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= 027296
         (225 letters)

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

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



>pdb|3MUN|A Chain A, Appep_pepclose Closed State
 pdb|3MUO|A Chain A, Appep_pepclose+pp Closed State
          Length = 693

 Score = 29.3 bits (64), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 11/24 (45%), Positives = 17/24 (70%)

Query: 180 GTNAAVIRGALRAERPDLLTVILP 203
           G+N  ++ GA+  +RPDL+ V LP
Sbjct: 540 GSNGGLLVGAVMTQRPDLMRVALP 563


>pdb|3IUN|A Chain A, Appep_d622n Opened State
 pdb|3IUQ|A Chain A, Appep_d622n+pp Closed State
 pdb|3IUR|A Chain A, Appep_d266nx+h2h3 Opened State
          Length = 693

 Score = 29.3 bits (64), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 11/24 (45%), Positives = 17/24 (70%)

Query: 180 GTNAAVIRGALRAERPDLLTVILP 203
           G+N  ++ GA+  +RPDL+ V LP
Sbjct: 540 GSNGGLLVGAVMTQRPDLMRVALP 563


>pdb|3CA8|A Chain A, Crystal Structure Of Escherichia Coli Ydcf, An
           S-Adenosyl-L-Methionine Utilizing Enzyme
 pdb|3CA8|B Chain B, Crystal Structure Of Escherichia Coli Ydcf, An
           S-Adenosyl-L-Methionine Utilizing Enzyme
          Length = 266

 Score = 28.5 bits (62), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 12/31 (38%), Positives = 18/31 (58%)

Query: 86  NVIGMFGSDEDVGTQIPTQAQSVVEGSGAVM 116
           NVIG + + +D   ++P QA  V+    AVM
Sbjct: 18  NVIGQWLAQDDFSGEVPYQADCVILAGNAVM 48


>pdb|3IVM|A Chain A, Appep_wt+pp Closed State
          Length = 693

 Score = 28.1 bits (61), Expect = 4.5,   Method: Composition-based stats.
 Identities = 11/24 (45%), Positives = 16/24 (66%)

Query: 180 GTNAAVIRGALRAERPDLLTVILP 203
           G+N  ++ GA+  +RPDL  V LP
Sbjct: 540 GSNGGLLVGAVXTQRPDLXRVALP 563


>pdb|3IUJ|A Chain A, Appep_wt2 Opened State
 pdb|3IUL|A Chain A, Appep_wt1 Opened State
 pdb|3IUM|A Chain A, Appep_wtx Opened State
          Length = 693

 Score = 28.1 bits (61), Expect = 4.5,   Method: Composition-based stats.
 Identities = 11/24 (45%), Positives = 16/24 (66%)

Query: 180 GTNAAVIRGALRAERPDLLTVILP 203
           G+N  ++ GA+  +RPDL  V LP
Sbjct: 540 GSNGGLLVGAVXTQRPDLXRVALP 563


  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
   0.317    0.131    0.377 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,366,505
Number of Sequences: 62578
Number of extensions: 252862
Number of successful extensions: 476
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 471
Number of HSP's gapped (non-prelim): 5
length of query: 225
length of database: 14,973,337
effective HSP length: 95
effective length of query: 130
effective length of database: 9,028,427
effective search space: 1173695510
effective search space used: 1173695510
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)