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= psy9877
         (1447 letters)

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

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



>pdb|2EC7|A Chain A, Solution Structure Of Human Immunodificiency Virus Type-2
           Nucleocapsid Protein
          Length = 49

 Score = 36.6 bits (83), Expect = 0.11,   Method: Composition-based stats.
 Identities = 18/48 (37%), Positives = 26/48 (54%), Gaps = 5/48 (10%)

Query: 257 SQRQDIIRNKQVCYACLKFGHRVSRCRTKSRLKCEKCG-SRHLTILCP 303
           +Q++ +IR    C+ C K GH   +CR   R  C KCG + H+   CP
Sbjct: 1   AQQRKVIR----CWNCGKEGHSARQCRAPRRQGCWKCGKTGHVMAKCP 44


>pdb|2A51|A Chain A, Structure Of The (13-51) Domain Of The Nucleocapsid
           Protein Ncp8 From Sivlhoest
          Length = 39

 Score = 31.6 bits (70), Expect = 3.2,   Method: Composition-based stats.
 Identities = 14/37 (37%), Positives = 18/37 (48%), Gaps = 1/37 (2%)

Query: 269 CYACLKFGHRVSRCRTKSRLKCEKCGSR-HLTILCPR 304
           C+ C K GH    CR   +  C  CGS+ H    CP+
Sbjct: 3   CFNCGKPGHTARMCRQPRQEGCWNCGSKEHRFAQCPK 39


>pdb|2UVP|A Chain A, Crystal Structure Of Hoba (Hp1230)from Helicobacter Pylori
          Length = 186

 Score = 31.2 bits (69), Expect = 4.5,   Method: Composition-based stats.
 Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 8/77 (10%)

Query: 330 VKIRGKDGKQDKLARLMIDTG---SQQSYVLEQTMNSLSYTPITKQSMRHALFGGSI--- 383
           V IR      D +   + D G   +QQS  LE  +   SY  +  Q++ H L GGS+   
Sbjct: 2   VSIRSMKNFYDWIKEFIRDQGEFIAQQSGWLE--LERSSYAKLIAQTISHVLNGGSLLVS 59

Query: 384 TDAMDHNLFKIVISNLD 400
            D+  H     ++SNL+
Sbjct: 60  ADSSRHWFLNYILSNLN 76


>pdb|2UVP|B Chain B, Crystal Structure Of Hoba (Hp1230)from Helicobacter Pylori
 pdb|2UVP|C Chain C, Crystal Structure Of Hoba (Hp1230)from Helicobacter Pylori
 pdb|2UVP|D Chain D, Crystal Structure Of Hoba (Hp1230)from Helicobacter Pylori
          Length = 186

 Score = 30.8 bits (68), Expect = 5.2,   Method: Composition-based stats.
 Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 8/77 (10%)

Query: 330 VKIRGKDGKQDKLARLMIDTG---SQQSYVLEQTMNSLSYTPITKQSMRHALFGGSI--- 383
           V IR      D +   + D G   +QQS  LE  +   SY  +  Q++ H L GGS+   
Sbjct: 2   VSIRSMKNFYDWIKEFVRDQGEFIAQQSGWLE--LERSSYAKLIAQTISHVLNGGSLLVS 59

Query: 384 TDAMDHNLFKIVISNLD 400
            D+  H     ++SNL+
Sbjct: 60  ADSSRHWFLNYILSNLN 76


  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    0.133    0.404 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 41,561,509
Number of Sequences: 62578
Number of extensions: 1689361
Number of successful extensions: 3905
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: 3903
Number of HSP's gapped (non-prelim): 7
length of query: 1447
length of database: 14,973,337
effective HSP length: 111
effective length of query: 1336
effective length of database: 8,027,179
effective search space: 10724311144
effective search space used: 10724311144
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 58 (26.9 bits)