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= 023404
         (282 letters)

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

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



>pdb|2DUL|A Chain A, Crystal Structure Of Trna G26 Methyltransferase Trm1 In
           Apo Form From Pyrococcus Horikoshii
 pdb|2EJT|A Chain A, Complex Structure Of Trm1 From Pyrococcus Horikoshii With
           S-Adenosyl- L-Methionine
 pdb|2EJU|A Chain A, Complex Structure Of Trm1 From Pyrococcus Horikoshii With
           S-Adenosyl- L-Homocystein
 pdb|2YTZ|A Chain A, Complex Structure Of Trm1 From Pyrococcus Horikoshii With
           S- Adenosyl-l-homocystein In The Orthorhombic
           Crystal-lattice
 pdb|2YTZ|B Chain B, Complex Structure Of Trm1 From Pyrococcus Horikoshii With
           S- Adenosyl-l-homocystein In The Orthorhombic
           Crystal-lattice
          Length = 378

 Score = 27.7 bits (60), Expect = 6.5,   Method: Compositional matrix adjust.
 Identities = 14/52 (26%), Positives = 24/52 (46%), Gaps = 3/52 (5%)

Query: 9   TRCLRKKLKIRMRCLKKVEQAVEVYHDEEYRSKRWHFPSYNFSVSVIWSPFL 60
           T  + ++LKI     KKVE+ +    ++ Y + R HF       S  +  F+
Sbjct: 324 THAIGRRLKIET---KKVEEIISALREQGYEATRTHFSPTGIKTSAPYEVFI 372


>pdb|1US8|B Chain B, The Rad50 Signature Motif: Essential To Atp Binding And
           Biological Function
          Length = 144

 Score = 27.7 bits (60), Expect = 7.6,   Method: Compositional matrix adjust.
 Identities = 14/32 (43%), Positives = 18/32 (56%)

Query: 13  RKKLKIRMRCLKKVEQAVEVYHDEEYRSKRWH 44
           RK + I  R LKK+ Q + V HDEE +    H
Sbjct: 96  RKLITIMERYLKKIPQVILVSHDEELKDAADH 127


>pdb|1F2T|B Chain B, Crystal Structure Of Atp-free Rad50 Abc-atpase
 pdb|1F2U|B Chain B, Crystal Structure Of Rad50 Abc-Atpase
 pdb|1F2U|D Chain D, Crystal Structure Of Rad50 Abc-Atpase
          Length = 148

 Score = 27.7 bits (60), Expect = 7.6,   Method: Compositional matrix adjust.
 Identities = 14/32 (43%), Positives = 18/32 (56%)

Query: 13  RKKLKIRMRCLKKVEQAVEVYHDEEYRSKRWH 44
           RK + I  R LKK+ Q + V HDEE +    H
Sbjct: 100 RKLITIMERYLKKIPQVILVSHDEELKDAADH 131


>pdb|3QKT|A Chain A, Rad50 Abc-Atpase With Adjacent Coiled-Coil Region In
           Complex With Amp- Pnp
 pdb|3QKT|B Chain B, Rad50 Abc-Atpase With Adjacent Coiled-Coil Region In
           Complex With Amp- Pnp
 pdb|3QKT|C Chain C, Rad50 Abc-Atpase With Adjacent Coiled-Coil Region In
           Complex With Amp- Pnp
 pdb|3QKT|D Chain D, Rad50 Abc-Atpase With Adjacent Coiled-Coil Region In
           Complex With Amp- Pnp
          Length = 339

 Score = 27.7 bits (60), Expect = 7.7,   Method: Compositional matrix adjust.
 Identities = 14/32 (43%), Positives = 18/32 (56%)

Query: 13  RKKLKIRMRCLKKVEQAVEVYHDEEYRSKRWH 44
           RK + I  R LKK+ Q + V HDEE +    H
Sbjct: 291 RKLITIMERYLKKIPQVILVSHDEELKDAADH 322


>pdb|3QKU|A Chain A, Mre11 Rad50 Binding Domain In Complex With Rad50 And
           Amp-Pnp
 pdb|3QKU|B Chain B, Mre11 Rad50 Binding Domain In Complex With Rad50 And
           Amp-Pnp
          Length = 359

 Score = 27.7 bits (60), Expect = 8.2,   Method: Compositional matrix adjust.
 Identities = 14/32 (43%), Positives = 18/32 (56%)

Query: 13  RKKLKIRMRCLKKVEQAVEVYHDEEYRSKRWH 44
           RK + I  R LKK+ Q + V HDEE +    H
Sbjct: 311 RKLITIMERYLKKIPQVILVSHDEELKDAADH 342


  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    0.436 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,605,724
Number of Sequences: 62578
Number of extensions: 341788
Number of successful extensions: 637
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 630
Number of HSP's gapped (non-prelim): 11
length of query: 282
length of database: 14,973,337
effective HSP length: 98
effective length of query: 184
effective length of database: 8,840,693
effective search space: 1626687512
effective search space used: 1626687512
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)