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= 036263
         (305 letters)

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

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



>pdb|2GIB|A Chain A, Crystal Structure Of The Sars Coronavirus Nucleocapsid
           Protein Dimerization Domain
 pdb|2GIB|B Chain B, Crystal Structure Of The Sars Coronavirus Nucleocapsid
           Protein Dimerization Domain
          Length = 103

 Score = 30.4 bits (67), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 21/82 (25%), Positives = 30/82 (36%), Gaps = 4/82 (4%)

Query: 137 FVKRDYFEEALEYFRVMQISGVEPDYLTIISVLNVCANVRTLGIGLWMHRYVPKQD---- 192
           F  +D   +  +Y    QI+   P       +  +   V   G  L  H  +   D    
Sbjct: 20  FGDQDLIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYHGAIKLDDKDPQ 79

Query: 193 FKDNVRVCNTLMDVYSRFGCIE 214
           FKDNV + N  +D Y  F   E
Sbjct: 80  FKDNVILLNKHIDAYKTFPPTE 101


>pdb|2CJR|A Chain A, Crystal Structure Of Oligomerization Domain Of Sars
           Coronavirus Nucleocapsid Protein.
 pdb|2CJR|B Chain B, Crystal Structure Of Oligomerization Domain Of Sars
           Coronavirus Nucleocapsid Protein.
 pdb|2CJR|C Chain C, Crystal Structure Of Oligomerization Domain Of Sars
           Coronavirus Nucleocapsid Protein.
 pdb|2CJR|D Chain D, Crystal Structure Of Oligomerization Domain Of Sars
           Coronavirus Nucleocapsid Protein.
 pdb|2CJR|E Chain E, Crystal Structure Of Oligomerization Domain Of Sars
           Coronavirus Nucleocapsid Protein.
 pdb|2CJR|F Chain F, Crystal Structure Of Oligomerization Domain Of Sars
           Coronavirus Nucleocapsid Protein.
 pdb|2CJR|G Chain G, Crystal Structure Of Oligomerization Domain Of Sars
           Coronavirus Nucleocapsid Protein.
 pdb|2CJR|H Chain H, Crystal Structure Of Oligomerization Domain Of Sars
           Coronavirus Nucleocapsid Protein.
 pdb|2JW8|A Chain A, Solution Structure Of Stereo-Array Isotope Labelled (Sail)
           C-Terminal Dimerization Domain Of Sars Coronavirus
           Nucleocapsid Protein
 pdb|2JW8|B Chain B, Solution Structure Of Stereo-Array Isotope Labelled (Sail)
           C-Terminal Dimerization Domain Of Sars Coronavirus
           Nucleocapsid Protein
          Length = 128

 Score = 28.9 bits (63), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 20/78 (25%), Positives = 29/78 (37%), Gaps = 4/78 (5%)

Query: 137 FVKRDYFEEALEYFRVMQISGVEPDYLTIISVLNVCANVRTLGIGLWMHRYVPKQD---- 192
           F  +D   +  +Y    QI+   P       +  +   V   G  L  H  +   D    
Sbjct: 50  FGDQDLIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYHGAIKLDDKDPQ 109

Query: 193 FKDNVRVCNTLMDVYSRF 210
           FKDNV + N  +D Y  F
Sbjct: 110 FKDNVILLNKHIDAYKTF 127


>pdb|3Q8N|A Chain A, Crystal Structure Of 4-Aminobutyrate Transaminase From
           Mycobacterium Smegmatis
 pdb|3Q8N|B Chain B, Crystal Structure Of 4-Aminobutyrate Transaminase From
           Mycobacterium Smegmatis
 pdb|3Q8N|C Chain C, Crystal Structure Of 4-Aminobutyrate Transaminase From
           Mycobacterium Smegmatis
 pdb|3Q8N|D Chain D, Crystal Structure Of 4-Aminobutyrate Transaminase From
           Mycobacterium Smegmatis
          Length = 453

 Score = 28.5 bits (62), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 19/51 (37%), Positives = 24/51 (47%), Gaps = 10/51 (19%)

Query: 241 NGFVGEALEYFNLMQK------GVFKTDEV----SFTGALTACSHAGLIED 281
            GFV  A  +   +QK       VF  DEV    + TGAL AC H  ++ D
Sbjct: 241 GGFVVPAPGFLGALQKWCTDNGAVFVADEVQTGFARTGALFACEHENVVPD 291


>pdb|1QVW|A Chain A, Crystal Structure Of The S. Cerevisiae Ydr533c Protein
 pdb|1QVW|B Chain B, Crystal Structure Of The S. Cerevisiae Ydr533c Protein
          Length = 237

 Score = 27.7 bits (60), Expect = 9.4,   Method: Compositional matrix adjust.
 Identities = 19/51 (37%), Positives = 24/51 (47%), Gaps = 2/51 (3%)

Query: 228 LVSWNSIIV--GFAVNGFVGEALEYFNLMQKGVFKTDEVSFTGALTACSHA 276
           L S+N +    G     FV EAL  FN  +K  F+ D VS TG      H+
Sbjct: 10  LTSYNDVFYSDGMKTGVFVVEALHPFNTFRKEGFEVDFVSETGKFGWDEHS 60


  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
   0.326    0.138    0.426 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,746,512
Number of Sequences: 62578
Number of extensions: 332151
Number of successful extensions: 738
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 738
Number of HSP's gapped (non-prelim): 8
length of query: 305
length of database: 14,973,337
effective HSP length: 98
effective length of query: 207
effective length of database: 8,840,693
effective search space: 1830023451
effective search space used: 1830023451
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.3 bits)