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= 047513
(221 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 8e-05, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 7/79 (8%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEV 115
LY+ + G ++ + FS FGTI ++ ++ G+SK FGF+ F+ PE A
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKV-------MMEGGRSKGFGFVCFSSPEEATK 70
Query: 116 VADAMHGYLLFEHILQVHL 134
M+G ++ L V L
Sbjct: 71 AVTEMNGRIVATKPLYVAL 89
>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 = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 47/80 (58%), Gaps = 10/80 (12%)
Query: 43 LPEEKPLVNKAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHF 102
LPE K + N +++G I E E+ +FF+++G++K ++I ++ TG SK +
Sbjct: 2 LPEGKIMPN---TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR------TGVSKGY 52
Query: 103 GFIEF-NDPEVAEVVADAMH 121
GF+ F ND +V ++V ++
Sbjct: 53 GFVSFYNDVDVQKIVESQIN 72
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 43/79 (54%), Gaps = 5/79 (6%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEV 115
L+I + F + ++ + F FG + ++ +K+ T SK FGF+ F++P+ A+V
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQ-----TSLSKCFGFVSFDNPDSAQV 97
Query: 116 VADAMHGYLLFEHILQVHL 134
AM+G+ + L+V L
Sbjct: 98 AIKAMNGFQVGTKRLKVQL 116
>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 = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 47/80 (58%), Gaps = 10/80 (12%)
Query: 43 LPEEKPLVNKAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHF 102
LPE K + N +++G I E E+ +FF+++G++K ++I ++ TG SK +
Sbjct: 2 LPEGKIMPN---TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR------TGVSKGY 52
Query: 103 GFIEF-NDPEVAEVVADAMH 121
GF+ F ND +V ++V ++
Sbjct: 53 GFVSFYNDVDVQKIVESQIN 72
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 32/114 (28%), Positives = 54/114 (47%), Gaps = 11/114 (9%)
Query: 16 VSSQLPVSSDRK-DAADFLPLEGGPGRKL-PEEKPLVNKAAV--LYIGRIRHGFYEKEMH 71
V+ Q P ++R D +F ++G P R + + P + K+ V ++I + K ++
Sbjct: 57 VNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALY 116
Query: 72 AFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEVVADAMHGYLL 125
FS FG I ++ V + SK +GF+ F E AE + M+G LL
Sbjct: 117 DTFSAFGNILSCKV-------VCDENGSKGYGFVHFETQEAAERAIEKMNGMLL 163
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 38/70 (54%), Gaps = 5/70 (7%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEV 115
LY+G + E + F FG I+ +++ + + TG+SK +GFI F+D E A+
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSE-----TGRSKGYGFITFSDSECAKK 83
Query: 116 VADAMHGYLL 125
+ ++G+ L
Sbjct: 84 ALEQLNGFEL 93
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 42/82 (51%), Gaps = 5/82 (6%)
Query: 51 NKAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDP 110
+ ++ LY+G + E + F FG I + + ++ +TG+SK +GFI F+D
Sbjct: 3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDS-----DTGRSKGYGFITFSDS 57
Query: 111 EVAEVVADAMHGYLLFEHILQV 132
E A + ++G+ L ++V
Sbjct: 58 ECARRALEQLNGFELAGRPMRV 79
>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 = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 42/79 (53%), Gaps = 7/79 (8%)
Query: 39 PGRKLPEEKPLVNKAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGK 98
P R +P ++ +K +++G I KE FFSQ+GTI ++ +K +TG+
Sbjct: 75 PKRAIPRDEQ--DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDK-----DTGQ 127
Query: 99 SKHFGFIEFNDPEVAEVVA 117
S+ FGF+ ++ + + V
Sbjct: 128 SRGFGFVTYDSADAVDRVC 146
Score = 40.8 bits (94), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 12/85 (14%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEV 115
++IG + E + +F ++GT+ L+I ++ TG+S+ FGF+ F P +
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPA-----TGRSRGFGFLSFEKPSSVDE 60
Query: 116 VADAMHGYLLFEHILQVHLIPPEHV 140
V +HIL +I P+
Sbjct: 61 VVKT-------QHILDGKVIDPKRA 78
>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 = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 33/144 (22%), Positives = 67/144 (46%), Gaps = 19/144 (13%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEV 115
+Y+G I + E + F+ FG IK + ++ + T K K F F+E+ PE A++
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSV-----TMKHKGFAFVEYEVPEAAQL 85
Query: 116 VADAMHGYLLFEHILQVHLIPPEHVHLKLWRGFNC-QYKP-LDWVEVECKRLNKVRTLEE 173
+ M+ +L ++K+ R N Q +P +D + E + N++
Sbjct: 86 ALEQMNSVMLGGR------------NIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASV 133
Query: 174 HKKLMEKILKHDQKRRKRIEAASI 197
H+ L + +K + +I++A++
Sbjct: 134 HQDLSDDDIKSVFEAFGKIKSATL 157
Score = 40.8 bits (94), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 26/98 (26%), Positives = 47/98 (47%), Gaps = 10/98 (10%)
Query: 42 KLPEEKPLVNKAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKH 101
+L EE N+ +Y+ + + ++ + F FG IK +AR+ TGK K
Sbjct: 117 QLAEEARAFNR---IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDP-----TTGKHKG 168
Query: 102 FGFIEFNDPEVAEVVADAMHGYLLFEHILQV--HLIPP 137
+GFIE+ + ++ +M+ + L L+V + PP
Sbjct: 169 YGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPP 206
>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
pdb|4F02|D Chain D, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
Length = 213
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 32/114 (28%), Positives = 54/114 (47%), Gaps = 11/114 (9%)
Query: 16 VSSQLPVSSDRK-DAADFLPLEGGPGRKL-PEEKPLVNKAAV--LYIGRIRHGFYEKEMH 71
V+ Q P ++R D +F ++G P R + + P + K+ V ++I + K ++
Sbjct: 62 VNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALY 121
Query: 72 AFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEVVADAMHGYLL 125
FS FG I ++ V + SK +GF+ F E AE + M+G LL
Sbjct: 122 DTFSAFGNILSCKV-------VCDENGSKGYGFVHFETQEAAERAIEKMNGMLL 168
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 41/83 (49%), Gaps = 5/83 (6%)
Query: 55 VLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAE 114
VLY+G + +K +HA F FG I ++I + + T K + F F+EF E A
Sbjct: 14 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYE-----TEKHRGFAFVEFELAEDAA 68
Query: 115 VVADAMHGYLLFEHILQVHLIPP 137
D M+ LF ++V+L P
Sbjct: 69 AAIDNMNESELFGRTIRVNLAKP 91
>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 = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 26/98 (26%), Positives = 47/98 (47%), Gaps = 10/98 (10%)
Query: 42 KLPEEKPLVNKAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKH 101
+L EE N+ +Y+ + + ++ + F FG IK +AR+ TGK K
Sbjct: 102 QLAEEARAFNR---IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDP-----TTGKHKG 153
Query: 102 FGFIEFNDPEVAEVVADAMHGYLLFEHILQV--HLIPP 137
+GFIE+ + ++ +M+ + L L+V + PP
Sbjct: 154 YGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPP 191
Score = 40.4 bits (93), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 31/131 (23%), Positives = 59/131 (45%), Gaps = 19/131 (14%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEV 115
+Y+G I + E + F+ FG IK + ++ + T K K F F+E+ PE A++
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSV-----TMKHKGFAFVEYEVPEAAQL 70
Query: 116 VADAMHGYLLFEHILQVHLIPPEHVHLKLWRGFNC-QYKP-LDWVEVECKRLNKVRTLEE 173
+ M+ +L ++K+ R N Q +P +D + E + N++
Sbjct: 71 ALEQMNSVMLGGR------------NIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASV 118
Query: 174 HKKLMEKILKH 184
H+ L + +K
Sbjct: 119 HQDLSDDDIKS 129
>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 = 40.4 bits (93), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 42/86 (48%), Gaps = 11/86 (12%)
Query: 42 KLPEEKPLVNKAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKH 101
+L EE N+ +Y+ + + ++ + F FG IK +AR+ TGK K
Sbjct: 101 QLAEEARAFNR---IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDP-----TTGKHKG 152
Query: 102 FGFIEFNDPEVAEVVADAMHGYLLFE 127
+GFIE+ E A+ DA+ LF+
Sbjct: 153 YGFIEY---EKAQSSQDAVSSXNLFD 175
Score = 36.6 bits (83), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 33/130 (25%), Positives = 56/130 (43%), Gaps = 19/130 (14%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEV 115
+Y+G I + E + F+ FG IK + + + T K K F F+E+ PE A+
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSV-----TXKHKGFAFVEYEVPEAAQ- 68
Query: 116 VADAMHGYLLFEHILQVHLIPPEHVHLKLWRGFNC-QYKP-LDWVEVECKRLNKVRTLEE 173
L E V L ++K+ R N Q +P +D + E + N++
Sbjct: 69 --------LALEQXNSVXL---GGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASV 117
Query: 174 HKKLMEKILK 183
H+ L + +K
Sbjct: 118 HQDLSDDDIK 127
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 40.4 bits (93), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 43/84 (51%), Gaps = 6/84 (7%)
Query: 53 AAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIAR--NKKLRVLNTGKSKHFGFIEFNDP 110
++ L+I + E+ + FS+ G IK I++ NK +L+ G FGF+E+ P
Sbjct: 5 SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMG----FGFVEYKKP 60
Query: 111 EVAEVVADAMHGYLLFEHILQVHL 134
E A+ + G+ + H L+V +
Sbjct: 61 EQAQKALKQLQGHTVDGHKLEVRI 84
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 40.4 bits (93), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 19/88 (21%), Positives = 40/88 (45%), Gaps = 5/88 (5%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEV 115
L + + + E + F G I+ ++ R+K TG+S +GF+ ++DP A+
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKI-----TGQSLGYGFVNYSDPNDADK 61
Query: 116 VADAMHGYLLFEHILQVHLIPPEHVHLK 143
+ ++G L ++V P ++
Sbjct: 62 AINTLNGLKLQTKTIKVSYARPSSASIR 89
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 40.4 bits (93), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 40/80 (50%), Gaps = 5/80 (6%)
Query: 55 VLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAE 114
VLY+G + +K +HA F FG I ++I + + T K + F F+EF E A
Sbjct: 65 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYE-----TEKHRGFAFVEFELAEDAA 119
Query: 115 VVADAMHGYLLFEHILQVHL 134
D M+ LF ++V+L
Sbjct: 120 AAIDNMNESELFGRTIRVNL 139
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/88 (21%), Positives = 40/88 (45%), Gaps = 5/88 (5%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEV 115
L + + + E + F G I+ ++ R+K TG+S +GF+ ++DP A+
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKI-----TGQSLGYGFVNYSDPNDADK 61
Query: 116 VADAMHGYLLFEHILQVHLIPPEHVHLK 143
+ ++G L ++V P ++
Sbjct: 62 AINTLNGLKLQTKTIKVSYARPSSASIR 89
Score = 35.8 bits (81), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 33/69 (47%), Gaps = 5/69 (7%)
Query: 54 AVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVA 113
A LY+ + +KEM FSQ+G I RI ++ TG S+ GFI F+ A
Sbjct: 91 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQA-----TGVSRGVGFIRFDKRIEA 145
Query: 114 EVVADAMHG 122
E ++G
Sbjct: 146 EEAIKGLNG 154
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 46/85 (54%), Gaps = 16/85 (18%)
Query: 38 GPGRKLPEEKPLVNKAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTG 97
G G+ +P +++G I E E+ +FF+++G++K ++I ++ TG
Sbjct: 4 GSGKIMPN---------TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR------TG 48
Query: 98 KSKHFGFIEF-NDPEVAEVVADAMH 121
SK +GF+ F ND +V ++V ++
Sbjct: 49 VSKGYGFVSFYNDVDVQKIVESQIN 73
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 37/67 (55%), Gaps = 6/67 (8%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPE-VAE 114
L++G + ++ + ++FSQ+G + I ++K T +S+ FGF++F DP V
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDK-----TTNQSRGFGFVKFKDPNCVGT 73
Query: 115 VVADAMH 121
V+A H
Sbjct: 74 VLASRPH 80
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 28/102 (27%), Positives = 43/102 (42%), Gaps = 7/102 (6%)
Query: 37 GGPGRKLPEEKPLVNKAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNT 96
G G P + N A + + + E ++ F FG+I R+ +A++K T
Sbjct: 1 GSSGSSGPNRRADDN--ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDK-----TT 53
Query: 97 GKSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPE 138
G+SK F FI F+ E A + G+ IL V P
Sbjct: 54 GQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPS 95
>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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/88 (22%), Positives = 41/88 (46%), Gaps = 5/88 (5%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEV 115
L + + ++E + F G I+ ++ R+K TG+S +GF+ + DP+ AE
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKI-----TGQSLGYGFVNYIDPKDAEK 59
Query: 116 VADAMHGYLLFEHILQVHLIPPEHVHLK 143
+ ++G L ++V P ++
Sbjct: 60 AINTLNGLRLQTKTIKVSYARPSSASIR 87
Score = 33.5 bits (75), Expect = 0.095, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 5/69 (7%)
Query: 54 AVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVA 113
A LY+ + +KE+ FSQ+G I RI ++ TG S+ GFI F+ A
Sbjct: 89 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQV-----TGVSRGVGFIRFDKRIEA 143
Query: 114 EVVADAMHG 122
E ++G
Sbjct: 144 EEAIKGLNG 152
>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 = 0.002, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 40/86 (46%), Gaps = 11/86 (12%)
Query: 53 AAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEV 112
A ++G + +K++ +F++FG + I + NTG+S+ FGFI F D
Sbjct: 11 AGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDP-----NTGRSRGFGFILFKDAAS 65
Query: 113 AEVVADAMHGYLLFEHILQVHLIPPE 138
E V D EH L +I P+
Sbjct: 66 VEKVLDQK------EHRLDGRVIDPK 85
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 40/80 (50%), Gaps = 5/80 (6%)
Query: 55 VLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAE 114
VLY+G + +K +HA F FG I ++I + + T K + F F+EF E A
Sbjct: 4 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYE-----TEKHRGFAFVEFELAEDAA 58
Query: 115 VVADAMHGYLLFEHILQVHL 134
D M+ LF ++V+L
Sbjct: 59 AAIDNMNESELFGRTIRVNL 78
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 40/80 (50%), Gaps = 5/80 (6%)
Query: 55 VLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAE 114
VLY+G + +K +HA F FG I ++I + + T K + F F+EF E A
Sbjct: 9 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYE-----TEKHRGFAFVEFELAEDAA 63
Query: 115 VVADAMHGYLLFEHILQVHL 134
D M+ LF ++V+L
Sbjct: 64 AAIDNMNESELFGRTIRVNL 83
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
Length = 124
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 6/73 (8%)
Query: 35 LEGGPGRKLPEEKPLVNKAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVL 94
EG P EEK ++K +V Y+G + +G +++ A FS G+I R+ I +K
Sbjct: 19 TEGPPQPLSAEEKKEIDKRSV-YVGNVDYGSTAQDLEAHFSSCGSINRITILCDK----- 72
Query: 95 NTGKSKHFGFIEF 107
+G K + +IEF
Sbjct: 73 FSGHPKGYAYIEF 85
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 40/80 (50%), Gaps = 5/80 (6%)
Query: 55 VLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAE 114
VLY+G + +K +HA F FG I ++I + + T K + F F+EF E A
Sbjct: 7 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYE-----TEKHRGFAFVEFELAEDAA 61
Query: 115 VVADAMHGYLLFEHILQVHL 134
D M+ LF ++V+L
Sbjct: 62 AAIDNMNESELFGRTIRVNL 81
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 10/79 (12%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEV 115
+Y+G + G + E+ FS +G ++ + IARN F F+EF DP AE
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----------PPGFAFVEFEDPRDAED 52
Query: 116 VADAMHGYLLFEHILQVHL 134
+ G ++ ++V L
Sbjct: 53 AVRGLDGKVICGSRVRVEL 71
>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 84
Score = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 5/78 (6%)
Query: 55 VLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAE 114
V+Y+G I + E+++ S G + L++ + + TG+SK + FIEF D E +
Sbjct: 6 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQ-----TGRSKGYAFIEFRDLESSA 60
Query: 115 VVADAMHGYLLFEHILQV 132
++GY L L+
Sbjct: 61 SAVRNLNGYQLGSRFLKC 78
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 37.7 bits (86), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 5/78 (6%)
Query: 55 VLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAE 114
V+Y+G I + E+++ S G + L++ + + TG+SK + FIEF D E +
Sbjct: 4 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQ-----TGRSKGYAFIEFRDLESSA 58
Query: 115 VVADAMHGYLLFEHILQV 132
++GY L L+
Sbjct: 59 SAVRNLNGYQLGSRFLKC 76
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 4/81 (4%)
Query: 53 AAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEV 112
++ ++IG + EK ++ FS FG I + K +R +TG SK + FI F +
Sbjct: 5 SSGIFIGNLDPEIDEKLLYDTFSAFGVI----LQTPKIMRDPDTGNSKGYAFINFASFDA 60
Query: 113 AEVVADAMHGYLLFEHILQVH 133
++ +AM+G L + V
Sbjct: 61 SDAAIEAMNGQYLCNRPITVS 81
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 37.4 bits (85), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 6/77 (7%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEV 115
L+IG + EK + A F + G I + + +++ T KS+ F FI F +P A+
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR------TSKSRGFAFITFENPADAKN 63
Query: 116 VADAMHGYLLFEHILQV 132
A M+G L ++V
Sbjct: 64 AAKDMNGKSLHGKAIKV 80
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 37.4 bits (85), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 29/66 (43%), Gaps = 6/66 (9%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEV 115
L+IG I E ++ FS FG I+ RI R G S+ F+ F +A+
Sbjct: 110 LFIGMISKKCTENDIRVMFSSFGQIEECRILRGPD------GLSRGCAFVTFTTRAMAQT 163
Query: 116 VADAMH 121
AMH
Sbjct: 164 AIKAMH 169
Score = 33.5 bits (75), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 17/69 (24%), Positives = 35/69 (50%), Gaps = 3/69 (4%)
Query: 53 AAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEV 112
A +++G++ + EK++ F Q+G + + + R+ R N +SK F+ F +
Sbjct: 15 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRD---RSQNPPQSKGCCFVTFYTRKA 71
Query: 113 AEVVADAMH 121
A +A+H
Sbjct: 72 ALEAQNALH 80
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 37.4 bits (85), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 29/66 (43%), Gaps = 6/66 (9%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEV 115
L+IG I E ++ FS FG I+ RI R G S+ F+ F +A+
Sbjct: 98 LFIGMISKKCTENDIRVMFSSFGQIEECRILRGPD------GLSRGCAFVTFTTRAMAQT 151
Query: 116 VADAMH 121
AMH
Sbjct: 152 AIKAMH 157
Score = 33.1 bits (74), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 36/71 (50%), Gaps = 3/71 (4%)
Query: 51 NKAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDP 110
+ A +++G++ + EK++ F Q+G + + + R+ R N +SK F+ F
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRD---RSQNPPQSKGCCFVTFYTR 57
Query: 111 EVAEVVADAMH 121
+ A +A+H
Sbjct: 58 KAALEAQNALH 68
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 5/78 (6%)
Query: 55 VLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAE 114
V+Y+G I + E+++ S G + L++ + + TG+SK + FIEF D E +
Sbjct: 5 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQ-----TGRSKGYAFIEFRDLESSA 59
Query: 115 VVADAMHGYLLFEHILQV 132
++GY L L+
Sbjct: 60 SAVRNLNGYQLGSRFLKC 77
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 36.6 bits (83), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 35/62 (56%), Gaps = 5/62 (8%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEV 115
+Y+G + + +++ FSQFG + +++ +++ T K K FGF+E + V+E
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRE-----TKKPKGFGFVEMQEESVSEA 58
Query: 116 VA 117
+A
Sbjct: 59 IA 60
>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 = 36.6 bits (83), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 43/83 (51%), Gaps = 5/83 (6%)
Query: 52 KAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPE 111
+ A L+I + F ++++ F FG + ++ +K+ + SK FGF+ +++P
Sbjct: 24 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNL-----SKCFGFVSYDNPV 78
Query: 112 VAEVVADAMHGYLLFEHILQVHL 134
A+ +M+G+ + L+V L
Sbjct: 79 SAQAAIQSMNGFQIGMKRLKVQL 101
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 36.6 bits (83), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 18/81 (22%), Positives = 40/81 (49%), Gaps = 5/81 (6%)
Query: 54 AVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVA 113
+ +Y+ + +++ FS++G + ++ I ++K R KSK FI F D + A
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTR-----KSKGVAFILFLDKDSA 71
Query: 114 EVVADAMHGYLLFEHILQVHL 134
+ A++ LF +++ +
Sbjct: 72 QNCTRAINNKQLFGRVIKASI 92
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 36.2 bits (82), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 43/87 (49%), Gaps = 6/87 (6%)
Query: 48 PLVNKAA-VLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIE 106
P V+++ +++G I + E+++ FS+ G + R+ +++ TGK K +GF E
Sbjct: 2 PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRE-----TGKPKGYGFCE 56
Query: 107 FNDPEVAEVVADAMHGYLLFEHILQVH 133
+ D E A ++G L+V
Sbjct: 57 YQDQETALSAMRNLNGREFSGRALRVD 83
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 35.4 bits (80), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 33/69 (47%), Gaps = 5/69 (7%)
Query: 54 AVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVA 113
A LY+ + +KEM FSQ+G I RI ++ TG S+ GFI F+ A
Sbjct: 2 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQA-----TGVSRGVGFIRFDKRIEA 56
Query: 114 EVVADAMHG 122
E ++G
Sbjct: 57 EEAIKGLNG 65
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 35.4 bits (80), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 5/59 (8%)
Query: 53 AAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPE 111
A +Y+G + +G +E+ A F G++ R+ I +K +G K F +IEF+D E
Sbjct: 5 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDK-----FSGHPKGFAYIEFSDKE 58
>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 = 35.4 bits (80), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 5/70 (7%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEV 115
+++G + +++ A F+ FG I R+ ++ + TGKSK +GF+ F + AE
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKD-----MATGKSKGYGFVSFFNKWDAEN 72
Query: 116 VADAMHGYLL 125
M G L
Sbjct: 73 AIQQMGGQWL 82
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 35.4 bits (80), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 37/80 (46%), Gaps = 9/80 (11%)
Query: 48 PLVNKAAV--LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFI 105
P + K+ V ++I + K ++ FS FG I ++ V + SK +GF+
Sbjct: 4 PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKV-------VCDENGSKGYGFV 56
Query: 106 EFNDPEVAEVVADAMHGYLL 125
F E AE + M+G LL
Sbjct: 57 HFETQEAAERAIEKMNGMLL 76
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 35.0 bits (79), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 9/72 (12%)
Query: 74 FSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH 133
F ++G + + I R++ T +S+ F F+ F+D AE DAM G +L L+V
Sbjct: 91 FEKYGRVGDVYIPRDRY-----TKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQ 145
Query: 134 LI----PPEHVH 141
+ PP+ H
Sbjct: 146 MARYGRPPDSHH 157
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of Hypothetical
Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens
At 1.95 A Resolution
Length = 89
Score = 35.0 bits (79), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 5/59 (8%)
Query: 53 AAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPE 111
A +Y+G + +G +E+ A F G++ R+ I +K +G K F +IEF+D E
Sbjct: 6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKF-----SGHPKGFAYIEFSDKE 59
>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 = 35.0 bits (79), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 42/85 (49%), Gaps = 11/85 (12%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEV 115
++IG + +K++ +FS+FG + + KL + TG+S+ FGF+ F + E +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTL----KLDPI-TGRSRGFGFVLFKESESVDK 56
Query: 116 VADAMHGYLLFEHILQVHLIPPEHV 140
V D EH L +I P+
Sbjct: 57 VMDQK------EHKLNGKVIDPKRA 75
>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 = 35.0 bits (79), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 25/98 (25%), Positives = 43/98 (43%), Gaps = 9/98 (9%)
Query: 48 PLVNKAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEF 107
P V L + + + + F ++G + + I R++ T +S+ F F+ F
Sbjct: 42 PDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRY-----TKESRGFAFVRF 96
Query: 108 NDPEVAEVVADAMHGYLLFEHILQVHLI----PPEHVH 141
+D AE DAM G +L L+V + PP+ H
Sbjct: 97 HDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDSHH 134
>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|C Chain C, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|B Chain B, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|D Chain D, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
Length = 88
Score = 34.3 bits (77), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 36/72 (50%), Gaps = 3/72 (4%)
Query: 51 NKAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDP 110
+ A +++G++ + EK++ F Q+G + + + R+ R N +SK F+ F
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRD---RSQNPPQSKGCCFVTFYTR 57
Query: 111 EVAEVVADAMHG 122
+ A +A+H
Sbjct: 58 KAALEAQNALHN 69
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 34.3 bits (77), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 26/110 (23%), Positives = 48/110 (43%), Gaps = 13/110 (11%)
Query: 23 SSDRKDAADFLPLEGGPGRKLPEEKPLVNKAAVLYIGRIRHGFYEKEMHAFFSQFGTIKR 82
S +R D LE GP R + + +L++ I E E+ F +G IK
Sbjct: 4 SYERVRNEDDDELEPGPQRSV--------EGWILFVTSIHEEAQEDEIQEKFCDYGEIKN 55
Query: 83 LRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV 132
+ + +++ TG SK + +E+ + A +A++G + +QV
Sbjct: 56 IHLNLDRR-----TGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV 100
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 34.3 bits (77), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 5/75 (6%)
Query: 47 KPLVNKAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIE 106
K V K + L + + E+++ +FS FG + +++ ++ L TG SK FGF+
Sbjct: 9 KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKD-----LKTGHSKGFGFVR 63
Query: 107 FNDPEVAEVVADAMH 121
F + E V H
Sbjct: 64 FTEYETQVKVMSQRH 78
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 33.9 bits (76), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 39/80 (48%), Gaps = 6/80 (7%)
Query: 43 LPEEKPLVNKAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHF 102
+P + + ++IG + ++ + +F QFG +K + R+ T +S+ F
Sbjct: 15 VPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPL-----TKRSRGF 69
Query: 103 GFIEFND-PEVAEVVADAMH 121
GF+ F D V +V+A + H
Sbjct: 70 GFVTFMDQAGVDKVLAQSRH 89
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 33.9 bits (76), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 18/79 (22%), Positives = 37/79 (46%), Gaps = 6/79 (7%)
Query: 55 VLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAE 114
+++G + E+ ++ F Q G + ++ I ++++ GK K FGF+ F PE
Sbjct: 18 TVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE------GKPKSFGFVCFKHPESVS 71
Query: 115 VVADAMHGYLLFEHILQVH 133
++G L+ + V
Sbjct: 72 YAIALLNGIRLYGRPINVS 90
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 33.9 bits (76), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 21/87 (24%), Positives = 37/87 (42%), Gaps = 8/87 (9%)
Query: 48 PLVNKAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEF 107
P N +Y+G + K++ F ++G I+ + + +N++ F F+EF
Sbjct: 17 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL-KNRR-------GGPPFAFVEF 68
Query: 108 NDPEVAEVVADAMHGYLLFEHILQVHL 134
DP AE GY + L+V
Sbjct: 69 EDPRDAEDAVYGRDGYDYDGYRLRVEF 95
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 33.5 bits (75), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 37/67 (55%), Gaps = 5/67 (7%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEV 115
L++G + E+ + FS++G I + + ++++ T +S+ FGF+ F + + A+
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRE-----TQRSRGFGFVTFENIDDAKD 69
Query: 116 VADAMHG 122
AM+G
Sbjct: 70 AMMAMNG 76
>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 = 33.5 bits (75), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 21/89 (23%), Positives = 45/89 (50%), Gaps = 5/89 (5%)
Query: 44 PEEKPLVNKAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFG 103
E++ L+ K+ LY+G + E++++ FS+ G IK++ + +K + + F
Sbjct: 30 EEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKT-----ACGFC 84
Query: 104 FIEFNDPEVAEVVADAMHGYLLFEHILQV 132
F+E+ AE ++G L + I++
Sbjct: 85 FVEYYSRADAENAMRYINGTRLDDRIIRT 113
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 33.5 bits (75), Expect = 0.091, Method: Compositional matrix adjust.
Identities = 21/89 (23%), Positives = 43/89 (48%), Gaps = 6/89 (6%)
Query: 44 PEEKPLVNKAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFG 103
E++ L+ K+ LY+G + E++++ FS+ G IK++ + +K F
Sbjct: 9 EEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACG------FC 62
Query: 104 FIEFNDPEVAEVVADAMHGYLLFEHILQV 132
F+E+ AE ++G L + I++
Sbjct: 63 FVEYYSRADAENAMRYINGTRLDDRIIRT 91
>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
At Ph 6.0
pdb|4F26|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
A Ph 9.0
Length = 115
Score = 33.5 bits (75), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 32/70 (45%), Gaps = 7/70 (10%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEV 115
++I + K ++ FS FG I ++ V + SK +GF+ F E AE
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKV-------VCDENGSKGYGFVHFETQEAAER 60
Query: 116 VADAMHGYLL 125
+ M+G LL
Sbjct: 61 AIEKMNGMLL 70
>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 = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 27/66 (40%), Gaps = 6/66 (9%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEV 115
L+IG I E ++ FS FG I+ RI R G S+ F+ F A+
Sbjct: 98 LFIGXISKKCTENDIRVXFSSFGQIEECRILRGPD------GLSRGCAFVTFTTRAXAQT 151
Query: 116 VADAMH 121
A H
Sbjct: 152 AIKAXH 157
Score = 32.0 bits (71), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 16/65 (24%), Positives = 33/65 (50%), Gaps = 3/65 (4%)
Query: 57 YIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEVV 116
++G++ + EK++ F Q+G + + + R+ R N +SK F+ F + A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRD---RSQNPPQSKGCCFVTFYTRKAALEA 63
Query: 117 ADAMH 121
+A+H
Sbjct: 64 QNALH 68
>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1HL6|C Chain C, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1RK8|A Chain A, Structure Of The Cytosolic Protein Pym Bound To The Mago-
Y14 Core Of The Exon Junction Complex
pdb|2X1G|A Chain A, Crystal Structure Of Importin13 - Mago-Y14 Complex
pdb|2X1G|C Chain C, Crystal Structure Of Importin13 - Mago-Y14 Complex
Length = 165
Score = 33.1 bits (74), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 24/102 (23%), Positives = 45/102 (44%), Gaps = 13/102 (12%)
Query: 31 DFLPLEGGPGRKLPEEKPLVNKAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKK 90
D LE GP R + + +L++ I E E+ F +G IK + + +++
Sbjct: 58 DDDELEPGPQRSV--------EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRR 109
Query: 91 LRVLNTGKSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV 132
TG SK + +E+ + A +A++G + +QV
Sbjct: 110 -----TGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV 146
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 33.1 bits (74), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 7/70 (10%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEV 115
L++ I F + ++ F QFG I + I + N SK FGF+ F + A+
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEI-------IFNERGSKGFGFVTFENSADADR 84
Query: 116 VADAMHGYLL 125
+ +HG ++
Sbjct: 85 AREKLHGTVV 94
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 33.1 bits (74), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 7/78 (8%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEV 115
L++ I F + ++ F QFG I + I + N SK FGF+ F + A+
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEI-------IFNERGSKGFGFVTFENSADADR 70
Query: 116 VADAMHGYLLFEHILQVH 133
+ +HG ++ ++V+
Sbjct: 71 AREKLHGTVVEGRKIEVN 88
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 33.1 bits (74), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 40/85 (47%), Gaps = 10/85 (11%)
Query: 37 GGPGRKLPEEKPLVNKAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNT 96
G G P + +K L++ + E+ + F G++ R RI +++ T
Sbjct: 1 GSSGSSGPNARSQPSK--TLFVKGLSEDTTEETLKESFD--GSV-RARIVTDRE-----T 50
Query: 97 GKSKHFGFIEFNDPEVAEVVADAMH 121
G SK FGF++FN E A+ +AM
Sbjct: 51 GSSKGFGFVDFNSEEDAKAAKEAME 75
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 32.7 bits (73), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 39/84 (46%), Gaps = 12/84 (14%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDP-EVAE 114
+Y+G + + + E+ F +G ++ + +ARN F F+EF DP + A+
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARN----------PPGFAFVEFEDPRDAAD 125
Query: 115 VVADAMHGYLLFEHILQVHLIPPE 138
V D + G L ++V L E
Sbjct: 126 AVRD-LDGRTLCGCRVRVELSNGE 148
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 32.7 bits (73), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 35/83 (42%), Gaps = 10/83 (12%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEV 115
+Y+G + + + E+ F +G ++ + +ARN F F+EF DP A
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARN----------PPGFAFVEFEDPRDAAD 125
Query: 116 VADAMHGYLLFEHILQVHLIPPE 138
+ G L ++V L E
Sbjct: 126 AVRELDGRTLCGCRVRVELSNGE 148
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 32.3 bits (72), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 20/85 (23%), Positives = 42/85 (49%), Gaps = 10/85 (11%)
Query: 48 PLVNKAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEF 107
P VN+ +LYI + + +EM+ F ++G I+++R+ NT +++ ++ +
Sbjct: 15 PEVNR--ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVG--------NTPETRGTAYVVY 64
Query: 108 NDPEVAEVVADAMHGYLLFEHILQV 132
D A+ D + G+ + L V
Sbjct: 65 EDIFDAKNACDHLSGFNVCNRYLVV 89
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 32.3 bits (72), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 5/69 (7%)
Query: 53 AAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEV 112
A L+IG+I EK++ F +FG I L + +++ TG K F+ + + E
Sbjct: 13 AIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDR-----FTGMHKGCAFLTYCERES 67
Query: 113 AEVVADAMH 121
A A+H
Sbjct: 68 ALKAQSALH 76
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 32.3 bits (72), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 35/67 (52%), Gaps = 6/67 (8%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPE-VAE 114
++IG + ++ + +F QFG +K + R+ T +S+ FGF+ F D V +
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPL-----TKRSRGFGFVTFMDQAGVDK 57
Query: 115 VVADAMH 121
V+A + H
Sbjct: 58 VLAQSRH 64
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 32.3 bits (72), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 35/70 (50%), Gaps = 5/70 (7%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEV 115
+++G + +++ + F+ FG I R+ ++ + TGKSK +GF+ F + AE
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKD-----MATGKSKGYGFVSFYNKLDAEN 72
Query: 116 VADAMHGYLL 125
M G L
Sbjct: 73 AIVHMGGQWL 82
>pdb|1W63|M Chain M, Ap1 Clathrin Adaptor Core
pdb|1W63|N Chain N, Ap1 Clathrin Adaptor Core
pdb|1W63|O Chain O, Ap1 Clathrin Adaptor Core
pdb|1W63|P Chain P, Ap1 Clathrin Adaptor Core
pdb|1W63|R Chain R, Ap1 Clathrin Adaptor Core
pdb|1W63|V Chain V, Ap1 Clathrin Adaptor Core
Length = 423
Score = 32.3 bits (72), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 33/135 (24%), Positives = 57/135 (42%), Gaps = 19/135 (14%)
Query: 69 EMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEVVADAMHGYLLFEH 128
+M F S + LR+ N K+ NTG+ K +E D + + V + FE+
Sbjct: 199 KMRVFLS---GMPELRLGLNDKVLFDNTGRGKSKS-VELEDVKFHQCVRLSR-----FEN 249
Query: 129 ILQVHLIPPEHVHLKLWRGFNCQYKPLDWVEVECKRLNKVRTLEEHK-KLMEKILKHDQK 187
+ IPP+ + N KPL W+E +E+H +E ++K +
Sbjct: 250 DRTISFIPPDGEFELMSYRLNTHVKPLIWIE---------SVIEKHSHSRIEYMVKAKSQ 300
Query: 188 RRKRIEAASIEYECP 202
++R A ++E P
Sbjct: 301 FKRRSTANNVEIHIP 315
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 32.3 bits (72), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 5/74 (6%)
Query: 50 VNKAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFND 109
V K A LYI + +K++ FS+FG RI ++ L TG S+ FI F+
Sbjct: 85 VIKDANLYISGLPRTMTQKDVEDMFSRFG-----RIINSRVLVDQTTGLSRGVAFIRFDK 139
Query: 110 PEVAEVVADAMHGY 123
AE + +G+
Sbjct: 140 RSEAEEAITSFNGH 153
>pdb|4EN2|M Chain M, Hiv-1 Nef In Complex With Mhc-I Cytoplasmic Domain And Mu1
Adaptin Subunit Of Ap1 Adaptor (Second Domain)
pdb|4EN2|A Chain A, Hiv-1 Nef In Complex With Mhc-I Cytoplasmic Domain And Mu1
Adaptin Subunit Of Ap1 Adaptor (Second Domain)
Length = 266
Score = 32.3 bits (72), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 33/135 (24%), Positives = 57/135 (42%), Gaps = 19/135 (14%)
Query: 69 EMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEVVADAMHGYLLFEH 128
+M F S + LR+ N K+ NTG+ K +E D + + V + FE+
Sbjct: 42 KMRVFLS---GMPELRLGLNDKVLFDNTGRGKSKS-VELEDVKFHQCVRLSR-----FEN 92
Query: 129 ILQVHLIPPEHVHLKLWRGFNCQYKPLDWVEVECKRLNKVRTLEEHK-KLMEKILKHDQK 187
+ IPP+ + N KPL W+E +E+H +E ++K +
Sbjct: 93 DRTISFIPPDGEFELMSYRLNTHVKPLIWIE---------SVIEKHSHSRIEYMVKAKSQ 143
Query: 188 RRKRIEAASIEYECP 202
++R A ++E P
Sbjct: 144 FKRRSTANNVEIHIP 158
>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 = 32.3 bits (72), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 5/74 (6%)
Query: 50 VNKAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFND 109
V K A LYI + +K++ FS+FG RI ++ L TG S+ FI F+
Sbjct: 85 VIKDANLYISGLPRTMTQKDVEDMFSRFG-----RIINSRVLVDQTTGLSRGVAFIRFDK 139
Query: 110 PEVAEVVADAMHGY 123
AE + +G+
Sbjct: 140 RSEAEEAITSFNGH 153
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 32.3 bits (72), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 36/79 (45%), Gaps = 6/79 (7%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEV 115
L+I + ++E+ GT+K LR+ N+ GK K ++E+ + A
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR------AGKPKGLAYVEYENESQASQ 73
Query: 116 VADAMHGYLLFEHILQVHL 134
M G + E+I++V +
Sbjct: 74 AVMKMDGMTIKENIIKVAI 92
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 32.0 bits (71), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 14/54 (25%), Positives = 29/54 (53%), Gaps = 5/54 (9%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFND 109
+++G I+ E + +F Q+G I+ + I ++ +GK + F F+ F+D
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR-----GSGKKRGFAFVTFDD 155
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 32.0 bits (71), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 14/54 (25%), Positives = 29/54 (53%), Gaps = 5/54 (9%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFND 109
+++G I+ E + +F Q+G I+ + I ++ +GK + F F+ F+D
Sbjct: 105 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR-----GSGKKRGFAFVTFDD 153
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 32.0 bits (71), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 23/95 (24%), Positives = 47/95 (49%), Gaps = 16/95 (16%)
Query: 43 LPEEKPLVNKAAVLYIG----RIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGK 98
+PE +P +YI +I+ +K ++A FSQFG I + ++R+ K+R G+
Sbjct: 2 VPETRP----NHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMR----GQ 53
Query: 99 SKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH 133
+ F+ F + A +M G+ ++ +++
Sbjct: 54 A----FVIFKEVSSATNALRSMQGFPFYDKPMRIQ 84
>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 = 32.0 bits (71), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 14/54 (25%), Positives = 29/54 (53%), Gaps = 5/54 (9%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFND 109
+++G I+ E + +F Q+G I+ + I ++ +GK + F F+ F+D
Sbjct: 100 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR-----GSGKKRGFAFVTFDD 148
>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 = 32.0 bits (71), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 23/95 (24%), Positives = 47/95 (49%), Gaps = 16/95 (16%)
Query: 43 LPEEKPLVNKAAVLYIG----RIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGK 98
+PE +P +YI +I+ +K +HA FS+FG I + ++R+ K+R G+
Sbjct: 3 VPETRP----NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR----GQ 54
Query: 99 SKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH 133
+ F+ F + A +M G+ ++ +++
Sbjct: 55 A----FVIFKEVSSATNALRSMQGFPFYDKPMRIQ 85
>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 = 32.0 bits (71), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 14/54 (25%), Positives = 29/54 (53%), Gaps = 5/54 (9%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFND 109
+++G I+ E + +F Q+G I+ + I ++ +GK + F F+ F+D
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR-----GSGKKRGFAFVTFDD 155
>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 = 32.0 bits (71), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 14/54 (25%), Positives = 29/54 (53%), Gaps = 5/54 (9%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFND 109
+++G I+ E + +F Q+G I+ + I ++ +GK + F F+ F+D
Sbjct: 106 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR-----GSGKKRGFAFVTFDD 154
>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 = 32.0 bits (71), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 23/95 (24%), Positives = 46/95 (48%), Gaps = 16/95 (16%)
Query: 43 LPEEKPLVNKAAVLYIG----RIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGK 98
+PE +P +YI +I+ +K +HA FS+FG I + ++R+ K+R G+
Sbjct: 3 VPETRP----NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR----GQ 54
Query: 99 SKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH 133
F+ F + A +M G+ ++ +++
Sbjct: 55 ----AFVIFKEVSSATNALRSMQGFPFYDKPMRIQ 85
>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 = 32.0 bits (71), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 23/95 (24%), Positives = 47/95 (49%), Gaps = 16/95 (16%)
Query: 43 LPEEKPLVNKAAVLYIG----RIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGK 98
+PE +P +YI +I+ +K +HA FS+FG I + ++R+ K+R G+
Sbjct: 2 VPETRP----NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR----GQ 53
Query: 99 SKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH 133
+ F+ F + A +M G+ ++ +++
Sbjct: 54 A----FVIFKEVSSATNALRSMQGFPFYDKPMRIQ 84
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 32.0 bits (71), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 16/65 (24%), Positives = 31/65 (47%), Gaps = 5/65 (7%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEV 115
LYI ++ G ++++ +G +I K + T K K +GF++F+ P A+
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYG-----KIVSTKAILDKTTNKCKGYGFVDFDSPSAAQK 62
Query: 116 VADAM 120
A+
Sbjct: 63 AVTAL 67
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 32.0 bits (71), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 20/85 (23%), Positives = 42/85 (49%), Gaps = 10/85 (11%)
Query: 48 PLVNKAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEF 107
P VN+ +LYI + + +EM+ F ++G I+++R+ NT +++ ++ +
Sbjct: 5 PEVNR--ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVG--------NTPETRGTAYVVY 54
Query: 108 NDPEVAEVVADAMHGYLLFEHILQV 132
D A+ D + G+ + L V
Sbjct: 55 EDIFDAKNAVDHLSGFNVSNRYLVV 79
>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 = 32.0 bits (71), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 23/95 (24%), Positives = 47/95 (49%), Gaps = 16/95 (16%)
Query: 43 LPEEKPLVNKAAVLYIG----RIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGK 98
+PE +P +YI +I+ +K +HA FS+FG I + ++R+ K+R G+
Sbjct: 2 VPETRP----NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR----GQ 53
Query: 99 SKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH 133
+ F+ F + A +M G+ ++ +++
Sbjct: 54 A----FVIFKEVSSATNALRSMQGFPFYDKPMRIQ 84
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 32.0 bits (71), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 22/93 (23%), Positives = 44/93 (47%), Gaps = 10/93 (10%)
Query: 40 GRKLPEEKPLVNKAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKS 99
GR P VN+ +LYI + + +EM+ F ++G I+++R+ NT ++
Sbjct: 1 GRANIRLPPEVNR--ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVG--------NTPET 50
Query: 100 KHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV 132
+ ++ + D A+ D + G+ + L V
Sbjct: 51 RGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVV 83
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 32.0 bits (71), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 14/54 (25%), Positives = 29/54 (53%), Gaps = 5/54 (9%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFND 109
+++G I+ E + +F Q+G I+ + I ++ +GK + F F+ F+D
Sbjct: 108 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR-----GSGKKRGFAFVTFDD 156
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 32.0 bits (71), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 23/91 (25%), Positives = 41/91 (45%), Gaps = 14/91 (15%)
Query: 51 NKAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDP 110
+ ++ +++GR E E+ FFSQ+G + + I K R F F+ F D
Sbjct: 3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP--KPFRA--------FAFVTFADD 52
Query: 111 EVAEVVADAMHGYLLFEHILQVHLIPPEHVH 141
++A+ ++ G L + VH+ E H
Sbjct: 53 QIAQ----SLCGEDLIIKGISVHISNAEPKH 79
>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 = 31.6 bits (70), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 25/52 (48%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEF 107
LY+G I G E+ M FF+ + L A + + + K+F F+EF
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEF 58
>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 = 31.6 bits (70), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 23/95 (24%), Positives = 47/95 (49%), Gaps = 16/95 (16%)
Query: 43 LPEEKPLVNKAAVLYIG----RIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGK 98
+PE +P +YI +I+ +K +HA FS+FG I + ++R+ K+R G+
Sbjct: 2 VPETRP----NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR----GQ 53
Query: 99 SKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH 133
+ F+ F + A +M G+ ++ +++
Sbjct: 54 A----FVIFKEVSSATNALRSMQGFPFYDKPMRIQ 84
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 31.6 bits (70), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 23/95 (24%), Positives = 47/95 (49%), Gaps = 16/95 (16%)
Query: 43 LPEEKPLVNKAAVLYIG----RIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGK 98
+PE +P +YI +I+ +K ++A FSQFG I + ++R+ K+R G+
Sbjct: 3 VPETRP----NHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMR----GQ 54
Query: 99 SKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH 133
+ F+ F + A +M G+ ++ +++
Sbjct: 55 A----FVIFKEVSSATNALRSMQGFPFYDKPMRIQ 85
>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 = 31.6 bits (70), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 23/94 (24%), Positives = 46/94 (48%), Gaps = 16/94 (17%)
Query: 44 PEEKPLVNKAAVLYIG----RIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKS 99
PE +P +YI +I+ +K +HA FS+FG I + ++R+ K+R G++
Sbjct: 1 PETRP----NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR----GQA 52
Query: 100 KHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH 133
F+ F + A +M G+ ++ +++
Sbjct: 53 ----FVIFKEVSSATNALRSMQGFPFYDKPMRIQ 82
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 31.6 bits (70), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 31/54 (57%), Gaps = 4/54 (7%)
Query: 67 EKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEVVADAM 120
++E+ FS FG +K +R+ + ++ TG + FGF++F + A+ +A+
Sbjct: 29 QREIRELFSTFGELKTVRLPK----KMTGTGAHRGFGFVDFITKQDAKKAFNAL 78
>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 = 31.6 bits (70), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 39/74 (52%), Gaps = 8/74 (10%)
Query: 60 RIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEVVADA 119
+I+ +K ++A FSQFG I + ++R+ K+R G++ F+ F + A +
Sbjct: 20 KIKKDELKKSLYAIFSQFGQILDILVSRSLKMR----GQA----FVIFKEVSSATNALRS 71
Query: 120 MHGYLLFEHILQVH 133
M G+ ++ +++
Sbjct: 72 MQGFPFYDKPMRIQ 85
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 31.2 bits (69), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 12/47 (25%), Positives = 24/47 (51%)
Query: 50 VNKAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNT 96
V A L + + G + ++ F++FGT+K+ + ++ R L T
Sbjct: 32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGT 78
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 30.8 bits (68), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 12/47 (25%), Positives = 24/47 (51%)
Query: 50 VNKAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNT 96
V A L + + G + ++ F++FGT+K+ + ++ R L T
Sbjct: 32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGT 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 = 30.8 bits (68), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 25/52 (48%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEF 107
LY+G I G E+ M FF+ + L A + + + K+F F+EF
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEF 60
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 30.8 bits (68), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 19/82 (23%), Positives = 35/82 (42%), Gaps = 11/82 (13%)
Query: 52 KAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPE 111
K +Y G I G ++ M FS FG I +R+ K + F+ F+ E
Sbjct: 24 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG-----------YSFVRFSTHE 72
Query: 112 VAEVVADAMHGYLLFEHILQVH 133
A +++G + H+++ +
Sbjct: 73 SAAHAIVSVNGTTIEGHVVKCY 94
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 30.8 bits (68), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 25/52 (48%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEF 107
LY+G I G E+ M FF+ + L A + + + K+F F+EF
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEF 58
>pdb|1U2F|A Chain A, Solution Structure Of The First Rna-Binding Domain Of
Hu2af65
Length = 90
Score = 30.8 bits (68), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 25/52 (48%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEF 107
LY+G I G E+ M FF+ + L A + + + K+F F+EF
Sbjct: 4 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEF 55
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 30.8 bits (68), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 21/41 (51%)
Query: 94 LNTGKSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL 134
+ GKSK G ++F PEVAE M+G L + V +
Sbjct: 42 MENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRI 82
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 30.8 bits (68), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 42/89 (47%), Gaps = 14/89 (15%)
Query: 52 KAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPE 111
K VL++ + + E+ + FSQFG ++R++ K K + FI F++ +
Sbjct: 10 KVKVLFVRNLANTVTEEILEKAFSQFGKLERVK-------------KLKDYAFIHFDERD 56
Query: 112 VAEVVADAMHGY-LLFEHILQVHLIPPEH 139
A + M+G L E+I V PP+
Sbjct: 57 GAVKAMEEMNGKDLEGENIEIVFAKPPDQ 85
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 30.8 bits (68), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 30/67 (44%), Gaps = 6/67 (8%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEV 115
L++G + E ++ F FG I+ I R G SK F++++ A+
Sbjct: 18 LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPD------GNSKGCAFVKYSSHAEAQA 71
Query: 116 VADAMHG 122
+A+HG
Sbjct: 72 AINALHG 78
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 30.4 bits (67), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 37/75 (49%), Gaps = 6/75 (8%)
Query: 48 PLVNKAAV-LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIE 106
P+ + A+ L++G+I G E+++ F +FG I L + +++ TG K F+
Sbjct: 9 PMKDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRL-----TGLHKGCAFLT 63
Query: 107 FNDPEVAEVVADAMH 121
+ + A A+H
Sbjct: 64 YCARDSALKAQSALH 78
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 30.4 bits (67), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 21/41 (51%)
Query: 94 LNTGKSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL 134
+ GKSK G ++F PEVAE M+G L + V +
Sbjct: 39 MENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRI 79
>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 = 30.4 bits (67), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 39/74 (52%), Gaps = 8/74 (10%)
Query: 60 RIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEVVADA 119
+I+ +K +HA FS+FG I + ++R+ K+R G++ F+ F + A +
Sbjct: 16 KIKKDELKKSLHAIFSRFGQILDILVSRSLKMR----GQA----FVIFKEVSSATNALRS 67
Query: 120 MHGYLLFEHILQVH 133
M G+ ++ +++
Sbjct: 68 MQGFPFYDKPMRIQ 81
>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 = 30.4 bits (67), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 39/74 (52%), Gaps = 8/74 (10%)
Query: 60 RIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEVVADA 119
+I+ +K +HA FS+FG I + ++R+ K+R G++ F+ F + A +
Sbjct: 15 KIKKDELKKSLHAIFSRFGQILDILVSRSLKMR----GQA----FVIFKEVSSATNALRS 66
Query: 120 MHGYLLFEHILQVH 133
M G+ ++ +++
Sbjct: 67 MQGFPFYDKPMRIQ 80
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 30.4 bits (67), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 22/89 (24%), Positives = 39/89 (43%), Gaps = 14/89 (15%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEV 115
+++GR +E+ FF Q+G + + I + + F F+ F D +VA+
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPK----------PFRAFAFVTFADDKVAQ- 62
Query: 116 VADAMHGYLLFEHILQVHLIPPEHVHLKL 144
++ G L + VH+ E H KL
Sbjct: 63 ---SLCGEDLIIKGISVHISNAEPKHNKL 88
>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 = 30.4 bits (67), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 39/74 (52%), Gaps = 8/74 (10%)
Query: 60 RIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEVVADA 119
+I+ +K +HA FS+FG I + ++R+ K+R G++ F+ F + A +
Sbjct: 14 KIKKDELKKSLHAIFSRFGQILDILVSRSLKMR----GQA----FVIFKEVSSATNALRS 65
Query: 120 MHGYLLFEHILQVH 133
M G+ ++ +++
Sbjct: 66 MQGFPFYDKPMRIQ 79
>pdb|2HZC|A Chain A, Crystal Structure Of The N-terminal Rrm Of The U2af Large
Subunit
Length = 87
Score = 30.4 bits (67), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 25/52 (48%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEF 107
LY+G I G E+ M FF+ + L A + + + K+F F+EF
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEF 60
>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second
Rna-Binding Domain Of Sex-Lethal Determined By
Multidimensional Heteronuclear Magnetic Resonance
Spectroscopy
Length = 97
Score = 30.4 bits (67), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 16/73 (21%), Positives = 34/73 (46%), Gaps = 5/73 (6%)
Query: 52 KAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPE 111
K LY+ + + ++ F ++G+I + I R+K TG+ + F+ +N E
Sbjct: 12 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKL-----TGRPRGVAFVRYNKRE 66
Query: 112 VAEVVADAMHGYL 124
A+ A++ +
Sbjct: 67 EAQEAISALNNVI 79
>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|B Chain B, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|C Chain C, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
Length = 184
Score = 30.0 bits (66), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 16/73 (21%), Positives = 34/73 (46%), Gaps = 5/73 (6%)
Query: 52 KAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPE 111
K LY+ + + ++ F ++G+I + I R+K TG+ + F+ +N E
Sbjct: 99 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKL-----TGRPRGVAFVRYNKRE 153
Query: 112 VAEVVADAMHGYL 124
A+ A++ +
Sbjct: 154 EAQEAISALNNVI 166
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 30.0 bits (66), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 12/47 (25%), Positives = 24/47 (51%)
Query: 50 VNKAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNT 96
V A L + + G + ++ F++FGT+K+ + ++ R L T
Sbjct: 85 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGT 131
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 16/70 (22%), Positives = 33/70 (47%), Gaps = 5/70 (7%)
Query: 52 KAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPE 111
K LY+ + + ++ F ++G+I + I R+K TG+ + F+ +N E
Sbjct: 88 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKL-----TGRPRGVAFVRYNKRE 142
Query: 112 VAEVVADAMH 121
A+ A++
Sbjct: 143 EAQEAISALN 152
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 29.6 bits (65), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 19/83 (22%), Positives = 38/83 (45%), Gaps = 5/83 (6%)
Query: 51 NKAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDP 110
N+ A +Y+G + E + F Q G + + +++ TG+ + +GF+EF
Sbjct: 13 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRV-----TGQHQGYGFVEFLSE 67
Query: 111 EVAEVVADAMHGYLLFEHILQVH 133
E A+ M L+ ++V+
Sbjct: 68 EDADYAIKIMDMIKLYGKPIRVN 90
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 29.6 bits (65), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 34/81 (41%), Gaps = 15/81 (18%)
Query: 38 GPGRKLPEEKPLVNKAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTG 97
G E+K + LY+G + E ++ F QFG I+ + + + ++
Sbjct: 1 GSSGSSGEDKTIT----TLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQC------ 50
Query: 98 KSKHFGFIEFNDPEVAEVVAD 118
FI+F + AEV A+
Sbjct: 51 -----AFIQFATRQAAEVAAE 66
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 18/80 (22%), Positives = 36/80 (45%), Gaps = 5/80 (6%)
Query: 54 AVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVA 113
A+L + + +++ FG+++R + +++ TG+SK +GF E+ + A
Sbjct: 96 ALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSER-----TGQSKGYGFAEYMKKDSA 150
Query: 114 EVVADAMHGYLLFEHILQVH 133
+ G L L VH
Sbjct: 151 ARAKSDLLGKPLGPRTLYVH 170
>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 = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 23/42 (54%)
Query: 84 RIARNKKLRVLNTGKSKHFGFIEFNDPEVAEVVADAMHGYLL 125
RI+ + ++ + TGKSK +GF+ F + AE M G L
Sbjct: 32 RISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWL 73
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 29.3 bits (64), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 18/80 (22%), Positives = 36/80 (45%), Gaps = 5/80 (6%)
Query: 54 AVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVA 113
A+L + + +++ FG+++R + +++ TG+SK +GF E+ + A
Sbjct: 96 ALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSER-----TGQSKGYGFAEYMKKDSA 150
Query: 114 EVVADAMHGYLLFEHILQVH 133
+ G L L VH
Sbjct: 151 ARAKSDLLGKPLGPRTLYVH 170
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 29.3 bits (64), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 14/59 (23%), Positives = 30/59 (50%), Gaps = 5/59 (8%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAE 114
+++G + + + + +F FG I+ + +++ TGKS+ +GF+ D AE
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQ-----TGKSRGYGFVTMADRAAAE 73
>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 = 29.3 bits (64), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 18/80 (22%), Positives = 36/80 (45%), Gaps = 5/80 (6%)
Query: 54 AVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVA 113
A+L + + +++ FG+++R + +++ TG+SK +GF E+ + A
Sbjct: 94 ALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSER-----TGQSKGYGFAEYMKKDSA 148
Query: 114 EVVADAMHGYLLFEHILQVH 133
+ G L L VH
Sbjct: 149 ARAKSDLLGKPLGPRTLYVH 168
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 29.3 bits (64), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 29/70 (41%), Gaps = 13/70 (18%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEV 115
L+IG + E+E+ + F Q+G + I +N +GF+ D AE
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDIIKN-------------YGFVHIEDKTAAED 57
Query: 116 VADAMHGYLL 125
+H Y L
Sbjct: 58 AIRNLHHYKL 67
>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 = 29.3 bits (64), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 15/78 (19%), Positives = 39/78 (50%), Gaps = 5/78 (6%)
Query: 55 VLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAE 114
+L++ + E+++H F+++G IK + + +++ TG K + +E+ + A+
Sbjct: 25 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRR-----TGYLKGYTLVEYETYKEAQ 79
Query: 115 VVADAMHGYLLFEHILQV 132
+ ++G L + V
Sbjct: 80 AAMEGLNGQDLMGQPISV 97
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 28.9 bits (63), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 18/82 (21%), Positives = 39/82 (47%), Gaps = 6/82 (7%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEV 115
+++G I H E E+ +F +FG + + + + + + + + FGFI F D + +
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQ-----RPRGFGFITFEDEQSVDQ 67
Query: 116 VADAMHGYLLFEHILQVHLIPP 137
+ MH + + ++V P
Sbjct: 68 AVN-MHFHDIMGKKVEVKRAEP 88
>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 = 28.9 bits (63), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 15/78 (19%), Positives = 39/78 (50%), Gaps = 5/78 (6%)
Query: 55 VLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAE 114
+L++ + E+++H F+++G IK + + +++ TG K + +E+ + A+
Sbjct: 24 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRR-----TGYLKGYTLVEYETYKEAQ 78
Query: 115 VVADAMHGYLLFEHILQV 132
+ ++G L + V
Sbjct: 79 AAMEGLNGQDLMGQPISV 96
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 28.9 bits (63), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 10/29 (34%), Positives = 17/29 (58%)
Query: 94 LNTGKSKHFGFIEFNDPEVAEVVADAMHG 122
+ TG S+ +GF+ F + A+ D+M G
Sbjct: 123 MQTGSSRGYGFVSFTSQDDAQNAMDSMQG 151
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 28.9 bits (63), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 28/70 (40%), Gaps = 6/70 (8%)
Query: 56 LYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEV 115
LYI + E+E+ FG + RI R+ ++G S+ GF E E
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRILRD------SSGTSRGVGFARMESTEKCEA 81
Query: 116 VADAMHGYLL 125
V +G +
Sbjct: 82 VIGHFNGKFI 91
>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 = 28.9 bits (63), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 15/78 (19%), Positives = 39/78 (50%), Gaps = 5/78 (6%)
Query: 55 VLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAE 114
+L++ + E+++H F+++G IK + + +++ TG K + +E+ + A+
Sbjct: 9 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRR-----TGYLKGYTLVEYETYKEAQ 63
Query: 115 VVADAMHGYLLFEHILQV 132
+ ++G L + V
Sbjct: 64 AAMEGLNGQDLMGQPISV 81
>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 = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 15/78 (19%), Positives = 39/78 (50%), Gaps = 5/78 (6%)
Query: 55 VLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAE 114
+L++ + E+++H F+++G IK + + +++ TG K + +E+ + A+
Sbjct: 11 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRR-----TGYLKGYTLVEYETYKEAQ 65
Query: 115 VVADAMHGYLLFEHILQV 132
+ ++G L + V
Sbjct: 66 AAMEGLNGQDLMGQPISV 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 = 28.5 bits (62), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 10/29 (34%), Positives = 17/29 (58%)
Query: 94 LNTGKSKHFGFIEFNDPEVAEVVADAMHG 122
+ TG S+ +GF+ F + A+ D+M G
Sbjct: 37 MQTGSSRGYGFVSFTSQDDAQNAMDSMQG 65
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 28.5 bits (62), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 15/78 (19%), Positives = 39/78 (50%), Gaps = 5/78 (6%)
Query: 55 VLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAE 114
+L++ + E+++H F+++G IK + + +++ TG K + +E+ + A+
Sbjct: 9 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRR-----TGYLKGYTLVEYETYKEAQ 63
Query: 115 VVADAMHGYLLFEHILQV 132
+ ++G L + V
Sbjct: 64 AAMEGLNGQDLMGQPISV 81
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 28.5 bits (62), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 40/80 (50%), Gaps = 5/80 (6%)
Query: 55 VLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAE 114
VLY+ + E+++ + F++F K I + R++ TG+ + FI F + E+A
Sbjct: 27 VLYLKNLSPRVTERDLVSLFARFQEKKGPPI----QFRMM-TGRMRGQAFITFPNKEIAW 81
Query: 115 VVADAMHGYLLFEHILQVHL 134
++GY L+ IL +
Sbjct: 82 QALHLVNGYKLYGKILVIEF 101
>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 = 28.5 bits (62), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 13/68 (19%), Positives = 36/68 (52%), Gaps = 5/68 (7%)
Query: 55 VLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAE 114
+L++ + E+++H F+++G IK + + +++ TG K + +E+ + A+
Sbjct: 9 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRR-----TGYLKGYTLVEYETYKEAQ 63
Query: 115 VVADAMHG 122
+ ++G
Sbjct: 64 AAMEGLNG 71
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 27.7 bits (60), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 29/54 (53%), Gaps = 8/54 (14%)
Query: 43 LPEEKPLVNKAAVLYIG----RIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLR 92
+PE +P +YI +I+ +K +HA FS+FG I + ++R+ K R
Sbjct: 2 VPETRP----NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXR 51
>pdb|3CUL|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUL|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3EGZ|A Chain A, Crystal Structure Of An In Vitro Evolved Tetracycline
Aptamer And Artificial Riboswitch
Length = 98
Score = 27.7 bits (60), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 29/54 (53%), Gaps = 8/54 (14%)
Query: 43 LPEEKPLVNKAAVLYIG----RIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLR 92
+PE +P +YI +I+ +K +HA FS+FG I + ++R+ K R
Sbjct: 3 VPETRP----NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXR 52
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 27.3 bits (59), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 13/74 (17%)
Query: 49 LVNKAAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFN 108
++ K VL++ + E+ + FS+FG ++R++ K K + F+ F
Sbjct: 11 VMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVK-------------KLKDYAFVHFE 57
Query: 109 DPEVAEVVADAMHG 122
D A D M+G
Sbjct: 58 DRGAAVKAMDEMNG 71
>pdb|2ONG|A Chain A, Crystal Structure Of Of Limonene Synthase With 2-
Fluorogeranyl Diphosphate (Fgpp).
pdb|2ONG|B Chain B, Crystal Structure Of Of Limonene Synthase With 2-
Fluorogeranyl Diphosphate (Fgpp).
pdb|2ONH|A Chain A, Crystal Structure Of Of Limonene Synthase With 2-
Fluorolinalyl Diphosphate(flpp)
pdb|2ONH|B Chain B, Crystal Structure Of Of Limonene Synthase With 2-
Fluorolinalyl Diphosphate(flpp)
Length = 543
Score = 27.3 bits (59), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 33/61 (54%), Gaps = 4/61 (6%)
Query: 41 RKLPEEKPLVNKAAVLYIGRIRHGFYE--KEMHAFFSQFGTIKRLRIARNKKLRV--LNT 96
RK P+ P+V + A+L + ++ F E KE ++ G +++L AR++ + NT
Sbjct: 211 RKRPDMNPVVLELAILDLNIVQAQFQEELKESFRWWRNTGFVEKLPFARDRLVECYFWNT 270
Query: 97 G 97
G
Sbjct: 271 G 271
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 26.9 bits (58), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 8/53 (15%)
Query: 44 PEEKPLVNKAAVLYIG----RIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLR 92
PE +P +YI +I+ +K +HA FS+FG I + ++R+ K R
Sbjct: 1 PETRP----NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXR 49
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 26.9 bits (58), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 29/66 (43%), Gaps = 13/66 (19%)
Query: 67 EKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEVAEVVADAMHGYLLF 126
E E++ F FG +K ++I LN F F+EF + E A + +HG
Sbjct: 45 ESELNEIFGPFGPMKEVKI--------LNG-----FAFVEFEEAESAAKAIEEVHGKSFA 91
Query: 127 EHILQV 132
L+V
Sbjct: 92 NQPLEV 97
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 26.9 bits (58), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 18/82 (21%), Positives = 34/82 (41%), Gaps = 6/82 (7%)
Query: 53 AAVLYIGRIRHGFYEKEMHAFFSQFGTIKRLRIARNKKLRVLNTGKSKHFGFIEFNDPEV 112
+ +++ + + K++ FS G + R I +K GKS+ G + F
Sbjct: 15 GSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD------GKSRGIGTVTFEQSIE 68
Query: 113 AEVVADAMHGYLLFEHILQVHL 134
A +G LLF+ + V +
Sbjct: 69 AVQAISMFNGQLLFDRPMHVKM 90
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
0.323 0.140 0.424
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,166,581
Number of Sequences: 62578
Number of extensions: 253607
Number of successful extensions: 679
Number of sequences better than 100.0: 144
Number of HSP's better than 100.0 without gapping: 66
Number of HSP's successfully gapped in prelim test: 78
Number of HSP's that attempted gapping in prelim test: 574
Number of HSP's gapped (non-prelim): 154
length of query: 221
length of database: 14,973,337
effective HSP length: 95
effective length of query: 126
effective length of database: 9,028,427
effective search space: 1137581802
effective search space used: 1137581802
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 49 (23.5 bits)