Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel).

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 2418430171  8 GRTTGPHWHPMTFQMIYVLKGWVKFWYErEGELMLKAGDFVYHPPRAAHDL 58
Cdd:pfam07883  8 GESSPPHRHPGEDEFFYVLEGEGELTVD-GEEVVLKAGDSVYFPAGVPHRF 57

RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP (deoxythymidine diphosphates)-4-dehydrorhamnose 3,5-epimerase)-like cupins. RmlC is a dTDP-sugar isomerase involved in the synthesis of L-rhamnose, a saccharide required for the virulence of some pathogenic bacteria. Cupins are a functionally diverse superfamily originally discovered based on the highly conserved motif found in germin and germin-like proteins. This conserved motif forms a beta-barrel fold found in all of the cupins, giving rise to the name cupin ('cupa' is the Latin term for small barrel). The active site of members of this superfamily is generally located at the center of a conserved barrel and usually includes a metal ion. The different functional classes in this superfamily include single domain bacterial isomerases and epimerases involved in the modification of cell wall carbohydrates, two domain bicupins such as the desiccation-tolerant seed storage globulins, and multidomain nuclear transcription factors involved in legume root nodulation.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 2418430171  8 GRTTGPHWHPMTFQMIYVLKGWVKFWYEREGELMLKAGDFVYHPPRAAH 56
Cdd:cd02208    9 GTSSPPHWHPEQDEIFYVLSGEGELTLDDGETVELKAGDIVLIPPGVPH 57

quercetinase, N- and C-terminal cupin domains; This family contains quercetinase (also known as quercetin 2,3-dioxygenase, 2,3QD, QDO and YxaG; EC 1.13.11.24), a mononuclear copper-dependent dioxygenase that catalyzes the cleavage of the flavonol quercetin (5,7,3',4'-tetrahydroxyflavonol) heterocyclic ring to produce 2-protocatechuoyl-phloroglucinol carboxylic acid and carbon monoxide. Bacillus subtilis quercetin 2,3-dioxygenase (QDO) is a homodimer that shows oxygenase activity with several divalent metals such as Mn2+, Co2+, Fe2+, and Cu2+, although the preferred one appears to be Mn2+. The dioxygen binds to the metal ion of the Cu-QDO-quercetin complex, yielding a Cu2+-superoxo quercetin radical intermediate, which then forms a Cu2+-alkylperoxo complex which then evolves into endoperoxide intermediate that decomposes to the product. Quercetinase is a bicupin with two tandem cupin beta-barrel domains, both of which are included in this alignment model. The pirins, which also belong to the cupin domain family, have been shown to catalyze a reaction involving quercetin and may have a function similar to that of quercetinase.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2418430171   8 GRTTGPHWHPMTFQMIYVLKGWVKFWYEREGElMLKAGDFVYHPPRAAH 56
Cdd:cd02215    42 GDAIPPHYHKRHHETFYVLEGRLQLWLDGESR-LLTPGDFASVPPGTIH 89

Uncharacterized conserved protein, cupin superfamily [Function unknown];

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2418430171   8 GRTTGPHWHPMTFQMIYVLKGWVKFWYErEGELMLKAGDFVYHPPRAAH 56
Cdd:COG3837    39 ASSSPYHAHSAEEEFVYVLEGELTLRIG-GEEYVLEPGDSVGFPAGVPH 86

Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism];

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2418430171   8 GRTTGPHWHPMTFQMIYVLKGWVKFWYErEGELMLKAGDFVYHPPRAAHDL 58
Cdd:COG0662    37 GAELSLHVHPHRDEFFYVLEGTGEVTIG-DEEVELKAGDSVYIPAGVPHRL 86

AraC/XylS family transcriptional regulators similar to HpaA, N-terminal cupin domain; Members of this family contain an N-terminal cupin domain and a C-terminal AraC/XylS family helix-turn-helix (HTH) DNA-binding domain, similar to Escherichia coli 4-hydroxyphenylacetate catabolism regulatory protein HpaA (also known as 4HPA). HpaA is encoded by the hpaA gene which is located upstream of hpaBC. It is activated by 4-HPA, 3-HPA and phenylacetate, and represents a member of the AraC/XylS family of regulators that recognizes aromatic effectors. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 2418430171  2 TRAKELGRTTGPHWHPMTFQMIYVLKGWVKFWYErEGELMLKAGDFVYHPPRAAH 56
Cdd:cd06999   26 ARSRLHDWEIAPHRHADLFQVLYIESGGGEVRLD-GRTHPLSAPALVVVPPGVVH 79

Uncharacterized conserved protein, RmlC-like cupin domain [General function prediction only];

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2418430171   8 GRTTGPHWHPMTFQMIYVLKGWVKFWY-ER-EGELMLKAGDFVYHPP 52
Cdd:COG4101    56 GARAKAHHHGEHETAIYVLSGRAETRYgERlEHRVVTEPGDFIFIPP 102

Oxalate decarboxylase (OxDC)-like cupin domain; This subfamily contains bacterial and eukaryotic cupin domains of proteins homologous to oxalate decarboxylase (OxDC; EC 4.1.1.2) such as MSMEG_2254, a putative OxDC from Mycobacterium smegmatis. OxDC is a manganese-dependent bicupin that catalyzes the conversion of oxalate to formate and carbon dioxide, utilizing dioxygen as a cofactor. It is evolutionarily related to oxalate oxidase (OxOx or germin; EC 1.2.3.4) which, in contrast, converts oxalate and dioxygen to carbon dioxide and hydrogen peroxide. OxDC is classified as a bicupin because it contains two cupin folds with each domain containing one manganese binding site, with four manganese binding residues (three histidines and one glutamate) conserved as well as a number of hydrophobic residues.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2418430171  13 PHWHPMTFQMIYVLKGWVKF-WYEREGELM---LKAGDFVYHPPRAAH 56
Cdd:cd20306    49 PHWHPNANELGYVISGEARVsILDPTGSLDtftVKPGQVVFIPQGWLH 96

Chromobacterium violaceum CV2614 and related proteins, cupin domain; This family includes mostly bacterial proteins homologous to CV2614, a Chromobacterium violaceum protein of unknown function. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 2418430171   8 GRTTGPHWHPMtFQMIYVLKGWVKFWYEREGELMLKAGDFV 48
Cdd:cd02236    32 GAELPWHTHPV-PNAGYVLSGELTVEYEDGKKRTFKAGDAF 71

2,4'-Dihydroxyacetophenone dioxygenase (DAD), cupin domain; 2,4'-Dihydroxyacetophenone dioxygenase (DAD) catalyzes the oxidation of 2,4'-dihydroxyacetophenone to 4-hydroxybenzoate and formate as part of the 4-hydroxyacetophenone catabolic pathway. This enzyme is a homo-tetramer containing one iron per molecule of enzyme. This enzyme is an unusual dioxygenase in that it cleaves a C-C bond in a substituent of the aromatic ring rather than within the ring itself. As a bacterial dioxygenase, DAD plays an important environmental role in the aerobic catabolism of aromatic compounds; expression of this enzyme in appropriately engineered microorganisms has the potential to use these aromatic pollutants as a carbon source and thus remove them from the environment. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2418430171   8 GRTTGPHWHPMTFQmIYVLKGwvkFWYEREGELMLKAGDFVYHPPRAAHDL 58
Cdd:cd20302    35 GGSLPRHRHTGPVH-AYTLSG---SWRYLEHDWVATAGSYVYEPAGSIHTL 81

Oxalate decarboxylase/archaeal phosphoglucose isomerase, cupin superfamily [Carbohydrate transport and metabolism]; Oxalate decarboxylase/archaeal phosphoglucose isomerase, cupin superfamily is part of the Pathway/BioSystem: Glycolysis

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2418430171   8 GRTTGPHWHPMTFQMIYVLKGWVKFW-YEREGELM---LKAGDFVYHPPRAAH 56
Cdd:COG2140    13 GGVREEHWHPNAAEWYYVLSGEARMTvQDPPGRARtvdVGPGDVVYVPPGYGH 65

XRE (Xenobiotic Response Element) family transcriptional regulators, C-terminal cupin domain; This family contains transcriptional regulators containing an N-terminal XRE (Xenobiotic Response Element) family helix-turn-helix (HTH) DNA-binding domain and a C-terminal cupin domain. Included in this family is Escherichia coli transcription factor SutR (YdcN) that plays a regulatory role in sulfur utilization; it regulates a set of genes involved in the generation of sulfate and its reduction, the synthesis of cysteine, the synthesis of enzymes containing Fe-S as cofactors, and the modification of tRNA with use of sulfur-containing substrates. This family belongs to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.

                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 2418430171 21 QMIYVLKGWVKFWYEREgELMLKAGDFVYHPPRAAH 56
Cdd:cd02209   39 EFGYVLEGELELTVGGE-TYVLEAGDSIYFDSDVPH 73