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= 025555
         (251 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 = 28.9 bits (63), Expect = 2.6,   Method: Composition-based stats.
 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 = 27.3 bits (59), Expect = 7.7,   Method: Compositional matrix adjust.
 Identities = 12/25 (48%), Positives = 17/25 (68%)

Query: 62 PADGLAVVKQGLLAGRVPGLSEPDE 86
          P + LA VKQ +L G +P L+EP+ 
Sbjct: 64 PHNDLASVKQAVLEGALPTLAEPER 88


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

 Score = 27.3 bits (59), Expect = 8.2,   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


>pdb|1Y4Q|B Chain B, T-To-T(High) Quaternary Transitions In Human Hemoglobin:
           Betaf42a Deoxy Low-Salt (1 Test Set)
 pdb|1Y4Q|D Chain D, T-To-T(High) Quaternary Transitions In Human Hemoglobin:
           Betaf42a Deoxy Low-Salt (1 Test Set)
          Length = 146

 Score = 27.3 bits (59), Expect = 9.1,   Method: Compositional matrix adjust.
 Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 3/48 (6%)

Query: 145 GRLFVIVAPVLRFADDLGDDATIEKI-GPPEKVINAFGPEVIGENVEG 191
           GRL V+     RFA+  GD +T + + G P+  + A G +V+G   +G
Sbjct: 29  GRLLVVYPWTQRFAESFGDLSTPDAVMGNPK--VKAHGKKVLGAFSDG 74


>pdb|3DEC|A Chain A, Crystal Structure Of A Glycosyl Hydrolases Family 2
           Protein From Bacteroides Thetaiotaomicron
          Length = 1000

 Score = 27.3 bits (59), Expect = 9.3,   Method: Composition-based stats.
 Identities = 19/71 (26%), Positives = 32/71 (45%), Gaps = 11/71 (15%)

Query: 85  DEQGWRTYRRPDDKSGGHGVGWSPIIPYLFSVPQEWDEVPVSIADLGGTEIDLRFASPKK 144
           DEQ     R PD +       W+   P L+++  E  +    + ++ GT++  R +  K 
Sbjct: 290 DEQ-----RLPDVRR------WNAEHPELYTLLLELKDAGGKVTEITGTKVGFRTSEIKN 338

Query: 145 GRLFVIVAPVL 155
           GR  +   PVL
Sbjct: 339 GRFCINGVPVL 349


>pdb|1YEN|B Chain B, T-To-T(High) Quaternary Transitions In Human Hemoglobin:
           Betap36a Oxy (2mm Ihp, 20% Peg) (10 Test Sets)
 pdb|1YEN|D Chain D, T-To-T(High) Quaternary Transitions In Human Hemoglobin:
           Betap36a Oxy (2mm Ihp, 20% Peg) (10 Test Sets)
 pdb|1Y45|B Chain B, T-To-T(High) Quaternary Transitions In Human Hemoglobin:
           Betap36a Deoxy Low-Salt (10 Test Sets)
 pdb|1Y45|D Chain D, T-To-T(High) Quaternary Transitions In Human Hemoglobin:
           Betap36a Deoxy Low-Salt (10 Test Sets)
          Length = 146

 Score = 26.9 bits (58), Expect = 9.7,   Method: Compositional matrix adjust.
 Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 3/48 (6%)

Query: 145 GRLFVIVAPVLRFADDLGDDATIEKI-GPPEKVINAFGPEVIGENVEG 191
           GRL V+ A   RF +  GD +T + + G P+  + A G +V+G   +G
Sbjct: 29  GRLLVVYAWTQRFFESFGDLSTPDAVMGNPK--VKAHGKKVLGAFSDG 74


  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    0.414 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,121,216
Number of Sequences: 62578
Number of extensions: 368923
Number of successful extensions: 798
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: 791
Number of HSP's gapped (non-prelim): 10
length of query: 251
length of database: 14,973,337
effective HSP length: 96
effective length of query: 155
effective length of database: 8,965,849
effective search space: 1389706595
effective search space used: 1389706595
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)