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= 039495
         (327 letters)

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

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



>pdb|1RO0|A Chain A, Bifunctional Dna PrimasePOLYMERASE DOMAIN OF ORF904 FROM
           The Archaeal Plasmid Prn1- Triple Mutant F50mL107ML110M
           Semet Remote
 pdb|1RO2|A Chain A, Bifunctional Dna PrimasePOLYMERASE DOMAIN OF ORF904 FROM
           The Archaeal Plasmid Prn1- Triple Mutant F50mL107ML110M
           Manganese Soak
          Length = 216

 Score = 30.4 bits (67), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 11/40 (27%), Positives = 23/40 (57%), Gaps = 4/40 (10%)

Query: 292 CENQPLGSLAVF----DTPPYALAPIFQKDSTGIVQTRSH 327
           C N   G + ++    D PP+ + P+F+++  GI+  +S+
Sbjct: 97  CTNTVHGGIHIYVLSNDIPPHKINPLFEENGKGIIDLQSY 136


>pdb|3M1M|A Chain A, Crystal Structure Of The Primase-Polymerase From
           Sulfolobus Islandicus
          Length = 335

 Score = 30.4 bits (67), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 11/40 (27%), Positives = 23/40 (57%), Gaps = 4/40 (10%)

Query: 292 CENQPLGSLAVF----DTPPYALAPIFQKDSTGIVQTRSH 327
           C N   G + ++    D PP+ + P+F+++  GI+  +S+
Sbjct: 101 CTNTVHGGIHIYVLSNDIPPHKINPLFEENGKGIIDLQSY 140


>pdb|1RNI|A Chain A, Bifunctional Dna PrimasePOLYMERASE DOMAIN OF ORF904 FROM
           THE ARCHAEAL Plasmid Prn1
          Length = 216

 Score = 30.0 bits (66), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 11/40 (27%), Positives = 23/40 (57%), Gaps = 4/40 (10%)

Query: 292 CENQPLGSLAVF----DTPPYALAPIFQKDSTGIVQTRSH 327
           C N   G + ++    D PP+ + P+F+++  GI+  +S+
Sbjct: 97  CTNTVHGGIHIYVLSNDIPPHKINPLFEENGKGIIDLQSY 136


>pdb|2GV9|A Chain A, Crystal Structure Of The Herpes Simplex Virus Type 1 Dna
           Polymerase
 pdb|2GV9|B Chain B, Crystal Structure Of The Herpes Simplex Virus Type 1 Dna
           Polymerase
          Length = 1193

 Score = 28.5 bits (62), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 8/54 (14%)

Query: 232 VLVECNS--------HEAVKCLELPASFLDPNRALILSCREYLCRNWDCKLQLI 277
           + V CNS        H  + CL + A+     R ++L+ REY+   W    QL+
Sbjct: 768 IKVVCNSVYGFTGVQHGLLPCLHVAATVTTIGREMLLATREYVHARWAAFEQLL 821


  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
   0.318    0.134    0.422 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,898,652
Number of Sequences: 62578
Number of extensions: 384662
Number of successful extensions: 730
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 729
Number of HSP's gapped (non-prelim): 8
length of query: 327
length of database: 14,973,337
effective HSP length: 99
effective length of query: 228
effective length of database: 8,778,115
effective search space: 2001410220
effective search space used: 2001410220
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: 52 (24.6 bits)