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Conserved domains on  [gi|488971937|ref|WP_002882865|]
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MULTISPECIES: helix-turn-helix domain-containing protein [Klebsiella]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 18527266)

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:0003677
PubMed:  10473770|15808743|10556324

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];
1-70 1.47e-17

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 73.11  E-value: 1.47e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971937   1 MTQPISVIAKSLVRERARTGLSLAEVARRAGIAKSTLSQLESGNGNPSLETLWSLCVALDIPFARLLEPQ 70
Cdd:COG1396    1 MSTLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGA 70
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
101-178 6.15e-09

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


:

Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 51.00  E-value: 6.15e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488971937 101 PPGARRDIYLLLTQPGADRISHPHPpgSVEHIIVTQGRARVGLTSAPEELGEGDYICYPADQEHVFQALEPDTQALLI 178
Cdd:COG1917   18 DGEDELEVVRVTFEPGARTPWHSHP--GEELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFRNLGDEPAVLLV 93
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-70 1.47e-17

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 73.11  E-value: 1.47e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971937   1 MTQPISVIAKSLVRERARTGLSLAEVARRAGIAKSTLSQLESGNGNPSLETLWSLCVALDIPFARLLEPQ 70
Cdd:COG1396    1 MSTLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGA 70
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 9-66 5.17e-13

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: 60.64  E-value: 5.17e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 488971937   9 AKSLVRERARTGLSLAEVARRAGIAKSTLSQLESGNGNPSLETLWSLCVALDIPFARL 66
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
12-66 1.79e-11

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 56.76  E-value: 1.79e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 488971937    12 LVRERARTGLSLAEVARRAGIAKSTLSQLESGNGNPSLETLWSLCVALDIPFARL 66
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 14-66 2.28e-10

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: 53.70  E-value: 2.28e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 488971937   14 RERARTGLSLAEVARRAGIAKSTLSQLESGNGNPSLETLWSLCVALDIPFARL 66
Cdd:pfam01381   3 ELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
101-178 6.15e-09

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


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 51.00  E-value: 6.15e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488971937 101 PPGARRDIYLLLTQPGADRISHPHPpgSVEHIIVTQGRARVGLTSAPEELGEGDYICYPADQEHVFQALEPDTQALLI 178
Cdd:COG1917   18 DGEDELEVVRVTFEPGARTPWHSHP--GEELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFRNLGDEPAVLLV 93
PRK13890 PRK13890
conjugal transfer protein TrbA; Provisional
 12-68 2.76e-08

conjugal transfer protein TrbA; Provisional


Pssm-ID: 237547 [Multi-domain]  Cd Length: 120  Bit Score: 49.75  E-value: 2.76e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 488971937  12 LVRERartGLSLAEVARRAGIAKSTLSQLESGNGNPSLETLWSLCVALDIPFARLLE 68
Cdd:PRK13890  13 LLDER---HMTKKELSERSGVSISFLSDLTTGKANPSLKVMEAIADALETPLPLLLE 66
cupin_XRE_C cd02209
XRE (Xenobiotic Response Element) family transcriptional regulators, C-terminal cupin domain; ...
 91-178 4.88e-07

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: 45.58  E-value: 4.88e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971937  91 NYQAILLAACPPGARRDIYLLLTQPGADRI-SHPHPpgSVEHIIVTQGRARVGLTSAPEELGEGDYICYPADQEHVFQAL 169
Cdd:cd02209    1 GYTYELLSPGLPGRKMEPFLVTLPPGGSGGePYSHE--GEEFGYVLEGELELTVGGETYVLEAGDSIYFDSDVPHRYRNP 78

                         90
                 ....*....|
gi 488971937 170 -EPDTQALLI 178
Cdd:cd02209   79 gDEPARVLWV 88
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 114-166 2.05e-06

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: 43.40  E-value: 2.05e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 488971937  114 QPGADRISHPHPpGSVEHIIVTQGRARVGLTSAPEELGEGDYICYPADQEHVF 166
Cdd:pfam07883   6 PPGESSPPHRHP-GEDEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPHRF 57
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-70 1.47e-17

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 73.11  E-value: 1.47e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971937   1 MTQPISVIAKSLVRERARTGLSLAEVARRAGIAKSTLSQLESGNGNPSLETLWSLCVALDIPFARLLEPQ 70
Cdd:COG1396    1 MSTLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGA 70
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 9-66 5.17e-13

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: 60.64  E-value: 5.17e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 488971937   9 AKSLVRERARTGLSLAEVARRAGIAKSTLSQLESGNGNPSLETLWSLCVALDIPFARL 66
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
8-70 9.14e-13

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 60.25  E-value: 9.14e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488971937   8 IAKSLVRERARTGLSLAEVARRAGIAKSTLSQLESGNGNPSLETLWSLCVALDIPFARLLEPQ 70
Cdd:COG1476    5 LGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLE 67
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
12-66 1.79e-11

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 56.76  E-value: 1.79e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 488971937    12 LVRERARTGLSLAEVARRAGIAKSTLSQLESGNGNPSLETLWSLCVALDIPFARL 66
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 14-66 2.28e-10

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: 53.70  E-value: 2.28e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 488971937   14 RERARTGLSLAEVARRAGIAKSTLSQLESGNGNPSLETLWSLCVALDIPFARL 66
Cdd:pfam01381   3 ELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
101-178 6.15e-09

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


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 51.00  E-value: 6.15e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488971937 101 PPGARRDIYLLLTQPGADRISHPHPpgSVEHIIVTQGRARVGLTSAPEELGEGDYICYPADQEHVFQALEPDTQALLI 178
Cdd:COG1917   18 DGEDELEVVRVTFEPGARTPWHSHP--GEELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFRNLGDEPAVLLV 93
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 8-67 1.05e-08

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: 1.05e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971937   8 IAKSLVRERARTGLSLAEVARRAGIAKSTLSQLESGNGNPSLETLWSLCVALDIPFARLL 67
Cdd:COG3620   18 LGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVL 77
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 8-64 1.96e-08

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: 48.78  E-value: 1.96e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 488971937   8 IAKSLVRERARTGLSLAEVARRAGIAKSTLSQLESGNGNPSLETLWSLCVALDIPFA 64
Cdd:COG1813   13 YGERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISLA 69
PRK13890 PRK13890
conjugal transfer protein TrbA; Provisional
 12-68 2.76e-08

conjugal transfer protein TrbA; Provisional


Pssm-ID: 237547 [Multi-domain]  Cd Length: 120  Bit Score: 49.75  E-value: 2.76e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 488971937  12 LVRERartGLSLAEVARRAGIAKSTLSQLESGNGNPSLETLWSLCVALDIPFARLLE 68
Cdd:PRK13890  13 LLDER---HMTKKELSERSGVSISFLSDLTTGKANPSLKVMEAIADALETPLPLLLE 66
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
17-68 1.09e-07

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 47.06  E-value: 1.09e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 488971937  17 ARTGLSLAEVARRAGIAKSTLSQLESGNG-NPSLETLWSLCVALDIPFARLLE 68
Cdd:COG3655   11 AERGMTKKELAEATGISRATLSRLKNGKAkAVRLDTLEKICKALDCQPGDLLE 63
cupin_XRE_C cd02209
XRE (Xenobiotic Response Element) family transcriptional regulators, C-terminal cupin domain; ...
 91-178 4.88e-07

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: 45.58  E-value: 4.88e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971937  91 NYQAILLAACPPGARRDIYLLLTQPGADRI-SHPHPpgSVEHIIVTQGRARVGLTSAPEELGEGDYICYPADQEHVFQAL 169
Cdd:cd02209    1 GYTYELLSPGLPGRKMEPFLVTLPPGGSGGePYSHE--GEEFGYVLEGELELTVGGETYVLEAGDSIYFDSDVPHRYRNP 78

                         90
                 ....*....|
gi 488971937 170 -EPDTQALLI 178
Cdd:cd02209   79 gDEPARVLWV 88
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 14-62 6.23e-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: 6.23e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 488971937   14 RERARTGLSLAEVARRAGIAKSTLSQLESG-NGNPSLETLWSLCVALDIP 62
Cdd:pfam13560   8 RLRERAGLSQEALARRLGVSRSTLSRLETGrRGRPSPAVVERLARALGVD 57
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 20-70 7.81e-07

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: 44.45  E-value: 7.81e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 488971937   20 GLSLAEVARRAGIAKSTLSQLESGN-GNPSLETLWSLCVALDIPFARLLEPQ 70
Cdd:pfam13443  10 GISKSDLARATGISRATLSRLRKGKpKRVSLDTLDKICDALGCQPGDLLEYV 61
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 114-166 2.05e-06

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: 43.40  E-value: 2.05e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 488971937  114 QPGADRISHPHPpGSVEHIIVTQGRARVGLTSAPEELGEGDYICYPADQEHVF 166
Cdd:pfam07883   6 PPGESSPPHRHP-GEDEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPHRF 57
PRK08154 PRK08154
anaerobic benzoate catabolism transcriptional regulator; Reviewed
 13-69 3.37e-06

anaerobic benzoate catabolism transcriptional regulator; Reviewed


Pssm-ID: 236167 [Multi-domain]  Cd Length: 309  Bit Score: 46.10  E-value: 3.37e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 488971937  13 VRE-RARTGLSLAEVARRAGIAKSTLSQLESGNGNPSLETLWSLCVALDIPFARLLEP 69
Cdd:PRK08154  33 VRTlRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCSLADLLGD 90
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 20-67 5.53e-06

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: 42.28  E-value: 5.53e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 488971937   20 GLSLAEVARRAGIAKSTLSQLESGNGNPSLETLWSLCVALDIPFARLL 67
Cdd:pfam12844  12 GLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLL 59
ManC COG0662
Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism];
114-177 1.07e-05

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


Pssm-ID: 440426 [Multi-domain]  Cd Length: 114  Bit Score: 42.82  E-value: 1.07e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488971937 114 QPGADRISHPHPPGSvEHIIVTQGRARVGLTSAPEELGEGDYICYPADQEHVFQALEPDTQALL 177
Cdd:COG0662   35 PPGAELSLHVHPHRD-EFFYVLEGTGEVTIGDEEVELKAGDSVYIPAGVPHRLRNPGDEPLELL 97
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 12-67 7.50e-05

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: 39.40  E-value: 7.50e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488971937  12 LVRERARTGLSLAEVARRAGIAKSTLSQLESGN------GNPSLETLWSLCVALDIPFARLL 67
Cdd:COG1426   10 LRQAREAKGLSLEDVAERTKISVSYLEAIEEGDfdalpgPVYVRGFLRSYARALGLDPEELL 71
cupin_RmlC-like cd02208
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 108-178 1.07e-04

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: 39.00  E-value: 1.07e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488971937 108 IYLLLTQPGADRISHPHPPGSvEHIIVTQGRARVGL-TSAPEELGEGDYICYPADQEHVFQALEPDTQALLI 178
Cdd:cd02208    1 ISVVTLPPGTSSPPHWHPEQD-EIFYVLSGEGELTLdDGETVELKAGDIVLIPPGVPHSFVNTSDEPAVFLV 71
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
16-62 5.21e-04

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 36.84  E-value: 5.21e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 488971937  16 RARTGLSLAEVARRAGIAKSTLSQLESGNGNPSLETLWSLCVALDIP 62
Cdd:COG2944   15 RERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGAALKLLRLLEKHP 61
COG1395 COG1395
Predicted transcriptional regulator [Transcription];
12-51 1.46e-03

Predicted transcriptional regulator [Transcription];


Pssm-ID: 441005 [Multi-domain]  Cd Length: 313  Bit Score: 38.28  E-value: 1.46e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 488971937  12 LVRERARTGLSLAEVARRAGIAKSTLSQLESGNGNPSLET 51
Cdd:COG1395  132 LRELREERGLSLGELASELGVSRRTISKYERGEMDASIEV 171
cupin_UGlyAH_N cd02211
(S)-ureidoglycine aminohydrolase and related proteins, N-terminal cupin domain; This family ...
 109-178 1.46e-03

(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: 36.73  E-value: 1.46e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488971937 109 YLLLTQPGAdRISHPHPPGSVEHII-VTQGRARVGLTSAPEELGEGDYICYPADQEHVFQALEP-DTQALLI 178
Cdd:cd02211   28 YLVEVEPGG-GSTAPEGGEGIERFLyVLEGEVELTVGGETHTLTAGGYAYLPPGTKHSLRNAGDePARLLWY 98
PRK09726 PRK09726
type II toxin-antitoxin system antitoxin HipB;
16-61 3.35e-03

type II toxin-antitoxin system antitoxin HipB;


Pssm-ID: 182049  Cd Length: 88  Bit Score: 35.34  E-value: 3.35e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 488971937  16 RARTGLSLAEVARRAGIAKSTLSQLESGNGNPSLETLWSLCVALDI 61
Cdd:PRK09726  21 RQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLEL 66
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 20-62 3.69e-03

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 35.17  E-value: 3.69e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 488971937  20 GLSLAEVARRAGIAKSTLSQLESGNGNPSLETLWSLCVALDIP 62
Cdd:COG3093   22 GLSQTELAKALGVSRQRISEILNGKRAITADTALRLARAFGTS 64
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
10-71 4.41e-03

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 36.31  E-value: 4.41e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488971937  10 KSLVRERARTGLSLAEVARRAGIAKSTLSQLESGNGNPSLETLWSLCVALDIPFARLL-------EPQV 71
Cdd:PRK09943  10 KRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEFFsepekpdEPQV 78
Cupin_1 pfam00190
Cupin; This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' ...
 104-179 5.78e-03

Cupin; This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel). This family contains 11S and 7S plant seed storage proteins, and germins. Plant seed storage proteins provide the major nitrogen source for the developing plant.


Pssm-ID: 395138  Cd Length: 151  Bit Score: 35.77  E-value: 5.78e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971937  104 ARRDIYllltqPGADRISHPHPPGSvEHIIVTQGRARVGLTSAPE-------ELGEGDYICYPADQEHVFQALEpDTQAL 176
Cdd:pfam00190  36 ARVDLA-----PGGMNPPHWHPNAT-EILYVLQGRGRVGFVVPGNgnrvfhkVLREGDVFVVPQGLPHFQYNIG-DEPAV 108


                  ...
gi 488971937  177 LIA 179
Cdd:pfam00190 109 AFV 111
cupin_TM1459-like cd02222
Thermotoga maritima TM1459 and related proteins, cupin domain; This family includes bacterial ...
 121-168 7.57e-03

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: 34.35  E-value: 7.57e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 488971937 121 SHPHppgsvEH-IIVTQGRARVGLTSAPEELGEGDYICYPADQEHVFQA 168
Cdd:cd02222   34 THPW-----EHeVYVLRGKGVVVIGGEEYPVKPGDVVYIPPNEPHQFRN 77
cupin_DddK cd06988
Dimethylsulfoniopropionate lyase DddK and related proteins, cupin domain; This family includes ...
 115-167 8.73e-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: 33.75  E-value: 8.73e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 488971937 115 PGADriSHPHPPGSVEHIIVTQGRARVGLTSAPEELGEGDYICYPADQEHVFQ 167
Cdd:cd06988   11 PGTT--STPHSHHEYEIFIVISGKGIVVVDGEREPVKAGDVVYIPPGTEHYVK 61
COG3837 COG3837
Uncharacterized conserved protein, cupin superfamily [Function unknown];
85-166 8.97e-03

Uncharacterized conserved protein, cupin superfamily [Function unknown];


Pssm-ID: 443048 [Multi-domain]  Cd Length: 115  Bit Score: 34.61  E-value: 8.97e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971937  85 VVAEQANYQAILLAACPPGARRDIYLLLTQPGAdRISHPH-PPGSVEHIIVTQGRARVGLTSAPEELGEGDYICYPADQE 163
Cdd:COG3837    7 LPGPEAGRRYRRLGDALGLTRLGVNLITLPPGA-SSSPYHaHSAEEEFVYVLEGELTLRIGGEEYVLEPGDSVGFPAGVP 85


                 ...
gi 488971937 164 HVF 166
Cdd:COG3837   86 HRL 88
cupin_DAD_ChrR cd02237
2,4'-Dihydroxyacetophenone dioxygenase (DAD) and anti-sigma factor ChrR, and similar proteins; ...
 102-179 9.36e-03

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: 33.91  E-value: 9.36e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488971937 102 PGARRDIYLLLTQPGADRISHPHPPGsvEHIIVTQGRarvgLTSAPEELGEGDYICYPADQEHVFQAlePDTQALLIA 179
Cdd:cd02237   10 PNTGLITAILRMAPGARLPDHEHVGG--EEFYVLDGA----LTDEDGTAGAGDFVREPPGSRHSAVA--PREGCLILV 79
PRK04140 PRK04140
transcriptional regulator;
12-69 9.91e-03

transcriptional regulator;


Pssm-ID: 235224 [Multi-domain]  Cd Length: 317  Bit Score: 35.60  E-value: 9.91e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488971937  12 LVRERARTGLSLAEVARRAGIAKSTLSQLESGNGNPSLETLWSLCVALDIPFAR---LLEP 69
Cdd:PRK04140 131 LREAREELGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEILDVPLTKpidILEK 191
 
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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