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I'm working on my first sequencing related project and I'm trying to find proteins with a specific PFAM ID (PF11999). The project is called "MMETSP", I searched the annotations for that ID, identified signal peptides using SignalP and their target locations with a tool called MultiLoc2 (I was looking for extracellular targets only).

Out of the very few sequences that where left after all this filtering, none of the DNA-bits started with the basepair-code "ATG", for Methionine. How can this be?

I used the shell to calculate that only 1,83% of all the sequences start with ATG.
Any ideas on this?

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    $\begingroup$ Exactly what sequences are you searching? $\endgroup$ – Devon Ryan Jul 28 '16 at 12:43
  • $\begingroup$ I'm looking for Antifreeze proteins (PF11999) in marine diatoms, that are located in the extracellular region. Using the cleavage site provided by SignalP I can isolate the targeting peptide. However, these peptides seem to have no "start"-code. I got the sequences by looking up the protein IDs in the fasta files that I got from the annotation-search. $\endgroup$ – Birg3r Jul 28 '16 at 14:17
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    $\begingroup$ You're just looking at the cleaved peptide sequence then? There's no reason those need to start with a methionine unless they're type-I and don't receive further N-terminal processing. $\endgroup$ – Devon Ryan Jul 28 '16 at 18:57
  • $\begingroup$ Well, I'm looking at the DNA coding the peptide. The peptide is located in front of the "maternal" protein, so the ORF should start with a methionine, shouldn't it? $\endgroup$ – Birg3r Jul 29 '16 at 8:28
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    $\begingroup$ If there are no UTRs in this species and the CDS is annotated as full length then yes. Otherwise no. $\endgroup$ – Devon Ryan Jul 29 '16 at 12:33
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If anyone stumbles across this question, I found out what the problem was in the end:
contrarily to my assumption that the DNA sequences where all in proper 5'3'-direction, it turned out that we found the exact ORF on the complementary strand in the other direction and who knows where else. Luckily, the MMETSP-Data also featured a /pep directory, in which the needed sequences where found in a clean version. Thanks for reading and good Luck.

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