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= 041390
         (639 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
           From Hypothetical Protein Bab23448
          Length = 99

 Score = 36.2 bits (82), Expect = 0.061,   Method: Compositional matrix adjust.
 Identities = 17/43 (39%), Positives = 26/43 (60%), Gaps = 4/43 (9%)

Query: 323 TFREEDVSNYFSIYGPVHDVRIPY----QQKRMFGFVTFVYPE 361
           T  EED+   FS YGP+ ++  P     ++ + F FVTF++PE
Sbjct: 19  TSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPE 61


>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
           Daz-Associated Protein 1
          Length = 105

 Score = 34.3 bits (77), Expect = 0.19,   Method: Composition-based stats.
 Identities = 25/68 (36%), Positives = 32/68 (47%), Gaps = 5/68 (7%)

Query: 321 DSTFREEDVSNYFSIYGPVHDVRI----PYQQKRMFGFVTFVYPETVKLILAKGNPHFVC 376
           D +  +E + +YFS YG V D  I       Q R FGFV F  P  V  +LA   PH + 
Sbjct: 25  DWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLD 83

Query: 377 DSRVLVKP 384
              +  KP
Sbjct: 84  GRNIDPKP 91


>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
           Beta Protein In Complex With Rna (Gaagaa)
          Length = 99

 Score = 34.3 bits (77), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 20/40 (50%), Positives = 23/40 (57%), Gaps = 3/40 (7%)

Query: 326 EEDVSNYFSIYGPVHDVRIPYQQ--KRMFGFVTFVYPETV 363
           E D+   FS YGP+ DV I Y Q  +R  GF  FVY E V
Sbjct: 29  ERDLREVFSKYGPIADVSIVYDQQSRRSRGFA-FVYFENV 67


>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
           Aagaac Rna
          Length = 129

 Score = 34.3 bits (77), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 20/40 (50%), Positives = 23/40 (57%), Gaps = 3/40 (7%)

Query: 326 EEDVSNYFSIYGPVHDVRIPYQQ--KRMFGFVTFVYPETV 363
           E D+   FS YGP+ DV I Y Q  +R  GF  FVY E V
Sbjct: 60  ERDLREVFSKYGPIADVSIVYDQQSRRSRGF-AFVYFENV 98


>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
           Protein
          Length = 96

 Score = 33.5 bits (75), Expect = 0.39,   Method: Composition-based stats.
 Identities = 20/40 (50%), Positives = 23/40 (57%), Gaps = 3/40 (7%)

Query: 326 EEDVSNYFSIYGPVHDVRIPY--QQKRMFGFVTFVYPETV 363
           E D+   FS YGP+ DV I Y  Q +R  GF  FVY E V
Sbjct: 26  ERDLREVFSKYGPIADVSIVYDQQSRRSRGF-AFVYFENV 64


>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
           ArginineSERINE-Rich Splicing Factor 10
          Length = 95

 Score = 33.1 bits (74), Expect = 0.47,   Method: Composition-based stats.
 Identities = 20/40 (50%), Positives = 23/40 (57%), Gaps = 3/40 (7%)

Query: 326 EEDVSNYFSIYGPVHDVRIPY--QQKRMFGFVTFVYPETV 363
           E D+   FS YGP+ DV I Y  Q +R  GF  FVY E V
Sbjct: 29  ERDLREVFSKYGPIADVSIVYDQQSRRSRGF-AFVYFENV 67


>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
           Protein- 43
          Length = 88

 Score = 30.8 bits (68), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 16/32 (50%), Positives = 21/32 (65%), Gaps = 1/32 (3%)

Query: 326 EEDVSNYFSIYGPVHDVRIPYQQKRMFGFVTF 357
           E+++  +FS YG V DV IP +  R F FVTF
Sbjct: 19  EDELREFFSQYGDVMDVFIP-KPFRAFAFVTF 49


>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 = 30.4 bits (67), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 14/32 (43%), Positives = 18/32 (56%), Gaps = 1/32 (3%)

Query: 195 CLYFAKGFCKNGTACKF-HHIHSPEAATAAAI 225
           CL+FAKG C  G  C++ HHI   E     A+
Sbjct: 73  CLFFAKGMCCLGPKCEYLHHIPDEEDIGKLAL 104


>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 = 30.4 bits (67), Expect = 3.5,   Method: Composition-based stats.
 Identities = 15/42 (35%), Positives = 24/42 (57%), Gaps = 4/42 (9%)

Query: 326 EEDVSNYFSIYGPVHDVRI----PYQQKRMFGFVTFVYPETV 363
           E+++  YF  YG V D++I       + R FGF++F  P +V
Sbjct: 17  EDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSV 58


>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
 pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
          Length = 75

 Score = 30.0 bits (66), Expect = 3.9,   Method: Composition-based stats.
 Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 4/44 (9%)

Query: 327 EDVSNYFSIYGPVHDVRIPYQQK----RMFGFVTFVYPETVKLI 366
           EDV +YF  +G V D  + + +     R FGFVTF   + V+ +
Sbjct: 14  EDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKV 57


>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 = 30.0 bits (66), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 14/32 (43%), Positives = 18/32 (56%), Gaps = 1/32 (3%)

Query: 195 CLYFAKGFCKNGTACKF-HHIHSPEAATAAAI 225
           CL+FAKG C  G  C++ HHI   E     A+
Sbjct: 75  CLFFAKGMCCLGPKCEYLHHIPDEEDIGKLAL 106


  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
   0.320    0.134    0.407 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,025,626
Number of Sequences: 62578
Number of extensions: 482374
Number of successful extensions: 12503
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 12496
Number of HSP's gapped (non-prelim): 18
length of query: 639
length of database: 14,973,337
effective HSP length: 105
effective length of query: 534
effective length of database: 8,402,647
effective search space: 4487013498
effective search space used: 4487013498
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)