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 15597508  98 FTSRALFPFDVARQVEFYELRLRGlGQEDAEAHAPGTQENLVVAQGVLEVRVNEERFLLATGDSILFYADQPHSYRNPAD 177
Cdd:cd02209   2 YTYELLSPGLPGRKMEPFLVTLPP-GGSGGEPYSHEGEEFGYVLEGELELTVGGETYVLEAGDSIYFDSDVPHRYRNPGD 80

                        90
                ....*....|
gi 15597508 178 SEALAYLVMT 187
Cdd:cd02209  81 EPARVLWVIT 90

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 15597508  98 FTSRALFPFDVARQVEFYELRLRGlGQEDAEAHAPGTQENLVVAQGVLEVRVNEERFLLATGDSILFYADQPHSYRNPAD 177
Cdd:cd02209   2 YTYELLSPGLPGRKMEPFLVTLPP-GGSGGEPYSHEGEEFGYVLEGELELTVGGETYVLEAGDSIYFDSDVPHRYRNPGD 80

                        90
                ....*....|
gi 15597508 178 SEALAYLVMT 187
Cdd:cd02209  81 EPARVLWVIT 90

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 15597508  14 AHNLLRLRGKRNLSLDALARISGVSRAMLAQIESGRSVPSIKVLCKIAQGLKVSVAAF 71
Cdd:cd00093   1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58

Uncharacterized conserved protein, cupin superfamily [Function unknown];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597508  91 LVSADGAFTSRALFPFDVARQVEFYELRLRgLGQEDAEAHAPGTQENLV-VAQGVLEVRVNEERFLLATGDSILFYADQP 169
Cdd:COG3837   7 LPGPEAGRRYRRLGDALGLTRLGVNLITLP-PGASSSPYHAHSAEEEFVyVLEGELTLRIGGEEYVLEPGDSVGFPAGVP 85

                        90       100
                ....*....|....*....|....*..
gi 15597508 170 HSYRNPADSEALAYLVMT---YPERLD 193
Cdd:COG3837  86 HRLRNRGDEPARYLVVGTrapYPDSFD 112

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 15597508   125 EDAEAHA-PGTQENLVVAQGVLEVRVNEERFLLATGDSILFYADQPHSYRNPADSEALAYLVM 186
Cdd:pfam07883   9 ESSPPHRhPGEDEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPHRFRNTGDEPARLLDVY 71

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 15597508  98 FTSRALFPFDVARQVEFYELRLRGlGQEDAEAHAPGTQENLVVAQGVLEVRVNEERFLLATGDSILFYADQPHSYRNPAD 177
Cdd:cd02209   2 YTYELLSPGLPGRKMEPFLVTLPP-GGSGGEPYSHEGEEFGYVLEGELELTVGGETYVLEAGDSIYFDSDVPHRYRNPGD 80

                        90
                ....*....|
gi 15597508 178 SEALAYLVMT 187
Cdd:cd02209  81 EPARVLWVIT 90

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

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15597508  11 QRVAHNLLRLRGKRNLSLDALARISGVSRAMLAQIESGRSVPSIKVLCKIAQGLKVSVAAFLDD 74
Cdd:COG1476   3 KKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSL 66

Helix-turn-helix XRE-family like proteins;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 15597508     16 NLLRLRGKRNLSLDALARISGVSRAMLAQIESGRSVPSIKVLCKIAQGLKVSVAAF 71
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 15597508    17 LLRLRGKRNLSLDALARISGVSRAMLAQIESGRSVPSIKVLCKIAQGLKVSVAAF 71
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597508  96 GAFTSRALFPFDvaRQVEFYELRLRGlGQEdAEAHAPGTQENLVVAQGVLEVRVNEERFLLATGDSILFYADQPHSYRNP 175
Cdd:COG1917   9 TGVSVRVLADGE--DELEVVRVTFEP-GAR-TPWHSHPGEELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFRNL 84

                        90
                ....*....|....*.
gi 15597508 176 ADSEAlAYLVMTYPER 191
Cdd:COG1917  85 GDEPA-VLLVVFSPGL 99

Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. This family contains many example antitoxins from bacterial toxin-antitoxin systems. These antitoxins are likely to be DNA-binding domains.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15597508    10 GQRvahnLLRLRGKRNLSLDALARISGVSRAMLAQIESGRSVPSIKVLCKIAQGLKVSVAAFL 72
Cdd:pfam12844   1 GER----LRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLL 59

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597508 107 DVARQVEFYELRLRGLGQEDAEAHaPGTQENLVVAQGVLEVRVNEERFLLATGDSILFYADQPHSYRNPADsEALAYLVM 186
Cdd:COG0662  22 EGGERLSVKRITVPPGAELSLHVH-PHRDEFFYVLEGTGEVTIGDEEVELKAGDSVYIPAGVPHRLRNPGD-EPLELLEV 99

                ....*..
gi 15597508 187 TYPERLD 193
Cdd:COG0662 100 QAPAYLG 106

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 15597508 123 GQEDAEAHAPGTQENLVVAQGVLEVRVNEERFLLATGDSILFYADQPHSYRNPADSEALA 182
Cdd:cd06991  29 GERVSEHYHPYSEEFLYVVRGRLVVRVDGEPVVLEAGEALLVPRGVRHRLENAGDEPARL 88

conjugal transfer protein TrbA; Provisional

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 15597508   16 NLLRLRGKRNLSLDALARISGVSRAMLAQIESGRSVPSIKVLCKIAQGLKVSVAAFLD 73
Cdd:PRK13890   9 NVLRLLDERHMTKKELSERSGVSISFLSDLTTGKANPSLKVMEAIADALETPLPLLLE 66

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 15597508 140 VAQGVLEVRVNEERFLLATGDSILFYADQPHSYRNPADSEAL 181
Cdd:cd02238  53 VLSGRFEFTIGGETRILKPGDSYYIPPNVPHGAEALEDSVLL 94

DNA-binding transcriptional regulator, XRE family [Transcription];

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15597508  13 VAHNLLRLRGKRNLSLDALARISGVSRAMLAQIESGRSV-PSIKVLCKIAQGLKVSVAAFLD 73
Cdd:COG3655   2 IYVKLDELLAERGMTKKELAEATGISRATLSRLKNGKAKaVRLDTLEKICKALDCQPGDLLE 63

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 15597508 125 EDAEAHAPGTQENLVVAQGVLEVRVNEERFLLATGDSILFYADQPHSYRNPADSE 179
Cdd:cd06988  13 TTSTPHSHHEYEIFIVISGKGIVVVDGEREPVKAGDVVYIPPGTEHYVKNDGDED 67

centromere-binding protein CENP-C, C-terminal cupin domain; This family includes centromeric protein C (CENP-C; known as Mif2 in budding yeast and centromere protein 3 or cnp3 in fission yeast), which is an inner kinetochore centromere (CEN)-binding protein found in fungi and metazoans. CENP-C is a component of the CENP-A nucleosome-associated complex (NAC) that plays a central role in assembly of kinetochore proteins, mitotic progression and chromosome segregation. CENP-C localizes to the inner kinetochore plates adjacent to the centromeric DNA and is known to have DNA-binding ability. CENP-C, along with CENP-H, provides a platform onto which the mitotic kinetochore is assembled and thus plays a critical role in the structuring of kinethocore chromatin. The cupin domain at the C-terminus forms a homodimer which is part of an enhanceosome-like structure that nucleates kinetochore assembly in budding yeast. 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 15597508 140 VAQGVLEVRVNEERFLLATGDSilFYADQPHSY--RNPADSEALAYLV 185
Cdd:cd06993  30 VIQGAVEVTLHETTFVVTKGCS--FQVPRGNYYsiKNIGNKEARLFFV 75

Predicted transcriptional regulator [Transcription];

                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 15597508  17 LLR-LRGKRNLSLDALARISGVSRAMLAQIESGRSVPSIKV 56
Cdd:COG1395 131 KLReLREERGLSLGELASELGVSRRTISKYERGEMDASIEV 171