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 557613310   3 VIPVSAERTTEVLDGVHLAQAAAGERASVQHFRIEPGATVDRHAHENEQLGWLAAGSLVFRLDGETVTVEAGDSYAIGGG 82
Cdd:cd02238    1 FVKWDELPWEELGPGVRRKILAGGEKLMLVEVRFEKGAVVPLHSHPHEQIGYVLSGRFEFTIGGETRILKPGDSYYIPPN 80

                         90       100
                 ....*....|....*....|....
gi 557613310  83 ERHGAHNRgdEDAVGVEVFVPPRE 106
Cdd:cd02238   81 VPHGAEAL--EDSVLLDVFSPPRE 102

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 557613310   3 VIPVSAERTTEVLDGVHLAQAAAGERASVQHFRIEPGATVDRHAHENEQLGWLAAGSLVFRLDGETVTVEAGDSYAIGGG 82
Cdd:cd02238    1 FVKWDELPWEELGPGVRRKILAGGEKLMLVEVRFEKGAVVPLHSHPHEQIGYVLSGRFEFTIGGETRILKPGDSYYIPPN 80

                         90       100
                 ....*....|....*....|....
gi 557613310  83 ERHGAHNRgdEDAVGVEVFVPPRE 106
Cdd:cd02238   81 VPHGAEAL--EDSVLLDVFSPPRE 102

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 557613310   33 HFRIEPGATVDRHAHENE-QLGWLAAGSLVFRLDGETVTVEAGDSYAIGGGERHGAHNRGDEDAVGVEVF 101
Cdd:pfam07883   2 LVTLPPGESSPPHRHPGEdEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPHRFRNTGDEPARLLDVY 71

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 557613310   3 VIPVSAERTTEVLDGVHLAQAAAGERASVQHFRIEPGATVDRHAHENEQLGWLAAGSLVFRLDGETVTVEAGDSYAIGGG 82
Cdd:cd02238    1 FVKWDELPWEELGPGVRRKILAGGEKLMLVEVRFEKGAVVPLHSHPHEQIGYVLSGRFEFTIGGETRILKPGDSYYIPPN 80

                         90       100
                 ....*....|....*....|....
gi 557613310  83 ERHGAHNRgdEDAVGVEVFVPPRE 106
Cdd:cd02238   81 VPHGAEAL--EDSVLLDVFSPPRE 102

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557613310   6 VSAERTTEVLDGVHLAQAAAGERASVQHFRIEPGATVDRHAHEN-EQLGWLAAGSLVFRLDGETVTVEAGDSYAIGGGER 84
Cdd:COG0662    4 VNIEELKAIGWGSYEVLGEGGERLSVKRITVPPGAELSLHVHPHrDEFFYVLEGTGEVTIGDEEVELKAGDSVYIPAGVP 83

                         90       100
                 ....*....|....*....|
gi 557613310  85 HGAHNRGDEDAVGVEVFVPP 104
Cdd:COG0662   84 HRLRNPGDEPLELLEVQAPA 103

Uncharacterized conserved protein, cupin superfamily [Function unknown];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557613310  20 LAQAAAGERASVQHFRIEPGA-TVDRHAH-ENEQLGWLAAGSLVFRLDGETVTVEAGDSYAIGGGERHGAHNRGDEDAVG 97
Cdd:COG3837   19 LGDALGLTRLGVNLITLPPGAsSSPYHAHsAEEEFVYVLEGELTLRIGGEEYVLEPGDSVGFPAGVPHRLRNRGDEPARY 98

                         90
                 ....*....|....
gi 557613310  98 VEVFVPPRESPPWE 111
Cdd:COG3837   99 LVVGTRAPYPDSFD 112

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 557613310  31 VQHFRIEPGATVDRHAHENEQLGWLAAGSLVFRLDGETVTVEA-GDSYAIGGGERHGAHNRGDEDAVGVEV 100
Cdd:cd20307   26 VQLSYIAPGAVVELHQHPESQIGMVLSGELEMNVGGVKKVMEPlQDVYVAPPNVPHGAVNPSSEEAVGLDI 96

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 557613310  36 IEPGATVDRHAHENEQLGWLAAGSLVFRLDGETVTVEAGDSYAIGGGERHGAHNRGDEDAVGVEVFV 102
Cdd:cd10547   26 IPPGGKMPLHQHRGEQIGIILNGKYDMTVGGEEQELGYGKIYYAPPNVSHSGYNDSDETATLINIFI 92

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        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557613310  10 RTTEVLDGVHLAQAAAGERASVQHFRIEPGATVDRHAHENEQLGWLAAGSL-VFRLDGETVTVEAGDSYAIGGGERHGAH 88
Cdd:cd02236    3 KTTTTWDGQPIPYPEGQPEITVLRITIPPGAELPWHTHPVPNAGYVLSGELtVEYEDGKKRTFKAGDAFVEAVNTWHRGR 82

                 ....*...
gi 557613310  89 NRGDEDAV 96
Cdd:cd02236   83 NGGDEPVE 90

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        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 557613310  33 HFRIEPGATVDRHAHEN-EQLGWLAAGSLVFRLD-GETVTVEAGDSYAIGGGERHGAHNRGDEDAVGVEVF 101
Cdd:cd02208    3 VVTLPPGTSSPPHWHPEqDEIFYVLSGEGELTLDdGETVELKAGDIVLIPPGVPHSFVNTSDEPAVFLVVS 73

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 557613310  36 IEPGATVDRHAHENEQLGWL-AAGSLVFRLDGETVTVEAGDSYAIGGGERHGAHNRGDEDAV 96
Cdd:cd02221   26 LPPGSSIGYHQHEGEFEIYYiLSGEGLYTDNGKEYEVKAGDVTFTRDGESHGIENTGDEDLV 87

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 557613310  34 FRIEPGATVDRHAHENEQLGWLAAGSLVFRLDGETVTVEAGDSYAIGGGERHGAHNRGDED 94
Cdd:cd02222   22 FEIEPGGHTPLHTHPWEHEVYVLRGKGVVVIGGEEYPVKPGDVVYIPPNEPHQFRNTGDEP 82

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        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557613310  18 VHLAQAAAGERASVQHFRIEPGA-TVDRHAHE-NEQLGWLAAGSLVFRLDGETVTVEAGDSYA--IGGGERHGAHNRGDE 93
Cdd:cd02224    6 RSLGDAAGLTQLGVNLERLPPGArSSPRHWHSaEEEFVYVLSGEGTLRLDGEEVLPRPGDFVGfpAGTGVAHQLINRSDE 85

                 ...
gi 557613310  94 DAV 96
Cdd:cd02224   86 PLV 88

Oxalate decarboxylase (OxDC), cupin domain; Oxalate decarboxylase (OxDC; EC 4.1.1.2) 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 and both domains are included in this alignment. Each OxDC cupin domain contains one manganese binding site, with four manganese binding residues (three histidines and one glutamate) conserved as well as a number of hydrophobic residues. Members of this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 557613310  35 RIEPGATVDRHAHENE-QLGWLAAGSL---VFRLDG--ETVTVEAGDSYAIGGGERHGAHNRGDEDAVGVEVF 101
Cdd:cd02240   33 RVAPGAMRELHWHPNTaEWQYVISGSArvtVFDEDGrfETFNLGAGDVGYVPSGSGHHIENIGDEDAEFLLIF 105

Rhizobium leguminosarum YP_766765.1 and related proteins, cupin domain; This family includes mostly bacterial proteins homologous to Rhizobium leguminosarum YP_766765.1, a 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 557613310  27 ERASVQHFRIEPGATVDRHAHENEQLGWLAAGSLVFRLDGETVTVEAGDSYAIGGGERHGAHNRGDEDA 95
Cdd:cd20299   15 ECAWVGLSHFLPGGGAETDASPREKVYVVLEGELTVTTDGEEVVLGPGDSCYIPPGETRSIDNRTNGPA 83