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= psy6927
         (93 letters)

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

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



>pdb|1ICH|A Chain A, Solution Structure Of The Tumor Necrosis Factor
          Receptor-1 Death Domain
          Length = 112

 Score = 26.6 bits (57), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 12/24 (50%), Positives = 14/24 (58%), Gaps = 2/24 (8%)

Query: 29 DGDSQVALYWI--SSPPLRWKTFV 50
          D D    LY +  + PPLRWK FV
Sbjct: 9  DTDDPATLYAVVENVPPLRWKEFV 32


>pdb|4AY8|A Chain A, Semet-Derivative Of A Methyltransferase From M. Mazei
 pdb|4AY8|B Chain B, Semet-Derivative Of A Methyltransferase From M. Mazei
          Length = 348

 Score = 26.6 bits (57), Expect = 3.7,   Method: Composition-based stats.
 Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 9/60 (15%)

Query: 39  ISSP----PLRWKTFVANRVSKIQELVSEDKWFHVKGTENP-----ADCLSRGITPKELI 89
           ++SP    P  ++ F+ +R+ K    V+     H+ G  NP     ADC   G++ +E I
Sbjct: 213 VASPDLXSPDSFRQFLKSRLQKFASSVNSVTVLHICGNVNPILSDXADCGFEGLSVEEKI 272


>pdb|4AY7|A Chain A, Methyltransferase From Methanosarcina Mazei
 pdb|4AY7|B Chain B, Methyltransferase From Methanosarcina Mazei
          Length = 348

 Score = 26.6 bits (57), Expect = 3.7,   Method: Composition-based stats.
 Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 9/60 (15%)

Query: 39  ISSP----PLRWKTFVANRVSKIQELVSEDKWFHVKGTENP-----ADCLSRGITPKELI 89
           ++SP    P  ++ F+ +R+ K    V+     H+ G  NP     ADC   G++ +E I
Sbjct: 213 VASPDLMSPDSFRQFLKSRLQKFASSVNSVTVLHICGNVNPILSDMADCGFEGLSVEEKI 272


  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
   0.320    0.133    0.426 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,835,054
Number of Sequences: 62578
Number of extensions: 88993
Number of successful extensions: 250
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 250
Number of HSP's gapped (non-prelim): 3
length of query: 93
length of database: 14,973,337
effective HSP length: 60
effective length of query: 33
effective length of database: 11,218,657
effective search space: 370215681
effective search space used: 370215681
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: 45 (21.9 bits)