Powering down the Pfam website
On October 5th, we began redirecting traffic from Pfam (pfam.xfam.org) to InterPro (www.ebi.ac.uk/interpro). The Pfam website will remain available at pfam-legacy.xfam.org until January 2023, when it will be decommissioned. You can read more about the sunset period in our blog post.

Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
3307  structures 9137  species 0  interactions 477355  sequences 5156  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 69 families and the total number of domains in the clan is 477355. 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 69 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 2OG-FeII_Oxy_6 3-HAO AIM24 AraC_binding AraC_binding_2 AraC_N ARD Asp_Arg_Hydrox AUDH_Cupin Auxin_BP CDO_I CENP-C_C cNMP_binding CsiD Cupin_1 Cupin_2 Cupin_3 Cupin_5 Cupin_6 Cupin_7 Cupin_8 DIOX_N DMSP_lyase dTDP_sugar_isom DUF1479 DUF1971 DUF386 DUF4437 DUF4867 DUF5070 DUF6016 Ectoine_synth ERG2_Sigma1R EutQ FdtA FTO_NTD GPI HgmA_C HgmA_N HutD JmjC JmjC_2 JmjN KduI Lyx_isomer MannoseP_isomer Ofd1_CTDD Oxygenase-NA PCO_ADO PhyH Pirin Pirin_C Pirin_C_2 PMI_typeI_C PMI_typeI_cat Popeye Pox_C4_C10 Ppnp TauD Tet_JBP Ureidogly_lyase 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
cNMP_binding (PF00027) 87173 (18.3%) View
2OG-FeII_Oxy (PF03171) 37065 (7.8%) View
AraC_binding (PF02311) 37024 (7.8%) View
DIOX_N (PF14226) 34382 (7.2%) View
Cupin_1 (PF00190) 22409 (4.7%) View
JmjC (PF02373) 20428 (4.3%) View
2OG-FeII_Oxy_3 (PF13640) 18586 (3.9%) View
TauD (PF02668) 18506 (3.9%) View
PhyH (PF05721) 17077 (3.6%) View
Pirin (PF02678) 14141 (3.0%) View
2OG-FeII_Oxy_2 (PF13532) 13132 (2.8%) View
Cupin_8 (PF13621) 10916 (2.3%) View
Pirin_C (PF05726) 9281 (1.9%) View
JmjN (PF02375) 8894 (1.9%) View
dTDP_sugar_isom (PF00908) 7886 (1.7%) View
AIM24 (PF01987) 7524 (1.6%) View
Cupin_3 (PF05899) 6668 (1.4%) View
PMI_typeI_cat (PF20511) 6581 (1.4%) View
VIT (PF08487) 6310 (1.3%) View
MannoseP_isomer (PF01050) 5726 (1.2%) View
HgmA_N (PF20510) 5269 (1.1%) View
AraC_binding_2 (PF14525) 4733 (1.0%) View
HgmA_C (PF04209) 4457 (0.9%) View
Cupin_6 (PF12852) 4308 (0.9%) View
KduI (PF04962) 4117 (0.9%) View
JmjC_2 (PF08007) 3912 (0.8%) View
Cupin_7 (PF12973) 3873 (0.8%) View
Pirin_C_2 (PF17954) 3866 (0.8%) View
CDO_I (PF05995) 3512 (0.7%) View
Asp_Arg_Hydrox (PF05118) 3464 (0.7%) View
Cupin_5 (PF06172) 3293 (0.7%) View
AraC_N (PF06719) 3222 (0.7%) View
ARD (PF03079) 3147 (0.7%) View
PCO_ADO (PF07847) 2280 (0.5%) View
Ureidogly_lyase (PF04115) 2266 (0.5%) View
Pfam family Num. domains Alignment
3-HAO (PF06052) 2193 (0.5%) View
2OG-FeII_Oxy_4 (PF13661) 1697 (0.4%) View
PMI_typeI_C (PF01238) 1672 (0.4%) View
Ectoine_synth (PF06339) 1588 (0.3%) View
DUF386 (PF04074) 1574 (0.3%) View
DUF1479 (PF07350) 1552 (0.3%) View
Ofd1_CTDD (PF10637) 1469 (0.3%) View
HutD (PF05962) 1451 (0.3%) View
Tet_JBP (PF12851) 1407 (0.3%) View
2OG-FeII_Oxy_5 (PF13759) 1391 (0.3%) View
Popeye (PF04831) 1389 (0.3%) View
FdtA (PF05523) 1375 (0.3%) View
ERG2_Sigma1R (PF04622) 1368 (0.3%) View
Ppnp (PF06865) 1346 (0.3%) View
EutQ (PF06249) 1241 (0.3%) View
CENP-C_C (PF11699) 1189 (0.2%) View
2OG-Fe_Oxy_2 (PF10014) 1049 (0.2%) View
2OG-FeII_Oxy_6 (PF20515) 1031 (0.2%) View
Oxygenase-NA (PF09859) 916 (0.2%) View
FTO_NTD (PF12933) 736 (0.2%) View
Lyx_isomer (PF07385) 653 (0.1%) View
VIT_2 (PF13757) 576 (0.1%) View
DUF1971 (PF09313) 523 (0.1%) View
Auxin_BP (PF02041) 449 (0.1%) View
GPI (PF06560) 409 (0.1%) View
DMSP_lyase (PF16867) 399 (0.1%) View
DUF4437 (PF14499) 385 (0.1%) View
DUF4867 (PF16161) 313 (0.1%) View
DUF6016 (PF19480) 292 (0.1%) View
CsiD (PF08943) 154 (0.0%) View
AUDH_Cupin (PF18637) 93 (0.0%) View
Pox_C4_C10 (PF03336) 45 (0.0%) View
DUF5070 (PF16802) 2 (0.0%) View
Cupin_2 (PF07883) 0 (0.0%) View
Total: 69 Total: 477355
No alignment ℹ

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...

Species distribution

Tree controls


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



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.

Loading structure mapping...