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= 028177
         (212 letters)

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

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



>pdb|2W96|A Chain A, Crystal Structure Of Cdk4 In Complex With A D-Type Cyclin
 pdb|2W99|A Chain A, Crystal Structure Of Cdk4 In Complex With A D-Type Cyclin
 pdb|2W9F|A Chain A, Crystal Structure Of Cdk4 In Complex With A D-Type Cyclin
          Length = 271

 Score = 30.0 bits (66), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 11/43 (25%), Positives = 26/43 (60%)

Query: 59  LQPIRESNLQLFALIALWISSKIHDSRPVSVKSFKSLGDKIIK 101
           L+P+++S LQL     ++++SK+ ++ P++ +      D  I+
Sbjct: 91  LEPVKKSRLQLLGATCMFVASKMKETIPLTAEKLCIYTDNSIR 133


>pdb|2W9Z|A Chain A, Crystal Structure Of Cdk4 In Complex With A D-Type Cyclin
          Length = 257

 Score = 30.0 bits (66), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 11/43 (25%), Positives = 26/43 (60%)

Query: 59  LQPIRESNLQLFALIALWISSKIHDSRPVSVKSFKSLGDKIIK 101
           L+P+++S LQL     ++++SK+ ++ P++ +      D  I+
Sbjct: 77  LEPVKKSRLQLLGATCMFVASKMKETIPLTAEKLCIYTDNSIR 119


>pdb|3G33|B Chain B, Crystal Structure Of Cdk4CYCLIN D3
 pdb|3G33|D Chain D, Crystal Structure Of Cdk4CYCLIN D3
          Length = 306

 Score = 29.3 bits (64), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 13/66 (19%), Positives = 34/66 (51%), Gaps = 5/66 (7%)

Query: 61  PIRESNLQLFALIALWISSKIHDSRPVSVKSFKSLGDKIIKDEHFTTRDFLEAEIVFMQV 120
           P R++ LQL   + + ++SK+ ++ P++++        I  D   + R   + E++ +  
Sbjct: 107 PTRKAQLQLLGAVCMLLASKLRETTPLTIEKL-----CIYTDHAVSPRQLRDWEVLVLGK 161

Query: 121 LDFEIG 126
           L +++ 
Sbjct: 162 LKWDLA 167


  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
   0.324    0.137    0.415 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,708,952
Number of Sequences: 62578
Number of extensions: 200508
Number of successful extensions: 444
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 442
Number of HSP's gapped (non-prelim): 3
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: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 bits)