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= 047471
         (579 letters)

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

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



>pdb|3MKQ|A Chain A, Crystal Structure Of Yeast AlphaBETAPRIME-Cop Subcomplex
           Of The Copi Vesicular Coat
 pdb|3MKQ|C Chain C, Crystal Structure Of Yeast AlphaBETAPRIME-Cop Subcomplex
           Of The Copi Vesicular Coat
 pdb|3MKQ|E Chain E, Crystal Structure Of Yeast AlphaBETAPRIME-Cop Subcomplex
           Of The Copi Vesicular Coat
          Length = 814

 Score = 33.5 bits (75), Expect = 0.32,   Method: Compositional matrix adjust.
 Identities = 25/92 (27%), Positives = 43/92 (46%), Gaps = 7/92 (7%)

Query: 31  MGIQPDVIVSNHVLNLYAKCGKMILARKVF-DEMSERNLVSWSAMISGHHQAGEHLLALE 89
           + I PD    +    L  K G++ LAR +  DE +E   + W A+     Q     LA+E
Sbjct: 649 LNISPD---QDQKFELALKVGQLTLARDLLTDESAE---MKWRALGDASLQRFNFKLAIE 702

Query: 90  FFSQMHLLPNEYIFASAISACAGIQSLVKGQQ 121
            F+  H L + ++  S+ +   G+ +L K  +
Sbjct: 703 AFTNAHDLESLFLLHSSFNNKEGLVTLAKDAE 734


>pdb|2HYP|A Chain A, Crystal Structure Of Rv0805 D66a Mutant
          Length = 280

 Score = 32.3 bits (72), Expect = 0.76,   Method: Compositional matrix adjust.
 Identities = 15/37 (40%), Positives = 23/37 (62%), Gaps = 4/37 (10%)

Query: 377 AAHANHRLGGSALKLFEQMKATGIKPDSVTFIGLLTA 413
           A  A+ RLG    +L EQ+  +G++PD++ F G L A
Sbjct: 36  AVDADDRLG----ELLEQLNQSGLRPDAIVFTGDLAA 68


>pdb|3BIL|A Chain A, Crystal Structure Of A Probable Laci Family
           Transcriptional Regulator From Corynebacterium
           Glutamicum
 pdb|3BIL|B Chain B, Crystal Structure Of A Probable Laci Family
           Transcriptional Regulator From Corynebacterium
           Glutamicum
          Length = 348

 Score = 28.5 bits (62), Expect = 10.0,   Method: Compositional matrix adjust.
 Identities = 15/33 (45%), Positives = 20/33 (60%)

Query: 388 ALKLFEQMKATGIKPDSVTFIGLLTACNHAGLV 420
           A KL +Q   T    DS+  IG++ AC+ AGLV
Sbjct: 234 ATKLLDQGAKTLFAGDSMMTIGVIEACHKAGLV 266


  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
   0.322    0.136    0.399 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,533,012
Number of Sequences: 62578
Number of extensions: 665792
Number of successful extensions: 1527
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1523
Number of HSP's gapped (non-prelim): 8
length of query: 579
length of database: 14,973,337
effective HSP length: 104
effective length of query: 475
effective length of database: 8,465,225
effective search space: 4020981875
effective search space used: 4020981875
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (25.4 bits)