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Conserved domains on  [gi|489080153|ref|WP_002990090|]
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XRE family transcriptional regulator [Streptococcus pyogenes]

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: ...
 132-244 1.59e-32

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


:

Pssm-ID: 442176  Cd Length: 121  Bit Score: 115.06  E-value: 1.59e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489080153 132 YYDHAASAGTGQYLNDVQ-VETIELP-VDYDADFVIPVHGDSMEPKYHSGDYVFVKLSV-ELADGDIGVFEYYGDAYIKQ 208
Cdd:COG2932    3 LYDGEASAGGGAFNEVEEpVDKLEFPgLPPDNLFAVRVSGDSMEPTIRDGDIVLVDPSDtEIRDGGIYVVRTDGELLVKR 82

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 489080153 209 LLINDEGAF-LHSLNSKYEDIPVDRD--SDFRIIGEVVG 244
Cdd:COG2932   83 LQRRPDGKLrLISDNPAYPPIEIPPEdaDEIEIIGRVVW 121
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-74 4.37e-15

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 68.48  E-value: 4.37e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489080153   1 MNILGNSIKEIRKSKKMTQKELAKLTGFKQNTISNHENGNRQLDEVDIRKYAKALKIEPQQLFDYSSSPTNPQV 74
Cdd:COG1396    5 KKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELPEAL 78
 
Name Accession Description Interval E-value
COG2932 COG2932
Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: ...
 132-244 1.59e-32

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


Pssm-ID: 442176  Cd Length: 121  Bit Score: 115.06  E-value: 1.59e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489080153 132 YYDHAASAGTGQYLNDVQ-VETIELP-VDYDADFVIPVHGDSMEPKYHSGDYVFVKLSV-ELADGDIGVFEYYGDAYIKQ 208
Cdd:COG2932    3 LYDGEASAGGGAFNEVEEpVDKLEFPgLPPDNLFAVRVSGDSMEPTIRDGDIVLVDPSDtEIRDGGIYVVRTDGELLVKR 82

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 489080153 209 LLINDEGAF-LHSLNSKYEDIPVDRD--SDFRIIGEVVG 244
Cdd:COG2932   83 LQRRPDGKLrLISDNPAYPPIEIPPEdaDEIEIIGRVVW 121
Peptidase_S24 pfam00717
Peptidase S24-like;
137-243 8.36e-28

Peptidase S24-like;


Pssm-ID: 425835  Cd Length: 116  Bit Score: 102.67  E-value: 8.36e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489080153  137 ASAGTGQYLNDVQVETIELPVDY----DADFVIPVHGDSMEPKYHSGDYVFVKLSVELADGDIGVFEYYGDAYIKQLLIN 212
Cdd:pfam00717   6 VAAGAPILAEEEIEGYLPLPESLlsppGNLFALRVKGDSMEPGIPDGDLVLVDPSREARNGDIVVARLDGEATVKRLYRD 85

                          90       100       110
                  ....*....|....*....|....*....|.
gi 489080153  213 DEGAFLHSLNSKYEDIPVDRDSDFRIIGEVV 243
Cdd:pfam00717  86 GGGIRLISLNPEYPPIELPAEDDVEIIGRVV 116
S24_LexA-like cd06529
Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of ...
 163-243 1.47e-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: 88.00  E-value: 1.47e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489080153 163 FVIPVHGDSMEPKYHSGDYVFVKLSVELADGDIGVFEYYGDAYIKQLLINDEGAF-LHSLNSKYEDIPVDRDsDFRIIGE 241
Cdd:cd06529    1 FALRVKGDSMEPTIPDGDLVLVDPSDTPRDGDIVVARLDGELTVKRLQRRGGGRLrLISDNPAYPPIEIDEE-ELEIVGV 79


                 ..
gi 489080153 242 VV 243
Cdd:cd06529   80 VG 81
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-74 4.37e-15

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 68.48  E-value: 4.37e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489080153   1 MNILGNSIKEIRKSKKMTQKELAKLTGFKQNTISNHENGNRQLDEVDIRKYAKALKIEPQQLFDYSSSPTNPQV 74
Cdd:COG1396    5 KKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELPEAL 78
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 5-62 6.09e-15

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: 67.19  E-value: 6.09e-15
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 489080153   5 GNSIKEIRKSKKMTQKELAKLTGFKQNTISNHENGNRQLDEVDIRKYAKALKIEPQQL 62
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
8-62 3.74e-13

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 62.15  E-value: 3.74e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 489080153     8 IKEIRKSKKMTQKELAKLTGFKQNTISNHENGNRQLDEVDIRKYAKALKIEPQQL 62
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 8-62 2.08e-11

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: 57.55  E-value: 2.08e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 489080153    8 IKEIRKSKKMTQKELAKLTGFKQNTISNHENGNRQLDEVDIRKYAKALKIEPQQL 62
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
lexA TIGR00498
SOS regulatory protein LexA; LexA acts as a homodimer to repress a number of genes involved in ...
 150-250 7.41e-07

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: 48.17  E-value: 7.41e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489080153  150 VETIE--LPVDYD------ADFVIPVHGDSM-EPKYHSGDYVFVKLSVELADGDIGVFEYYGDAYIKQLLINDEGAFLHS 220
Cdd:TIGR00498  91 EQHIEeyFPIDFSllkkpsAVFLLKVMGDSMvDAGICDGDLLIVRSQKDARNGEIVAAMIDGEVTVKRFYKDGTKVELKP 170

                          90       100       110
                  ....*....|....*....|....*....|
gi 489080153  221 LNSKYEDIPVdRDSDFRIIGEVVGSYSGNH 250
Cdd:TIGR00498 171 ENPEFDPIVL-NAEDVTILGKVVGVIRNFQ 199
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 4-122 8.67e-07

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 47.16  E-value: 8.67e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489080153   4 LGNSIKEIRKSKKMTQKELAKLTGFKQNTISNHENGNRQLDEVDIRKYAKALKIEPQQLF--DYSSSPTNPQVELIPSTL 81
Cdd:PRK09706   6 LGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCSPTWLLfgDEDKQPTPPVPLNQPVEL 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 489080153  82 qkitsTSSQLEHKRQLNVLDYAE--TQL-EQQNTVESNKDIVEE 122
Cdd:PRK09706  86 -----SEDQKELLELFDALPESEqdAQLsEMRARVENFNKLFEE 124
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 3-39 1.60e-06

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: 46.08  E-value: 1.60e-06
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 489080153    3 ILGNSIKEIRKSKKMTQKELAKLTGFKQNTISNHENG 39
Cdd:TIGR03830  65 LTGPEIRRIRKKLGLSQREAAELLGGGVNAFSRYERG 101
PRK10276 PRK10276
translesion error-prone DNA polymerase V autoproteolytic subunit;
161-242 2.37e-03

translesion error-prone DNA polymerase V autoproteolytic subunit;


Pssm-ID: 182350  Cd Length: 139  Bit Score: 37.47  E-value: 2.37e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489080153 161 ADFVIPVHGDSM-EPKYHSGDYVFVKLSVELADGDIGVFEYYGDAYIKQLLINDEGAfLHSLNSKYEDIPVDRDSDFRII 239
Cdd:PRK10276  50 ATYFVKASGDSMiDAGISDGDLLIVDSAITASHGDIVIAAVDGEFTVKKLQLRPTVQ-LIPMNSAYSPITISSEDTLDVF 128


                 ...
gi 489080153 240 GEV 242
Cdd:PRK10276 129 GVV 131
 
Name Accession Description Interval E-value
COG2932 COG2932
Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: ...
 132-244 1.59e-32

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


Pssm-ID: 442176  Cd Length: 121  Bit Score: 115.06  E-value: 1.59e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489080153 132 YYDHAASAGTGQYLNDVQ-VETIELP-VDYDADFVIPVHGDSMEPKYHSGDYVFVKLSV-ELADGDIGVFEYYGDAYIKQ 208
Cdd:COG2932    3 LYDGEASAGGGAFNEVEEpVDKLEFPgLPPDNLFAVRVSGDSMEPTIRDGDIVLVDPSDtEIRDGGIYVVRTDGELLVKR 82

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 489080153 209 LLINDEGAF-LHSLNSKYEDIPVDRD--SDFRIIGEVVG 244
Cdd:COG2932   83 LQRRPDGKLrLISDNPAYPPIEIPPEdaDEIEIIGRVVW 121
Peptidase_S24 pfam00717
Peptidase S24-like;
137-243 8.36e-28

Peptidase S24-like;


Pssm-ID: 425835  Cd Length: 116  Bit Score: 102.67  E-value: 8.36e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489080153  137 ASAGTGQYLNDVQVETIELPVDY----DADFVIPVHGDSMEPKYHSGDYVFVKLSVELADGDIGVFEYYGDAYIKQLLIN 212
Cdd:pfam00717   6 VAAGAPILAEEEIEGYLPLPESLlsppGNLFALRVKGDSMEPGIPDGDLVLVDPSREARNGDIVVARLDGEATVKRLYRD 85

                          90       100       110
                  ....*....|....*....|....*....|.
gi 489080153  213 DEGAFLHSLNSKYEDIPVDRDSDFRIIGEVV 243
Cdd:pfam00717  86 GGGIRLISLNPEYPPIELPAEDDVEIIGRVV 116
S24_LexA-like cd06529
Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of ...
 163-243 1.47e-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: 88.00  E-value: 1.47e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489080153 163 FVIPVHGDSMEPKYHSGDYVFVKLSVELADGDIGVFEYYGDAYIKQLLINDEGAF-LHSLNSKYEDIPVDRDsDFRIIGE 241
Cdd:cd06529    1 FALRVKGDSMEPTIPDGDLVLVDPSDTPRDGDIVVARLDGELTVKRLQRRGGGRLrLISDNPAYPPIEIDEE-ELEIVGV 79


                 ..
gi 489080153 242 VV 243
Cdd:cd06529   80 VG 81
LexA COG1974
SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase) [Transcription, ...
 151-246 7.26e-21

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


Pssm-ID: 441577 [Multi-domain]  Cd Length: 199  Bit Score: 86.89  E-value: 7.26e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489080153 151 ETIELPVDY----DADFVIPVHGDSM-EPKYHSGDYVFVKLSVELADGDIGVFEYYGDAYIKQLLINDEGAFLHSLNSKY 225
Cdd:COG1974   97 EYLDLPEELvknpGATFALRVKGDSMiDAGILDGDLVIVDRQLEAENGDIVVALIDGEATVKRLYKEGGRVRLQPENPAY 176

                         90       100
                 ....*....|....*....|.
gi 489080153 226 EDIPVDRDsDFRIIGEVVGSY 246
Cdd:COG1974  177 PPIIIEGD-DVEILGVVVGVI 196
Peptidase_S24_S26 cd06462
The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal ...
 163-242 3.43e-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: 73.84  E-value: 3.43e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489080153 163 FVIPVHGDSMEPKYHSGDYVFV-KLSVELADGDIGVFEYYGD-AYIKQlLINDEGA---FLHSLNSKYEDIPVDRDSDFR 237
Cdd:cd06462    1 FALRVEGDSMEPTIPDGDLVLVdKSSYEPKRGDIVVFRLPGGeLTVKR-VIGLPGEghyFLLGDNPNSPDSRIDGPPELD 79


                 ....*
gi 489080153 238 IIGEV 242
Cdd:cd06462   80 IVGVV 84
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-74 4.37e-15

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 68.48  E-value: 4.37e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489080153   1 MNILGNSIKEIRKSKKMTQKELAKLTGFKQNTISNHENGNRQLDEVDIRKYAKALKIEPQQLFDYSSSPTNPQV 74
Cdd:COG1396    5 KKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELPEAL 78
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 5-62 6.09e-15

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: 67.19  E-value: 6.09e-15
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 489080153   5 GNSIKEIRKSKKMTQKELAKLTGFKQNTISNHENGNRQLDEVDIRKYAKALKIEPQQL 62
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-66 1.40e-14

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 66.41  E-value: 1.40e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489080153   1 MN-ILGNSIKEIRKSKKMTQKELAKLTGFKQNTISNHENGNRQLDEVDIRKYAKALKIEPQQLFDYS 66
Cdd:COG1476    1 MKkKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLE 67
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
8-62 3.74e-13

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 62.15  E-value: 3.74e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 489080153     8 IKEIRKSKKMTQKELAKLTGFKQNTISNHENGNRQLDEVDIRKYAKALKIEPQQL 62
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 8-62 2.08e-11

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: 57.55  E-value: 2.08e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 489080153    8 IKEIRKSKKMTQKELAKLTGFKQNTISNHENGNRQLDEVDIRKYAKALKIEPQQL 62
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 4-58 2.87e-11

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: 57.64  E-value: 2.87e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 489080153   4 LGNSIKEIRKSKKMTQKELAKLTGFKQNTISNHENGNRQLDEVDIRKYAKALKIE 58
Cdd:COG1813   13 YGERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGIS 67
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 4-63 9.35e-09

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: 50.96  E-value: 9.35e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489080153   4 LGNSIKEIRKSKKMTQKELAKLTGFKQNTISNHENGNRQLDEVD------IRKYAKALKIEPQQLF 63
Cdd:COG1426    6 IGELLRQAREAKGLSLEDVAERTKISVSYLEAIEEGDFDALPGPvyvrgfLRSYARALGLDPEELL 71
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 5-63 9.95e-09

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: 50.36  E-value: 9.95e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 489080153    5 GNSIKEIRKSKKMTQKELAKLTGFKQNTISNHENGNRQLDEVDIRKYAKALKIEPQQLF 63
Cdd:pfam12844   1 GERLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLL 59
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 4-62 5.61e-08

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: 49.25  E-value: 5.61e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 489080153   4 LGNSIKEIRKSKKMTQKELAKLTGFKQNTISNHENGNRQLDEVDIRKYAKALKIEPQQL 62
Cdd:COG3620   18 LGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAV 76
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 8-65 4.48e-07

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


Pssm-ID: 433211 [Multi-domain]  Cd Length: 63  Bit Score: 45.99  E-value: 4.48e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 489080153    8 IKEIRKSKKMTQKELAKLTGFKQNTISNHENGN-RQLDEVDIRKYAKALKIEPQQLFDY 65
Cdd:pfam13443   2 LRKLMADRGISKSDLARATGISRATLSRLRKGKpKRVSLDTLDKICDALGCQPGDLLEY 60
lexA TIGR00498
SOS regulatory protein LexA; LexA acts as a homodimer to repress a number of genes involved in ...
 150-250 7.41e-07

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: 48.17  E-value: 7.41e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489080153  150 VETIE--LPVDYD------ADFVIPVHGDSM-EPKYHSGDYVFVKLSVELADGDIGVFEYYGDAYIKQLLINDEGAFLHS 220
Cdd:TIGR00498  91 EQHIEeyFPIDFSllkkpsAVFLLKVMGDSMvDAGICDGDLLIVRSQKDARNGEIVAAMIDGEVTVKRFYKDGTKVELKP 170

                          90       100       110
                  ....*....|....*....|....*....|
gi 489080153  221 LNSKYEDIPVdRDSDFRIIGEVVGSYSGNH 250
Cdd:TIGR00498 171 ENPEFDPIVL-NAEDVTILGKVVGVIRNFQ 199
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 4-122 8.67e-07

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 47.16  E-value: 8.67e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489080153   4 LGNSIKEIRKSKKMTQKELAKLTGFKQNTISNHENGNRQLDEVDIRKYAKALKIEPQQLF--DYSSSPTNPQVELIPSTL 81
Cdd:PRK09706   6 LGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCSPTWLLfgDEDKQPTPPVPLNQPVEL 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 489080153  82 qkitsTSSQLEHKRQLNVLDYAE--TQL-EQQNTVESNKDIVEE 122
Cdd:PRK09706  86 -----SEDQKELLELFDALPESEqdAQLsEMRARVENFNKLFEE 124
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 3-39 1.60e-06

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: 46.08  E-value: 1.60e-06
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 489080153    3 ILGNSIKEIRKSKKMTQKELAKLTGFKQNTISNHENG 39
Cdd:TIGR03830  65 LTGPEIRRIRKKLGLSQREAAELLGGGVNAFSRYERG 101
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
8-42 2.33e-06

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 44.15  E-value: 2.33e-06
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 489080153   8 IKEIRKSKKMTQKELAKLTGFKQNTISNHENGNRQ 42
Cdd:COG2944   11 IRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRK 45
LepB COG0681
Signal peptidase I [Intracellular trafficking, secretion, and vesicular transport];
163-207 2.61e-06

Signal peptidase I [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 440445 [Multi-domain]  Cd Length: 189  Bit Score: 46.77  E-value: 2.61e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 489080153 163 FVIPvhGDSMEPKYHSGDYVFV-KLSVELAD---GDIGVFEYYGD---AYIK 207
Cdd:COG0681   36 FVIP--SGSMEPTLLVGDRLLVnKLSYGFGEpkrGDIVVFKYPEDpskDYIK 85
S26_SPase_I cd06530
The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4. ...
 163-207 2.26e-05

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: 41.80  E-value: 2.26e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 489080153 163 FVIPVHGDSMEPKYHSGDYVFV-KLSVELAD---GDIGVFEYYGDA---YIK 207
Cdd:cd06530    1 EPVVVPGGSMEPTLQPGDLVLVnKLSYGFREpkrGDVVVFKSPGDPgkpIIK 52
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
8-65 2.75e-05

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 41.28  E-value: 2.75e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 489080153   8 IKEIRKSKKMTQKELAKLTGFKQNTISNHENG-NRQLDEVDIRKYAKALKIEPQQLFDY 65
Cdd:COG3655    6 LDELLAERGMTKKELAEATGISRATLSRLKNGkAKAVRLDTLEKICKALDCQPGDLLEY 64
PRK09726 PRK09726
type II toxin-antitoxin system antitoxin HipB;
4-38 3.27e-05

type II toxin-antitoxin system antitoxin HipB;


Pssm-ID: 182049  Cd Length: 88  Bit Score: 41.50  E-value: 3.27e-05
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 489080153   4 LGNSIKEIRKSKKMTQKELAKLTGFKQNTISNHEN 38
Cdd:PRK09726  13 LANAMKLVRQQNGWTQSELAKKIGIKQATISNFEN 47
sigpep_I_bact TIGR02227
signal peptidase I, bacterial type; This model represents signal peptidase I from most ...
 163-214 3.55e-04

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: 39.52  E-value: 3.55e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489080153  163 FVIPVHGDSMEPKYHSGDYVFV-KLSVELAD---GDIGVFEY---YGDAYIK---------------QLLINDE 214
Cdd:TIGR02227   4 FPYKIPGGSMEPTLKEGDRILVnKFAYRTSDpkrGDIVVFKDpdtNKNIYVKriiglpgdkvefrdgKLYINGK 77
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 4-59 8.73e-04

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: 36.74  E-value: 8.73e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 489080153    4 LGNSIKEIRKSKKMTQKELAKLTGFKQNTISNHENGNRQL-DEVDIRKYAKALKIEP 59
Cdd:pfam13560   2 LGARLRRLRERAGLSQEALARRLGVSRSTLSRLETGRRGRpSPAVVERLARALGVDG 58
PRK10276 PRK10276
translesion error-prone DNA polymerase V autoproteolytic subunit;
161-242 2.37e-03

translesion error-prone DNA polymerase V autoproteolytic subunit;


Pssm-ID: 182350  Cd Length: 139  Bit Score: 37.47  E-value: 2.37e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489080153 161 ADFVIPVHGDSM-EPKYHSGDYVFVKLSVELADGDIGVFEYYGDAYIKQLLINDEGAfLHSLNSKYEDIPVDRDSDFRII 239
Cdd:PRK10276  50 ATYFVKASGDSMiDAGISDGDLLIVDSAITASHGDIVIAAVDGEFTVKKLQLRPTVQ-LIPMNSAYSPITISSEDTLDVF 128


                 ...
gi 489080153 240 GEV 242
Cdd:PRK10276 129 GVV 131
Peptidase_S26 pfam10502
Signal peptidase, peptidase S26; This is a family of membrane signal serine endopeptidases ...
 163-207 3.09e-03

Signal peptidase, peptidase S26; This is a family of membrane signal serine endopeptidases which function in the processing of newly-synthesized secreted proteins. Peptidase S26 removes the hydrophobic, N-terminal, signal peptides as proteins are translocated across membranes. The active site residues take the form of a catalytic dyad that is Ser, Lys in subfamily S26A; the Ser is the nucleophile in catalysis, and the Lys is the general base.


Pssm-ID: 431321 [Multi-domain]  Cd Length: 162  Bit Score: 37.18  E-value: 3.09e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 489080153  163 FVIPVHgdSMEPKYHSGDYVFVKLSV----ELADGDIGVF---EYYGDAYIK 207
Cdd:pfam10502  26 YVVPGG--SMSPTLPIGDYLIVNKFSyglgEPKRGDIVVFrppEGPGVPLIK 75
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 10-60 4.28e-03

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 35.56  E-value: 4.28e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 489080153  10 EIRKSKKMTQKELAKLTGFKQNTISNHENGNRQLDEVDIRKYAKALKIEPQ 60
Cdd:COG3093   16 EFLEPLGLSQTELAKALGVSRQRISEILNGKRAITADTALRLARAFGTSAE 66
HTH_37 pfam13744
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain.
 8-50 6.77e-03

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


Pssm-ID: 433449 [Multi-domain]  Cd Length: 80  Bit Score: 34.51  E-value: 6.77e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 489080153    8 IKEIRKSKKMTQKELAKLTGFKQNTISNHENGnrQLDEVDIRK 50
Cdd:pfam13744  23 IARLIEGRGLSQQEAAALLGIAQPKVSALLKG--KLSRFSLDK 63
 
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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