It is different for two sectors. Zeta Andromedae and Orellius. I wouldn't suggest either of those before at or at least near the level cap, and I'd suggest getting geared up a bit before Orellius, that one can be pretty brutal.
For every other sector, the enemies are level 45. You get adjusted to that level, which makes up for the fact that your equipment and skills are weak, but not for the fact that a higher tier ship has more equipment slots and skill slots available. If you end up with a strong team, commander level is enough to hold your own. To be safe, captain might be a better idea, since there's not a huge difference between a tier 4 and tier 5 ship.
Avoid tactical cubes, and when you're fighting the boss, stay away from the ends. Kill regeneration probes and plasma balls, ignore the other probe types unless you're getting overwhelmed (in which case it's usually not going to be a kill anyway).
Make sure to bring kinetic and plasma resist powers and gear to avoid being oneshotted. Activate brace for impact and if possible aux to inertial dampers when you see the boss preparing a torpedo spread. That should let you survive long enough to fire off heals after that. By staying alive alone you stay usefull, since you can keep up dps.
Make sure you are teamed with the others, so they can easily see when you are in distress andbe able to help.