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= 013065
         (450 letters)

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

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



>pdb|3DDM|A Chain A, Crystal Structure Of Mandelate RacemaseMUCONATE
           Lactonizing Enzyme From Bordetella Bronchiseptica Rb50
 pdb|3DDM|B Chain B, Crystal Structure Of Mandelate RacemaseMUCONATE
           Lactonizing Enzyme From Bordetella Bronchiseptica Rb50
 pdb|3DDM|C Chain C, Crystal Structure Of Mandelate RacemaseMUCONATE
           Lactonizing Enzyme From Bordetella Bronchiseptica Rb50
 pdb|3DDM|D Chain D, Crystal Structure Of Mandelate RacemaseMUCONATE
           Lactonizing Enzyme From Bordetella Bronchiseptica Rb50
          Length = 392

 Score = 34.3 bits (77), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 4/71 (5%)

Query: 297 RGGDQEYLYVDGVGIKTGDYFQFYQPDHNAALAACRNASENIRNLKLNSSGKGFLGRRDV 356
           R G   + ++ G G + G Y     P++   + A R A+E  R  KL     GF   RDV
Sbjct: 131 RAGQPLWAWLGGSGDRIGVYASGINPENPEDVVA-RKAAEGYRAFKLKV---GFDDARDV 186

Query: 357 ANSIDRKEVLG 367
            N++  +E+LG
Sbjct: 187 RNALHVRELLG 197


>pdb|3NZZ|A Chain A, Crystal Structure Of The Salmonella Type Iii Secretion
           System Tip Protein Sipd
 pdb|3NZZ|B Chain B, Crystal Structure Of The Salmonella Type Iii Secretion
           System Tip Protein Sipd
 pdb|3O02|A Chain A, The Crystal Structure Of The Salmonella Type Iii Secretion
           System Tip Protein Sipd In Complex With
           Chenodeoxycholate
 pdb|3O02|B Chain B, The Crystal Structure Of The Salmonella Type Iii Secretion
           System Tip Protein Sipd In Complex With
           Chenodeoxycholate
          Length = 308

 Score = 28.9 bits (63), Expect = 6.2,   Method: Compositional matrix adjust.
 Identities = 23/101 (22%), Positives = 44/101 (43%), Gaps = 13/101 (12%)

Query: 179 AFISDAVALVFASDKDKPHAGTGEIQFHLAMSEGVSAIGPRH-----KAVSVRANHAEGS 233
           AF +   AL  AS   +P     + +    +S+ +SAIG  +       V+V  +  +  
Sbjct: 73  AFSAPTSALFSASPMAQPRTTISDAEIWDMVSQNISAIGDSYLGVYENVVAVYTDFYQAF 132

Query: 234 T--------WLTAKREGHHVILDGEQILRHIDQLENRFPQV 266
           +        WL   ++G+ V LD   +   ++ L N++ Q+
Sbjct: 133 SDILSKMGGWLLPGKDGNTVKLDVTSLKNDLNSLVNKYNQI 173


>pdb|3O00|A Chain A, Crystal Structure Of The Salmonella Type Iii Secretion
           System Tip Protein Sipd-C244s
 pdb|3O00|B Chain B, Crystal Structure Of The Salmonella Type Iii Secretion
           System Tip Protein Sipd-C244s
 pdb|3O01|A Chain A, The Crystal Structure Of The Salmonella Type Iii Secretion
           System Tip Protein Sipd In Complex With Deoxycholate
 pdb|3O01|B Chain B, The Crystal Structure Of The Salmonella Type Iii Secretion
           System Tip Protein Sipd In Complex With Deoxycholate
          Length = 308

 Score = 28.9 bits (63), Expect = 6.9,   Method: Compositional matrix adjust.
 Identities = 23/101 (22%), Positives = 44/101 (43%), Gaps = 13/101 (12%)

Query: 179 AFISDAVALVFASDKDKPHAGTGEIQFHLAMSEGVSAIGPRH-----KAVSVRANHAEGS 233
           AF +   AL  AS   +P     + +    +S+ +SAIG  +       V+V  +  +  
Sbjct: 73  AFSAPTSALFSASPMAQPRTTISDAEIWDMVSQNISAIGDSYLGVYENVVAVYTDFYQAF 132

Query: 234 T--------WLTAKREGHHVILDGEQILRHIDQLENRFPQV 266
           +        WL   ++G+ V LD   +   ++ L N++ Q+
Sbjct: 133 SDILSKMGGWLLPGKDGNTVKLDVTSLKNDLNSLVNKYNQI 173


>pdb|2YM9|A Chain A, Sipd From Salmonella Typhimurium
 pdb|2YM9|B Chain B, Sipd From Salmonella Typhimurium
 pdb|2YM9|C Chain C, Sipd From Salmonella Typhimurium
 pdb|2YM9|D Chain D, Sipd From Salmonella Typhimurium
          Length = 346

 Score = 28.5 bits (62), Expect = 8.1,   Method: Compositional matrix adjust.
 Identities = 23/101 (22%), Positives = 44/101 (43%), Gaps = 13/101 (12%)

Query: 179 AFISDAVALVFASDKDKPHAGTGEIQFHLAMSEGVSAIGPRH-----KAVSVRANHAEGS 233
           AF +   AL  AS   +P     + +    +S+ +SAIG  +       V+V  +  +  
Sbjct: 111 AFSAPTSALFSASPMAQPRTTISDAEIWDMVSQNISAIGDSYLGVYENVVAVYTDFYQAF 170

Query: 234 T--------WLTAKREGHHVILDGEQILRHIDQLENRFPQV 266
           +        WL   ++G+ V LD   +   ++ L N++ Q+
Sbjct: 171 SDILSKMGGWLLPGKDGNTVKLDVTSLKNDLNSLVNKYNQI 211


  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    0.139    0.414 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,767,809
Number of Sequences: 62578
Number of extensions: 596337
Number of successful extensions: 1366
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1364
Number of HSP's gapped (non-prelim): 9
length of query: 450
length of database: 14,973,337
effective HSP length: 102
effective length of query: 348
effective length of database: 8,590,381
effective search space: 2989452588
effective search space used: 2989452588
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)