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 489005398   2 FIFHKDTTLEDLGNGVTRRILAHDGKMMAVEVNFAAGAVGPMHNHPHEQLTYVLSGEFEFTIGEETRVVSAGDTLYKRPG 81
Cdd:cd02238    1 FVKWDELPWEELGPGVRRKILAGGEKLMLVEVRFEKGAVVPLHSHPHEQIGYVLSGRFEFTIGGETRILKPGDSYYIPPN 80

                         90       100
                 ....*....|....*....|....
gi 489005398  82 IMHGCVCLQPGTLLDTFTPIREDF 105
Cdd:cd02238   81 VPHGAEALEDSVLLDVFSPPREDF 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 489005398   2 FIFHKDTTLEDLGNGVTRRILAHDGKMMAVEVNFAAGAVGPMHNHPHEQLTYVLSGEFEFTIGEETRVVSAGDTLYKRPG 81
Cdd:cd02238    1 FVKWDELPWEELGPGVRRKILAGGEKLMLVEVRFEKGAVVPLHSHPHEQIGYVLSGRFEFTIGGETRILKPGDSYYIPPN 80

                         90       100
                 ....*....|....*....|....
gi 489005398  82 IMHGCVCLQPGTLLDTFTPIREDF 105
Cdd:cd02238   81 VPHGAEALEDSVLLDVFSPPREDF 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
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 489005398   31 VEVNFAAGAVGPMHNHPHE-QLTYVLSGEFEFTIGEETRVVSAGDTLYKRPGIMHG 85
Cdd:pfam07883   1 GLVTLPPGESSPPHRHPGEdEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPHR 56

(S)-ureidoglycine aminohydrolase;

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 489005398  31 VEVNFAAGAVGPMHNHPHEQLTYVLSGEFEFTIGEETRVVSAGDTLYKRPGIMH 84
Cdd:PRK11171  66 VEVEPGGGSDQPEPDEGAETFLFVVEGEITLTLEGKTHALSEGGYAYLPPGSDW 119

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 489005398   2 FIFHKDTTLEDLGNGVTRRILAHDGKMMAVEVNFAAGAVGPMHNHPHEQLTYVLSGEFEFTIGEETRVVSAGDTLYKRPG 81
Cdd:cd02238    1 FVKWDELPWEELGPGVRRKILAGGEKLMLVEVRFEKGAVVPLHSHPHEQIGYVLSGRFEFTIGGETRILKPGDSYYIPPN 80

                         90       100
                 ....*....|....*....|....
gi 489005398  82 IMHGCVCLQPGTLLDTFTPIREDF 105
Cdd:cd02238   81 VPHGAEALEDSVLLDVFSPPREDF 104

Bradyrhizobium japonicum BLR7677 and related proteins, cupin domain; This family includes bacterial and fungal proteins homologous to BLR7677, a Bradyrhizobium japonicum 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 489005398  25 DGKMMAVEVNFAAGAVGPMHNHPHEQLTYVLSGEFEFTI-GEETRVVSAGDTLYKRPGIMH 84
Cdd:cd02234   16 GKEVTVLLVTYPPGAASPPHRHPGFVFAYVLEGEVRSQVnGGPPRVYKAGESFYEPPGAHH 76

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
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 489005398   31 VEVNFAAGAVGPMHNHPHE-QLTYVLSGEFEFTIGEETRVVSAGDTLYKRPGIMHG 85
Cdd:pfam07883   1 GLVTLPPGESSPPHRHPGEdEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPHR 56

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489005398  16 GVTRRILAH---DGKMMAVEVNFAAGA-VGPMHNHPHEQLTYVLSGEFEFTIGEETRVVSAGDTLY 77
Cdd:cd02209    1 GYTYELLSPglpGRKMEPFLVTLPPGGsGGEPYSHEGEEFGYVLEGELELTVGGETYVLEAGDSIY 66

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        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489005398  20 RILAH----DGKMMAVEVNFAAGAVGPMHNHPHEQLT-YVLSGEFEFTIGEETRVVSAGDTLYKRPGIMHGCVCLQPGT- 93
Cdd:cd02215   20 TVLATgestGGAFTLVTTEGPKGDAIPPHYHKRHHETfYVLEGRLQLWLDGESRLLTPGDFASVPPGTIHAYRMLSPDTr 99

                 ....*..
gi 489005398  94 LLDTFTP 100
Cdd:cd02215  100 FLGVITP 106

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
                 ....*....|....*....|....*....|....*....|....*....|.
gi 489005398  36 AAGAVGPMHNHPHEQLTYVLSGEFEFTIGEETRVVSA-GDTLYKRPGIMHG 85
Cdd:cd06975   27 PPGAKMPLHQHREEQIGMILNGELEMTVGGEEQELEPlGDVYYAPPNVPHG 77

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
                 ....*....|....*....|....*....|....*....|....*....|...
gi 489005398  36 AAGAVGPMHNHPHEQLTYVLSGEFEFTIGEETRVVSAGDTLY-KRPGIMHGCV 87
Cdd:cd20307   32 APGAVVELHQHPESQIGMVLSGELEMNVGGVKKVMEPLQDVYvAPPNVPHGAV 84

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 489005398  30 AVEVNFAAGAVGPMHNHP-HEQLTYVLSGEFEFTIG-EETRVVSAGDTLYKRPGIMHGCV 87
Cdd:cd02208    1 ISVVTLPPGTSSPPHWHPeQDEIFYVLSGEGELTLDdGETVELKAGDIVLIPPGVPHSFV 60

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
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 489005398  23 AHDGKMMAVEVNFAAGAVGPMHNHPHEQLTYVLSGEFEFTIGE-ETRVVSAGDTL 76
Cdd:cd02236   17 EGQPEITVLRITIPPGAELPWHTHPVPNAGYVLSGELTVEYEDgKKRTFKAGDAF 71

uncharacterized protein bxe_c0505, cupin domain; This family includes mostly bacterial proteins homologous to bxe_c0505, a Burkholderia xenovorans 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 489005398  23 AHDGKMMAVEVNFAAGAVGPMHNHPHE---QLTYVLSG--EFEFTIGEETRVvSAGDTLYKRPGIMH 84
Cdd:cd06980   16 ATGGRVGAHVIRATGGGEGPTGWHYHDcdfQMVYVLKGwvKFEFEGGGEVRL-EAGDCVYQPPGIRH 81

Pseudomonas aeruginosa PA3510 and related proteins, cupin domain; This family includes bacterial proteins homologous to PA3510, a Pseudomonas aeruginosa protein of unknown function with a beta-barrel fold that belongs to the cupin superfamily.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 489005398  37 AGAVGPMHNHPHEQLTYVLSGEFEFTIGEE----TRVVSAGDTLYKRPGIMHG 85
Cdd:cd02225   62 PGQGGALHTHEVEEVFFVLQGRLTVFWEDEgeehERELGPRDMISVPAGVYRG 114

AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization domain of the bacterial gene regulatory protein AraC. The domain is found in conjunction with the helix-turn-helix (HTH) DNA-binding motif pfam00165. This domain is distantly related to the Cupin domain pfam00190.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 489005398   42 PMHNHPHEQLTYVLSGEFEFTIGEETRVVSAGDTLYKRPGIMH 84
Cdd:pfam02311  17 PPHVHDFYVIGYIERGVGRFRLNGRTYHLGPGDLFLLPPGEPH 59

Bradyrhizobium japonicum BLR2406 and related proteins, cupin domain; This family includes bacterial and fungal proteins homologous to BLR2406, a Bradyrhizobium japonicum protein of unknown function with a cupin beta barrel domain. Proteins in this subfamily appear to align closest to RmlC carbohydrate epimerase which is involved in dTDP-L-rhamnose production, and belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 489005398  33 VNFAAGAVGPMHNHP-HEQLTYVLSGEFEFTIG---EETRVVSAGDTLYKRPGIMH 84
Cdd:cd02210   16 VTIPPGARTGAHHHGeHETAIYVLSGRAETRYGdrlEHRAEAGPGDFIYIPPGVPH 71

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
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489005398    28 MMAVEVNFAAGAVGPMHNHPH-EQLTYVLSGEFEFTIGEE------TRVVSAGDTLYKRPGIMH 84
Cdd:smart00835  30 ISAARVNLEPGGMLPPHYHPRaTELLYVVRGEGRVGVVDPngnkvyDARLREGDVFVVPQGHPH 93

ChrR Cupin-like domain; Members of this family are part of the cupin superfamily. This family includes the transcriptional activator ChrR.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489005398   16 GVTRRILAHDGKMMAVEVN---FAAGAVGPMHNHPHEQLTYVLSGEFEftigEETRVVSAGDTLYKRPGIMH------GC 86
Cdd:pfam12973   9 GVERKPLHRDGGEKARATSlvrYAPGSRFPAHRHPGGEEILVLEGVFS----DEHGDYPAGTYLRNPPGSSHapfseeGC 84

                  ...
gi 489005398   87 VCL 89
Cdd:pfam12973  85 TIF 87

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
                 ....*....|....*....|....*....|....*....|....
gi 489005398  43 MHNHPHEQLTY-VLSGEFEFTIGEETRVVSAGDTLYKRPGIMHG 85
Cdd:cd02221   34 YHQHEGEFEIYyILSGEGLYTDNGKEYEVKAGDVTFTRDGESHG 77

(S)-ureidoglycine aminohydrolase;

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 489005398  31 VEVNFAAGAVGPMHNHPHEQLTYVLSGEFEFTIGEETRVVSAGDTLYKRPGIMH 84
Cdd:PRK11171  66 VEVEPGGGSDQPEPDEGAETFLFVVEGEITLTLEGKTHALSEGGYAYLPPGSDW 119

AraC/XylS family transcriptional regulators similar to NimR, N-terminal cupin domain; This family contains mostly bacterial proteins containing an AraC/XylS family helix-turn-helix (HTH) DNA-binding domain C-terminal to a cupin domain, and may be possible transcriptional regulators. Included in this family is Escherichia coli HTH-type transcriptional regulator NimR (also called YeaM) that negatively regulates expression of the nimT operon and its own expression. 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 489005398  28 MMAVEVNFAAGAVGPMHNHPHEQLTYVLSGEFEFTIGEETRVVSAGDTLYKRPGIMHGCVCLQP 91
Cdd:cd06124    1 VLARAADYPAGHRTPWHSHPWGQLLYASSGVMTVETEDGRWLVPPQRAVWIPAGVEHSVRMLGA 64

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 489005398  28 MMAVEVnFAAGAVGPMHNHPH-EQLTYVLSGEFEFTIGEETRVVSAGDTLYKRPGIMHG 85
Cdd:cd06987   29 TVVVEI-FDPGGRTPPNTHPAaHEMFFVLAGEGRAYCDGQRVPLRPGDALVVPPGSEHV 86