SupplementaryTable 1.Protein sequences included in the representative set.

PDB ID / accession no. / Name / Description / Species
1eo6 / GATE-16 / Golgi-associated atpase enhancer of 16 kd / Bostaurus
1gnu / GABARAP / gamma-aminobutyric acid (GABA-A) receptor-associated protein / Homo sapiens
1kjt / GABARAP / gamma-aminobutyric acid (GABA-A) receptor-associated protein / Rattusnorvegicus
1v49 / LC3 / Microtubule-associated proteins 1A/1B light chain 3 / Homo sapiens
1ugm / LC3 / Microtubule-associated proteins 1A/1B light chain 3 / Rattusnorvegicus
NP_789776 / MoaD / molybdopterinsynthase small subunit / Homo sapiens
Q9Z224 / MoaD / molybdopterinsynthase small subunit / Musmusculus
XP_682412 / MoaD / molybdopterinsynthase small subunit / Aspergillusnidulans
1fma / MoaD / molybdopterinsynthase small subunit / Pyrococcusfuriosus
1vjk / MoaD / molybdopterinsynthase small subunit / Escherichia coli
1v8c / MoaD / molybdopterinsynthase small subunit / Thermusthermophilus
AAH03581 / Urm1 / ubiquitin-related modifier-1 / Homo sapiens
1xo3 / Urm1 / ubiquitin-related modifier-1 / Musmusculus
2ax5 / Urm1 / ubiquitin-related modifier-1 / Saccharomycescerevisiae
CAG31999 / Urm1 / ubiquitin-related modifier-1 / Gallus gallus
NP_996018 / Urm1 / ubiquitin-related modifier-1 / Drosophila melanogaster
AAX79740 / Urm1 / ubiquitin-related modifier-1 / Trypanosomabrucei
1ubi / UBIQUITIN / ubiquitin / Homo sapiens
2d3g / UBIQUITIN / ubiquitin / Bostaurus
1otr / UBIQUITIN / ubiquitin / Saccharomycescerevisiae
2dx5 / UBIQUITIN / ubiquitin / Musmusculus
2k39 / UBIQUITIN / ubiquitin / Xenopuslaevis
1ndd / NEDD8 / Neural precursor cell expressed, developmentally down-regulated gene 8 / Homo sapiens
AAH04625 / NEDD8 / Neural precursor cell expressed, developmentally down-regulated gene 8 / Musmusculus
AAF53724 / NEDD8 / Neural precursor cell expressed, developmentally down-regulated gene 8 / Drosophila melanogaster
AAF73911 / NEDD8 / Neural precursor cell expressed, developmentally down-regulated gene 8 / Bostaurus
NP_194414 / Smt3 / small ubiquitin-related modifier / Arabidopsis thaliana
2bf8 / smtc / small ubiquitin-related modifier / Bostaurus
1l2n / Smt3 / small ubiquitin-related modifier / Saccharomycescerevisiae
1a5r / SUMO-1 / small ubiquitin-related modifier 1 / Homo sapiens
1wm3 / SUMO-2 / small ubiquitin-related modifier 2 / Homo sapiens
1u4a / SUMO-3 / small ubiquitin-related modifier 3 / Homo sapiens
NP_776791 / ISG15 / interferon-stimulated gene-15 / Bostaurus
1z2m / ISG15 / interferon-stimulated gene-15 / Homo sapiens
Q64339 / ISG15 / interferon-stimulated gene-15 / Musmusculus
AAH44145 / Ufm1 / ubiquitin-fold-modifier 1 / Daniorerio
1l7y / Ufm1 / ubiquitin-fold-modifier 1 / Caenorhabditiselegans
1wxs / Ufm1 / ubiquitin-fold-modifier 1 / Homo sapiens
1J0G / Ufm1 / ubiquitin-fold-modifier 1 / Musmusculus
NP_177894 / Ufm1 / ubiquitin-fold-modifier 1 / Arabidopsis thaliana
1f0z / ThiS / involved in thiamin biosynthesis / Escherichia coli
1ryj / ThiS / involved in thiamin biosynthesis / Pyrococcusfuriosus
1tyg / ThiS / involved in thiamin biosynthesis / Bacillus subtilis
YP_155158 / ThiS / involved in thiamin biosynthesis / Idiomarinaloihiensis
1uh6 / Hub / ubiquitin like protein 5 / Arabidopsis thaliana
NP_190104 / Hub / ubiquitin like protein 5 / Musmusculus
1m94 / Hub1 / ubiquitin like protein 5 / Saccharomycescerevisiae
1p0r / UBL5 / ubiquitin like protein 5 / Homo sapiens
NP_079677 / Ubl5 / ubiquitin like protein 5 / Musmusculus
p11441 / Ubl4 / ubiquitin like protein 4 / Homo sapiens
p21126 / Ubl4 / ubiquitin like protein 4 / Musmusculus
1iyf / Parkin / product of the causative gene of autosomal-recessive juvenile parkinsonism / Homo sapiens
1mg8 / Parkin / product of the causative gene of autosomal-recessive juvenile parkinsonism / Musmusculus
NP_064478 / Parkin / product of the causative gene of autosomal-recessive juvenile parkinsonism / Rattusnorvegicus
1wx7 / UBQLN3 / Ubiquilin 3 / Homo sapiens
1p1a / HHR23B / Rad23 / Homo sapiens
1p98 / HHR23A / Rad23 / Homo sapiens
NP_033036 / MHR23a / Rad23 / Musmusculus
NP_033037 / Rad23b / Rad23 / Musmusculus
1wz3 / ATG12 / autophagy related protein / Arabidopsis thaliana
O94817 / ATG12 / autophagy related protein / Homo sapiens
BAB62092 / APG12 / autophagy related protein / Musmusculus
AAM10266 / APG8 / autophagy related protein / Arabidopsis thaliana
CAD21230 / APG8 / autophagy related protein / Neurosporacrassa
1wgg / USP14 / Ubiquitin Specific Protease 14 / Musmusculus
NP_005142 / USP14 / Ubiquitin Specific Protease 14 / Homo sapiens
1bt0 / Rub1 / related to ubiquitin-1 / Arabidopsis thaliana
Q03919 / Rub1 / related to ubiquitin-1 / Saccharomycescerevisiae
AAD52982 / Fat10 / human leukocyte antigen-F adjacent transcripts / Homo sapiens
AAG27477 / Fat10 / human leukocyte antigen-F adjacent transcripts / Musmusculus
XP_580689 / Fat10 / human leukocyte antigen-F adjacent transcripts / Bostaurus
CAC42833 / Fat10 / human leukocyte antigen-F adjacent transcripts / Rattusnorvegicus
AAK61367 / ubiquilin / ubiquilin / Bostaurus
NP_038466 / ubiquilin / ubiquilin / Homo sapiens
AAD02323 / HCG-1 / human chorionic gonadotrophin-like / Homo sapiens
AAD02325 / HCG-1 / human chorionic gonadotrophin-like / Musmusculus
1wgh / UBL3 / Ubiquitin-like 3 / Musmusculus
NP_009039 / elongin B / transcription elongation factor B / Homo sapiens
NP_112391 / elongin B / transcription elongation factor B / Rattusnorvegicus
1t0y / TSC-b / Tubulin-binding Cofactor B / Caenorhabditiselegans
1v6e / TSC-b / Tubulin-specific Chaperone B / Musmusculus
1c1y / RAF-1 / Ras-binding domain of the serine/threoninekinase c-Raf1 / Homo sapiens
1rrb / RAF / Ras-binding domain of Raf-1 / Rattusnorvegicus
1ef5 / Ral / Ras-binding domain of Ral / Musmusculus
1lxd / Ral / Ras-interacting domain of RalGDS / Rattusnorvegicus

SupplementaryTable 2.Representative members of the ubiquitinsuperfamily.

Protein family / Description / Classification / Function / Substrate
ubiquitin / UBL / protein degradation
ISG15 / interferon-stimulated gene-15 / UBL / activated by interferon / serine protease inhibitor 2a and others
Nedd8/Rub1 / neural precursor cell-expressed developmentally downregulated-8/related to ubiquitin 1 / UBL / cell cycle control / cullin,VCEligase complex,p53
Rad23 / UDP / DNA repair / Rad4
Fat10 / F-adjacent transcripts 10 / UBL / cell cycle control, apoptosis / MAD2
ubiquilin / UBL / modulator of presenilin protein accumulation / presenilin-1,2
Parkin / product of the causative gene of autosomal-recessive juvenile parkinsonism / UDP / E3 enzyme of ubiquitin
SUMO / Small ubiquitin-Related Modifier / UBL / nuclear transport, transcriptional regulation, chromosome segregation and cell cycle control / RanGAP1,PML
Hub/UBL5 / homolog to ubiquitin-1 / UBL / cell polarity / Sph1,Hbt1,CLK4
Ufm / ubiquitin fold modifier 1 / UBL / endoplasmic stress response
LC_3 / microtubule-associated protein 1 light chain 3 / UBL / autophagy
GATE-16 / Golgi-associated atpase enhancer of 16 kd / UBL / autophagy,intra-Golgi transport / N-ethylmaleimide-sensitive fusion protein,SNAREs
GABARAP / gamma-aminobutyric acid (GABA-A) receptor-associated protein / UBL / autophagy,proteins trafficking / transferrinreceptor,DDX 47
Urm1 / ubiquitin related modifier 1 / UBL / sulphurcarrier,proteinmodification / Ahp1
MoaD / molybdopterinsynthase small subunit / UBL / sulphur carrier
ThiS / involved in thiamin biosynthesis / UBL / sulphur carrier
ATG12 / autophagy related protein / UBL / autophagy, cytoplasm to vacuole targeting / APG5
APG8 / autophagy related protein / UBL / autophagy / PtdEtn
Ral/RGL / Ras-interacting domain of RalGDS/Ras-binding domain of RGL / UDP / adaptor
Raf / Ras-binding domain of Raf-1 / UDP / adaptor
USP14 / Ubiquitin Specific Protease 14 / UDP / deubiquitination enzyme
HCG / human chorionic gonadotrophin-like / UDP / unknown
elongin B / transcription elongation factor B / UDP / transcriptional regulation