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= 036944
         (370 letters)

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

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



>pdb|1W98|B Chain B, The Structural Basis Of Cdk2 Activation By Cyclin E
          Length = 283

 Score = 34.7 bits (78), Expect = 0.084,   Method: Compositional matrix adjust.
 Identities = 30/111 (27%), Positives = 55/111 (49%), Gaps = 13/111 (11%)

Query: 41  LRKVALNVILKNSKCFNFDAFIPYLAMNYFDLFISRNQLPNVLGRVRDDIVLAAICCLTL 100
           +R + L+ +++  + +       YLA ++FD +++  +  NV   V+  + L  I  L +
Sbjct: 49  MRAILLDWLMEVCEVYKLHRETFYLAQDFFDRYMATQE--NV---VKTLLQLIGISSLFI 103

Query: 101 AWKVRN----QAFRFIYFERDNNLNEDYKRHILSMELQILKGINWRLRAVT 147
           A K+      +  +F Y   D   + D    IL+MEL I+K + WRL  +T
Sbjct: 104 AAKLEEIYPPKLHQFAYVT-DGACSGD---EILTMELMIMKALKWRLSPLT 150


>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 = 32.7 bits (73), Expect = 0.34,   Method: Compositional matrix adjust.
 Identities = 34/133 (25%), Positives = 58/133 (43%), Gaps = 17/133 (12%)

Query: 65  LAMNYFDLFISRNQLPNVLGRVRDDIVLAAICCLTLAWKVRNQ----AFRFIYFERDNNL 120
           LAMNY D F+S   +       +  + L    C+ +A K++      A +   +  DN++
Sbjct: 80  LAMNYLDRFLSLEPVK------KSRLQLLGATCMFVASKMKETIPLTAEKLCIYT-DNSI 132

Query: 121 NEDYKRHILSMELQILKGINWRLRAVTAMYFKEFFVGKIPVG---KGIMRRTLNEIIIQA 177
             +       MEL ++  + W L A+T   F E F+ K+P     K I+R+     +   
Sbjct: 133 RPEELL---QMELLLVNKLKWNLAAMTPHDFIEHFLSKMPEAEENKQIIRKHAQTFVALC 189

Query: 178 QGDINFTQYKPSV 190
             D+ F    PS+
Sbjct: 190 ATDVKFISNPPSM 202


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

 Score = 32.7 bits (73), Expect = 0.37,   Method: Compositional matrix adjust.
 Identities = 34/133 (25%), Positives = 58/133 (43%), Gaps = 17/133 (12%)

Query: 65  LAMNYFDLFISRNQLPNVLGRVRDDIVLAAICCLTLAWKVRNQ----AFRFIYFERDNNL 120
           LAMNY D F+S   +       +  + L    C+ +A K++      A +   +  DN++
Sbjct: 66  LAMNYLDRFLSLEPVK------KSRLQLLGATCMFVASKMKETIPLTAEKLCIYT-DNSI 118

Query: 121 NEDYKRHILSMELQILKGINWRLRAVTAMYFKEFFVGKIPVG---KGIMRRTLNEIIIQA 177
             +       MEL ++  + W L A+T   F E F+ K+P     K I+R+     +   
Sbjct: 119 RPEELL---QMELLLVNKLKWNLAAMTPHDFIEHFLSKMPEAEENKQIIRKHAQTFVALC 175

Query: 178 QGDINFTQYKPSV 190
             D+ F    PS+
Sbjct: 176 ATDVKFISNPPSM 188


>pdb|2IDL|A Chain A, Crystal Structure Of Conserved Protein Of Unknown Function
           From Streptococcus Pneumoniae
 pdb|2IDL|B Chain B, Crystal Structure Of Conserved Protein Of Unknown Function
           From Streptococcus Pneumoniae
          Length = 117

 Score = 30.8 bits (68), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 5/74 (6%)

Query: 84  GRVRDDIVLAAICCLTLAWKVRNQAFRFIYFERDNNLNEDYKRHILSMELQILKGINWRL 143
           G    D+V A++   TLA    N   +F  +E    LNED   +++   ++I K +    
Sbjct: 29  GEYGLDVVCASVS--TLAINFINSIEKFAGYEPILELNEDEGGYLM---VEIPKDLPSHQ 83

Query: 144 RAVTAMYFKEFFVG 157
           R +T ++F+ FF+G
Sbjct: 84  REMTQLFFESFFLG 97


  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
   0.321    0.137    0.408 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,006,054
Number of Sequences: 62578
Number of extensions: 446546
Number of successful extensions: 879
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 875
Number of HSP's gapped (non-prelim): 4
length of query: 370
length of database: 14,973,337
effective HSP length: 100
effective length of query: 270
effective length of database: 8,715,537
effective search space: 2353194990
effective search space used: 2353194990
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)