Also automatic gearboxes can change gears usually much faster than humans. Operating the clutch is hard and when not done in the correct way, letting the clutch slip too much, waste energy.
Taking this all into account, in many cases, an automatic transmission might be more efficient.
I have been driving cars with manual transmissions all my life. My current car as indicator lights telling you when to change gears up and down. I often find myself skipping gears, especially when accelerating in the city, I often skip fourth gear. The car has six gears and you should already switch to the fifth gear when driving 50Km/h. My first car only had four gears, and the fourth gear was only used when driving over sixty. If a car has more gears it also means that you have to shift more often, which might make driving less efficient in city traffic due to the many more moments you shift slightly at the wrong moment.