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= psy15639
         (135 letters)

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

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



>pdb|1X4U|A Chain A, Solution Structure Of The Fyve Domain From Human Fyve
          Domain Containing 27 Isoform B Protein
          Length = 84

 Score = 30.8 bits (68), Expect = 0.26,   Method: Compositional matrix adjust.
 Identities = 20/73 (27%), Positives = 28/73 (38%), Gaps = 9/73 (12%)

Query: 6  PAARLGNCRVCLKSFKPDDYSRVCYECHQKVCEDCASY--------SKLDENQDENTWRC 57
          P    GNC  C  +F      R C  C    C  C S+        +   E Q E  + C
Sbjct: 10 PTNNFGNCTGCSATFSVLKKRRSCSNCGNSFCSRCCSFKVPKSSMGATAPEAQRETVFVC 69

Query: 58 SICRRKLQSRAQP 70
          + C + L S++ P
Sbjct: 70 ASCNQTL-SKSGP 81


>pdb|2RAD|A Chain A, Crystal Structure Of The Succinoglycan Biosynthesis
           Protein. Northeast Structural Genomics Consortium Target
           Bcr135
 pdb|2RAD|B Chain B, Crystal Structure Of The Succinoglycan Biosynthesis
           Protein. Northeast Structural Genomics Consortium Target
           Bcr135
 pdb|3B55|A Chain A, Crystal Structure Of The Q81bn2_baccr Protein From
           Bacillus Cereus. Nesg Target Bcr135
          Length = 451

 Score = 28.9 bits (63), Expect = 0.80,   Method: Composition-based stats.
 Identities = 16/43 (37%), Positives = 24/43 (55%)

Query: 64  LQSRAQPVLSQNSTDSLLDVPVLEALQRRHSDVKIGSANSGAH 106
           L++ A+P+ + N T SL D+  L+      S V +G A  GAH
Sbjct: 46  LEAHAKPLKTTNPTASLNDLKPLKNXVGSASIVGLGEATHGAH 88


>pdb|2A20|A Chain A, Solution Structure Of Rim2 Zinc Finger Domain
 pdb|2CJS|C Chain C, Structural Basis For A Munc13-1 Dimeric - Munc13-1 - Rim
          Heterodimer Switch: C2-domains As Versatile Protein-
          Protein Interaction Modules
          Length = 62

 Score = 27.7 bits (60), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 18/62 (29%), Positives = 25/62 (40%), Gaps = 7/62 (11%)

Query: 2  KSDKPAARLGNCRVCLKSFKPDDYSRVCYECHQKVCEDCASYSKLDENQDENTWRCSICR 61
          K D P      C +C K+   D     C  C  K C  C     L  N+    W C++CR
Sbjct: 6  KGDAPT-----CGICHKTKFADGCGHNCSYCQTKFCARCGGRVSLRSNKV--MWVCNLCR 58

Query: 62 RK 63
          ++
Sbjct: 59 KQ 60


>pdb|2CSZ|A Chain A, Solution Structure Of The Ring Domain Of The
          Synaptotagmin- Like Protein 4
          Length = 76

 Score = 26.9 bits (58), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 19/58 (32%), Positives = 27/58 (46%), Gaps = 11/58 (18%)

Query: 3  SDKPAARLGNCRVCLKSFKPDDYSRVCYECHQKVCEDCASYSKLDENQDENTWRCSIC 60
          SD+  AR   C+  L    P   +  C  C+  VC DC    ++ E+    TWRC +C
Sbjct: 24 SDRTCAR---CQESLGRLSPK--TNTCRGCNHLVCRDC----RIQES--NGTWRCKVC 70


>pdb|2JM1|A Chain A, Structures And Chemical Shift Assignments For The Add
           Domain Of The Atrx Protein
          Length = 141

 Score = 25.8 bits (55), Expect = 7.5,   Method: Compositional matrix adjust.
 Identities = 21/79 (26%), Positives = 28/79 (35%), Gaps = 24/79 (30%)

Query: 6   PAARLGNCRVCLKSFKPDDYSR-------------------VCYECHQKVCEDCA----S 42
           P+ ++  C+ C K +  DD SR                    C  CH   C+ C      
Sbjct: 35  PSLQVLICKNCFKYYMSDDISRDSDGMDEQCRWCAEGGNLICCDFCHNAFCKKCILRNLG 94

Query: 43  YSKLDENQDENT-WRCSIC 60
             +L    DEN  W C IC
Sbjct: 95  RKELSTIMDENNQWYCYIC 113


>pdb|2LD1|A Chain A, Structures And Chemical Shift Assignments For The Add
           Domain Of The Atrx Protein
 pdb|2LBM|A Chain A, Solution Structure Of The Add Domain Of Atrx Complexed
           With Histone Tail H3 1-15 K9me3
          Length = 142

 Score = 25.8 bits (55), Expect = 7.6,   Method: Compositional matrix adjust.
 Identities = 21/80 (26%), Positives = 28/80 (35%), Gaps = 24/80 (30%)

Query: 6   PAARLGNCRVCLKSFKPDDYSR-------------------VCYECHQKVCEDCA----S 42
           P+ ++  C+ C K +  DD SR                    C  CH   C+ C      
Sbjct: 36  PSLQVLICKNCFKYYMSDDISRDSDGMDEQCRWCAEGGNLICCDFCHNAFCKKCILRNLG 95

Query: 43  YSKLDENQDENT-WRCSICR 61
             +L    DEN  W C IC 
Sbjct: 96  RKELSTIMDENNQWYCYICH 115


>pdb|4FO9|A Chain A, Crystal Structure Of The E3 Sumo Ligase Pias2
          Length = 360

 Score = 25.4 bits (54), Expect = 9.7,   Method: Compositional matrix adjust.
 Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 2/32 (6%)

Query: 32  CHQKVCEDCASYSKLDENQDENTWRCSICRRK 63
           C    C D A Y  L  N+ + TW C +C +K
Sbjct: 234 CTHLQCFDAALY--LQMNEKKPTWICPVCDKK 263


  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
   0.315    0.129    0.395 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,138,532
Number of Sequences: 62578
Number of extensions: 153614
Number of successful extensions: 404
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 19
Number of HSP's that attempted gapping in prelim test: 389
Number of HSP's gapped (non-prelim): 29
length of query: 135
length of database: 14,973,337
effective HSP length: 88
effective length of query: 47
effective length of database: 9,466,473
effective search space: 444924231
effective search space used: 444924231
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 46 (22.3 bits)