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Conserved domains on  [gi|84379808|gb|EAP96659|]
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DNA-binding protein [Vibrio splendidus 12B01]

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];
1-82 9.77e-20

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 78.89  E-value: 9.77e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84379808   1 MQTEIK-VGVNLKRLRQEKGWSLDKTAKETGVSKAMLGQIERGESSPTVAKLWQIASGFEVSLSSFIAASSNSELTSLFR 79
Cdd:COG1396   1 MSTLKKaLGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELPEALLS 80


                ...
gi 84379808  80 DAN 82
Cdd:COG1396  81 EEE 83
cupin_XRE_C cd02209
XRE (Xenobiotic Response Element) family transcriptional regulators, C-terminal cupin domain; ...
 92-182 1.59e-19

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: 78.70  E-value: 1.59e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84379808  92 GFFVSLLFPFEEALGFEIFELTLAP-DYQHESAPHnaGVTEHILCISGEMEVMFDGEWHTLRAGQAVRFNANQNHGYKNI 170
Cdd:cd02209   1 GYTYELLSPGLPGRKMEPFLVTLPPgGSGGEPYSH--EGEEFGYVLEGELELTVGGETYVLEAGDSIYFDSDVPHRYRNP 78

                        90
                ....*....|..
gi 84379808 171 GEGNVVFHNVIH 182
Cdd:cd02209  79 GDEPARVLWVIT 90
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-82 9.77e-20

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 78.89  E-value: 9.77e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84379808   1 MQTEIK-VGVNLKRLRQEKGWSLDKTAKETGVSKAMLGQIERGESSPTVAKLWQIASGFEVSLSSFIAASSNSELTSLFR 79
Cdd:COG1396   1 MSTLKKaLGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELPEALLS 80


                ...
gi 84379808  80 DAN 82
Cdd:COG1396  81 EEE 83
cupin_XRE_C cd02209
XRE (Xenobiotic Response Element) family transcriptional regulators, C-terminal cupin domain; ...
 92-182 1.59e-19

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: 78.70  E-value: 1.59e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84379808  92 GFFVSLLFPFEEALGFEIFELTLAP-DYQHESAPHnaGVTEHILCISGEMEVMFDGEWHTLRAGQAVRFNANQNHGYKNI 170
Cdd:cd02209   1 GYTYELLSPGLPGRKMEPFLVTLPPgGSGGEPYSH--EGEEFGYVLEGELELTVGGETYVLEAGDSIYFDSDVPHRYRNP 78

                        90
                ....*....|..
gi 84379808 171 GEGNVVFHNVIH 182
Cdd:cd02209  79 GDEPARVLWVIT 90
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 8-65 5.89e-15

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: 66.04  E-value: 5.89e-15
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 84379808   8 GVNLKRLRQEKGWSLDKTAKETGVSKAMLGQIERGESSPTVAKLWQIASGFEVSLSSF 65
Cdd:cd00093   1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
92-184 1.01e-14

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


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 66.41  E-value: 1.01e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84379808  92 GFFVSLLFPFEEalGFEIFELTLAPDyqHESAPHNAGVTEHILCISGEMEVMFDGEWHTLRAGQAVRFNANQNHGYKNIG 171
Cdd:COG1917  10 GVSVRVLADGED--ELEVVRVTFEPG--ARTPWHSHPGEELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFRNLG 85

                        90
                ....*....|...
gi 84379808 172 EGNVVFHnVIHYP 184
Cdd:COG1917  86 DEPAVLL-VVFSP 97
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
10-65 7.24e-14

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 62.92  E-value: 7.24e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 84379808     10 NLKRLRQEKGWSLDKTAKETGVSKAMLGQIERGESSPTVAKLWQIASGFEVSLSSF 65
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 11-65 4.36e-13

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: 61.02  E-value: 4.36e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 84379808    11 LKRLRQEKGWSLDKTAKETGVSKAMLGQIERGESSPTVAKLWQIASGFEVSLSSF 65
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 110-181 1.55e-11

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: 57.27  E-value: 1.55e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 84379808   110 FELTLAPDYQHESAPHnAGVTEHILCISGEMEVMFDGEWHTLRAGQAVRFNANQNHGYKNIGEGNVVFHNVI 181
Cdd:pfam07883   1 GLVTLPPGESSPPHRH-PGEDEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPHRFRNTGDEPARLLDVY 71
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
4-169 8.06e-06

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 44.40  E-value: 8.06e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84379808    4 EIKVGVNLKRLRQEKGWSLDKTAKETGVSKAMLGQIERGESSPTVAKLWQIASGFEVSLSSFIAASSNSELTSLFRDANE 83
Cdd:PRK09943   5 GLAPGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEFFSEPEKPDEPQVVINQDD 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84379808   84 LrheeYNIGF-FVSLLFPF----EEALGFeIFElTLAPDYQHESAPHNAGvtEHI-LCISGEMEVMFDGEWHTLRAGQAV 157
Cdd:PRK09943  85 L----IEMGSqGVSMKLVHngnpNRTLAM-IFE-TYQPGTTTGERIKHQG--EEIgTVLEGEIVLTINGQDYHLVAGQSY 156

                        170
                 ....*....|..
gi 84379808  158 RFNANQNHGYKN 169
Cdd:PRK09943 157 AINTGIPHSFSN 168
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-82 9.77e-20

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 78.89  E-value: 9.77e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84379808   1 MQTEIK-VGVNLKRLRQEKGWSLDKTAKETGVSKAMLGQIERGESSPTVAKLWQIASGFEVSLSSFIAASSNSELTSLFR 79
Cdd:COG1396   1 MSTLKKaLGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELPEALLS 80


                ...
gi 84379808  80 DAN 82
Cdd:COG1396  81 EEE 83
cupin_XRE_C cd02209
XRE (Xenobiotic Response Element) family transcriptional regulators, C-terminal cupin domain; ...
 92-182 1.59e-19

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: 78.70  E-value: 1.59e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84379808  92 GFFVSLLFPFEEALGFEIFELTLAP-DYQHESAPHnaGVTEHILCISGEMEVMFDGEWHTLRAGQAVRFNANQNHGYKNI 170
Cdd:cd02209   1 GYTYELLSPGLPGRKMEPFLVTLPPgGSGGEPYSH--EGEEFGYVLEGELELTVGGETYVLEAGDSIYFDSDVPHRYRNP 78

                        90
                ....*....|..
gi 84379808 171 GEGNVVFHNVIH 182
Cdd:cd02209  79 GDEPARVLWVIT 90
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 8-65 5.89e-15

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: 66.04  E-value: 5.89e-15
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 84379808   8 GVNLKRLRQEKGWSLDKTAKETGVSKAMLGQIERGESSPTVAKLWQIASGFEVSLSSF 65
Cdd:cd00093   1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
92-184 1.01e-14

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


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 66.41  E-value: 1.01e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84379808  92 GFFVSLLFPFEEalGFEIFELTLAPDyqHESAPHNAGVTEHILCISGEMEVMFDGEWHTLRAGQAVRFNANQNHGYKNIG 171
Cdd:COG1917  10 GVSVRVLADGED--ELEVVRVTFEPG--ARTPWHSHPGEELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFRNLG 85

                        90
                ....*....|...
gi 84379808 172 EGNVVFHnVIHYP 184
Cdd:COG1917  86 DEPAVLL-VVFSP 97
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
10-65 7.24e-14

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 62.92  E-value: 7.24e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 84379808     10 NLKRLRQEKGWSLDKTAKETGVSKAMLGQIERGESSPTVAKLWQIASGFEVSLSSF 65
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 11-65 4.36e-13

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: 61.02  E-value: 4.36e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 84379808    11 LKRLRQEKGWSLDKTAKETGVSKAMLGQIERGESSPTVAKLWQIASGFEVSLSSF 65
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
6-66 1.05e-12

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 60.25  E-value: 1.05e-12
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 84379808   6 KVGVNLKRLRQEKGWSLDKTAKETGVSKAMLGQIERGESSPTVAKLWQIASGFEVSLSSFI 66
Cdd:COG1476   4 KLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELF 64
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 7-63 1.15e-11

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: 57.64  E-value: 1.15e-11
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 84379808   7 VGVNLKRLRQEKGWSLDKTAKETGVSKAMLGQIERGESSPTVAKLWQIASGFEVSLS 63
Cdd:COG1813  13 YGERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISLA 69
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 110-181 1.55e-11

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: 57.27  E-value: 1.55e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 84379808   110 FELTLAPDYQHESAPHnAGVTEHILCISGEMEVMFDGEWHTLRAGQAVRFNANQNHGYKNIGEGNVVFHNVI 181
Cdd:pfam07883   1 GLVTLPPGESSPPHRH-PGEDEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPHRFRNTGDEPARLLDVY 71
ManC COG0662
Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism];
106-180 3.44e-11

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


Pssm-ID: 440426 [Multi-domain]  Cd Length: 114  Bit Score: 57.46  E-value: 3.44e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 84379808 106 GFEIFELTLAPDyqHESAPH-NAGVTEHILCISGEMEVMFDGEWHTLRAGQAVRFNANQNHGYKNIGEGNVVFHNV 180
Cdd:COG0662  26 RLSVKRITVPPG--AELSLHvHPHRDEFFYVLEGTGEVTIGDEEVELKAGDSVYIPAGVPHRLRNPGDEPLELLEV 99
COG3837 COG3837
Uncharacterized conserved protein, cupin superfamily [Function unknown];
80-184 7.09e-11

Uncharacterized conserved protein, cupin superfamily [Function unknown];


Pssm-ID: 443048 [Multi-domain]  Cd Length: 115  Bit Score: 56.95  E-value: 7.09e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84379808  80 DANELRHEEYniGFFVSLLFPFEEALGFEIFELTLAPDyqHESAP---HNAGvTEHILCISGEMEVMFDGEWHTLRAGQA 156
Cdd:COG3837   3 NLDDLPGPEA--GRRYRRLGDALGLTRLGVNLITLPPG--ASSSPyhaHSAE-EEFVYVLEGELTLRIGGEEYVLEPGDS 77

                        90       100       110
                ....*....|....*....|....*....|.
gi 84379808 157 VRFNANQNHGYKNIGEGNVVFHNVI---HYP 184
Cdd:COG3837  78 VGFPAGVPHRLRNRGDEPARYLVVGtraPYP 108
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 2-66 9.45e-09

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: 50.40  E-value: 9.45e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 84379808   2 QTEIKVGVNLKRLRQEKGWSLDKTAKETGVSKAMLGQIERGESSPTVAKLWQIASGFEVSLSSFI 66
Cdd:COG3620  13 SPDDTLGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVL 77
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 8-67 3.43e-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: 48.44  E-value: 3.43e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 84379808     8 GVNLKRLRQEKGWSLDKTAKETGVSKAMLGQIERGESSPTVAKLWQIASGFEVSLSSFIA 67
Cdd:pfam12844   1 GERLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLLQ 60
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 2-43 1.29e-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: 44.02  E-value: 1.29e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 84379808   2 QTEIKVGVNLKRLRQEKGWSLDKTAKETGVSKAMLGQIERGE 43
Cdd:COG1426   1 EALETIGELLRQAREAKGLSLEDVAERTKISVSYLEAIEEGD 42
cupin_TM1459-like cd02222
Thermotoga maritima TM1459 and related proteins, cupin domain; This family includes bacterial ...
 97-177 3.49e-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: 43.59  E-value: 3.49e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84379808  97 LLFPFEEALGFEIFELTLAPDYQ--HESAPHnagvtEH-ILCISGEMEVMFDGEWHTLRAGQAVRFNANQNHGYKNIGEG 173
Cdd:cd02222   7 LIGPEDGAPNFAMRYFEIEPGGHtpLHTHPW-----EHeVYVLRGKGVVVIGGEEYPVKPGDVVYIPPNEPHQFRNTGDE 81


                ....
gi 84379808 174 NVVF 177
Cdd:cd02222  82 PLGF 85
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 11-61 6.72e-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: 42.13  E-value: 6.72e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 84379808    11 LKRLRQEKGWSLDKTAKETGVSKAMLGQIERGE-SSPTVAKLWQIASGFEVS 61
Cdd:pfam13560   6 LRRLRERAGLSQEALARRLGVSRSTLSRLETGRrGRPSPAVVERLARALGVD 57
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
4-169 8.06e-06

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 44.40  E-value: 8.06e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84379808    4 EIKVGVNLKRLRQEKGWSLDKTAKETGVSKAMLGQIERGESSPTVAKLWQIASGFEVSLSSFIAASSNSELTSLFRDANE 83
Cdd:PRK09943   5 GLAPGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEFFSEPEKPDEPQVVINQDD 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84379808   84 LrheeYNIGF-FVSLLFPF----EEALGFeIFElTLAPDYQHESAPHNAGvtEHI-LCISGEMEVMFDGEWHTLRAGQAV 157
Cdd:PRK09943  85 L----IEMGSqGVSMKLVHngnpNRTLAM-IFE-TYQPGTTTGERIKHQG--EEIgTVLEGEIVLTINGQDYHLVAGQSY 156

                        170
                 ....*....|..
gi 84379808  158 RFNANQNHGYKN 169
Cdd:PRK09943 157 AINTGIPHSFSN 168
cupin_RmlC-like cd02208
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 109-181 1.53e-05

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: 41.31  E-value: 1.53e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 84379808 109 IFELTLAPDyqHESAPH-NAGVTEHILCISGEMEVMFD-GEWHTLRAGQAVRFNANQNHGYKNIGEGNVVFHNVI 181
Cdd:cd02208   1 ISVVTLPPG--TSSPPHwHPEQDEIFYVLSGEGELTLDdGETVELKAGDIVLIPPGVPHSFVNTSDEPAVFLVVS 73
cupin_TcmJ-like cd06991
TcmJ monooxygenase and related proteins, cupin domain; This family includes TcmJ, a subunit of ...
 131-178 4.00e-05

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: 41.13  E-value: 4.00e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 84379808 131 EHILCISGEMEVMFDGEWHTLRAGQAVRFNANQNHGYKNIG--EGNVVFH 178
Cdd:cd06991  42 EFLYVVRGRLVVRVDGEPVVLEAGEALLVPRGVRHRLENAGdePARLVFH 91
cupin_SPO2919-like cd02224
Silicibacter pomeroyi SPO2919 and related proteins, uncharacterized sugar phosphate isomerase ...
 131-184 1.34e-04

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: 39.39  E-value: 1.34e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 84379808 131 EHILCISGEMEVMFDGEWHTLRAGQAVRFNANQN--HGYKNIGEGNVVF--------HNVIHYP 184
Cdd:cd02224  41 EFVYVLSGEGTLRLDGEEVLPRPGDFVGFPAGTGvaHQLINRSDEPLVYlvvgtrlpDDVCTYP 104
PRK04140 PRK04140
transcriptional regulator;
11-116 1.79e-04

transcriptional regulator;


Pssm-ID: 235224 [Multi-domain]  Cd Length: 317  Bit Score: 41.00  E-value: 1.79e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 84379808   11 LKRLRQEKGWSLDKTAKETGVSKAMLGQIERGESSPTV---AKLWQIasgFEVSLSSFIaassnseltSLFR--DANELR 85
Cdd:PRK04140 131 LREAREELGLSLGELASELGVSRRTISKYENGGMNASIevaIKLEEI---LDVPLTKPI---------DILEkvRDDEVT 198

                         90       100       110
                 ....*....|....*....|....*....|.
gi 84379808   86 HEEYNIGFFVSLLFPFEEALGFEIFELTLAP 116
Cdd:PRK04140 199 PEDPEEDPFEKEILNVLTRLGFDVLPTKKAP 229
cupin_DddK cd06988
Dimethylsulfoniopropionate lyase DddK and related proteins, cupin domain; This family includes ...
 121-177 2.05e-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: 38.37  E-value: 2.05e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 84379808 121 ESAPHNAGVTEHILCISGEMEVMFDGEWHTLRAGQAVRFNANQNHGYKNIGEGNVVF 177
Cdd:cd06988  14 TSTPHSHHEYEIFIVISGKGIVVVDGEREPVKAGDVVYIPPGTEHYVKNDGDEDFEF 70
PRK08154 PRK08154
anaerobic benzoate catabolism transcriptional regulator; Reviewed
 7-80 2.93e-04

anaerobic benzoate catabolism transcriptional regulator; Reviewed


Pssm-ID: 236167 [Multi-domain]  Cd Length: 309  Bit Score: 40.32  E-value: 2.93e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 84379808    7 VGVNLKRLRQEKGWSLDKTAKETGVSKAMLGQIERGESSPTVAKLWQIASGFEVSLSSFIAA--SSNSELTsLFRD 80
Cdd:PRK08154  29 LGERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCSLADLLGDvdTSSPDWL-LIRE 103
PRK09726 PRK09726
type II toxin-antitoxin system antitoxin HipB;
11-68 3.73e-04

type II toxin-antitoxin system antitoxin HipB;


Pssm-ID: 182049  Cd Length: 88  Bit Score: 38.04  E-value: 3.73e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 84379808   11 LKRLRQEKGWSLDKTAKETGVSKAMLGQIERGESSPTVAKLWQIASGFEVSLSSFIAA 68
Cdd:PRK09726  17 MKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMTLCDAK 74
cupin_HP0902-like cd02230
Helicobacter pylori HP0902 and related proteins, cupin domain; This family includes ...
 122-166 3.96e-04

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: 37.87  E-value: 3.96e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 84379808 122 SAPHNAGVTehilCISGEMEVMFDGEWHTLRAGQAVRFNANQNHG 166
Cdd:cd02230  28 TAPGDATVQ----VLEGEAEFTIGGETVTLKAGELIVMPANVPHA 68
COG1395 COG1395
Predicted transcriptional regulator [Transcription];
11-48 6.43e-04

Predicted transcriptional regulator [Transcription];


Pssm-ID: 441005 [Multi-domain]  Cd Length: 313  Bit Score: 39.43  E-value: 6.43e-04
                        10        20        30
                ....*....|....*....|....*....|....*...
gi 84379808  11 LKRLRQEKGWSLDKTAKETGVSKAMLGQIERGESSPTV 48
Cdd:COG1395 132 LRELREERGLSLGELASELGVSRRTISKYERGEMDASI 169
HTH_25 pfam13413
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 11-45 6.86e-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: 6.86e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 84379808    11 LKRLRQEKGWSLDKTAKETGVSKAMLGQIERGESS 45
Cdd:pfam13413   2 LRAAREARGLSLEDVAERTKIRPRYLEALEEDDFD 36
cupin_KdgF cd02238
pectin degradation protein KdgF and related proteins, cupin domain; This family includes ...
 135-176 7.79e-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: 7.79e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 84379808 135 CISGEMEVMFDGEWHTLRAGQAVRFNANQNHGYKNIGEGNVV 176
Cdd:cd02238  53 VLSGRFEFTIGGETRILKPGDSYYIPPNVPHGAEALEDSVLL 94
PHA01976 PHA01976
helix-turn-helix protein
 9-70 1.56e-03

helix-turn-helix protein


Pssm-ID: 177330 [Multi-domain]  Cd Length: 67  Bit Score: 35.70  E-value: 1.56e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 84379808    9 VNLKRLRQEKGWSLDKTAKETGVSKAMLGQIERGESSPTVAKLWQIASGFEVSLSSFIAASS 70
Cdd:PHA01976   5 IQLIKARNARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGVTLDWLCGRCG 66
cupin_MJ1618 cd02214
Methanocaldococcus jannaschii MJ1618 and related proteins, cupin domain; This family includes ...
 121-177 1.75e-03

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: 36.34  E-value: 1.75e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 84379808 121 ESAPHN-AGVTE--HILCISGEMEVmfDGEWHTLRAGQAVRFNANQNHGYKNIGEGNVVF 177
Cdd:cd02214  31 STLPHRlKGSEEvyYILEGEGTMEI--DGEPREVGPGDAVLIPPGAVQRIENTGEEDLVF 88
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
1-60 2.44e-03

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 34.91  E-value: 2.44e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 84379808   1 MQTEIKVGVNLKRLRQEKGWSLDKTAKETGVSKAMLGQIERGESSPT---VAKLWQIASGFEV 60
Cdd:COG2944   1 MTKKPLTPEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSgaaLKLLRLLEKHPEL 63
cupin_dsy2733 cd06983
Desulfitobacterium hafniense dsy2733 and related proteins, cupin domain; This family includes ...
 133-166 2.49e-03

Desulfitobacterium hafniense dsy2733 and related proteins, cupin domain; This family includes bacterial proteins homologous to dsy2733, a Desulfitobacterium hafniense 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: 380388 [Multi-domain]  Cd Length: 81  Bit Score: 35.30  E-value: 2.49e-03
                        10        20        30
                ....*....|....*....|....*....|....
gi 84379808 133 ILCISGEMEVMFDGEWHTLRAGQAVRFNANQNHG 166
Cdd:cd06983  34 YYVLEGEAEITIGDEKHRLKAGDVLAVPAGVLHA 67
AraC_binding pfam02311
AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization ...
 110-180 4.13e-03

AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization domain of the bacterial gene regulatory protein AraC. The domain is found in conjunction with the helix-turn-helix (HTH) DNA-binding motif pfam00165. This domain is distantly related to the Cupin domain pfam00190.


Pssm-ID: 396749 [Multi-domain]  Cd Length: 134  Bit Score: 35.87  E-value: 4.13e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 84379808   110 FELTLAPDYQHESAPHNAGVTEHILCISGEMEVMFDGEWHTLRAGQAVRFNANQNHGYKNIGEGNVVFHNV 180
Cdd:pfam02311   4 LEGIEARYPGHSFPPHVHDFYVIGYIERGVGRFRLNGRTYHLGPGDLFLLPPGEPHDYEPESEDGWRYRWL 74
 
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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