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= 002482
(917 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2CPI|A Chain A, Solution Structure Of The Rna Recognition Motif Of Cnot4
Length = 111
Score = 96.3 bits (238), Expect = 7e-20, Method: Composition-based stats.
Identities = 46/96 (47%), Positives = 68/96 (70%), Gaps = 2/96 (2%)
Query: 26 VRVIQRNLVYIIGLPINLADEDLLQRKEYFGQYGKVLKVSISRTATGDIQHSANNSCCVY 85
VRV+Q+NLV+++GL LAD ++L+R EYFG++GK+ KV I+ + + S S Y
Sbjct: 10 VRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTS--YAGSQGPSASAY 67
Query: 86 ITYSREDDAIRCIQSVHSYILDGRPLRACFGTTKYC 121
+TY R +DA+R IQ V++ ++DGR L+A GTTKYC
Sbjct: 68 VTYIRSEDALRAIQCVNNVVVDGRTLKASLGTTKYC 103
>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 = 0.011, Method: Composition-based stats.
Identities = 23/83 (27%), Positives = 46/83 (55%), Gaps = 8/83 (9%)
Query: 31 RNLVYIIGLPINLADEDLLQRKEYFGQYGKVLKVSISRTATGDIQHSANNSCCVYITYSR 90
++ VY+ LP +L + DL + F +YGKV+KV+I + + + + +I +
Sbjct: 16 KSTVYVSNLPFSLTNNDLYR---IFSKYGKVVKVTIMKD-----KDTRKSKGVAFILFLD 67
Query: 91 EDDAIRCIQSVHSYILDGRPLRA 113
+D A C +++++ L GR ++A
Sbjct: 68 KDSAQNCTRAINNKQLFGRVIKA 90
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 37.0 bits (84), Expect = 0.044, Method: Composition-based stats.
Identities = 27/109 (24%), Positives = 47/109 (43%), Gaps = 27/109 (24%)
Query: 11 KAKPKPSEGRMHLTNVRVIQRNLVYIIGLPINLADEDLLQRKEYFGQYGKVLKVSISRTA 70
K++PK R+H++N+ P D DL ++ FGQ+GK+L V I
Sbjct: 26 KSQPK----RLHVSNI-------------PFRFRDPDL---RQMFGQFGKILDVEIIFNE 65
Query: 71 TGDIQHSANNSCCVYITYSREDDAIRCIQSVHSYILDGRPLRACFGTTK 119
G ++T+ DA R + +H +++GR + T +
Sbjct: 66 RGSKGFG-------FVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107
>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 = 37.0 bits (84), Expect = 0.050, Method: Composition-based stats.
Identities = 25/82 (30%), Positives = 41/82 (50%), Gaps = 6/82 (7%)
Query: 24 TNVRVIQRNLVYIIGLPINLADEDLLQRKEYFGQYGKVLKVSISRTATGDIQHSANNSCC 83
T+ ++ + I L L DE+LL +E F +G + K++I G +HS NN CC
Sbjct: 203 TDSATLEGREIXIRNLSTELLDENLL--RESFEGFGSIEKINIP---AGQKEHSFNN-CC 256
Query: 84 VYITYSREDDAIRCIQSVHSYI 105
+ + +D A R +Q S +
Sbjct: 257 AFXVFENKDSAERALQXNRSLL 278
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 35.0 bits (79), Expect = 0.17, Method: Composition-based stats.
Identities = 25/87 (28%), Positives = 38/87 (43%), Gaps = 8/87 (9%)
Query: 36 IIGLPINLADEDLLQRKEYFGQYGKVLKVSISRTATGDIQHSANNSCCVYITYSREDDAI 95
+ GL + + DL +E F +YG + VSI Q S + ++ + DDA
Sbjct: 17 VFGLSLYTTERDL---REVFSKYGPIADVSIVYD-----QQSRRSRGFAFVYFENVDDAK 68
Query: 96 RCIQSVHSYILDGRPLRACFGTTKYCH 122
+ + LDGR +R F TK H
Sbjct: 69 EAKERANGMELDGRRIRVDFSITKRPH 95
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 35.0 bits (79), Expect = 0.17, Method: Composition-based stats.
Identities = 25/87 (28%), Positives = 38/87 (43%), Gaps = 8/87 (9%)
Query: 36 IIGLPINLADEDLLQRKEYFGQYGKVLKVSISRTATGDIQHSANNSCCVYITYSREDDAI 95
+ GL + + DL +E F +YG + VSI Q S + ++ + DDA
Sbjct: 51 VFGLSLYTTERDL---REVFSKYGPIADVSIVYD-----QQSRRSRGFAFVYFENVDDAK 102
Query: 96 RCIQSVHSYILDGRPLRACFGTTKYCH 122
+ + LDGR +R F TK H
Sbjct: 103 EAKERANGMELDGRRIRVDFSITKRPH 129
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 35.0 bits (79), Expect = 0.17, Method: Composition-based stats.
Identities = 21/86 (24%), Positives = 39/86 (45%), Gaps = 10/86 (11%)
Query: 34 VYIIGLPINLADEDLLQRKEYFGQYGKVLKVSISRTATGDIQHSANNSCCVYITYSREDD 93
+++ +P D DL ++ FGQ+GK+L V I G ++T+ D
Sbjct: 18 LHVSNIPFRFRDPDL---RQMFGQFGKILDVEIIFNERGSKGFG-------FVTFENSAD 67
Query: 94 AIRCIQSVHSYILDGRPLRACFGTTK 119
A R + +H +++GR + T +
Sbjct: 68 ADRAREKLHGTVVEGRKIEVNNATAR 93
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 34.7 bits (78), Expect = 0.25, Method: Composition-based stats.
Identities = 25/87 (28%), Positives = 38/87 (43%), Gaps = 8/87 (9%)
Query: 36 IIGLPINLADEDLLQRKEYFGQYGKVLKVSISRTATGDIQHSANNSCCVYITYSREDDAI 95
+ GL + + DL +E F +YG + VSI Q S + ++ + DDA
Sbjct: 20 VFGLSLYTTERDL---REVFSKYGPIADVSIVYD-----QQSRRSRGFAFVYFENVDDAK 71
Query: 96 RCIQSVHSYILDGRPLRACFGTTKYCH 122
+ + LDGR +R F TK H
Sbjct: 72 EAKERANGMELDGRRIRVDFSITKRPH 98
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 30.4 bits (67), Expect = 4.3, Method: Composition-based stats.
Identities = 14/47 (29%), Positives = 23/47 (48%), Gaps = 1/47 (2%)
Query: 73 DIQHSANNSCCVYITYSREDDAIRCIQSVHSYILDGRPLRACFGTTK 119
D +H CC +I Y + A CI ++ ++ GR LR +G +
Sbjct: 56 DFKHYPEKGCC-FIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKER 101
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 30.4 bits (67), Expect = 4.8, Method: Composition-based stats.
Identities = 17/73 (23%), Positives = 36/73 (49%), Gaps = 9/73 (12%)
Query: 39 LPINLADEDLLQRKEYFGQYGKVLKVSISRTATGDIQHSANNSCCVYITYSREDDAIRCI 98
L ++D D+ +E F ++G + K ++ +G +A+ + + R DA++ +
Sbjct: 43 LDFGVSDADI---QELFAEFGTLKKAAVDYDRSGRSLGTAD------VHFERRADALKAM 93
Query: 99 QSVHSYILDGRPL 111
+ LDGRP+
Sbjct: 94 KQYKGVPLDGRPM 106
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 30.4 bits (67), Expect = 5.0, Method: Composition-based stats.
Identities = 17/73 (23%), Positives = 36/73 (49%), Gaps = 9/73 (12%)
Query: 39 LPINLADEDLLQRKEYFGQYGKVLKVSISRTATGDIQHSANNSCCVYITYSREDDAIRCI 98
L ++D D+ +E F ++G + K ++ +G +A+ + + R DA++ +
Sbjct: 43 LDFGVSDADI---QELFAEFGTLKKAAVDYDRSGRSLGTAD------VHFERRADALKAM 93
Query: 99 QSVHSYILDGRPL 111
+ LDGRP+
Sbjct: 94 KQYKGVPLDGRPM 106
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 30.0 bits (66), Expect = 6.6, Method: Composition-based stats.
Identities = 17/73 (23%), Positives = 38/73 (52%), Gaps = 9/73 (12%)
Query: 39 LPINLADEDLLQRKEYFGQYGKVLKVSISRTATGDIQHSANNSCCVYITYSREDDAIRCI 98
L ++D D+ +E F ++G + K ++ +G +A+ + + R+ DA++ +
Sbjct: 36 LDFGVSDADI---QELFAEFGTLKKAAVHYDRSGRSLGTAD------VHFERKADALKAM 86
Query: 99 QSVHSYILDGRPL 111
+ + LDGRP+
Sbjct: 87 KQYNGVPLDGRPM 99
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 29.6 bits (65), Expect = 8.2, Method: Composition-based stats.
Identities = 20/84 (23%), Positives = 46/84 (54%), Gaps = 11/84 (13%)
Query: 27 RVIQRNL-VYIIGLPINLADEDLLQRKEYFGQYGKVLKVSISRTATGDIQHSANNSCCVY 85
R +Q+ + ++GLP ++DL KEYF +G+VL V + + D++ + ++ +
Sbjct: 10 RAVQKTSDLIVLGLPWKTTEQDL---KEYFSTFGEVLMVQVKK----DLK-TGHSKGFGF 61
Query: 86 ITYSREDDAIRCIQSVHSYILDGR 109
+ ++ + ++ + H ++DGR
Sbjct: 62 VRFTEYETQVKVMSQRH--MIDGR 83
>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 = 29.6 bits (65), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 19/87 (21%), Positives = 41/87 (47%), Gaps = 8/87 (9%)
Query: 32 NLVYIIGLPINLADEDLLQRKEYFGQYGKVLKVSISRTATGDIQHSANNSCCVYITYSRE 91
N +Y+ + +L+D+D+ K F +GK+ +++R T + + +I Y +
Sbjct: 126 NRIYVASVHQDLSDDDI---KSVFEAFGKIKSATLARDPT-----TGKHKGYGFIEYEKA 177
Query: 92 DDAIRCIQSVHSYILDGRPLRACFGTT 118
+ + S++ + L G+ LR T
Sbjct: 178 QSSQDAVSSMNLFDLGGQYLRVGKAVT 204
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
0.313 0.128 0.376
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 26,575,664
Number of Sequences: 62578
Number of extensions: 1077298
Number of successful extensions: 1654
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 25
Number of HSP's that attempted gapping in prelim test: 1647
Number of HSP's gapped (non-prelim): 29
length of query: 917
length of database: 14,973,337
effective HSP length: 108
effective length of query: 809
effective length of database: 8,214,913
effective search space: 6645864617
effective search space used: 6645864617
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)