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= psy6355
(83 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 63.9 bits (154), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 31/46 (67%), Positives = 36/46 (78%)
Query: 5 TDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPS 50
T R +GFIRFD+RIEAE AI+ LNG P G+ EPITVKFAN+PS
Sbjct: 39 TGVSRGVGFIRFDKRIEAEEAIKGLNGQKPLGAAEPITVKFANNPS 84
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 63.5 bits (153), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 31/46 (67%), Positives = 36/46 (78%)
Query: 5 TDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPS 50
T R +GFIRFD+RIEAE AI+ LNG P G+ EPITVKFAN+PS
Sbjct: 128 TGVSRGVGFIRFDKRIEAEEAIKGLNGQKPLGAAEPITVKFANNPS 173
>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 = 58.2 bits (139), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 28/42 (66%), Positives = 32/42 (76%)
Query: 5 TDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFA 46
T R +GFIRFD+RIEAE AI+ LNG P G+ EPITVKFA
Sbjct: 126 TGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167
>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 = 52.8 bits (125), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 26/42 (61%), Positives = 29/42 (69%)
Query: 5 TDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFA 46
T R + FIRFD+R EAE AI NG P GS+EPITVKFA
Sbjct: 126 TGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPITVKFA 167
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 50.4 bits (119), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 25/42 (59%), Positives = 28/42 (66%)
Query: 5 TDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFA 46
T R + FIRFD+R EAE AI NG P GS+EPITV FA
Sbjct: 126 TGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPITVXFA 167
>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 = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 29/43 (67%)
Query: 4 FTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFA 46
T R + F+R+++R EA+ AI LN IP+G ++P++V+ A
Sbjct: 50 LTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 92
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 41.2 bits (95), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 28/38 (73%)
Query: 9 RYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFA 46
R + F+R+++R EA+ AI LN IP+G ++P++V+ A
Sbjct: 131 RGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168
>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 = 41.2 bits (95), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 28/38 (73%)
Query: 9 RYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFA 46
R + F+R+++R EA+ AI LN IP+G ++P++V+ A
Sbjct: 142 RGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 179
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 32.0 bits (71), Expect = 0.080, Method: Composition-based stats.
Identities = 19/43 (44%), Positives = 26/43 (60%), Gaps = 2/43 (4%)
Query: 4 FTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFA 46
F + R GFIR + R AE A EL+GTI K + P+ ++FA
Sbjct: 53 FINRDRGFGFIRLESRTLAEIAKAELDGTILK--SRPLRIRFA 93
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 31.6 bits (70), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 6/54 (11%)
Query: 1 MKGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSNK 54
+K D+ FI FD+R A +A++E+NG +G N I + FA P K
Sbjct: 41 VKKLKDYA----FIHFDERDGAVKAMEEMNGKDLEGEN--IEIVFAKPPDQKRK 88
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 30.4 bits (67), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 30/62 (48%), Gaps = 13/62 (20%)
Query: 3 GFTDFCRYL----------GFIRFDQRIEAERAIQELNG--TIPKGSNEPITVKFANSPS 50
G D C L F++F EA+ AI L+G T+P G++ + VKFA++
Sbjct: 40 GVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMP-GASSSLVVKFADTDK 98
Query: 51 SS 52
S
Sbjct: 99 ES 100
>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 = 30.0 bits (66), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 10/27 (37%), Positives = 17/27 (62%)
Query: 5 TDFCRYLGFIRFDQRIEAERAIQELNG 31
T+ + GF+ +D + A+ AIQ +NG
Sbjct: 63 TNLSKCFGFVSYDNPVSAQAAIQSMNG 89
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 28.5 bits (62), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 26/42 (61%), Gaps = 3/42 (7%)
Query: 13 FIRFDQRIEAERAIQELNG--TIPKGSNEPITVKFANSPSSS 52
F+++ EA+ AI L+G T+P G++ + VKFA++ S
Sbjct: 60 FVKYSSHAEAQAAINALHGSQTMP-GASSSLVVKFADTDKES 100
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif In Trna Selenocysteine Associated Protein
Length = 104
Score = 28.1 bits (61), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 5 TDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFA 46
T + GF++F +E +RA+ E G + GS +P+ + A
Sbjct: 47 TGVSKGYGFVKFTDELEQKRALTECQGAVGLGS-KPVRLSVA 87
>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 = 27.7 bits (60), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 10/22 (45%), Positives = 17/22 (77%)
Query: 12 GFIRFDQRIEAERAIQELNGTI 33
GF+ F+ + AERAI+++NG +
Sbjct: 146 GFVHFETQEAAERAIEKMNGML 167
>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 = 27.3 bits (59), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 10/22 (45%), Positives = 17/22 (77%)
Query: 12 GFIRFDQRIEAERAIQELNGTI 33
GF+ F+ + AERAI+++NG +
Sbjct: 141 GFVHFETQEAAERAIEKMNGML 162
>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 = 27.3 bits (59), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 10/22 (45%), Positives = 17/22 (77%)
Query: 12 GFIRFDQRIEAERAIQELNGTI 33
GF+ F+ + AERAI+++NG +
Sbjct: 48 GFVHFETQEAAERAIEKMNGML 69
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 27.3 bits (59), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 10/22 (45%), Positives = 17/22 (77%)
Query: 12 GFIRFDQRIEAERAIQELNGTI 33
GF+ F+ + AERAI+++NG +
Sbjct: 54 GFVHFETQEAAERAIEKMNGML 75
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 26.6 bits (57), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 10/26 (38%), Positives = 19/26 (73%)
Query: 11 LGFIRFDQRIEAERAIQELNGTIPKG 36
GF+ F+ +A+RA ++L+GT+ +G
Sbjct: 57 FGFVTFENSADADRAREKLHGTVVEG 82
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1
In Complex With Ugcaugu
Length = 109
Score = 26.6 bits (57), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 10/26 (38%), Positives = 19/26 (73%)
Query: 11 LGFIRFDQRIEAERAIQELNGTIPKG 36
GF+ F+ +A+RA ++L+GT+ +G
Sbjct: 71 FGFVTFENSADADRAREKLHGTVVEG 96
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
0.324 0.141 0.429
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,243,117
Number of Sequences: 62578
Number of extensions: 64408
Number of successful extensions: 146
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 120
Number of HSP's gapped (non-prelim): 29
length of query: 83
length of database: 14,973,337
effective HSP length: 51
effective length of query: 32
effective length of database: 11,781,859
effective search space: 377019488
effective search space used: 377019488
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 45 (21.9 bits)