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= 028027
(215 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 52.4 bits (124), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 44/74 (59%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
L+I +P F + ++ + F FG + ++ +K+T SK FGF+ F++P+ A+V AM
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 116 HGYLLFEHILQVHL 129
+G+ + L+V L
Sbjct: 103 NGFQVGTKRLKVQL 116
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 52.0 bits (123), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 43/87 (49%)
Query: 50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE 109
++ T L + +P + E ++ F G I+ ++ R+K TGQS +GF+ ++DP A+
Sbjct: 1 MDSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDAD 60
Query: 110 VVADAMHGYLLFEHILQVHLIPPEHVH 136
+ ++G L ++V P
Sbjct: 61 KAINTLNGLKLQTKTIKVSYARPSSAS 87
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 52.0 bits (123), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 43/87 (49%)
Query: 50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE 109
++ T L + +P + E ++ F G I+ ++ R+K TGQS +GF+ ++DP A+
Sbjct: 1 MDSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDAD 60
Query: 110 VVADAMHGYLLFEHILQVHLIPPEHVH 136
+ ++G L ++V P
Sbjct: 61 KAINTLNGLKLQTKTIKVSYARPSSAS 87
Score = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 34/62 (54%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
LY+ +P +KEM+ FSQ+G I RI ++ TG S+ GFI F+ AE +
Sbjct: 93 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 152
Query: 116 HG 117
+G
Sbjct: 153 NG 154
>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 = 50.8 bits (120), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 42/83 (50%)
Query: 54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
T L + +P ++E ++ F G I+ ++ R+K TGQS +GF+ + DP+ AE +
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 114 AMHGYLLFEHILQVHLIPPEHVH 136
++G L ++V P
Sbjct: 63 TLNGLRLQTKTIKVSYARPSSAS 85
Score = 43.5 bits (101), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 34/62 (54%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
LY+ +P +KE++ FSQ+G I RI ++ TG S+ GFI F+ AE +
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 116 HG 117
+G
Sbjct: 151 NG 152
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/95 (28%), Positives = 48/95 (50%), Gaps = 5/95 (5%)
Query: 51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEV 110
+ ++ LY+G + E ++ F FG I + + ++ TG+SK +GFI F+D E A
Sbjct: 3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62
Query: 111 VADAMHGYLLFEHILQVHLIPPEHVHPKLWRGFNP 145
+ ++G+ L ++V HV +L G P
Sbjct: 63 ALEQLNGFELAGRPMRVG-----HVTERLDGGSGP 92
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/90 (28%), Positives = 44/90 (48%), Gaps = 9/90 (10%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
L++G + ++ ++++FSQ+G + I ++K T QS+ FGF++F DP V +
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASR 78
Query: 116 HGYLLFEHILQVHLIPPEHVHPKLWRGFNP 145
H L I P+ P RG P
Sbjct: 79 ------PHTLDGRNIDPKPCTP---RGMQP 99
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 48.1 bits (113), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 39/65 (60%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
LY+G + E ++ F FG I+ +++ + +TG+SK +GFI F+D E A+ + +
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 116 HGYLL 120
+G+ L
Sbjct: 89 NGFEL 93
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 48.1 bits (113), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 35/67 (52%)
Query: 67 EKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQ 126
E ++Q F FG+I R+ +A++K TGQSK F FI F+ E A + G+ IL
Sbjct: 29 ETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILN 88
Query: 127 VHLIPPE 133
V P
Sbjct: 89 VEWAKPS 95
>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 = 47.4 bits (111), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 40/73 (54%)
Query: 55 VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
V+Y+G IP+ E+++ S G + L++ + +TG+SK + FIEF D E +
Sbjct: 6 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 65
Query: 115 MHGYLLFEHILQV 127
++GY L L+
Sbjct: 66 LNGYQLGSRFLKC 78
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 47.0 bits (110), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 40/73 (54%)
Query: 55 VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
V+Y+G IP+ E+++ S G + L++ + +TG+SK + FIEF D E +
Sbjct: 4 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63
Query: 115 MHGYLLFEHILQV 127
++GY L L+
Sbjct: 64 LNGYQLGSRFLKC 76
>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 = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 42/83 (50%), Gaps = 7/83 (8%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
++IG + E ++ +F ++G + L+I ++ TG+S+ FGF+ F P + V
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT- 64
Query: 116 HGYLLFEHILQVHLIPPEHVHPK 138
+HIL +I P+ P+
Sbjct: 65 ------QHILDGKVIDPKRAIPR 81
Score = 44.7 bits (104), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 35/62 (56%)
Query: 51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEV 110
+K +++G I KE + FFSQ+G I ++ +K TGQS+ FGF+ ++ + +
Sbjct: 85 DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDR 144
Query: 111 VA 112
V
Sbjct: 145 VC 146
>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 = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 40/73 (54%)
Query: 55 VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
V+Y+G IP+ E+++ S G + L++ + +TG+SK + FIEF D E +
Sbjct: 5 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 64
Query: 115 MHGYLLFEHILQV 127
++GY L L+
Sbjct: 65 LNGYQLGSRFLKC 77
>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 = 46.2 bits (108), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 40/67 (59%), Gaps = 1/67 (1%)
Query: 36 EGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSK 95
EG P EEK ++K +V Y+G + +G ++++A FS G+I R+ I +K +G K
Sbjct: 20 EGPPQPLSAEEKKEIDKRSV-YVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPK 78
Query: 96 HFGFIEF 102
+ +IEF
Sbjct: 79 GYAYIEF 85
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 42/71 (59%), Gaps = 1/71 (1%)
Query: 48 PLVNKAT-VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPE 106
P V+++ +++G IP+ E++++ FS+ G + R+ +++TG+ K +GF E+ D E
Sbjct: 2 PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61
Query: 107 VAEVVADAMHG 117
A ++G
Sbjct: 62 TALSAMRNLNG 72
>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 = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 48/93 (51%), Gaps = 5/93 (5%)
Query: 42 KLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIE 101
+L EE N+ +Y+ + + ++++ F FG IK +AR+ TG+ K +GFIE
Sbjct: 102 QLAEEARAFNR---IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIE 158
Query: 102 FNDPEVAEVVADAMHGYLLFEHILQV--HLIPP 132
+ + ++ +M+ + L L+V + PP
Sbjct: 159 YEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPP 191
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 37/147 (25%), Positives = 66/147 (44%), Gaps = 9/147 (6%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
+Y+G I + E ++ F+ FG IK + ++ + T + K F F+E+ PE A++ + M
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 116 HGYLLFEHILQV----HLIPPEHVHPKL---WRGFNPRYKPVDRVQVERKLQNKERTLEE 168
+ +L ++V ++ + + +L R FN Y V V + + + E
Sbjct: 76 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIY--VASVHQDLSDDDIKSVFEA 133
Query: 169 HKKLVEKILKRDQKRRKRIEAAGIEYE 195
K+ L RD K IEYE
Sbjct: 134 FGKIKSCTLARDPTTGKHKGYGFIEYE 160
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 34/62 (54%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
LY+ +P +KEM+ FSQ+G I RI ++ TG S+ GFI F+ AE +
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 116 HG 117
+G
Sbjct: 64 NG 65
>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 = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 43/81 (53%), Gaps = 6/81 (7%)
Query: 42 KLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIE 101
+L EE N+ +Y+ + + ++++ F FG IK +AR+ TG+ K +GFIE
Sbjct: 101 QLAEEARAFNR---IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIE 157
Query: 102 FNDPEVAEVVADAMHGYLLFE 122
+ E A+ DA+ LF+
Sbjct: 158 Y---EKAQSSQDAVSSXNLFD 175
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 36/147 (24%), Positives = 63/147 (42%), Gaps = 9/147 (6%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
+Y+G I + E ++ F+ FG IK + + + T + K F F+E+ PE A++ +
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 116 HGYLLFEHILQV----HLIPPEHVHPKL---WRGFNPRYKPVDRVQVERKLQNKERTLEE 168
+ L ++V ++ + + +L R FN Y V V + + + E
Sbjct: 75 NSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIY--VASVHQDLSDDDIKSVFEA 132
Query: 169 HKKLVEKILKRDQKRRKRIEAAGIEYE 195
K+ L RD K IEYE
Sbjct: 133 FGKIKSCTLARDPTTGKHKGYGFIEYE 159
>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 = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 42/74 (56%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
L+I +P F ++++ F FG + ++ +K+T SK FGF+ +++P A+ +M
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 116 HGYLLFEHILQVHL 129
+G+ + L+V L
Sbjct: 88 NGFQIGMKRLKVQL 101
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 44/84 (52%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
L + IP E +++ F ++G I+ ++I +++T QS+ +GF++F A+ +
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 116 HGYLLFEHILQVHLIPPEHVHPKL 139
+G+ + L+V L H P +
Sbjct: 105 NGFNILNKRLKVALAASGHQRPGI 128
>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 = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 48/93 (51%), Gaps = 5/93 (5%)
Query: 42 KLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIE 101
+L EE N+ +Y+ + + ++++ F FG IK +AR+ TG+ K +GFIE
Sbjct: 117 QLAEEARAFNR---IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIE 173
Query: 102 FNDPEVAEVVADAMHGYLLFEHILQV--HLIPP 132
+ + ++ +M+ + L L+V + PP
Sbjct: 174 YEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPP 206
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 37/147 (25%), Positives = 66/147 (44%), Gaps = 9/147 (6%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
+Y+G I + E ++ F+ FG IK + ++ + T + K F F+E+ PE A++ + M
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 116 HGYLLFEHILQV----HLIPPEHVHPKL---WRGFNPRYKPVDRVQVERKLQNKERTLEE 168
+ +L ++V ++ + + +L R FN Y V V + + + E
Sbjct: 91 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIY--VASVHQDLSDDDIKSVFEA 148
Query: 169 HKKLVEKILKRDQKRRKRIEAAGIEYE 195
K+ L RD K IEYE
Sbjct: 149 FGKIKSATLARDPTTGKHKGYGFIEYE 175
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 44.7 bits (104), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 38/70 (54%)
Query: 47 KPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPE 106
K V K + L + +P E++++ +FS FG + +++ ++ KTG SK FGF+ F + E
Sbjct: 9 KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYE 68
Query: 107 VAEVVADAMH 116
V H
Sbjct: 69 TQVKVMSQRH 78
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 44.3 bits (103), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 35/64 (54%)
Query: 53 ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVA 112
A L+IG+IP EK+++ F +FG I L + +++ TG K F+ + + E A
Sbjct: 13 AIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQ 72
Query: 113 DAMH 116
A+H
Sbjct: 73 SALH 76
>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 = 43.9 bits (102), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 26/93 (27%), Positives = 45/93 (48%), Gaps = 4/93 (4%)
Query: 48 PLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEV 107
P V T L + + + ++ F ++G + + I R++ T +S+ F F+ F+D
Sbjct: 42 PDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRD 101
Query: 108 AEVVADAMHGYLLFEHILQVHLI----PPEHVH 136
AE DAM G +L L+V + PP+ H
Sbjct: 102 AEDAMDAMDGAVLDGRELRVQMARYGRPPDSHH 134
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 43.9 bits (102), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 33/54 (61%)
Query: 53 ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPE 106
A +Y+G + +G +E++A F G++ R+ I +K +G K F +IEF+D E
Sbjct: 5 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKE 58
>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 = 43.9 bits (102), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 33/54 (61%)
Query: 53 ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPE 106
A +Y+G + +G +E++A F G++ R+ I +K +G K F +IEF+D E
Sbjct: 6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKE 59
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 43.5 bits (101), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEV 110
+K+TV Y+ +P ++ FS++G + ++ I ++K T +SK FI F D + A+
Sbjct: 15 SKSTV-YVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQN 73
Query: 111 VADAMHGYLLFEHILQVHL 129
A++ LF +++ +
Sbjct: 74 CTRAINNKQLFGRVIKASI 92
>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 = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/100 (25%), Positives = 46/100 (46%), Gaps = 3/100 (3%)
Query: 54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
+L + +P +++ + FG+++R + +++TGQSK +GF E+ + A
Sbjct: 94 ALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKS 153
Query: 114 AMHGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRV 153
+ G L L VH + P L + R VDR+
Sbjct: 154 DLLGKPLGPRTLYVHWTDAGQLTPAL---LHSRCLCVDRL 190
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 41/82 (50%), Gaps = 3/82 (3%)
Query: 48 PLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEV 107
P N +Y+G +P K+++ F ++GAI+ + + +N++ G F F+EF DP
Sbjct: 17 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL-KNRRGGPP--FAFVEFEDPRD 73
Query: 108 AEVVADAMHGYLLFEHILQVHL 129
AE GY + L+V
Sbjct: 74 AEDAVYGRDGYDYDGYRLRVEF 95
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/100 (25%), Positives = 46/100 (46%), Gaps = 3/100 (3%)
Query: 54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
+L + +P +++ + FG+++R + +++TGQSK +GF E+ + A
Sbjct: 96 ALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKS 155
Query: 114 AMHGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRV 153
+ G L L VH + P L + R VDR+
Sbjct: 156 DLLGKPLGPRTLYVHWTDAGQLTPAL---LHSRCLCVDRL 192
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/100 (25%), Positives = 46/100 (46%), Gaps = 3/100 (3%)
Query: 54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
+L + +P +++ + FG+++R + +++TGQSK +GF E+ + A
Sbjct: 96 ALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKS 155
Query: 114 AMHGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRV 153
+ G L L VH + P L + R VDR+
Sbjct: 156 DLLGKPLGPRTLYVHWTDAGQLTPAL---LHSRCLCVDRL 192
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 41/81 (50%)
Query: 55 VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
VLY+G + +K + A F FG I ++I + +T + + F F+EF E A D
Sbjct: 14 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 73
Query: 115 MHGYLLFEHILQVHLIPPEHV 135
M+ LF ++V+L P +
Sbjct: 74 MNESELFGRTIRVNLAKPMRI 94
>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 = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 6/77 (7%)
Query: 57 YIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMH 116
++G + +K+++ +F++FG + I + TG+S+ FGFI F D E V D
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQK- 73
Query: 117 GYLLFEHILQVHLIPPE 133
EH L +I P+
Sbjct: 74 -----EHRLDGRVIDPK 85
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 42/62 (67%), Gaps = 2/62 (3%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEF-NDPEVAEVVADA 114
+++G I E E+++FF+++G++K ++I + +TG SK +GF+ F ND +V ++V
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 115 MH 116
++
Sbjct: 71 IN 72
>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|B Chain B, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|C Chain C, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|D Chain D, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
Length = 84
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/96 (23%), Positives = 43/96 (44%), Gaps = 12/96 (12%)
Query: 38 GPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHF 97
GPGR T L + +P + E+++ FS G ++ ++ R+K G S +
Sbjct: 1 GPGR------------TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGY 48
Query: 98 GFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPE 133
GF+ + + AE + ++G L ++V P
Sbjct: 49 GFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPS 84
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 42/64 (65%), Gaps = 2/64 (3%)
Query: 54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEF-NDPEVAEVVA 112
+++G I E E+++FF+++G++K ++I + +TG SK +GF+ F ND +V ++V
Sbjct: 11 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVE 69
Query: 113 DAMH 116
++
Sbjct: 70 SQIN 73
>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 = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 42/64 (65%), Gaps = 2/64 (3%)
Query: 54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEF-NDPEVAEVVA 112
+++G I E E+++FF+++G++K ++I + +TG SK +GF+ F ND +V ++V
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVE 68
Query: 113 DAMH 116
++
Sbjct: 69 SQIN 72
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 36/66 (54%)
Query: 51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEV 110
+ A L++G+IP G E++++ F +FG I L + +++ TG K F+ + + A
Sbjct: 13 HDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALK 72
Query: 111 VADAMH 116
A+H
Sbjct: 73 AQSALH 78
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 36/57 (63%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVA 112
+Y+G + + ++++ FSQFG + +++ +++T + K FGF+E + V+E +A
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIA 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 = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 36/68 (52%)
Query: 52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
K T LY+ +P + ++ F ++G+I + I R+K TG+ + F+ +N E A+
Sbjct: 12 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 71
Query: 112 ADAMHGYL 119
A++ +
Sbjct: 72 ISALNNVI 79
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 43/80 (53%), Gaps = 3/80 (3%)
Query: 53 ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNK-KTG--QSKHFGFIEFNDPEVAE 109
++ L+I + E+ ++ FS+ GAIK I++ K K G S FGF+E+ PE A+
Sbjct: 5 SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQ 64
Query: 110 VVADAMHGYLLFEHILQVHL 129
+ G+ + H L+V +
Sbjct: 65 KALKQLQGHTVDGHKLEVRI 84
>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 = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 39/81 (48%)
Query: 54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
T L + +P + E+++ FS G ++ ++ R+K G S +GF+ + + AE +
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 114 AMHGYLLFEHILQVHLIPPEH 134
++G L ++V P
Sbjct: 63 TLNGLRLQSKTIKVSYARPSS 83
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 34/63 (53%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
LYI +P +K+++ FS+FG I R+ ++ TG S+ FI F+ AE +
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 116 HGY 118
+G+
Sbjct: 151 NGH 153
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 25/92 (27%), Positives = 44/92 (47%), Gaps = 4/92 (4%)
Query: 50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE 109
V T L + + + ++ F ++G + + I R++ T +S+ F F+ F+D AE
Sbjct: 67 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAE 126
Query: 110 VVADAMHGYLLFEHILQVHLI----PPEHVHP 137
DAM G +L L+V + PP+ H
Sbjct: 127 DAMDAMDGAVLDGRELRVQMARYGRPPDSHHS 158
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 39/81 (48%)
Query: 54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
T L + +P + E+++ FS G ++ ++ R+K G S +GF+ + + AE +
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 114 AMHGYLLFEHILQVHLIPPEH 134
++G L ++V P
Sbjct: 63 TLNGLRLQSKTIKVSYARPSS 83
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 34/63 (53%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
LYI +P +K+++ FS+FG I R+ ++ TG S+ FI F+ AE +
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 116 HGY 118
+G+
Sbjct: 151 NGH 153
>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 = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 36/68 (52%)
Query: 52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
K T LY+ +P + ++ F ++G+I + I R+K TG+ + F+ +N E A+
Sbjct: 99 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 158
Query: 112 ADAMHGYL 119
A++ +
Sbjct: 159 ISALNNVI 166
Score = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 36/79 (45%)
Query: 54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
T L + +P ++E+ A F G I RI R+ KTG S + F++F ++
Sbjct: 15 TNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIK 74
Query: 114 AMHGYLLFEHILQVHLIPP 132
++G + L+V P
Sbjct: 75 VLNGITVRNKRLKVSYARP 93
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 36/79 (45%)
Query: 54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
T L + +P ++E+ A F G I RI R+ KTG S + F++F ++
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 114 AMHGYLLFEHILQVHLIPP 132
++G + L+V P
Sbjct: 64 VLNGITVRNKRLKVSYARP 82
Score = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 36/68 (52%)
Query: 52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
K T LY+ +P + ++ F ++G+I + I R+K TG+ + F+ +N E A+
Sbjct: 88 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 147
Query: 112 ADAMHGYL 119
A++ +
Sbjct: 148 ISALNNVI 155
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 47/94 (50%), Gaps = 7/94 (7%)
Query: 36 EGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSK 95
G G ++T + +VN LY+ + G ++ ++ FS FG I ++ + G+SK
Sbjct: 3 SGSSGDRITRYQ-VVN----LYVKNLDDGIDDERLRKAFSPFGTITSAKVM--MEGGRSK 55
Query: 96 HFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL 129
FGF+ F+ PE A M+G ++ L V L
Sbjct: 56 GFGFVCFSSPEEATKAVTEMNGRIVATKPLYVAL 89
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 37/73 (50%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
L+IG +P+ + +++ + FG +K + ++ TG SK + F E+ D V + +
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176
Query: 116 HGYLLFEHILQVH 128
+G L + L V
Sbjct: 177 NGMQLGDKKLLVQ 189
Score = 31.2 bits (69), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 5/52 (9%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNK-----KTGQSKHFGFIEF 102
LY+G IP G E+ M FF+ + L A + Q K+F F+EF
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEF 58
>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 = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 38/69 (55%), Gaps = 2/69 (2%)
Query: 51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTG--QSKHFGFIEFNDPEVA 108
+ A +++G++P + EK+++ F Q+GA+ + + R++ QSK F+ F + A
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 109 EVVADAMHG 117
+A+H
Sbjct: 61 LEAQNALHN 69
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 37/73 (50%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
L+IG +P+ + +++ + FG +K + ++ TG SK + F E+ D V + +
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 116 HGYLLFEHILQVH 128
+G L + L V
Sbjct: 64 NGMQLGDKKLLVQ 76
>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 = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 41/78 (52%), Gaps = 6/78 (7%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
++IG + +K+++ +FS+FG + + + TG+S+ FGF+ F + E + V D
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 116 HGYLLFEHILQVHLIPPE 133
EH L +I P+
Sbjct: 62 ------EHKLNGKVIDPK 73
>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 = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 25/97 (25%), Positives = 46/97 (47%), Gaps = 8/97 (8%)
Query: 31 DFLPLEGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKK 90
D LE GP R + + +L++ I E E+Q F +G IK + + +++
Sbjct: 58 DDDELEPGPQRSV--------EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRR 109
Query: 91 TGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV 127
TG SK + +E+ + A +A++G + +QV
Sbjct: 110 TGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV 146
>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|B Chain B, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|C Chain C, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|D Chain D, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
Length = 99
Score = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 19/82 (23%), Positives = 40/82 (48%)
Query: 52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
+ T L + +P + E+++ FS G ++ ++ R+K G S +GF+ + + AE
Sbjct: 18 QGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 77
Query: 112 ADAMHGYLLFEHILQVHLIPPE 133
+ ++G L ++V P
Sbjct: 78 INTLNGLRLQSKTIKVSYARPS 99
>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 = 40.8 bits (94), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 37/73 (50%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
L+IG +P+ + +++ + FG +K + ++ TG SK + F E+ D V + +
Sbjct: 99 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 158
Query: 116 HGYLLFEHILQVH 128
+G L + L V
Sbjct: 159 NGMQLGDKKLLVQ 171
Score = 32.0 bits (71), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 34/114 (29%), Positives = 48/114 (42%), Gaps = 11/114 (9%)
Query: 50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNK-----KTGQSKHFGFIEFND 104
+ A LY+G IP G E+ M FF+ + L A + Q K+F F+EF
Sbjct: 3 LGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFR- 61
Query: 105 PEVAEVV-ADAMHGYLLFEHILQV---HLIPPEHVHPKLWRGFNPRYKPVDRVQ 154
V E A A G + L++ H P KL+ G P Y D+V+
Sbjct: 62 -SVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVK 114
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 40.8 bits (94), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 39/75 (52%)
Query: 55 VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
VLY+G + +K + A F FG I ++I + +T + + F F+EF E A D
Sbjct: 65 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 124
Query: 115 MHGYLLFEHILQVHL 129
M+ LF ++V+L
Sbjct: 125 MNESELFGRTIRVNL 139
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 40.8 bits (94), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 37/73 (50%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
L+IG +P+ + +++ + FG +K + ++ TG SK + F E+ D V + +
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 116 HGYLLFEHILQVH 128
+G L + L V
Sbjct: 157 NGMQLGDKKLLVQ 169
Score = 32.0 bits (71), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 34/114 (29%), Positives = 48/114 (42%), Gaps = 11/114 (9%)
Query: 50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNK-----KTGQSKHFGFIEFND 104
+ A LY+G IP G E+ M FF+ + L A + Q K+F F+EF
Sbjct: 1 LGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFR- 59
Query: 105 PEVAEVV-ADAMHGYLLFEHILQV---HLIPPEHVHPKLWRGFNPRYKPVDRVQ 154
V E A A G + L++ H P KL+ G P Y D+V+
Sbjct: 60 -SVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVK 112
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 40.8 bits (94), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 24/93 (25%), Positives = 45/93 (48%), Gaps = 8/93 (8%)
Query: 35 LEGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQS 94
LE GP R + + +L++ I E E+Q F +G IK + + +++TG S
Sbjct: 16 LEPGPQRSV--------EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFS 67
Query: 95 KHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV 127
K + +E+ + A +A++G + +QV
Sbjct: 68 KGYALVEYETHKQALAAKEALNGAEIMGQTIQV 100
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 40.8 bits (94), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 38/68 (55%), Gaps = 2/68 (2%)
Query: 51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTG--QSKHFGFIEFNDPEVA 108
+ A +++G++P + EK+++ F Q+GA+ + + R++ QSK F+ F + A
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 109 EVVADAMH 116
+A+H
Sbjct: 61 LEAQNALH 68
Score = 40.0 bits (92), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 30/61 (49%), Gaps = 1/61 (1%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
L+IG I E +++ FS FG I+ RI R G S+ F+ F +A+ AM
Sbjct: 98 LFIGMISKKCTENDIRVMFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRAMAQTAIKAM 156
Query: 116 H 116
H
Sbjct: 157 H 157
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 40.8 bits (94), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 34/104 (32%), Positives = 48/104 (46%), Gaps = 16/104 (15%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
+Y+G + G + E++ FS +G ++ + IARN F F+EF DP AE DA+
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAE---DAV 54
Query: 116 HGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRVQVERKL 159
G L +I V +L G PR DR RKL
Sbjct: 55 RG-------LDGKVICGSRVRVELSTGM-PRRSRFDRPPARRKL 90
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 40.8 bits (94), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 36/79 (45%)
Query: 54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
T L + +P ++E+ A F G I RI R+ KTG S + F++F ++
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 114 AMHGYLLFEHILQVHLIPP 132
++G + L+V P
Sbjct: 64 VLNGITVRNKRLKVSYARP 82
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 40.4 bits (93), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 37/66 (56%), Gaps = 2/66 (3%)
Query: 53 ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTG--QSKHFGFIEFNDPEVAEV 110
A +++G++P + EK+++ F Q+GA+ + + R++ QSK F+ F + A
Sbjct: 15 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALE 74
Query: 111 VADAMH 116
+A+H
Sbjct: 75 AQNALH 80
Score = 40.0 bits (92), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 30/61 (49%), Gaps = 1/61 (1%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
L+IG I E +++ FS FG I+ RI R G S+ F+ F +A+ AM
Sbjct: 110 LFIGMISKKCTENDIRVMFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRAMAQTAIKAM 168
Query: 116 H 116
H
Sbjct: 169 H 169
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 40.4 bits (93), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 38/62 (61%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
L++G + E+ ++ FS++G I + + ++++T +S+ FGF+ F + + A+ AM
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 116 HG 117
+G
Sbjct: 75 NG 76
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 40.0 bits (92), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 39/75 (52%)
Query: 55 VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
VLY+G + +K + A F FG I ++I + +T + + F F+EF E A D
Sbjct: 7 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66
Query: 115 MHGYLLFEHILQVHL 129
M+ LF ++V+L
Sbjct: 67 MNESELFGRTIRVNL 81
>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 = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 39/75 (52%)
Query: 55 VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
VLY+G + +K + A F FG I ++I + +T + + F F+EF E A D
Sbjct: 9 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 68
Query: 115 MHGYLLFEHILQVHL 129
M+ LF ++V+L
Sbjct: 69 MNESELFGRTIRVNL 83
>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 = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 39/75 (52%)
Query: 55 VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
VLY+G + +K + A F FG I ++I + +T + + F F+EF E A D
Sbjct: 4 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 63
Query: 115 MHGYLLFEHILQVHL 129
M+ LF ++V+L
Sbjct: 64 MNESELFGRTIRVNL 78
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 35/62 (56%), Gaps = 3/62 (4%)
Query: 55 VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
L++ + E+ ++ F G++ R RI +++TG SK FGF++FN E A+ +A
Sbjct: 17 TLFVKGLSEDTTEETLKESFD--GSV-RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEA 73
Query: 115 MH 116
M
Sbjct: 74 ME 75
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 53 ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRL-RIARNKKTGQSKHFGFIEFNDPEVAEVV 111
++ ++IG + EK + FS FG I + +I R+ TG SK + FI F + ++
Sbjct: 5 SSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAA 64
Query: 112 ADAMHGYLLFEHILQVH 128
+AM+G L + V
Sbjct: 65 IEAMNGQYLCNRPITVS 81
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/94 (26%), Positives = 47/94 (50%), Gaps = 7/94 (7%)
Query: 36 EGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSK 95
G G++L E P Y+G +P + ++ A F +I+ +R+ R+K T + K
Sbjct: 3 SGSSGKELPTEPPYT-----AYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFK 56
Query: 96 HFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL 129
F ++EF++ + + A G LL + L+V +
Sbjct: 57 GFCYVEFDEVDSLK-EALTYDGALLGDRSLRVDI 89
>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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 35/62 (56%), Gaps = 2/62 (3%)
Query: 57 YIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTG--QSKHFGFIEFNDPEVAEVVADA 114
++G++P + EK+++ F Q+GA+ + + R++ QSK F+ F + A +A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 115 MH 116
+H
Sbjct: 67 LH 68
Score = 36.2 bits (82), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 28/61 (45%), Gaps = 1/61 (1%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
L+IG I E +++ FS FG I+ RI R G S+ F+ F A+ A
Sbjct: 98 LFIGXISKKCTENDIRVXFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRAXAQTAIKAX 156
Query: 116 H 116
H
Sbjct: 157 H 157
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 33/56 (58%)
Query: 54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE 109
T +++G +P+ + ++ +F FG I+ + +++TG+S+ +GF+ D AE
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAE 73
>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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 35/65 (53%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
+++G + ++++A F+ FG I R+ ++ TG+SK +GF+ F + AE M
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 116 HGYLL 120
G L
Sbjct: 78 GGQWL 82
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 37/67 (55%), Gaps = 1/67 (1%)
Query: 51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFND-PEVAE 109
+ ++IG + ++ ++ +F QFG +K + R+ T +S+ FGF+ F D V +
Sbjct: 23 SSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDK 82
Query: 110 VVADAMH 116
V+A + H
Sbjct: 83 VLAQSRH 89
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 36/65 (55%), Gaps = 2/65 (3%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
L++ IP F + +++ F QFG I + I N++ SK FGF+ F + A+ + +
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKL 89
Query: 116 HGYLL 120
HG ++
Sbjct: 90 HGTVV 94
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 36/65 (55%), Gaps = 2/65 (3%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
L++ IP F + +++ F QFG I + I N++ SK FGF+ F + A+ + +
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKL 75
Query: 116 HGYLL 120
HG ++
Sbjct: 76 HGTVV 80
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 36/62 (58%), Gaps = 1/62 (1%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPE-VAEVVADA 114
++IG + ++ ++ +F QFG +K + R+ T +S+ FGF+ F D V +V+A +
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62
Query: 115 MH 116
H
Sbjct: 63 RH 64
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
L+IG + EK ++A F + G I + + +++ T +S+ F FI F +P A+ A M
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDM 68
Query: 116 HGYLLFEHILQV 127
+G L ++V
Sbjct: 69 NGKSLHGKAIKV 80
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
+++G IPH E E++ +F +FG + + + + + + + FGFI F D + + + M
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-M 71
Query: 116 H 116
H
Sbjct: 72 H 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 = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 30/104 (28%), Positives = 51/104 (49%), Gaps = 8/104 (7%)
Query: 23 PSDKKGAAD---FLPLEGGPGRKL-TEEKPLVNKATV--LYIGRIPHGFYEKEMQAFFSQ 76
P+D + A D F ++G P R + ++ P + K+ V ++I + K + FS
Sbjct: 62 PADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSA 121
Query: 77 FGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLL 120
FG I ++ ++ SK +GF+ F E AE + M+G LL
Sbjct: 122 FGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKMNGMLL 163
>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 = 37.7 bits (86), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 30/104 (28%), Positives = 51/104 (49%), Gaps = 8/104 (7%)
Query: 23 PSDKKGAAD---FLPLEGGPGRKL-TEEKPLVNKATV--LYIGRIPHGFYEKEMQAFFSQ 76
P+D + A D F ++G P R + ++ P + K+ V ++I + K + FS
Sbjct: 67 PADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSA 126
Query: 77 FGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLL 120
FG I ++ ++ SK +GF+ F E AE + M+G LL
Sbjct: 127 FGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKMNGMLL 168
>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|X Chain X, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|Y Chain Y, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2V|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
pdb|1N52|B Chain B, Cap Binding Complex
pdb|1N54|B Chain B, Cap Binding Complex M7gpppg Free
pdb|3FEX|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex.
pdb|3FEY|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex
Length = 156
Score = 37.4 bits (85), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 44/85 (51%), Gaps = 4/85 (4%)
Query: 45 EEKPLVNKATVLYIGRIPHGFYEKEMQAF--FSQFGAIKRLRIARNKKTGQSKHFGFIEF 102
E++ L+ K+ LY+G + FY E Q + FS+ G IK++ + +K + F F+E+
Sbjct: 31 EQEKLLKKSCTLYVGNLS--FYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEY 88
Query: 103 NDPEVAEVVADAMHGYLLFEHILQV 127
AE ++G L + I++
Sbjct: 89 YSRADAENAMRYINGTRLDDRIIRT 113
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 37.0 bits (84), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 9/79 (11%)
Query: 39 PGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFG 98
PG LT +K +++G I E ++ +F Q+G I+ + I ++ +G+ + F
Sbjct: 98 PGAHLTVKK--------IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFA 149
Query: 99 FIEFNDPE-VAEVVADAMH 116
F+ F+D + V ++V H
Sbjct: 150 FVTFDDHDSVDKIVIQKYH 168
Score = 33.5 bits (75), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 14/59 (23%), Positives = 31/59 (52%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
L+IG + ++ +++ F Q+G + + R+ T +S+ FGF+ + E + +A
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 37.0 bits (84), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 9/79 (11%)
Query: 39 PGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFG 98
PG LT +K +++G I E ++ +F Q+G I+ + I ++ +G+ + F
Sbjct: 96 PGAHLTVKK--------IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFA 147
Query: 99 FIEFNDPE-VAEVVADAMH 116
F+ F+D + V ++V H
Sbjct: 148 FVTFDDHDSVDKIVIQKYH 166
Score = 33.5 bits (75), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 14/59 (23%), Positives = 31/59 (52%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
L+IG + ++ +++ F Q+G + + R+ T +S+ FGF+ + E + +A
Sbjct: 14 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 72
>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 = 37.0 bits (84), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 9/79 (11%)
Query: 39 PGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFG 98
PG LT +K +++G I E ++ +F Q+G I+ + I ++ +G+ + F
Sbjct: 91 PGAHLTVKK--------IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFA 142
Query: 99 FIEFNDPE-VAEVVADAMH 116
F+ F+D + V ++V H
Sbjct: 143 FVTFDDHDSVDKIVIQKYH 161
Score = 33.5 bits (75), Expect = 0.091, Method: Compositional matrix adjust.
Identities = 14/59 (23%), Positives = 31/59 (52%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
L+IG + ++ +++ F Q+G + + R+ T +S+ FGF+ + E + +A
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67
>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 = 37.0 bits (84), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 9/79 (11%)
Query: 39 PGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFG 98
PG LT +K +++G I E ++ +F Q+G I+ + I ++ +G+ + F
Sbjct: 98 PGAHLTVKK--------IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFA 149
Query: 99 FIEFNDPE-VAEVVADAMH 116
F+ F+D + V ++V H
Sbjct: 150 FVTFDDHDSVDKIVIQKYH 168
Score = 33.5 bits (75), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 14/59 (23%), Positives = 31/59 (52%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
L+IG + ++ +++ F Q+G + + R+ T +S+ FGF+ + E + +A
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
>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 = 37.0 bits (84), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 9/79 (11%)
Query: 39 PGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFG 98
PG LT +K +++G I E ++ +F Q+G I+ + I ++ +G+ + F
Sbjct: 97 PGAHLTVKK--------IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFA 148
Query: 99 FIEFNDPE-VAEVVADAMH 116
F+ F+D + V ++V H
Sbjct: 149 FVTFDDHDSVDKIVIQKYH 167
Score = 33.5 bits (75), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 14/59 (23%), Positives = 31/59 (52%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
L+IG + ++ +++ F Q+G + + R+ T +S+ FGF+ + E + +A
Sbjct: 15 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 73
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 37.0 bits (84), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 9/79 (11%)
Query: 39 PGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFG 98
PG LT +K +++G I E ++ +F Q+G I+ + I ++ +G+ + F
Sbjct: 99 PGAHLTVKK--------IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFA 150
Query: 99 FIEFNDPE-VAEVVADAMH 116
F+ F+D + V ++V H
Sbjct: 151 FVTFDDHDSVDKIVIQKYH 169
Score = 33.5 bits (75), Expect = 0.096, Method: Compositional matrix adjust.
Identities = 14/59 (23%), Positives = 31/59 (52%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
L+IG + ++ +++ F Q+G + + R+ T +S+ FGF+ + E + +A
Sbjct: 17 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 75
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 36.6 bits (83), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 35/65 (53%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
+++G + +++++ F+ FG I R+ ++ TG+SK +GF+ F + AE M
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 116 HGYLL 120
G L
Sbjct: 78 GGQWL 82
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 36.6 bits (83), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 31/65 (47%), Gaps = 8/65 (12%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
L+IG +P E+E+++ F Q+G + I +N +GF+ D AE +
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFVHIEDKTAAEDAIRNL 62
Query: 116 HGYLL 120
H Y L
Sbjct: 63 HHYKL 67
>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|6 Chain 6, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|7 Chain 7, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|8 Chain 8, Crystal Structure Of Human Spliceosomal U1 Snrnp
Length = 216
Score = 36.6 bits (83), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 13/48 (27%), Positives = 30/48 (62%)
Query: 55 VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEF 102
L++ R+ + E +++ F +G IKR+ + +K++G+ + + FIE+
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEY 151
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 36.2 bits (82), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 13/48 (27%), Positives = 30/48 (62%)
Query: 55 VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEF 102
L++ R+ + E +++ F +G IKR+ + +K++G+ + + FIE+
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEY 151
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 36.2 bits (82), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 30/67 (44%), Gaps = 1/67 (1%)
Query: 54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
T LYI +P E+E++ FG + RI R+ +G S+ GF E E V
Sbjct: 26 TNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIG 84
Query: 114 AMHGYLL 120
+G +
Sbjct: 85 HFNGKFI 91
>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 = 35.4 bits (80), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
L+I +P ++E++ G +K LR+ N + G+ K ++E+ + A M
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTN-RAGKPKGLAYVEYENESQASQAVMKM 78
Query: 116 HGYLLFEHILQVHL 129
G + E+I++V +
Sbjct: 79 DGMTIKENIIKVAI 92
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 35.4 bits (80), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 31/65 (47%)
Query: 51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEV 110
N+ +Y+G + E + F Q G + + +++ TGQ + +GF+EF E A+
Sbjct: 13 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 72
Query: 111 VADAM 115
M
Sbjct: 73 AIKIM 77
>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 = 35.4 bits (80), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 41/80 (51%), Gaps = 5/80 (6%)
Query: 48 PLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEV 107
P VN+ +LYI +P+ +EM F ++G I+++R+ T +++ ++ + D
Sbjct: 15 PEVNR--ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVG---NTPETRGTAYVVYEDIFD 69
Query: 108 AEVVADAMHGYLLFEHILQV 127
A+ D + G+ + L V
Sbjct: 70 AKNACDHLSGFNVCNRYLVV 89
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 35.0 bits (79), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 6/60 (10%)
Query: 54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
T LY+G + E +++ F QFG I+ + + Q + FI+F + AEV A+
Sbjct: 13 TTLYVGGLGDTITETDLRNHFYQFGEIRTITVV------QRQQCAFIQFATRQAAEVAAE 66
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 35.0 bits (79), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 7/79 (8%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDP-EVAEVVADA 114
+Y+G + + + E++ F +G ++ + +ARN F F+EF DP + A+ V D
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRD- 129
Query: 115 MHGYLLFEHILQVHLIPPE 133
+ G L ++V L E
Sbjct: 130 LDGRTLCGCRVRVELSNGE 148
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 35.0 bits (79), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 22/88 (25%), Positives = 43/88 (48%), Gaps = 5/88 (5%)
Query: 40 GRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGF 99
GR P VN+ +LYI +P+ +EM F ++G I+++R+ T +++ +
Sbjct: 1 GRANIRLPPEVNR--ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVG---NTPETRGTAY 55
Query: 100 IEFNDPEVAEVVADAMHGYLLFEHILQV 127
+ + D A+ D + G+ + L V
Sbjct: 56 VVYEDIFDAKNACDHLSGFNVCNRYLVV 83
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 34.7 bits (78), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 36/78 (46%), Gaps = 5/78 (6%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
+Y+G + + + E++ F +G ++ + +ARN F F+EF DP A +
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVREL 130
Query: 116 HGYLLFEHILQVHLIPPE 133
G L ++V L E
Sbjct: 131 DGRTLCGCRVRVELSNGE 148
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 34.7 bits (78), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 53 ATVLYIGRIPHGFYEKEMQAFFSQFGAIKR-LRIARNKKTGQSKHFGFIEFN 103
+ ++ + +P E +++ G R +R+ RNK +GQS+ F F+EF+
Sbjct: 1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFS 52
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 34.7 bits (78), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 40/84 (47%), Gaps = 9/84 (10%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
+++GR +E+Q FF Q+G + + I + + F F+ F D +VA+ ++
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRA-----FAFVTFADDKVAQ----SL 64
Query: 116 HGYLLFEHILQVHLIPPEHVHPKL 139
G L + VH+ E H KL
Sbjct: 65 CGEDLIIKGISVHISNAEPKHNKL 88
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 34.3 bits (77), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 30/60 (50%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
LYI + G ++++ +G I + +K T + K +GF++F+ P A+ A+
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
>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 = 34.3 bits (77), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 44/84 (52%), Gaps = 3/84 (3%)
Query: 45 EEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNK-KTGQSKHFGFIEFN 103
E++ L+ K+ LY+G + E+++ FS+ G IK++ + +K KT F F+E+
Sbjct: 10 EQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACG--FCFVEYY 67
Query: 104 DPEVAEVVADAMHGYLLFEHILQV 127
AE ++G L + I++
Sbjct: 68 SRADAENAMRYINGTRLDDRIIRT 91
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 34.3 bits (77), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 41/80 (51%), Gaps = 5/80 (6%)
Query: 48 PLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEV 107
P VN+ +LYI +P+ +EM F ++G I+++R+ T +++ ++ + D
Sbjct: 5 PEVNR--ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVG---NTPETRGTAYVVYEDIFD 59
Query: 108 AEVVADAMHGYLLFEHILQV 127
A+ D + G+ + L V
Sbjct: 60 AKNAVDHLSGFNVSNRYLVV 79
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 33.5 bits (75), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 36/77 (46%), Gaps = 6/77 (7%)
Query: 52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
K +Y G I G ++ M+ FS FG I +R+ K + F+ F+ E A
Sbjct: 24 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG------YSFVRFSTHESAAHA 77
Query: 112 ADAMHGYLLFEHILQVH 128
+++G + H+++ +
Sbjct: 78 IVSVNGTTIEGHVVKCY 94
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 33.5 bits (75), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 4/75 (5%)
Query: 48 PLVNKATV--LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDP 105
P + K+ V ++I + K + FS FG I ++ ++ SK +GF+ F
Sbjct: 4 PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQ 61
Query: 106 EVAEVVADAMHGYLL 120
E AE + M+G LL
Sbjct: 62 EAAERAIEKMNGMLL 76
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 33.5 bits (75), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 33/57 (57%), Gaps = 2/57 (3%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVA 112
L+IG + E+ ++ ++ Q+G + + R+ + +S+ FGF+ F+ +AEV A
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSS--MAEVDA 84
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 33.5 bits (75), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 37/77 (48%), Gaps = 2/77 (2%)
Query: 53 ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVA 112
A +++ +P F K ++ F++ G + I + G+SK G ++F PEVAE
Sbjct: 8 ACQIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVKFESPEVAERAC 65
Query: 113 DAMHGYLLFEHILQVHL 129
M+G L + V +
Sbjct: 66 RMMNGMKLSGREIDVRI 82
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 33.1 bits (74), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 21/86 (24%), Positives = 42/86 (48%), Gaps = 9/86 (10%)
Query: 51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEV 110
+ ++ +++GR E E++ FFSQ+G + + I + + F F+ F D ++A+
Sbjct: 3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRA-----FAFVTFADDQIAQ- 56
Query: 111 VADAMHGYLLFEHILQVHLIPPEHVH 136
++ G L + VH+ E H
Sbjct: 57 ---SLCGEDLIIKGISVHISNAEPKH 79
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 33.1 bits (74), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 39/74 (52%), Gaps = 2/74 (2%)
Query: 44 TEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFN 103
+++ +VN A V+ ++P +K + + FS+ G + + ++ TG++K F F+E
Sbjct: 5 SDQYIVVNGAPVIPSAKVP--VLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECG 62
Query: 104 DPEVAEVVADAMHG 117
A+ + + HG
Sbjct: 63 SMNDAKKIIKSFHG 76
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 33.1 bits (74), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 35/62 (56%), Gaps = 3/62 (4%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKH--FGFIEFNDPEVAEVVAD 113
+ + IP ++E++ FS FG +K +R+ + K TG H FGF++F + A+ +
Sbjct: 18 ILVRNIPFQANQREIRELFSTFGELKTVRLPK-KMTGTGAHRGFGFVDFITKQDAKKAFN 76
Query: 114 AM 115
A+
Sbjct: 77 AL 78
>pdb|3NS6|A Chain A, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
pdb|3NS6|B Chain B, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
Length = 100
Score = 32.7 bits (73), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 39/74 (52%), Gaps = 2/74 (2%)
Query: 44 TEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFN 103
+++ +VN A V+ ++P +K + + FS+ G + + ++ TG++K F F+E
Sbjct: 5 SDQYIVVNGAPVIPSAKVP--VLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECG 62
Query: 104 DPEVAEVVADAMHG 117
A+ + + HG
Sbjct: 63 SMNDAKKIIKSFHG 76
>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 = 32.7 bits (73), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 23/44 (52%)
Query: 77 FGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLL 120
FG I R+ ++ TG+SK +GF+ F + AE M G L
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWL 73
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 32.7 bits (73), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 13/58 (22%), Positives = 31/58 (53%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
+++G + ++++ +F QFG + + +K T + + FGF+ F ++ E V +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 32.7 bits (73), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 38/77 (49%), Gaps = 2/77 (2%)
Query: 53 ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVA 112
++ +++ +P F K ++ F++ G + I + G+SK G ++F PEVAE
Sbjct: 5 SSGIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVKFESPEVAERAC 62
Query: 113 DAMHGYLLFEHILQVHL 129
M+G L + V +
Sbjct: 63 RMMNGMKLSGREIDVRI 79
>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 = 32.7 bits (73), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 31/65 (47%), Gaps = 2/65 (3%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
++I + K + FS FG I ++ ++ SK +GF+ F E AE + M
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAAERAIEKM 65
Query: 116 HGYLL 120
+G LL
Sbjct: 66 NGMLL 70
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 32.7 bits (73), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 34/74 (45%), Gaps = 6/74 (8%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
L++G +P E++ + F ++G + I R++ FGFI +AE+ +
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLESRTLAEIAKAEL 78
Query: 116 HGYLLFEHILQVHL 129
G +L L++
Sbjct: 79 DGTILKSRPLRIRF 92
>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 = 32.3 bits (72), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 14/62 (22%), Positives = 31/62 (50%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
L++G + ++ ++ F F + + + +TG S+ +GF+ F + A+ D+M
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 116 HG 117
G
Sbjct: 64 QG 65
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 32.3 bits (72), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 36/74 (48%), Gaps = 1/74 (1%)
Query: 55 VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
+++G + E+ + F Q G + ++ I ++++ G+ K FGF+ F PE
Sbjct: 18 TVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIAL 76
Query: 115 MHGYLLFEHILQVH 128
++G L+ + V
Sbjct: 77 LNGIRLYGRPINVS 90
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 32.3 bits (72), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 14/62 (22%), Positives = 31/62 (50%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
L++G + ++ ++ F F + + + +TG S+ +GF+ F + A+ D+M
Sbjct: 90 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 149
Query: 116 HG 117
G
Sbjct: 150 QG 151
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 32.3 bits (72), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 43/84 (51%), Gaps = 9/84 (10%)
Query: 52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
K VL++ + + E+ ++ FSQFG ++R++ + K + FI F++ + A
Sbjct: 10 KVKVLFVRNLANTVTEEILEKAFSQFGKLERVK--------KLKDYAFIHFDERDGAVKA 61
Query: 112 ADAMHGYLL-FEHILQVHLIPPEH 134
+ M+G L E+I V PP+
Sbjct: 62 MEEMNGKDLEGENIEIVFAKPPDQ 85
>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
pdb|2F9J|B Chain B, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
Length = 125
Score = 32.3 bits (72), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 40/80 (50%), Gaps = 5/80 (6%)
Query: 48 PLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEV 107
P VN+ +L I +P+ +EM F ++G I+++R+ T +++ ++ + D
Sbjct: 15 PEVNR--ILMIRNLPYKITAEEMYDIFGKYGPIRQIRVG---NTPETRGTAYVVYEDIFD 69
Query: 108 AEVVADAMHGYLLFEHILQV 127
A+ D + G+ + L V
Sbjct: 70 AKNACDHLSGFNVCNRYLVV 89
>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 = 31.6 bits (70), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 14/76 (18%), Positives = 39/76 (51%)
Query: 52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
+ +L++ + E+++ F+++G IK + + +++TG K + +E+ + A+
Sbjct: 22 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 81
Query: 112 ADAMHGYLLFEHILQV 127
+ ++G L + V
Sbjct: 82 MEGLNGQDLMGQPISV 97
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 31.6 bits (70), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 36/75 (48%)
Query: 55 VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
VLY+ + E+++ + F++F K I TG+ + FI F + E+A
Sbjct: 27 VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86
Query: 115 MHGYLLFEHILQVHL 129
++GY L+ IL +
Sbjct: 87 VNGYKLYGKILVIEF 101
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 31.6 bits (70), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 12/66 (18%), Positives = 36/66 (54%)
Query: 52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
+ +L++ + E+++ F+++G IK + + +++TG K + +E+ + A+
Sbjct: 21 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 80
Query: 112 ADAMHG 117
+ ++G
Sbjct: 81 MEGLNG 86
>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 = 31.2 bits (69), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 12/66 (18%), Positives = 36/66 (54%)
Query: 52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
+ +L++ + E+++ F+++G IK + + +++TG K + +E+ + A+
Sbjct: 6 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 65
Query: 112 ADAMHG 117
+ ++G
Sbjct: 66 MEGLNG 71
>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 = 31.2 bits (69), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 12/66 (18%), Positives = 36/66 (54%)
Query: 52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
+ +L++ + E+++ F+++G IK + + +++TG K + +E+ + A+
Sbjct: 8 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 67
Query: 112 ADAMHG 117
+ ++G
Sbjct: 68 MEGLNG 73
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 31.2 bits (69), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 12/66 (18%), Positives = 36/66 (54%)
Query: 52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
+ +L++ + E+++ F+++G IK + + +++TG K + +E+ + A+
Sbjct: 6 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 65
Query: 112 ADAMHG 117
+ ++G
Sbjct: 66 MEGLNG 71
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 31.2 bits (69), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 11/50 (22%), Positives = 28/50 (56%)
Query: 53 ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEF 102
A ++ ++ ++++ FFS G ++ +RI ++ + +SK ++EF
Sbjct: 25 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEF 74
>pdb|3N09|A Chain A, Atomic Model Of An Infectious Rotavirus Particle
pdb|3N09|B Chain B, Atomic Model Of An Infectious Rotavirus Particle
Length = 800
Score = 31.2 bits (69), Expect = 0.50, Method: Composition-based stats.
Identities = 16/35 (45%), Positives = 21/35 (60%), Gaps = 2/35 (5%)
Query: 130 IPPEHV--HPKLWRGFNPRYKPVDRVQVERKLQNK 162
I PE V KL+R F PR PV R E++L+N+
Sbjct: 31 IKPEQVKKQTKLFRIFEPRQLPVYRANGEKELRNR 65
>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 = 30.8 bits (68), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 12/63 (19%), Positives = 35/63 (55%)
Query: 55 VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
+L++ + E+++ F+++G IK + + +++TG K + +E+ + A+ +
Sbjct: 9 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 68
Query: 115 MHG 117
++G
Sbjct: 69 LNG 71
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 30.4 bits (67), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 6/56 (10%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
L++G +P E+EM+ F ++G + I ++ K FGFI +AE+
Sbjct: 25 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIA 74
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 30.4 bits (67), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 31/74 (41%), Gaps = 8/74 (10%)
Query: 54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
T L++ P E E+ F FG +K ++I F F+EF + E A +
Sbjct: 32 TRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG--------FAFVEFEEAESAAKAIE 83
Query: 114 AMHGYLLFEHILQV 127
+HG L+V
Sbjct: 84 EVHGKSFANQPLEV 97
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 30.4 bits (67), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 17/69 (24%), Positives = 34/69 (49%), Gaps = 8/69 (11%)
Query: 49 LVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVA 108
++ K VL++ + E+ ++ FS+FG ++R++ + K + F+ F D A
Sbjct: 11 VMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVK--------KLKDYAFVHFEDRGAA 62
Query: 109 EVVADAMHG 117
D M+G
Sbjct: 63 VKAMDEMNG 71
>pdb|1U2F|A Chain A, Solution Structure Of The First Rna-Binding Domain Of
Hu2af65
Length = 90
Score = 30.0 bits (66), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 5/52 (9%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNK-----KTGQSKHFGFIEF 102
LY+G IP G E+ M FF+ + L A + Q K+F F+EF
Sbjct: 4 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEF 55
>pdb|2D7I|A Chain A, Crsytal Structure Of Pp-Galnac-T10 With Udp, Galnac And
Mn2+
pdb|2D7R|A Chain A, Crystal Structure Of Pp-galnac-t10 Complexed With
Galnac-ser On Lectin Domain
Length = 570
Score = 30.0 bits (66), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 23/50 (46%)
Query: 84 RIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPE 133
RIARN+KT I+ +D DAM G +E + IPPE
Sbjct: 220 RIARNRKTIVCPMIDVIDHDDFRYETQAGDAMRGAFDWEMYYKRIPIPPE 269
>pdb|2HZC|A Chain A, Crystal Structure Of The N-terminal Rrm Of The U2af Large
Subunit
Length = 87
Score = 30.0 bits (66), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 27/58 (46%), Gaps = 5/58 (8%)
Query: 50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNK-----KTGQSKHFGFIEF 102
+ A LY+G IP G E+ M FF+ + L A + Q K+F F+EF
Sbjct: 3 LGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEF 60
>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
pdb|2RS8|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
Length = 99
Score = 30.0 bits (66), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 6/56 (10%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
L++G +P E+EM+ F ++G + I ++ K FGFI +AE+
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIA 67
>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D (Auf1) With Telomere Dna
pdb|1X0F|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D(Auf1) With Telomeric Dna
Length = 79
Score = 30.0 bits (66), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 16/75 (21%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPE-VAEVVADA 114
+++G + E++++ +F FG ++ + + + KT + + F FI F + E V +++
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 63
Query: 115 MHGYLLFEHILQVHL 129
H L + ++V +
Sbjct: 64 YHNVGLSKCEIKVAM 78
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 28/64 (43%), Gaps = 8/64 (12%)
Query: 54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
T L++ P E E+ F FG +K ++I F F+EF + E A +
Sbjct: 5 TRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG--------FAFVEFEEAESAAKAIE 56
Query: 114 AMHG 117
+HG
Sbjct: 57 EVHG 60
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 19/82 (23%), Positives = 35/82 (42%)
Query: 48 PLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEV 107
P V+ L + + + ++ F ++G + + I R T + F F+ F+D
Sbjct: 8 PDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRD 67
Query: 108 AEVVADAMHGYLLFEHILQVHL 129
A+ AM G L L+V +
Sbjct: 68 AQDAEAAMDGAELDGRELRVQV 89
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 1/66 (1%)
Query: 53 ATVLYIGRIPHGFYEKEMQAFFSQFG-AIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
A L++G + E + F+ G + ++I RN+ TG + F+EF D AE
Sbjct: 9 AASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKC 68
Query: 112 ADAMHG 117
++G
Sbjct: 69 LHKING 74
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 29.6 bits (65), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 12/51 (23%), Positives = 29/51 (56%)
Query: 56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPE 106
+++G + E++++ +F FG ++ + + + KT + + F FI F + E
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEE 52
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 29.6 bits (65), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 13/54 (24%), Positives = 32/54 (59%)
Query: 67 EKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLL 120
E++++ FS++G I + I ++++ +S+ F F+ F + + A+ + +G L
Sbjct: 26 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 79
>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 = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 33/63 (52%), Gaps = 5/63 (7%)
Query: 67 EKEMQAFFSQFGAIKRLRIARNKKT-GQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHIL 125
+K + A FSQFG I + ++R+ K GQ+ F+ F + A +M G+ ++ +
Sbjct: 27 KKSLYAIFSQFGQILDILVSRSLKMRGQA----FVIFKEVSSATNALRSMQGFPFYDKPM 82
Query: 126 QVH 128
++
Sbjct: 83 RIQ 85
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 28/67 (41%), Gaps = 6/67 (8%)
Query: 52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
+ T YIG IPH E ++ F FG I K K FI+++ E A V
Sbjct: 26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDF------KHYPEKGCCFIKYDTHEQAAVC 79
Query: 112 ADAMHGY 118
A+ +
Sbjct: 80 IVALANF 86
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 28.9 bits (63), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 13/54 (24%), Positives = 32/54 (59%)
Query: 67 EKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLL 120
E++++ FS++G I + I ++++ +S+ F F+ F + + A+ + +G L
Sbjct: 29 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 82
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 28.9 bits (63), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 13/54 (24%), Positives = 32/54 (59%)
Query: 67 EKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLL 120
E++++ FS++G I + I ++++ +S+ F F+ F + + A+ + +G L
Sbjct: 60 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 113
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 28.9 bits (63), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 13/54 (24%), Positives = 32/54 (59%)
Query: 67 EKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLL 120
E++++ FS++G I + I ++++ +S+ F F+ F + + A+ + +G L
Sbjct: 29 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 82
>pdb|3U1L|A Chain A, Structure Of The Mrna Splicing Complex Component Cwc2
pdb|3U1M|A Chain A, Structure Of The Mrna Splicing Complex Component Cwc2
Length = 240
Score = 28.5 bits (62), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 32/79 (40%), Gaps = 15/79 (18%)
Query: 52 KATVLYIGRIPHGFYEKEMQA---------FFSQFGAIKRLRIARNKKTGQSKHFGFIEF 102
K LY+G I K ++ FS+ G I R+R +SK+ GF++F
Sbjct: 133 KNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV------ESKNCGFVKF 186
Query: 103 NDPEVAEVVADAMHGYLLF 121
AE +AM L
Sbjct: 187 KYQANAEFAKEAMSNQTLL 205
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 28.5 bits (62), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 17/77 (22%), Positives = 35/77 (45%), Gaps = 1/77 (1%)
Query: 53 ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVA 112
+ +++ + + K+++ FS G + R I +K G+S+ G + F A
Sbjct: 15 GSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTFEQSIEAVQAI 73
Query: 113 DAMHGYLLFEHILQVHL 129
+G LLF+ + V +
Sbjct: 74 SMFNGQLLFDRPMHVKM 90
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 28.5 bits (62), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 32/63 (50%), Gaps = 5/63 (7%)
Query: 67 EKEMQAFFSQFGAIKRLRIARN-KKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHIL 125
+K + A FSQFG I + ++R+ K GQ F+ F + A +M G+ ++ +
Sbjct: 26 KKSLYAIFSQFGQILDILVSRSLKMRGQ----AFVIFKEVSSATNALRSMQGFPFYDKPM 81
Query: 126 QVH 128
++
Sbjct: 82 RIQ 84
>pdb|3TP2|A Chain A, Crystal Structure Of The Splicing Factor Cwc2 From Yeast
pdb|3TP2|B Chain B, Crystal Structure Of The Splicing Factor Cwc2 From Yeast
Length = 229
Score = 28.1 bits (61), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 32/79 (40%), Gaps = 15/79 (18%)
Query: 52 KATVLYIGRIPHGFYEKEMQ---------AFFSQFGAIKRLRIARNKKTGQSKHFGFIEF 102
K LY+G I K ++ FS+ G I R+R +SK+ GF++F
Sbjct: 135 KNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV------ESKNCGFVKF 188
Query: 103 NDPEVAEVVADAMHGYLLF 121
AE +AM L
Sbjct: 189 KYQANAEFAKEAMSNQTLL 207
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 27.7 bits (60), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 32/63 (50%), Gaps = 5/63 (7%)
Query: 67 EKEMQAFFSQFGAIKRLRIARNKKT-GQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHIL 125
+K + A FSQFG I + ++R+ K GQ F+ F + A +M G+ ++ +
Sbjct: 27 KKSLYAIFSQFGQILDILVSRSLKMRGQ----AFVIFKEVSSATNALRSMQGFPFYDKPM 82
Query: 126 QVH 128
++
Sbjct: 83 RIQ 85
>pdb|1UOK|A Chain A, Crystal Structure Of B. Cereus Oligo-1,6-Glucosidase
Length = 558
Score = 27.7 bits (60), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 21/35 (60%), Gaps = 3/35 (8%)
Query: 140 WRGFNPRYKPVDRVQVERKLQNKERTLEEHKKLVE 174
W NP YK ++ V++ +QNK+ +KKL+E
Sbjct: 438 WITVNPNYKEIN---VKQAIQNKDSIFYYYKKLIE 469
>pdb|1YVU|A Chain A, Crystal Structure Of A. Aeolicus Argonaute
Length = 706
Score = 26.9 bits (58), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 24/50 (48%), Gaps = 4/50 (8%)
Query: 105 PEVAEVVADAMHGYLLFEHILQVHLIPPEHVHPKLWRG-FNP---RYKPV 150
PEV E V + GY L L+ + P E + L R FNP R KP+
Sbjct: 139 PEVNEKVLKSEEGYFLLHLDLKFRIQPFETLQTLLERNDFNPKRIRVKPI 188
>pdb|2F8S|A Chain A, Crystal Structure Of Aa-Ago With Externally-Bound Sirna
pdb|2F8S|B Chain B, Crystal Structure Of Aa-Ago With Externally-Bound Sirna
pdb|2F8T|A Chain A, Crystal Structure Of Aa-Ago With Externally-Bound Sirna
pdb|2F8T|B Chain B, Crystal Structure Of Aa-Ago With Externally-Bound Sirna
pdb|2NUB|A Chain A, Structure Of Aquifex Aeolicus Argonuate
Length = 706
Score = 26.9 bits (58), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 24/50 (48%), Gaps = 4/50 (8%)
Query: 105 PEVAEVVADAMHGYLLFEHILQVHLIPPEHVHPKLWRG-FNP---RYKPV 150
PEV E V + GY L L+ + P E + L R FNP R KP+
Sbjct: 139 PEVNEKVLKSEEGYFLLHLDLKFRIQPFETLQTLLERNDFNPKRIRVKPI 188
>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 = 26.6 bits (57), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 33/63 (52%), Gaps = 5/63 (7%)
Query: 67 EKEMQAFFSQFGAIKRLRIARNKKT-GQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHIL 125
+K + A FS+FG I + ++R+ K GQ+ F+ F + A +M G+ ++ +
Sbjct: 27 KKSLHAIFSRFGQILDILVSRSLKMRGQA----FVIFKEVSSATNALRSMQGFPFYDKPM 82
Query: 126 QVH 128
++
Sbjct: 83 RIQ 85
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
0.319 0.139 0.412
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,347,028
Number of Sequences: 62578
Number of extensions: 261724
Number of successful extensions: 930
Number of sequences better than 100.0: 175
Number of HSP's better than 100.0 without gapping: 125
Number of HSP's successfully gapped in prelim test: 50
Number of HSP's that attempted gapping in prelim test: 769
Number of HSP's gapped (non-prelim): 202
length of query: 215
length of database: 14,973,337
effective HSP length: 95
effective length of query: 120
effective length of database: 9,028,427
effective search space: 1083411240
effective search space used: 1083411240
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)