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Conserved domains on  [gi|446320023|ref|WP_000397878|]
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helix-turn-helix domain-containing protein [Bacillus anthracis]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 15193285)

helix-turn-helix domain-containing protein such as an XRE (Xenobiotic Response Element) family transcriptional regulator

Gene Ontology:  GO:0003677
PubMed:  10473770|15808743|10556324

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNPP_C super family cl40071
RNPP family C-terminal domain; The bacterial PIcR helix-turn-helix transcription factor ...
 87-274 2.63e-22

RNPP family C-terminal domain; The bacterial PIcR helix-turn-helix transcription factor includes five TPR units of different lengths. This entry represents the TPR containing domain as a whole. This family is called RNPP after (Rapm NprR, PrgX, and PlcR).


The actual alignment was detected with superfamily member pfam18768:

Pssm-ID: 436723  Cd Length: 213  Bit Score: 92.20  E-value: 2.63e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446320023   87 RQHQYKELYEIVTKEKNLNNFRMKEDKQFLIWHEAIAIYRVNNL-IKTALTLLNNAL-KITVTNIDFLteREIDIMQTMA 164
Cdd:pfam18768   9 REKQYEEIYQRIEKLLQNQDKFHIEFSKYLLWQYTVAAFHLGRIsAEECITELNLLLlEKDDTNIRHH--LHLHIKNSLA 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446320023  165 IFHAENKEYKESINILKRCLNNFDKLDFPRDkEIKLKIIYNLAKCLNYTYQYEEAKKYIDKGIKLAINLNTLYLLGELYY 244
Cdd:pfam18768  87 NLYAEEGKTNQSIQYYQQVITSSEANELDYD-VLKIKVMYNYSKLLYDKNDYDSSLEVINQGIASSIEKENMSLLGQLYY 165

                         170       180       190
                  ....*....|....*....|....*....|
gi 446320023  245 EKGSNLLKLEQSNkEEVADNMKTALFIFEL 274
Cdd:pfam18768 166 QRGECLEKLDGSE-EEIAESYQRALFFFEL 194
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
5-70 9.58e-12

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 60.01  E-value: 9.58e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446320023   5 DLGITIKELRIKKNISQSELCH--GIcSQSQISKIEKGVIYPSSILLYQLSERLGIDPNNIFALTQNK 70
Cdd:COG1396    7 ALGERLRELRKARGLTQEELAErlGV-SRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEE 73
 
Name Accession Description Interval E-value
RNPP_C pfam18768
RNPP family C-terminal domain; The bacterial PIcR helix-turn-helix transcription factor ...
 87-274 2.63e-22

RNPP family C-terminal domain; The bacterial PIcR helix-turn-helix transcription factor includes five TPR units of different lengths. This entry represents the TPR containing domain as a whole. This family is called RNPP after (Rapm NprR, PrgX, and PlcR).


Pssm-ID: 436723  Cd Length: 213  Bit Score: 92.20  E-value: 2.63e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446320023   87 RQHQYKELYEIVTKEKNLNNFRMKEDKQFLIWHEAIAIYRVNNL-IKTALTLLNNAL-KITVTNIDFLteREIDIMQTMA 164
Cdd:pfam18768   9 REKQYEEIYQRIEKLLQNQDKFHIEFSKYLLWQYTVAAFHLGRIsAEECITELNLLLlEKDDTNIRHH--LHLHIKNSLA 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446320023  165 IFHAENKEYKESINILKRCLNNFDKLDFPRDkEIKLKIIYNLAKCLNYTYQYEEAKKYIDKGIKLAINLNTLYLLGELYY 244
Cdd:pfam18768  87 NLYAEEGKTNQSIQYYQQVITSSEANELDYD-VLKIKVMYNYSKLLYDKNDYDSSLEVINQGIASSIEKENMSLLGQLYY 165

                         170       180       190
                  ....*....|....*....|....*....|
gi 446320023  245 EKGSNLLKLEQSNkEEVADNMKTALFIFEL 274
Cdd:pfam18768 166 QRGECLEKLDGSE-EEIAESYQRALFFFEL 194
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
5-70 9.58e-12

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 60.01  E-value: 9.58e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446320023   5 DLGITIKELRIKKNISQSELCH--GIcSQSQISKIEKGVIYPSSILLYQLSERLGIDPNNIFALTQNK 70
Cdd:COG1396    7 ALGERLRELRKARGLTQEELAErlGV-SRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEE 73
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 7-60 3.24e-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: 49.09  E-value: 3.24e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 446320023   7 GITIKELRIKKNISQSELCHGI-CSQSQISKIEKGVIYPSSILLYQLSERLGIDP 60
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLgVSRSTISRIENGKRNPSLETLEKLAKALGVSL 55
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
10-60 4.44e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 48.67  E-value: 4.44e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 446320023    10 IKELRIKKNISQSELCHGI-CSQSQISKIEKGVIYPSSILLYQLSERLGIDP 60
Cdd:smart00530   2 LKELREEKGLTQEELAEKLgVSRSTLSRIENGKRKPSLETLKKLAKALGVSL 53
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 10-60 1.92e-07

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: 47.15  E-value: 1.92e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 446320023   10 IKELRIKKNISQSELCHGIC-SQSQISKIEKGVIYPSSILLYQLSERLGIDP 60
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGvSRSTISKIENGKREPSLETLKKLAEALGVSL 52
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
 163-247 5.69e-04

Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443378 [Multi-domain]  Cd Length: 131  Bit Score: 39.22  E-value: 5.69e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446320023 163 MAIFHAENKEYKESINILKRCLnnfdKLDfPRDKEIKLkiiyNLAKCLNYTYQYEEAKKYIDKGIKLA-INLNTLYLLGE 241
Cdd:COG4235   23 LGRAYLRLGRYDEALAAYEKAL----RLD-PDNADALL----DLAEALLAAGDTEEAEELLERALALDpDNPEALYLLGL 93


                 ....*.
gi 446320023 242 LYYEKG 247
Cdd:COG4235   94 AAFQQG 99
 
Name Accession Description Interval E-value
RNPP_C pfam18768
RNPP family C-terminal domain; The bacterial PIcR helix-turn-helix transcription factor ...
 87-274 2.63e-22

RNPP family C-terminal domain; The bacterial PIcR helix-turn-helix transcription factor includes five TPR units of different lengths. This entry represents the TPR containing domain as a whole. This family is called RNPP after (Rapm NprR, PrgX, and PlcR).


Pssm-ID: 436723  Cd Length: 213  Bit Score: 92.20  E-value: 2.63e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446320023   87 RQHQYKELYEIVTKEKNLNNFRMKEDKQFLIWHEAIAIYRVNNL-IKTALTLLNNAL-KITVTNIDFLteREIDIMQTMA 164
Cdd:pfam18768   9 REKQYEEIYQRIEKLLQNQDKFHIEFSKYLLWQYTVAAFHLGRIsAEECITELNLLLlEKDDTNIRHH--LHLHIKNSLA 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446320023  165 IFHAENKEYKESINILKRCLNNFDKLDFPRDkEIKLKIIYNLAKCLNYTYQYEEAKKYIDKGIKLAINLNTLYLLGELYY 244
Cdd:pfam18768  87 NLYAEEGKTNQSIQYYQQVITSSEANELDYD-VLKIKVMYNYSKLLYDKNDYDSSLEVINQGIASSIEKENMSLLGQLYY 165

                         170       180       190
                  ....*....|....*....|....*....|
gi 446320023  245 EKGSNLLKLEQSNkEEVADNMKTALFIFEL 274
Cdd:pfam18768 166 QRGECLEKLDGSE-EEIAESYQRALFFFEL 194
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
5-70 9.58e-12

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 60.01  E-value: 9.58e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446320023   5 DLGITIKELRIKKNISQSELCH--GIcSQSQISKIEKGVIYPSSILLYQLSERLGIDPNNIFALTQNK 70
Cdd:COG1396    7 ALGERLRELRKARGLTQEELAErlGV-SRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEE 73
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
6-68 2.60e-09

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 52.54  E-value: 2.60e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446320023   6 LGITIKELRIKKNISQSELCHGI-CSQSQISKIEKGVIYPSSILLYQLSERLGIDPNNIFALTQ 68
Cdd:COG1476    5 LGNRLKELRKERGLTQEELAELLgVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLEE 68
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 7-60 3.24e-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: 49.09  E-value: 3.24e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 446320023   7 GITIKELRIKKNISQSELCHGI-CSQSQISKIEKGVIYPSSILLYQLSERLGIDP 60
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLgVSRSTISRIENGKRNPSLETLEKLAKALGVSL 55
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
10-60 4.44e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 48.67  E-value: 4.44e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 446320023    10 IKELRIKKNISQSELCHGI-CSQSQISKIEKGVIYPSSILLYQLSERLGIDP 60
Cdd:smart00530   2 LKELREEKGLTQEELAEKLgVSRSTLSRIENGKRKPSLETLKKLAKALGVSL 53
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 5-59 4.53e-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: 49.17  E-value: 4.53e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446320023   5 DLGITIKELRIKKNISQSELCHGI-CSQSQISKIEKGVIYPSSILLYQLSERLGID 59
Cdd:COG1813   12 DYGERIREAREARGLSQEELAEKLgVSESTIRRIERGEATPSLDTLRKLEKALGIS 67
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 10-60 1.92e-07

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: 47.15  E-value: 1.92e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 446320023   10 IKELRIKKNISQSELCHGIC-SQSQISKIEKGVIYPSSILLYQLSERLGIDP 60
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGvSRSTISKIENGKREPSLETLKKLAEALGVSL 52
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 7-67 9.04e-07

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: 45.36  E-value: 9.04e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446320023    7 GITIKELRIKKNISQSELCH--GIcSQSQISKIEKGVIYPSSILLYQLSERLGIDPNNIFALT 67
Cdd:pfam12844   1 GERLRKAREERGLTQEELAErlGI-SRSQLSAIENGKSVPPAETLYKIAELLGVPANWLLQGE 62
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
 163-247 5.69e-04

Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443378 [Multi-domain]  Cd Length: 131  Bit Score: 39.22  E-value: 5.69e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446320023 163 MAIFHAENKEYKESINILKRCLnnfdKLDfPRDKEIKLkiiyNLAKCLNYTYQYEEAKKYIDKGIKLA-INLNTLYLLGE 241
Cdd:COG4235   23 LGRAYLRLGRYDEALAAYEKAL----RLD-PDNADALL----DLAEALLAAGDTEEAEELLERALALDpDNPEALYLLGL 93


                 ....*.
gi 446320023 242 LYYEKG 247
Cdd:COG4235   94 AAFQQG 99
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 6-70 8.29e-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: 38.08  E-value: 8.29e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446320023   6 LGITIKELRIKKNISQSELCH--GIcSQSQISKIEKGVIYPSSILLYQLSERLGIDPNNIFALTQNK 70
Cdd:COG3620   18 LGEALRLMRKELGLSQLPVAElvGV-SQSDILRIESGKRDPTVSTLEKIAEALGKELSAVLVVDDGK 83
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 121-247 1.87e-03

Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 37.86  E-value: 1.87e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446320023 121 AIAIYRVNNLiKTALTLLNNALKITVTNIDFLtereidimQTMAIFHAENKEYKESINILKRCLnnfdKLDfPRDKEIKl 200
Cdd:COG4783   11 AQALLLAGDY-DEAEALLEKALELDPDNPEAF--------ALLGEILLQLGDLDEAIVLLHEAL----ELD-PDEPEAR- 75

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 446320023 201 kiiYNLAKCLNYTYQYEEAKKYIDKGIKLA-INLNTLYLLGELYYEKG 247
Cdd:COG4783   76 ---LNLGLALLKAGDYDEALALLEKALKLDpEHPEAYLRLARAYRALG 120
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 154-247 3.13e-03

Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 37.09  E-value: 3.13e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446320023 154 EREIDIMQTMAIFHAENKEYKESINILKRCLNNFdkldfPRDKEIklkiIYNLAKCLNYTYQYEEAKKYIDKGIKLA-IN 232
Cdd:COG4783    1 AACAEALYALAQALLLAGDYDEAEALLEKALELD-----PDNPEA----FALLGEILLQLGDLDEAIVLLHEALELDpDE 71

                         90
                 ....*....|....*
gi 446320023 233 LNTLYLLGELYYEKG 247
Cdd:COG4783   72 PEARLNLGLALLKAG 86
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
134-247 3.34e-03

Tetratricopeptide (TPR) repeat [General function prediction only];


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 38.06  E-value: 3.34e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446320023 134 ALTLLNNALKITvtnidfltEREIDIMQTMAIFHAENKEYKESINILKRCLnnfdKLDfPRDKEIklkiIYNLAKCLNYT 213
Cdd:COG0457   27 AIEDYEKALELD--------PDDAEALYNLGLAYLRLGRYEEALADYEQAL----ELD-PDDAEA----LNNLGLALQAL 89

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 446320023 214 YQYEEAKKYIDKGIKLAI-NLNTLYLLGELYYEKG 247
Cdd:COG0457   90 GRYEEALEDYDKALELDPdDAEALYNLGLALLELG 124
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 87-247 5.67e-03

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 37.79  E-value: 5.67e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446320023  87 RQHQYKELYEIVTKEKNLNnfrmkeDKQFLIWHEAIAIYRVNNLIKTALTLLNNALKITVTNIDFLTEreidimqtMAIF 166
Cdd:COG2956  122 QEGDWEKAIEVLERLLKLG------PENAHAYCELAELYLEQGDYDEAIEALEKALKLDPDCARALLL--------LAEL 187

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446320023 167 HAENKEYKESINILKRCLNnfdkldfpRDKEiKLKIIYNLAKCLNYTYQYEEAKKYIDKGIKLAINLNTLYLLGELYYEK 246
Cdd:COG2956  188 YLEQGDYEEAIAALERALE--------QDPD-YLPALPRLAELYEKLGDPEEALELLRKALELDPSDDLLLALADLLERK 258


                 .
gi 446320023 247 G 247
Cdd:COG2956  259 E 259
 
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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