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= 006830
         (629 letters)

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

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



>pdb|1JCH|A Chain A, Crystal Structure Of Colicin E3 In Complex With Its
           Immunity Protein
 pdb|1JCH|C Chain C, Crystal Structure Of Colicin E3 In Complex With Its
           Immunity Protein
          Length = 551

 Score = 32.7 bits (73), Expect = 0.57,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 37/71 (52%), Gaps = 1/71 (1%)

Query: 42  RAR-ELHMARRDISRYKESRKAAESVKAQAESELSTARKTVKDLACRIEKTNHQAIPSMR 100
           RAR EL+ A  D++R +E +  A  V    +SEL  A KT+ D    I++ N  A   M 
Sbjct: 325 RARAELNQANEDVARNQERQAKAVQVYNSRKSELDAANKTLADAIAEIKQFNRFAHDPMA 384

Query: 101 YVERLEKSSGI 111
              R+ + +G+
Sbjct: 385 GGHRMWQMAGL 395


>pdb|2B5U|A Chain A, Crystal Structure Of Colicin E3 V206c Mutant In Complex
           With Its Immunity Protein
 pdb|2B5U|C Chain C, Crystal Structure Of Colicin E3 V206c Mutant In Complex
           With Its Immunity Protein
          Length = 551

 Score = 32.7 bits (73), Expect = 0.61,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 37/71 (52%), Gaps = 1/71 (1%)

Query: 42  RAR-ELHMARRDISRYKESRKAAESVKAQAESELSTARKTVKDLACRIEKTNHQAIPSMR 100
           RAR EL+ A  D++R +E +  A  V    +SEL  A KT+ D    I++ N  A   M 
Sbjct: 325 RARAELNQANEDVARNQERQAKAVQVYNSRKSELDAANKTLADAIAEIKQFNRFAHDPMA 384

Query: 101 YVERLEKSSGI 111
              R+ + +G+
Sbjct: 385 GGHRMWQMAGL 395


>pdb|2YSU|B Chain B, Structure Of The Complex Between Btub And Colicin E2
           Receptor Binding Domain
          Length = 135

 Score = 31.6 bits (70), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 25/80 (31%), Positives = 41/80 (51%), Gaps = 1/80 (1%)

Query: 33  LDIPESSSSRAR-ELHMARRDISRYKESRKAAESVKAQAESELSTARKTVKDLACRIEKT 91
           ++  E +  RAR EL+ A  D++R +E +  A  V    +SEL  A KT+ D    I++ 
Sbjct: 4   VEAAERNYERARAELNQANEDVARNQERQAKAVQVYNSRKSELDAANKTLADAIAEIKQF 63

Query: 92  NHQAIPSMRYVERLEKSSGI 111
           N  A   M    R+ + +G+
Sbjct: 64  NRFAHDPMAGGHRMWQMAGL 83


>pdb|1UJW|B Chain B, Structure Of The Complex Between Btub And Colicin E3
           Receptor Binding Domain
          Length = 135

 Score = 31.2 bits (69), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 25/80 (31%), Positives = 41/80 (51%), Gaps = 1/80 (1%)

Query: 33  LDIPESSSSRAR-ELHMARRDISRYKESRKAAESVKAQAESELSTARKTVKDLACRIEKT 91
           ++  E +  RAR EL+ A  D++R +E +  A  V    +SEL  A KT+ D    I++ 
Sbjct: 3   VEAAERNYERARAELNQANEDVARNQERQAKAVQVYNSRKSELDAANKTLADAIAEIKQF 62

Query: 92  NHQAIPSMRYVERLEKSSGI 111
           N  A   M    R+ + +G+
Sbjct: 63  NRFAHDPMAGGHRMWQMAGL 82


>pdb|2FIC|A Chain A, The Crystal Structure Of The Bar Domain From Human
           Bin1AMPHIPHYSIN II And Its Implications For Molecular
           Recognition
 pdb|2FIC|B Chain B, The Crystal Structure Of The Bar Domain From Human
           Bin1AMPHIPHYSIN II And Its Implications For Molecular
           Recognition
          Length = 251

 Score = 31.2 bits (69), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 29/110 (26%), Positives = 52/110 (47%), Gaps = 13/110 (11%)

Query: 34  DIPESSSSRAREL---HMARRDISRYKESRKAAESVKAQAESELSTARKTVKDLACRIEK 90
           DI    + R R+L     AR      + ++K  E+  A+AE EL  A+K  +++   ++ 
Sbjct: 145 DIKSRIAKRGRKLVDYDSARHHYESLQTAKKKDEAKIAKAEEELIKAQKVFEEMNVDLQ- 203

Query: 91  TNHQAIPSMR------YVERLEKSSGIEENVLAERSRESHRYAEVMRELE 134
              + +PS+       YV   +  +G+EEN   E S+ +    +V+  LE
Sbjct: 204 ---EELPSLWNSRVGFYVNTFQSIAGLEENFHKEMSKLNQNLNDVLVGLE 250


  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
   0.309    0.123    0.317 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,628,773
Number of Sequences: 62578
Number of extensions: 397203
Number of successful extensions: 1284
Number of sequences better than 100.0: 34
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 30
Number of HSP's that attempted gapping in prelim test: 1246
Number of HSP's gapped (non-prelim): 67
length of query: 629
length of database: 14,973,337
effective HSP length: 105
effective length of query: 524
effective length of database: 8,402,647
effective search space: 4402987028
effective search space used: 4402987028
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 54 (25.4 bits)