Deck gear boxes transmit the power from the mid-PTO to the mower deck blades. Often times this requires a 90 degree turn of the power. These gear boxes take an extreme amount of abuse. 

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Below is a set of three videos I made while rebuilding a gear box. Part number MIA12567. 

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John Deere deck gear boxes have many part numbers - most but not all of the garden tractor gear boxes all substitute to the most recent AUC10298.

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Generally these gear boxes are considered a whole component with limited rebuild options. Even within the parts diagram aside from the seals and the two vertical shaft bearing there is a limited number of parts that can be ordered from John Deere (as shown below, in the parts diagram). The most likely reason for this is the shims and tension required for the input shaft. Watching the videos may explain this issues some more.