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= 002856
         (873 letters)

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

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



>pdb|2OEV|A Chain A, Crystal Structure Of AlixAIP1
          Length = 705

 Score = 32.0 bits (71), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 31/115 (26%), Positives = 50/115 (43%), Gaps = 8/115 (6%)

Query: 225 DVDELYHLLPLDKVESLEDLVTIGPPGLVKATVIST--HQQVTSVQEQGEDTASQDSNSD 282
           D D +YH    D+V  L+DL  IG   LVK+T ++    Q+ T + E+    + Q S + 
Sbjct: 321 DNDFIYH----DRVPDLKDLDPIGKATLVKSTPVNVPISQKFTDLFEKMVPVSVQQSLAA 376

Query: 283 VAARTPPAKSSGVGSTASTPAVGPATPISINVPAQTLSNASNTSP--VLPGSSSV 335
              R     +  +        +      S+N+PA     + +T P  +L  S SV
Sbjct: 377 YNQRKADLVNRSIAQMREATTLANGVLASLNLPAAIEDVSGDTVPQSILTKSRSV 431


>pdb|2R02|A Chain A, Crystal Structure Of AlixAIP1 IN COMPLEX WITH THE HIV-1
           Ypltsl Late Domain
 pdb|2R03|A Chain A, Crystal Structure Of AlixAIP1 IN COMPLEX WITH THE YPDL
           Late Domain
 pdb|2R05|A Chain A, Crystal Structure Of AlixAIP1 IN COMPLEX WITH THE HIV-1
           Yplasl Late Domain
          Length = 697

 Score = 32.0 bits (71), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 31/115 (26%), Positives = 50/115 (43%), Gaps = 8/115 (6%)

Query: 225 DVDELYHLLPLDKVESLEDLVTIGPPGLVKATVIST--HQQVTSVQEQGEDTASQDSNSD 282
           D D +YH    D+V  L+DL  IG   LVK+T ++    Q+ T + E+    + Q S + 
Sbjct: 313 DNDFIYH----DRVPDLKDLDPIGKATLVKSTPVNVPISQKFTDLFEKMVPVSVQQSLAA 368

Query: 283 VAARTPPAKSSGVGSTASTPAVGPATPISINVPAQTLSNASNTSP--VLPGSSSV 335
              R     +  +        +      S+N+PA     + +T P  +L  S SV
Sbjct: 369 YNQRKADLVNRSIAQMREATTLANGVLASLNLPAAIEDVSGDTVPQSILTKSRSV 423


>pdb|2XS1|A Chain A, Crystal Structure Of Alix In Complex With The Sivmac239
           Pykevtedl Late Domain
 pdb|2XS8|A Chain A, Crystal Structure Of Alix In Complex With The Sivagmtan-1
           Aydparkll Late Domain
          Length = 704

 Score = 32.0 bits (71), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 31/115 (26%), Positives = 50/115 (43%), Gaps = 8/115 (6%)

Query: 225 DVDELYHLLPLDKVESLEDLVTIGPPGLVKATVIST--HQQVTSVQEQGEDTASQDSNSD 282
           D D +YH    D+V  L+DL  IG   LVK+T ++    Q+ T + E+    + Q S + 
Sbjct: 320 DNDFIYH----DRVPDLKDLDPIGKATLVKSTPVNVPISQKFTDLFEKMVPVSVQQSLAA 375

Query: 283 VAARTPPAKSSGVGSTASTPAVGPATPISINVPAQTLSNASNTSP--VLPGSSSV 335
              R     +  +        +      S+N+PA     + +T P  +L  S SV
Sbjct: 376 YNQRKADLVNRSIAQMREATTLANGVLASLNLPAAIEDVSGDTVPQSILTKSRSV 430


>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
           Murine Apaf-1
          Length = 1256

 Score = 30.4 bits (67), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 22/87 (25%), Positives = 40/87 (45%), Gaps = 6/87 (6%)

Query: 788 YYQQNTYQQYLAAKELKKQSWRYHRKYNTWFQRHEEPKVANDEFEQGTYVY--FDFHIAN 845
           YY  +    +L  K  + Q    HRK  T FQR+ +P   + + E   Y Y    +H+A+
Sbjct: 442 YYLHDLQVDFLTEKN-RSQLQDLHRKMVTQFQRYYQPHTLSPDQEDCMYWYNFLAYHMAS 500

Query: 846 DDLQHGWCQRIKTEFTFEYNYLEDELI 872
            ++    C  +   F+ ++   + EL+
Sbjct: 501 ANMHKELCALM---FSLDWIKAKTELV 524


>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
          Length = 1249

 Score = 30.0 bits (66), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 22/87 (25%), Positives = 40/87 (45%), Gaps = 6/87 (6%)

Query: 788 YYQQNTYQQYLAAKELKKQSWRYHRKYNTWFQRHEEPKVANDEFEQGTYVY--FDFHIAN 845
           YY  +    +L  K  + Q    HRK  T FQR+ +P   + + E   Y Y    +H+A+
Sbjct: 435 YYLHDLQVDFLTEKN-RSQLQDLHRKMVTQFQRYYQPHTLSPDQEDCMYWYNFLAYHMAS 493

Query: 846 DDLQHGWCQRIKTEFTFEYNYLEDELI 872
            ++    C  +   F+ ++   + EL+
Sbjct: 494 ANMHKELCALM---FSLDWIKAKTELV 517


  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
   0.311    0.128    0.363 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 24,203,534
Number of Sequences: 62578
Number of extensions: 973048
Number of successful extensions: 2129
Number of sequences better than 100.0: 43
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 41
Number of HSP's that attempted gapping in prelim test: 2126
Number of HSP's gapped (non-prelim): 44
length of query: 873
length of database: 14,973,337
effective HSP length: 107
effective length of query: 766
effective length of database: 8,277,491
effective search space: 6340558106
effective search space used: 6340558106
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 56 (26.2 bits)