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= 043204
         (504 letters)

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

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



>pdb|1WD7|A Chain A, Crystal Structure Of Uroporphyrinogen Iii Synthase From An
           Extremely Thermophilic Bacterium Thermus Thermophilus
           Hb8 (Wild Type, Native, Form-2 Crystal)
 pdb|1WD7|B Chain B, Crystal Structure Of Uroporphyrinogen Iii Synthase From An
           Extremely Thermophilic Bacterium Thermus Thermophilus
           Hb8 (Wild Type, Native, Form-2 Crystal)
 pdb|1WCW|A Chain A, Crystal Structure Of Uroporphyrinogen Iii Synthase From An
           Extremely Thermophilic Bacterium Thermus Thermophilus
           Hb8 (Wild Type, Native, Form-1 Crystal)
          Length = 261

 Score = 30.4 bits (67), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 27/80 (33%), Positives = 39/80 (48%), Gaps = 2/80 (2%)

Query: 232 LFALCDQGKIQDAMQILEKILRKGLKAPKSRRHRI-DLCPCNDGEDIEGAKSLINEALIR 290
           L  L  QG+   A+Q+  K L     A   R +R+  L P     D EG   L  EAL+R
Sbjct: 123 LLPLLPQGRGVAALQLYGKPLPLLENALAERGYRVLPLMPYRHLPDPEGILRL-EEALLR 181

Query: 291 GGIPSLASYSAMAIDLYNEG 310
           G + +LA  +A+ ++   EG
Sbjct: 182 GEVDALAFVAAIQVEFLFEG 201


>pdb|1WCX|A Chain A, Crystal Structure Of Mutant Uroporphyrinogen Iii Synthase
           From An Extremely Thermophilic Bacterium Thermus
           Thermophilus Hb8 (L75mI193ML248M, SEMET DERIVATIVE,
           FORM-1 Crystal)
          Length = 261

 Score = 29.6 bits (65), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 27/80 (33%), Positives = 38/80 (47%), Gaps = 2/80 (2%)

Query: 232 LFALCDQGKIQDAMQILEKILRKGLKAPKSRRHRI-DLCPCNDGEDIEGAKSLINEALIR 290
           L  L  QG+   A+Q+  K L     A   R +R+  L P     D EG   L  EAL+R
Sbjct: 123 LLPLLPQGRGVAALQLYGKPLPLLENALAERGYRVLPLXPYRHLPDPEGILRL-EEALLR 181

Query: 291 GGIPSLASYSAMAIDLYNEG 310
           G + +LA  +A  ++   EG
Sbjct: 182 GEVDALAFVAAXQVEFLFEG 201


>pdb|1VPB|A Chain A, Crystal Structure Of A Putative Modulator Of Dna Gyrase
           (Bt3649) From Bacteroides Thetaiotaomicron Vpi-5482 At
           1.75 A Resolution
          Length = 451

 Score = 29.3 bits (64), Expect = 6.0,   Method: Compositional matrix adjust.
 Identities = 15/36 (41%), Positives = 21/36 (58%)

Query: 325 KGFWPSLVMYEAKLAALFKDGMVDEALEVIEEEMVK 360
           KG  P L +Y+AK A+L  D  ++ A  V EE + K
Sbjct: 120 KGGKPDLKLYDAKFASLNPDDKIEMAKAVAEEALGK 155


  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
   0.322    0.136    0.408 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,031,190
Number of Sequences: 62578
Number of extensions: 559372
Number of successful extensions: 1486
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1483
Number of HSP's gapped (non-prelim): 6
length of query: 504
length of database: 14,973,337
effective HSP length: 103
effective length of query: 401
effective length of database: 8,527,803
effective search space: 3419649003
effective search space used: 3419649003
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: 54 (25.4 bits)