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= 040346
         (237 letters)

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

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



>pdb|2WSS|S Chain S, The Structure Of The Membrane Extrinsic Region Of Bovine
           Atp Synthase
 pdb|2WSS|W Chain W, The Structure Of The Membrane Extrinsic Region Of Bovine
           Atp Synthase
          Length = 190

 Score = 37.4 bits (85), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 28/130 (21%), Positives = 59/130 (45%)

Query: 94  YAAALLDKALCHSSLEAVQRDVLKLSRLLKNEQIQAVCADPFVGDKDKGQIVKELLSSWK 153
           YA AL   A   + LE V++++L++ ++LK  +  A   +P+V    K + + +  +  K
Sbjct: 18  YATALYSAASKQNKLEQVEKELLRVGQILKEPKXAASLLNPYVKRSVKVKSLSDXTAKEK 77

Query: 154 VNSYLAALLRMLIERNKVAMVSDVLEEFQRIYDDLIGTRVVFVSSAKKMEEDQLFHIAKR 213
            +   + L+ +L E  ++     V+  F        G     V++A  ++E  L  +   
Sbjct: 78  FSPLTSNLINLLAENGRLTNTPAVISAFSTXXSVHRGEVPCTVTTASALDETTLTELKTV 137

Query: 214 VQNLCGAAQV 223
           +++     QV
Sbjct: 138 LKSFLSKGQV 147


>pdb|2BO5|A Chain A, Bovine Oligomycin Sensitivity Conferral Protein N-Terminal
           Domain
 pdb|2JMX|A Chain A, Oscp-Nt (1-120) In Complex With N-Terminal (1-25) Alpha
           Subunit From F1-Atpase
 pdb|4B2Q|W Chain W, Model Of The Yeast F1fo-Atp Synthase Dimer Based On
           Subtomogram Average
 pdb|4B2Q|WW Chain w, Model Of The Yeast F1fo-Atp Synthase Dimer Based On
           Subtomogram Average
          Length = 120

 Score = 37.4 bits (85), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 21/88 (23%), Positives = 46/88 (52%)

Query: 94  YAAALLDKALCHSSLEAVQRDVLKLSRLLKNEQIQAVCADPFVGDKDKGQIVKELLSSWK 153
           YA AL   A   + LE V++++L++ ++LK  ++ A   +P+V    K + + ++ +  K
Sbjct: 18  YATALYSAASKQNKLEQVEKELLRVGQILKEPKMAASLLNPYVKRSVKVKSLSDMTAKEK 77

Query: 154 VNSYLAALLRMLIERNKVAMVSDVLEEF 181
            +   + L+ +L E  ++     V+  F
Sbjct: 78  FSPLTSNLINLLAENGRLTNTPAVISAF 105


>pdb|2A7U|B Chain B, Nmr Solution Structure Of The E.Coli F-Atpase Delta
           Subunit N-Terminal Domain In Complex With Alpha Subunit
           N-Terminal 22 Residues
 pdb|1ABV|A Chain A, N-Terminal Domain Of The Delta Subunit Of The F1f0-Atp
           Synthase From Escherichia Coli, Nmr, Minimized Average
           Structure
          Length = 134

 Score = 30.8 bits (68), Expect = 0.69,   Method: Compositional matrix adjust.
 Identities = 35/133 (26%), Positives = 59/133 (44%), Gaps = 24/133 (18%)

Query: 94  YAAALLDKALCHSSLEAVQRDVLKLSRLLKNEQIQAVCADPFVGDKDKGQIVKELLSSWK 153
           YA A  D A+ H S+E  Q  +   + + KNEQ+  + +         G +  E L+   
Sbjct: 10  YAKAAFDFAVEHQSVERWQDMLAFAAEVTKNEQMAELLS---------GALAPETLA--- 57

Query: 154 VNSYLAA-----------LLRMLIERNKVAMVSDVLEEFQRIYDDLIGTRVVFVSSAKKM 202
             S++A            L+R++ E  ++  + DVLE+F  +      T  V V SA  +
Sbjct: 58  -ESFIAVCGEQLDENGQNLIRVMAENGRLNALPDVLEQFIHLRAVSEATAEVDVISAAAL 116

Query: 203 EEDQLFHIAKRVQ 215
            E QL  I+  ++
Sbjct: 117 SEQQLAKISAAME 129


>pdb|3U5C|H Chain H, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 40s
           Subunit, Ribosome A
 pdb|3U5G|H Chain H, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 40s
           Subunit, Ribosome B
          Length = 190

 Score = 27.7 bits (60), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 15/54 (27%), Positives = 28/54 (51%), Gaps = 7/54 (12%)

Query: 142 GQIVKELLSSWKVNSYLAALLRMLIERNKVAMVSDVLEEFQRIYDDLIGTRVVF 195
           G+ V+ L+   K+        ++L++   V  +   LE FQ +Y+ L G ++VF
Sbjct: 137 GKRVRYLVGGNKIQ-------KVLLDSKDVQQIDYKLESFQAVYNKLTGKQIVF 183


  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
   0.318    0.130    0.365 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,018,743
Number of Sequences: 62578
Number of extensions: 148171
Number of successful extensions: 404
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: 398
Number of HSP's gapped (non-prelim): 5
length of query: 237
length of database: 14,973,337
effective HSP length: 96
effective length of query: 141
effective length of database: 8,965,849
effective search space: 1264184709
effective search space used: 1264184709
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)