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= psy17189
         (95 letters)

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

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



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

 Score = 53.1 bits (126), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 30/69 (43%), Positives = 39/69 (56%), Gaps = 2/69 (2%)

Query: 1  MELYCSENLNTDRCTAGRDATMYTDSRVMENLITSEQHNGVPPVDYFVSVQTEIKPYMRK 60
          MEL C E        AG D  +  D RV+++L+  E+   VP   YF  VQ EIKP+MRK
Sbjct: 15 MELLCCEG-TRHAPRAGPDPRLLGDQRVLQSLLRLEERY-VPRASYFQCVQREIKPHMRK 72

Query: 61 IVNSWMQEV 69
          ++  WM EV
Sbjct: 73 MLAYWMLEV 81


>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 = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 28/68 (41%), Positives = 37/68 (54%), Gaps = 4/68 (5%)

Query: 2  ELYCSENLNTDRCTAGRDATMYTDSRVMENLITSEQHNGVPPVDYFVSVQTEIKPYMRKI 61
          +L C E     R  A  DA +  D RV+  ++ +E+    P V YF  VQ E+ P MRKI
Sbjct: 4  QLLCCEVETIRR--AYPDANLLND-RVLRAMLKAEE-TCAPSVSYFKCVQKEVLPSMRKI 59

Query: 62 VNSWMQEV 69
          V +WM EV
Sbjct: 60 VATWMLEV 67


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

 Score = 43.9 bits (102), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 23/51 (45%), Positives = 31/51 (60%), Gaps = 2/51 (3%)

Query: 19 DATMYTDSRVMENLITSEQHNGVPPVDYFVSVQTEIKPYMRKIVNSWMQEV 69
          DA +  D RV+  ++ +E+    P V YF  VQ E+ P MRKIV +WM EV
Sbjct: 5  DANLLND-RVLRAMLKAEE-TCAPSVSYFKCVQKEVLPSMRKIVATWMLEV 53


>pdb|4EWV|A Chain A, Crystal Structure Of Gh3.12 In Complex With Ampcpp
 pdb|4EWV|B Chain B, Crystal Structure Of Gh3.12 In Complex With Ampcpp
 pdb|4EPM|A Chain A, Crystal Structure Of Arabidopsis Gh3.12 (Pbs3) In Complex
           With Amp
 pdb|4EQL|A Chain A, Crystal Structure Of Gh3.12 In Complex With Amp And
           Salicylate
 pdb|4EQL|B Chain B, Crystal Structure Of Gh3.12 In Complex With Amp And
           Salicylate
          Length = 581

 Score = 26.9 bits (58), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 15/44 (34%), Positives = 20/44 (45%), Gaps = 5/44 (11%)

Query: 41  VPPVDYFVSVQTEIKPYMRKIVNSWMQEVSFPHIFHAFCLSGGA 84
           VP V Y      +IKPY+ ++VN    +V        F LS G 
Sbjct: 66  VPIVSY-----EDIKPYLDRVVNGESSDVISARTITGFLLSSGT 104


>pdb|4EQ4|A Chain A, Crystal Structure Of Seleno-Methionine Derivatized Gh3.12
 pdb|4EQ4|B Chain B, Crystal Structure Of Seleno-Methionine Derivatized Gh3.12
          Length = 581

 Score = 25.8 bits (55), Expect = 6.1,   Method: Composition-based stats.
 Identities = 15/43 (34%), Positives = 20/43 (46%), Gaps = 5/43 (11%)

Query: 41  VPPVDYFVSVQTEIKPYMRKIVNSWMQEVSFPHIFHAFCLSGG 83
           VP V Y      +IKPY+ ++VN    +V        F LS G
Sbjct: 66  VPIVSY-----EDIKPYLDRVVNGESSDVISARTITGFLLSSG 103


>pdb|3DS8|A Chain A, The Crysatl Structure Of The Gene Lin2722 Products From
           Listeria Innocua
          Length = 254

 Score = 25.4 bits (54), Expect = 7.5,   Method: Compositional matrix adjust.
 Identities = 9/21 (42%), Positives = 12/21 (57%)

Query: 39  NGVPPVDYFVSVQTEIKPYMR 59
           N  P  DYF+  QTE+ P + 
Sbjct: 153 NSTPQXDYFIKNQTEVSPDLE 173


  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
   0.325    0.136    0.430 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,810,429
Number of Sequences: 62578
Number of extensions: 91620
Number of successful extensions: 217
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 213
Number of HSP's gapped (non-prelim): 6
length of query: 95
length of database: 14,973,337
effective HSP length: 62
effective length of query: 33
effective length of database: 11,093,501
effective search space: 366085533
effective search space used: 366085533
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: 45 (21.9 bits)