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= 028762
         (204 letters)

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

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



>pdb|3MCB|A Chain A, Crystal Structure Of Nac Domains Of Human Nascent
           Polypeptide- Associated Complex (Nac)
          Length = 54

 Score = 92.8 bits (229), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 42/54 (77%), Positives = 50/54 (92%)

Query: 70  AMLKLGMKPIPGVSRVTVKKSKNILFVISKPDVFKSPTSDTYIVFGEAKIEDLS 123
           AM KLG++ + GV+RVT++KSKNILFVI+KPDV+KSP SDTYIVFGEAKIEDLS
Sbjct: 1   AMSKLGLRQVTGVTRVTIRKSKNILFVITKPDVYKSPASDTYIVFGEAKIEDLS 54


>pdb|3LKX|B Chain B, Human Nac Dimerization Domain
          Length = 54

 Score = 90.9 bits (224), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 40/53 (75%), Positives = 48/53 (90%)

Query: 75  GMKPIPGVSRVTVKKSKNILFVISKPDVFKSPTSDTYIVFGEAKIEDLSSQLQ 127
           G++ + GV+RVT++KSKNILFVI+KPDV+KSP SDTYIVFGEAKIEDLS Q Q
Sbjct: 2   GLRQVTGVTRVTIRKSKNILFVITKPDVYKSPASDTYIVFGEAKIEDLSQQAQ 54


>pdb|3MCE|A Chain A, Crystal Structure Of The Nac Domain Of Alpha Subunit Of
           Nascent Polypeptide-Associated Complex(Nac)
 pdb|3MCE|B Chain B, Crystal Structure Of The Nac Domain Of Alpha Subunit Of
           Nascent Polypeptide-Associated Complex(Nac)
 pdb|3MCE|C Chain C, Crystal Structure Of The Nac Domain Of Alpha Subunit Of
           Nascent Polypeptide-Associated Complex(Nac)
 pdb|3MCE|D Chain D, Crystal Structure Of The Nac Domain Of Alpha Subunit Of
           Nascent Polypeptide-Associated Complex(Nac)
          Length = 61

 Score = 88.6 bits (218), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 40/51 (78%), Positives = 48/51 (94%)

Query: 73  KLGMKPIPGVSRVTVKKSKNILFVISKPDVFKSPTSDTYIVFGEAKIEDLS 123
           KLG++ + GV+RVT++KSKNILFVI+KPDV+KSP SDTYIVFGEAKIEDLS
Sbjct: 10  KLGLRQVTGVTRVTIRKSKNILFVITKPDVYKSPASDTYIVFGEAKIEDLS 60


>pdb|1TR8|A Chain A, Crystal Structure Of Archaeal Nascent
           Polypeptide-Associated Complex (Aenac)
 pdb|1TR8|B Chain B, Crystal Structure Of Archaeal Nascent
           Polypeptide-Associated Complex (Aenac)
          Length = 102

 Score = 34.7 bits (78), Expect = 0.036,   Method: Compositional matrix adjust.
 Identities = 16/35 (45%), Positives = 20/35 (57%)

Query: 169 DIELVMTQAGVPRSRAVKALKAADGDIVSAIMELT 203
           DIELV  Q G  R  A +AL+   GD+  AI  L+
Sbjct: 68  DIELVXNQTGASREDATRALQETGGDLAEAIXRLS 102


>pdb|2ZBK|B Chain B, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
           Insights Into Dna Transfer Mechanisms
 pdb|2ZBK|D Chain D, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
           Insights Into Dna Transfer Mechanisms
 pdb|2ZBK|F Chain F, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
           Insights Into Dna Transfer Mechanisms
 pdb|2ZBK|H Chain H, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
           Insights Into Dna Transfer Mechanisms
          Length = 530

 Score = 26.6 bits (57), Expect = 9.7,   Method: Compositional matrix adjust.
 Identities = 15/46 (32%), Positives = 26/46 (56%)

Query: 75  GMKPIPGVSRVTVKKSKNILFVISKPDVFKSPTSDTYIVFGEAKIE 120
           G+KP   V  +T ++   ++    K + F+SP++D+  V GE  IE
Sbjct: 278 GLKPNKKVKNLTEEEITRLVETFKKDEDFRSPSADSLSVIGEDLIE 323


>pdb|1MU5|A Chain A, Structure Of Topoisomerase Subunit
          Length = 471

 Score = 26.6 bits (57), Expect = 9.9,   Method: Compositional matrix adjust.
 Identities = 15/46 (32%), Positives = 26/46 (56%)

Query: 75  GMKPIPGVSRVTVKKSKNILFVISKPDVFKSPTSDTYIVFGEAKIE 120
           G+KP   V  +T ++   ++    K + F+SP++D+  V GE  IE
Sbjct: 279 GLKPNKKVKNLTEEEITRLVETFKKYEDFRSPSADSLSVIGEDLIE 324


  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
   0.309    0.126    0.335 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,527,170
Number of Sequences: 62578
Number of extensions: 119906
Number of successful extensions: 272
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: 263
Number of HSP's gapped (non-prelim): 9
length of query: 204
length of database: 14,973,337
effective HSP length: 94
effective length of query: 110
effective length of database: 9,091,005
effective search space: 1000010550
effective search space used: 1000010550
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 49 (23.5 bits)