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= 005528
         (692 letters)

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

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



>pdb|2OAU|A Chain A, Mechanosensitive Channel Of Small Conductance (Mscs)
 pdb|2OAU|B Chain B, Mechanosensitive Channel Of Small Conductance (Mscs)
 pdb|2OAU|C Chain C, Mechanosensitive Channel Of Small Conductance (Mscs)
 pdb|2OAU|D Chain D, Mechanosensitive Channel Of Small Conductance (Mscs)
 pdb|2OAU|E Chain E, Mechanosensitive Channel Of Small Conductance (Mscs)
 pdb|2OAU|F Chain F, Mechanosensitive Channel Of Small Conductance (Mscs)
 pdb|2OAU|G Chain G, Mechanosensitive Channel Of Small Conductance (Mscs)
 pdb|4HWA|A Chain A, Crystal Structure Of Escherichia Coli Mscs Wildtype (open
           State)
 pdb|4HWA|B Chain B, Crystal Structure Of Escherichia Coli Mscs Wildtype (open
           State)
 pdb|4HWA|C Chain C, Crystal Structure Of Escherichia Coli Mscs Wildtype (open
           State)
 pdb|4HWA|D Chain D, Crystal Structure Of Escherichia Coli Mscs Wildtype (open
           State)
 pdb|4HWA|E Chain E, Crystal Structure Of Escherichia Coli Mscs Wildtype (open
           State)
 pdb|4HWA|F Chain F, Crystal Structure Of Escherichia Coli Mscs Wildtype (open
           State)
 pdb|4HWA|G Chain G, Crystal Structure Of Escherichia Coli Mscs Wildtype (open
           State)
          Length = 306

 Score = 35.4 bits (80), Expect = 0.099,   Method: Compositional matrix adjust.
 Identities = 17/59 (28%), Positives = 28/59 (47%)

Query: 513 IFLYVMHPFDVGDRCIIDGVQMVVEDIRILTTTLVRYDNEKVFYPNSVLATKPITNFYR 571
           + L +  PF  G+   + GV   V  ++I +TT+   D + +  PN  +    I NF R
Sbjct: 142 VLLVMFRPFRAGEYVDLGGVAGTVLSVQIFSTTMRTADGKIIVIPNGKIIAGNIINFSR 200


>pdb|4AGE|A Chain A, Mtssl Spin Labeled D67c Mutant Of Mscs In The Open Form
 pdb|4AGE|B Chain B, Mtssl Spin Labeled D67c Mutant Of Mscs In The Open Form
 pdb|4AGE|C Chain C, Mtssl Spin Labeled D67c Mutant Of Mscs In The Open Form
 pdb|4AGE|D Chain D, Mtssl Spin Labeled D67c Mutant Of Mscs In The Open Form
 pdb|4AGE|E Chain E, Mtssl Spin Labeled D67c Mutant Of Mscs In The Open Form
 pdb|4AGE|F Chain F, Mtssl Spin Labeled D67c Mutant Of Mscs In The Open Form
 pdb|4AGE|G Chain G, Mtssl Spin Labeled D67c Mutant Of Mscs In The Open Form
          Length = 286

 Score = 35.4 bits (80), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 17/59 (28%), Positives = 28/59 (47%)

Query: 513 IFLYVMHPFDVGDRCIIDGVQMVVEDIRILTTTLVRYDNEKVFYPNSVLATKPITNFYR 571
           + L +  PF  G+   + GV   V  ++I +TT+   D + +  PN  +    I NF R
Sbjct: 122 VLLVMFRPFRAGEYVDLGGVAGTVLSVQIFSTTMRTADGKIIVIPNGKIIAGNIINFSR 180


>pdb|2VV5|A Chain A, The Open Structure Of Mscs
 pdb|2VV5|B Chain B, The Open Structure Of Mscs
 pdb|2VV5|C Chain C, The Open Structure Of Mscs
 pdb|2VV5|D Chain D, The Open Structure Of Mscs
 pdb|2VV5|E Chain E, The Open Structure Of Mscs
 pdb|2VV5|F Chain F, The Open Structure Of Mscs
 pdb|2VV5|G Chain G, The Open Structure Of Mscs
          Length = 286

 Score = 35.4 bits (80), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 17/59 (28%), Positives = 28/59 (47%)

Query: 513 IFLYVMHPFDVGDRCIIDGVQMVVEDIRILTTTLVRYDNEKVFYPNSVLATKPITNFYR 571
           + L +  PF  G+   + GV   V  ++I +TT+   D + +  PN  +    I NF R
Sbjct: 122 VLLVMFRPFRAGEYVDLGGVAGTVLSVQIFSTTMRTADGKIIVIPNGKIIAGNIINFSR 180


>pdb|4AGF|A Chain A, Mtssl Spin Labeled L124c Mutant Of Mscs In The Open Form
 pdb|4AGF|B Chain B, Mtssl Spin Labeled L124c Mutant Of Mscs In The Open Form
 pdb|4AGF|C Chain C, Mtssl Spin Labeled L124c Mutant Of Mscs In The Open Form
 pdb|4AGF|D Chain D, Mtssl Spin Labeled L124c Mutant Of Mscs In The Open Form
 pdb|4AGF|E Chain E, Mtssl Spin Labeled L124c Mutant Of Mscs In The Open Form
 pdb|4AGF|F Chain F, Mtssl Spin Labeled L124c Mutant Of Mscs In The Open Form
 pdb|4AGF|G Chain G, Mtssl Spin Labeled L124c Mutant Of Mscs In The Open Form
          Length = 286

 Score = 33.5 bits (75), Expect = 0.45,   Method: Compositional matrix adjust.
 Identities = 16/59 (27%), Positives = 27/59 (45%)

Query: 513 IFLYVMHPFDVGDRCIIDGVQMVVEDIRILTTTLVRYDNEKVFYPNSVLATKPITNFYR 571
           +   +  PF  G+   + GV   V  ++I +TT+   D + +  PN  +    I NF R
Sbjct: 122 VLCVMFRPFRAGEYVDLGGVAGTVLSVQIFSTTMRTADGKIIVIPNGKIIAGNIINFSR 180


>pdb|3T9N|A Chain A, Crystal Structure Of A Membrane Protein
 pdb|3T9N|B Chain B, Crystal Structure Of A Membrane Protein
 pdb|3T9N|C Chain C, Crystal Structure Of A Membrane Protein
 pdb|3T9N|D Chain D, Crystal Structure Of A Membrane Protein
 pdb|3T9N|E Chain E, Crystal Structure Of A Membrane Protein
 pdb|3T9N|F Chain F, Crystal Structure Of A Membrane Protein
 pdb|3T9N|G Chain G, Crystal Structure Of A Membrane Protein
          Length = 282

 Score = 33.1 bits (74), Expect = 0.54,   Method: Compositional matrix adjust.
 Identities = 36/154 (23%), Positives = 67/154 (43%), Gaps = 11/154 (7%)

Query: 490 ITSQLVLA-----AFMFG--NTVKNIFESIIFLYVMHPFDVGDRCIIDGVQMVVEDIRIL 542
           +TS L +A     A  FG  N VK++     F+     F VGD   I+G+   VE+I + 
Sbjct: 92  MTSLLAVAGIGSLAIGFGAQNLVKDMISGF-FIIFEDQFSVGDYVTINGISGTVEEIGLR 150

Query: 543 TTTLVRYDNEKVFYPNSVLATKPITNFYRSTGNMKDSVEFTIDASMSTVSIEALKSRIQD 602
            T +  + +     PN     K +TN  + +     ++ F ID  +  + IE L+   ++
Sbjct: 151 VTKIRGFSDGLHIIPNG--EIKMVTNLTKDSMMAVVNIAFPIDEDVDKI-IEGLQEICEE 207

Query: 603 YLNSKPEHWRPQHKVVVKEIEDANKIRMALHVTH 636
              S+ +       + + +++D+  + M    T 
Sbjct: 208 VKKSRDDLIEGPTVLGITDMQDSKLVIMVYAKTQ 241


>pdb|3UDC|A Chain A, Crystal Structure Of A Membrane Protein
 pdb|3UDC|B Chain B, Crystal Structure Of A Membrane Protein
 pdb|3UDC|C Chain C, Crystal Structure Of A Membrane Protein
 pdb|3UDC|D Chain D, Crystal Structure Of A Membrane Protein
 pdb|3UDC|E Chain E, Crystal Structure Of A Membrane Protein
 pdb|3UDC|F Chain F, Crystal Structure Of A Membrane Protein
 pdb|3UDC|G Chain G, Crystal Structure Of A Membrane Protein
          Length = 285

 Score = 33.1 bits (74), Expect = 0.56,   Method: Compositional matrix adjust.
 Identities = 36/154 (23%), Positives = 67/154 (43%), Gaps = 11/154 (7%)

Query: 490 ITSQLVLA-----AFMFG--NTVKNIFESIIFLYVMHPFDVGDRCIIDGVQMVVEDIRIL 542
           +TS L +A     A  FG  N VK++     F+     F VGD   I+G+   VE+I + 
Sbjct: 92  MTSLLAVAGIGSLAIGFGAQNLVKDMISGF-FIIFEDQFSVGDYVTINGISGTVEEIGLR 150

Query: 543 TTTLVRYDNEKVFYPNSVLATKPITNFYRSTGNMKDSVEFTIDASMSTVSIEALKSRIQD 602
            T +  + +     PN     K +TN  + +     ++ F ID  +  + IE L+   ++
Sbjct: 151 VTKIRGFSDGLHIIPNG--EIKMVTNLTKDSMMAVVNIAFPIDEDVDKI-IEGLQEICEE 207

Query: 603 YLNSKPEHWRPQHKVVVKEIEDANKIRMALHVTH 636
              S+ +       + + +++D+  + M    T 
Sbjct: 208 VKKSRDDLIEGPTVLGITDMQDSKLVIMVYAKTQ 241


>pdb|4H0A|A Chain A, Crystal Structure Of A Hypothetical Protein (Sav1118) From
           Staphylococcus Aureus Subsp. Aureus Mu50 At 1.90 A
           Resolution
 pdb|4H0A|B Chain B, Crystal Structure Of A Hypothetical Protein (Sav1118) From
           Staphylococcus Aureus Subsp. Aureus Mu50 At 1.90 A
           Resolution
          Length = 323

 Score = 30.4 bits (67), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 16/29 (55%), Positives = 17/29 (58%)

Query: 558 NSVLATKPITNFYRSTGNMKDSVEFTIDA 586
           NS LA     N Y +T N  DSVEFT DA
Sbjct: 228 NSDLAHIASNNLYEATSNGSDSVEFTEDA 256


>pdb|4HW9|A Chain A, Crystal Structure Of Helicobacter Pylori Mscs (closed
           State)
 pdb|4HW9|B Chain B, Crystal Structure Of Helicobacter Pylori Mscs (closed
           State)
 pdb|4HW9|C Chain C, Crystal Structure Of Helicobacter Pylori Mscs (closed
           State)
 pdb|4HW9|D Chain D, Crystal Structure Of Helicobacter Pylori Mscs (closed
           State)
 pdb|4HW9|E Chain E, Crystal Structure Of Helicobacter Pylori Mscs (closed
           State)
 pdb|4HW9|F Chain F, Crystal Structure Of Helicobacter Pylori Mscs (closed
           State)
 pdb|4HW9|G Chain G, Crystal Structure Of Helicobacter Pylori Mscs (closed
           State)
          Length = 309

 Score = 28.9 bits (63), Expect = 9.1,   Method: Compositional matrix adjust.
 Identities = 15/44 (34%), Positives = 21/44 (47%)

Query: 519 HPFDVGDRCIIDGVQMVVEDIRILTTTLVRYDNEKVFYPNSVLA 562
           HPF  GD   I G++  VE +    T+L  +D      PN  +A
Sbjct: 141 HPFKKGDIIEISGLEGKVEALNFFNTSLRLHDGRLAVLPNRSVA 184


  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
   0.322    0.135    0.385 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,540,901
Number of Sequences: 62578
Number of extensions: 580281
Number of successful extensions: 1301
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1294
Number of HSP's gapped (non-prelim): 9
length of query: 692
length of database: 14,973,337
effective HSP length: 106
effective length of query: 586
effective length of database: 8,340,069
effective search space: 4887280434
effective search space used: 4887280434
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.8 bits)