Table 1 CAFA target prediction examples for PFP, ESG, and BLAST

T06450, E. coli A34 Protein trbA

F1 measure

PFP:0.9

ESG:0.2

BLAST:0

Selected CAFA Target

Annotations

GO:0008152

GO:0044238

GO:0044237

GO:0043170

GO:0044260

GO:0019538

GO:0044267

GO:0006457

GO:0042026

metabolic process

primary metabolic process

cellular metabolic process

macromolecule metabolic process

cellular macromolecule metabolic process

protein metabolic process

cellular protein metabolic process

protein folding

protein refolding

Selected PFP Annotations

GO:0044260

GO:0015804

GO:0046483

GO:0009110

GO:0019538

GO:0009110

GO:0019538

cellular protein metabolic process

carboxylic acid metabolic process

cellular macromolecule metabolic process

neutral amino acid transport

heterocycle metabolic process

vitamin biosynthetic process

protein metabolic process

0.99

0.81

0.81

0.8

0.8

0.77

0.77

Selected ESG Annotations

GO:0000746

GO:0006810

GO:0008643

GO:0007165

GO:0008152

GO:0008652

conjugation

transport

carbohydrate transport

signal transduction

metabolic process

amino acid biosynthetic process

0.61

0.2

0.12

0.09

0.05

0.05

Selected BLAST

Annotations

T06299, E. coli rutE

F1 measure

PFP:0.18

ESG:0.13

BLAST:0

Selected CAFA Target

Annotations

GO:0019740

GO:0008152

GO:0034641

GO:0006139

GO:0006206

GO:0019860

GO:0006208

GO:0006212

nitrogen utilization

metabolic process

cellular nitrogen compound metabolic process

nucleobase, nucleoside, nucleotide and nucleic acid metabolic process

pyrimidine base metabolic process

uracil metabolic process

pyrimidine base catabolic process

uracil catabolic process

Selected PFP Annotations

GO:0006139

GO:0046131

nucleobase, nucleoside, nucleotide and nucleic acid metabolism

pyrimidine ribonucleoside metabolism

1

1

Selected ESG Annotations

GO:0055114

oxidation-reduction process

1

Selected BLAST

Annotations

T05345, E. coli Sensor protein CpxA

F1 measure

PFP:0.32

ESG:0.68

BLAST:0.43

Selected CAFA Target

Annotations

GO:0008152

GO:0044237

GO:0006796

GO:0016310

GO:0044260

GO:0006464

GO:0043687

GO:0006468

GO:0046777

metabolic process

cellular metabolic process

phosphate metabolic process

phosphorylation

cellular macromolecule metabolic process

protein modification process

post-translational protein modification

protein amino acid phosphorylation

protein amino acid auto phosphorylation

Selected PFP Annotations

GO:0007165

GO:0016310

GO:0006139

GO:0019222

GO:0043283

signal transduction

phosphorylation

nucleobase, nucleoside, nucleotide and nucleic acid metabolism

regulation of metabolism

biopolymer metabolism

1

1

1

1

1

GO:0006464

GO:0006468

GO:0015698

protein modification

protein amino acid phosphorylation

inorganic anion transport

0.99

0.99

0.99

Selected ESG Annotations

GO:0000160

GO:0007165

GO:0018106

GO:0016310

GO:0009405

GO:0006950

two-component signal transduction system (phosphorelay)

signal transduction

peptidyl-histidine phosphorylation

phosphorylation

pathogenesis

response to stress

1

1

1

0.93

0.39

0.33

Selected BLAST

Annotations

GO:0000160

GO:0006950

GO:0009987

GO:0009628

GO:0006979

GO:0044260

GO:0043687

GO:0006468

GO:0046777

two-component signal transduction system (phosphorelay)

response to stress

cellular process

response to abiotic stimulus

response to oxidative stress

cellular macromolecule metabolic process

post-translational protein modification

protein amino acid phosphorylation

protein amino acid auto-phosphorylation

0.39

0.39

0.39

0.39

0.39

0.28

0.28

0.28

0.25

T18799, Homo sapiens Ribonuclease H2 subunit B

F1 measure

PFP:0.5

ESG:0.47

BLAST:0.79

Selected CAFA Target

Annotations

GO:0006139

GO:0006401

GO:0006401

GO:0044248

GO:0034641

GO:0044260

GO:0090304

nucleobase, nucleoside, nucleotide and nucleic acid metabolic process

RNA catabolic process

RNA catabolic process

cellular catabolic process

cellular nitrogen compound metabolic process

cellular macromolecule metabolic process

nucleic acid metabolic process

Selected PFP Annotations

GO:0050789

GO:0044267

GO:0046451

GO:0006351

GO:0044260

GO:0006721

GO:0044238

GO:0016070

regulation of biological process

cellular protein metabolism

diaminopimelate metabolism

transcription, DNA-dependent

cellular macromolecule metabolism

terpenoid metabolism

primary metabolism

RNA metabolism

1

0.9

0.86

0.83

0.83

0.82

0.81

0.41

Selected ESG Annotations

GO:0006412

GO:0006418

GO:0006429

translation

tRNA aminoacylation for protein translation

leucyl-tRNA aminoacylation

0.02

0.01

0.01

Selected BLAST

Annotations

GO:0006139

GO:0006259

GO:0006260

GO:0006261

GO:0006271

GO:0006401

GO:0006807

nucleobase, nucleoside, nucleotide and nucleic acid metabolic process

DNA metabolic process

DNA replication

DNA-dependent DNA replication

DNA strand elongation involved in DNA replication

RNA catabolic process

nitrogen compound metabolic process

0.4

0.4

0.4

0.4

0.4

0.4

0.4