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Conserved domains on  [gi|635773349|gb|KDF54801|]
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hypothetical protein AF40_03754 [Enterobacter roggenkampii MGH 54]

Protein Classification

transcriptional regulator( domain architecture ID 10793339)

helix-turn-helix-type transcriptional regulator

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK10072 PRK10072
HTH-type transcriptional regulator;
1-94 3.40e-57

HTH-type transcriptional regulator;


:

Pssm-ID: 182222  Cd Length: 96  Bit Score: 171.13  E-value: 3.40e-57
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 635773349  1 MEYKDPEFELLSSLEQIIFKDVPQTITLQQKSNPFTEYEQLRKGTGLKTEEFARAMGVSVAMVQEWESKREKPTPTELRL 80
Cdd:PRK10072  1 MEYKDPMFELLSSLEQIVFKDETQKITLTQKTTSFTEFEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRVKPSSAELKL 80

                        90
                ....*....|....
gi 635773349 81 MRLIQANPALSKQI 94
Cdd:PRK10072 81 MRLIQANPALSKQL 94
 
Name Accession Description Interval E-value
PRK10072 PRK10072
HTH-type transcriptional regulator;
1-94 3.40e-57

HTH-type transcriptional regulator;


Pssm-ID: 182222  Cd Length: 96  Bit Score: 171.13  E-value: 3.40e-57
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 635773349  1 MEYKDPEFELLSSLEQIIFKDVPQTITLQQKSNPFTEYEQLRKGTGLKTEEFARAMGVSVAMVQEWESKREKPTPTELRL 80
Cdd:PRK10072  1 MEYKDPMFELLSSLEQIVFKDETQKITLTQKTTSFTEFEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRVKPSSAELKL 80

                        90
                ....*....|....
gi 635773349 81 MRLIQANPALSKQI 94
Cdd:PRK10072 81 MRLIQANPALSKQL 94
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
40-90 5.40e-15

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 63.03  E-value: 5.40e-15
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 635773349 40 QLRKGTGLKTEEFARAMGVSVAMVQEWESKREKPTPTELRLMRLIQANPAL 90
Cdd:COG2944  13 ALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGAALKLLRLLEKHPEL 63
NadS NF041265
NadS family protein;
9-95 1.00e-07

NadS family protein;


Pssm-ID: 469165  Cd Length: 94  Bit Score: 45.55  E-value: 1.00e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 635773349  9 ELLSSLEQIIfkDVPQTItlqQKSNPFTEYE-----QLRKGTGLKTEEFARAMGVSVAMVQEWESKREKPTPTELRLMRL 83
Cdd:NF041265  6 ELKASLEEAV--EIKNGV---KAPARVTRYEvadvkAIRAQLNVSQAEMAKALGTSVDTIKSWESKRRNPTGLAAKVLAT 80

                        90
                ....*....|..
gi 635773349 84 IQANPALSKQIA 95
Cdd:NF041265 81 IQDNPAFFKELA 92
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 40-81 1.38e-05

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: 39.07  E-value: 1.38e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 635773349 40 QLRKGTGLKTEEFARAMGVSVAMVQEWESKREKPTPTELRLM 81
Cdd:cd00093   6 ELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKL 47
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
40-81 2.02e-05

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 38.65  E-value: 2.02e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 635773349   40 QLRKGTGLKTEEFARAMGVSVAMVQEWESKREKPTPTELRLM 81
Cdd:smart00530  4 ELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKL 45
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 40-95 1.36e-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: 38.00  E-value: 1.36e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 635773349   40 QLRKGTGLKTEEFARAMGVSVAMVQEWESKREKPTPTELRLMRLIQANPALSKQIA 95
Cdd:TIGR03830  72 RIRKKLGLSQREAAELLGGGVNAFSRYERGEVRPSKALDKLLRLLDKHPELLEELR 127
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 40-90 3.45e-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: 3.45e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 635773349  40 QLRKGTGLKTEEFARAMGVSVAMVQEWES-KREKPTPTEL-RLMRLIQANPAL 90
Cdd:pfam13560  8 RLRERAGLSQEALARRLGVSRSTLSRLETgRRGRPSPAVVeRLARALGVDGAE 60
VC1465_fam NF040522
VC1465 family Xer recombination activation factor;
42-86 6.19e-03

VC1465 family Xer recombination activation factor;


Pssm-ID: 439737 [Multi-domain]  Cd Length: 111  Bit Score: 33.19  E-value: 6.19e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 635773349  42 RKGTGLKTEEFARAMGVSVAMVQEWESKREKPTPTELRLMRLIQA 86
Cdd:NF040522   5 REKAGLTRQQAAEMLRVSLRTVQNWETGKVPMPYCAFKLERRLIP 49
 
Name Accession Description Interval E-value
PRK10072 PRK10072
HTH-type transcriptional regulator;
1-94 3.40e-57

HTH-type transcriptional regulator;


Pssm-ID: 182222  Cd Length: 96  Bit Score: 171.13  E-value: 3.40e-57
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 635773349  1 MEYKDPEFELLSSLEQIIFKDVPQTITLQQKSNPFTEYEQLRKGTGLKTEEFARAMGVSVAMVQEWESKREKPTPTELRL 80
Cdd:PRK10072  1 MEYKDPMFELLSSLEQIVFKDETQKITLTQKTTSFTEFEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRVKPSSAELKL 80

                        90
                ....*....|....
gi 635773349 81 MRLIQANPALSKQI 94
Cdd:PRK10072 81 MRLIQANPALSKQL 94
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
40-90 5.40e-15

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 63.03  E-value: 5.40e-15
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 635773349 40 QLRKGTGLKTEEFARAMGVSVAMVQEWESKREKPTPTELRLMRLIQANPAL 90
Cdd:COG2944  13 ALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGAALKLLRLLEKHPEL 63
NadS NF041265
NadS family protein;
9-95 1.00e-07

NadS family protein;


Pssm-ID: 469165  Cd Length: 94  Bit Score: 45.55  E-value: 1.00e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 635773349  9 ELLSSLEQIIfkDVPQTItlqQKSNPFTEYE-----QLRKGTGLKTEEFARAMGVSVAMVQEWESKREKPTPTELRLMRL 83
Cdd:NF041265  6 ELKASLEEAV--EIKNGV---KAPARVTRYEvadvkAIRAQLNVSQAEMAKALGTSVDTIKSWESKRRNPTGLAAKVLAT 80

                        90
                ....*....|..
gi 635773349 84 IQANPALSKQIA 95
Cdd:NF041265 81 IQDNPAFFKELA 92
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 40-81 1.38e-05

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: 39.07  E-value: 1.38e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 635773349 40 QLRKGTGLKTEEFARAMGVSVAMVQEWESKREKPTPTELRLM 81
Cdd:cd00093   6 ELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKL 47
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
40-81 2.02e-05

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 38.65  E-value: 2.02e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 635773349   40 QLRKGTGLKTEEFARAMGVSVAMVQEWESKREKPTPTELRLM 81
Cdd:smart00530  4 ELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKL 45
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
40-79 8.39e-05

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 37.67  E-value: 8.39e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 635773349 40 QLRKGTGLKTEEFARAMGVSVAMVQEWESKREKPTPTELR 79
Cdd:COG1396  14 ELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLL 53
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 40-95 1.36e-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: 38.00  E-value: 1.36e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 635773349   40 QLRKGTGLKTEEFARAMGVSVAMVQEWESKREKPTPTELRLMRLIQANPALSKQIA 95
Cdd:TIGR03830  72 RIRKKLGLSQREAAELLGGGVNAFSRYERGEVRPSKALDKLLRLLDKHPELLEELR 127
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 40-90 3.45e-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: 3.45e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 635773349  40 QLRKGTGLKTEEFARAMGVSVAMVQEWES-KREKPTPTEL-RLMRLIQANPAL 90
Cdd:pfam13560  8 RLRERAGLSQEALARRLGVSRSTLSRLETgRRGRPSPAVVeRLARALGVDGAE 60
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 39-81 5.12e-04

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: 34.82  E-value: 5.12e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 635773349  39 EQLRKGTGLKTEEFARAMGVSVAMVQEWESKREKPTPTELRLM 81
Cdd:pfam01381  2 KELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKL 44
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 40-81 1.16e-03

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: 34.53  E-value: 1.16e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 635773349 40 QLRKGTGLKTEEFARAMGVSVAMVQEWESKREKPTPTELRLM 81
Cdd:COG1813  19 EAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKL 60
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
40-79 1.47e-03

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 34.05  E-value: 1.47e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 635773349 40 QLRKGTGLKTEEFARAMGVSVAMVQEWESKREKPTPTELR 79
Cdd:COG1476  11 ELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELAL 50
VC1465_fam NF040522
VC1465 family Xer recombination activation factor;
42-86 6.19e-03

VC1465 family Xer recombination activation factor;


Pssm-ID: 439737 [Multi-domain]  Cd Length: 111  Bit Score: 33.19  E-value: 6.19e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 635773349  42 RKGTGLKTEEFARAMGVSVAMVQEWESKREKPTPTELRLMRLIQA 86
Cdd:NF040522   5 REKAGLTRQQAAEMLRVSLRTVQNWETGKVPMPYCAFKLERRLIP 49
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 37-87 6.73e-03

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: 32.68  E-value: 6.73e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 635773349 37 EYEQLRKGTGLKTEEFARAMGVSVAMVQEWESKREKPTPTEL-RLMRLIQAN 87
Cdd:COG3620  21 ALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLeKIAEALGKE 72
 
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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