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= 047577
         (194 letters)

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

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



>pdb|3BPJ|A Chain A, Crystal Structure Of Human Translation Initiation Factor
           3, Subunit 1 Alpha
 pdb|3BPJ|B Chain B, Crystal Structure Of Human Translation Initiation Factor
           3, Subunit 1 Alpha
 pdb|3BPJ|C Chain C, Crystal Structure Of Human Translation Initiation Factor
           3, Subunit 1 Alpha
 pdb|3BPJ|D Chain D, Crystal Structure Of Human Translation Initiation Factor
           3, Subunit 1 Alpha
          Length = 80

 Score = 43.9 bits (102), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 21/60 (35%), Positives = 34/60 (56%)

Query: 115 LDNFIPKSESDFMEYAELISHKLRPYEKSYHYIGLLKAVMRLSMTSLKAADAKDVASSIT 174
           +D   P S  DF E+ +L+  K+  YEKS +Y   L+ ++R    SL+  D K + +S+T
Sbjct: 5   IDAMNPSSRDDFTEFGKLLKDKITQYEKSLYYASFLEVLVRDVCISLEIDDLKKITNSLT 64


>pdb|2JT1|A Chain A, Solution Nmr Structure Of Pefi (Plasmid-Encoded Fimbriae
           Regulatory) Protein From Salmonella Typhimurium.
           Northeast Structural Genomics Target Str82
          Length = 77

 Score = 26.6 bits (57), Expect = 8.4,   Method: Compositional matrix adjust.
 Identities = 12/43 (27%), Positives = 24/43 (55%)

Query: 111 DEKNLDNFIPKSESDFMEYAELISHKLRPYEKSYHYIGLLKAV 153
           + +N+D+  P    D  + A L  +++R Y +  H +G+L+ V
Sbjct: 15  ERQNMDDGAPVKTRDIADAAGLSIYQVRLYLEQLHDVGVLEKV 57


>pdb|4AF5|A Chain A, Structure Of The C. Glutamicum Acnr Crystal Form I
          Length = 190

 Score = 26.6 bits (57), Expect = 10.0,   Method: Compositional matrix adjust.
 Identities = 16/43 (37%), Positives = 24/43 (55%), Gaps = 2/43 (4%)

Query: 92  RLVEEADYKSTKELFGKGGDEKNLDNFIPKSESDFMEYAELIS 134
           R +EEA  KS   +F   GD++NL  F+  +  D    AE++S
Sbjct: 37  RRLEEATGKSRGAIFHHFGDKENL--FLALAREDAARMAEVVS 77


  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
   0.312    0.130    0.355 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,169,073
Number of Sequences: 62578
Number of extensions: 100360
Number of successful extensions: 264
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 262
Number of HSP's gapped (non-prelim): 4
length of query: 194
length of database: 14,973,337
effective HSP length: 94
effective length of query: 100
effective length of database: 9,091,005
effective search space: 909100500
effective search space used: 909100500
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 bits)