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= 006596
         (639 letters)

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

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



>pdb|3KLN|A Chain A, Vibrio Cholerae Vpst
 pdb|3KLN|B Chain B, Vibrio Cholerae Vpst
 pdb|3KLN|C Chain C, Vibrio Cholerae Vpst
 pdb|3KLN|D Chain D, Vibrio Cholerae Vpst
 pdb|3KLO|A Chain A, Vibrio Cholerae Vpst Bound To C-Di-Gmp
 pdb|3KLO|B Chain B, Vibrio Cholerae Vpst Bound To C-Di-Gmp
 pdb|3KLO|C Chain C, Vibrio Cholerae Vpst Bound To C-Di-Gmp
 pdb|3KLO|D Chain D, Vibrio Cholerae Vpst Bound To C-Di-Gmp
          Length = 225

 Score = 30.0 bits (66), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 3/72 (4%)

Query: 239 AFTVKDHRGELYKKHYPPALNDDVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQ 298
            F + D    L K      L D++W   K+ ++   H R  N+ + S + + +L  R+ Q
Sbjct: 109 VFYIDDDMDTLIKG-MSKILQDEMWLTRKLAQEYILHYRAGNSVVTS-QMYAKLTKREQQ 166

Query: 299 KLRSILGSGMSN 310
            ++ +LGSG SN
Sbjct: 167 IIK-LLGSGASN 177


>pdb|2P6R|A Chain A, Crystal Structure Of Superfamily 2 Helicase Hel308 In
           Complex With Unwound Dna
 pdb|2P6U|A Chain A, Apo Structure Of The Hel308 Superfamily 2 Helicase
          Length = 702

 Score = 29.3 bits (64), Expect = 6.9,   Method: Compositional matrix adjust.
 Identities = 17/53 (32%), Positives = 33/53 (62%), Gaps = 6/53 (11%)

Query: 264 RLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEAL 316
           R+  IG+  +  ++L NAGI + ED    +VR  +K+ S++G G++ ++ E +
Sbjct: 636 RIRHIGRVRA--RKLYNAGIRNAED----IVRHREKVASLIGRGIAERVVEGI 682


  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
   0.314    0.132    0.380 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,279,927
Number of Sequences: 62578
Number of extensions: 831905
Number of successful extensions: 1421
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1421
Number of HSP's gapped (non-prelim): 7
length of query: 639
length of database: 14,973,337
effective HSP length: 105
effective length of query: 534
effective length of database: 8,402,647
effective search space: 4487013498
effective search space used: 4487013498
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 55 (25.8 bits)