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= psy2997
         (415 letters)

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

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



>pdb|2Y69|D Chain D, Bovine Heart Cytochrome C Oxidase Re-Refined With
           Molecular Oxygen
 pdb|2Y69|Q Chain Q, Bovine Heart Cytochrome C Oxidase Re-Refined With
           Molecular Oxygen
          Length = 169

 Score = 73.9 bits (180), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 49/169 (28%), Positives = 75/169 (44%), Gaps = 17/169 (10%)

Query: 36  TRLFPFTGNRE------VVGHGR------NGIAAYGDNVLCPFPAIRY-KVFDSDLLLLR 82
           TR+F   G R       V  HG         + +Y D    P P + + K   +    L+
Sbjct: 4   TRVFSLIGRRAISTSVCVRAHGSVVKSEDYALPSYVDRRDYPLPDVAHVKNLSASQKALK 63

Query: 83  EKEKGHWNALSKEEKKMLYRASFRQTFAEFTRHGAYPDTEYLGSVGLSMVVIAVSXXXXX 142
           EKEK  W++LS +EK  LYR  F+++FAE  R       E+   VG +M  I  +     
Sbjct: 64  EKEKASWSSLSIDEKVELYRLKFKESFAEMNR----STNEWKTVVGAAMFFIGFTALLLI 119

Query: 143 XXXXXXXPPLPATMTPEGWENTVTKMIQLQWNPITGMASKWDYENDRWR 191
                   P+P T   E       +M+ ++  PI G ++KWDY+ + W+
Sbjct: 120 WEKHYVYGPIPHTFEEEWVAKQTKRMLDMKVAPIQGFSAKWDYDKNEWK 168



 Score = 57.8 bits (138), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 48/167 (28%), Positives = 73/167 (43%), Gaps = 24/167 (14%)

Query: 225 HGNREVVGHGRNGIAAYGDNVLCPFPAIRY-KVFDSDLLLLREKEKGHWNALSKEEKKML 283
           HG+  VV      + +Y D    P P + + K   +    L+EKEK  W++LS +EK  L
Sbjct: 24  HGS--VVKSEDYALPSYVDRRDYPLPDVAHVKNLSASQKALKEKEKASWSSLSIDEKVEL 81

Query: 284 YRASFRQTFAEFTRHGAYPDTEYLGGVGLSMVVIAEITIFLITNFLSHSTVSXXXXXXXX 343
           YR  F+++FAE  R       E+   VG +M  I    + LI  +  H            
Sbjct: 82  YRLKFKESFAEMNR----STNEWKTVVGAAMFFIGFTALLLI--WEKHYVYG-------- 127

Query: 344 XXXXXXXXXXXXXEGWENTVTK-MIQLQWNPITGMASKWDYENDRWR 389
                        E W    TK M+ ++  PI G ++KWDY+ + W+
Sbjct: 128 ------PIPHTFEEEWVAKQTKRMLDMKVAPIQGFSAKWDYDKNEWK 168


>pdb|1OCC|D Chain D, Structure Of Bovine Heart Cytochrome C Oxidase At The
           Fully Oxidized State
 pdb|1OCC|Q Chain Q, Structure Of Bovine Heart Cytochrome C Oxidase At The
           Fully Oxidized State
 pdb|2OCC|D Chain D, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
           State
 pdb|2OCC|Q Chain Q, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
           State
 pdb|1OCO|D Chain D, Bovine Heart Cytochrome C Oxidase In Carbon Monoxide-bound
           State
 pdb|1OCO|Q Chain Q, Bovine Heart Cytochrome C Oxidase In Carbon Monoxide-bound
           State
 pdb|1OCR|D Chain D, Bovine Heart Cytochrome C Oxidase In The Fully Reduced
           State
 pdb|1OCR|Q Chain Q, Bovine Heart Cytochrome C Oxidase In The Fully Reduced
           State
 pdb|1OCZ|D Chain D, Bovine Heart Cytochrome C Oxidase In Azide-Bound State
 pdb|1OCZ|Q Chain Q, Bovine Heart Cytochrome C Oxidase In Azide-Bound State
 pdb|1V54|D Chain D, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
           State
 pdb|1V54|Q Chain Q, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
           State
 pdb|1V55|D Chain D, Bovine Heart Cytochrome C Oxidase At The Fully Reduced
           State
 pdb|1V55|Q Chain Q, Bovine Heart Cytochrome C Oxidase At The Fully Reduced
           State
 pdb|2DYR|D Chain D, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
           State
 pdb|2DYR|Q Chain Q, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
           State
 pdb|2DYS|D Chain D, Bovine Heart Cytochrome C Oxidase Modified By Dccd
 pdb|2DYS|Q Chain Q, Bovine Heart Cytochrome C Oxidase Modified By Dccd
 pdb|2EIJ|D Chain D, Bovine Heart Cytochrome C Oxidase In The Fully Reduced
           State
 pdb|2EIJ|Q Chain Q, Bovine Heart Cytochrome C Oxidase In The Fully Reduced
           State
 pdb|2EIK|D Chain D, Cadmium Ion Binding Structure Of Bovine Heart Cytochrome C
           Oxidase In The Fully Reduced State
 pdb|2EIK|Q Chain Q, Cadmium Ion Binding Structure Of Bovine Heart Cytochrome C
           Oxidase In The Fully Reduced State
 pdb|2EIL|D Chain D, Cadmium Ion Binding Structure Of Bovine Heart Cytochrome C
           Oxidase In The Fully Oxidized State
 pdb|2EIL|Q Chain Q, Cadmium Ion Binding Structure Of Bovine Heart Cytochrome C
           Oxidase In The Fully Oxidized State
 pdb|2EIM|D Chain D, Zinc Ion Binding Structure Of Bovine Heart Cytochrome C
           Oxidase In The Fully Reduced State
 pdb|2EIM|Q Chain Q, Zinc Ion Binding Structure Of Bovine Heart Cytochrome C
           Oxidase In The Fully Reduced State
 pdb|2EIN|D Chain D, Zinc Ion Binding Structure Of Bovine Heart Cytochrome C
           Oxidase In The Fully Oxidized State
 pdb|2EIN|Q Chain Q, Zinc Ion Binding Structure Of Bovine Heart Cytochrome C
           Oxidase In The Fully Oxidized State
 pdb|2ZXW|D Chain D, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
           State (1-S X-Ray Exposure Dataset)
 pdb|2ZXW|Q Chain Q, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
           State (1-S X-Ray Exposure Dataset)
 pdb|3ABL|D Chain D, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
           State (15-S X-Ray Exposure Dataset)
 pdb|3ABL|Q Chain Q, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
           State (15-S X-Ray Exposure Dataset)
 pdb|3ABM|D Chain D, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
           State (200-S X-Ray Exposure Dataset)
 pdb|3ABM|Q Chain Q, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
           State (200-S X-Ray Exposure Dataset)
 pdb|3ABK|D Chain D, Bovine Heart Cytochrome C Oxidase At The No-Bound Fully
           Reduced State (50k)
 pdb|3ABK|Q Chain Q, Bovine Heart Cytochrome C Oxidase At The No-Bound Fully
           Reduced State (50k)
 pdb|3AG1|D Chain D, Bovine Heart Cytochrome C Oxidase In The Carbon
           Monoxide-Bou Reduced State At 280 K
 pdb|3AG1|Q Chain Q, Bovine Heart Cytochrome C Oxidase In The Carbon
           Monoxide-Bou Reduced State At 280 K
 pdb|3AG2|D Chain D, Bovine Heart Cytochrome C Oxidase In The Carbon
           Monoxide-Bou Reduced State At 100 K
 pdb|3AG2|Q Chain Q, Bovine Heart Cytochrome C Oxidase In The Carbon
           Monoxide-Bou Reduced State At 100 K
 pdb|3AG3|D Chain D, Bovine Heart Cytochrome C Oxidase In The Nitric
           Oxide-Bound Reduced State At 100 K
 pdb|3AG3|Q Chain Q, Bovine Heart Cytochrome C Oxidase In The Nitric
           Oxide-Bound Reduced State At 100 K
 pdb|3AG4|D Chain D, Bovine Heart Cytochrome C Oxidase In The Cyanide Ion-Bound
           F Reduced State At 100 K
 pdb|3AG4|Q Chain Q, Bovine Heart Cytochrome C Oxidase In The Cyanide Ion-Bound
           F Reduced State At 100 K
 pdb|3ASN|D Chain D, Bovine Heart Cytochrome C Oxidase In The Fully Oxidized
           State Measured At 1.7470 Angstrom Wavelength
 pdb|3ASN|Q Chain Q, Bovine Heart Cytochrome C Oxidase In The Fully Oxidized
           State Measured At 1.7470 Angstrom Wavelength
 pdb|3ASO|D Chain D, Bovine Heart Cytochrome C Oxidase In The Fully Oxidized
           State Measured At 0.9 Angstrom Wavelength
 pdb|3ASO|Q Chain Q, Bovine Heart Cytochrome C Oxidase In The Fully Oxidized
           State Measured At 0.9 Angstrom Wavelength
 pdb|2YBB|O Chain O, Fitted Model For Bovine  Mitochondrial Supercomplex
           I1iii2iv1 By Single Particle Cryo-Em (Emd-1876)
          Length = 147

 Score = 71.6 bits (174), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 43/146 (29%), Positives = 68/146 (46%), Gaps = 5/146 (3%)

Query: 47  VVGHGRNGIAAYGDNVLCPFPAIRY-KVFDSDLLLLREKEKGHWNALSKEEKKMLYRASF 105
           VV      + +Y D    P P + + K   +    L+EKEK  W++LS +EK  LYR  F
Sbjct: 5   VVKSEDYALPSYVDRRDYPLPDVAHVKNLSASQKALKEKEKASWSSLSIDEKVELYRLKF 64

Query: 106 RQTFAEFTRHGAYPDTEYLGSVGLSMVVIAVSXXXXXXXXXXXXPPLPATMTPEGWENTV 165
           +++FAE  R       E+   VG +M  I  +             P+P T   E      
Sbjct: 65  KESFAEMNR----STNEWKTVVGAAMFFIGFTALLLIWEKHYVYGPIPHTFEEEWVAKQT 120

Query: 166 TKMIQLQWNPITGMASKWDYENDRWR 191
            +M+ ++  PI G ++KWDY+ + W+
Sbjct: 121 KRMLDMKVAPIQGFSAKWDYDKNEWK 146



 Score = 58.2 bits (139), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 48/167 (28%), Positives = 73/167 (43%), Gaps = 24/167 (14%)

Query: 225 HGNREVVGHGRNGIAAYGDNVLCPFPAIRY-KVFDSDLLLLREKEKGHWNALSKEEKKML 283
           HG+  VV      + +Y D    P P + + K   +    L+EKEK  W++LS +EK  L
Sbjct: 2   HGS--VVKSEDYALPSYVDRRDYPLPDVAHVKNLSASQKALKEKEKASWSSLSIDEKVEL 59

Query: 284 YRASFRQTFAEFTRHGAYPDTEYLGGVGLSMVVIAEITIFLITNFLSHSTVSXXXXXXXX 343
           YR  F+++FAE  R       E+   VG +M  I    + LI  +  H            
Sbjct: 60  YRLKFKESFAEMNR----STNEWKTVVGAAMFFIGFTALLLI--WEKHYVYG-------- 105

Query: 344 XXXXXXXXXXXXXEGWENTVTK-MIQLQWNPITGMASKWDYENDRWR 389
                        E W    TK M+ ++  PI G ++KWDY+ + W+
Sbjct: 106 ------PIPHTFEEEWVAKQTKRMLDMKVAPIQGFSAKWDYDKNEWK 146


  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    0.137    0.441 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,973,365
Number of Sequences: 62578
Number of extensions: 525120
Number of successful extensions: 1128
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: 1118
Number of HSP's gapped (non-prelim): 8
length of query: 415
length of database: 14,973,337
effective HSP length: 101
effective length of query: 314
effective length of database: 8,652,959
effective search space: 2717029126
effective search space used: 2717029126
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)