Table 2 Model organism distributions

From: The topological properties of the protein universe

Organism

Proteins

Residues

A

Loops/res

Voids/res

B

Largest loop/res

Largest void/res

Aedes aegypti

17359

427.62 ± 251.92

2.22 ± 0.15

1.45 ± 0.15

0.34 ± 0.11

0.12 ± 0.05

Apis mellifera

10987

447.53 ± 262.66

2.22 ± 0.11

1.47 ± 0.11

0.32 ± 0.08

0.11 ± 0.04

Arabidopsis thaliana

78842

423.01 ± 250.48

2.21 ± 0.31

1.43 ± 0.30

0.33 ± 0.24

0.13 ± 0.12

Azotobacter vinelandii

8851

324.32 ± 200.62

2.23 ± 0.02

1.42 ± 0.02

0.38 ± 0.01

0.16 ± 0.01

Bacillus subtilis

67815

302.46 ± 185.85

2.37 ± 0.21

1.58 ± 0.21

0.39 ± 0.17

0.14 ± 0.07

Bacteroides thetaiotaomicron

48267

416.85 ± 257.44

2.31 ± 0.20

1.45 ± 0.21

0.3  ± 0.18

0.13 ± 0.07

Caenorhabditis elegans

17106

400.49 ± 280.59

2.22 ± 0.15

1.47 ± 0.15

0.35 ± 0.12

0.13 ± 0.05

Canis lupus

26159

450.14 ± 284.27

2.23 ± 0.04

1.58 ± 0.03

0.31 ± 0.02

0.13 ± 0.01

Chlamydomonas reinhardtii

11199

376.57 ± 228.87

2.17 ± 0.11

1.42 ± 0.11

0.35 ± 0.09

0.12 ± 0.04

Ciona intestinalis

10492

345.55 ± 228.70

2.15 ± 0.12

1.41 ± 0.12

0.32 ± 0.09

0.12 ± 0.04

Danio rerio

38420

437.22 ± 301.55

2.13 ± 0.22

1.37 ± 0.22

0.32 ± 0.17

0.11 ± 0.07

Dictyostelium discoideum

7440

451.37 ± 354.80

2.20 ± 0.10

1.41 ± 0.09

0.33 ± 0.08

0.13 ± 0.04

Drosophila melanogaster

20021

412.36 ± 289.59

2.16 ± 0.17

1.41 ± 0.16

0.34 ± 0.12

0.12 ± 0.05

Escherichia coli

1231178

317.38 ± 213.47

2.24 ± 1.01

1.45 ± 0.98

0.37 ± 0.73

0.13 ± 0.30

Felis catus

21428

455.05 ± 269.37

2.13 ± 0.16

1.38 ± 0.16

0.33 ± 0.12

0.11 ± 0.05

Galleria mellonella

10274

381.47 ± 239.33

2.16 ± 0.12

1.41 ± 0.12

0.33 ± 0.09

0.12 ± 0.04

Gallus gallus

19838

431.24 ± 279.30

2.12 ± 0.16

1.36 ± 0.16

0.32 ± 0.12

0.12 ± 0.05

Halobacterium salinarum

10117

297.93 ± 190.55

2.34 ± 0.05

1.52 ± 0.05

0.39 ± 0.04

0.15 ± 0.02

Haloferax volcanii

9676

293.52 ± 184.23

2.29 ± 0.07

1.49 ± 0.06

0.39 ± 0.05

0.15 ± 0.02

Homo sapiens

125847

267.58 ± 228.53

2.00 ± 0.41

1.19 ± 0.42

0.34 ± 0.29

0.13 ± 0.13

Hydra vulgaris

4598

415.93 ± 233.97

2.25 ± 0.07

1.48 ± 0.07

0.33 ± 0.06

0.12 ± 0.02

Macaca mulatta

44295

423.04 ± 266.77

2.10 ± 0.24

1.34 ± 0.24

0.32 ± 0.17

0.11 ± 0.07

Methanococcus maripaludis

24655

307.42 ± 184.66

2.41 ± 0.11

1.58 ± 0.12

0.40 ± 0.10

0.15 ± 0.05

Methanosarcina barkeri

18136

314.44 ± 202.72

2.30 ± 0.01

1.51 ± 0.01

0.40 ± 0.01

0.18 ± 0.01

Mus musculus

48222

362.49 ± 289.31

2.05 ± 0.29

1.32 ± 0.27

0.33 ± 0.19

0.12 ± 0.08

Mycoplasmoides genitalium

1132

291.66 ±  25.62

1.80 ± 0.04

0.90 ± 0.03

0.42 ± 0.03

0.12 ± 0.01

Neurospora crassa

10707

447.68 ± 243.85

2.21 ± 0.08

1.44 ± 0.07

0.36 ± 0.06

0.12 ± 0.03

Oryza sativa

81003

408.99 ± 249.70

2.19 ± 0.06

1.41 ± 0.06

0.33 ± 0.04

0.13 ± 0.02

Oryzias latipes

58331

474.59 ± 265.89

2.18 ± 0.25

1.40 ± 0.26

0.33 ± 0.20

0.11 ± 0.09

Pyrococcus abyssi

2003

296.69 ± 185.09

2.08 ± 0.01

1.35 ± 0.01

0.31 ± 0.00

0.12 ± 0.00

Pyrococcus furiosus

5648

290.31 ± 177.69

2.36 ± 0.01

1.52 ± 0.01

0.41 ± 0.01

0.16 ± 0.00

Rattus norvegicus

23236

426.28 ± 312.62

2.14 ± 0.19

1.40 ± 0.18

0.35 ± 0.14

0.12 ± 0.06

Saccharomyces cerevisiae

51363

446.54 ± 257.76

2.28 ± 0.14

1.51 ± 0.13

0.36 ± 0.12

0.11 ± 0.04

Salmonella enterica

2010110

331.18 ± 210.85

2.32 ± 0.68

1.51 ± 0.70

0.38 ± 0.53

0.13 ± 0.22

Schizosaccharomyces pombe

4038

437.07 ± 322.44

2.07 ± 0.01

1.37 ± 0.01

0.36 ± 0.01

0.13 ± 0.00

Staphylococcus aureus

116248

295.43 ± 199.82

2.26 ± 0.30

1.50 ± 0.29

0.37 ± 0.22

0.13 ± 0.09

Streptomyces coelicolor

13460

338.39 ± 195.27

2.34 ± 0.08

1.53 ± 0.08

0.39 ± 0.07

0.14 ± 0.03

Strongylocentrotus purpuratus

18147

452.89 ± 253.41

2.21 ± 0.13

1.43 ± 0.14

0.34 ± 0.12

0.12 ± 0.05

Sulfolobus islandicus

23763

287.96 ± 183.27

2.09 ± 0.01

1.41 ± 0.02

0.33 ± 0.02

0.14 ± 0.01

Sus scrofa

66130

461.47 ± 273.30

2.16 ± 0.28

1.40 ± 0.28

0.33 ± 0.22

0.11 ± 0.09

Tetrahymena thermophila

10721

408.02 ± 245.33

2.25 ± 0.02

1.46 ± 0.02

0.37 ± 0.02

0.12 ± 0.01

Xenopus laevis

29810

404.72 ± 250.70

2.14 ± 0.19

1.39 ± 0.19

0.33 ± 0.15

0.12 ± 0.06

Zea mays

96737

404.08 ± 256.06

2.17 ± 0.36

1.41 ± 0.33

0.33 ± 0.26

0.12 ± 0.11

  1. Proteins = Number of protein structures predicted by AlphaFold2. Residues = Average and stddev. of protein chain length. Loops/res = Average and std. err. for the number of loops divided by protein chain length. Voids/res = Same as loops, but for voids. Largest loop/res = Average and std. err. for max. number of loop simplices divided by protein chain length. Largest void/res = Same as loops. Charts A and B depict species-wise distributions for comparisons to Fig. 2A and B, respectively.
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