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Conserved domains on  [gi|15597212|ref|NP_250706|]
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liu genes regulator [Pseudomonas aeruginosa PAO1]

Protein Classification

MerR family transcriptional regulator( domain architecture ID 10140965)

MerR family transcriptional regulator activates transcription through protein-dependent DNA distortion and the majority of regulators in the family respond to environmental stimuli, such as oxidative stress, heavy metals or antibiotics

CATH:  1.10.10.10
Gene Ontology:  GO:0003677|GO:0003700|GO:0006355
PubMed:  15808743|12829265|17302809|35130613
SCOP:  3000158

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_GnyR cd04776
Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Putative helix-turn-helix ...
 5-123 1.44e-57

Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.


:

Pssm-ID: 133403  Cd Length: 118  Bit Score: 174.26  E-value: 1.44e-57
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212   5 YTISDLARELDITTRAIRFYEEQGLLSPERRGQERIYSPRDKVSLKLILRGKRIGFSLAECRELIELYDPDPssGNQKQL 84
Cdd:cd04776   1 YTISELAREFDVTPRTLRFYEDKGLLSPERRGQTRVYSRRDRARLKLILRGKRLGFSLEEIRELLDLYDPPG--GNRKQL 78

                        90       100       110
                ....*....|....*....|....*....|....*....
gi 15597212  85 NTMLEKIAERRAQLEQQLLDIEQMQLELDTAEERCRAAL 123
Cdd:cd04776  79 EKMLEKIEKRRAELEQQRRDIDAALAELDAAEERCRERL 117
 
Name Accession Description Interval E-value
HTH_GnyR cd04776
Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Putative helix-turn-helix ...
 5-123 1.44e-57

Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.


Pssm-ID: 133403  Cd Length: 118  Bit Score: 174.26  E-value: 1.44e-57
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212   5 YTISDLARELDITTRAIRFYEEQGLLSPERRGQERIYSPRDKVSLKLILRGKRIGFSLAECRELIELYDPDPssGNQKQL 84
Cdd:cd04776   1 YTISELAREFDVTPRTLRFYEDKGLLSPERRGQTRVYSRRDRARLKLILRGKRLGFSLEEIRELLDLYDPPG--GNRKQL 78

                        90       100       110
                ....*....|....*....|....*....|....*....
gi 15597212  85 NTMLEKIAERRAQLEQQLLDIEQMQLELDTAEERCRAAL 123
Cdd:cd04776  79 EKMLEKIEKRRAELEQQRRDIDAALAELDAAEERCRERL 117
SoxR COG0789
DNA-binding transcriptional regulator, MerR family [Transcription];
7-112 9.00e-22

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


Pssm-ID: 440552 [Multi-domain]  Cd Length: 100  Bit Score: 83.03  E-value: 9.00e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212   7 ISDLARELDITTRAIRFYEEQGLLSPERR--GQERIYSPRDKVSLKLILRGKRIGFSLAECRELIELYDPDPSsgnqkql 84
Cdd:COG0789   1 IGEVARLTGVSVRTLRYYERIGLLPPPERteGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLDDGEE------- 73

                        90       100
                ....*....|....*....|....*...
gi 15597212  85 nTMLEKIAERRAQLEQQLLDIEQMQLEL 112
Cdd:COG0789  74 -EVRELLEEHLAELEAQIAELQALRAEL 100
PRK10227 PRK10227
HTH-type transcriptional regulator CueR;
7-119 6.29e-19

HTH-type transcriptional regulator CueR;


Pssm-ID: 182320  Cd Length: 135  Bit Score: 76.61  E-value: 6.29e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212    7 ISDLARELDITTRAIRFYEEQGLLSPERRGQE--RIYSPRDKVSLKLILRGKRIGFSLAECRELIELY-DPDPSSGNQKQ 83
Cdd:PRK10227   3 ISDVAKITGLTSKAIRFYEEKGLVTPPMRSENgyRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFnDPQRHSADVKR 82

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 15597212   84 lnTMLEKIAErraqLEQQLLDIEQMQLELDTAEERC 119
Cdd:PRK10227  83 --RTLEKVAE----IERHIEELQSMRDQLLALANAC 112
HTH_MERR smart00422
helix_turn_helix, mercury resistance;
5-72 5.87e-17

helix_turn_helix, mercury resistance;


Pssm-ID: 197716  Cd Length: 70  Bit Score: 69.86  E-value: 5.87e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212      5 YTISDLARELDITTRAIRFYEEQGLLSPERR--GQERIYSPRDKVSLKLILRGKRIGFSLAECRELIELY 72
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRteGGYRLYSDEDLERLRFIKRLKELGFSLEEIKELLELL 70
CueR TIGR02044
Cu(I)-responsive transcriptional regulator; This model represents the copper-, silver- and ...
 7-119 6.11e-16

Cu(I)-responsive transcriptional regulator; This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue. [Regulatory functions, DNA interactions]


Pssm-ID: 131099 [Multi-domain]  Cd Length: 127  Bit Score: 68.63  E-value: 6.11e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212     7 ISDLARELDITTRAIRFYEEQGLLSPERR--GQERIYSPRDKVSLKLILRGKRIGFSLAECRELIELY-DPDPSSGNQKQ 83
Cdd:TIGR02044   3 IGQVAKLTGLSSKMIRYYEEKGLIPPPLRseGGYRTYTQQHLDELRLISRARQVGFSLEECKELLNLWnDPNRTSADVKA 82

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 15597212    84 LNtmLEKIAErraqLEQQLLDIEQMQLELDTAEERC 119
Cdd:TIGR02044  83 RT--LEKVAE----IERKISELQSMRDQLEALAQAC 112
MerR_1 pfam13411
MerR HTH family regulatory protein;
5-69 2.16e-13

MerR HTH family regulatory protein;


Pssm-ID: 463870  Cd Length: 66  Bit Score: 60.65  E-value: 2.16e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15597212     5 YTISDLARELDITTRAIRFYEEQGLLSPERRGQE-RIYSPRDKVSLKLILRGKRIGFSLAECRELI 69
Cdd:pfam13411   1 YTISELARLLGVTPRTLRYWEREGLLPPPRTERGrRYYTDEDVERLRLIKALLERGLSLKEIKELL 66
 
Name Accession Description Interval E-value
HTH_GnyR cd04776
Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Putative helix-turn-helix ...
 5-123 1.44e-57

Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.


Pssm-ID: 133403  Cd Length: 118  Bit Score: 174.26  E-value: 1.44e-57
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212   5 YTISDLARELDITTRAIRFYEEQGLLSPERRGQERIYSPRDKVSLKLILRGKRIGFSLAECRELIELYDPDPssGNQKQL 84
Cdd:cd04776   1 YTISELAREFDVTPRTLRFYEDKGLLSPERRGQTRVYSRRDRARLKLILRGKRLGFSLEEIRELLDLYDPPG--GNRKQL 78

                        90       100       110
                ....*....|....*....|....*....|....*....
gi 15597212  85 NTMLEKIAERRAQLEQQLLDIEQMQLELDTAEERCRAAL 123
Cdd:cd04776  79 EKMLEKIEKRRAELEQQRRDIDAALAELDAAEERCRERL 117
HTH_MerR-like cd00592
Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators; Helix-turn-helix ...
 5-109 3.06e-23

Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators; Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.


Pssm-ID: 133378 [Multi-domain]  Cd Length: 100  Bit Score: 86.53  E-value: 3.06e-23
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212   5 YTISDLARELDITTRAIRFYEEQGLLSPERR-GQERIYSPRDKVSLKLILRGKRIGFSLAECRELIELYDPDPSSGNQKQ 83
Cdd:cd00592   1 YTIGEVAKLLGVSVRTLRYYEEKGLLPPERSeNGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLDARDEELSLAALLA 80

                        90       100
                ....*....|....*....|....*.
gi 15597212  84 LntmlekIAERRAQLEQQLLDIEQMQ 109
Cdd:cd00592  81 L------LDEKLAELEEKIARLEALL 100
SoxR COG0789
DNA-binding transcriptional regulator, MerR family [Transcription];
7-112 9.00e-22

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


Pssm-ID: 440552 [Multi-domain]  Cd Length: 100  Bit Score: 83.03  E-value: 9.00e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212   7 ISDLARELDITTRAIRFYEEQGLLSPERR--GQERIYSPRDKVSLKLILRGKRIGFSLAECRELIELYDPDPSsgnqkql 84
Cdd:COG0789   1 IGEVARLTGVSVRTLRYYERIGLLPPPERteGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLDDGEE------- 73

                        90       100
                ....*....|....*....|....*...
gi 15597212  85 nTMLEKIAERRAQLEQQLLDIEQMQLEL 112
Cdd:COG0789  74 -EVRELLEEHLAELEAQIAELQALRAEL 100
HTH_CueR cd01108
Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Helix-turn-helix ...
 5-119 2.86e-20

Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.


Pssm-ID: 133383 [Multi-domain]  Cd Length: 127  Bit Score: 79.91  E-value: 2.86e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212   5 YTISDLARELDITTRAIRFYEEQGLLSPERRGQE--RIYSPRDKVSLKLILRGKRIGFSLAECRELIELY-DPDPSSGNQ 81
Cdd:cd01108   1 MNIGEAAKLTGLSAKMIRYYEEIGLIPPPSRSDNgyRVYNQRDIEELRFIRRARDLGFSLEEIRELLALWrDPSRASADV 80

                        90       100       110
                ....*....|....*....|....*....|....*...
gi 15597212  82 KQLntMLEKIAErraqLEQQLLDIEQMQLELDTAEERC 119
Cdd:cd01108  81 KAL--ALEHIAE----LERKIAELQAMRRTLQQLADSC 112
HTH_HMRTR cd04770
Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators; ...
 5-121 4.73e-19

Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators; Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.


Pssm-ID: 133398 [Multi-domain]  Cd Length: 123  Bit Score: 76.83  E-value: 4.73e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212   5 YTISDLARELDITTRAIRFYEEQGLLSPERRGQE--RIYSPRDKVSLKLILRGKRIGFSLAECRELIELYD-PDPSSGNQ 81
Cdd:cd04770   1 MKIGELAKAAGVSPDTIRYYERIGLLPPPQRSENgyRLYGEADLARLRFIRRAQALGFSLAEIRELLSLRDdGAAPCAEV 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|
gi 15597212  82 KQLntmlekIAERRAQLEQQLLDIEQMQLELDTAEERCRA 121
Cdd:cd04770  81 RAL------LEEKLAEVEAKIAELQALRAELAGLLSACDG 114
PRK10227 PRK10227
HTH-type transcriptional regulator CueR;
7-119 6.29e-19

HTH-type transcriptional regulator CueR;


Pssm-ID: 182320  Cd Length: 135  Bit Score: 76.61  E-value: 6.29e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212    7 ISDLARELDITTRAIRFYEEQGLLSPERRGQE--RIYSPRDKVSLKLILRGKRIGFSLAECRELIELY-DPDPSSGNQKQ 83
Cdd:PRK10227   3 ISDVAKITGLTSKAIRFYEEKGLVTPPMRSENgyRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFnDPQRHSADVKR 82

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 15597212   84 lnTMLEKIAErraqLEQQLLDIEQMQLELDTAEERC 119
Cdd:PRK10227  83 --RTLEKVAE----IERHIEELQSMRDQLLALANAC 112
HTH_MERR smart00422
helix_turn_helix, mercury resistance;
5-72 5.87e-17

helix_turn_helix, mercury resistance;


Pssm-ID: 197716  Cd Length: 70  Bit Score: 69.86  E-value: 5.87e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212      5 YTISDLARELDITTRAIRFYEEQGLLSPERR--GQERIYSPRDKVSLKLILRGKRIGFSLAECRELIELY 72
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRteGGYRLYSDEDLERLRFIKRLKELGFSLEEIKELLELL 70
CueR TIGR02044
Cu(I)-responsive transcriptional regulator; This model represents the copper-, silver- and ...
 7-119 6.11e-16

Cu(I)-responsive transcriptional regulator; This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue. [Regulatory functions, DNA interactions]


Pssm-ID: 131099 [Multi-domain]  Cd Length: 127  Bit Score: 68.63  E-value: 6.11e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212     7 ISDLARELDITTRAIRFYEEQGLLSPERR--GQERIYSPRDKVSLKLILRGKRIGFSLAECRELIELY-DPDPSSGNQKQ 83
Cdd:TIGR02044   3 IGQVAKLTGLSSKMIRYYEEKGLIPPPLRseGGYRTYTQQHLDELRLISRARQVGFSLEECKELLNLWnDPNRTSADVKA 82

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 15597212    84 LNtmLEKIAErraqLEQQLLDIEQMQLELDTAEERC 119
Cdd:TIGR02044  83 RT--LEKVAE----IERKISELQSMRDQLEALAQAC 112
zntR PRK09514
Zn(2+)-responsive transcriptional regulator;
5-112 6.46e-16

Zn(2+)-responsive transcriptional regulator;


Pssm-ID: 181924 [Multi-domain]  Cd Length: 140  Bit Score: 69.23  E-value: 6.46e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212    5 YTISDLARELDITTRAIRFYEEQGLLSPERRGQE--RIYSPRDKVSLKLILRGKRIGFSLAECRELIELyDPDPSSGNQK 82
Cdd:PRK09514   2 YRIGELAKLAEVTPDTLRFYEKQGLMDPEVRTEGgyRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLSI-RLDPEHHTCQ 80

                         90       100       110
                 ....*....|....*....|....*....|
gi 15597212   83 QLNTMLEKiaeRRAQLEQQLLDIEQMQLEL 112
Cdd:PRK09514  81 EVKGIVDE---KLAEVEAKIAELQHMRRSL 107
HTH_TipAL-Mta cd01106
Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA; ...
 5-109 7.57e-16

Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA; Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Unique to this family, is a TipAL-like, lineage specific Bacilli subgroup, which has five conserved cysteines in the C-terminus of the protein.


Pssm-ID: 133381 [Multi-domain]  Cd Length: 103  Bit Score: 67.90  E-value: 7.57e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212   5 YTISDLARELDITTRAIRFYEEQGLLSPERRGQE--RIYSPRDKVSLKLILRGKRIGFSLAECRELIElydpDPSSGNQK 82
Cdd:cd01106   1 YTVGEVAKLTGVSVRTLHYYDEIGLLKPSRRTENgyRLYTEEDLERLQQILFLKELGFSLKEIKELLK----DPSEDLLE 76

                        90       100
                ....*....|....*....|....*..
gi 15597212  83 QLNTMLEKIAERRAQLEQQLLDIEQMQ 109
Cdd:cd01106  77 ALREQKELLEEKKERLDKLIKTIDRTL 103
HTH_CadR-PbrR-like cd04785
Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators; ...
 5-120 2.56e-14

Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators; Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.


Pssm-ID: 133412 [Multi-domain]  Cd Length: 126  Bit Score: 64.49  E-value: 2.56e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212   5 YTISDLARELDITTRAIRFYEEQGLLSPERR--GQERIYSPRDKVSLKLILRGKRIGFSLAECRELIELYD-PDPSSGNQ 81
Cdd:cd04785   1 LSIGELARRTGVNVETIRYYESIGLLPEPARtaGGYRLYGAAHVERLRFIRRARDLGFSLEEIRALLALSDrPDRSCAEA 80

                        90       100       110
                ....*....|....*....|....*....|....*....
gi 15597212  82 KQLntmlekIAERRAQLEQQLLDIEQMQLELDTAEERCR 120
Cdd:cd04785  81 DAI------ARAHLADVRARIADLRRLEAELKRMVAACS 113
HTH_BmrR cd01107
Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator; Helix-turn-helix (HTH) ...
 5-114 1.17e-13

Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator; Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.


Pssm-ID: 133382 [Multi-domain]  Cd Length: 108  Bit Score: 62.54  E-value: 1.17e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212   5 YTISDLARELDITTRAIRFYEEQGLLSPERRGQE---RIYSPRDKVSLKLILRGKRIGFSLAECRELIELYDPDpssgnq 81
Cdd:cd01107   1 FTIGEFAKLSNLSIKALRYYDKIGLLKPAYVDPDtgyRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDADNDD------ 74

                        90       100       110
                ....*....|....*....|....*....|...
gi 15597212  82 kqlnTMLEKIAERRAQLEQQLLDIEQMQLELDT 114
Cdd:cd01107  75 ----ELRKLLREKLAELEAEIEELQRILRLLED 103
MerR_1 pfam13411
MerR HTH family regulatory protein;
5-69 2.16e-13

MerR HTH family regulatory protein;


Pssm-ID: 463870  Cd Length: 66  Bit Score: 60.65  E-value: 2.16e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15597212     5 YTISDLARELDITTRAIRFYEEQGLLSPERRGQE-RIYSPRDKVSLKLILRGKRIGFSLAECRELI 69
Cdd:pfam13411   1 YTISELARLLGVTPRTLRYWEREGLLPPPRTERGrRYYTDEDVERLRLIKALLERGLSLKEIKELL 66
HTH_MerR-like_sg6 cd04781
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 6-122 9.49e-13

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.


Pssm-ID: 133408  Cd Length: 120  Bit Score: 60.37  E-value: 9.49e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212   6 TISDLARELDITTRAIRFYEEQGLL-SPERRGQERIYSPRDKVSLKLILRGKRIGFSLAECRELIElyDPDPSSGNQKQL 84
Cdd:cd04781   2 DIAEVARQSGLPASTLRYYEEKGLIaSIGRRGLRRQYDPQVLDRLALIALGRAAGFSLDEIQAMLS--HDGKPPIDRQLL 79

                        90       100       110
                ....*....|....*....|....*....|....*...
gi 15597212  85 ntmlekiAERRAQLEQQLLDIEQMQLELDTAeERCRAA 122
Cdd:cd04781  80 -------KAKAAELDQQIQRLQAMRELLRHV-AQCPAP 109
HTH_MerR-SF cd04761
Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; ...
 5-52 1.15e-12

Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.


Pssm-ID: 133389 [Multi-domain]  Cd Length: 49  Bit Score: 58.37  E-value: 1.15e-12
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 15597212   5 YTISDLARELDITTRAIRFYEEQGLLSPERR-GQERIYSPRDKVSLKLI 52
Cdd:cd04761   1 YTIGELAKLTGVSPSTLRYYERIGLLSPARTeGGYRLYSDADLERLRLI 49
HTH_YyaN cd01109
Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB; ...
 5-123 1.28e-12

Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB; Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.


Pssm-ID: 133384 [Multi-domain]  Cd Length: 113  Bit Score: 59.78  E-value: 1.28e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212   5 YTISDLARELDITTRAIRFYEEQGLLSPERRGQE--RIYSPRDKVSLKLILRGKRIGFSLAECRELIELYDPDPSSgnqk 82
Cdd:cd01109   1 YTIKEVAEKTGLSADTLRYYEKEGLLPPVKRDENgiRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAELRREGDST---- 76

                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
gi 15597212  83 qlntmlekIAERRAQLEQQLLDIEQMQLELdtaeERCRAAL 123
Cdd:cd01109  77 --------IPERLELLEEHREELEEQIAEL----QETLAYL 105
HTH_MerR1 cd04783
Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator; Helix-turn-helix ...
 5-119 7.53e-12

Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator; Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.


Pssm-ID: 133410 [Multi-domain]  Cd Length: 126  Bit Score: 58.01  E-value: 7.53e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212   5 YTISDLARELDITTRAIRFYEEQGLLS-PER-RGQERIYSPRDKVSLKLILRGKRIGFSLAECRELIELYDPDPSSgnqk 82
Cdd:cd04783   1 LTIGELAKAAGVNVETIRYYQRRGLLPePPRpEGGYRRYPEETVTRLRFIKRAQELGFTLDEIAELLELDDGTDCS---- 76

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 15597212  83 qlnTMLEKIAERRAQLEQQLLDIEQMQLELDTAEERC 119
Cdd:cd04783  77 ---EARELAEQKLAEVDEKIADLQRMRASLQELVSQC 110
HTH_MerR2 cd04769
Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators; Helix-turn-helix ...
 6-123 1.46e-11

Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators; Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.


Pssm-ID: 133397 [Multi-domain]  Cd Length: 116  Bit Score: 56.99  E-value: 1.46e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212   6 TISDLARELDITTRAIRFYEEQGLL-SPERRGQERIYSPRDKVSLKLILRGKRIGFSLAECRELIELYDPDPSSgnqkQL 84
Cdd:cd04769   2 YIGELAQQTGVTIKAIRLYEEKGLLpSPKRSGNYRVYDAQHVECLRFIKEARQLGFTLAELKAIFAGHEGRAVL----PW 77

                        90       100       110
                ....*....|....*....|....*....|....*....
gi 15597212  85 NTMLEKIAERRAQLEQQLLDIEQMQLELDTAEERCRAAL 123
Cdd:cd04769  78 PHLQQALEDKKQEIRAQITELQQLLARLDAFEASLKDAL 116
HTH_CadR-PbrR cd04784
Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; ...
 7-122 5.71e-11

Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.


Pssm-ID: 133411  Cd Length: 127  Bit Score: 56.04  E-value: 5.71e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212   7 ISDLARELDITTRAIRFYEEQGLLSPERRGQE--RIYSPRDKVSLKLILRGKRIGFSLAECRELIELYDpDPssgnQKQL 84
Cdd:cd04784   3 IGELAKKTGCSVETIRYYEKEGLLPAPARSANnyRLYDEEHLERLLFIRRCRSLDMSLDEIRTLLQLQD-DP----EASC 77

                        90       100       110
                ....*....|....*....|....*....|....*...
gi 15597212  85 NTMLEKIAERRAQLEQQLLDIEQMQLELDTAEERCRAA 122
Cdd:cd04784  78 AEVNALIDEHLAHVRARIAELQALEKQLQALRERCDGA 115
HTH_HMRTR_unk cd04787
Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription ...
 6-132 5.81e-11

Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators; Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the conserved, metal-binding cysteines seen in the MerR1 group.


Pssm-ID: 133414 [Multi-domain]  Cd Length: 133  Bit Score: 56.16  E-value: 5.81e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212   6 TISDLARELDITTRAIRFYEEQGLLSPER--RGQERIYSPRDKVSLKLILRGKRIGFSLAECRELIELYDPDPSSGNQ-K 82
Cdd:cd04787   2 KVKELANAAGVTPDTVRFYTRIGLLRPTRdpVNGYRLYSEKDLSRLRFILSARQLGFSLKDIKEILSHADQGESPCPMvR 81

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|
gi 15597212  83 QLntmlekIAERRAQLEQQLLDIEQMQLELDTAEERCRAALIKSYNKHTV 132
Cdd:cd04787  82 RL------IEQRLAETERRIKELLKLRDRMQQAVSQWQQMPDGAPDGHSI 125
HTH_NolA-AlbR cd04788
Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR; ...
 7-100 7.58e-11

Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR; Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.


Pssm-ID: 133415 [Multi-domain]  Cd Length: 96  Bit Score: 54.69  E-value: 7.58e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212   7 ISDLARELDITTRAIRFYEEQGLLSPERR--GQERIYSPRDKVSLKLILRGKRIGFSLAECRELIELYDPDPSSGNQKQl 84
Cdd:cd04788   3 IGELARRTGLSVRTLHHYDHIGLLSPSQRteGGHRLYDRADIRRLHQIIALRRLGFSLREIGRALDGPDFDPLELLRRQ- 81

                        90
                ....*....|....*.
gi 15597212  85 ntmLEKIAERRAQLEQ 100
Cdd:cd04788  82 ---LARLEEQLELATR 94
HTH_MerR-like_sg3 cd01282
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 7-113 9.08e-11

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.


Pssm-ID: 133388  Cd Length: 112  Bit Score: 54.92  E-value: 9.08e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212   7 ISDLARELDITTRAIRFYEEQGLLSPERRGQ-ERIYSPRDKVSLKLILRGKRIGFSLAECRELIE-LYDPDPSSGNQKQl 84
Cdd:cd01282   3 IGELAARTGVSVRSLRYYEEQGLLVPERSANgYRDYDEAAVDRVRQIRRLLAAGLTLEEIREFLPcLRGGEPTFRPCPD- 81

                        90       100
                ....*....|....*....|....*....
gi 15597212  85 ntMLEKIAERRAQLEQQLLDIEQMQLELD 113
Cdd:cd01282  82 --LLAVLRRELARIDRQIADLTRSRDRLD 108
HTH_YfmP cd04774
Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator; Helix-turn-helix (HTH) ...
 5-102 9.12e-11

Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator; Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.


Pssm-ID: 133401 [Multi-domain]  Cd Length: 96  Bit Score: 54.83  E-value: 9.12e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212   5 YTISDLARELDITTRAIRFYEEQGLLSPER-RGQERIYSPRDKVSLKLILRGKR-IGFSLAECRELIELyDPDPSSGNQK 82
Cdd:cd04774   1 YKVDEVAKRLGLTKRTLKYYEEIGLVSPERsEGRYRLYSEEDLKRLERILRLREvLGFSLQEVTHFLER-PLEPVDGGHR 79

                        90       100
                ....*....|....*....|
gi 15597212  83 QLNTMLEKIAErraQLEQQL 102
Cdd:cd04774  80 YSAESLREIHD---ALAQQV 96
MerR-DNA-bind pfam09278
MerR, DNA binding; Members of this family of DNA-binding domains are predominantly found in ...
 49-114 5.66e-10

MerR, DNA binding; Members of this family of DNA-binding domains are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold.


Pssm-ID: 462739  Cd Length: 65  Bit Score: 51.73  E-value: 5.66e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15597212    49 LKLILRGKRIGFSLAECRELIELYDpdpssGNQKQLNTMLEKIAERRAQLEQQLLDIEQMQLELDT 114
Cdd:pfam09278   4 LAFIRRARRLGFSLEEIRELLALYD-----DPGPPCADVRALLREKLAELEARIAELQALRDELDA 64
HTH_MerR-like_sg2 cd04778
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 4-73 9.46e-10

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 2). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.


Pssm-ID: 133405 [Multi-domain]  Cd Length: 219  Bit Score: 54.32  E-value: 9.46e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15597212   4 TYTISDLARELDITTRAIRFYEEQGLLSP-ERRGQERIYSPRDKVSLKLILRGKRIGFSLAECRELIELYD 73
Cdd:cd04778   1 EYRIDDLARAAGTTVRNVRAYQDRGLLPPpRRRGRVAIYNDSHLARLRLINQLLERGYTLAHIAELLAAWE 71
HTH_BmrR-like cd04768
Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators; Helix-turn-helix ...
 5-109 9.69e-10

Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators; Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.


Pssm-ID: 133396 [Multi-domain]  Cd Length: 96  Bit Score: 51.97  E-value: 9.69e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212   5 YTISDLARELDITTRAIRFYEEQGLLSPERRGQE--RIYSPRDKVSLKLILRGKRIGFSLAECRELIelydpdpsSGNQK 82
Cdd:cd04768   1 LTIGEFAKLAGVSIRTLRHYDDIGLFKPAKIAENgyRYYSYAQLYQLQFILFLRELGFSLAEIKELL--------DTEME 72

                        90       100
                ....*....|....*....|....*..
gi 15597212  83 QLNTMLEkiaERRAQLEQQLLDIEQMQ 109
Cdd:cd04768  73 ELTAMLL---EKKQAIQQKIDRLQQLE 96
HTH_MerR-like_sg7 cd04786
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 7-116 6.86e-09

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.


Pssm-ID: 133413 [Multi-domain]  Cd Length: 131  Bit Score: 50.59  E-value: 6.86e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212   7 ISDLARELDITTRAIRFYEEQGLLSPERRGQE--RIYSPRDKVSLKLILRGKRIGFSLAECRELIElydPDPSSGNQKQL 84
Cdd:cd04786   3 IGELAKRSGMAASRIRFYEAEGLLSSVERSANgyRDYPPETVWVLEIISSAQQAGFSLDEIRQLLP---ADASNWQHDEL 79

                        90       100       110       120
                ....*....|....*....|....*....|....*....|...
gi 15597212  85 NTMLE-KIAE------RRAQLEQQLL----DIEQMQLELDTAE 116
Cdd:cd04786  80 LAALErKVADiealeaRLAQNKAQLLvlidLIESKPDEMDCAD 122
HTH_TioE_rpt2 cd04773
Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE; Putative ...
 5-104 1.40e-08

Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE; Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.


Pssm-ID: 133400  Cd Length: 108  Bit Score: 49.28  E-value: 1.40e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212   5 YTISDLARELDITTRAIRFYEEQGLLSPERRGQE--RIYSPRDKVSLKLILRGKRIGFSLAECRELIELYDPDPSSGnqk 82
Cdd:cd04773   1 MTIGELAHLLGVPPSTLRHWEKEGLLSPDREPETgyRVYDPSDVRDARLIHLLRRGGYLLEQIATVVEQLRHAGGTE--- 77

                        90       100
                ....*....|....*....|..
gi 15597212  83 QLNTMLEKIAERRAQLEQQLLD 104
Cdd:cd04773  78 ALAAALEQRRVALTQRGRAMLD 99
HTH_Cfa-like_unk cd04790
Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators; Putative ...
 4-97 2.64e-08

Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators; Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.


Pssm-ID: 133417 [Multi-domain]  Cd Length: 172  Bit Score: 49.74  E-value: 2.64e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212   4 TYTISDLARELDITTRAIRFYEEQGLLSPERR--GQERIYSPRDKVSLKLILRGKRIGFSLAECRELIELYDPDPSSGNQ 81
Cdd:cd04790   1 MLTISQLARQFGLSRSTLLYYERIGLLSPSARseSNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQQPGDDATDVLR 80

                        90
                ....*....|....*.
gi 15597212  82 KQLNTMLEKIAERRAQ 97
Cdd:cd04790  81 RRLAELNREIQRLRQQ 96
MerR pfam00376
MerR family regulatory protein;
6-37 3.00e-08

MerR family regulatory protein;


Pssm-ID: 425647 [Multi-domain]  Cd Length: 38  Bit Score: 46.64  E-value: 3.00e-08
                          10        20        30
                  ....*....|....*....|....*....|..
gi 15597212     6 TISDLARELDITTRAIRFYEEQGLLSPERRGQ 37
Cdd:pfam00376   1 TIGEVAKLLGVSPRTLRYYEKIGLLPPPERTE 32
HTH_GlnR-like cd01105
Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators; Helix-turn-helix ...
 4-70 5.83e-08

Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators; Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.


Pssm-ID: 133380  Cd Length: 88  Bit Score: 47.22  E-value: 5.83e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15597212   4 TYTISDLARELDITTRAIRFYEEQGLLSPER--RGQERIYSPRDKVSLKLILRGKRIGFSLAECRELIE 70
Cdd:cd01105   1 VIGIGEVSKLTGVSPRQLRYWEEKGLIKSIRsdGGGQRKYSLADVDRLLVIKELLDEGFTLAAAVEKLR 69
HTH_BltR cd04782
Helix-Turn-Helix DNA binding domain of the BltR transcription regulator; Helix-turn-helix (HTH) ...
 5-109 3.24e-07

Helix-Turn-Helix DNA binding domain of the BltR transcription regulator; Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.


Pssm-ID: 133409 [Multi-domain]  Cd Length: 97  Bit Score: 45.30  E-value: 3.24e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212   5 YTISDLARELDITTRAIRFYEEQGLLSPERRGQE--RIYSPRDKVSLKLILRGKRIGFSLAECRELIELYDPDpssgnqk 82
Cdd:cd04782   1 FTTGEFAKLCGISKQTLFHYDKIGLFKPEIVKENgyRYYTLEQFEQLDIILLLKELGISLKEIKDYLDNRNPD------- 73

                        90       100
                ....*....|....*....|....*..
gi 15597212  83 qlnTMLEKIAERRAQLEQQLLDIEQMQ 109
Cdd:cd04782  74 ---ELIELLKKQEKEIKEEIEELQKIK 97
HTH_SoxR cd01110
Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator; Helix-turn-helix (HTH) ...
 6-113 5.13e-07

Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator; Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.


Pssm-ID: 133385 [Multi-domain]  Cd Length: 139  Bit Score: 45.65  E-value: 5.13e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212   6 TISDLARELDITTRAIRFYEEQGLLSPER-RGQERIYSPRDKVSLKLILRGKRIGFSLAECRELIELYDPD--PSSGNQK 82
Cdd:cd01110   3 SVGEVAKRSGVAVSALHFYEQKGLIASWRnAGNQRRYPRDVLRRIAFIKVAQRLGLSLAEIAEALATLPEDrtPTKADWE 82

                        90       100       110
                ....*....|....*....|....*....|.
gi 15597212  83 QLNTMLekiaerRAQLEQQLLDIEQMQLELD 113
Cdd:cd01110  83 RLSRAW------RDRLDERIAELQQLRDQLD 107
PRK13752 PRK13752
mercuric resistance operon transcriptional regulator MerR;
6-105 9.43e-07

mercuric resistance operon transcriptional regulator MerR;


Pssm-ID: 184302  Cd Length: 144  Bit Score: 45.28  E-value: 9.43e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212    6 TISDLARELDITTRAIRFYEEQGLLS-PER-RGQERIYSPRDKVSLKLILRGKRIGFSLAECRELIELYD----PDPSSG 79
Cdd:PRK13752   9 TIGVFAKAAGVNVETIRFYQRKGLLPePDKpYGSIRRYGEADVTRVRFVKSAQRLGFSLDEIAELLRLEDgthcEEASSL 88

                         90       100
                 ....*....|....*....|....*.
gi 15597212   80 NQKQLNTMLEKIAErRAQLEQQLLDI 105
Cdd:PRK13752  89 AEHKLKDVREKMAD-LARMEAVLSEL 113
HTH_MerR-like_sg1 cd04777
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 7-69 2.64e-06

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.


Pssm-ID: 133404 [Multi-domain]  Cd Length: 107  Bit Score: 43.17  E-value: 2.64e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15597212   7 ISDLARELDITTRAIRFYEEQGLLSPERRGQERIYSPRDKVSLKLILRGKRIGFSLAECRELI 69
Cdd:cd04777   3 IGKFAKKNNITIDTVRHYIDLGLLIPEKKGGQYFFDEKCQDDLEFILELKGLGFSLIEIQKIF 65
HTH_HspR-like_MBC cd04767
Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators; Putative ...
 5-72 6.14e-06

Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators; Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.


Pssm-ID: 133395  Cd Length: 120  Bit Score: 42.48  E-value: 6.14e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15597212   5 YTISDLARELDITTRAIRFYEEQGLLSPERRGQERIYSPRDKVSLKLIlrgKRI----GFSLAECRELIELY 72
Cdd:cd04767   2 YPIGVVAELLNIHPETLRIWERHGLIKPARRNGQRLYSNNDLKRLRFI---KKLinekGLNIAGVKQILSMY 70
HTH_TioE_rpt1 cd04772
First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE; Putative ...
 5-41 4.36e-05

First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE; Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.


Pssm-ID: 133399  Cd Length: 99  Bit Score: 39.68  E-value: 4.36e-05
                        10        20        30
                ....*....|....*....|....*....|....*....
gi 15597212   5 YTISDLARELDITTRAIRFYEEQGLLSPERRG--QERIY 41
Cdd:cd04772   1 YRTVDLARAIGLSPQTVRNYESLGLIPPAERTanGYRIY 39
HTH_MerD cd01111
Helix-Turn-Helix DNA binding domain of the MerD transcription regulator; Helix-turn-helix (HTH) ...
 5-102 4.41e-05

Helix-Turn-Helix DNA binding domain of the MerD transcription regulator; Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs, and organic substrates.


Pssm-ID: 133386  Cd Length: 107  Bit Score: 40.06  E-value: 4.41e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212   5 YTISDLARELDITTRAIRFYEEQGLLSPERR--GQERIYSPRDKVSLKLILRGKRIGFSLAECRELIELYDPDPSSGNQK 82
Cdd:cd01111   1 YSISQLALDAGVSVHIVRDYLLRGLLHPVARteGGYGLFDDCALQRLRFVRAAFEAGIGLDELARLCRALDAGDGKQPEA 80

                        90       100
                ....*....|....*....|...
gi 15597212  83 QLNTMLEKIAERRAQL---EQQL 102
Cdd:cd01111  81 CLAQLRQKIEVRRAALnalTTQL 103
HTH_HspR cd04766
Helix-Turn-Helix DNA binding domain of the HspR transcription regulator; Helix-turn-helix (HTH) ...
 5-100 3.35e-04

Helix-Turn-Helix DNA binding domain of the HspR transcription regulator; Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.


Pssm-ID: 133394 [Multi-domain]  Cd Length: 91  Bit Score: 37.24  E-value: 3.35e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212   5 YTISDLARELDITTRAIRFYEEQGLLSPER-RGQERIYSPRDKVSLKLILRGKR-IGFSLAECRELIELydpdpssgnQK 82
Cdd:cd04766   2 YVISVAAELSGMHPQTLRLYERLGLLSPSRtDGGTRRYSERDIERLRRIQRLTQeLGVNLAGVKRILEL---------EE 72

                        90
                ....*....|....*...
gi 15597212  83 QLNTMLEKIAERRAQLEQ 100
Cdd:cd04766  73 ELAELRAELDELRARLRR 90
HTH_Cfa-like cd04775
Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators; Putative ...
 5-101 4.23e-04

Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators; Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.


Pssm-ID: 133402 [Multi-domain]  Cd Length: 102  Bit Score: 37.13  E-value: 4.23e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212   5 YTISDLARELDITTRAIRFYEEQGLLSPERRGQE-RIYSPRDKVSLKLILRGKRIGFSLAECRELIElydpdpSSGNQKQ 83
Cdd:cd04775   2 YTIGQMSRKFGVSRSTLLYYESIGLIPSARSEANyRLYSEADLSRLEKIVFLQAGGLPLEEIAGCLA------QPHVQAI 75

                        90
                ....*....|....*...
gi 15597212  84 LNTMLEKIAERRAQLEQQ 101
Cdd:cd04775  76 LEERLQSLNREIQRLRQQ 93
HTH_MlrA-CarA cd01104
Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; ...
 5-68 5.08e-04

Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.


Pssm-ID: 133379  Cd Length: 68  Bit Score: 36.06  E-value: 5.08e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15597212   5 YTISDLARELDITTRAIRFYEEQ-GLLSPER-RGQERIYSPRDKVSLKLILRGKRIGFSLAECREL 68
Cdd:cd01104   1 YTIGAVARLTGVSPDTLRAWERRyGLPAPQRtDGGHRLYSEADVARLRLIRRLTSEGVRISQAAAL 66
HTH_MerR-like_sg4 cd04779
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 5-116 5.33e-04

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.


Pssm-ID: 133406 [Multi-domain]  Cd Length: 134  Bit Score: 37.49  E-value: 5.33e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212   5 YTISDLARELDITTRAIRFYEEQGLLSPERRGQERIYSPRDKV-SLKLILRGKRIGFSLAECRELIElyDPDPSSGNQKQ 83
Cdd:cd04779   1 YRIGQLAHLAGVSKRTIDYYTNLGLLTPERSDSNYRYYDETALdRLQLIEHLKGQRLSLAEIKDQLE--EVQRSDKEQRE 78

                        90       100       110
                ....*....|....*....|....*....|...
gi 15597212  84 LNTMLEKIAERRAQLEQQLLDIEQMQLELDTAE 116
Cdd:cd04779  79 VAQEVQLVCDQIDGLEHRLKQLKPIASQTDRAQ 111
HTH_MlrA-like_sg1 cd04764
Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Putative ...
 5-70 8.22e-04

Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.


Pssm-ID: 133392  Cd Length: 67  Bit Score: 35.77  E-value: 8.22e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15597212   5 YTISDLARELDITTRAIRFYEEQ-GLLSPERRGQERIYSPRDKVSLKLILRGKRIGFSLAECRELIE 70
Cdd:cd04764   1 YTIKEVSEIIGVKPHTLRYYEKEfNLYIPRTENGRRYYTDEDIELLKKIKTLLEKGLSIKEIKEILN 67
HTH_MlrA-like_sg2 cd04765
Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Putative ...
 5-102 1.29e-03

Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.


Pssm-ID: 133393  Cd Length: 99  Bit Score: 35.69  E-value: 1.29e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212   5 YTISDLARELDITTRAIRFYEEQ--GLLSPERRGQERIYSPRDkvsLKLILRGKRI----GFSLAECRELIElyDPDPSS 78
Cdd:cd04765   1 FSIGEVAEILGLPPHVLRYWETEfpQLKPVKRAGGRRYYRPKD---VELLLLIKHLlyekGYTIEGAKQALK--EDGAAA 75

                        90       100
                ....*....|....*....|....
gi 15597212  79 GNQKQLNTMLEKIAERRAQLEQQL 102
Cdd:cd04765  76 IREEEAEERLPSIRAELLDLRDQL 99
HTH_HspR-like cd01279
Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators; Helix-turn-helix ...
 4-72 1.83e-03

Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators; Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.


Pssm-ID: 133387  Cd Length: 98  Bit Score: 35.27  E-value: 1.83e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15597212   4 TYTISDLARELDITTRAIRFYEEQGLLSPERR-GQERIYSPRDKVSLKLILR-GKRIGFSLAECRELIELY 72
Cdd:cd01279   1 LYPISVAAELLGIHPQTLRVYDRLGLVSPARTnGGGRRYSNNDLELLRQVQRlSQDEGFNLAGIKRIIELY 71
HTH_Cfa cd04789
Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator; Putative ...
 5-100 2.43e-03

Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator; Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.


Pssm-ID: 133416  Cd Length: 102  Bit Score: 35.16  E-value: 2.43e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597212   5 YTISDLARELDITTRAIRFYEEQGLLSPERRGQE-RIYSPRDKVSLKLILRGKRIGFSLAECRELIElydpdpSSGNQKQ 83
Cdd:cd04789   2 YTISELAEKAGISRSTLLYYEKLGLITGTRNANGyRLYPDSDLQRLLLIQQLQAGGLSLKECLACLQ------GKLTRSL 75

                        90
                ....*....|....*..
gi 15597212  84 LNTMLEKIAERRAQLEQ 100
Cdd:cd04789  76 LLERLSSLAEQIARKQQ 92
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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