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945  structures 6529  species 29  interactions 112082  sequences 1162  architectures

Clan: Cupin (CL0029)


Cupin fold Add an annotation

This clan represents the conserved barrel domain of the 'cupin' superfamily [1] ('cupa' is the Latin term for a small barrel). The cupin fold is found in a wide variety of enzymes, but notably contains the non-enzymatic seed storage proteins also.

This clan contains 53 families and the total number of domains in the clan is 112082. The clan was built by A Bateman.

Literature references

  1. Dunwell JM; , Biotechnol Genet Eng Rev 1998;15:1-32.: Cupins: a new superfamily of functionally diverse proteins that include germins and plant storage proteins. PUBMED:9573603 EPMC:9573603


This clan contains the following 53 member families:

2OG-Fe_Oxy_2 2OG-FeII_Oxy 2OG-FeII_Oxy_2 2OG-FeII_Oxy_3 2OG-FeII_Oxy_4 2OG-FeII_Oxy_5 3-HAO AraC_binding AraC_binding_2 AraC_N ARD Asp_Arg_Hydrox Auxin_BP CDO_I CENP-C_C CsiD Cupin_1 Cupin_2 Cupin_3 Cupin_4 Cupin_5 Cupin_6 Cupin_7 Cupin_8 dTDP_sugar_isom DUF1255 DUF1479 DUF1498 DUF1637 DUF1971 DUF386 DUF4437 Ectoine_synth EutQ FdtA FTO_NTD GPI HgmA HutD JmjC KduI MannoseP_isomer Ofd1_CTDD Oxygenase-NA PhyH Pirin Pirin_C PMI_typeI Pox_C4_C10 TauD Tet_JBP VIT VIT_2

External database links

Domain organisation

Below is a listing of the unique domain organisations or architectures from this clan. More...

Loading domain graphics...


The table below shows the number of occurrences of each domain throughout the sequence database. More...

Pfam family Num. domains Alignment
Cupin_2 (PF07883) 20335 (18.1%) View
AraC_binding (PF02311) 10833 (9.7%) View
2OG-FeII_Oxy (PF03171) 7390 (6.6%) View
TauD (PF02668) 5659 (5.0%) View
Pirin (PF02678) 4965 (4.4%) View
PMI_typeI (PF01238) 4066 (3.6%) View
2OG-FeII_Oxy_3 (PF13640) 3739 (3.3%) View
Cupin_1 (PF00190) 3563 (3.2%) View
dTDP_sugar_isom (PF00908) 3552 (3.2%) View
DUF386 (PF04074) 3287 (2.9%) View
2OG-FeII_Oxy_2 (PF13532) 3255 (2.9%) View
PhyH (PF05721) 3239 (2.9%) View
JmjC (PF02373) 2778 (2.5%) View
MannoseP_isomer (PF01050) 2703 (2.4%) View
Pirin_C (PF05726) 2522 (2.3%) View
Cupin_8 (PF13621) 2241 (2.0%) View
KduI (PF04962) 2006 (1.8%) View
AraC_binding_2 (PF14525) 1819 (1.6%) View
Cupin_4 (PF08007) 1723 (1.5%) View
Cupin_6 (PF12852) 1675 (1.5%) View
AraC_N (PF06719) 1635 (1.5%) View
Cupin_3 (PF05899) 1583 (1.4%) View
Cupin_5 (PF06172) 1200 (1.1%) View
DUF1971 (PF09313) 1196 (1.1%) View
HgmA (PF04209) 1185 (1.1%) View
Asp_Arg_Hydrox (PF05118) 1101 (1.0%) View
Cupin_7 (PF12973) 1076 (1.0%) View
Pfam family Num. domains Alignment
DUF1255 (PF06865) 1071 (1.0%) View
VIT (PF08487) 1019 (0.9%) View
HutD (PF05962) 985 (0.9%) View
ARD (PF03079) 964 (0.9%) View
CDO_I (PF05995) 920 (0.8%) View
EutQ (PF06249) 785 (0.7%) View
DUF1479 (PF07350) 709 (0.6%) View
FdtA (PF05523) 624 (0.6%) View
CsiD (PF08943) 476 (0.4%) View
Ectoine_synth (PF06339) 443 (0.4%) View
2OG-Fe_Oxy_2 (PF10014) 432 (0.4%) View
3-HAO (PF06052) 387 (0.3%) View
DUF1498 (PF07385) 356 (0.3%) View
DUF1637 (PF07847) 328 (0.3%) View
Tet_JBP (PF12851) 327 (0.3%) View
2OG-FeII_Oxy_5 (PF13759) 313 (0.3%) View
Oxygenase-NA (PF09859) 288 (0.3%) View
Ofd1_CTDD (PF10637) 253 (0.2%) View
GPI (PF06560) 215 (0.2%) View
CENP-C_C (PF11699) 190 (0.2%) View
2OG-FeII_Oxy_4 (PF13661) 165 (0.1%) View
Pox_C4_C10 (PF03336) 127 (0.1%) View
VIT_2 (PF13757) 116 (0.1%) View
FTO_NTD (PF12933) 102 (0.1%) View
DUF4437 (PF14499) 81 (0.1%) View
Auxin_BP (PF02041) 80 (0.1%) View
Total: 53 Total: 112082 Clan alignment

Please note: Clan alignments can be very large and can cause problems for some browsers. Read the note above before viewing.

Family relationships

This diagram shows the relationships between members of this clan. More...

We could not retrieve a family relationship diagram for this clan.

Species distribution

Tree controls


This tree shows the occurrence of the domains in this clan across different species. More...



There are 29 interactions for this clan. More...

Interacting families
HgmA HgmA
CsiD CsiD
Pirin_C Pirin
AraC_binding AraC_binding
Cupin_1 Cupin_1
PhyH PhyH
PMI_typeI PMI_typeI
Cupin_2 HTH_3
DUF1255 DUF1255
2OG-FeII_Oxy 2OG-FeII_Oxy
MannoseP_isomer NTP_transferase
Cupin_4 Cupin_4
Asp_Arg_Hydrox Pro_3_hydrox_C
FdtA FdtA
TauD TauD
HutD HutD
JmjC JmjC
Cupin_5 Cupin_5
dTDP_sugar_isom dTDP_sugar_isom
DUF386 DUF386
Cupin_3 Cupin_3
Pirin Pirin_C


For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the MSD group, to allow us to map Pfam domains onto UniProt three-dimensional structures. The table below shows the mapping between the Pfam families in this clan, the corresponding UniProt entries, and the region of the three-dimensional structures that are available for that sequence.

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