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MULTISPECIES: S24 family peptidase [unclassified Staphylococcus]

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

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List of domain hits

 Name Accession Description Interval E-value
LexA COG1974
SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase) [Transcription, ...
 8-201 1.54e-38

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


:

Pssm-ID: 441577 [Multi-domain]  Cd Length: 199  Bit Score: 131.58  E-value: 1.54e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2617418074   8 RRKELNLTLEQVGDLVGVGKSTVRKWetgdienmkrdkIVKLAKAlrvspSYIMGIDEEQRQLETLP----VKKIPVVSK 83
Cdd:COG1974    20 RERGYPPSQREIAEALGLSSSAVHRH------------LKALEKK-----GYLRRDPGKSRAIELLPaspeVVGLPLLGR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2617418074  84 ISAGLPIYSEENLIDYIYFATNKLNSDKEEFGLKVSGDSM-DKIFQDGDIVVVEKDSVVENGQLGVVMINGyNATVKRIR 162
Cdd:COG1974    83 VAAGFPIPAEENIEEYLDLPEELVKNPGATFALRVKGDSMiDAGILDGDLVIVDRQLEAENGDIVVALIDG-EATVKRLY 161

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2617418074 163 YNGDQIILIPEsNnsSHYPQVYGKDDEVKIIGRVVASQK 201
Cdd:COG1974   162 KEGGRVRLQPE-N--PAYPPIIIEGDDVEILGVVVGVIR 197
 
Name Accession Description Interval E-value
LexA COG1974
SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase) [Transcription, ...
 8-201 1.54e-38

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


Pssm-ID: 441577 [Multi-domain]  Cd Length: 199  Bit Score: 131.58  E-value: 1.54e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2617418074   8 RRKELNLTLEQVGDLVGVGKSTVRKWetgdienmkrdkIVKLAKAlrvspSYIMGIDEEQRQLETLP----VKKIPVVSK 83
Cdd:COG1974    20 RERGYPPSQREIAEALGLSSSAVHRH------------LKALEKK-----GYLRRDPGKSRAIELLPaspeVVGLPLLGR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2617418074  84 ISAGLPIYSEENLIDYIYFATNKLNSDKEEFGLKVSGDSM-DKIFQDGDIVVVEKDSVVENGQLGVVMINGyNATVKRIR 162
Cdd:COG1974    83 VAAGFPIPAEENIEEYLDLPEELVKNPGATFALRVKGDSMiDAGILDGDLVIVDRQLEAENGDIVVALIDG-EATVKRLY 161

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2617418074 163 YNGDQIILIPEsNnsSHYPQVYGKDDEVKIIGRVVASQK 201
Cdd:COG1974   162 KEGGRVRLQPE-N--PAYPPIIIEGDDVEILGVVVGVIR 197
Peptidase_S24 pfam00717
Peptidase S24-like;
79-197 9.35e-32

Peptidase S24-like;


Pssm-ID: 425835  Cd Length: 116  Bit Score: 111.53  E-value: 9.35e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2617418074  79 PVVSKISAGLPIYSEENLIDYIYFATNKLNSDKEEFGLKVSGDSMDKIFQDGDIVVVEKDSVVENGQLGVVMINGYnATV 158
Cdd:pfam00717   1 PLIGRVAAGAPILAEEEIEGYLPLPESLLSPPGNLFALRVKGDSMEPGIPDGDLVLVDPSREARNGDIVVARLDGE-ATV 79

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 2617418074 159 KRIRYNGDQIILIPEsnNSSHYPQVYGKDDEVKIIGRVV 197
Cdd:pfam00717  80 KRLYRDGGGIRLISL--NPEYPPIELPAEDDVEIIGRVV 116
lexA TIGR00498
SOS regulatory protein LexA; LexA acts as a homodimer to repress a number of genes involved in ...
 76-197 5.31e-21

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: 85.92  E-value: 5.31e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2617418074  76 KKIPVVSKISAGLPIYSEENLIDYIYFATNKLNSDKEEFGLKVSGDSMDKIF-QDGDIVVVEKDSVVENGQLGVVMINGy 154
Cdd:TIGR00498  74 KGVPLIGRVAAGEPILAEQHIEEYFPIDFSLLKKPSAVFLLKVMGDSMVDAGiCDGDLLIVRSQKDARNGEIVAAMIDG- 152

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2617418074 155 NATVKRIRYNGDQIILIPEsnNSSHYPQVyGKDDEVKIIGRVV 197
Cdd:TIGR00498 153 EVTVKRFYKDGTKVELKPE--NPEFDPIV-LNAEDVTILGKVV 192
S24_LexA-like cd06529
Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of ...
 114-197 2.19e-15

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: 67.97  E-value: 2.19e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2617418074 114 FGLKVSGDSMDKIFQDGDIVVVEKDSVVENGQLGVVMINGYnATVKRIRY-NGDQIILIPEsnNSSHYPQVYgKDDEVKI 192
Cdd:cd06529     1 FALRVKGDSMEPTIPDGDLVLVDPSDTPRDGDIVVARLDGE-LTVKRLQRrGGGRLRLISD--NPAYPPIEI-DEEELEI 76


                  ....*
gi 2617418074 193 IGRVV 197
Cdd:cd06529    77 VGVVG 81
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
5-60 2.15e-12

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 59.45  E-value: 2.15e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2617418074    5 IKSRRKELNLTLEQVGDLVGVGKSTVRKWETGDIeNMKRDKIVKLAKALRVSPSYI 60
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKR-KPSLETLKKLAKALGVSLDEL 56
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 5-67 1.03e-09

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 54.47  E-value: 1.03e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2617418074   5 IKSRRKELNLTLEQVGDLVGVGKSTVRKWETGDIENmKRDKIVKLAKALRVSPSYIMGIDEEQ 67
Cdd:PRK09706   10 IRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEP-TGKNLFALAKALQCSPTWLLFGDEDK 71
VC1465_fam NF040522
VC1465 family Xer recombination activation factor;
5-36 7.53e-04

VC1465 family Xer recombination activation factor;


Pssm-ID: 439737 [Multi-domain]  Cd Length: 111  Bit Score: 37.81  E-value: 7.53e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2617418074   5 IKSRRKELNLTLEQVGDLVGVGKSTVRKWETG 36
Cdd:NF040522    1 IKETREKAGLTRQQAAEMLRVSLRTVQNWETG 32
 
Name Accession Description Interval E-value
LexA COG1974
SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase) [Transcription, ...
 8-201 1.54e-38

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


Pssm-ID: 441577 [Multi-domain]  Cd Length: 199  Bit Score: 131.58  E-value: 1.54e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2617418074   8 RRKELNLTLEQVGDLVGVGKSTVRKWetgdienmkrdkIVKLAKAlrvspSYIMGIDEEQRQLETLP----VKKIPVVSK 83
Cdd:COG1974    20 RERGYPPSQREIAEALGLSSSAVHRH------------LKALEKK-----GYLRRDPGKSRAIELLPaspeVVGLPLLGR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2617418074  84 ISAGLPIYSEENLIDYIYFATNKLNSDKEEFGLKVSGDSM-DKIFQDGDIVVVEKDSVVENGQLGVVMINGyNATVKRIR 162
Cdd:COG1974    83 VAAGFPIPAEENIEEYLDLPEELVKNPGATFALRVKGDSMiDAGILDGDLVIVDRQLEAENGDIVVALIDG-EATVKRLY 161

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2617418074 163 YNGDQIILIPEsNnsSHYPQVYGKDDEVKIIGRVVASQK 201
Cdd:COG1974   162 KEGGRVRLQPE-N--PAYPPIIIEGDDVEILGVVVGVIR 197
Peptidase_S24 pfam00717
Peptidase S24-like;
79-197 9.35e-32

Peptidase S24-like;


Pssm-ID: 425835  Cd Length: 116  Bit Score: 111.53  E-value: 9.35e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2617418074  79 PVVSKISAGLPIYSEENLIDYIYFATNKLNSDKEEFGLKVSGDSMDKIFQDGDIVVVEKDSVVENGQLGVVMINGYnATV 158
Cdd:pfam00717   1 PLIGRVAAGAPILAEEEIEGYLPLPESLLSPPGNLFALRVKGDSMEPGIPDGDLVLVDPSREARNGDIVVARLDGE-ATV 79

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 2617418074 159 KRIRYNGDQIILIPEsnNSSHYPQVYGKDDEVKIIGRVV 197
Cdd:pfam00717  80 KRLYRDGGGIRLISL--NPEYPPIELPAEDDVEIIGRVV 116
lexA TIGR00498
SOS regulatory protein LexA; LexA acts as a homodimer to repress a number of genes involved in ...
 76-197 5.31e-21

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: 85.92  E-value: 5.31e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2617418074  76 KKIPVVSKISAGLPIYSEENLIDYIYFATNKLNSDKEEFGLKVSGDSMDKIF-QDGDIVVVEKDSVVENGQLGVVMINGy 154
Cdd:TIGR00498  74 KGVPLIGRVAAGEPILAEQHIEEYFPIDFSLLKKPSAVFLLKVMGDSMVDAGiCDGDLLIVRSQKDARNGEIVAAMIDG- 152

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2617418074 155 NATVKRIRYNGDQIILIPEsnNSSHYPQVyGKDDEVKIIGRVV 197
Cdd:TIGR00498 153 EVTVKRFYKDGTKVELKPE--NPEFDPIV-LNAEDVTILGKVV 192
COG2932 COG2932
Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: ...
 78-197 1.94e-16

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


Pssm-ID: 442176  Cd Length: 121  Bit Score: 71.92  E-value: 1.94e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2617418074  78 IPVVS-KISAGLPIYSE-ENLIDYIYFATNklnSDKEEFGLKVSGDSMDKIFQDGDIVVVEK-DSVVENGQLGVVMINGy 154
Cdd:COG2932     1 VPLYDgEASAGGGAFNEvEEPVDKLEFPGL---PPDNLFAVRVSGDSMEPTIRDGDIVLVDPsDTEIRDGGIYVVRTDG- 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2617418074 155 NATVKRIRYNGD-QIILIpeSNNSSHYPQVYGKDD--EVKIIGRVV 197
Cdd:COG2932    77 ELLVKRLQRRPDgKLRLI--SDNPAYPPIEIPPEDadEIEIIGRVV 120
S24_LexA-like cd06529
Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of ...
 114-197 2.19e-15

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: 67.97  E-value: 2.19e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2617418074 114 FGLKVSGDSMDKIFQDGDIVVVEKDSVVENGQLGVVMINGYnATVKRIRY-NGDQIILIPEsnNSSHYPQVYgKDDEVKI 192
Cdd:cd06529     1 FALRVKGDSMEPTIPDGDLVLVDPSDTPRDGDIVVARLDGE-LTVKRLQRrGGGRLRLISD--NPAYPPIEI-DEEELEI 76


                  ....*
gi 2617418074 193 IGRVV 197
Cdd:cd06529    77 VGVVG 81
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
5-74 1.84e-14

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 65.79  E-value: 1.84e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2617418074   5 IKSRRKELNLTLEQVGDLVGVGKSTVRKWETGDIeNMKRDKIVKLAKALRVSPSYIMGIDEEQRQLETLP 74
Cdd:COG1396    12 LRELRKARGLTQEELAERLGVSRSTISRIERGRR-NPSLETLLKLAKALGVSLDELLGGADEELPEALLS 80
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 5-60 7.92e-13

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: 60.64  E-value: 7.92e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2617418074   5 IKSRRKELNLTLEQVGDLVGVGKSTVRKWETGDIeNMKRDKIVKLAKALRVSPSYI 60
Cdd:cd00093     4 LKELRKEKGLTQEELAEKLGVSRSTISRIENGKR-NPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
5-60 2.15e-12

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 59.45  E-value: 2.15e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2617418074    5 IKSRRKELNLTLEQVGDLVGVGKSTVRKWETGDIeNMKRDKIVKLAKALRVSPSYI 60
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKR-KPSLETLKKLAKALGVSLDEL 56
Peptidase_S24_S26 cd06462
The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal ...
 114-196 5.12e-12

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: 59.20  E-value: 5.12e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2617418074 114 FGLKVSGDSMDKIFQDGDIVVVEKDSV-VENGQLGVVMINGYNATVKRI--RYNGDQIILIPESNNSShyPQVYGKDDEV 190
Cdd:cd06462     1 FALRVEGDSMEPTIPDGDLVLVDKSSYePKRGDIVVFRLPGGELTVKRVigLPGEGHYFLLGDNPNSP--DSRIDGPPEL 78


                  ....*.
gi 2617418074 191 KIIGRV 196
Cdd:cd06462    79 DIVGVV 84
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-65 7.62e-11

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 55.62  E-value: 7.62e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2617418074   1 MKPDIKSRRKELNLTLEQVGDLVGVGKSTVRKWETGDIeNMKRDKIVKLAKALRVSPSYIMGIDE 65
Cdd:COG1476     5 LGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKY-NPSLELALKIARALGVSLEELFSLEE 68
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 5-60 5.70e-10

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: 52.93  E-value: 5.70e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2617418074   5 IKSRRKELNLTLEQVGDLVGVGKSTVRKWETGDIeNMKRDKIVKLAKALRVSPSYI 60
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKR-EPSLETLKKLAEALGVSLDEL 55
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 5-67 1.03e-09

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 54.47  E-value: 1.03e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2617418074   5 IKSRRKELNLTLEQVGDLVGVGKSTVRKWETGDIENmKRDKIVKLAKALRVSPSYIMGIDEEQ 67
Cdd:PRK09706   10 IRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEP-TGKNLFALAKALQCSPTWLLFGDEDK 71
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 5-58 4.63e-09

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: 50.99  E-value: 4.63e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2617418074   5 IKSRRKELNLTLEQVGDLVGVGKSTVRKWETGDIENMKRDKIVKLAKALRVSPS 58
Cdd:pfam13560   6 LRRLRERAGLSQEALARRLGVSRSTLSRLETGRRGRPSPAVVERLARALGVDGA 59
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
3-37 3.08e-07

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 46.08  E-value: 3.08e-07
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 2617418074   3 PDIKSRRKELNLTLEQVGDLVGVGKSTVRKWETGD 37
Cdd:COG2944     9 EEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGR 43
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 5-59 3.83e-07

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: 45.70  E-value: 3.83e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2617418074   5 IKSRRKELNLTLEQVGDLVGVGKSTVRKWETGDIeNMKRDKIVKLAKALRVSPSY 59
Cdd:COG1813    17 IREAREARGLSQEELAEKLGVSESTIRRIERGEA-TPSLDTLRKLEKALGISLAE 70
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 5-67 6.44e-06

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: 43.08  E-value: 6.44e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2617418074   5 IKSRRKELNLTLEQVGDLVGVGKSTVRKWETGDiENMKRDKIVKLAKALRVSPSYIMGIDEEQ 67
Cdd:COG3620    22 LRLMRKELGLSQLPVAELVGVSQSDILRIESGK-RDPTVSTLEKIAEALGKELSAVLVVDDGK 83
PRK10276 PRK10276
translesion error-prone DNA polymerase V autoproteolytic subunit;
116-196 6.58e-06

translesion error-prone DNA polymerase V autoproteolytic subunit;


Pssm-ID: 182350  Cd Length: 139  Bit Score: 44.02  E-value: 6.58e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2617418074 116 LKVSGDSM-DKIFQDGDIVVVEKDSVVENGQLGVVMINGyNATVKRIRYNgDQIILIPEsnNSSHYPQVYGKDDEVKIIG 194
Cdd:PRK10276   54 VKASGDSMiDAGISDGDLLIVDSAITASHGDIVIAAVDG-EFTVKKLQLR-PTVQLIPM--NSAYSPITISSEDTLDVFG 129


                  ..
gi 2617418074 195 RV 196
Cdd:PRK10276  130 VV 131
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 5-55 1.05e-05

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: 41.49  E-value: 1.05e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2617418074   5 IKSRRKELNLTLEQVGDLVGVGKSTVRkwetgDIENMKRDkiVKLAKALRV 55
Cdd:TIGR03070   7 VRARRKALGLTQADLADLAGVGLRFIR-----DLENGKPT--VRLDKVLRV 50
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 3-52 3.12e-05

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: 41.85  E-value: 3.12e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2617418074   3 PDIKSRRKELNLTLEQVGDLVGVGKSTVRKWETGDIENMKR-DKIVKLAKA 52
Cdd:TIGR03830  68 PEIRRIRKKLGLSQREAAELLGGGVNAFSRYERGEVRPSKAlDKLLRLLDK 118
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 5-61 6.31e-05

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: 39.58  E-value: 6.31e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2617418074   5 IKSRRKELNLTLEQVGDLVGVGKSTVRKWETGDIeNMKRDKIVKLAKALRVSPSYIM 61
Cdd:pfam12844   4 LRKAREERGLTQEELAERLGISRSQLSAIENGKS-VPPAETLYKIAELLGVPANWLL 59
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 5-61 7.78e-05

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: 39.40  E-value: 7.78e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2617418074   5 IKSRRKELNLTLEQVGDLVGVGKSTVRKWETGDIENM-----KRDKIVKLAKALRVSPSYIM 61
Cdd:COG1426    10 LRQAREAKGLSLEDVAERTKISVSYLEAIEEGDFDALpgpvyVRGFLRSYARALGLDPEELL 71
VC1465_fam NF040522
VC1465 family Xer recombination activation factor;
5-36 7.53e-04

VC1465 family Xer recombination activation factor;


Pssm-ID: 439737 [Multi-domain]  Cd Length: 111  Bit Score: 37.81  E-value: 7.53e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2617418074   5 IKSRRKELNLTLEQVGDLVGVGKSTVRKWETG 36
Cdd:NF040522    1 IKETREKAGLTRQQAAEMLRVSLRTVQNWETG 32
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 5-66 3.82e-03

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: 34.44  E-value: 3.82e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2617418074   5 IKSRRKELNLTLEQVGDLVGVGKSTVRKWETGDIENMKRDKIVKLAKALRVSPSYIMGIDEE 66
Cdd:pfam13443   2 LRKLMADRGISKSDLARATGISRATLSRLRKGKPKRVSLDTLDKICDALGCQPGDLLEYVPD 63
PRK13355 PRK13355
bifunctional HTH-domain containing protein/aminotransferase; Provisional
 5-69 4.84e-03

bifunctional HTH-domain containing protein/aminotransferase; Provisional


Pssm-ID: 237361 [Multi-domain]  Cd Length: 517  Bit Score: 37.41  E-value: 4.84e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2617418074   5 IKSRRKELNLTLEQVGDL-----VGVGKSTVRKWETGdIENMKRDKIVKLAKALRVSPSYIMGIDEEQRQ 69
Cdd:PRK13355    8 LKQAMKARGLKQEDLVHAaeargVKLGKSHISQYVSG-KTGPRRDVLPFLAAILGVSEDWLLGGESPADQ 76
 
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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