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= 038384
         (283 letters)

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

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



>pdb|2ZBK|A Chain A, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
           Insights Into Dna Transfer Mechanisms
 pdb|2ZBK|C Chain C, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
           Insights Into Dna Transfer Mechanisms
 pdb|2ZBK|E Chain E, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
           Insights Into Dna Transfer Mechanisms
 pdb|2ZBK|G Chain G, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
           Insights Into Dna Transfer Mechanisms
          Length = 389

 Score = 85.5 bits (210), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 54/172 (31%), Positives = 83/172 (48%), Gaps = 38/172 (22%)

Query: 5   DAVFHRLANDQYCTRNRCIVITGRGYPDISTRRFLRLLIEKLRLPTFCLVDCDPYGFDIL 64
           DAVF +L    +  + + I+IT  G PD +TRRF+R L E+L+LP + L D DPYG+ I 
Sbjct: 211 DAVFQQLHRAGFWKQYKSILITSAGQPDRATRRFVRRLNEELKLPVYILTDADPYGWYIF 270

Query: 65  TTYRFGSMQMAYDAKFLRIPEMHWLG---------------------------AFPSDFE 97
           + +R GS+ ++Y+++ L  P+  +LG                           A  +D +
Sbjct: 271 SVFRIGSISLSYESERLATPDAKFLGVSMGDIFGNSRKKPYLSEAERKNYIIKAKDADIK 330

Query: 98  KYGLPKN---CRLKLTVEGV--------KFEIEAFCACSFSFLSEKYIPSKI 138
           +    KN    + K   E +        K EIEA  +    FL+ +YIP KI
Sbjct: 331 RAEEIKNYEWFKTKAWQEEINTFLQRKAKLEIEAMASKGLKFLAFQYIPEKI 382


>pdb|1D3Y|A Chain A, Structure Of The Dna Topoisomerase Vi A Subunit
 pdb|1D3Y|B Chain B, Structure Of The Dna Topoisomerase Vi A Subunit
          Length = 301

 Score = 68.6 bits (166), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 38/115 (33%), Positives = 61/115 (53%), Gaps = 5/115 (4%)

Query: 6   AVFHRLANDQYCTRNRCIVITGRGYPDISTRRFLRLLIEKLRLPTFCLVDCDPYGF-DIL 64
            +F RL  +++  ++ CI+++ +G P  +TRRF++ L E+  LP     D DPYG+ +I 
Sbjct: 132 GMFARLNAERFWDKHNCILVSLKGVPARATRRFIKRLHEEHDLPVLVFTDGDPYGYLNIY 191

Query: 65  TTYRFGSMQMAYDAKFLRIPEMHWLGAFPSDFEKYGLP----KNCRLKLTVEGVK 115
            T + GS +  + A  L IP    +G  P D   Y LP    K   +K   +G+K
Sbjct: 192 RTLKVGSGKAIHLADKLSIPAARLIGVTPQDIIDYDLPTHPLKEQDIKRIKDGLK 246


>pdb|2Q2E|A Chain A, Crystal Structure Of The Topoisomerase Vi Holoenzyme From
           Methanosarcina Mazei
          Length = 369

 Score = 65.5 bits (158), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 38/161 (23%), Positives = 75/161 (46%), Gaps = 28/161 (17%)

Query: 6   AVFHRLANDQYCTRNRCIVITGRGYPDISTRRFLRLLIEKLRLPTFCLVDCDPYGFDILT 65
            ++ RL  + +      I++  +G P  STRR ++ + E+L +P     D DP+ + I  
Sbjct: 205 GMYARLMENGFDEAYNAILVHLKGQPARSTRRIIKRMNEELGIPVAVFTDGDPWSYRIYA 264

Query: 66  TYRFGSMQMAYDAKFLRIPEMHWLGAFPSDFEKYGLP----------------------- 102
           +  +G+++ A+ ++F+  P   +LG  PSD  +Y L                        
Sbjct: 265 SVAYGAIKSAHLSEFMATPAAKFLGLQPSDIVEYELSTDKLTEQDVSALRSELSDPRFES 324

Query: 103 ----KNCRLKLTVEGVKFEIEAFCACSFSFLSEKYIPSKIQ 139
               +  +L+L + G K E +AF      F++E Y+P++++
Sbjct: 325 DYWKEQIQLQLDI-GKKAEQQAFAGKGLDFVTEVYLPNRLK 364


  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
   0.325    0.140    0.438 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,764,434
Number of Sequences: 62578
Number of extensions: 311786
Number of successful extensions: 653
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 648
Number of HSP's gapped (non-prelim): 4
length of query: 283
length of database: 14,973,337
effective HSP length: 98
effective length of query: 185
effective length of database: 8,840,693
effective search space: 1635528205
effective search space used: 1635528205
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (24.3 bits)