGRRLNVKWG 84
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 33.1 bits (74), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 30/67 (44%), Gaps = 5/67 (7%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
+YVG L N+ L AF +G ++ V + F FV F + DA A+ +
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSV-----WVARNPPGFAFVEFEDPRDAADAVREL 130
Query: 71 DGAELYG 77
DG L G
Sbjct: 131 DGRTLCG 137
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 32.7 bits (73), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 35/75 (46%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
L++GGL +N+ + FG +K D AT + + F +++ QA+ +
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 71 DGAELYGRVLTVNYA 85
+G +L + L V A
Sbjct: 64 NGMQLGDKKLLVQRA 78
>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 = 32.3 bits (72), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 35/75 (46%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
L++GGL +N+ + FG +K D AT + + F +++ QA+ +
Sbjct: 99 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 158
Query: 71 DGAELYGRVLTVNYA 85
+G +L + L V A
Sbjct: 159 NGMQLGDKKLLVQRA 173
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 32.3 bits (72), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 35/75 (46%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
L++GGL +N+ + FG +K D AT + + F +++ QA+ +
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 71 DGAELYGRVLTVNYA 85
+G +L + L V A
Sbjct: 157 NGMQLGDKKLLVQRA 171
>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 = 32.3 bits (72), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 35/75 (46%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
L++GGL +N+ + FG +K D AT + + F +++ QA+ +
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176
Query: 71 DGAELYGRVLTVNYA 85
+G +L + L V A
Sbjct: 177 NGMQLGDKKLLVQRA 191
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 32.3 bits (72), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 30/56 (53%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
L+VG + ++E L F FG I ++ D+ T H+ F+T+ ++ A++A
Sbjct: 18 LFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKA 73
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 32.3 bits (72), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 35/82 (42%), Gaps = 3/82 (3%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
+YVG L ++ + F +G I+D+ + + F FV F + DA A+
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDL---KNRRGGPPFAFVEFEDPRDAEDAVYGR 81
Query: 71 DGAELYGRVLTVNYALPERIKG 92
DG + G L V + R G
Sbjct: 82 DGYDYDGYRLRVEFPRSGRGTG 103
>pdb|2CPI|A Chain A, Solution Structure Of The Rna Recognition Motif Of Cnot4
Length = 111
Score = 32.0 bits (71), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 44/83 (53%), Gaps = 10/83 (12%)
Query: 6 VQKNTLYVGGLAEEVNEA-ILHAA--FIPFGDIKDVKTPLDQATQKHRSFG-----FVTF 57
VQKN ++V GL++ + + +L F FG I K ++ +T S G +VT+
Sbjct: 13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIH--KVVINNSTSYAGSQGPSASAYVTY 70
Query: 58 LEKEDAIQAMDNMDGAELYGRVL 80
+ EDA++A+ ++ + GR L
Sbjct: 71 IRSEDALRAIQCVNNVVVDGRTL 93
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 32.0 bits (71), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 34/74 (45%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
L V L + + PFG ++ + T + + +GF +++K+ A +A ++
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 71 DGAELYGRVLTVNY 84
G L R L V++
Sbjct: 158 LGKPLGPRTLYVHW 171
>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 = 32.0 bits (71), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 34/74 (45%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
L V L + + PFG ++ + T + + +GF +++K+ A +A ++
Sbjct: 96 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Query: 71 DGAELYGRVLTVNY 84
G L R L V++
Sbjct: 156 LGKPLGPRTLYVHW 169
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 32.0 bits (71), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 34/74 (45%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
L V L + + PFG ++ + T + + +GF +++K+ A +A ++
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 71 DGAELYGRVLTVNY 84
G L R L V++
Sbjct: 158 LGKPLGPRTLYVHW 171
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 32.0 bits (71), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 39/85 (45%), Gaps = 8/85 (9%)
Query: 9 NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKT---PL-----DQATQKHRSFGFVTFLEK 60
NT++V GL E V + F G IK K P+ D+ T K + V+F +
Sbjct: 8 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 67
Query: 61 EDAIQAMDNMDGAELYGRVLTVNYA 85
A A+D DG E G + V++A
Sbjct: 68 PSAKAAIDWFDGKEFSGNPIKVSFA 92
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 31.6 bits (70), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 39/85 (45%), Gaps = 8/85 (9%)
Query: 9 NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKT---PL-----DQATQKHRSFGFVTFLEK 60
NT++V GL E V + F G IK K P+ D+ T K + V+F +
Sbjct: 14 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 73
Query: 61 EDAIQAMDNMDGAELYGRVLTVNYA 85
A A+D DG E G + V++A
Sbjct: 74 PSAKAAIDWFDGKEFSGNPIKVSFA 98
>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 = 30.4 bits (67), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 3 NLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKED 62
N AV+ L++G ++++ E + F FG I++ + L R FVTF +
Sbjct: 90 NNAVEDRKLFIGXISKKCTENDIRVXFSSFGQIEECRI-LRGPDGLSRGCAFVTFTTRAX 148
Query: 63 AIQAM 67
A A+
Sbjct: 149 AQTAI 153
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
28
Length = 111
Score = 30.4 bits (67), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 39/87 (44%), Gaps = 6/87 (6%)
Query: 6 VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQ 65
+ T+++ L+ + E L FGD+K V+ L T+ + F F+ +E A +
Sbjct: 13 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQK 72
Query: 66 AMDNMD------GAELYGRVLTVNYAL 86
+ G +L GR L V+ A+
Sbjct: 73 CLAAASLEAEGGGLKLDGRQLKVDLAV 99
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 30.0 bits (66), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 4/81 (4%)
Query: 7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
+ TL + L+ E L F +K P +Q K + + F+ F EDA +A
Sbjct: 14 ESKTLVLSNLSYSATEETLQEVF---EKATFIKVPQNQ-NGKSKGYAFIEFASFEDAKEA 69
Query: 67 MDNMDGAELYGRVLTVNYALP 87
+++ + E+ GR + + P
Sbjct: 70 LNSCNKREIEGRAIRLELQGP 90
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 30.0 bits (66), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 24/42 (57%)
Query: 49 HRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALPERI 90
H+ F FV ++ + +A A+ DG + G+VL +N A ++
Sbjct: 49 HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPKV 90
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor
9g8
Length = 101
Score = 29.6 bits (65), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 36/83 (43%), Gaps = 7/83 (8%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
+YVG L + L AF +G ++ V + F FV F + DA A+ +
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTV-----WIARNPPGFAFVEFEDPRDAEDAVRGL 57
Query: 71 DGAELYGRVLTV--NYALPERIK 91
DG + G + V + +P R +
Sbjct: 58 DGKVICGSRVRVELSTGMPRRSR 80
>pdb|2X4F|A Chain A, The Crystal Structure Of The Human Myosin Light Chain
Kinase Loc340156.
pdb|2X4F|B Chain B, The Crystal Structure Of The Human Myosin Light Chain
Kinase Loc340156
Length = 373
Score = 29.3 bits (64), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 57 FLEKEDAIQAMDNMDGAELYGRVLTVNYALPE 88
F K D + M+ +DG EL+ R++ +Y L E
Sbjct: 155 FESKNDIVLVMEYVDGGELFDRIIDESYNLTE 186
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 28.9 bits (63), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 5/53 (9%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDA 63
++VG ++ E L F +GD+ DV P + R+F FVTF + + A
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQIA 55
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 28.5 bits (62), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 5/49 (10%)
Query: 9 NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTF 57
+ ++VG E++ L F +G++ DV P + R+F FVTF
Sbjct: 12 SKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIP-----KPFRAFAFVTF 55
>pdb|3S8S|A Chain A, Crystal Structure Of The Rrm Domain Of Human Setd1a
Length = 110
Score = 28.5 bits (62), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 15/65 (23%), Positives = 29/65 (44%)
Query: 16 LAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAEL 75
L + V E L +G++++V+ L T+KH V F A + + N+ +
Sbjct: 14 LNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSV 73
Query: 76 YGRVL 80
G ++
Sbjct: 74 MGNII 78
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 28.1 bits (61), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 3/50 (6%)
Query: 42 LDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNY---ALPE 88
L+ K R G VTF + +A+QA+ +G L+ R + V ALP+
Sbjct: 48 LEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALPK 97
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 28.1 bits (61), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 13/54 (24%), Positives = 32/54 (59%), Gaps = 1/54 (1%)
Query: 36 KDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD-NMDGAELYGRVLTVNYALPE 88
++V+ ++++ + R F FV F +DA + M+ N + G+ ++++Y+ P+
Sbjct: 30 REVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSDPK 83
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 28.1 bits (61), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 35/77 (45%), Gaps = 8/77 (10%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
L+VGGL + A L F FG I+ + D K SF ++ + + A A M
Sbjct: 20 LWVGGLGPNTSLAALAREFDRFGSIRTI----DHV--KGDSFAYIQYESLDAAQAACAKM 73
Query: 71 DGAELYG--RVLTVNYA 85
G L G R L V++A
Sbjct: 74 RGFPLGGPDRRLRVDFA 90
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 26.9 bits (58), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 26/51 (50%)
Query: 25 LHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAEL 75
L + F G + +++ P+D+AT K + F FV DA + + + G L
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRL 79
>pdb|3NS6|A Chain A, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
pdb|3NS6|B Chain B, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
Length = 100
Score = 26.6 bits (57), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 26/51 (50%)
Query: 25 LHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAEL 75
L + F G + +++ P+D+AT K + F FV DA + + + G L
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRL 79
>pdb|2XRG|A Chain A, Crystal Structure Of Autotaxin (Enpp2) In Complex With The
Ha155 Boronic Acid Inhibitor
Length = 862
Score = 26.6 bits (57), Expect = 7.8, Method: Composition-based stats.
Identities = 11/35 (31%), Positives = 16/35 (45%)
Query: 72 GAELYGRVLTVNYALPERIKGGEQGWAAQPIWADA 106
G +Y V ++ L R K + W QP+W A
Sbjct: 229 GNSMYDPVFDASFHLRGREKFNHRWWGGQPLWITA 263
>pdb|2XR9|A Chain A, Crystal Structure Of Autotaxin (Enpp2)
Length = 827
Score = 26.6 bits (57), Expect = 7.8, Method: Composition-based stats.
Identities = 11/35 (31%), Positives = 16/35 (45%)
Query: 72 GAELYGRVLTVNYALPERIKGGEQGWAAQPIWADA 106
G +Y V ++ L R K + W QP+W A
Sbjct: 194 GNSMYDPVFDASFHLRGREKFNHRWWGGQPLWITA 228
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.316 0.130 0.379
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,847,347
Number of Sequences: 62578
Number of extensions: 134519
Number of successful extensions: 417
Number of sequences better than 100.0: 151
Number of HSP's better than 100.0 without gapping: 123
Number of HSP's successfully gapped in prelim test: 28
Number of HSP's that attempted gapping in prelim test: 270
Number of HSP's gapped (non-prelim): 168
length of query: 174
length of database: 14,973,337
effective HSP length: 92
effective length of query: 82
effective length of database: 9,216,161
effective search space: 755725202
effective search space used: 755725202
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 bits)