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= psy15836
         (74 letters)

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

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



>pdb|4APY|A Chain A, Ethylene Glycol-bound Form Of P450 Cyp125a3 From
           Mycobacterium Smegmatis
          Length = 433

 Score = 28.9 bits (63), Expect = 0.67,   Method: Composition-based stats.
 Identities = 9/22 (40%), Positives = 13/22 (59%)

Query: 3   WSVDFTSRAKSDLPAPPGYCPI 24
           W VD+T   K+ +   PG CP+
Sbjct: 404 WQVDYTGAGKASVSGAPGTCPV 425


>pdb|1BDF|A Chain A, Structure Of Escherichia Coli Rna Polymerase Alpha Subunit
           N-Terminal Domain
 pdb|1BDF|B Chain B, Structure Of Escherichia Coli Rna Polymerase Alpha Subunit
           N-Terminal Domain
 pdb|1BDF|C Chain C, Structure Of Escherichia Coli Rna Polymerase Alpha Subunit
           N-Terminal Domain
 pdb|1BDF|D Chain D, Structure Of Escherichia Coli Rna Polymerase Alpha Subunit
           N-Terminal Domain
          Length = 235

 Score = 26.2 bits (56), Expect = 5.0,   Method: Composition-based stats.
 Identities = 10/41 (24%), Positives = 22/41 (53%), Gaps = 4/41 (9%)

Query: 20  GYCPINNSVQSDVTNQTDGNLLIKKCWEVALAPIKQVPMNI 60
           GY P +  + S+   +  G LL+  C+    +P++++  N+
Sbjct: 151 GYVPASTRIHSEEDERPIGRLLVDACY----SPVERIAYNV 187


>pdb|3IYD|A Chain A, Three-Dimensional Em Structure Of An Intact
           Activator-Dependent Transcription Initiation Complex
 pdb|3IYD|B Chain B, Three-Dimensional Em Structure Of An Intact
           Activator-Dependent Transcription Initiation Complex
 pdb|3LU0|A Chain A, Molecular Model Of Escherichia Coli Core Rna Polymerase
 pdb|3LU0|B Chain B, Molecular Model Of Escherichia Coli Core Rna Polymerase
 pdb|4IGC|A Chain A, X-ray Crystal Structure Of Escherichia Coli Sigma70
           Holoenzyme
 pdb|4IGC|B Chain B, X-ray Crystal Structure Of Escherichia Coli Sigma70
           Holoenzyme
 pdb|4IGC|F Chain F, X-ray Crystal Structure Of Escherichia Coli Sigma70
           Holoenzyme
 pdb|4IGC|G Chain G, X-ray Crystal Structure Of Escherichia Coli Sigma70
           Holoenzyme
          Length = 329

 Score = 26.2 bits (56), Expect = 5.0,   Method: Composition-based stats.
 Identities = 10/41 (24%), Positives = 22/41 (53%), Gaps = 4/41 (9%)

Query: 20  GYCPINNSVQSDVTNQTDGNLLIKKCWEVALAPIKQVPMNI 60
           GY P +  + S+   +  G LL+  C+    +P++++  N+
Sbjct: 151 GYVPASTRIHSEEDERPIGRLLVDACY----SPVERIAYNV 187


  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    0.133    0.428 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,199,618
Number of Sequences: 62578
Number of extensions: 69634
Number of successful extensions: 120
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 119
Number of HSP's gapped (non-prelim): 3
length of query: 74
length of database: 14,973,337
effective HSP length: 44
effective length of query: 30
effective length of database: 12,219,905
effective search space: 366597150
effective search space used: 366597150
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: 45 (21.9 bits)