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= 031214
         (164 letters)

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

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



>pdb|2Y69|F Chain F, Bovine Heart Cytochrome C Oxidase Re-Refined With
           Molecular Oxygen
 pdb|2Y69|S Chain S, Bovine Heart Cytochrome C Oxidase Re-Refined With
           Molecular Oxygen
          Length = 129

 Score = 59.7 bits (143), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 42/118 (35%), Positives = 56/118 (47%), Gaps = 7/118 (5%)

Query: 30  SIASRSLISR-PLFASRHFSADSGTSVKKRVEDVNPVATGHXXXXXXXXXXGKNILEIDY 88
           ++AS++L +R P   S   S  SG  V    E     ATG           G++   I  
Sbjct: 11  ALASQALRARGPNGVSVVRSMASGGGVPTDEEQ----ATGLEREVMLAARKGQDPYNILA 66

Query: 89  PTGPFGTKDAPAVVKSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKPHECPVCSQYFVL 146
           P    GTK+ P +V S  +KRIVGC   E  D   V+WFWL KG+   CP C  ++ L
Sbjct: 67  PKATSGTKEDPNLVPSITNKRIVGCICEE--DNSTVIWFWLHKGEAQRCPSCGTHYKL 122


>pdb|1OCC|F Chain F, Structure Of Bovine Heart Cytochrome C Oxidase At The
           Fully Oxidized State
 pdb|1OCC|S Chain S, Structure Of Bovine Heart Cytochrome C Oxidase At The
           Fully Oxidized State
 pdb|2OCC|F Chain F, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
           State
 pdb|2OCC|S Chain S, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
           State
 pdb|1OCO|F Chain F, Bovine Heart Cytochrome C Oxidase In Carbon Monoxide-bound
           State
 pdb|1OCO|S Chain S, Bovine Heart Cytochrome C Oxidase In Carbon Monoxide-bound
           State
 pdb|1OCR|F Chain F, Bovine Heart Cytochrome C Oxidase In The Fully Reduced
           State
 pdb|1OCR|S Chain S, Bovine Heart Cytochrome C Oxidase In The Fully Reduced
           State
 pdb|1OCZ|F Chain F, Bovine Heart Cytochrome C Oxidase In Azide-Bound State
 pdb|1OCZ|S Chain S, Bovine Heart Cytochrome C Oxidase In Azide-Bound State
 pdb|1V54|F Chain F, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
           State
 pdb|1V54|S Chain S, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
           State
 pdb|1V55|F Chain F, Bovine Heart Cytochrome C Oxidase At The Fully Reduced
           State
 pdb|1V55|S Chain S, Bovine Heart Cytochrome C Oxidase At The Fully Reduced
           State
 pdb|2DYR|F Chain F, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
           State
 pdb|2DYR|S Chain S, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
           State
 pdb|2DYS|F Chain F, Bovine Heart Cytochrome C Oxidase Modified By Dccd
 pdb|2DYS|S Chain S, Bovine Heart Cytochrome C Oxidase Modified By Dccd
 pdb|2EIJ|F Chain F, Bovine Heart Cytochrome C Oxidase In The Fully Reduced
           State
 pdb|2EIJ|S Chain S, Bovine Heart Cytochrome C Oxidase In The Fully Reduced
           State
 pdb|2EIK|F Chain F, Cadmium Ion Binding Structure Of Bovine Heart Cytochrome C
           Oxidase In The Fully Reduced State
 pdb|2EIK|S Chain S, Cadmium Ion Binding Structure Of Bovine Heart Cytochrome C
           Oxidase In The Fully Reduced State
 pdb|2EIL|F Chain F, Cadmium Ion Binding Structure Of Bovine Heart Cytochrome C
           Oxidase In The Fully Oxidized State
 pdb|2EIL|S Chain S, Cadmium Ion Binding Structure Of Bovine Heart Cytochrome C
           Oxidase In The Fully Oxidized State
 pdb|2EIM|F Chain F, Zinc Ion Binding Structure Of Bovine Heart Cytochrome C
           Oxidase In The Fully Reduced State
 pdb|2EIM|S Chain S, Zinc Ion Binding Structure Of Bovine Heart Cytochrome C
           Oxidase In The Fully Reduced State
 pdb|2EIN|F Chain F, Zinc Ion Binding Structure Of Bovine Heart Cytochrome C
           Oxidase In The Fully Oxidized State
 pdb|2EIN|S Chain S, Zinc Ion Binding Structure Of Bovine Heart Cytochrome C
           Oxidase In The Fully Oxidized State
 pdb|2ZXW|F Chain F, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
           State (1-S X-Ray Exposure Dataset)
 pdb|2ZXW|S Chain S, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
           State (1-S X-Ray Exposure Dataset)
 pdb|3ABL|F Chain F, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
           State (15-S X-Ray Exposure Dataset)
 pdb|3ABL|S Chain S, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
           State (15-S X-Ray Exposure Dataset)
 pdb|3ABM|F Chain F, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
           State (200-S X-Ray Exposure Dataset)
 pdb|3ABM|S Chain S, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
           State (200-S X-Ray Exposure Dataset)
 pdb|3ABK|F Chain F, Bovine Heart Cytochrome C Oxidase At The No-Bound Fully
           Reduced State (50k)
 pdb|3ABK|S Chain S, Bovine Heart Cytochrome C Oxidase At The No-Bound Fully
           Reduced State (50k)
 pdb|3AG1|F Chain F, Bovine Heart Cytochrome C Oxidase In The Carbon
           Monoxide-Bou Reduced State At 280 K
 pdb|3AG1|S Chain S, Bovine Heart Cytochrome C Oxidase In The Carbon
           Monoxide-Bou Reduced State At 280 K
 pdb|3AG2|F Chain F, Bovine Heart Cytochrome C Oxidase In The Carbon
           Monoxide-Bou Reduced State At 100 K
 pdb|3AG2|S Chain S, Bovine Heart Cytochrome C Oxidase In The Carbon
           Monoxide-Bou Reduced State At 100 K
 pdb|3AG3|F Chain F, Bovine Heart Cytochrome C Oxidase In The Nitric
           Oxide-Bound Reduced State At 100 K
 pdb|3AG3|S Chain S, Bovine Heart Cytochrome C Oxidase In The Nitric
           Oxide-Bound Reduced State At 100 K
 pdb|3AG4|F Chain F, Bovine Heart Cytochrome C Oxidase In The Cyanide Ion-Bound
           F Reduced State At 100 K
 pdb|3AG4|S Chain S, Bovine Heart Cytochrome C Oxidase In The Cyanide Ion-Bound
           F Reduced State At 100 K
 pdb|3ASN|F Chain F, Bovine Heart Cytochrome C Oxidase In The Fully Oxidized
           State Measured At 1.7470 Angstrom Wavelength
 pdb|3ASN|S Chain S, Bovine Heart Cytochrome C Oxidase In The Fully Oxidized
           State Measured At 1.7470 Angstrom Wavelength
 pdb|3ASO|F Chain F, Bovine Heart Cytochrome C Oxidase In The Fully Oxidized
           State Measured At 0.9 Angstrom Wavelength
 pdb|3ASO|S Chain S, Bovine Heart Cytochrome C Oxidase In The Fully Oxidized
           State Measured At 0.9 Angstrom Wavelength
 pdb|2YBB|Q Chain Q, Fitted Model For Bovine  Mitochondrial Supercomplex
           I1iii2iv1 By Single Particle Cryo-Em (Emd-1876)
          Length = 98

 Score = 57.0 bits (136), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 31/81 (38%), Positives = 40/81 (49%), Gaps = 2/81 (2%)

Query: 66  ATGHXXXXXXXXXXGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEGEDEHDVV 125
           ATG           G++   I  P    GTK+ P +V S  +KRIVGC   E  D   V+
Sbjct: 13  ATGLEREVMLAARKGQDPYNILAPKATSGTKEDPNLVPSITNKRIVGCICEE--DNSTVI 70

Query: 126 WFWLEKGKPHECPVCSQYFVL 146
           WFWL KG+   CP C  ++ L
Sbjct: 71  WFWLHKGEAQRCPSCGTHYKL 91


>pdb|2JRR|A Chain A, Solution Nmr Structure Of Q5lls5 From Silicibacter
           Pomeroyi. Northeast Structural Genomics Consortium
           Target Sir90
          Length = 67

 Score = 29.6 bits (65), Expect = 0.75,   Method: Compositional matrix adjust.
 Identities = 18/42 (42%), Positives = 21/42 (50%), Gaps = 1/42 (2%)

Query: 107 DKRIVGCPGGEGEDEHDVVWFWL-EKGKPHECPVCSQYFVLE 147
           DK  V C GGEG   H  VW  + E     ECP C   +VL+
Sbjct: 12  DKSRVACDGGEGALGHPRVWLQIPEDTGWVECPYCDCKYVLK 53


>pdb|2ODX|A Chain A, Solution Structure Of Zn(Ii)cox4
          Length = 80

 Score = 29.6 bits (65), Expect = 0.81,   Method: Compositional matrix adjust.
 Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 1/56 (1%)

Query: 94  GTKDAPAVVKSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKPHECPVCSQYFVLEVV 149
           GT   P +++SY D R VGC G      H ++W      +   C  C   + L  V
Sbjct: 17  GTMKDPIIIESYDDYRYVGCTGSPA-GSHTIMWLKPTVNEVARCWECGSVYKLNPV 71


  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
   0.319    0.136    0.441 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,408,314
Number of Sequences: 62578
Number of extensions: 173093
Number of successful extensions: 323
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 318
Number of HSP's gapped (non-prelim): 5
length of query: 164
length of database: 14,973,337
effective HSP length: 91
effective length of query: 73
effective length of database: 9,278,739
effective search space: 677347947
effective search space used: 677347947
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)