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Conserved domains on  [gi|446722829|ref|WP_000800142|]
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LexA family transcriptional regulator [Escherichia coli]

Protein Classification

XRE family transcriptional regulator( domain architecture ID 11443577)

XRE (Xenobiotic Response Element) family transcriptional regulator is a helix-turn-helix domain-containing transcriptional regulator with a peptidase S24 LexA-like domain

Gene Ontology:  GO:0003677
PubMed:  10473770|15808743|10556324

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
COG2932 COG2932
Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: ...
 91-218 7.25e-30

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


:

Pssm-ID: 442176  Cd Length: 121  Bit Score: 107.35  E-value: 7.25e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446722829  91 VLDVEFSCGDGTHVRGDliDVVRSIELDPEYARRLvgnRAFKnieignARGDSMAPTISPGDLLFLDKTVTYFDGDGIYA 170
Cdd:COG2932    3 LYDGEASAGGGAFNEVE--EPVDKLEFPGLPPDNL---FAVR------VSGDSMEPTIRDGDIVLVDPSDTEIRDGGIYV 71

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 446722829 171 FCFDGECYIKRLQKI-GSKIMVLSDNPNYQPWSIEKEGMALLYIQSKVI 218
Cdd:COG2932   72 VRTDGELLVKRLQRRpDGKLRLISDNPAYPPIEIPPEDADEIEIIGRVV 120
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
9-73 1.11e-10

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 56.16  E-value: 1.11e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446722829   9 NRIAMMLKTKGWSQAELARKLGVSAQSVQYWTTGKTFPRSDKLAQLSVISGYPQSWFLGEDTSST 73
Cdd:COG1396   10 ERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEEL 74
 
Name Accession Description Interval E-value
COG2932 COG2932
Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: ...
 91-218 7.25e-30

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


Pssm-ID: 442176  Cd Length: 121  Bit Score: 107.35  E-value: 7.25e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446722829  91 VLDVEFSCGDGTHVRGDliDVVRSIELDPEYARRLvgnRAFKnieignARGDSMAPTISPGDLLFLDKTVTYFDGDGIYA 170
Cdd:COG2932    3 LYDGEASAGGGAFNEVE--EPVDKLEFPGLPPDNL---FAVR------VSGDSMEPTIRDGDIVLVDPSDTEIRDGGIYV 71

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 446722829 171 FCFDGECYIKRLQKI-GSKIMVLSDNPNYQPWSIEKEGMALLYIQSKVI 218
Cdd:COG2932   72 VRTDGELLVKRLQRRpDGKLRLISDNPAYPPIEIPPEDADEIEIIGRVV 120
S24_LexA-like cd06529
Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of ...
 139-213 1.60e-22

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: 87.23  E-value: 1.60e-22
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446722829 139 ARGDSMAPTISPGDLLFLDKTVTYFDGDgIYAFCFDGECYIKRLQKIG-SKIMVLSDNPNYQPWSIEKEGMALLYI 213
Cdd:cd06529    5 VKGDSMEPTIPDGDLVLVDPSDTPRDGD-IVVARLDGELTVKRLQRRGgGRLRLISDNPAYPPIEIDEEELEIVGV 79
Peptidase_S24 pfam00717
Peptidase S24-like;
139-218 1.44e-19

Peptidase S24-like;


Pssm-ID: 425835  Cd Length: 116  Bit Score: 80.71  E-value: 1.44e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446722829  139 ARGDSMAPTISPGDLLFLDKTVTYFDGDgIYAFCFDGECYIKRLQKIGSKIMVLSDNPNYQPWSIEKEGMalLYIQSKVI 218
Cdd:pfam00717  40 VKGDSMEPGIPDGDLVLVDPSREARNGD-IVVARLDGEATVKRLYRDGGGIRLISLNPEYPPIELPAEDD--VEIIGRVV 116
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
9-73 1.11e-10

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 56.16  E-value: 1.11e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446722829   9 NRIAMMLKTKGWSQAELARKLGVSAQSVQYWTTGKTFPRSDKLAQLSVISGYPQSWFLGEDTSST 73
Cdd:COG1396   10 ERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEEL 74
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 9-55 6.22e-09

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: 50.63  E-value: 6.22e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 446722829   9 NRIAMMLKTKGWSQAELARKLGVSAQSVQYWTTGKTFPRSDKLAQLS 55
Cdd:cd00093    2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLA 48
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
10-55 1.17e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 49.82  E-value: 1.17e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 446722829    10 RIAMMLKTKGWSQAELARKLGVSAQSVQYWTTGKTFPRSDKLAQLS 55
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLA 46
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 11-55 1.15e-06

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: 44.45  E-value: 1.15e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 446722829   11 IAMMLKTKGWSQAELARKLGVSAQSVQYWTTGKTFPRSDKLAQLS 55
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLA 45
PRK13355 PRK13355
bifunctional HTH-domain containing protein/aminotransferase; Provisional
 10-87 3.84e-06

bifunctional HTH-domain containing protein/aminotransferase; Provisional


Pssm-ID: 237361 [Multi-domain]  Cd Length: 517  Bit Score: 47.04  E-value: 3.84e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446722829  10 RIAMMLKTKGWSQAELAR-------KLGVSAQSvqYWTTGKTFPRSDKLAQLSVISGYPQSWFLGE--------DTSSTL 74
Cdd:PRK13355   7 RLKQAMKARGLKQEDLVHaaeargvKLGKSHIS--QYVSGKTGPRRDVLPFLAAILGVSEDWLLGGespadqesDASAVV 84

                         90
                 ....*....|...
gi 446722829  75 SSAEKHHTREDSV 87
Cdd:PRK13355  85 ESAPNSHLADPSA 97
PRK10276 PRK10276
translesion error-prone DNA polymerase V autoproteolytic subunit;
139-206 8.04e-06

translesion error-prone DNA polymerase V autoproteolytic subunit;


Pssm-ID: 182350  Cd Length: 139  Bit Score: 44.02  E-value: 8.04e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446722829 139 ARGDSMAPT-ISPGDLLFLDKTVTYFDGDGIYAfCFDGECYIKRLQKIGSkIMVLSDNPNYQPWSIEKE 206
Cdd:PRK10276  56 ASGDSMIDAgISDGDLLIVDSAITASHGDIVIA-AVDGEFTVKKLQLRPT-VQLIPMNSAYSPITISSE 122
lexA TIGR00498
SOS regulatory protein LexA; LexA acts as a homodimer to repress a number of genes involved in ...
 141-200 1.07e-03

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: 38.93  E-value: 1.07e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446722829  141 GDSMAPT-ISPGDLLFLDKTVTYFDGDgIYAFCFDGECYIKRLQKIGSKIMVLSDNPNYQP 200
Cdd:TIGR00498 118 GDSMVDAgICDGDLLIVRSQKDARNGE-IVAAMIDGEVTVKRFYKDGTKVELKPENPEFDP 177
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 11-54 4.01e-03

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: 34.56  E-value: 4.01e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 446722829   11 IAMMLKTK----GWSQAELARKLGVSAQSVQYWTTGKTFPRSDKLAQL 54
Cdd:TIGR03070   3 IGILVRARrkalGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRV 50
 
Name Accession Description Interval E-value
COG2932 COG2932
Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: ...
 91-218 7.25e-30

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


Pssm-ID: 442176  Cd Length: 121  Bit Score: 107.35  E-value: 7.25e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446722829  91 VLDVEFSCGDGTHVRGDliDVVRSIELDPEYARRLvgnRAFKnieignARGDSMAPTISPGDLLFLDKTVTYFDGDGIYA 170
Cdd:COG2932    3 LYDGEASAGGGAFNEVE--EPVDKLEFPGLPPDNL---FAVR------VSGDSMEPTIRDGDIVLVDPSDTEIRDGGIYV 71

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 446722829 171 FCFDGECYIKRLQKI-GSKIMVLSDNPNYQPWSIEKEGMALLYIQSKVI 218
Cdd:COG2932   72 VRTDGELLVKRLQRRpDGKLRLISDNPAYPPIEIPPEDADEIEIIGRVV 120
S24_LexA-like cd06529
Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of ...
 139-213 1.60e-22

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: 87.23  E-value: 1.60e-22
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446722829 139 ARGDSMAPTISPGDLLFLDKTVTYFDGDgIYAFCFDGECYIKRLQKIG-SKIMVLSDNPNYQPWSIEKEGMALLYI 213
Cdd:cd06529    5 VKGDSMEPTIPDGDLVLVDPSDTPRDGD-IVVARLDGELTVKRLQRRGgGRLRLISDNPAYPPIEIDEEELEIVGV 79
Peptidase_S24 pfam00717
Peptidase S24-like;
139-218 1.44e-19

Peptidase S24-like;


Pssm-ID: 425835  Cd Length: 116  Bit Score: 80.71  E-value: 1.44e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446722829  139 ARGDSMAPTISPGDLLFLDKTVTYFDGDgIYAFCFDGECYIKRLQKIGSKIMVLSDNPNYQPWSIEKEGMalLYIQSKVI 218
Cdd:pfam00717  40 VKGDSMEPGIPDGDLVLVDPSREARNGD-IVVARLDGEATVKRLYRDGGGIRLISLNPEYPPIELPAEDD--VEIIGRVV 116
Peptidase_S24_S26 cd06462
The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal ...
 139-203 4.76e-17

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: 73.07  E-value: 4.76e-17
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446722829 139 ARGDSMAPTISPGDLLFLDKTVTYFDGDGIYAFCFDG-ECYIKRLQKIG--SKIMVLSDNPNYQPWSI 203
Cdd:cd06462    5 VEGDSMEPTIPDGDLVLVDKSSYEPKRGDIVVFRLPGgELTVKRVIGLPgeGHYFLLGDNPNSPDSRI 72
LexA COG1974
SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase) [Transcription, ...
 9-221 5.11e-12

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


Pssm-ID: 441577 [Multi-domain]  Cd Length: 199  Bit Score: 62.62  E-value: 5.11e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446722829   9 NRIAMMLKTKGW--SQAELARKLGVSAQSVQYWTTgktfprsdKLAQLSVIsgypqswflgEDTSSTLSSAEKHHTREDS 86
Cdd:COG1974   13 DFIKEYIRERGYppSQREIAEALGLSSSAVHRHLK--------ALEKKGYL----------RRDPGKSRAIELLPASPEV 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446722829  87 VVFNVLDvefscgdgtHVR-GDLI----DVVRSIELDPEyarrLVGNR----AFKnieignARGDSM-APTISPGDLLFL 156
Cdd:COG1974   75 VGLPLLG---------RVAaGFPIpaeeNIEEYLDLPEE----LVKNPgatfALR------VKGDSMiDAGILDGDLVIV 135

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446722829 157 DKTVTYFDGDgIYAFCFDGECYIKRLQKIGSKIMVLSDNPNYQPwsIEKEGMAlLYIQSKVISSV 221
Cdd:COG1974  136 DRQLEAENGD-IVVALIDGEATVKRLYKEGGRVRLQPENPAYPP--IIIEGDD-VEILGVVVGVI 196
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
9-73 1.11e-10

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 56.16  E-value: 1.11e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446722829   9 NRIAMMLKTKGWSQAELARKLGVSAQSVQYWTTGKTFPRSDKLAQLSVISGYPQSWFLGEDTSST 73
Cdd:COG1396   10 ERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEEL 74
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 9-55 6.22e-09

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: 50.63  E-value: 6.22e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 446722829   9 NRIAMMLKTKGWSQAELARKLGVSAQSVQYWTTGKTFPRSDKLAQLS 55
Cdd:cd00093    2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLA 48
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
9-55 7.12e-09

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 50.62  E-value: 7.12e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 446722829   9 NRIAMMLKTKGWSQAELARKLGVSAQSVQYWTTGKTFPRSDKLAQLS 55
Cdd:COG1476    7 NRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIA 53
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
1-62 8.88e-09

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 50.32  E-value: 8.88e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446722829   1 MKNVKSTENRIAMMLKTKGWSQAELARKLGVSAQSVQYWTTGKTFPRSDKLAQLSVISGYPQ 62
Cdd:COG2944    1 MTKKPLTPEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGAALKLLRLLEKHPE 62
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
10-55 1.17e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 49.82  E-value: 1.17e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 446722829    10 RIAMMLKTKGWSQAELARKLGVSAQSVQYWTTGKTFPRSDKLAQLS 55
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLA 46
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 10-55 9.42e-08

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: 47.63  E-value: 9.42e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 446722829  10 RIAMMLKTKGWSQAELARKLGVSAQSVQYWTTGKTFPRSDKLAQLS 55
Cdd:COG1813   16 RIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLE 61
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 11-55 1.15e-06

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: 44.45  E-value: 1.15e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 446722829   11 IAMMLKTKGWSQAELARKLGVSAQSVQYWTTGKTFPRSDKLAQLS 55
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLA 45
PRK13355 PRK13355
bifunctional HTH-domain containing protein/aminotransferase; Provisional
 10-87 3.84e-06

bifunctional HTH-domain containing protein/aminotransferase; Provisional


Pssm-ID: 237361 [Multi-domain]  Cd Length: 517  Bit Score: 47.04  E-value: 3.84e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446722829  10 RIAMMLKTKGWSQAELAR-------KLGVSAQSvqYWTTGKTFPRSDKLAQLSVISGYPQSWFLGE--------DTSSTL 74
Cdd:PRK13355   7 RLKQAMKARGLKQEDLVHaaeargvKLGKSHIS--QYVSGKTGPRRDVLPFLAAILGVSEDWLLGGespadqesDASAVV 84

                         90
                 ....*....|...
gi 446722829  75 SSAEKHHTREDSV 87
Cdd:PRK13355  85 ESAPNSHLADPSA 97
PRK10276 PRK10276
translesion error-prone DNA polymerase V autoproteolytic subunit;
139-206 8.04e-06

translesion error-prone DNA polymerase V autoproteolytic subunit;


Pssm-ID: 182350  Cd Length: 139  Bit Score: 44.02  E-value: 8.04e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446722829 139 ARGDSMAPT-ISPGDLLFLDKTVTYFDGDGIYAfCFDGECYIKRLQKIGSkIMVLSDNPNYQPWSIEKE 206
Cdd:PRK10276  56 ASGDSMIDAgISDGDLLIVDSAITASHGDIVIA-AVDGEFTVKKLQLRPT-VQLIPMNSAYSPITISSE 122
S26_SPase_I cd06530
The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4. ...
 141-197 1.46e-04

The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are translocated across biological membranes. The bacterial signal peptidase I, which is the most intensively studied, has two N-terminal transmembrane segments inserted in the plasma membrane and a hydrophilic, C-terminal catalytic region that is located in the periplasmic space. Although the bacterial signal peptidase I is monomeric, signal peptidases of eukaryotic cells commonly function as oligomeric complexes containing two divergent copies of the catalytic monomer. These are the IMP1 and IMP2 signal peptidases of the mitochondrial inner membrane that remove leader peptides from nuclear- and mitochondrial-encoded proteins. Also, two components of the endoplasmic reticulum signal peptidase in mammals (18-kDa and 21-kDa) belong to this family and they process many proteins that enter the ER for retention or for export to the Golgi apparatus, secretory vesicles, plasma membranes or vacuole. An atypical member of the S26 SPase type I family is the TraF peptidase which has the remarkable activity of producing a cyclic protein of the Pseudomonas pilin system. The type I signal peptidases are unique serine proteases that utilize a serine/lysine catalytic dyad mechanism in place of the classical serine/histidine/aspartic acid catalytic triad mechanism.


Pssm-ID: 119398 [Multi-domain]  Cd Length: 85  Bit Score: 39.49  E-value: 1.46e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446722829 141 GDSMAPTISPGDLLFLDKTVTYFD----GDgIYAFCFDGEC---YIKRLqkIGskIMVLSDNPN 197
Cdd:cd06530    7 GGSMEPTLQPGDLVLVNKLSYGFRepkrGD-VVVFKSPGDPgkpIIKRV--IG--YFVLGDNRN 65
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 6-54 2.36e-04

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: 39.23  E-value: 2.36e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 446722829   6 STENRIAMMLKTKGWSQAELARKLGVSAQSVQYWTTGKTFPRSDKLAQL 54
Cdd:COG3620   17 TLGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKI 65
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 10-66 4.05e-04

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: 37.65  E-value: 4.05e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 446722829   10 RIAMMLKTKGWSQAELARKLGVSAQSVQYWTTGKTFPRSDKLAQLSVISGYPQSWFL 66
Cdd:pfam12844   3 RLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLL 59
YdaS COG4197
DNA-binding transcriptional regulator YdaS, prophage-encoded, Cro superfamily [Transcription];
21-43 4.56e-04

DNA-binding transcriptional regulator YdaS, prophage-encoded, Cro superfamily [Transcription];


Pssm-ID: 443351  Cd Length: 68  Bit Score: 37.58  E-value: 4.56e-04
                         10        20
                 ....*....|....*....|...
gi 446722829  21 SQAELARKLGVSAQSVQYWTTGK 43
Cdd:COG4197   10 SQSALARALGVSQQAVSQWLNGK 32
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 15-44 7.44e-04

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 37.48  E-value: 7.44e-04
                         10        20        30
                 ....*....|....*....|....*....|
gi 446722829  15 LKTKGWSQAELARKLGVSAQSVQYWTTGKT 44
Cdd:COG3093   18 LEPLGLSQTELAKALGVSRQRISEILNGKR 47
PHA01976 PHA01976
helix-turn-helix protein
 10-67 8.57e-04

helix-turn-helix protein


Pssm-ID: 177330 [Multi-domain]  Cd Length: 67  Bit Score: 36.86  E-value: 8.57e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 446722829  10 RIAMMLKTKGWSQAELARKLGVSAQSVQYWTTGKTFPRSDKLAQLSVISGYPQSWFLG 67
Cdd:PHA01976   6 QLIKARNARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGVTLDWLCG 63
lexA TIGR00498
SOS regulatory protein LexA; LexA acts as a homodimer to repress a number of genes involved in ...
 141-200 1.07e-03

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: 38.93  E-value: 1.07e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446722829  141 GDSMAPT-ISPGDLLFLDKTVTYFDGDgIYAFCFDGECYIKRLQKIGSKIMVLSDNPNYQP 200
Cdd:TIGR00498 118 GDSMVDAgICDGDLLIVRSQKDARNGE-IVAAMIDGEVTVKRFYKDGTKVELKPENPEFDP 177
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 1-66 1.17e-03

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 37.91  E-value: 1.17e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446722829   1 MKNvKSTENRIAMMLKTKGWSQAELARKLGVSAQSVQYWTTGKTFPRSDKLAQLSVISGYPQSWFL 66
Cdd:PRK09706   1 MKN-LTLGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCSPTWLL 65
Csa3 COG3415
CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein ...
 12-39 2.09e-03

CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein Csa3, CARF domain is part of the Pathway/BioSystem: CRISPR-Cas system


Pssm-ID: 442641 [Multi-domain]  Cd Length: 325  Bit Score: 38.68  E-value: 2.09e-03
                         10        20
                 ....*....|....*....|....*...
gi 446722829  12 AMMLKTKGWSQAELARKLGVSAQSVQYW 39
Cdd:COG3415   31 AVLLLAEGLSVREIAERLGVSRSTVYRW 58
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 11-54 4.01e-03

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: 34.56  E-value: 4.01e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 446722829   11 IAMMLKTK----GWSQAELARKLGVSAQSVQYWTTGKTFPRSDKLAQL 54
Cdd:TIGR03070   3 IGILVRARrkalGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRV 50
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
9-44 4.18e-03

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 34.73  E-value: 4.18e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 446722829   9 NRIAMMLKTKGWSQAELARKLGVSAQSVQYWTTGKT 44
Cdd:COG3655    4 VKLDELLAERGMTKKELAEATGISRATLSRLKNGKA 39
Terminase_5 pfam06056
Putative ATPase subunit of terminase (gpP-like); This family of proteins are annotated as ...
 10-39 4.75e-03

Putative ATPase subunit of terminase (gpP-like); This family of proteins are annotated as ATPase subunits of phage terminase after. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.


Pssm-ID: 428745 [Multi-domain]  Cd Length: 58  Bit Score: 34.28  E-value: 4.75e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 446722829   10 RIAMMLKTKGWSQAELARKLGVSAQSVQYW 39
Cdd:pfam06056   4 RQARFLYWQGYRPAEIAEMLGLKEATVYSW 33
sigpep_I_bact TIGR02227
signal peptidase I, bacterial type; This model represents signal peptidase I from most ...
 141-182 5.74e-03

signal peptidase I, bacterial type; This model represents signal peptidase I from most bacteria. Eukaryotic sequences are likely organellar. Several bacteria have multiple paralogs, but these represent isozymes of signal peptidase I. Virtually all known bacteria may be presumed to A related model finds a simlar protein in many archaea and a few bacteria, as well as a microsomal (endoplasmic reticulum) protein in eukaryotes. [Protein fate, Protein and peptide secretion and trafficking]


Pssm-ID: 274044 [Multi-domain]  Cd Length: 142  Bit Score: 36.05  E-value: 5.74e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 446722829  141 GDSMAPTISPGDLLFLDKTVTYFD----GDGI--YAFCFDGECYIKRL 182
Cdd:TIGR02227  10 GGSMEPTLKEGDRILVNKFAYRTSdpkrGDIVvfKDPDTNKNIYVKRI 57
HTH_28 pfam13518
Helix-turn-helix domain; This helix-turn-helix domain is often found in transposases and is ...
 12-39 7.72e-03

Helix-turn-helix domain; This helix-turn-helix domain is often found in transposases and is likely to be DNA-binding.


Pssm-ID: 463908 [Multi-domain]  Cd Length: 52  Bit Score: 33.72  E-value: 7.72e-03
                          10        20
                  ....*....|....*....|....*...
gi 446722829   12 AMMLKTKGWSQAELARKLGVSAQSVQYW 39
Cdd:pfam13518   5 IVLLALEGESIKEAARLFGISRSTVYRW 32
 
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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