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= 023059
         (288 letters)

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

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



>pdb|3DEL|B Chain B, The Structure Of Ct381, The Arginine Binding Protein From
           The Periplasm Chlamydia Trachomatis
 pdb|3DEL|C Chain C, The Structure Of Ct381, The Arginine Binding Protein From
           The Periplasm Chlamydia Trachomatis
 pdb|3DEL|D Chain D, The Structure Of Ct381, The Arginine Binding Protein From
           The Periplasm Chlamydia Trachomatis
 pdb|3DEL|F Chain F, The Structure Of Ct381, The Arginine Binding Protein From
           The Periplasm Chlamydia Trachomatis
          Length = 242

 Score = 28.9 bits (63), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 8/72 (11%)

Query: 222 IIRAQGEATSAQLIGQAIAKNPAFITLRK--------IEAAREIAQTISKSSNKVYLNAD 273
            ++  G++ S + I    A  P F  + K        I+ AREI+  + K+ +    + D
Sbjct: 1   CLKEGGDSNSEKFIVGTNATYPPFEFVDKRGEVVGFDIDLAREISNKLGKTLDVREFSFD 60

Query: 274 DLLLNLQEMKLD 285
            L+LNL++ ++D
Sbjct: 61  ALILNLKQHRID 72


>pdb|3E98|A Chain A, Crystal Structure Of A Gaf Domain Containing Protein That
           Belongs To Pfam Duf484 Family (Pa5279) From Pseudomonas
           Aeruginosa At 2.43 A Resolution
 pdb|3E98|B Chain B, Crystal Structure Of A Gaf Domain Containing Protein That
           Belongs To Pfam Duf484 Family (Pa5279) From Pseudomonas
           Aeruginosa At 2.43 A Resolution
          Length = 252

 Score = 28.1 bits (61), Expect = 6.5,   Method: Compositional matrix adjust.
 Identities = 23/94 (24%), Positives = 47/94 (50%), Gaps = 8/94 (8%)

Query: 188 KEFTFAIEAKQVAAQEAERAKFIVEKAEQDKKGAIIRAQGEATSAQLIGQAIAKNPAFIT 247
           +E T A++A+QVAA  ++  +F VE  E   +  I    G+A S       + +    + 
Sbjct: 25  QEPTAALDAEQVAAYLSQHPEFFVEHDELIPELRIPHQPGDAVS------LVERQVRLLR 78

Query: 248 LRKIEAAREIAQ--TISKSSNKVYLNADDLLLNL 279
            R IE    ++Q   +++ +++++     L+L+L
Sbjct: 79  ERNIEXRHRLSQLXDVARENDRLFDKTRRLVLDL 112


  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
   0.317    0.132    0.360 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,170,058
Number of Sequences: 62578
Number of extensions: 258265
Number of successful extensions: 640
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 639
Number of HSP's gapped (non-prelim): 11
length of query: 288
length of database: 14,973,337
effective HSP length: 98
effective length of query: 190
effective length of database: 8,840,693
effective search space: 1679731670
effective search space used: 1679731670
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)