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= 022994
         (289 letters)

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

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



>pdb|2PRV|A Chain A, Crystal Structure Of An Uncharacterized Protein (Yobk,
           Bsu18990) From Bacillus Subtilis At 1.30 A Resolution
 pdb|2PRV|B Chain B, Crystal Structure Of An Uncharacterized Protein (Yobk,
           Bsu18990) From Bacillus Subtilis At 1.30 A Resolution
          Length = 153

 Score = 33.9 bits (76), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 25/88 (28%), Positives = 39/88 (44%), Gaps = 5/88 (5%)

Query: 138 AQLMYSVMMTGYMFKNAQYRLELQQSLEQVALPE---VLDKKDTPDYAPGTQKNVSGE-- 192
           A  ++ V++ GY F +A       +  E   L +   V++  D   Y   T K   GE  
Sbjct: 53  AGGLFGVLVLGYNFDHASVVNRTNEYKEHYGLTDGLVVIEDVDYFAYCLDTNKXKDGECP 112

Query: 193 VFRWNNVSGPEKIDAKKYIEFLEAEIEE 220
           V  W+ V G +   A  +IEF   +I+E
Sbjct: 113 VVEWDRVIGYQDTVADSFIEFFYNKIQE 140


>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 = 0.60,   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 = 0.60,   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|2QTV|A Chain A, Structure Of Sec23-Sar1 Complexed With The Active Fragment
           Of Sec31
          Length = 772

 Score = 28.1 bits (61), Expect = 5.7,   Method: Compositional matrix adjust.
 Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 1/61 (1%)

Query: 88  KNVQPEFMELFVKRAPEQVVDAMRQTVTNMIGTLPPQ-FFAVTVTTVAENLAQLMYSVMM 146
            ++ P++  L  +  P ++     + +TN   T+PP  FF V +T+  ENL  L  S++ 
Sbjct: 91  NHLPPQYTNLSQENMPLELQSTTIEYITNKPVTVPPIFFFVVDLTSETENLDSLKESIIT 150

Query: 147 T 147
           +
Sbjct: 151 S 151


>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 = 5.8,   Method: Compositional matrix adjust.
 Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 1/61 (1%)

Query: 88  KNVQPEFMELFVKRAPEQVVDAMRQTVTNMIGTLPPQ-FFAVTVTTVAENLAQLMYSVMM 146
            ++ P++  L  +  P ++     + +TN   T+PP  FF V +T+  ENL  L  S++ 
Sbjct: 87  NHLPPQYTNLSQENMPLELQSTTIEYITNKPVTVPPIFFFVVDLTSETENLDSLKESIIT 146

Query: 147 T 147
           +
Sbjct: 147 S 147


  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
   0.319    0.135    0.387 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,436,278
Number of Sequences: 62578
Number of extensions: 271634
Number of successful extensions: 715
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 711
Number of HSP's gapped (non-prelim): 7
length of query: 289
length of database: 14,973,337
effective HSP length: 98
effective length of query: 191
effective length of database: 8,840,693
effective search space: 1688572363
effective search space used: 1688572363
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)