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= 016113
         (395 letters)

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

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



>pdb|3QC1|A Chain A, Protein Phosphatase Subunit: Alpha4
          Length = 243

 Score = 62.0 bits (149), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 47/161 (29%), Positives = 77/161 (47%), Gaps = 20/161 (12%)

Query: 15  FERGRKIHQ---IATE---SGCDPDAVRKGCEVLEKCEDMVGKLGLFSSNETKDDISTAN 68
           FE  +K+ +   +ATE   S    D V KG E+LEK   M+ +L LFS NE  ++I++ +
Sbjct: 37  FETSKKLLEDVEVATEPTGSRTIQDKVSKGLELLEKAAGMLSQLDLFSRNEDLEEIASTD 96

Query: 69  LKYILVPYFLGEL-IEKIAQDDRLQILKASQAKLKEFISFC-----------EIMXXXXX 116
           LKY++VP   G L ++++    RL  L+ ++     F++ C           +       
Sbjct: 97  LKYLMVPALQGALTMKQVNPSKRLDHLQRAREHFVHFLTQCHCYHVAEFQLPQTKTNSAE 156

Query: 117 XXXXXXXQAKP--TAFTDQRARKIARFKRQRAAESKLQEIK 155
                   A P   A   QR  KI R+K+++  E +L  +K
Sbjct: 157 NNTASSSMAYPNLVAMASQRQAKIERYKQKKEVEHRLSALK 197


>pdb|2V0P|A Chain A, The Structure Of Tap42 Alpha4 Subunit
 pdb|2V0P|B Chain B, The Structure Of Tap42 Alpha4 Subunit
          Length = 234

 Score = 48.1 bits (113), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 44/73 (60%), Gaps = 12/73 (16%)

Query: 48  MVGKLGLFSSNETKDDISTANLKYILVPYFLGELIEKIAQDD---------RLQILKASQ 98
           +  +L LFS+NET DD+STA++K++ V Y+LG LI +   +D         +L  LK S 
Sbjct: 49  IFDRLALFSTNETIDDVSTASIKFLAVDYYLGLLISRRQSNDSDVAQRQSXKLIYLKKS- 107

Query: 99  AKLKEFISFCEIM 111
             ++ FI+F  ++
Sbjct: 108 --VESFINFLTLL 118


>pdb|1CM8|A Chain A, Phosphorylated Map Kinase P38-Gamma
 pdb|1CM8|B Chain B, Phosphorylated Map Kinase P38-Gamma
          Length = 367

 Score = 32.3 bits (72), Expect = 0.47,   Method: Compositional matrix adjust.
 Identities = 22/71 (30%), Positives = 40/71 (56%), Gaps = 9/71 (12%)

Query: 46  EDMVGKLGLFSSNETKDDISTANLKYILVPYF---LGELI--EKIAQDDRLQILKASQAK 100
           E+++G L +F+ +ET DD +     Y+++P+    LG+L+  EK+ + DR+Q L     K
Sbjct: 84  ENVIGLLDVFTPDETLDDFTDF---YLVMPFMGTDLGKLMKHEKLGE-DRIQFLVYQMLK 139

Query: 101 LKEFISFCEIM 111
              +I    I+
Sbjct: 140 GLRYIHAAGII 150


  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
   0.315    0.129    0.372 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,746,822
Number of Sequences: 62578
Number of extensions: 330679
Number of successful extensions: 746
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 737
Number of HSP's gapped (non-prelim): 10
length of query: 395
length of database: 14,973,337
effective HSP length: 101
effective length of query: 294
effective length of database: 8,652,959
effective search space: 2543969946
effective search space used: 2543969946
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)