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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446503179  92 IVYDVLTPDfmKARIEVLMMDLNKQAnTTESHYsHEDkEEIAVIMKGEVYVELEGKEYFLEEGDVVRIPPNVKHRFLNKS 171
Cdd:COG1917   11 VSVRVLADG--EDELEVVRVTFEPGA-RTPWHS-HPG-EELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFRNLG 85

                         90
                 ....*....|....
gi 446503179 172 DESNHILFVLTPSL 185
Cdd:COG1917   86 DEPAVLLVVFSPGL 99

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446503179  92 IVYDVLTPDfmKARIEVLMMDLNKQAnTTESHYsHEDkEEIAVIMKGEVYVELEGKEYFLEEGDVVRIPPNVKHRFLNKS 171
Cdd:COG1917   11 VSVRVLADG--EDELEVVRVTFEPGA-RTPWHS-HPG-EELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFRNLG 85

                         90
                 ....*....|....
gi 446503179 172 DESNHILFVLTPSL 185
Cdd:COG1917   86 DEPAVLLVVFSPGL 99

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        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446503179  92 IVYDVLTPDFMKARIEVLMMDLNKQANTTEShYSHEDkEEIAVIMKGEVYVELEGKEYFLEEGDVVRIPPNVKHRFLNKS 171
Cdd:cd02209    2 YTYELLSPGLPGRKMEPFLVTLPPGGSGGEP-YSHEG-EEFGYVLEGELELTVGGETYVLEAGDSIYFDSDVPHRYRNPG 79

                         90
                 ....*....|.
gi 446503179 172 DESNHILFVLT 182
Cdd:cd02209   80 DEPARVLWVIT 90

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 446503179  119 TTESHYsHEDKEEIAVIMKGEVYVELEGKEYFLEEGDVVRIPPNVKHRFLNKSDESNHILFV 180
Cdd:pfam07883  10 SSPPHR-HPGEDEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPHRFRNTGDEPARLLDV 70

conjugal transfer protein TrbA; Provisional

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446503179  10 VLSYRKKNNMTIREFADYAGISTSLISQIERGHANPSLNVLELIAKALNVPLFTLF-INDIDTDSL 74
Cdd:PRK13890  10 VLRLLDERHMTKKELSERSGVSISFLSDLTTGKANPSLKVMEAIADALETPLPLLLeSTDLDKEAL 75

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446503179  92 IVYDVLTPDfmKARIEVLMMDLNKQAnTTESHYsHEDkEEIAVIMKGEVYVELEGKEYFLEEGDVVRIPPNVKHRFLNKS 171
Cdd:COG1917   11 VSVRVLADG--EDELEVVRVTFEPGA-RTPWHS-HPG-EELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFRNLG 85

                         90
                 ....*....|....
gi 446503179 172 DESNHILFVLTPSL 185
Cdd:COG1917   86 DEPAVLLVVFSPGL 99

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        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446503179  92 IVYDVLTPDFMKARIEVLMMDLNKQANTTEShYSHEDkEEIAVIMKGEVYVELEGKEYFLEEGDVVRIPPNVKHRFLNKS 171
Cdd:cd02209    2 YTYELLSPGLPGRKMEPFLVTLPPGGSGGEP-YSHEG-EEFGYVLEGELELTVGGETYVLEAGDSIYFDSDVPHRYRNPG 79

                         90
                 ....*....|.
gi 446503179 172 DESNHILFVLT 182
Cdd:cd02209   80 DEPARVLWVIT 90

Helix-turn-helix XRE-family like proteins;

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 446503179    13 YRKKNNMTIREFADYAGISTSLISQIERGHANPSLNVLELIAKALNVPL 61
Cdd:smart00530   5 LREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSL 53

Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and HTH domains [Translation, ribosomal structure and biogenesis];

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446503179   1 MIHDRLGQTVLSYRKKNNMTIREFADYAGISTSLISQIERGHANPSLNVLELIAKALNVPL 61
Cdd:COG1813    8 ELVEDYGERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISL 68

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

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446503179 125 SHEDKEEIAVIMKGEVYVELEGKEYFLEEGDVVRIPPNVKHRFLNKSDESNHILFVLTPS 184
Cdd:COG0662   44 VHPHRDEFFYVLEGTGEVTIGDEEVELKAGDSVYIPAGVPHRLRNPGDEPLELLEVQAPA 103

conjugal transfer protein TrbA; Provisional

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446503179  10 VLSYRKKNNMTIREFADYAGISTSLISQIERGHANPSLNVLELIAKALNVPLFTLF-INDIDTDSL 74
Cdd:PRK13890  10 VLRLLDERHMTKKELSERSGVSISFLSDLTTGKANPSLKVMEAIADALETPLPLLLeSTDLDKEAL 75

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        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 446503179 119 TTESHYSHEDkeEIAVIMKGEVYVELEGKEYFLEEGDVVRIPPNVKHRFLNKSDESNHI 177
Cdd:cd06988   14 TSTPHSHHEY--EIFIVISGKGIVVVDGEREPVKAGDVVYIPPGTEHYVKNDGDEDFEF 70

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        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446503179  98 TPDFMKARIEVLMMDLNKQANTTESHYsHEDKEEIAVIMKGEVYVELEGKEYFLEEGDVVRIPPNVKHRFLNKSDESNHI 177
Cdd:cd06979    9 TKDGTADRFDLFEFEVSPNAGMPPPHY-HEDWEETIYGLEGSVTLTLPGKTVEVGPGDSIFIPRGEVHGFVNRSGGPTCR 87

                 ....*.
gi 446503179 178 LFVLTP 183
Cdd:cd06979   88 LCVLAP 93

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 446503179 119 TTESHYsHEDKEEIAVIMKGEVYVELEGKEYFLEEGDVVRIPPNVKHRFLNKSDESNHILFVLTP 183
Cdd:cd02214   31 STLPHR-LKGSEEVYYILEGEGTMEIDGEPREVGPGDAVLIPPGAVQRIENTGEEDLVFLCICSP 94

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 446503179 121 ESHYsHEDKEEIAVIMKGEVYVELEGKEYFLEEGDVVRIPPNVKHRFLNK 170
Cdd:cd20295   34 EEHY-HKKSTEIYYVLEGEGIFELDGEAVPVKPGDLVLIPPGTRHRAVGK 82

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
                 ....*....|....*....|....*....|....*....|....*....|.
gi 446503179 123 HYSHEDKEEIAVIMKGEVYVELEGKEYFLEEGDVVRIPPNVKHRFLNKSDE 173
Cdd:cd06985   30 VHSHKENEEIYIILKGKGEFQVDGEVFPVKEGSVIRVAPDGKRSWRNTSDE 80

DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446503179   1 MIHDRL-GQTVLSYRKKNNMTIREFADYAGISTSLISQIERGHANPSLNVLELIAKALNVP 60
Cdd:COG2944    1 MTKKPLtPEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGAALKLLRLLEKHP 61

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
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446503179 119 TTESHYsHEDKEEIAVIMKGEVYVELEGKEYFLEEGDVVRIPPNVK--HRFLNKSDE 173
Cdd:cd02224   30 SSPRHW-HSAEEEFVYVLSGEGTLRLDGEEVLPRPGDFVGFPAGTGvaHQLINRSDE 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        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446503179 123 HYsHEDKEEIAVIMKGEVYVELEGKEYFLEEGDVVRIPPNVKHRFLNKSDESNHILFVLTP 183
Cdd:cd06991   35 HY-HPYSEEFLYVVRGRLVVRVDGEPVVLEAGEALLVPRGVRHRLENAGDEPARLVFHLSP 94

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 446503179  126 HEDKEEIAVIMKGEVYVELEGKEYFLEEGDVVRIPPNVKHRF 167
Cdd:pfam02311  20 VHDFYVIGYIERGVGRFRLNGRTYHLGPGDLFLLPPGEPHDY 61

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 446503179 126 HEDKEEIAVIMKG--EVYVELEGKEYFLE--EGDVVRIPPNVKHRFLNKSDE 173
Cdd:cd02225   70 THEVEEVFFVLQGrlTVFWEDEGEEHERElgPRDMISVPAGVYRGFKNIGEE 121

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446503179 123 HYsHEDKEEIAVIMKGEVYVELEGKEYFLEEGDVVRIPPNVKHRFLNKSDEsNHILFVLTP 183
Cdd:cd02215   48 HY-HKRHHETFYVLEGRLQLWLDGESRLLTPGDFASVPPGTIHAYRMLSPD-TRFLGVITP 106

transcriptional repressor DicA; Reviewed

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446503179   6 LGQTVLSYRKKNNMTIREFADYAGISTSLISQIERGHANPSLNVLELIAKALNV-PLFTLF 65
Cdd:PRK09706   6 LGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCsPTWLLF 66

ARD/ARD' family; The two acireductone dioxygenase enzymes (ARD and ARD', previously known as E-2 and E-2') from Klebsiella pneumoniae share the same amino acid sequence, but bind different metal ions: ARD binds Ni2+, ARD' binds Fe2+. ARD and ARD' can be experimentally interconverted by removal of the bound metal ion and reconstitution with the appropriate metal ion. The two enzymes share the same substrate, 1,2-dihydroxy-3-keto-5-(methylthio)pentene, but yield different products. ARD' yields the alpha-keto precursor of methionine (and formate), thus forming part of the ubiquitous methionine salvage pathway that converts 5'-methylthioadenosine (MTA) to methionine. This pathway is responsible for the tight control of the concentration of MTA, which is a powerful inhibitor of polyamine biosynthesis and transmethylation reactions. ARD yields methylthiopropanoate, carbon monoxide and formate, and thus prevents the conversion of MTA to methionine. The role of the ARD catalyzed reaction is unclear: methylthiopropanoate is cytotoxic, and carbon monoxide can activate guanylyl cyclase, leading to increased intracellular cGMP levels. This family also contains other members, whose functions are not well characterized.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446503179   71 TDSLISKKKDRKKVYRENNDHIVYDVLTPDFMkARIEVLMmdlnkqANTTESHySHEDkEEIAVIMKGEVYVELEGKE-- 148
Cdd:pfam03079  43 DDEETAEDLLRILKYKHYDDVDIDVTVCPETT-PNFDEKL------EKFFEEH-LHTD-EEIRYIVEGTGYFDVRDKDdv 113

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 446503179  149 ---YFLEEGDVVRIPPNVKHRFlnKSDESNHI----LFVLTP 183
Cdd:pfam03079 114 wirVFVEKGDLISLPAGIYHRF--TTTPDNYVkalrLFVTKP 153

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        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446503179 111 MDLNKQANTTESHYSHEDKEEIA----------VIMKGEVYVELEGKEYFLEEGDVVRIPPNVKH 165
Cdd:cd06983    2 MALSNSDNVQISLFAFADGESVSeeeyfgdtlyYVLEGEAEITIGDEKHRLKAGDVLAVPAGVLH 66

gentisate 1,2-dioxygenase, 1-hydroxy-2-naphthoate dioxygenase, and salicylate 1,2-dioxygenase bicupin aromatic ring-cleaving dioxygenases, C-terminal cupin domain; This model represents the C-terminal cupin domains of three closely related bicupin aromatic ring-cleaving dioxygenases: gentisate 1,2-dioxygenase (GDO), salicylate 1,2-dioxygenase (SDO), and 1-hydroxy-2-naphthoate dioxygenase (NDO). GDO catalyzes the cleavage of the gentisate (2,5-dihydroxybenzoate) aromatic ring, a key step in the gentisate degradation pathway allowing soil bacteria to utilize 2,5-xylenol, 3,5-xylenol, and m-cresol as sole carbon and energy sources. NDO catalyzes the cleavage of 1-hydroxy-2-naphthoate as part of the bacterial phenanthrene degradation pathway. SDO is a ring cleavage dioxygenase from Pseudaminobacter salicylatoxidans that oxidizes salicylate to 2-oxohepta-3,5-dienedioic acid via a novel ring fission mechanism. SDO differs from other known GDO's and NDO's in its unique ability to oxidatively cleave many different salicylate, gentisate, and 1-hydroxy-2- naphthoate substrates with high catalytic efficiency. The active site of this enzyme is located in the N-terminal domain but could be influenced by changes in the C-terminal domain, which lacks the strictly conserved metal-binding residues found in other cupin domains and is thought to be an inactive vestigial remnant.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 446503179 132 IAVIMKGEVYVELEGKEYFLEEGDVVRIPPNVKHRFLNKSDESnhILF 179
Cdd:cd06992   42 VYHVVEGSGRTVIGGKTFEWEPGDVFVVPSWAWHSHEADSEDA--VLF 87

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

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446503179 120 TESHYsHEDKEEIAVIMKGEV---YVELEGKEYFLEEGDVVRIPPNVKHRFLNKSDE 173
Cdd:COG4101   59 AKAHH-HGEHETAIYVLSGRAetrYGERLEHRVVTEPGDFIFIPPGVPHQEINLSDT 114

AraC/XylS family transcriptional regulators similar to Bacillus subtilis YbfI, 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, including YbfI, an uncharacterized Bacillus subtilis. In Pseudomonas putida, this protein is thought to regulate the expression of phenylserine aldolase. 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 446503179 124 YSHEDKEEIAVIMKGEVYVELEGKEYFLEEGDVVRIPPNVKHR 166
Cdd:cd07001   17 NHFHDFYVIGFIESGQRTLFCEGKEYTVEPGDLLLINPRDVHS 59

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
                 ....*....|....*....|....*....|....*....|..
gi 446503179 125 SHEDKEEIAVIMKGEVYVELEGKEYFLEEGDVVRIPPNVKHR 166
Cdd:cd02226   39 KHDDEDELFLVLEGELTIDFRDRDVTLGPGEFFVVPKGVEHR 80

Ureidoglycine aminohydrolase [Nucleotide transport and metabolism];

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 446503179 135 IMKGEVYVELEGKEYFLEEGDVVRIPPNVKHRFLNKSDESNHILFV 180
Cdd:COG3257   87 VLEGEVTLTLGGETHELTPGGYAYLPPGTPWTLRNAGDEPARFHWI 132

acireductone dioxygenase (ARD), cupin domain; Acireductone dioxygenase (ARD; also known as 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase) catalyzes the oxidation of 1,2-dihydroxy-3-keto-5-methylthiopentene to yield two different products depending on which active site metal is present (Fe2+ or Ni2+) as part of the methionine salvage pathway. The ARD apo-enzyme, obtained after the metal is removed, is catalytically inactive. The Fe(II)-ARD reaction yields an alpha-keto acid and formic acid, while Ni(II)-ARD instead catalyzes a shunt out of the methionine salvage pathway, yielding methylthiocarboxylic acid, formic acid, and CO. ARD belongs to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446503179 126 HEDkEEIAVIMKGEVY--VELEGKEYF---LEEGDVVRIPPNVKHRFlnKSDESNHI 177
Cdd:cd02232   67 HED-DEVRFILDGSGYfdVRDKDDEWIrilVEKGDLIVVPAGIYHRF--TLDENPYI 120

(S)-ureidoglycine aminohydrolase;

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 446503179 135 IMKGEVYVELEGKEYFLEEGDVVRIPPNVKHRFLNKSDESNHILFV 180
Cdd:PRK11171  89 VVEGEITLTLEGKTHALSEGGYAYLPPGSDWTLRNAGAEDARFHWI 134

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        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 446503179 130 EEIAVIMKGEVYVELEGKEYFLEEGDVVRIPPNVKHRFlnKSDESNHILFV 180
Cdd:cd02228   34 DEIKYVLEGELEITDDGQTVTAKPGDVLFIPKGSKITF--STPDYAKFFYV 82

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 446503179 120 TESHYsHEDKEEIAVIMKGEVYV----ELEgkEYF-LEEGDVVRIPPNVKHRFLNKSD 172
Cdd:cd02210   24 TGAHH-HGEHETAIYVLSGRAETrygdRLE--HRAeAGPGDFIYIPPGVPHQEVNLSD 78

Ethanolamine utilization protein EutQ, cupin superfamily (function unknown) [Amino acid transport and metabolism];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446503179  73 SLISKKKDRKKVYRENNDHIVY--DVLTPDFmKARIEVLMMDLNKQANTTESHYshedkEEIAVIMKGEVYVELEGKEYF 150
Cdd:COG4766   15 SGIKVSVKDERFDTGGPGDKVYlkDVVTLEE-SSRMGAGFMRLEKTTFPWTLTY-----DEVDYVLEGTLTIEIDGETVT 88

                         90       100       110
                 ....*....|....*....|....*....|....
gi 446503179 151 LEEGDVVRIPPNVKHRFlnKSDESNHILFVLTPS 184
Cdd:COG4766   89 AGPGDVIYIPKGSSITF--STPEKARFFYVTYPA 120