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= 043389
         (223 letters)

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

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



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

 Score = 61.6 bits (148), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 39/142 (27%), Positives = 79/142 (55%), Gaps = 2/142 (1%)

Query: 4   LFGK--RKTPAELLRENKRMLDKSIREIERERQGLQTQEKKLISEIKKSAKQGQMGAVKV 61
           LFGK   K P EL+ E    + K +R ++R+ + +Q +E+K+   +K +AK+GQ     V
Sbjct: 5   LFGKTQEKPPKELVNEWSLKIRKEMRVVDRQIRDIQREEEKVKRSVKDAAKKGQKDVCIV 64

Query: 62  MAKDLIRTRHQIEKFYKLKSQLQGVSLRIQTLKSTQAMGEAMKGVTKAMGQMNRQMNLPS 121
           +AK++IR+R  + K Y  K+ +  V + ++   +   +  +++  T+ M  M   + +P 
Sbjct: 65  LAKEMIRSRKAVSKLYASKAHMNSVLMGMKNQLAVLRVAGSLQKSTEVMKAMQSLVKIPE 124

Query: 122 LQKIMQEFERQNEKMEMVTEVM 143
           +Q  M+E  ++  K  ++ E++
Sbjct: 125 IQATMRELSKEMMKAGIIEEML 146


>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 = 58.9 bits (141), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 35/135 (25%), Positives = 75/135 (55%)

Query: 9   KTPAELLRENKRMLDKSIREIERERQGLQTQEKKLISEIKKSAKQGQMGAVKVMAKDLIR 68
           K P EL+ E    + K +R ++R+ + +Q +E+K+   +K +AK+GQ     V+AK++IR
Sbjct: 6   KPPKELVNEWSLKIRKEMRVVDRQIRDIQREEEKVKRSVKDAAKKGQKDVCIVLAKEMIR 65

Query: 69  TRHQIEKFYKLKSQLQGVSLRIQTLKSTQAMGEAMKGVTKAMGQMNRQMNLPSLQKIMQE 128
           +R  + K Y  K+ +  V + ++   +   +  +++  T+ M  M   + +P +Q  M+E
Sbjct: 66  SRKAVSKLYASKAHMNSVLMGMKNQLAVLRVAGSLQKSTEVMKAMQSLVKIPEIQATMRE 125

Query: 129 FERQNEKMEMVTEVM 143
             ++  K  ++ E++
Sbjct: 126 LSKEMMKAGIIEEML 140


>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 = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 36/139 (25%), Positives = 73/139 (52%), Gaps = 8/139 (5%)

Query: 9   KTPAELLRENKRMLDKSIREIERERQGLQTQEKKLISEIKKSAKQGQMGAVKVMAKDLIR 68
           K P EL+ E    + K  R ++R+ + +Q +E+K+   +K +AK+GQ     V+AK+ IR
Sbjct: 6   KPPKELVNEWSLKIRKEXRVVDRQIRDIQREEEKVKRSVKDAAKKGQKDVCIVLAKEXIR 65

Query: 69  TRHQIEKFYKLKSQ----LQGVSLRIQTLKSTQAMGEAMKGVTKAMGQMNRQMNLPSLQK 124
           +R  + K Y  K+     L G   ++  L+   ++ ++ + V KA   +   + +P +Q 
Sbjct: 66  SRKAVSKLYASKAHXNSVLXGXKNQLAVLRVAGSLQKSTE-VXKAXQSL---VKIPEIQA 121

Query: 125 IMQEFERQNEKMEMVTEVM 143
             +E  ++  K  ++ E++
Sbjct: 122 TXRELSKEXXKAGIIEEML 140


  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
   0.314    0.128    0.330 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,730,463
Number of Sequences: 62578
Number of extensions: 146082
Number of successful extensions: 413
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 401
Number of HSP's gapped (non-prelim): 16
length of query: 223
length of database: 14,973,337
effective HSP length: 95
effective length of query: 128
effective length of database: 9,028,427
effective search space: 1155638656
effective search space used: 1155638656
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 49 (23.5 bits)