Table 2. Application of exclusion criteria to potential FFAT motifs in yeast.
| A. Motifs with FFAT scores 0.0 to 1.5 | |||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Name | FFAT score | Exclusion criteria | |||||||||||||||
| 1. loc | 2. struct | 3. Conservation (family of orthologues) | |||||||||||||||
| FFAT score ≤2.5 | size of fam. | observed motifs | expected background (random) | p-value (-log10) | |||||||||||||
| if not cyto. | if not IDR | 2.5 | 2.0 | 1.5 | 0.0-1.0 | 2.5 | 2.0 | 1.5 | 0.0-1.0 | ≤2.5 | ≤2.0 | ≤1.5 | 0.0-1.0 | ||||
| Opi1 er | 0 | H b | 13% | 151 | 1 | 3 | 2 | 13 | 2.2 | 0.7 | 0.0 | 0.0 | 3.2 | 4.2 | 4.0 | 3.5 | |
| Osh1 er | 0 | 99% | 154 | 55 | 26 | 3 | 149 | 9.2 | 2.7 | 0.5 | 0.1 | 44 | 38 | 34 | 34 | ||
| Bbc1 | 1 | H b | 20% | 168 | 15 | 8 | 4 | 7 | 7.0 | 1.6 | 0.4 | 0.0 | 3.9 | 3.7 | 2.8 | 2.1 | |
| Kri1 | 1 | H b | 23% | 154 | 14 | 3 | 5 | 19 | 12 | 5.0 | 1.1 | 0.4 | 2.4 | 3.4 | 5 | 4.6 | |
| Osh2 er | 1 | H b | as Osh1 | ||||||||||||||
| Osh3 er | 1 | 74% | 156 | 13 | 31 | 23 | 62 | 6.6 | 1.2 | 0.0 | 0.0 | 24 | 26 | 20 | 15 | ||
| Seg2 | 1.2 | 33% | 21 | 3 | 1 | 1 | 2 | 0.1 | 0.0 | 0.0 | 0.0 | 2.0 | 1.3 | 1.1 | 0.8 | ||
| Ypr097w | 1 | 14% | 168 | 7 | 6 | 4 | 7 | 9.0 | 1.7 | 0.3 | 0.1 | 1.5 | 3.2 | 2.8 | 2.0 | ||
| Asg7 | 1.5 | lumen | 11% | 18 | 0 | 1 | 1 | 0 | 0.2 | 0.0 | 0.0 | 0.0 | 0.6 | 0.8 | / | / | |
| Ede1 | 1.5 | 18% | 221 | 16 | 7 | 11 | 5 | 12 | 2.6 | 0.3 | 0.0 | 3.0 | 4.1 | 4.0 | 1.6 | ||
| ‡ Erb1 er | 1.5 | 31% | 125 | 25 | 10 | 11 | 0 | 5.3 | 2.3 | 0.5 | 0.0 | 7 | 3.7 | 2.7 | / | ||
| Exo1 | 1.5 | E | 9.9% | 171 | 17 | 0 | 1 | 0 | 4.7 | 0.7 | 0.2 | 0.0 | 2.0 | / | / | / | |
| Mcm3 | 1.5 | H b | 3.1% | 732 | 18 | 4 | 1 | 0 | 26 | 6.0 | 2.0 | 0.2 | / | / | / | / | |
| Nop2 | 1.5 | H | 85% | 145 | 62 | 18 | 46 | 16 | 5.9 | 1.3 | 0.8 | 0.2 | 27 | 17 | 14 | 4.1 | |
| 12% | 17 | 4 | 9 | 0 | 4 | 1.1 | 2.2 | 0.7 | 1.2 | ||||||||
| ‡ Ost1 er | 1.5 | lumen | E | 2.0% | 148 | 2 | 0 | 1 | 0 | 1.9 | 0.6 | 0.2 | 0.0 | 0.0 | / | / | / |
| Pet123 | 1.5 | mito. | 5.7% | 35 | 0 | 1 | 1 | 0 | 0.4 | 0.0 | 0.0 | 0.0 | 0.5 | 0.8 | / | / | |
| Rqc1 | 1.5 | 20% | 151 | 7 | 9 | 6 | 8 | 6.9 | 1.7 | 0.1 | 0.1 | 3.2 | 4.6 | 3.6 | 2.4 | ||
| Sfb3 er | 1.5 | 7.4% | 274 | 10 | 4 | 6 | 0 | 6.8 | 1.9 | 0.1 | 0.1 | 1.4 | 1.6 | 1.7 | / | ||
| Skp2 | 1.5 | 5.4% | 37 | 1 | 0 | 1 | 0 | 0.6 | 0.4 | 0.0 | 0.0 | 0.2 | / | / | / | ||
| Ste13 | 1.5 | lumen | E | 4.8% | 230 | 8 | 2 | 2 | 0 | 10 | 2.4 | 0.7 | 0.1 | / | 0.1 | 0.3 | / |
| Tub1 | 1.5 | H | 100% | 74 | 2 | 0 | 71 | 0 | 3.0 | 0.4 | 0.0 | 0.0 | 15 | 16 | 17 | / | |
| Tub3 | 1.5 | H | as Tub1 | ||||||||||||||
| Ubp10 | 1.5 | H b | 8.1% | 533 | 20 | 14 | 8 | 4 | 24 | 6.2 | 1.0 | 0.1 | 1 | 2.9 | 2.6 | 1.3 | |
| Ubr1 | 1.5 | H b | 18% | 186 | 18 | 13 | 9 | 3 | 19 | 3.6 | 1.1 | 0.1 | 1.7 | 3.7 | 2.5 | 1.0 | |
| Vid27 | 1.5 | 39% | 155 | 17 | 25 | 17 | 15 | 12 | 1.5 | 0.7 | 0.0 | 10 | 12 | 7 | 4.0 | ||
| Wsc2 | 1.5 | 1.9% | 105 | 1 | 0 | 1 | 0 | 1.6 | 0.2 | 0.0 | 0.0 | 0.0 | / | / | / | ||
| Ylr149c | 1.5 | H b | 5.1% | 99 | 3 | 1 | 1 | 0 | 2.9 | 0.6 | 0.2 | 0.1 | 0.2 | 0.3 | / | / | |
| Yor238w | 1.5 | H b | 0.9% | 117 | 1 | 0 | 0 | 0 | 1.3 | 0.1 | 0.1 | 0.0 | / | / | / | / | |
| B. Samples of motifs with FFAT scores 2.0 and 2.5 | |||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Name | FFAT score | Exclusion criteria | |||||||||||||||
| 1. loc | 2. struct | 3. Conservation (family of orthologues) | |||||||||||||||
| FFAT score ≤2.5 | size of fam. | observed motifs | expected background (random) | p-value (-log10) | |||||||||||||
| if not cyto. | if not IDR | 2.5 | 2.0 | 1.5 | 0.0-1.0 | 2.5 | 2.0 | 1.5 | 0.0-1.0 | ≤2.5 | ≤2.0 | ≤1.5 | 0.0-1.0 | ||||
| Acs1 | 2.0 | E | 10% | 240 | 12 | 11 | 1 | 0 | 5.1 | 1.3 | 0.2 | 0.0 | 2.8 | 2.4 | / | / | |
| Ecm13 | 2.0 | 27% | 123 | 24 | 12 | 0 | 2 | 5.7 | 2.7 | 0.7 | 0.1 | 4.6 | 1.9 | 0.3 | 0.7 | ||
| Efr3 | 2.0 | 8.2% | 159 | 4 | 2 | 6 | 1 | 4.3 | 0.6 | 0.1 | 0.0 | 1.2 | 2.1 | 2.0 | / | ||
| Ent3 | 2.0 | 71% | 139 | 85 | 19 | 0 | 0 | 3.4 | 0.6 | 0.2 | 0.0 | 21 | 4.4 | / | / | ||
| Irr1 | 2.0 | 9.9% | 302 | 23 | 8 | 0 | 0 | 24.3 | 5.9 | 2.0 | 0.6 | 0.1 | 0.0 | / | / | ||
| Kar2 er | 2.0 | lumen | 3.1% | 413 | 6 | 13 | 0 | 0 | 13.1 | 3.5 | 1.3 | 0.0 | 0.1 | 1.3 | / | / | |
| Met4 | 2.0 | 5.0% | 20 | 1 | 0 | 0 | 0 | 0.4 | 0.0 | 0.1 | 0.0 | / | / | / | / | ||
| Mgr3 | 2.0 | mito. | 33% | 43 | 2 | 12 | 0 | 0 | 0.7 | 0.0 | 0.1 | 0.1 | 3.2 | 3.1 | / | / | |
| Msh6 | 2.0 | 13% | 563 | 57 | 20 | 1 | 1 | 26.7 | 5.6 | 1.3 | 0.3 | 4.7 | 2.2 | 0.1 | / | ||
| Rkr1 | 2.0 | 4.5% | 154 | 5 | 2 | 0 | 0 | 9.9 | 1.9 | 0.5 | 0.0 | / | / | / | / | ||
| Sxm1 | 2.0 | 19% | 158 | 27 | 4 | 1 | 4 | 12.8 | 3.2 | 0.3 | 0.1 | 2.2 | 0.9 | 1.3 | 1.3 | ||
| ‡ Utp9 | 2.0 | 38% | 13 | 1 | 4 | 0 | 0 | 0.2 | 0 | 0 | 0 | 1.5 | 1.3 | / | / | ||
| Yhl026c | 2.0 | 3.7% | 54 | 0 | 2 | 0 | 0 | 0.7 | 0.0 | 0.1 | 0.0 | 0.3 | 0.7 | / | / | ||
| Aim44 | 2.5 | 35% | 20 | 5 | 2 | 0 | 0 | 0.8 | 0.1 | 0.1 | 0.0 | 1.5 | 0.6 | / | / | ||
| Chm7 er | 2.5 | 7.4% | 149 | 11 | 0 | 0 | 0 | 3.0 | 0.7 | 0.1 | 0.1 | 1.2 | / | / | / | ||
| Dyn1 | 2.5 | 2.3% | 175 | 4 | 0 | 0 | 0 | 23.8 | 4.7 | 0.9 | 0.4 | / | / | / | / | ||
| ‡ Epo1 er | 2.5 | 24% | 38 | 8 | 2 | 0 | 0 | 0.6 | 0.1 | 0.0 | 0.0 | 2.4 | 0.7 | / | / | ||
| Kxd1 (x2) | 2.5 | H b | 6.0% | 83 | 6 | 1 | 0 | 0 | 0.5 | 0.8 | 0.0 | 0.0 | 1.3 | / | / | / | |
| Mdv1 | 2.5 | E | 4.1% | 765 | 25 | 5 | 0 | 0 | 16.2 | 3.2 | 0.6 | 0.2 | 0.8 | 0.1 | / | / | |
| Mga2er | 2.5 | 7.1% | 311 | 13 | 5 | 3 | 0 | 7.2 | 2.1 | 0.3 | 0.1 | 1.4 | 1.0 | 0.8 | / | ||
| ‡ Num1 er | 2.5 | 52% | 42 | 15 | 7 | 4 | 1 | 6.9 | 2.3 | 0.0 | 0.0 | 2.5 | 2.0 | 1.6 | / | ||
| Pbi1 ‡ | 2.5 | H | 4.2% | 24 | 1 | 0 | 0 | 0 | 0.5 | 0.3 | 0.0 | 0.0 | 0.1 | / | / | / | |
| Sec2 | 2.5 | 20% | 163 | 24 | 7 | 9 | 0 | 4.6 | 1.7 | 0.2 | 0.1 | 6 | 3.0 | 2.4 | / | ||
| Sec27 | 2.5 | 3.2% | 1157 | 26 | 10 | 2 | 0 | 35.8 | 7.6 | 1.1 | 0.3 | 0.3 | 0.3 | 0.1 | / | ||
| Sec63 | 2.5 | lumen | 6.4% | 141 | 4 | 4 | 1 | 0 | 6.9 | 1.2 | 0.3 | 0.0 | 0.1 | 0.8 | / | / | |
| Sec66 | 2.5 | lumen | 2.2% | 136 | 2 | 0 | 1 | 0 | 1.2 | 0.5 | 0.0 | 0.0 | 0.3 | / | / | / | |
| Tor1 (x2) | 2.5 | H (x2) | 75% | 158 | 133 | 1 | 0 | 0 | 9.3 | 1.2 | 0.1 | 0.0 | 24 | / | / | / | |
| Ubp1 er | 2.5 | 5.2% | 154 | 3 | 4 | 1 | 0 | 5.5 | 1.0 | 0.3 | 0.0 | 0.1 | 0.9 | / | / | ||
| Ubp2 | 2.5 | H | 11% | 154 | 18 | 1 | 0 | 0 | 13.9 | 2.7 | 0.8 | 0.3 | 0.1 | / | / | / | |
| Vps13 er | 2.5 | 48% | 142 | 27 | 24 | 10 | 14 | 23.0 | 4.7 | 1.2 | 0.3 | 5 | 8 | 5 | 3.5 | ||
| Yml002w | 2.5 | H | 11% | 113 | 11 | 0 | 1 | 0 | 5.2 | 1.1 | 0.3 | 0.0 | 0.7 | / | / | / | |
| Ypt7 | 2.5 | 11% | 38 | 3 | 1 | 0 | 0 | 0.9 | 0.2 | 0.0 | 0.0 | 0.7 | / | / | / | ||
Notes: Sequences in order of increasing FFAT score. Red text, yellow fill indicates motif excluded and exclusion criterion: Location: lumen = translocated; mito. = mitochondrion; empty: cytoplasm. Structure: H helix, E sheet (red confirmed, black predicted, H b indicates helix between domains); empty: loop. Conservation: exclusion either if observed motifs ≤ expected (numbers of motifs in red) or if all p values for excess motifs with FFAT score ≤2.5/2.0/1.5/1.0 ≥0.01 (i.e. -1*log10 p value <2.0). Display of p value: nonsignificant (p>10-2); borderline (10-3≤p<10-2): pink, or only 2 motifs: grey; positive (p≤10-3): blue. The most significant Chi2 is used to colour the protein name. Chi2 is not valid if all expected values =0, and not given if only 1 motif was observed (“/”). ‡Erb1 and Ost1 have been previously identified as binding yeast VAP (Chatr-Aryamontri et al., 2017). Superscript er: known on ER. NOP2 has motifs of 2 main types: one in a confirmed helix and others in a loop.
Notes: colouring, p-values and exclusions as in part A. Kxd1 and Tor1 have 2 motifs with FFAT score =2.5. ‡ Epo1, Num1 and Pbi1 have been reported to bind VAP, but potential FFAT motifs have not been tested (Chao et al., 2014; Riekhof et al., 2014). Superscript er: known on ER.