NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1469803557|gb|RGT62438|]
View 

helix-turn-helix domain-containing protein [Coprobacillus sp. AF18-40]

Protein Classification

LexA family protein( domain architecture ID 11449429)

LexA family protein may function as a transcriptional regulator involved in the repression of one or more genes involved in the response to DNA damage (SOS response), including recA and lexA and/or may contain a S24 peptidase domain such as in the translesion error-prone DNA polymerase V autoproteolytic subunit

Gene Ontology:  GO:0003677|GO:0045892
PubMed:  10679470|10908318

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
LexA COG1974
SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase) [Transcription, ...
 4-203 3.11e-40

SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase) [Transcription, Signal transduction mechanisms];


:

Pssm-ID: 441577 [Multi-domain]  Cd Length: 199  Bit Score: 135.81  E-value: 3.11e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469803557   4 ERIKKLRKEKGL--TQQQLGEMLGVQKSAIAKYengrvpnlkketISRLAEI--FNVTPNYLLGIDepSLHGHSHNIDIP 79
Cdd:COG1974    13 DFIKEYIRERGYppSQREIAEALGLSSSAVHRH------------LKALEKKgyLRRDPGKSRAIE--LLPASPEVVGLP 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469803557  80 LYSDVCCGDGIFVEDNIEEYISLPESLLSSRKDYFCQYADGDSMIDENIQSGDLIIFEKTQQLNNGDVGCFGIEDNiATC 159
Cdd:COG1974    79 LLGRVAAGFPIPAEENIEEYLDLPEELVKNPGATFALRVKGDSMIDAGILDGDLVIVDRQLEAENGDIVVALIDGE-ATV 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1469803557 160 KKYFNDSKQhcIILQPANDKYSPIIINEynyHEFKIIGKLALVI 203
Cdd:COG1974   158 KRLYKEGGR--VRLQPENPAYPPIIIEG---DDVEILGVVVGVI 196
 
Name Accession Description Interval E-value
LexA COG1974
SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase) [Transcription, ...
 4-203 3.11e-40

SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase) [Transcription, Signal transduction mechanisms];


Pssm-ID: 441577 [Multi-domain]  Cd Length: 199  Bit Score: 135.81  E-value: 3.11e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469803557   4 ERIKKLRKEKGL--TQQQLGEMLGVQKSAIAKYengrvpnlkketISRLAEI--FNVTPNYLLGIDepSLHGHSHNIDIP 79
Cdd:COG1974    13 DFIKEYIRERGYppSQREIAEALGLSSSAVHRH------------LKALEKKgyLRRDPGKSRAIE--LLPASPEVVGLP 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469803557  80 LYSDVCCGDGIFVEDNIEEYISLPESLLSSRKDYFCQYADGDSMIDENIQSGDLIIFEKTQQLNNGDVGCFGIEDNiATC 159
Cdd:COG1974    79 LLGRVAAGFPIPAEENIEEYLDLPEELVKNPGATFALRVKGDSMIDAGILDGDLVIVDRQLEAENGDIVVALIDGE-ATV 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1469803557 160 KKYFNDSKQhcIILQPANDKYSPIIINEynyHEFKIIGKLALVI 203
Cdd:COG1974   158 KRLYKEGGR--VRLQPENPAYPPIIIEG---DDVEILGVVVGVI 196
Peptidase_S24 pfam00717
Peptidase S24-like;
79-199 1.19e-25

Peptidase S24-like;


Pssm-ID: 425835  Cd Length: 116  Bit Score: 95.73  E-value: 1.19e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469803557  79 PLYSDVCCGDGIFVEDNIEEYISLPESLLSSRKDYFCQYADGDSMIDEnIQSGDLIIFEKTQQLNNGDVGCFgIEDNIAT 158
Cdd:pfam00717   1 PLIGRVAAGAPILAEEEIEGYLPLPESLLSPPGNLFALRVKGDSMEPG-IPDGDLVLVDPSREARNGDIVVA-RLDGEAT 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1469803557 159 CKKYFNDSKQhcIILQPANDKYSPIIINEynYHEFKIIGKL 199
Cdd:pfam00717  79 VKRLYRDGGG--IRLISLNPEYPPIELPA--EDDVEIIGRV 115
lexA TIGR00498
SOS regulatory protein LexA; LexA acts as a homodimer to repress a number of genes involved in ...
 78-205 2.05e-22

SOS regulatory protein LexA; LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA. [DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 273106 [Multi-domain]  Cd Length: 199  Bit Score: 89.77  E-value: 2.05e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469803557  78 IPLYSDVCCGDGIFVEDNIEEYISLPESLLSSRKDYFCQYADGDSMIDENIQSGDLIIFEKTQQLNNGDVGCFGIEDNIa 157
Cdd:TIGR00498  76 VPLIGRVAAGEPILAEQHIEEYFPIDFSLLKKPSAVFLLKVMGDSMVDAGICDGDLLIVRSQKDARNGEIVAAMIDGEV- 154

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1469803557 158 TCKKYFNDSKQhcIILQPANDKYSPIIINEYNyheFKIIGKLALVISK 205
Cdd:TIGR00498 155 TVKRFYKDGTK--VELKPENPEFDPIVLNAED---VTILGKVVGVIRN 197
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 3-61 5.48e-19

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.


Pssm-ID: 238045 [Multi-domain]  Cd Length: 58  Bit Score: 76.82  E-value: 5.48e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1469803557   3 GERIKKLRKEKGLTQQQLGEMLGVQKSAIAKYENGRVpNLKKETISRLAEIFNVTPNYL 61
Cdd:cd00093     1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKR-NPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
5-61 8.81e-17

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 71.01  E-value: 8.81e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1469803557    5 RIKKLRKEKGLTQQQLGEMLGVQKSAIAKYENGRVpNLKKETISRLAEIFNVTPNYL 61
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKR-KPSLETLKKLAKALGVSLDEL 56
PRK10276 PRK10276
translesion error-prone DNA polymerase V autoproteolytic subunit;
74-185 5.97e-12

translesion error-prone DNA polymerase V autoproteolytic subunit;


Pssm-ID: 182350  Cd Length: 139  Bit Score: 60.58  E-value: 5.97e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469803557  74 HNIDIPLYSD-VCCGDGIFVEDNIEEYISLPESLLS-SRKDYFCQyADGDSMIDENIQSGDLIIFEKTQQLNNGDVGCFG 151
Cdd:PRK10276   11 EIVTFPLFSDlVQCGFPSPAADYVEQRIDLNELLIQhPSATYFVK-ASGDSMIDAGISDGDLLIVDSAITASHGDIVIAA 89

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1469803557 152 IEDNIaTCKKYfndSKQHCIILQPANDKYSPIII 185
Cdd:PRK10276   90 VDGEF-TVKKL---QLRPTVQLIPMNSAYSPITI 119
 
Name Accession Description Interval E-value
LexA COG1974
SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase) [Transcription, ...
 4-203 3.11e-40

SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase) [Transcription, Signal transduction mechanisms];


Pssm-ID: 441577 [Multi-domain]  Cd Length: 199  Bit Score: 135.81  E-value: 3.11e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469803557   4 ERIKKLRKEKGL--TQQQLGEMLGVQKSAIAKYengrvpnlkketISRLAEI--FNVTPNYLLGIDepSLHGHSHNIDIP 79
Cdd:COG1974    13 DFIKEYIRERGYppSQREIAEALGLSSSAVHRH------------LKALEKKgyLRRDPGKSRAIE--LLPASPEVVGLP 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469803557  80 LYSDVCCGDGIFVEDNIEEYISLPESLLSSRKDYFCQYADGDSMIDENIQSGDLIIFEKTQQLNNGDVGCFGIEDNiATC 159
Cdd:COG1974    79 LLGRVAAGFPIPAEENIEEYLDLPEELVKNPGATFALRVKGDSMIDAGILDGDLVIVDRQLEAENGDIVVALIDGE-ATV 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1469803557 160 KKYFNDSKQhcIILQPANDKYSPIIINEynyHEFKIIGKLALVI 203
Cdd:COG1974   158 KRLYKEGGR--VRLQPENPAYPPIIIEG---DDVEILGVVVGVI 196
Peptidase_S24 pfam00717
Peptidase S24-like;
79-199 1.19e-25

Peptidase S24-like;


Pssm-ID: 425835  Cd Length: 116  Bit Score: 95.73  E-value: 1.19e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469803557  79 PLYSDVCCGDGIFVEDNIEEYISLPESLLSSRKDYFCQYADGDSMIDEnIQSGDLIIFEKTQQLNNGDVGCFgIEDNIAT 158
Cdd:pfam00717   1 PLIGRVAAGAPILAEEEIEGYLPLPESLLSPPGNLFALRVKGDSMEPG-IPDGDLVLVDPSREARNGDIVVA-RLDGEAT 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1469803557 159 CKKYFNDSKQhcIILQPANDKYSPIIINEynYHEFKIIGKL 199
Cdd:pfam00717  79 VKRLYRDGGG--IRLISLNPEYPPIELPA--EDDVEIIGRV 115
lexA TIGR00498
SOS regulatory protein LexA; LexA acts as a homodimer to repress a number of genes involved in ...
 78-205 2.05e-22

SOS regulatory protein LexA; LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA. [DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 273106 [Multi-domain]  Cd Length: 199  Bit Score: 89.77  E-value: 2.05e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469803557  78 IPLYSDVCCGDGIFVEDNIEEYISLPESLLSSRKDYFCQYADGDSMIDENIQSGDLIIFEKTQQLNNGDVGCFGIEDNIa 157
Cdd:TIGR00498  76 VPLIGRVAAGEPILAEQHIEEYFPIDFSLLKKPSAVFLLKVMGDSMVDAGICDGDLLIVRSQKDARNGEIVAAMIDGEV- 154

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1469803557 158 TCKKYFNDSKQhcIILQPANDKYSPIIINEYNyheFKIIGKLALVISK 205
Cdd:TIGR00498 155 TVKRFYKDGTK--VELKPENPEFDPIVLNAED---VTILGKVVGVIRN 197
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
3-69 5.23e-21

Transcriptional regulator, contains XRE-family HTH domain [Transcription];


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 82.74  E-value: 5.23e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1469803557   3 GERIKKLRKEKGLTQQQLGEMLGVQKSAIAKYENGRVpNLKKETISRLAEIFNVTPNYLLGIDEPSL 69
Cdd:COG1396     9 GERLRELRKARGLTQEELAERLGVSRSTISRIERGRR-NPSLETLLKLAKALGVSLDELLGGADEEL 74
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 3-61 5.48e-19

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.


Pssm-ID: 238045 [Multi-domain]  Cd Length: 58  Bit Score: 76.82  E-value: 5.48e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1469803557   3 GERIKKLRKEKGLTQQQLGEMLGVQKSAIAKYENGRVpNLKKETISRLAEIFNVTPNYL 61
Cdd:cd00093     1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKR-NPSLETLEKLAKALGVSLDEL 58
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-66 2.28e-18

DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 75.65  E-value: 2.28e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1469803557   1 MTGERIKKLRKEKGLTQQQLGEMLGVQKSAIAKYENGR-VPNLkkETISRLAEIFNVTPNYLLGIDE 66
Cdd:COG1476     4 KLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKyNPSL--ELALKIARALGVSLEELFSLEE 68
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
5-61 8.81e-17

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 71.01  E-value: 8.81e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1469803557    5 RIKKLRKEKGLTQQQLGEMLGVQKSAIAKYENGRVpNLKKETISRLAEIFNVTPNYL 61
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKR-KPSLETLKKLAKALGVSLDEL 56
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 3-57 5.25e-15

Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and HTH domains [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441418 [Multi-domain]  Cd Length: 70  Bit Score: 66.89  E-value: 5.25e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1469803557   3 GERIKKLRKEKGLTQQQLGEMLGVQKSAIAKYENGR-VPNLkkETISRLAEIFNVT 57
Cdd:COG1813    14 GERIREAREARGLSQEELAEKLGVSESTIRRIERGEaTPSL--DTLRKLEKALGIS 67
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 6-61 1.09e-14

Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and CI. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteriztic of the whole family.


Pssm-ID: 460181 [Multi-domain]  Cd Length: 55  Bit Score: 65.64  E-value: 1.09e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1469803557   6 IKKLRKEKGLTQQQLGEMLGVQKSAIAKYENGRVpNLKKETISRLAEIFNVTPNYL 61
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKR-EPSLETLKKLAEALGVSLDEL 55
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 3-62 1.25e-14

Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. This family contains many example antitoxins from bacterial toxin-antitoxin systems. These antitoxins are likely to be DNA-binding domains.


Pssm-ID: 463728 [Multi-domain]  Cd Length: 64  Bit Score: 65.77  E-value: 1.25e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469803557   3 GERIKKLRKEKGLTQQQLGEMLGVQKSAIAKYENGRVpNLKKETISRLAEIFNVTPNYLL 62
Cdd:pfam12844   1 GERLRKAREERGLTQEELAERLGISRSQLSAIENGKS-VPPAETLYKIAELLGVPANWLL 59
COG2932 COG2932
Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: ...
 78-198 1.59e-14

Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: prophages, transposons];


Pssm-ID: 442176  Cd Length: 121  Bit Score: 66.91  E-value: 1.59e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469803557  78 IPLYS-DVCCGDGIFVE-DNIEEYISLPESllsSRKDYFCQYADGDSMIDEnIQSGDLIIFEKTQ-QLNNGDVGCFGIED 154
Cdd:COG2932     1 VPLYDgEASAGGGAFNEvEEPVDKLEFPGL---PPDNLFAVRVSGDSMEPT-IRDGDIVLVDPSDtEIRDGGIYVVRTDG 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1469803557 155 NIaTCKKYFNDsKQHCIILQPANDKYSPIIINEYNYHEFKIIGK 198
Cdd:COG2932    77 EL-LVKRLQRR-PDGKLRLISDNPAYPPIEIPPEDADEIEIIGR 118
S24_LexA-like cd06529
Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of ...
 114-197 1.10e-13

Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The LexA-like proteins contain two-domains: an N-terminal DNA binding domain and a C-terminal domain (CTD) that provides LexA dimerization as well as cleavage activity. They undergo autolysis, cleaving at an Ala-Gly or a Cys-Gly bond, separating the DNA-binding domain from the rest of the protein. In the presence of single-stranded DNA, the LexA, UmuD and MucA proteins interact with RecA, activating self cleavage, thus either derepressing transcription in the case of LexA or activating the lesion-bypass polymerase in the case of UmuD and MucA. The LexA proteins are serine proteases that carry out catalysis using a serine/lysine dyad instead of the prototypical serine/histidine/aspartic acid triad found in most serine proteases. LexA sequence homologs are found in almost all of the bacterial genomes sequenced to date, covering a large number of phyla, suggesting both, an ancient origin and a widespread distribution of lexA and the SOS response.


Pssm-ID: 119397 [Multi-domain]  Cd Length: 81  Bit Score: 63.73  E-value: 1.10e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469803557 114 FCQYADGDSMIDEnIQSGDLIIFEKTQQLNNGDVGCFGIeDNIATCKKYFNDSKQHcIILQPANDKYSPIIINEYNYHEF 193
Cdd:cd06529     1 FALRVKGDSMEPT-IPDGDLVLVDPSDTPRDGDIVVARL-DGELTVKRLQRRGGGR-LRLISDNPAYPPIEIDEEELEIV 77


                  ....
gi 1469803557 194 KIIG 197
Cdd:cd06529    78 GVVG 81
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 3-58 3.76e-12

Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.


Pssm-ID: 433309 [Multi-domain]  Cd Length: 64  Bit Score: 59.08  E-value: 3.76e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1469803557   3 GERIKKLRKEKGLTQQQLGEMLGVQKSAIAKYENGRVPNLKKETISRLAEIFNVTP 58
Cdd:pfam13560   3 GARLRRLRERAGLSQEALARRLGVSRSTLSRLETGRRGRPSPAVVERLARALGVDG 58
PRK10276 PRK10276
translesion error-prone DNA polymerase V autoproteolytic subunit;
74-185 5.97e-12

translesion error-prone DNA polymerase V autoproteolytic subunit;


Pssm-ID: 182350  Cd Length: 139  Bit Score: 60.58  E-value: 5.97e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469803557  74 HNIDIPLYSD-VCCGDGIFVEDNIEEYISLPESLLS-SRKDYFCQyADGDSMIDENIQSGDLIIFEKTQQLNNGDVGCFG 151
Cdd:PRK10276   11 EIVTFPLFSDlVQCGFPSPAADYVEQRIDLNELLIQhPSATYFVK-ASGDSMIDAGISDGDLLIVDSAITASHGDIVIAA 89

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1469803557 152 IEDNIaTCKKYfndSKQHCIILQPANDKYSPIII 185
Cdd:PRK10276   90 VDGEF-TVKKL---QLRPTVQLIPMNSAYSPITI 119
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 3-71 1.21e-10

Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain CBS pair) [Transcription];


Pssm-ID: 442838 [Multi-domain]  Cd Length: 95  Bit Score: 56.18  E-value: 1.21e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469803557   3 GERIKKLRKEKGLTQQQLGEMLGVQKSAIAKYENGRV-PNLkkETISRLAEIFNVTPNYLLGIDEPSLHG 71
Cdd:COG3620    19 GEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRdPTV--STLEKIAEALGKELSAVLVVDDGKLVG 86
Peptidase_S24_S26 cd06462
The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal ...
 114-198 3.04e-10

The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the transport of proteins across membranes in all living organisms. All members in this superfamily are unique serine proteases that carry out catalysis using a serine/lysine dyad instead of the prototypical serine/histidine/aspartic acid triad found in most serine proteases.


Pssm-ID: 119396 [Multi-domain]  Cd Length: 84  Bit Score: 54.58  E-value: 3.04e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469803557 114 FCQYADGDSMIDEnIQSGDLIIFEKTQ-QLNNGDVGCFGIEDNIATCKKYFNDSKQHCIILQPANDKYSPIIIneYNYHE 192
Cdd:cd06462     1 FALRVEGDSMEPT-IPDGDLVLVDKSSyEPKRGDIVVFRLPGGELTVKRVIGLPGEGHYFLLGDNPNSPDSRI--DGPPE 77


                  ....*.
gi 1469803557 193 FKIIGK 198
Cdd:cd06462    78 LDIVGV 83
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 1-40 1.09e-09

putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.


Pssm-ID: 274805 [Multi-domain]  Cd Length: 127  Bit Score: 54.17  E-value: 1.09e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1469803557   1 MTGERIKKLRKEKGLTQQQLGEMLGVQKSAIAKYENGRVP 40
Cdd:TIGR03830  65 LTGPEIRRIRKKLGLSQREAAELLGGGVNAFSRYERGEVR 104
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
1-39 1.22e-09

DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 52.63  E-value: 1.22e-09
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1469803557   1 MTGERIKKLRKEKGLTQQQLGEMLGVQKSAIAKYENGRV 39
Cdd:COG2944     6 LTPEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRR 44
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 3-62 1.71e-08

Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 441035 [Multi-domain]  Cd Length: 71  Bit Score: 49.42  E-value: 1.71e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1469803557   3 GERIKKLRKEKGLTQQQLGEMLGVQKSAIAKYENGRVPNL-----KKETISRLAEIFNVTPNYLL 62
Cdd:COG1426     7 GELLRQAREAKGLSLEDVAERTKISVSYLEAIEEGDFDALpgpvyVRGFLRSYARALGLDPEELL 71
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 1-105 2.40e-08

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 51.01  E-value: 2.40e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469803557   1 MTGERIKKLRKEKGLTQQQLGEMLGVQKSAIAKYENGRV-PnlKKETISRLAEIFNVTPNYLLGIDEPSLHGHSHNIDIP 79
Cdd:PRK09706    5 TLGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETeP--TGKNLFALAKALQCSPTWLLFGDEDKQPTPPVPLNQP 82

                          90       100
                  ....*....|....*....|....*....
gi 1469803557  80 LYSDvccgdgifvEDN---IEEYISLPES 105
Cdd:PRK09706   83 VELS---------EDQkelLELFDALPES 102
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 3-64 1.28e-07

Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense mechanisms];


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 47.50  E-value: 1.28e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1469803557   3 GERIK-KLRKEKGLTQQQLGEMLGVQKSAIAKYENGRVPnLKKETISRLAEIFNVTPNYLLGI 64
Cdd:COG3093    10 GEILReEFLEPLGLSQTELAKALGVSRQRISEILNGKRA-ITADTALRLARAFGTSAEFWLNL 71
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 3-57 4.53e-07

transcriptional regulator, y4mF family; Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems. [Regulatory functions, DNA interactions]


Pssm-ID: 213767 [Multi-domain]  Cd Length: 58  Bit Score: 45.34  E-value: 4.53e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1469803557   3 GERIKKLRKEKGLTQQQLGEMLGVQKSAIAKYENGRvPNLKKETISRLAEIFNVT 57
Cdd:TIGR03070   4 GILVRARRKALGLTQADLADLAGVGLRFIRDLENGK-PTVRLDKVLRVLDALGLE 57
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 5-62 7.11e-07

Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to DNA.


Pssm-ID: 433211 [Multi-domain]  Cd Length: 63  Bit Score: 44.84  E-value: 7.11e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1469803557   5 RIKKLRKEKGLTQQQLGEMLGVQKSAIAKYENGRVPNLKKETISRLAEIFNVTPNYLL 62
Cdd:pfam13443   1 KLRKLMADRGISKSDLARATGISRATLSRLRKGKPKRVSLDTLDKICDALGCQPGDLL 58
PRK13355 PRK13355
bifunctional HTH-domain containing protein/aminotransferase; Provisional
 3-68 1.53e-06

bifunctional HTH-domain containing protein/aminotransferase; Provisional


Pssm-ID: 237361 [Multi-domain]  Cd Length: 517  Bit Score: 47.81  E-value: 1.53e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1469803557   3 GERIKKLRKEKGLTQQQLGEMLG-----VQKSAIAKYENGR-VPnlKKETISRLAEIFNVTPNYLLGIDEPS 68
Cdd:PRK13355    5 AERLKQAMKARGLKQEDLVHAAEargvkLGKSHISQYVSGKtGP--RRDVLPFLAAILGVSEDWLLGGESPA 74
COG1395 COG1395
Predicted transcriptional regulator [Transcription];
3-56 1.73e-05

Predicted transcriptional regulator [Transcription];


Pssm-ID: 441005 [Multi-domain]  Cd Length: 313  Bit Score: 44.44  E-value: 1.73e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1469803557   3 GERIKKLRKEKGLTQQQLGEMLGVQKSAIAKYENGRV-PNLkkETISRLAEIFNV 56
Cdd:COG1395   129 GEKLRELREERGLSLGELASELGVSRRTISKYERGEMdASI--EVALKLEEILGE 181
HTH_37 pfam13744
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain.
 5-55 2.89e-05

Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain.


Pssm-ID: 433449 [Multi-domain]  Cd Length: 80  Bit Score: 41.06  E-value: 2.89e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1469803557   5 RIKKLRKEKGLTQQQLGEMLGVQKSAIAKYENGRVPNLkkeTISRLAEIFN 55
Cdd:pfam13744  22 AIARLIEGRGLSQQEAAALLGIAQPKVSALLKGKLSRF---SLDKLLDFLT 69
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
1-56 8.63e-05

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 41.70  E-value: 8.63e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1469803557   1 MTGERIKKLRKEKGLTQQQLGEMLGVQKSAIAKYENGRVpnlkKETISRLAEIFNV 56
Cdd:PRK09943    7 APGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKV----SPAISTLQKLLKV 58
PRK04140 PRK04140
transcriptional regulator;
3-56 1.17e-04

transcriptional regulator;


Pssm-ID: 235224 [Multi-domain]  Cd Length: 317  Bit Score: 41.77  E-value: 1.17e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1469803557   3 GERIKKLRKEKGLTQQQLGEMLGVQKSAIAKYENGRVpNLKKETISRLAEIFNV 56
Cdd:PRK04140  128 GDVLREAREELGLSLGELASELGVSRRTISKYENGGM-NASIEVAIKLEEILDV 180
PHA01976 PHA01976
helix-turn-helix protein
 5-63 3.14e-04

helix-turn-helix protein


Pssm-ID: 177330 [Multi-domain]  Cd Length: 67  Bit Score: 38.01  E-value: 3.14e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469803557   5 RIKKLRKEKGLTQQQLGEMLGVQKSAIAKYENG-RVPNLKkeTISRLAEIFNVTPNYLLG 63
Cdd:PHA01976    6 QLIKARNARAWSAPELSRRAGVRHSLIYDFEADkRLPNLK--TLLRLADALGVTLDWLCG 63
MqsA_antitoxin pfam15731
Antitoxin component of bacterial toxin-antitoxin system, MqsA; MqsA_antitoxin is a family of ...
 3-39 6.12e-04

Antitoxin component of bacterial toxin-antitoxin system, MqsA; MqsA_antitoxin is a family of prokaryotic proteins that act as antidotes to the mRNA interferase MqsR. It has a zinc-binding at the very N-terminus indicating its DNA-binding capacity. MqsR is the gene most highly upregulated in E. Colo MqsR_toxin is a family of bacterial toxins that act as an mRNA interferase. MqsR is the gene most highly upregulated in E. coli persister cells and it plays an essential role in biofilm regulation and cell signalling. It forms part of a bacterial toxin-antitoxin TA system, and as expected for a TA system, the expression of the MqsR toxin leads to growth arrest, while co-expression with its antitoxin, MqsA, rescues the growth arrest phenotype. In addition, MqsR associates with MqsA to form a tight, non-toxic complex and both MqsA alone and the MqsR:MqsA2:MqsR complex bind and regulate the mqsR promoter. The structure of MqsR shows that is is a member of the RelE/YoeB family of bacterial RNases that are structurally and functionally characterized bacterial toxins.


Pssm-ID: 292359 [Multi-domain]  Cd Length: 131  Bit Score: 38.51  E-value: 6.12e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1469803557   3 GERIKKLRKEKGLTQQQLGEMLGVQKSAIAKYENGRV 39
Cdd:pfam15731  71 PAFIARVRKKLGLDQREAAEIFGGGVNAFSRYENGKT 107
AF0184 COG2522
Predicted transcriptional regulator, contains XRE-type HTH domain [Transcription];
6-52 9.27e-04

Predicted transcriptional regulator, contains XRE-type HTH domain [Transcription];


Pssm-ID: 442012 [Multi-domain]  Cd Length: 99  Bit Score: 37.11  E-value: 9.27e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1469803557   6 IKKLRKEkGLTQQQLGEMLGVQKSAIAKYENGRVPNLK--------KETISRLAE 52
Cdd:COG2522    21 AKELVER-GLSQSEIAKLLGITQAAVSQYLSGKRGASEriefdeeiKELIEELAE 74
COG1709 COG1709
Predicted transcriptional regulator,contains XRE-type HTH domain [Transcription];
3-38 9.38e-04

Predicted transcriptional regulator,contains XRE-type HTH domain [Transcription];


Pssm-ID: 441315  Cd Length: 234  Bit Score: 39.00  E-value: 9.38e-04
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1469803557   3 GERIKKLRKEKGLTQQQLGEMLGVQKSAIAKYENGR 38
Cdd:COG1709    24 GETLRKWREDFGISQTELARELGVSPSVISDYESGR 59
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH