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Conserved domains on  [gi|490521965|ref|WP_004387402|]
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helix-turn-helix domain-containing protein [Cronobacter sakazakii]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK11832 super family cl32729
hydrogen peroxide resistance inhibitor IprA;
39-208 1.37e-20

hydrogen peroxide resistance inhibitor IprA;


The actual alignment was detected with superfamily member PRK11832:

Pssm-ID: 183332 [Multi-domain]  Cd Length: 207  Bit Score: 85.32  E-value: 1.37e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490521965  39 NEESVNILLSGSLALTRDwDNLIFFETNRPNIFGIS--LQPNNArfeHFRLIIKEDSLVKRISRADFLAVIEEQKLWKEL 116
Cdd:PRK11832  40 NNEDTFVILEGVISLRRE-ENVLIGITQAPYIMGLAdgLMKNDI---PYKLISEGNCTGYHLPAKQTITLIEQNQLWRDA 115

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490521965 117 SHVISFYYYVLLWKNYHFYAADSYMLVRKSLITLGEMPLESRININASQYITSTTNLSKSYVMKVIQELRKGGYIEIQRG 196
Cdd:PRK11832 116 FYWLAWQNRILELRDVQLIGHNSYEQIRATLLSMIDWNEELRSRIGVMNYIHQRTRISRSVVAEVLAALRKGGYIEMNKG 195

                        170
                 ....*....|..
gi 490521965 197 RLLSIGKLPQKY 208
Cdd:PRK11832 196 KLVAINRLPSEY 207
 
Name Accession Description Interval E-value
PRK11832 PRK11832
hydrogen peroxide resistance inhibitor IprA;
39-208 1.37e-20

hydrogen peroxide resistance inhibitor IprA;


Pssm-ID: 183332 [Multi-domain]  Cd Length: 207  Bit Score: 85.32  E-value: 1.37e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490521965  39 NEESVNILLSGSLALTRDwDNLIFFETNRPNIFGIS--LQPNNArfeHFRLIIKEDSLVKRISRADFLAVIEEQKLWKEL 116
Cdd:PRK11832  40 NNEDTFVILEGVISLRRE-ENVLIGITQAPYIMGLAdgLMKNDI---PYKLISEGNCTGYHLPAKQTITLIEQNQLWRDA 115

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490521965 117 SHVISFYYYVLLWKNYHFYAADSYMLVRKSLITLGEMPLESRININASQYITSTTNLSKSYVMKVIQELRKGGYIEIQRG 196
Cdd:PRK11832 116 FYWLAWQNRILELRDVQLIGHNSYEQIRATLLSMIDWNEELRSRIGVMNYIHQRTRISRSVVAEVLAALRKGGYIEMNKG 195

                        170
                 ....*....|..
gi 490521965 197 RLLSIGKLPQKY 208
Cdd:PRK11832 196 KLVAINRLPSEY 207
HTH_46 pfam15977
Winged helix-turn-helix DNA binding;
139-205 4.55e-20

Winged helix-turn-helix DNA binding;


Pssm-ID: 435049 [Multi-domain]  Cd Length: 68  Bit Score: 80.01  E-value: 4.55e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490521965  139 SYMLVRKSLITLGEMPLESRININASQYITSTTNLSKSYVMKVIQELRKGGYIEIQRGRLLSIGKLP 205
Cdd:pfam15977   1 SYDIIRALLLELMDLPEEFRENISVLNYIQQRTHLSRSSIMKILSELKKGGYIEIDRGRLVAINNLP 67
IscR COG1959
DNA-binding transcriptional regulator, IscR family [Transcription];
139-197 1.42e-05

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


Pssm-ID: 441562  Cd Length: 141  Bit Score: 43.29  E-value: 1.42e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 490521965 139 SYMLvrKSLITLGEMPLESRININAsqyITSTTNLSKSYVMKVIQELRKGGYIEIQRGR 197
Cdd:COG1959    7 DYAL--RALLYLALHPGGEPVTSKE---IAERQGISPSYLEKILQKLRKAGLVESVRGP 60
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 10-110 9.21e-04

effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels


Pssm-ID: 237999 [Multi-domain]  Cd Length: 115  Bit Score: 37.69  E-value: 9.21e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490521965  10 PDAQINALINAFHchgtIKEYPRGSCL-AQNE--ESVNILLSGSLALTRDWDN---LIFFETNRPNIFG-ISLQPNNARf 82
Cdd:cd00038    6 DDEELEELADALE----ERRFPAGEVIiRQGDpaDSLYIVLSGSVEVYKLDEDgreQIVGFLGPGDLFGeLALLGNGPR- 80

                         90       100
                 ....*....|....*....|....*...
gi 490521965  83 eHFRLIIKEDSLVKRISRADFLAVIEEQ 110
Cdd:cd00038   81 -SATVRALTDSELLVLPRSDFRRLLQEY 107
rrf2_super TIGR00738
Rrf2 family protein; This model represents a superfamily of probable transcriptional ...
 143-197 2.75e-03

Rrf2 family protein; This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency. [Unknown function, General]


Pssm-ID: 273242  Cd Length: 132  Bit Score: 36.46  E-value: 2.75e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 490521965  143 VRKSLITLGEMPLESRININASQYITSTTNLSKSYVMKVIQELRKGGYIEIQRGR 197
Cdd:TIGR00738   7 TEYALRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRKAGLVESVRGP 61
 
Name Accession Description Interval E-value
PRK11832 PRK11832
hydrogen peroxide resistance inhibitor IprA;
39-208 1.37e-20

hydrogen peroxide resistance inhibitor IprA;


Pssm-ID: 183332 [Multi-domain]  Cd Length: 207  Bit Score: 85.32  E-value: 1.37e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490521965  39 NEESVNILLSGSLALTRDwDNLIFFETNRPNIFGIS--LQPNNArfeHFRLIIKEDSLVKRISRADFLAVIEEQKLWKEL 116
Cdd:PRK11832  40 NNEDTFVILEGVISLRRE-ENVLIGITQAPYIMGLAdgLMKNDI---PYKLISEGNCTGYHLPAKQTITLIEQNQLWRDA 115

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490521965 117 SHVISFYYYVLLWKNYHFYAADSYMLVRKSLITLGEMPLESRININASQYITSTTNLSKSYVMKVIQELRKGGYIEIQRG 196
Cdd:PRK11832 116 FYWLAWQNRILELRDVQLIGHNSYEQIRATLLSMIDWNEELRSRIGVMNYIHQRTRISRSVVAEVLAALRKGGYIEMNKG 195

                        170
                 ....*....|..
gi 490521965 197 RLLSIGKLPQKY 208
Cdd:PRK11832 196 KLVAINRLPSEY 207
HTH_46 pfam15977
Winged helix-turn-helix DNA binding;
139-205 4.55e-20

Winged helix-turn-helix DNA binding;


Pssm-ID: 435049 [Multi-domain]  Cd Length: 68  Bit Score: 80.01  E-value: 4.55e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490521965  139 SYMLVRKSLITLGEMPLESRININASQYITSTTNLSKSYVMKVIQELRKGGYIEIQRGRLLSIGKLP 205
Cdd:pfam15977   1 SYDIIRALLLELMDLPEEFRENISVLNYIQQRTHLSRSSIMKILSELKKGGYIEIDRGRLVAINNLP 67
IscR COG1959
DNA-binding transcriptional regulator, IscR family [Transcription];
139-197 1.42e-05

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


Pssm-ID: 441562  Cd Length: 141  Bit Score: 43.29  E-value: 1.42e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 490521965 139 SYMLvrKSLITLGEMPLESRININAsqyITSTTNLSKSYVMKVIQELRKGGYIEIQRGR 197
Cdd:COG1959    7 DYAL--RALLYLALHPGGEPVTSKE---IAERQGISPSYLEKILQKLRKAGLVESVRGP 60
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 16-198 1.43e-05

cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms];


Pssm-ID: 440428 [Multi-domain]  Cd Length: 207  Bit Score: 44.21  E-value: 1.43e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490521965  16 ALINAFHCHGTIKEYPRGSCLAQNEESVN---ILLSGSLALTRDWDN---LIFFETNRPNIFG-ISLQPNNARfeHFRLI 88
Cdd:COG0664    7 EELEALLAHLELRTLKKGEVLFREGDPADhlyFVLSGLVKLYRISEDgreQILGFLGPGDFFGeLSLLGGEPS--PATAE 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490521965  89 IKEDSLVKRISRADFLAVIEEQ-KLWKELSHVISFYYYVLLWKNYHFYAADSYMLVRKSLITLGEmPLESRININASQ-Y 166
Cdd:COG0664   85 ALEDSELLRIPREDLEELLERNpELARALLRLLARRLRQLQERLVSLAFLSAEERLARFLLELAD-RLDGRIDLPLTQeE 163

                        170       180       190
                 ....*....|....*....|....*....|..
gi 490521965 167 ITSTTNLSKSYVMKVIQELRKGGYIEIQRGRL 198
Cdd:COG0664  164 IASYLGLTRETVSRILKKLEKEGLIELERGRI 195
Rrf2 pfam02082
Iron-dependent Transcriptional regulator; Several proteins in this family form iron-sulfur ...
 164-197 4.68e-05

Iron-dependent Transcriptional regulator; Several proteins in this family form iron-sulfur clusters enabling iron dependent DNA transcription regulation. The iron binding is mediated by three conserved cysteine residues. Members of this family can also bind O-acetyl-L-serine, [Fe-S] and nitric oxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 396591 [Multi-domain]  Cd Length: 131  Bit Score: 41.38  E-value: 4.68e-05
                          10        20        30
                  ....*....|....*....|....*....|....
gi 490521965  164 SQYITSTTNLSKSYVMKVIQELRKGGYIEIQRGR 197
Cdd:pfam02082  26 SEEIAERQNISPVYLEKILAKLRKAGLVESVRGA 59
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 10-110 9.21e-04

effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels


Pssm-ID: 237999 [Multi-domain]  Cd Length: 115  Bit Score: 37.69  E-value: 9.21e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490521965  10 PDAQINALINAFHchgtIKEYPRGSCL-AQNE--ESVNILLSGSLALTRDWDN---LIFFETNRPNIFG-ISLQPNNARf 82
Cdd:cd00038    6 DDEELEELADALE----ERRFPAGEVIiRQGDpaDSLYIVLSGSVEVYKLDEDgreQIVGFLGPGDLFGeLALLGNGPR- 80

                         90       100
                 ....*....|....*....|....*...
gi 490521965  83 eHFRLIIKEDSLVKRISRADFLAVIEEQ 110
Cdd:cd00038   81 -SATVRALTDSELLVLPRSDFRRLLQEY 107
rrf2_super TIGR00738
Rrf2 family protein; This model represents a superfamily of probable transcriptional ...
 143-197 2.75e-03

Rrf2 family protein; This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency. [Unknown function, General]


Pssm-ID: 273242  Cd Length: 132  Bit Score: 36.46  E-value: 2.75e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 490521965  143 VRKSLITLGEMPLESRININASQYITSTTNLSKSYVMKVIQELRKGGYIEIQRGR 197
Cdd:TIGR00738   7 TEYALRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRKAGLVESVRGP 61
 
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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