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= 041834
         (189 letters)

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

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



>pdb|3BT7|A Chain A, Structure Of E. Coli 5-Methyluridine Methyltransferase
           Trma In Complex With 19 Nucleotide T-Arm Analogue
 pdb|3BT7|B Chain B, Structure Of E. Coli 5-Methyluridine Methyltransferase
           Trma In Complex With 19 Nucleotide T-Arm Analogue
          Length = 369

 Score = 27.7 bits (60), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 14/29 (48%), Positives = 19/29 (65%), Gaps = 1/29 (3%)

Query: 28  YQQEATKLRRQIREIQNLNRHILGEALST 56
           ++QEA  LR  +R  QNLN H++G A  T
Sbjct: 135 WRQEAEALRDALRA-QNLNVHLIGRATKT 162


  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
   0.314    0.129    0.355 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,590,452
Number of Sequences: 62578
Number of extensions: 151859
Number of successful extensions: 312
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 310
Number of HSP's gapped (non-prelim): 11
length of query: 189
length of database: 14,973,337
effective HSP length: 93
effective length of query: 96
effective length of database: 9,153,583
effective search space: 878743968
effective search space used: 878743968
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 48 (23.1 bits)