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Yes, an onset is a prosodic position that, at least in most cases in most languages, is filled by a consonant. (The only potential exception I can think of involves diphthongs, but even there the onset can be analyzed as containing a glide consonant.)

The onset is a unit within a syllable, not a word. So it is not the case that a word like "obligate" has an onset. Rather, each of the syllables making up that word can potentially have an onset.

"Obligate" has three syllables:

  • [ɑb]
  • [lɪ]
  • [ɡeɪt]

The second and third syllables have the consonants [l] and [g], respectively, in onset position. I believe what's confusing you is the fact that the first syllable doesn't have an onset. Not all syllables do. For example, the words axe, ill, up, end, and oar (all one-syllable words) do not have onsets.

I hope this clears up your confusion!