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= 008379
         (568 letters)

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

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



>pdb|1H6K|A Chain A, Nuclear Cap Binding Complex
 pdb|1H6K|B Chain B, Nuclear Cap Binding Complex
 pdb|1H6K|C Chain C, Nuclear Cap Binding Complex
          Length = 757

 Score = 30.4 bits (67), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 16/60 (26%), Positives = 32/60 (53%)

Query: 68  PGFTDVFAALVAVVNTKFTAVGELLLKRIVLQLKRAYKRNDKPQLLAAVKFIAHLVNQQV 127
           P    ++  LV ++N +    G   ++ ++ QLK + K N+  + +  V+F++ LVN  V
Sbjct: 61  PEKLTIYTTLVGLLNARNYNFGGEFVEAMIRQLKESLKANNYNEAVYLVRFLSDLVNCHV 120


>pdb|1N52|A Chain A, Cap Binding Complex
 pdb|1N54|A Chain A, Cap Binding Complex M7gpppg Free
 pdb|3FEX|A Chain A, Crystal Structure Of The Cbc-Importin Alpha Complex.
 pdb|3FEY|A Chain A, Crystal Structure Of The Cbc-Importin Alpha Complex
          Length = 790

 Score = 30.4 bits (67), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 16/60 (26%), Positives = 32/60 (53%)

Query: 68  PGFTDVFAALVAVVNTKFTAVGELLLKRIVLQLKRAYKRNDKPQLLAAVKFIAHLVNQQV 127
           P    ++  LV ++N +    G   ++ ++ QLK + K N+  + +  V+F++ LVN  V
Sbjct: 80  PEKLTIYTTLVGLLNARNYNFGGEFVEAMIRQLKESLKANNYNEAVYLVRFLSDLVNCHV 139


>pdb|1H2V|C Chain C, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
          Length = 771

 Score = 30.4 bits (67), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 16/60 (26%), Positives = 32/60 (53%)

Query: 68  PGFTDVFAALVAVVNTKFTAVGELLLKRIVLQLKRAYKRNDKPQLLAAVKFIAHLVNQQV 127
           P    ++  LV ++N +    G   ++ ++ QLK + K N+  + +  V+F++ LVN  V
Sbjct: 61  PEKLTIYTTLVGLLNARNYNFGGEFVEAMIRQLKESLKANNYNEAVYLVRFLSDLVNCHV 120


>pdb|1H2T|C Chain C, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
           In Complex With A Cap Analogue M7gpppg
 pdb|1H2U|A Chain A, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
           In Complex With A Cap Analogue M7gpppg
 pdb|1H2U|B Chain B, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
           In Complex With A Cap Analogue M7gpppg
          Length = 723

 Score = 30.4 bits (67), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 15/55 (27%), Positives = 31/55 (56%)

Query: 73  VFAALVAVVNTKFTAVGELLLKRIVLQLKRAYKRNDKPQLLAAVKFIAHLVNQQV 127
           ++  LV ++N +    G   ++ ++ QLK + K N+  + +  V+F++ LVN  V
Sbjct: 66  IYTTLVGLLNARNYNFGGEFVEAMIRQLKESLKANNYNEAVYLVRFLSDLVNCHV 120


>pdb|3BRY|A Chain A, Crystal Structure Of The Ralstonia Pickettii Toluene
           Transporter Tbux
 pdb|3BRY|B Chain B, Crystal Structure Of The Ralstonia Pickettii Toluene
           Transporter Tbux
          Length = 441

 Score = 29.6 bits (65), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 17/54 (31%), Positives = 29/54 (53%), Gaps = 1/54 (1%)

Query: 10  SAEYQRLTWDALRKSIN-GLVNKVNATNIKNIIPELFAENLIRGRGLFCRSCMK 62
           SA+YQR+ W ++ K +N G V   +A N+   +P+ + +  + G G   R   K
Sbjct: 296 SADYQRVFWSSVMKDMNVGFVQSGSAANLDLSLPQNYRDISVFGIGAEYRYNAK 349


>pdb|3LNL|A Chain A, Crystal Structure Of Staphylococcus Aureus Protein Sa1388
 pdb|3LNL|B Chain B, Crystal Structure Of Staphylococcus Aureus Protein Sa1388
          Length = 370

 Score = 28.9 bits (63), Expect = 7.7,   Method: Compositional matrix adjust.
 Identities = 18/72 (25%), Positives = 36/72 (50%), Gaps = 9/72 (12%)

Query: 185 GEIDK-------RVQFLIEGLFAIRKAKF--QGYPAVRPELDLVDIEDQLTHEISLQDEI 235
           G+IDK       +++F+I+     R  +   Q +P   P  D ++I+    + + +  E+
Sbjct: 189 GQIDKIEDVDEVKIEFMIDAYQKSRAEQLIKQYHPYETPVFDFIEIKQTSLYGLGVMAEV 248

Query: 236 DPEITLDIFKPD 247
           D ++TL+ F  D
Sbjct: 249 DNQMTLEDFAAD 260


>pdb|2NYD|A Chain A, Crystal Structure Of Staphylococcus Aureus Hypothetical
           Protein Sa1388
 pdb|2NYD|B Chain B, Crystal Structure Of Staphylococcus Aureus Hypothetical
           Protein Sa1388
          Length = 370

 Score = 28.9 bits (63), Expect = 8.0,   Method: Compositional matrix adjust.
 Identities = 18/72 (25%), Positives = 36/72 (50%), Gaps = 9/72 (12%)

Query: 185 GEIDK-------RVQFLIEGLFAIRKAKF--QGYPAVRPELDLVDIEDQLTHEISLQDEI 235
           G+IDK       +++F+I+     R  +   Q +P   P  D ++I+    + + +  E+
Sbjct: 189 GQIDKIEDVDEVKIEFMIDAYQKSRAEQLIKQYHPYETPVFDFIEIKQTSLYGLGVMAEV 248

Query: 236 DPEITLDIFKPD 247
           D ++TL+ F  D
Sbjct: 249 DNQMTLEDFAAD 260


  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
   0.323    0.139    0.400 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,011,119
Number of Sequences: 62578
Number of extensions: 493580
Number of successful extensions: 995
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 991
Number of HSP's gapped (non-prelim): 7
length of query: 568
length of database: 14,973,337
effective HSP length: 104
effective length of query: 464
effective length of database: 8,465,225
effective search space: 3927864400
effective search space used: 3927864400
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: 54 (25.4 bits)