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= 039791
         (552 letters)

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

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



>pdb|3OPG|A Chain A, Crystal Structure Of Human Mitochondrial Transcription
           Termination Factor 3
          Length = 298

 Score = 34.3 bits (77), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 28/92 (30%), Positives = 43/92 (46%), Gaps = 8/92 (8%)

Query: 232 DICRKIRVFYDFRFEKGKLGELMGRNKSIFLDYPEEVLVQKVEYFCRFGVGNEDVGLLLL 291
           DI + +    D   E  +LG  + +N +IF +  E  L  +V Y         DV  ++ 
Sbjct: 68  DIKQMLLFLKDVGIEDNQLGAFLTKNHAIFSEDLEN-LKTRVAYLHSKNFSKADVAQMVR 126

Query: 292 KSPEILSFDLETQVISVKGLLNHLGLSAKELK 323
           K+P +L+F       SV+ L N LG   KEL+
Sbjct: 127 KAPFLLNF-------SVERLDNRLGFFQKELE 151



 Score = 32.0 bits (71), Expect = 0.83,   Method: Compositional matrix adjust.
 Identities = 29/102 (28%), Positives = 45/102 (44%), Gaps = 9/102 (8%)

Query: 403 LTFLHGIGYGENTLTLKVLAKAHGTGSE----LQERFDCLLRNGVAFSKLCMMIRLTPKI 458
           L FL  +G  +N L    L K H   SE    L+ R   L     + + +  M+R  P +
Sbjct: 73  LLFLKDVGIEDNQLG-AFLTKNHAIFSEDLENLKTRVAYLHSKNFSKADVAQMVRKAPFL 131

Query: 459 LNQNPETIEQKLDFLCQDLGSSL----DYLYAFPTFLCFDLE 496
           LN + E ++ +L F  ++L  S+    D +   P  L   LE
Sbjct: 132 LNFSVERLDNRLGFFQKELELSVKKTRDLVVRLPRLLTGSLE 173



 Score = 30.8 bits (68), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 36/150 (24%), Positives = 62/150 (41%), Gaps = 8/150 (5%)

Query: 51  FTYAEHISKHSLNTLSKLIADLGVSYSA----PSFSSTFQRFLRYHPINEFEFFFESIGI 106
           FT  +++  HS  TL KL+  LGV  S     P  ++   R      I +   F + +GI
Sbjct: 25  FTLRDYVD-HS-ETLQKLVL-LGVDLSKIEKHPEAANLLLRLDFEKDIKQMLLFLKDVGI 81

Query: 107 DHAEVSCFLPANKFFLSEDSCLLNAACA-LSSFGFPWDKLGKLYKEEVSIFSQSSQDLTA 165
           +  ++  FL  N    SED   L    A L S  F    + ++ ++   + + S + L  
Sbjct: 82  EDNQLGAFLTKNHAIFSEDLENLKTRVAYLHSKNFSKADVAQMVRKAPFLLNFSVERLDN 141

Query: 166 KLSRLKNYYGFSNVILVGICLGFPHVLAGN 195
           +L   +     S      + +  P +L G+
Sbjct: 142 RLGFFQKELELSVKKTRDLVVRLPRLLTGS 171


>pdb|3M66|A Chain A, Crystal Structure Of Human Mitochondrial Transcription
           Termination Factor 3
          Length = 270

 Score = 33.9 bits (76), Expect = 0.24,   Method: Compositional matrix adjust.
 Identities = 28/92 (30%), Positives = 43/92 (46%), Gaps = 8/92 (8%)

Query: 232 DICRKIRVFYDFRFEKGKLGELMGRNKSIFLDYPEEVLVQKVEYFCRFGVGNEDVGLLLL 291
           DI + +    D   E  +LG  + +N +IF +  E  L  +V Y         DV  ++ 
Sbjct: 40  DIKQMLLFLKDVGIEDNQLGAFLTKNHAIFSEDLEN-LKTRVAYLHSKNFSKADVAQMVR 98

Query: 292 KSPEILSFDLETQVISVKGLLNHLGLSAKELK 323
           K+P +L+F       SV+ L N LG   KEL+
Sbjct: 99  KAPFLLNF-------SVERLDNRLGFFQKELE 123



 Score = 32.0 bits (71), Expect = 0.89,   Method: Compositional matrix adjust.
 Identities = 29/102 (28%), Positives = 45/102 (44%), Gaps = 9/102 (8%)

Query: 403 LTFLHGIGYGENTLTLKVLAKAHGTGSE----LQERFDCLLRNGVAFSKLCMMIRLTPKI 458
           L FL  +G  +N L    L K H   SE    L+ R   L     + + +  M+R  P +
Sbjct: 45  LLFLKDVGIEDNQLG-AFLTKNHAIFSEDLENLKTRVAYLHSKNFSKADVAQMVRKAPFL 103

Query: 459 LNQNPETIEQKLDFLCQDLGSSL----DYLYAFPTFLCFDLE 496
           LN + E ++ +L F  ++L  S+    D +   P  L   LE
Sbjct: 104 LNFSVERLDNRLGFFQKELELSVKKTRDLVVRLPRLLTGSLE 145


  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
   0.323    0.139    0.421 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,567,827
Number of Sequences: 62578
Number of extensions: 705379
Number of successful extensions: 1538
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1533
Number of HSP's gapped (non-prelim): 11
length of query: 552
length of database: 14,973,337
effective HSP length: 104
effective length of query: 448
effective length of database: 8,465,225
effective search space: 3792420800
effective search space used: 3792420800
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (25.4 bits)