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Conserved domains on  [gi|1471545580|gb|RHJ29548|]
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helix-turn-helix domain-containing protein [Collinsella sp. AM12-1]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SORL COG2033
Desulfoferrodoxin, superoxide reductase-like (SORL) domain [Energy production and conversion];
93-198 8.12e-22

Desulfoferrodoxin, superoxide reductase-like (SORL) domain [Energy production and conversion];


:

Pssm-ID: 441636 [Multi-domain]  Cd Length: 125  Bit Score: 86.14  E-value: 8.12e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1471545580  93 FYVCPICGNVVHAL--GEGSFSCCGSTMFPQEAEEPDAD---HAFSIERIEDDWYVTL---DHPMTKDHYISFVAYATMD 164
Cdd:COG2033     5 FYKCEKCGNIVEVVhgGGGPLVCCGEPMELLVANTADAAkekHVPVIEAEGFGVKVKVgevPHPMTEEHYIEWIELYTGD 84

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1471545580 165 GISFKKLYPEQSVQPRFHITGRGRIFL---YCNQHGL 198
Cdd:COG2033    85 GVGRKELKPGDEPEATFKVKDKSGTLTareYCNLHGL 121
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
16-77 5.23e-19

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 77.73  E-value: 5.23e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1471545580  16 AHAIKRLREERGLTQRALAESLGVTDKAVSKWESGRGLPDISLVEPLAQRLGISVAELLAGD 77
Cdd:COG1396     9 GERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGA 70
 
Name Accession Description Interval E-value
SORL COG2033
Desulfoferrodoxin, superoxide reductase-like (SORL) domain [Energy production and conversion];
93-198 8.12e-22

Desulfoferrodoxin, superoxide reductase-like (SORL) domain [Energy production and conversion];


Pssm-ID: 441636 [Multi-domain]  Cd Length: 125  Bit Score: 86.14  E-value: 8.12e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1471545580  93 FYVCPICGNVVHAL--GEGSFSCCGSTMFPQEAEEPDAD---HAFSIERIEDDWYVTL---DHPMTKDHYISFVAYATMD 164
Cdd:COG2033     5 FYKCEKCGNIVEVVhgGGGPLVCCGEPMELLVANTADAAkekHVPVIEAEGFGVKVKVgevPHPMTEEHYIEWIELYTGD 84

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1471545580 165 GISFKKLYPEQSVQPRFHITGRGRIFL---YCNQHGL 198
Cdd:COG2033    85 GVGRKELKPGDEPEATFKVKDKSGTLTareYCNLHGL 121
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
16-77 5.23e-19

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 77.73  E-value: 5.23e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1471545580  16 AHAIKRLREERGLTQRALAESLGVTDKAVSKWESGRGLPDISLVEPLAQRLGISVAELLAGD 77
Cdd:COG1396     9 GERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGA 70
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 16-73 1.67e-16

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: 70.27  E-value: 1.67e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1471545580  16 AHAIKRLREERGLTQRALAESLGVTDKAVSKWESGRGLPDISLVEPLAQRLGISVAEL 73
Cdd:cd00093     1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
19-73 6.84e-16

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 68.70  E-value: 6.84e-16
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1471545580   19 IKRLREERGLTQRALAESLGVTDKAVSKWESGRGLPDISLVEPLAQRLGISVAEL 73
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 19-73 1.65e-15

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: 67.57  E-value: 1.65e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1471545580  19 IKRLREERGLTQRALAESLGVTDKAVSKWESGRGLPDISLVEPLAQRLGISVAEL 73
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
SORL cd00524
Superoxide reductase-like (SORL) domain; present in a family of mononuclear non-heme iron ...
 129-198 3.64e-11

Superoxide reductase-like (SORL) domain; present in a family of mononuclear non-heme iron proteins that includes superoxide reductase and desulfoferrodoxin. Superoxide reductase-like proteins scavenge superoxide anion radicals as a defense mechanism against reactive oxygen species and are found in anaerobic bacteria and archeae, and microaerophilic Treponema pallidum. The SORL domain contains an active iron site, Fe[His4Cys(Glu)], which in the reduced state loses the glutamate ligand. Superoxide reductase (class II) forms a homotetramer with four Fe[His4Cys(Glu)] centers. Desulfoferrodoxin (class I) is a homodimeric protein, with each protomer comprised of two domains, the N-terminal desulforedoxin (DSRD) domain and C-terminal SORL domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].


Pssm-ID: 238290  Cd Length: 86  Bit Score: 56.95  E-value: 3.64e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1471545580 129 DHAFSIERIE----DDWYVTLD---HPMTKDHYISFVAYATMDG-ISFKKLYPEQSVQPRFHI----TGRGRIFLYCNQH 196
Cdd:cd00524     3 KHVPVIEKPDsvepFDVKVKVGsvpHPMTEEHYIEWIELYFGDEkVGRVELTPGTKPEATFTVkapkKGKLVALSYCNLH 82


                  ..
gi 1471545580 197 GL 198
Cdd:cd00524    83 GL 84
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 14-59 2.76e-09

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: 53.02  E-value: 2.76e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1471545580  14 LAAHAIKRLREERGLTQRALAESLGVTDKAVSKWESGRGLPDISLV 59
Cdd:TIGR03830  65 LTGPEIRRIRKKLGLSQREAAELLGGGVNAFSRYERGEVRPSKALD 110
PRK08154 PRK08154
anaerobic benzoate catabolism transcriptional regulator; Reviewed
 13-77 2.74e-06

anaerobic benzoate catabolism transcriptional regulator; Reviewed


Pssm-ID: 236167 [Multi-domain]  Cd Length: 309  Bit Score: 46.87  E-value: 2.74e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1471545580  13 FLAA--HAIKRLREERGLTQRALAESLGVTDKAVSKWESGRGLPDISLVEPLAQRLGISVAELLAGD 77
Cdd:PRK08154   25 FLAAlgERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCSLADLLGDV 91
VC1465_fam NF040522
VC1465 family Xer recombination activation factor;
19-51 8.52e-04

VC1465 family Xer recombination activation factor;


Pssm-ID: 439737 [Multi-domain]  Cd Length: 111  Bit Score: 37.81  E-value: 8.52e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1471545580  19 IKRLREERGLTQRALAESLGVTDKAVSKWESGR 51
Cdd:NF040522    1 IKETREKAGLTRQQAAEMLRVSLRTVQNWETGK 33
Desulfoferrodox pfam01880
Desulfoferrodoxin; Desulfoferrodoxins contains two types of iron: an Fe-S4 site very similar ...
 144-198 2.36e-03

Desulfoferrodoxin; Desulfoferrodoxins contains two types of iron: an Fe-S4 site very similar to that found in desulforedoxin from Desulfovibrio gigas and an octahedral coordinated high-spin ferrous site most probably with nitrogen/oxygen-containing ligands. Due to this rather unusual combination of active centres, this novel protein is named desulfoferrodoxin.


Pssm-ID: 396450  Cd Length: 97  Bit Score: 36.16  E-value: 2.36e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1471545580 144 TLDHPMTKDHYISFVAYATMD-GISFKKLYPEqSVQPR--FHI--TGRGRI--FLYCNQHGL 198
Cdd:pfam01880  33 KIPHPMTEEHHIAWIELYFGEeGLARAEFTPH-ETEPEvtFTVklKKSGKLyaLSYCNLHGL 93
neela_ferrous TIGR00332
desulfoferrodoxin ferrous iron-binding domain; This domain comprises essentially the full ...
 147-201 5.04e-03

desulfoferrodoxin ferrous iron-binding domain; This domain comprises essentially the full length of neelaredoxin, a monomeric, blue, non-heme iron protein of Desulfovibrio gigas said to bind two iron atoms per monomer with identical spectral properties. Neelaredoxin was shown recently to have significant superoxide dismutase activity. This domain is also found (in a form in which the distance between the motifs H[HWYF]IXW and CN[IL]HGXW is somewhat shorter) as the C-terminal domain of desulfoferrodoxin, which is said to bind a single ferrous iron atom.The N-terminal domain of desulfoferrodoxin is described in a separate model, dfx_rbo (TIGR00320). [Energy metabolism, Electron transport]


Pssm-ID: 273018  Cd Length: 106  Bit Score: 35.34  E-value: 5.04e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1471545580 147 HPMTKDHYISFVAyATMDGISFKKLYPEQSVQP----------RFHITGRGRIFLYCNQHGLFTS 201
Cdd:TIGR00332  36 HPMEENHHIAWIE-LIFGDEVSRKPLVPGDAPFaefasvdgpnKVEMSGKLTARSYCNIHGLWMY 99
 
Name Accession Description Interval E-value
SORL COG2033
Desulfoferrodoxin, superoxide reductase-like (SORL) domain [Energy production and conversion];
93-198 8.12e-22

Desulfoferrodoxin, superoxide reductase-like (SORL) domain [Energy production and conversion];


Pssm-ID: 441636 [Multi-domain]  Cd Length: 125  Bit Score: 86.14  E-value: 8.12e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1471545580  93 FYVCPICGNVVHAL--GEGSFSCCGSTMFPQEAEEPDAD---HAFSIERIEDDWYVTL---DHPMTKDHYISFVAYATMD 164
Cdd:COG2033     5 FYKCEKCGNIVEVVhgGGGPLVCCGEPMELLVANTADAAkekHVPVIEAEGFGVKVKVgevPHPMTEEHYIEWIELYTGD 84

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1471545580 165 GISFKKLYPEQSVQPRFHITGRGRIFL---YCNQHGL 198
Cdd:COG2033    85 GVGRKELKPGDEPEATFKVKDKSGTLTareYCNLHGL 121
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
16-77 5.23e-19

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 77.73  E-value: 5.23e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1471545580  16 AHAIKRLREERGLTQRALAESLGVTDKAVSKWESGRGLPDISLVEPLAQRLGISVAELLAGD 77
Cdd:COG1396     9 GERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGA 70
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
16-77 2.87e-17

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 72.57  E-value: 2.87e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1471545580  16 AHAIKRLREERGLTQRALAESLGVTDKAVSKWESGRGLPDISLVEPLAQRLGISVAELLAGD 77
Cdd:COG1476     6 GNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLE 67
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 19-72 7.17e-17

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: 71.51  E-value: 7.17e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1471545580  19 IKRLREERGLTQRALAESLGVTDKAVSKWESGRGLPDISLVEPLAQRLGISVAE 72
Cdd:COG1813    17 IREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISLAE 70
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 16-73 1.67e-16

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: 70.27  E-value: 1.67e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1471545580  16 AHAIKRLREERGLTQRALAESLGVTDKAVSKWESGRGLPDISLVEPLAQRLGISVAEL 73
Cdd:cd00093     1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
19-73 6.84e-16

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 68.70  E-value: 6.84e-16
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1471545580   19 IKRLREERGLTQRALAESLGVTDKAVSKWESGRGLPDISLVEPLAQRLGISVAEL 73
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 19-73 1.65e-15

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: 67.57  E-value: 1.65e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1471545580  19 IKRLREERGLTQRALAESLGVTDKAVSKWESGRGLPDISLVEPLAQRLGISVAEL 73
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 16-73 1.04e-11

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: 57.92  E-value: 1.04e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1471545580  16 AHAIKRLREERGLTQRALAESLGVTDKAVSKWESGR-GLPDISLVEPLAQRLGISVAEL 73
Cdd:pfam13560   3 GARLRRLRERAGLSQEALARRLGVSRSTLSRLETGRrGRPSPAVVERLARALGVDGAER 61
SORL cd00524
Superoxide reductase-like (SORL) domain; present in a family of mononuclear non-heme iron ...
 129-198 3.64e-11

Superoxide reductase-like (SORL) domain; present in a family of mononuclear non-heme iron proteins that includes superoxide reductase and desulfoferrodoxin. Superoxide reductase-like proteins scavenge superoxide anion radicals as a defense mechanism against reactive oxygen species and are found in anaerobic bacteria and archeae, and microaerophilic Treponema pallidum. The SORL domain contains an active iron site, Fe[His4Cys(Glu)], which in the reduced state loses the glutamate ligand. Superoxide reductase (class II) forms a homotetramer with four Fe[His4Cys(Glu)] centers. Desulfoferrodoxin (class I) is a homodimeric protein, with each protomer comprised of two domains, the N-terminal desulforedoxin (DSRD) domain and C-terminal SORL domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].


Pssm-ID: 238290  Cd Length: 86  Bit Score: 56.95  E-value: 3.64e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1471545580 129 DHAFSIERIE----DDWYVTLD---HPMTKDHYISFVAYATMDG-ISFKKLYPEQSVQPRFHI----TGRGRIFLYCNQH 196
Cdd:cd00524     3 KHVPVIEKPDsvepFDVKVKVGsvpHPMTEEHYIEWIELYFGDEkVGRVELTPGTKPEATFTVkapkKGKLVALSYCNLH 82


                  ..
gi 1471545580 197 GL 198
Cdd:cd00524    83 GL 84
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 19-76 4.50e-11

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: 56.14  E-value: 4.50e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1471545580  19 IKRLREERGLTQRALAESLGVTDKAVSKWESGRGLPDISLVEPLAQRLGISVAELLAG 76
Cdd:pfam12844   4 LRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLLQG 61
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 16-77 5.89e-11

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: 56.95  E-value: 5.89e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1471545580  16 AHAIKRLREERGLTQRALAESLGVTDKAVSKWESGRGLPDISLVEPLAQRLGISVAELLAGD 77
Cdd:COG3620    19 GEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVLVVD 80
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
10-55 1.80e-10

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 54.55  E-value: 1.80e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1471545580  10 SHTFLAAHAIKRLREERGLTQRALAESLGVTDKAVSKWESGRGLPD 55
Cdd:COG2944     2 TKKPLTPEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPS 47
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 14-59 2.76e-09

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: 53.02  E-value: 2.76e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1471545580  14 LAAHAIKRLREERGLTQRALAESLGVTDKAVSKWESGRGLPDISLV 59
Cdd:TIGR03830  65 LTGPEIRRIRKKLGLSQREAAELLGGGVNAFSRYERGEVRPSKALD 110
SORL_Dfx_classI cd03171
Superoxide reductase-like (SORL) domain, class I; SORL-domains are present in a family of ...
 130-198 3.07e-07

Superoxide reductase-like (SORL) domain, class I; SORL-domains are present in a family of mononuclear non-heme iron proteins that includes superoxide reductase and desulfoferrodoxin. Superoxide reductase-like proteins scavenge superoxide anion radicals as a defense mechanism against reactive oxygen species and are found in anaerobic bacteria and archeae, and microaerophilic Treponema pallidum. Desulfoferrodoxin (class I) is a homodimeric protein, with each protomer comprised of two domains, the N-terminal desulforedoxin (DSRD) domain and C-terminal SORL domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].


Pssm-ID: 239421  Cd Length: 78  Bit Score: 46.22  E-value: 3.07e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1471545580 130 HAFSIERIEDDWYVTL---DHPMTKDHYISFVAYATMDGISFKKLYPEQSVQPRFHIT-GRGRIFLYCNQHGL 198
Cdd:cd03171     4 HVPVIEKIGGGIKVKVgsvAHPMEEKHYIEWIELLADGKVYRKHLKPGDAPEAEFSVDaDVVTARAYCNLHGL 76
PRK08154 PRK08154
anaerobic benzoate catabolism transcriptional regulator; Reviewed
 13-77 2.74e-06

anaerobic benzoate catabolism transcriptional regulator; Reviewed


Pssm-ID: 236167 [Multi-domain]  Cd Length: 309  Bit Score: 46.87  E-value: 2.74e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1471545580  13 FLAA--HAIKRLREERGLTQRALAESLGVTDKAVSKWESGRGLPDISLVEPLAQRLGISVAELLAGD 77
Cdd:PRK08154   25 FLAAlgERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCSLADLLGDV 91
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 21-77 5.05e-06

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 44.46  E-value: 5.05e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1471545580  21 RLREER---GLTQRALAESLGVTDKAVSKWESGRGLPDISLVEPLAQRLGISVAELLAGD 77
Cdd:PRK09706    9 RIRYRRkqlKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCSPTWLLFGD 68
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 11-75 3.21e-05

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 40.95  E-value: 3.21e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1471545580  11 HTFLAAHAIKRLREE----RGLTQRALAESLGVTDKAVSKWESG-RGL-PDISLVepLAQRLGISVAELLA 75
Cdd:COG3093     2 NKRNPIHPGEILREEflepLGLSQTELAKALGVSRQRISEILNGkRAItADTALR--LARAFGTSAEFWLN 70
HTH_37 pfam13744
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain.
 16-70 4.59e-05

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: 40.29  E-value: 4.59e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1471545580  16 AHAIKRLREERGLTQRALAESLGVTDKAVSKWESGRgLPDISL------VEPLAQRLGISV 70
Cdd:pfam13744  20 ARAIARLIEGRGLSQQEAAALLGIAQPKVSALLKGK-LSRFSLdklldfLTALGQDVEIVV 79
PHA01976 PHA01976
helix-turn-helix protein
 19-76 5.34e-05

helix-turn-helix protein


Pssm-ID: 177330 [Multi-domain]  Cd Length: 67  Bit Score: 39.94  E-value: 5.34e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1471545580  19 IKRLREERGLTQRALAESLGVTDKAVSKWESGRGLPDISLVEPLAQRLGISVAELLAG 76
Cdd:PHA01976    7 LIKARNARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGVTLDWLCGR 64
COG1395 COG1395
Predicted transcriptional regulator [Transcription];
19-72 8.67e-05

Predicted transcriptional regulator [Transcription];


Pssm-ID: 441005 [Multi-domain]  Cd Length: 313  Bit Score: 42.13  E-value: 8.67e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1471545580  19 IKRLREERGLTQRALAESLGVTDKAVSKWESGRGLPDISLVEPLAQRLGISVAE 72
Cdd:COG1395   132 LRELREERGLSLGELASELGVSRRTISKYERGEMDASIEVALKLEEILGEPIVK 185
PRK13355 PRK13355
bifunctional HTH-domain containing protein/aminotransferase; Provisional
 19-83 8.83e-05

bifunctional HTH-domain containing protein/aminotransferase; Provisional


Pssm-ID: 237361 [Multi-domain]  Cd Length: 517  Bit Score: 42.42  E-value: 8.83e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1471545580  19 IKRLREERGLTQRALAESLG-----VTDKAVSKWESGRGLPDISLVEPLAQRLGISVAELLAGDIRANAN 83
Cdd:PRK13355    8 LKQAMKARGLKQEDLVHAAEargvkLGKSHISQYVSGKTGPRRDVLPFLAAILGVSEDWLLGGESPADQE 77
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 19-74 1.50e-04

Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 441035 [Multi-domain]  Cd Length: 71  Bit Score: 38.63  E-value: 1.50e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1471545580  19 IKRLREERGLTQRALAESLGVTDKAVSKWESGR--GLPD----ISLVEPLAQRLGISVAELL 74
Cdd:COG1426    10 LRQAREAKGLSLEDVAERTKISVSYLEAIEEGDfdALPGpvyvRGFLRSYARALGLDPEELL 71
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 18-68 1.53e-04

transcriptional regulator, y4mF family; Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems. [Regulatory functions, DNA interactions]


Pssm-ID: 213767 [Multi-domain]  Cd Length: 58  Bit Score: 38.41  E-value: 1.53e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1471545580  18 AIKRLREERGLTQRALAESLGVTDKAVSKWESGRGLPDISLVEPLAQRLGI 68
Cdd:TIGR03070   6 LVRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDALGL 56
AF0184 COG2522
Predicted transcriptional regulator, contains XRE-type HTH domain [Transcription];
19-99 1.66e-04

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


Pssm-ID: 442012 [Multi-domain]  Cd Length: 99  Bit Score: 39.42  E-value: 1.66e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1471545580  19 IKRLREeRGLTQRALAESLGVTDKAVSKWESG-RGLPDISLVEPLAQRLGISVAELLAgdirananrAGNMLKGVFYVCP 97
Cdd:COG2522    21 AKELVE-RGLSQSEIAKLLGITQAAVSQYLSGkRGASERIEFDEEIKELIEELAEGLA---------SGKPEDALAEICR 90


                  ..
gi 1471545580  98 IC 99
Cdd:COG2522    91 LC 92
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 16-46 1.72e-04

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: 41.13  E-value: 1.72e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1471545580  16 AHAIKRLREERGLTQRALAESLGVTDKAVSK 46
Cdd:COG1475   109 ARAYQRLLEEFGLTQEEIAERLGKSRSEVSN 139
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
19-75 4.20e-04

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 39.78  E-value: 4.20e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1471545580  19 IKRLREERGLTQRALAESLGVTDKAVSKWESGRGLPDISLVEPLAQRLGISVAELLA 75
Cdd:PRK09943   12 LSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEFFS 68
MqsA_antitoxin pfam15731
Antitoxin component of bacterial toxin-antitoxin system, MqsA; MqsA_antitoxin is a family of ...
 5-62 4.23e-04

Antitoxin component of bacterial toxin-antitoxin system, MqsA; MqsA_antitoxin is a family of prokaryotic proteins that act as antidotes to the mRNA interferase MqsR. It has a zinc-binding at the very N-terminus indicating its DNA-binding capacity. MqsR is the gene most highly upregulated in E. Colo MqsR_toxin is a family of bacterial toxins that act as an mRNA interferase. MqsR is the gene most highly upregulated in E. coli persister cells and it plays an essential role in biofilm regulation and cell signalling. It forms part of a bacterial toxin-antitoxin TA system, and as expected for a TA system, the expression of the MqsR toxin leads to growth arrest, while co-expression with its antitoxin, MqsA, rescues the growth arrest phenotype. In addition, MqsR associates with MqsA to form a tight, non-toxic complex and both MqsA alone and the MqsR:MqsA2:MqsR complex bind and regulate the mqsR promoter. The structure of MqsR shows that is is a member of the RelE/YoeB family of bacterial RNases that are structurally and functionally characterized bacterial toxins.


Pssm-ID: 292359 [Multi-domain]  Cd Length: 131  Bit Score: 38.90  E-value: 4.23e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1471545580   5 RQTNAShtFLAAHAIKRLREERGLTQRALAESLGVTDKAVSKWESGRGLPDISLVEPL 62
Cdd:pfam15731  62 RQVNAV--LIDPAFIARVRKKLGLDQREAAEIFGGGVNAFSRYENGKTRPPLALVKLL 117
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
19-74 4.46e-04

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 37.43  E-value: 4.46e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1471545580  19 IKRLREERGLTQRALAESLGVTDKAVSKWESGRGL-PDISLVEPLAQRLGISVAELL 74
Cdd:COG3655     6 LDELLAERGMTKKELAEATGISRATLSRLKNGKAKaVRLDTLEKICKALDCQPGDLL 62
YdaS COG4197
DNA-binding transcriptional regulator YdaS, prophage-encoded, Cro superfamily [Transcription];
19-52 5.84e-04

DNA-binding transcriptional regulator YdaS, prophage-encoded, Cro superfamily [Transcription];


Pssm-ID: 443351  Cd Length: 68  Bit Score: 37.20  E-value: 5.84e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1471545580  19 IKRLREERGlTQRALAESLGVTDKAVSKWESGRG 52
Cdd:COG4197     1 LEKAIEALG-SQSALARALGVSQQAVSQWLNGKR 33
VC1465_fam NF040522
VC1465 family Xer recombination activation factor;
19-51 8.52e-04

VC1465 family Xer recombination activation factor;


Pssm-ID: 439737 [Multi-domain]  Cd Length: 111  Bit Score: 37.81  E-value: 8.52e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1471545580  19 IKRLREERGLTQRALAESLGVTDKAVSKWESGR 51
Cdd:NF040522    1 IKETREKAGLTRQQAAEMLRVSLRTVQNWETGK 33
DSRD cd00974
Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin ...
 94-118 1.41e-03

Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].


Pssm-ID: 238478 [Multi-domain]  Cd Length: 34  Bit Score: 35.00  E-value: 1.41e-03
                          10        20
                  ....*....|....*....|....*..
gi 1471545580  94 YVCPICGNVVHAL--GEGSFSCCGSTM 118
Cdd:cd00974     5 YKCEICGNIVEVLnvGGGTLVCCGQPM 31
YdaS_antitoxin pfam15943
Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT; YdaS_antitoxin is a family ...
 19-52 1.61e-03

Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT; YdaS_antitoxin is a family of putative bacterial antitoxins, neutralising the toxin YdaT, family pfam06254.


Pssm-ID: 435033  Cd Length: 65  Bit Score: 35.78  E-value: 1.61e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1471545580  19 IKRLREERGlTQRALAESLGVTDKAVSKWESGRG 52
Cdd:pfam15943   1 IKKAIEIVG-GQKALAEALGVTQQAVSQWLHGKK 33
COG1709 COG1709
Predicted transcriptional regulator,contains XRE-type HTH domain [Transcription];
18-51 2.07e-03

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


Pssm-ID: 441315  Cd Length: 234  Bit Score: 37.85  E-value: 2.07e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1471545580  18 AIKRLREERGLTQRALAESLGVTDKAVSKWESGR 51
Cdd:COG1709    26 TLRKWREDFGISQTELARELGVSPSVISDYESGR 59
PRK04140 PRK04140
transcriptional regulator;
19-50 2.07e-03

transcriptional regulator;


Pssm-ID: 235224 [Multi-domain]  Cd Length: 317  Bit Score: 38.30  E-value: 2.07e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1471545580  19 IKRLREERGLTQRALAESLGVTDKAVSKWESG 50
Cdd:PRK04140  131 LREAREELGLSLGELASELGVSRRTISKYENG 162
Desulfoferrodox pfam01880
Desulfoferrodoxin; Desulfoferrodoxins contains two types of iron: an Fe-S4 site very similar ...
 144-198 2.36e-03

Desulfoferrodoxin; Desulfoferrodoxins contains two types of iron: an Fe-S4 site very similar to that found in desulforedoxin from Desulfovibrio gigas and an octahedral coordinated high-spin ferrous site most probably with nitrogen/oxygen-containing ligands. Due to this rather unusual combination of active centres, this novel protein is named desulfoferrodoxin.


Pssm-ID: 396450  Cd Length: 97  Bit Score: 36.16  E-value: 2.36e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1471545580 144 TLDHPMTKDHYISFVAYATMD-GISFKKLYPEqSVQPR--FHI--TGRGRI--FLYCNQHGL 198
Cdd:pfam01880  33 KIPHPMTEEHHIAWIELYFGEeGLARAEFTPH-ETEPEvtFTVklKKSGKLyaLSYCNLHGL 93
neela_ferrous TIGR00332
desulfoferrodoxin ferrous iron-binding domain; This domain comprises essentially the full ...
 147-201 5.04e-03

desulfoferrodoxin ferrous iron-binding domain; This domain comprises essentially the full length of neelaredoxin, a monomeric, blue, non-heme iron protein of Desulfovibrio gigas said to bind two iron atoms per monomer with identical spectral properties. Neelaredoxin was shown recently to have significant superoxide dismutase activity. This domain is also found (in a form in which the distance between the motifs H[HWYF]IXW and CN[IL]HGXW is somewhat shorter) as the C-terminal domain of desulfoferrodoxin, which is said to bind a single ferrous iron atom.The N-terminal domain of desulfoferrodoxin is described in a separate model, dfx_rbo (TIGR00320). [Energy metabolism, Electron transport]


Pssm-ID: 273018  Cd Length: 106  Bit Score: 35.34  E-value: 5.04e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1471545580 147 HPMTKDHYISFVAyATMDGISFKKLYPEQSVQP----------RFHITGRGRIFLYCNQHGLFTS 201
Cdd:TIGR00332  36 HPMEENHHIAWIE-LIFGDEVSRKPLVPGDAPFaefasvdgpnKVEMSGKLTARSYCNIHGLWMY 99
 
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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