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= 000259
         (1771 letters)

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

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



>pdb|2F7F|A Chain A, Crystal Structure Of Enterococcus Faecalis Putative
           Nicotinate Phosphoribosyltransferase, New York
           Structural Genomics Consortium
          Length = 494

 Score = 35.4 bits (80), Expect = 0.31,   Method: Compositional matrix adjust.
 Identities = 35/134 (26%), Positives = 56/134 (41%), Gaps = 28/134 (20%)

Query: 142 KSNIWLSDRSSDQRRELLYVSLYLLIWGEAANLRFMPECLCYIFHNMAMELNKILEDYID 201
           K  +W   R SD++ E  YV+L    W E        E   Y+FH +   +NK + D+  
Sbjct: 362 KKQVWRITRKSDKKSEGDYVTL----WNEDPR----QEEEIYMFHPVHTFINKYVRDF-- 411

Query: 202 ENTGQPVMPSISGENAFLNCVVKPIYETVKAEVESSKNGSAPHYAWRNYDDINEYFWSKR 261
               +PV+  I  E        K +YE    +           YA  N D ++E +  KR
Sbjct: 412 --EARPVLQDIFVEG-------KRVYELPTLD-------EIKQYAKENLDSLHEEY--KR 453

Query: 262 CFQKLKWPIDVGSN 275
                K+P+D+ ++
Sbjct: 454 DLNPQKYPVDLSTD 467


>pdb|2ZNL|A Chain A, Crystal Structure Of Pa-Pb1 Complex Form Influenza Virus Rna
            Polymerase
          Length = 478

 Score = 32.0 bits (71), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 18/85 (21%), Positives = 43/85 (50%), Gaps = 3/85 (3%)

Query: 1118 LVKYDKQLEKEVEIYRVKLPGPLKLGEGKPENQNHAFIFTRGDAVQTIDMNQDNYFEEAL 1177
            L +  K++   +E +    P PL+L  G P +Q   F+    DA++ + +   ++  E +
Sbjct: 8    LSQMSKEVNARIEPFLKTTPRPLRLPNGPPCSQRSKFLLM--DALK-LSIEDPSHEGEGI 64

Query: 1178 KMRNLLEEYRHYYGIRKPTILGVRE 1202
             + + ++  R ++G ++P ++   E
Sbjct: 65   PLYDAIKCMRTFFGWKEPNVVKPHE 89


  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    0.139    0.430 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 49,605,647
Number of Sequences: 62578
Number of extensions: 2011663
Number of successful extensions: 4918
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: 4918
Number of HSP's gapped (non-prelim): 3
length of query: 1771
length of database: 14,973,337
effective HSP length: 113
effective length of query: 1658
effective length of database: 7,902,023
effective search space: 13101554134
effective search space used: 13101554134
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 59 (27.3 bits)