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= 045334
         (80 letters)

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

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



>pdb|2RN9|A Chain A, Solution Structure Of Human Apocox17
 pdb|2RNB|A Chain A, Solution Structure Of Human Cu(I)cox17
          Length = 67

 Score = 63.5 bits (153), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 32/51 (62%), Positives = 38/51 (74%), Gaps = 2/51 (3%)

Query: 32 ESKPKK--KICCACPETKKLRDECIVEHGEEACAKWIEAHRKCLRAEGFNV 80
          ES+ KK  K CCACPETKK RD CI+E GEE C   IEAH++C+RA GF +
Sbjct: 17 ESQEKKPLKPCCACPETKKARDACIIEKGEEHCGHLIEAHKECMRALGFKI 67


>pdb|2L0Y|B Chain B, Complex Hmia40-Hcox17
          Length = 67

 Score = 58.9 bits (141), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 33/72 (45%), Positives = 39/72 (54%), Gaps = 13/72 (18%)

Query: 9  ASSTLALPGSQPNQGLEVTKSGTESKPKKKICCACPETKKLRDECIVEHGEEACAKWIEA 68
            S  ALP SQ  + L             K CC CPETKK RD CI+E GEE C   IEA
Sbjct: 9  VDSNPALPESQEKRPL-------------KPCCTCPETKKARDACIIEKGEEHCGHLIEA 55

Query: 69 HRKCLRAEGFNV 80
          H++ +RA GF +
Sbjct: 56 HKESMRALGFKI 67


>pdb|2LGQ|A Chain A, Human C30sC59S-Cox17 Mutant
          Length = 67

 Score = 58.2 bits (139), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 30/51 (58%), Positives = 36/51 (70%), Gaps = 2/51 (3%)

Query: 32 ESKPKK--KICCACPETKKLRDECIVEHGEEACAKWIEAHRKCLRAEGFNV 80
          ES+ KK  K CCA PETKK RD CI+E GEE C   IEAH++ +RA GF +
Sbjct: 17 ESQEKKPLKPCCASPETKKARDACIIEKGEEHCGHLIEAHKESMRALGFKI 67


>pdb|1U96|A Chain A, Solution Structure Of Yeast Cox17 With Copper Bound
 pdb|1U97|A Chain A, Solution Structure Of Apo Yeast Cox17
 pdb|1Z2G|A Chain A, Solution Structure Of Apo, Oxidized Yeast Cox17
          Length = 69

 Score = 38.9 bits (89), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 20/51 (39%), Positives = 32/51 (62%), Gaps = 2/51 (3%)

Query: 32 ESKPKKKICCACPETKKLRDECIVEHGE--EACAKWIEAHRKCLRAEGFNV 80
          E + K K CC C   K+ RD CI+ +G+  E C ++IE +++C++  GF V
Sbjct: 15 ECEDKPKPCCVCKPEKEERDTCILFNGQDSEKCKEFIEKYKECMKGYGFEV 65


>pdb|3PZP|A Chain A, Human Dna Polymerase Kappa Extending Opposite A Cis-Syn
          Thymine Dimer
 pdb|3PZP|B Chain B, Human Dna Polymerase Kappa Extending Opposite A Cis-Syn
          Thymine Dimer
          Length = 517

 Score = 25.0 bits (53), Expect = 9.7,   Method: Composition-based stats.
 Identities = 11/24 (45%), Positives = 14/24 (58%)

Query: 16 PGSQPNQGLEVTKSGTESKPKKKI 39
          PG  P+ GL   K+G E   K+KI
Sbjct: 2  PGGDPHMGLNDNKAGMEGLDKEKI 25


  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    0.131    0.409 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,566,663
Number of Sequences: 62578
Number of extensions: 82769
Number of successful extensions: 92
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 86
Number of HSP's gapped (non-prelim): 5
length of query: 80
length of database: 14,973,337
effective HSP length: 49
effective length of query: 31
effective length of database: 11,907,015
effective search space: 369117465
effective search space used: 369117465
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 45 (21.9 bits)