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= psy17858
         (157 letters)

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

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



>pdb|2QKO|A Chain A, Crystal Structure Of Transcriptional Regulator Rha06399
           From Rhodococcus Sp. Rha1
 pdb|2QKO|B Chain B, Crystal Structure Of Transcriptional Regulator Rha06399
           From Rhodococcus Sp. Rha1
 pdb|2QKO|C Chain C, Crystal Structure Of Transcriptional Regulator Rha06399
           From Rhodococcus Sp. Rha1
 pdb|2QKO|D Chain D, Crystal Structure Of Transcriptional Regulator Rha06399
           From Rhodococcus Sp. Rha1
          Length = 215

 Score = 28.1 bits (61), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 18/49 (36%), Positives = 26/49 (53%), Gaps = 7/49 (14%)

Query: 70  PQHVACMAHF----WGPITRSGTGFLAVQDV---AKREPGFRVIATGTI 111
           PQ++     +    +G ITR  TG+LA+Q++   A R P  R   T TI
Sbjct: 101 PQNLELAIEYXQGLFGRITRDRTGYLALQELRLEAVRRPELRTTLTRTI 149


>pdb|4DVZ|A Chain A, Crystal Structure Of The Helicobacter Pylori Caga
           Oncoprotein
          Length = 569

 Score = 26.9 bits (58), Expect = 5.1,   Method: Composition-based stats.
 Identities = 21/68 (30%), Positives = 31/68 (45%), Gaps = 5/68 (7%)

Query: 89  GFLAVQDVAKREPGFRVIATGTILDANQ---TAEVTKKL--KLTGVPMKIYKKTAFIKDM 143
           G  A   V+  E GF  +A   + D N    T+ V + L  KLT   + + +    IKD 
Sbjct: 263 GVGATNGVSHLEAGFNKVAVFNLPDLNNLAITSFVRRNLENKLTAKGLSLQEANKLIKDF 322

Query: 144 FNSTLEVA 151
            +S  E+A
Sbjct: 323 LSSNKELA 330


>pdb|4DVY|P Chain P, Crystal Structure Of The Helicobacter Pylori Caga
           Oncoprotein
          Length = 876

 Score = 26.9 bits (58), Expect = 5.2,   Method: Composition-based stats.
 Identities = 21/68 (30%), Positives = 31/68 (45%), Gaps = 5/68 (7%)

Query: 89  GFLAVQDVAKREPGFRVIATGTILDANQ---TAEVTKKL--KLTGVPMKIYKKTAFIKDM 143
           G  A   V+  E GF  +A   + D N    T+ V + L  KLT   + + +    IKD 
Sbjct: 523 GVGATNGVSHLEAGFNKVAVFNLPDLNNLAITSFVRRNLENKLTAKGLSLQEANKLIKDF 582

Query: 144 FNSTLEVA 151
            +S  E+A
Sbjct: 583 LSSNKELA 590


>pdb|4G0H|A Chain A, Crystal Structure Of The N-Terminal Domain Of Helicobacter
           Pylori Caga Protein
          Length = 916

 Score = 26.9 bits (58), Expect = 5.3,   Method: Composition-based stats.
 Identities = 21/68 (30%), Positives = 31/68 (45%), Gaps = 5/68 (7%)

Query: 89  GFLAVQDVAKREPGFRVIATGTILDANQ---TAEVTKKL--KLTGVPMKIYKKTAFIKDM 143
           G  A   V+  E GF  +A   + D N    T+ V + L  KLT   + + +    IKD 
Sbjct: 523 GVGATNGVSHLEAGFNKVAVFNLPDLNNLAITSFVRRNLENKLTAKGLSLQEANKLIKDF 582

Query: 144 FNSTLEVA 151
            +S  E+A
Sbjct: 583 LSSNKELA 590


  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    0.137    0.419 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,443,427
Number of Sequences: 62578
Number of extensions: 168509
Number of successful extensions: 482
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 481
Number of HSP's gapped (non-prelim): 5
length of query: 157
length of database: 14,973,337
effective HSP length: 91
effective length of query: 66
effective length of database: 9,278,739
effective search space: 612396774
effective search space used: 612396774
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 47 (22.7 bits)