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Conserved domains on  [gi|503338886|ref|WP_013573547|]
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MULTISPECIES: NadS family protein [Rahnella]

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 super family cl49308
NadS family protein;
5-93 4.36e-20

NadS family protein;


The actual alignment was detected with superfamily member NF041265:

Pssm-ID: 469165  Cd Length: 94  Bit Score: 77.14  E-value: 4.36e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503338886  5 FFEELRQSAEEMVAIHKGEMTPAHITRVAMPEVKQIRTKAGIKQDEFARLLGVSPSLVQAWEQQKRLPNGAALKLLKMLE 84
Cdd:NF041265  3 FFDELKASLEEAVEIKNGVKAPARVTRYEVADVKAIRAQLNVSQAEMAKALGTSVDTIKSWESKRRNPTGLAAKVLATIQ 82


                ....*....
gi 503338886 85 LNPQIIQTL 93
Cdd:NF041265 83 DNPAFFKEL 91
 
Name Accession Description Interval E-value
NadS NF041265
NadS family protein;
5-93 4.36e-20

NadS family protein;


Pssm-ID: 469165  Cd Length: 94  Bit Score: 77.14  E-value: 4.36e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503338886  5 FFEELRQSAEEMVAIHKGEMTPAHITRVAMPEVKQIRTKAGIKQDEFARLLGVSPSLVQAWEQQKRLPNGAALKLLKMLE 84
Cdd:NF041265  3 FFDELKASLEEAVEIKNGVKAPARVTRYEVADVKAIRAQLNVSQAEMAKALGTSVDTIKSWESKRRNPTGLAAKVLATIQ 82


                ....*....
gi 503338886 85 LNPQIIQTL 93
Cdd:NF041265 83 DNPAFFKEL 91
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
30-90 2.47e-18

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 71.89  E-value: 2.47e-18
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 503338886 30 TRVAMPEVKQIRTKAGIKQDEFARLLGVSPSLVQAWEQQKRLPNGAALKLLKMLELNPQII 90
Cdd:COG2944   4 KPLTPEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGAALKLLRLLEKHPELL 64
PRK10072 PRK10072
HTH-type transcriptional regulator;
2-93 1.18e-14

HTH-type transcriptional regulator;


Pssm-ID: 182222  Cd Length: 96  Bit Score: 63.27  E-value: 1.18e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503338886  2 TKEFFEELRQSAEEMVAIHKGEMTPAHITRVAMPEVKQIRTKAGIKQDEFARLLGVSPSLVQAWEQQKRLPNGAALKLLK 81
Cdd:PRK10072  3 YKDPMFELLSSLEQIVFKDETQKITLTQKTTSFTEFEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRVKPSSAELKLMR 82

                        90
                ....*....|..
gi 503338886 82 MLELNPQIIQTL 93
Cdd:PRK10072 83 LIQANPALSKQL 94
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 7-94 4.14e-11

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: 54.94  E-value: 4.14e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503338886    7 EELRQSAEEMVAIHK---GEMTPahitrvamPEVKQIRTKAGIKQDEFARLLGVSPSLVQAWEQQKRLPNGAALKLLKML 83
Cdd:TIGR03830  45 EDSKRNSAALADFYRkvdGLLTG--------PEIRRIRKKLGLSQREAAELLGGGVNAFSRYERGEVRPSKALDKLLRLL 116

                          90
                  ....*....|.
gi 503338886   84 ELNPQIIQTLK 94
Cdd:TIGR03830 117 DKHPELLEELR 127
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 37-90 2.59e-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: 46.01  E-value: 2.59e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 503338886 37 VKQIRTKAGIKQDEFARLLGVSPSLVQAWEQQKRLPNGAAL-KLLKMLELNPQII 90
Cdd:cd00093   4 LKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLeKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
36-90 5.42e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 45.20  E-value: 5.42e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 503338886   36 EVKQIRTKAGIKQDEFARLLGVSPSLVQAWEQQKRLPNGAAL-KLLKMLELNPQII 90
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLkKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 37-90 1.58e-06

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: 41.37  E-value: 1.58e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 503338886  37 VKQIRTKAGIKQDEFARLLGVSPSLVQAWEQQKRLPNGAAL-KLLKMLELNPQII 90
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLkKLAEALGVSLDEL 55
 
Name Accession Description Interval E-value
NadS NF041265
NadS family protein;
5-93 4.36e-20

NadS family protein;


Pssm-ID: 469165  Cd Length: 94  Bit Score: 77.14  E-value: 4.36e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503338886  5 FFEELRQSAEEMVAIHKGEMTPAHITRVAMPEVKQIRTKAGIKQDEFARLLGVSPSLVQAWEQQKRLPNGAALKLLKMLE 84
Cdd:NF041265  3 FFDELKASLEEAVEIKNGVKAPARVTRYEVADVKAIRAQLNVSQAEMAKALGTSVDTIKSWESKRRNPTGLAAKVLATIQ 82


                ....*....
gi 503338886 85 LNPQIIQTL 93
Cdd:NF041265 83 DNPAFFKEL 91
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
30-90 2.47e-18

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 71.89  E-value: 2.47e-18
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 503338886 30 TRVAMPEVKQIRTKAGIKQDEFARLLGVSPSLVQAWEQQKRLPNGAALKLLKMLELNPQII 90
Cdd:COG2944   4 KPLTPEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGAALKLLRLLEKHPELL 64
PRK10072 PRK10072
HTH-type transcriptional regulator;
2-93 1.18e-14

HTH-type transcriptional regulator;


Pssm-ID: 182222  Cd Length: 96  Bit Score: 63.27  E-value: 1.18e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503338886  2 TKEFFEELRQSAEEMVAIHKGEMTPAHITRVAMPEVKQIRTKAGIKQDEFARLLGVSPSLVQAWEQQKRLPNGAALKLLK 81
Cdd:PRK10072  3 YKDPMFELLSSLEQIVFKDETQKITLTQKTTSFTEFEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRVKPSSAELKLMR 82

                        90
                ....*....|..
gi 503338886 82 MLELNPQIIQTL 93
Cdd:PRK10072 83 LIQANPALSKQL 94
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 7-94 4.14e-11

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: 54.94  E-value: 4.14e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503338886    7 EELRQSAEEMVAIHK---GEMTPahitrvamPEVKQIRTKAGIKQDEFARLLGVSPSLVQAWEQQKRLPNGAALKLLKML 83
Cdd:TIGR03830  45 EDSKRNSAALADFYRkvdGLLTG--------PEIRRIRKKLGLSQREAAELLGGGVNAFSRYERGEVRPSKALDKLLRLL 116

                          90
                  ....*....|.
gi 503338886   84 ELNPQIIQTLK 94
Cdd:TIGR03830 117 DKHPELLEELR 127
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 37-90 2.59e-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: 46.01  E-value: 2.59e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 503338886 37 VKQIRTKAGIKQDEFARLLGVSPSLVQAWEQQKRLPNGAAL-KLLKMLELNPQII 90
Cdd:cd00093   4 LKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLeKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
36-90 5.42e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 45.20  E-value: 5.42e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 503338886   36 EVKQIRTKAGIKQDEFARLLGVSPSLVQAWEQQKRLPNGAAL-KLLKMLELNPQII 90
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLkKLAKALGVSLDEL 56
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
37-85 9.56e-08

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 44.84  E-value: 9.56e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 503338886 37 VKQIRTKAGIKQDEFARLLGVSPSLVQAWEQQKRLPN-GAALKLLKMLEL 85
Cdd:COG1476   9 LKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSlELALKIARALGV 58
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 37-84 1.24e-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: 44.54  E-value: 1.24e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 503338886 37 VKQIRTKAGIKQDEFARLLGVSPSLVQAWEQQKRLPNgaaLKLLKMLE 84
Cdd:COG1813  17 IREAREARGLSQEELAEKLGVSESTIRRIERGEATPS---LDTLRKLE 61
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
37-87 2.47e-07

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 44.22  E-value: 2.47e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 503338886 37 VKQIRTKAGIKQDEFARLLGVSPSLVQAWEQQKRLPNGAAL-KLLKMLELNP 87
Cdd:COG1396  12 LRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLlKLAKALGVSL 63
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 37-90 1.58e-06

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: 41.37  E-value: 1.58e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 503338886  37 VKQIRTKAGIKQDEFARLLGVSPSLVQAWEQQKRLPNGAAL-KLLKMLELNPQII 90
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLkKLAEALGVSLDEL 55
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 36-93 3.86e-04

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: 35.58  E-value: 3.86e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 503338886  36 EVKQIRTKAGIKQDEFARLLGVSPSLVQAWEQ--QKRLPNGAALKLLKMLELNPQIIQTL 93
Cdd:pfam13560  5 RLRRLRERAGLSQEALARRLGVSRSTLSRLETgrRGRPSPAVVERLARALGVDGAERAEL 64
MqsA_antitoxin pfam15731
Antitoxin component of bacterial toxin-antitoxin system, MqsA; MqsA_antitoxin is a family of ...
 7-94 3.50e-03

Antitoxin component of bacterial toxin-antitoxin system, MqsA; MqsA_antitoxin is a family of prokaryotic proteins that act as antidotes to the mRNA interferase MqsR. It has a zinc-binding at the very N-terminus indicating its DNA-binding capacity. MqsR is the gene most highly upregulated in E. Colo MqsR_toxin is a family of bacterial toxins that act as an mRNA interferase. MqsR is the gene most highly upregulated in E. coli persister cells and it plays an essential role in biofilm regulation and cell signalling. It forms part of a bacterial toxin-antitoxin TA system, and as expected for a TA system, the expression of the MqsR toxin leads to growth arrest, while co-expression with its antitoxin, MqsA, rescues the growth arrest phenotype. In addition, MqsR associates with MqsA to form a tight, non-toxic complex and both MqsA alone and the MqsR:MqsA2:MqsR complex bind and regulate the mqsR promoter. The structure of MqsR shows that is is a member of the RelE/YoeB family of bacterial RNases that are structurally and functionally characterized bacterial toxins.


Pssm-ID: 292359 [Multi-domain]  Cd Length: 131  Bit Score: 34.28  E-value: 3.50e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503338886    7 EELRQSAEEMVAIHKgemtpaHI-TRVAMPE-VKQIRTKAGIKQDEFARLLGVSPSLVQAWEQQKRLPNGAALKLLKMLE 84
Cdd:pfam15731  48 EEGDRYSALALAFNR------QVnAVLIDPAfIARVRKKLGLDQREAAEIFGGGVNAFSRYENGKTRPPLALVKLLRLLD 121

                          90
                  ....*....|
gi 503338886   85 LNPQIIQTLK 94
Cdd:pfam15731 122 RHPELLEEIR 131
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 37-88 7.00e-03

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: 32.26  E-value: 7.00e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 503338886  37 VKQIRTKAGIKQDEFARLLGVSPSLVQAWEQQKRLPNGA-ALKLLKMLELNPQ 88
Cdd:pfam12844  4 LRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAEtLYKIAELLGVPAN 56
COG2452 COG2452
Predicted site-specific integrase-resolvase [Mobilome: prophages, transposons];
50-72 7.32e-03

Predicted site-specific integrase-resolvase [Mobilome: prophages, transposons];


Pssm-ID: 441988 [Multi-domain]  Cd Length: 178  Bit Score: 33.81  E-value: 7.32e-03
                         10        20
                 ....*....|....*....|...
gi 503338886  50 EFARLLGVSPSLVQAWEQQKRLP 72
Cdd:COG2452    5 EAAELLGVSPKTLRRWEKEGKLP 27
PHA01976 PHA01976
helix-turn-helix protein
 39-73 7.70e-03

helix-turn-helix protein


Pssm-ID: 177330 [Multi-domain]  Cd Length: 67  Bit Score: 32.24  E-value: 7.70e-03
                        10        20        30
                ....*....|....*....|....*....|....*
gi 503338886 39 QIRTKAGIKQDEFARLLGVSPSLVQAWEQQKRLPN 73
Cdd:PHA01976  9 KARNARAWSAPELSRRAGVRHSLIYDFEADKRLPN 43
HTH_MerR-trunc cd04762
Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family ...
 50-72 8.57e-03

Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.


Pssm-ID: 133390 [Multi-domain]  Cd Length: 49  Bit Score: 31.79  E-value: 8.57e-03
                        10        20
                ....*....|....*....|...
gi 503338886 50 EFARLLGVSPSLVQAWEQQKRLP 72
Cdd:cd04762   5 EAAELLGVSPSTLRRWVKEGKLK 27
 
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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