| Cluster | CG0005: |
| YGL161C | 10 | 6 | weak similarity to TRCDSEMBL:HS167A19_1 dJ167A19.1 human (Class IV) |
| YGL198W | 10 | 5 | weak similarity to YIP1P (Class III) |
| YGR172C | YIP1 | 16 | 7 | golgi membrane protein |
| YPL095C | 4 | 4 | strong similarity to YBR177C (Class IV) |
| YDR425W | 7 | 3 | similarity to hypothetical protein YDL113C (Class IV) |
| YDL226C | GCS1 | 15 | 3 | ADP-ribosylation factor GTPase-activating protein (ARF-GAP) |
| YDR100W | 6 | 2 | similarity to Dictyostelium development-specific membrane protein (Class III) |
| YDR468C | TLG1 | 7 | 2 | member of the syntaxin family of t-SNAREs |
| YNL044W | YIP3 | 10 | 2 | protein of unknown function |
| Cluster | CG0006: |
| YDR244W | PEX5 | 4 | 3 | peroxisomal targeting signal receptor |
| YGL153W | PEX14 | 14 | 3 | peroxisomal protein involved in protein import - peroxin |
| YLR191W | PEX13 | 6 | 3 | peroxisomal protein involved in protein import - peroxin |
| YNL214W | PEX17 | 4 | 3 | component of the peroxisomal protein translocation - peroxin |
| Cluster | CG0009: |
| YFL059W | SNZ3 | 9 | 6 | strong similarity to Para rubber tree ethylene-responsive protein1 (Class II) |
| YMR095C | SNO1 | 3 | 3 | similarity to M.leprae hisH protein (Class III) |
| YMR096W | SNZ1 | 5 | 5 | stationary phase protein |
| YNL333W | SNZ2 | 8 | 6 | putative pyridoxine (vitamin B6) biosynthetic enzyme |
| YFL060C | SNO3 | 4 | 3 | strong similarity to SNO1 and SNO2 (Class IV) |
| YMR322C | 4 | 3 | strong similarity to YPL280W, YOR391C andYDR533C (Class IV) |
| YNL334C | SNO2 | 5 | 2 | strong similarity to hypothetical proteins YFL060C and YMR095C (Class IV) |
| Cluster | SP0045: |
| YCL019W | 4 | 2 |
| YCL020W | 4 | 2 |
| YDR261W-A | 4 | 3 |
| YDR261W-B | 3 | 3 |
| Cluster | NN0514: |
| YBR270C | 20 | 2 | strong similarity to hypothetical protein YJL058C (Class IV) |
| YIL105C | 8 | 4 | weak similarity to probable transcription factor ASK10P (Class III) |
| YMR068W | 4 | 2 | weak similarity to mouse transcription factor NF-kappa B (Class III) |
| YNL047C | 9 | 4 | similarity to probable transcription factor ASK10P and hypothetical protein YPR115W, and strong similarity to hypothetical protein YIL105C (Class III) |
| YPL059W | GRX5 | 5 | 2 | member of the subfamily of yeast glutaredoxins (Grx3, GRX4, and Grx5) |
| Cluster | NN0519: |
| YDR120C | TRM1 | 4 | 2 | N2,N2-dimethylguanine tRNA methyltransferase |
| YEL017W | 12 | 4 | hypothetical protein (Class V) |
| YGR121C | MEP1 | 2 | 2 | ammonia permease of high capacity and moderate affinity |
| YHR123W | EPT1 | 3 | 2 | sn-1,2-diacylglycerol ethanolamine- and cholinephosphotransferase |
| YIR038C | GTT1 | 23 | 4 | glutathione S-transferase |
| Cluster | NN0631: |
| YBR172C | SMY2 | 2 | 2 | kinesin-related protein |
| YKL074C | MUD2 | 8 | 5 | pre-mRNA splicing factor |
| YLR116W | MSL5 | 18 | 5 | branch point bridging protein |
| YML046W | PRP39 | 2 | 2 | pre-mRNA splicing factor |
| YPL016W | SWI1 | 6 | 2 | component of SWI/SNF global transcription activator complex |
| YPL105C | 5 | 2 | similarity to SMY2P (Class III) |
| Cluster | NN0637: |
| YBL078C | AUT7 | 4 | 2 | essential for autophagy |
| YBR217W | APG12 | 11 | 4 | component of the autophagic system |
| YHR171W | APG7 | 5 | 4 | component of the autophagic system |
| YMR159C | APG16 | 11 | 2 | coiled-coil protein required for autophagy |
| YNR007C | AUT1 | 5 | 3 | essential for autophagocytosis |
| YPL149W | APG5 | 4 | 3 | involved in autophagy and nutrient starvation |