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Conserved domains on  [gi|1895173470|ref|WP_186179839|]
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mercury resistance co-regulator MerD [Escherichia coli]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK13749 super family cl29192
HTH-type transcriptional regulator MerD;
17-135 6.11e-56

HTH-type transcriptional regulator MerD;


The actual alignment was detected with superfamily member PRK13749:

Pssm-ID: 184299  Cd Length: 121  Bit Score: 170.48  E-value: 6.11e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895173470  17 NVRRVSQLAHNAGVSVHIVRDYLVRGLLRPVACTTGGYGVFDDAALQRLCFVRAAFEAGIGLDALARLCRALDAADGAQA 96
Cdd:PRK13749    2 SAYTVSRLALDAGVSVHIVRDYLLRGLLRPVACTTGGYGLFDDAALQRLCFVRAAFEAGIGLDALARLCRALDAADGDEA 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1895173470  97 AAQLAVLRQLVERRRAALAHLDAQLASMPAERA-HEEALP 135
Cdd:PRK13749   82 AAQLAVLRQLVERRREALADLEVQLATMPTEPAqHAESLP 121
 
Name Accession Description Interval E-value
PRK13749 PRK13749
HTH-type transcriptional regulator MerD;
17-135 6.11e-56

HTH-type transcriptional regulator MerD;


Pssm-ID: 184299  Cd Length: 121  Bit Score: 170.48  E-value: 6.11e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895173470  17 NVRRVSQLAHNAGVSVHIVRDYLVRGLLRPVACTTGGYGVFDDAALQRLCFVRAAFEAGIGLDALARLCRALDAADGAQA 96
Cdd:PRK13749    2 SAYTVSRLALDAGVSVHIVRDYLLRGLLRPVACTTGGYGLFDDAALQRLCFVRAAFEAGIGLDALARLCRALDAADGDEA 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1895173470  97 AAQLAVLRQLVERRRAALAHLDAQLASMPAERA-HEEALP 135
Cdd:PRK13749   82 AAQLAVLRQLVERRREALADLEVQLATMPTEPAqHAESLP 121
HTH_MerD cd01111
Helix-Turn-Helix DNA binding domain of the MerD transcription regulator; Helix-turn-helix (HTH) ...
 21-125 4.76e-44

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: 139.83  E-value: 4.76e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895173470  21 VSQLAHNAGVSVHIVRDYLVRGLLRPVACTTGGYGVFDDAALQRLCFVRAAFEAGIGLDALARLCRALDAADGAQAAAQL 100
Cdd:cd01111     3 ISQLALDAGVSVHIVRDYLLRGLLHPVARTEGGYGLFDDCALQRLRFVRAAFEAGIGLDELARLCRALDAGDGKQPEACL 82

                          90       100
                  ....*....|....*....|....*
gi 1895173470 101 AVLRQLVERRRAALAHLDAQLASMP 125
Cdd:cd01111    83 AQLRQKIEVRRAALNALTTQLAEMA 107
MerD TIGR02054
mercuric resistence transcriptional repressor protein MerD; This model represents a ...
 17-133 3.72e-42

mercuric resistence transcriptional repressor protein MerD; This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon. [Cellular processes, Detoxification]


Pssm-ID: 131109  Cd Length: 120  Bit Score: 135.39  E-value: 3.72e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895173470  17 NVRRVSQLAHNAGVSVHIVRDYLVRGLLRPVACTTGGYGVFDDAALQRLCFVRAAFEAGIGLDALARLCRALDAADGAQA 96
Cdd:TIGR02054   2 NAYTISRLAEDAGVSVHVVRDYLLRGLLHPVRRTTSGYGIFDDASLQRLRFVRAAFEAGIGLGELARLCRALDAANGDDT 81

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1895173470  97 AAQLAVLRQLVERRRAALAHLDAQLASMPAERAHEEA 133
Cdd:TIGR02054  82 AACLAVLRQLVEARREALAALEVQLAAMPTAAAQHSE 118
HTH_MERR smart00422
helix_turn_helix, mercury resistance;
20-86 1.95e-16

helix_turn_helix, mercury resistance;


Pssm-ID: 197716  Cd Length: 70  Bit Score: 68.32  E-value: 1.95e-16
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1895173470   20 RVSQLAHNAGVSVHIVRDYLVRGLLRPVACTTGGYGVFDDAALQRLCFVRAAFEAGIGLDALARLCR 86
Cdd:smart00422   2 TIGEVAKLAGVSVRTLRYYERIGLLPPPIRTEGGYRLYSDEDLERLRFIKRLKELGFSLEEIKELLE 68
SoxR COG0789
DNA-binding transcriptional regulator, MerR family [Transcription];
21-121 5.56e-12

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


Pssm-ID: 440552 [Multi-domain]  Cd Length: 100  Bit Score: 57.99  E-value: 5.56e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895173470  21 VSQLAHNAGVSVHIVRDYLVRGLLRPVACTTGGYGVFDDAALQRLCFVRAAFEAGIGLDALARLCRALDAADGAQAAAQL 100
Cdd:COG0789     1 IGEVARLTGVSVRTLRYYERIGLLPPPERTEGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLDDGEEEVRELLE 80

                          90       100
                  ....*....|....*....|.
gi 1895173470 101 AVLRQLvERRRAALAHLDAQL 121
Cdd:COG0789    81 EHLAEL-EAQIAELQALRAEL 100
MerR_1 pfam13411
MerR HTH family regulatory protein;
20-85 2.31e-11

MerR HTH family regulatory protein;


Pssm-ID: 463870  Cd Length: 66  Bit Score: 55.25  E-value: 2.31e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1895173470  20 RVSQLAHNAGVSVHIVRDYLVRGLLRPVAcTTGGYGVFDDAALQRLCFVRAAFEAGIGLDALARLC 85
Cdd:pfam13411   2 TISELARLLGVTPRTLRYWEREGLLPPPR-TERGRRYYTDEDVERLRLIKALLERGLSLKEIKELL 66
 
Name Accession Description Interval E-value
PRK13749 PRK13749
HTH-type transcriptional regulator MerD;
17-135 6.11e-56

HTH-type transcriptional regulator MerD;


Pssm-ID: 184299  Cd Length: 121  Bit Score: 170.48  E-value: 6.11e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895173470  17 NVRRVSQLAHNAGVSVHIVRDYLVRGLLRPVACTTGGYGVFDDAALQRLCFVRAAFEAGIGLDALARLCRALDAADGAQA 96
Cdd:PRK13749    2 SAYTVSRLALDAGVSVHIVRDYLLRGLLRPVACTTGGYGLFDDAALQRLCFVRAAFEAGIGLDALARLCRALDAADGDEA 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1895173470  97 AAQLAVLRQLVERRRAALAHLDAQLASMPAERA-HEEALP 135
Cdd:PRK13749   82 AAQLAVLRQLVERRREALADLEVQLATMPTEPAqHAESLP 121
HTH_MerD cd01111
Helix-Turn-Helix DNA binding domain of the MerD transcription regulator; Helix-turn-helix (HTH) ...
 21-125 4.76e-44

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: 139.83  E-value: 4.76e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895173470  21 VSQLAHNAGVSVHIVRDYLVRGLLRPVACTTGGYGVFDDAALQRLCFVRAAFEAGIGLDALARLCRALDAADGAQAAAQL 100
Cdd:cd01111     3 ISQLALDAGVSVHIVRDYLLRGLLHPVARTEGGYGLFDDCALQRLRFVRAAFEAGIGLDELARLCRALDAGDGKQPEACL 82

                          90       100
                  ....*....|....*....|....*
gi 1895173470 101 AVLRQLVERRRAALAHLDAQLASMP 125
Cdd:cd01111    83 AQLRQKIEVRRAALNALTTQLAEMA 107
MerD TIGR02054
mercuric resistence transcriptional repressor protein MerD; This model represents a ...
 17-133 3.72e-42

mercuric resistence transcriptional repressor protein MerD; This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon. [Cellular processes, Detoxification]


Pssm-ID: 131109  Cd Length: 120  Bit Score: 135.39  E-value: 3.72e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895173470  17 NVRRVSQLAHNAGVSVHIVRDYLVRGLLRPVACTTGGYGVFDDAALQRLCFVRAAFEAGIGLDALARLCRALDAADGAQA 96
Cdd:TIGR02054   2 NAYTISRLAEDAGVSVHVVRDYLLRGLLHPVRRTTSGYGIFDDASLQRLRFVRAAFEAGIGLGELARLCRALDAANGDDT 81

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1895173470  97 AAQLAVLRQLVERRRAALAHLDAQLASMPAERAHEEA 133
Cdd:TIGR02054  82 AACLAVLRQLVEARREALAALEVQLAAMPTAAAQHSE 118
HTH_MERR smart00422
helix_turn_helix, mercury resistance;
20-86 1.95e-16

helix_turn_helix, mercury resistance;


Pssm-ID: 197716  Cd Length: 70  Bit Score: 68.32  E-value: 1.95e-16
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1895173470   20 RVSQLAHNAGVSVHIVRDYLVRGLLRPVACTTGGYGVFDDAALQRLCFVRAAFEAGIGLDALARLCR 86
Cdd:smart00422   2 TIGEVAKLAGVSVRTLRYYERIGLLPPPIRTEGGYRLYSDEDLERLRFIKRLKELGFSLEEIKELLE 68
HTH_MerR-like cd00592
Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators; Helix-turn-helix ...
 20-121 3.66e-12

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: 58.41  E-value: 3.66e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895173470  20 RVSQLAHNAGVSVHIVRDYLVRGLLRPvACTTGGYGVFDDAALQRLCFVRAAFEAGIGLDALARLCRalDAADGAQAAAQ 99
Cdd:cd00592     2 TIGEVAKLLGVSVRTLRYYEEKGLLPP-ERSENGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLD--ARDEELSLAAL 78

                          90       100
                  ....*....|....*....|..
gi 1895173470 100 LAVLRQLVERRRAALAHLDAQL 121
Cdd:cd00592    79 LALLDEKLAELEEKIARLEALL 100
SoxR COG0789
DNA-binding transcriptional regulator, MerR family [Transcription];
21-121 5.56e-12

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


Pssm-ID: 440552 [Multi-domain]  Cd Length: 100  Bit Score: 57.99  E-value: 5.56e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895173470  21 VSQLAHNAGVSVHIVRDYLVRGLLRPVACTTGGYGVFDDAALQRLCFVRAAFEAGIGLDALARLCRALDAADGAQAAAQL 100
Cdd:COG0789     1 IGEVARLTGVSVRTLRYYERIGLLPPPERTEGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLDDGEEEVRELLE 80

                          90       100
                  ....*....|....*....|.
gi 1895173470 101 AVLRQLvERRRAALAHLDAQL 121
Cdd:COG0789    81 EHLAEL-EAQIAELQALRAEL 100
MerR_1 pfam13411
MerR HTH family regulatory protein;
20-85 2.31e-11

MerR HTH family regulatory protein;


Pssm-ID: 463870  Cd Length: 66  Bit Score: 55.25  E-value: 2.31e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1895173470  20 RVSQLAHNAGVSVHIVRDYLVRGLLRPVAcTTGGYGVFDDAALQRLCFVRAAFEAGIGLDALARLC 85
Cdd:pfam13411   2 TISELARLLGVTPRTLRYWEREGLLPPPR-TERGRRYYTDEDVERLRLIKALLERGLSLKEIKELL 66
HTH_MerR-SF cd04761
Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; ...
 20-68 2.07e-10

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: 52.59  E-value: 2.07e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1895173470  20 RVSQLAHNAGVSVHIVRDYLVRGLLRPvACTTGGYGVFDDAALQRLCFV 68
Cdd:cd04761     2 TIGELAKLTGVSPSTLRYYERIGLLSP-ARTEGGYRLYSDADLERLRLI 49
HTH_MerR1 cd04783
Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator; Helix-turn-helix ...
 20-84 9.44e-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: 52.61  E-value: 9.44e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1895173470  20 RVSQLAHNAGVSVHIVRDYLVRGLLRPVACTTGGYGVFDDAALQRLCFVRAAFEAGIGLDALARL 84
Cdd:cd04783     2 TIGELAKAAGVNVETIRYYQRRGLLPEPPRPEGGYRRYPEETVTRLRFIKRAQELGFTLDEIAEL 66
HTH_HMRTR cd04770
Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators; ...
 20-123 2.26e-09

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: 51.79  E-value: 2.26e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895173470  20 RVSQLAHNAGVSVHIVRDYLVRGLLRPVACTTGGYGVFDDAALQRLCFVRAAFEAGIGLDALARLCRALDAADGAQAAAQ 99
Cdd:cd04770     2 KIGELAKAAGVSPDTIRYYERIGLLPPPQRSENGYRLYGEADLARLRFIRRAQALGFSLAEIRELLSLRDDGAAPCAEVR 81

                          90       100
                  ....*....|....*....|....*.
gi 1895173470 100 LAVLRQL--VERRRAALAHLDAQLAS 123
Cdd:cd04770    82 ALLEEKLaeVEAKIAELQALRAELAG 107
HTH_CadR-PbrR cd04784
Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; ...
 20-124 1.74e-08

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: 49.49  E-value: 1.74e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895173470  20 RVSQLAHNAGVSVHIVRDYLVRGLLRPVACTTGGYGVFDDAALQRLCFVRAAFEAGIGLDALARLCRALDAADGAQAAAQ 99
Cdd:cd04784     2 KIGELAKKTGCSVETIRYYEKEGLLPAPARSANNYRLYDEEHLERLLFIRRCRSLDMSLDEIRTLLQLQDDPEASCAEVN 81

                          90       100
                  ....*....|....*....|....*..
gi 1895173470 100 LAVLRQL--VERRRAALAHLDAQLASM 124
Cdd:cd04784    82 ALIDEHLahVRARIAELQALEKQLQAL 108
HTH_CadR-PbrR-like cd04785
Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators; ...
 23-124 1.72e-07

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: 46.77  E-value: 1.72e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895173470  23 QLAHNAGVSVHIVRDYLVRGLLRPVACTTGGYGVFDDAALQRLCFVRAAFEAGIGLDALARLCRALDAADGAQAAAQLAV 102
Cdd:cd04785     5 ELARRTGVNVETIRYYESIGLLPEPARTAGGYRLYGAAHVERLRFIRRARDLGFSLEEIRALLALSDRPDRSCAEADAIA 84

                          90       100
                  ....*....|....*....|....
gi 1895173470 103 LRQL--VERRRAALAHLDAQLASM 124
Cdd:cd04785    85 RAHLadVRARIADLRRLEAELKRM 108
HTH_HMRTR_unk cd04787
Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription ...
 20-71 3.45e-07

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: 46.14  E-value: 3.45e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1895173470  20 RVSQLAHNAGVSVHIVRDYLVRGLLRPVACTTGGYGVFDDAALQRLCFVRAA 71
Cdd:cd04787     2 KVKELANAAGVTPDTVRFYTRIGLLRPTRDPVNGYRLYSEKDLSRLRFILSA 53
zntR PRK09514
Zn(2+)-responsive transcriptional regulator;
20-84 6.06e-07

Zn(2+)-responsive transcriptional regulator;


Pssm-ID: 181924 [Multi-domain]  Cd Length: 140  Bit Score: 45.73  E-value: 6.06e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1895173470  20 RVSQLAHNAGVSVHIVRDYLVRGLLRPVACTTGGYGVFDDAALQRLCFVRAAFEAGIGLDALARL 84
Cdd:PRK09514    3 RIGELAKLAEVTPDTLRFYEKQGLMDPEVRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIREL 67
HTH_MerR-like_sg3 cd01282
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 20-126 1.59e-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 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: 43.75  E-value: 1.59e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895173470  20 RVSQLAHNAGVSVHIVRDYLVRGLLRPVAcTTGGYGVFDDAALQRLCFVRAAFEAGIGLDALARL--CRALDAADGAQAA 97
Cdd:cd01282     2 RIGELAARTGVSVRSLRYYEEQGLLVPER-SANGYRDYDEAAVDRVRQIRRLLAAGLTLEEIREFlpCLRGGEPTFRPCP 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1895173470  98 AQLAVLR---QLVERRRAALAHLDAQLASMPA 126
Cdd:cd01282    81 DLLAVLRrelARIDRQIADLTRSRDRLDAYLA 112
HTH_CueR cd01108
Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Helix-turn-helix ...
 21-84 4.69e-05

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: 40.24  E-value: 4.69e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1895173470  21 VSQLAHNAGVSVHIVRDYLVRGLLRPVACTTGGYGVFDDAALQRLCFVRAAFEAGIGLDALARL 84
Cdd:cd01108     3 IGEAAKLTGLSAKMIRYYEEIGLIPPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIREL 66
HTH_NolA-AlbR cd04788
Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR; ...
 19-84 1.88e-04

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: 38.13  E-value: 1.88e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1895173470  19 RRVSQLAHNAGVSVHIVRDYLVRGLLRPVACTTGGYGVFDDAALQRLCFVRAAFEAGIGLDALARL 84
Cdd:cd04788     1 WKIGELARRTGLSVRTLHHYDHIGLLSPSQRTEGGHRLYDRADIRRLHQIIALRRLGFSLREIGRA 66
HTH_TipAL-Mta cd01106
Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA; ...
 21-65 2.01e-04

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: 38.24  E-value: 2.01e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1895173470  21 VSQLAHNAGVSVHIVRDYLVRGLLRPVACTTGGYGVFDDAALQRL 65
Cdd:cd01106     3 VGEVAKLTGVSVRTLHYYDEIGLLKPSRRTENGYRLYTEEDLERL 47
HTH_Cfa-like_unk cd04790
Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators; Putative ...
 20-84 1.13e-03

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: 37.03  E-value: 1.13e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1895173470  20 RVSQLAHNAGVSVHIVRDYLVRGLLRPVACTTGGYGVFDDAALQRL---CFVRaafEAGIGLDALARL 84
Cdd:cd04790     3 TISQLARQFGLSRSTLLYYERIGLLSPSARSESNYRLYGERDLERLeqiCAYR---SAGVSLEDIRSL 67
HTH_MerR-like_sg4 cd04779
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 20-68 2.05e-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 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: 35.94  E-value: 2.05e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1895173470  20 RVSQLAHNAGVSVHIVRDYLVRGLLRPVAcTTGGYGVFDDAALQRLCFV 68
Cdd:cd04779     2 RIGQLAHLAGVSKRTIDYYTNLGLLTPER-SDSNYRYYDETALDRLQLI 49
HTH_YyaN cd01109
Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB; ...
 29-86 2.72e-03

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: 35.13  E-value: 2.72e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1895173470  29 GVSVHIVRDYLVRGLLRPVACTTGGYGVFDDAALQRLCFVRAAFEAGIGLDAL---ARLCR 86
Cdd:cd01109    11 GLSADTLRYYEKEGLLPPVKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIkeyAELRR 71
PRK13752 PRK13752
mercuric resistance operon transcriptional regulator MerR;
24-86 2.76e-03

mercuric resistance operon transcriptional regulator MerR;


Pssm-ID: 184302  Cd Length: 144  Bit Score: 35.65  E-value: 2.76e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1895173470  24 LAHNAGVSVHIVRDYLVRGLLRPVACTTGGYGVFDDAALQRLCFVRAAFEAGIGLDALARLCR 86
Cdd:PRK13752   13 FAKAAGVNVETIRFYQRKGLLPEPDKPYGSIRRYGEADVTRVRFVKSAQRLGFSLDEIAELLR 75
HTH_SoxR cd01110
Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator; Helix-turn-helix (HTH) ...
 21-84 3.09e-03

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: 35.25  E-value: 3.09e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1895173470  21 VSQLAHNAGVSVHIVRDYLVRGLLRPVAcTTGGYGVFDDAALQRLCFVRAAFEAGIGLD----ALARL 84
Cdd:cd01110     4 VGEVAKRSGVAVSALHFYEQKGLIASWR-NAGNQRRYPRDVLRRIAFIKVAQRLGLSLAeiaeALATL 70
HTH_TioE_rpt1 cd04772
First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE; Putative ...
 20-71 4.89e-03

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: 34.29  E-value: 4.89e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1895173470  20 RVSQLAHNAGVSVHIVRDYLVRGLLRPVACTTGGYGVFDDAALQRLCFVRAA 71
Cdd:cd04772     2 RTVDLARAIGLSPQTVRNYESLGLIPPAERTANGYRIYTDKHIAALRAYRAL 53
 
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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