BLASTP 2.2.1 [Apr-13-2001]


Reference:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer, 
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.

Query= gi|15646056|ref|NP_208238.1| ribosomal protein L34
(rpl34) [Helicobacter pylori 26695]
         (44 letters)

Database: /var/www/html/HP/blast_new/blast/db/pdbaa
           13,198 sequences; 2,899,336 total letters

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

pdb|1LNR|2  Chain 2, Crystal Structure Of The Large Ribosoma...    63  8e-12
pdb|1LNR|M  Chain M, Crystal Structure Of The Large Ribosoma...    23  9.2

>pdb|1LNR|2 Chain 2, Crystal Structure Of The Large Ribosomal Subunit From
          Deinococcus Radiodurans
          Length = 47

 Score = 62.8 bits (151), Expect = 8e-12
 Identities = 28/44 (63%), Positives = 35/44 (78%)

Query: 1  MKRTYQPHNTPRKRTHGFLVRMKTKNGRKVINARRAKGRKKLSV 44
          MKRTYQP+N  R +THGF  RMKTK+GR ++  RRAKGR +L+V
Sbjct: 1  MKRTYQPNNRKRAKTHGFRARMKTKSGRNILARRRAKGRHQLTV 44



>pdb|1LNR|M Chain M, Crystal Structure Of The Large Ribosomal Subunit From
          Deinococcus Radiodurans
          Length = 113

 Score = 22.7 bits (47), Expect = 9.2
 Identities = 11/25 (44%), Positives = 14/25 (56%)

Query: 20 VRMKTKNGRKVINARRAKGRKKLSV 44
          +R K +  RKV     A GR +LSV
Sbjct: 6  IRRKLRTRRKVRTTTAASGRLRLSV 30



  Database: /var/www/html/HP/blast_new/blast/db/pdbaa
    Posted date:  Dec 20, 2002 11:08 AM
  Number of letters in database: 2,899,336
  Number of sequences in database:  13,198
  
Lambda     K      H
   0.322    0.133    0.383 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 235,677
Number of Sequences: 13198
Number of extensions: 5105
Number of successful extensions: 13
Number of sequences better than 10.0: 2
Number of HSP's better than 10.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 11
Number of HSP's gapped (non-prelim): 2
length of query: 44
length of database: 2,899,336
effective HSP length: 20
effective length of query: 24
effective length of database: 2,635,376
effective search space: 63249024
effective search space used: 63249024
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: 47 (22.7 bits)