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 1770065902   4 FFINNEQPWEELGGGIKRKIVAYTDDLMAVHLSFDKGAIGHPHTHEiHDQIGYVVRGSFEAEIEGEKKVLKEGDAYFARK 83
Cdd:cd02238     1 FVKWDELPWEELGPGVRRKILAGGEKLMLVEVRFEKGAVVPLHSHP-HEQIGYVLSGRFEFTIGGETRILKPGDSYYIPP 79

                          90       100
                  ....*....|....*....|....*.
gi 1770065902  84 HMMHGAVALEqDSILLDIFNPAREDF 109
Cdd:cd02238    80 NVPHGAEALE-DSVLLDVFSPPREDF 104

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 1770065902   4 FFINNEQPWEELGGGIKRKIVAYTDDLMAVHLSFDKGAIGHPHTHEiHDQIGYVVRGSFEAEIEGEKKVLKEGDAYFARK 83
Cdd:cd02238     1 FVKWDELPWEELGPGVRRKILAGGEKLMLVEVRFEKGAVVPLHSHP-HEQIGYVLSGRFEFTIGGETRILKPGDSYYIPP 79

                          90       100
                  ....*....|....*....|....*.
gi 1770065902  84 HMMHGAVALEqDSILLDIFNPAREDF 109
Cdd:cd02238    80 NVPHGAEALE-DSVLLDVFSPPREDF 104

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 1770065902  33 VHLSFDKGAIGHPHTHEIHDQIGYVVRGSFEAEIEGEKKVLKEGDAYFARKHMMHGAVAL-EQDSILLDIF 102
Cdd:pfam07883   1 GLVTLPPGESSPPHRHPGEDEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPHRFRNTgDEPARLLDVY 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 1770065902   4 FFINNEQPWEELGGGIKRKIVAYTDDLMAVHLSFDKGAIGHPHTHEiHDQIGYVVRGSFEAEIEGEKKVLKEGDAYFARK 83
Cdd:cd02238     1 FVKWDELPWEELGPGVRRKILAGGEKLMLVEVRFEKGAVVPLHSHP-HEQIGYVLSGRFEFTIGGETRILKPGDSYYIPP 79

                          90       100
                  ....*....|....*....|....*.
gi 1770065902  84 HMMHGAVALEqDSILLDIFNPAREDF 109
Cdd:cd02238    80 NVPHGAEALE-DSVLLDVFSPPREDF 104

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1770065902  40 GAIGHPHTHEiHDQIGYVVRGSFEAEIEGEKKVLK-EGDAYFARKHMMHGAV-ALEQDSILLDIF 102
Cdd:cd06975    29 GAKMPLHQHR-EEQIGMILNGELEMTVGGEEQELEpLGDVYYAPPNVPHGAVnPSDETAVLLDIK 92

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1770065902  40 GAIGHPHTHEIHdQIGYVVRGSFEAEIEGEKKVLK-EGDAYFARKHMMHGAV-ALEQDSILLDI 101
Cdd:cd20307    34 GAVVELHQHPES-QIGMVLSGELEMNVGGVKKVMEpLQDVYVAPPNVPHGAVnPSSEEAVGLDI 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
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1770065902  45 PHTHEiHDQIGYVVRGSFEAEIEGEKKVLKEGDAYFARKHMMHGAV-ALEQDSILLDIF 102
Cdd:cd10547    34 LHQHR-GEQIGIILNGKYDMTVGGEEQELGYGKIYYAPPNVSHSGYnDSDETATLINIF 91

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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1770065902  18 GIKRKIVAYTD------DLMAVHLSFDKGAIGHPHTHEiHDQIGYVVRGSFEAEIEGE-KKVLKEGDAYF 80
Cdd:cd02235     1 GIKRTVLQRTDlsvpgrEVVQVRVEIPPGAVAGRHTHP-GEESGYVLEGSLELEVDGQpPVTLKAGDSFF 69

Uncharacterized conserved protein, cupin superfamily [Function unknown];

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1770065902  40 GAIGHPHTHEIHDQIGYVVRGSFEAEIEGEKKVLKEGDAYFARKHMMHG 88
Cdd:COG3837    39 ASSSPYHAHSAEEEFVYVLEGELTLRIGGEEYVLEPGDSVGFPAGVPHR 87

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        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1770065902   7 NNEQPWEELGGGIKRKIVAY---TDDLMAVHLSFDKGAIGHPHTHEIHDQIGYVVRGS-----FEAEIEGEKKVLKEGDA 78
Cdd:cd02240     1 DSEPIEENAGGSVRIATVTNfpiSKDLSSALVRVAPGAMRELHWHPNTAEWQYVISGSarvtvFDEDGRFETFNLGAGDV 80

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1770065902  79 YFARKHMMHGAVAL-EQDSILLDIF-NPAREDFL 110
Cdd:cd02240    81 GYVPSGSGHHIENIgDEDAEFLLIFdDGTFADVS 114

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
                  ....*....|....*....|....*....|....*....|....
gi 1770065902  45 PHTHEIHDQIGYVVRGSFEAEIEGEKKVLKEGDAYFARKHMMHG 88
Cdd:cd06122    42 VHAHAGSDKVYFVLEGEGRFTVGDEERELGAGEAVLAPAGVPHG 85

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
                  ....*....|....*....|....*....|....*....|..
gi 1770065902  46 HTHEIHDQIGYVVRGSFEAEIEGEKKVLKEGDAYFARKHMMH 87
Cdd:cd06991    35 HYHPYSEEFLYVVRGRLVVRVDGEPVVLEAGEALLVPRGVRH 76

quercetinase, N- and C-terminal cupin domains; This family contains quercetinase (also known as quercetin 2,3-dioxygenase, 2,3QD, QDO and YxaG; EC 1.13.11.24), a mononuclear copper-dependent dioxygenase that catalyzes the cleavage of the flavonol quercetin (5,7,3',4'-tetrahydroxyflavonol) heterocyclic ring to produce 2-protocatechuoyl-phloroglucinol carboxylic acid and carbon monoxide. Bacillus subtilis quercetin 2,3-dioxygenase (QDO) is a homodimer that shows oxygenase activity with several divalent metals such as Mn2+, Co2+, Fe2+, and Cu2+, although the preferred one appears to be Mn2+. The dioxygen binds to the metal ion of the Cu-QDO-quercetin complex, yielding a Cu2+-superoxo quercetin radical intermediate, which then forms a Cu2+-alkylperoxo complex which then evolves into endoperoxide intermediate that decomposes to the product. Quercetinase is a bicupin with two tandem cupin beta-barrel domains, both of which are included in this alignment model. The pirins, which also belong to the cupin domain family, have been shown to catalyze a reaction involving quercetin and may have a function similar to that of quercetinase.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1770065902  27 TDDLM-AVHLSFDKGAIGHPHTHEIHDQIGYVVRGSFEAEIEGEKKVLKEGD 77
Cdd:cd02215    28 TGGAFtLVTTEGPKGDAIPPHYHKRHHETFYVLEGRLQLWLDGESRLLTPGD 79

Helicobacter pylori HP0902 and related proteins, cupin domain; This family includes prokaryotic and archaeal proteins homologous to HP0902, a functionally uncharacterized protein from Helicobacter pylori and Spy1581, a protein of unknown function from Streptococcus pyogenes. These proteins demonstrate all-beta cupin folds that cannot bind metal ions due to the absence of a metal-binding histidine that is conserved in many metallo-cupins. HP0902 is able to bind bacterial endotoxin lipopolysaccharides (LPS) through its surface-exposed loops, where metal-binding sites are usually found in other metallo-cupins, and thus may have a putative role in H. pylori pathogenicity.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1770065902  22 KIVAYTDDLMAVHLSFDKGAIGHPHTHEiHDQIGYVVRGSFEAEIEGEKKVLKEGDAYFARKHMMHGAVALEQDSILL 99
Cdd:cd02230     3 RTLVQDDGLRVTLFAFDAGQELSEHTAP-GDATVQVLEGEAEFTIGGETVTLKAGELIVMPANVPHALKAEEDFKMLL 79

Bacillus subtilis YdbB and related proteins, cupin domain; This family includes bacterial proteins homologous to YdbB, a Bacillus subtilis protein of unknown function. It also includes protein Nmb1881 From Neisseria meningitidis, also 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 1770065902  44 HPHTHEIHDQIGYVVRGSFEAEIEGEKKVLKEGDAYFARKHMMHGAVALEQDSILL 99
Cdd:cd02226    36 VWHKHDDEDELFLVLEGELTIDFRDRDVTLGPGEFFVVPKGVEHRPVAEEETVVLL 91