Skip to main content

Table 2 Manually Evaluated Nickel Protein Candidates

From: A Computational Framework for Proteome-Wide Pursuit and Prediction of Metalloproteins using ICP-MS and MS/MS Data

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

  1. 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.