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= 028937
         (201 letters)

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

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



>pdb|2HPI|A Chain A, Eubacterial And Eukaryotic Replicative Dna Polymerases Are
           Not Homologous: X-Ray Structure Of Dna Polymerase Iii
 pdb|2HPM|A Chain A, Eubacterial And Eukaryotic Replicative Dna Polymerases Are
           Not Homologous: X-ray Structure Of Dna Polymerase Iii
          Length = 1220

 Score = 31.6 bits (70), Expect = 0.28,   Method: Composition-based stats.
 Identities = 16/54 (29%), Positives = 33/54 (61%), Gaps = 5/54 (9%)

Query: 71  PNGALPKGRRDILLEYVKNVQPEFMELFVKRAPEQVVDAMRQTVTNMIGTLPPQ 124
           P   LP+GR +   +Y++ +   F+ L ++R P+++ +A  + V  ++GT+PP 
Sbjct: 296 PRFPLPEGRTEA--QYLRELT--FLGL-LRRYPDRITEAFYREVLRLLGTMPPH 344


>pdb|3E0D|A Chain A, Insights Into The Replisome From The Crystral Structure Of
           The Ternary Complex Of The Eubacterial Dna Polymerase
           Iii Alpha-Subunit
 pdb|3E0D|B Chain B, Insights Into The Replisome From The Crystral Structure Of
           The Ternary Complex Of The Eubacterial Dna Polymerase
           Iii Alpha-Subunit
          Length = 1220

 Score = 31.6 bits (70), Expect = 0.28,   Method: Composition-based stats.
 Identities = 16/54 (29%), Positives = 33/54 (61%), Gaps = 5/54 (9%)

Query: 71  PNGALPKGRRDILLEYVKNVQPEFMELFVKRAPEQVVDAMRQTVTNMIGTLPPQ 124
           P   LP+GR +   +Y++ +   F+ L ++R P+++ +A  + V  ++GT+PP 
Sbjct: 296 PRFPLPEGRTEA--QYLRELT--FLGL-LRRYPDRITEAFYREVLRLLGTMPPH 344


>pdb|1M2O|A Chain A, Crystal Structure Of The Sec23-Sar1 Complex
 pdb|1M2O|C Chain C, Crystal Structure Of The Sec23-Sar1 Complex
 pdb|1M2V|A Chain A, Crystal Structure Of The Yeast Sec2324 HETERODIMER
          Length = 768

 Score = 28.1 bits (61), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 92  PEFMELFVKRAPEQVVDAMRQTVTNMIGTLPPQ-FFAVTVTTVAENLAQLMYSVMMT 147
           P++  L  +  P ++     + +TN   T+PP  FF V +T+  ENL  L  S++ +
Sbjct: 91  PQYTNLSQENMPLELQSTTIEYITNKPVTVPPIFFFVVDLTSETENLDSLKESIITS 147


>pdb|2QTV|A Chain A, Structure Of Sec23-Sar1 Complexed With The Active Fragment
           Of Sec31
          Length = 772

 Score = 28.1 bits (61), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 92  PEFMELFVKRAPEQVVDAMRQTVTNMIGTLPPQ-FFAVTVTTVAENLAQLMYSVMMT 147
           P++  L  +  P ++     + +TN   T+PP  FF V +T+  ENL  L  S++ +
Sbjct: 95  PQYTNLSQENMPLELQSTTIEYITNKPVTVPPIFFFVVDLTSETENLDSLKESIITS 151


  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    0.133    0.389 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,047,354
Number of Sequences: 62578
Number of extensions: 117913
Number of successful extensions: 333
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 327
Number of HSP's gapped (non-prelim): 6
length of query: 201
length of database: 14,973,337
effective HSP length: 94
effective length of query: 107
effective length of database: 9,091,005
effective search space: 972737535
effective search space used: 972737535
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: 49 (23.5 bits)