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= 030235
         (181 letters)

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

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



>pdb|2YR1|A Chain A, Crystal Structure Of 3-Dehydroquinate Dehydratase From
           Geobacillus Kaustophilus Hta426
 pdb|2YR1|B Chain B, Crystal Structure Of 3-Dehydroquinate Dehydratase From
           Geobacillus Kaustophilus Hta426
          Length = 257

 Score = 28.9 bits (63), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 15/40 (37%), Positives = 21/40 (52%)

Query: 90  VPVSPSDKLTMYFQADGAMNETAIPAVTQALQGTEGISDL 129
           +P SP D L +    + A  E AIP +T A+ G   I+ L
Sbjct: 178 MPKSPEDVLVLLQATEEARRELAIPLITMAMGGLGAITRL 217


>pdb|3DIN|A Chain A, Crystal Structure Of The Protein-Translocation Complex
           Formed By The Secy Channel And The Seca Atpase
 pdb|3DIN|B Chain B, Crystal Structure Of The Protein-Translocation Complex
           Formed By The Secy Channel And The Seca Atpase
          Length = 871

 Score = 26.2 bits (56), Expect = 9.5,   Method: Composition-based stats.
 Identities = 24/82 (29%), Positives = 35/82 (42%), Gaps = 8/82 (9%)

Query: 96  DKLTMYFQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVEKQTTVQATGVAANL 155
           +K+  +  AD  + E A   V +A + T G+    VQV+ GIA  E +     TG    L
Sbjct: 45  EKVNSFEDADEHLFE-AFALVREAARRTLGMRPFDVQVMGGIALHEGKVAEMKTGEGKTL 103

Query: 156 VEIIQ-------GSGFKLQTLN 170
              +        G G  L T+N
Sbjct: 104 AATMPIYLNALIGKGVHLVTVN 125


>pdb|3JUX|A Chain A, Structure Of The Translocation Atpase Seca From Thermotoga
           Maritima
          Length = 822

 Score = 26.2 bits (56), Expect = 9.5,   Method: Composition-based stats.
 Identities = 24/82 (29%), Positives = 35/82 (42%), Gaps = 8/82 (9%)

Query: 96  DKLTMYFQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVEKQTTVQATGVAANL 155
           +K+  +  AD  + E A   V +A + T G+    VQV+ GIA  E +     TG    L
Sbjct: 45  EKVNSFEDADEHLFE-AFALVREAARRTLGMRPFDVQVMGGIALHEGKVAEMKTGEGKTL 103

Query: 156 VEIIQ-------GSGFKLQTLN 170
              +        G G  L T+N
Sbjct: 104 AATMPIYLNALIGKGVHLVTVN 125


  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
   0.316    0.130    0.354 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,615,661
Number of Sequences: 62578
Number of extensions: 100690
Number of successful extensions: 293
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 291
Number of HSP's gapped (non-prelim): 4
length of query: 181
length of database: 14,973,337
effective HSP length: 93
effective length of query: 88
effective length of database: 9,153,583
effective search space: 805515304
effective search space used: 805515304
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 bits)