A CLBING BE58 OVERSHOT HIS ALT WHEN LOSS OF ACFT CTL OCCURS. ACFT WAS NEAR A TSTM AND WAS CAUGHT UP IN UPDRAFT. EVENT CREATED A POTENTIAL CONFLICT.

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DEPARTED ATHENS; TX; IFR FOR CLT. REQUESTED 17000 FT; WAS ASSIGNED TO CLB TO 16000 FT EBOUND. HEARD ATC CALLING US OUT AS TFC TO A COMMUTER FLT. I WAS NEVER GIVEN THE COMMUTER TFC CALL; AND DID NOT KNOW THEIR POS OR ALT. I ENCOUNTERED A SEVERE TSTM AHEAD AND ASKED FOR A DEV TO THE N. ATC ASKED IF I NEEDED TO GO S. I SAID 'NO; N WOULD BE FINE.' HE (ATC) APPROVED MY DEV TO THE N. ON THE DEV WE CONTINUED TO CLB TO 16000 FT. AS WE NEARED AND CIRCUMNAVED THE TSTM CELL; THE ACFT WAS CAUGHT IN A SUDDEN UPDRAFT. AS THE ACFT ASCENDED I EXERTED MAX CTL DEFLECTION AVAILABLE WITHOUT EXCEEDING THE ACFT LIMITATIONS. TURB MADE THIS DIFFICULT. AT ONE POINT MY ALTIMETER INDICATED WE WERE A LITTLE ABOVE 16300 FT. FINALLY; I WAS ABLE TO SLOW THE ACFT ENOUGH TO DROP THE GEAR; AND BEGIN THE DSCNT. AT THIS TIME I FELT THE ACFT WAS UNDER CTL AND STABLE ENOUGH FOR ME TO NOTIFY ATC THAT WE HAD EXCEEDED OUR ASSIGNED ALT. AT THE SAME TIME HOUSTON REQUESTED OUR ALT. I ANSWERED 'OUT OF 16100 FT FOR 16000 FT.' BETTER PLT/CTLR COM COULD HAVE HELPED THIS SIT. HAD I BEEN AWARE OF THE NEAR PROX OF THE COMMUTER FLT; I WOULD HAVE MADE A GREATER DEV TO THE N; OR WOULD HAVE NEGOTIATED A DIFFERENT ALT. HAD THE CTLR KNOWN HOW BAD THE WX WAS IN MY AREA HE COULD HAVE MADE OTHER DECISIONS AS WELL.