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= 005397
         (698 letters)

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

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



>pdb|3AQM|A Chain A, Structure Of Bacterial Protein (Form Ii)
 pdb|3AQM|B Chain B, Structure Of Bacterial Protein (Form Ii)
          Length = 415

 Score = 32.3 bits (72), Expect = 0.93,   Method: Compositional matrix adjust.
 Identities = 20/55 (36%), Positives = 28/55 (50%), Gaps = 2/55 (3%)

Query: 7   DDDFPSIESITPQS--KIDSVYQSHTEKGIRKLCCELLDLKDAVENLCGNMHTKY 59
           D+ F SIE    +    I+S+Y S  +  +R     + DLKD V  L GN  T+Y
Sbjct: 121 DNIFGSIEEDAQRRDFTINSLYYSVADFTVRDYVGGMKDLKDGVIRLIGNPETRY 175


>pdb|3AQK|A Chain A, Structure Of Bacterial Protein (Apo Form I)
          Length = 414

 Score = 32.3 bits (72), Expect = 0.95,   Method: Compositional matrix adjust.
 Identities = 20/55 (36%), Positives = 28/55 (50%), Gaps = 2/55 (3%)

Query: 7   DDDFPSIESITPQS--KIDSVYQSHTEKGIRKLCCELLDLKDAVENLCGNMHTKY 59
           D+ F SIE    +    I+S+Y S  +  +R     + DLKD V  L GN  T+Y
Sbjct: 120 DNIFGSIEEDAQRRDFTINSLYYSVADFTVRDYVGGMKDLKDGVIRLIGNPETRY 174


>pdb|3AQL|A Chain A, Structure Of Bacterial Protein (Apo Form Ii)
 pdb|3AQL|B Chain B, Structure Of Bacterial Protein (Apo Form Ii)
 pdb|3AQN|A Chain A, Complex Structure Of Bacterial Protein (Apo Form Ii)
 pdb|3AQN|B Chain B, Complex Structure Of Bacterial Protein (Apo Form Ii)
          Length = 415

 Score = 32.3 bits (72), Expect = 0.95,   Method: Compositional matrix adjust.
 Identities = 20/55 (36%), Positives = 28/55 (50%), Gaps = 2/55 (3%)

Query: 7   DDDFPSIESITPQS--KIDSVYQSHTEKGIRKLCCELLDLKDAVENLCGNMHTKY 59
           D+ F SIE    +    I+S+Y S  +  +R     + DLKD V  L GN  T+Y
Sbjct: 121 DNIFGSIEEDAQRRDFTINSLYYSVADFTVRDYVGGMKDLKDGVIRLIGNPETRY 175


>pdb|2D2S|A Chain A, Crystal Structure Of The Exo84p C-Terminal Domains
          Length = 235

 Score = 29.6 bits (65), Expect = 6.7,   Method: Compositional matrix adjust.
 Identities = 43/181 (23%), Positives = 79/181 (43%), Gaps = 7/181 (3%)

Query: 139 LEKIDVLLAEHKVEEAIEVLDAEERNFPELRXXXXXXXXXXXXFKS-DFLKRKAMVEDQL 197
           +E+ID+ LA  + E A+E L   E    +L               S    +R+  +  +L
Sbjct: 22  VEEIDIELARLRFESAVETLLDIESQLEDLSERISDEELMLLNLISLKIEQRREAISSKL 81

Query: 198 VKITEQPSIGILELKKALTDLIKLGKGPLAHQLLLKYYASRLQRSFEVYLPSSSV-CPEV 256
            + +   S  I+ LK    ++IKLG    A  L L+  ++ +Q   ++ L   SV  P  
Sbjct: 82  SQ-SILSSNEIVHLKSGTENMIKLGLPEQALDLFLQNRSNFIQ---DLILQIGSVDNPTN 137

Query: 257 FPATISKLVFSTVSLTTKDSGLIFGD-NPVYSNRVVQWAEWEIEYFVRLVKENAPPSETI 315
           +   ++ + F T+  T +D   IF +     S+ +V W   E++   +L+ +     E +
Sbjct: 138 YLTQLAVIRFQTIKKTVEDFQDIFKELGAKISSILVDWCSDEVDNHFKLIDKQLLNDEML 197

Query: 316 S 316
           S
Sbjct: 198 S 198


  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
   0.318    0.134    0.386 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,088,802
Number of Sequences: 62578
Number of extensions: 684168
Number of successful extensions: 1618
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1618
Number of HSP's gapped (non-prelim): 5
length of query: 698
length of database: 14,973,337
effective HSP length: 106
effective length of query: 592
effective length of database: 8,340,069
effective search space: 4937320848
effective search space used: 4937320848
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: 55 (25.8 bits)