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Conserved domains on  [gi|490826349|ref|WP_004688439|]
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MerR family DNA-binding transcriptional regulator [Brucella neotomae]

Protein Classification

MerR family transcriptional regulator( domain architecture ID 10140965)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_GnyR cd04776
Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Putative helix-turn-helix ...
 5-122 3.60e-51

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: 157.69  E-value: 3.60e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490826349   5 YTITELTREFGISTRTLRFYEDEGLIAPVRRGRTRLFRPSDRHLLKQIMRGKRLGFSIAEIHEIIQMYREPPGETGQLKL 84
Cdd:cd04776    1 YTISELAREFDVTPRTLRFYEDKGLLSPERRGQTRVYSRRDRARLKLILRGKRLGFSLEEIRELLDLYDPPGGNRKQLEK 80

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 490826349  85 LMKRVEEKRADLRQKRRDIDETLGELDQVEEACIERLA 122
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 ...
 5-122 3.60e-51

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: 157.69  E-value: 3.60e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490826349   5 YTITELTREFGISTRTLRFYEDEGLIAPVRRGRTRLFRPSDRHLLKQIMRGKRLGFSIAEIHEIIQMYREPPGETGQLKL 84
Cdd:cd04776    1 YTISELAREFDVTPRTLRFYEDKGLLSPERRGQTRVYSRRDRARLKLILRGKRLGFSLEEIRELLDLYDPPGGNRKQLEK 80

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 490826349  85 LMKRVEEKRADLRQKRRDIDETLGELDQVEEACIERLA 122
Cdd:cd04776   81 MLEKIEKRRAELEQQRRDIDAALAELDAAEERCRERLA 118
SoxR COG0789
DNA-binding transcriptional regulator, MerR family [Transcription];
7-110 3.97e-21

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


Pssm-ID: 440552 [Multi-domain]  Cd Length: 100  Bit Score: 81.11  E-value: 3.97e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490826349   7 ITELTREFGISTRTLRFYEDEGLIAPVRR--GRTRLFRPSDRHLLKQIMRGKRLGFSIAEIHEIIQMYREPPGETGQLkl 84
Cdd:COG0789    1 IGEVARLTGVSVRTLRYYERIGLLPPPERteGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLDDGEEEVREL-- 78

                         90       100
                 ....*....|....*....|....*.
gi 490826349  85 lmkrVEEKRADLRQKRRDIDETLGEL 110
Cdd:COG0789   79 ----LEEHLAELEAQIAELQALRAEL 100
HTH_MERR smart00422
helix_turn_helix, mercury resistance;
5-72 1.59e-15

helix_turn_helix, mercury resistance;


Pssm-ID: 197716  Cd Length: 70  Bit Score: 66.00  E-value: 1.59e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490826349     5 YTITELTREFGISTRTLRFYEDEGLIAPVRR--GRTRLFRPSDRHLLKQIMRGKRLGFSIAEIHEIIQMY 72
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRteGGYRLYSDEDLERLRFIKRLKELGFSLEEIKELLELL 70
MerR_1 pfam13411
MerR HTH family regulatory protein;
5-69 1.94e-13

MerR HTH family regulatory protein;


Pssm-ID: 463870  Cd Length: 66  Bit Score: 60.26  E-value: 1.94e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490826349    5 YTITELTREFGISTRTLRFYEDEGLIAPVRRGRT-RLFRPSDRHLLKQIMRGKRLGFSIAEIHEII 69
Cdd:pfam13411   1 YTISELARLLGVTPRTLRYWEREGLLPPPRTERGrRYYTDEDVERLRLIKALLERGLSLKEIKELL 66
zntR PRK09514
Zn(2+)-responsive transcriptional regulator;
5-101 3.14e-11

Zn(2+)-responsive transcriptional regulator;


Pssm-ID: 181924 [Multi-domain]  Cd Length: 140  Bit Score: 56.52  E-value: 3.14e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490826349   5 YTITELTREFGISTRTLRFYEDEGLIAPVRR--GRTRLFRPSDRHLLKQIMRGKRLGFSIAEIHEIIQMYREPPGETGQ- 81
Cdd:PRK09514   2 YRIGELAKLAEVTPDTLRFYEKQGLMDPEVRteGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLSIRLDPEHHTCQe 81

                         90       100
                 ....*....|....*....|....
gi 490826349  82 LKLL----MKRVEEKRADLRQKRR 101
Cdd:PRK09514  82 VKGIvdekLAEVEAKIAELQHMRR 105
 
Name Accession Description Interval E-value
HTH_GnyR cd04776
Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Putative helix-turn-helix ...
 5-122 3.60e-51

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: 157.69  E-value: 3.60e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490826349   5 YTITELTREFGISTRTLRFYEDEGLIAPVRRGRTRLFRPSDRHLLKQIMRGKRLGFSIAEIHEIIQMYREPPGETGQLKL 84
Cdd:cd04776    1 YTISELAREFDVTPRTLRFYEDKGLLSPERRGQTRVYSRRDRARLKLILRGKRLGFSLEEIRELLDLYDPPGGNRKQLEK 80

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 490826349  85 LMKRVEEKRADLRQKRRDIDETLGELDQVEEACIERLA 122
Cdd:cd04776   81 MLEKIEKRRAELEQQRRDIDAALAELDAAEERCRERLA 118
SoxR COG0789
DNA-binding transcriptional regulator, MerR family [Transcription];
7-110 3.97e-21

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


Pssm-ID: 440552 [Multi-domain]  Cd Length: 100  Bit Score: 81.11  E-value: 3.97e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490826349   7 ITELTREFGISTRTLRFYEDEGLIAPVRR--GRTRLFRPSDRHLLKQIMRGKRLGFSIAEIHEIIQMYREPPGETGQLkl 84
Cdd:COG0789    1 IGEVARLTGVSVRTLRYYERIGLLPPPERteGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLDDGEEEVREL-- 78

                         90       100
                 ....*....|....*....|....*.
gi 490826349  85 lmkrVEEKRADLRQKRRDIDETLGEL 110
Cdd:COG0789   79 ----LEEHLAELEAQIAELQALRAEL 100
HTH_YyaN cd01109
Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB; ...
 5-112 6.52e-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: 78.27  E-value: 6.52e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490826349   5 YTITELTREFGISTRTLRFYEDEGLIAPVRR--GRTRLFRPSDRHLLKQIMRGKRLGFSIAEIHEIIQMYREPPGETGQL 82
Cdd:cd01109    1 YTIKEVAEKTGLSADTLRYYEKEGLLPPVKRdeNGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAELRREGDSTIPER 80

                         90       100       110
                 ....*....|....*....|....*....|
gi 490826349  83 KLLMkrvEEKRADLRQKRRDIDETLGELDQ 112
Cdd:cd01109   81 LELL---EEHREELEEQIAELQETLAYLDY 107
HTH_MerR-like cd00592
Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators; Helix-turn-helix ...
 5-107 1.20e-19

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: 77.28  E-value: 1.20e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490826349   5 YTITELTREFGISTRTLRFYEDEGLIAPVRR-GRTRLFRPSDRHLLKQIMRGKRLGFSIAEIHEIIQMYREPPGETGQLK 83
Cdd:cd00592    1 YTIGEVAKLLGVSVRTLRYYEEKGLLPPERSeNGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLDARDEELSLAALLA 80

                         90       100
                 ....*....|....*....|....
gi 490826349  84 LLmkrvEEKRADLRQKRRDIDETL 107
Cdd:cd00592   81 LL----DEKLAELEEKIARLEALL 100
HTH_HMRTR cd04770
Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators; ...
 5-123 3.14e-16

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: 69.13  E-value: 3.14e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490826349   5 YTITELTREFGISTRTLRFYEDEGLIAPVRR--GRTRLFRPSDRHLLKQIMRGKRLGFSIAEIHEIIQMYREPPGETGQL 82
Cdd:cd04770    1 MKIGELAKAAGVSPDTIRYYERIGLLPPPQRseNGYRLYGEADLARLRFIRRAQALGFSLAEIRELLSLRDDGAAPCAEV 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 490826349  83 KLLmkrVEEKRADLRQKRRDIDETLGELDQVEEACIERLAE 123
Cdd:cd04770   81 RAL---LEEKLAEVEAKIAELQALRAELAGLLSACDGDESV 118
HTH_MERR smart00422
helix_turn_helix, mercury resistance;
5-72 1.59e-15

helix_turn_helix, mercury resistance;


Pssm-ID: 197716  Cd Length: 70  Bit Score: 66.00  E-value: 1.59e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490826349     5 YTITELTREFGISTRTLRFYEDEGLIAPVRR--GRTRLFRPSDRHLLKQIMRGKRLGFSIAEIHEIIQMY 72
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRteGGYRLYSDEDLERLRFIKRLKELGFSLEEIKELLELL 70
HTH_CueR cd01108
Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Helix-turn-helix ...
 5-117 1.51e-14

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: 64.89  E-value: 1.51e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490826349   5 YTITELTREFGISTRTLRFYEDEGLIAPVRRGRT--RLFRPSDRHLLKQIMRGKRLGFSIAEIHEIIQMYREPPGETGQL 82
Cdd:cd01108    1 MNIGEAAKLTGLSAKMIRYYEEIGLIPPPSRSDNgyRVYNQRDIEELRFIRRARDLGFSLEEIRELLALWRDPSRASADV 80

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 490826349  83 KllmKRVEEKRADLRQKRRDIDETLGELDQVEEAC 117
Cdd:cd01108   81 K---ALALEHIAELERKIAELQAMRRTLQQLADSC 112
MerR_1 pfam13411
MerR HTH family regulatory protein;
5-69 1.94e-13

MerR HTH family regulatory protein;


Pssm-ID: 463870  Cd Length: 66  Bit Score: 60.26  E-value: 1.94e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490826349    5 YTITELTREFGISTRTLRFYEDEGLIAPVRRGRT-RLFRPSDRHLLKQIMRGKRLGFSIAEIHEII 69
Cdd:pfam13411   1 YTISELARLLGVTPRTLRYWEREGLLPPPRTERGrRYYTDEDVERLRLIKALLERGLSLKEIKELL 66
HTH_MerR-like_sg6 cd04781
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 6-116 9.57e-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: 59.99  E-value: 9.57e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490826349   6 TITELTREFGISTRTLRFYEDEGLIAPV-RRGRTRLFRPSDRHLLKQIMRGKRLGFSIAEIHEIIQMYREPPGEtgqlkl 84
Cdd:cd04781    2 DIAEVARQSGLPASTLRYYEEKGLIASIgRRGLRRQYDPQVLDRLALIALGRAAGFSLDEIQAMLSHDGKPPID------ 75

                         90       100       110
                 ....*....|....*....|....*....|..
gi 490826349  85 lmkrveekRADLRQKRRDIDETLGELDQVEEA 116
Cdd:cd04781   76 --------RQLLKAKAAELDQQIQRLQAMREL 99
HTH_TipAL-Mta cd01106
Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA; ...
 5-107 1.61e-12

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: 59.04  E-value: 1.61e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490826349   5 YTITELTREFGISTRTLRFYEDEGLIAPVRRGRT--RLFRPSDRHLLKQIMRGKRLGFSIAEIHEIIQMYREPPGETgqL 82
Cdd:cd01106    1 YTVGEVAKLTGVSVRTLHYYDEIGLLKPSRRTENgyRLYTEEDLERLQQILFLKELGFSLKEIKELLKDPSEDLLEA--L 78

                         90       100
                 ....*....|....*....|....*
gi 490826349  83 KLLMKRVEEKRADLRQKRRDIDETL 107
Cdd:cd01106   79 REQKELLEEKKERLDKLIKTIDRTL 103
HTH_MerR2 cd04769
Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators; Helix-turn-helix ...
 6-116 2.03e-12

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: 59.30  E-value: 2.03e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490826349   6 TITELTREFGISTRTLRFYEDEGLIAPVRR-GRTRLFRPSDRHLLKQIMRGKRLGFSIAEIHEIIQMYREPPGETGQlkL 84
Cdd:cd04769    2 YIGELAQQTGVTIKAIRLYEEKGLLPSPKRsGNYRVYDAQHVECLRFIKEARQLGFTLAELKAIFAGHEGRAVLPWP--H 79

                         90       100       110
                 ....*....|....*....|....*....|..
gi 490826349  85 LMKRVEEKRADLRQKRRDIDETLGELDQVEEA 116
Cdd:cd04769   80 LQQALEDKKQEIRAQITELQQLLARLDAFEAS 111
HTH_BmrR cd01107
Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator; Helix-turn-helix (HTH) ...
 5-107 4.17e-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: 58.30  E-value: 4.17e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490826349   5 YTITELTREFGISTRTLRFYEDEGLIAPVRRGRT---RLFRPSDRHLLKQIMRGKRLGFSIAEIHEIIQmYREPPGETGQ 81
Cdd:cd01107    1 FTIGEFAKLSNLSIKALRYYDKIGLLKPAYVDPDtgyRYYSAEQLERLNRIKYLRDLGFPLEEIKEILD-ADNDDELRKL 79

                         90       100
                 ....*....|....*....|....*.
gi 490826349  82 LKLLMKRVEEKRADLRQKRRDIDETL 107
Cdd:cd01107   80 LREKLAELEAEIEELQRILRLLEDRL 105
HTH_BmrR-like cd04768
Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators; Helix-turn-helix ...
 5-114 2.19e-11

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: 56.21  E-value: 2.19e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490826349   5 YTITELTREFGISTRTLRFYEDEGLIAPVRRGRT--RLFRPSDRHLLKQIMRGKRLGFSIAEIHEIIQmyreppGETGQL 82
Cdd:cd04768    1 LTIGEFAKLAGVSIRTLRHYDDIGLFKPAKIAENgyRYYSYAQLYQLQFILFLRELGFSLAEIKELLD------TEMEEL 74

                         90       100       110
                 ....*....|....*....|....*....|..
gi 490826349  83 KllmkrveekrADLRQKRRDIDETLGELDQVE 114
Cdd:cd04768   75 T----------AMLLEKKQAIQQKIDRLQQLE 96
zntR PRK09514
Zn(2+)-responsive transcriptional regulator;
5-101 3.14e-11

Zn(2+)-responsive transcriptional regulator;


Pssm-ID: 181924 [Multi-domain]  Cd Length: 140  Bit Score: 56.52  E-value: 3.14e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490826349   5 YTITELTREFGISTRTLRFYEDEGLIAPVRR--GRTRLFRPSDRHLLKQIMRGKRLGFSIAEIHEIIQMYREPPGETGQ- 81
Cdd:PRK09514   2 YRIGELAKLAEVTPDTLRFYEKQGLMDPEVRteGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLSIRLDPEHHTCQe 81

                         90       100
                 ....*....|....*....|....
gi 490826349  82 LKLL----MKRVEEKRADLRQKRR 101
Cdd:PRK09514  82 VKGIvdekLAEVEAKIAELQHMRR 105
HTH_CadR-PbrR-like cd04785
Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators; ...
 5-117 2.58e-10

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: 54.09  E-value: 2.58e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490826349   5 YTITELTREFGISTRTLRFYEDEGLIAPVRR--GRTRLFRPSDRHLLKQIMRGKRLGFSIAEIHEIIQMYREPPGETGQL 82
Cdd:cd04785    1 LSIGELARRTGVNVETIRYYESIGLLPEPARtaGGYRLYGAAHVERLRFIRRARDLGFSLEEIRALLALSDRPDRSCAEA 80

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 490826349  83 KLLMKR----VEEKRADLRQKRRdidetlgELDQVEEAC 117
Cdd:cd04785   81 DAIARAhladVRARIADLRRLEA-------ELKRMVAAC 112
HTH_MerR-like_sg3 cd01282
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 7-122 5.78e-10

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 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: 52.61  E-value: 5.78e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490826349   7 ITELTREFGISTRTLRFYEDEGLIAPVRRGRT-RLFRPSDRHLLKQIMRGKRLGFSIAEIHEIIQMYREPPGETGQlkll 85
Cdd:cd01282    3 IGELAARTGVSVRSLRYYEEQGLLVPERSANGyRDYDEAAVDRVRQIRRLLAAGLTLEEIREFLPCLRGGEPTFRP---- 78

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 490826349  86 mkrVEEKRADLRQKRRDIDETLGELDQVEEACIERLA 122
Cdd:cd01282   79 ---CPDLLAVLRRELARIDRQIADLTRSRDRLDAYLA 112
PRK10227 PRK10227
HTH-type transcriptional regulator CueR;
7-117 1.22e-09

HTH-type transcriptional regulator CueR;


Pssm-ID: 182320  Cd Length: 135  Bit Score: 52.35  E-value: 1.22e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490826349   7 ITELTREFGISTRTLRFYEDEGLIAPVRRGRTRLFRPSDRHL--LKQIMRGKRLGFSIAEIHEIIQMYREPPGETGQLKl 84
Cdd:PRK10227   3 ISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLneLTLLRQARQVGFNLEESGELVNLFNDPQRHSADVK- 81

                         90       100       110
                 ....*....|....*....|....*....|...
gi 490826349  85 lmKRVEEKRADLRQKRRDIDETLGELDQVEEAC 117
Cdd:PRK10227  82 --RRTLEKVAEIERHIEELQSMRDQLLALANAC 112
HTH_MerR-SF cd04761
Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; ...
 5-52 4.30e-09

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: 48.74  E-value: 4.30e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 490826349   5 YTITELTREFGISTRTLRFYEDEGLIAPVRR-GRTRLFRPSDRHLLKQI 52
Cdd:cd04761    1 YTIGELAKLTGVSPSTLRYYERIGLLSPARTeGGYRLYSDADLERLRLI 49
HTH_MerR1 cd04783
Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator; Helix-turn-helix ...
 5-120 4.39e-09

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: 50.69  E-value: 4.39e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490826349   5 YTITELTREFGISTRTLRFYEDEGLIAPVRR--GRTRLFRPSDRHLLKQIMRGKRLGFSIAEIHEIIQMYREPPGETGQl 82
Cdd:cd04783    1 LTIGELAKAAGVNVETIRYYQRRGLLPEPPRpeGGYRRYPEETVTRLRFIKRAQELGFTLDEIAELLELDDGTDCSEAR- 79

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 490826349  83 kllmKRVEEKRADLRQKRRDIDETLGELDQVEEACIER 120
Cdd:cd04783   80 ----ELAEQKLAEVDEKIADLQRMRASLQELVSQCAAT 113
HTH_MerR-like_sg2 cd04778
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 5-126 4.92e-09

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 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: 52.01  E-value: 4.92e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490826349   5 YTITELTREFGISTRTLRFYEDEGLIAPVRR-GRTRLFrpSDRHL--LKQIMRGKRLGFSIAEIHEIIQMYREPPGETGQ 81
Cdd:cd04778    2 YRIDDLARAAGTTVRNVRAYQDRGLLPPPRRrGRVAIY--NDSHLarLRLINQLLERGYTLAHIAELLAAWEQGRDLGDV 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 490826349  82 LKLlmKRVEEKRADLRQKRRDIDETLGELdQVEEACIERLAELGV 126
Cdd:cd04778   80 LGL--QAAIDGPWSTEEPGTALLAELQSE-FGDERALARAVALGL 121
HTH_Cfa-like_unk cd04790
Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators; Putative ...
 5-109 1.07e-08

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


Pssm-ID: 133417 [Multi-domain]  Cd Length: 172  Bit Score: 50.51  E-value: 1.07e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490826349   5 YTITELTREFGISTRTLRFYEDEGLIAPVRR--GRTRLFRPSDRHLLKQIMRGKRLGFSIAEIHEIIQmyREPPGETGQL 82
Cdd:cd04790    2 LTISQLARQFGLSRSTLLYYERIGLLSPSARseSNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQ--QPGDDATDVL 79

                         90       100
                 ....*....|....*....|....*..
gi 490826349  83 KLLMKRVEEKRADLRQKRRDIDETLGE 109
Cdd:cd04790   80 RRRLAELNREIQRLRQQQRAIATLLKQ 106
HTH_HMRTR_unk cd04787
Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription ...
 6-98 1.26e-08

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: 49.61  E-value: 1.26e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490826349   6 TITELTREFGISTRTLRFYEDEGLIAPVRRGRT--RLFRPSDRHLLKQIMRGKRLGFSIAEIHEIIQMYREPPGETGQLK 83
Cdd:cd04787    2 KVKELANAAGVTPDTVRFYTRIGLLRPTRDPVNgyRLYSEKDLSRLRFILSARQLGFSLKDIKEILSHADQGESPCPMVR 81

                         90
                 ....*....|....*.
gi 490826349  84 -LLMKRVEEKRADLRQ 98
Cdd:cd04787   82 rLIEQRLAETERRIKE 97
HTH_SoxR cd01110
Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator; Helix-turn-helix (HTH) ...
 6-67 1.52e-08

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: 49.50  E-value: 1.52e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 490826349   6 TITELTREFGISTRTLRFYEDEGLIAPVR-RGRTRLFRPSDRHLLKQIMRGKRLGFSIAEIHE 67
Cdd:cd01110    3 SVGEVAKRSGVAVSALHFYEQKGLIASWRnAGNQRRYPRDVLRRIAFIKVAQRLGLSLAEIAE 65
MerR-DNA-bind pfam09278
MerR, DNA binding; Members of this family of DNA-binding domains are predominantly found in ...
 46-113 3.17e-08

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: 47.11  E-value: 3.17e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 490826349   46 RHLLKQIMRGKRLGFSIAEIHEIIQMYREPPGETGQLKLLmkrVEEKRADLRQKRRDIDETLGELDQV 113
Cdd:pfam09278   1 LRRLAFIRRARRLGFSLEEIRELLALYDDPGPPCADVRAL---LREKLAELEARIAELQALRDELDAL 65
MerR pfam00376
MerR family regulatory protein;
6-41 7.66e-08

MerR family regulatory protein;


Pssm-ID: 425647 [Multi-domain]  Cd Length: 38  Bit Score: 45.49  E-value: 7.66e-08
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 490826349    6 TITELTREFGISTRTLRFYEDEGLIAPVRR--GRTRLF 41
Cdd:pfam00376   1 TIGEVAKLLGVSPRTLRYYEKIGLLPPPERteGGYRRY 38
HTH_CadR-PbrR cd04784
Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; ...
 7-75 1.13e-07

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: 47.18  E-value: 1.13e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490826349   7 ITELTREFGISTRTLRFYEDEGLIAPVRR--GRTRLFRPSDRHLLKQIMRGKRLGFSIAEIHEIIQMYREP 75
Cdd:cd04784    3 IGELAKKTGCSVETIRYYEKEGLLPAPARsaNNYRLYDEEHLERLLFIRRCRSLDMSLDEIRTLLQLQDDP 73
HTH_NolA-AlbR cd04788
Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR; ...
 7-100 1.22e-07

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: 46.22  E-value: 1.22e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490826349   7 ITELTREFGISTRTLRFYEDEGLIAPVRR--GRTRLFRPSDRHLLKQIMRGKRLGFSIAEIHEIIQMYREPPGETGQLKL 84
Cdd:cd04788    3 IGELARRTGLSVRTLHHYDHIGLLSPSQRteGGHRLYDRADIRRLHQIIALRRLGFSLREIGRALDGPDFDPLELLRRQL 82

                         90
                 ....*....|....*.
gi 490826349  85 lmKRVEEKRADLRQKR 100
Cdd:cd04788   83 --ARLEEQLELATRLR 96
HTH_YfmP cd04774
Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator; Helix-turn-helix (HTH) ...
 5-75 1.33e-07

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: 46.35  E-value: 1.33e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 490826349   5 YTITELTREFGISTRTLRFYEDEGLIAPVR-RGRTRLFRPSDRHLLKQIMRGKR-LGFSIAEIHEIIQMYREP 75
Cdd:cd04774    1 YKVDEVAKRLGLTKRTLKYYEEIGLVSPERsEGRYRLYSEEDLKRLERILRLREvLGFSLQEVTHFLERPLEP 73
HTH_HspR-like_MBC cd04767
Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators; Putative ...
 5-72 1.65e-07

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: 46.33  E-value: 1.65e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490826349   5 YTITELTREFGISTRTLRFYEDEGLIAPVRRGRTRLFRPSDRHLLKQImrgKRL----GFSIAEIHEIIQMY 72
Cdd:cd04767    2 YPIGVVAELLNIHPETLRIWERHGLIKPARRNGQRLYSNNDLKRLRFI---KKLinekGLNIAGVKQILSMY 70
HTH_TioE_rpt2 cd04773
Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE; Putative ...
 5-102 3.78e-07

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: 45.43  E-value: 3.78e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490826349   5 YTITELTREFGISTRTLRFYEDEGLIAPVRRGRT--RLFRPSDRHLLKQIMRGKRLGFSIAEIHEIIQMYReppgETGQL 82
Cdd:cd04773    1 MTIGELAHLLGVPPSTLRHWEKEGLLSPDREPETgyRVYDPSDVRDARLIHLLRRGGYLLEQIATVVEQLR----HAGGT 76

                         90       100
                 ....*....|....*....|
gi 490826349  83 KLLMKRVEEKRADLRQKRRD 102
Cdd:cd04773   77 EALAAALEQRRVALTQRGRA 96
HTH_MlrA-like_sg2 cd04765
Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Putative ...
 5-110 4.89e-07

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: 44.94  E-value: 4.89e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490826349   5 YTITELTREFGISTRTLRFYEDE-GLIAPVRR-GRTRLFRPSDRHLLKQImrgKRL----GFSIAEIHEIIQMYREPPGe 78
Cdd:cd04765    1 FSIGEVAEILGLPPHVLRYWETEfPQLKPVKRaGGRRYYRPKDVELLLLI---KHLlyekGYTIEGAKQALKEDGAAAI- 76

                         90       100       110
                 ....*....|....*....|....*....|..
gi 490826349  79 tgqlkllmkRVEEKRADLRQKRRDIDETLGEL 110
Cdd:cd04765   77 ---------REEEAEERLPSIRAELLDLRDQL 99
HTH_GlnR-like cd01105
Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators; Helix-turn-helix ...
 5-77 1.82e-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: 42.99  E-value: 1.82e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 490826349   5 YTITELTREFGISTRTLRFYEDEGLIAPVR--RGRTRLFRPSDRHLLKQIMRGKRLGFSIAEIHEIIQMYREPPG 77
Cdd:cd01105    2 IGIGEVSKLTGVSPRQLRYWEEKGLIKSIRsdGGGQRKYSLADVDRLLVIKELLDEGFTLAAAVEKLRRRRVQAE 76
HTH_MlrA-like_sg1 cd04764
Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Putative ...
 5-70 2.49e-06

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: 42.32  E-value: 2.49e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 490826349   5 YTITELTREFGISTRTLRFYEDE--GLIAPVRRGRtRLFRPSDRHLLKQIMRGKRLGFSIAEIHEIIQ 70
Cdd:cd04764    1 YTIKEVSEIIGVKPHTLRYYEKEfnLYIPRTENGR-RYYTDEDIELLKKIKTLLEKGLSIKEIKEILN 67
HTH_MerR-like_sg7 cd04786
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 7-123 3.01e-06

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 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: 43.28  E-value: 3.01e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490826349   7 ITELTREFGISTRTLRFYEDEGLIAPVRRGRT--RLFRPSDRHLLKQIMRGKRLGFSIAEIHEIIqmyrePPGETGQlkl 84
Cdd:cd04786    3 IGELAKRSGMAASRIRFYEAEGLLSSVERSANgyRDYPPETVWVLEIISSAQQAGFSLDEIRQLL-----PADASNW--- 74

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 490826349  85 lmkRVEEKRADLRQKRRDIdetlgeldqveEACIERLAE 123
Cdd:cd04786   75 ---QHDELLAALERKVADI-----------EALEARLAQ 99
HTH_Cfa-like cd04775
Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators; Putative ...
 5-108 3.96e-06

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: 42.53  E-value: 3.96e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490826349   5 YTITELTREFGISTRTLRFYEDEGLIAPVRR-GRTRLFRPSDRHLLKQIMRGKRLGFSIAEIHEIIQMYREPpgetGQLK 83
Cdd:cd04775    2 YTIGQMSRKFGVSRSTLLYYESIGLIPSARSeANYRLYSEADLSRLEKIVFLQAGGLPLEEIAGCLAQPHVQ----AILE 77

                         90       100
                 ....*....|....*....|....*
gi 490826349  84 LLMKRVEEKRADLRQKRRDIDETLG 108
Cdd:cd04775   78 ERLQSLNREIQRLRQQQQVLAAILG 102
HTH_TioE_rpt1 cd04772
First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE; Putative ...
 5-49 4.18e-06

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: 42.38  E-value: 4.18e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 490826349   5 YTITELTREFGISTRTLRFYEDEGLIAPVRRGRT--RLFrpSDRHLL 49
Cdd:cd04772    1 YRTVDLARAIGLSPQTVRNYESLGLIPPAERTANgyRIY--TDKHIA 45
HTH_MerR-like_sg1 cd04777
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 7-107 4.32e-06

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


Pssm-ID: 133404 [Multi-domain]  Cd Length: 107  Bit Score: 42.40  E-value: 4.32e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490826349   7 ITELTREFGISTRTLRFYEDEGLIAPVRRGRTRLFRPSDRHLLKQIMRGKRLGFSIAEIHEIIQMYREPPGETGQLKLLM 86
Cdd:cd04777    3 IGKFAKKNNITIDTVRHYIDLGLLIPEKKGGQYFFDEKCQDDLEFILELKGLGFSLIEIQKIFSYKRLTKSRTHEDQDYY 82

                         90       100
                 ....*....|....*....|..
gi 490826349  87 KRV-EEKRADLRQKRRDIDETL 107
Cdd:cd04777   83 KSFlKNKKDELEKEIEDLKKAI 104
HTH_HspR cd04766
Helix-Turn-Helix DNA binding domain of the HspR transcription regulator; Helix-turn-helix (HTH) ...
 4-91 1.09e-05

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: 41.10  E-value: 1.09e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490826349   4 YYTITELTREFGISTRTLRFYEDEGLIAPVR-RGRTRLFRPSDRHLLKQIMRGKR-LGFSIAEIHEIIQMYREPPGETGQ 81
Cdd:cd04766    1 VYVISVAAELSGMHPQTLRLYERLGLLSPSRtDGGTRRYSERDIERLRRIQRLTQeLGVNLAGVKRILELEEELAELRAE 80

                         90
                 ....*....|
gi 490826349  82 LKLLMKRVEE 91
Cdd:cd04766   81 LDELRARLRR 90
PRK13752 PRK13752
mercuric resistance operon transcriptional regulator MerR;
3-96 2.92e-05

mercuric resistance operon transcriptional regulator MerR;


Pssm-ID: 184302  Cd Length: 144  Bit Score: 41.04  E-value: 2.92e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490826349   3 EYYTITELTREFGISTRTLRFYEDEGLIAPVRR--GRTRLFRPSDRHLLKQIMRGKRLGFSIAEIHEIIQM----YREPP 76
Cdd:PRK13752   6 ENLTIGVFAKAAGVNVETIRFYQRKGLLPEPDKpyGSIRRYGEADVTRVRFVKSAQRLGFSLDEIAELLRLedgtHCEEA 85

                         90       100
                 ....*....|....*....|
gi 490826349  77 GETGQLKLlmKRVEEKRADL 96
Cdd:PRK13752  86 SSLAEHKL--KDVREKMADL 103
HTH_BltR cd04782
Helix-Turn-Helix DNA binding domain of the BltR transcription regulator; Helix-turn-helix (HTH) ...
 5-98 6.93e-05

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


Pssm-ID: 133409 [Multi-domain]  Cd Length: 97  Bit Score: 39.14  E-value: 6.93e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490826349   5 YTITELTREFGISTRTLRFYEDEGLIAPVRRGRT--RLFRPSDRHLLKQIMRGKRLGFSIAEIHEIIQMyREPPGETGQL 82
Cdd:cd04782    1 FTTGEFAKLCGISKQTLFHYDKIGLFKPEIVKENgyRYYTLEQFEQLDIILLLKELGISLKEIKDYLDN-RNPDELIELL 79

                         90
                 ....*....|....*.
gi 490826349  83 KLLMKRVEEKRADLRQ 98
Cdd:cd04782   80 KKQEKEIKEEIEELQK 95
HTH_MlrA-like cd04763
Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators; Helix-turn-helix ...
 5-69 1.46e-04

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: 37.51  E-value: 1.46e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490826349   5 YTITELTREFGISTRTLRFYEDE-GLIAPVR-RGRTRLFRPSDRHLLKQIMRGKRLGFSIAEIHEII 69
Cdd:cd04763    1 YTIGEVALLTGIKPHVLRAWEREfGLLKPQRsDGGHRLFNDADIDRILEIKRWIDNGVQVSKVKKLL 67
HTH_MlrA-CarA cd01104
Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; ...
 5-65 1.95e-04

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


Pssm-ID: 133379  Cd Length: 68  Bit Score: 37.22  E-value: 1.95e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 490826349   5 YTITELTREFGISTRTLRFYEDE-GLIAPVR-RGRTRLFRPSDRHLLKQIMRGKRLGFSIAEI 65
Cdd:cd01104    1 YTIGAVARLTGVSPDTLRAWERRyGLPAPQRtDGGHRLYSEADVARLRLIRRLTSEGVRISQA 63
HTH_17 pfam12728
Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.
 4-45 3.36e-04

Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.


Pssm-ID: 463684 [Multi-domain]  Cd Length: 51  Bit Score: 36.28  E-value: 3.36e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 490826349    4 YYTITELTREFGISTRTLRFYEDEGLIAPVRRGRTRLFRPSD 45
Cdd:pfam12728   1 LLTVEEAAELLGVSRRTVYRLIRSGELPAAKIGRRWRIRKSD 42
HTH_HspR-like cd01279
Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators; Helix-turn-helix ...
 5-72 5.11e-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: 36.81  E-value: 5.11e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490826349   5 YTITELTREFGISTRTLRFYEDEGLIAPVRR-GRTRLFRPSDRHLLKQIMR-GKRLGFSIAEIHEIIQMY 72
Cdd:cd01279    2 YPISVAAELLGIHPQTLRVYDRLGLVSPARTnGGGRRYSNNDLELLRQVQRlSQDEGFNLAGIKRIIELY 71
HTH_Cfa cd04789
Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator; Putative ...
 5-100 8.12e-04

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: 36.31  E-value: 8.12e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490826349   5 YTITELTREFGISTRTLRFYEDEGLIAPVRRGRT-RLFRPSDRHLLKQIMRGKRLGFSIAEIHEIIQMYREPpgetGQLK 83
Cdd:cd04789    2 YTISELAEKAGISRSTLLYYEKLGLITGTRNANGyRLYPDSDLQRLLLIQQLQAGGLSLKECLACLQGKLTR----SLLL 77

                         90
                 ....*....|....*..
gi 490826349  84 LLMKRVEEKRADLRQKR 100
Cdd:cd04789   78 ERLSSLAEQIARKQQAR 94
COG2452 COG2452
Predicted site-specific integrase-resolvase [Mobilome: prophages, transposons];
5-45 1.72e-03

Predicted site-specific integrase-resolvase [Mobilome: prophages, transposons];


Pssm-ID: 441988 [Multi-domain]  Cd Length: 178  Bit Score: 36.51  E-value: 1.72e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 490826349   5 YTITELTREFGISTRTLRFYEDEGLIAPVRR-GRTRLFRPSD 45
Cdd:COG2452    1 LTPGEAAELLGVSPKTLRRWEKEGKLPAIRTpGGHRRYPESE 42
 
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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