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Conserved domains on  [gi|635780959|gb|KDF62381|]
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hypothetical protein AF40_01159 [Enterobacter roggenkampii MGH 54]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 14302692)

helix-turn-helix domain-containing protein such as an XRE (Xenobiotic Response Element) family transcriptional regulator containing a cupin-like domain, controls the expression of genes involved in stress response

Gene Ontology:  GO:0003700|GO:0006355|GO:0003677
PubMed:  10473770|15808743|10556324|14697267

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-74 2.84e-22

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 85.05  E-value: 2.84e-22
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 635780959   1 MD-ITQHLAATLKTLRQARGWSLSKLADETGVSKAMLGQIERNESSPTVSTLWKIATGLNVPFSTFITPEADRQA 74
Cdd:COG1396    1 MStLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELP 75
cupin_XRE_C cd02209
XRE (Xenobiotic Response Element) family transcriptional regulators, C-terminal cupin domain; ...
 83-172 3.96e-13

XRE (Xenobiotic Response Element) family transcriptional regulators, C-terminal cupin domain; This family contains transcriptional regulators containing an N-terminal XRE (Xenobiotic Response Element) family helix-turn-helix (HTH) DNA-binding domain and a C-terminal cupin domain. Included in this family is Escherichia coli transcription factor SutR (YdcN) that plays a regulatory role in sulfur utilization; it regulates a set of genes involved in the generation of sulfate and its reduction, the synthesis of cysteine, the synthesis of enzymes containing Fe-S as cofactors, and the modification of tRNA with use of sulfur-containing substrates. This family belongs to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


:

Pssm-ID: 380339 [Multi-domain]  Cd Length: 90  Bit Score: 61.75  E-value: 3.96e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 635780959  83 MVVKPLFPWDEALRFDYFSITLVPGA-LSESTPHEagVIEHVVVVSGELEMKLEGKWKTISADSGVRFAGDKPHAYRNSS 161
Cdd:cd02209    2 YTYELLSPGLPGRKMEPFLVTLPPGGsGGEPYSHE--GEEFGYVLEGELELTVGGETYVLEAGDSIYFDSDVPHRYRNPG 79

                         90
                 ....*....|.
gi 635780959 162 DRTVHFHSLIH 172
Cdd:cd02209   80 DEPARVLWVIT 90
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-74 2.84e-22

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 85.05  E-value: 2.84e-22
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 635780959   1 MD-ITQHLAATLKTLRQARGWSLSKLADETGVSKAMLGQIERNESSPTVSTLWKIATGLNVPFSTFITPEADRQA 74
Cdd:COG1396    1 MStLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELP 75
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 11-65 6.98e-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: 67.96  E-value: 6.98e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 635780959  11 LKTLRQARGWSLSKLADETGVSKAMLGQIERNESSPTVSTLWKIATGLNVPFSTF 65
Cdd:cd00093    4 LKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 11-65 9.03e-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: 64.87  E-value: 9.03e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 635780959   11 LKTLRQARGWSLSKLADETGVSKAMLGQIERNESSPTVSTLWKIATGLNVPFSTF 65
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
11-65 9.81e-15

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 64.85  E-value: 9.81e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 635780959    11 LKTLRQARGWSLSKLADETGVSKAMLGQIERNESSPTVSTLWKIATGLNVPFSTF 65
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
cupin_XRE_C cd02209
XRE (Xenobiotic Response Element) family transcriptional regulators, C-terminal cupin domain; ...
 83-172 3.96e-13

XRE (Xenobiotic Response Element) family transcriptional regulators, C-terminal cupin domain; This family contains transcriptional regulators containing an N-terminal XRE (Xenobiotic Response Element) family helix-turn-helix (HTH) DNA-binding domain and a C-terminal cupin domain. Included in this family is Escherichia coli transcription factor SutR (YdcN) that plays a regulatory role in sulfur utilization; it regulates a set of genes involved in the generation of sulfate and its reduction, the synthesis of cysteine, the synthesis of enzymes containing Fe-S as cofactors, and the modification of tRNA with use of sulfur-containing substrates. This family belongs to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380339 [Multi-domain]  Cd Length: 90  Bit Score: 61.75  E-value: 3.96e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 635780959  83 MVVKPLFPWDEALRFDYFSITLVPGA-LSESTPHEagVIEHVVVVSGELEMKLEGKWKTISADSGVRFAGDKPHAYRNSS 161
Cdd:cd02209    2 YTYELLSPGLPGRKMEPFLVTLPPGGsGGEPYSHE--GEEFGYVLEGELELTVGGETYVLEAGDSIYFDSDVPHRYRNPG 79

                         90
                 ....*....|.
gi 635780959 162 DRTVHFHSLIH 172
Cdd:cd02209   80 DEPARVLWVIT 90
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
81-172 2.12e-09

Cupin domain protein related to quercetin dioxygenase [General function prediction only];


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 52.16  E-value: 2.12e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 635780959  81 QAMVVKPLFpwDEALRFDYFSITLVPGAlsESTPHEAGVIEHVVVVSGELEMKLEGKWKTISADSGVRFAGDKPHAYRNS 160
Cdd:COG1917    9 TGVSVRVLA--DGEDELEVVRVTFEPGA--RTPWHSHPGEELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFRNL 84

                         90
                 ....*....|..
gi 635780959 161 SDRTVHFHSLIH 172
Cdd:COG1917   85 GDEPAVLLVVFS 96
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 102-171 2.66e-08

Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel).


Pssm-ID: 462300 [Multi-domain]  Cd Length: 71  Bit Score: 48.41  E-value: 2.66e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 635780959  102 ITLVPGALSESTPHEaGVIEHVVVVSGELEMKLEGKWKTISADSGVRFAGDKPHAYRNSSDRTVHFHSLI 171
Cdd:pfam07883   3 VTLPPGESSPPHRHP-GEDEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPHRFRNTGDEPARLLDVY 71
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
2-164 3.03e-07

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 47.87  E-value: 3.03e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 635780959   2 DITQHLAATLKTLRQARGWSLSKLADETGVSKAMLGQIERNESSPTVSTLWKIATGLNVPFST-FITPEADR--QAVFDP 78
Cdd:PRK09943   3 DEGLAPGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEfFSEPEKPDepQVVINQ 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 635780959  79 QQ------QAMVVKPLFPWDEALRFDYFSITLVPGALSESTPHEAGviEHV-VVVSGELEMKLEGKWKTISADSGVRFAG 151
Cdd:PRK09943  83 DDliemgsQGVSMKLVHNGNPNRTLAMIFETYQPGTTTGERIKHQG--EEIgTVLEGEIVLTINGQDYHLVAGQSYAINT 160

                        170
                 ....*....|...
gi 635780959 152 DKPHAYRNSSDRT 164
Cdd:PRK09943 161 GIPHSFSNTSAGI 173
PRK09726 PRK09726
type II toxin-antitoxin system antitoxin HipB;
7-70 1.99e-06

type II toxin-antitoxin system antitoxin HipB;


Pssm-ID: 182049  Cd Length: 88  Bit Score: 43.82  E-value: 1.99e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 635780959   7 LAATLKTLRQARGWSLSKLADETGVSKAMLGQIERNESSPTVSTLWKIATGLNVPFSTFITPEA 70
Cdd:PRK09726  13 LANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMTLCDAKNA 76
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 7-59 1.79e-03

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: 35.33  E-value: 1.79e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 635780959    7 LAATLKTLRQARGWSLSKLADETGVSKAMLGQIERNESSPTVSTLWKIATGLN 59
Cdd:TIGR03070   3 IGILVRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDALG 55
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-74 2.84e-22

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 85.05  E-value: 2.84e-22
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 635780959   1 MD-ITQHLAATLKTLRQARGWSLSKLADETGVSKAMLGQIERNESSPTVSTLWKIATGLNVPFSTFITPEADRQA 74
Cdd:COG1396    1 MStLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELP 75
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 11-65 6.98e-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: 67.96  E-value: 6.98e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 635780959  11 LKTLRQARGWSLSKLADETGVSKAMLGQIERNESSPTVSTLWKIATGLNVPFSTF 65
Cdd:cd00093    4 LKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
4-69 2.37e-15

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 66.80  E-value: 2.37e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 635780959   4 TQHLAATLKTLRQARGWSLSKLADETGVSKAMLGQIERNESSPTVSTLWKIATGLNVPFSTFITPE 69
Cdd:COG1476    2 KKKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLE 67
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 11-65 9.03e-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: 64.87  E-value: 9.03e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 635780959   11 LKTLRQARGWSLSKLADETGVSKAMLGQIERNESSPTVSTLWKIATGLNVPFSTF 65
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
11-65 9.81e-15

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 64.85  E-value: 9.81e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 635780959    11 LKTLRQARGWSLSKLADETGVSKAMLGQIERNESSPTVSTLWKIATGLNVPFSTF 65
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 2-63 1.15e-13

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: 62.65  E-value: 1.15e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 635780959   2 DITQHLAATLKTLRQARGWSLSKLADETGVSKAMLGQIERNESSPTVSTLWKIATGLNVPFS 63
Cdd:COG1813    8 ELVEDYGERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISLA 69
cupin_XRE_C cd02209
XRE (Xenobiotic Response Element) family transcriptional regulators, C-terminal cupin domain; ...
 83-172 3.96e-13

XRE (Xenobiotic Response Element) family transcriptional regulators, C-terminal cupin domain; This family contains transcriptional regulators containing an N-terminal XRE (Xenobiotic Response Element) family helix-turn-helix (HTH) DNA-binding domain and a C-terminal cupin domain. Included in this family is Escherichia coli transcription factor SutR (YdcN) that plays a regulatory role in sulfur utilization; it regulates a set of genes involved in the generation of sulfate and its reduction, the synthesis of cysteine, the synthesis of enzymes containing Fe-S as cofactors, and the modification of tRNA with use of sulfur-containing substrates. This family belongs to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380339 [Multi-domain]  Cd Length: 90  Bit Score: 61.75  E-value: 3.96e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 635780959  83 MVVKPLFPWDEALRFDYFSITLVPGA-LSESTPHEagVIEHVVVVSGELEMKLEGKWKTISADSGVRFAGDKPHAYRNSS 161
Cdd:cd02209    2 YTYELLSPGLPGRKMEPFLVTLPPGGsGGEPYSHE--GEEFGYVLEGELELTVGGETYVLEAGDSIYFDSDVPHRYRNPG 79

                         90
                 ....*....|.
gi 635780959 162 DRTVHFHSLIH 172
Cdd:cd02209   80 DEPARVLWVIT 90
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 4-72 5.77e-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: 53.49  E-value: 5.77e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 635780959   4 TQHLAATLKTLRQARGWSLSKLADETGVSKAMLGQIERNESSPTVSTLWKIATGLNVPFSTFITPEADR 72
Cdd:COG3620   15 DDTLGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVLVVDDGK 83
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
81-172 2.12e-09

Cupin domain protein related to quercetin dioxygenase [General function prediction only];


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 52.16  E-value: 2.12e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 635780959  81 QAMVVKPLFpwDEALRFDYFSITLVPGAlsESTPHEAGVIEHVVVVSGELEMKLEGKWKTISADSGVRFAGDKPHAYRNS 160
Cdd:COG1917    9 TGVSVRVLA--DGEDELEVVRVTFEPGA--RTPWHSHPGEELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFRNL 84

                         90
                 ....*....|..
gi 635780959 161 SDRTVHFHSLIH 172
Cdd:COG1917   85 GDEPAVLLVVFS 96
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 11-71 1.80e-08

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: 48.82  E-value: 1.80e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 635780959   11 LKTLRQARGWSLSKLADETGVSKAMLGQIERNESSPTVSTLWKIATGLNVPFSTFITPEAD 71
Cdd:pfam12844   4 LRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLLQGEGE 64
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 102-171 2.66e-08

Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel).


Pssm-ID: 462300 [Multi-domain]  Cd Length: 71  Bit Score: 48.41  E-value: 2.66e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 635780959  102 ITLVPGALSESTPHEaGVIEHVVVVSGELEMKLEGKWKTISADSGVRFAGDKPHAYRNSSDRTVHFHSLI 171
Cdd:pfam07883   3 VTLPPGESSPPHRHP-GEDEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPHRFRNTGDEPARLLDVY 71
COG3837 COG3837
Uncharacterized conserved protein, cupin superfamily [Function unknown];
82-175 5.71e-08

Uncharacterized conserved protein, cupin superfamily [Function unknown];


Pssm-ID: 443048 [Multi-domain]  Cd Length: 115  Bit Score: 48.86  E-value: 5.71e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 635780959  82 AMVVKPLFPWDEALRFDYFSITLVPGALSESTPHEAGVIEHVVVVSGELEMKLEGKWKTISADSGVRFAGDKPHAYRNSS 161
Cdd:COG3837   13 GRRYRRLGDALGLTRLGVNLITLPPGASSSPYHAHSAEEEFVYVLEGELTLRIGGEEYVLEPGDSVGFPAGVPHRLRNRG 92

                         90
                 ....*....|....*..
gi 635780959 162 DRTVHF---HSLIHYPR 175
Cdd:COG3837   93 DEPARYlvvGTRAPYPD 109
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
2-164 3.03e-07

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 47.87  E-value: 3.03e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 635780959   2 DITQHLAATLKTLRQARGWSLSKLADETGVSKAMLGQIERNESSPTVSTLWKIATGLNVPFST-FITPEADR--QAVFDP 78
Cdd:PRK09943   3 DEGLAPGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEfFSEPEKPDepQVVINQ 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 635780959  79 QQ------QAMVVKPLFPWDEALRFDYFSITLVPGALSESTPHEAGviEHV-VVVSGELEMKLEGKWKTISADSGVRFAG 151
Cdd:PRK09943  83 DDliemgsQGVSMKLVHNGNPNRTLAMIFETYQPGTTTGERIKHQG--EEIgTVLEGEIVLTINGQDYHLVAGQSYAINT 160

                        170
                 ....*....|...
gi 635780959 152 DKPHAYRNSSDRT 164
Cdd:PRK09943 161 GIPHSFSNTSAGI 173
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 6-61 4.48e-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: 44.83  E-value: 4.48e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 635780959    6 HLAATLKTLRQARGWSLSKLADETGVSKAMLGQIERNE-SSPTVSTLWKIATGLNVP 61
Cdd:pfam13560   1 ELGARLRRLRERAGLSQEALARRLGVSRSTLSRLETGRrGRPSPAVVERLARALGVD 57
ManC COG0662
Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism];
102-174 1.04e-06

Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism];


Pssm-ID: 440426 [Multi-domain]  Cd Length: 114  Bit Score: 45.52  E-value: 1.04e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 635780959 102 ITLVPGAlsESTPHE-AGVIEHVVVVSGELEMKLEGKWKTISADSGVRFAGDKPHAYRNSSDRTVHFHSlIHYP 174
Cdd:COG0662   32 ITVPPGA--ELSLHVhPHRDEFFYVLEGTGEVTIGDEEVELKAGDSVYIPAGVPHRLRNPGDEPLELLE-VQAP 102
cupin_TM1459-like cd02222
Thermotoga maritima TM1459 and related proteins, cupin domain; This family includes bacterial ...
 92-167 1.80e-06

Thermotoga maritima TM1459 and related proteins, cupin domain; This family includes bacterial and archaeal proteins homologous to Thermotoga maritima TM1459, a manganese-containing cupin that has been shown to cleave C=C bonds in the presence of alkylperoxide as oxidant in vitro. Its biological function is still unknown. This family also includes Halorhodospira halophila Hhal_0468. Structures of these proteins show a cupin fold with a conserved "jelly roll-like" beta-barrel fold that form a homodimer.


Pssm-ID: 380351 [Multi-domain]  Cd Length: 91  Bit Score: 43.98  E-value: 1.80e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 635780959  92 DEALRFDYFSITLVPGAlseSTPHEAGVIEHVV-VVSGELEMKLEGKWKTISADSGVRFAGDKPHAYRNSSDRTVHF 167
Cdd:cd02222   12 DGAPNFAMRYFEIEPGG---HTPLHTHPWEHEVyVLRGKGVVVIGGEEYPVKPGDVVYIPPNEPHQFRNTGDEPLGF 85
PRK09726 PRK09726
type II toxin-antitoxin system antitoxin HipB;
7-70 1.99e-06

type II toxin-antitoxin system antitoxin HipB;


Pssm-ID: 182049  Cd Length: 88  Bit Score: 43.82  E-value: 1.99e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 635780959   7 LAATLKTLRQARGWSLSKLADETGVSKAMLGQIERNESSPTVSTLWKIATGLNVPFSTFITPEA 70
Cdd:PRK09726  13 LANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMTLCDAKNA 76
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 2-43 4.75e-06

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: 42.48  E-value: 4.75e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 635780959   2 DITQHLAATLKTLRQARGWSLSKLADETGVSKAMLGQIERNE 43
Cdd:COG1426    1 EALETIGELLRQAREAKGLSLEDVAERTKISVSYLEAIEEGD 42
PRK04140 PRK04140
transcriptional regulator;
10-62 1.94e-05

transcriptional regulator;


Pssm-ID: 235224 [Multi-domain]  Cd Length: 317  Bit Score: 43.69  E-value: 1.94e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 635780959  10 TLKTLRQARGWSLSKLADETGVSKAMLGQIERNESSPTVSTLWKIATGLNVPF 62
Cdd:PRK04140 130 VLREAREELGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEILDVPL 182
COG1395 COG1395
Predicted transcriptional regulator [Transcription];
11-63 1.98e-05

Predicted transcriptional regulator [Transcription];


Pssm-ID: 441005 [Multi-domain]  Cd Length: 313  Bit Score: 43.67  E-value: 1.98e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 635780959  11 LKTLRQARGWSLSKLADETGVSKAMLGQIERNESSPTVSTLWKIATGLNVPFS 63
Cdd:COG1395  132 LRELREERGLSLGELASELGVSRRTISKYERGEMDASIEVALKLEEILGEPIV 184
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 11-71 6.36e-05

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: 39.06  E-value: 6.36e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 635780959   11 LKTLRQARGWSLSKLADETGVSKAMLGQIERNES-SPTVSTLWKIATGLNVPFSTFITPEAD 71
Cdd:pfam13443   2 LRKLMADRGISKSDLARATGISRATLSRLRKGKPkRVSLDTLDKICDALGCQPGDLLEYVPD 63
cupin_DddK cd06988
Dimethylsulfoniopropionate lyase DddK and related proteins, cupin domain; This family includes ...
 106-170 1.26e-04

Dimethylsulfoniopropionate lyase DddK and related proteins, cupin domain; This family includes mostly bacterial proteins homologous to dimethylsulfoniopropionate lyase DddK from marine bacterium Pelagibacter. DddK cleaves dimethylsulfoniopropionate (DMSP), the organic osmolyte and antioxidant produced in marine environments, and yields acrylate and the climate-active gas dimethyl sulfide (DMS). DddK contains a double-stranded beta-helical motif which utilizes various divalent metal ions as cofactors for catalytic activity; however, nickel, an abundant metal ion in marine environments, confers the highest DMSP lyase activity. Also included in this family is Plu4264, a Photorhabdus luminescens manganese-containing cupin shown to have similar metal binding site to TM1287 decarboxylase, but two very different substrate binding pockets. The Plu4264 binding pocket shows a cavity and substrate entry point more than twice as large as and more hydrophobic than TM1287, suggesting that Plu4264 accepts a substrate that is significantly larger than that of TM1287, a putative oxalate decarboxylase. Thus, the function of Plu4264 could be similar to that of TM1287 but with a larger, less charged substrate. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.


Pssm-ID: 380393 [Multi-domain]  Cd Length: 76  Bit Score: 38.76  E-value: 1.26e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 635780959 106 PGalSESTPHEAGVIEHVVVVSGELEMKLEGKWKTISADSGVRFAGDKPHAYRNSSDRTVHFHSL 170
Cdd:cd06988   11 PG--TTSTPHSHHEYEIFIVISGKGIVVVDGEREPVKAGDVVYIPPGTEHYVKNDGDEDFEFYSI 73
PRK08154 PRK08154
anaerobic benzoate catabolism transcriptional regulator; Reviewed
 7-70 2.16e-04

anaerobic benzoate catabolism transcriptional regulator; Reviewed


Pssm-ID: 236167 [Multi-domain]  Cd Length: 309  Bit Score: 40.32  E-value: 2.16e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 635780959   7 LAATLKTLRQARGWSLSKLADETGVSKAMLGQIERNESSPTVSTLWKIATGLNVPFSTFITPEA 70
Cdd:PRK08154  29 LGERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCSLADLLGDVD 92
cupin_UGlyAH_N cd02211
(S)-ureidoglycine aminohydrolase and related proteins, N-terminal cupin domain; This family ...
 96-168 3.53e-04

(S)-ureidoglycine aminohydrolase and related proteins, N-terminal cupin domain; This family includes the N-terminal cupin domain of (S)-ureidoglycine aminohydrolase (UGlyAH), an enzyme that converts (S)-ureidoglycine into (S)-ureidoglycolate and ammonia, providing the final substrate to the ureide pathway. The ureide pathway has recently been identified as the metabolic route of purine catabolism in plants and some bacteria where, uric acid, which is a major product of the early stage of purine catabolism, is degraded into glyoxylate and ammonia via stepwise reactions by seven different enzymes. Thus, this pathway has a possible physiological role in mobilization of purine ring nitrogen for further assimilation. This enzyme from Arabidopsis thaliana(AtUGlyAH) has been shown to bind a Mn2+ ion, via the C-terminal cupin domain, which acts as a molecular anchor to bind (S)-ureidoglycine, and its binding mode dictates the enantioselectivity of the reaction. The structure of AtUGlyAH shows a bi-cupin fold with a conserved "jelly roll-like" beta-barrel fold and an octameric functional unit. Several structural homologs of UGlyAH, including the Escherichia coli ortholog YlbA (also known as GlxB6), also exhibit similar features.


Pssm-ID: 380341 [Multi-domain]  Cd Length: 117  Bit Score: 38.27  E-value: 3.53e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 635780959  96 RFDYFSITLVPGALSESTPHEAGvIEHVV-VVSGELEMKLEGKWKTISADSGVRFAGDKPHAYRNSSDRTVHFH 168
Cdd:cd02211   24 TFVQYLVEVEPGGGSTAPEGGEG-IERFLyVLEGEVELTVGGETHTLTAGGYAYLPPGTKHSLRNAGDEPARLL 96
PRK13890 PRK13890
conjugal transfer protein TrbA; Provisional
 18-96 4.23e-04

conjugal transfer protein TrbA; Provisional


Pssm-ID: 237547 [Multi-domain]  Cd Length: 120  Bit Score: 38.19  E-value: 4.23e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 635780959  18 RGWSLSKLADETGVSKAMLGQIERNESSPTVSTLWKIATGLNVPF-----STFITPEA-----------------DRQAV 75
Cdd:PRK13890  17 RHMTKKELSERSGVSISFLSDLTTGKANPSLKVMEAIADALETPLpllleSTDLDKEAldalaggkaprslppgfERVAA 96

                         90       100
                 ....*....|....*....|.
gi 635780959  76 FDPQQQAMVVKplfPWDEALR 96
Cdd:PRK13890  97 VLPEHQAFIVK---KWGEATR 114
HTH_25 pfam13413
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 10-45 6.82e-04

Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.


Pssm-ID: 433187 [Multi-domain]  Cd Length: 62  Bit Score: 36.32  E-value: 6.82e-04
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 635780959   10 TLKTLRQARGWSLSKLADETGVSKAMLGQIERNESS 45
Cdd:pfam13413   1 RLRAAREARGLSLEDVAERTKIRPRYLEALEEDDFD 36
PRK11171 PRK11171
(S)-ureidoglycine aminohydrolase;
96-168 1.16e-03

(S)-ureidoglycine aminohydrolase;


Pssm-ID: 183011 [Multi-domain]  Cd Length: 266  Bit Score: 38.34  E-value: 1.16e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 635780959  96 RFDYFSITLVPGALSESTPHEAGvIEHVV-VVSGELEMKLEGKWKTISADSGVRFAGDKPHAYRNSSDRTVHFH 168
Cdd:PRK11171  60 TFSQYLVEVEPGGGSDQPEPDEG-AETFLfVVEGEITLTLEGKTHALSEGGYAYLPPGSDWTLRNAGAEDARFH 132
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 7-59 1.79e-03

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: 35.33  E-value: 1.79e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 635780959    7 LAATLKTLRQARGWSLSKLADETGVSKAMLGQIERNESSPTVSTLWKIATGLN 59
Cdd:TIGR03070   3 IGILVRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDALG 55
HigA COG5499
Antitoxin component HigA of the HigAB toxin-antitoxin module, contains an N-terminal HTH ...
 9-68 2.00e-03

Antitoxin component HigA of the HigAB toxin-antitoxin module, contains an N-terminal HTH domain [Defense mechanisms];


Pssm-ID: 444250  Cd Length: 127  Bit Score: 36.35  E-value: 2.00e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 635780959   9 ATLKTLRQARGWSLSKLADETGvSKAMLGQIERNESSPTVSTLWKIATGLNVPFSTFITP 68
Cdd:COG5499   68 EALKFLMEQHGLTQKDLAPEIG-SKSRVSEILNGKRSLTLEMIRKLAERFGIPAELFIQP 126
cupin_BacB cd06975
Bacillus subtilis bacilysin and related proteins, cupin domain; Bacilysin (BacB, also known as ...
 124-165 2.65e-03

Bacillus subtilis bacilysin and related proteins, cupin domain; Bacilysin (BacB, also known as AerE in Microcystis aeruginosa) is a non-ribosomally synthesized dipeptide antibiotic that is produced and excreted by certain strains of Bacillus subtilis. It is an oxidase that catalyzes the synthesis of 2-oxo-3-(4-oxocyclohexa-2,5-dienyl)propanoic acid, a precursor to L-anticapsin. Each bacilysin monomer has two tandem cupin domains. It is active against a wide range of bacteria and some fungi. The antimicrobial activity of bacilysin is antagonized by glucosamine and N-acetyl glucosamine, indicating that bacilysin interferes with glucosamine synthesis, and thus, with the synthesis of microbial cell walls. AerE is thought to be involved in the formation of the 2-carboxy-6-hydroxyoctahydroindole (Choi) moiety found on all aeruginosin tetrapeptides, based on gene knock-out experiments. It is encoded by the aerE gene of the aerABCDEF aeruginosin biosynthesis gene cluster in Microcystis aeruginosa.


Pssm-ID: 380380 [Multi-domain]  Cd Length: 93  Bit Score: 35.63  E-value: 2.65e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 635780959 124 VVVSGELEMKLEGKWKTISADSGVRFAGDK-PHAYRNSSDRTV 165
Cdd:cd06975   44 MILNGELEMTVGGEEQELEPLGDVYYAPPNvPHGAVNPSDETA 86
PHA01976 PHA01976
helix-turn-helix protein
 14-60 2.86e-03

helix-turn-helix protein


Pssm-ID: 177330 [Multi-domain]  Cd Length: 67  Bit Score: 34.93  E-value: 2.86e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 635780959  14 LRQARGWSLSKLADETGVSKAMLGQIERNESSPTVSTLWKIATGLNV 60
Cdd:PHA01976  10 ARNARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGV 56
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
1-51 3.94e-03

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 34.52  E-value: 3.94e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 635780959   1 MDITQHLAATLKTLRQARGWSLSKLADETGVSKAMLGQIERNESSPTVSTL 51
Cdd:COG2944    1 MTKKPLTPEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGAAL 51
 
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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