HTH-type transcriptional regulator PuuR;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 902775142  16 GMRLRHARLAQEITLKQLAQKVGCSESLLSKLENEAASPSLAMLHRLASALETNISDLMAESWVADSP--VLKPAQrsrk 93
Cdd:PRK09943   9 GKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEFFSEPEKPDEPqvVINQDD---- 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 902775142  94 rFVHRSKQGgIELETLTHHHKGGLLQGNIHIIEPGVASDGQIEHHGEEMGYVLEGEIALYLGEETYTLSVGDSFYFPSNV 173
Cdd:PRK09943  85 -LIEMGSQG-VSMKLVHNGNPNRTLAMIFETYQPGTTTGERIKHQGEEIGTVLEGEIVLTINGQDYHLVAGQSYAINTGI 162

                        170       180
                 ....*....|....*....|...
gi 902775142 174 PHGYRNVGESVARVLWVNTPVTF 196
Cdd:PRK09943 163 PHSFSNTSAGICRIISAHTPTTF 185

Uncharacterized conserved protein, cupin superfamily [Function unknown];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 902775142 102 GGIELETLTHHHKGGLLQGNIHIIEPGVASDGQIEHH-GEEMGYVLEGEIALYLGEETYTLSVGDSFYFPSNVPHGYRNV 180
Cdd:COG3837   12 AGRRYRRLGDALGLTRLGVNLITLPPGASSSPYHAHSaEEEFVYVLEGELTLRIGGEEYVLEPGDSVGFPAGVPHRLRNR 91

                         90
                 ....*....|...
gi 902775142 181 GESVARVLWVNTP 193
Cdd:COG3837   92 GDEPARYLVVGTR 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 902775142  122 IHIIEPGvASDGQIEHHGE-EMGYVLEGEIALYLGEETYTLSVGDSFYFPSNVPHGYRNVGESVARVLWV 190
Cdd:pfam07883   2 LVTLPPG-ESSPPHRHPGEdEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPHRFRNTGDEPARLLDV 70

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 902775142  16 GMRLRHARLAQEITLKQLAQKVGCSESLLSKLENEAASPSLAMLHRLASALETNISDL 73
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58

Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 902775142   14 DLGMRLRHARLAQEITLKQLAQKVGCSESLLSKLEN-EAASPSLAMLHRLASALET 68
Cdd:pfam13560   1 ELGARLRRLRERAGLSQEALARRLGVSRSTLSRLETgRRGRPSPAVVERLARALGV 56

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 902775142   125 IEPGvasdGQIEHH----GEEMGYVLEGEIALYLGEE------TYTLSVGDSFYFPSNVPHGYRNVGESVARVLWVNT 192
Cdd:smart00835  37 LEPG----GMLPPHyhprATELLYVVRGEGRVGVVDPngnkvyDARLREGDVFVVPQGHPHFQVNSGDENLEFVAFNT 110

Uncharacterized conserved protein, cupin superfamily [Function unknown];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 902775142 102 GGIELETLTHHHKGGLLQGNIHIIEPGVASDGQIEHH-GEEMGYVLEGEIALYLGEETYTLSVGDSFYFPSNVPHGYRNV 180
Cdd:COG3837   12 AGRRYRRLGDALGLTRLGVNLITLPPGASSSPYHAHSaEEEFVYVLEGELTLRIGGEEYVLEPGDSVGFPAGVPHRLRNR 91

                         90
                 ....*....|...
gi 902775142 181 GESVARVLWVNTP 193
Cdd:COG3837   92 GDEPARYLVVGTR 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 902775142  122 IHIIEPGvASDGQIEHHGE-EMGYVLEGEIALYLGEETYTLSVGDSFYFPSNVPHGYRNVGESVARVLWV 190
Cdd:pfam07883   2 LVTLPPG-ESSPPHRHPGEdEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPHRFRNTGDEPARLLDV 70

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

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 902775142 124 IIEPGVASDGQIEHHGEEMGYVLEGEIALYLGEETYTLSVGDSFYFPSNVPHGYRNVGESVARVLWVNTPVTF 196
Cdd:COG0662   33 TVPPGAELSLHVHPHRDEFFYVLEGTGEVTIGDEEVELKAGDSVYIPAGVPHRLRNPGDEPLELLEVQAPAYL 105

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 902775142 137 HHGEEMGYVLEGEIALYLGEETYTLSVGDSFYFPSNVPHGYRNVGESVA 185
Cdd:cd02238   45 HPHEQIGYVLSGRFEFTIGGETRILKPGDSYYIPPNVPHGAEALEDSVL 93

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 902775142 125 IEPGVASdGQIEHHGEEMGYVLEGEIALYL-GEETYTLSVGDSFYFPSNVPHGYRNVGESVARVL 188
Cdd:cd02235   26 IPPGAVA-GRHTHPGEESGYVLEGSLELEVdGQPPVTLKAGDSFFIPAGTVHNAKNVGSGPAKLL 89

Helix-turn-helix XRE-family like proteins;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 902775142    18 RLRHARLAQEITLKQLAQKVGCSESLLSKLENEAASPSLAMLHRLASALETNISDL 73
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56

Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 902775142   14 DLGMRLRHARLAQEITLKQLAQKVGCSESLLSKLEN-EAASPSLAMLHRLASALET 68
Cdd:pfam13560   1 ELGARLRRLRERAGLSQEALARRLGVSRSTLSRLETgRRGRPSPAVVERLARALGV 56

Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and CI. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteriztic of the whole family.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 902775142   19 LRHARLAQEITLKQLAQKVGCSESLLSKLENEAASPSLAMLHRLASALETNISDL 73
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55

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 902775142 125 IEPGvasdGQIEHH---GEEMGYVLEGEIALYLGEETYTLSVGDSFYFPSNVPHGYRNVGESVAR 186
Cdd:cd02222   24 IEPG----GHTPLHthpWEHEVYVLRGKGVVVIGGEEYPVKPGDVVYIPPNEPHQFRNTGDEPLG 84

Ureidoglycine aminohydrolase [Nucleotide transport and metabolism];

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 902775142 125 IEPGVASD-GQIEHHGEEMGYVLEGEIALYLGEETYTLSVGDSFYFPSNVPHGYRNVGESVARVLWV 190
Cdd:COG3257   66 VAPGGGSDrPEPDPGAETFLFVLEGEVTLTLGGETHELTPGGYAYLPPGTPWTLRNAGDEPARFHWI 132

Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain CBS pair) [Transcription];

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 902775142  15 LGMRLRHARLAQEITLKQLAQKVGCSESLLSKLENEAASPSLAMLHRLASALETNISDL 73
Cdd:COG3620   18 LGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAV 76

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 902775142 125 IEPGvasdGQI---EHHGEEMGYVLEGEIALYLGEETYTLSVGDSFYFPSNVPH-GYRNVGESV 184
Cdd:cd10547   26 IPPG----GKMplhQHRGEQIGIILNGKYDMTVGGEEQELGYGKIYYAPPNVSHsGYNDSDETA 85

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 902775142 124 IIEPGVASDGQIEHHGEEMGYVLEGEIALYLGEETYTLSVGDSFYFPSNVPHGYRNVGESVARVLWVNTP 193
Cdd:cd02214   25 RVPPGESTLPHRLKGSEEVYYILEGEGTMEIDGEPREVGPGDAVLIPPGAVQRIENTGEEDLVFLCICSP 94

Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell division, chromosome partitioning];

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 902775142  11 ALSDLGMRLRHARLAQEITLKQLAQKVGCSESLLSKLENE------AASPSLAMLHRLASALETNISDLM 74
Cdd:COG1426    2 ALETIGELLRQAREAKGLSLEDVAERTKISVSYLEAIEEGdfdalpGPVYVRGFLRSYARALGLDPEELL 71

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
                 ....*....|....*....|....*....|....*....|...
gi 902775142 136 EH--HGEEMGYVLEGEIALYLGEETYTLSVGDSFYFPSNVPHG 176
Cdd:cd02230   26 EHtaPGDATVQVLEGEAEFTIGGETVTLKAGELIVMPANVPHA 68

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        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 902775142 121 NIHIIEPGVASdgQIEHHG--EEMGYVLEGEIALYLG---EETYTLSVGDSFYFPSNVPH 175
Cdd:cd02210   14 GVVTIPPGART--GAHHHGehETAIYVLSGRAETRYGdrlEHRAEAGPGDFIYIPPGVPH 71

Uncharacterized conserved protein, RmlC-like cupin domain [General function prediction only];

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 902775142 125 IEPGVASDGQieHHG--EEMGYVLEGEIALYLG---EETYTLSVGDSFYFPSNVPHGYRNVGES 183
Cdd:COG4101   53 IPPGARAKAH--HHGehETAIYVLSGRAETRYGerlEHRVVTEPGDFIFIPPGVPHQEINLSDT 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        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 902775142 144 YVLEGEIALYLGEETYTLSVGDSFYFPSNVPHGYRNVGESVARVLWVNTP 193
Cdd:cd06122   53 FVLEGEGRFTVGDEERELGAGEAVLAPAGVPHGVRNTGAERLVLLVFMAP 102

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        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 902775142 136 EH---HGEEMGYVLEGEIALYLGEETYTLSVGDSFYFPSNVPHGYRNVGESVARV 187
Cdd:cd06991   34 EHyhpYSEEFLYVVRGRLVVRVDGEPVVLEAGEALLVPRGVRHRLENAGDEPARL 88

Streptomyces resistomycificus RemF cyclase and related proteins, cupin domain; RemF cyclase is a manganese-containing polyketide cyclase present in bacteria that is involved in the biosynthesis of resistomycin, the aromatic pentacyclic metabolite in Streptomyces resistomycificus. Structure of this enzyme shows a cupin fold with a conserved "jelly roll-like" beta-barrel fold that forms a homodimer. It contains an unusual octahedral zinc-binding site in a large hydrophobic pocket that may represent the active site. The zinc ion, coordinated to four histidine side chains and two water molecules, could act as a Lewis acid in the aldol condensation reaction catalyzed by RemF, reminiscent of class II aldolases.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 902775142 140 EEMGYVLEGEIALYLGEETYTLSVGDSFYFPSNVPHGYRNVGESVARVLWVNTP 193
Cdd:cd06979   40 EETIYGLEGSVTLTLPGKTVEVGPGDSIFIPRGEVHGFVNRSGGPTCRLCVLAP 93

Clostridium difficile EutQ and related proteins, cupin domain; This family includes bacterial and fungal proteins homologous to ethanolamine utilization protein EutQ found in Clostridium difficile, as well as in other bacteria, including the enteric pathogens Salmonella enterica and Enterococcus faecalis. EutQ is encoded by the eutQ gene which is part of the eut (ethanolamine utilization) operon found to be essential during anoxic growth of S. enterica on ethanolamine and tetrathionate. In C. difficile, inability to utilize ethanolamine results in greater virulence and a shorter time to morbidity in the animal model, suggesting that, in contrast to other intestinal pathogens, the metabolism of ethanolamine can delay the onset of disease. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization. In contrast to the metal-binding catalytic cupins, the EutQ family does not possess the histidine residues that are responsible for metal coordination in the oxidoreductase and epimerase classes of cupins.

                         10        20        30
                 ....*....|....*....|....*....|...
gi 902775142 140 EEMGYVLEGEIALYLGEETYTLSVGDSFYFPSN 172
Cdd:cd02228   34 DEIKYVLEGELEITDDGQTVTAKPGDVLFIPKG 66

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 902775142 125 IEPGVASDGQiEHHGEEMGYVLEGEIALYLGEETYTLSVGDSFYF-PSNVPHGYRNVGESVARVL 188
Cdd:cd20307   31 IAPGAVVELH-QHPESQIGMVLSGELEMNVGGVKKVMEPLQDVYVaPPNVPHGAVNPSSEEAVGL 94

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        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 902775142 122 IHIIEPGVASDGQIEHHGEEMGYVLEGEIALYLGEETYTLSVGDSFYFPSNVPHGYRNVGESVARVLWVNTP 193
Cdd:cd06987   32 VEIFDPGGRTPPNTHPAAHEMFFVLAGEGRAYCDGQRVPLRPGDALVVPPGSEHVIENTGSGRLYCLTLMVP 103

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
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 902775142 134 QIEHHGEEMGYVLEGEIALYLGEETYTLSVGDSFYFPSNVPHGYRNVGESVARVL 188
Cdd:cd02213   56 QRHHHRSEHWVVVSGTAEVTLDGKEKLLKEGESIYIPKGTKHRLENPGKIPLEII 110

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
                 ....*....|....*....|....*....|....*....|....*....|.
gi 902775142 126 EPGVASDGQiEHHGEEMGYVLEGEIALYL-GEETYTLSVGDSFYFPSNVPH 175
Cdd:cd02234   27 PPGAASPPH-RHPGFVFAYVLEGEVRSQVnGGPPRVYKAGESFYEPPGAHH 76

EutQ-like cupin domain; This entry represents the cupin domain, with a conserved jelly roll-like beta-barrel fold capable of homodimerization found in bacteria, plant and fungi. It is present in EutQ family from the eut operon, involved in ethanolamine degradation. EutQ is essential during anoxic growth and has acetate kinase activity. The cupin domain from EutQ does not possess the His residues responsible for metal coordination in other classes of cupins. This domain is also found in (S)-ureidoglycine aminohydrolase (UGlyAH) from E.coli, which is involved in the anaerobic nitrogen utilization via the assimilation of allantoin. It catalyzes the deamination of allantoin to produce S-ureidoglycolate and ammonia from S-ureidoglycine.

                          10        20        30
                  ....*....|....*....|....*....|.
gi 902775142  141 EMGYVLEGEIALY-LGEETYTLSVGDSFYFP 170
Cdd:pfam05899  27 ETCYILSGEVTVTpEGGKTVTLRAGDLVVLP 57

Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense mechanisms];

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 902775142  16 GMRLRHARL-AQEITLKQLAQKVGCSESLLSKLENEAASPSLAMLHRLASALETNisdlmAESW 78
Cdd:COG3093   10 GEILREEFLePLGLSQTELAKALGVSRQRISEILNGKRAITADTALRLARAFGTS-----AEFW 68

Desulfitobacterium hafniense dsy2733 and related proteins, cupin domain; This family includes bacterial proteins homologous to dsy2733, a Desulfitobacterium hafniense 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
                 ....*....|....*....|....*....|....*...
gi 902775142 139 GEEMGYVLEGEIALYLGEETYTLSVGDSFYFPSNVPHG 176
Cdd:cd06983   30 GDTLYYVLEGEAEITIGDEKHRLKAGDVLAVPAGVLHA 67

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 902775142 124 IIEPGvASDGQIEHHGE-EMGYVLEGEIALYLGEETYTLSVGDSFYFPSNVPHGYRNVGE 182
Cdd:cd02221   25 TLPPG-SSIGYHQHEGEfEIYYILSGEGLYTDNGKEYEVKAGDVTFTRDGESHGIENTGD 83

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        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 902775142 119 QGNIHIIEpgVASDGQIEHHGE--EMGYVLEGEIALYLGEETYTLSVGDSFYFPSNVPHgyRNVGEsvARVLWVNTP 193
Cdd:cd20295   21 PASVHLVE--VEEGHEEHYHKKstEIYYVLEGEGIFELDGEAVPVKPGDLVLIPPGTRH--RAVGK--MKILLIVIP 91

AraC/XylS family transcriptional regulators similar to MmsR, N-terminal cupin domain; This family contains 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 is MmsR, a bacterial transcriptional regulator thought to positively regulate the expression of the mmsAB operon. The mmsAB operon contains two structural genes involved in valine metabolism: mmsA which encodes methylmalonate-semialdehyde dehydrogenase, and mmsB which encodes 3-hydroxyisobutyrate dehydrogenase. The cupin domain of members of this subfamily does not contain a metal binding site.

                         10        20        30
                 ....*....|....*....|....*....|....
gi 902775142 144 YVLEGEIALYLGEETYTLSVGDSFYFPSNVPHGY 177
Cdd:cd06986   33 YVLSGKGTFSVNGKTYHLKAGQGFLIPPGEPHSY 66

3-hydroxyanthranilate 3,4-dioxygenase; Provisional

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 902775142 139 GEEMGYVLEGEIALYLGEE----TYTLSVGDSFYFPSNVPH 175
Cdd:PRK13264  54 GEEFFYQLEGDMYLKVQEDgkrrDVPIREGEMFLLPPHVPH 94

Oxalate decarboxylase (OxDC)-like cupin domain; This subfamily contains bacterial and eukaryotic cupin domains of proteins homologous to oxalate decarboxylase (OxDC; EC 4.1.1.2) such as MSMEG_2254, a putative OxDC from Mycobacterium smegmatis. OxDC 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 with each domain containing one manganese binding site, with four manganese binding residues (three histidines and one glutamate) conserved as well as a number of hydrophobic residues.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 902775142 141 EMGYVLEGEIALYL----GE-ETYTLSVGDSFYFPSNVPHGYRNVGESVARVL 188
Cdd:cd20306   57 ELGYVISGEARVSIldptGSlDTFTVKPGQVVFIPQGWLHWIENVGDEEAHLL 109

Mannose-6-phosphate isomerase; All of the members of this Pfam entry belong to family 2 of the mannose-6-phosphate isomerases. The type II phosphomannose isomerases are bifunctional enzymes. This Pfam entry covers the isomerase domain. The guanosine diphospho-D-mannose pyrophosphorylase domain is in another Pfam entry, see pfam00483.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 902775142  113 HKGGLLQGNIHIIEPGVASDGQIEHHGEEMGYVLEGEIALYLGEETYTLSVGDSFYFPSNVPHGYRNVG 181
Cdd:pfam01050  58 DEGERYQVKRITVKPGARLSLQMHHHRAEHWIVVSGTARVTKGGETFLLTENESTYIPLGTIHRLENPG 126