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 488376789  86 GYILNWLVTNSNEFDMEPLILTLRPNASYKNFKPSESDTFIYCLNGEVSLQLGNQVYKACKEDVLYFKAKDKHRLYNETN 165
Cdd:cd02209    1 GYTYELLSPGLPGRKMEPFLVTLPPGGSGGEPYSHEGEEFGYVLEGELELTVGGETYVLEAGDSIYFDSDVPHRYRNPGD 80

                         90
                 ....*....|
gi 488376789 166 KEVKVLIVAT 175
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 488376789   4 GYKLRNLRRIKNLTQEELAERTDLSKGYISQIESNHASPSMETFLNLIEVLGTSASDF 61
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58

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 488376789  86 GYILNWLVTNSNEFDMEPLILTLRPNASYKNFKPSESDTFIYCLNGEVSLQLGNQVYKACKEDVLYFKAKDKHRLYNETN 165
Cdd:cd02209    1 GYTYELLSPGLPGRKMEPFLVTLPPGGSGGEPYSHEGEEFGYVLEGELELTVGGETYVLEAGDSIYFDSDVPHRYRNPGD 80

                         90
                 ....*....|
gi 488376789 166 KEVKVLIVAT 175
Cdd:cd02209   81 EPARVLWVIT 90

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 488376789    7 LRNLRRIKNLTQEELAERTDLSKGYISQIESNHASPSMETFLNLIEVLGTSASDF 61
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55

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 488376789  104 LILTLRPNASYKNFKPSESDTFIYCLNGEVSLQLGNQVYKACKEDVLYFKAKDKHRLYNETNKEVKVLIV 173
Cdd:pfam07883   1 GLVTLPPGESSPPHRHPGEDEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPHRFRNTGDEPARLLDV 70

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

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488376789   1 MDIGYKLRNLRRIKNLTQEELAERTDLSKGYISQIESNHASPSMETFLNLIEVLGTSASDFFKES 65
Cdd:COG1476    3 KKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLE 67

Helix-turn-helix XRE-family like proteins;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 488376789     6 KLRNLRRIKNLTQEELAERTDLSKGYISQIESNHASPSMETFLNLIEVLGTSASDF 61
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56

Uncharacterized conserved protein, cupin superfamily [Function unknown];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488376789  84 DKGYILNWLVTNSNEFDMEPLILTLRPNASYK-NFKPSESDTFIYCLNGEVSLQLGNQVYKACKEDVLYFKAKDKHRLYN 162
Cdd:COG3837   11 EAGRRYRRLGDALGLTRLGVNLITLPPGASSSpYHAHSAEEEFVYVLEGELTLRIGGEEYVLEPGDSVGFPAGVPHRLRN 90

                         90
                 ....*....|...
gi 488376789 163 ETNKEVKVLIVAT 175
Cdd:COG3837   91 RGDEPARYLVVGT 103

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

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 488376789   2 DIGYKLRNLRRIKNLTQEELAERTDLSKGYISQIESNHASPSMETFLNLIEVLGTSASD 60
Cdd:COG1813   12 DYGERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISLAE 70

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 488376789    4 GYKLRNLRRIKNLTQEELAERTDLSKGYISQIESNHASPSMETFLNLIEVLGTSASDFFK 63
Cdd:pfam12844   1 GERLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLLQ 60

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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 488376789    7 LRNLRRIKNLTQEELAERTDLSKGYISQIES-NHASPSMETFLNLIEVLGTSASD 60
Cdd:pfam13560   6 LRRLRERAGLSQEALARRLGVSRSTLSRLETgRRGRPSPAVVERLARALGVDGAE 60

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 488376789  104 LILTLRPNASYKNFKPSESDTFIYCLNGEVSLQLGNQVYKACKEDVLYFKAKDKHRLYNETNKEVKVLIV 173
Cdd:pfam07883   1 GLVTLPPGESSPPHRHPGEDEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPHRFRNTGDEPARLLDV 70

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488376789  96 SNEFDMEPLILTLRPNASYKNFKpSESDTFIYCLNGEVSLQLGNQVYKACKEDVLYFKAKDKHRLYNETNKEVKVLIVAT 175
Cdd:COG1917   18 DGEDELEVVRVTFEPGARTPWHS-HPGEELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFRNLGDEPAVLLVVFS 96

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

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 488376789  14 KNLTQEELAERTDLSKGYISQIESNHASPSMETFLNLIEVLGTSA 58
Cdd:COG3093   21 LGLSQTELAKALGVSRQRISEILNGKRAITADTALRLARAFGTSA 65

RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP (deoxythymidine diphosphates)-4-dehydrorhamnose 3,5-epimerase)-like cupins. RmlC is a dTDP-sugar isomerase involved in the synthesis of L-rhamnose, a saccharide required for the virulence of some pathogenic bacteria. 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). The active site of members of this superfamily is generally located at the center of a conserved barrel and usually includes a metal ion. The different functional classes in this superfamily include single domain bacterial isomerases and epimerases involved in the modification of cell wall carbohydrates, two domain bicupins such as the desiccation-tolerant seed storage globulins, and multidomain nuclear transcription factors involved in legume root nodulation.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488376789 105 ILTLRPNASYKNFKPSESDTFIYCLNGEVSLQLGNQVYKACKE-DVLYFKAKDKHRLYNETNKEVKVLIV 173
Cdd:cd02208    3 VVTLPPGTSSPPHWHPEQDEIFYVLSGEGELTLDDGETVELKAgDIVLIPPGVPHSFVNTSDEPAVFLVV 72

(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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488376789 105 ILTLRPNAsyKNFKPSESD---TFIYCLNGEVSLQLGNQVYKACKEDVLYFKAKDKHRLYNETNKEVKVLIV 173
Cdd:cd02211   29 LVEVEPGG--GSTAPEGGEgieRFLYVLEGEVELTVGGETHTLTAGGYAYLPPGTKHSLRNAGDEPARLLWY 98

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.

                          10        20
                  ....*....|....*....|....*...
gi 488376789   10 LRRIKNLTQEELAERTDLSKGYISQIES 37
Cdd:pfam04545  15 LRYGEGLTLEEIGERLGISRERVRQIEK 42

Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).

                         10        20
                 ....*....|....*....|....*...
gi 488376789  10 LRRIKNLTQEELAERTDLSKGYISQIES 37
Cdd:cd06171   21 LRFGEGLSYEEIAEILGISRSTVRQRLH 48