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= 003233
         (837 letters)

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

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



>pdb|3MK7|B Chain B, The Structure Of Cbb3 Cytochrome Oxidase
 pdb|3MK7|E Chain E, The Structure Of Cbb3 Cytochrome Oxidase
 pdb|3MK7|H Chain H, The Structure Of Cbb3 Cytochrome Oxidase
 pdb|3MK7|L Chain L, The Structure Of Cbb3 Cytochrome Oxidase
          Length = 203

 Score = 33.5 bits (75), Expect = 0.47,   Method: Composition-based stats.
 Identities = 13/38 (34%), Positives = 24/38 (63%)

Query: 398 PWGIENKLKSTDASSESKALQSEAVIHSQEEVAGSEDT 435
           PW +EN L   D + +  AL+   V +++E++AG+ D+
Sbjct: 141 PWLVENTLDGKDTAKKMSALRMLGVPYTEEDIAGARDS 178


>pdb|1U3C|A Chain A, Crystal Structure Of The Phr Domain Of Cryptochrome 1 From
           Arabidopsis Thaliana
 pdb|1U3D|A Chain A, Crystal Structure Of The Phr Domain Of Cryptochrome 1 From
           Arabidopsis Thaliana With Amppnp Bound
          Length = 509

 Score = 30.4 bits (67), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 22/83 (26%), Positives = 37/83 (44%), Gaps = 6/83 (7%)

Query: 386 EEEGHTPDGALEPWGIENKLKSTDASSESKAL------QSEAVIHSQEEVAGSEDTEIKE 439
           EEEGH   G +  W ++N L   D+S  S          +++V    + V  +  ++I  
Sbjct: 48  EEEGHYHPGRVSRWWLKNSLAQLDSSLRSLGTCLITKRSTDSVASLLDVVKSTGASQIFF 107

Query: 440 KHLIEAISEVRTEENQCKKTIEG 462
            HL + +S VR    +   T +G
Sbjct: 108 NHLYDPLSLVRDHRAKDVLTAQG 130


>pdb|3ROH|A Chain A, Crystal Structure Of Leukotoxin (Luke) From Staphylococcus
           Aureus Subsp. Aureus Col
          Length = 329

 Score = 29.3 bits (64), Expect = 9.0,   Method: Compositional matrix adjust.
 Identities = 17/52 (32%), Positives = 27/52 (51%), Gaps = 2/52 (3%)

Query: 702 ERKTEKSALMDSATASLTDPLQSSRIETTKVAEQVGEGGEPKGRTEEIQTKQ 753
           ++K   + L     A L  P+Q SR  T    E +G+G E   RTE++ +K+
Sbjct: 21  KKKMLAATLSVGLIAPLASPIQESRANTN--IENIGDGAEVIKRTEDVSSKK 70


  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
   0.299    0.120    0.316 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,206,245
Number of Sequences: 62578
Number of extensions: 786791
Number of successful extensions: 1151
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1148
Number of HSP's gapped (non-prelim): 14
length of query: 837
length of database: 14,973,337
effective HSP length: 107
effective length of query: 730
effective length of database: 8,277,491
effective search space: 6042568430
effective search space used: 6042568430
T: 11
A: 40
X1: 17 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (21.6 bits)
S2: 56 (26.2 bits)