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= 025184
         (256 letters)

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

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



>pdb|3BGA|A Chain A, Crystal Structure Of Beta-Galactosidase From Bacteroides
           Thetaiotaomicron Vpi-5482
 pdb|3BGA|B Chain B, Crystal Structure Of Beta-Galactosidase From Bacteroides
           Thetaiotaomicron Vpi-5482
          Length = 1010

 Score = 29.3 bits (64), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 16/60 (26%), Positives = 27/60 (45%)

Query: 96  DDKSGGHGVGWSPIIPYLFSVPQEWDEVPVSIADLGGTEIDLRFASPKKGRLFVIVAPVL 155
           D+K       W+   P L+++  E  +    + +L G E+  R +  K GR  +   PVL
Sbjct: 294 DEKKIAEVKAWNAEHPNLYTLVLELKDAQGKVTELTGCEVGFRTSEIKDGRFCINGVPVL 353


>pdb|1U5K|A Chain A, Recombinational Repair Protein Reco
 pdb|1U5K|B Chain B, Recombinational Repair Protein Reco
 pdb|1W3S|A Chain A, The Crystal Structure Of Reco From Deinococcus
          Radiodurans.
 pdb|1W3S|B Chain B, The Crystal Structure Of Reco From Deinococcus
          Radiodurans.
 pdb|2V1C|C Chain C, Crystal Structure And Mutational Study Of Recor Provide
          Insight Into Its Role In Dna Repair
          Length = 244

 Score = 27.7 bits (60), Expect = 7.3,   Method: Compositional matrix adjust.
 Identities = 12/28 (42%), Positives = 18/28 (64%)

Query: 62 PADGLAVVKQGLLAGRVPGLSEPDEQGW 89
          P + LA VKQ +L G +P L+EP+   +
Sbjct: 64 PHNDLASVKQAVLEGALPTLAEPERYAF 91


>pdb|2LFU|A Chain A, The Structure Of A N. Meningitides Protein Targeted For
           Vaccine Development
          Length = 193

 Score = 26.9 bits (58), Expect = 9.9,   Method: Compositional matrix adjust.
 Identities = 24/79 (30%), Positives = 34/79 (43%), Gaps = 1/79 (1%)

Query: 27  AVACSTGSDSVDGVMKRRSVLVSGASLISSAVLGFPADGLAVVKQGL-LAGRVPGLSEPD 85
           A     GS SVDG++     L  G     +A+ G    G      G  ++GR  G +  +
Sbjct: 99  AAKVDFGSKSVDGIIDSGDDLHMGTQKFKAAIDGNGFKGTWTENGGGDVSGRFYGPAGEE 158

Query: 86  EQGWRTYRRPDDKSGGHGV 104
             G  +YR  D + GG GV
Sbjct: 159 VAGKYSYRPTDAEKGGFGV 177


  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    0.138    0.412 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,320,214
Number of Sequences: 62578
Number of extensions: 377409
Number of successful extensions: 857
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 850
Number of HSP's gapped (non-prelim): 10
length of query: 256
length of database: 14,973,337
effective HSP length: 97
effective length of query: 159
effective length of database: 8,903,271
effective search space: 1415620089
effective search space used: 1415620089
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: 50 (23.9 bits)