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Conserved domains on  [gi|15595808|ref|NP_249302|]
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HTH-type transcriptional regulator PrtR [Pseudomonas aeruginosa PAO1]

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: ...
 111-242 1.24e-34

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


:

Pssm-ID: 442176  Cd Length: 121  Bit Score: 120.84  E-value: 1.24e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595808 111 LPLYkEVEMSAGAGRTAVREIEGRKLRFSyatlrasGVDPSAAICAQLTGNSMEPLIMDGSTIGVDTATTHITDGEIYAL 190
Cdd:COG2932   1 VPLY-DGEASAGGGAFNEVEEPVDKLEFP-------GLPPDNLFAVRVSGDSMEPTIRDGDIVLVDPSDTEIRDGGIYVV 72

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 15595808 191 EHDGMLRVKFVYRLPGGGIRLRSFNrEEYPDEEYSPEDMrsRQISMIGWVFW 242
Cdd:COG2932  73 RTDGELLVKRLQRRPDGKLRLISDN-PAYPPIEIPPEDA--DEIEIIGRVVW 121
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
11-83 1.09e-13

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 64.63  E-value: 1.09e-13
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15595808  11 SFAARLKQAMAMRNLKQETLAEAAGVSQNTIHKLTSGKAQ-STRKLIEIAAALGVSPVWLQTGEGAPAARSAVS 83
Cdd:COG1396   7 ALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNpSLETLLKLAKALGVSLDELLGGADEELPEALLS 80
 
Name Accession Description Interval E-value
COG2932 COG2932
Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: ...
 111-242 1.24e-34

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


Pssm-ID: 442176  Cd Length: 121  Bit Score: 120.84  E-value: 1.24e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595808 111 LPLYkEVEMSAGAGRTAVREIEGRKLRFSyatlrasGVDPSAAICAQLTGNSMEPLIMDGSTIGVDTATTHITDGEIYAL 190
Cdd:COG2932   1 VPLY-DGEASAGGGAFNEVEEPVDKLEFP-------GLPPDNLFAVRVSGDSMEPTIRDGDIVLVDPSDTEIRDGGIYVV 72

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 15595808 191 EHDGMLRVKFVYRLPGGGIRLRSFNrEEYPDEEYSPEDMrsRQISMIGWVFW 242
Cdd:COG2932  73 RTDGELLVKRLQRRPDGKLRLISDN-PAYPPIEIPPEDA--DEIEIIGRVVW 121
Peptidase_S24 pfam00717
Peptidase S24-like;
112-241 3.55e-27

Peptidase S24-like;


Pssm-ID: 425835  Cd Length: 116  Bit Score: 101.13  E-value: 3.55e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595808   112 PLYKEVemSAGAGRTAVREIEGRkLRFSYATLRAsgvdPSAAICAQLTGNSMEPLIMDGSTIGVDTaTTHITDGEIYALE 191
Cdd:pfam00717   1 PLIGRV--AAGAPILAEEEIEGY-LPLPESLLSP----PGNLFALRVKGDSMEPGIPDGDLVLVDP-SREARNGDIVVAR 72

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 15595808   192 HDGMLRVKFVYRlPGGGIRLRSFNReEYPDEEYSPEDmrsrQISMIGWVF 241
Cdd:pfam00717  73 LDGEATVKRLYR-DGGGIRLISLNP-EYPPIELPAED----DVEIIGRVV 116
S24_LexA-like cd06529
Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of ...
 154-230 4.21e-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: 81.45  E-value: 4.21e-20
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15595808 154 ICAQLTGNSMEPLIMDGSTIGVDTATThITDGEIYALEHDGMLRVKFVYRLPGGGIRLRSFNrEEYPDEEYSPEDMR 230
Cdd:cd06529   1 FALRVKGDSMEPTIPDGDLVLVDPSDT-PRDGDIVVARLDGELTVKRLQRRGGGRLRLISDN-PAYPPIEIDEEELE 75
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
11-83 1.09e-13

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 64.63  E-value: 1.09e-13
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15595808  11 SFAARLKQAMAMRNLKQETLAEAAGVSQNTIHKLTSGKAQ-STRKLIEIAAALGVSPVWLQTGEGAPAARSAVS 83
Cdd:COG1396   7 ALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNpSLETLLKLAKALGVSLDELLGGADEELPEALLS 80
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
15-69 4.15e-12

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 59.45  E-value: 4.15e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 15595808     15 RLKQAMAMRNLKQETLAEAAGVSQNTIHKLTSGKAQ-STRKLIEIAAALGVSPVWL 69
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKpSLETLKKLAKALGVSLDEL 56
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 13-69 1.28e-11

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: 58.33  E-value: 1.28e-11
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 15595808  13 AARLKQAMAMRNLKQETLAEAAGVSQNTIHKLTSGKAQ-STRKLIEIAAALGVSPVWL 69
Cdd:cd00093   1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNpSLETLEKLAKALGVSLDEL 58
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 16-69 2.08e-10

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


Pssm-ID: 460181 [Multi-domain]  Cd Length: 55  Bit Score: 54.85  E-value: 2.08e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 15595808    16 LKQAMAMRNLKQETLAEAAGVSQNTIHKLTSGKAQ-STRKLIEIAAALGVSPVWL 69
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREpSLETLKKLAEALGVSLDEL 55
PRK13355 PRK13355
bifunctional HTH-domain containing protein/aminotransferase; Provisional
 11-88 3.49e-09

bifunctional HTH-domain containing protein/aminotransferase; Provisional


Pssm-ID: 237361 [Multi-domain]  Cd Length: 517  Bit Score: 56.67  E-value: 3.49e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595808   11 SFAARLKQAMAMRNLKQETLAEAAG-----VSQNTIHKLTSGKAQSTRKLIEI-AAALGVSPVWLQTGEGA----PAARS 80
Cdd:PRK13355   3 TFAERLKQAMKARGLKQEDLVHAAEargvkLGKSHISQYVSGKTGPRRDVLPFlAAILGVSEDWLLGGESPadqeSDASA 82


                 ....*...
gi 15595808   81 AVSVADGS 88
Cdd:PRK13355  83 VVESAPNS 90
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 12-63 1.37e-05

transcriptional regulator, y4mF family; Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems. [Regulatory functions, DNA interactions]


Pssm-ID: 213767 [Multi-domain]  Cd Length: 58  Bit Score: 41.88  E-value: 1.37e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 15595808    12 FAARLKQAMAMRNLKQETLAEAAGVSQNTIHKLTSGKAQST-RKLIEIAAALG 63
Cdd:TIGR03070   3 IGILVRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRlDKVLRVLDALG 55
 
Name Accession Description Interval E-value
COG2932 COG2932
Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: ...
 111-242 1.24e-34

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


Pssm-ID: 442176  Cd Length: 121  Bit Score: 120.84  E-value: 1.24e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595808 111 LPLYkEVEMSAGAGRTAVREIEGRKLRFSyatlrasGVDPSAAICAQLTGNSMEPLIMDGSTIGVDTATTHITDGEIYAL 190
Cdd:COG2932   1 VPLY-DGEASAGGGAFNEVEEPVDKLEFP-------GLPPDNLFAVRVSGDSMEPTIRDGDIVLVDPSDTEIRDGGIYVV 72

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 15595808 191 EHDGMLRVKFVYRLPGGGIRLRSFNrEEYPDEEYSPEDMrsRQISMIGWVFW 242
Cdd:COG2932  73 RTDGELLVKRLQRRPDGKLRLISDN-PAYPPIEIPPEDA--DEIEIIGRVVW 121
Peptidase_S24 pfam00717
Peptidase S24-like;
112-241 3.55e-27

Peptidase S24-like;


Pssm-ID: 425835  Cd Length: 116  Bit Score: 101.13  E-value: 3.55e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595808   112 PLYKEVemSAGAGRTAVREIEGRkLRFSYATLRAsgvdPSAAICAQLTGNSMEPLIMDGSTIGVDTaTTHITDGEIYALE 191
Cdd:pfam00717   1 PLIGRV--AAGAPILAEEEIEGY-LPLPESLLSP----PGNLFALRVKGDSMEPGIPDGDLVLVDP-SREARNGDIVVAR 72

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 15595808   192 HDGMLRVKFVYRlPGGGIRLRSFNReEYPDEEYSPEDmrsrQISMIGWVF 241
Cdd:pfam00717  73 LDGEATVKRLYR-DGGGIRLISLNP-EYPPIELPAED----DVEIIGRVV 116
S24_LexA-like cd06529
Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of ...
 154-230 4.21e-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: 81.45  E-value: 4.21e-20
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15595808 154 ICAQLTGNSMEPLIMDGSTIGVDTATThITDGEIYALEHDGMLRVKFVYRLPGGGIRLRSFNrEEYPDEEYSPEDMR 230
Cdd:cd06529   1 FALRVKGDSMEPTIPDGDLVLVDPSDT-PRDGDIVVARLDGELTVKRLQRRGGGRLRLISDN-PAYPPIEIDEEELE 75
Peptidase_S24_S26 cd06462
The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal ...
 160-229 9.87e-14

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: 64.98  E-value: 9.87e-14
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15595808 160 GNSMEPLIMDGSTIGVDTATTHITDGEIYALEHDG-MLRVKFVYRLPG-GGIRLRSFNrEEYPDEEYSPEDM 229
Cdd:cd06462   7 GDSMEPTIPDGDLVLVDKSSYEPKRGDIVVFRLPGgELTVKRVIGLPGeGHYFLLGDN-PNSPDSRIDGPPE 77
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
11-83 1.09e-13

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 64.63  E-value: 1.09e-13
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15595808  11 SFAARLKQAMAMRNLKQETLAEAAGVSQNTIHKLTSGKAQ-STRKLIEIAAALGVSPVWLQTGEGAPAARSAVS 83
Cdd:COG1396   7 ALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNpSLETLLKLAKALGVSLDELLGGADEELPEALLS 80
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
15-69 4.15e-12

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 59.45  E-value: 4.15e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 15595808     15 RLKQAMAMRNLKQETLAEAAGVSQNTIHKLTSGKAQ-STRKLIEIAAALGVSPVWL 69
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKpSLETLKKLAKALGVSLDEL 56
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 13-69 1.28e-11

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: 58.33  E-value: 1.28e-11
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 15595808  13 AARLKQAMAMRNLKQETLAEAAGVSQNTIHKLTSGKAQ-STRKLIEIAAALGVSPVWL 69
Cdd:cd00093   1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNpSLETLEKLAKALGVSLDEL 58
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
11-69 1.02e-10

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 56.01  E-value: 1.02e-10
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595808  11 SFAARLKQAMAMRNLKQETLAEAAGVSQNTIHKLTSGKAQ-STRKLIEIAAALGVSPVWL 69
Cdd:COG1476   4 KLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNpSLELALKIARALGVSLEEL 63
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 16-69 2.08e-10

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


Pssm-ID: 460181 [Multi-domain]  Cd Length: 55  Bit Score: 54.85  E-value: 2.08e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 15595808    16 LKQAMAMRNLKQETLAEAAGVSQNTIHKLTSGKAQ-STRKLIEIAAALGVSPVWL 69
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREpSLETLKKLAEALGVSLDEL 55
PRK13355 PRK13355
bifunctional HTH-domain containing protein/aminotransferase; Provisional
 11-88 3.49e-09

bifunctional HTH-domain containing protein/aminotransferase; Provisional


Pssm-ID: 237361 [Multi-domain]  Cd Length: 517  Bit Score: 56.67  E-value: 3.49e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595808   11 SFAARLKQAMAMRNLKQETLAEAAG-----VSQNTIHKLTSGKAQSTRKLIEI-AAALGVSPVWLQTGEGA----PAARS 80
Cdd:PRK13355   3 TFAERLKQAMKARGLKQEDLVHAAEargvkLGKSHISQYVSGKTGPRRDVLPFlAAILGVSEDWLLGGESPadqeSDASA 82


                 ....*...
gi 15595808   81 AVSVADGS 88
Cdd:PRK13355  83 VVESAPNS 90
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 10-68 1.21e-08

Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and HTH domains [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441418 [Multi-domain]  Cd Length: 70  Bit Score: 50.71  E-value: 1.21e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595808  10 DSFAARLKQAMAMRNLKQETLAEAAGVSQNTIHKLTSGKAQSTRKLIE-IAAALGVSPVW 68
Cdd:COG1813  11 EDYGERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRkLEKALGISLAE 70
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
15-66 1.21e-08

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 50.53  E-value: 1.21e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 15595808  15 RLKQAMAMRNLKQETLAEAAGVSQNTIHKLTSGKAQSTR--KLIEIAAALGVSP 66
Cdd:COG3655   5 KLDELLAERGMTKKELAEATGISRATLSRLKNGKAKAVRldTLEKICKALDCQP 58
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 15-74 7.84e-08

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: 48.05  E-value: 7.84e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15595808    15 RLKQAMAMRNLKQETLAEAAGVSQNTIHKLTSGKAQ-STRKLIEIAAALGVSPVWLQTGEG 74
Cdd:pfam12844   3 RLRKAREERGLTQEELAERLGISRSQLSAIENGKSVpPAETLYKIAELLGVPANWLLQGEG 63
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 15-66 3.17e-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: 46.38  E-value: 3.17e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 15595808    15 RLKQAMAMRNLKQETLAEAAGVSQNTIHKLTSGKAQ--STRKLIEIAAALGVSP 66
Cdd:pfam13443   1 KLRKLMADRGISKSDLARATGISRATLSRLRKGKPKrvSLDTLDKICDALGCQP 54
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 12-67 5.19e-06

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: 42.90  E-value: 5.19e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 15595808    12 FAARLKQAMAMRNLKQETLAEAAGVSQNTIHKLTSGKAQ--STRKLIEIAAALGVSPV 67
Cdd:pfam13560   2 LGARLRRLRERAGLSQEALARRLGVSRSTLSRLETGRRGrpSPAVVERLARALGVDGA 59
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 12-63 1.37e-05

transcriptional regulator, y4mF family; Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems. [Regulatory functions, DNA interactions]


Pssm-ID: 213767 [Multi-domain]  Cd Length: 58  Bit Score: 41.88  E-value: 1.37e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 15595808    12 FAARLKQAMAMRNLKQETLAEAAGVSQNTIHKLTSGKAQST-RKLIEIAAALG 63
Cdd:TIGR03070   3 IGILVRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRlDKVLRVLDALG 55
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 8-69 6.53e-05

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: 40.77  E-value: 6.53e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15595808   8 PPDSFAARLKQAMAMRNLKQETLAEAAGVSQNTIHKLTSGKAQ-STRKLIEIAAALGVSPVWL 69
Cdd:COG3620  14 PDDTLGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDpTVSTLEKIAEALGKELSAV 76
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 23-69 1.81e-04

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 39.41  E-value: 1.81e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 15595808  23 RNLKQETLAEAAGVSQNTIHKLTSGKAQ-STRKLIEIAAALGVSP-VWL 69
Cdd:COG3093  21 LGLSQTELAKALGVSRQRISEILNGKRAiTADTALRLARAFGTSAeFWL 69
PHA01976 PHA01976
helix-turn-helix protein
 10-74 3.07e-03

helix-turn-helix protein


Pssm-ID: 177330 [Multi-domain]  Cd Length: 67  Bit Score: 35.32  E-value: 3.07e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15595808   10 DSFAARLKQAMAMRNLKQETLAEAAGVSQNTIHKLTSGKA-QSTRKLIEIAAALGVSPVWLQTGEG 74
Cdd:PHA01976   1 MSFAIQLIKARNARAWSAPELSRRAGVRHSLIYDFEADKRlPNLKTLLRLADALGVTLDWLCGRCG 66
Phage_CI_repr pfam07022
Bacteriophage CI repressor helix-turn-helix domain; This family consists of several phage CI ...
 15-76 7.31e-03

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: 34.23  E-value: 7.31e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15595808    15 RLKQAMAMRNLKQetLAEAAGVSQNTIHKLTSGKAQSTRKLIEIAAALGVSPVWLQTGEGAP 76
Cdd:pfam07022   5 RLMKAYGFKSRQE--LADHLGVSKSTLSTWYTRDSFPAELVVRCALETGVSLEWLATGDGEL 64
 
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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