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Conserved domains on  [gi|1547349409|ref|WP_126956135|]
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MULTISPECIES: helix-turn-helix transcriptional regulator [Enterobacteriaceae]

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: ...
 94-224 3.02e-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: 113.90  E-value: 3.02e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547349409  94 IEALDFCVSAGPGAINsEFVEVLRSVEysvedarrmFNGRKAEQIRIINVRGDSMSGTIEPGDLLFVDISVQHFDGDGIY 173
Cdd:COG2932     1 VPLYDGEASAGGGAFN-EVEEPVDKLE---------FPGLPPDNLFAVRVSGDSMEPTIRDGDIVLVDPSDTEIRDGGIY 70

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1547349409 174 AFIYDDTSHVKRLQKMKD-KLLVISDNKTYRPWEpIEKEEMNKIFVFGKVIG 224
Cdd:COG2932    71 VVRTDGELLVKRLQRRPDgKLRLISDNPAYPPIE-IPPEDADEIEIIGRVVW 121
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
3-78 9.34e-10

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 53.85  E-value: 9.34e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1547349409   3 KETLAERLNQAMELSGMSQGALAKAAGIAQPTIWRLTSGNARGS-TKIVEIANALGVRTEWLSTGVGPMRADGQTPE 78
Cdd:COG1396     5 KKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSlETLLKLAKALGVSLDELLGGADEELPEALLSE 81
 
Name Accession Description Interval E-value
COG2932 COG2932
Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: ...
 94-224 3.02e-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: 113.90  E-value: 3.02e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547349409  94 IEALDFCVSAGPGAINsEFVEVLRSVEysvedarrmFNGRKAEQIRIINVRGDSMSGTIEPGDLLFVDISVQHFDGDGIY 173
Cdd:COG2932     1 VPLYDGEASAGGGAFN-EVEEPVDKLE---------FPGLPPDNLFAVRVSGDSMEPTIRDGDIVLVDPSDTEIRDGGIY 70

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1547349409 174 AFIYDDTSHVKRLQKMKD-KLLVISDNKTYRPWEpIEKEEMNKIFVFGKVIG 224
Cdd:COG2932    71 VVRTDGELLVKRLQRRPDgKLRLISDNPAYPPIE-IPPEDADEIEIIGRVVW 121
S24_LexA-like cd06529
Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of ...
 139-220 9.38e-20

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: 80.30  E-value: 9.38e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547349409 139 RIINVRGDSMSGTIEPGDLLFVDISVQHFDGDgIYAFIYDDTSHVKRLQKMKD-KLLVISDNKTYRPWEpIEKEEMNKIF 217
Cdd:cd06529     1 FALRVKGDSMEPTIPDGDLVLVDPSDTPRDGD-IVVARLDGELTVKRLQRRGGgRLRLISDNPAYPPIE-IDEEELEIVG 78


                  ...
gi 1547349409 218 VFG 220
Cdd:cd06529    79 VVG 81
Peptidase_S24 pfam00717
Peptidase S24-like;
100-223 9.10e-18

Peptidase S24-like;


Pssm-ID: 425835  Cd Length: 116  Bit Score: 76.09  E-value: 9.10e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547349409 100 CVSAG-PGAINSEFVEVLRSVEYSVEDARRMFngrkaeqirIINVRGDSMSGTIEPGDLLFVDISVQHFDGDgIYAFIYD 178
Cdd:pfam00717   5 RVAAGaPILAEEEIEGYLPLPESLLSPPGNLF---------ALRVKGDSMEPGIPDGDLVLVDPSREARNGD-IVVARLD 74

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1547349409 179 DTSHVKRLQKMKDKLLVISDNKTYRPWEpIEKEEMNKIfvFGKVI 223
Cdd:pfam00717  75 GEATVKRLYRDGGGIRLISLNPEYPPIE-LPAEDDVEI--IGRVV 116
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
3-78 9.34e-10

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 53.85  E-value: 9.34e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1547349409   3 KETLAERLNQAMELSGMSQGALAKAAGIAQPTIWRLTSGNARGS-TKIVEIANALGVRTEWLSTGVGPMRADGQTPE 78
Cdd:COG1396     5 KKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSlETLLKLAKALGVSLDELLGGADEELPEALLSE 81
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 7-63 5.74e-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: 51.01  E-value: 5.74e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1547349409   7 AERLNQAMELSGMSQGALAKAAGIAQPTIWRLTSGNARGS-TKIVEIANALGVRTEWL 63
Cdd:cd00093     1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSlETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
9-63 6.87e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 47.90  E-value: 6.87e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1547349409    9 RLNQAMELSGMSQGALAKAAGIAQPTIWRLTSGNARGSTKIVE-IANALGVRTEWL 63
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKkLAKALGVSLDEL 56
PRK13355 PRK13355
bifunctional HTH-domain containing protein/aminotransferase; Provisional
 3-82 3.70e-06

bifunctional HTH-domain containing protein/aminotransferase; Provisional


Pssm-ID: 237361 [Multi-domain]  Cd Length: 517  Bit Score: 47.04  E-value: 3.70e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547349409   3 KETLAERLNQAMELSGMSQGALAKAAGIAQPTIWR-LTSGNARGSTKIVE-----IANALGVRTEWLSTGVGPMRADGQT 76
Cdd:PRK13355    1 KTTFAERLKQAMKARGLKQEDLVHAAEARGVKLGKsHISQYVSGKTGPRRdvlpfLAAILGVSEDWLLGGESPADQESDA 80


                  ....*.
gi 1547349409  77 PEISQP 82
Cdd:PRK13355   81 SAVVES 86
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 10-63 9.80e-06

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


Pssm-ID: 460181 [Multi-domain]  Cd Length: 55  Bit Score: 41.76  E-value: 9.80e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1547349409  10 LNQAMELSGMSQGALAKAAGIAQPTIWRLTSGNAR-GSTKIVEIANALGVRTEWL 63
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREpSLETLKKLAEALGVSLDEL 55
PRK10276 PRK10276
translesion error-prone DNA polymerase V autoproteolytic subunit;
141-223 1.94e-04

translesion error-prone DNA polymerase V autoproteolytic subunit;


Pssm-ID: 182350  Cd Length: 139  Bit Score: 40.17  E-value: 1.94e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547349409 141 INVRGDSM-SGTIEPGDLLFVDISVQHFDGDGIYAFIyDDTSHVKRLQKmKDKLLVISDNKTYRPWePIEKEEmnKIFVF 219
Cdd:PRK10276   54 VKASGDSMiDAGISDGDLLIVDSAITASHGDIVIAAV-DGEFTVKKLQL-RPTVQLIPMNSAYSPI-TISSED--TLDVF 128


                  ....
gi 1547349409 220 GKVI 223
Cdd:PRK10276  129 GVVT 132
 
Name Accession Description Interval E-value
COG2932 COG2932
Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: ...
 94-224 3.02e-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: 113.90  E-value: 3.02e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547349409  94 IEALDFCVSAGPGAINsEFVEVLRSVEysvedarrmFNGRKAEQIRIINVRGDSMSGTIEPGDLLFVDISVQHFDGDGIY 173
Cdd:COG2932     1 VPLYDGEASAGGGAFN-EVEEPVDKLE---------FPGLPPDNLFAVRVSGDSMEPTIRDGDIVLVDPSDTEIRDGGIY 70

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1547349409 174 AFIYDDTSHVKRLQKMKD-KLLVISDNKTYRPWEpIEKEEMNKIFVFGKVIG 224
Cdd:COG2932    71 VVRTDGELLVKRLQRRPDgKLRLISDNPAYPPIE-IPPEDADEIEIIGRVVW 121
S24_LexA-like cd06529
Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of ...
 139-220 9.38e-20

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: 80.30  E-value: 9.38e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547349409 139 RIINVRGDSMSGTIEPGDLLFVDISVQHFDGDgIYAFIYDDTSHVKRLQKMKD-KLLVISDNKTYRPWEpIEKEEMNKIF 217
Cdd:cd06529     1 FALRVKGDSMEPTIPDGDLVLVDPSDTPRDGD-IVVARLDGELTVKRLQRRGGgRLRLISDNPAYPPIE-IDEEELEIVG 78


                  ...
gi 1547349409 218 VFG 220
Cdd:cd06529    79 VVG 81
Peptidase_S24 pfam00717
Peptidase S24-like;
100-223 9.10e-18

Peptidase S24-like;


Pssm-ID: 425835  Cd Length: 116  Bit Score: 76.09  E-value: 9.10e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547349409 100 CVSAG-PGAINSEFVEVLRSVEYSVEDARRMFngrkaeqirIINVRGDSMSGTIEPGDLLFVDISVQHFDGDgIYAFIYD 178
Cdd:pfam00717   5 RVAAGaPILAEEEIEGYLPLPESLLSPPGNLF---------ALRVKGDSMEPGIPDGDLVLVDPSREARNGD-IVVARLD 74

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1547349409 179 DTSHVKRLQKMKDKLLVISDNKTYRPWEpIEKEEMNKIfvFGKVI 223
Cdd:pfam00717  75 GEATVKRLYRDGGGIRLISLNPEYPPIE-LPAEDDVEI--IGRVV 116
Peptidase_S24_S26 cd06462
The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal ...
 139-222 9.82e-16

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: 69.60  E-value: 9.82e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547349409 139 RIINVRGDSMSGTIEPGDLLFVDISVQHFDGDGIYAFIYDDTS-HVKRLQKM--KDKLLVISDNKTYRPWEPIEKEEMNk 215
Cdd:cd06462     1 FALRVEGDSMEPTIPDGDLVLVDKSSYEPKRGDIVVFRLPGGElTVKRVIGLpgEGHYFLLGDNPNSPDSRIDGPPELD- 79


                  ....*..
gi 1547349409 216 ifVFGKV 222
Cdd:cd06462    80 --IVGVV 84
LexA COG1974
SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase) [Transcription, ...
 143-226 3.91e-10

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


Pssm-ID: 441577 [Multi-domain]  Cd Length: 199  Bit Score: 57.23  E-value: 3.91e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547349409 143 VRGDSMSG-TIEPGDLLFVDISVQHFDGDgIYAFIYDDTSHVKRLQKMKDKLLVISDNKTYrpwEPIEKEEMNkIFVFGK 221
Cdd:COG1974   117 VKGDSMIDaGILDGDLVIVDRQLEAENGD-IVVALIDGEATVKRLYKEGGRVRLQPENPAY---PPIIIEGDD-VEILGV 191


                  ....*
gi 1547349409 222 VIGSM 226
Cdd:COG1974   192 VVGVI 196
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
3-78 9.34e-10

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 53.85  E-value: 9.34e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1547349409   3 KETLAERLNQAMELSGMSQGALAKAAGIAQPTIWRLTSGNARGS-TKIVEIANALGVRTEWLSTGVGPMRADGQTPE 78
Cdd:COG1396     5 KKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSlETLLKLAKALGVSLDELLGGADEELPEALLSE 81
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 7-63 5.74e-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: 51.01  E-value: 5.74e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1547349409   7 AERLNQAMELSGMSQGALAKAAGIAQPTIWRLTSGNARGS-TKIVEIANALGVRTEWL 63
Cdd:cd00093     1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSlETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
9-63 6.87e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 47.90  E-value: 6.87e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1547349409    9 RLNQAMELSGMSQGALAKAAGIAQPTIWRLTSGNARGSTKIVE-IANALGVRTEWL 63
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKkLAKALGVSLDEL 56
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
3-63 2.77e-07

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 46.38  E-value: 2.77e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1547349409   3 KETLAERLNQAMELSGMSQGALAKAAGIAQPTIWRLTSGNARGSTKIV-EIANALGVRTEWL 63
Cdd:COG1476     2 KKKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELAlKIARALGVSLEEL 63
PRK13355 PRK13355
bifunctional HTH-domain containing protein/aminotransferase; Provisional
 3-82 3.70e-06

bifunctional HTH-domain containing protein/aminotransferase; Provisional


Pssm-ID: 237361 [Multi-domain]  Cd Length: 517  Bit Score: 47.04  E-value: 3.70e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547349409   3 KETLAERLNQAMELSGMSQGALAKAAGIAQPTIWR-LTSGNARGSTKIVE-----IANALGVRTEWLSTGVGPMRADGQT 76
Cdd:PRK13355    1 KTTFAERLKQAMKARGLKQEDLVHAAEARGVKLGKsHISQYVSGKTGPRRdvlpfLAAILGVSEDWLLGGESPADQESDA 80


                  ....*.
gi 1547349409  77 PEISQP 82
Cdd:PRK13355   81 SAVVES 86
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 10-63 9.80e-06

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


Pssm-ID: 460181 [Multi-domain]  Cd Length: 55  Bit Score: 41.76  E-value: 9.80e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1547349409  10 LNQAMELSGMSQGALAKAAGIAQPTIWRLTSGNAR-GSTKIVEIANALGVRTEWL 63
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREpSLETLKKLAEALGVSLDEL 55
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 4-62 4.12e-05

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: 40.69  E-value: 4.12e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547349409   4 ETLAERLNQAMELSGMSQGALAKAAGIAQPTIWRLTSGNARGSTKIVE-IANALGVRTEW 62
Cdd:COG1813    11 EDYGERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRkLEKALGISLAE 70
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 6-58 8.80e-05

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: 39.43  E-value: 8.80e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1547349409   6 LAERLNQAMELSGMSQGALAKAAGIAQPTIWRLTSGNAR--GSTKIVEIANALGV 58
Cdd:pfam13560   2 LGARLRRLRERAGLSQEALARRLGVSRSTLSRLETGRRGrpSPAVVERLARALGV 56
PRK08154 PRK08154
anaerobic benzoate catabolism transcriptional regulator; Reviewed
 6-78 1.26e-04

anaerobic benzoate catabolism transcriptional regulator; Reviewed


Pssm-ID: 236167 [Multi-domain]  Cd Length: 309  Bit Score: 42.25  E-value: 1.26e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1547349409   6 LAERLNQAMELSGMSQGALAKAAGIAQPTIWRLTSGnaRGSTKIV---EIANALGVRTEWLstgVGPmrADGQTPE 78
Cdd:PRK08154   29 LGERVRTLRARRGMSRKVLAQASGVSERYLAQLESG--QGNVSILllrRVARALGCSLADL---LGD--VDTSSPD 97
PRK10276 PRK10276
translesion error-prone DNA polymerase V autoproteolytic subunit;
141-223 1.94e-04

translesion error-prone DNA polymerase V autoproteolytic subunit;


Pssm-ID: 182350  Cd Length: 139  Bit Score: 40.17  E-value: 1.94e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547349409 141 INVRGDSM-SGTIEPGDLLFVDISVQHFDGDGIYAFIyDDTSHVKRLQKmKDKLLVISDNKTYRPWePIEKEEmnKIFVF 219
Cdd:PRK10276   54 VKASGDSMiDAGISDGDLLIVDSAITASHGDIVIAAV-DGEFTVKKLQL-RPTVQLIPMNSAYSPI-TISSED--TLDVF 128


                  ....
gi 1547349409 220 GKVI 223
Cdd:PRK10276  129 GVVT 132
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 4-63 2.83e-04

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


Pssm-ID: 442838 [Multi-domain]  Cd Length: 95  Bit Score: 38.85  E-value: 2.83e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1547349409   4 ETLAERLNQAMELSGMSQGALAKAAGIAQPTIWRLTSGNARGS-TKIVEIANALGVRTEWL 63
Cdd:COG3620    16 DTLGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTvSTLEKIAEALGKELSAV 76
Phage_CI_repr pfam07022
Bacteriophage CI repressor helix-turn-helix domain; This family consists of several phage CI ...
 8-71 4.53e-04

Bacteriophage CI repressor helix-turn-helix domain; This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic.


Pssm-ID: 311152  Cd Length: 65  Bit Score: 37.69  E-value: 4.53e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1547349409   8 ERLNQAMELSGMS-QGALAKAAGIAQPTIWRLTSGNARGSTKIVEIANALGVRTEWLSTGVGPMR 71
Cdd:pfam07022   1 AVIERLMKAYGFKsRQELADHLGVSKSTLSTWYTRDSFPAELVVRCALETGVSLEWLATGDGELY 65
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 8-68 8.58e-04

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


Pssm-ID: 463728 [Multi-domain]  Cd Length: 64  Bit Score: 36.88  E-value: 8.58e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1547349409   8 ERLNQAMELSGMSQGALAKAAGIAQPTIWRLTSGNAR-GSTKIVEIANALGVRTEWLSTGVG 68
Cdd:pfam12844   2 ERLRKAREERGLTQEELAERLGISRSQLSAIENGKSVpPAETLYKIAELLGVPANWLLQGEG 63
COG5606 COG5606
Predicted DNA-binding protein, XRE-type HTH domain [General function prediction only];
3-61 1.12e-03

Predicted DNA-binding protein, XRE-type HTH domain [General function prediction only];


Pssm-ID: 444337  Cd Length: 105  Bit Score: 37.55  E-value: 1.12e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1547349409   3 KETLAERLNQAMELSGMSQGALAKAAGIAQPTIWRLTSGNARGST--KIVEIANALGVRTE 61
Cdd:COG5606    30 KAQLMAAIRKLIKERGLTQAEAAELLGITQPRVSDLLRGKISKFSldKLVNMLARLGQDVE 90
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 1-130 1.18e-03

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 37.91  E-value: 1.18e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547349409   1 MKKETLAERLNQAMELSGMSQGALAKAAGIAQPTIWRLTSGNARGSTK-IVEIANALGVRTEWLSTGvgpmrADGQTPEI 79
Cdd:PRK09706    1 MKNLTLGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKnLFALAKALQCSPTWLLFG-----DEDKQPTP 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1547349409  80 SQPK---TELAPTDTFRIEALDfcvsAGPgaiNSEFVEVLRSVEYSVEDARRMF 130
Cdd:PRK09706   76 PVPLnqpVELSEDQKELLELFD----ALP---ESEQDAQLSEMRARVENFNKLF 122
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
3-58 1.21e-03

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 36.27  E-value: 1.21e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1547349409   3 KETLAERlnqamelsGMSQGALAKAAGIAQPTIWRLTSGNARG---STkIVEIANALGV 58
Cdd:COG3655     7 DELLAER--------GMTKKELAEATGISRATLSRLKNGKAKAvrlDT-LEKICKALDC 56
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 9-59 2.03e-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: 35.59  E-value: 2.03e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1547349409   9 RLNQAMELSGMSQGALAKAAGIAQPTIWRLTSGNARG-STKIVE-IANALGVR 59
Cdd:pfam13443   1 KLRKLMADRGISKSDLARATGISRATLSRLRKGKPKRvSLDTLDkICDALGCQ 53
YdaS_antitoxin pfam15943
Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT; YdaS_antitoxin is a family ...
 10-50 2.53e-03

Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT; YdaS_antitoxin is a family of putative bacterial antitoxins, neutralising the toxin YdaT, family pfam06254.


Pssm-ID: 435033  Cd Length: 65  Bit Score: 35.40  E-value: 2.53e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1547349409  10 LNQAMELSGmSQGALAKAAGIAQPTIWRLTSGNARGSTKIV 50
Cdd:pfam15943   1 IKKAIEIVG-GQKALAEALGVTQQAVSQWLHGKKGIPAEYC 40
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 4-63 5.02e-03

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 35.17  E-value: 5.02e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1547349409   4 ETLAERLnqaMELSGMSQGALAKAAGIAQPTIWRLTSGNARGSTKI-VEIANALGVRTE-WL 63
Cdd:COG3093    11 EILREEF---LEPLGLSQTELAKALGVSRQRISEILNGKRAITADTaLRLARAFGTSAEfWL 69
 
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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