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= 048516
         (389 letters)

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

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



>pdb|3MVB|O Chain O, Crystal Structure Of A Triple Rfy Mutant Of Human Mterf1
           Bound To The Termination Sequence
          Length = 343

 Score = 30.8 bits (68), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 3/72 (4%)

Query: 266 LKLKLFRSLGFSEDNILSMFRSMPPAFTVSERKIRSVVETLLRRRDVDISSIVNNASLFL 325
           +K KLF SLG +E+ +     S P    ++E+K    ++ L+   ++ IS I+ N  +  
Sbjct: 243 IKEKLF-SLGCTEEEVQKFVLSYPDVIFLAEKKFNDKIDCLM-EENISISQIIENPRVLD 300

Query: 326 CSIESNLKPRMR 337
            SI S LK R++
Sbjct: 301 SSI-STLKSRIK 311


>pdb|3MVA|O Chain O, Crystal Structure Of Human Mterf1 Bound To The Termination
           Sequence
          Length = 343

 Score = 30.8 bits (68), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 3/72 (4%)

Query: 266 LKLKLFRSLGFSEDNILSMFRSMPPAFTVSERKIRSVVETLLRRRDVDISSIVNNASLFL 325
           +K KLF SLG +E+ +     S P    ++E+K    ++ L+   ++ IS I+ N  +  
Sbjct: 243 IKEKLF-SLGCTEEEVQKFVLSYPDVIFLAEKKFNDKIDCLM-EENISISQIIENPRVLD 300

Query: 326 CSIESNLKPRMR 337
            SI S LK R++
Sbjct: 301 SSI-STLKSRIK 311


>pdb|3N6S|A Chain A, Crystal Structure Of Human Mitochondrial Mterf In Complex
           With A 15- Mer Dna Encompassing The Trnaleu(Uur) Binding
           Sequence
          Length = 353

 Score = 30.8 bits (68), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 3/72 (4%)

Query: 266 LKLKLFRSLGFSEDNILSMFRSMPPAFTVSERKIRSVVETLLRRRDVDISSIVNNASLFL 325
           +K KLF SLG +E+ +     S P    ++E+K    ++ L+   ++ IS I+ N  +  
Sbjct: 244 IKEKLF-SLGCTEEEVQKFVLSYPDVIFLAEKKFNDKIDCLM-EENISISQIIENPRVLD 301

Query: 326 CSIESNLKPRMR 337
            SI S LK R++
Sbjct: 302 SSI-STLKSRIK 312


>pdb|3N7Q|A Chain A, Crystal Structure Of Human Mitochondrial Mterf Fragment
           (Aa 99-399) In Complex With A 12-Mer Dna Encompassing
           The Trnaleu(Uur) Binding Sequence
          Length = 310

 Score = 30.8 bits (68), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 3/72 (4%)

Query: 266 LKLKLFRSLGFSEDNILSMFRSMPPAFTVSERKIRSVVETLLRRRDVDISSIVNNASLFL 325
           +K KLF SLG +E+ +     S P    ++E+K    ++ L+   ++ IS I+ N  +  
Sbjct: 201 IKEKLF-SLGCTEEEVQKFVLSYPDVIFLAEKKFNDKIDCLM-EENISISQIIENPRVLD 258

Query: 326 CSIESNLKPRMR 337
            SI S LK R++
Sbjct: 259 SSI-STLKSRIK 269


  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
   0.322    0.135    0.393 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,362,784
Number of Sequences: 62578
Number of extensions: 320320
Number of successful extensions: 710
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 710
Number of HSP's gapped (non-prelim): 4
length of query: 389
length of database: 14,973,337
effective HSP length: 101
effective length of query: 288
effective length of database: 8,652,959
effective search space: 2492052192
effective search space used: 2492052192
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: 52 (24.6 bits)