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= 028984
         (200 letters)

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

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



>pdb|1JSU|C Chain C, P27(Kip1)CYCLIN ACDK2 COMPLEX
          Length = 84

 Score = 32.0 bits (71), Expect = 0.24,   Method: Compositional matrix adjust.
 Identities = 11/25 (44%), Positives = 17/25 (68%)

Query: 175 KYNYDIVNDLPLEGRYQWVRLNEAS 199
           K+N+D  N  PLEG+Y+W  + + S
Sbjct: 37  KWNFDFQNHKPLEGKYEWQEVEKGS 61


>pdb|1YUB|A Chain A, Solution Structure Of An Rrna Methyltransferase (Ermam)
           That Confers Macrolide-Lincosamide-Streptogramin
           Antibiotic Resistance, Nmr, Minimized Average Structure
          Length = 245

 Score = 31.6 bits (70), Expect = 0.30,   Method: Compositional matrix adjust.
 Identities = 31/113 (27%), Positives = 51/113 (45%), Gaps = 18/113 (15%)

Query: 73  SENFSTSRSSSDDVIKSADLKATSFETEVSTCNNKFSKEETSPLSEICGDSEDQTSMDKP 132
           S+NF TS    + +IK  +LK T    E+ T         T+ L++I   S+  TS++  
Sbjct: 8   SQNFLTSEKVLNQIIKQLNLKETDTVYEIGTGKGHL----TTKLAKI---SKQVTSIE-- 58

Query: 133 SKTPPESHRRKPSSEEEKIPSAAEIDEFFTAAEKREQERFAEKYNYDIVNDLP 185
                +SH    SSE+ K+ +   +       +   Q +F  K  Y IV ++P
Sbjct: 59  ----LDSHLFNLSSEKLKLNTRVTL-----IHQDILQFQFPNKQRYKIVGNIP 102


>pdb|2ICS|A Chain A, Crystal Structure Of An Adenine Deaminase
          Length = 379

 Score = 27.3 bits (59), Expect = 6.5,   Method: Compositional matrix adjust.
 Identities = 14/54 (25%), Positives = 27/54 (50%), Gaps = 5/54 (9%)

Query: 73  SENFSTSRSSSDDVIKSADLKATSFETEVSTCNN-----KFSKEETSPLSEICG 121
           +ENF  ++  + ++ K ADL   + + E  T  +     + +KE+  P+  I G
Sbjct: 312 AENFHLTQKGTLEIGKDADLTIFTIQAEEKTLTDSNGLTRVAKEQIRPIKTIIG 365


  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
   0.303    0.120    0.324 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,813,997
Number of Sequences: 62578
Number of extensions: 165039
Number of successful extensions: 300
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 288
Number of HSP's gapped (non-prelim): 20
length of query: 200
length of database: 14,973,337
effective HSP length: 94
effective length of query: 106
effective length of database: 9,091,005
effective search space: 963646530
effective search space used: 963646530
T: 11
A: 40
X1: 17 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (21.9 bits)
S2: 49 (23.5 bits)