Granulicella tundricola hydroxynitrile lyase (GtHNL) and related proteins, cupin domain; This family includes archaeal, eukaryotic, and bacterial proteins homologous to hydroxynitrile lyase from Granulicella tundricola (GtHNL), a novel class of HNLs that does not show any sequence or structural similarity to any other HNL and does not contain conserved motifs typical of HNLs. HNLs comprise a diverse group of enzymes that vary in terms of their substrate specificity, enantioselectivity and the need for a co-factor. In plants, they catalyze the reversible cleavage of cyanohydrins, yielding HCN and aldehydes or ketones. Also included in this family is TM1010 from Thermotoga maritima, a protein of unknown function. Some but not all members of this family have N- or C-terminal carboxymuconolactone decarboxylase domains in addition to the cupin domain. Members of this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383354  19 FTGCVRIDAPFQATEPAKVGGATVTFEPGARTAWHTHPLGQTLIVTQGRGWLQEWGKEAEPLNQGDIAWIPPGVKHWHGA 98
Cdd:cd02233    1 FTGTVWLDPLFPADEPSRVSVANVTFEPGARTAWHTHPGGQILIVTSGVGWVQEEGGPPQELRPGDVVWIPPGVKHWHGA 80

                         90       100
                 ....*....|....*....|....*.
gi 505383354  99 SAQTAMTHIAIAEAVDGSPVAWLEKV 124
Cdd:cd02233   81 APDSAMTHLAITEALDGGGVEWLEPV 106

Granulicella tundricola hydroxynitrile lyase (GtHNL) and related proteins, cupin domain; This family includes archaeal, eukaryotic, and bacterial proteins homologous to hydroxynitrile lyase from Granulicella tundricola (GtHNL), a novel class of HNLs that does not show any sequence or structural similarity to any other HNL and does not contain conserved motifs typical of HNLs. HNLs comprise a diverse group of enzymes that vary in terms of their substrate specificity, enantioselectivity and the need for a co-factor. In plants, they catalyze the reversible cleavage of cyanohydrins, yielding HCN and aldehydes or ketones. Also included in this family is TM1010 from Thermotoga maritima, a protein of unknown function. Some but not all members of this family have N- or C-terminal carboxymuconolactone decarboxylase domains in addition to the cupin domain. Members of this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383354  19 FTGCVRIDAPFQATEPAKVGGATVTFEPGARTAWHTHPLGQTLIVTQGRGWLQEWGKEAEPLNQGDIAWIPPGVKHWHGA 98
Cdd:cd02233    1 FTGTVWLDPLFPADEPSRVSVANVTFEPGARTAWHTHPGGQILIVTSGVGWVQEEGGPPQELRPGDVVWIPPGVKHWHGA 80

                         90       100
                 ....*....|....*....|....*.
gi 505383354  99 SAQTAMTHIAIAEAVDGSPVAWLEKV 124
Cdd:cd02233   81 APDSAMTHLAITEALDGGGVEWLEPV 106

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 505383354   42 VTFEPGARTAWHTHP-LGQTLIVTQGRGWLQEwGKEAEPLNQGDIAWIPPGVKHWHGA 98
Cdd:pfam07883   3 VTLPPGESSPPHRHPgEDEFFYVLEGEGELTV-DGEEVVLKAGDSVYFPAGVPHRFRN 59

Granulicella tundricola hydroxynitrile lyase (GtHNL) and related proteins, cupin domain; This family includes archaeal, eukaryotic, and bacterial proteins homologous to hydroxynitrile lyase from Granulicella tundricola (GtHNL), a novel class of HNLs that does not show any sequence or structural similarity to any other HNL and does not contain conserved motifs typical of HNLs. HNLs comprise a diverse group of enzymes that vary in terms of their substrate specificity, enantioselectivity and the need for a co-factor. In plants, they catalyze the reversible cleavage of cyanohydrins, yielding HCN and aldehydes or ketones. Also included in this family is TM1010 from Thermotoga maritima, a protein of unknown function. Some but not all members of this family have N- or C-terminal carboxymuconolactone decarboxylase domains in addition to the cupin domain. Members of this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383354  19 FTGCVRIDAPFQATEPAKVGGATVTFEPGARTAWHTHPLGQTLIVTQGRGWLQEWGKEAEPLNQGDIAWIPPGVKHWHGA 98
Cdd:cd02233    1 FTGTVWLDPLFPADEPSRVSVANVTFEPGARTAWHTHPGGQILIVTSGVGWVQEEGGPPQELRPGDVVWIPPGVKHWHGA 80

                         90       100
                 ....*....|....*....|....*.
gi 505383354  99 SAQTAMTHIAIAEAVDGSPVAWLEKV 124
Cdd:cd02233   81 APDSAMTHLAITEALDGGGVEWLEPV 106

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        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 505383354  41 TVTFEPGARTAWHTHPLG-QTLIVTQGRGWLQEWGKEAEPLNQGDIAWIPPGVKHW 95
Cdd:cd02208    3 VVTLPPGTSSPPHWHPEQdEIFYVLSGEGELTLDDGETVELKAGDIVLIPPGVPHS 58

Thermotoga maritima TM1459 and related proteins, cupin domain; This family includes bacterial and archaeal proteins homologous to Thermotoga maritima TM1459, a manganese-containing cupin that has been shown to cleave C=C bonds in the presence of alkylperoxide as oxidant in vitro. Its biological function is still unknown. This family also includes Halorhodospira halophila Hhal_0468. Structures of these proteins show a cupin fold with a conserved "jelly roll-like" beta-barrel fold that form a homodimer.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 505383354  43 TFEPGARTAWHTHPLGQTLIVTQGRGWLQEwGKEAEPLNQGDIAWIPPGVKHW 95
Cdd:cd02222   23 EIEPGGHTPLHTHPWEHEVYVLRGKGVVVI-GGEEYPVKPGDVVYIPPNEPHQ 74

Bradyrhizobium diazoefficiens BLL4011 and related proteins, cupin domain; This family includes bacterial and fungal proteins homologous to BLL4011, a Bradyrhizobium diazoefficiens 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        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 505383354  40 ATVTFEPGARTAWHTHPLGQTLIVTQGRGWLQEWGKEAEPLNQGDIAWIPPGVKH 94
Cdd:cd02235   22 VRVEIPPGAVAGRHTHPGEESGYVLEGSLELEVDGQPPVTLKAGDSFFIPAGTVH 76

Methanocaldococcus jannaschii MJ1618 and related proteins, cupin domain; This family includes bacterial and archaeal proteins homologous to MJ1618, a Methanocaldococcus jannaschii protein of unknown function with a cupin beta barrel domain. The active site of members of the cupin superfamily is generally located at the center of a conserved barrel and usually includes a metal ion.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 505383354  40 ATVTFEPGARTAWHTHPlGQTLI--VTQGRGwLQEWGKEAEPLNQGDIAWIPPGVKHW 95
Cdd:cd02214   22 AHARVPPGESTLPHRLK-GSEEVyyILEGEG-TMEIDGEPREVGPGDAVLIPPGAVQR 77

AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization domain of the bacterial gene regulatory protein AraC. The domain is found in conjunction with the helix-turn-helix (HTH) DNA-binding motif pfam00165. This domain is distantly related to the Cupin domain pfam00190.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 505383354   46 PGARTAWHTHPLGQTLIVTQGRGWLQEWGKEaEPLNQGDIAWIPPGVKH 94
Cdd:pfam02311  12 PGHSFPPHVHDFYVIGYIERGVGRFRLNGRT-YHLGPGDLFLLPPGEPH 59

AraC/XylS family transcriptional regulators similar to NimR, N-terminal cupin domain; This family contains mostly bacterial proteins containing an AraC/XylS family helix-turn-helix (HTH) DNA-binding domain C-terminal to a cupin domain, and may be possible transcriptional regulators. Included in this family is Escherichia coli HTH-type transcriptional regulator NimR (also called YeaM) that negatively regulates expression of the nimT operon and its own expression. 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        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505383354  37 VGGATVTFEPGARTAWHTHPLGQ-------TLIVTQGRG-WLQewgkeaePLNQGdiAWIPPGVKHWHGASAQTAMTHIA 108
Cdd:cd06124    1 VLARAADYPAGHRTPWHSHPWGQllyassgVMTVETEDGrWLV-------PPQRA--VWIPAGVEHSVRMLGAVELRSLY 71

                         90
                 ....*....|
gi 505383354 109 IA-EAVDGSP 117
Cdd:cd06124   72 IDpEAAAGLP 81

pectin degradation protein KdgF and related proteins, cupin domain; This family includes bacterial and archaeal pectin degradation protein KdgF that catalyzes the linearization of unsaturated uronates from both pectin and alginate, which are polysaccharides found in the cell walls of plants and brown algae, respectively, and represent an important source of carbon. These polysaccharides, mostly consisting of chains of uronates, can be metabolized by bacteria through a pathway of enzymatic steps to the key metabolite 2-keto-3-deoxygluconate (KDG). Pectin degradation is used by many plant-pathogenic bacteria during infection, and also, pectin and alginate can both represent abundant sources of carbohydrate for the production of biofuels. These proteins belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 505383354  42 VTFEPGARTAWHTHPLGQTLIVTQGRGWLQEwGKEAEPLNQGDIAWIPPGVKH 94
Cdd:cd02238   32 VRFEKGAVVPLHSHPHEQIGYVLSGRFEFTI-GGETRILKPGDSYYIPPNVPH 83

uncharacterized protein bxe_c0505, cupin domain; This family includes mostly bacterial proteins homologous to bxe_c0505, a Burkholderia xenovorans 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        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 505383354  35 AKVGGATVTFEPGarTAWHTHPLG-QTLIVTqgRGWLQEW--GKEAEPLNQGDIAWIPPGVKH 94
Cdd:cd06980   23 AHVIRATGGGEGP--TGWHYHDCDfQMVYVL--KGWVKFEfeGGGEVRLEAGDCVYQPPGIRH 81

AraC/XylS family transcriptional regulators similar to MmsR, N-terminal cupin domain; This family contains bacterial proteins containing an AraC/XylS family helix-turn-helix (HTH) DNA-binding domain C-terminal to a cupin domain, and may be possible transcriptional regulators. Included is MmsR, a bacterial transcriptional regulator thought to positively regulate the expression of the mmsAB operon. The mmsAB operon contains two structural genes involved in valine metabolism: mmsA which encodes methylmalonate-semialdehyde dehydrogenase, and mmsB which encodes 3-hydroxyisobutyrate dehydrogenase. The cupin domain of members of this subfamily does not contain a metal binding site.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 505383354  62 IVTQGRGWLQEWGKEAEpLNQGDIAWIPPGVKHWHGASAQT 102
Cdd:cd06986   33 YVLSGKGTFSVNGKTYH-LKAGQGFLIPPGEPHSYGADEDD 72

TcmJ monooxygenase and related proteins, cupin domain; This family includes TcmJ, a subunit of the tetracenomycin (TCM) polyketide synthase (PKS) type II complex in Streptomyces glaucescens. TcmJ is a quinone-forming monooxygenase involved in the modification of aromatic polyketides synthesized by polyketide synthases of types II and III. Orthologs of TcmJ include the Streptomyces BenD (benastatin biosynthetic pathway), the Streptomyces olivaceus ElmJ (polyketide antibiotic elloramycin biosynthetic pathway), the Actinomadura hibisca PdmL (pradimicin biosynthetic pathway), the Streptomyces cyaneus CurC (curamycin biosynthetic pathway), the Streptomyces rishiriensis Lct30 (lactonamycin biosynthetic pathway), and the Streptomyces WhiE II (spore pigment polyketide biosynthetic pathway). 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        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 505383354  34 PAKVGG-----ATVTFEPGARTAWHTHPLG-QTLIVTQGRGWLQEWGKEAePLNQGDIAWIPPGVKH 94
Cdd:cd06991   11 PKTVGAtsgfmGTLTLAPGERVSEHYHPYSeEFLYVVRGRLVVRVDGEPV-VLEAGEALLVPRGVRH 76