When I try to start my car it get a message that says the key is not recognized. I have the key with me and have checked the key battery and it is fine.

It sounds like your anti theft has kicked in. You should call the nearest GM dealer and see if they have a technician you can pay to have come to you and reprogram your keys and fobs with their scanners.

There's an antenna for the transponder receiver built into the key surround on the 9-5, it could have had a knock or be faulty.

On the 9-5 if the transponder stops working and you get a key not accepted message then you can override it by pushing the unlock button on the key remote with the ignition turned to on and it should let you start the car.

The key codes work in sequence. Each time you press a button on the key, it generates a new code. The car knows what code is next, and the few that come after.
If you accidentally press the button when the key is out of range of the car, the code the key sends isn't recognized by the car as "current". The next time you press it, the car does recognize it, as it's re-synchronized.
It's possible that the battery in the key is getting weak, and that is simply time-related. Car batteries have a similar lifetime. I'm a little surprised that your alternator went out, too, but that does happen.

Wait for the new key, honda is the only one that can deal with it unless you can find a lock smith that deals with those.

use a code reader to reset the CPU as the program is corrupted.

Yes the your Lexus does have a physical key slot to start the car

Car not starting or turning over indicates towards multiple possibilities. It can be issue with battery or weak battery. But if battery checks out ok, then it can be starter issue or faulty alternator or problem with low fuel pressure or no spark at spark plugs due to dirty spark plugs or faulty ignition coil or injectors getting cracked or dirty and needs to be cleaned.

To confirm the problem, the basic troubleshooting is required.

Click this link below and follow the troubleshooting:------

http://technoanswers.blogspot.in/2012/02/car-starting-issues.html

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This will help.

Thanks.

MAKE SURE YOU DONT HAVE THE WRONG KEY.TRY ANOTHER KEY.PUT KEY IN THE IGNITION SWITCH.TURN IGNITION TO THE ON POSITION.WHEN LED FLASHES TWICE THAT INDICATE KEY IS RECOGNIZED.IF KEY CODE NOT RECOGNIZED A MESSAGE ON THE TRIP COMPUTER WILL BE DISPLAYED.TO ENABLE ENGINE TO START WHEN KEY CODE NOT RECOGNIZED.SWITCH THE IGNITION ON.PRESS ANY KEY REMOTE TRANSMITTER BUTTON ONCE START THE ENGINE.IF ALL FAILS. THE KEY SWITCH TRANSPONDER FAILED OR THE KEY LOCK CYLINDER BROKEN, IMMOBILIZER MODULE FAULTY VECHICLE HAS TO BE SCANNED TO LOOK FOR FAULTY IMMOBILIZER MODULE.

seems like your key is not being recognized, possible your tumbler..the ring around your ignition switch is bad

The car is not reading the key and thinks someone is trying to steal it. Try another key or see a dealer.