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= 009379
         (536 letters)

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

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



>pdb|1TIF|A Chain A, Translation Initiation Factor 3 N-terminal Domain
          Length = 78

 Score = 51.6 bits (122), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 29/72 (40%), Positives = 46/72 (63%), Gaps = 2/72 (2%)

Query: 83  LNDKINAQFVRLVLDEGHK--VVSRHEALALARSLQCDLVEVDRKANPPVCKIMDFHKEK 140
           +N++I A+ VRL+   G +  + S+ EAL +A     DLV V   A PPVC+IMD+ K +
Sbjct: 7   INEQIRAREVRLIDQNGDQLGIKSKQEALEIAARRNLDLVLVAPNAKPPVCRIMDYGKFR 66

Query: 141 YQKELKEKDRAK 152
           ++++ KEK+  K
Sbjct: 67  FEQQKKEKEARK 78


>pdb|1I96|V Chain V, Crystal Structure Of The 30s Ribosomal Subunit From
           Thermus Thermophilus In Complex With The Translation
           Initiation Factor If3 (C-Terminal Domain)
          Length = 89

 Score = 42.4 bits (98), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 24/86 (27%), Positives = 49/86 (56%), Gaps = 1/86 (1%)

Query: 163 DCKEVRFSGKIEQKDLQMKADTVKRLMDKGYRVKCMALPVGKKEETEDLGG-YLSRLIDL 221
           + K ++F  KI++ D Q K   +KR + +G++VK   +  G++    +LG   L+R+ + 
Sbjct: 1   EVKSIKFRVKIDEHDYQTKLGHIKRFLQEGHKVKVTIMFRGREVAHPELGERILNRVTED 60

Query: 222 IEDISVVESGPHVERKQAYAIIRHVK 247
           ++D++VVE  P +  +    ++  VK
Sbjct: 61  LKDLAVVEMKPEMLGRDMNMLLAPVK 86


>pdb|1TIG|A Chain A, Translation Initiation Factor 3 C-Terminal Domain
          Length = 94

 Score = 42.0 bits (97), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 24/82 (29%), Positives = 44/82 (53%), Gaps = 1/82 (1%)

Query: 163 DCKEVRFSGKIEQKDLQMKADTVKRLMDKGYRVKCMALPVGKKEETEDLGG-YLSRLIDL 221
           + KEVR S  IE+ D   K    ++ ++KG +VK      G+    +++G   L RL + 
Sbjct: 6   NVKEVRLSPTIEEHDFNTKLRNARKFLEKGDKVKATIRFKGRAITHKEIGQRVLDRLSEA 65

Query: 222 IEDISVVESGPHVERKQAYAII 243
             DI+VVE+ P ++ +  + ++
Sbjct: 66  CADIAVVETAPKMDGRNMFLVL 87


>pdb|2IFE|A Chain A, Translation Initiation Factor If3 From Escherichia Coli
           Ribosome Binding Domain (Residues 84-180)
          Length = 100

 Score = 32.0 bits (71), Expect = 0.96,   Method: Composition-based stats.
 Identities = 20/80 (25%), Positives = 46/80 (57%), Gaps = 2/80 (2%)

Query: 166 EVRFSGKIEQKDLQMKADTVKRLMDKGYRVKCMALPVGKKEETEDLG-GYLSRLIDLIED 224
           E++F    ++ D Q+K  ++ R +++G + K      G++   + +G   L+R+ D +++
Sbjct: 15  EIKFRPGTDEGDYQVKLRSLIRFLEEGDKAKITLRFRGREMAHQQIGMEVLNRVKDDLQE 74

Query: 225 ISVVESGP-HVERKQAYAII 243
           ++VVES P  +E +Q   ++
Sbjct: 75  LAVVESFPTKIEGRQMIMVL 94


  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    0.376 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,226,703
Number of Sequences: 62578
Number of extensions: 603247
Number of successful extensions: 1042
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1037
Number of HSP's gapped (non-prelim): 8
length of query: 536
length of database: 14,973,337
effective HSP length: 103
effective length of query: 433
effective length of database: 8,527,803
effective search space: 3692538699
effective search space used: 3692538699
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: 54 (25.4 bits)