Engine judder under braking

I have a 1999 Mk4 petrol Golf (74000mls), went pretty good up till now, but there have been problems of late. When the car is accelerating up through the gears, everything runs smoothly. However once you start slowing down, the engine growls roughly. When the clutch is to the floor the sound diminishes, but can still be heard faintly. Seems to be especially bad from 3000-2000rpm in second and third. Any suggestions as to what the problem is?

Do you think it might be coming from the transmission?