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= psy2782
         (147 letters)

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

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



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

 Score =  100 bits (250), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 46/53 (86%), Positives = 51/53 (96%)

Query: 76  GLKQIQGVSRVTIRKSKNILFVINKPDVFKNPASDTYIVFGEAKIEDLSQQAQ 128
           GL+Q+ GV+RVTIRKSKNILFVI KPDV+K+PASDTYIVFGEAKIEDLSQQAQ
Sbjct: 2   GLRQVTGVTRVTIRKSKNILFVITKPDVYKSPASDTYIVFGEAKIEDLSQQAQ 54


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

 Score =  100 bits (250), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 46/53 (86%), Positives = 51/53 (96%)

Query: 72  MSKLGLKQIQGVSRVTIRKSKNILFVINKPDVFKNPASDTYIVFGEAKIEDLS 124
           MSKLGL+Q+ GV+RVTIRKSKNILFVI KPDV+K+PASDTYIVFGEAKIEDLS
Sbjct: 2   MSKLGLRQVTGVTRVTIRKSKNILFVITKPDVYKSPASDTYIVFGEAKIEDLS 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 = 99.8 bits (247), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 46/54 (85%), Positives = 51/54 (94%)

Query: 72  MSKLGLKQIQGVSRVTIRKSKNILFVINKPDVFKNPASDTYIVFGEAKIEDLSQ 125
            SKLGL+Q+ GV+RVTIRKSKNILFVI KPDV+K+PASDTYIVFGEAKIEDLSQ
Sbjct: 8   FSKLGLRQVTGVTRVTIRKSKNILFVITKPDVYKSPASDTYIVFGEAKIEDLSQ 61


>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 = 30.0 bits (66), Expect = 0.45,   Method: Compositional matrix adjust.
 Identities = 20/61 (32%), Positives = 33/61 (54%)

Query: 61  QSRGEKKARKIMSKLGLKQIQGVSRVTIRKSKNILFVINKPDVFKNPASDTYIVFGEAKI 120
           QS G+  A KI+   GLK  + V  +T  +   ++    K + F++P++D+  V GE  I
Sbjct: 263 QSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKKDEDFRSPSADSLSVIGEDLI 322

Query: 121 E 121
           E
Sbjct: 323 E 323


>pdb|1MX0|A Chain A, Structure Of Topoisomerase Subunit
 pdb|1MX0|B Chain B, Structure Of Topoisomerase Subunit
 pdb|1MX0|C Chain C, Structure Of Topoisomerase Subunit
 pdb|1MX0|D Chain D, Structure Of Topoisomerase Subunit
 pdb|1MX0|E Chain E, Structure Of Topoisomerase Subunit
 pdb|1MX0|F Chain F, Structure Of Topoisomerase Subunit
          Length = 472

 Score = 30.0 bits (66), Expect = 0.45,   Method: Compositional matrix adjust.
 Identities = 20/61 (32%), Positives = 33/61 (54%)

Query: 61  QSRGEKKARKIMSKLGLKQIQGVSRVTIRKSKNILFVINKPDVFKNPASDTYIVFGEAKI 120
           QS G+  A KI+   GLK  + V  +T  +   ++    K + F++P++D+  V GE  I
Sbjct: 265 QSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKKYEDFRSPSADSLSVIGEDLI 324

Query: 121 E 121
           E
Sbjct: 325 E 325


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

 Score = 30.0 bits (66), Expect = 0.45,   Method: Compositional matrix adjust.
 Identities = 20/61 (32%), Positives = 33/61 (54%)

Query: 61  QSRGEKKARKIMSKLGLKQIQGVSRVTIRKSKNILFVINKPDVFKNPASDTYIVFGEAKI 120
           QS G+  A KI+   GLK  + V  +T  +   ++    K + F++P++D+  V GE  I
Sbjct: 264 QSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKKYEDFRSPSADSLSVIGEDLI 323

Query: 121 E 121
           E
Sbjct: 324 E 324


>pdb|1Z59|A Chain A, Topoisomerase Vi-B, Adp-Bound Monomer Form
 pdb|1Z5C|A Chain A, Topoisomerase Vi-B, Adp Pi Bound Dimer Form
 pdb|1Z5C|B Chain B, Topoisomerase Vi-B, Adp Pi Bound Dimer Form
          Length = 469

 Score = 30.0 bits (66), Expect = 0.47,   Method: Compositional matrix adjust.
 Identities = 20/61 (32%), Positives = 33/61 (54%)

Query: 61  QSRGEKKARKIMSKLGLKQIQGVSRVTIRKSKNILFVINKPDVFKNPASDTYIVFGEAKI 120
           QS G+  A KI+   GLK  + V  +T  +   ++    K + F++P++D+  V GE  I
Sbjct: 262 QSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKKYEDFRSPSADSLSVIGEDLI 321

Query: 121 E 121
           E
Sbjct: 322 E 322


>pdb|1Z5A|A Chain A, Topoisomerase Vi-B, Adp-Bound Dimer Form
 pdb|1Z5A|B Chain B, Topoisomerase Vi-B, Adp-Bound Dimer Form
 pdb|1Z5B|A Chain A, Topoisomerase Vi-B, Adp Alf4- Bound Dimer Form
 pdb|1Z5B|B Chain B, Topoisomerase Vi-B, Adp Alf4- Bound Dimer Form
 pdb|2HKJ|A Chain A, Topoisomerase Vi-B Bound To Radicicol
          Length = 469

 Score = 30.0 bits (66), Expect = 0.49,   Method: Compositional matrix adjust.
 Identities = 20/61 (32%), Positives = 33/61 (54%)

Query: 61  QSRGEKKARKIMSKLGLKQIQGVSRVTIRKSKNILFVINKPDVFKNPASDTYIVFGEAKI 120
           QS G+  A KI+   GLK  + V  +T  +   ++    K + F++P++D+  V GE  I
Sbjct: 262 QSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKKYEDFRSPSADSLSVIGEDLI 321

Query: 121 E 121
           E
Sbjct: 322 E 322


>pdb|2VU9|A Chain A, Crystal Structure Of Botulinum Neurotoxin Serotype A
           Binding Domain In Complex With Gt1b
 pdb|2VUA|A Chain A, Crystal Structure Of The Botulinum Neurotoxin Serotype A
           Binding Domain
          Length = 444

 Score = 25.8 bits (55), Expect = 9.5,   Method: Composition-based stats.
 Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 5/52 (9%)

Query: 54  DLVSKAKQSR-----GEKKARKIMSKLGLKQIQGVSRVTIRKSKNILFVINK 100
           ++V K K+ R      +    KI+S L +  +  +S+V + KSKN   + NK
Sbjct: 330 NVVVKNKEYRLATNASQAGVEKILSALEIPDVGNLSQVVVMKSKNDQGITNK 381


  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    0.127    0.333 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,546,938
Number of Sequences: 62578
Number of extensions: 115062
Number of successful extensions: 238
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 225
Number of HSP's gapped (non-prelim): 16
length of query: 147
length of database: 14,973,337
effective HSP length: 90
effective length of query: 57
effective length of database: 9,341,317
effective search space: 532455069
effective search space used: 532455069
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: 47 (22.7 bits)