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= 005161
         (711 letters)

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

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



>pdb|3SPA|A Chain A, Crystal Structure Of Human Mitochondrial Rna Polymerase
          Length = 1134

 Score = 36.6 bits (83), Expect = 0.055,   Method: Compositional matrix adjust.
 Identities = 26/83 (31%), Positives = 42/83 (50%), Gaps = 9/83 (10%)

Query: 597 RRMKETSCTFDHYTYNIMIDIYGEQGWINEVVGVLTELKECGLRPDLCSYNTLIKAYGI- 655
           +R K    T D   YN ++  +  QG   E+V VL  +K+ GL PDL SY   ++  G  
Sbjct: 156 QRQKRKLLTLD--MYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQ 213

Query: 656 ---AGMVEDAVGLVKEMRENGIE 675
              AG +E     +++M + G++
Sbjct: 214 DQDAGTIERC---LEQMSQEGLK 233



 Score = 30.4 bits (67), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 13/45 (28%), Positives = 23/45 (51%)

Query: 157 YNTLMTGYGKVSNMEAAQRLFLSIKDVGLEPDETTYRSMIEGWGR 201
           YN +M G+ +    +    +   +KD GL PD  +Y + ++  GR
Sbjct: 168 YNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGR 212


  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
   0.322    0.136    0.407 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,052,446
Number of Sequences: 62578
Number of extensions: 887306
Number of successful extensions: 2122
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 2111
Number of HSP's gapped (non-prelim): 16
length of query: 711
length of database: 14,973,337
effective HSP length: 106
effective length of query: 605
effective length of database: 8,340,069
effective search space: 5045741745
effective search space used: 5045741745
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: 55 (25.8 bits)