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= psy928
         (88 letters)

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

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



>pdb|2A3J|A Chain A, Structure Of Urndesign, A Complete Computational Redesign
           Of Human U1a Protein
          Length = 127

 Score = 25.8 bits (55), Expect = 6.2,   Method: Compositional matrix adjust.
 Identities = 15/63 (23%), Positives = 31/63 (49%), Gaps = 3/63 (4%)

Query: 7   PREAVATALLSVAEARAKSLDLVAKALETKDGRSA---ASLSIAEQYVKAFNELAKTNNT 63
           P+E +   L ++A ++   LD+V    +   G++    A+   A+ +V+AF       N 
Sbjct: 42  PKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNP 101

Query: 64  LIV 66
           L++
Sbjct: 102 LVI 104


>pdb|4EUV|A Chain A, Crystal Structure Of Peld 158-Ct From Pseudomonas
           Aeruginosa Pao1, In Complex With C-Di-Gmp, Form 1
          Length = 297

 Score = 25.4 bits (54), Expect = 8.2,   Method: Composition-based stats.
 Identities = 18/54 (33%), Positives = 24/54 (44%)

Query: 3   LKKSPREAVATALLSVAEARAKSLDLVAKALETKDGRSAASLSIAEQYVKAFNE 56
           L++    +V   LL   E RA S   V   L   DGR  A L++ +     FNE
Sbjct: 80  LERGELVSVRQELLERGEQRAHSAAAVCVPLVDTDGRILALLAVEQMPFFVFNE 133


>pdb|4EU0|A Chain A, Crystal Structure Of Peld 158-Ct From Pseudomonas
           Aeruginosa Pao1
          Length = 298

 Score = 25.4 bits (54), Expect = 8.2,   Method: Composition-based stats.
 Identities = 18/54 (33%), Positives = 24/54 (44%)

Query: 3   LKKSPREAVATALLSVAEARAKSLDLVAKALETKDGRSAASLSIAEQYVKAFNE 56
           L++    +V   LL   E RA S   V   L   DGR  A L++ +     FNE
Sbjct: 80  LERGELVSVRQELLERGEQRAHSAAAVCVPLVDTDGRILALLAVEQMPFFVFNE 133


>pdb|3IFE|A Chain A, 1.55 Angstrom Resolution Crystal Structure Of Peptidase T
           (Pept-1) From Bacillus Anthracis Str. 'ames Ancestor'
          Length = 434

 Score = 25.0 bits (53), Expect = 9.7,   Method: Composition-based stats.
 Identities = 13/40 (32%), Positives = 23/40 (57%), Gaps = 3/40 (7%)

Query: 20  EARAKSLDLVAKALETKDGRSAASLSIAEQYVKAFNELAK 59
           EAR  +++ + K ++ K G+ A  L + +QY   +N L K
Sbjct: 315 EARKNTIENIVKQMQEKYGQDAVVLEMNDQY---YNMLEK 351


  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
   0.308    0.118    0.289 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,714,450
Number of Sequences: 62578
Number of extensions: 42895
Number of successful extensions: 142
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 129
Number of HSP's gapped (non-prelim): 14
length of query: 88
length of database: 14,973,337
effective HSP length: 56
effective length of query: 32
effective length of database: 11,468,969
effective search space: 367007008
effective search space used: 367007008
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 45 (21.9 bits)