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= psy8093
         (148 letters)

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

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



>pdb|3M4A|A Chain A, Crystal Structure Of A Bacterial Topoisomerase Ib In
           Complex With Dna Reveals A Secondary Dna Binding Site
          Length = 346

 Score = 28.5 bits (62), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 19/72 (26%), Positives = 32/72 (44%), Gaps = 17/72 (23%)

Query: 42  SSSGLRGDQKGNRQYLVDILKFIGPELGCDPRMKEYFLMDTPVPMLVTLASYI---FFVN 98
           +  G    ++  ++ LVD +KF+  +LG  P               VT  SYI    F  
Sbjct: 252 AQQGTESSERQAKKVLVDCVKFVADDLGNTP--------------AVTRGSYICPVIFDR 297

Query: 99  YLGPKLMENRKP 110
           YL  K++++ +P
Sbjct: 298 YLDGKVLDDYEP 309


>pdb|2F4Q|A Chain A, Crystal Structure Of Deinococcus Radiodurans Topoisomerase
           Ib
          Length = 346

 Score = 28.5 bits (62), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 19/72 (26%), Positives = 32/72 (44%), Gaps = 17/72 (23%)

Query: 42  SSSGLRGDQKGNRQYLVDILKFIGPELGCDPRMKEYFLMDTPVPMLVTLASYI---FFVN 98
           +  G    ++  ++ LVD +KF+  +LG  P               VT  SYI    F  
Sbjct: 252 AQQGTESSERQAKKVLVDCVKFVADDLGNTP--------------AVTRGSYICPVIFDR 297

Query: 99  YLGPKLMENRKP 110
           YL  K++++ +P
Sbjct: 298 YLDGKVLDDYEP 309


>pdb|3F8T|A Chain A, Crystal Structure Analysis Of A Full-Length Mcm Homolog
           From Methanopyrus Kandleri
          Length = 506

 Score = 27.7 bits (60), Expect = 2.6,   Method: Composition-based stats.
 Identities = 26/98 (26%), Positives = 36/98 (36%), Gaps = 26/98 (26%)

Query: 14  NPLKQWREDPLSFRLLHCDVSYQHGFGSSSSGLRGDQKGNRQYLVDILKFIGPELGCDPR 73
           NP +QW  DP   R+   D  +   F                   D++ F    LG DPR
Sbjct: 347 NPGEQWPSDPPIARI-DLDQDFLSHF-------------------DLIAF----LGVDPR 382

Query: 74  MKEYFLMDTPVPMLVTLASYIFFV--NYLGPKLMENRK 109
             E    DT VP    L  Y+ +    +  P+L E  +
Sbjct: 383 PGEPEEQDTEVPSYTLLRRYLLYAIREHPAPELTEEAR 420


  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
   0.326    0.141    0.462 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,770,972
Number of Sequences: 62578
Number of extensions: 183829
Number of successful extensions: 348
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 348
Number of HSP's gapped (non-prelim): 4
length of query: 148
length of database: 14,973,337
effective HSP length: 90
effective length of query: 58
effective length of database: 9,341,317
effective search space: 541796386
effective search space used: 541796386
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 47 (22.7 bits)