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possibly have a site not show up on SERPs for certain keywords because it is linked to from an unrelated site
I have 2 sites that are related in theme. #1 is LocationWidgets.com and #2 is Name1-Name2.com which is very focused on yellow widgets in a sub-location of website #1. They both link to each other from every page (in the menu bar). They are both number 1 in the SERPs for a number of different competitive terms (1 to 4 million results).
It makes sense that they wouldn't both rank for the same term because it would be spamming the SERPs. But as site #1 continues to grow it can't ever seem to rank for the word "yellow" because site #2 already ranks for that word. So if I try to do a page on site #1 for "yellow widgets" or "yellow doo-hickies" in different locations, Google keeps the new page at position #100. This ends up being frustrating because site #2 shows up for searches where it doesn't belong and site #1, which should show up, is locked in the SERPs between 90 and 100.
Anybody out there follow that?
Although its nice to have two sites doing well, it ends up being confusing for the user. If I were to do it over again, I would have never built site #2 and just made its topic a sub-page of site #1.
At first I was thinking that Google is acting as if your sites are one site because they are linked together from every page. But sometimes Google does show pages from the same site at the top of the SERPs for a search (when the second page is indented.)
Here's a possibility: there may be a filter keeping one of your sites from ranking well for the same words as your other site because they link to each other from every page. Not a heavy interlinking penalty, just a filter to allow only one of the heavily interlinked sites from showing well in SERPs for the same search.
I don't interlink my sites at all, so I don't have first hand experience. In my searches, though, I haven't seen two or more sites heavily interlinked together showing well in the SERPs for the same search. Maybe one of them, as in your case.
It makes sense that they wouldn't both rank for the same term because it would be spamming the SERPs.
I suppose if the pages were identical, it would be seen as spam. Not because you happen to own both sites and that they rank well for the same term. So, if the "yellow" page on site #2 is different than the "yellow" page on site #1, you can try getting them both ranking well for "yellow" by taking out some of the interlinking. If site #1 is your main site, take out as many links as you can going from it to site #2 and leave links going from site #2 to site #1. Users at site #2 can still navigate to your main site.
Yes, it seems to behave as though Google considers them the same site and automatically applies some filter which is okay with me. It's just that the filter doesn't quite get it right. It might be nice if Google did show the second site indented, but I've never seen that.