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Conserved domains on  [gi|446635057|ref|WP_000712403|]
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MULTISPECIES: helix-turn-helix transcriptional regulator [Salmonella]

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: ...
 89-219 8.43e-33

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: 8.43e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446635057  89 IDILDLEVSAGPGVINrEFVEILRSVEysqddarhmFDGRKAENIRIINVRGDSMSGTIEPGDLLFVDVSIKNFDGDGIY 168
Cdd:COG2932    1 VPLYDGEASAGGGAFN-EVEEPVDKLE---------FPGLPPDNLFAVRVSGDSMEPTIRDGDIVLVDPSDTEIRDGGIY 70

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 446635057 169 AFLYDDTAHVKRLQKMKD-KLLVISDNKSYSAWDpIERDEMNRVFVFGKVIG 219
Cdd:COG2932   71 VVRTDGELLVKRLQRRPDgKLRLISDNPAYPPIE-IPPEDADEIEIIGRVVW 121
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
3-66 3.57e-09

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 51.92  E-value: 3.57e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446635057   3 KETLSDRLNKAMELAGMSQGALAKASGVAQPTIWRLTSGNARGS-TKIVEIANALGVNSEWLSTG 66
Cdd:COG1396    5 KKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSlETLLKLAKALGVSLDELLGG 69
 
Name Accession Description Interval E-value
COG2932 COG2932
Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: ...
 89-219 8.43e-33

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: 8.43e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446635057  89 IDILDLEVSAGPGVINrEFVEILRSVEysqddarhmFDGRKAENIRIINVRGDSMSGTIEPGDLLFVDVSIKNFDGDGIY 168
Cdd:COG2932    1 VPLYDGEASAGGGAFN-EVEEPVDKLE---------FPGLPPDNLFAVRVSGDSMEPTIRDGDIVLVDPSDTEIRDGGIY 70

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 446635057 169 AFLYDDTAHVKRLQKMKD-KLLVISDNKSYSAWDpIERDEMNRVFVFGKVIG 219
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 ...
 134-215 2.17e-19

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: 79.14  E-value: 2.17e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446635057 134 RIINVRGDSMSGTIEPGDLLFVDVSIKNFDGDgIYAFLYDDTAHVKRLQKMKD-KLLVISDNKSYSAWDpIERDEMNRVF 212
Cdd:cd06529    1 FALRVKGDSMEPTIPDGDLVLVDPSDTPRDGD-IVVARLDGELTVKRLQRRGGgRLRLISDNPAYPPIE-IDEEELEIVG 78


                 ...
gi 446635057 213 VFG 215
Cdd:cd06529   79 VVG 81
Peptidase_S24 pfam00717
Peptidase S24-like;
95-218 1.72e-16

Peptidase S24-like;


Pssm-ID: 425835  Cd Length: 116  Bit Score: 72.62  E-value: 1.72e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446635057   95 EVSAGPGVINREfvEILRSVEYSQDDARHmfdgrkAENIRIINVRGDSMSGTIEPGDLLFVDVSIKNFDGDgIYAFLYDD 174
Cdd:pfam00717   5 RVAAGAPILAEE--EIEGYLPLPESLLSP------PGNLFALRVKGDSMEPGIPDGDLVLVDPSREARNGD-IVVARLDG 75

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 446635057  175 TAHVKRLQKMKDKLLVISDNKSYsawDPIERDEMNRVFVFGKVI 218
Cdd:pfam00717  76 EATVKRLYRDGGGIRLISLNPEY---PPIELPAEDDVEIIGRVV 116
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
3-66 3.57e-09

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 51.92  E-value: 3.57e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446635057   3 KETLSDRLNKAMELAGMSQGALAKASGVAQPTIWRLTSGNARGS-TKIVEIANALGVNSEWLSTG 66
Cdd:COG1396    5 KKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSlETLLKLAKALGVSLDELLGG 69
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 7-63 1.60e-08

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: 49.47  E-value: 1.60e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 446635057   7 SDRLNKAMELAGMSQGALAKASGVAQPTIWRLTSGNARGS-TKIVEIANALGVNSEWL 63
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSlETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
9-63 5.47e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 47.90  E-value: 5.47e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 446635057     9 RLNKAMELAGMSQGALAKASGVAQPTIWRLTSGNARGSTKIVE-IANALGVNSEWL 63
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKkLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 10-63 7.09e-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: 42.14  E-value: 7.09e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 446635057   10 LNKAMELAGMSQGALAKASGVAQPTIWRLTSGNAR-GSTKIVEIANALGVNSEWL 63
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREpSLETLKKLAEALGVSLDEL 55
PRK13355 PRK13355
bifunctional HTH-domain containing protein/aminotransferase; Provisional
 3-98 1.01e-05

bifunctional HTH-domain containing protein/aminotransferase; Provisional


Pssm-ID: 237361 [Multi-domain]  Cd Length: 517  Bit Score: 45.88  E-value: 1.01e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446635057   3 KETLSDRLNKAMELAGMSQGALAKASGVAQPTIWR-LTSGNARGSTKIVE-----IANALGVNSEWLSTGIGPMKKDGTT 76
Cdd:PRK13355   1 KTTFAERLKQAMKARGLKQEDLVHAAEARGVKLGKsHISQYVSGKTGPRRdvlpfLAAILGVSEDWLLGGESPADQESDA 80

                         90       100
                 ....*....|....*....|..
gi 446635057  77 PINASPSSNTFKIDILDLEVSA 98
Cdd:PRK13355  81 SAVVESAPNSHLADPSAPTTPI 102
PRK10276 PRK10276
translesion error-prone DNA polymerase V autoproteolytic subunit;
136-218 3.09e-04

translesion error-prone DNA polymerase V autoproteolytic subunit;


Pssm-ID: 182350  Cd Length: 139  Bit Score: 39.78  E-value: 3.09e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446635057 136 INVRGDSM-SGTIEPGDLLFVDVSIKNFDGDGIYAFLyDDTAHVKRLQKmKDKLLVISDNKSYSawdPI---ERDEMNrv 211
Cdd:PRK10276  54 VKASGDSMiDAGISDGDLLIVDSAITASHGDIVIAAV-DGEFTVKKLQL-RPTVQLIPMNSAYS---PItisSEDTLD-- 126


                 ....*..
gi 446635057 212 fVFGKVI 218
Cdd:PRK10276 127 -VFGVVT 132
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 14-63 6.02e-03

addiction module antidote protein, HigA family; Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair. [Regulatory functions, DNA interactions, Regulatory functions, Protein interactions, Mobile and extrachromosomal element functions, Other]


Pssm-ID: 274228 [Multi-domain]  Cd Length: 78  Bit Score: 34.52  E-value: 6.02e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 446635057   14 MELAGMSQGALAKASGVAQPTIWRLTSGNARGSTKI-VEIANALGVNSE-WL 63
Cdd:TIGR02607  14 LEPLGLSVRALAKALGVSRSTLSRIVNGRAAITADMaLRLAKALGTSPEfWL 65
 
Name Accession Description Interval E-value
COG2932 COG2932
Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: ...
 89-219 8.43e-33

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: 8.43e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446635057  89 IDILDLEVSAGPGVINrEFVEILRSVEysqddarhmFDGRKAENIRIINVRGDSMSGTIEPGDLLFVDVSIKNFDGDGIY 168
Cdd:COG2932    1 VPLYDGEASAGGGAFN-EVEEPVDKLE---------FPGLPPDNLFAVRVSGDSMEPTIRDGDIVLVDPSDTEIRDGGIY 70

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 446635057 169 AFLYDDTAHVKRLQKMKD-KLLVISDNKSYSAWDpIERDEMNRVFVFGKVIG 219
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 ...
 134-215 2.17e-19

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: 79.14  E-value: 2.17e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446635057 134 RIINVRGDSMSGTIEPGDLLFVDVSIKNFDGDgIYAFLYDDTAHVKRLQKMKD-KLLVISDNKSYSAWDpIERDEMNRVF 212
Cdd:cd06529    1 FALRVKGDSMEPTIPDGDLVLVDPSDTPRDGD-IVVARLDGELTVKRLQRRGGgRLRLISDNPAYPPIE-IDEEELEIVG 78


                 ...
gi 446635057 213 VFG 215
Cdd:cd06529   79 VVG 81
Peptidase_S24 pfam00717
Peptidase S24-like;
95-218 1.72e-16

Peptidase S24-like;


Pssm-ID: 425835  Cd Length: 116  Bit Score: 72.62  E-value: 1.72e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446635057   95 EVSAGPGVINREfvEILRSVEYSQDDARHmfdgrkAENIRIINVRGDSMSGTIEPGDLLFVDVSIKNFDGDgIYAFLYDD 174
Cdd:pfam00717   5 RVAAGAPILAEE--EIEGYLPLPESLLSP------PGNLFALRVKGDSMEPGIPDGDLVLVDPSREARNGD-IVVARLDG 75

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 446635057  175 TAHVKRLQKMKDKLLVISDNKSYsawDPIERDEMNRVFVFGKVI 218
Cdd:pfam00717  76 EATVKRLYRDGGGIRLISLNPEY---PPIELPAEDDVEIIGRVV 116
Peptidase_S24_S26 cd06462
The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal ...
 134-217 3.36e-15

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: 68.06  E-value: 3.36e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446635057 134 RIINVRGDSMSGTIEPGDLLFVDVSIKNFDGDGIYAFLYDD-TAHVKRLQKM--KDKLLVISDNKSYSawdPIERDEMNR 210
Cdd:cd06462    1 FALRVEGDSMEPTIPDGDLVLVDKSSYEPKRGDIVVFRLPGgELTVKRVIGLpgEGHYFLLGDNPNSP---DSRIDGPPE 77


                 ....*..
gi 446635057 211 VFVFGKV 217
Cdd:cd06462   78 LDIVGVV 84
LexA COG1974
SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase) [Transcription, ...
 138-221 3.49e-12

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


Pssm-ID: 441577 [Multi-domain]  Cd Length: 199  Bit Score: 63.01  E-value: 3.49e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446635057 138 VRGDSMSG-TIEPGDLLFVDVSIKNFDGDgIYAFLYDDTAHVKRLQKMKDKLLVISDNksySAWDPIERDEMNrVFVFGK 216
Cdd:COG1974  117 VKGDSMIDaGILDGDLVIVDRQLEAENGD-IVVALIDGEATVKRLYKEGGRVRLQPEN---PAYPPIIIEGDD-VEILGV 191


                 ....*
gi 446635057 217 VIGSM 221
Cdd:COG1974  192 VVGVI 196
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
3-66 3.57e-09

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 51.92  E-value: 3.57e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446635057   3 KETLSDRLNKAMELAGMSQGALAKASGVAQPTIWRLTSGNARGS-TKIVEIANALGVNSEWLSTG 66
Cdd:COG1396    5 KKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSlETLLKLAKALGVSLDELLGG 69
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 7-63 1.60e-08

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: 49.47  E-value: 1.60e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 446635057   7 SDRLNKAMELAGMSQGALAKASGVAQPTIWRLTSGNARGS-TKIVEIANALGVNSEWL 63
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSlETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
9-63 5.47e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 47.90  E-value: 5.47e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 446635057     9 RLNKAMELAGMSQGALAKASGVAQPTIWRLTSGNARGSTKIVE-IANALGVNSEWL 63
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKkLAKALGVSLDEL 56
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
3-63 5.94e-07

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 45.61  E-value: 5.94e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446635057   3 KETLSDRLNKAMELAGMSQGALAKASGVAQPTIWRLTSGNARGSTKIV-EIANALGVNSEWL 63
Cdd:COG1476    2 KKKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELAlKIARALGVSLEEL 63
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 10-63 7.09e-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: 42.14  E-value: 7.09e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 446635057   10 LNKAMELAGMSQGALAKASGVAQPTIWRLTSGNAR-GSTKIVEIANALGVNSEWL 63
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREpSLETLKKLAEALGVSLDEL 55
PRK13355 PRK13355
bifunctional HTH-domain containing protein/aminotransferase; Provisional
 3-98 1.01e-05

bifunctional HTH-domain containing protein/aminotransferase; Provisional


Pssm-ID: 237361 [Multi-domain]  Cd Length: 517  Bit Score: 45.88  E-value: 1.01e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446635057   3 KETLSDRLNKAMELAGMSQGALAKASGVAQPTIWR-LTSGNARGSTKIVE-----IANALGVNSEWLSTGIGPMKKDGTT 76
Cdd:PRK13355   1 KTTFAERLKQAMKARGLKQEDLVHAAEARGVKLGKsHISQYVSGKTGPRRdvlpfLAAILGVSEDWLLGGESPADQESDA 80

                         90       100
                 ....*....|....*....|..
gi 446635057  77 PINASPSSNTFKIDILDLEVSA 98
Cdd:PRK13355  81 SAVVESAPNSHLADPSAPTTPI 102
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 4-62 1.08e-04

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: 39.15  E-value: 1.08e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446635057   4 ETLSDRLNKAMELAGMSQGALAKASGVAQPTIWRLTSGNARGSTKIVE-IANALGVNSEW 62
Cdd:COG1813   11 EDYGERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRkLEKALGISLAE 70
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 4-63 2.36e-04

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


Pssm-ID: 442838 [Multi-domain]  Cd Length: 95  Bit Score: 39.23  E-value: 2.36e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446635057   4 ETLSDRLNKAMELAGMSQGALAKASGVAQPTIWRLTSGNARGS-TKIVEIANALGVNSEWL 63
Cdd:COG3620   16 DTLGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTvSTLEKIAEALGKELSAV 76
PRK10276 PRK10276
translesion error-prone DNA polymerase V autoproteolytic subunit;
136-218 3.09e-04

translesion error-prone DNA polymerase V autoproteolytic subunit;


Pssm-ID: 182350  Cd Length: 139  Bit Score: 39.78  E-value: 3.09e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446635057 136 INVRGDSM-SGTIEPGDLLFVDVSIKNFDGDGIYAFLyDDTAHVKRLQKmKDKLLVISDNKSYSawdPI---ERDEMNrv 211
Cdd:PRK10276  54 VKASGDSMiDAGISDGDLLIVDSAITASHGDIVIAAV-DGEFTVKKLQL-RPTVQLIPMNSAYS---PItisSEDTLD-- 126


                 ....*..
gi 446635057 212 fVFGKVI 218
Cdd:PRK10276 127 -VFGVVT 132
Phage_CI_repr pfam07022
Bacteriophage CI repressor helix-turn-helix domain; This family consists of several phage CI ...
 8-71 6.55e-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: 36.92  E-value: 6.55e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446635057    8 DRLNKAMELAGMS-QGALAKASGVAQPTIWRLTSGNARGSTKIVEIANALGVNSEWLSTGIGPMK 71
Cdd:pfam07022   1 AVIERLMKAYGFKsRQELADHLGVSKSTLSTWYTRDSFPAELVVRCALETGVSLEWLATGDGELY 65
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 6-58 8.37e-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: 8.37e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 446635057    6 LSDRLNKAMELAGMSQGALAKASGVAQPTIWRLTSGNAR--GSTKIVEIANALGV 58
Cdd:pfam13560   2 LGARLRRLRERAGLSQEALARRLGVSRSTLSRLETGRRGrpSPAVVERLARALGV 56
YdaS_antitoxin pfam15943
Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT; YdaS_antitoxin is a family ...
 10-50 9.83e-04

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: 36.55  E-value: 9.83e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 446635057   10 LNKAMELAGmSQGALAKASGVAQPTIWRLTSGNARGSTKIV 50
Cdd:pfam15943   1 IKKAIEIVG-GQKALAEALGVTQQAVSQWLHGKKGIPAEYC 40
YdaS COG4197
DNA-binding transcriptional regulator YdaS, prophage-encoded, Cro superfamily [Transcription];
10-57 1.02e-03

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


Pssm-ID: 443351  Cd Length: 68  Bit Score: 36.43  E-value: 1.02e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 446635057  10 LNKAMELAGmSQGALAKASGVAQPTIWRLTSGNAR-GSTKIVEIANALG 57
Cdd:COG4197    1 LEKAIEALG-SQSALARALGVSQQAVSQWLNGKRRvPAERCLAIERATG 48
PRK08154 PRK08154
anaerobic benzoate catabolism transcriptional regulator; Reviewed
 6-63 1.24e-03

anaerobic benzoate catabolism transcriptional regulator; Reviewed


Pssm-ID: 236167 [Multi-domain]  Cd Length: 309  Bit Score: 39.17  E-value: 1.24e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446635057   6 LSDRLNKAMELAGMSQGALAKASGVAQPTIWRLTSGnaRGSTKIV---EIANALGVNSEWL 63
Cdd:PRK08154  29 LGERVRTLRARRGMSRKVLAQASGVSERYLAQLESG--QGNVSILllrRVARALGCSLADL 87
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 14-63 6.02e-03

addiction module antidote protein, HigA family; Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair. [Regulatory functions, DNA interactions, Regulatory functions, Protein interactions, Mobile and extrachromosomal element functions, Other]


Pssm-ID: 274228 [Multi-domain]  Cd Length: 78  Bit Score: 34.52  E-value: 6.02e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 446635057   14 MELAGMSQGALAKASGVAQPTIWRLTSGNARGSTKI-VEIANALGVNSE-WL 63
Cdd:TIGR02607  14 LEPLGLSVRALAKALGVSRSTLSRIVNGRAAITADMaLRLAKALGTSPEfWL 65
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
9-59 6.03e-03

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 34.35  E-value: 6.03e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 446635057   9 RLNKAMELAGMSQGALAKASGVAQPTIWRLTSGNARG---STkIVEIANALGVN 59
Cdd:COG3655    5 KLDELLAERGMTKKELAEATGISRATLSRLKNGKAKAvrlDT-LEKICKALDCQ 57
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 4-63 6.43e-03

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 34.78  E-value: 6.43e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446635057   4 ETLSDRLNKAMelaGMSQGALAKASGVAQPTIWRLTSGNARGSTKI-VEIANALGVNSE-WL 63
Cdd:COG3093   11 EILREEFLEPL---GLSQTELAKALGVSRQRISEILNGKRAITADTaLRLARAFGTSAEfWL 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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