The clerk opened fire during a robbery Wednesday night at Mike's Liquor Store in the 8700 block of MLK Boulevard near Reed.
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Houston police said that at least two armed suspects went into the store, where two employees were working at the time.
One of the employees had a concealed handgun license and got into a shootout with the suspects.
The robbery suspect who was shot managed to escape, but died a short time later just south of the store.
The suspect's body was found by police, who put two and two together after receiving a call for a robbery at the store.
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The employees were not injured.
Officers are searching for the second suspect, who is believed to have fled into a nearby neighborhood.
Police are asking people who live in the area to be on the lookout.