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= 043608
         (579 letters)

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

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



>pdb|3T4E|A Chain A, 1.95 Angstrom Crystal Structure Of Shikimate
           5-Dehydrogenase (Aroe) From Salmonella Enterica Subsp.
           Enterica Serovar Typhimurium In Complex With Nad
 pdb|3T4E|B Chain B, 1.95 Angstrom Crystal Structure Of Shikimate
           5-Dehydrogenase (Aroe) From Salmonella Enterica Subsp.
           Enterica Serovar Typhimurium In Complex With Nad
          Length = 312

 Score = 30.0 bits (66), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 15/44 (34%), Positives = 22/44 (50%)

Query: 6   VSSLCKQNLYNEALVAYDFSQNNTNIRIRPSTYAGLISACSSLR 49
           V+ L  Q+ + EAL + D   N T + ++P     LI   S LR
Sbjct: 205 VTDLADQHAFTEALASADILTNGTKVGMKPLENESLIGDVSLLR 248


>pdb|1FFT|B Chain B, The Structure Of Ubiquinol Oxidase From Escherichia Coli
 pdb|1FFT|G Chain G, The Structure Of Ubiquinol Oxidase From Escherichia Coli
          Length = 315

 Score = 29.6 bits (65), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 18/77 (23%), Positives = 35/77 (45%)

Query: 214 KLGYELEALCHFNEMLHHGAYQPNEFIFGSVFSACSNFARILFNEIDSPDLASWNALIAG 273
           +LG ++ A+      LH  A +P  +   S   +   F+ + F  I +PD A+++  +A 
Sbjct: 178 RLGSQIYAMAGMQTRLHLIANEPGTYDGISASYSGPGFSGMKFKAIATPDRAAFDQWVAK 237

Query: 274 VASHSNANEAMSLFSEM 290
                N    M+ F ++
Sbjct: 238 AKQSPNTMSDMAAFEKL 254


  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
   0.324    0.136    0.415 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,780,860
Number of Sequences: 62578
Number of extensions: 662687
Number of successful extensions: 1823
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1820
Number of HSP's gapped (non-prelim): 4
length of query: 579
length of database: 14,973,337
effective HSP length: 104
effective length of query: 475
effective length of database: 8,465,225
effective search space: 4020981875
effective search space used: 4020981875
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (25.4 bits)