Update: This is what i get after BLAST! 

Thank you very much :)

I am unable to understand your point! Here is the whole genome sequence link

http://www.ncbi.nlm.nih.gov/nuccore/489481747?report=fasta

I tried to extract the 16s rRNA information from this link previously. Can you tell me how can I get the 16s rRNA sequence from the whole genome data? 

Thanks

I understand your point now. Yes, it is just first contig. There are 28 more. Here is the complete information on WGS.

http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=APBN&display=contigs&search=APBN01000000

So, my question is, how can I get the 16S from all these contigs information? 

Thanks

Blast against the Ribosomal Database Project. You are right that sometimes it is not easy to extract 16S rDNA genes from NCBI. 

http://rdp.cme.msu.edu/seqmatch/seqmatch_intro.jsp

Hi Muhammad,

In the your alignment, You are looking at description tab. Go to the alignment tab. then scroll down to go to match with your sequence you will find a link to GenBank entry for that range from the whole genome sequence. shown below in bold face.

Hope this helps.

Plus/Plus Range 1: 2299023 to 2300546 GenBank

GraphicsNext MatchPrevious Match

Query 1 TATAGAGTTTGATCCTGGCTCAGATTGAACGCTAGCGGCATGCTTTACACATGCAAGTCG 60 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 2299023 TATAGAGTTTGATCCTGGCTCAGATTGAACGCTAGCGGCATGCTTTACACATGCAAGTCG 2299082