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        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1770576969  21 GAIDIYRAFRRKDFDGAWDFAIRVVMPPGSSMGEHTHGDDEEMYIILKGEGTMIIEGEKRPVSDGDMIVNQRFGTHGLVN 100
Cdd:cd02221     1 GTVTVYHLLTPEELKGKGRLFARVTLPPGSSIGYHQHEGEFEIYYILSGEGLYTDNGKEYEVKAGDVTFTRDGESHGIEN 80

                          90
                  ....*....|.
gi 1770576969 101 TSNHDIELLII 111
Cdd:cd02221    81 TGDEDLVFIAL 91

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        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1770576969  21 GAIDIYRAFRRKDFDGAWDFAIRVVMPPGSSMGEHTHGDDEEMYIILKGEGTMIIEGEKRPVSDGDMIVNQRFGTHGLVN 100
Cdd:cd02221     1 GTVTVYHLLTPEELKGKGRLFARVTLPPGSSIGYHQHEGEFEIYYILSGEGLYTDNGKEYEVKAGDVTFTRDGESHGIEN 80

                          90
                  ....*....|.
gi 1770576969 101 TSNHDIELLII 111
Cdd:cd02221    81 TGDEDLVFIAL 91

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 1770576969  43 RVVMPPGSSMGEHTHGDDEEMYIILKGEGTMIIEGEKRPVSDGDMIVNQRFGTHGLVNTSNHDIELLII 111
Cdd:pfam07883   2 LVTLPPGESSPPHRHPGEDEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPHRFRNTGDEPARLLDV 70

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        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1770576969  21 GAIDIYRAFRRKDFDGAWDFAIRVVMPPGSSMGEHTHGDDEEMYIILKGEGTMIIEGEKRPVSDGDMIVNQRFGTHGLVN 100
Cdd:cd02221     1 GTVTVYHLLTPEELKGKGRLFARVTLPPGSSIGYHQHEGEFEIYYILSGEGLYTDNGKEYEVKAGDVTFTRDGESHGIEN 80

                          90
                  ....*....|.
gi 1770576969 101 TSNHDIELLII 111
Cdd:cd02221    81 TGDEDLVFIAL 91

Bacteroides fragilis BF4112 and related proteins, cupin domain; This family includes archaeal and bacterial proteins homologous to BF4112, a Bacteroides fragilis 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 1770576969  45 VMPPGSSMG-EHTHGDDEEMYIILKGEGTMIIEGEKRPVSDGDMI-VNQRfGTHGLVNTSNHDIELLIIQA 113
Cdd:cd06985    20 SLPAGAAVPfVHSHKENEEIYIILKGKGEFQVDGEVFPVKEGSVIrVAPD-GKRSWRNTSDEPLIYICIQA 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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1770576969  43 RVVMPPGSSMGEHTHGDDEEMYIILKGEGTMIIEGEKRPVSDGDMIVNQRFGTHGLVNTSNHDIELLII 111
Cdd:pfam07883   2 LVTLPPGESSPPHRHPGEDEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPHRFRNTGDEPARLLDV 70

Uncharacterized conserved protein, cupin superfamily [Function unknown];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1770576969  12 VDTNSHDGEGAIDIYRAFRrkDFDGAWDFAIRVV-MPPGSSMGE-HTHGDDEEMYIILKGEGTMIIEGEKRPVSDGDMIV 89
Cdd:COG3837     2 VNLDDLPGPEAGRRYRRLG--DALGLTRLGVNLItLPPGASSSPyHAHSAEEEFVYVLEGELTLRIGGEEYVLEPGDSVG 79

                          90       100
                  ....*....|....*....|....
gi 1770576969  90 NQRFGTHGLVNTSNHDIELLIIQA 113
Cdd:COG3837    80 FPAGVPHRLRNRGDEPARYLVVGT 103

Methanocaldococcus jannaschii MJ1618 and related proteins, cupin domain; This family includes bacterial and archaeal proteins homologous to MJ1618, a Methanocaldococcus jannaschii protein of unknown function with a cupin beta barrel domain. The active site of members of the cupin superfamily is generally located at the center of a conserved barrel and usually includes a metal ion.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1770576969  43 RVVMPPGSSMGEHTHGDDEEMYIILKGEGTMIIEGEKRPVSDGDMIV---NQRfgtHGLVNTSNHDIELLII 111
Cdd:cd02214    23 HARVPPGESTLPHRLKGSEEVYYILEGEGTMEIDGEPREVGPGDAVLippGAV---QRIENTGEEDLVFLCI 91

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1770576969  44 VVMPPG--SSMGeHTHGDDEEMYIILKGEGTMIIEGEKRPVSDGDMI---VNQRFGtHGLVNTSNHDIELLII 111
Cdd:cd02224    22 ERLPPGarSSPR-HWHSAEEEFVYVLSGEGTLRLDGEEVLPRPGDFVgfpAGTGVA-HQLINRSDEPLVYLVV 92

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1770576969  46 MPPGSSMGEHTHGDDEEMYIILKGEGTMII-EGEKRPVSDGDMIVNQRFGTHGLVNTSNHD 105
Cdd:cd07008    34 VKPGQEIAAHIHPHGQDTWIVLSGEGEYLLgDGQTVPIKAGDIVIAPAGQVHGARNTGDEP 94

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 1770576969  48 PGSSMGEHTHGDDEEMYIILKGEGTMIIEGEKRPVSDGDMIVnQRFGT-HGLVNTSNHDIELLIIQA 113
Cdd:cd06122    36 PGQSQKVHAHAGSDKVYFVLEGEGRFTVGDEERELGAGEAVL-APAGVpHGVRNTGAERLVLLVFMA 101

Phosphomannose isomerase type II, C-terminal cupin domain; This family includes the C-terminal cupin domain of mannose-6-phosphate isomerases (MPIs) which have been classified broadly into two groups, type I and type II, based on domain organization. This family contains type II phosphomannose isomerase (also known as PMI-GDP, phosphomannose isomerase/GDP-D-mannose pyrophosphorylase), a bifunctional enzyme with two domains that catalyze the first and third steps in the GDP-mannose pathway in which fructose 6-phosphate is converted to GDP-D-mannose. The N-terminal domain catalyzes the first and rate-limiting step, the isomerization from D-fructose-6-phosphate to D-mannose-6-phosphate, while the C-terminal cupin domain (represented in this alignment model) converts mannose 1-phosphate to GDP-D-mannose in the final step of the reaction. Although these two domains occur together in one protein in most organisms, they occur as separate proteins in certain cyanobacterial organisms. Also, although type I and type II MPIs have no overall sequence similarity, they share a conserved catalytic motif.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1770576969  43 RVVMPPGSSMGEHTHGDDEEMYIILKGEGTMIIEGEKRPVSDGDMIVNQRFGTHGLVNTSNHDIELLIIQ 112
Cdd:cd02213    44 RLTVNPGKRLSLQRHHHRSEHWVVVSGTAEVTLDGKEKLLKEGESIYIPKGTKHRLENPGKIPLEIIEVQ 113

monomeric dehydratase Pac13 and related proteins, cupin domain; This family includes a small monomeric dehydratase Pac13 that mediates the formation of the 3'-deoxynucleotide of pacidamycins, which are uradyl peptide antibiotics (UPAs). Pac13 is involved in the formation of the unique 3'-deoxyuridine moiety found in these UPAs; it catalyzes the dehydration of uridine-5'-aldehyde. The similarity of the 3'-deoxy pacidamycin moiety with synthetic anti-retrovirals, offers a potential opportunity for the utilization of Pac13 in the biocatalytic generation of antiviral compounds. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1770576969  54 EHTHGDDEEMYIILKGEGTMIIEGEKRPVSDGDMIV 89
Cdd:cd20295    35 EHYHKKSTEIYYVLEGEGIFELDGEAVPVKPGDLVL 70

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 1770576969  39 DFAIRVV-MPPGSSMGEHTHgDDEEMYIILKGEGTMIIEGEKRPVsdgdmivnQRFGT---------HGLVNTSNHDIEL 108
Cdd:cd06975    18 WTEIMLSyIPPGAKMPLHQH-REEQIGMILNGELEMTVGGEEQEL--------EPLGDvyyappnvpHGAVNPSDETAVL 88

                  ...
gi 1770576969 109 LII 111
Cdd:cd06975    89 LDI 91

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 1770576969  41 AIRVVMPPGSSMGEHTHGddeemYI----ILKGEGTMIIE-GEKRPVSDGDMI---VNQrfgTHGLVNTSNHDIELLIIQ 112
Cdd:cd02236    24 VLRITIPPGAELPWHTHP-----VPnagyVLSGELTVEYEdGKKRTFKAGDAFveaVNT---WHRGRNGGDEPVELLVFY 95

                  ....
gi 1770576969 113 ASLK 116
Cdd:cd02236    96 AGAK 99

Cupin; This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel). This family contains 11S and 7S plant seed storage proteins, and germins. Plant seed storage proteins provide the major nitrogen source for the developing plant.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1770576969   41 AIRVVMPPGSSMGEHTHGDDEEMYIILKGEGTMII---EGEKR---PVSDGDMIVNQRFGTHGLVNTSNHDIELLI 110
Cdd:smart00835  32 AARVNLEPGGMLPPHYHPRATELLYVVRGEGRVGVvdpNGNKVydaRLREGDVFVVPQGHPHFQVNSGDENLEFVA 107

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1770576969  42 IRVVMPPGSSMGEHTHGDDEEMYIiLKGEGTMIIEGEKRPVSDGDMIVNQRFGTHGLVNTSNHDIELLII 111
Cdd:cd06984    14 VHITLKPGESLKKHITPVDVFFYV-LEGEGIVEIGEEKQEVEADTLIESPANIPHCLYNESDADLRVLVI 82

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
                  ....*....|....*....|....*....|....*
gi 1770576969  55 HTHGDDEEMYIILKGEGTMIIEGEKRPVSDGDMIV 89
Cdd:cd02226    38 HKHDDEDELFLVLEGELTIDFRDRDVTLGPGEFFV 72

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
                  ....*....|....*....|....*....|....*....|....*..
gi 1770576969  43 RVVMPPGSSMGEHTHgDDEEMYIILKGEGTMIIEGEKRPVSDGDMIV 89
Cdd:cd02238    31 EVRFEKGAVVPLHSH-PHEQIGYVLSGRFEFTIGGETRILKPGDSYY 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 1770576969  30 RRKDFDGAWDFAIrVVMPPGSSMGEHTHGDDEEMYIILKGEGTMIIEGEKRPVSDGDMI 88
Cdd:cd02215    24 TGESTGGAFTLVT-TEGPKGDAIPPHYHKRHHETFYVLEGRLQLWLDGESRLLTPGDFA 81