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= 005538
         (691 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 = 31.6 bits (70), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 31/115 (26%), Positives = 50/115 (43%), Gaps = 8/115 (6%)

Query: 43  DVDELYHLLPLDKVESLEDLVTIGPPGLVKATVIST--HQQVTSVQEQGEDTASQDSNSD 100
           D D +YH    D+V  L+DL  IG   LVK+T ++    Q+ T + E+    + Q S + 
Sbjct: 321 DNDFIYH----DRVPDLKDLDPIGKATLVKSTPVNVPISQKFTDLFEKMVPVSVQQSLAA 376

Query: 101 VAARTPPAKSSGVGSTASTPAVGPATPISINVPAQTLSNASNTSP--VLPGSSSV 153
              R     +  +        +      S+N+PA     + +T P  +L  S SV
Sbjct: 377 YNQRKADLVNRSIAQMREATTLANGVLASLNLPAAIEDVSGDTVPQSILTKSRSV 431


>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 = 31.6 bits (70), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 31/115 (26%), Positives = 50/115 (43%), Gaps = 8/115 (6%)

Query: 43  DVDELYHLLPLDKVESLEDLVTIGPPGLVKATVIST--HQQVTSVQEQGEDTASQDSNSD 100
           D D +YH    D+V  L+DL  IG   LVK+T ++    Q+ T + E+    + Q S + 
Sbjct: 320 DNDFIYH----DRVPDLKDLDPIGKATLVKSTPVNVPISQKFTDLFEKMVPVSVQQSLAA 375

Query: 101 VAARTPPAKSSGVGSTASTPAVGPATPISINVPAQTLSNASNTSP--VLPGSSSV 153
              R     +  +        +      S+N+PA     + +T P  +L  S SV
Sbjct: 376 YNQRKADLVNRSIAQMREATTLANGVLASLNLPAAIEDVSGDTVPQSILTKSRSV 430


>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 = 31.6 bits (70), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 31/115 (26%), Positives = 50/115 (43%), Gaps = 8/115 (6%)

Query: 43  DVDELYHLLPLDKVESLEDLVTIGPPGLVKATVIST--HQQVTSVQEQGEDTASQDSNSD 100
           D D +YH    D+V  L+DL  IG   LVK+T ++    Q+ T + E+    + Q S + 
Sbjct: 313 DNDFIYH----DRVPDLKDLDPIGKATLVKSTPVNVPISQKFTDLFEKMVPVSVQQSLAA 368

Query: 101 VAARTPPAKSSGVGSTASTPAVGPATPISINVPAQTLSNASNTSP--VLPGSSSV 153
              R     +  +        +      S+N+PA     + +T P  +L  S SV
Sbjct: 369 YNQRKADLVNRSIAQMREATTLANGVLASLNLPAAIEDVSGDTVPQSILTKSRSV 423


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

 Score = 30.0 bits (66), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 22/87 (25%), Positives = 40/87 (45%), Gaps = 6/87 (6%)

Query: 606 YYQQNTYQQYLAAKELKKQSWRYHRKYNTWFQRHEEPKVANDEFEQGTYVY--FDFHIAN 663
           YY  +    +L  K  + Q    HRK  T FQR+ +P   + + E   Y Y    +H+A+
Sbjct: 442 YYLHDLQVDFLTEKN-RSQLQDLHRKMVTQFQRYYQPHTLSPDQEDCMYWYNFLAYHMAS 500

Query: 664 DDLQHGWCQRIKTEFTFEYNYLEDELI 690
            ++    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 = 4.9,   Method: Compositional matrix adjust.
 Identities = 22/87 (25%), Positives = 40/87 (45%), Gaps = 6/87 (6%)

Query: 606 YYQQNTYQQYLAAKELKKQSWRYHRKYNTWFQRHEEPKVANDEFEQGTYVY--FDFHIAN 663
           YY  +    +L  K  + Q    HRK  T FQR+ +P   + + E   Y Y    +H+A+
Sbjct: 435 YYLHDLQVDFLTEKN-RSQLQDLHRKMVTQFQRYYQPHTLSPDQEDCMYWYNFLAYHMAS 493

Query: 664 DDLQHGWCQRIKTEFTFEYNYLEDELI 690
            ++    C  +   F+ ++   + EL+
Sbjct: 494 ANMHKELCALM---FSLDWIKAKTELV 517


>pdb|1ZN6|A Chain A, X-Ray Crystal Structure Of Protein Q7wlm8 From Bordetella
           Bronchiseptica. Northeast Structural Genomics Consortium
           Target Bor19
          Length = 227

 Score = 29.3 bits (64), Expect = 6.9,   Method: Composition-based stats.
 Identities = 12/38 (31%), Positives = 18/38 (47%), Gaps = 2/38 (5%)

Query: 554 KDSERARSYIPRHPAVTPPS--YPQVQAPIVSNPAFWE 589
           KD ER R Y   HP+   P+  +P+     +  P  W+
Sbjct: 9   KDQERXRKYFAAHPSAEVPADXWPRYXGAFIRRPLEWD 46


  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    0.129    0.367 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,071,858
Number of Sequences: 62578
Number of extensions: 758774
Number of successful extensions: 1405
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 1402
Number of HSP's gapped (non-prelim): 15
length of query: 691
length of database: 14,973,337
effective HSP length: 106
effective length of query: 585
effective length of database: 8,340,069
effective search space: 4878940365
effective search space used: 4878940365
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: 55 (25.8 bits)