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= 031557
         (157 letters)

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

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



>pdb|2D8M|A Chain A, Solution Structure Of The First Brct Domain Of Dna-Repair
           Protein Xrcc1
          Length = 129

 Score = 31.6 bits (70), Expect = 0.18,   Method: Compositional matrix adjust.
 Identities = 13/29 (44%), Positives = 20/29 (68%)

Query: 124 IKVTLSGNQQPVRTEITEAAMELGAEVKT 152
           + V LSG Q P R+E+ + A+ELGA+ + 
Sbjct: 26  VVVVLSGFQNPFRSELRDKALELGAKYRP 54


>pdb|3M9U|A Chain A, Crystal Structure Of Geranylgeranyl Pyrophosphate Synthase
           From Lactobacillus Brevis Atcc 367
 pdb|3M9U|B Chain B, Crystal Structure Of Geranylgeranyl Pyrophosphate Synthase
           From Lactobacillus Brevis Atcc 367
 pdb|3M9U|C Chain C, Crystal Structure Of Geranylgeranyl Pyrophosphate Synthase
           From Lactobacillus Brevis Atcc 367
 pdb|3M9U|D Chain D, Crystal Structure Of Geranylgeranyl Pyrophosphate Synthase
           From Lactobacillus Brevis Atcc 367
 pdb|3PDE|A Chain A, Crystal Structure Of Geranylgeranyl Pyrophosphate Synthase
           From Lactobacillus Brevis Atcc 367 Complexed With
           Isoprenyl Diphosphate And Magnesium
 pdb|3PDE|B Chain B, Crystal Structure Of Geranylgeranyl Pyrophosphate Synthase
           From Lactobacillus Brevis Atcc 367 Complexed With
           Isoprenyl Diphosphate And Magnesium
 pdb|3PDE|C Chain C, Crystal Structure Of Geranylgeranyl Pyrophosphate Synthase
           From Lactobacillus Brevis Atcc 367 Complexed With
           Isoprenyl Diphosphate And Magnesium
 pdb|3PDE|D Chain D, Crystal Structure Of Geranylgeranyl Pyrophosphate Synthase
           From Lactobacillus Brevis Atcc 367 Complexed With
           Isoprenyl Diphosphate And Magnesium
          Length = 309

 Score = 30.0 bits (66), Expect = 0.50,   Method: Compositional matrix adjust.
 Identities = 16/51 (31%), Positives = 26/51 (50%)

Query: 65  KKDNNEKGDDAPSKAGILGNMQNLYETVKKAQMVVQVEAVRVQKELAAAEF 115
           +KD +E  +  P K G++G  Q L +T+   Q  +Q      Q++  AA F
Sbjct: 242 QKDADEAKNTYPGKLGLIGANQALIDTIHSGQAALQGLPTSTQRDDLAAFF 292


>pdb|1PUG|A Chain A, Structure Of E. Coli Ybab
 pdb|1PUG|B Chain B, Structure Of E. Coli Ybab
 pdb|1PUG|C Chain C, Structure Of E. Coli Ybab
 pdb|1PUG|D Chain D, Structure Of E. Coli Ybab
          Length = 109

 Score = 28.5 bits (62), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 4/63 (6%)

Query: 83  GNMQNLYETVKKAQMVVQVEAVRVQKELAAAEFDGYCEGELIKVTLSGNQQPVRTEITEA 142
           G + NL +  ++ Q  +Q    ++Q+E+A  E  G     L+KVT++G     R EI  +
Sbjct: 5   GGLGNLMKQAQQMQEKMQ----KMQEEIAQLEVTGESGAGLVKVTINGAHNCRRVEIDPS 60

Query: 143 AME 145
            +E
Sbjct: 61  LLE 63


  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
   0.312    0.126    0.345 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,666,788
Number of Sequences: 62578
Number of extensions: 121026
Number of successful extensions: 224
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 220
Number of HSP's gapped (non-prelim): 7
length of query: 157
length of database: 14,973,337
effective HSP length: 91
effective length of query: 66
effective length of database: 9,278,739
effective search space: 612396774
effective search space used: 612396774
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 47 (22.7 bits)