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= psy4474
         (2174 letters)

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

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



>pdb|2AP3|A Chain A, 1.6 A Crystal Structure Of A Conserved Protein Of Unknown
            Function From Staphylococcus Aureus
          Length = 199

 Score = 32.0 bits (71), Expect = 4.4,   Method: Compositional matrix adjust.
 Identities = 32/139 (23%), Positives = 71/139 (51%), Gaps = 11/139 (7%)

Query: 925  KETKAQSDRIQDALKTLNQLIGHRKEFEVDVENVEAKLKELEVA------VEGDVKTNNV 978
            K+T  +   ++D +K  +  +   KEFE + + ++   ++ + A      ++ DVK   V
Sbjct: 59   KDTAVRGKAVKDLIKNADDRL---KEFEKEEDAIKKSEQDFKKAKSHVDNIDNDVKRKEV 115

Query: 979  LMLQELLN-KYAQLNEEAGELNMMISNVSIATEHMNLNDADRLTVNDSVSSMQKRYAQLS 1037
              L ++L  KY   ++ A      +++     +++N NDA +  VN+   ++++ Y +L 
Sbjct: 116  KQLDDVLKEKYKLHSDYAKAYKKAVNSEKTLFKYLNQNDATQQGVNEKSKAIEQNYKKL- 174

Query: 1038 RTIEDRISTVNNKLQSVKR 1056
            + + D+ + V NK+Q  K+
Sbjct: 175  KEVSDKYTKVLNKVQKEKQ 193


>pdb|2VSG|A Chain A, A Structural Motif In The Variant Surface Glycoproteins Of
            Trypanosoma Brucei
 pdb|2VSG|B Chain B, A Structural Motif In The Variant Surface Glycoproteins Of
            Trypanosoma Brucei
          Length = 358

 Score = 31.2 bits (69), Expect = 6.1,   Method: Compositional matrix adjust.
 Identities = 20/57 (35%), Positives = 29/57 (50%), Gaps = 8/57 (14%)

Query: 1929 KEEVEAWLHKAHATVQECDELEAGIKEEQKNIETQYLQWNSFRETLAQMTAWLDSVE 1985
            + + +    KAHA++ E  +L  G K  Q  +ET  L        LAQ TA LDS++
Sbjct: 233  RNQADTLYGKAHASITELLQLAQGPKPGQTEVETMKL--------LAQKTAALDSIK 281


>pdb|3KTZ|A Chain A, Structure Of Gap31
 pdb|3KTZ|B Chain B, Structure Of Gap31
 pdb|3KU0|A Chain A, Structure Of Gap31 With Adenine At Its Binding Pocket
 pdb|3KU0|B Chain B, Structure Of Gap31 With Adenine At Its Binding Pocket
          Length = 251

 Score = 31.2 bits (69), Expect = 6.3,   Method: Composition-based stats.
 Identities = 19/84 (22%), Positives = 38/84 (45%), Gaps = 15/84 (17%)

Query: 2086 DKVYESTSEPGHEPLRVQMEKLQQAVEALYDKITVTESLIL---------------SQVE 2130
            +K Y  T++ G EPLR+ ++KL +     Y    +  SL++               +Q+ 
Sbjct: 119  EKAYRETTDLGIEPLRIGIKKLDENAIDNYKPTEIASSLLVVIQMVSEAARFTFIENQIR 178

Query: 2131 AKYAKLIEPETSYEELQKRQGQLT 2154
              + + I P  +   L+ + G+L+
Sbjct: 179  NNFQQRIRPANNTISLENKWGKLS 202


  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
   0.311    0.127    0.349 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 57,420,543
Number of Sequences: 62578
Number of extensions: 2259178
Number of successful extensions: 6567
Number of sequences better than 100.0: 60
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 51
Number of HSP's that attempted gapping in prelim test: 6403
Number of HSP's gapped (non-prelim): 193
length of query: 2174
length of database: 14,973,337
effective HSP length: 114
effective length of query: 2060
effective length of database: 7,839,445
effective search space: 16149256700
effective search space used: 16149256700
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 59 (27.3 bits)