Table 5. Homolog protein to accessory proteins of the mammalian circadian clock.
| Organism | Protein | Clock function | C. elegans homolog | E value | |
| ROR | ROR-A | 2nd loop | C01H6.5b (NHR-23b) | 1.40E-70 | |
| Mus musculus | REB-ERVa | ROR-B | 2nd loop | C01H6.5a (NHR-23a) | 4.50E-73 |
| NR1D1 | 2nd loop | W05B5.3a (NHR-85a) | 8.10E-47 | ||
| NR1D2 | 2nd loop | W05B5.3a (NHR-85a) | 8.70E-55 | ||
| DBP | 3rd loop | ZK909.4 (CES-2) | 1.50E-18 | ||
| CSNK | CSNK1a | Modulator | C03C10.1 (KIN-19) | 4.30E-204 | |
| CSNK1d | Modulator | F46F2.2b (KIN-20b) | 1.40E-172 | ||
| CSNK1e | Modulator | F46F2.2b (KIN-20b) | 5.00E-172 | ||
| CCRN4L | Modulator | ZC518.3c (CCR-4c) | 3.50E-21 | ||
| DEC1 | Modulator | Y54G2A.1 (LIN-22) | 4.20E-05 | ||
| DEC2 | Modulator | Y54G2A.1 (LIN-22) | 1.50E-05 | ||
| FBXL-3 | Modulator | C02F5.7a | 5.20E-04 | ||
| PPARGC1a | Modulator | F18H3.3b (PAB-2b) | 6.10E-08 | ||
| MEL receptor | MEL1A | Output | F41E7.3 (NPR-6) | 1.00E-26 | |
| MEL1B | Output | F41E7.3 (NPR-6) | 1.10E-31 | ||
| OPN4 | Input | T11B7.4e (ALP-1e) | 5.20E-61 | ||
| PKC2 | Output | None | None | ||
| VIP | Output | None | None | ||
| VPAC2 | Output | C18B12.2 (SEB-3) | 1.60E-37 | ||
| PRDX-2 | Output | F09E5.15a (PRDX-2a) | 1.70E-104 | ||
| WD-REP | Output | C14B1.4 (WDR-5.1) | 2.70E-159 | ||
These proteins are the best hits found by probabilistic inference search based on Hidden Markov Models built upon multiple protein alignments of the accessory proteins of the circadian clock of mammals (M. musculus). Those proteins that did not possess the same domains that the query profile are highlighted (bold). Common C. elegans names are enclosed between parenthesis when available.