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Conserved domains on  [gi|1277172724|gb|PIR70714|]
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hypothetical protein COU46_00035, partial [Candidatus Niyogibacteria bacterium CG10_big_fil_rev_8_21_14_0_10_42_19]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 11443570)

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

Gene Ontology:  GO:0003677
PubMed:  37972151

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-56 9.53e-15

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 61.55  E-value: 9.53e-15
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 1277172724  1 KVRNKLGLTQDDLVRKSGVKHTTLTKIESNVViKPSVQTVAKIAKALGVPMEDLVK 56
Cdd:COG1396   14 ELRKARGLTQEELAERLGVSRSTISRIERGRR-NPSLETLLKLAKALGVSLDELLG 68
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-56 9.53e-15

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 61.55  E-value: 9.53e-15
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 1277172724  1 KVRNKLGLTQDDLVRKSGVKHTTLTKIESNVViKPSVQTVAKIAKALGVPMEDLVK 56
Cdd:COG1396   14 ELRKARGLTQEELAERLGVSRSTISRIERGRR-NPSLETLLKLAKALGVSLDELLG 68
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
1-54 8.35e-13

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 55.60  E-value: 8.35e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1277172724   1 KVRNKLGLTQDDLVRKSGVKHTTLTKIESNVViKPSVQTVAKIAKALGVPMEDL 54
Cdd:smart00530  4 ELREEKGLTQEELAEKLGVSRSTLSRIENGKR-KPSLETLKKLAKALGVSLDEL 56
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 1-54 3.75e-12

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: 54.10  E-value: 3.75e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 1277172724  1 KVRNKLGLTQDDLVRKSGVKHTTLTKIESNVViKPSVQTVAKIAKALGVPMEDL 54
Cdd:cd00093    6 ELRKEKGLTQEELAEKLGVSRSTISRIENGKR-NPSLETLEKLAKALGVSLDEL 58
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 1-54 1.36e-11

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: 52.54  E-value: 1.36e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 1277172724  1 KVRNKLGLTQDDLVRKSGVKHTTLTKIESNvVIKPSVQTVAKIAKALGVPMEDL 54
Cdd:pfam01381  3 ELREELGLSQEELAEKLGVSRSTISKIENG-KREPSLETLKKLAEALGVSLDEL 55
PRK09726 PRK09726
type II toxin-antitoxin system antitoxin HipB;
2-51 1.61e-06

type II toxin-antitoxin system antitoxin HipB;


Pssm-ID: 182049  Cd Length: 88  Bit Score: 40.73  E-value: 1.61e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 1277172724  2 VRNKLGLTQDDLVRKSGVKHTTLTKIESNVViKPSVQTVAKIAKALGVPM 51
Cdd:PRK09726  20 VRQQNGWTQSELAKKIGIKQATISNFENNPD-NTTLTTFFKILQSLELSM 68
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-56 9.53e-15

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 61.55  E-value: 9.53e-15
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 1277172724  1 KVRNKLGLTQDDLVRKSGVKHTTLTKIESNVViKPSVQTVAKIAKALGVPMEDLVK 56
Cdd:COG1396   14 ELRKARGLTQEELAERLGVSRSTISRIERGRR-NPSLETLLKLAKALGVSLDELLG 68
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-55 2.13e-13

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 57.55  E-value: 2.13e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 1277172724  1 KVRNKLGLTQDDLVRKSGVKHTTLTKIESNvVIKPSVQTVAKIAKALGVPMEDLV 55
Cdd:COG1476   11 ELRKERGLTQEELAELLGVSRQTISAIENG-KYNPSLELALKIARALGVSLEELF 64
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
1-54 8.35e-13

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 55.60  E-value: 8.35e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1277172724   1 KVRNKLGLTQDDLVRKSGVKHTTLTKIESNVViKPSVQTVAKIAKALGVPMEDL 54
Cdd:smart00530  4 ELREEKGLTQEELAEKLGVSRSTLSRIENGKR-KPSLETLKKLAKALGVSLDEL 56
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 1-54 3.75e-12

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: 54.10  E-value: 3.75e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 1277172724  1 KVRNKLGLTQDDLVRKSGVKHTTLTKIESNVViKPSVQTVAKIAKALGVPMEDL 54
Cdd:cd00093    6 ELRKEKGLTQEELAEKLGVSRSTISRIENGKR-NPSLETLEKLAKALGVSLDEL 58
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 1-54 1.36e-11

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: 52.54  E-value: 1.36e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 1277172724  1 KVRNKLGLTQDDLVRKSGVKHTTLTKIESNvVIKPSVQTVAKIAKALGVPMEDL 54
Cdd:pfam01381  3 ELREELGLSQEELAEKLGVSRSTISKIENG-KREPSLETLKKLAEALGVSLDEL 55
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 3-53 2.77e-10

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: 49.94  E-value: 2.77e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 1277172724  3 RNKLGLTQDDLVRKSGVKHTTLTKIESNvVIKPSVQTVAKIAKALGVPMED 53
Cdd:COG1813   21 REARGLSQEELAEKLGVSESTIRRIERG-EATPSLDTLRKLEKALGISLAE 70
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 3-54 2.79e-09

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: 47.14  E-value: 2.79e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 1277172724  3 RNKLGLTQDDLVRKSGVKHTTLTKIESNVVIKPSVQTVAKIAKALGVPMEDL 54
Cdd:pfam13560 10 RERAGLSQEALARRLGVSRSTLSRLETGRRGRPSPAVVERLARALGVDGAER 61
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 1-56 7.86e-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: 40.73  E-value: 7.86e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 1277172724  1 KVRNKLGLTQDDLVRKSGVKHTTLTKIESNvVIKPSVQTVAKIAKALGVPMEDLVK 56
Cdd:pfam12844  6 KAREERGLTQEELAERLGISRSQLSAIENG-KSVPPAETLYKIAELLGVPANWLLQ 60
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 1-55 9.98e-07

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: 41.54  E-value: 9.98e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 1277172724  1 KVRNKLGLTQDDLVRKSGVKHTTLTKIESNVViKPSVQTVAKIAKALGVPMEDLV 55
Cdd:COG3620   24 LMRKELGLSQLPVAELVGVSQSDILRIESGKR-DPTVSTLEKIAEALGKELSAVL 77
PRK09726 PRK09726
type II toxin-antitoxin system antitoxin HipB;
2-51 1.61e-06

type II toxin-antitoxin system antitoxin HipB;


Pssm-ID: 182049  Cd Length: 88  Bit Score: 40.73  E-value: 1.61e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 1277172724  2 VRNKLGLTQDDLVRKSGVKHTTLTKIESNVViKPSVQTVAKIAKALGVPM 51
Cdd:PRK09726  20 VRQQNGWTQSELAKKIGIKQATISNFENNPD-NTTLTTFFKILQSLELSM 68
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 7-56 2.90e-06

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: 39.45  E-value: 2.90e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 1277172724  7 GLTQDDLVRKSGVKHTTLTKIESNVVIKPSVQTVAKIAKALGVPMEDLVK 56
Cdd:pfam13443 10 GISKSDLARATGISRATLSRLRKGKPKRVSLDTLDKICDALGCQPGDLLE 59
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
1-56 1.80e-05

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 37.43  E-value: 1.80e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1277172724  1 KVRNKL-------GLTQDDLVRKSGVKHTTLTKIESNVVIKPSVQTVAKIAKALGVPMEDLVK 56
Cdd:COG3655    1 MIYVKLdellaerGMTKKELAEATGISRATLSRLKNGKAKAVRLDTLEKICKALDCQPGDLLE 63
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 3-55 7.31e-05

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: 35.94  E-value: 7.31e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 1277172724  3 RNKLGLTQDDLVRKSGVKHTTLTKIESNVVIKPSVQTVAK-----IAKALGVPMEDLV 55
Cdd:COG1426   14 REAKGLSLEDVAERTKISVSYLEAIEEGDFDALPGPVYVRgflrsYARALGLDPEELL 71
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
1-51 9.10e-05

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 37.47  E-value: 9.10e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1277172724   1 KVRNKLGLTQDDLVRKSGVKHTTLTKIESNVViKPSVQTVAKIAKALGVPM 51
Cdd:PRK09943   14 EIRQQQGLSQRRAAELSGLTHSAISTIEQDKV-SPAISTLQKLLKVYGLSL 63
SfsB COG3423
Predicted transcriptional regulator, lambda repressor-like DNA-binding domain [Transcription];
5-54 2.04e-04

Predicted transcriptional regulator, lambda repressor-like DNA-binding domain [Transcription];


Pssm-ID: 442649 [Multi-domain]  Cd Length: 69  Bit Score: 34.81  E-value: 2.04e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 1277172724  5 KLGLTQDDLVRKSGVKHTTLtkieSNVVIKPSVQTVAKIAKALGVPMEDL 54
Cdd:COG3423   18 KRGTSLAALAREAGLSSSTL----SNALTRPWPKGERAIAEALGVPPEEI 63
PRK08154 PRK08154
anaerobic benzoate catabolism transcriptional regulator; Reviewed
 3-55 9.23e-04

anaerobic benzoate catabolism transcriptional regulator; Reviewed


Pssm-ID: 236167 [Multi-domain]  Cd Length: 309  Bit Score: 34.54  E-value: 9.23e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1277172724   3 RNKLGLTQDDLVRKSGVKHTTLTKIES---NVvikpSVQTVAKIAKALGVPMEDLV 55
Cdd:PRK08154   37 RARRGMSRKVLAQASGVSERYLAQLESgqgNV----SILLLRRVARALGCSLADLL 88
PHA01976 PHA01976
helix-turn-helix protein
 1-55 8.04e-03

helix-turn-helix protein


Pssm-ID: 177330 [Multi-domain]  Cd Length: 67  Bit Score: 30.69  E-value: 8.04e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 1277172724  1 KVRNKLGLTQDDLVRKSGVKHTTLTKIESNVVIkPSVQTVAKIAKALGVPMEDLV 55
Cdd:PHA01976   9 KARNARAWSAPELSRRAGVRHSLIYDFEADKRL-PNLKTLLRLADALGVTLDWLC 62
 
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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