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= 028201
         (212 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 = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 40/153 (26%), Positives = 71/153 (46%), Gaps = 12/153 (7%)

Query: 1   MNIFSK---KPNPKEALRESKREMQHATRGMEKEIGALQQEEKKLVAEIKRTAKTGNEGA 57
           M +F K   KP PKE + E   +++   R ++++I  +Q+EE+K+   +K  AK G +  
Sbjct: 3   MGLFGKTQEKP-PKELVNEWSLKIRKEMRVVDRQIRDIQREEEKVKRSVKDAAKKGQKDV 61

Query: 58  TKILARQLIRLRQQIANLQGSRAQ----IRGIATHTQAMHAHSSVXXXXXXXXXXXXXXX 113
             +LA+++IR R+ ++ L  S+A     + G+      +    S+               
Sbjct: 62  CIVLAKEMIRSRKAVSKLYASKAHMNSVLMGMKNQLAVLRVAGSLQKSTEVMKAMQSLVK 121

Query: 114 XQMEPAKQAKVMREFQKQSAQMDMTTEMMSDTI 146
               P  QA  MRE  K+  +  +  EM+ DT 
Sbjct: 122 I---PEIQA-TMRELSKEMMKAGIIEEMLEDTF 150


>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 = 44.7 bits (104), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 34/140 (24%), Positives = 66/140 (47%), Gaps = 1/140 (0%)

Query: 7   KPNPKEALRESKREMQHATRGMEKEIGALQQEEKKLVAEIKRTAKTGNEGATKILARQLI 66
           KP PKE + E   +++   R ++++I  +Q+EE+K+   +K  AK G +    +LA+++I
Sbjct: 6   KP-PKELVNEWSLKIRKEMRVVDRQIRDIQREEEKVKRSVKDAAKKGQKDVCIVLAKEMI 64

Query: 67  RLRQQIANLQGSRAQIRGIATHTQAMHAHSSVXXXXXXXXXXXXXXXXQMEPAKQAKVMR 126
           R R+ ++ L  S+A +  +    +   A   V                 ++  +    MR
Sbjct: 65  RSRKAVSKLYASKAHMNSVLMGMKNQLAVLRVAGSLQKSTEVMKAMQSLVKIPEIQATMR 124

Query: 127 EFQKQSAQMDMTTEMMSDTI 146
           E  K+  +  +  EM+ DT 
Sbjct: 125 ELSKEMMKAGIIEEMLEDTF 144


>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 = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 38/143 (26%), Positives = 69/143 (48%), Gaps = 3/143 (2%)

Query: 5   SKKPNPKEALRESKREMQHATRGMEKEIGALQQEEKKLVAEIKRTAKTGNEGATKILARQ 64
           ++KP PKE + E   +++   R ++++I  +Q+EE+K+   +K  AK G +    +LA++
Sbjct: 4   AEKP-PKELVNEWSLKIRKEXRVVDRQIRDIQREEEKVKRSVKDAAKKGQKDVCIVLAKE 62

Query: 65  LIRLRQQIANLQGSRAQIRGIATHTQAMHAHSSVXXXXXXXXXXXXXXXXQME-PAKQAK 123
            IR R+ ++ L  S+A    +    +   A   V                 ++ P  QA 
Sbjct: 63  XIRSRKAVSKLYASKAHXNSVLXGXKNQLAVLRVAGSLQKSTEVXKAXQSLVKIPEIQA- 121

Query: 124 VMREFQKQSAQMDMTTEMMSDTI 146
             RE  K+  +  +  EM+ DT 
Sbjct: 122 TXRELSKEXXKAGIIEEMLEDTF 144


>pdb|1DH3|A Chain A, Crystal Structure Of A Creb Bzip-Cre Complex Reveals The
          Basis For Creb Faimly Selective Dimerization And Dna
          Binding
 pdb|1DH3|C Chain C, Crystal Structure Of A Creb Bzip-Cre Complex Reveals The
          Basis For Creb Faimly Selective Dimerization And Dna
          Binding
          Length = 55

 Score = 27.7 bits (60), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 12/37 (32%), Positives = 23/37 (62%)

Query: 11 KEALRESKREMQHATRGMEKEIGALQQEEKKLVAEIK 47
          +EA RES+R+ +   + +E  +  L+ + K L+ E+K
Sbjct: 10 REAARESRRKKKEYVKSLENRVAVLENQNKTLIEELK 46


  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    0.312 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,009,669
Number of Sequences: 62578
Number of extensions: 107356
Number of successful extensions: 302
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 294
Number of HSP's gapped (non-prelim): 11
length of query: 212
length of database: 14,973,337
effective HSP length: 95
effective length of query: 117
effective length of database: 9,028,427
effective search space: 1056325959
effective search space used: 1056325959
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: 49 (23.5 bits)