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Conserved domains on  [gi|1543063251|ref|WP_125971253|]
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helix-turn-helix domain-containing protein [Iodobacter ciconiae]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 10009472)

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
COG5606 COG5606
Predicted DNA-binding protein, XRE-type HTH domain [General function prediction only];
5-90 3.09e-37

Predicted DNA-binding protein, XRE-type HTH domain [General function prediction only];


:

Pssm-ID: 444337  Cd Length: 105  Bit Score: 120.76  E-value: 3.09e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543063251   5 IIESSGNVFADLGVSPEESTLLGLRSGLMNELRQTLQEKNWTQQQAAAALGVSQARISDLMRGKWEKFSLDMLVTLASHA 84
Cdd:COG5606     6 IEESSGNVFADLGFPDEEAEELKLKAQLMAAIRKLIKERGLTQAEAAELLGITQPRVSDLLRGKISKFSLDKLVNMLARL 85


                  ....*.
gi 1543063251  85 GRKISL 90
Cdd:COG5606    86 GQDVEI 91
 
Name Accession Description Interval E-value
COG5606 COG5606
Predicted DNA-binding protein, XRE-type HTH domain [General function prediction only];
5-90 3.09e-37

Predicted DNA-binding protein, XRE-type HTH domain [General function prediction only];


Pssm-ID: 444337  Cd Length: 105  Bit Score: 120.76  E-value: 3.09e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543063251   5 IIESSGNVFADLGVSPEESTLLGLRSGLMNELRQTLQEKNWTQQQAAAALGVSQARISDLMRGKWEKFSLDMLVTLASHA 84
Cdd:COG5606     6 IEESSGNVFADLGFPDEEAEELKLKAQLMAAIRKLIKERGLTQAEAAELLGITQPRVSDLLRGKISKFSLDKLVNMLARL 85


                  ....*.
gi 1543063251  85 GRKISL 90
Cdd:COG5606    86 GQDVEI 91
HTH_37 pfam13744
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain.
 12-91 1.34e-17

Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain.


Pssm-ID: 433449 [Multi-domain]  Cd Length: 80  Bit Score: 70.33  E-value: 1.34e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543063251 12 VFADLGVSPEESTLLglRSGLMNELRQTLQEKNWTQQQAAAALGVSQARISDLMRGKWEKFSLDMLVTLASHAGRKISLM 91
Cdd:pfam13744  1 VFADLGFEDAEELQA--KAQLARAIARLIEGRGLSQQEAAALLGIAQPKVSALLKGKLSRFSLDKLLDFLTALGQDVEIV 78
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
35-81 7.61e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 44.82  E-value: 7.61e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1543063251  35 ELRQTLQEKNWTQQQAAAALGVSQARISDLMRGKWeKFSLDMLVTLA 81
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKR-KPSLETLKKLA 46
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 33-81 1.02e-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: 1.02e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 1543063251 33 MNELRQTLQEKNWTQQQAAAALGVSQARISDLMRGKwEKFSLDMLVTLA 81
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGK-RNPSLETLEKLA 48
 
Name Accession Description Interval E-value
COG5606 COG5606
Predicted DNA-binding protein, XRE-type HTH domain [General function prediction only];
5-90 3.09e-37

Predicted DNA-binding protein, XRE-type HTH domain [General function prediction only];


Pssm-ID: 444337  Cd Length: 105  Bit Score: 120.76  E-value: 3.09e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543063251   5 IIESSGNVFADLGVSPEESTLLGLRSGLMNELRQTLQEKNWTQQQAAAALGVSQARISDLMRGKWEKFSLDMLVTLASHA 84
Cdd:COG5606     6 IEESSGNVFADLGFPDEEAEELKLKAQLMAAIRKLIKERGLTQAEAAELLGITQPRVSDLLRGKISKFSLDKLVNMLARL 85


                  ....*.
gi 1543063251  85 GRKISL 90
Cdd:COG5606    86 GQDVEI 91
HTH_37 pfam13744
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain.
 12-91 1.34e-17

Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain.


Pssm-ID: 433449 [Multi-domain]  Cd Length: 80  Bit Score: 70.33  E-value: 1.34e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543063251 12 VFADLGVSPEESTLLglRSGLMNELRQTLQEKNWTQQQAAAALGVSQARISDLMRGKWEKFSLDMLVTLASHAGRKISLM 91
Cdd:pfam13744  1 VFADLGFEDAEELQA--KAQLARAIARLIEGRGLSQQEAAALLGIAQPKVSALLKGKLSRFSLDKLLDFLTALGQDVEIV 78
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
35-81 7.61e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 44.82  E-value: 7.61e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1543063251  35 ELRQTLQEKNWTQQQAAAALGVSQARISDLMRGKWeKFSLDMLVTLA 81
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKR-KPSLETLKKLA 46
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 33-81 1.02e-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: 1.02e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 1543063251 33 MNELRQTLQEKNWTQQQAAAALGVSQARISDLMRGKwEKFSLDMLVTLA 81
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGK-RNPSLETLEKLA 48
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 35-85 1.14e-06

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: 41.74  E-value: 1.14e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 1543063251 35 ELRQTLQEKNWTQQQAAAALGVSQARISDLMRGKWEKFSLDMLVTLASHAG 85
Cdd:pfam13560  5 RLRRLRERAGLSQEALARRLGVSRSTLSRLETGRRGRPSPAVVERLARALG 55
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
32-88 2.82e-06

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 40.99  E-value: 2.82e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 1543063251 32 LMNELRQTLQEKNWTQQQAAAALGVSQARISDLMRGKwEKFSLDMLVTLASHAGRKI 88
Cdd:COG1476    5 LGNRLKELRKERGLTQEELAELLGVSRQTISAIENGK-YNPSLELALKIARALGVSL 60
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 40-81 3.03e-06

Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense mechanisms];


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 41.33  E-value: 3.03e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 1543063251 40 LQEKNWTQQQAAAALGVSQARISDLMRGKwEKFSLDMLVTLA 81
Cdd:COG3093   18 LEPLGLSQTELAKALGVSRQRISEILNGK-RAITADTALRLA 58
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 36-89 3.32e-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: 40.60  E-value: 3.32e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 1543063251 36 LRQTLQEKNWTQQQAAAALGVSQARISDLMRGKwEKFSLDMLVTLASHAGRKIS 89
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGK-REPSLETLKKLAEALGVSLD 53
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
28-81 7.33e-06

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 40.37  E-value: 7.33e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 1543063251 28 LRSGLMNELRQTLQEKNWTQQQAAAALGVSQARISDLMRGKwEKFSLDMLVTLA 81
Cdd:COG1396    4 LKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGR-RNPSLETLLKLA 56
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 36-81 1.27e-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: 34.14  E-value: 1.27e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 1543063251 36 LRQTLQEKNWTQQQAAAALGVSQARISDLMRGKwEKFSLDMLVTLA 81
Cdd:COG1813   17 IREAREARGLSQEELAEKLGVSESTIRRIERGE-ATPSLDTLRKLE 61
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 32-89 3.68e-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: 33.45  E-value: 3.68e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 1543063251 32 LMNELRQTLQEKNWTQQQAAAALGVSQARISDLMRGKwEKFSLDMLVTLASHAGRKIS 89
Cdd:COG3620   18 LGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGK-RDPTVSTLEKIAEALGKELS 74
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 36-83 5.04e-03

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: 32.51  E-value: 5.04e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 1543063251 36 LRQTLQEKNWTQQQAAAALGVSQARISDLMRGKWEKFSLDMLVTLASH 83
Cdd:pfam13443  2 LRKLMADRGISKSDLARATGISRATLSRLRKGKPKRVSLDTLDKICDA 49
AF0184 COG2522
Predicted transcriptional regulator, contains XRE-type HTH domain [Transcription];
28-68 6.74e-03

Predicted transcriptional regulator, contains XRE-type HTH domain [Transcription];


Pssm-ID: 442012 [Multi-domain]  Cd Length: 99  Bit Score: 32.87  E-value: 6.74e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 1543063251 28 LRSGLMNELRqtlqEKNWTQQQAAAALGVSQARISDLMRGK 68
Cdd:COG2522   16 IRALLAKELV----ERGLSQSEIAKLLGITQAAVSQYLSGK 52
 
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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