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= 023862
         (276 letters)

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

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



>pdb|3B39|A Chain A, Structure Of The Dnag Primase Catalytic Domain Bound To
           Ssdna
 pdb|3B39|B Chain B, Structure Of The Dnag Primase Catalytic Domain Bound To
           Ssdna
          Length = 322

 Score = 32.7 bits (73), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 1/44 (2%)

Query: 12  PKSRFFFTPLRPSINLKPPDSFPRIQPLPFPRISGKIPGSRVLV 55
           P S F F  L P ++L  PD   R+  L  P IS ++PG  + +
Sbjct: 260 PLSAFLFNSLMPQVDLSTPDGRARLSTLALPLIS-QVPGETLRI 302


>pdb|1EQN|A Chain A, E.Coli Primase Catalytic Core
 pdb|1EQN|B Chain B, E.Coli Primase Catalytic Core
 pdb|1EQN|C Chain C, E.Coli Primase Catalytic Core
 pdb|1EQN|D Chain D, E.Coli Primase Catalytic Core
 pdb|1EQN|E Chain E, E.Coli Primase Catalytic Core
          Length = 321

 Score = 32.7 bits (73), Expect = 0.23,   Method: Compositional matrix adjust.
 Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 1/44 (2%)

Query: 12  PKSRFFFTPLRPSINLKPPDSFPRIQPLPFPRISGKIPGSRVLV 55
           P S F F  L P ++L  PD   R+  L  P IS ++PG  + +
Sbjct: 259 PLSAFLFNSLXPQVDLSTPDGRARLSTLALPLIS-QVPGETLRI 301


>pdb|1DD9|A Chain A, Structure Of The Dnag Catalytic Core
 pdb|1DDE|A Chain A, Structure Of The Dnag Catalytic Core
          Length = 338

 Score = 32.3 bits (72), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 1/44 (2%)

Query: 12  PKSRFFFTPLRPSINLKPPDSFPRIQPLPFPRISGKIPGSRVLV 55
           P S F F  L P ++L  PD   R+  L  P IS ++PG  + +
Sbjct: 272 PLSAFLFNSLMPQVDLSTPDGRARLSTLALPLIS-QVPGETLRI 314


  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
   0.321    0.138    0.407 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,098,682
Number of Sequences: 62578
Number of extensions: 256081
Number of successful extensions: 488
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 485
Number of HSP's gapped (non-prelim): 6
length of query: 276
length of database: 14,973,337
effective HSP length: 97
effective length of query: 179
effective length of database: 8,903,271
effective search space: 1593685509
effective search space used: 1593685509
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)