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Conserved domains on  [gi|496402095|ref|WP_009111085|]
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MULTISPECIES: NadS family protein [Brenneria]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 709729)

helix-turn-helix (HTH) domain-containing protein with an XRE (Xenobiotic Response Element) family HTH domain, binds DNA and may function as a transcriptional regulator

CATH:  1.10.10.10
Gene Ontology:  GO:0003677
PubMed:  15808743|2644244|8831795
SCOP:  4000362

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NadS NF041265
NadS family protein;
1-94 4.78e-31

NadS family protein;


:

Pssm-ID: 469165  Cd Length: 94  Bit Score: 104.87  E-value: 4.78e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496402095  1 MSdFFNDLMTSVNEAVAISEGKTTAARITRYEMPDVKAIRTLSGLKQDDFASALGVSPSLVQAWEQHRRQPTGTALKVLN 80
Cdd:NF041265  1 MS-FFDELKASLEEAVEIKNGVKAPARVTRYEVADVKAIRAQLNVSQAEMAKALGTSVDTIKSWESKRRNPTGLAAKVLA 79

                        90
                ....*....|....
gi 496402095 81 ILKNKPDFIKVLKA 94
Cdd:NF041265 80 TIQDNPAFFKELAA 93
 
Name Accession Description Interval E-value
NadS NF041265
NadS family protein;
1-94 4.78e-31

NadS family protein;


Pssm-ID: 469165  Cd Length: 94  Bit Score: 104.87  E-value: 4.78e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496402095  1 MSdFFNDLMTSVNEAVAISEGKTTAARITRYEMPDVKAIRTLSGLKQDDFASALGVSPSLVQAWEQHRRQPTGTALKVLN 80
Cdd:NF041265  1 MS-FFDELKASLEEAVEIKNGVKAPARVTRYEVADVKAIRAQLNVSQAEMAKALGTSVDTIKSWESKRRNPTGLAAKVLA 79

                        90
                ....*....|....
gi 496402095 81 ILKNKPDFIKVLKA 94
Cdd:NF041265 80 TIQDNPAFFKELAA 93
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
29-89 3.12e-19

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 73.81  E-value: 3.12e-19
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 496402095 29 TRYEMPDVKAIRTLSGLKQDDFASALGVSPSLVQAWEQHRRQPTGTALKVLNILKNKPDFI 89
Cdd:COG2944   4 KPLTPEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGAALKLLRLLEKHPELL 64
PRK10072 PRK10072
HTH-type transcriptional regulator;
7-86 4.49e-13

HTH-type transcriptional regulator;


Pssm-ID: 182222  Cd Length: 96  Bit Score: 59.42  E-value: 4.49e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496402095  7 DLMTSVNEAVAISEGKTTAARITRYEMPDVKAIRTLSGLKQDDFASALGVSPSLVQAWEQHRRQPTGTALKVLNILKNKP 86
Cdd:PRK10072  9 ELLSSLEQIVFKDETQKITLTQKTTSFTEFEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRVKPSSAELKLMRLIQANP 88
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
36-89 4.77e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 45.20  E-value: 4.77e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 496402095   36 VKAIRTLSGLKQDDFASALGVSPSLVQAWEQHRRQPT-GTALKVLNILKNKPDFI 89
Cdd:smart00530  2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSlETLKKLAKALGVSLDEL 56
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 36-89 1.04e-07

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: 44.47  E-value: 1.04e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 496402095 36 VKAIRTLSGLKQDDFASALGVSPSLVQAWEQHRRQPT-GTALKVLNILKNKPDFI 89
Cdd:cd00093   4 LKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSlETLEKLAKALGVSLDEL 58
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 36-89 6.53e-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: 42.53  E-value: 6.53e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 496402095  36 VKAIRTLSGLKQDDFASALGVSPSLVQAWEQHRRQPTG-TALKVLNILKNKPDFI 89
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLeTLKKLAEALGVSLDEL 55
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 34-93 3.89e-04

putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.


Pssm-ID: 274805 [Multi-domain]  Cd Length: 127  Bit Score: 36.45  E-value: 3.89e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 496402095   34 PDVKAIRTLSGLKQDDFASALGVSPSLVQAWEQHRRQPTGTALKVLNILKNKPDFIKVLK 93
Cdd:TIGR03830  68 PEIRRIRKKLGLSQREAAELLGGGVNAFSRYERGEVRPSKALDKLLRLLDKHPELLEELR 127
 
Name Accession Description Interval E-value
NadS NF041265
NadS family protein;
1-94 4.78e-31

NadS family protein;


Pssm-ID: 469165  Cd Length: 94  Bit Score: 104.87  E-value: 4.78e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496402095  1 MSdFFNDLMTSVNEAVAISEGKTTAARITRYEMPDVKAIRTLSGLKQDDFASALGVSPSLVQAWEQHRRQPTGTALKVLN 80
Cdd:NF041265  1 MS-FFDELKASLEEAVEIKNGVKAPARVTRYEVADVKAIRAQLNVSQAEMAKALGTSVDTIKSWESKRRNPTGLAAKVLA 79

                        90
                ....*....|....
gi 496402095 81 ILKNKPDFIKVLKA 94
Cdd:NF041265 80 TIQDNPAFFKELAA 93
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
29-89 3.12e-19

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 73.81  E-value: 3.12e-19
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 496402095 29 TRYEMPDVKAIRTLSGLKQDDFASALGVSPSLVQAWEQHRRQPTGTALKVLNILKNKPDFI 89
Cdd:COG2944   4 KPLTPEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGAALKLLRLLEKHPELL 64
PRK10072 PRK10072
HTH-type transcriptional regulator;
7-86 4.49e-13

HTH-type transcriptional regulator;


Pssm-ID: 182222  Cd Length: 96  Bit Score: 59.42  E-value: 4.49e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496402095  7 DLMTSVNEAVAISEGKTTAARITRYEMPDVKAIRTLSGLKQDDFASALGVSPSLVQAWEQHRRQPTGTALKVLNILKNKP 86
Cdd:PRK10072  9 ELLSSLEQIVFKDETQKITLTQKTTSFTEFEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRVKPSSAELKLMRLIQANP 88
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
36-89 4.77e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 45.20  E-value: 4.77e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 496402095   36 VKAIRTLSGLKQDDFASALGVSPSLVQAWEQHRRQPT-GTALKVLNILKNKPDFI 89
Cdd:smart00530  2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSlETLKKLAKALGVSLDEL 56
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
36-83 6.08e-08

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 45.22  E-value: 6.08e-08
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 496402095 36 VKAIRTLSGLKQDDFASALGVSPSLVQAWEQHRRQPT-GTALKVLNILK 83
Cdd:COG1476   9 LKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSlELALKIARALG 57
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 36-89 1.04e-07

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: 44.47  E-value: 1.04e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 496402095 36 VKAIRTLSGLKQDDFASALGVSPSLVQAWEQHRRQPT-GTALKVLNILKNKPDFI 89
Cdd:cd00093   4 LKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSlETLEKLAKALGVSLDEL 58
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
36-82 1.41e-07

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 44.60  E-value: 1.41e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 496402095 36 VKAIRTLSGLKQDDFASALGVSPSLVQAWEQHRRQPT-GTALKVLNIL 82
Cdd:COG1396  12 LRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSlETLLKLAKAL 59
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 36-81 2.19e-07

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: 43.77  E-value: 2.19e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 496402095 36 VKAIRTLSGLKQDDFASALGVSPSLVQAWEQHRRQPTGTAL----KVLNI 81
Cdd:COG1813  17 IREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLrkleKALGI 66
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 36-89 6.53e-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: 42.53  E-value: 6.53e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 496402095  36 VKAIRTLSGLKQDDFASALGVSPSLVQAWEQHRRQPTG-TALKVLNILKNKPDFI 89
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLeTLKKLAEALGVSLDEL 55
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 7-91 3.63e-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: 38.85  E-value: 3.63e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496402095  7 DLMTSvnEAVAISEGKTTAARItryempdvKAIRTLSGLKQDDFASALGVSPSLVQAWEQHRRQPT-GTALKVLNILKNK 85
Cdd:COG3620   3 DLMSR--DVVTVSPDDTLGEAL--------RLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTvSTLEKIAEALGKE 72


                ....*.
gi 496402095 86 PDFIKV 91
Cdd:COG3620  73 LSAVLV 78
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 34-93 3.89e-04

putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.


Pssm-ID: 274805 [Multi-domain]  Cd Length: 127  Bit Score: 36.45  E-value: 3.89e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 496402095   34 PDVKAIRTLSGLKQDDFASALGVSPSLVQAWEQHRRQPTGTALKVLNILKNKPDFIKVLK 93
Cdd:TIGR03830  68 PEIRRIRKKLGLSQREAAELLGGGVNAFSRYERGEVRPSKALDKLLRLLDKHPELLEELR 127
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 36-94 7.18e-04

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: 34.96  E-value: 7.18e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 496402095  36 VKAIRTLSGLKQDDFASALGVSPSLVQAWEQHRRQPT-GTALKVLNILKNKPDFIKVLKA 94
Cdd:pfam12844  4 LRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPaETLYKIAELLGVPANWLLQGEG 63
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 37-71 3.43e-03

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: 32.89  E-value: 3.43e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 496402095  37 KAIRTLSGLKQDDFASALGVSPSLVQAWEQHRRQP 71
Cdd:pfam13560  7 RRLRERAGLSQEALARRLGVSRSTLSRLETGRRGR 41
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 44-89 3.86e-03

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 34.06  E-value: 3.86e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 496402095  44 GLKQDDFASALGVSPSLVQAWEQHRRQPTGTALKVL-NILKNKPDFI 89
Cdd:PRK09706  18 KLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALaKALQCSPTWL 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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