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= 024274
         (270 letters)

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

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



>pdb|2EBI|A Chain A, Arabidopsis Gt-1 Dna-Binding Domain With T133d
          Phosphomimetic Mutation
          Length = 86

 Score = 60.8 bits (146), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 29/75 (38%), Positives = 44/75 (58%)

Query: 12 QAVQWGNEETRDLIVIRGETERDLVGIKRNKTIWEIVSVKLRERGYSRTPDQCKCKWKNL 71
          +A  W  +ETR LI+ R   +      K NK +WE +S K+RE+G+ R+PD C  KW+NL
Sbjct: 3  RAETWVQDETRSLIMFRRGMDGLFNTSKSNKHLWEQISSKMREKGFDRSPDMCTDKWRNL 62

Query: 72 VNRYKGKETSDPDSG 86
          +  +K  +  D  +G
Sbjct: 63 LKEFKKAKHHDRGNG 77


>pdb|2JMW|A Chain A, Structure Of Dna-Binding Domain Of Arabidopsis Gt-1
          Length = 86

 Score = 58.2 bits (139), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 28/75 (37%), Positives = 43/75 (57%)

Query: 12 QAVQWGNEETRDLIVIRGETERDLVGIKRNKTIWEIVSVKLRERGYSRTPDQCKCKWKNL 71
          +A  W  +ETR LI+ R   +      K NK +WE +S K+RE+G+ R+P  C  KW+NL
Sbjct: 3  RAETWVQDETRSLIMFRRGMDGLFNTSKSNKHLWEQISSKMREKGFDRSPTMCTDKWRNL 62

Query: 72 VNRYKGKETSDPDSG 86
          +  +K  +  D  +G
Sbjct: 63 LKEFKKAKHHDRGNG 77


>pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact
           Activator-Dependent Transcription Initiation Complex
          Length = 613

 Score = 30.0 bits (66), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 4/52 (7%)

Query: 62  DQCKCKWKNLVNRYKGKETSD----PDSGRQCPFFNELHAVFTERAKNMQRL 109
           +QCK   KN +  + G ETSD           P+  +LH V  E  + +Q+L
Sbjct: 293 EQCKMPKKNFITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKL 344


>pdb|4IGC|X Chain X, X-ray Crystal Structure Of Escherichia Coli Sigma70
           Holoenzyme
 pdb|4IGC|Y Chain Y, X-ray Crystal Structure Of Escherichia Coli Sigma70
           Holoenzyme
          Length = 613

 Score = 30.0 bits (66), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 4/52 (7%)

Query: 62  DQCKCKWKNLVNRYKGKETSD----PDSGRQCPFFNELHAVFTERAKNMQRL 109
           +QCK   KN +  + G ETSD           P+  +LH V  E  + +Q+L
Sbjct: 293 EQCKMPKKNFITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKL 344


>pdb|1SIG|A Chain A, Crystal Structure Of A Sigma70 Subunit Fragment From
           Escherichia Coli Rna Polymerase
          Length = 339

 Score = 29.3 bits (64), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 4/52 (7%)

Query: 62  DQCKCKWKNLVNRYKGKETSD----PDSGRQCPFFNELHAVFTERAKNMQRL 109
           +QCK   KN +  + G ETSD           P+  +LH V  E  + +Q+L
Sbjct: 184 EQCKMPKKNFITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKL 235


  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
   0.317    0.130    0.386 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,874,784
Number of Sequences: 62578
Number of extensions: 188314
Number of successful extensions: 368
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 366
Number of HSP's gapped (non-prelim): 6
length of query: 270
length of database: 14,973,337
effective HSP length: 97
effective length of query: 173
effective length of database: 8,903,271
effective search space: 1540265883
effective search space used: 1540265883
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)