BLASTN 2.2.15 [Oct-15-2006]


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.

Query= V00339 V00339.1 E. coli operon rpoBC coding for the beta- and
beta'-subunits of RNA polymerase (genes rpoC and rpoB), and genes
rplL, rlpJ, rplA, and rplK coding for 50S ribosomal subunit proteins
L7/L12, L10, L1, and L11, respectively. (Map position 89-90 min.)
         (366 letters)

Database: all 
           884 sequences; 12,243,887 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AE008894 AE006468 |AE008894| Salmonella typhimurium LT2, section...   412   e-115
embl|AE006211|AE006211 Pasteurella multocida subsp. multocida st...    70   4e-12

>AE008894 AE006468 |AE008894| Salmonella typhimurium LT2, section 198
            of 220 of the complete genome.
          Length = 23650

 Score =  412 bits (208), Expect = e-115
 Identities = 229/236 (97%)
 Strand = Plus / Plus

                                                                        
Query: 131  gcccggttgaagctgctgaagaaaaaactgaattcgacgtaattctgaaagctgctggcg 190
            |||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2366 gcccggctgaagctgctgaagaaaaaactgaattcgacgtaattctgaaagctgctggcg 2425

                                                                        
Query: 191  ctaacaaagttgctgttatcaaagcagtacgtggcgcaactggcctgggtctgaaagaag 250
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2426 ctaacaaagttgctgttatcaaagcagtacgtggcgcaactggcctgggtctgaaagaag 2485

                                                                        
Query: 251  ctaaagacttggtagaatctgcaccggctgctctgaaagaaggcgtgagcaaagacgacg 310
            |||||||| ||||||||||||| ||||| |||||||||||||||||||||||||| ||||
Sbjct: 2486 ctaaagacctggtagaatctgctccggccgctctgaaagaaggcgtgagcaaagatgacg 2545

                                                                    
Query: 311  cagaagcactgaaaaaagctctggaagaagctggcgctgaagttgaagttaaataa 366
            | ||||||||||||||| ||||||||||||||||||||||||||||||||||||||
Sbjct: 2546 ctgaagcactgaaaaaatctctggaagaagctggcgctgaagttgaagttaaataa 2601



 Score =  163 bits (82), Expect = 4e-40
 Identities = 97/102 (95%)
 Strand = Plus / Plus

                                                                        
Query: 1    atgtctatcactaaagatcaaatcattgaagcagttgcagctatgtctgtaatggacgtt 60
            |||||||||||||||||||||||||||||||||||  | |||||||| ||||||||||||
Sbjct: 2236 atgtctatcactaaagatcaaatcattgaagcagtatccgctatgtccgtaatggacgtt 2295

                                                      
Query: 61   gtagaactgatctctgcaatggaagaaaaattcggtgtttcc 102
            ||||||||||| ||||||||||||||||||||||||||||||
Sbjct: 2296 gtagaactgatttctgcaatggaagaaaaattcggtgtttcc 2337


>embl|AE006211|AE006211 Pasteurella multocida subsp. multocida str.
            Pm70 section 178 of 204 of the complete genome.
          Length = 10859

 Score = 69.9 bits (35), Expect = 4e-12
 Identities = 110/135 (81%)
 Strand = Plus / Minus

                                                                        
Query: 138  tgaagctgctgaagaaaaaactgaattcgacgtaattctgaaagctgctggcgctaacaa 197
            |||||| |||||||| |||||||||||||||||| | ||   ||  || || || |||||
Sbjct: 4617 tgaagcagctgaagagaaaactgaattcgacgtagtacttgcaggcgcaggtgcgaacaa 4558

                                                                        
Query: 198  agttgctgttatcaaagcagtacgtggcgcaactggcctgggtctgaaagaagctaaaga 257
            |||||| || |||||||| |||||||| ||||||||  | ||  | |||||||| |||||
Sbjct: 4557 agttgcagtaatcaaagcggtacgtggtgcaactggtttaggcttaaaagaagcgaaaga 4498

                           
Query: 258  cttggtagaatctgc 272
            ||| || ||||||||
Sbjct: 4497 cttagttgaatctgc 4483



 Score = 42.1 bits (21), Expect = 9e-04
 Identities = 36/41 (87%)
 Strand = Plus / Minus

                                                     
Query: 61   gtagaactgatctctgcaatggaagaaaaattcggtgtttc 101
            |||||| | ||| |||| |||||||||||||| ||||||||
Sbjct: 4697 gtagaattaatcgctgcgatggaagaaaaatttggtgtttc 4657


  Database: all
    Posted date:  Oct 28, 2008 10:42 PM
  Number of letters in database: 12,243,887
  Number of sequences in database:  884
  
Lambda     K      H
    1.37    0.711     1.31 

Gapped
Lambda     K      H
    1.37    0.711     1.31 


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Sequences: 884
Number of Hits to DB: 47,271
Number of extensions: 3044
Number of successful extensions: 68
Number of sequences better than 1.0e-03: 2
Number of HSP's gapped: 68
Number of HSP's successfully gapped: 5
Length of query: 366
Length of database: 12,243,887
Length adjustment: 16
Effective length of query: 350
Effective length of database: 12,229,743
Effective search space: 4280410050
Effective search space used: 4280410050
X1: 11 (21.8 bits)
X2: 15 (29.7 bits)
X3: 25 (49.6 bits)
S1: 14 (28.2 bits)
S2: 21 (42.1 bits)