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= 008185
         (574 letters)

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

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



>pdb|4GF4|A Chain A, Low Ph Structure Of Pseudomonas Putida Oprb
          Length = 436

 Score = 36.2 bits (82), Expect = 0.045,   Method: Compositional matrix adjust.
 Identities = 23/85 (27%), Positives = 36/85 (42%)

Query: 249 QSYAFMAAASGGILGNLFGGYFLLKTPPTTMFLVFAVLLSLQLAISFSAREESLGLAQVS 308
           + Y F     G + GNL GGY   KT   +        L LQ  + +   E  L + + S
Sbjct: 40  KGYDFTLDYVGEVAGNLHGGYNDDKTARYSDQFALGAHLDLQKILGWHDAEFKLAITERS 99

Query: 309 YQNVASKSIAQSIKKQFSDLIATIG 333
            +N+++  I+     QFS +    G
Sbjct: 100 GRNLSNDRISDPRAGQFSSVQEVWG 124


>pdb|4GEY|A Chain A, High Ph Structure Of Pseudomonas Putida Oprb
          Length = 436

 Score = 36.2 bits (82), Expect = 0.045,   Method: Compositional matrix adjust.
 Identities = 23/85 (27%), Positives = 36/85 (42%)

Query: 249 QSYAFMAAASGGILGNLFGGYFLLKTPPTTMFLVFAVLLSLQLAISFSAREESLGLAQVS 308
           + Y F     G + GNL GGY   KT   +        L LQ  + +   E  L + + S
Sbjct: 40  KGYDFTLDYVGEVAGNLHGGYNDDKTARYSDQFALGAHLDLQKILGWHDAEFKLAITERS 99

Query: 309 YQNVASKSIAQSIKKQFSDLIATIG 333
            +N+++  I+     QFS +    G
Sbjct: 100 GRNLSNDRISDPRAGQFSSVQEVWG 124


>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 = 28.5 bits (62), Expect = 9.6,   Method: Compositional matrix adjust.
 Identities = 14/36 (38%), Positives = 23/36 (63%), Gaps = 1/36 (2%)

Query: 211 LPNLMACVLLSNL-GASITEVAKDALVAEYGQKNGI 245
           L N +  +LLS++ G ++TEV  D ++ EY  K G+
Sbjct: 39  LGNALRAILLSSMPGCAVTEVEIDGVLHEYSTKEGV 74


  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
   0.325    0.139    0.418 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,113,088
Number of Sequences: 62578
Number of extensions: 399549
Number of successful extensions: 954
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 952
Number of HSP's gapped (non-prelim): 3
length of query: 574
length of database: 14,973,337
effective HSP length: 104
effective length of query: 470
effective length of database: 8,465,225
effective search space: 3978655750
effective search space used: 3978655750
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (25.4 bits)