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= psy9518
         (132 letters)

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

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



>pdb|1VHN|A Chain A, Crystal Structure Of A Putative Flavin Oxidoreductase With
           Flavin
          Length = 318

 Score = 28.9 bits (63), Expect = 0.91,   Method: Compositional matrix adjust.
 Identities = 9/18 (50%), Positives = 16/18 (88%)

Query: 1   MIGRGALIKPWIFQEIKE 18
           ++ RGA+ +PWIF++IK+
Sbjct: 211 LVARGAIGRPWIFKQIKD 228


>pdb|1A41|A Chain A, Type 1-Topoisomerase Catalytic Fragment From Vaccinia
           Virus
          Length = 234

 Score = 28.5 bits (62), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 3/49 (6%)

Query: 2   IGRGALIKPWIFQEIKEKKLFDISSAERFDILKEYVNYGLEHWGSDTRG 50
           I + A +   I + +K+K   D+ S   FD   E+++  ++H  S T G
Sbjct: 189 ISKRAYMATTILEMVKDKNFLDVVSKTTFD---EFLSIVVDHVKSSTDG 234


>pdb|2H7F|X Chain X, Structure Of Variola Topoisomerase Covalently Bound To Dna
          Length = 314

 Score = 27.7 bits (60), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 3/49 (6%)

Query: 2   IGRGALIKPWIFQEIKEKKLFDISSAERFDILKEYVNYGLEHWGSDTRG 50
           I + A +   I + +K+K   D+ S   FD   E+++  ++H  S T G
Sbjct: 269 ISKRAXMATTILEMVKDKNFLDVVSKTTFD---EFLSIVVDHVKSSTDG 314


>pdb|2H7G|X Chain X, Structure Of Variola Topoisomerase Non-Covalently Bound To
           Dna
 pdb|3IGC|A Chain A, Smallpox Virus Topoisomerase-Dna Transition State
          Length = 314

 Score = 27.7 bits (60), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 3/49 (6%)

Query: 2   IGRGALIKPWIFQEIKEKKLFDISSAERFDILKEYVNYGLEHWGSDTRG 50
           I + A +   I + +K+K   D+ S   FD   E+++  ++H  S T G
Sbjct: 269 ISKRAYMATTILEMVKDKNFLDVVSKTTFD---EFLSIVVDHVKSSTDG 314


>pdb|2W61|A Chain A, Saccharomyces Cerevisiae Gas2p Apostructure (E176q Mutant)
          Length = 555

 Score = 27.3 bits (59), Expect = 2.7,   Method: Composition-based stats.
 Identities = 21/77 (27%), Positives = 37/77 (48%), Gaps = 6/77 (7%)

Query: 13  FQEIKEKKLFDISSAERFDILKEYVNYGLEHWGSDTRGVETTRRFL-----LEWLSFLHR 67
           F+E  E  +  I+  +  DIL ++ N   E   +D +G+ T   +L      E  S    
Sbjct: 310 FEEENEYGVVKINDNDGVDILPDFKNLKKEFAKADPKGI-TEEEYLTAKEPTEVESVECP 368

Query: 68  YIPVGLLESTQKMNQRP 84
           +I VG+ E+ +K+ + P
Sbjct: 369 HIAVGVWEANEKLPETP 385


>pdb|2W62|A Chain A, Saccharomyces Cerevisiae Gas2p In Complex With
           Laminaripentaose
 pdb|2W63|A Chain A, Saccharomyces Cerevisiae Gas2p In Complex With
           Laminaritriose And Laminaritetraose
          Length = 555

 Score = 27.3 bits (59), Expect = 2.7,   Method: Composition-based stats.
 Identities = 21/77 (27%), Positives = 37/77 (48%), Gaps = 6/77 (7%)

Query: 13  FQEIKEKKLFDISSAERFDILKEYVNYGLEHWGSDTRGVETTRRFL-----LEWLSFLHR 67
           F+E  E  +  I+  +  DIL ++ N   E   +D +G+ T   +L      E  S    
Sbjct: 310 FEEENEYGVVKINDNDGVDILPDFKNLKKEFAKADPKGI-TEEEYLTAKEPTEVESVECP 368

Query: 68  YIPVGLLESTQKMNQRP 84
           +I VG+ E+ +K+ + P
Sbjct: 369 HIAVGVWEANEKLPETP 385


>pdb|1T8H|A Chain A, 1.8 A Crystal Structure Of An Uncharacterized B.
          Stearothermophilus Protein
          Length = 277

 Score = 26.9 bits (58), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 16/34 (47%), Positives = 20/34 (58%), Gaps = 2/34 (5%)

Query: 37 VNYGLEHWGSDTRGVETTRRFLLEWLSF-LHRYI 69
          +N GL H G D   V   RR L EWL+F L R++
Sbjct: 45 LNMGL-HVGDDRTDVVNNRRRLAEWLAFPLERWV 77


  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
   0.321    0.137    0.434 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,137,045
Number of Sequences: 62578
Number of extensions: 156377
Number of successful extensions: 406
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 403
Number of HSP's gapped (non-prelim): 10
length of query: 132
length of database: 14,973,337
effective HSP length: 88
effective length of query: 44
effective length of database: 9,466,473
effective search space: 416524812
effective search space used: 416524812
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 46 (22.3 bits)