I think this question is asking about how a gene that is inserted is different from the resident genes within the organism. It is an important question, but the answer is complex, so I’ll provide a starting point. I’m glad to go deeper for you if you’d like, so contact me directly or I can continue answering here on GMOAnswers.com.
First, a quick lesson in how genes work. When we think of a “gene,” this is the information that leads to a trait, PLUS the information that regulates it. All genes are composed of the same basic building blocks, adenine, thymidine, cytosine and guanine, the A,T,C and G in the genetic code. The order of A’s, T’s, G’s and C’s encodes the information to produce a trait. Again, some of the code is the information for the trait. The rest of the code simply turns it on and off.
So if you wanted to make a GE plant, like a banana that could help the developing world by producing more beta-carotene (the carrot vitamin), you might take the sequences from carrots or daffodils and place them in banana, downstream of a strong regulatory sequence that turns them on all the time. This is seriously just biological Legos.
The major production traits are glyphosate tolerance and insect resistance. In both of these cases a sequence from bacteria is added to the plant, under the control of sequences that turn them on at high levels. While these both come from bacteria, it does not matter too much. Bacteria use the same A,G,C,T code, they just have a little different hardware to process that from information to final product. It is like how your USB drive works in any computer—while Macs and PCs are different, they know how to use the same information.
So the best answer to your question is that they are the same in their composition, nothing weird or magical. They are different in that their functional units might be mixed and matched in ways that allow the trait to be expressed in ways that best support the trait. That trait might be to help the farmer use less insecticide or fuel. In the future, new technologies will help in other ways, like providing higher quality fruits and vegetables, or producing plants that can help the neediest. That’s pretty exciting, and all from the same basic code.