Bacillus subtilis bacilysin and related proteins, N-terminal cupin domain; This model represents the N-terminal domain of bacilysin (BacB, also known as AerE in Microcystis aeruginosa), a non-ribosomally synthesized dipeptide antibiotic that is produced and excreted by certain strains of Bacillus subtilis. Bacilysin is an oxidase that catalyzes the synthesis of 2-oxo-3-(4-oxocyclohexa-2,5-dienyl)propanoic acid, a precursor to L-anticapsin. Each bacilysin monomer has two tandem cupin domains. It is active against a wide range of bacteria and some fungi. The antimicrobial activity of bacilysin is antagonized by glucosamine and N-acetyl glucosamine, indicating that bacilysin interferes with glucosamine synthesis, and thus, with the synthesis of microbial cell walls. AerE is thought to be involved in the formation of the 2-carboxy-6-hydroxyoctahydroindole (Choi) moiety found on all aeruginosin tetrapeptides, based on gene knock-out experiments. It is encoded by the aerE gene of the aerABCDEF Aeruginosin biosynthesis gene cluster in Microcystis aeruginosa. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837885258  11 YFPTPKLIEWENGVRQYSTVRGDTEVLMSYVPPHTNVEPHQHKEVQIGMVVSGELMMTVGDVTRKMTALESAYIAPPHVP 90
Cdd:cd20307     1 FFPVPKTIKLENGVELYSFQCQDTVVQLSYIAPGAVVELHQHPESQIGMVLSGELEMNVGGVKKVMEPLQDVYVAPPNVP 80

                          90       100
                  ....*....|....*....|
gi 1837885258  91 HGARNDTDQEVIAIDIKRLK 110
Cdd:cd20307    81 HGAVNPSSEEAVGLDIKRLK 100

Bacillus subtilis bacilysin and related proteins, N-terminal cupin domain; This model represents the N-terminal domain of bacilysin (BacB, also known as AerE in Microcystis aeruginosa), a non-ribosomally synthesized dipeptide antibiotic that is produced and excreted by certain strains of Bacillus subtilis. Bacilysin is an oxidase that catalyzes the synthesis of 2-oxo-3-(4-oxocyclohexa-2,5-dienyl)propanoic acid, a precursor to L-anticapsin. Each bacilysin monomer has two tandem cupin domains. It is active against a wide range of bacteria and some fungi. The antimicrobial activity of bacilysin is antagonized by glucosamine and N-acetyl glucosamine, indicating that bacilysin interferes with glucosamine synthesis, and thus, with the synthesis of microbial cell walls. AerE is thought to be involved in the formation of the 2-carboxy-6-hydroxyoctahydroindole (Choi) moiety found on all aeruginosin tetrapeptides, based on gene knock-out experiments. It is encoded by the aerE gene of the aerABCDEF Aeruginosin biosynthesis gene cluster in Microcystis aeruginosa. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837885258  11 YFPTPKLIEWENGVRQYSTVRGDTEVLMSYVPPHTNVEPHQHKEVQIGMVVSGELMMTVGDVTRKMTALESAYIAPPHVP 90
Cdd:cd20307     1 FFPVPKTIKLENGVELYSFQCQDTVVQLSYIAPGAVVELHQHPESQIGMVLSGELEMNVGGVKKVMEPLQDVYVAPPNVP 80

                          90       100
                  ....*....|....*....|
gi 1837885258  91 HGARNDTDQEVIAIDIKRLK 110
Cdd:cd20307    81 HGAVNPSSEEAVGLDIKRLK 100

Cupin domain protein related to quercetin dioxygenase [General function prediction only];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837885258  22 NGVRQYSTVRGDTEVLMSYV--PPHTNVEPHQHKEVQIGMVVSGELMMTVGDVTRKMTALESAYIaPPHVPHGARNDTDQ 99
Cdd:COG1917     9 TGVSVRVLADGEDELEVVRVtfEPGARTPWHSHPGEELIYVLEGEGEVEVGGEEYELKPGDVVFI-PPGVPHAFRNLGDE 87

                  ....*..
gi 1837885258 100 EVIAIDI 106
Cdd:COG1917    88 PAVLLVV 94

Cupin domain protein related to quercetin dioxygenase [General function prediction only];

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1837885258 156 GGEMPFHKHRNEQIGICIGGGYDMTVEGCTVEMKFGTAYFCEPREDHGAINRSEKESKSINIFFPPR 222
Cdd:COG1917    33 GARTPWHSHPGEELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFRNLGDEPAVLLVVFSPGL 99

Bacillus subtilis bacilysin and related proteins, N-terminal cupin domain; This model represents the N-terminal domain of bacilysin (BacB, also known as AerE in Microcystis aeruginosa), a non-ribosomally synthesized dipeptide antibiotic that is produced and excreted by certain strains of Bacillus subtilis. Bacilysin is an oxidase that catalyzes the synthesis of 2-oxo-3-(4-oxocyclohexa-2,5-dienyl)propanoic acid, a precursor to L-anticapsin. Each bacilysin monomer has two tandem cupin domains. It is active against a wide range of bacteria and some fungi. The antimicrobial activity of bacilysin is antagonized by glucosamine and N-acetyl glucosamine, indicating that bacilysin interferes with glucosamine synthesis, and thus, with the synthesis of microbial cell walls. AerE is thought to be involved in the formation of the 2-carboxy-6-hydroxyoctahydroindole (Choi) moiety found on all aeruginosin tetrapeptides, based on gene knock-out experiments. It is encoded by the aerE gene of the aerABCDEF Aeruginosin biosynthesis gene cluster in Microcystis aeruginosa. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837885258  11 YFPTPKLIEWENGVRQYSTVRGDTEVLMSYVPPHTNVEPHQHKEVQIGMVVSGELMMTVGDVTRKMTALESAYIAPPHVP 90
Cdd:cd20307     1 FFPVPKTIKLENGVELYSFQCQDTVVQLSYIAPGAVVELHQHPESQIGMVLSGELEMNVGGVKKVMEPLQDVYVAPPNVP 80

                          90       100
                  ....*....|....*....|
gi 1837885258  91 HGARNDTDQEVIAIDIKRLK 110
Cdd:cd20307    81 HGAVNPSSEEAVGLDIKRLK 100

Bacillus subtilis bacilysin and related proteins, cupin domain; Bacilysin (BacB, also known as AerE in Microcystis aeruginosa) is a non-ribosomally synthesized dipeptide antibiotic that is produced and excreted by certain strains of Bacillus subtilis. It is an oxidase that catalyzes the synthesis of 2-oxo-3-(4-oxocyclohexa-2,5-dienyl)propanoic acid, a precursor to L-anticapsin. Each bacilysin monomer has two tandem cupin domains. It is active against a wide range of bacteria and some fungi. The antimicrobial activity of bacilysin is antagonized by glucosamine and N-acetyl glucosamine, indicating that bacilysin interferes with glucosamine synthesis, and thus, with the synthesis of microbial cell walls. AerE is thought to be involved in the formation of the 2-carboxy-6-hydroxyoctahydroindole (Choi) moiety found on all aeruginosin tetrapeptides, based on gene knock-out experiments. It is encoded by the aerE gene of the aerABCDEF aeruginosin biosynthesis gene cluster in Microcystis aeruginosa.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837885258  16 KLIEWENGVRQYSTVRGDTEVLMSYVPPHTNVEPHQHKEVQIGMVVSGELMMTVGDVTRKMTALESAYIAPPHVPHGARN 95
Cdd:cd06975     1 KTIKLETGVELQFFVGSWTEIMLSYIPPGAKMPLHQHREEQIGMILNGELEMTVGGEEQELEPLGDVYYAPPNVPHGAVN 80

                          90
                  ....*....|...
gi 1837885258  96 DTDQEVIAIDIKR 108
Cdd:cd06975    81 PSDETAVLLDIKR 93

Bacillus subtilis bacilysin and related proteins, C-terminal cupin domain; This model represents the C-terminal domain of bacilysin (BacB, also known as AerE in Microcystis aeruginosa), a non-ribosomally synthesized dipeptide antibiotic that is produced and excreted by certain strains of Bacillus subtilis. Bacilysin is an oxidase that catalyzes the synthesis of 2-oxo-3-(4-oxocyclohexa-2,5-dienyl)propanoic acid, a precursor to L-anticapsin. Each bacilysin monomer has two tandem cupin domains. It is active against a wide range of bacteria and some fungi. The antimicrobial activity of bacilysin is antagonized by glucosamine and N-acetyl glucosamine, indicating that bacilysin interferes with glucosamine synthesis, and thus, with the synthesis of microbial cell walls. AerE is thought to be involved in the formation of the 2-carboxy-6-hydroxyoctahydroindole (Choi) moiety found on all aeruginosin tetrapeptides, based on gene knock-out experiments. It is encoded by the aerE gene of the aerABCDEF aeruginosin biosynthesis gene cluster in Microcystis aeruginosa. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1837885258  35 EVLMSYVPPHTNVEPHQHKEVQIGMVVSGELMMTVGDVTRKMTaLESAYIAPPHVPHGARNDTDQEVIAIDI 106
Cdd:cd10547    20 EIMISQIPPGGKMPLHQHRGEQIGIILNGKYDMTVGGEEQELG-YGKIYYAPPNVSHSGYNDSDETATLINI 90

Cupin domain protein related to quercetin dioxygenase [General function prediction only];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837885258  22 NGVRQYSTVRGDTEVLMSYV--PPHTNVEPHQHKEVQIGMVVSGELMMTVGDVTRKMTALESAYIaPPHVPHGARNDTDQ 99
Cdd:COG1917     9 TGVSVRVLADGEDELEVVRVtfEPGARTPWHSHPGEELIYVLEGEGEVEVGGEEYELKPGDVVFI-PPGVPHAFRNLGDE 87

                  ....*..
gi 1837885258 100 EVIAIDI 106
Cdd:COG1917    88 PAVLLVV 94

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        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837885258 129 RDLLPGMEVTFFVED----WVEIMLAKipgnGGEMPFHKHRNEQIGICIGGGYDMTVEGCTVEMKFGTAYFCEPREDHGA 204
Cdd:cd02238    10 EELGPGVRRKILAGGeklmLVEVRFEK----GAVVPLHSHPHEQIGYVLSGRFEFTIGGETRILKPGDSYYIPPNVPHGA 85

                          90
                  ....*....|....*...
gi 1837885258 205 INRseKESKSINIFFPPR 222
Cdd:cd02238    86 EAL--EDSVLLDVFSPPR 101

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 1837885258  41 VPPHTNVEPHQHKEVQIGMVVSGELMMTVGDVTRKMTALESAYIaPPHVPHGARNDTDQEVIAIDI 106
Cdd:cd06988     9 VRPGTTSTPHSHHEYEIFIVISGKGIVVVDGEREPVKAGDVVYI-PPGTEHYVKNDGDEDFEFYSI 73

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 1837885258 156 GGEMPFHKHRNE-QIGICIGGGYDMTVEGCTVEMKFGTAYFCEPREDHGAINRSEKESKSINIF 218
Cdd:pfam07883   8 GESSPPHRHPGEdEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPHRFRNTGDEPARLLDVY 71

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        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1837885258  35 EVLMSYVPPH-TNVEPHQHKEVQIGMVVSGELMMTVGDVTRKMTALESAYIaPPHVPHGARNDTDQEVIAI 104
Cdd:cd02209    17 EPFLVTLPPGgSGGEPYSHEGEEFGYVLEGELELTVGGETYVLEAGDSIYF-DSDVPHRYRNPGDEPARVL 86

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 1837885258  40 YVPPHTNvePHQHkEVqigMVVSGELMMTVGDVTRKMTALESAYIaPPHVPHGARNDTDQE 100
Cdd:cd02222    29 HTPLHTH--PWEH-EV---YVLRGKGVVVIGGEEYPVKPGDVVYI-PPNEPHQFRNTGDEP 82

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 1837885258 156 GGEMPFHKHRN-EQIGICI-GGGYDMTVEGCTVEMKFGTAYFCEPREDHGAINRSEKESKSINIF 218
Cdd:cd02208     9 GTSSPPHWHPEqDEIFYVLsGEGELTLDDGETVELKAGDIVLIPPGVPHSFVNTSDEPAVFLVVS 73

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 1837885258 156 GGEMPFHKHRNEQIGICIGGGYDMTVEGCTVEMKFGTAYFCEPREDHGAINRSEKE 211
Cdd:cd02222    27 GGHTPLHTHPWEHEVYVLRGKGVVVIGGEEYPVKPGDVVYIPPNEPHQFRNTGDEP 82

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        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1837885258  41 VPPHTNVEPHQHKEVQIGMVVSGELMMTV-GDVTRKMTALESAYIaPPHVPHGARNDTDQEV 101
Cdd:cd02235    26 IPPGAVAGRHTHPGEESGYVLEGSLELEVdGQPPVTLKAGDSFFI-PAGTVHNAKNVGSGPA 86