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Conserved domains on  [gi|446349782|ref|WP_000427637|]
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MULTISPECIES: helix-turn-helix domain-containing protein [Bacillus]

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
cupin_XRE_C cd02209
XRE (Xenobiotic Response Element) family transcriptional regulators, C-terminal cupin domain; ...
 88-177 6.70e-20

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: 79.47  E-value: 6.70e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446349782  88 NLSYEMLSPDFTGN-LATAIMTVPPNTASSEnVLEHKGEELAFVLDGKITLYLNEEEYVLETGDSVKIPAYLKHKWVNHF 166
Cdd:cd02209    1 GYTYELLSPGLPGRkMEPFLVTLPPGGSGGE-PYSHEGEEFGYVLEGELELTVGGETYVLEAGDSIYFDSDVPHRYRNPG 79

                         90
                 ....*....|.
gi 446349782 167 EKNAIVLFSVT 177
Cdd:cd02209   80 DEPARVLWVIT 90
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-72 1.15e-19

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 78.50  E-value: 1.15e-19
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446349782   1 MENI--DIGKKIEKQRKEKGLTSKELAKMADITPSMLSQIERGSANPSIQTLKVLAKALDVPTfSFLLEDTNTD 72
Cdd:COG1396    1 MSTLkkALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSL-DELLGGADEE 73
 
Name Accession Description Interval E-value
cupin_XRE_C cd02209
XRE (Xenobiotic Response Element) family transcriptional regulators, C-terminal cupin domain; ...
 88-177 6.70e-20

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: 79.47  E-value: 6.70e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446349782  88 NLSYEMLSPDFTGN-LATAIMTVPPNTASSEnVLEHKGEELAFVLDGKITLYLNEEEYVLETGDSVKIPAYLKHKWVNHF 166
Cdd:cd02209    1 GYTYELLSPGLPGRkMEPFLVTLPPGGSGGE-PYSHEGEEFGYVLEGELELTVGGETYVLEAGDSIYFDSDVPHRYRNPG 79

                         90
                 ....*....|.
gi 446349782 167 EKNAIVLFSVT 177
Cdd:cd02209   80 DEPARVLWVIT 90
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-72 1.15e-19

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 78.50  E-value: 1.15e-19
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446349782   1 MENI--DIGKKIEKQRKEKGLTSKELAKMADITPSMLSQIERGSANPSIQTLKVLAKALDVPTfSFLLEDTNTD 72
Cdd:COG1396    1 MSTLkkALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSL-DELLGGADEE 73
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
2-181 1.96e-19

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 80.99  E-value: 1.96e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446349782   2 ENIDIGKKIEKQRKEKGLTSKELAKMADITPSMLSQIERGSANPSIQTLKVLAKALDVPTFSFLLEDTNTDD--LIVRSH 79
Cdd:PRK09943   4 EGLAPGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEFFSEPEKPDEpqVVINQD 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446349782  80 KRKKMIIDNLSYEML-SPDFTGNLATAIMTVPPNTASSENVlEHKGEELAFVLDGKITLYLNEEEYVLETGDSVKIPAYL 158
Cdd:PRK09943  84 DLIEMGSQGVSMKLVhNGNPNRTLAMIFETYQPGTTTGERI-KHQGEEIGTVLEGEIVLTINGQDYHLVAGQSYAINTGI 162

                        170       180
                 ....*....|....*....|...
gi 446349782 159 KHKWVNHFEKNAIVLFSVTPPIF 181
Cdd:PRK09943 163 PHSFSNTSAGICRIISAHTPTTF 185
COG3837 COG3837
Uncharacterized conserved protein, cupin superfamily [Function unknown];
90-179 4.87e-19

Uncharacterized conserved protein, cupin superfamily [Function unknown];


Pssm-ID: 443048 [Multi-domain]  Cd Length: 115  Bit Score: 78.14  E-value: 4.87e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446349782  90 SYEMLSPDFTG-NLATAIMTVPPNTASSENVLEHKGEELAFVLDGKITLYLNEEEYVLETGDSVKIPAYLKHKWVNHFEK 168
Cdd:COG3837   15 RYRRLGDALGLtRLGVNLITLPPGASSSPYHAHSAEEEFVYVLEGELTLRIGGEEYVLEPGDSVGFPAGVPHRLRNRGDE 94

                         90
                 ....*....|.
gi 446349782 169 NAIVLFSVTPP 179
Cdd:COG3837   95 PARYLVVGTRA 105
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 7-60 5.80e-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: 68.35  E-value: 5.80e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 446349782   7 GKKIEKQRKEKGLTSKELAKMADITPSMLSQIERGSANPSIQTLKVLAKALDVP 60
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVS 54
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
9-60 4.80e-15

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 66.00  E-value: 4.80e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 446349782     9 KIEKQRKEKGLTSKELAKMADITPSMLSQIERGSANPSIQTLKVLAKALDVP 60
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVS 52
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 10-60 1.10e-14

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: 1.10e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 446349782   10 IEKQRKEKGLTSKELAKMADITPSMLSQIERGSANPSIQTLKVLAKALDVP 60
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVS 51
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 105-174 1.25e-14

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: 65.36  E-value: 1.25e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446349782  105 AIMTVPPNTASSENVleHKGE-ELAFVLDGKITLYLNEEEYVLETGDSVKIPAYLKHKWVNHFEKNAIVLF 174
Cdd:pfam07883   1 GLVTLPPGESSPPHR--HPGEdEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPHRFRNTGDEPARLLD 69
PRK13890 PRK13890
conjugal transfer protein TrbA; Provisional
 16-72 8.70e-12

conjugal transfer protein TrbA; Provisional


Pssm-ID: 237547 [Multi-domain]  Cd Length: 120  Bit Score: 59.00  E-value: 8.70e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446349782  16 EKGLTSKELAKMADITPSMLSQIERGSANPSIQTLKVLAKALDVPtFSFLLEDTNTD 72
Cdd:PRK13890  16 ERHMTKKELSERSGVSISFLSDLTTGKANPSLKVMEAIADALETP-LPLLLESTDLD 71
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 5-57 2.38e-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: 37.64  E-value: 2.38e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 446349782    5 DIGKKIEKQRKEKGLTSKELAKMADITPSMLSQIERGSANPSIQTLKVLAKAL 57
Cdd:TIGR03070   2 QIGILVRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDAL 54
 
Name Accession Description Interval E-value
cupin_XRE_C cd02209
XRE (Xenobiotic Response Element) family transcriptional regulators, C-terminal cupin domain; ...
 88-177 6.70e-20

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: 79.47  E-value: 6.70e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446349782  88 NLSYEMLSPDFTGN-LATAIMTVPPNTASSEnVLEHKGEELAFVLDGKITLYLNEEEYVLETGDSVKIPAYLKHKWVNHF 166
Cdd:cd02209    1 GYTYELLSPGLPGRkMEPFLVTLPPGGSGGE-PYSHEGEEFGYVLEGELELTVGGETYVLEAGDSIYFDSDVPHRYRNPG 79

                         90
                 ....*....|.
gi 446349782 167 EKNAIVLFSVT 177
Cdd:cd02209   80 DEPARVLWVIT 90
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-72 1.15e-19

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 78.50  E-value: 1.15e-19
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446349782   1 MENI--DIGKKIEKQRKEKGLTSKELAKMADITPSMLSQIERGSANPSIQTLKVLAKALDVPTfSFLLEDTNTD 72
Cdd:COG1396    1 MSTLkkALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSL-DELLGGADEE 73
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
2-181 1.96e-19

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 80.99  E-value: 1.96e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446349782   2 ENIDIGKKIEKQRKEKGLTSKELAKMADITPSMLSQIERGSANPSIQTLKVLAKALDVPTFSFLLEDTNTDD--LIVRSH 79
Cdd:PRK09943   4 EGLAPGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEFFSEPEKPDEpqVVINQD 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446349782  80 KRKKMIIDNLSYEML-SPDFTGNLATAIMTVPPNTASSENVlEHKGEELAFVLDGKITLYLNEEEYVLETGDSVKIPAYL 158
Cdd:PRK09943  84 DLIEMGSQGVSMKLVhNGNPNRTLAMIFETYQPGTTTGERI-KHQGEEIGTVLEGEIVLTINGQDYHLVAGQSYAINTGI 162

                        170       180
                 ....*....|....*....|...
gi 446349782 159 KHKWVNHFEKNAIVLFSVTPPIF 181
Cdd:PRK09943 163 PHSFSNTSAGICRIISAHTPTTF 185
COG3837 COG3837
Uncharacterized conserved protein, cupin superfamily [Function unknown];
90-179 4.87e-19

Uncharacterized conserved protein, cupin superfamily [Function unknown];


Pssm-ID: 443048 [Multi-domain]  Cd Length: 115  Bit Score: 78.14  E-value: 4.87e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446349782  90 SYEMLSPDFTG-NLATAIMTVPPNTASSENVLEHKGEELAFVLDGKITLYLNEEEYVLETGDSVKIPAYLKHKWVNHFEK 168
Cdd:COG3837   15 RYRRLGDALGLtRLGVNLITLPPGASSSPYHAHSAEEEFVYVLEGELTLRIGGEEYVLEPGDSVGFPAGVPHRLRNRGDE 94

                         90
                 ....*....|.
gi 446349782 169 NAIVLFSVTPP 179
Cdd:COG3837   95 PARYLVVGTRA 105
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 7-60 5.80e-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: 68.35  E-value: 5.80e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 446349782   7 GKKIEKQRKEKGLTSKELAKMADITPSMLSQIERGSANPSIQTLKVLAKALDVP 60
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVS 54
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 5-60 1.65e-15

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: 67.66  E-value: 1.65e-15
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446349782   5 DIGKKIEKQRKEKGLTSKELAKMADITPSMLSQIERGSANPSIQTLKVLAKALDVP 60
Cdd:COG1813   12 DYGERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGIS 67
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
3-68 2.56e-15

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 66.80  E-value: 2.56e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446349782   3 NIDIGKKIEKQRKEKGLTSKELAKMADITPSMLSQIERGSANPSIQTLKVLAKALDVPTFSFLLED 68
Cdd:COG1476    2 KKKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLE 67
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
9-60 4.80e-15

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 66.00  E-value: 4.80e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 446349782     9 KIEKQRKEKGLTSKELAKMADITPSMLSQIERGSANPSIQTLKVLAKALDVP 60
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVS 52
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 10-60 1.10e-14

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: 1.10e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 446349782   10 IEKQRKEKGLTSKELAKMADITPSMLSQIERGSANPSIQTLKVLAKALDVP 60
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVS 51
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 105-174 1.25e-14

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: 65.36  E-value: 1.25e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446349782  105 AIMTVPPNTASSENVleHKGE-ELAFVLDGKITLYLNEEEYVLETGDSVKIPAYLKHKWVNHFEKNAIVLF 174
Cdd:pfam07883   1 GLVTLPPGESSPPHR--HPGEdEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPHRFRNTGDEPARLLD 69
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
80-179 7.86e-14

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


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 64.10  E-value: 7.86e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446349782  80 KRKKMIIDNLSYEMLSPDfTGNLATAIMTVPPNTASSENVleHKGEELAFVLDGKITLYLNEEEYVLETGDSVKIPAYLK 159
Cdd:COG1917    2 RLAEIALTGVSVRVLADG-EDELEVVRVTFEPGARTPWHS--HPGEELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVP 78

                         90       100
                 ....*....|....*....|
gi 446349782 160 HKWVNHFEKNAIVLFSVTPP 179
Cdd:COG1917   79 HAFRNLGDEPAVLLVVFSPG 98
ManC COG0662
Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism];
97-181 3.87e-12

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


Pssm-ID: 440426 [Multi-domain]  Cd Length: 114  Bit Score: 59.77  E-value: 3.87e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446349782  97 DFTGNLATAIMTVPPNTASSENVLEHkGEELAFVLDGKITLYLNEEEYVLETGDSVKIPAYLKHKWVNHFEKNAIVLFSV 176
Cdd:COG0662   22 EGGERLSVKRITVPPGAELSLHVHPH-RDEFFYVLEGTGEVTIGDEEVELKAGDSVYIPAGVPHRLRNPGDEPLELLEVQ 100


                 ....*
gi 446349782 177 TPPIF 181
Cdd:COG0662  101 APAYL 105
PRK13890 PRK13890
conjugal transfer protein TrbA; Provisional
 16-72 8.70e-12

conjugal transfer protein TrbA; Provisional


Pssm-ID: 237547 [Multi-domain]  Cd Length: 120  Bit Score: 59.00  E-value: 8.70e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446349782  16 EKGLTSKELAKMADITPSMLSQIERGSANPSIQTLKVLAKALDVPtFSFLLEDTNTD 72
Cdd:PRK13890  16 ERHMTKKELSERSGVSISFLSDLTTGKANPSLKVMEAIADALETP-LPLLLESTDLD 71
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 7-65 1.50e-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: 56.91  E-value: 1.50e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 446349782    7 GKKIEKQRKEKGLTSKELAKMADITPSMLSQIERGSANPSIQTLKVLAKALDVPTFSFL 65
Cdd:pfam12844   1 GERLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLL 59
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 6-68 2.78e-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: 57.34  E-value: 2.78e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446349782   6 IGKKIEKQRKEKGLTSKELAKMADITPSMLSQIERGSANPSIQTLKVLAKALDVPTFSFLLED 68
Cdd:COG3620   18 LGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVLVVD 80
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 1-57 2.09e-08

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 50.62  E-value: 2.09e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446349782   1 MENIDIGKKIEKQRKEKGLTSKELAKMADITPSMLSQIERGSANPSIQTLKVLAKAL 57
Cdd:PRK09706   1 MKNLTLGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKAL 57
cupin_RmlC-like cd02208
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 106-174 2.89e-07

RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP (deoxythymidine diphosphates)-4-dehydrorhamnose 3,5-epimerase)-like cupins. RmlC is a dTDP-sugar isomerase involved in the synthesis of L-rhamnose, a saccharide required for the virulence of some pathogenic bacteria. Cupins are a functionally diverse superfamily originally discovered based on the highly conserved motif found in germin and germin-like proteins. This conserved motif forms a beta-barrel fold found in all of the cupins, giving rise to the name cupin ('cupa' is the Latin term for small barrel). The active site of members of this superfamily is generally located at the center of a conserved barrel and usually includes a metal ion. The different functional classes in this superfamily include single domain bacterial isomerases and epimerases involved in the modification of cell wall carbohydrates, two domain bicupins such as the desiccation-tolerant seed storage globulins, and multidomain nuclear transcription factors involved in legume root nodulation.


Pssm-ID: 380338 [Multi-domain]  Cd Length: 73  Bit Score: 45.94  E-value: 2.89e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446349782 106 IMTVPPNTASsenvLEH---KGEELAFVLDGKITLYLN-EEEYVLETGDSVKIPAYLKHKWVNHFEKNAIVLF 174
Cdd:cd02208    3 VVTLPPGTSS----PPHwhpEQDEIFYVLSGEGELTLDdGETVELKAGDIVLIPPGVPHSFVNTSDEPAVFLV 71
PRK08154 PRK08154
anaerobic benzoate catabolism transcriptional regulator; Reviewed
 7-60 4.32e-07

anaerobic benzoate catabolism transcriptional regulator; Reviewed


Pssm-ID: 236167 [Multi-domain]  Cd Length: 309  Bit Score: 48.41  E-value: 4.32e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 446349782   7 GKKIEKQRKEKGLTSKELAKMADITPSMLSQIERGSANPSIQTLKVLAKALDVP 60
Cdd:PRK08154  30 GERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCS 83
cupin_SPO2919-like cd02224
Silicibacter pomeroyi SPO2919 and related proteins, uncharacterized sugar phosphate isomerase ...
 106-156 1.11e-06

Silicibacter pomeroyi SPO2919 and related proteins, uncharacterized sugar phosphate isomerase with a cupin domain; This family includes proteins similar to sugar phosphate isomerase SPO2919 from Silicibacter pomeroyi and Afe_0303 from Acidithiobacillus ferrooxidans, but are as yet uncharacterized. Structures of these proteins show a cupin fold with a conserved "jelly roll-like" beta-barrel fold that form a homodimer.


Pssm-ID: 380353 [Multi-domain]  Cd Length: 105  Bit Score: 45.17  E-value: 1.11e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 446349782 106 IMTVPPNTASSENVLEHKGEELAFVLDGKITLYLNEEEYVLETGDSVKIPA 156
Cdd:cd02224   21 LERLPPGARSSPRHWHSAEEEFVYVLSGEGTLRLDGEEVLPRPGDFVGFPA 71
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 14-60 1.32e-06

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


Pssm-ID: 433309 [Multi-domain]  Cd Length: 64  Bit Score: 43.67  E-value: 1.32e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 446349782   14 RKEKGLTSKELAKMADITPSMLSQIERGSAN-PSIQTLKVLAKALDVP 60
Cdd:pfam13560  10 RERAGLSQEALARRLGVSRSTLSRLETGRRGrPSPAVVERLARALGVD 57
cupin_QDO_N_C cd02215
quercetinase, N- and C-terminal cupin domains; This family contains quercetinase (also known ...
 129-181 1.86e-06

quercetinase, N- and C-terminal cupin domains; This family contains quercetinase (also known as quercetin 2,3-dioxygenase, 2,3QD, QDO and YxaG; EC 1.13.11.24), a mononuclear copper-dependent dioxygenase that catalyzes the cleavage of the flavonol quercetin (5,7,3',4'-tetrahydroxyflavonol) heterocyclic ring to produce 2-protocatechuoyl-phloroglucinol carboxylic acid and carbon monoxide. Bacillus subtilis quercetin 2,3-dioxygenase (QDO) is a homodimer that shows oxygenase activity with several divalent metals such as Mn2+, Co2+, Fe2+, and Cu2+, although the preferred one appears to be Mn2+. The dioxygen binds to the metal ion of the Cu-QDO-quercetin complex, yielding a Cu2+-superoxo quercetin radical intermediate, which then forms a Cu2+-alkylperoxo complex which then evolves into endoperoxide intermediate that decomposes to the product. Quercetinase is a bicupin with two tandem cupin beta-barrel domains, both of which are included in this alignment model. The pirins, which also belong to the cupin domain family, have been shown to catalyze a reaction involving quercetin and may have a function similar to that of quercetinase.


Pssm-ID: 380345 [Multi-domain]  Cd Length: 122  Bit Score: 44.83  E-value: 1.86e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446349782 129 FVLDGKITLYLNEEEYVLETGDSVKIPAYLKHKWVNHFEKNAIVLFSvTPPIF 181
Cdd:cd02215   58 YVLEGRLQLWLDGESRLLTPGDFASVPPGTIHAYRMLSPDTRFLGVI-TPGGF 109
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 6-60 2.36e-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: 43.25  E-value: 2.36e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446349782   6 IGKKIEKQRKEKGLTSKELAKMADITPSMLSQIERG------SANPSIQTLKVLAKALDVP 60
Cdd:COG1426    6 IGELLRQAREAKGLSLEDVAERTKISVSYLEAIEEGdfdalpGPVYVRGFLRSYARALGLD 66
cupin_TcmJ-like cd06991
TcmJ monooxygenase and related proteins, cupin domain; This family includes TcmJ, a subunit of ...
 93-178 3.49e-06

TcmJ monooxygenase and related proteins, cupin domain; This family includes TcmJ, a subunit of the tetracenomycin (TCM) polyketide synthase (PKS) type II complex in Streptomyces glaucescens. TcmJ is a quinone-forming monooxygenase involved in the modification of aromatic polyketides synthesized by polyketide synthases of types II and III. Orthologs of TcmJ include the Streptomyces BenD (benastatin biosynthetic pathway), the Streptomyces olivaceus ElmJ (polyketide antibiotic elloramycin biosynthetic pathway), the Actinomadura hibisca PdmL (pradimicin biosynthetic pathway), the Streptomyces cyaneus CurC (curamycin biosynthetic pathway), the Streptomyces rishiriensis Lct30 (lactonamycin biosynthetic pathway), and the Streptomyces WhiE II (spore pigment polyketide biosynthetic pathway). Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380396 [Multi-domain]  Cd Length: 105  Bit Score: 43.82  E-value: 3.49e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446349782  93 MLSPDFTGnlATA----IMTVPPntasSENVLEH---KGEELAFVLDGKITLYLNEEEYVLETGDSVKIPAYLKHKWVNH 165
Cdd:cd06991    8 LLSPKTVG--ATSgfmgTLTLAP----GERVSEHyhpYSEEFLYVVRGRLVVRVDGEPVVLEAGEALLVPRGVRHRLENA 81

                         90
                 ....*....|...
gi 446349782 166 FEKNAIVLFSVTP 178
Cdd:cd06991   82 GDEPARLVFHLSP 94
cupin_MJ1618 cd02214
Methanocaldococcus jannaschii MJ1618 and related proteins, cupin domain; This family includes ...
 91-179 3.69e-06

Methanocaldococcus jannaschii MJ1618 and related proteins, cupin domain; This family includes bacterial and archaeal proteins homologous to MJ1618, a Methanocaldococcus jannaschii protein of unknown function with a cupin beta barrel domain. The active site of members of the cupin superfamily is generally located at the center of a conserved barrel and usually includes a metal ion.


Pssm-ID: 380344 [Multi-domain]  Cd Length: 100  Bit Score: 43.66  E-value: 3.69e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446349782  91 YEMLSPDFTGN----LATAimTVPPNTASSENVLEHKgEELAFVLDGKITLYLNEEEYVLETGDSVKIPAYLKHKWVNHF 166
Cdd:cd02214    6 RELLHPDNDGDprysLAHA--RVPPGESTLPHRLKGS-EEVYYILEGEGTMEIDGEPREVGPGDAVLIPPGAVQRIENTG 82

                         90
                 ....*....|...
gi 446349782 167 EKNAIVLFSVTPP 179
Cdd:cd02214   83 EEDLVFLCICSPA 95
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 11-83 7.52e-06

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 42.49  E-value: 7.52e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446349782  11 EKQRKEKGLTSKELAKMADITPSMLSQIERGSANPSIQTLKVLAKALDVPTFSFLLEDTNTDDLIVRSHKRKK 83
Cdd:COG3093   15 EEFLEPLGLSQTELAKALGVSRQRISEILNGKRAITADTALRLARAFGTSAEFWLNLQAAYDLWLARQKAGEE 87
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
7-60 3.60e-05

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 39.92  E-value: 3.60e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 446349782   7 GKKIEKQRKEKGLTSKELAKMADITPSMLSQIERGSANPSIQTLKVLAKALDVP 60
Cdd:COG2944    8 PEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGAALKLLRLLEKHP 61
AllE COG3257
Ureidoglycine aminohydrolase [Nucleotide transport and metabolism];
106-156 5.01e-05

Ureidoglycine aminohydrolase [Nucleotide transport and metabolism];


Pssm-ID: 442488 [Multi-domain]  Cd Length: 262  Bit Score: 42.50  E-value: 5.01e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 446349782 106 IMTVPPNTASSENVLEHKGEELAFVLDGKITLYLNEEEYVLETGDSVKIPA 156
Cdd:COG3257   63 IVEVAPGGGSDRPEPDPGAETFLFVLEGEVTLTLGGETHELTPGGYAYLPP 113
PRK11171 PRK11171
(S)-ureidoglycine aminohydrolase;
95-165 8.80e-05

(S)-ureidoglycine aminohydrolase;


Pssm-ID: 183011 [Multi-domain]  Cd Length: 266  Bit Score: 41.81  E-value: 8.80e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446349782  95 SPDFTGNLATAIMTVPPNTASSENVLEHKGEELAFVLDGKITLYLNEEEYVLETGDSVKIPAYLKHKWVNH 165
Cdd:PRK11171  54 RPGLGATFSQYLVEVEPGGGSDQPEPDEGAETFLFVVEGEITLTLEGKTHALSEGGYAYLPPGSDWTLRNA 124
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 9-67 8.88e-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: 8.88e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446349782    9 KIEKQRKEKGLTSKELAKMADITPSMLSQIERG-SANPSIQTLKVLAKALDVpTFSFLLE 67
Cdd:pfam13443   1 KLRKLMADRGISKSDLARATGISRATLSRLRKGkPKRVSLDTLDKICDALGC-QPGDLLE 59
cupin_UGlyAH_N cd02211
(S)-ureidoglycine aminohydrolase and related proteins, N-terminal cupin domain; This family ...
 106-174 1.10e-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: 39.81  E-value: 1.10e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446349782 106 IMTVPPNTASSENVLEHKGEELAFVLDGKITLYLNEEEYVLETGDSVKIPAYLKHKWVNHFEKNA-IVLF 174
Cdd:cd02211   29 LVEVEPGGGSTAPEGGEGIERFLYVLEGEVELTVGGETHTLTAGGYAYLPPGTKHSLRNAGDEPArLLWY 98
cupin_TM1459-like cd02222
Thermotoga maritima TM1459 and related proteins, cupin domain; This family includes bacterial ...
 107-164 1.36e-04

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: 38.97  E-value: 1.36e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 446349782 107 MTVPPNTASSenvLE-HKGEELAFVLDGKITLYLNEEEYVLETGDSVKIPAYLKHKWVN 164
Cdd:cd02222   22 FEIEPGGHTP---LHtHPWEHEVYVLRGKGVVVIGGEEYPVKPGDVVYIPPNEPHQFRN 77
cupin_BacB cd06975
Bacillus subtilis bacilysin and related proteins, cupin domain; Bacilysin (BacB, also known as ...
 106-173 1.95e-04

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: 38.71  E-value: 1.95e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446349782 106 IMTVPPNTASSENvlEHKGEELAFVLDGKITLYLNEEEYVLETGDSVKI-PAYLKHKWVNHFEKNAIVL 173
Cdd:cd06975   23 LSYIPPGAKMPLH--QHREEQIGMILNGELEMTVGGEEQELEPLGDVYYaPPNVPHGAVNPSDETAVLL 89
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 5-57 2.38e-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: 37.64  E-value: 2.38e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 446349782    5 DIGKKIEKQRKEKGLTSKELAKMADITPSMLSQIERGSANPSIQTLKVLAKAL 57
Cdd:TIGR03070   2 QIGILVRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDAL 54
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 2-55 4.42e-04

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: 38.38  E-value: 4.42e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 446349782    2 ENIDIGKKIEKQRKEKGLTSKELAKMADITPSMLSQIERGSANPS---IQTLKVLAK 55
Cdd:TIGR03830  62 DGLLTGPEIRRIRKKLGLSQREAAELLGGGVNAFSRYERGEVRPSkalDKLLRLLDK 118
cupin_DAD_ChrR cd02237
2,4'-Dihydroxyacetophenone dioxygenase (DAD) and anti-sigma factor ChrR, and similar proteins; ...
 94-174 5.89e-04

2,4'-Dihydroxyacetophenone dioxygenase (DAD) and anti-sigma factor ChrR, and similar proteins; cupin domain; This family includes the proteins 2,4'-Dihydroxyacetophenone dioxygenase (DAD) and anti-sigma factor ChrR. DAD catalyzes the oxidation of 2,4'-dihydroxyacetophenone to 4-hydroxybenzoate and formate as part of the 4-hydroxyacetophenone catabolic pathway. The enzyme is a homotetramer containing one iron per molecule of enzyme. Anti-sigma factor ChrR is a member of the ZAS (Zn2+ anti-sigma) subfamily of group IV anti-sigmas. It inhibits transcriptional activity by binding to the Rsp extra cytoplasmic function (ECF) sigma factor E (sigmaE). Some ChrR members contain tandem repeats of two distinct homologous functional domains. Members of this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.


Pssm-ID: 380365 [Multi-domain]  Cd Length: 82  Bit Score: 36.99  E-value: 5.89e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446349782  94 LSPDFTGNLATAIMTVPPNTASSENvlEHKGEELAFVLDGKITlylnEEEYVLETGDSVKIPAYLKHKWVNhFEKNAIVL 173
Cdd:cd02237    6 LLIDPNTGLITAILRMAPGARLPDH--EHVGGEEFYVLDGALT----DEDGTAGAGDFVREPPGSRHSAVA-PREGCLIL 78


                 .
gi 446349782 174 F 174
Cdd:cd02237   79 V 79
cupin_KdgF cd02238
pectin degradation protein KdgF and related proteins, cupin domain; This family includes ...
 125-160 6.89e-04

pectin degradation protein KdgF and related proteins, cupin domain; This family includes bacterial and archaeal pectin degradation protein KdgF that catalyzes the linearization of unsaturated uronates from both pectin and alginate, which are polysaccharides found in the cell walls of plants and brown algae, respectively, and represent an important source of carbon. These polysaccharides, mostly consisting of chains of uronates, can be metabolized by bacteria through a pathway of enzymatic steps to the key metabolite 2-keto-3-deoxygluconate (KDG). Pectin degradation is used by many plant-pathogenic bacteria during infection, and also, pectin and alginate can both represent abundant sources of carbohydrate for the production of biofuels. These proteins belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.


Pssm-ID: 380366 [Multi-domain]  Cd Length: 104  Bit Score: 37.45  E-value: 6.89e-04
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 446349782 125 EELAFVLDGKITLYLNEEEYVLETGDSVKIPAYLKH 160
Cdd:cd02238   48 EQIGYVLSGRFEFTIGGETRILKPGDSYYIPPNVPH 83
cupin_HP0902-like cd02230
Helicobacter pylori HP0902 and related proteins, cupin domain; This family includes ...
 121-160 1.13e-03

Helicobacter pylori HP0902 and related proteins, cupin domain; This family includes prokaryotic and archaeal proteins homologous to HP0902, a functionally uncharacterized protein from Helicobacter pylori and Spy1581, a protein of unknown function from Streptococcus pyogenes. These proteins demonstrate all-beta cupin folds that cannot bind metal ions due to the absence of a metal-binding histidine that is conserved in many metallo-cupins. HP0902 is able to bind bacterial endotoxin lipopolysaccharides (LPS) through its surface-exposed loops, where metal-binding sites are usually found in other metallo-cupins, and thus may have a putative role in H. pylori pathogenicity.


Pssm-ID: 380358 [Multi-domain]  Cd Length: 83  Bit Score: 36.33  E-value: 1.13e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 446349782 121 EHK--GEELAFVLDGKITLYLNEEEYVLETGDSVKIPAYLKH 160
Cdd:cd02230   26 EHTapGDATVQVLEGEAEFTIGGETVTLKAGELIVMPANVPH 67
cupin_BacB_C cd10547
Bacillus subtilis bacilysin and related proteins, C-terminal cupin domain; This model ...
 104-173 1.68e-03

Bacillus subtilis bacilysin and related proteins, C-terminal cupin domain; This model represents the C-terminal domain of bacilysin (BacB, also known as AerE in Microcystis aeruginosa), a non-ribosomally synthesized dipeptide antibiotic that is produced and excreted by certain strains of Bacillus subtilis. Bacilysin 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. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.


Pssm-ID: 380415 [Multi-domain]  Cd Length: 92  Bit Score: 36.09  E-value: 1.68e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446349782 104 TAIMTVPPNTASSENvlEHKGEELAFVLDGKITLYLNEEEYVLETGDSVKIPAYLKHKWVNHFEKNAIVL 173
Cdd:cd10547   21 IMISQIPPGGKMPLH--QHRGEQIGIILNGKYDMTVGGEEQELGYGKIYYAPPNVSHSGYNDSDETATLI 88
cupin_RemF-like cd06979
Streptomyces resistomycificus RemF cyclase and related proteins, cupin domain; RemF cyclase is ...
 95-178 1.71e-03

Streptomyces resistomycificus RemF cyclase and related proteins, cupin domain; RemF cyclase is a manganese-containing polyketide cyclase present in bacteria that is involved in the biosynthesis of resistomycin, the aromatic pentacyclic metabolite in Streptomyces resistomycificus. Structure of this enzyme shows a cupin fold with a conserved "jelly roll-like" beta-barrel fold that forms a homodimer. It contains an unusual octahedral zinc-binding site in a large hydrophobic pocket that may represent the active site. The zinc ion, coordinated to four histidine side chains and two water molecules, could act as a Lewis acid in the aldol condensation reaction catalyzed by RemF, reminiscent of class II aldolases.


Pssm-ID: 380384 [Multi-domain]  Cd Length: 93  Bit Score: 36.29  E-value: 1.71e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446349782  95 SPDFTGN-LATAIMTVPPNTASSENVLEHKGEELAFVLDGKITLYLNEEEYVLETGDSVKIPAYLKHKWVNHFEKNAIVL 173
Cdd:cd06979    9 TKDGTADrFDLFEFEVSPNAGMPPPHYHEDWEETIYGLEGSVTLTLPGKTVEVGPGDSIFIPRGEVHGFVNRSGGPTCRL 88


                 ....*
gi 446349782 174 FSVTP 178
Cdd:cd06979   89 CVLAP 93
cupin_YP766765-like cd20299
Rhizobium leguminosarum YP_766765.1 and related proteins, cupin domain; This family includes ...
 125-156 2.71e-03

Rhizobium leguminosarum YP_766765.1 and related proteins, cupin domain; This family includes mostly bacterial proteins homologous to Rhizobium leguminosarum YP_766765.1, a protein of unknown function. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380433 [Multi-domain]  Cd Length: 90  Bit Score: 35.34  E-value: 2.71e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 446349782 125 EELAFVLDGKITLYLNEEEYVLETGDSVKIPA 156
Cdd:cd20299   38 EKVYVVLEGELTVTTDGEEVVLGPGDSCYIPP 69
cupin_DddK cd06988
Dimethylsulfoniopropionate lyase DddK and related proteins, cupin domain; This family includes ...
 108-164 5.25e-03

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: 34.52  E-value: 5.25e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446349782 108 TVPPNTASSENVleHKGEELAFVLDGKITLYLNEEEYVLETGDSVKIPAYLKHKWVN 164
Cdd:cd06988    8 VVRPGTTSTPHS--HHEYEIFIVISGKGIVVVDGEREPVKAGDVVYIPPGTEHYVKN 62
TIGR00270 TIGR00270
TIGR00270 family protein; [Hypothetical proteins, Conserved]
 5-74 9.39e-03

TIGR00270 family protein; [Hypothetical proteins, Conserved]


Pssm-ID: 129371 [Multi-domain]  Cd Length: 154  Bit Score: 35.27  E-value: 9.39e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446349782    5 DIGKKIEKQRKEKGLTSKELAKMADITPSMLSQIERGSANPSIQTLKVLAKALDVPtfsfLLEDTNTDDL 74
Cdd:TIGR00270  69 DYGIIIRREREKRGWSQEQLAKKIQEKESLIKKIENAEIEPEPKVVEKLEKLLKIK----LREQVPEIKI 134
 
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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