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Conserved domains on  [gi|1311729724|ref|WP_101230597|]
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MerR family DNA-binding transcriptional regulator [Colwellia sp. 75C3]

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 ...
 10-127 1.86e-55

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: 168.86  E-value: 1.86e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1311729724  10 YSISDLSKEFDITTRSIRFYEDQGLVSPARKGQTRIYNQRDKVRLKLILRGKRLGFSLAETGRLFELYDVDKTSAKQLNS 89
Cdd:cd04776     1 YTISELAREFDVTPRTLRFYEDKGLLSPERRGQTRVYSRRDRARLKLILRGKRLGFSLEEIRELLDLYDPPGGNRKQLEK 80

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1311729724  90 IMELIHNKKRDLTQQLEDINAVLIELNDLEDNCQETLR 127
Cdd:cd04776    81 MLEKIEKRRAELEQQRRDIDAALAELDAAEERCRERLA 118
 
Name Accession Description Interval E-value
HTH_GnyR cd04776
Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Putative helix-turn-helix ...
 10-127 1.86e-55

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: 168.86  E-value: 1.86e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1311729724  10 YSISDLSKEFDITTRSIRFYEDQGLVSPARKGQTRIYNQRDKVRLKLILRGKRLGFSLAETGRLFELYDVDKTSAKQLNS 89
Cdd:cd04776     1 YTISELAREFDVTPRTLRFYEDKGLLSPERRGQTRVYSRRDRARLKLILRGKRLGFSLEEIRELLDLYDPPGGNRKQLEK 80

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1311729724  90 IMELIHNKKRDLTQQLEDINAVLIELNDLEDNCQETLR 127
Cdd:cd04776    81 MLEKIEKRRAELEQQRRDIDAALAELDAAEERCRERLA 118
SoxR COG0789
DNA-binding transcriptional regulator, MerR family [Transcription];
12-115 1.73e-21

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


Pssm-ID: 440552 [Multi-domain]  Cd Length: 100  Bit Score: 82.26  E-value: 1.73e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1311729724  12 ISDLSKEFDITTRSIRFYEDQGLVSPARK--GQTRIYNQRDKVRLKLILRGKRLGFSLAETGRLFELYDVDKTSAKqlns 89
Cdd:COG0789     1 IGEVARLTGVSVRTLRYYERIGLLPPPERteGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLDDGEEEVR---- 76

                          90       100
                  ....*....|....*....|....*.
gi 1311729724  90 imELIHNKKRDLTQQLEDINAVLIEL 115
Cdd:COG0789    77 --ELLEEHLAELEAQIAELQALRAEL 100
zntR PRK09514
Zn(2+)-responsive transcriptional regulator;
10-124 1.10e-16

Zn(2+)-responsive transcriptional regulator;


Pssm-ID: 181924 [Multi-domain]  Cd Length: 140  Bit Score: 71.15  E-value: 1.10e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1311729724  10 YSISDLSKEFDITTRSIRFYEDQGLVSPARKGQT--RIYNQRDKVRLKLILRGKRLGFSLAETGRLFELyDVDKT--SAK 85
Cdd:PRK09514    2 YRIGELAKLAEVTPDTLRFYEKQGLMDPEVRTEGgyRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLSI-RLDPEhhTCQ 80

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1311729724  86 QLNSIMElihnkkrdltQQLEDINAVLIELNDLEDNCQE 124
Cdd:PRK09514   81 EVKGIVD----------EKLAEVEAKIAELQHMRRSLQR 109
HTH_MERR smart00422
helix_turn_helix, mercury resistance;
10-77 1.20e-16

helix_turn_helix, mercury resistance;


Pssm-ID: 197716  Cd Length: 70  Bit Score: 68.70  E-value: 1.20e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1311729724   10 YSISDLSKEFDITTRSIRFYEDQGLVSPARK--GQTRIYNQRDKVRLKLILRGKRLGFSLAETGRLFELY 77
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRteGGYRLYSDEDLERLRFIKRLKELGFSLEEIKELLELL 70
CueR TIGR02044
Cu(I)-responsive transcriptional regulator; This model represents the copper-, silver- and ...
 12-123 1.36e-12

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: 60.15  E-value: 1.36e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1311729724  12 ISDLSKEFDITTRSIRFYEDQGLVSPARK--GQTRIYNQRDKVRLKLILRGKRLGFSLAETGRLFELY-DVDKTSAkqln 88
Cdd:TIGR02044   3 IGQVAKLTGLSSKMIRYYEEKGLIPPPLRseGGYRTYTQQHLDELRLISRARQVGFSLEECKELLNLWnDPNRTSA---- 78

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1311729724  89 SIMELIHNKKRDLTQQLEDINAVLIELNDLEDNCQ 123
Cdd:TIGR02044  79 DVKARTLEKVAEIERKISELQSMRDQLEALAQACP 113
MerR_1 pfam13411
MerR HTH family regulatory protein;
10-69 5.03e-12

MerR HTH family regulatory protein;


Pssm-ID: 463870  Cd Length: 66  Bit Score: 56.79  E-value: 5.03e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1311729724  10 YSISDLSKEFDITTRSIRFYEDQGLVSPARKGQT-RIYNQRDKVRLKLILRGKRLGFSLAE 69
Cdd:pfam13411   1 YTISELARLLGVTPRTLRYWEREGLLPPPRTERGrRYYTDEDVERLRLIKALLERGLSLKE 61
 
Name Accession Description Interval E-value
HTH_GnyR cd04776
Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Putative helix-turn-helix ...
 10-127 1.86e-55

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: 168.86  E-value: 1.86e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1311729724  10 YSISDLSKEFDITTRSIRFYEDQGLVSPARKGQTRIYNQRDKVRLKLILRGKRLGFSLAETGRLFELYDVDKTSAKQLNS 89
Cdd:cd04776     1 YTISELAREFDVTPRTLRFYEDKGLLSPERRGQTRVYSRRDRARLKLILRGKRLGFSLEEIRELLDLYDPPGGNRKQLEK 80

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1311729724  90 IMELIHNKKRDLTQQLEDINAVLIELNDLEDNCQETLR 127
Cdd:cd04776    81 MLEKIEKRRAELEQQRRDIDAALAELDAAEERCRERLA 118
HTH_MerR-like cd00592
Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators; Helix-turn-helix ...
 10-112 5.89e-22

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: 83.45  E-value: 5.89e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1311729724  10 YSISDLSKEFDITTRSIRFYEDQGLVSPAR-KGQTRIYNQRDKVRLKLILRGKRLGFSLAETGRLFELYDVDKTSAKQLN 88
Cdd:cd00592     1 YTIGEVAKLLGVSVRTLRYYEEKGLLPPERsENGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLDARDEELSLAALLA 80

                          90       100
                  ....*....|....*....|....
gi 1311729724  89 SIMElihnKKRDLTQQLEDINAVL 112
Cdd:cd00592    81 LLDE----KLAELEEKIARLEALL 100
SoxR COG0789
DNA-binding transcriptional regulator, MerR family [Transcription];
12-115 1.73e-21

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


Pssm-ID: 440552 [Multi-domain]  Cd Length: 100  Bit Score: 82.26  E-value: 1.73e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1311729724  12 ISDLSKEFDITTRSIRFYEDQGLVSPARK--GQTRIYNQRDKVRLKLILRGKRLGFSLAETGRLFELYDVDKTSAKqlns 89
Cdd:COG0789     1 IGEVARLTGVSVRTLRYYERIGLLPPPERteGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLDDGEEEVR---- 76

                          90       100
                  ....*....|....*....|....*.
gi 1311729724  90 imELIHNKKRDLTQQLEDINAVLIEL 115
Cdd:COG0789    77 --ELLEEHLAELEAQIAELQALRAEL 100
HTH_HMRTR cd04770
Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators; ...
 10-128 1.08e-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: 78.37  E-value: 1.08e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1311729724  10 YSISDLSKEFDITTRSIRFYEDQGLVSPARKGQT--RIYNQRDKVRLKLILRGKRLGFSLAETGRLFELYDVDKTSAKQl 87
Cdd:cd04770     1 MKIGELAKAAGVSPDTIRYYERIGLLPPPQRSENgyRLYGEADLARLRFIRRAQALGFSLAEIRELLSLRDDGAAPCAE- 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1311729724  88 nsIMELIHNKKRDLTQQLEDINAVLIELNDLEDNCQETLRT 128
Cdd:cd04770    80 --VRALLEEKLAEVEAKIAELQALRAELAGLLSACDGDESV 118
HTH_CueR cd01108
Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Helix-turn-helix ...
 12-123 5.36e-17

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: 71.44  E-value: 5.36e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1311729724  12 ISDLSKEFDITTRSIRFYEDQGLVSPARKGQT--RIYNQRDKVRLKLILRGKRLGFSLAETGRLFELY-DVDKTSA--KQ 86
Cdd:cd01108     3 IGEAAKLTGLSAKMIRYYEEIGLIPPPSRSDNgyRVYNQRDIEELRFIRRARDLGFSLEEIRELLALWrDPSRASAdvKA 82

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1311729724  87 LNSimelihNKKRDLTQQLEDINAVLIELNDLEDNCQ 123
Cdd:cd01108    83 LAL------EHIAELERKIAELQAMRRTLQQLADSCH 113
zntR PRK09514
Zn(2+)-responsive transcriptional regulator;
10-124 1.10e-16

Zn(2+)-responsive transcriptional regulator;


Pssm-ID: 181924 [Multi-domain]  Cd Length: 140  Bit Score: 71.15  E-value: 1.10e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1311729724  10 YSISDLSKEFDITTRSIRFYEDQGLVSPARKGQT--RIYNQRDKVRLKLILRGKRLGFSLAETGRLFELyDVDKT--SAK 85
Cdd:PRK09514    2 YRIGELAKLAEVTPDTLRFYEKQGLMDPEVRTEGgyRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLSI-RLDPEhhTCQ 80

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1311729724  86 QLNSIMElihnkkrdltQQLEDINAVLIELNDLEDNCQE 124
Cdd:PRK09514   81 EVKGIVD----------EKLAEVEAKIAELQHMRRSLQR 109
HTH_MERR smart00422
helix_turn_helix, mercury resistance;
10-77 1.20e-16

helix_turn_helix, mercury resistance;


Pssm-ID: 197716  Cd Length: 70  Bit Score: 68.70  E-value: 1.20e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1311729724   10 YSISDLSKEFDITTRSIRFYEDQGLVSPARK--GQTRIYNQRDKVRLKLILRGKRLGFSLAETGRLFELY 77
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRteGGYRLYSDEDLERLRFIKRLKELGFSLEEIKELLELL 70
HTH_MerR2 cd04769
Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators; Helix-turn-helix ...
 12-120 9.92e-16

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: 67.78  E-value: 9.92e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1311729724  12 ISDLSKEFDITTRSIRFYEDQGLVSPA-RKGQTRIYNQRDKVRLKLILRGKRLGFSLAETGRLFElyDVDKTSAKQLNSI 90
Cdd:cd04769     3 IGELAQQTGVTIKAIRLYEEKGLLPSPkRSGNYRVYDAQHVECLRFIKEARQLGFTLAELKAIFA--GHEGRAVLPWPHL 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 1311729724  91 MELIHNKKRDLTQQLEDINAVLIELNDLED 120
Cdd:cd04769    81 QQALEDKKQEIRAQITELQQLLARLDAFEA 110
HTH_TipAL-Mta cd01106
Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA; ...
 10-112 5.03e-14

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: 63.27  E-value: 5.03e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1311729724  10 YSISDLSKEFDITTRSIRFYEDQGLVSPARKGQT--RIYNQRDKVRLKLILRGKRLGFSLAETGRLFELYDVDKTSAkqL 87
Cdd:cd01106     1 YTVGEVAKLTGVSVRTLHYYDEIGLLKPSRRTENgyRLYTEEDLERLQQILFLKELGFSLKEIKELLKDPSEDLLEA--L 78

                          90       100
                  ....*....|....*....|....*
gi 1311729724  88 NSIMELIHNKKRDLTQQLEDINAVL 112
Cdd:cd01106    79 REQKELLEEKKERLDKLIKTIDRTL 103
HTH_CadR-PbrR cd04784
Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; ...
 12-123 1.90e-13

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: 62.20  E-value: 1.90e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1311729724  12 ISDLSKEFDITTRSIRFYEDQGLVSPARKGQT--RIYNQRDKVRLKLILRGKRLGFSLAETGRLFELYDvdkTSAKQLNS 89
Cdd:cd04784     3 IGELAKKTGCSVETIRYYEKEGLLPAPARSANnyRLYDEEHLERLLFIRRCRSLDMSLDEIRTLLQLQD---DPEASCAE 79

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1311729724  90 IMELIHNKKRDLTQQLEDINAVLIELNDLEDNCQ 123
Cdd:cd04784    80 VNALIDEHLAHVRARIAELQALEKQLQALRERCD 113
HTH_MerR-like_sg6 cd04781
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 11-111 2.46e-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: 61.92  E-value: 2.46e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1311729724  11 SISDLSKEFDITTRSIRFYEDQGLV-SPARKGQTRIYNQRDKVRLKLILRGKRLGFSLAETGRLFE---LYDVDKTSAKQ 86
Cdd:cd04781     2 DIAEVARQSGLPASTLRYYEEKGLIaSIGRRGLRRQYDPQVLDRLALIALGRAAGFSLDEIQAMLShdgKPPIDRQLLKA 81

                          90       100
                  ....*....|....*....|....*
gi 1311729724  87 lnsimelihnKKRDLTQQLEDINAV 111
Cdd:cd04781    82 ----------KAAELDQQIQRLQAM 96
PRK10227 PRK10227
HTH-type transcriptional regulator CueR;
11-122 3.80e-13

HTH-type transcriptional regulator CueR;


Pssm-ID: 182320  Cd Length: 135  Bit Score: 61.59  E-value: 3.80e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1311729724  11 SISDLSKEFDITTRSIRFYEDQGLVSPARKGQT--RIYNQRDKVRLKLILRGKRLGFSLAETGRLFELY-DVDKTSAKQL 87
Cdd:PRK10227    2 NISDVAKITGLTSKAIRFYEEKGLVTPPMRSENgyRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFnDPQRHSADVK 81

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1311729724  88 NSIMElihnKKRDLTQQLEDINAVLIELNDLEDNC 122
Cdd:PRK10227   82 RRTLE----KVAEIERHIEELQSMRDQLLALANAC 112
CueR TIGR02044
Cu(I)-responsive transcriptional regulator; This model represents the copper-, silver- and ...
 12-123 1.36e-12

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: 60.15  E-value: 1.36e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1311729724  12 ISDLSKEFDITTRSIRFYEDQGLVSPARK--GQTRIYNQRDKVRLKLILRGKRLGFSLAETGRLFELY-DVDKTSAkqln 88
Cdd:TIGR02044   3 IGQVAKLTGLSSKMIRYYEEKGLIPPPLRseGGYRTYTQQHLDELRLISRARQVGFSLEECKELLNLWnDPNRTSA---- 78

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1311729724  89 SIMELIHNKKRDLTQQLEDINAVLIELNDLEDNCQ 123
Cdd:TIGR02044  79 DVKARTLEKVAEIERKISELQSMRDQLEALAQACP 113
MerR_1 pfam13411
MerR HTH family regulatory protein;
10-69 5.03e-12

MerR HTH family regulatory protein;


Pssm-ID: 463870  Cd Length: 66  Bit Score: 56.79  E-value: 5.03e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1311729724  10 YSISDLSKEFDITTRSIRFYEDQGLVSPARKGQT-RIYNQRDKVRLKLILRGKRLGFSLAE 69
Cdd:pfam13411   1 YTISELARLLGVTPRTLRYWEREGLLPPPRTERGrRYYTDEDVERLRLIKALLERGLSLKE 61
HTH_BmrR cd01107
Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator; Helix-turn-helix (HTH) ...
 10-118 7.25e-12

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: 57.53  E-value: 7.25e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1311729724  10 YSISDLSKEFDITTRSIRFYEDQGLVSPARKGQT---RIYNQRDKVRLKLILRGKRLGFSLAETGRLFELYDVDKtsakq 86
Cdd:cd01107     1 FTIGEFAKLSNLSIKALRYYDKIGLLKPAYVDPDtgyRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDADNDDE----- 75

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1311729724  87 lnsIMELIHNKKRDLTQQLEDINAVLIELNDL 118
Cdd:cd01107    76 ---LRKLLREKLAELEAEIEELQRILRLLEDR 104
HTH_MerR-SF cd04761
Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; ...
 10-57 7.74e-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: 56.06  E-value: 7.74e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1311729724  10 YSISDLSKEFDITTRSIRFYEDQGLVSPARK-GQTRIYNQRDKVRLKLI 57
Cdd:cd04761     1 YTIGELAKLTGVSPSTLRYYERIGLLSPARTeGGYRLYSDADLERLRLI 49
HTH_YyaN cd01109
Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB; ...
 10-117 8.20e-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: 57.47  E-value: 8.20e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1311729724  10 YSISDLSKEFDITTRSIRFYEDQGLVSPARKGQT--RIYNQRDKVRLKLILRGKRLGFSLAETGRLFELY-DVDKTSAKQ 86
Cdd:cd01109     1 YTIKEVAEKTGLSADTLRYYEKEGLLPPVKRDENgiRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAELRrEGDSTIPER 80

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1311729724  87 LnsimELIHNKKRDLTQQLEDINAVLIELND 117
Cdd:cd01109    81 L----ELLEEHREELEEQIAELQETLAYLDY 107
HTH_CadR-PbrR-like cd04785
Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators; ...
 10-120 4.49e-11

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: 56.02  E-value: 4.49e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1311729724  10 YSISDLSKEFDITTRSIRFYEDQGLVS-PARK-GQTRIYNQRDKVRLKLILRGKRLGFSLAETGRLFELYDVDKTSAKQL 87
Cdd:cd04785     1 LSIGELARRTGVNVETIRYYESIGLLPePARTaGGYRLYGAAHVERLRFIRRARDLGFSLEEIRALLALSDRPDRSCAEA 80

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1311729724  88 NSIMElihnkkrdltQQLEDINAVLIELNDLED 120
Cdd:cd04785    81 DAIAR----------AHLADVRARIADLRRLEA 103
HTH_MerR-like_sg2 cd04778
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 10-93 6.39e-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 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: 57.40  E-value: 6.39e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1311729724  10 YSISDLSKEFDITTRSIRFYEDQGLVSPARK-GQTRIYNQRDKVRLKLILRGKRLGFSLAETGRLFELYDvdktSAKQLN 88
Cdd:cd04778     2 YRIDDLARAAGTTVRNVRAYQDRGLLPPPRRrGRVAIYNDSHLARLRLINQLLERGYTLAHIAELLAAWE----QGRDLG 77


                  ....*
gi 1311729724  89 SIMEL 93
Cdd:cd04778    78 DVLGL 82
HTH_MerR-like_sg1 cd04777
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 12-109 6.54e-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 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: 55.11  E-value: 6.54e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1311729724  12 ISDLSKEFDITTRSIRFYEDQGLVSPARKGQTRIYNQRDKVRLKLILRGKRLGFSLAETGRLFELYDVDKTSAKQLNS-I 90
Cdd:cd04777     3 IGKFAKKNNITIDTVRHYIDLGLLIPEKKGGQYFFDEKCQDDLEFILELKGLGFSLIEIQKIFSYKRLTKSRTHEDQDyY 82

                          90
                  ....*....|....*....
gi 1311729724  91 MELIHNKKRDLTQQLEDIN 109
Cdd:cd04777    83 KSFLKNKKDELEKEIEDLK 101
HTH_MerR1 cd04783
Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator; Helix-turn-helix ...
 10-125 2.67e-10

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: 54.15  E-value: 2.67e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1311729724  10 YSISDLSKEFDITTRSIRFYEDQGLVS-PAR-KGQTRIYNQRDKVRLKLILRGKRLGFSLAETGRLFELYDVDKTSAKQl 87
Cdd:cd04783     1 LTIGELAKAAGVNVETIRYYQRRGLLPePPRpEGGYRRYPEETVTRLRFIKRAQELGFTLDEIAELLELDDGTDCSEAR- 79

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1311729724  88 nsimELIHNKKRDLTQQLEDINAVLIELNDLEDNCQET 125
Cdd:cd04783    80 ----ELAEQKLAEVDEKIADLQRMRASLQELVSQCAAT 113
MerR-DNA-bind pfam09278
MerR, DNA binding; Members of this family of DNA-binding domains are predominantly found in ...
 53-118 4.99e-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: 4.99e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1311729724  53 RLKLILRGKRLGFSLAETGRLFELYDVDKTSAKQLNsimELIHNKKRDLTQQLEDINAVLIELNDL 118
Cdd:pfam09278   3 RLAFIRRARRLGFSLEEIRELLALYDDPGPPCADVR---ALLREKLAELEARIAELQALRDELDAL 65
HTH_YfmP cd04774
Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator; Helix-turn-helix (HTH) ...
 10-105 9.16e-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: 52.13  E-value: 9.16e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1311729724  10 YSISDLSKEFDITTRSIRFYEDQGLVSPAR-KGQTRIYNQRDKVRLKLILRGKR-LGFSLAETGRLFELYDVDKTSAKQL 87
Cdd:cd04774     1 YKVDEVAKRLGLTKRTLKYYEEIGLVSPERsEGRYRLYSEEDLKRLERILRLREvLGFSLQEVTHFLERPLEPVDGGHRY 80

                          90
                  ....*....|....*...
gi 1311729724  88 NSimELIHNKKRDLTQQL 105
Cdd:cd04774    81 SA--ESLREIHDALAQQV 96
HTH_NolA-AlbR cd04788
Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR; ...
 12-92 1.19e-09

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: 51.61  E-value: 1.19e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1311729724  12 ISDLSKEFDITTRSIRFYEDQGLVSPARK--GQTRIYNQRDKVRLKLILRGKRLGFSLAETGRLFE--LYDVDKTSAKQL 87
Cdd:cd04788     3 IGELARRTGLSVRTLHHYDHIGLLSPSQRteGGHRLYDRADIRRLHQIIALRRLGFSLREIGRALDgpDFDPLELLRRQL 82


                  ....*
gi 1311729724  88 NSIME 92
Cdd:cd04788    83 ARLEE 87
HTH_HMRTR_unk cd04787
Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription ...
 12-128 1.59e-09

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: 52.31  E-value: 1.59e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1311729724  12 ISDLSKEFDITTRSIRFYEDQGLVSPARKGQT--RIYNQRDKVRLKLILRGKRLGFSLAETGRLFELYDVDKTSAKQLns 89
Cdd:cd04787     3 VKELANAAGVTPDTVRFYTRIGLLRPTRDPVNgyRLYSEKDLSRLRFILSARQLGFSLKDIKEILSHADQGESPCPMV-- 80

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1311729724  90 imelihnkKRDLTQQLEDINAVLIELNDLEDNCQETLRT 128
Cdd:cd04787    81 --------RRLIEQRLAETERRIKELLKLRDRMQQAVSQ 111
PRK13752 PRK13752
mercuric resistance operon transcriptional regulator MerR;
11-115 1.64e-08

mercuric resistance operon transcriptional regulator MerR;


Pssm-ID: 184302  Cd Length: 144  Bit Score: 49.90  E-value: 1.64e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1311729724  11 SISDLSKEFDITTRSIRFYEDQGLVSPARK--GQTRIYNQRDKVRLKLILRGKRLGFSLAETGRLFELYdvDKTSAKQLN 88
Cdd:PRK13752    9 TIGVFAKAAGVNVETIRFYQRKGLLPEPDKpyGSIRRYGEADVTRVRFVKSAQRLGFSLDEIAELLRLE--DGTHCEEAS 86

                          90       100       110
                  ....*....|....*....|....*....|
gi 1311729724  89 SIMElihNKKRDLTQQLEDI---NAVLIEL 115
Cdd:PRK13752   87 SLAE---HKLKDVREKMADLarmEAVLSEL 113
HTH_BmrR-like cd04768
Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators; Helix-turn-helix ...
 10-103 4.01e-08

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: 47.73  E-value: 4.01e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1311729724  10 YSISDLSKEFDITTRSIRFYEDQGLVSPARKGQT--RIYNQRDKVRLKLILRGKRLGFSLAETGRLFELYDVDKTsaKQL 87
Cdd:cd04768     1 LTIGEFAKLAGVSIRTLRHYDDIGLFKPAKIAENgyRYYSYAQLYQLQFILFLRELGFSLAEIKELLDTEMEELT--AML 78

                          90
                  ....*....|....*.
gi 1311729724  88 NSIMELIHNKKRDLTQ 103
Cdd:cd04768    79 LEKKQAIQQKIDRLQQ 94
HTH_SoxR cd01110
Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator; Helix-turn-helix (HTH) ...
 11-86 1.12e-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: 47.57  E-value: 1.12e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1311729724  11 SISDLSKEFDITTRSIRFYEDQGLVSPAR-KGQTRIYNQRDKVRLKLILRGKRLGFSLAETGRLFELYDVDKTSAKQ 86
Cdd:cd01110     3 SVGEVAKRSGVAVSALHFYEQKGLIASWRnAGNQRRYPRDVLRRIAFIKVAQRLGLSLAEIAEALATLPEDRTPTKA 79
MerR pfam00376
MerR family regulatory protein;
11-46 2.32e-07

MerR family regulatory protein;


Pssm-ID: 425647 [Multi-domain]  Cd Length: 38  Bit Score: 44.33  E-value: 2.32e-07
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1311729724  11 SISDLSKEFDITTRSIRFYEDQGLVSPARKGQT--RIY 46
Cdd:pfam00376   1 TIGEVAKLLGVSPRTLRYYEKIGLLPPPERTEGgyRRY 38
HTH_MerR-like_sg3 cd01282
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 12-73 3.08e-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 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: 45.68  E-value: 3.08e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1311729724  12 ISDLSKEFDITTRSIRFYEDQGLVSPAR--KGQtRIYNQRDKVRLKLILRGKRLGFSLAETGRL 73
Cdd:cd01282     3 IGELAARTGVSVRSLRYYEEQGLLVPERsaNGY-RDYDEAAVDRVRQIRRLLAAGLTLEEIREF 65
HTH_GlnR-like cd01105
Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators; Helix-turn-helix ...
 10-68 6.91e-07

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: 44.14  E-value: 6.91e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1311729724  10 YSISDLSKEFDITTRSIRFYEDQGLVSPAR--KGQTRIYNQRDKVRLKLIlrgKRL---GFSLA 68
Cdd:cd01105     2 IGIGEVSKLTGVSPRQLRYWEEKGLIKSIRsdGGGQRKYSLADVDRLLVI---KELldeGFTLA 62
HTH_Cfa-like_unk cd04790
Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators; Putative ...
 10-69 2.59e-06

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: 44.34  E-value: 2.59e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1311729724  10 YSISDLSKEFDITTRSIRFYEDQGLVSPARK--GQTRIYNQRDKVRLKLILRGKRLGFSLAE 69
Cdd:cd04790     2 LTISQLARQFGLSRSTLLYYERIGLLSPSARseSNYRLYGERDLERLEQICAYRSAGVSLED 63
HTH_HspR-like_MBC cd04767
Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators; Putative ...
 10-77 3.36e-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: 43.25  E-value: 3.36e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1311729724  10 YSISDLSKEFDITTRSIRFYEDQGLVSPARKGQTRIYNQRDKVRLKLIlrgKRL----GFSLAETGRLFELY 77
Cdd:cd04767     2 YPIGVVAELLNIHPETLRIWERHGLIKPARRNGQRLYSNNDLKRLRFI---KKLinekGLNIAGVKQILSMY 70
HTH_HspR cd04766
Helix-Turn-Helix DNA binding domain of the HspR transcription regulator; Helix-turn-helix (HTH) ...
 10-76 9.18e-06

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: 41.48  E-value: 9.18e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1311729724  10 YSISDLSKEFDITTRSIRFYEDQGLVSPAR-KGQTRIYNQRDKVRLKLILRGKR-LGFSLAETGRLFEL 76
Cdd:cd04766     2 YVISVAAELSGMHPQTLRLYERLGLLSPSRtDGGTRRYSERDIERLRRIQRLTQeLGVNLAGVKRILEL 70
HTH_TioE_rpt1 cd04772
First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE; Putative ...
 10-72 2.31e-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: 40.45  E-value: 2.31e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1311729724  10 YSISDLSKEFDITTRSIRFYEDQGLVSPARKGQT--RIYNQRDKVRLKlILRGKRLGFSLAETGR 72
Cdd:cd04772     1 YRTVDLARAIGLSPQTVRNYESLGLIPPAERTANgyRIYTDKHIAALR-AYRALLPGYGYRVAQR 64
HTH_TioE_rpt2 cd04773
Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE; Putative ...
 10-75 8.78e-05

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: 39.27  E-value: 8.78e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1311729724  10 YSISDLSKEFDITTRSIRFYEDQGLVSPARKGQT--RIYNQRDkvrlkliLRGKRLGFSLAETGRLFE 75
Cdd:cd04773     1 MTIGELAHLLGVPPSTLRHWEKEGLLSPDREPETgyRVYDPSD-------VRDARLIHLLRRGGYLLE 61
HTH_MerR-like_sg4 cd04779
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 10-132 1.53e-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: 39.03  E-value: 1.53e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1311729724  10 YSISDLSKEFDITTRSIRFYEDQGLVSPAR-KGQTRIYNQRDKVRLKLILRGKRLGFSLAETGRLFElyDVDKTSAKQLN 88
Cdd:cd04779     1 YRIGQLAHLAGVSKRTIDYYTNLGLLTPERsDSNYRYYDETALDRLQLIEHLKGQRLSLAEIKDQLE--EVQRSDKEQRE 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1311729724  89 SIMELIHnkkrdLTQQLEDINAVLIELNDLEDNCQETLRTLETK 132
Cdd:cd04779    79 VAQEVQL-----VCDQIDGLEHRLKQLKPIASQTDRAQRMKMTK 117
HTH_MlrA-like_sg2 cd04765
Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Putative ...
 10-105 2.56e-04

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: 37.62  E-value: 2.56e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1311729724  10 YSISDLSKEFDITTRSIRFYEDQ-GLVSPA-RKGQTRIYNQRDkvrLKLILRGKRL----GFSLAETGRLFELYDVDKTS 83
Cdd:cd04765     1 FSIGEVAEILGLPPHVLRYWETEfPQLKPVkRAGGRRYYRPKD---VELLLLIKHLlyekGYTIEGAKQALKEDGAAAIR 77

                          90       100
                  ....*....|....*....|..
gi 1311729724  84 AKQLNSIMELIHNKKRDLTQQL 105
Cdd:cd04765    78 EEEAEERLPSIRAELLDLRDQL 99
HTH_HspR-like cd01279
Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators; Helix-turn-helix ...
 10-77 2.91e-04

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: 37.58  E-value: 2.91e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1311729724  10 YSISDLSKEFDITTRSIRFYEDQGLVSPARK-GQTRIYNQRDKVRLKLILR-GKRLGFSLAETGRLFELY 77
Cdd:cd01279     2 YPISVAAELLGIHPQTLRVYDRLGLVSPARTnGGGRRYSNNDLELLRQVQRlSQDEGFNLAGIKRIIELY 71
HTH_Cfa-like cd04775
Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators; Putative ...
 10-98 6.40e-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: 36.75  E-value: 6.40e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1311729724  10 YSISDLSKEFDITTRSIRFYEDQGLVSPARK-GQTRIYNQRDKVRLKLILRGKRLGFSLAETGRLFELYDVDKTSAKQLN 88
Cdd:cd04775     2 YTIGQMSRKFGVSRSTLLYYESIGLIPSARSeANYRLYSEADLSRLEKIVFLQAGGLPLEEIAGCLAQPHVQAILEERLQ 81

                          90
                  ....*....|
gi 1311729724  89 SIMELIHNKK 98
Cdd:cd04775    82 SLNREIQRLR 91
HTH_MerR-like_sg7 cd04786
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 12-69 1.63e-03

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: 35.96  E-value: 1.63e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1311729724  12 ISDLSKEFDITTRSIRFYEDQGLVSPARKGQT--RIYNQRDKVRLKLILRGKRLGFSLAE 69
Cdd:cd04786     3 IGELAKRSGMAASRIRFYEAEGLLSSVERSANgyRDYPPETVWVLEIISSAQQAGFSLDE 62
HTH_MlrA-CarA cd01104
Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; ...
 10-73 1.73e-03

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: 34.91  E-value: 1.73e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1311729724  10 YSISDLSKEFDITTRSIRFYEDQ-GLVSPAR-KGQTRIYNQRDKVRLKLILRGKRLGFSLAETGRL 73
Cdd:cd01104     1 YTIGAVARLTGVSPDTLRAWERRyGLPAPQRtDGGHRLYSEADVARLRLIRRLTSEGVRISQAAAL 66
HTH_MerD cd01111
Helix-Turn-Helix DNA binding domain of the MerD transcription regulator; Helix-turn-helix (HTH) ...
 10-106 2.15e-03

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: 35.44  E-value: 2.15e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1311729724  10 YSISDLSKEFDITTRSIRFYEDQGLVSPARK--GQTRIYNQRDKVRLKLILRGKRLGFSLAETGRLFELYDVD--KTSAK 85
Cdd:cd01111     1 YSISQLALDAGVSVHIVRDYLLRGLLHPVARteGGYGLFDDCALQRLRFVRAAFEAGIGLDELARLCRALDAGdgKQPEA 80

                          90       100
                  ....*....|....*....|....
gi 1311729724  86 QLNSIMELIHNKKR---DLTQQLE 106
Cdd:cd01111    81 CLAQLRQKIEVRRAalnALTTQLA 104
 
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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