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= psy1866
         (235 letters)

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

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



>pdb|2DF4|B Chain B, Structure Of Trna-Dependent Amidotransferase Gatcab
           Complexed With Mn2+
 pdb|2DQN|B Chain B, Structure Of Trna-Dependent Amidotransferase Gatcab
           Complexed With Asn
 pdb|2F2A|B Chain B, Structure Of Trna-Dependent Amidotransferase Gatcab
           Complexed With Gln
 pdb|2G5H|B Chain B, Structure Of Trna-Dependent Amidotransferase Gatcab
 pdb|2G5I|B Chain B, Structure Of Trna-dependent Amidotransferase Gatcab
           Complexed With Adp-alf4
 pdb|3IP4|B Chain B, The High Resolution Structure Of Gatcab
          Length = 483

 Score = 30.4 bits (67), Expect = 0.79,   Method: Compositional matrix adjust.
 Identities = 18/55 (32%), Positives = 31/55 (56%), Gaps = 2/55 (3%)

Query: 178 RALPHLEPKAQNSKKKICKDLEAVFQMSDEAVILKVKDNVHDSNLERITNKKYGR 232
           +  P L  K  N+K+ I +D   + Q+SDEA +LK  +   D+N + + + K G+
Sbjct: 388 KVFPELAAKGGNAKQ-IMED-NGLVQISDEATLLKFVNEALDNNEQSVEDYKNGK 440


  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
   0.316    0.130    0.364 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,549,792
Number of Sequences: 62578
Number of extensions: 176186
Number of successful extensions: 465
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 464
Number of HSP's gapped (non-prelim): 2
length of query: 235
length of database: 14,973,337
effective HSP length: 96
effective length of query: 139
effective length of database: 8,965,849
effective search space: 1246253011
effective search space used: 1246253011
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)