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 640582091  26 FKGTSYLKPLAESKE-AKTAVHNVSFEPGCRNNWHMHSVPQILIAVAGEGWYQEEGKPAQKLVPGDVVIVNPNTKHWHGA 104
Cdd:cd02233    1 FTGTVWLDPLFPADEpSRVSVANVTFEPGARTAWHTHPGGQILIVTSGVGWVQEEGGPPQELRPGDVVWIPPGVKHWHGA 80

                         90       100
                 ....*....|....*....|....*.
gi 640582091 105 TKDSWFAHLAIMVG--DSKNTWLKPV 128
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 640582091  26 FKGTSYLKPLAESKE-AKTAVHNVSFEPGCRNNWHMHSVPQILIAVAGEGWYQEEGKPAQKLVPGDVVIVNPNTKHWHGA 104
Cdd:cd02233    1 FTGTVWLDPLFPADEpSRVSVANVTFEPGARTAWHTHPGGQILIVTSGVGWVQEEGGPPQELRPGDVVWIPPGVKHWHGA 80

                         90       100
                 ....*....|....*....|....*.
gi 640582091 105 TKDSWFAHLAIMVG--DSKNTWLKPV 128
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        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 640582091   48 VSFEPGCRNNWHMHSV-PQILIAVAGEGWYQEEGKPaQKLVPGDVVIVNPNTKHWHGATKD 107
Cdd:pfam07883   3 VTLPPGESSPPHRHPGeDEFFYVLEGEGELTVDGEE-VVLKAGDSVYFPAGVPHRFRNTGD 62

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 640582091  26 FKGTSYLKPLAESKE-AKTAVHNVSFEPGCRNNWHMHSVPQILIAVAGEGWYQEEGKPAQKLVPGDVVIVNPNTKHWHGA 104
Cdd:cd02233    1 FTGTVWLDPLFPADEpSRVSVANVTFEPGARTAWHTHPGGQILIVTSGVGWVQEEGGPPQELRPGDVVWIPPGVKHWHGA 80

                         90       100
                 ....*....|....*....|....*.
gi 640582091 105 TKDSWFAHLAIMVG--DSKNTWLKPV 128
Cdd:cd02233   81 APDSAMTHLAITEAldGGGVEWLEPV 106

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 640582091  48 VSFEPGCRNNWHMHSVPQILIAVAGEGWYQEEGKPAQKLVPGDVVIVNPNTKH 100
Cdd:cd02235   24 VEIPPGAVAGRHTHPGEESGYVLEGSLELEVDGQPPVTLKAGDSFFIPAGTVH 76

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        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 640582091  45 VHNVSFEPGCRNNWHMHSV-PQILIAVAGEGWYQEEGKPAQKLVPGDVVIVNPNTKHWHGATKD 107
Cdd:cd02208    1 ISVVTLPPGTSSPPHWHPEqDEIFYVLSGEGELTLDDGETVELKAGDIVLIPPGVPHSFVNTSD 64

dimethylsulfoniopropionate lyase DddQ, cupin domain; Dimethylsulfoniopropionate (DMSP) is produced worldwide in large amounts, mainly by marine phytoplankton and macroalgae. DMSP lyase catalyzes the cleavage of DMSP to generate the volatile dimethyl sulfide (DMS) and plays a major role in the biogeochemical cycling of sulfur. When released into the atmosphere from the oceans, DMS is oxidized, forming cloud condensation nuclei that may influence weather and climate. DMSP lyase belongs to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 640582091  58 WHMHSVPQILIAVAGEGWYQEEGKPAQKLVPGDVVIVNPNTKHW 101
Cdd:cd20282   35 WHHHAAEEIYLVLAGSAEFLSEGQPPRRLGPGDTVFHASNQPHA 78

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 640582091  50 FEPGCRNNWHMHSVPQILIAVAGEGWYQEEGKPaQKLVPGDVVIVNPNTKHW 101
Cdd:cd02222   24 IEPGGHTPLHTHPWEHEVYVLRGKGVVVIGGEE-YPVKPGDVVYIPPNEPHQ 74

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        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 640582091  47 NVSFEPGCRNNWHMHSVpqiliaVAGEGWYQEEGKpAQKLVPGDVVIVNPNTKHWHGA-TKDSW 109
Cdd:cd06986   18 GHSYGPAVRDYYILHYV------LSGKGTFSVNGK-TYHLKAGQGFLIPPGEPHSYGAdEDDPW 74