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= 009405
         (535 letters)

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

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



>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
           Pspc1NONO
          Length = 261

 Score = 33.5 bits (75), Expect = 0.32,   Method: Compositional matrix adjust.
 Identities = 37/149 (24%), Positives = 60/149 (40%), Gaps = 14/149 (9%)

Query: 362 RIRVAHEHGTLVVLENLDPSYTSTVVEDLVWHAFKE-NCSAKMIPRVAFASPYFGQSFVI 420
           RIR A  HG  + ++NL P     V  +L+  AF +     K +  V       G+ FV 
Sbjct: 89  RIRFAT-HGAALTVKNLSP----VVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVE 143

Query: 421 FKTREVAELVVTKLEEGCLLLSNGRPLLGSIGTPCFTGKQSKFVGHLAL-DKLKFQMQRE 479
           F  +  A   + +  +G  LL+       +   P       +F     L +KL  + Q+ 
Sbjct: 144 FAAKPPARKALERCGDGAFLLT-------TTPRPVIVEPMEQFDDEDGLPEKLMQKTQQY 196

Query: 480 MREAVSTSHCSQPNSLEYDMAIEWSLLQE 508
            +E       +QP + E++ A  W  L E
Sbjct: 197 HKEREQPPRFAQPGTFEFEYASRWKALDE 225


>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
           Pspc1NONO
          Length = 261

 Score = 28.9 bits (63), Expect = 7.7,   Method: Compositional matrix adjust.
 Identities = 37/148 (25%), Positives = 58/148 (39%), Gaps = 12/148 (8%)

Query: 362 RIRVAHEHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIF 421
           R+R A    +L V  NL P Y S  + +  +  F +   A +I  V       G+  V F
Sbjct: 89  RVRFACHSASLTV-RNL-PQYVSNELLEEAFSVFGQVERAVVI--VDDRGRPSGKGIVEF 144

Query: 422 KTREVAELVVTKLEEGCLLLSNGRPLLGSIGTPCFTGKQSKFVGHLAL-DKLKFQMQREM 480
             +  A   + +  EG  LL+       +   P       +      L +KL  + Q+  
Sbjct: 145 SGKPAARKALDRCSEGSFLLT-------TFPRPVTVEPMDQLDDEEGLPEKLVIKNQQFH 197

Query: 481 REAVSTSHCSQPNSLEYDMAIEWSLLQE 508
           +E       +QP S EY+ A+ W  L E
Sbjct: 198 KEREQPPRFAQPGSFEYEYAMRWKALIE 225


  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
   0.312    0.128    0.360 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,752,977
Number of Sequences: 62578
Number of extensions: 469119
Number of successful extensions: 867
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 863
Number of HSP's gapped (non-prelim): 8
length of query: 535
length of database: 14,973,337
effective HSP length: 103
effective length of query: 432
effective length of database: 8,527,803
effective search space: 3684010896
effective search space used: 3684010896
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: 54 (25.4 bits)