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= 029928
         (185 letters)

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

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



>pdb|3FRT|A Chain A, The Structure Of Human Chmp3 (Residues 8 - 222).
 pdb|3FRT|B Chain B, The Structure Of Human Chmp3 (Residues 8 - 222)
          Length = 218

 Score = 37.4 bits (85), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 30/123 (24%), Positives = 56/123 (45%), Gaps = 8/123 (6%)

Query: 1   MEKEIGALQQEEKKLVAEIKRTAKTGNEGATKILARQLIRLRQQIANLQGSRAQIR---- 56
           ++++I  +Q+EE+K+   +K  AK G +    +LA+++IR R+ ++ L  S+A +     
Sbjct: 26  VDRQIRDIQREEEKVKRSVKDAAKKGQKDVCIVLAKEMIRSRKAVSKLYASKAHMNSVLM 85

Query: 57  GIATHTQAMHAHSSVXXXXXXXXXXXXXXXXQMEPAKQAKVMREFQKQSAQMDMTTEMMS 116
           G+      +    S+                   P  QA  MRE  K+  +  +  EM+ 
Sbjct: 86  GMKNQLAVLRVAGSLQKSTEVMKAMQSLVKI---PEIQA-TMRELSKEMMKAGIIEEMLE 141

Query: 117 DTI 119
           DT 
Sbjct: 142 DTF 144


>pdb|3FRV|A Chain A, Structure Of Human Chmp3 (Residues 1-150)
          Length = 152

 Score = 36.6 bits (83), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 30/123 (24%), Positives = 56/123 (45%), Gaps = 8/123 (6%)

Query: 1   MEKEIGALQQEEKKLVAEIKRTAKTGNEGATKILARQLIRLRQQIANLQGSRAQIR---- 56
           ++++I  +Q+EE+K+   +K  AK G +    +LA+++IR R+ ++ L  S+A +     
Sbjct: 32  VDRQIRDIQREEEKVKRSVKDAAKKGQKDVCIVLAKEMIRSRKAVSKLYASKAHMNSVLM 91

Query: 57  GIATHTQAMHAHSSVXXXXXXXXXXXXXXXXQMEPAKQAKVMREFQKQSAQMDMTTEMMS 116
           G+      +    S+                   P  QA  MRE  K+  +  +  EM+ 
Sbjct: 92  GMKNQLAVLRVAGSLQKSTEVMKAMQSLVKI---PEIQA-TMRELSKEMMKAGIIEEMLE 147

Query: 117 DTI 119
           DT 
Sbjct: 148 DTF 150


>pdb|2GD5|A Chain A, Structural Basis For Budding By The Escrtiii Factor Chmp3
 pdb|2GD5|B Chain B, Structural Basis For Budding By The Escrtiii Factor Chmp3
 pdb|2GD5|C Chain C, Structural Basis For Budding By The Escrtiii Factor Chmp3
 pdb|2GD5|D Chain D, Structural Basis For Budding By The Escrtiii Factor Chmp3
          Length = 179

 Score = 34.7 bits (78), Expect = 0.035,   Method: Compositional matrix adjust.
 Identities = 31/120 (25%), Positives = 56/120 (46%), Gaps = 2/120 (1%)

Query: 1   MEKEIGALQQEEKKLVAEIKRTAKTGNEGATKILARQLIRLRQQIANLQGSRAQIRGIAT 60
           ++++I  +Q+EE+K+   +K  AK G +    +LA++ IR R+ ++ L  S+A    +  
Sbjct: 26  VDRQIRDIQREEEKVKRSVKDAAKKGQKDVCIVLAKEXIRSRKAVSKLYASKAHXNSVLX 85

Query: 61  HTQAMHAHSSVXXXXXXXXXXXXXXXXQME-PAKQAKVMREFQKQSAQMDMTTEMMSDTI 119
             +   A   V                 ++ P  QA   RE  K+  +  +  EM+ DT 
Sbjct: 86  GXKNQLAVLRVAGSLQKSTEVXKAXQSLVKIPEIQA-TXRELSKEXXKAGIIEEMLEDTF 144


  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
   0.310    0.122    0.307 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,263,230
Number of Sequences: 62578
Number of extensions: 80392
Number of successful extensions: 221
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 213
Number of HSP's gapped (non-prelim): 8
length of query: 185
length of database: 14,973,337
effective HSP length: 93
effective length of query: 92
effective length of database: 9,153,583
effective search space: 842129636
effective search space used: 842129636
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 48 (23.1 bits)