Table 2.
Manually Evaluated Nickel Protein Candidates
| Cluster number |
ORF | Annotation | Crystal structure homolog |
Metal In structure |
IPM prediction |
|---|---|---|---|---|---|
| 2 | PF0144 | Aldolase-type TIM barrel | Fe | ||
| 2 | PF1881 | Alba archaeal DNA/RNA-binding protein | 2Z7C | ||
| 3 | PF0038 | Beta-lactamase-like glyoxalase II family member | Zn | ||
| 4 | PF1916 | Glycosyl transferase, family 2 | |||
| 4 | PF1987 | Conserved hypothetical protein | |||
| 5 | PF0056 | Carbohydrate binding protein | 1VJ2 | Mn | Mn |
| 5 | PF0138 | Uncharacterized rubrerythrin domain protein | 2FZF | Fe | |
| 6 | PF1664 | Phosphoribosyl-AMP cyclohydrolase | 1ZPS | Cd | Zn |
| 6 | PF2038 | Adenosylcobalamin biosynthesis | 1G5T | Mg | Co |
| 7 | PF1329 | Hydrogenase II beta | Fe | ||
| 7 | PF1331 | Hydrogenase II delta | Fe | ||
| 7 | PF1332 | Hydrogenase II alpha | Fe,Ni | ||
| 8 | PF0891 | Hydrogenase I beta | Fe | ||
| 8 | PF0894 | Hydrogenase I alpha | Fe,Ni | ||
| 8 | PF1500 | PRC-barrel-like | |||
| 8 | PF1529 | Pyroxidine biosynthesis protein | 2YZR | ||
| 12 | PF1401 | Peptidyl-prolyl cis-trans isomerase | |||
| 13 | PF0086 | Alanyl-tRNA synthetase, class IIc | 2E1B | Zn | |
| 13 | PF0615 | Hydrogenase expression/formation protein A | 3A43 | Zn | Ni |
| 13 | PF1272 | LamB/YcsF | 1V6T | ||
| 13 | PF1684 | Acetylglutamate kinase | 2EGX | ||
| 13 | PF1861 | Lysyl aminopeptidase | 2PE3 | Zn | |
Cluster number refers to hierarchical clustering with dynamic hybrid partitioning, see Figure 4 for explanation and supplementary tables 1-8 in Additional File 9 for complete cluster tables. Crystal structures obtained from PDB with sequence similarity >50%. ORF numbers in bold have been previously characterized in P. furiosus, those in italics were characterized by metal-targeted purification.