Table 1.

Mass spectrometry analysis of proteins co-immunoprecipitated with GFP-tagged Fap43p or biotinylated in cells expressing either Fap43–HA–BirA* or Fap44–HA–BirA*

Protein	Total number of peptides
	Number in TGD	GFP–Fap43p–oex	Fap43p–GFP native	Fap43p–BirA* native	Fap44p–BirA* native
Fap43	TTHERM_00196190	682/454	12/7	74/52	32/18
Fap44	TTHERM_00498220	215/188	13/9	57/37	31/18
Fap57A	TTHERM_00105300	0	0	31/19	56/30
Fap57B	TTHERM_00052490	0	0	6/4	3/2
Fap57C	TTHERM_00214710	0	0	3/3	4/3
Dyh6	TTHERM_00688470	0	0	1/1	2/2
Dyh7	TTHERM_00912290	0	0	0	0
Dyh3	TTHERM_01276420	10/10	0	1/1	0/0
Dyh4	TTHERM_00499300	11/11	0	2/2	2/2
Dyh5	TTHERM_00486600	15/15	0	0/0	0/0

In the corresponding control samples, the proteins listed in the table were not identified. Note that the number of identified peptides of Fap43p and Fap44p is significantly larger than the number of peptides of other proteins. In Tetrahymena cells, the excess of the overexpressed GFP–Fap43p accumulates near the basal bodies (Fig. S2). Co-precipitation of ODA dynein heavy chains in cells overexpressing GFP–Fap43p is likely due to their accumulation at the cilia base before transport to the cilia (in the case of overexpressed GFP–Fap43p, the cytoskeletal fraction was analyzed). Note that only 1–2 peptides of Dyh3p and Dyh4p were detected in samples prepared from cells expressing either Fap43p or Fap44p at the native level (similar to the number of the Dyh6 peptides; however, in contrast to IDA I1, there are four ODAs in each axonemal unit). All proteins identified in the experimental and control samples are listed in Tables S2–S5