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= psy2389
         (172 letters)

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

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



>pdb|1FFT|C Chain C, The Structure Of Ubiquinol Oxidase From Escherichia Coli
 pdb|1FFT|H Chain H, The Structure Of Ubiquinol Oxidase From Escherichia Coli
          Length = 204

 Score =  141 bits (356), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 76/171 (44%), Positives = 99/171 (57%)

Query: 1   MSDCLIFSSLFAIYAVLGHNYAEGPTAIQIFKLPSVALNTIIXXXXXXXCGFAIIQAQKK 60
           MSDC++FS LFA YAVL +  A GPT   IF+LP V + T +        G A I   K 
Sbjct: 34  MSDCILFSILFATYAVLVNGTAGGPTGKDIFELPFVLVETFLLLFSSITYGMAAIAMYKN 93

Query: 61  YVNGVIFWLSITTLLGFFFVILELNEFIELINRNFGPWRSAFLSSFFVLVGMHGXXXXXX 120
             + VI WL++T L G  F+ +E+ EF  LI    GP RS FLS+FF LVG HG      
Sbjct: 94  NKSQVISWLALTWLFGAGFIGMEIYEFHHLIVNGMGPDRSGFLSAFFALVGTHGLHVTSG 153

Query: 121 XXXXXXXXXQIKKYNLILENQRRIICLSMFWHFLDIIWIGIFTFIYLIGTL 171
                    QI +  L   N+ RI+CLS+FWHFLD++WI +FT +YL+G +
Sbjct: 154 LIWMAVLMVQIARRGLTSTNRTRIMCLSLFWHFLDVVWICVFTVVYLMGAM 204


>pdb|2YEV|A Chain A, Structure Of Caa3-Type Cytochrome Oxidase
 pdb|2YEV|D Chain D, Structure Of Caa3-Type Cytochrome Oxidase
          Length = 791

 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 33/131 (25%), Positives = 58/131 (44%), Gaps = 3/131 (2%)

Query: 38  LNTIIXXXXXXXCGFAIIQAQKKYVNGVIFWLSITTLLGFFFVILELNEFIELINRNFGP 97
           LNT +         FA    ++   N   F L +T +LG  F +++  EF +  + +   
Sbjct: 662 LNTFLLVSSSFTVHFAHHDLRRGRFNPFRFGLLVTIILGVLFFLVQSWEFYQFYHHS--S 719

Query: 98  WRSA-FLSSFFVLVGMHGXXXXXXXXXXXXXXXQIKKYNLILENQRRIICLSMFWHFLDI 156
           W+   + ++FF +VG+HG               Q  +  + L N   +   SM+WH +D 
Sbjct: 720 WQENLWTAAFFTIVGLHGLHVVIGGFGLILAYLQALRGKITLHNHGTLEAASMYWHLVDA 779

Query: 157 IWIGIFTFIYL 167
           +W+ I T  Y+
Sbjct: 780 VWLVIVTIFYV 790


>pdb|1V54|C Chain C, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
           State
 pdb|1V54|P Chain P, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
           State
 pdb|1V55|C Chain C, Bovine Heart Cytochrome C Oxidase At The Fully Reduced
           State
 pdb|1V55|P Chain P, Bovine Heart Cytochrome C Oxidase At The Fully Reduced
           State
 pdb|2DYR|C Chain C, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
           State
 pdb|2DYR|P Chain P, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
           State
 pdb|2EIJ|C Chain C, Bovine Heart Cytochrome C Oxidase In The Fully Reduced
           State
 pdb|2EIJ|P Chain P, Bovine Heart Cytochrome C Oxidase In The Fully Reduced
           State
 pdb|2EIK|C Chain C, Cadmium Ion Binding Structure Of Bovine Heart Cytochrome C
           Oxidase In The Fully Reduced State
 pdb|2EIK|P Chain P, Cadmium Ion Binding Structure Of Bovine Heart Cytochrome C
           Oxidase In The Fully Reduced State
 pdb|2EIL|C Chain C, Cadmium Ion Binding Structure Of Bovine Heart Cytochrome C
           Oxidase In The Fully Oxidized State
 pdb|2EIL|P Chain P, Cadmium Ion Binding Structure Of Bovine Heart Cytochrome C
           Oxidase In The Fully Oxidized State
 pdb|2EIM|C Chain C, Zinc Ion Binding Structure Of Bovine Heart Cytochrome C
           Oxidase In The Fully Reduced State
 pdb|2EIM|P Chain P, Zinc Ion Binding Structure Of Bovine Heart Cytochrome C
           Oxidase In The Fully Reduced State
 pdb|2EIN|C Chain C, Zinc Ion Binding Structure Of Bovine Heart Cytochrome C
           Oxidase In The Fully Oxidized State
 pdb|2EIN|P Chain P, Zinc Ion Binding Structure Of Bovine Heart Cytochrome C
           Oxidase In The Fully Oxidized State
 pdb|2ZXW|C Chain C, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
           State (1-S X-Ray Exposure Dataset)
 pdb|2ZXW|P Chain P, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
           State (1-S X-Ray Exposure Dataset)
 pdb|3ABL|C Chain C, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
           State (15-S X-Ray Exposure Dataset)
 pdb|3ABL|P Chain P, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
           State (15-S X-Ray Exposure Dataset)
 pdb|3ABM|C Chain C, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
           State (200-S X-Ray Exposure Dataset)
 pdb|3ABM|P Chain P, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
           State (200-S X-Ray Exposure Dataset)
 pdb|3ABK|C Chain C, Bovine Heart Cytochrome C Oxidase At The No-Bound Fully
           Reduced State (50k)
 pdb|3ABK|P Chain P, Bovine Heart Cytochrome C Oxidase At The No-Bound Fully
           Reduced State (50k)
 pdb|3AG1|C Chain C, Bovine Heart Cytochrome C Oxidase In The Carbon
           Monoxide-Bou Reduced State At 280 K
 pdb|3AG1|P Chain P, Bovine Heart Cytochrome C Oxidase In The Carbon
           Monoxide-Bou Reduced State At 280 K
 pdb|3AG2|C Chain C, Bovine Heart Cytochrome C Oxidase In The Carbon
           Monoxide-Bou Reduced State At 100 K
 pdb|3AG2|P Chain P, Bovine Heart Cytochrome C Oxidase In The Carbon
           Monoxide-Bou Reduced State At 100 K
 pdb|3AG3|C Chain C, Bovine Heart Cytochrome C Oxidase In The Nitric
           Oxide-Bound Reduced State At 100 K
 pdb|3AG3|P Chain P, Bovine Heart Cytochrome C Oxidase In The Nitric
           Oxide-Bound Reduced State At 100 K
 pdb|3AG4|C Chain C, Bovine Heart Cytochrome C Oxidase In The Cyanide Ion-Bound
           F Reduced State At 100 K
 pdb|3AG4|P Chain P, Bovine Heart Cytochrome C Oxidase In The Cyanide Ion-Bound
           F Reduced State At 100 K
 pdb|2Y69|C Chain C, Bovine Heart Cytochrome C Oxidase Re-Refined With
           Molecular Oxygen
 pdb|2Y69|P Chain P, Bovine Heart Cytochrome C Oxidase Re-Refined With
           Molecular Oxygen
 pdb|3ASN|C Chain C, Bovine Heart Cytochrome C Oxidase In The Fully Oxidized
           State Measured At 1.7470 Angstrom Wavelength
 pdb|3ASN|P Chain P, Bovine Heart Cytochrome C Oxidase In The Fully Oxidized
           State Measured At 1.7470 Angstrom Wavelength
 pdb|3ASO|C Chain C, Bovine Heart Cytochrome C Oxidase In The Fully Oxidized
           State Measured At 0.9 Angstrom Wavelength
 pdb|3ASO|P Chain P, Bovine Heart Cytochrome C Oxidase In The Fully Oxidized
           State Measured At 0.9 Angstrom Wavelength
 pdb|2YBB|N Chain N, Fitted Model For Bovine  Mitochondrial Supercomplex
           I1iii2iv1 By Single Particle Cryo-Em (Emd-1876)
 pdb|2DYS|C Chain C, Bovine Heart Cytochrome C Oxidase Modified By Dccd
 pdb|2DYS|P Chain P, Bovine Heart Cytochrome C Oxidase Modified By Dccd
          Length = 261

 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 27/118 (22%), Positives = 55/118 (46%), Gaps = 6/118 (5%)

Query: 53  AIIQAQKKYVNGVIFWLSITTLLGFFFVILELNEFIELINRNFGPWRSAFLSSFFVLVGM 112
           ++++  +K++   +F   IT  LG +F +L+ +E+ E     F      + S+FFV  G 
Sbjct: 150 SLMEGDRKHMLQALF---ITITLGVYFTLLQASEYYE---APFTISDGVYGSTFFVATGF 203

Query: 113 HGXXXXXXXXXXXXXXXQIKKYNLILENQRRIICLSMFWHFLDIIWIGIFTFIYLIGT 170
           HG               +  K++    +       + +WHF+D++W+ ++  IY  G+
Sbjct: 204 HGLHVIIGSTFLIVCFFRQLKFHFTSNHHFGFEAAAWYWHFVDVVWLFLYVSIYWWGS 261


>pdb|1OCC|C Chain C, Structure Of Bovine Heart Cytochrome C Oxidase At The
           Fully Oxidized State
 pdb|1OCC|P Chain P, Structure Of Bovine Heart Cytochrome C Oxidase At The
           Fully Oxidized State
 pdb|2OCC|C Chain C, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
           State
 pdb|2OCC|P Chain P, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
           State
 pdb|1OCO|C Chain C, Bovine Heart Cytochrome C Oxidase In Carbon Monoxide-bound
           State
 pdb|1OCO|P Chain P, Bovine Heart Cytochrome C Oxidase In Carbon Monoxide-bound
           State
 pdb|1OCR|C Chain C, Bovine Heart Cytochrome C Oxidase In The Fully Reduced
           State
 pdb|1OCR|P Chain P, Bovine Heart Cytochrome C Oxidase In The Fully Reduced
           State
 pdb|1OCZ|C Chain C, Bovine Heart Cytochrome C Oxidase In Azide-Bound State
 pdb|1OCZ|P Chain P, Bovine Heart Cytochrome C Oxidase In Azide-Bound State
          Length = 261

 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 27/118 (22%), Positives = 55/118 (46%), Gaps = 6/118 (5%)

Query: 53  AIIQAQKKYVNGVIFWLSITTLLGFFFVILELNEFIELINRNFGPWRSAFLSSFFVLVGM 112
           ++++  +K++   +F   IT  LG +F +L+ +E+ E     F      + S+FFV  G 
Sbjct: 150 SLMEGDRKHMLQALF---ITITLGVYFTLLQASEYYE---APFTISDGVYGSTFFVATGF 203

Query: 113 HGXXXXXXXXXXXXXXXQIKKYNLILENQRRIICLSMFWHFLDIIWIGIFTFIYLIGT 170
           HG               +  K++    +       + +WHF+D++W+ ++  IY  G+
Sbjct: 204 HGLHVIIGSTFLIVCFFRQLKFHFTSNHHFGFEAGAWYWHFVDVVWLFLYVSIYWWGS 261


>pdb|1QLE|C Chain C, Cryo-structure Of The Paracoccus Denitrificans
           Four-subunit Cytochrome C Oxidase In The Completely
           Oxidized State Complexed With An Antibody Fv Fragment
          Length = 273

 Score = 38.9 bits (89), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 26/118 (22%), Positives = 52/118 (44%), Gaps = 7/118 (5%)

Query: 52  FAIIQAQKKYVNGVIFWLSITTLLGFFFVILELNEFIELINRNFGPWRSAFLSSFFVLVG 111
           F +   +K  +NG+I    +  +LG  F  L+  E+    +  FG   + +  +F++  G
Sbjct: 162 FVLEGDRKTTINGLI----VAVILGVCFTGLQAYEYS---HAAFGLADTVYAGAFYMATG 214

Query: 112 MHGXXXXXXXXXXXXXXXQIKKYNLILENQRRIICLSMFWHFLDIIWIGIFTFIYLIG 169
            HG               ++ K  +  +        + +WHF+D++W+ +F  IY+ G
Sbjct: 215 FHGAHVIIGTIFLFVCLIRLLKGQMTQKQHVGFEAAAWYWHFVDVVWLFLFVVIYIWG 272


>pdb|1M56|C Chain C, Structure Of Cytochrome C Oxidase From Rhodobactor
           Sphaeroides (Wild Type)
 pdb|1M56|I Chain I, Structure Of Cytochrome C Oxidase From Rhodobactor
           Sphaeroides (Wild Type)
 pdb|1M57|C Chain C, Structure Of Cytochrome C Oxidase From Rhodobacter
           Sphaeroides (Eq(I-286) Mutant))
 pdb|1M57|I Chain I, Structure Of Cytochrome C Oxidase From Rhodobacter
           Sphaeroides (Eq(I-286) Mutant))
          Length = 266

 Score = 33.1 bits (74), Expect = 0.079,   Method: Compositional matrix adjust.
 Identities = 15/66 (22%), Positives = 30/66 (45%)

Query: 104 SSFFVLVGMHGXXXXXXXXXXXXXXXQIKKYNLILENQRRIICLSMFWHFLDIIWIGIFT 163
           ++FF+  G HG               ++++ +   E          +WHF+D++W+ +F 
Sbjct: 200 ANFFMATGFHGFHVIVGTIFLLVCLIRVQRGHFTPEKHVGFEAAIWYWHFVDVVWLFLFA 259

Query: 164 FIYLIG 169
            IY+ G
Sbjct: 260 SIYIWG 265


  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
   0.335    0.148    0.475 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,995,087
Number of Sequences: 62578
Number of extensions: 111283
Number of successful extensions: 219
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 207
Number of HSP's gapped (non-prelim): 7
length of query: 172
length of database: 14,973,337
effective HSP length: 92
effective length of query: 80
effective length of database: 9,216,161
effective search space: 737292880
effective search space used: 737292880
T: 11
A: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.6 bits)
S2: 48 (23.1 bits)