It had been nine months since Dillon Gee climbed a major league mound and pitched in a game that counted.

The Mets starter’s first outing was positive in every category except the win/loss one.

Gee pitched 6 1/3 innings, allowing one run on three hits with four strikeouts and three walks in a 2-1 loss to the Padres. He pitched well enough to win but the Mets’ bats went cold after scoring 19 runs in the first two games of the season. It was Gee’s first outing since a blood clot was discovered in his right shoulder last July, which required surgery on an artery.

“I put it behind me a long time ago, but it definitely feels nice to get out there and get back in the regular season and get back on a big-league mound,” Gee said. “It’s a turning point and hopefully I can keep building from there.”

The Mets need him to. With starters Johan Santana and Shaun Marcum sidelined by injuries, the Mets are relying on Gee to be a solid No. 3 starter behind Jon Niese and Matt Harvey. Gee did not allow a hit yesterday through the first three innings, despite struggling with his command.

“Nothing really felt that great, but getting that competitiveness back and figuring out how to keep people out when you’re not feeling good,” Gee said. “I think I did a good job of battling and just staying in there and making decent pitches when I had to. I was able to minimize the damage.”

The Padres broke through with a Mark Kotsay base hit in the fourth that was just out of the reach of Mets shortstop Ruben Tejada and fell into short left field. Kotsay later scored on a Jedd Gyorko double that gave San Diego a 1-0 lead.

Gee threw 93 pitches before being pulled in the seventh after hitting Cameron Maybin with a pitch.