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= 002225
         (951 letters)

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

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



>pdb|3IYD|D Chain D, Three-Dimensional Em Structure Of An Intact
           Activator-Dependent Transcription Initiation Complex
          Length = 1413

 Score = 30.4 bits (67), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 35/126 (27%), Positives = 59/126 (46%), Gaps = 16/126 (12%)

Query: 751 RQQILISKSSKEFNDLKGNLTDALEQIE--QYKLEVHDLKQKLELAMKELRDTNEETR-- 806
           RQQIL  +   +  +  G+  DA    E  Q  L+  DL+Q+ E   +EL +TN ET+  
Sbjct: 156 RQQILTEEQYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKRK 215

Query: 807 ---KQVQLLVIFIQGLSK---------TVADFECRAVADIERCNFRLDSLSSQSKRLILK 854
              K+++LL  F+Q  +K          V   + R +  ++   F    L+   +R+I +
Sbjct: 216 KLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINR 275

Query: 855 ANVITR 860
            N + R
Sbjct: 276 NNRLKR 281


>pdb|3LU0|D Chain D, Molecular Model Of Escherichia Coli Core Rna Polymerase
 pdb|4IGC|D Chain D, X-ray Crystal Structure Of Escherichia Coli Sigma70
           Holoenzyme
 pdb|4IGC|I Chain I, X-ray Crystal Structure Of Escherichia Coli Sigma70
           Holoenzyme
          Length = 1407

 Score = 30.4 bits (67), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 35/126 (27%), Positives = 59/126 (46%), Gaps = 16/126 (12%)

Query: 751 RQQILISKSSKEFNDLKGNLTDALEQIE--QYKLEVHDLKQKLELAMKELRDTNEETR-- 806
           RQQIL  +   +  +  G+  DA    E  Q  L+  DL+Q+ E   +EL +TN ET+  
Sbjct: 156 RQQILTEEQYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKRK 215

Query: 807 ---KQVQLLVIFIQGLSK---------TVADFECRAVADIERCNFRLDSLSSQSKRLILK 854
              K+++LL  F+Q  +K          V   + R +  ++   F    L+   +R+I +
Sbjct: 216 KLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINR 275

Query: 855 ANVITR 860
            N + R
Sbjct: 276 NNRLKR 281


>pdb|3TC1|A Chain A, Crystal Structure Of Octaprenyl Pyrophosphate Synthase
           From Helicobacter Pylori
 pdb|3TC1|B Chain B, Crystal Structure Of Octaprenyl Pyrophosphate Synthase
           From Helicobacter Pylori
          Length = 315

 Score = 30.4 bits (67), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 13/31 (41%), Positives = 21/31 (67%)

Query: 236 QGEIEDMVIMNCFRSLKEEFEERLCDQSAQF 266
           +GEIED+ +  CF S K+++   L D++A F
Sbjct: 136 RGEIEDVFVGECFNSDKQKYWRILEDKTAHF 166


>pdb|3V39|A Chain A, Bd3459, A Predatory Peptidoglycan Endopeptidase From
           Bdellovibrio Bacteriovorus
          Length = 418

 Score = 29.6 bits (65), Expect = 8.2,   Method: Compositional matrix adjust.
 Identities = 16/37 (43%), Positives = 23/37 (62%), Gaps = 1/37 (2%)

Query: 683 NQKYFMETELRRLEVAEKEKLK-QETRLLSSLVEEKE 718
           N  YF+ +EL R+++ + EKL   E  LL+ L EEK 
Sbjct: 83  NMSYFLISELNRMKITKIEKLTFDENFLLAWLAEEKP 119


  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
   0.313    0.130    0.356 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 23,808,111
Number of Sequences: 62578
Number of extensions: 912649
Number of successful extensions: 2532
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 26
Number of HSP's that attempted gapping in prelim test: 2512
Number of HSP's gapped (non-prelim): 47
length of query: 951
length of database: 14,973,337
effective HSP length: 108
effective length of query: 843
effective length of database: 8,214,913
effective search space: 6925171659
effective search space used: 6925171659
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 56 (26.2 bits)