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= 027566
         (222 letters)

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

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



>pdb|1TZA|A Chain A, X-Ray Structure Of Northeast Structural Genomics
           Consortium Target Sor45
 pdb|1TZA|B Chain B, X-Ray Structure Of Northeast Structural Genomics
           Consortium Target Sor45
          Length = 134

 Score = 63.5 bits (153), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 28/56 (50%), Positives = 38/56 (67%)

Query: 166 IRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTENI 221
           IRV+V++ YIE +S P   +Y F+Y + I N  E+  +L  RHWIITDANGKT  +
Sbjct: 8   IRVEVKTEYIEQQSSPEDEKYLFSYTITIINLGEQAAKLETRHWIITDANGKTSEV 63


>pdb|1XQ4|A Chain A, Crystal Structure Of The Putative Apaa Protein From
           Bordetella Pertussis, Northeast Structural Genomics
           Target Ber40
 pdb|1XQ4|B Chain B, Crystal Structure Of The Putative Apaa Protein From
           Bordetella Pertussis, Northeast Structural Genomics
           Target Ber40
 pdb|1XQ4|C Chain C, Crystal Structure Of The Putative Apaa Protein From
           Bordetella Pertussis, Northeast Structural Genomics
           Target Ber40
 pdb|1XQ4|D Chain D, Crystal Structure Of The Putative Apaa Protein From
           Bordetella Pertussis, Northeast Structural Genomics
           Target Ber40
          Length = 139

 Score = 58.9 bits (141), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 24/56 (42%), Positives = 34/56 (60%)

Query: 166 IRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTENI 221
           + V V   Y+ ++S P + QY FAY VRITN    P Q++ RHWIITD   + + +
Sbjct: 13  LTVSVTPRYVPEQSDPSQQQYVFAYTVRITNTGSHPAQVISRHWIITDGEERVQEV 68


>pdb|2F1E|A Chain A, Solution Structure Of Apag Protein
          Length = 127

 Score = 57.8 bits (138), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 24/56 (42%), Positives = 36/56 (64%)

Query: 166 IRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTENI 221
           + V+V   ++  +S P +G+Y FAY +RI N    P +L+ RHW ITD NG+TE +
Sbjct: 9   VEVEVSPRFLAHQSTPDEGRYAFAYSIRIQNAGAVPARLVARHWQITDGNGRTEQV 64


>pdb|1XVS|A Chain A, Crystal Structure Of Apag Protein From Vibrio Cholerae
 pdb|1XVS|B Chain B, Crystal Structure Of Apag Protein From Vibrio Cholerae
          Length = 126

 Score = 55.1 bits (131), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 26/58 (44%), Positives = 39/58 (67%)

Query: 160 DATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGK 217
           D +   I++QV++ YIE++S P   ++ FAY + I N S + VQL  R W+ITDA+GK
Sbjct: 2   DVSLPCIKIQVQTRYIEEQSNPEYQRFVFAYLITIKNLSSQTVQLXSRRWLITDADGK 59


>pdb|1A76|A Chain A, Flap Endonuclease-1 From Methanococcus Jannaschii
 pdb|1A77|A Chain A, Flap Endonuclease-1 From Methanococcus Jannaschii
          Length = 326

 Score = 31.2 bits (69), Expect = 0.44,   Method: Compositional matrix adjust.
 Identities = 14/40 (35%), Positives = 24/40 (60%)

Query: 127 MKEAVAEERFEDAARYRDKLKEIAPNSLLKCLSDATTLGI 166
           MKEA+ +E FE+AA+Y  ++  + P  +  C    + +GI
Sbjct: 105 MKEAIKKEDFEEAAKYAKRVSYLTPKMVENCKYLLSLMGI 144


>pdb|3Q0I|A Chain A, Methionyl-Trna Formyltransferase From Vibrio Cholerae
          Length = 318

 Score = 29.3 bits (64), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 12/27 (44%), Positives = 17/27 (62%)

Query: 134 ERFEDAARYRDKLKEIAPNSLLKCLSD 160
           E  + +A   DKL E+ P +LL+CL D
Sbjct: 163 EASDTSASXYDKLAELGPQALLECLQD 189


  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
   0.321    0.134    0.381 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,129,563
Number of Sequences: 62578
Number of extensions: 167150
Number of successful extensions: 480
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 469
Number of HSP's gapped (non-prelim): 11
length of query: 222
length of database: 14,973,337
effective HSP length: 95
effective length of query: 127
effective length of database: 9,028,427
effective search space: 1146610229
effective search space used: 1146610229
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: 49 (23.5 bits)