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= 025488
         (252 letters)

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

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



>pdb|2Z7C|B Chain B, Crystal Structure Of Chromatin Protein Alba From
          Hyperthermophilic Archaeon Pyrococcus Horikoshii
 pdb|2Z7C|D Chain D, Crystal Structure Of Chromatin Protein Alba From
          Hyperthermophilic Archaeon Pyrococcus Horikoshii
 pdb|2Z7C|A Chain A, Crystal Structure Of Chromatin Protein Alba From
          Hyperthermophilic Archaeon Pyrococcus Horikoshii
 pdb|2Z7C|C Chain C, Crystal Structure Of Chromatin Protein Alba From
          Hyperthermophilic Archaeon Pyrococcus Horikoshii
          Length = 93

 Score = 37.0 bits (84), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 22/67 (32%), Positives = 35/67 (52%), Gaps = 3/67 (4%)

Query: 29 IRNYITYATTLLQEKHAKEIVLKAMGQAINKTVAIAEIIKKRIPQLHQDTAISSVSITDT 88
          + NY+    T   E  AKE+ +KA G+AI++ V +AEI++ R   L  D  +  + I   
Sbjct: 14 VMNYVLAVITQFHE-GAKEVSIKARGRAISRAVDVAEIVRNRF--LKDDVDVKEIKIGTE 70

Query: 89 WEPIEEG 95
            P  +G
Sbjct: 71 ELPTADG 77


>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 = 36.6 bits (83), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 27/42 (64%), Gaps = 1/42 (2%)

Query: 29 IRNYITYATTLLQEKHAKEIVLKAMGQAINKTVAIAEIIKKR 70
          + NY+  A TLL +    EIV+KA G+AI+K V   EI++ R
Sbjct: 19 VMNYVLAALTLLNQ-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 = 36.6 bits (83), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 27/42 (64%), Gaps = 1/42 (2%)

Query: 29 IRNYITYATTLLQEKHAKEIVLKAMGQAINKTVAIAEIIKKR 70
          + NY+  A TLL +    EIV+KA G+AI+K V   EI++ R
Sbjct: 19 VMNYVLAALTLLNQ-GVSEIVIKARGRAISKAVDTVEIVRNR 59


>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 = 36.6 bits (83), Expect = 0.014,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 27/42 (64%), Gaps = 1/42 (2%)

Query: 29 IRNYITYATTLLQEKHAKEIVLKAMGQAINKTVAIAEIIKKR 70
          + NY+  A TLL +    EIV+KA G+AI+K V   EI++ R
Sbjct: 22 VMNYVLAALTLLNQ-GVSEIVIKARGRAISKAVDTVEIVRNR 62


>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 = 36.2 bits (82), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 19/54 (35%), Positives = 32/54 (59%), Gaps = 1/54 (1%)

Query: 20 EIRITTQGAIRNYITYATTLLQEKHAKEIVLKAMGQAINKTVAIAEIIKKRIPQ 73
          E+RI  +  + NY+    T L E+   ++V+KA G+ IN+ V   EI++KR  +
Sbjct: 8  EVRIGRK-PVMNYVLAILTTLMEQGTNQVVVKARGRNINRAVDAVEIVRKRFAK 60


>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 = 36.2 bits (82), Expect = 0.019,   Method: Compositional matrix adjust.
 Identities = 18/42 (42%), Positives = 28/42 (66%), Gaps = 1/42 (2%)

Query: 29 IRNYITYATTLLQEKHAKEIVLKAMGQAINKTVAIAEIIKKR 70
          + NY+    T L E  A E+V+KA G+AI++ V +AEI++ R
Sbjct: 13 VMNYVLATLTQLNE-GADEVVIKARGRAISRAVDVAEIVRNR 53


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

 Score = 34.7 bits (78), Expect = 0.054,   Method: Compositional matrix adjust.
 Identities = 17/42 (40%), Positives = 26/42 (61%), Gaps = 2/42 (4%)

Query: 29 IRNYITYATTLLQEKHAKEIVLKAMGQAINKTVAIAEIIKKR 70
          + NY+    T L      E+++KA G+AINK V +AE+I+ R
Sbjct: 12 VMNYVVAVLTQLTSND--EVIIKARGKAINKAVDVAEMIRNR 51


>pdb|3TOE|A Chain A, Structure Of Mth10b
 pdb|3TOE|B Chain B, Structure Of Mth10b
          Length = 91

 Score = 32.3 bits (72), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 17/48 (35%), Positives = 28/48 (58%), Gaps = 2/48 (4%)

Query: 29 IRNYITYATTLLQEKHAKEIVLKAMGQAINKTVAIAEIIKKR-IPQLH 75
          + NY+    T +      E++LKA G AI++ V +AEI++ R IP + 
Sbjct: 14 VMNYVLAVVTQMN-GGTSEVILKARGIAISRAVDVAEIVRNRFIPDIQ 60


  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
   0.311    0.128    0.361 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,512,987
Number of Sequences: 62578
Number of extensions: 134334
Number of successful extensions: 228
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 219
Number of HSP's gapped (non-prelim): 9
length of query: 252
length of database: 14,973,337
effective HSP length: 97
effective length of query: 155
effective length of database: 8,903,271
effective search space: 1380007005
effective search space used: 1380007005
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 50 (23.9 bits)