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= psy13278
         (174 letters)

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

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



>pdb|2F6H|X Chain X, Myosin V Cargo Binding Domain
          Length = 419

 Score = 32.0 bits (71), Expect = 0.16,   Method: Compositional matrix adjust.
 Identities = 20/59 (33%), Positives = 35/59 (59%), Gaps = 2/59 (3%)

Query: 69  SQLLQARK-TQEDVNTVCEMCNKMSTNQIIKLLNLYTPADDYEERISQSFIHLIQEKLK 126
           ++LLQ RK T ED++ +  +C  ++  Q+ KL++ Y  A DYE  I Q  +  + + +K
Sbjct: 292 AKLLQVRKYTIEDIDILRGICYSLTPAQLQKLISQYQVA-DYESPIPQEILRYVADIVK 349


>pdb|1Q5D|A Chain A, Epothilone B-Bound Cytochrome P450epok
 pdb|1Q5E|A Chain A, Substrate-Free Cytochrome P450epok
          Length = 419

 Score = 29.6 bits (65), Expect = 0.90,   Method: Compositional matrix adjust.
 Identities = 23/86 (26%), Positives = 36/86 (41%), Gaps = 1/86 (1%)

Query: 52  TSQVRDLNRIKSVHKVASQLLQARKTQEDVNTVCEMCNKMSTNQIIKLLNLYTPADDYEE 111
           TS+  DL R + + +   QLL AR  QE+ + V +    +    I  LL +    D+   
Sbjct: 115 TSRAIDLLRAE-IQRTVDQLLDARSGQEEFDVVRDYAEGIPMRAISALLKVPAECDEKFR 173

Query: 112 RISQSFIHLIQEKLKERPQSEQSTLL 137
           R   +    +   L  R   E  TL+
Sbjct: 174 RFGSATARALGVGLVPRVDEETKTLV 199


>pdb|1PKF|A Chain A, Crystal Structure Of Epothilone D-Bound Cytochrome
           P450epok
          Length = 419

 Score = 29.6 bits (65), Expect = 0.91,   Method: Compositional matrix adjust.
 Identities = 23/86 (26%), Positives = 36/86 (41%), Gaps = 1/86 (1%)

Query: 52  TSQVRDLNRIKSVHKVASQLLQARKTQEDVNTVCEMCNKMSTNQIIKLLNLYTPADDYEE 111
           TS+  DL R + + +   QLL AR  QE+ + V +    +    I  LL +    D+   
Sbjct: 115 TSRAIDLLRAE-IQRTVDQLLDARSGQEEFDVVRDYAEGIPMRAISALLKVPAECDEKFR 173

Query: 112 RISQSFIHLIQEKLKERPQSEQSTLL 137
           R   +    +   L  R   E  TL+
Sbjct: 174 RFGSATARALGVGLVPRVDEETKTLV 199


>pdb|3AQ2|A Chain A, Molecular Insights Into Plant Cell Proliferation
          Disturbance By Agrobacterium Protein 6b
 pdb|3AQ2|B Chain B, Molecular Insights Into Plant Cell Proliferation
          Disturbance By Agrobacterium Protein 6b
          Length = 207

 Score = 27.3 bits (59), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 14/26 (53%), Positives = 17/26 (65%)

Query: 1  VSTSQVRDLNRIKSVHKVASQLLQAR 26
          V T QVRDL RI  V +++  L QAR
Sbjct: 6  VPTWQVRDLRRILRVSELSQHLRQAR 31



 Score = 27.3 bits (59), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 14/26 (53%), Positives = 17/26 (65%)

Query: 50 VSTSQVRDLNRIKSVHKVASQLLQAR 75
          V T QVRDL RI  V +++  L QAR
Sbjct: 6  VPTWQVRDLRRILRVSELSQHLRQAR 31


  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
   0.317    0.127    0.341 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,828,650
Number of Sequences: 62578
Number of extensions: 116910
Number of successful extensions: 724
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 718
Number of HSP's gapped (non-prelim): 13
length of query: 174
length of database: 14,973,337
effective HSP length: 92
effective length of query: 82
effective length of database: 9,216,161
effective search space: 755725202
effective search space used: 755725202
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)