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 495983956 111 GTEVSWGHDTDEYGLIMEGSLIFEVNGEKYLVEEGDTIYIKAGMPHKWRKAGEGRCVSYW 170
Cdd:cd02209   28 SGGEPYSHEGEEFGYVLEGELELTVGGETYVLEAGDSIYFDSDVPHRYRNPGDEPARVLW 87

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 495983956 111 GTEVSWGHDTDEYGLIMEGSLIFEVNGEKYLVEEGDTIYIKAGMPHKWRKAGEGRCVSYW 170
Cdd:cd02209   28 SGGEPYSHEGEEFGYVLEGELELTVGGETYVLEAGDSIYFDSDVPHRYRNPGDEPARVLW 87

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 495983956   3 GKKIKYYRKQASLTLQEISARTGLSIGYLSNLERDLTSPSFDNLCSICNALSVNVVDL 60
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58

Helix-turn-helix XRE-family like proteins;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 495983956     5 KIKYYRKQASLTLQEISARTGLSIGYLSNLERDLTSPSFDNLCSICNALSVNVVDL 60
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56

HTH-type transcriptional regulator PuuR;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495983956   1 MIGKKIKYYRKQASLTLQEISARTGLSIGYLSNLERDLTSPSFDNLCSIcnalsVNVVDLiknSLSYKPLLKKADRTPVY 80
Cdd:PRK09943   7 APGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKL-----LKVYGL---SLSEFFSEPEKPDEPQV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495983956  81 ARDyrtryefttAQDLNLLG-----MCLI-----------LEEDYY-----GTEVSwgHDTDEYGLIMEGSLIFEVNGEK 139
Cdd:PRK09943  79 VIN---------QDDLIEMGsqgvsMKLVhngnpnrtlamIFETYQpgtttGERIK--HQGEEIGTVLEGEIVLTINGQD 147

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 495983956 140 YLVEEGDTIYIKAGMPHKWRKAGEGRC--VSYWTKLNY 175
Cdd:PRK09943 148 YHLVAGQSYAINTGIPHSFSNTSAGICriISAHTPTTF 185

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 495983956 111 GTEVSWGHDTDEYGLIMEGSLIFEVNGEKYLVEEGDTIYIKAGMPHKWRKAGEGRCVSYW 170
Cdd:cd02209   28 SGGEPYSHEGEEFGYVLEGELELTVGGETYVLEAGDSIYFDSDVPHRYRNPGDEPARVLW 87

Cupin domain protein related to quercetin dioxygenase [General function prediction only];

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 495983956 111 GTEVSW-GHDTDEYGLIMEGSLIFEVNGEKYLVEEGDTIYIKAGMPHKWRKAGEGRCVSYW 170
Cdd:COG1917   33 GARTPWhSHPGEELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFRNLGDEPAVLLV 93

Uncharacterized conserved protein, cupin superfamily [Function unknown];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495983956  85 RTRYEFTTAQDLNLLGMCLI-LEEdyyGTEVSWGH---DTDEYGLIMEGSLIFEVNGEKYLVEEGDTIYIKAGMPHKWRK 160
Cdd:COG3837   14 RRYRRLGDALGLTRLGVNLItLPP---GASSSPYHahsAEEEFVYVLEGELTLRIGGEEYVLEPGDSVGFPAGVPHRLRN 90

                 ....*..
gi 495983956 161 AGEGRCV 167
Cdd:COG3837   91 RGDEPAR 97

Helix-turn-helix XRE-family like proteins;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 495983956     5 KIKYYRKQASLTLQEISARTGLSIGYLSNLERDLTSPSFDNLCSICNALSVNVVDL 60
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 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 495983956    6 IKYYRKQASLTLQEISARTGLSIGYLSNLERDLTSPSFDNLCSICNALSVNVVDL 60
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55

HTH-type transcriptional regulator PuuR;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495983956   1 MIGKKIKYYRKQASLTLQEISARTGLSIGYLSNLERDLTSPSFDNLCSIcnalsVNVVDLiknSLSYKPLLKKADRTPVY 80
Cdd:PRK09943   7 APGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKL-----LKVYGL---SLSEFFSEPEKPDEPQV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495983956  81 ARDyrtryefttAQDLNLLG-----MCLI-----------LEEDYY-----GTEVSwgHDTDEYGLIMEGSLIFEVNGEK 139
Cdd:PRK09943  79 VIN---------QDDLIEMGsqgvsMKLVhngnpnrtlamIFETYQpgtttGERIK--HQGEEIGTVLEGEIVLTINGQD 147

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 495983956 140 YLVEEGDTIYIKAGMPHKWRKAGEGRC--VSYWTKLNY 175
Cdd:PRK09943 148 YHLVAGQSYAINTGIPHSFSNTSAGICriISAHTPTTF 185

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

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 495983956   2 IGKKIKYYRKQASLTLQEISARTGLSIGYLSNLERD----LTSPSF--DNLCSICNALSVNVVDLI 61
Cdd:COG1426    6 IGELLRQAREAKGLSLEDVAERTKISVSYLEAIEEGdfdaLPGPVYvrGFLRSYARALGLDPEELL 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
                 ....*....|....*....|....*....|...
gi 495983956 124 GLIMEGSLIFEVNGEKYLVEEGDTIYIKAGMPH 156
Cdd:cd02238   51 GYVLSGRFEFTIGGETRILKPGDSYYIPPNVPH 83

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 495983956 119 DTDEYGLIMEGSLIFEVNGEKYLVEEGDTIYIKAGMPHKWRKAGEGR------CVSYWTK 172
Cdd:cd02214   39 GSEEVYYILEGEGTMEIDGEPREVGPGDAVLIPPGAVQRIENTGEEDlvflciCSPAWSP 98

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
                 ....*....|....*....|....*....|....*..
gi 495983956 121 DEYGLIMEGSLIFEVNGEKYLVEEGDTIYIKAGMPHK 157
Cdd:cd02213   62 SEHWVVVSGTAEVTLDGKEKLLKEGESIYIPKGTKHR 98

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
                 ....*....|....*....|....*....|.
gi 495983956 126 IMEGSLIFEVNGEKYLVEEGDTIYIKAGMPH 156
Cdd:cd02230   37 VLEGEAEFTIGGETVTLKAGELIVMPANVPH 67

transcriptional repressor DicA; Reviewed

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 495983956   1 MIGKKIKYYRKQASLTLQEISARTGLSIGYLSNLERDLTSPSFDNLCSICNAL 53
Cdd:PRK09706   5 TLGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKAL 57

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
                 ....*....|....*....|....*....|....*....|..
gi 495983956 118 HDTDEYGLIMEGSLIFEVNGEKYLVEEGDTIYIKAGMPHKWR 159
Cdd:cd02215   51 KRHHETFYVLEGRLQLWLDGESRLLTPGDFASVPPGTIHAYR 92

(S)-ureidoglycine aminohydrolase and related proteins, N-terminal cupin domain; This family includes the N-terminal cupin domain of (S)-ureidoglycine aminohydrolase (UGlyAH), an enzyme that converts (S)-ureidoglycine into (S)-ureidoglycolate and ammonia, providing the final substrate to the ureide pathway. The ureide pathway has recently been identified as the metabolic route of purine catabolism in plants and some bacteria where, uric acid, which is a major product of the early stage of purine catabolism, is degraded into glyoxylate and ammonia via stepwise reactions by seven different enzymes. Thus, this pathway has a possible physiological role in mobilization of purine ring nitrogen for further assimilation. This enzyme from Arabidopsis thaliana(AtUGlyAH) has been shown to bind a Mn2+ ion, via the C-terminal cupin domain, which acts as a molecular anchor to bind (S)-ureidoglycine, and its binding mode dictates the enantioselectivity of the reaction. The structure of AtUGlyAH shows a bi-cupin fold with a conserved "jelly roll-like" beta-barrel fold and an octameric functional unit. Several structural homologs of UGlyAH, including the Escherichia coli ortholog YlbA (also known as GlxB6), also exhibit similar features.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 495983956 126 IMEGSLIFEVNGEKYLVEEGDTIYIKAGMPHKWRKAGEGRCVSYWTKLNYI 176
Cdd:cd02211   53 VLEGEVELTVGGETHTLTAGGYAYLPPGTKHSLRNAGDEPARLLWYKKRYE 103

conjugal transfer protein TrbA; Provisional

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 495983956  15 LTLQEISARTGLSIGYLSNLERDLTSPSFDNLCSICNALSVNV------VDLIKNSLS 66
Cdd:PRK13890  19 MTKKELSERSGVSISFLSDLTTGKANPSLKVMEAIADALETPLplllesTDLDKEALD 76

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 495983956 120 TDEYGLIMEGSLIFEVNGEKYLVEEGDTIYIKAGMPHKWRKAGEG 164
Cdd:cd06991   40 SEEFLYVVRGRLVVRVDGEPVVLEAGEALLVPRGVRHRLENAGDE 84

Dimethylsulfoniopropionate lyase DddK and related proteins, cupin domain; This family includes mostly bacterial proteins homologous to dimethylsulfoniopropionate lyase DddK from marine bacterium Pelagibacter. DddK cleaves dimethylsulfoniopropionate (DMSP), the organic osmolyte and antioxidant produced in marine environments, and yields acrylate and the climate-active gas dimethyl sulfide (DMS). DddK contains a double-stranded beta-helical motif which utilizes various divalent metal ions as cofactors for catalytic activity; however, nickel, an abundant metal ion in marine environments, confers the highest DMSP lyase activity. Also included in this family is Plu4264, a Photorhabdus luminescens manganese-containing cupin shown to have similar metal binding site to TM1287 decarboxylase, but two very different substrate binding pockets. The Plu4264 binding pocket shows a cavity and substrate entry point more than twice as large as and more hydrophobic than TM1287, suggesting that Plu4264 accepts a substrate that is significantly larger than that of TM1287, a putative oxalate decarboxylase. Thus, the function of Plu4264 could be similar to that of TM1287 but with a larger, less charged substrate. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 495983956 117 GHDTDEYGLIMEGSLIFEVNGEKYLVEEGDTIYIKAGMPH 156
Cdd:cd06988   19 SHHEYEIFIVISGKGIVVVDGEREPVKAGDVVYIPPGTEH 58

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
                 ....*....|....*....|....*....|....*...
gi 495983956 126 IMEGSLIFEVNGEKYLVEEGDTIYIKAGMPHKWRKAGE 163
Cdd:cd06984   37 VLEGEGIVEIGEEKQEVEADTLIESPANIPHCLYNESD 74

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
                 ....*....|....*....|....*....|....*....|....*....|..
gi 495983956 112 TEVSWGH------DTDEYGLIMEGSLIFEVNGEKYLVEEGDTIYIKAGMPHK 157
Cdd:cd20295   27 VEVEEGHeehyhkKSTEIYYVLEGEGIFELDGEAVPVKPGDLVLIPPGTRHR 78