I am trying to find the full plasmid sequence for pMG101. I have been looking through other papers that have sequenced this plasmid. The GenBank access numbers I got are the following: AY009372–AY009396, ASRI00000000. However, when I go on genbank it gives me a result saying it is not there..... I am stuck and not sure how I am suppose to find this full plasmid sequence. Does anyone know another way to find it?
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2 Answers
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Looks as if you'll have to do some reconstruction work building the full sequence from the information here and elsewhere in this paper:
Nucleotide sequence accession numbers.The DDBJ/EMBL/GenBank accession numbers for the sequences reported in this paper are AB031076(the SalI-XhoI 3.0-kb fragment of pMG101), D84187(rDNA for strain S55), D86354 (rDNA for USDA 4362), D86355 (rDNA for USDA 4377), AB031077 (plasmid pMG103), and AB031078 (plasmid pMG105).
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$\begingroup$ See I do not need the whole sequence, I just need the SilR SilS and SilE, but not as an individual protein, but all together. Also what do you mean my reconstruction work, like I need to sequence it again, or need to start putting the plasmid together based off of already sequenced parts? $\endgroup$ Commented Jul 21, 2016 at 13:34
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$\begingroup$ Just from a quick skim of the paper, it seems like the information you need is all there, you just have to piece it together. $\endgroup$– iayorkCommented Jul 21, 2016 at 13:35
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$\begingroup$ So I found this: ncbi.nlm.nih.gov/nuccore/AF067954.1. This is the part of the plasmid I am looking for, however, this plasmid pMG101 was not isolated from the same bacterial strain that I am using. I am going to be doing primer design, does this matter? $\endgroup$ Commented Jul 22, 2016 at 12:08
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$\begingroup$ We have no way of telling. Primers are cheap; if you have good controls downstream, consider making the primers and seeing if they work. $\endgroup$– iayorkCommented Jul 22, 2016 at 13:58
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$\begingroup$ I just found out it is the same sequence. E. Coli J53's plasmid was derived from this bacterial plasmid. $\endgroup$ Commented Jul 28, 2016 at 13:03
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Here it is: http://www.ncbi.nlm.nih.gov/nuccore/4206623?report=graph
This is the same plasmid as in E. Coli J53. This is the newest sequence.
answered Jul 28, 2016 at 18:28