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Conserved domains on  [gi|490280271|ref|WP_004176198|]
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MULTISPECIES: type II toxin-antitoxin system antitoxin HipB [Klebsiella]

Protein Classification

type II toxin-antitoxin system HipB family antitoxin( domain architecture ID 10793307)

type II toxin-antitoxin (TA) system HipB family antitoxin similar to Escherichia coli HipB, which binds to operator sites with the consensus sequence 5'-TATCCN(8)GGATA-3' to repress the hipBA operon promoter, and is also the antitoxin component of the HipA-HipB TA module, neutralizing the toxic effect of cognate toxin HipA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK09726 PRK09726
type II toxin-antitoxin system antitoxin HipB;
1-88 4.92e-47

type II toxin-antitoxin system antitoxin HipB;


:

Pssm-ID: 182049  Cd Length: 88  Bit Score: 144.74  E-value: 4.92e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490280271  1 MNSPQIYSPVQLANYLKLLRQQNHWTQDALARRIGIKQATLSNFENHPDKTTLTTLFKILQSLGVVMMLnAKAAETAPAP 80
Cdd:PRK09726  2 MSFQKIYSPTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMTL-CDAKNASPES 80


                ....*...
gi 490280271 81 DNNTDLDW 88
Cdd:PRK09726 81 TEQQDLEW 88
 
Name Accession Description Interval E-value
PRK09726 PRK09726
type II toxin-antitoxin system antitoxin HipB;
1-88 4.92e-47

type II toxin-antitoxin system antitoxin HipB;


Pssm-ID: 182049  Cd Length: 88  Bit Score: 144.74  E-value: 4.92e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490280271  1 MNSPQIYSPVQLANYLKLLRQQNHWTQDALARRIGIKQATLSNFENHPDKTTLTTLFKILQSLGVVMMLnAKAAETAPAP 80
Cdd:PRK09726  2 MSFQKIYSPTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMTL-CDAKNASPES 80


                ....*...
gi 490280271 81 DNNTDLDW 88
Cdd:PRK09726 81 TEQQDLEW 88
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
11-65 6.02e-13

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 58.08  E-value: 6.02e-13
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 490280271 11 QLANYLKLLRQQNHWTQDALARRIGIKQATLSNFENHPDKTTLTTLFKILQSLGV 65
Cdd:COG1396   7 ALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGV 61
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 13-65 2.47e-12

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: 56.02  E-value: 2.47e-12
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 490280271 13 ANYLKLLRQQNHWTQDALARRIGIKQATLSNFENHPDKTTLTTLFKILQSLGV 65
Cdd:cd00093   1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGV 53
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
16-65 2.91e-12

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 55.60  E-value: 2.91e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 490280271   16 LKLLRQQNHWTQDALARRIGIKQATLSNFENHPDKTTLTTLFKILQSLGV 65
Cdd:smart00530  2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGV 51
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 16-65 1.62e-11

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: 53.70  E-value: 1.62e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 490280271  16 LKLLRQQNHWTQDALARRIGIKQATLSNFENHPDKTTLTTLFKILQSLGV 65
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGV 50
 
Name Accession Description Interval E-value
PRK09726 PRK09726
type II toxin-antitoxin system antitoxin HipB;
1-88 4.92e-47

type II toxin-antitoxin system antitoxin HipB;


Pssm-ID: 182049  Cd Length: 88  Bit Score: 144.74  E-value: 4.92e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490280271  1 MNSPQIYSPVQLANYLKLLRQQNHWTQDALARRIGIKQATLSNFENHPDKTTLTTLFKILQSLGVVMMLnAKAAETAPAP 80
Cdd:PRK09726  2 MSFQKIYSPTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMTL-CDAKNASPES 80


                ....*...
gi 490280271 81 DNNTDLDW 88
Cdd:PRK09726 81 TEQQDLEW 88
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
11-65 6.02e-13

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 58.08  E-value: 6.02e-13
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 490280271 11 QLANYLKLLRQQNHWTQDALARRIGIKQATLSNFENHPDKTTLTTLFKILQSLGV 65
Cdd:COG1396   7 ALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGV 61
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
11-65 2.33e-12

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 56.39  E-value: 2.33e-12
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 490280271 11 QLANYLKLLRQQNHWTQDALARRIGIKQATLSNFENHPDKTTLTTLFKILQSLGV 65
Cdd:COG1476   4 KLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGV 58
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 13-65 2.47e-12

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: 56.02  E-value: 2.47e-12
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 490280271 13 ANYLKLLRQQNHWTQDALARRIGIKQATLSNFENHPDKTTLTTLFKILQSLGV 65
Cdd:cd00093   1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGV 53
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
16-65 2.91e-12

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 55.60  E-value: 2.91e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 490280271   16 LKLLRQQNHWTQDALARRIGIKQATLSNFENHPDKTTLTTLFKILQSLGV 65
Cdd:smart00530  2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGV 51
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 16-65 1.62e-11

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: 53.70  E-value: 1.62e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 490280271  16 LKLLRQQNHWTQDALARRIGIKQATLSNFENHPDKTTLTTLFKILQSLGV 65
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGV 50
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 12-64 1.56e-10

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: 52.33  E-value: 1.56e-10
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 490280271 12 LANYLKLLRQQNHWTQDALARRIGIKQATLSNFENHPDKTTLTTLFKILQSLG 64
Cdd:COG3620  18 LGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALG 70
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 12-65 1.61e-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: 44.16  E-value: 1.61e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 490280271 12 LANYLKLLRQQNHWTQDALARRIGIKQATLSNFENHPDKTTLTTLFKILQSLGV 65
Cdd:COG1813  13 YGERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGI 66
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 15-65 5.66e-07

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: 42.66  E-value: 5.66e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 490280271  15 YLKLLRQQNHWTQDALARRIGIKQATLSNFENHPDKTTLTTLFKILQSLGV 65
Cdd:pfam12844  3 RLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGV 53
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 11-46 9.25e-07

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: 42.13  E-value: 9.25e-07
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 490280271  11 QLANYLKLLRQQNHWTQDALARRIGIKQATLSNFEN 46
Cdd:pfam13560  1 ELGARLRRLRERAGLSQEALARRLGVSRSTLSRLET 36
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
16-61 1.21e-05

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 39.15  E-value: 1.21e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 490280271 16 LKLLRQQNHWTQDALARRIGIKQATLSNFEN---HPDKTTLtTLFKILQ 61
Cdd:COG2944  11 IRALRERLGLSQAEFAALLGVSVSTVRRWEQgrrKPSGAAL-KLLRLLE 58
HTH_37 pfam13744
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain.
 10-64 3.41e-04

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: 35.66  E-value: 3.41e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 490280271  10 VQLANYLKLLRQQNHWTQDALARRIGIKQATLSNFEN-HPDKTTLTTLFKILQSLG 64
Cdd:pfam13744 17 AQLARAIARLIEGRGLSQQEAAALLGIAQPKVSALLKgKLSRFSLDKLLDFLTALG 72
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 16-65 3.68e-04

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: 35.21  E-value: 3.68e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 490280271  16 LKLLRQQNHWTQDALARRIGIKQATLSNFENHPDKT-TLTTLFKILQSLGV 65
Cdd:pfam13443  2 LRKLMADRGISKSDLARATGISRATLSRLRKGKPKRvSLDTLDKICDALGC 52
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
16-65 6.24e-04

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 34.73  E-value: 6.24e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 490280271 16 LKLLRQQNHWTQDALARRIGIKQATLSNFENHPDKT-TLTTLFKILQSLGV 65
Cdd:COG3655   6 LDELLAERGMTKKELAEATGISRATLSRLKNGKAKAvRLDTLEKICKALDC 56
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 8-43 2.32e-03

Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 441084 [Multi-domain]  Cd Length: 241  Bit Score: 34.96  E-value: 2.32e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 490280271   8 SPVQLANYLKLLRQQNHWTQDALARRIGIKQATLSN 43
Cdd:COG1475  104 NPLEEARAYQRLLEEFGLTQEEIAERLGKSRSEVSN 139
PHA01976 PHA01976
helix-turn-helix protein
 16-67 8.74e-03

helix-turn-helix protein


Pssm-ID: 177330 [Multi-domain]  Cd Length: 67  Bit Score: 31.85  E-value: 8.74e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 490280271 16 LKLLRQQNH--WTQDALARRIGIKQATLSNFENHPDKTTLTTLFKILQSLGVVM 67
Cdd:PHA01976  5 IQLIKARNAraWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGVTL 58
 
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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