NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|445929581|ref|WP_000007436|]
View 

MULTISPECIES: NadS family protein [Gammaproteobacteria]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
NadS NF041265
NadS family protein;
1-94 7.92e-66

NadS family protein;


:

Pssm-ID: 469165  Cd Length: 94  Bit Score: 192.70  E-value: 7.92e-66
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445929581  1 MSFFDELKTSLEEAVEIKQGLKEPARVTRYEIADVKAIREQLNVSQSEMAKALGTSVDTIKSWESKRRNPTGLAAKVLAT 80
Cdd:NF041265  1 MSFFDELKASLEEAVEIKNGVKAPARVTRYEVADVKAIRAQLNVSQAEMAKALGTSVDTIKSWESKRRNPTGLAAKVLAT 80

                        90
                ....*....|....
gi 445929581 81 IKENPAFFRELASH 94
Cdd:NF041265 81 IQDNPAFFKELAAH 94
 
Name Accession Description Interval E-value
NadS NF041265
NadS family protein;
1-94 7.92e-66

NadS family protein;


Pssm-ID: 469165  Cd Length: 94  Bit Score: 192.70  E-value: 7.92e-66
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445929581  1 MSFFDELKTSLEEAVEIKQGLKEPARVTRYEIADVKAIREQLNVSQSEMAKALGTSVDTIKSWESKRRNPTGLAAKVLAT 80
Cdd:NF041265  1 MSFFDELKASLEEAVEIKNGVKAPARVTRYEVADVKAIRAQLNVSQAEMAKALGTSVDTIKSWESKRRNPTGLAAKVLAT 80

                        90
                ....*....|....
gi 445929581 81 IKENPAFFRELASH 94
Cdd:NF041265 81 IQDNPAFFKELAAH 94
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
28-88 6.11e-17

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 68.04  E-value: 6.11e-17
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 445929581 28 TRYEIADVKAIREQLNVSQSEMAKALGTSVDTIKSWESKRRNPTGLAAKVLATIKENPAFF 88
Cdd:COG2944   4 KPLTPEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGAALKLLRLLEKHPELL 64
PRK10072 PRK10072
HTH-type transcriptional regulator;
6-91 1.99e-09

HTH-type transcriptional regulator;


Pssm-ID: 182222  Cd Length: 96  Bit Score: 49.79  E-value: 1.99e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445929581  6 ELKTSLEEAVEIKQGLKEPARVTRYEIADVKAIREQLNVSQSEMAKALGTSVDTIKSWESKRRNPTGLAAKVLATIKENP 85
Cdd:PRK10072  9 ELLSSLEQIVFKDETQKITLTQKTTSFTEFEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRVKPSSAELKLMRLIQANP 88


                ....*.
gi 445929581 86 AFFREL 91
Cdd:PRK10072 89 ALSKQL 94
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
35-79 9.06e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 44.43  E-value: 9.06e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 445929581   35 VKAIREQLNVSQSEMAKALGTSVDTIKSWESKRRNPTGLAAKVLA 79
Cdd:smart00530  2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLA 46
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 35-79 2.97e-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: 43.30  E-value: 2.97e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 445929581  35 VKAIREQLNVSQSEMAKALGTSVDTIKSWESKRRNPTGLAAKVLA 79
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLA 45
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 35-79 1.13e-06

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: 41.77  E-value: 1.13e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 445929581 35 VKAIREQLNVSQSEMAKALGTSVDTIKSWESKRRNPTGLAAKVLA 79
Cdd:cd00093   4 LKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLA 48
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 22-92 1.39e-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: 37.61  E-value: 1.39e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 445929581   22 KEPARVTRYEIadvKAIREQLNVSQSEMAKALGTSVDTIKSWESKRRNPTGLAAKVLATIKENPAFFRELA 92
Cdd:TIGR03830  60 KVDGLLTGPEI---RRIRKKLGLSQREAAELLGGGVNAFSRYERGEVRPSKALDKLLRLLDKHPELLEELR 127
 
Name Accession Description Interval E-value
NadS NF041265
NadS family protein;
1-94 7.92e-66

NadS family protein;


Pssm-ID: 469165  Cd Length: 94  Bit Score: 192.70  E-value: 7.92e-66
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445929581  1 MSFFDELKTSLEEAVEIKQGLKEPARVTRYEIADVKAIREQLNVSQSEMAKALGTSVDTIKSWESKRRNPTGLAAKVLAT 80
Cdd:NF041265  1 MSFFDELKASLEEAVEIKNGVKAPARVTRYEVADVKAIRAQLNVSQAEMAKALGTSVDTIKSWESKRRNPTGLAAKVLAT 80

                        90
                ....*....|....
gi 445929581 81 IKENPAFFRELASH 94
Cdd:NF041265 81 IQDNPAFFKELAAH 94
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
28-88 6.11e-17

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 68.04  E-value: 6.11e-17
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 445929581 28 TRYEIADVKAIREQLNVSQSEMAKALGTSVDTIKSWESKRRNPTGLAAKVLATIKENPAFF 88
Cdd:COG2944   4 KPLTPEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGAALKLLRLLEKHPELL 64
PRK10072 PRK10072
HTH-type transcriptional regulator;
6-91 1.99e-09

HTH-type transcriptional regulator;


Pssm-ID: 182222  Cd Length: 96  Bit Score: 49.79  E-value: 1.99e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445929581  6 ELKTSLEEAVEIKQGLKEPARVTRYEIADVKAIREQLNVSQSEMAKALGTSVDTIKSWESKRRNPTGLAAKVLATIKENP 85
Cdd:PRK10072  9 ELLSSLEQIVFKDETQKITLTQKTTSFTEFEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRVKPSSAELKLMRLIQANP 88


                ....*.
gi 445929581 86 AFFREL 91
Cdd:PRK10072 89 ALSKQL 94
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 35-81 8.27e-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: 44.93  E-value: 8.27e-08
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 445929581 35 VKAIREQLNVSQSEMAKALGTSVDTIKSWESKRRNPTGLAAKVLATI 81
Cdd:COG1813  17 IREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKA 63
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
35-79 9.06e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 44.43  E-value: 9.06e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 445929581   35 VKAIREQLNVSQSEMAKALGTSVDTIKSWESKRRNPTGLAAKVLA 79
Cdd:smart00530  2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLA 46
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 35-79 2.97e-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: 43.30  E-value: 2.97e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 445929581  35 VKAIREQLNVSQSEMAKALGTSVDTIKSWESKRRNPTGLAAKVLA 79
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLA 45
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
35-81 5.30e-07

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 42.91  E-value: 5.30e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 445929581 35 VKAIREQLNVSQSEMAKALGTSVDTIKSWESKRRNPTGLAAKVLATI 81
Cdd:COG1476   9 LKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARA 55
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
35-71 6.97e-07

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 43.06  E-value: 6.97e-07
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 445929581 35 VKAIREQLNVSQSEMAKALGTSVDTIKSWESKRRNPT 71
Cdd:COG1396  12 LRELRKARGLTQEELAERLGVSRSTISRIERGRRNPS 48
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 35-79 1.13e-06

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: 41.77  E-value: 1.13e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 445929581 35 VKAIREQLNVSQSEMAKALGTSVDTIKSWESKRRNPTGLAAKVLA 79
Cdd:cd00093   4 LKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLA 48
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 22-92 1.39e-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: 37.61  E-value: 1.39e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 445929581   22 KEPARVTRYEIadvKAIREQLNVSQSEMAKALGTSVDTIKSWESKRRNPTGLAAKVLATIKENPAFFRELA 92
Cdd:TIGR03830  60 KVDGLLTGPEI---RRIRKKLGLSQREAAELLGGGVNAFSRYERGEVRPSKALDKLLRLLDKHPELLEELR 127
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 35-71 2.17e-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: 36.92  E-value: 2.17e-04
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 445929581 35 VKAIREQLNVSQSEMAKALGTSVDTIKSWESKRRNPT 71
Cdd:COG3620  22 LRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPT 58
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 35-86 1.87e-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: 33.80  E-value: 1.87e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 445929581  35 VKAIREQLNVSQSEMAKALGTSVDTIKSWESKRRNPTGLAAKVLATIKENPA 86
Cdd:pfam12844  4 LRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPA 55
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 39-72 6.66e-03

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 33.29  E-value: 6.66e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 445929581  39 REQLNVSQSEMAKALGTSVDTIKSWESKRRNPTG 72
Cdd:PRK09706  14 RKQLKLSQRSLAKAVKVSHVSISQWERDETEPTG 47
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH