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= 002067
(973 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2E62|A Chain A, Solution Structure Of The Cwf21 Domain In Protein Aak25922
Length = 61
Score = 75.1 bits (183), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 37/52 (71%), Positives = 48/52 (92%)
Query: 819 MNEEQRQKLRRLEVSLIEYRESLEERGIKSSEEIEKKVAIHRKRLESEYGLA 870
M+EEQRQK RR+EV+LIEYRE+LEE+G+K+ EEIE+KV I+RKRLE +YGL+
Sbjct: 10 MDEEQRQKRRRIEVALIEYRETLEEQGMKNPEEIERKVEINRKRLEVDYGLS 61
>pdb|1UG0|A Chain A, Solution Structure Of Surp Domain In Bab30904
Length = 88
Score = 51.6 bits (122), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/58 (43%), Positives = 33/58 (56%)
Query: 321 DIMVIPPEDRHLRHVIDTLALYVLDGGCAFEQAIMERGRGNPLFNFLFELGSKEHTYY 378
+I V PPE R VI+ LA +V +GG E+ ME + NP F FL + S+E YY
Sbjct: 16 EIKVSPPEGAETRRVIEKLARFVAEGGPELEKVAMEDYKDNPAFTFLHDKNSREFLYY 73
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 50.4 bits (119), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 33/86 (38%), Positives = 43/86 (50%), Gaps = 7/86 (8%)
Query: 179 DDGDPQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFM 238
DDG P+T LYVGNLS V E +L+ F + GP S K++ T + C FV F
Sbjct: 11 DDGQPRT--LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPY----C-FVEFY 63
Query: 239 NRADGQAAKDEMQGVVVYEYELKIGW 264
D AA M G + E+K+ W
Sbjct: 64 EHRDAAAALAAMNGRKILGKEVKVNW 89
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 50.1 bits (118), Expect = 6e-06, Method: Composition-based stats.
Identities = 29/81 (35%), Positives = 41/81 (50%), Gaps = 3/81 (3%)
Query: 185 TTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQ 244
T NL+VG+L+ VD+ L F F S +MW + + R GFV+F ++ D Q
Sbjct: 87 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW---DMQTGSSRGYGFVSFTSQDDAQ 143
Query: 245 AAKDEMQGVVVYEYELKIGWG 265
A D MQG + L+I W
Sbjct: 144 NAMDSMQGQDLNGRPLRINWA 164
Score = 42.0 bits (97), Expect = 0.002, Method: Composition-based stats.
Identities = 25/78 (32%), Positives = 37/78 (47%), Gaps = 4/78 (5%)
Query: 188 LYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAAK 247
LYVGNL + E+ L + F GPIA++KIM ++ + N FV + D A
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMI----DKNNKNVNYAFVEYHQSHDANIAL 58
Query: 248 DEMQGVVVYEYELKIGWG 265
+ G + +KI W
Sbjct: 59 QTLNGKQIENNIVKINWA 76
>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 = 48.9 bits (115), Expect = 1e-05, Method: Composition-based stats.
Identities = 29/81 (35%), Positives = 41/81 (50%), Gaps = 3/81 (3%)
Query: 185 TTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQ 244
T NL+VG+L+ VD+ L F F S +MW + + R GFV+F ++ D Q
Sbjct: 1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW---DMQTGSSRGYGFVSFTSQDDAQ 57
Query: 245 AAKDEMQGVVVYEYELKIGWG 265
A D MQG + L+I W
Sbjct: 58 NAMDSMQGQDLNGRPLRINWA 78
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 47.4 bits (111), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 41/79 (51%), Gaps = 4/79 (5%)
Query: 188 LYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAAK 247
L++G L+ + +E L FG+ GPI+ V ++ RT + R F+ F N AD + A
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTS----KSRGFAFITFENPADAKNAA 65
Query: 248 DEMQGVVVYEYELKIGWGK 266
+M G ++ +K+ K
Sbjct: 66 KDMNGKSLHGKAIKVEQAK 84
>pdb|1X4O|A Chain A, Solution Structure Of Surp Domain In Splicing Factor 4
Length = 78
Score = 46.6 bits (109), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 35/62 (56%)
Query: 324 VIPPEDRHLRHVIDTLALYVLDGGCAFEQAIMERGRGNPLFNFLFELGSKEHTYYVWRLY 383
V PPED +++ + LA ++ DGG E ++ R N F+FL++ S+ + YY +L
Sbjct: 9 VSPPEDEEAKNLAEKLARFIADGGPEVETIALQNNRENQAFSFLYDPNSQGYRYYRQKLD 68
Query: 384 SF 385
F
Sbjct: 69 EF 70
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 46.2 bits (108), Expect = 9e-05, Method: Composition-based stats.
Identities = 30/81 (37%), Positives = 40/81 (49%), Gaps = 3/81 (3%)
Query: 187 NLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAA 246
NL V + VDE L + F R+GPI SVKI+ R E R+ R GFV F + + Q A
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDR---ETRQSRGYGFVKFQSGSSAQQA 100
Query: 247 KDEMQGVVVYEYELKIGWGKS 267
+ G + LK+ S
Sbjct: 101 IAGLNGFNILNKRLKVALAAS 121
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 46.2 bits (108), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 27/72 (37%), Positives = 35/72 (48%), Gaps = 5/72 (6%)
Query: 184 QTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADG 243
Q NLYV NL +D+ L + F FG I S K+M E R + GFV F + +
Sbjct: 14 QVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMM-----EGGRSKGFGFVCFSSPEEA 68
Query: 244 QAAKDEMQGVVV 255
A EM G +V
Sbjct: 69 TKAVTEMNGRIV 80
>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 = 42.7 bits (99), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 38/81 (46%), Gaps = 3/81 (3%)
Query: 186 TNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQA 245
+LYVG+L P V E L F GPI S+++ + RR +V F AD +
Sbjct: 16 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVC---RDMITRRSLGYAYVNFQQPADAER 72
Query: 246 AKDEMQGVVVYEYELKIGWGK 266
A D M V+ ++I W +
Sbjct: 73 ALDTMNFDVIKGKPVRIMWSQ 93
Score = 38.5 bits (88), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 41/81 (50%), Gaps = 5/81 (6%)
Query: 187 NLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAA 246
N+++ NL +D L TF FG I S K++ + + GFV F + + A
Sbjct: 105 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC-----DENGSKGYGFVHFETQEAAERA 159
Query: 247 KDEMQGVVVYEYELKIGWGKS 267
++M G+++ + ++ +G KS
Sbjct: 160 IEKMNGMLLNDRKVFVGRFKS 180
>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|B Chain B, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|C Chain C, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|D Chain D, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|E Chain E, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|F Chain F, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|G Chain G, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|H Chain H, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
Length = 190
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 38/81 (46%), Gaps = 3/81 (3%)
Query: 186 TNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQA 245
+LYVG+L P V E L F GPI S+++ + RR +V F AD +
Sbjct: 11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVC---RDMITRRSLGYAYVNFQQPADAER 67
Query: 246 AKDEMQGVVVYEYELKIGWGK 266
A D M V+ ++I W +
Sbjct: 68 ALDTMNFDVIKGKPVRIMWSQ 88
Score = 38.1 bits (87), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 41/81 (50%), Gaps = 5/81 (6%)
Query: 187 NLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAA 246
N+++ NL +D L TF FG I S K++ + + GFV F + + A
Sbjct: 100 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC-----DENGSKGYGFVHFETQEAAERA 154
Query: 247 KDEMQGVVVYEYELKIGWGKS 267
++M G+++ + ++ +G KS
Sbjct: 155 IEKMNGMLLNDRKVFVGRFKS 175
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 3/75 (4%)
Query: 188 LYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAAK 247
L+VG LS +E L + F ++G I+ V ++ R E +R R GFV F N D + A
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDR---ETQRSRGFGFVTFENIDDAKDAM 71
Query: 248 DEMQGVVVYEYELKI 262
M G V ++++
Sbjct: 72 MAMNGKSVDGRQIRV 86
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 39/78 (50%), Gaps = 4/78 (5%)
Query: 176 GSFDDGDPQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFV 235
GS + DP L V LS E L F ++GPIA V I++ +++ RR R FV
Sbjct: 4 GSRANPDPNCC-LGVFGLSLYTTERDLREVFSKYGPIADVSIVY---DQQSRRSRGFAFV 59
Query: 236 AFMNRADGQAAKDEMQGV 253
F N D + AK+ G+
Sbjct: 60 YFENVDDAKEAKERANGM 77
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 40.8 bits (94), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 36/72 (50%), Gaps = 4/72 (5%)
Query: 182 DPQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRA 241
DP L V LS E L F ++GPIA V I++ +++ RR R FV F N
Sbjct: 13 DPNCC-LGVFGLSLYTTERDLREVFSKYGPIADVSIVY---DQQSRRSRGFAFVYFENVD 68
Query: 242 DGQAAKDEMQGV 253
D + AK+ G+
Sbjct: 69 DAKEAKERANGM 80
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 40.4 bits (93), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 36/72 (50%), Gaps = 4/72 (5%)
Query: 182 DPQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRA 241
DP L V LS E L F ++GPIA V I++ +++ RR R FV F N
Sbjct: 13 DPNCC-LGVFGLSLYTTERDLREVFSKYGPIADVSIVY---DQQSRRSRGFAFVYFENVD 68
Query: 242 DGQAAKDEMQGV 253
D + AK+ G+
Sbjct: 69 DAKEAKERANGM 80
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 40.4 bits (93), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 42/79 (53%), Gaps = 5/79 (6%)
Query: 184 QTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADG 243
Q L+V N+ + + L + FG+FG I V+I++ R + GFV F N AD
Sbjct: 28 QPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIF-----NERGSKGFGFVTFENSADA 82
Query: 244 QAAKDEMQGVVVYEYELKI 262
A++++ G VV ++++
Sbjct: 83 DRAREKLHGTVVEGRKIEV 101
>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 = 40.4 bits (93), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 41/78 (52%), Gaps = 3/78 (3%)
Query: 187 NLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAA 246
+++VG+LSP++ + F FG I+ +++ + + + GFV+F N+ D + A
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVV---KDMATGKSKGYGFVSFFNKWDAENA 73
Query: 247 KDEMQGVVVYEYELKIGW 264
+M G + +++ W
Sbjct: 74 IQQMGGQWLGGRQIRTNW 91
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 40.4 bits (93), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 41/75 (54%), Gaps = 5/75 (6%)
Query: 188 LYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAAK 247
L+V N+ + + L + FG+FG I V+I++ R + GFV F N AD A+
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIF-----NERGSKGFGFVTFENSADADRAR 72
Query: 248 DEMQGVVVYEYELKI 262
+++ G VV ++++
Sbjct: 73 EKLHGTVVEGRKIEV 87
>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 = 40.0 bits (92), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 3/77 (3%)
Query: 186 TNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQA 245
T+L V NL+ + + L R F ++G + V I R +E R FV F ++ D +
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKE---SRGFAFVRFHDKRDAED 104
Query: 246 AKDEMQGVVVYEYELKI 262
A D M G V+ EL++
Sbjct: 105 AMDAMDGAVLDGRELRV 121
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 40.0 bits (92), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 3/77 (3%)
Query: 186 TNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQA 245
T+L V NL+ + + L R F ++G + V I R +E R FV F ++ D +
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKE---SRGFAFVRFHDKRDAED 127
Query: 246 AKDEMQGVVVYEYELKI 262
A D M G V+ EL++
Sbjct: 128 AMDAMDGAVLDGRELRV 144
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 40.0 bits (92), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 36/72 (50%), Gaps = 4/72 (5%)
Query: 182 DPQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRA 241
DP L V LS E L F ++GPIA V I++ +++ RR R FV F N
Sbjct: 44 DPNCC-LGVFGLSLYTTERDLREVFSKYGPIADVSIVY---DQQSRRSRGFAFVYFENVD 99
Query: 242 DGQAAKDEMQGV 253
D + AK+ G+
Sbjct: 100 DAKEAKERANGM 111
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 39.7 bits (91), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 30/95 (31%), Positives = 44/95 (46%), Gaps = 12/95 (12%)
Query: 177 SFDDGDPQTTNLYVGNLSPQVDENFLLRTFGRF----GPIASVKIMWPRTEEERRRQRNC 232
S++ G+P LY+ NLSP+V E L+ F RF GP ++M R R
Sbjct: 18 SYNPGEPNKV-LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM-------TGRMRGQ 69
Query: 233 GFVAFMNRADGQAAKDEMQGVVVYEYELKIGWGKS 267
F+ F N+ A + G +Y L I +GK+
Sbjct: 70 AFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKN 104
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 39.7 bits (91), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 40/78 (51%), Gaps = 3/78 (3%)
Query: 187 NLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAA 246
+++VG+LSP++ + F FG I+ +++ + + + GFV+F N+ D + A
Sbjct: 17 HVFVGDLSPEITTEDIKSAFAPFGKISDARVV---KDMATGKSKGYGFVSFYNKLDAENA 73
Query: 247 KDEMQGVVVYEYELKIGW 264
M G + +++ W
Sbjct: 74 IVHMGGQWLGGRQIRTNW 91
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 39.3 bits (90), Expect = 0.009, Method: Composition-based stats.
Identities = 23/86 (26%), Positives = 39/86 (45%), Gaps = 10/86 (11%)
Query: 182 DPQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRA 241
D T LYVG L + E L F +FG I ++ ++ +++ C F+ F R
Sbjct: 9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVV---------QRQQCAFIQFATRQ 59
Query: 242 DGQ-AAKDEMQGVVVYEYELKIGWGK 266
+ AA+ ++V L + WG+
Sbjct: 60 AAEVAAEKSFNKLIVNGRRLNVKWGR 85
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 39.3 bits (90), Expect = 0.010, Method: Composition-based stats.
Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 3/62 (4%)
Query: 183 PQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRAD 242
P + +YV NL + N L R F ++G + V IM +++ R+ + F+ F+++
Sbjct: 14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIM---KDKDTRKSKGVAFILFLDKDS 70
Query: 243 GQ 244
Q
Sbjct: 71 AQ 72
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 38.1 bits (87), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 36/79 (45%), Gaps = 3/79 (3%)
Query: 188 LYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAAK 247
LYVG L+ +VD+ L F FG I ++I + E + R FV F D AA
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPL---DYETEKHRGFAFVEFELAEDAAAAI 71
Query: 248 DEMQGVVVYEYELKIGWGK 266
D M ++ +++ K
Sbjct: 72 DNMNESELFGRTIRVNLAK 90
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 38.1 bits (87), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 36/82 (43%), Gaps = 9/82 (10%)
Query: 184 QTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADG 243
Q L+VGNL + E R F R+G + V I R R GF+ +R
Sbjct: 21 QRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFI---------NRDRGFGFIRLESRTLA 71
Query: 244 QAAKDEMQGVVVYEYELKIGWG 265
+ AK E+ G ++ L+I +
Sbjct: 72 EIAKAELDGTILKSRPLRIRFA 93
Score = 32.0 bits (71), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 28/59 (47%), Gaps = 4/59 (6%)
Query: 188 LYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAA 246
L V NLSP V L + F +FGP+ ++ ++R R GFV F + + A
Sbjct: 99 LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVV----DDRGRATGKGFVEFAAKPPARKA 153
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 37.7 bits (86), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 3/76 (3%)
Query: 188 LYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAAK 247
LYVG+L + E+ L F FG I S+++M + E R + GF+ F + + A
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMM---DSETGRSKGYGFITFSDSECAKKAL 85
Query: 248 DEMQGVVVYEYELKIG 263
+++ G + +K+G
Sbjct: 86 EQLNGFELAGRPMKVG 101
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet
Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 37.4 bits (85), Expect = 0.045, Method: Composition-based stats.
Identities = 26/92 (28%), Positives = 45/92 (48%), Gaps = 4/92 (4%)
Query: 176 GSFDDGDPQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFV 235
GS +G P+ NL++ +L + + LL+ F FG + S K+ +++ + GFV
Sbjct: 17 GSQKEG-PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVF---IDKQTNLSKCFGFV 72
Query: 236 AFMNRADGQAAKDEMQGVVVYEYELKIGWGKS 267
++ N QAA M G + LK+ +S
Sbjct: 73 SYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRS 104
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 37.0 bits (84), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 31/64 (48%), Gaps = 3/64 (4%)
Query: 188 LYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAAK 247
LYVG L+ +VD+ L F FG I ++I P + E + R FV F D AA
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQI--P-LDYETEKHRGFAFVEFELAEDAAAAI 122
Query: 248 DEMQ 251
D M
Sbjct: 123 DNMN 126
>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 = 36.6 bits (83), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 40/78 (51%), Gaps = 3/78 (3%)
Query: 186 TNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQA 245
+ +YVG++ ++ E+ + + F FGPI S+ + W + + + FV + Q
Sbjct: 29 SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSW---DSVTMKHKGFAFVEYEVPEAAQL 85
Query: 246 AKDEMQGVVVYEYELKIG 263
A ++M V++ +K+G
Sbjct: 86 ALEQMNSVMLGGRNIKVG 103
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 36.6 bits (83), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 34/76 (44%), Gaps = 15/76 (19%)
Query: 181 GDPQTTN----LYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVA 236
GDP+ L+V NL+ V E L ++F FG + VK + ++ FV
Sbjct: 7 GDPEVMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVK-----------KLKDYAFVH 55
Query: 237 FMNRADGQAAKDEMQG 252
F +R A DEM G
Sbjct: 56 FEDRGAAVKAMDEMNG 71
>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 = 36.6 bits (83), Expect = 0.069, Method: Composition-based stats.
Identities = 22/81 (27%), Positives = 41/81 (50%), Gaps = 5/81 (6%)
Query: 187 NLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAA 246
N+++ NL +D L TF FG I S K++ + + GFV F + + A
Sbjct: 7 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC-----DENGSKGYGFVHFETQEAAERA 61
Query: 247 KDEMQGVVVYEYELKIGWGKS 267
++M G+++ + ++ +G KS
Sbjct: 62 IEKMNGMLLNDRKVFVGRFKS 82
>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 = 36.6 bits (83), Expect = 0.073, Method: Composition-based stats.
Identities = 24/79 (30%), Positives = 36/79 (45%), Gaps = 3/79 (3%)
Query: 188 LYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAAK 247
LYVG L+ +VD+ L F FG I ++I + E + R FV F D AA
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQI---PLDYETEKHRGFAFVEFELAEDAAAAI 66
Query: 248 DEMQGVVVYEYELKIGWGK 266
D M ++ +++ K
Sbjct: 67 DNMNESELFGRTIRVNLAK 85
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 36.6 bits (83), Expect = 0.076, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 5/64 (7%)
Query: 187 NLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRR--QRNCGFVAFMNRADGQ 244
++VG L P +DE+ + +F RFGP+ + WP E + + F+ F + Q
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLV---VDWPHKAESKSYFPPKGYAFLLFQEESSVQ 66
Query: 245 AAKD 248
A D
Sbjct: 67 ALID 70
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 36.6 bits (83), Expect = 0.079, Method: Composition-based stats.
Identities = 24/79 (30%), Positives = 36/79 (45%), Gaps = 3/79 (3%)
Query: 188 LYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAAK 247
LYVG L+ +VD+ L F FG I ++I + E + R FV F D AA
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQI---PLDYETEKHRGFAFVEFELAEDAAAAI 64
Query: 248 DEMQGVVVYEYELKIGWGK 266
D M ++ +++ K
Sbjct: 65 DNMNESELFGRTIRVNLAK 83
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 36.2 bits (82), Expect = 0.085, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 4/73 (5%)
Query: 181 GDPQTTNLYVGNLSPQVDENFLLRTFGRFGPIASV-KIMWPRTEEERRRQRNCGFVAFMN 239
G ++ +++GNL P++DE L TF FG I KIM + + + F+ F +
Sbjct: 1 GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIM---RDPDTGNSKGYAFINFAS 57
Query: 240 RADGQAAKDEMQG 252
AA + M G
Sbjct: 58 FDASDAAIEAMNG 70
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 36.2 bits (82), Expect = 0.085, Method: Composition-based stats.
Identities = 22/81 (27%), Positives = 41/81 (50%), Gaps = 5/81 (6%)
Query: 187 NLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAA 246
N+++ NL +D L TF FG I S K++ + + GFV F + + A
Sbjct: 13 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC-----DENGSKGYGFVHFETQEAAERA 67
Query: 247 KDEMQGVVVYEYELKIGWGKS 267
++M G+++ + ++ +G KS
Sbjct: 68 IEKMNGMLLNDRKVFVGRFKS 88
>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 = 36.2 bits (82), Expect = 0.099, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 39/76 (51%), Gaps = 3/76 (3%)
Query: 188 LYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAAK 247
+YVG++ ++ E+ + + F FGPI S+ + W + + + FV + Q A
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSW---DSVTMKHKGFAFVEYEVPEAAQLAL 72
Query: 248 DEMQGVVVYEYELKIG 263
++M V++ +K+G
Sbjct: 73 EQMNSVMLGGRNIKVG 88
>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 = 35.8 bits (81), Expect = 0.10, Method: Composition-based stats.
Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 4/68 (5%)
Query: 177 SFDDGDPQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVA 236
S +G ++VG + ++DE + F R+G + VKI+ RT + GFV+
Sbjct: 1 SLPEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGV----SKGYGFVS 56
Query: 237 FMNRADGQ 244
F N D Q
Sbjct: 57 FYNDVDVQ 64
>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 = 35.8 bits (81), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 32/69 (46%), Gaps = 3/69 (4%)
Query: 186 TNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQA 245
TNLYV NL + ++ L FG++G I I+ + R R FV + R + Q
Sbjct: 14 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTG---RPRGVAFVRYNKREEAQE 70
Query: 246 AKDEMQGVV 254
A + V+
Sbjct: 71 AISALNNVI 79
>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 = 35.8 bits (81), Expect = 0.11, Method: Composition-based stats.
Identities = 23/63 (36%), Positives = 30/63 (47%), Gaps = 3/63 (4%)
Query: 188 LYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAAK 247
LYVG L+ +VD+ L F FG I ++I + E + R FV F D AA
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQI---PLDYETEKHRGFAFVEFELAEDAAAAI 61
Query: 248 DEM 250
D M
Sbjct: 62 DNM 64
>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 = 35.8 bits (81), Expect = 0.12, Method: Composition-based stats.
Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 4/68 (5%)
Query: 177 SFDDGDPQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVA 236
S +G ++VG + ++DE + F R+G + VKI+ RT + GFV+
Sbjct: 1 SLPEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGV----SKGYGFVS 56
Query: 237 FMNRADGQ 244
F N D Q
Sbjct: 57 FYNDVDVQ 64
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 35.8 bits (81), Expect = 0.12, Method: Composition-based stats.
Identities = 21/69 (30%), Positives = 32/69 (46%), Gaps = 4/69 (5%)
Query: 176 GSFDDGDPQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFV 235
G G ++VG + ++DE + F R+G + VKI+ RT + GFV
Sbjct: 1 GPLGSGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGV----SKGYGFV 56
Query: 236 AFMNRADGQ 244
+F N D Q
Sbjct: 57 SFYNDVDVQ 65
>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|B Chain B, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|C Chain C, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
Length = 184
Score = 35.8 bits (81), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 32/69 (46%), Gaps = 3/69 (4%)
Query: 186 TNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQA 245
TNLYV NL + ++ L FG++G I I+ + R R FV + R + Q
Sbjct: 101 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTG---RPRGVAFVRYNKREEAQE 157
Query: 246 AKDEMQGVV 254
A + V+
Sbjct: 158 AISALNNVI 166
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 35.4 bits (80), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 3/56 (5%)
Query: 186 TNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRA 241
+++G LS Q + L FG+FG + +M + +R R GFV FM++A
Sbjct: 26 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVM---RDPLTKRSRGFGFVTFMDQA 78
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 35.4 bits (80), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 37/76 (48%), Gaps = 3/76 (3%)
Query: 187 NLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAA 246
L V NL+ + + L R F ++G + V I PR E + R FV F +R D Q A
Sbjct: 15 TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYI--PR-EPHTKAPRGFAFVRFHDRRDAQDA 71
Query: 247 KDEMQGVVVYEYELKI 262
+ M G + EL++
Sbjct: 72 EAAMDGAELDGRELRV 87
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 35.0 bits (79), Expect = 0.19, Method: Composition-based stats.
Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 3/71 (4%)
Query: 184 QTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADG 243
+ TNLYV NL + ++ L FG++G I I+ ++ R R FV + R +
Sbjct: 88 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNIL---RDKLTGRPRGVAFVRYNKREEA 144
Query: 244 QAAKDEMQGVV 254
Q A + V+
Sbjct: 145 QEAISALNNVI 155
Score = 30.8 bits (68), Expect = 3.8, Method: Composition-based stats.
Identities = 22/81 (27%), Positives = 34/81 (41%), Gaps = 3/81 (3%)
Query: 186 TNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQA 245
TNL V L + + L F GPI + +IM + + FV F + D Q
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIM---RDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 246 AKDEMQGVVVYEYELKIGWGK 266
A + G+ V LK+ + +
Sbjct: 61 AIKVLNGITVRNKRLKVSYAR 81
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 35.0 bits (79), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 32/70 (45%), Gaps = 4/70 (5%)
Query: 183 PQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRAD 242
P L+VG L+ Q E+ + R F FG I I+ + C FV + + A+
Sbjct: 13 PSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTIL----RGPDGNSKGCAFVKYSSHAE 68
Query: 243 GQAAKDEMQG 252
QAA + + G
Sbjct: 69 AQAAINALHG 78
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 35.0 bits (79), Expect = 0.22, Method: Composition-based stats.
Identities = 18/54 (33%), Positives = 29/54 (53%), Gaps = 3/54 (5%)
Query: 188 LYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRA 241
+++G LS Q + L FG+FG + +M + +R R GFV FM++A
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVM---RDPLTKRSRGFGFVTFMDQA 53
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 35.0 bits (79), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 41/83 (49%), Gaps = 3/83 (3%)
Query: 181 GDPQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNR 240
G ++ LYVG+L + E+ L F FG I ++ +M + + R + GF+ F +
Sbjct: 1 GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLM---KDSDTGRSKGYGFITFSDS 57
Query: 241 ADGQAAKDEMQGVVVYEYELKIG 263
+ A +++ G + +++G
Sbjct: 58 ECARRALEQLNGFELAGRPMRVG 80
>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 = 35.0 bits (79), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 27/108 (25%), Positives = 44/108 (40%), Gaps = 14/108 (12%)
Query: 165 PDDFDPSGKLPGSFDDGDPQTTN-----LYVGNLSPQVDENFLLRTFGRFGPIASVKIMW 219
P P +PG P + N L++ NL + +E L F +F V+++
Sbjct: 182 PGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVP 241
Query: 220 PRTEEERRRQRNCGFVAFMNRADGQAAKDEMQGVVVYEYE-LKIGWGK 266
R + FV F N AA+D +QG + + +KI + K
Sbjct: 242 GR--------HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK 281
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 34.7 bits (78), Expect = 0.26, Method: Composition-based stats.
Identities = 23/80 (28%), Positives = 37/80 (46%), Gaps = 3/80 (3%)
Query: 183 PQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRAD 242
P+ NL++ +L + + L TF FG + S K+ +++ + GFV+F N
Sbjct: 38 PEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVF---IDKQTSLSKCFGFVSFDNPDS 94
Query: 243 GQAAKDEMQGVVVYEYELKI 262
Q A M G V LK+
Sbjct: 95 AQVAIKAMNGFQVGTKRLKV 114
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 33.9 bits (76), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 27/64 (42%), Gaps = 4/64 (6%)
Query: 188 LYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAAK 247
L++G +S + EN + F FG I +I+ R C FV F RA Q A
Sbjct: 110 LFIGMISKKCTENDIRVMFSSFGQIEECRIL----RGPDGLSRGCAFVTFTTRAMAQTAI 165
Query: 248 DEMQ 251
M
Sbjct: 166 KAMH 169
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 33.9 bits (76), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 27/64 (42%), Gaps = 4/64 (6%)
Query: 188 LYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAAK 247
L++G +S + EN + F FG I +I+ R C FV F RA Q A
Sbjct: 98 LFIGMISKKCTENDIRVMFSSFGQIEECRIL----RGPDGLSRGCAFVTFTTRAMAQTAI 153
Query: 248 DEMQ 251
M
Sbjct: 154 KAMH 157
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 33.5 bits (75), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 29/65 (44%), Gaps = 4/65 (6%)
Query: 188 LYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAAK 247
L+VG L+ Q E +LR F FG I ++ + C FV F + + QAA
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVL----RGPDGSSKGCAFVKFSSHTEAQAAI 73
Query: 248 DEMQG 252
+ G
Sbjct: 74 HALHG 78
>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 = 33.1 bits (74), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 41/78 (52%), Gaps = 3/78 (3%)
Query: 187 NLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAA 246
+++VG+LSP++ + F FG I+ +++ + + + GFV+F N+ D + A
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVV---KDMATGKSKGYGFVSFFNKWDAENA 64
Query: 247 KDEMQGVVVYEYELKIGW 264
+M G + +++ W
Sbjct: 65 IQQMGGQWLGGRQIRTNW 82
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 33.1 bits (74), Expect = 0.73, Method: Composition-based stats.
Identities = 16/36 (44%), Positives = 24/36 (66%), Gaps = 1/36 (2%)
Query: 187 NLYVGNLSPQVDENFLLRTFGRFG-PIASVKIMWPR 221
+L++G+L P +DENF+ R F G + SVKI+ R
Sbjct: 11 SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNR 46
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 33.1 bits (74), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 36/79 (45%), Gaps = 3/79 (3%)
Query: 184 QTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADG 243
Q +YVG L +V E L F + GP+ + + P+ + Q GFV F++ D
Sbjct: 14 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHM--PKDRVTGQHQ-GYGFVEFLSEEDA 70
Query: 244 QAAKDEMQGVVVYEYELKI 262
A M + +Y +++
Sbjct: 71 DYAIKIMDMIKLYGKPIRV 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 = 33.1 bits (74), Expect = 0.85, Method: Composition-based stats.
Identities = 23/84 (27%), Positives = 33/84 (39%), Gaps = 5/84 (5%)
Query: 164 LPDDFDPSGKLPGSFDDGDP-QTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRT 222
LP P P + + + L++G +S + EN + F FG I +I+
Sbjct: 73 LPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQIEECRIL---- 128
Query: 223 EEERRRQRNCGFVAFMNRADGQAA 246
R C FV F RA Q A
Sbjct: 129 RGPDGLSRGCAFVTFTTRAXAQTA 152
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 32.7 bits (73), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 9/82 (10%)
Query: 184 QTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADG 243
Q + L+VGNL P + E + + F ++G V I + + GF+ R
Sbjct: 21 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI---------HKDKGFGFIRLETRTLA 71
Query: 244 QAAKDEMQGVVVYEYELKIGWG 265
+ AK E+ + + +L++ +
Sbjct: 72 EIAKVELDNMPLRGKQLRVRFA 93
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 32.7 bits (73), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 3/49 (6%)
Query: 187 NLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFV 235
N+YVGNL + F +FG + +VK+++ R E ++ + GFV
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDR---ETKKPKGFGFV 48
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 32.7 bits (73), Expect = 0.99, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 31/73 (42%), Gaps = 8/73 (10%)
Query: 180 DGDPQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMN 239
D P +YVGNL ++ L R FG +GP+ SV + R FV F +
Sbjct: 68 DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVA--------RNPPGFAFVEFED 119
Query: 240 RADGQAAKDEMQG 252
D A E+ G
Sbjct: 120 PRDAADAVRELDG 132
>pdb|2DT6|A Chain A, Solution Structure Of The First Surp Domain Of Human
Splicing Factor Sf3a120
Length = 64
Score = 32.3 bits (72), Expect = 1.3, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 332 LRHVIDTLALYVLDGGCAFEQAIMERGRGNPLFNFLFELGSKEHTYYVWRLYSFAQG 388
+R+++D A +V G FE I + NP FNFL H YY ++ F +G
Sbjct: 3 VRNIVDKTASFVARNGPEFEARIRQNEINNPKFNFL-NPNDPYHAYYRHKVSEFKEG 58
>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 = 32.0 bits (71), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 18/76 (23%), Positives = 36/76 (47%), Gaps = 3/76 (3%)
Query: 188 LYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAAK 247
+YVG++ ++ E+ + + F FGPI S+ W + + + FV + Q A
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSW---DSVTXKHKGFAFVEYEVPEAAQLAL 71
Query: 248 DEMQGVVVYEYELKIG 263
++ V + +K+G
Sbjct: 72 EQXNSVXLGGRNIKVG 87
>pdb|3O08|A Chain A, Crystal Structure Of Dimeric Klhxk1 In Crystal Form I
pdb|3O08|B Chain B, Crystal Structure Of Dimeric Klhxk1 In Crystal Form I
pdb|3O1B|A Chain A, Crystal Structure Of Dimeric Klhxk1 In Crystal Form Ii
pdb|3O1W|A Chain A, Crystal Structure Of Dimeric Klhxk1 In Crystal Form Iii
pdb|3O1W|B Chain B, Crystal Structure Of Dimeric Klhxk1 In Crystal Form Iii
pdb|3O4W|A Chain A, Crystal Structure Of Dimeric Klhxk1 In Crystal Form Iv
pdb|3O4W|B Chain B, Crystal Structure Of Dimeric Klhxk1 In Crystal Form Iv
pdb|3O5B|A Chain A, Crystal Structure Of Dimeric Klhxk1 In Crystal Form Vii
With Glucose Bound (Open State)
pdb|3O5B|B Chain B, Crystal Structure Of Dimeric Klhxk1 In Crystal Form Vii
With Glucose Bound (Open State)
pdb|3O6W|A Chain A, Crystal Structure Of Monomeric Klhxk1 In Crystal Form Viii
(Open State)
pdb|3O6W|B Chain B, Crystal Structure Of Monomeric Klhxk1 In Crystal Form Viii
(Open State)
pdb|3O80|A Chain A, Crystal Structure Of Monomeric Klhxk1 In Crystal Form Ix
(Open State)
pdb|3O8M|A Chain A, Crystal Structure Of Monomeric Klhxk1 In Crystal Form Xi
With Glucose Bound (Closed State)
Length = 485
Score = 32.0 bits (71), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 39/153 (25%), Positives = 65/153 (42%), Gaps = 38/153 (24%)
Query: 560 LKVLQVWSDWFLFSDAYVNGLRATFLRSGNSGVTPFHSICGDAPEIDKKNNSEDTCDLSK 619
L +L ++ F+F D ++ L+ ++ T + S D P N EDT DL K
Sbjct: 315 LVLLDLYDSGFIFKDQDISKLKEAYVMD-----TSYPSKIEDDP----FENLEDTDDLFK 365
Query: 620 TNQDTALAMGKGAAIKELMNLPLSELERRCRHNGLSLVGGR--EMMVARLLSLEDAEKQR 677
TN +N+ + +ER+ LVG R + V + ++ D +R
Sbjct: 366 TN----------------LNIETTVVERKLIRKLAELVGTRAARLTVCGVSAICD---KR 406
Query: 678 GYELDDDLKSAHSQSSSGRYSR--GWKETNMEA 708
GY K+AH + ++R G+KE +A
Sbjct: 407 GY------KTAHIAADGSVFNRYPGYKEKAAQA 433
>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 = 32.0 bits (71), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 37/81 (45%), Gaps = 9/81 (11%)
Query: 184 QTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADG 243
Q + L+VGNL P + E + + F ++G V I + + GF+ R
Sbjct: 14 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI---------HKDKGFGFIRLETRTLA 64
Query: 244 QAAKDEMQGVVVYEYELKIGW 264
+ AK E+ + + +L++ +
Sbjct: 65 EIAKVELDNMPLRGKQLRVRF 85
>pdb|2GHP|A Chain A, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|B Chain B, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|C Chain C, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|D Chain D, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|E Chain E, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|F Chain F, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|G Chain G, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|H Chain H, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
Length = 292
Score = 32.0 bits (71), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 29/60 (48%), Gaps = 3/60 (5%)
Query: 188 LYVGNLSPQV-DENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAA 246
+ + NLS ++ DEN L +F FG I + I P ++E C F F N+ + A
Sbjct: 213 IXIRNLSTELLDENLLRESFEGFGSIEKINI--PAGQKEHSFNNCCAFXVFENKDSAERA 270
>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 = 32.0 bits (71), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 29/54 (53%), Gaps = 3/54 (5%)
Query: 184 QTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAF 237
++ +++G L+ E+ L FG++G + +KIM + R R GF++F
Sbjct: 2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIM---KDPATGRSRGFGFLSF 52
>pdb|2LO6|A Chain A, Structure Of Nrd1 Cid Bound To Phosphorylated Rnap Ii Ctd
Length = 161
Score = 32.0 bits (71), Expect = 1.8, Method: Composition-based stats.
Identities = 28/147 (19%), Positives = 65/147 (44%), Gaps = 13/147 (8%)
Query: 447 QRDEFEDMLRALT--------LERSQIKEAMGFALDNADAAGEIVEVLTESLTLKETPIP 498
Q D+F++ + L + S+IK+ +ALD+ D +I+ ++ + L P
Sbjct: 3 QDDDFQNFVATLESFKDLKSGISGSRIKKLTTYALDHIDIESKIISLIIDYSRL--CPDS 60
Query: 499 TKVARLMLVSDVLHNSSAPVKNASAYRTKFEATLPDIMESFNDLYRSITGRITAEA---L 555
K+ L ++ + ++ S + T + + ++ + + A++
Sbjct: 61 HKLGSLYIIDSIGRAYLDETRSNSNSSSNKPGTCAHAINTLGEVIQELLSDAIAKSNQDH 120
Query: 556 KERVLKVLQVWSDWFLFSDAYVNGLRA 582
KE++ +L +W LF +Y+N +R+
Sbjct: 121 KEKIRMLLDIWDRSGLFQKSYLNAIRS 147
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 31.6 bits (70), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 5/69 (7%)
Query: 187 NLYVGNLSPQVDENFLLRTFGRFGPIA-SVKIMWPRTEEERRRQRNCGFVAFMNRADGQA 245
+L+VG+L+P VD+ L F + P K++ +T + GFV F + + +
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTG----VSKGYGFVKFTDELEQKR 66
Query: 246 AKDEMQGVV 254
A E QG V
Sbjct: 67 ALTECQGAV 75
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 31.6 bits (70), Expect = 2.5, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 31/73 (42%), Gaps = 8/73 (10%)
Query: 180 DGDPQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMN 239
D P +YVGNL ++ L R FG +GP+ SV + R FV F +
Sbjct: 68 DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVA--------RNPPGFAFVEFED 119
Query: 240 RADGQAAKDEMQG 252
D A ++ G
Sbjct: 120 PRDAADAVRDLDG 132
>pdb|3CLJ|A Chain A, Structure Of The Rna Polymerase Ii Ctd-Interacting Domain
Of Nrd1
Length = 157
Score = 31.6 bits (70), Expect = 2.5, Method: Composition-based stats.
Identities = 26/137 (18%), Positives = 63/137 (45%), Gaps = 7/137 (5%)
Query: 449 DEFEDMLRALTLERSQIKEAMGFALDNADAAGEIVEVLTESLTLKETPIPTKVARLMLVS 508
+ F+D+ ++ S+IK+ +ALD+ D +I+ ++ + L P K+ L ++
Sbjct: 11 ESFKDLKSGIS--GSRIKKLTTYALDHIDIESKIISLIIDYSRL--CPDSHKLGSLYIID 66
Query: 509 DVLHNSSAPVKNASAYRTKFEATLPDIMESFNDLYRSITGRITAEA---LKERVLKVLQV 565
+ ++ S + T + + ++ + + A++ KE++ +L +
Sbjct: 67 SIGRAYLDETRSNSNSSSNKPGTCAHAINTLGEVIQELLSDAIAKSNQDHKEKIRMLLDI 126
Query: 566 WSDWFLFSDAYVNGLRA 582
W LF +Y+N +R+
Sbjct: 127 WDRSGLFQKSYLNAIRS 143
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 31.2 bits (69), Expect = 2.8, Method: Composition-based stats.
Identities = 22/81 (27%), Positives = 34/81 (41%), Gaps = 3/81 (3%)
Query: 186 TNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQA 245
TNL V L + + L F GPI + +IM + + FV F + D Q
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIM---RDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 246 AKDEMQGVVVYEYELKIGWGK 266
A + G+ V LK+ + +
Sbjct: 61 AIKVLNGITVRNKRLKVSYAR 81
>pdb|1G29|1 Chain 1, Malk
pdb|1G29|2 Chain 2, Malk
Length = 372
Score = 31.2 bits (69), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 35/73 (47%), Gaps = 12/73 (16%)
Query: 282 QMAIRSKEGATVILSGPSGPPVTTV---------PSQNSELVLTPNVPDI---MVIPPED 329
+M++ K+G +IL GPSG TT PS+ + V D + +PP+D
Sbjct: 21 EMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQIYIGDKLVADPEKGIFVPPKD 80
Query: 330 RHLRHVIDTLALY 342
R + V + ALY
Sbjct: 81 RDIAMVFQSYALY 93
>pdb|3DDK|A Chain A, Coxsackievirus B3 3dpol Rna Dependent Rna Polymerase
Length = 462
Score = 31.2 bits (69), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 694 SGRYSRGWKETNMEAESMGLSGW-NGYEEDEKLSQAVGSVPLGTMLTTP 741
S R+++ K T S+ L W NG E E+ + + SVP+G LT P
Sbjct: 401 SIRWTKDPKNTQDHVRSLCLLAWHNGEHEYEEFIRKIRSVPVGRCLTLP 449
>pdb|3CDU|A Chain A, Crystal Structure Of Coxsackievirus B3 Rna-dependent Rna
Polymerase (3dpol) In Complex With A Pyrophosphate
pdb|3CDW|A Chain A, Crystal Structure Of Coxsackievirus B3 Rna-Dependent Rna
Polymerase (3dpol) In Complex With Protein Primer Vpg
And A Pyrophosphate
Length = 468
Score = 31.2 bits (69), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 694 SGRYSRGWKETNMEAESMGLSGW-NGYEEDEKLSQAVGSVPLGTMLTTP 741
S R+++ K T S+ L W NG E E+ + + SVP+G LT P
Sbjct: 401 SIRWTKDPKNTQDHVRSLCLLAWHNGEHEYEEFIRKIRSVPVGRCLTLP 449
>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 = 30.8 bits (68), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 33/76 (43%), Gaps = 18/76 (23%)
Query: 184 QTTNLYVG---------NLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGF 234
+ LYVG +L P E+ + F R G I ++ + +NCGF
Sbjct: 133 KNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV---------ESKNCGF 183
Query: 235 VAFMNRADGQAAKDEM 250
V F +A+ + AK+ M
Sbjct: 184 VKFKYQANAEFAKEAM 199
>pdb|3EGN|A Chain A, C-Terminal Rna Recognition Motif Of The U11U12 65K PROTEIN
Length = 143
Score = 30.8 bits (68), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 24/93 (25%), Positives = 42/93 (45%), Gaps = 3/93 (3%)
Query: 177 SFDDGDPQTTNLYVGNLSPQVDENFLLRTFGRFGPIAS--VKIMWPRTEEERRRQRNCGF 234
S++ G+P +YV NL+ V E L FGR+ +S +IM+ + R + F
Sbjct: 38 SYEPGEP-NCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAF 96
Query: 235 VAFMNRADGQAAKDEMQGVVVYEYELKIGWGKS 267
+ N A E G V++ + + + +S
Sbjct: 97 IGLPNEKAAAKALKEANGYVLFGKPMVVQFARS 129
>pdb|3S99|A Chain A, Crystal Structure Of A Basic Membrane Lipoprotein From
Brucella Melitensis, Iodide Soak
Length = 356
Score = 30.4 bits (67), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 36/83 (43%), Gaps = 2/83 (2%)
Query: 674 EKQRGYELDDDLKSAHSQSSSGRYSRGWKETNMEAESMGLSGWNGYEEDEKLSQAVGSVP 733
E GY+ D++ + +++ GRY +G M + G++G+ G ++ Q + S
Sbjct: 114 EHATGYKTADNMSAYNARFYEGRYVQGVIAAKMSKK--GIAGYIGSVPVPEVVQGINSFM 171
Query: 734 LGTMLTTPQPEIKAFTKKEKNDP 756
LG P +K DP
Sbjct: 172 LGAQSVNPDFRVKVIWVNSWFDP 194
>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 = 30.4 bits (67), Expect = 4.8, Method: Composition-based stats.
Identities = 21/83 (25%), Positives = 39/83 (46%), Gaps = 7/83 (8%)
Query: 184 QTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCG--FVAFMNRA 241
++ LYVGNLS E + F + G I + + ++ ++ CG FV + +RA
Sbjct: 38 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGL-----DKMKKTACGFCFVEYYSRA 92
Query: 242 DGQAAKDEMQGVVVYEYELKIGW 264
D + A + G + + ++ W
Sbjct: 93 DAENAMRYINGTRLDDRIIRTDW 115
>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 = 30.4 bits (67), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 33/76 (43%), Gaps = 18/76 (23%)
Query: 184 QTTNLYVG---------NLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGF 234
+ LYVG +L P E+ + F R G I ++ + +NCGF
Sbjct: 135 KNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV---------ESKNCGF 185
Query: 235 VAFMNRADGQAAKDEM 250
V F +A+ + AK+ M
Sbjct: 186 VKFKYQANAEFAKEAM 201
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 30.4 bits (67), Expect = 5.2, Method: Composition-based stats.
Identities = 17/88 (19%), Positives = 35/88 (39%), Gaps = 9/88 (10%)
Query: 179 DDGDPQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFM 238
+ P+ +Y G ++ + + + +TF FG I +++ ++ FV F
Sbjct: 19 NQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF---------PEKGYSFVRFS 69
Query: 239 NRADGQAAKDEMQGVVVYEYELKIGWGK 266
A + G + + +K WGK
Sbjct: 70 THESAAHAIVSVNGTTIEGHVVKCYWGK 97
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 30.0 bits (66), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 17/31 (54%)
Query: 185 TTNLYVGNLSPQVDENFLLRTFGRFGPIASV 215
TT L+VG L P L R F RFG I ++
Sbjct: 17 TTRLWVGGLGPNTSLAALAREFDRFGSIRTI 47
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 30.0 bits (66), Expect = 6.3, Method: Composition-based stats.
Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 4/69 (5%)
Query: 188 LYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAAK 247
++VGNL +V E L F + GP+ V I ++ + ++ GFV F + A
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTI----CKDREGKPKSFGFVCFKHPESVSYAI 74
Query: 248 DEMQGVVVY 256
+ G+ +Y
Sbjct: 75 ALLNGIRLY 83
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 30.0 bits (66), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 34/88 (38%), Gaps = 11/88 (12%)
Query: 179 DDGDPQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFM 238
+G+ T L+V V E+ L FG FGP+ VKI+ FV F
Sbjct: 25 QEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-----------NGFAFVEFE 73
Query: 239 NRADGQAAKDEMQGVVVYEYELKIGWGK 266
A +E+ G L++ + K
Sbjct: 74 EAESAAKAIEEVHGKSFANQPLEVVYSK 101
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 30.0 bits (66), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 26/50 (52%), Gaps = 3/50 (6%)
Query: 188 LYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAF 237
++VG + E L F +FG + V +++ + E++R R GF+ F
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIY---DAEKQRPRGFGFITF 59
>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 = 9.0, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 3/50 (6%)
Query: 188 LYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAF 237
++VG LSP E + FG FG + S+++ P + +R+ C F+ F
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIEL--PMDNKTNKRRGFC-FITF 48
>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 = 29.6 bits (65), Expect = 9.5, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 3/50 (6%)
Query: 188 LYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAF 237
++VG LSP E + FG FG + S+++ P + +R+ C F+ F
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIEL--PMDNKTNKRRGFC-FITF 50
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 29.3 bits (64), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 16/71 (22%), Positives = 33/71 (46%), Gaps = 3/71 (4%)
Query: 182 DPQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRA 241
D +++VGN+ + E L F GP+ S ++++ R E + + GF + ++
Sbjct: 5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDR---ETGKPKGYGFCEYQDQE 61
Query: 242 DGQAAKDEMQG 252
+A + G
Sbjct: 62 TALSAMRNLNG 72
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
0.314 0.132 0.383
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 25,404,899
Number of Sequences: 62578
Number of extensions: 1040467
Number of successful extensions: 2118
Number of sequences better than 100.0: 100
Number of HSP's better than 100.0 without gapping: 32
Number of HSP's successfully gapped in prelim test: 68
Number of HSP's that attempted gapping in prelim test: 2050
Number of HSP's gapped (non-prelim): 110
length of query: 973
length of database: 14,973,337
effective HSP length: 108
effective length of query: 865
effective length of database: 8,214,913
effective search space: 7105899745
effective search space used: 7105899745
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 56 (26.2 bits)