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= psy5305
         (947 letters)

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

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



>pdb|3EGT|A Chain A, T. Brucei Farnesyl Diphosphate Synthase Complexed With
           Bisphosphonate Bph-722
 pdb|3EGT|B Chain B, T. Brucei Farnesyl Diphosphate Synthase Complexed With
           Bisphosphonate Bph-722
          Length = 413

 Score = 32.0 bits (71), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 32/124 (25%), Positives = 49/124 (39%), Gaps = 27/124 (21%)

Query: 750 WFRVLDVVAKLAVISNAVLIAFTSNFIPRIMYKFLGSKNFTDEGFLNDTLSYFNTSDFQE 809
           W+R  DV  + A+    +L ++T           +    F D  FL D L  FN  D+  
Sbjct: 164 WYRHPDVTVQCAINDGLLLKSWT---------HMMAMHFFADRPFLQDLLCRFNRVDYTT 214

Query: 810 SARPLYPSINVTMCRYHNYRNPPWFEPNH--------------LKYKRSWYYWKLLAARL 855
           +   LY   +VT     N  +P   +P                +KYK ++Y + LL   +
Sbjct: 215 AVGQLY---DVTSMFDSNKLDPDVSQPTTTDFAEFTLSNYKRIVKYKTAYYTY-LLPLVM 270

Query: 856 GFIV 859
           G IV
Sbjct: 271 GLIV 274


>pdb|2EWG|A Chain A, T. Brucei Farnesyl Diphosphate Synthase Complexed With
           Minodronate
 pdb|2EWG|B Chain B, T. Brucei Farnesyl Diphosphate Synthase Complexed With
           Minodronate
 pdb|2I19|A Chain A, T. Brucei Farnesyl Diphosphate Synthase Complexed With
           Bisphosphonate
 pdb|2I19|B Chain B, T. Brucei Farnesyl Diphosphate Synthase Complexed With
           Bisphosphonate
 pdb|2OGD|A Chain A, T. Brucei Farnesyl Diphosphate Synthase Complexed With
           Bisphosphonate Bph-527
 pdb|2OGD|B Chain B, T. Brucei Farnesyl Diphosphate Synthase Complexed With
           Bisphosphonate Bph-527
 pdb|2P1C|A Chain A, T. Brucei Farnesyl Diphosphate Synthase Complexed With
           Bisphosphonate Bph-210
 pdb|2P1C|B Chain B, T. Brucei Farnesyl Diphosphate Synthase Complexed With
           Bisphosphonate Bph-210
 pdb|3DYF|A Chain A, T. Brucei Farnesyl Diphosphate Synthase Complexed With
           Bisphosphonate Bph-461 And Isopentyl Diphosphate
 pdb|3DYF|B Chain B, T. Brucei Farnesyl Diphosphate Synthase Complexed With
           Bisphosphonate Bph-461 And Isopentyl Diphosphate
 pdb|3DYG|A Chain A, T. Brucei Farnesyl Diphosphate Synthase Complexed With
           Bisphosphonate Bph-461
 pdb|3DYG|B Chain B, T. Brucei Farnesyl Diphosphate Synthase Complexed With
           Bisphosphonate Bph-461
 pdb|3DYH|A Chain A, T. Brucei Farnesyl Diphosphate Synthase Complexed With
           Bisphosphonate Bph-721
 pdb|3DYH|B Chain B, T. Brucei Farnesyl Diphosphate Synthase Complexed With
           Bisphosphonate Bph-721
 pdb|3EFQ|A Chain A, T. Brucei Farnesyl Diphosphate Synthase Complexed With
           Bisphosphonate Bph-714
 pdb|3EFQ|B Chain B, T. Brucei Farnesyl Diphosphate Synthase Complexed With
           Bisphosphonate Bph-714
          Length = 390

 Score = 32.0 bits (71), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 32/124 (25%), Positives = 49/124 (39%), Gaps = 27/124 (21%)

Query: 750 WFRVLDVVAKLAVISNAVLIAFTSNFIPRIMYKFLGSKNFTDEGFLNDTLSYFNTSDFQE 809
           W+R  DV  + A+    +L ++T           +    F D  FL D L  FN  D+  
Sbjct: 141 WYRHPDVTVQCAINDGLLLKSWT---------HMMAMHFFADRPFLQDLLCRFNRVDYTT 191

Query: 810 SARPLYPSINVTMCRYHNYRNPPWFEPNH--------------LKYKRSWYYWKLLAARL 855
           +   LY   +VT     N  +P   +P                +KYK ++Y + LL   +
Sbjct: 192 AVGQLY---DVTSMFDSNKLDPDVSQPTTTDFAEFTLSNYKRIVKYKTAYYTY-LLPLVM 247

Query: 856 GFIV 859
           G IV
Sbjct: 248 GLIV 251


  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
   0.324    0.138    0.426 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 28,095,845
Number of Sequences: 62578
Number of extensions: 1158813
Number of successful extensions: 2807
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 2806
Number of HSP's gapped (non-prelim): 3
length of query: 947
length of database: 14,973,337
effective HSP length: 108
effective length of query: 839
effective length of database: 8,214,913
effective search space: 6892312007
effective search space used: 6892312007
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 56 (26.2 bits)