Combine 2 Motifs?

[asusc...@gmail.com]

The MEME program has successfully found my OPR motif, but it has separated the motif into two.  Note Motif #1 and Motif #2: http://meme-suite.org/opal-jobs/appMEME_4.11.01452211932326-1646719899/meme.html

If you look in the middle of these two motifs, you can see the "LWALA" that is the most notable feature in this particular highly divergent motif.  (I'm using a PPR protein, MCA1, for comparison, which is motif 2.)

Is there any way to convince the program to make these two motifs that it has found into one motif through the settings?

In order to find the OPRs at all, I have to make sure to change the following settings:
Motif Site Distribution ANR: Any number of sites per sequence
Minimum Motif Width 28

Sorry, I'm a biologist by training, and I've stared at these sequences for so long that I can spot them visually when I work with the individual proteins, but I have a hard time convincing computer programs that they are there. Personally, I think that it's because mostly what we are seeing is an alpha helix that was highly repetitious originally, but has since degenerated.  But that's just my personal favorite hypothesis at the moment. Any help would be appreciated.

[CharlesEGrant]

Two things to keep in mind First, if you ask MEME to find 3  motifs, it will do its best to find 3 motifs. MEME will keep looking for motifs until if finds the number of motifs you requested or it reaches the running time limit. Second, MEME is a greedy algorithm. As soon as it has enough evidence to report a motif it will do so, and then begin looking for other motifs. As you say it seem likely that motif 1 and motif 3 really represent the same underlying motif, so the trick will be to increase the amount of evidence the MEME has to find before reporting a motif. Under the "Advanced options" settings, try increasing the minimum number of sites that must be identified as instances of the motif. You'll also have to increase the maximum number of sites that will be used, since the max has to be greater than the min. If you set the min sites to 70 and the max sites to 100, you should get 1 highly significant motif, and the remaining motifs MEME finds will be not at all significant.