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Conserved domains on  [gi|501535771|ref|WP_012541779|]
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MULTISPECIES: helix-turn-helix domain-containing protein [Klebsiella]

Protein Classification

HTH_XRE and 2TM domain-containing protein( domain architecture ID 11272085)

HTH_XRE and 2TM domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
5-60 2.54e-16

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


:

Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 68.72  E-value: 2.54e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 501535771   5 NQVKQLRLQRAWSQEQLAEMAGLSVRTIQRIENGER-PGLETLSALAAVFEVTVAEI 60
Cdd:COG1476    7 NRLKELRKERGLTQEELAELLGVSRQTISAIENGKYnPSLELALKIARALGVSLEEL 63
2TM pfam13239
2TM domain; This short region contains two transmembrane alpha helices that are found ...
 81-159 3.02e-06

2TM domain; This short region contains two transmembrane alpha helices that are found associated with a wide range of other domains. This domain may be involved in cell lysis or peptidoglycan turnover.


:

Pssm-ID: 463815  Cd Length: 80  Bit Score: 42.98  E-value: 3.02e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501535771   81 EEAKARVHQESRFFRSLSVALVVCVLLAVLNRFTNPQYYWSGWVALIWGALLVVRGLRLFVFGE-WIKNWRQARLQRLLR 159
Cdd:pfam13239   1 ERAKKRVKRKKGFYKHLGVYLIVNAFLILINLLTGGGLPWFLWPLLGWGLGLLLHAWNVFQTEPfEGKFWEEKKIEKLME 80
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
5-60 2.54e-16

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 68.72  E-value: 2.54e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 501535771   5 NQVKQLRLQRAWSQEQLAEMAGLSVRTIQRIENGER-PGLETLSALAAVFEVTVAEI 60
Cdd:COG1476    7 NRLKELRKERGLTQEELAELLGVSRQTISAIENGKYnPSLELALKIARALGVSLEEL 63
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
7-60 7.33e-14

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 62.15  E-value: 7.33e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 501535771     7 VKQLRLQRAWSQEQLAEMAGLSVRTIQRIENGER-PGLETLSALAAVFEVTVAEI 60
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRkPSLETLKKLAKALGVSLDEL 56
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 5-60 1.32e-13

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: 61.80  E-value: 1.32e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 501535771   5 NQVKQLRLQRAWSQEQLAEMAGLSVRTIQRIENGER-PGLETLSALAAVFEVTVAEI 60
Cdd:cd00093    2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRnPSLETLEKLAKALGVSLDEL 58
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 7-60 1.79e-13

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: 61.02  E-value: 1.79e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 501535771    7 VKQLRLQRAWSQEQLAEMAGLSVRTIQRIENGER-PGLETLSALAAVFEVTVAEI 60
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKRePSLETLKKLAEALGVSLDEL 55
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 5-53 1.93e-06

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: 43.03  E-value: 1.93e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 501535771    5 NQVKQLRLQRAWSQEQLAEMAGLSVRTIQRIENGE-RPGLETLSALAAVF 53
Cdd:TIGR03070   5 ILVRARRKALGLTQADLADLAGVGLRFIRDLENGKpTVRLDKVLRVLDAL 54
2TM pfam13239
2TM domain; This short region contains two transmembrane alpha helices that are found ...
 81-159 3.02e-06

2TM domain; This short region contains two transmembrane alpha helices that are found associated with a wide range of other domains. This domain may be involved in cell lysis or peptidoglycan turnover.


Pssm-ID: 463815  Cd Length: 80  Bit Score: 42.98  E-value: 3.02e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501535771   81 EEAKARVHQESRFFRSLSVALVVCVLLAVLNRFTNPQYYWSGWVALIWGALLVVRGLRLFVFGE-WIKNWRQARLQRLLR 159
Cdd:pfam13239   1 ERAKKRVKRKKGFYKHLGVYLIVNAFLILINLLTGGGLPWFLWPLLGWGLGLLLHAWNVFQTEPfEGKFWEEKKIEKLME 80
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
9-70 8.72e-06

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 43.63  E-value: 8.72e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 501535771   9 QLRLQRAWSQEQLAEMAGLSVRTIQRIENGE-RPGLETLSALAAVFEVTVAEIGGEASREGAP 70
Cdd:PRK09943  14 EIRQQQGLSQRRAAELSGLTHSAISTIEQDKvSPAISTLQKLLKVYGLSLSEFFSEPEKPDEP 76
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
5-60 2.54e-16

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 68.72  E-value: 2.54e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 501535771   5 NQVKQLRLQRAWSQEQLAEMAGLSVRTIQRIENGER-PGLETLSALAAVFEVTVAEI 60
Cdd:COG1476    7 NRLKELRKERGLTQEELAELLGVSRQTISAIENGKYnPSLELALKIARALGVSLEEL 63
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
5-60 3.46e-15

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 66.56  E-value: 3.46e-15
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 501535771   5 NQVKQLRLQRAWSQEQLAEMAGLSVRTIQRIENGER-PGLETLSALAAVFEVTVAEI 60
Cdd:COG1396   10 ERLRELRKARGLTQEELAERLGVSRSTISRIERGRRnPSLETLLKLAKALGVSLDEL 66
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
7-60 7.33e-14

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 62.15  E-value: 7.33e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 501535771     7 VKQLRLQRAWSQEQLAEMAGLSVRTIQRIENGER-PGLETLSALAAVFEVTVAEI 60
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRkPSLETLKKLAKALGVSLDEL 56
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 5-60 1.32e-13

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: 61.80  E-value: 1.32e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 501535771   5 NQVKQLRLQRAWSQEQLAEMAGLSVRTIQRIENGER-PGLETLSALAAVFEVTVAEI 60
Cdd:cd00093    2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRnPSLETLEKLAKALGVSLDEL 58
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 7-60 1.79e-13

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: 61.02  E-value: 1.79e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 501535771    7 VKQLRLQRAWSQEQLAEMAGLSVRTIQRIENGER-PGLETLSALAAVFEVTVAEI 60
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKRePSLETLKKLAEALGVSLDEL 55
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 6-59 2.69e-13

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: 61.11  E-value: 2.69e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 501535771   6 QVKQLRLQRAWSQEQLAEMAGLSVRTIQRIENGER-PGLETLSALAAVFEVTVAE 59
Cdd:COG1813   16 RIREAREARGLSQEELAEKLGVSESTIRRIERGEAtPSLDTLRKLEKALGISLAE 70
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 6-60 3.67e-09

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: 51.17  E-value: 3.67e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 501535771   6 QVKQLRLQRAWSQEQLAEMAGLSVRTIQRIENGER-PGLETLSALAAVFEVTVAEI 60
Cdd:COG3620   21 ALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRdPTVSTLEKIAEALGKELSAV 76
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
5-60 5.72e-09

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 49.76  E-value: 5.72e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 501535771   5 NQVKQLRLQRAWSQEQLAEMAGLSVRTIQRIENGE--RPGLETLSALAAVFEVTVAEI 60
Cdd:COG3655    4 VKLDELLAERGMTKKELAEATGISRATLSRLKNGKakAVRLDTLEKICKALDCQPGDL 61
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 8-60 1.69e-07

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


Pssm-ID: 433211 [Multi-domain]  Cd Length: 63  Bit Score: 45.99  E-value: 1.69e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 501535771    8 KQLRLQRAWSQEQLAEMAGLSVRTIQRIENGE--RPGLETLSALAAVFEVTVAEI 60
Cdd:pfam13443   3 RKLMADRGISKSDLARATGISRATLSRLRKGKpkRVSLDTLDKICDALGCQPGDL 57
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 6-60 6.47e-07

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: 44.44  E-value: 6.47e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 501535771    6 QVKQLRLQRAWSQEQLAEMAGLSVRTIQRIENGE--RPGLETLSALAAVFEVTVAEI 60
Cdd:pfam13560   5 RLRRLRERAGLSQEALARRLGVSRSTLSRLETGRrgRPSPAVVERLARALGVDGAER 61
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 5-53 1.93e-06

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: 43.03  E-value: 1.93e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 501535771    5 NQVKQLRLQRAWSQEQLAEMAGLSVRTIQRIENGE-RPGLETLSALAAVF 53
Cdd:TIGR03070   5 ILVRARRKALGLTQADLADLAGVGLRFIRDLENGKpTVRLDKVLRVLDAL 54
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 7-60 2.86e-06

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: 42.66  E-value: 2.86e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 501535771    7 VKQLRLQRAWSQEQLAEMAGLSVRTIQRIENGER-PGLETLSALAAVFEVTVAEI 60
Cdd:pfam12844   4 LRKAREERGLTQEELAERLGISRSQLSAIENGKSvPPAETLYKIAELLGVPANWL 58
2TM pfam13239
2TM domain; This short region contains two transmembrane alpha helices that are found ...
 81-159 3.02e-06

2TM domain; This short region contains two transmembrane alpha helices that are found associated with a wide range of other domains. This domain may be involved in cell lysis or peptidoglycan turnover.


Pssm-ID: 463815  Cd Length: 80  Bit Score: 42.98  E-value: 3.02e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501535771   81 EEAKARVHQESRFFRSLSVALVVCVLLAVLNRFTNPQYYWSGWVALIWGALLVVRGLRLFVFGE-WIKNWRQARLQRLLR 159
Cdd:pfam13239   1 ERAKKRVKRKKGFYKHLGVYLIVNAFLILINLLTGGGLPWFLWPLLGWGLGLLLHAWNVFQTEPfEGKFWEEKKIEKLME 80
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 6-43 8.07e-06

Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 441035 [Multi-domain]  Cd Length: 71  Bit Score: 41.71  E-value: 8.07e-06
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 501535771   6 QVKQLRLQRAWSQEQLAEMAGLSVRTIQRIENGERPGL 43
Cdd:COG1426    9 LLRQAREAKGLSLEDVAERTKISVSYLEAIEEGDFDAL 46
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
9-70 8.72e-06

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 43.63  E-value: 8.72e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 501535771   9 QLRLQRAWSQEQLAEMAGLSVRTIQRIENGE-RPGLETLSALAAVFEVTVAEIGGEASREGAP 70
Cdd:PRK09943  14 EIRQQQGLSQRRAAELSGLTHSAISTIEQDKvSPAISTLQKLLKVYGLSLSEFFSEPEKPDEP 76
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
3-52 2.73e-05

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 39.92  E-value: 2.73e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 501535771   3 SNNQVKQLRLQRAWSQEQLAEMAGLSVRTIQRIENGER-PGLETLSALAAV 52
Cdd:COG2944    7 TPEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRkPSGAALKLLRLL 57
COG1395 COG1395
Predicted transcriptional regulator [Transcription];
8-59 1.45e-04

Predicted transcriptional regulator [Transcription];


Pssm-ID: 441005 [Multi-domain]  Cd Length: 313  Bit Score: 40.59  E-value: 1.45e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 501535771   8 KQLRLQRAWSQEQLAEMAGLSVRTIQRIENGE-RPGLETLSALAAVFEVTVAE 59
Cdd:COG1395  133 RELREERGLSLGELASELGVSRRTISKYERGEmDASIEVALKLEEILGEPIVK 185
TIGR00270 TIGR00270
TIGR00270 family protein; [Hypothetical proteins, Conserved]
 7-73 5.45e-04

TIGR00270 family protein; [Hypothetical proteins, Conserved]


Pssm-ID: 129371 [Multi-domain]  Cd Length: 154  Bit Score: 38.35  E-value: 5.45e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 501535771    7 VKQLRLQRAWSQEQLAEMAGLSVRTIQRIENGE-RPGLETLSALAAVFEVTVAEIGGEASREGAPGPE 73
Cdd:TIGR00270  74 IRREREKRGWSQEQLAKKIQEKESLIKKIENAEiEPEPKVVEKLEKLLKIKLREQVPEIKIEKSGRKS 141
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 14-56 6.09e-04

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 36.71  E-value: 6.09e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 501535771  14 RAWSQEQLAEMAGLSVRTIQRIENGERP-GLETLSALAAVFEVT 56
Cdd:COG3093   21 LGLSQTELAKALGVSRQRISEILNGKRAiTADTALRLARAFGTS 64
PRK04140 PRK04140
transcriptional regulator;
8-59 1.37e-03

transcriptional regulator;


Pssm-ID: 235224 [Multi-domain]  Cd Length: 317  Bit Score: 37.91  E-value: 1.37e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 501535771   8 KQLRLQRAWSQEQLAEMAGLSVRTIQRIENGE-RPGLETLSALAAVFEVTVAE 59
Cdd:PRK04140 132 REAREELGLSLGELASELGVSRRTISKYENGGmNASIEVAIKLEEILDVPLTK 184
 
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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