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Conserved domains on  [gi|2416603799|ref|WP_269374897|]
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Cu(I)-responsive transcriptional regulator [Vibrio sinaloensis]

Protein Classification

MerR family transcriptional regulator( domain architecture ID 323)

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:0006355|GO:0003677|GO:0003700
PubMed:  17302809|12829265|15808743|35130613
SCOP:  3000158

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_MerR-SF super family cl02600
Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; ...
 1-126 5.36e-64

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.


The actual alignment was detected with superfamily member cd01108:

Pssm-ID: 470628 [Multi-domain]  Cd Length: 127  Bit Score: 190.85  E-value: 5.36e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416603799   1 MNIGAVSKLTGLSTKSIRLYEDKELITAPHRSESGYREYSDQHVQELNLISRAKNAGFSLIECKELVQLAHNSNRKSSEV 80
Cdd:cd01108     1 MNIGEAAKLTGLSAKMIRYYEEIGLIPPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLALWRDPSRASADV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2416603799  81 KAKAKEKLHEVEIKIRELQEIERQLKKWVSACPGDSGSNCPIIEDL 126
Cdd:cd01108    81 KALALEHIAELERKIAELQAMRRTLQQLADSCHGDDRPDCPILEGL 126
 
Name Accession Description Interval E-value
HTH_CueR cd01108
Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Helix-turn-helix ...
 1-126 5.36e-64

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: 190.85  E-value: 5.36e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416603799   1 MNIGAVSKLTGLSTKSIRLYEDKELITAPHRSESGYREYSDQHVQELNLISRAKNAGFSLIECKELVQLAHNSNRKSSEV 80
Cdd:cd01108     1 MNIGEAAKLTGLSAKMIRYYEEIGLIPPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLALWRDPSRASADV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2416603799  81 KAKAKEKLHEVEIKIRELQEIERQLKKWVSACPGDSGSNCPIIEDL 126
Cdd:cd01108    81 KALALEHIAELERKIAELQAMRRTLQQLADSCHGDDRPDCPILEGL 126
CueR TIGR02044
Cu(I)-responsive transcriptional regulator; This model represents the copper-, silver- and ...
 1-127 4.21e-63

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: 188.42  E-value: 4.21e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416603799   1 MNIGAVSKLTGLSTKSIRLYEDKELITAPHRSESGYREYSDQHVQELNLISRAKNAGFSLIECKELVQLAHNSNRKSSEV 80
Cdd:TIGR02044   1 MNIGQVAKLTGLSSKMIRYYEEKGLIPPPLRSEGGYRTYTQQHLDELRLISRARQVGFSLEECKELLNLWNDPNRTSADV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2416603799  81 KAKAKEKLHEVEIKIRELQEIERQLKKWVSACPGDSGSNCPIIEDLT 127
Cdd:TIGR02044  81 KARTLEKVAEIERKISELQSMRDQLEALAQACPGDDSPDCPIIENLS 127
PRK10227 PRK10227
HTH-type transcriptional regulator CueR;
1-127 1.65e-43

HTH-type transcriptional regulator CueR;


Pssm-ID: 182320  Cd Length: 135  Bit Score: 139.40  E-value: 1.65e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416603799   1 MNIGAVSKLTGLSTKSIRLYEDKELITAPHRSESGYREYSDQHVQELNLISRAKNAGFSLIECKELVQLAHNSNRKSSEV 80
Cdd:PRK10227    1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFNDPQRHSADV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2416603799  81 KAKAKEKLHEVEIKIRELQEIERQLKKWVSACPGDSGSNCPIIEDLT 127
Cdd:PRK10227   81 KRRTLEKVAEIERHIEELQSMRDQLLALANACPGDDSADCPIIENLS 127
SoxR COG0789
DNA-binding transcriptional regulator, MerR family [Transcription];
3-105 6.88e-29

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


Pssm-ID: 440552 [Multi-domain]  Cd Length: 100  Bit Score: 100.75  E-value: 6.88e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416603799   3 IGAVSKLTGLSTKSIRLYEDKELITAPHRSESGYREYSDQHVQELNLISRAKNAGFSLIECKELVQLAHNSNRkssEVKA 82
Cdd:COG0789     1 IGEVARLTGVSVRTLRYYERIGLLPPPERTEGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLDDGEE---EVRE 77

                          90       100
                  ....*....|....*....|...
gi 2416603799  83 KAKEKLHEVEIKIRELQEIERQL 105
Cdd:COG0789    78 LLEEHLAELEAQIAELQALRAEL 100
HTH_MERR smart00422
helix_turn_helix, mercury resistance;
1-69 1.83e-23

helix_turn_helix, mercury resistance;


Pssm-ID: 197716  Cd Length: 70  Bit Score: 86.03  E-value: 1.83e-23
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2416603799    1 MNIGAVSKLTGLSTKSIRLYEDKELITAPHRSESGYREYSDQHVQELNLISRAKNAGFSLIECKELVQL 69
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRTEGGYRLYSDEDLERLRFIKRLKELGFSLEEIKELLEL 69
MerR_1 pfam13411
MerR HTH family regulatory protein;
1-66 1.83e-16

MerR HTH family regulatory protein;


Pssm-ID: 463870  Cd Length: 66  Bit Score: 68.35  E-value: 1.83e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2416603799   1 MNIGAVSKLTGLSTKSIRLYEDKELItAPHRSESGYREYSDQHVQELNLISRAKNAGFSLIECKEL 66
Cdd:pfam13411   1 YTISELARLLGVTPRTLRYWEREGLL-PPPRTERGRRYYTDEDVERLRLIKALLERGLSLKEIKEL 65
 
Name Accession Description Interval E-value
HTH_CueR cd01108
Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Helix-turn-helix ...
 1-126 5.36e-64

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: 190.85  E-value: 5.36e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416603799   1 MNIGAVSKLTGLSTKSIRLYEDKELITAPHRSESGYREYSDQHVQELNLISRAKNAGFSLIECKELVQLAHNSNRKSSEV 80
Cdd:cd01108     1 MNIGEAAKLTGLSAKMIRYYEEIGLIPPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLALWRDPSRASADV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2416603799  81 KAKAKEKLHEVEIKIRELQEIERQLKKWVSACPGDSGSNCPIIEDL 126
Cdd:cd01108    81 KALALEHIAELERKIAELQAMRRTLQQLADSCHGDDRPDCPILEGL 126
CueR TIGR02044
Cu(I)-responsive transcriptional regulator; This model represents the copper-, silver- and ...
 1-127 4.21e-63

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: 188.42  E-value: 4.21e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416603799   1 MNIGAVSKLTGLSTKSIRLYEDKELITAPHRSESGYREYSDQHVQELNLISRAKNAGFSLIECKELVQLAHNSNRKSSEV 80
Cdd:TIGR02044   1 MNIGQVAKLTGLSSKMIRYYEEKGLIPPPLRSEGGYRTYTQQHLDELRLISRARQVGFSLEECKELLNLWNDPNRTSADV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2416603799  81 KAKAKEKLHEVEIKIRELQEIERQLKKWVSACPGDSGSNCPIIEDLT 127
Cdd:TIGR02044  81 KARTLEKVAEIERKISELQSMRDQLEALAQACPGDDSPDCPIIENLS 127
HTH_HMRTR cd04770
Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators; ...
 1-123 7.75e-47

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: 147.32  E-value: 7.75e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416603799   1 MNIGAVSKLTGLSTKSIRLYEDKELITAPHRSESGYREYSDQHVQELNLISRAKNAGFSLIECKELVQLAHNSNRKSSEV 80
Cdd:cd04770     1 MKIGELAKAAGVSPDTIRYYERIGLLPPPQRSENGYRLYGEADLARLRFIRRAQALGFSLAEIRELLSLRDDGAAPCAEV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2416603799  81 KAKAKEKLHEVEIKIRELQEIERQLKKWVSACPGDSGSNCPII 123
Cdd:cd04770    81 RALLEEKLAEVEAKIAELQALRAELAGLLSACDGDESVICPIL 123
PRK10227 PRK10227
HTH-type transcriptional regulator CueR;
1-127 1.65e-43

HTH-type transcriptional regulator CueR;


Pssm-ID: 182320  Cd Length: 135  Bit Score: 139.40  E-value: 1.65e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416603799   1 MNIGAVSKLTGLSTKSIRLYEDKELITAPHRSESGYREYSDQHVQELNLISRAKNAGFSLIECKELVQLAHNSNRKSSEV 80
Cdd:PRK10227    1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFNDPQRHSADV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2416603799  81 KAKAKEKLHEVEIKIRELQEIERQLKKWVSACPGDSGSNCPIIEDLT 127
Cdd:PRK10227   81 KRRTLEKVAEIERHIEELQSMRDQLLALANACPGDDSADCPIIENLS 127
HTH_CadR-PbrR-like cd04785
Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators; ...
 1-126 1.86e-34

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: 115.72  E-value: 1.86e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416603799   1 MNIGAVSKLTGLSTKSIRLYEDKELITAPHRSESGYREYSDQHVQELNLISRAKNAGFSLIECKELVQLAHNSNRKSSEV 80
Cdd:cd04785     1 LSIGELARRTGVNVETIRYYESIGLLPEPARTAGGYRLYGAAHVERLRFIRRARDLGFSLEEIRALLALSDRPDRSCAEA 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2416603799  81 KAKAKEKLHEVEIKIRELQEIERQLKKWVSACPGDSGSNCPIIEDL 126
Cdd:cd04785    81 DAIARAHLADVRARIADLRRLEAELKRMVAACSGGRVADCRIIEAL 126
HTH_CadR-PbrR cd04784
Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; ...
 1-126 9.52e-31

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: 106.50  E-value: 9.52e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416603799   1 MNIGAVSKLTGLSTKSIRLYEDKELITAPHRSESGYREYSDQHVQELNLISRAKNAGFSLIECKELVQLAHNSNRKSSEV 80
Cdd:cd04784     1 MKIGELAKKTGCSVETIRYYEKEGLLPAPARSANNYRLYDEEHLERLLFIRRCRSLDMSLDEIRTLLQLQDDPEASCAEV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2416603799  81 KAKAKEKLHEVEIKIRELQEIERQLKKWVSACPGDSG-SNCPIIEDL 126
Cdd:cd04784    81 NALIDEHLAHVRARIAELQALEKQLQALRERCDGARTiEECGILQGL 127
HTH_MerR1 cd04783
Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator; Helix-turn-helix ...
 1-126 1.83e-30

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: 105.77  E-value: 1.83e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416603799   1 MNIGAVSKLTGLSTKSIRLYEDKELITAPHRSESGYREYSDQHVQELNLISRAKNAGFSLIECKELVQLahNSNRKSSEV 80
Cdd:cd04783     1 LTIGELAKAAGVNVETIRYYQRRGLLPEPPRPEGGYRRYPEETVTRLRFIKRAQELGFTLDEIAELLEL--DDGTDCSEA 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2416603799  81 KAKAKEKLHEVEIKIRELQEIERQLKKWVSACPGDSGS-NCPIIEDL 126
Cdd:cd04783    79 RELAEQKLAEVDEKIADLQRMRASLQELVSQCAATKNNvSCPIIAAL 125
SoxR COG0789
DNA-binding transcriptional regulator, MerR family [Transcription];
3-105 6.88e-29

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


Pssm-ID: 440552 [Multi-domain]  Cd Length: 100  Bit Score: 100.75  E-value: 6.88e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416603799   3 IGAVSKLTGLSTKSIRLYEDKELITAPHRSESGYREYSDQHVQELNLISRAKNAGFSLIECKELVQLAHNSNRkssEVKA 82
Cdd:COG0789     1 IGEVARLTGVSVRTLRYYERIGLLPPPERTEGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLDDGEE---EVRE 77

                          90       100
                  ....*....|....*....|...
gi 2416603799  83 KAKEKLHEVEIKIRELQEIERQL 105
Cdd:COG0789    78 LLEEHLAELEAQIAELQALRAEL 100
zntR PRK09514
Zn(2+)-responsive transcriptional regulator;
3-126 2.98e-26

Zn(2+)-responsive transcriptional regulator;


Pssm-ID: 181924 [Multi-domain]  Cd Length: 140  Bit Score: 95.42  E-value: 2.98e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416603799   3 IGAVSKLTGLSTKSIRLYEDKELITAPHRSESGYREYSDQHVQELNLISRAKNAGFSLIECKELVQL-AHNSNRKSSEVK 81
Cdd:PRK09514    4 IGELAKLAEVTPDTLRFYEKQGLMDPEVRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLSIrLDPEHHTCQEVK 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2416603799  82 AKAKEKLHEVEIKIRELQEIERQLKKWVSACPG--DSGSNCPIIEDL 126
Cdd:PRK09514   84 GIVDEKLAEVEAKIAELQHMRRSLQRLNDACCGtaHSAVYCSILEAL 130
HTH_MerR-like cd00592
Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators; Helix-turn-helix ...
 1-102 7.57e-24

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: 88.07  E-value: 7.57e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416603799   1 MNIGAVSKLTGLSTKSIRLYEDKELITaPHRSESGYREYSDQHVQELNLISRAKNAGFSLIECKELVQLAhNSNRKSSEV 80
Cdd:cd00592     1 YTIGEVAKLLGVSVRTLRYYEEKGLLP-PERSENGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLDAR-DEELSLAAL 78

                          90       100
                  ....*....|....*....|..
gi 2416603799  81 KAKAKEKLHEVEIKIRELQEIE 102
Cdd:cd00592    79 LALLDEKLAELEEKIARLEALL 100
HTH_MERR smart00422
helix_turn_helix, mercury resistance;
1-69 1.83e-23

helix_turn_helix, mercury resistance;


Pssm-ID: 197716  Cd Length: 70  Bit Score: 86.03  E-value: 1.83e-23
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2416603799    1 MNIGAVSKLTGLSTKSIRLYEDKELITAPHRSESGYREYSDQHVQELNLISRAKNAGFSLIECKELVQL 69
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRTEGGYRLYSDEDLERLRFIKRLKELGFSLEEIKELLEL 69
HTH_MerR-like_sg6 cd04781
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 1-126 9.88e-22

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: 83.49  E-value: 9.88e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416603799   1 MNIGAVSKLTGLSTKSIRLYEDKELITAPHRsESGYREYSDQHVQELNLISRAKNAGFSLIECKELvqLAHNSNRKSSev 80
Cdd:cd04781     1 LDIAEVARQSGLPASTLRYYEEKGLIASIGR-RGLRRQYDPQVLDRLALIALGRAAGFSLDEIQAM--LSHDGKPPID-- 75

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2416603799  81 KAKAKEKLHEVEIKIRELQEIeRQLKKWVSACPGDSGSNCPIIEDL 126
Cdd:cd04781    76 RQLLKAKAAELDQQIQRLQAM-RELLRHVAQCPAPSHLDCPTFQRL 120
HTH_MerR2 cd04769
Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators; Helix-turn-helix ...
 1-111 1.54e-21

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: 82.80  E-value: 1.54e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416603799   1 MNIGAVSKLTGLSTKSIRLYEDKELITAPHRSESgYREYSDQHVQELNLISRAKNAGFSLIECKELVQlAHNSNRKSSEV 80
Cdd:cd04769     1 MYIGELAQQTGVTIKAIRLYEEKGLLPSPKRSGN-YRVYDAQHVECLRFIKEARQLGFTLAELKAIFA-GHEGRAVLPWP 78

                          90       100       110
                  ....*....|....*....|....*....|...
gi 2416603799  81 KAKA--KEKLHEVEIKIRELQEIERQLKKWVSA 111
Cdd:cd04769    79 HLQQalEDKKQEIRAQITELQQLLARLDAFEAS 111
HTH_MerR-like_sg3 cd01282
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 1-107 1.63e-21

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: 82.65  E-value: 1.63e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416603799   1 MNIGAVSKLTGLSTKSIRLYEDKELItAPHRSESGYREYSDQHVQELNLISRAKNAGFSLIECKEL---VQLAHNSNRKS 77
Cdd:cd01282     1 MRIGELAARTGVSVRSLRYYEEQGLL-VPERSANGYRDYDEAAVDRVRQIRRLLAAGLTLEEIREFlpcLRGGEPTFRPC 79

                          90       100       110
                  ....*....|....*....|....*....|
gi 2416603799  78 SEVKAKAKEKLHEVEIKIRELQEIERQLKK 107
Cdd:cd01282    80 PDLLAVLRRELARIDRQIADLTRSRDRLDA 109
HTH_YyaN cd01109
Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB; ...
 1-107 1.65e-20

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: 79.81  E-value: 1.65e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416603799   1 MNIGAVSKLTGLSTKSIRLYEDKELITAPHRSESGYREYSDQHVQELNLISRAKNAGFSLIECKELVQLAHNSNRKSSEV 80
Cdd:cd01109     1 YTIKEVAEKTGLSADTLRYYEKEGLLPPVKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAELRREGDSTIPER 80

                          90       100
                  ....*....|....*....|....*..
gi 2416603799  81 KAKAKEKLHEVEIKIRELQEIERQLKK 107
Cdd:cd01109    81 LELLEEHREELEEQIAELQETLAYLDY 107
HTH_BmrR cd01107
Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator; Helix-turn-helix (HTH) ...
 3-108 1.26e-17

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: 72.55  E-value: 1.26e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416603799   3 IGAVSKLTGLSTKSIRLYEDKELITaPHR--SESGYREYSDQHVQELNLISRAKNAGFSLIECKELVqlahnSNRKSSEV 80
Cdd:cd01107     3 IGEFAKLSNLSIKALRYYDKIGLLK-PAYvdPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEIL-----DADNDDEL 76

                          90       100
                  ....*....|....*....|....*...
gi 2416603799  81 KAKAKEKLHEVEIKIRELQEIERQLKKW 108
Cdd:cd01107    77 RKLLREKLAELEAEIEELQRILRLLEDR 104
HTH_MerR-like_sg7 cd04786
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 1-105 1.40e-16

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: 70.62  E-value: 1.40e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416603799   1 MNIGAVSKLTGLSTKSIRLYEDKELITAPHRSESGYREYSDQHVQELNLISRAKNAGFSLIECKELVQlAHNSNRKSSEV 80
Cdd:cd04786     1 MKIGELAKRSGMAASRIRFYEAEGLLSSVERSANGYRDYPPETVWVLEIISSAQQAGFSLDEIRQLLP-ADASNWQHDEL 79

                          90       100
                  ....*....|....*....|....*
gi 2416603799  81 KAKAKEKLHEVEIKIRELQEIERQL 105
Cdd:cd04786    80 LAALERKVADIEALEARLAQNKAQL 104
MerR_1 pfam13411
MerR HTH family regulatory protein;
1-66 1.83e-16

MerR HTH family regulatory protein;


Pssm-ID: 463870  Cd Length: 66  Bit Score: 68.35  E-value: 1.83e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2416603799   1 MNIGAVSKLTGLSTKSIRLYEDKELItAPHRSESGYREYSDQHVQELNLISRAKNAGFSLIECKEL 66
Cdd:pfam13411   1 YTISELARLLGVTPRTLRYWEREGLL-PPPRTERGRRYYTDEDVERLRLIKALLERGLSLKEIKEL 65
HTH_BmrR-like cd04768
Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators; Helix-turn-helix ...
 3-102 4.97e-15

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: 65.45  E-value: 4.97e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416603799   3 IGAVSKLTGLSTKSIRLYEDKELITAPHRSESGYREYSDQHVQELNLISRAKNAGFSLIECKELVQLahnsnrKSSEVKA 82
Cdd:cd04768     3 IGEFAKLAGVSIRTLRHYDDIGLFKPAKIAENGYRYYSYAQLYQLQFILFLRELGFSLAEIKELLDT------EMEELTA 76

                          90       100
                  ....*....|....*....|
gi 2416603799  83 KAKEKLHEVEIKIRELQEIE 102
Cdd:cd04768    77 MLLEKKQAIQQKIDRLQQLE 96
MerR-DNA-bind pfam09278
MerR, DNA binding; Members of this family of DNA-binding domains are predominantly found in ...
 44-106 6.66e-15

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: 64.06  E-value: 6.66e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2416603799  44 VQELNLISRAKNAGFSLIECKELVQLAHNSNRKSSEVKAKAKEKLHEVEIKIRELQEIERQLK 106
Cdd:pfam09278   1 LRRLAFIRRARRLGFSLEEIRELLALYDDPGPPCADVRALLREKLAELEARIAELQALRDELD 63
PRK13752 PRK13752
mercuric resistance operon transcriptional regulator MerR;
1-126 1.84e-14

mercuric resistance operon transcriptional regulator MerR;


Pssm-ID: 184302  Cd Length: 144  Bit Score: 65.31  E-value: 1.84e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416603799   1 MNIGAVSKLTGLSTKSIRLYEDKELITAPHRSESGYREYSDQHVQELNLISRAKNAGFSLIECKELVQLAHNSNrkSSEV 80
Cdd:PRK13752    8 LTIGVFAKAAGVNVETIRFYQRKGLLPEPDKPYGSIRRYGEADVTRVRFVKSAQRLGFSLDEIAELLRLEDGTH--CEEA 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2416603799  81 KAKAKEKLHEVEIKIRELQEIERQLKKWVSACPGDSGS-NCPIIEDL 126
Cdd:PRK13752   86 SSLAEHKLKDVREKMADLARMEAVLSELVCACHARKGNvSCPLIASL 132
HTH_MerR-SF cd04761
Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; ...
 1-50 2.73e-14

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: 62.22  E-value: 2.73e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2416603799   1 MNIGAVSKLTGLSTKSIRLYEDKELITaPHRSESGYREYSDQHVQELNLI 50
Cdd:cd04761     1 YTIGELAKLTGVSPSTLRYYERIGLLS-PARTEGGYRLYSDADLERLRLI 49
HTH_MlrA-CarA cd01104
Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; ...
 2-68 2.17e-13

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: 60.33  E-value: 2.17e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2416603799   2 NIGAVSKLTGLSTKSIRLYEDKELITAPHRSESGYREYSDQHVQELNLISRAKNAGFSLIECKELVQ 68
Cdd:cd01104     2 TIGAVARLTGVSPDTLRAWERRYGLPAPQRTDGGHRLYSEADVARLRLIRRLTSEGVRISQAAALAL 68
MerR pfam00376
MerR family regulatory protein;
2-39 1.95e-12

MerR family regulatory protein;


Pssm-ID: 425647 [Multi-domain]  Cd Length: 38  Bit Score: 57.04  E-value: 1.95e-12
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 2416603799   2 NIGAVSKLTGLSTKSIRLYEDKELITAPHRSESGYREY 39
Cdd:pfam00376   1 TIGEVAKLLGVSPRTLRYYEKIGLLPPPERTEGGYRRY 38
HTH_HMRTR_unk cd04787
Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription ...
 1-124 2.08e-12

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: 59.62  E-value: 2.08e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416603799   1 MNIGAVSKLTGLSTKSIRLYEDKELITAPHRSESGYREYSDQHVQELNLISRAKNAGFSLIECKELVQLAHNSNRKSSEV 80
Cdd:cd04787     1 MKVKELANAAGVTPDTVRFYTRIGLLRPTRDPVNGYRLYSEKDLSRLRFILSARQLGFSLKDIKEILSHADQGESPCPMV 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 2416603799  81 KAKAKEKLHEVEIKIRELQEIERQLKKWVSA------CPGDSGSNCPIIE 124
Cdd:cd04787    81 RRLIEQRLAETERRIKELLKLRDRMQQAVSQwqqmpdGAPDGHSICHLIE 130
HTH_TipAL-Mta cd01106
Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA; ...
 1-102 1.36e-11

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: 56.73  E-value: 1.36e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416603799   1 MNIGAVSKLTGLSTKSIRLYEDKELITAPHRSESGYREYSDQHVQELNLISRAKNAGFSLIECKELVQLAHNSNRKSSEV 80
Cdd:cd01106     1 YTVGEVAKLTGVSVRTLHYYDEIGLLKPSRRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELLKDPSEDLLEALRE 80

                          90       100
                  ....*....|....*....|...
gi 2416603799  81 KAKA-KEKLHEVEIKIRELQEIE 102
Cdd:cd01106    81 QKELlEEKKERLDKLIKTIDRTL 103
HTH_TioE_rpt1 cd04772
First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE; Putative ...
 6-102 6.28e-11

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: 55.09  E-value: 6.28e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416603799   6 VSKLTGLSTKSIRLYEDKELITAPHRSESGYREYSDQHVQELnLISRAKNAGFSLIECKELVQLAHNSNRKSSEVK-AKA 84
Cdd:cd04772     6 LARAIGLSPQTVRNYESLGLIPPAERTANGYRIYTDKHIAAL-RAYRALLPGYGYRVAQRIMRAVHAGIVASALALvDAA 84

                          90
                  ....*....|....*...
gi 2416603799  85 KEKLHeveikiRELQEIE 102
Cdd:cd04772    85 HALLQ------RYRQQLD 96
HTH_NolA-AlbR cd04788
Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR; ...
 1-64 6.73e-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: 6.73e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2416603799   1 MNIGAVSKLTGLSTKSIRLYEDKELITAPHRSESGYREYSDQHVQELNLISRAKNAGFSLIECK 64
Cdd:cd04788     1 WKIGELARRTGLSVRTLHHYDHIGLLSPSQRTEGGHRLYDRADIRRLHQIIALRRLGFSLREIG 64
HTH_GnyR cd04776
Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Putative helix-turn-helix ...
 1-100 8.69e-11

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: 55.23  E-value: 8.69e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416603799   1 MNIGAVSKLTGLSTKSIRLYEDKELITaPHRsESGYREYSDQHVQELNLISRAKNAGFSLIECKELVQL--AHNSNRKSS 78
Cdd:cd04776     1 YTISELAREFDVTPRTLRFYEDKGLLS-PER-RGQTRVYSRRDRARLKLILRGKRLGFSLEEIRELLDLydPPGGNRKQL 78

                          90       100
                  ....*....|....*....|...
gi 2416603799  79 E-VKAKAKEKLHEVEIKIRELQE 100
Cdd:cd04776    79 EkMLEKIEKRRAELEQQRRDIDA 101
HTH_YfmP cd04774
Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator; Helix-turn-helix (HTH) ...
 1-92 2.31e-10

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: 53.28  E-value: 2.31e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416603799   1 MNIGAVSKLTGLSTKSIRLYEDKELITaPHRSESGYREYSDQHVQELNLISRAKNA-GFSLIECKELVQLahnSNRKSSE 79
Cdd:cd04774     1 YKVDEVAKRLGLTKRTLKYYEEIGLVS-PERSEGRYRLYSEEDLKRLERILRLREVlGFSLQEVTHFLER---PLEPVDG 76

                          90
                  ....*....|...
gi 2416603799  80 VKAKAKEKLHEVE 92
Cdd:cd04774    77 GHRYSAESLREIH 89
HTH_Cfa-like_unk cd04790
Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators; Putative ...
 3-105 2.59e-09

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: 52.43  E-value: 2.59e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416603799   3 IGAVSKLTGLSTKSIRLYEDKELITAPHRSESGYREYSDQHVQELNLISRAKNAGFSLIECKELVQLAHnsnrksSEVKA 82
Cdd:cd04790     4 ISQLARQFGLSRSTLLYYERIGLLSPSARSESNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQQPG------DDATD 77

                          90       100
                  ....*....|....*....|...
gi 2416603799  83 KAKEKLHEVEIKIRELQEIERQL 105
Cdd:cd04790    78 VLRRRLAELNREIQRLRQQQRAI 100
HTH_MerD cd01111
Helix-Turn-Helix DNA binding domain of the MerD transcription regulator; Helix-turn-helix (HTH) ...
 6-107 1.29e-08

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: 49.31  E-value: 1.29e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416603799   6 VSKLT---GLSTKSIRLYEDKELITAPHRSESGYREYSDQHVQELNLISRAKNAGFSLIECKELVQLAHNSNRKssEVKA 82
Cdd:cd01111     3 ISQLAldaGVSVHIVRDYLLRGLLHPVARTEGGYGLFDDCALQRLRFVRAAFEAGIGLDELARLCRALDAGDGK--QPEA 80

                          90       100
                  ....*....|....*....|....*
gi 2416603799  83 KAKEKLHEVEIKIRELQEIERQLKK 107
Cdd:cd01111    81 CLAQLRQKIEVRRAALNALTTQLAE 105
HTH_Cfa-like cd04775
Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators; Putative ...
 3-100 5.70e-08

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: 47.53  E-value: 5.70e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416603799   3 IGAVSKLTGLSTKSIRLYEDKELITAPhRSESGYREYSDQHVQELNLISRAKNAGFSLIECKELVQLAHnsnrksseVKA 82
Cdd:cd04775     4 IGQMSRKFGVSRSTLLYYESIGLIPSA-RSEANYRLYSEADLSRLEKIVFLQAGGLPLEEIAGCLAQPH--------VQA 74

                          90
                  ....*....|....*...
gi 2416603799  83 KAKEKLHEVEIKIRELQE 100
Cdd:cd04775    75 ILEERLQSLNREIQRLRQ 92
HTH_MerR-like_sg4 cd04779
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 3-105 6.08e-07

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: 45.19  E-value: 6.08e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416603799   3 IGAVSKLTGLSTKSIRLYEDKELITaPHRSESGYREYSDQHVQELNLISRAKNAGFSLIECKELVQLAHNSNRKSSEVKA 82
Cdd:cd04779     3 IGQLAHLAGVSKRTIDYYTNLGLLT-PERSDSNYRYYDETALDRLQLIEHLKGQRLSLAEIKDQLEEVQRSDKEQREVAQ 81

                          90       100
                  ....*....|....*....|....*.
gi 2416603799  83 K---AKEKLHEVEIKIRELQEIERQL 105
Cdd:cd04779    82 EvqlVCDQIDGLEHRLKQLKPIASQT 107
HTH_GlnR-like cd01105
Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators; Helix-turn-helix ...
 2-74 4.51e-06

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: 41.83  E-value: 4.51e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2416603799   2 NIGAVSKLTGLSTKSIRLYEDKELITAPHRSESGYREYSDQHVQELNLISRAKNAGFSLIECKELVQLAHNSN 74
Cdd:cd01105     3 GIGEVSKLTGVSPRQLRYWEEKGLIKSIRSDGGGQRKYSLADVDRLLVIKELLDEGFTLAAAVEKLRRRRVQA 75
HTH_Cfa cd04789
Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator; Putative ...
 1-68 7.10e-06

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: 41.70  E-value: 7.10e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2416603799   1 MNIGAVSKLTGLSTKSIRLYEDKELITApHRSESGYREYSDQHVQELNLISRAKNAGFSLIECKELVQ 68
Cdd:cd04789     2 YTISELAEKAGISRSTLLYYEKLGLITG-TRNANGYRLYPDSDLQRLLLIQQLQAGGLSLKECLACLQ 68
HTH_MerR-like_sg1 cd04777
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 1-100 1.30e-05

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: 41.24  E-value: 1.30e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416603799   1 MNIGAVSKLTGLSTKSIRLYEDKELITaPHRsESGYREYSDQHVQELNLISRAKNAGFSLIECKELVQLAHNSNRKSSE- 79
Cdd:cd04777     1 MKIGKFAKKNNITIDTVRHYIDLGLLI-PEK-KGGQYFFDEKCQDDLEFILELKGLGFSLIEIQKIFSYKRLTKSRTHEd 78

                          90       100
                  ....*....|....*....|....
gi 2416603799  80 ---VKAKAKEKLHEVEIKIRELQE 100
Cdd:cd04777    79 qdyYKSFLKNKKDELEKEIEDLKK 102
HTH_MerR-like_sg2 cd04778
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 7-67 7.31e-05

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: 40.45  E-value: 7.31e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2416603799   7 SKLTGLSTKSIRLYEDKELITAPHR-SESGYreYSDQHVQELNLISRAKNAGFSLIECKELV 67
Cdd:cd04778     8 ARAAGTTVRNVRAYQDRGLLPPPRRrGRVAI--YNDSHLARLRLINQLLERGYTLAHIAELL 67
HTH_MerR-like_sg5 cd04780
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 1-68 9.38e-05

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), 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: 133407  Cd Length: 95  Bit Score: 38.85  E-value: 9.38e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2416603799   1 MNIGAVSKLTGLSTKSIRLYEDKELITAPHRSESGYREYSDQHVQELNLIsRA--KNAGFSLIECKELVQ 68
Cdd:cd04780     1 MRMSELSKRSGVSVATIKYYLREGLLPEGRRLAPNQAEYSEAHVERLRLI-RAlqQEGGLPISQIKEVLD 69
HTH_MlrA-like_sg1 cd04764
Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Putative ...
 3-68 1.88e-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: 37.31  E-value: 1.88e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2416603799   3 IGAVSKLTGLSTKSIRLYEdKELITAPHRSESGYREYSDQHVQELNLISRAKNAGFSLIECKELVQ 68
Cdd:cd04764     3 IKEVSEIIGVKPHTLRYYE-KEFNLYIPRTENGRRYYTDEDIELLKKIKTLLEKGLSIKEIKEILN 67
HTH_MerR-trunc cd04762
Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family ...
 1-47 2.52e-03

Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.


Pssm-ID: 133390 [Multi-domain]  Cd Length: 49  Bit Score: 33.71  E-value: 2.52e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2416603799   1 MNIGAVSKLTGLSTKSIRLYEDKELITApHRSESGYREYSDQHVQEL 47
Cdd:cd04762     1 LTTKEAAELLGVSPSTLRRWVKEGKLKA-IRTPGGHRRFPEEDLERL 46
HTH_MlrA-like cd04763
Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators; Helix-turn-helix ...
 3-67 2.86e-03

Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators; Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, 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-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: 133391  Cd Length: 68  Bit Score: 34.05  E-value: 2.86e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2416603799   3 IGAVSKLTGLSTKSIRLYEDKELITAPHRSESGYREYSDQHVQELNLISRAKNAGFSLIECKELV 67
Cdd:cd04763     3 IGEVALLTGIKPHVLRAWEREFGLLKPQRSDGGHRLFNDADIDRILEIKRWIDNGVQVSKVKKLL 67
 
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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