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= 035190
         (70 letters)

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

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



>pdb|2JNJ|A Chain A, Solution Structure Of The P8 Tfiih Subunit
 pdb|2JNJ|B Chain B, Solution Structure Of The P8 Tfiih Subunit
          Length = 74

 Score = 60.1 bits (144), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 25/66 (37%), Positives = 41/66 (62%)

Query: 1  MVNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEF 60
          MVN +KG+ I CD  M QF++ ++ S    +KFII  +D TH+FV   +  +++  + E 
Sbjct: 4  MVNVLKGVLIECDPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGEL 63

Query: 61 RDQNSY 66
           DQN++
Sbjct: 64 MDQNAF 69


>pdb|1YDL|A Chain A, Crystal Structure Of The Human Tfiih, Northeast
          Structural Genomics Target Hr2045
          Length = 79

 Score = 51.2 bits (121), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 21/61 (34%), Positives = 35/61 (57%)

Query: 6  KGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEFRDQNS 65
          KG  I CD    QF++ ++ S    +KFII  +D TH+FV   +  +++  + E  DQN+
Sbjct: 14 KGXLIECDPAXKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGELXDQNA 73

Query: 66 Y 66
          +
Sbjct: 74 F 74


>pdb|3DGP|B Chain B, Crystal Structure Of The Complex Between Tfb5 And The
          C-Terminal Domain Of Tfb2
 pdb|3DOM|B Chain B, Crystal Structure Of The Complex Between Tfb5 And The
          C-Terminal Domain Of Tfb2
 pdb|3DOM|D Chain D, Crystal Structure Of The Complex Between Tfb5 And The
          C-Terminal Domain Of Tfb2
          Length = 71

 Score = 38.1 bits (87), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 18/63 (28%), Positives = 30/63 (47%), Gaps = 3/63 (4%)

Query: 4  AIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEFRDQ 63
          A KG  + CD  +   I+ ++A M      ++  LD THL V P+  E ++  +     +
Sbjct: 3  ARKGALVQCDPSIKALILQIDAKMSD---IVLEELDDTHLLVNPSKVEFVKHELNRLLSK 59

Query: 64 NSY 66
          N Y
Sbjct: 60 NIY 62


  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
   0.326    0.134    0.385 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,645,845
Number of Sequences: 62578
Number of extensions: 42767
Number of successful extensions: 88
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 85
Number of HSP's gapped (non-prelim): 3
length of query: 70
length of database: 14,973,337
effective HSP length: 40
effective length of query: 30
effective length of database: 12,470,217
effective search space: 374106510
effective search space used: 374106510
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 45 (21.9 bits)