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A protein that catalyzes one reaction can theoretically be modified by mutations and natural selection and eventually catalyze another reaction completely unrelated to the original. Has this been observed, documented, or at least postulated to be where a certain protein(s) came from?

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What do you mean with "in real time"? Sequencing an organisms, adding an evolutionary pressure, sequencing again and suddenly finding a new protein? – Michael Kuhn Sep 13 '12 at 14:33
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The “real time” requirement is an incompatible criterion with the rest. It’s designed to make this question essentially unanswerable. – Konrad Rudolph Sep 13 '12 at 15:34
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Mutation of a (duplicated) existing protein is the usual way a new protein evolves. – Mechanical snail Sep 16 '12 at 22:37
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This sounds dangerously close to the fundamental biblical literalist Ken Ham's distinction between "Historical" versus "Observable" knowledge, which is utter tripe (refer to crime scene analogy). Especially with the odd parameter that "homologs don't count". As @KonradRudolph eluded to, this question is designed to be unanswerable, but fortunately, the more patient users on this site have provided awesome answers. – James Dec 16 '15 at 12:48
    
@James I apologize for the poor quality of the original question. I was fresh off a heated debate when I asked this question. I have modified it to better reflect my ignorance seeking understanding. – Dale Dec 17 '15 at 6:47

From the following free review:

Here we review some of the successful strategies in creating protein diversity and the more recent progress in directed protein evolution in a wide range of scientific disciplines and its impacts in chemical, pharmaceutical, and agricultural sciences.

Quoting three examples, but the article has much more:

Directed evolution has been successfully applied to DNA polymerase for enhanced activity (233) and conversion to an efficient RNA polymerase (232, 333).

Naumann and Reznikoff (216) used directed evolution to generate a mutated Tn5 bacterial transposase that could function on transposons with mutated end binding sequences.

Organophosphate-degrading enzymes have been evolved and selected for broadened substrate specificity (53, 335). Broadened substrate specificity of a biphenyl dioxygenase has also been achieved (33, 87, 164, 291). Efforts in cleaning underground water contamination prompted the evolution of an enzyme for chlorinated ethene degradation (41).

L. Yuan, I. Kurek et al: Laboratory-directed protein evolution. In: Microbiology and molecular biology reviews : MMBR. 69, 3, September 2005, 373–392. doi:10.1128/MMBR.69.3.373-392.2005. PMID 16148303. PMC 1197809.

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Assuming that the OP was really interested in "natural selection" I guess these don't provide an answer. Of course, in the broader sense, human activity could be deemed to be an agent of natural selection. – Alan Boyd Sep 13 '12 at 14:17
    
These are fascinating modifications of proteins. I was hoping for something more drastic than modified binding specificity and catalytic efficiency. Has there been a change in function from one reaction to a completely unrelated one? – Dale Dec 17 '15 at 6:52

How about EWS-FLI1 and other oncofusion proteins?

One could argue that cancer progression is as close to viewing "evolution in real time" (as you say) as possible.

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how was this a new protein from scratch? thnx – r2d2 Apr 28 '15 at 10:38
    
Oncofusion is very similar to homologues, especially when there is not modification of function. Your link on "EWS-FLI1" explains that a virus causes a cancer by modifying gene regulation, which is a change in DNA sequence not Protein amino acid sequence. I don't see how your answer addresses a change in reaction catalyzed. – Dale Dec 17 '15 at 6:34

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