Bacillus halodurans Bh2720 and related proteins, cupin domain; This family includes bacterial, archaeal, and eukaryotic proteins similar to Bh2720, a Bacillus halodurans protein of unknown function with a cupin beta-barrel fold.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1054968252  18 FQKEVYYDDNCQVVLMSIEPGEDIGEETH-DADQTTFFVAGEGQAVVDGSRTKVTPNHMIVIPKGAKHNIINKGDEPLKL 96
Cdd:cd02223     1 FRRVLWTGKNLQLVLMSIPPGEDIGLEVHdDVDQFLRIEEGEGKAIMGGFESEVKDGDAIIVPAGTWHNVINTGNEPLKL 80

                          90
                  ....*....|....*...
gi 1054968252  97 FTIYSPPAEEQGIAHKTK 114
Cdd:cd02223    81 YTIYAPPEHPDGTVHKTK 98

Bacillus halodurans Bh2720 and related proteins, cupin domain; This family includes bacterial, archaeal, and eukaryotic proteins similar to Bh2720, a Bacillus halodurans protein of unknown function with a cupin beta-barrel fold.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1054968252  18 FQKEVYYDDNCQVVLMSIEPGEDIGEETH-DADQTTFFVAGEGQAVVDGSRTKVTPNHMIVIPKGAKHNIINKGDEPLKL 96
Cdd:cd02223     1 FRRVLWTGKNLQLVLMSIPPGEDIGLEVHdDVDQFLRIEEGEGKAIMGGFESEVKDGDAIIVPAGTWHNVINTGNEPLKL 80

                          90
                  ....*....|....*...
gi 1054968252  97 FTIYSPPAEEQGIAHKTK 114
Cdd:cd02223    81 YTIYAPPEHPDGTVHKTK 98

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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1054968252  31 VLMSIEPGEDIGEETHDADQTTFFV-AGEGQAVVDGSRTKVTPNHMIVIPKGAKHNIINKGDEPLKLFTIY 100
Cdd:pfam07883   1 GLVTLPPGESSPPHRHPGEDEFFYVlEGEGELTVDGEEVVLKAGDSVYFPAGVPHRFRNTGDEPARLLDVY 71

Bacillus halodurans Bh2720 and related proteins, cupin domain; This family includes bacterial, archaeal, and eukaryotic proteins similar to Bh2720, a Bacillus halodurans protein of unknown function with a cupin beta-barrel fold.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1054968252  18 FQKEVYYDDNCQVVLMSIEPGEDIGEETH-DADQTTFFVAGEGQAVVDGSRTKVTPNHMIVIPKGAKHNIINKGDEPLKL 96
Cdd:cd02223     1 FRRVLWTGKNLQLVLMSIPPGEDIGLEVHdDVDQFLRIEEGEGKAIMGGFESEVKDGDAIIVPAGTWHNVINTGNEPLKL 80

                          90
                  ....*....|....*...
gi 1054968252  97 FTIYSPPAEEQGIAHKTK 114
Cdd:cd02223    81 YTIYAPPEHPDGTVHKTK 98

Xanthomonas campestris XcTcmJ and related proteins, cupin domain; This family includes bacterial and archaeal proteins homologous to plant pathogen Xanthomonas campestris tetracenomycin polyketide synthesis protein XcTcmJ, a protein encoded by the tcmJ gene. XcTcmJ is annotated as being involved in tetracenomycin polyketide biosynthesis. Also included is Xc5357 from a different strain of X. campestris. Structure studies show that binding of zinc induces conformational changes and serves a functional role in this cupin protein. 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 1054968252  25 DDNCQVVLMSIEPGEDIG--EETH-DADQTTFFVAGEGQAVVDGSRTKVTPNHMIVIPKGAKHNIINKGDEPLKLFTIYS 101
Cdd:cd07006     7 TERSQAATMVLAPGDTEGgpDNRHrGSDQWLYVVSGSGEAIVEGERVALKPGSLLLIEAGETHEIRNTGDEPLKTLNFYV 86

                  ...
gi 1054968252 102 PPA 104
Cdd:cd07006    87 PPA 89

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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1054968252  31 VLMSIEPGEDIGEETHDADQTTFFV-AGEGQAVVDGSRTKVTPNHMIVIPKGAKHNIINKGDEPLKLFTIY 100
Cdd:pfam07883   1 GLVTLPPGESSPPHRHPGEDEFFYVlEGEGELTVDGEEVVLKAGDSVYFPAGVPHRFRNTGDEPARLLDVY 71

Dimethylsulfoniopropionate lyase DddK and related proteins, cupin domain; This family includes mostly bacterial proteins homologous to dimethylsulfoniopropionate lyase DddK from marine bacterium Pelagibacter. DddK cleaves dimethylsulfoniopropionate (DMSP), the organic osmolyte and antioxidant produced in marine environments, and yields acrylate and the climate-active gas dimethyl sulfide (DMS). DddK contains a double-stranded beta-helical motif which utilizes various divalent metal ions as cofactors for catalytic activity; however, nickel, an abundant metal ion in marine environments, confers the highest DMSP lyase activity. Also included in this family is Plu4264, a Photorhabdus luminescens manganese-containing cupin shown to have similar metal binding site to TM1287 decarboxylase, but two very different substrate binding pockets. The Plu4264 binding pocket shows a cavity and substrate entry point more than twice as large as and more hydrophobic than TM1287, suggesting that Plu4264 accepts a substrate that is significantly larger than that of TM1287, a putative oxalate decarboxylase. Thus, the function of Plu4264 could be similar to that of TM1287 but with a larger, less charged substrate. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1054968252  35 IEPGEDIGEETHDADQTTFFVAGEGQAVVDGSRTKVTPNHMIVIPKGAKHNIINKGDEPLKLFTIY 100
Cdd:cd06988     9 VRPGTTSTPHSHHEYEIFIVISGKGIVVVDGEREPVKAGDVVYIPPGTEHYVKNDGDEDFEFYSIW 74

Thermotoga maritima TM1287 decarboxylase, cupin domain; This family includes bacterial proteins homologous to TM1287 decarboxylase, a Thermotoga maritima manganese-containing cupin thought to catalyze the conversion of oxalate to formate and carbon dioxide, due to its similarity to oxalate decarboxylase (OXDC) from Bacillus subtilis. TM1287 shows a cupin fold with a conserved "jelly roll-like" beta-barrel fold and forms a homodimer.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1054968252  33 MSIEPGEDIGEETHDADQTTFFV-AGEGQAVVDGSRTKVTPNHMIVIPKGAKHNIINKGDEPLKLF 97
Cdd:cd02221    24 VTLPPGSSIGYHQHEGEFEIYYIlSGEGLYTDNGKEYEVKAGDVTFTRDGESHGIENTGDEDLVFI 89

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        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1054968252  27 NCQVVLMSIEPGEDIGEETHDADQTTFFVAGEGQAVVDGSRTKVTPNHMIVIPKGAKHNIINKGDEPLK 95
Cdd:cd02222    16 NFAMRYFEIEPGGHTPLHTHPWEHEVYVLRGKGVVVIGGEEYPVKPGDVVYIPPNEPHQFRNTGDEPLG 84

Microcystis aeruginosa MAE_RS03005 and related proteins, cupin domain; This family includes bacterial and some eukaryotic proteins homologous to MAE_RS03005, a Microcystis aeruginosa 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 1054968252  45 THDADQTTFFV-AGEGQAVVDGSRTKVTPNHMIVIPKGAKHNIINKGDEPLKLFTIYSP 102
Cdd:cd06987    45 THPAAHEMFFVlAGEGRAYCDGQRVPLRPGDALVVPPGSEHVIENTGSGRLYCLTLMVP 103

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        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1054968252  31 VLMSIEPGEDIGEETH-DADQTTFFVAGEG----QAVVDGSRT-KVTPNHMIVIPKGAKHNIINKGDEPLKLFTIYSPPA 104
Cdd:COG2140     6 GLTVLEPGGVREEHWHpNAAEWYYVLSGEArmtvQDPPGRARTvDVGPGDVVYVPPGYGHYIINTGDEPLVFLAVFDDDA 85

Klebsiella pneumoniae yp_001338853.1 and related proteins, cupin domain; This family includes bacterial proteins homologous to Klebsiella pneumoniae yp_001338853.1, an uncharacterized conserved protein with double-stranded beta-helix domain. 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 1054968252  21 EVYYDDNCQVVLMSIEPGEDIGEETHDADQTTFFV-AGEGQAVVDGSRTK-VTPNHMIVIPKGAKHNIINKGDEPLKLFT 98
Cdd:cd07008    20 VITETDDSAIVVWHVKPGQEIAAHIHPHGQDTWIVlSGEGEYLLGDGQTVpIKAGDIVIAPAGQVHGARNTGDEPLVFVS 99

                  ..
gi 1054968252  99 IY 100
Cdd:cd07008   100 VV 101

uncharacterized Methanocaldococcus jannaschii Moth_1897 and related proteins, cupin domain; This family includes archaeal and bacterial proteins homologous to Moth_1897, a Methanocaldococcus jannaschii 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        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1054968252  20 KEVYYDDNCQVVLMSIEPGEDIGEETHDADQTTFFVAGEGQAVVDGSRTKVTPNHMIVIPKGAKHNIINKGDEPLKLFTI 99
Cdd:cd06984     3 RKLYDTEHAQIVHITLKPGESLKKHITPVDVFFYVLEGEGIVEIGEEKQEVEADTLIESPANIPHCLYNESDADLRVLVI 82

Thermus thermophilus TTHA0104 and related proteins, cupin domain; This family contains bacterial proteins including TTHA0104 (also called TT1209), a putative antibiotic synthesis protein from Thermus thermophilus. TTHA0104 is a cupin-like protein. The 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).

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1054968252  36 EPGEDIGEETH-DADQTTFFVAGEGQAVVDGSRTKVTPNHMIVIPKGAKHNIINKGDEPLKLFTIYSP 102
Cdd:cd06122    35 EPGQSQKVHAHaGSDKVYFVLEGEGRFTVGDEERELGAGEAVLAPAGVPHGVRNTGAERLVLLVFMAP 102

Desulfitobacterium hafniense dsy2733 and related proteins, cupin domain; This family includes bacterial proteins homologous to dsy2733, a Desulfitobacterium hafniense 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 1054968252  26 DNCQVVLMSIEPGEDIGEETHDADQTTFFVAGEGQAVVDGSRTKVTPNHMIVIPKGAKHNIINKGD 91
Cdd:cd06983     8 DNVQISLFAFADGESVSEEEYFGDTLYYVLEGEAEITIGDEKHRLKAGDVLAVPAGVLHAIGGLGA 73

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        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1054968252  58 EGQAVV-----DGSRT--KVTPNHMIVIPKGAKHNIINKGDEPLKLFTIYSPPAEE 106
Cdd:cd20306    63 SGEARVsildpTGSLDtfTVKPGQVVFIPQGWLHWIENVGDEEAHLLIFFNHETPE 118

acireductone dioxygenase (ARD), cupin domain; Acireductone dioxygenase (ARD; also known as 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase) catalyzes the oxidation of 1,2-dihydroxy-3-keto-5-methylthiopentene to yield two different products depending on which active site metal is present (Fe2+ or Ni2+) as part of the methionine salvage pathway. The ARD apo-enzyme, obtained after the metal is removed, is catalytically inactive. The Fe(II)-ARD reaction yields an alpha-keto acid and formic acid, while Ni(II)-ARD instead catalyzes a shunt out of the methionine salvage pathway, yielding methylthiocarboxylic acid, formic acid, and CO. ARD belongs to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1054968252  43 EETHDADQTTFFVAGEGQ-AVVDGS----RTKVTPNHMIVIPKGAKH 84
Cdd:cd02232    64 EHLHEDDEVRFILDGSGYfDVRDKDdewiRILVEKGDLIVVPAGIYH 110

Silicibacter pomeroyi SPO2919 and related proteins, uncharacterized sugar phosphate isomerase with a cupin domain; This family includes proteins similar to sugar phosphate isomerase SPO2919 from Silicibacter pomeroyi and Afe_0303 from Acidithiobacillus ferrooxidans, but are as yet uncharacterized. 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 1054968252  53 FFV-AGEGQAVVDGSRTKVTPNHMIVIPKGAK--HNIINKGDEPLKLFTI 99
Cdd:cd02224    43 VYVlSGEGTLRLDGEEVLPRPGDFVGFPAGTGvaHQLINRSDEPLVYLVV 92

gentisate 1,2-dioxygenase, 1-hydroxy-2-naphthoate dioxygenase, and salicylate 1,2-dioxygenase bicupin aromatic ring-cleaving dioxygenases, C-terminal cupin domain; This model represents the C-terminal cupin domains of three closely related bicupin aromatic ring-cleaving dioxygenases: gentisate 1,2-dioxygenase (GDO), salicylate 1,2-dioxygenase (SDO), and 1-hydroxy-2-naphthoate dioxygenase (NDO). GDO catalyzes the cleavage of the gentisate (2,5-dihydroxybenzoate) aromatic ring, a key step in the gentisate degradation pathway allowing soil bacteria to utilize 2,5-xylenol, 3,5-xylenol, and m-cresol as sole carbon and energy sources. NDO catalyzes the cleavage of 1-hydroxy-2-naphthoate as part of the bacterial phenanthrene degradation pathway. SDO is a ring cleavage dioxygenase from Pseudaminobacter salicylatoxidans that oxidizes salicylate to 2-oxohepta-3,5-dienedioic acid via a novel ring fission mechanism. SDO differs from other known GDO's and NDO's in its unique ability to oxidatively cleave many different salicylate, gentisate, and 1-hydroxy-2- naphthoate substrates with high catalytic efficiency. The active site of this enzyme is located in the N-terminal domain but could be influenced by changes in the C-terminal domain, which lacks the strictly conserved metal-binding residues found in other cupin domains and is thought to be an inactive vestigial remnant.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1054968252  55 VAGEGQAVVDGSRTKVTPNHMIVIPKGAKHNIINkGDEPLKLF 97
Cdd:cd06992    46 VEGSGRTVIGGKTFEWEPGDVFVVPSWAWHSHEA-DSEDAVLF 87

gentisate 1,2-dioxygenase, 1-hydroxy-2-naphthoate dioxygenase, and salicylate 1,2-dioxygenase, N-terminal cupin domain; This family includes the N-terminal cupin domains of three closely related bicupin aromatic ring-cleaving dioxygenases: gentisate 1,2-dioxygenase (GDO), salicylate 1,2-dioxygenase (SDO), and 1-hydroxy-2-naphthoate dioxygenase (NDO). GDO catalyzes the cleavage of the gentisate (2,5-dihydroxybenzoate) aromatic ring, a key step in the gentisate degradation pathway allowing soil bacteria to utilize 2,5-xylenol, 3,5-xylenol, and m-cresol as sole carbon and energy sources. NDO catalyzes the cleavage of 1-hydroxy-2-naphthoate as part of the bacterial phenanthrene degradation pathway. SDO is a ring cleavage dioxygenase from Pseudaminobacter salicylatoxidans that oxidizes salicylate to 2-oxohepta-3,5-dienedioic acid via a novel ring fission mechanism. SDO differs from other known GDOs and NDOs in its unique ability to oxidatively cleave many different salicylate, gentisate and 1-hydroxy-2-naphthoate substrates with high catalytic efficiency. The active site of these enzymes is located in the N-terminal domain but could be influenced by changes in the C-terminal domain, which lacks the strictly conserved metal-binding residues found in other cupin domains and is thought to be an inactive vestigial remnant.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1054968252  35 IEPGEDIGEETHDADQTTFFVAGEGQA-VVDGSRTKVTPNHMIVIPKGAKHNIINKGDEP 93
Cdd:cd02216    28 LPPGEVAPAHRHTPNALRFVLEGPGAYtTVDGERCDMEPGDLILTPPGTWHDHGNEGDEP 87

Acireductone dioxygenase (methionine salvage), cupin superfamily [Amino acid transport and metabolism];

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1054968252  43 EETHDADQTTFFVAGEGQ--AVVDGS--RTKVTPNHMIVIPKGAKH 84
Cdd:COG1791    95 EHTHTEDEVRFFVAGEGLfgLHLGGKvyEVLCEAGDLISVPAGTEH 140