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= 039428
         (335 letters)

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

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



>pdb|1UI6|A Chain A, Crystal Structure Of Gamma-Butyrolactone Receptor
           (Arpa-Like Protein)
 pdb|1UI6|B Chain B, Crystal Structure Of Gamma-Butyrolactone Receptor
           (Arpa-Like Protein)
          Length = 215

 Score = 29.6 bits (65), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 18/75 (24%), Positives = 33/75 (44%), Gaps = 4/75 (5%)

Query: 133 YDLSTWKRLFLTQLSGKSEEKSTADDIAVDAEGNAYVTDVVSSKIWKVGVEGQLLSIIRS 192
           +  + W+ +  ++L     +     DI VD+  +  V  VV +++    V G L    R 
Sbjct: 122 HPFTEWREIATSRLLDAVRQSDVHQDIDVDSVAHTLVCSVVGTRV----VGGTLEPAGRE 177

Query: 193 PLFTAKEWYKNVFGL 207
           P   A+ WY  + G+
Sbjct: 178 PRRLAEMWYILIRGM 192


>pdb|1UI5|A Chain A, Crystal Structure Of Gamma-Butyrolactone Receptor (Arpa
           Like Protein)
 pdb|1UI5|B Chain B, Crystal Structure Of Gamma-Butyrolactone Receptor (Arpa
           Like Protein)
          Length = 215

 Score = 29.3 bits (64), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 18/74 (24%), Positives = 32/74 (43%), Gaps = 4/74 (5%)

Query: 133 YDLSTWKRLFLTQLSGKSEEKSTADDIAVDAEGNAYVTDVVSSKIWKVGVEGQLLSIIRS 192
           +  + W+ +  ++L     +     DI VD+  +  V  VV +++    V G L    R 
Sbjct: 122 HPFTEWREIATSRLLDAVRQSDVHQDIDVDSVAHTLVCSVVGTRV----VGGTLEPAGRE 177

Query: 193 PLFTAKEWYKNVFG 206
           P   A+ WY  + G
Sbjct: 178 PRRLAEXWYILIRG 191


>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
 pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
          Length = 115

 Score = 28.9 bits (63), Expect = 4.5,   Method: Compositional matrix adjust.
 Identities = 18/56 (32%), Positives = 32/56 (57%), Gaps = 7/56 (12%)

Query: 196 TAKEWYKNVFGLNGIVYHPDGF------LIVIHMCSGNLF-KIDIRKEEEEVKLIE 244
           TA   Y+++F     V H  GF      L+V++  +   F K+D +K+EE++KL++
Sbjct: 49  TAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLLK 104


>pdb|1RWI|B Chain B, Extracellular Domain Of Mycobacterium Tuberculosis Pknd
 pdb|1RWI|A Chain A, Extracellular Domain Of Mycobacterium Tuberculosis Pknd
 pdb|1RWL|A Chain A, Extracellular Domain Of Mycobacterium Tuberculosis Pknd
          Length = 270

 Score = 28.1 bits (61), Expect = 7.3,   Method: Compositional matrix adjust.
 Identities = 12/27 (44%), Positives = 18/27 (66%)

Query: 157 DDIAVDAEGNAYVTDVVSSKIWKVGVE 183
           D +AVD  GN YVTD  ++++ K+  E
Sbjct: 153 DGVAVDNSGNVYVTDTDNNRVVKLEAE 179


  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
   0.319    0.135    0.406 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,535,397
Number of Sequences: 62578
Number of extensions: 306593
Number of successful extensions: 664
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 659
Number of HSP's gapped (non-prelim): 11
length of query: 335
length of database: 14,973,337
effective HSP length: 99
effective length of query: 236
effective length of database: 8,778,115
effective search space: 2071635140
effective search space used: 2071635140
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: 52 (24.6 bits)