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= psy2448
         (151 letters)

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

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



>pdb|2EBH|X Chain X, Crystal Structures Reveal A Thiol-Protease Like Catalytic
           Triad In The C-Terminal Region Of Pasteurella Multocida
           Toxin
          Length = 746

 Score = 28.1 bits (61), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 27/111 (24%), Positives = 40/111 (36%), Gaps = 18/111 (16%)

Query: 39  LPALKQLCKI------------FPVDLKARRVFVSAGGLKRVQALKPPAGSELCEAVTMI 86
           +P L Q  KI            F  D+ + RV +    L+  Q L PP G  L      +
Sbjct: 517 MPGLVQYLKIPATVVDSDGAWQFLPDVASSRVPIEVTELENWQVLTPPQGKILGLKQFKL 576

Query: 87  NSYFPEDIVRY------YSPRCTDHLLAKVDQFTPQVSLPLITCAPDTPSD 131
            + FP +  R        S    + L+ K+D     V +  + C     SD
Sbjct: 577 TAGFPTEQSRLPLLENSVSEDLREELMQKIDAIKNDVKMNSLVCMEAGSSD 627


>pdb|4IM7|A Chain A, Crystal Structure Of Fructuronate Reductase (ydfi) From E.
           Coli Cft073 (efi Target Efi-506389) Complexed With Nadh
           And D-mannonate
          Length = 506

 Score = 26.9 bits (58), Expect = 4.7,   Method: Composition-based stats.
 Identities = 13/40 (32%), Positives = 18/40 (45%)

Query: 87  NSYFPEDIVRYYSPRCTDHLLAKVDQFTPQVSLPLITCAP 126
           N  FP  +V    P  T+  LAK++Q T       + C P
Sbjct: 234 NVTFPSTMVDRIVPAVTEDTLAKIEQLTGVRDAAGVACEP 273


>pdb|2XSA|A Chain A, Ogoga Apostructure
 pdb|2XSB|A Chain A, Ogoga Pugnac Complex
          Length = 447

 Score = 26.6 bits (57), Expect = 5.1,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 35/81 (43%), Gaps = 4/81 (4%)

Query: 51  VDLKAR-RVFVSAGGLKRVQALKPPAGSELCEAVTMINSYFPEDIVRYYSPRCTDHLLAK 109
           V ++AR RV   A GL R+  L+  A +     +    S  P   V Y  P+    LLA+
Sbjct: 42  VHVRARWRVPYDAAGLARLTELRDAAAAR---GMVFYVSLAPCLDVTYSDPQDRAALLAR 98

Query: 110 VDQFTPQVSLPLITCAPDTPS 130
           VDQ        L+    D PS
Sbjct: 99  VDQLARAGLRNLVLLFDDIPS 119


>pdb|2EBF|X Chain X, Crystal Structures Reveal A Thiol-Protease Like Catalytic
           Triad In The C-Terminal Region Of Pasteurella Multocida
           Toxin
          Length = 746

 Score = 26.2 bits (56), Expect = 7.3,   Method: Compositional matrix adjust.
 Identities = 25/104 (24%), Positives = 38/104 (36%), Gaps = 18/104 (17%)

Query: 39  LPALKQLCKI------------FPVDLKARRVFVSAGGLKRVQALKPPAGSELCEAVTMI 86
           +P L Q  KI            F  D+ + RV +    L+  Q L PP G  L      +
Sbjct: 517 MPGLVQYLKIPATVVDSDGAWQFLPDVASSRVPIEVTELENWQVLTPPQGKILGLKQFKL 576

Query: 87  NSYFPEDIVRY------YSPRCTDHLLAKVDQFTPQVSLPLITC 124
            + FP +  R        S    + L+ K+D     V +  + C
Sbjct: 577 TAGFPTEQSRLPLLENSVSEDLREELMQKIDAIKNDVKMNSLVC 620


>pdb|3GHF|A Chain A, Crystal Structure Of The Septum Site-Determining Protein
          Minc From Salmonella Typhimurium
          Length = 120

 Score = 25.8 bits (55), Expect = 8.7,   Method: Compositional matrix adjust.
 Identities = 15/49 (30%), Positives = 25/49 (51%)

Query: 18 LSNVSFSFVDLLLYESPPEILLPALKQLCKIFPVDLKARRVFVSAGGLK 66
          L   SF+   + L+E+ PE++  AL+      P  LK   V ++  GL+
Sbjct: 10 LKGSSFTLSVVHLHEAEPEVIRQALEDKIAQAPAFLKHAPVVINVSGLE 58


  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
   0.319    0.136    0.404 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,633,255
Number of Sequences: 62578
Number of extensions: 171706
Number of successful extensions: 366
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 364
Number of HSP's gapped (non-prelim): 6
length of query: 151
length of database: 14,973,337
effective HSP length: 90
effective length of query: 61
effective length of database: 9,341,317
effective search space: 569820337
effective search space used: 569820337
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)