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= psy8283
         (285 letters)

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

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



>pdb|2LKI|A Chain A, Solution Nmr Structure Of Holo Acyl Carrier Protein Ne2163
           From Nitrosomonas Europaea. Northeast Structural
           Genomics Consortium Target Net1
          Length = 105

 Score = 32.0 bits (71), Expect = 0.40,   Method: Compositional matrix adjust.
 Identities = 17/42 (40%), Positives = 24/42 (57%)

Query: 95  DLPEDNREAAVNAITLPEVFHDFETTMPEINSVQFEPVKSLA 136
           ++PE +  A VN IT  E + DF     EI++  FE + SLA
Sbjct: 55  NIPELDSMAVVNVITALEEYFDFSVDDDEISAQTFETLGSLA 96


>pdb|3TDV|A Chain A, Structure Of The Gdp Complex Of Wild-Type Aminoglycoside
           2'- Phosphotransferase-Iiia
 pdb|3TDV|B Chain B, Structure Of The Gdp Complex Of Wild-Type Aminoglycoside
           2'- Phosphotransferase-Iiia
          Length = 306

 Score = 30.0 bits (66), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 18/46 (39%), Positives = 26/46 (56%), Gaps = 2/46 (4%)

Query: 73  YLLADCNEAFVKIKMAFRPGMVDLPEDNREAAVNAITLPEVFHDFE 118
           YLL DC E F +  MA+R G VDL    R+ ++  +T  +V +  E
Sbjct: 233 YLLEDCGELFTRQVMAYR-GEVDLDTHIRKVSL-FVTFDQVSYLLE 276


>pdb|3TDW|A Chain A, The Gdp Complex Of The Aminoglycoside
           2'-Phosphotransfere-Iiia F108l Mutant
          Length = 306

 Score = 30.0 bits (66), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 18/46 (39%), Positives = 26/46 (56%), Gaps = 2/46 (4%)

Query: 73  YLLADCNEAFVKIKMAFRPGMVDLPEDNREAAVNAITLPEVFHDFE 118
           YLL DC E F +  MA+R G VDL    R+ ++  +T  +V +  E
Sbjct: 233 YLLEDCGELFTRQVMAYR-GEVDLDTHIRKVSL-FVTFDQVSYLLE 276


>pdb|3TB4|A Chain A, Crystal Structure Of The Isc Domain Of Vibb
          Length = 223

 Score = 28.1 bits (61), Expect = 5.4,   Method: Compositional matrix adjust.
 Identities = 26/87 (29%), Positives = 38/87 (43%), Gaps = 2/87 (2%)

Query: 86  KMAFRPGMVDLPEDNREAAVNAITLPEVFHDFETTMPEINSVQFEPVKSLAPPTKRL-MH 144
           K+A  P  V LP +  +  ++A     + HD +         Q EP+ SL    ++L  H
Sbjct: 5   KIASYPLPVSLPTNKVDWRIDASRAVLLIHDMQEYFVHYFDSQAEPIPSLIKHIQQLKAH 64

Query: 145 WKESGGVEKLFALPGRPIPA-RALFKD 170
            K++G      A P    PA RAL  D
Sbjct: 65  AKQAGIPVVYTAQPANQDPAERALLSD 91


  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
   0.321    0.137    0.418 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,106,632
Number of Sequences: 62578
Number of extensions: 312840
Number of successful extensions: 528
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 526
Number of HSP's gapped (non-prelim): 7
length of query: 285
length of database: 14,973,337
effective HSP length: 98
effective length of query: 187
effective length of database: 8,840,693
effective search space: 1653209591
effective search space used: 1653209591
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)