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= 025552
         (251 letters)

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

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



>pdb|2H9U|A Chain A, Crystal Structure Of The Archaea Specific Dna Binding
           Protein
 pdb|3U6Y|A Chain A, Crystal Structure Of Alba2-Dna Complex
 pdb|3U6Y|C Chain C, Crystal Structure Of Alba2-Dna Complex
          Length = 102

 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 33/95 (34%), Positives = 49/95 (51%), Gaps = 5/95 (5%)

Query: 20  EIRITSQGRMRSYITYAMTLLQERGSNEIVFKAMGRAINKTVTIVELIKRRIVGLHQNTV 79
           E+RI  +  M +Y+   +T L E+G+N++V KA GR IN+ V  VE++++R     +N  
Sbjct: 8   EVRIGRKPVM-NYVLAILTTLMEQGTNQVVVKARGRNINRAVDAVEIVRKR---FAKNIE 63

Query: 80  IGSTDITDTWXXXXXXXXXXXTTRHVSMITITLSK 114
           I    I D+             TR VS I I L K
Sbjct: 64  IKDIKI-DSQEIEVQTPEGQTRTRRVSSIEICLEK 97


>pdb|1H0X|A Chain A, Structure Of Alba: An Archaeal Chromatin Protein
          Modulated By Acetylation
 pdb|1H0X|B Chain B, Structure Of Alba: An Archaeal Chromatin Protein
          Modulated By Acetylation
 pdb|1H0Y|A Chain A, Structure Of Alba: An Archaeal Chromatin Protein
          Modulated By Acetylation
          Length = 100

 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 27/64 (42%), Positives = 40/64 (62%), Gaps = 2/64 (3%)

Query: 7  VEKPKAETPIDENEIRITSQGRMRSYITYAMTLLQERGSNEIVFKAMGRAINKTVTIVEL 66
          +EK  + TP   N + I  +  M +Y+  A+TLL + G +EIV KA GRAI+K V  VE+
Sbjct: 1  MEKMSSGTPTPSNVVLIGKKPVM-NYVLAALTLLNQ-GVSEIVIKARGRAISKAVDTVEI 58

Query: 67 IKRR 70
          ++ R
Sbjct: 59 VRNR 62


>pdb|2BKY|A Chain A, Crystal Structure Of The Alba1:alba2 Heterodimer From
          Sulfolobus Solfataricus
 pdb|2BKY|B Chain B, Crystal Structure Of The Alba1:alba2 Heterodimer From
          Sulfolobus Solfataricus
          Length = 97

 Score = 41.2 bits (95), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 25/57 (43%), Positives = 36/57 (63%), Gaps = 2/57 (3%)

Query: 14 TPIDENEIRITSQGRMRSYITYAMTLLQERGSNEIVFKAMGRAINKTVTIVELIKRR 70
          TP   N + I  +  M +Y+  A+TLL + G +EIV KA GRAI+K V  VE+++ R
Sbjct: 5  TPTPSNVVLIGKKPVM-NYVLAALTLLNQ-GVSEIVIKARGRAISKAVDTVEIVRNR 59


>pdb|1Y9X|A Chain A, Solution Structure Of Archaeon Dna-Binding Protein
          Ssh10b
 pdb|1Y9X|B Chain B, Solution Structure Of Archaeon Dna-Binding Protein
          Ssh10b
          Length = 97

 Score = 40.8 bits (94), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 37/60 (61%), Gaps = 2/60 (3%)

Query: 14 TPIDENEIRITSQGRMRSYITYAMTLLQERGSNEIVFKAMGRAINKTVTIVELIKRRIVG 73
          TP   N + I  +  M +Y+  A+TLL + G +EIV KA GRAI+K V  VE+++ R + 
Sbjct: 5  TPTPSNVVLIGKKPVM-NYVLAALTLLNQ-GVSEIVIKARGRAISKAVDTVEIVRNRFLA 62


>pdb|1NFH|A Chain A, Structure Of A Sir2 Substrate, Alba, Reveals A Mechanism
          For Deactylation-Induced Enhancement Of Dna-Binding
 pdb|1NFH|B Chain B, Structure Of A Sir2 Substrate, Alba, Reveals A Mechanism
          For Deactylation-Induced Enhancement Of Dna-Binding
 pdb|1NFJ|A Chain A, Structure Of A Sir2 Substrate, Alba, Reveals A Mechanism
          For Deactylation-Induced Enhancement Of Dna-Binding
          Length = 89

 Score = 35.4 bits (80), Expect = 0.028,   Method: Compositional matrix adjust.
 Identities = 16/40 (40%), Positives = 28/40 (70%), Gaps = 1/40 (2%)

Query: 31 SYITYAMTLLQERGSNEIVFKAMGRAINKTVTIVELIKRR 70
          +Y+   +T L E G++E+V KA GRAI++ V + E+++ R
Sbjct: 15 NYVLATLTQLNE-GADEVVIKARGRAISRAVDVAEIVRNR 53


>pdb|1NH9|A Chain A, Crystal Structure Of A Dna Binding Protein Mja10b From
          The Hyperthermophile Methanococcus Jannaschii
          Length = 87

 Score = 34.3 bits (77), Expect = 0.066,   Method: Compositional matrix adjust.
 Identities = 16/42 (38%), Positives = 27/42 (64%), Gaps = 1/42 (2%)

Query: 30 RSYITYAMTLLQERGSN-EIVFKAMGRAINKTVTIVELIKRR 70
          +  + Y + +L +  SN E++ KA G+AINK V + E+I+ R
Sbjct: 10 KPVMNYVVAVLTQLTSNDEVIIKARGKAINKAVDVAEMIRNR 51


  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
   0.315    0.133    0.386 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,790,754
Number of Sequences: 62578
Number of extensions: 130967
Number of successful extensions: 200
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 194
Number of HSP's gapped (non-prelim): 11
length of query: 251
length of database: 14,973,337
effective HSP length: 96
effective length of query: 155
effective length of database: 8,965,849
effective search space: 1389706595
effective search space used: 1389706595
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)