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= 011280
         (489 letters)

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

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



>pdb|2CUN|A Chain A, Crystal Structure Of Phosphoglycerate Kinase From
           Pyrococcus Horikoshii Ot3
 pdb|2CUN|B Chain B, Crystal Structure Of Phosphoglycerate Kinase From
           Pyrococcus Horikoshii Ot3
          Length = 410

 Score = 31.2 bits (69), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 20/59 (33%), Positives = 32/59 (54%), Gaps = 2/59 (3%)

Query: 36  RCPVLVFINSKSGGQLGGDLLVTYRSLLNKNQVFDVGEEAPDKALRRIYLNLETLKANG 94
           R PV   ++ K G ++  DLL   R LL++ Q+ D+G+   +K  R I +    + ANG
Sbjct: 270 RTPVDFAVDYK-GERVEIDLLSENRGLLHQYQIMDIGKRTAEK-YREILMKARIIVANG 326


>pdb|3OKG|A Chain A, Crystal Structure Of Hsds Subunit From Thermoanaerobacter
           Tengcongensis
 pdb|3OKG|B Chain B, Crystal Structure Of Hsds Subunit From Thermoanaerobacter
           Tengcongensis
          Length = 412

 Score = 29.3 bits (64), Expect = 5.6,   Method: Compositional matrix adjust.
 Identities = 18/43 (41%), Positives = 21/43 (48%), Gaps = 4/43 (9%)

Query: 111 GGDGTAGWL---LGVVCDLKLSHPPPIATVPLGTGNNLPFAFG 150
           G D   GW    LG VCD+ +   PP +T     GN LPF  G
Sbjct: 221 GADLPPGWRWVRLGEVCDIIMGQSPPSSTYNF-EGNGLPFFQG 262


>pdb|3MA9|L Chain L, Crystal Structure Of Gp41 Derived Protein Complexed With
           Fab 8066
 pdb|3MAC|L Chain L, Crystal Structure Of Gp41-Derived Protein Complexed With
           Fab 8062
          Length = 213

 Score = 28.9 bits (63), Expect = 6.4,   Method: Compositional matrix adjust.
 Identities = 13/40 (32%), Positives = 24/40 (60%), Gaps = 7/40 (17%)

Query: 125 DLKLSHPPPIATVPLGT------GNNLPFAFG-WGKKNPG 157
           D++L+ PP ++ VP  T      G+N+P+ +  W ++ PG
Sbjct: 1   DIELTQPPSVSVVPGQTARISCSGDNIPYEYASWYQQKPG 40


>pdb|1UDI|E Chain E, Nucleotide Mimicry In The Crystal Structure Of The Uracil-
           Dna Glycosylase-Uracil Glycosylase Inhibitor Protein
           Complex
 pdb|1LAU|E Chain E, Uracil-Dna Glycosylase
 pdb|1UDG|A Chain A, The Structural Basis Of Specific Base Excision Repair By
           Uracil-Dna Glycosylase
 pdb|1UDH|A Chain A, The Structural Basis Of Specific Base Excision Repair By
           Uracil-Dna Glycosylase
          Length = 244

 Score = 28.5 bits (62), Expect = 8.4,   Method: Compositional matrix adjust.
 Identities = 12/20 (60%), Positives = 14/20 (70%)

Query: 122 VVCDLKLSHPPPIATVPLGT 141
           V C LK SHP P++ VP GT
Sbjct: 202 VHCVLKFSHPSPLSKVPFGT 221


  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    0.136    0.427 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,984,307
Number of Sequences: 62578
Number of extensions: 707071
Number of successful extensions: 1293
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1290
Number of HSP's gapped (non-prelim): 7
length of query: 489
length of database: 14,973,337
effective HSP length: 103
effective length of query: 386
effective length of database: 8,527,803
effective search space: 3291731958
effective search space used: 3291731958
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)