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LexA family transcriptional regulator [Hyphomicrobium sp. MC1]

Protein Classification

LexA family transcriptional regulator( domain architecture ID 11272004)

LexA family transcriptional regulator containing an XRE family helix-turn-helix (HTH) DNA-binding domain and a C-terminal S24 family peptidase domain that is responsible for dimerization and cleavage activity; similar to LexA that controls the SOS response to conditions that damage DNA or inhibit DNA replication

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Peptidase_S24 pfam00717
Peptidase S24-like;
110-209 8.06e-10

Peptidase S24-like;


:

Pssm-ID: 425835  Cd Length: 116  Bit Score: 54.52  E-value: 8.06e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503712776  110 DMLAVPESL----KECFAVSIGDNSMKPLYQEGDICIVDPSIGPNENDAVVVSFPGKALVLRTYVPRGadssgatAYDLQ 185
Cdd:pfam00717  20 GYLPLPESLlsppGNLFALRVKGDSMEPGIPDGDLVLVDPSREARNGDIVVARLDGEATVKRLYRDGG-------GIRLI 92

                          90       100
                  ....*....|....*....|....
gi 503712776  186 TPNADYKTLTVNSSHPADLLGVVV 209
Cdd:pfam00717  93 SLNPEYPPIELPAEDDVEIIGRVV 116
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
8-62 1.56e-09

Helix-turn-helix XRE-family like proteins;


:

Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 52.14  E-value: 1.56e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 503712776     8 ISDALDAQKMSHEDLARRLKVSRQAVSAWINGKNGPKRARAVAVAKILKIDVGLL 62
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
 
Name Accession Description Interval E-value
Peptidase_S24 pfam00717
Peptidase S24-like;
110-209 8.06e-10

Peptidase S24-like;


Pssm-ID: 425835  Cd Length: 116  Bit Score: 54.52  E-value: 8.06e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503712776  110 DMLAVPESL----KECFAVSIGDNSMKPLYQEGDICIVDPSIGPNENDAVVVSFPGKALVLRTYVPRGadssgatAYDLQ 185
Cdd:pfam00717  20 GYLPLPESLlsppGNLFALRVKGDSMEPGIPDGDLVLVDPSREARNGDIVVARLDGEATVKRLYRDGG-------GIRLI 92

                          90       100
                  ....*....|....*....|....
gi 503712776  186 TPNADYKTLTVNSSHPADLLGVVV 209
Cdd:pfam00717  93 SLNPEYPPIELPAEDDVEIIGRVV 116
COG2932 COG2932
Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: ...
 82-209 1.52e-09

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


Pssm-ID: 442176  Cd Length: 121  Bit Score: 53.81  E-value: 1.52e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503712776  82 IPLLRIEktilktGAALDLQSSLRAYAVDMLAVP-ESLKECFAVSIGDNSMKPLYQEGDICIVDPSIG-PNENDAVVVSF 159
Cdd:COG2932    1 VPLYDGE------ASAGGGAFNEVEEPVDKLEFPgLPPDNLFAVRVSGDSMEPTIRDGDIVLVDPSDTeIRDGGIYVVRT 74

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 503712776 160 PGKALVlRTYVPRGADSsgataYDLQTPNADYKTLTVNSSHPADL--LGVVV 209
Cdd:COG2932   75 DGELLV-KRLQRRPDGK-----LRLISDNPAYPPIEIPPEDADEIeiIGRVV 120
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
8-62 1.56e-09

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 52.14  E-value: 1.56e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 503712776     8 ISDALDAQKMSHEDLARRLKVSRQAVSAWINGKNGPKRARAVAVAKILKIDVGLL 62
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 5-62 1.88e-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: 51.78  E-value: 1.88e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 503712776   5 AKIISDALDAQKMSHEDLARRLKVSRQAVSAWINGKNGPKRARAVAVAKILKIDVGLL 62
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-62 8.77e-09

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 50.23  E-value: 8.77e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 503712776   1 MVSIAKIISDALDAQKMSHEDLARRLKVSRQAVSAWINGKNGPKRARAVAVAKILKIDVGLL 62
Cdd:COG1476    2 KKKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEEL 63
S24_LexA-like cd06529
Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of ...
 122-209 2.56e-08

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: 49.48  E-value: 2.56e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503712776 122 FAVSIGDNSMKPLYQEGDICIVDPSIGPNENDAVVVSFPGKALVlRTYVPRGADssgatAYDLQTPNADYKTLTVNSSHp 201
Cdd:cd06529    1 FALRVKGDSMEPTIPDGDLVLVDPSDTPRDGDIVVARLDGELTV-KRLQRRGGG-----RLRLISDNPAYPPIEIDEEE- 73


                 ....*...
gi 503712776 202 ADLLGVVV 209
Cdd:cd06529   74 LEIVGVVG 81
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 8-62 3.29e-08

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: 48.31  E-value: 3.29e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 503712776    8 ISDALDAQKMSHEDLARRLKVSRQAVSAWINGKNGPKRARAVAVAKILKIDVGLL 62
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
PRK13355 PRK13355
bifunctional HTH-domain containing protein/aminotransferase; Provisional
 8-62 7.87e-04

bifunctional HTH-domain containing protein/aminotransferase; Provisional


Pssm-ID: 237361 [Multi-domain]  Cd Length: 517  Bit Score: 39.72  E-value: 7.87e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 503712776   8 ISDALDAQKMSHEDLARRL-----KVSRQAVSAWINGKNGPKRARAVAVAKILKIDVGLL 62
Cdd:PRK13355   8 LKQAMKARGLKQEDLVHAAeargvKLGKSHISQYVSGKTGPRRDVLPFLAAILGVSEDWL 67
lysogeny_AimR NF038310
AimR family lysis-lysogeny pheromone receptor; The founding member of this family, AimR ...
 8-41 6.95e-03

AimR family lysis-lysogeny pheromone receptor; The founding member of this family, AimR (arbitrium receptor), is a DNA-binding phage regulatory protein that acts as a receptor for a 6-amino acid signaling peptide cleaved from the C-terminus of AimP. AimR controls expression of AimX, the third member of the quorum sensing-like arbitrium system and an inhibitor of phage lysogeny.


Pssm-ID: 468467  Cd Length: 363  Bit Score: 36.74  E-value: 6.95e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 503712776   8 ISDALDAQKMSHEDLARRLKVSRQAVSAWINGKN 41
Cdd:NF038310   1 IKNDLESKGITNRKLAKKIGVSKSTLSKFFNGKG 34
 
Name Accession Description Interval E-value
Peptidase_S24 pfam00717
Peptidase S24-like;
110-209 8.06e-10

Peptidase S24-like;


Pssm-ID: 425835  Cd Length: 116  Bit Score: 54.52  E-value: 8.06e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503712776  110 DMLAVPESL----KECFAVSIGDNSMKPLYQEGDICIVDPSIGPNENDAVVVSFPGKALVLRTYVPRGadssgatAYDLQ 185
Cdd:pfam00717  20 GYLPLPESLlsppGNLFALRVKGDSMEPGIPDGDLVLVDPSREARNGDIVVARLDGEATVKRLYRDGG-------GIRLI 92

                          90       100
                  ....*....|....*....|....
gi 503712776  186 TPNADYKTLTVNSSHPADLLGVVV 209
Cdd:pfam00717  93 SLNPEYPPIELPAEDDVEIIGRVV 116
COG2932 COG2932
Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: ...
 82-209 1.52e-09

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


Pssm-ID: 442176  Cd Length: 121  Bit Score: 53.81  E-value: 1.52e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503712776  82 IPLLRIEktilktGAALDLQSSLRAYAVDMLAVP-ESLKECFAVSIGDNSMKPLYQEGDICIVDPSIG-PNENDAVVVSF 159
Cdd:COG2932    1 VPLYDGE------ASAGGGAFNEVEEPVDKLEFPgLPPDNLFAVRVSGDSMEPTIRDGDIVLVDPSDTeIRDGGIYVVRT 74

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 503712776 160 PGKALVlRTYVPRGADSsgataYDLQTPNADYKTLTVNSSHPADL--LGVVV 209
Cdd:COG2932   75 DGELLV-KRLQRRPDGK-----LRLISDNPAYPPIEIPPEDADEIeiIGRVV 120
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
8-62 1.56e-09

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 52.14  E-value: 1.56e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 503712776     8 ISDALDAQKMSHEDLARRLKVSRQAVSAWINGKNGPKRARAVAVAKILKIDVGLL 62
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 5-62 1.88e-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: 51.78  E-value: 1.88e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 503712776   5 AKIISDALDAQKMSHEDLARRLKVSRQAVSAWINGKNGPKRARAVAVAKILKIDVGLL 62
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-62 8.77e-09

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 50.23  E-value: 8.77e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 503712776   1 MVSIAKIISDALDAQKMSHEDLARRLKVSRQAVSAWINGKNGPKRARAVAVAKILKIDVGLL 62
Cdd:COG1476    2 KKKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEEL 63
S24_LexA-like cd06529
Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of ...
 122-209 2.56e-08

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: 49.48  E-value: 2.56e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503712776 122 FAVSIGDNSMKPLYQEGDICIVDPSIGPNENDAVVVSFPGKALVlRTYVPRGADssgatAYDLQTPNADYKTLTVNSSHp 201
Cdd:cd06529    1 FALRVKGDSMEPTIPDGDLVLVDPSDTPRDGDIVVARLDGELTV-KRLQRRGGG-----RLRLISDNPAYPPIEIDEEE- 73


                 ....*...
gi 503712776 202 ADLLGVVV 209
Cdd:cd06529   74 LEIVGVVG 81
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 8-62 3.29e-08

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: 48.31  E-value: 3.29e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 503712776    8 ISDALDAQKMSHEDLARRLKVSRQAVSAWINGKNGPKRARAVAVAKILKIDVGLL 62
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
LexA COG1974
SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase) [Transcription, ...
 107-215 4.91e-08

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


Pssm-ID: 441577 [Multi-domain]  Cd Length: 199  Bit Score: 51.07  E-value: 4.91e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503712776 107 YAVDMLAVPESL----KECFAVSIGDNSMK-PLYQEGDICIVDPSIGPNENDAVVVSFPGKALVlRTYVPRGadssgaTA 181
Cdd:COG1974   94 NIEEYLDLPEELvknpGATFALRVKGDSMIdAGILDGDLVIVDRQLEAENGDIVVALIDGEATV-KRLYKEG------GR 166

                         90       100       110
                 ....*....|....*....|....*....|....
gi 503712776 182 YDLQTPNADYKTLTVNSSHpADLLGVVVEYRRKL 215
Cdd:COG1974  167 VRLQPENPAYPPIIIEGDD-VEILGVVVGVIRRL 199
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 4-58 9.72e-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: 9.72e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 503712776   4 IAKIISDALDAQKMSHEDLARRLKVSRQAVSAWINGKNGPKRARAVAVAKILKID 58
Cdd:COG1813   13 YGERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGIS 67
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-62 2.12e-07

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 46.91  E-value: 2.12e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 503712776   1 MVSIAKIISDALDAQKMSHEDLARRLKVSRQAVSAWINGKNGPKRARAVAVAKILKIDVGLL 62
Cdd:COG1396    5 KKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDEL 66
Peptidase_S24_S26 cd06462
The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal ...
 122-208 2.00e-06

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: 44.56  E-value: 2.00e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503712776 122 FAVSIGDNSMKPLYQEGDICIVDPSI-GPNENDAVVVSFPGKALVLRTYVPRGadssGATAYDLQTPNADYKTLTVNSSH 200
Cdd:cd06462    1 FALRVEGDSMEPTIPDGDLVLVDKSSyEPKRGDIVVFRLPGGELTVKRVIGLP----GEGHYFLLGDNPNSPDSRIDGPP 76


                 ....*...
gi 503712776 201 PADLLGVV 208
Cdd:cd06462   77 ELDIVGVV 84
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 6-62 8.29e-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: 8.29e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 503712776    6 KIISDALDAQKMSHEDLARRLKVSRQAVSAWINGKNGPKRARAVAVAKILKIDVGLL 62
Cdd:pfam12844   2 ERLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWL 58
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 12-40 1.17e-04

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 39.41  E-value: 1.17e-04
                         10        20
                 ....*....|....*....|....*....
gi 503712776  12 LDAQKMSHEDLARRLKVSRQAVSAWINGK 40
Cdd:COG3093   18 LEPLGLSQTELAKALGVSRQRISEILNGK 46
PRK13355 PRK13355
bifunctional HTH-domain containing protein/aminotransferase; Provisional
 8-62 7.87e-04

bifunctional HTH-domain containing protein/aminotransferase; Provisional


Pssm-ID: 237361 [Multi-domain]  Cd Length: 517  Bit Score: 39.72  E-value: 7.87e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 503712776   8 ISDALDAQKMSHEDLARRL-----KVSRQAVSAWINGKNGPKRARAVAVAKILKIDVGLL 62
Cdd:PRK13355   8 LKQAMKARGLKQEDLVHAAeargvKLGKSHISQYVSGKTGPRRDVLPFLAAILGVSEDWL 67
YdaS COG4197
DNA-binding transcriptional regulator YdaS, prophage-encoded, Cro superfamily [Transcription];
4-49 1.11e-03

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


Pssm-ID: 443351  Cd Length: 68  Bit Score: 36.43  E-value: 1.11e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 503712776   4 IAKIISdALDAQKmsheDLARRLKVSRQAVSAWINGKN--GPKRARAV 49
Cdd:COG4197    1 LEKAIE-ALGSQS----ALARALGVSQQAVSQWLNGKRrvPAERCLAI 43
lysogeny_AimR NF038310
AimR family lysis-lysogeny pheromone receptor; The founding member of this family, AimR ...
 8-41 6.95e-03

AimR family lysis-lysogeny pheromone receptor; The founding member of this family, AimR (arbitrium receptor), is a DNA-binding phage regulatory protein that acts as a receptor for a 6-amino acid signaling peptide cleaved from the C-terminus of AimP. AimR controls expression of AimX, the third member of the quorum sensing-like arbitrium system and an inhibitor of phage lysogeny.


Pssm-ID: 468467  Cd Length: 363  Bit Score: 36.74  E-value: 6.95e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 503712776   8 ISDALDAQKMSHEDLARRLKVSRQAVSAWINGKN 41
Cdd:NF038310   1 IKNDLESKGITNRKLAKKIGVSKSTLSKFFNGKG 34
 
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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