Supplement for
Loopy proteins appear conserved in evolution
Jinfeng Liu, Hepan Tan & Burkhard Rost
TOC:
· Table 1S: Number of NORS proteins predicted under different thresholds
· Table 2S: NORS predicted in proteomes
· Table 3S: NORS involved in protein-protein interactions listed in DIP
· Table 4S: Comparison between NORS and 'natively disordered regions'
· References for Supplement (all also quoted in manuscript)
Table 1S: Number of NORS proteins predicted under different thresholds
|
LenWina |
%secb |
accLenc |
nNORS_PDBd |
FP_PDBe |
nNors_Genf |
%Nors_Geng |
|
50 |
8 |
10 |
45 |
20 |
41757 |
23.0 |
|
50 |
8 |
15 |
19 |
5 |
32313 |
17.8 |
|
50 |
8 |
20 |
11 |
1 |
24927 |
13.7 |
|
50 |
10 |
10 |
50 |
24 |
44971 |
24.7 |
|
50 |
10 |
15 |
24 |
7 |
34311 |
18.9 |
|
50 |
10 |
20 |
12 |
2 |
26134 |
14.4 |
|
50 |
12 |
10 |
63 |
35 |
48047 |
26.4 |
|
50 |
12 |
15 |
27 |
9 |
36080 |
19.8 |
|
50 |
12 |
20 |
13 |
3 |
27174 |
14.9 |
|
50 |
14 |
10 |
73 |
44 |
51547 |
28.3 |
|
50 |
14 |
15 |
29 |
10 |
38181 |
21.0 |
|
50 |
14 |
20 |
14 |
4 |
28392 |
15.6 |
|
|
|
|
|
|
|
|
|
60 |
8 |
10 |
20 |
5 |
33857 |
18.6 |
|
60 |
8 |
15 |
7 |
0 |
27266 |
15.0 |
|
60 |
8 |
20 |
4 |
0 |
21653 |
11.9 |
|
60 |
10 |
10 |
25 |
6 |
37538 |
20.6 |
|
60 |
10 |
15 |
10 |
0 |
29653 |
16.3 |
|
60 |
10 |
20 |
5 |
0 |
23170 |
12.7 |
|
60 |
12 |
10 |
36 |
12 |
41532 |
22.8 |
|
60 |
12 |
15 |
16 |
2 |
32207 |
17.7 |
|
60 |
12 |
20 |
6 |
0 |
24760 |
13.6 |
|
60 |
14 |
10 |
47 |
22 |
44123 |
24.3 |
|
60 |
14 |
15 |
19 |
3 |
33825 |
18.6 |
|
60 |
14 |
20 |
7 |
0 |
25768 |
14.2 |
|
|
|
|
|
|
|
|
|
70 |
8 |
10 |
18 |
3 |
29935 |
16.5 |
|
70 |
8 |
15 |
7 |
0 |
24585 |
13.5 |
|
70 |
8 |
20 |
4 |
0 |
19789 |
10.9 |
|
70 |
10 |
10 |
21 |
5 |
33609 |
18.5 |
|
70 |
10 |
15 |
9 |
0 |
27065 |
14.9 |
|
70 |
10 |
20 |
4 |
0 |
21411 |
11.8 |
|
**70 |
12 |
10 |
23 |
5 |
36203 |
19.9 |
|
70 |
12 |
15 |
10 |
0 |
28791 |
15.8 |
|
70 |
12 |
20 |
4 |
0 |
22555 |
12.4 |
|
70 |
14 |
10 |
32 |
11 |
38243 |
21.0 |
|
70 |
14 |
15 |
13 |
2 |
30133 |
16.6 |
|
70 |
14 |
20 |
6 |
1 |
23450 |
12.9 |
|
|
|
|
|
|
|
|
|
80 |
8 |
10 |
15 |
4 |
26676 |
14.7 |
|
80 |
8 |
15 |
8 |
0 |
22323 |
12.3 |
|
80 |
8 |
20 |
3 |
0 |
18211 |
10.0 |
|
80 |
10 |
10 |
17 |
5 |
29841 |
16.4 |
|
80 |
10 |
15 |
9 |
0 |
24521 |
13.5 |
|
80 |
10 |
20 |
4 |
0 |
19667 |
10.8 |
|
80 |
12 |
10 |
20 |
5 |
31864 |
17.5 |
|
80 |
12 |
15 |
9 |
0 |
25885 |
14.2 |
|
80 |
12 |
20 |
4 |
0 |
20603 |
11.3 |
|
80 |
14 |
10 |
23 |
8 |
35380 |
19.5 |
|
80 |
14 |
15 |
11 |
1 |
28209 |
15.5 |
|
80 |
14 |
20 |
4 |
0 |
22135 |
12.2 |
|
|
|
|
|
|
|
|
|
90 |
8 |
10 |
8 |
1 |
23951 |
13.2 |
|
90 |
8 |
15 |
3 |
0 |
20263 |
11.1 |
|
90 |
8 |
20 |
1 |
0 |
16716 |
9.2 |
|
90 |
10 |
10 |
12 |
3 |
26239 |
14.4 |
|
90 |
10 |
15 |
5 |
0 |
21986 |
12.1 |
|
90 |
10 |
20 |
2 |
0 |
17897 |
9.8 |
|
90 |
12 |
10 |
14 |
3 |
28315 |
15.6 |
|
90 |
12 |
15 |
6 |
0 |
23442 |
12.9 |
|
90 |
12 |
20 |
2 |
0 |
18874 |
10.4 |
|
90 |
14 |
10 |
20 |
6 |
31272 |
17.2 |
|
90 |
14 |
15 |
9 |
1 |
25520 |
14.0 |
|
90 |
14 |
20 |
2 |
0 |
20271 |
11.1 |
|
|
|
|
|
|
|
|
|
100 |
8 |
10 |
4 |
1 |
21586 |
11.9 |
|
100 |
8 |
15 |
1 |
0 |
18533 |
10.2 |
|
100 |
8 |
20 |
1 |
0 |
15446 |
8.5 |
|
100 |
10 |
10 |
7 |
1 |
24088 |
13.2 |
|
100 |
10 |
15 |
3 |
0 |
20374 |
11.2 |
|
100 |
10 |
20 |
2 |
0 |
16718 |
9.2 |
|
100 |
12 |
10 |
11 |
2 |
26527 |
14.6 |
|
100 |
12 |
15 |
5 |
0 |
22183 |
12.2 |
|
100 |
12 |
20 |
2 |
0 |
17957 |
9.9 |
|
100 |
14 |
10 |
13 |
3 |
29108 |
16.0 |
|
100 |
14 |
15 |
6 |
0 |
23934 |
13.2 |
|
100 |
14 |
20 |
2 |
0 |
19150 |
10.5 |
aLenWin: Length of sequence window
b%Sec: Cutoff for percentage of secondary structure
caccLen: Cutoff for minimum length of continous exposed residues in the sequence window
dnNORS_PDB: number of NORS proteins predicted in PDBsub
eFP_PDB: number of false positives in previous column
fnNORS_Gen: number of NORS proteins predicted in all 31 proteomes
g%NORS_Gen: percentage of NORS proteins in all 31 proteomes.
** The threshold we used in the paper
Table 2S: NORS predicted in proteomes
|
Organism |
Number of proteins |
Percentage of NORS proteins |
Percentage of residues in NORS |
Archae bacteria |
|
|
|
Aeropyrum pernix K1 |
2694 |
13.1 |
6.8 |
|
Archaeoglobus fulgidus |
2383 |
1.1 |
0.4 |
|
Methanococcus jannaschii |
1735 |
0.6 |
0.3 |
|
Methanobacterium thermoautotrophicum |
1871 |
1.8 |
0.7 |
|
Pyrococcus abyssi |
1765 |
1.5 |
0.4 |
|
Pyrococcus horikoshii |
2064 |
3.0 |
1.1 |
Prokaryotes |
|
|
|
Aquifex aeolicus |
1522 |
1.4 |
0.4 |
|
Bacillus subtilis |
4099 |
1.3 |
0.5 |
|
Borrelia burgdorferi |
850 |
1.2 |
0.4 |
|
Campylobacter jejuni |
1731 |
1.6 |
0.5 |
|
Chlamydia pneumoniae |
1052 |
2.9 |
1.1 |
|
Chlamydia trachomatis |
894 |
2.9 |
1.0 |
|
Deinococcus radiodurans |
3103 |
4.8 |
1.9 |
|
Escherichia coli |
4285 |
4.8 |
0.6 |
|
Haemophilus influenzae |
1716 |
2.2 |
0.8 |
|
Helicobacter pylori |
1788 |
1.2 |
0.4 |
|
Mycoplasma genitalium |
470 |
3.0 |
0.9 |
|
M pneumoniae |
677 |
3.7 |
1.4 |
|
Mycobacterium tuberculosis |
3918 |
6.3 |
2.7 |
|
Neisseria meningitidis |
2081 |
3.4 |
1.4 |
|
Rickettsia prowazekii |
834 |
1.6 |
0.4 |
|
Synechocystis PCC6803 |
3169 |
2.8 |
1.1 |
|
Thermotoga maritima |
1846 |
1.6 |
0.5 |
|
Treponema pallidum |
1031 |
4.1 |
1.3 |
|
Ureaplasma urealyticum |
613 |
1.5 |
0.4 |
Eukaryotes |
|
|
|
Arabidopsis thaliana |
25445 |
20.3 |
7.2 |
|
Caenorhabditis elegans |
20011 |
17.5 |
6.8 |
|
Drosophila melanogaster |
14333 |
27.1 |
10.8 |
|
Saccharomyces cerevisiae |
6307 |
18.5 |
7.2 |
|
Mus musculus |
28097 |
29.1 |
13.8 |
|
Homo sapiens |
37313 |
30.2 |
14.9 |
Table 3S: NORS involved in protein-protein interactions listed in DIP [xxx 1]