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 1442580779  84 MVVTPVFPWDPQLRFDHFSITLAPGA-LSESTPHEkgVIEHVVVISGALELCLEGQWQTLQAGEGRRFAGDLAHAYRNSG 162
Cdd:cd02209     2 YTYELLSPGLPGRKMEPFLVTLPPGGsGGEPYSHE--GEEFGYVLEGELELTVGGETYVLEAGDSIYFDSDVPHRYRNPG 79

                          90
                  ....*....|.
gi 1442580779 163 AQTAHFHSLIH 173
Cdd:cd02209    80 DEPARVLWVIT 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 1442580779  84 MVVTPVFPWDPQLRFDHFSITLAPGA-LSESTPHEkgVIEHVVVISGALELCLEGQWQTLQAGEGRRFAGDLAHAYRNSG 162
Cdd:cd02209     2 YTYELLSPGLPGRKMEPFLVTLPPGGsGGEPYSHE--GEEFGYVLEGELELTVGGETYVLEAGDSIYFDSDVPHRYRNPG 79

                          90
                  ....*....|.
gi 1442580779 163 AQTAHFHSLIH 173
Cdd:cd02209    80 DEPARVLWVIT 90

Helix-turn-helix XRE-family like proteins;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1442580779   11 LKTLRQQRGWSLSRLAEETGVSKAMLGQIERNESSPTVATLWKIATGLNV 60
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGV 51

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442580779  93 DPQLRFDHFSITLAPGAlsESTPHEKGVIEHVVVISGALELCLEGQWQTLQAGEGRRFAGDLAHAYRNSGAQTAHFHSLI 172
Cdd:COG1917    18 DGEDELEVVRVTFEPGA--RTPWHSHPGEELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFRNLGDEPAVLLVVF 95

                  .
gi 1442580779 173 H 173
Cdd:COG1917    96 S 96

type II toxin-antitoxin system antitoxin HipB;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1442580779   7 LAATLKTLRQQRGWSLSRLAEETGVSKAMLGQIERNESSPTVATLWKIATGLNVAFSTFIV 67
Cdd:PRK09726   13 LANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMTLCDA 73

transcriptional regulator, y4mF family; Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems. [Regulatory functions, DNA interactions]

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1442580779   7 LAATLKTLRQQRGWSLSRLAEETGVSKAMLGQIERNESSPTVATLWKIATGLN 59
Cdd:TIGR03070   3 IGILVRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDALG 55

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 1442580779  84 MVVTPVFPWDPQLRFDHFSITLAPGA-LSESTPHEkgVIEHVVVISGALELCLEGQWQTLQAGEGRRFAGDLAHAYRNSG 162
Cdd:cd02209     2 YTYELLSPGLPGRKMEPFLVTLPPGGsGGEPYSHE--GEEFGYVLEGELELTVGGETYVLEAGDSIYFDSDVPHRYRNPG 79

                          90
                  ....*....|.
gi 1442580779 163 AQTAHFHSLIH 173
Cdd:cd02209    80 DEPARVLWVIT 90

Helix-turn-helix XRE-family like proteins;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1442580779   11 LKTLRQQRGWSLSRLAEETGVSKAMLGQIERNESSPTVATLWKIATGLNV 60
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGV 51

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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1442580779   4 AQHLAATLKTLRQQRGWSLSRLAEETGVSKAMLGQIERNESSPTVATLWKIATGLNV 60
Cdd:COG1476     2 KKKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGV 58

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

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1442580779   5 QHLAATLKTLRQQRGWSLSRLAEETGVSKAMLGQIERNESSPTVATLWKIATGLNVAFSTFIV 67
Cdd:COG3620    16 DTLGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVLV 78

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 1442580779 103 ITLAPGALSESTPHEkGVIEHVVVISGALELCLEGQWQTLQAGEGRRFAGDLAHAYRNSGAQTAHFHSLI 172
Cdd:pfam07883   3 VTLPPGESSPPHRHP-GEDEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPHRFRNTGDEPARLLDVY 71

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
                  ....*....|....*....|....*....|....*....|....*....|
gi 1442580779  11 LKTLRQQRGWSLSRLAEETGVSKAMLGQIERNESSPTVATLWKIATGLNV 60
Cdd:pfam12844   4 LRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGV 53

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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1442580779   6 HLAATLKTLRQQRGWSLSRLAEETGVSKAMLGQIERNE-SSPTVATLWKIATGLNV 60
Cdd:pfam13560   1 ELGARLRRLRERAGLSQEALARRLGVSRSTLSRLETGRrGRPSPAVVERLARALGV 56

(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        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442580779  94 PQL--RFDHFSITLAPGALSESTPHEKGvIEHVV-VISGALELCLEGQWQTLQAGEgrrFA---GDLAHAYRNSGAQTAH 167
Cdd:cd02211    19 PKLgaTFVQYLVEVEPGGGSTAPEGGEG-IERFLyVLEGEVELTVGGETHTLTAGG---YAylpPGTKHSLRNAGDEPAR 94

                          90
                  ....*....|....*
gi 1442580779 168 FHsLIHYPKEKAAGG 182
Cdd:cd02211    95 LL-WYKKRYEPLEGG 108

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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1442580779  11 LKTLRQQRGWSLSRLAEETGVSKAMLGQIERNE-SSPTVATLWKIATGLNV 60
Cdd:COG3655     6 LDELLAERGMTKKELAEATGISRATLSRLKNGKaKAVRLDTLEKICKALDC 56

Ureidoglycine aminohydrolase [Nucleotide transport and metabolism];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442580779  86 VTPVFP-WD---------PQL--RFDHFSITLAPGALSESTPHEKGvIEHVV-VISGALELCLEGQWQTLQAGEgrrFA- 151
Cdd:COG3257    35 VTSVLPgWEntrvwilarPLSgaTFSQYIVEVAPGGGSDRPEPDPG-AETFLfVLEGEVTLTLGGETHELTPGG---YAy 110

                          90       100
                  ....*....|....*....|
gi 1442580779 152 --GDLAHAYRNSGAQTAHFH 169
Cdd:COG3257   111 lpPGTPWTLRNAGDEPARFH 130

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

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1442580779 103 ITLAPGALSESTPHEKGViEHVVVISGALELCLEGQWQTLQAGEGRRFAGDLAHAYRNSGAQTAHFHSlIHYP 175
Cdd:COG0662    32 ITVPPGAELSLHVHPHRD-EFFYVLEGTGEVTIGDEEVELKAGDSVYIPAGVPHRLRNPGDEPLELLE-VQAP 102

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 1442580779 103 ITLAPGAlseSTPHEKGVIEHVV-VISGALELCLEGQWQTLQAGEGRRFAGDLAHAYRNSGAQTAHF 168
Cdd:cd02222    22 FEIEPGG---HTPLHTHPWEHEVyVLRGKGVVVIGGEEYPVKPGDVVYIPPNEPHQFRNTGDEPLGF 85

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        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1442580779 103 ITLAPGalSESTPHEKGVIEHVVVISGALELCLEGQWQTLQAGEGRRFAGDLAHAYRNSGAQTAHFHSL 171
Cdd:cd06988     7 CVVRPG--TTSTPHSHHEYEIFIVISGKGIVVVDGEREPVKAGDVVYIPPGTEHYVKNDGDEDFEFYSI 73

Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to DNA.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1442580779  11 LKTLRQQRGWSLSRLAEETGVSKAMLGQIERNES-SPTVATLWKIATGLNVAFSTFIV 67
Cdd:pfam13443   2 LRKLMADRGISKSDLARATGISRATLSRLRKGKPkRVSLDTLDKICDALGCQPGDLLE 59

transcriptional regulator, y4mF family; Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems. [Regulatory functions, DNA interactions]

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1442580779   7 LAATLKTLRQQRGWSLSRLAEETGVSKAMLGQIERNESSPTVATLWKIATGLN 59
Cdd:TIGR03070   3 IGILVRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDALG 55

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        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442580779 103 ITLAPGALSeSTPH-----EkgviEHVVVISGALELCLEGQWQTLQAGEGRRF-AGD-LAHAYRNSGAQTAHF------- 168
Cdd:cd02224    22 ERLPPGARS-SPRHwhsaeE----EFVYVLSGEGTLRLDGEEVLPRPGDFVGFpAGTgVAHQLINRSDEPLVYlvvgtrl 96

                  ....*...
gi 1442580779 169 -HSLIHYP 175
Cdd:cd02224    97 pDDVCTYP 104

helix-turn-helix protein

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1442580779  14 LRQQRGWSLSRLAEETGVSKAMLGQIERNESSPTVATLWKIATGLNVAF 62
Cdd:PHA01976   10 ARNARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGVTL 58