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= 009448
         (534 letters)

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

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



>pdb|2R6A|A Chain A, Crystal Form Bh1
 pdb|2R6A|B Chain B, Crystal Form Bh1
 pdb|2R6E|A Chain A, Crystal Form B2
 pdb|2R6E|B Chain B, Crystal Form B2
 pdb|2R6C|A Chain A, Crystal Form Bh2
 pdb|2R6C|B Chain B, Crystal Form Bh2
 pdb|2R6C|C Chain C, Crystal Form Bh2
 pdb|2R6C|D Chain D, Crystal Form Bh2
 pdb|2R6C|E Chain E, Crystal Form Bh2
 pdb|2R6C|F Chain F, Crystal Form Bh2
 pdb|2R6D|A Chain A, Crystal Form B1
 pdb|2R6D|B Chain B, Crystal Form B1
 pdb|2R6D|C Chain C, Crystal Form B1
 pdb|2R6D|D Chain D, Crystal Form B1
 pdb|2R6D|E Chain E, Crystal Form B1
 pdb|2R6D|F Chain F, Crystal Form B1
 pdb|4ESV|A Chain A, A New Twist On The Translocation Mechanism Of Helicases
           From The Structure Of Dnab With Its Substrates
 pdb|4ESV|B Chain B, A New Twist On The Translocation Mechanism Of Helicases
           From The Structure Of Dnab With Its Substrates
 pdb|4ESV|C Chain C, A New Twist On The Translocation Mechanism Of Helicases
           From The Structure Of Dnab With Its Substrates
 pdb|4ESV|D Chain D, A New Twist On The Translocation Mechanism Of Helicases
           From The Structure Of Dnab With Its Substrates
 pdb|4ESV|E Chain E, A New Twist On The Translocation Mechanism Of Helicases
           From The Structure Of Dnab With Its Substrates
 pdb|4ESV|F Chain F, A New Twist On The Translocation Mechanism Of Helicases
           From The Structure Of Dnab With Its Substrates
 pdb|4ESV|G Chain G, A New Twist On The Translocation Mechanism Of Helicases
           From The Structure Of Dnab With Its Substrates
 pdb|4ESV|H Chain H, A New Twist On The Translocation Mechanism Of Helicases
           From The Structure Of Dnab With Its Substrates
 pdb|4ESV|I Chain I, A New Twist On The Translocation Mechanism Of Helicases
           From The Structure Of Dnab With Its Substrates
 pdb|4ESV|J Chain J, A New Twist On The Translocation Mechanism Of Helicases
           From The Structure Of Dnab With Its Substrates
 pdb|4ESV|K Chain K, A New Twist On The Translocation Mechanism Of Helicases
           From The Structure Of Dnab With Its Substrates
 pdb|4ESV|L Chain L, A New Twist On The Translocation Mechanism Of Helicases
           From The Structure Of Dnab With Its Substrates
          Length = 454

 Score = 28.9 bits (63), Expect = 8.0,   Method: Compositional matrix adjust.
 Identities = 26/105 (24%), Positives = 46/105 (43%), Gaps = 13/105 (12%)

Query: 14  ISPSKLRMKLIGPHHNRKKDGSNSNSARTSPSRLDDSEFVRNSLLNGG-FDDEAPSLEVA 72
           +S  +L M+++    N   +  N  + + +P           SL N G + D+ PS+ V+
Sbjct: 242 MSAQQLVMRMLCAEGN--INAQNLRTGKLTPEDWGKLTMAMGSLSNAGIYIDDTPSIRVS 299

Query: 73  S----------EKGAGEVVLGHNQGEQASFQPNETLPRENTEVSR 107
                      E G G +V+ + Q  Q S +  E   +E +E+SR
Sbjct: 300 DIRAKCRRLKQESGLGMIVIDYLQLIQGSGRSKENRQQEVSEISR 344


>pdb|2VYE|A Chain A, Crystal Structure Of The Dnac-Ssdna Complex
 pdb|2VYE|B Chain B, Crystal Structure Of The Dnac-Ssdna Complex
 pdb|2VYF|A Chain A, Crystal Structure Of The Dnac
 pdb|2VYF|B Chain B, Crystal Structure Of The Dnac
          Length = 454

 Score = 28.5 bits (62), Expect = 9.4,   Method: Compositional matrix adjust.
 Identities = 27/105 (25%), Positives = 46/105 (43%), Gaps = 13/105 (12%)

Query: 14  ISPSKLRMKLIGPHHNRKKDGSNSNSARTSPSRLDDSEFVRNSLLNGG-FDDEAPSLEVA 72
           +S  +L M+++    N   +  N  + + +P           SL N G + D+ PS+ V+
Sbjct: 242 MSAQQLVMRMLCAEGN--INAQNLRTGKLTPEDWGKLTMAMGSLSNAGIYIDDTPSIRVS 299

Query: 73  S----------EKGAGEVVLGHNQGEQASFQPNETLPRENTEVSR 107
                      E G G VV+ + Q  Q S +  E   +E +E+SR
Sbjct: 300 DIRAKCRRLKQESGLGMVVIDYLQLIQGSGRNRENRQQEVSEISR 344


  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
   0.310    0.123    0.349 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,984,663
Number of Sequences: 62578
Number of extensions: 524607
Number of successful extensions: 986
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 972
Number of HSP's gapped (non-prelim): 28
length of query: 534
length of database: 14,973,337
effective HSP length: 103
effective length of query: 431
effective length of database: 8,527,803
effective search space: 3675483093
effective search space used: 3675483093
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: 54 (25.4 bits)