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Conserved domains on  [gi|1731510250|gb|QEI30709|]
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AraC family transcriptional regulator [Mediterraneibacter gnavus ATCC 29149]

Protein Classification

helix-turn-helix transcriptional regulator( domain architecture ID 11454547)

helix-turn-helix (HTH) transcriptional regulator containing an AraC family DNA-binding HTH domain controls the expression of genes with diverse biological functions including metabolism, stress response, and virulence

CATH:  1.10.10.1310
Gene Ontology:  GO:0003700|GO:0043565|GO:0006355
PubMed:  9409145|8831795|15808743|2644244
SCOP:  4000332

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
188-270 7.16e-26

helix_turn_helix, arabinose operon control protein;


:

Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 97.24  E-value: 7.16e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250  188 ITLDTLTGLTHMNKYYMVHSFTKYAGLSPIQYLNQTRLKRAQHLLKNTNYSISDIASSTGFSSQSYFTQIFRKNFNMTPV 267
Cdd:smart00342   2 LTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTPS 81


                   ...
gi 1731510250  268 KYR 270
Cdd:smart00342  82 EYR 84
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
31-276 1.54e-24

AraC-type DNA-binding domain and AraC-containing proteins [Transcription];


:

Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 99.08  E-value: 1.54e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250  31 DWKSIMHTHHFTELLFVVSGEGSFSFNQEQSPLRRGDLVIIPPYTEHTERSSQNHPLEYYVLGIDGISFLSQKDRECAQV 110
Cdd:COG2207    12 LLLALLLLLLLLLLLLILLLLALVLLLLLLALLLLLLLLLGLLGGLLLLLLLLLLLGLLLLLLLLLLGLLLLALLALLLL 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250 111 FCNFEHDPSIHELFRQMLYEIRTAQYGSQTICQHLLEILILKIIRSQQLIPVSINSIRMTKECAQIKEYLDSNYAEHITL 190
Cdd:COG2207    92 VGLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTL 171

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250 191 DTLTGLTHMNKYYMVHSFTKYAGLSPIQYLNQTRLKRAQHLLKNTNYSISDIASSTGFSSQSYFTQIFRKNFNMTPVKYR 270
Cdd:COG2207   172 EELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSEYR 251


                  ....*.
gi 1731510250 271 QEHAKN 276
Cdd:COG2207   252 KRLRAR 257
 
Name Accession Description Interval E-value
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
188-270 7.16e-26

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 97.24  E-value: 7.16e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250  188 ITLDTLTGLTHMNKYYMVHSFTKYAGLSPIQYLNQTRLKRAQHLLKNTNYSISDIASSTGFSSQSYFTQIFRKNFNMTPV 267
Cdd:smart00342   2 LTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTPS 81


                   ...
gi 1731510250  268 KYR 270
Cdd:smart00342  82 EYR 84
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
31-276 1.54e-24

AraC-type DNA-binding domain and AraC-containing proteins [Transcription];


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 99.08  E-value: 1.54e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250  31 DWKSIMHTHHFTELLFVVSGEGSFSFNQEQSPLRRGDLVIIPPYTEHTERSSQNHPLEYYVLGIDGISFLSQKDRECAQV 110
Cdd:COG2207    12 LLLALLLLLLLLLLLLILLLLALVLLLLLLALLLLLLLLLGLLGGLLLLLLLLLLLGLLLLLLLLLLGLLLLALLALLLL 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250 111 FCNFEHDPSIHELFRQMLYEIRTAQYGSQTICQHLLEILILKIIRSQQLIPVSINSIRMTKECAQIKEYLDSNYAEHITL 190
Cdd:COG2207    92 VGLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTL 171

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250 191 DTLTGLTHMNKYYMVHSFTKYAGLSPIQYLNQTRLKRAQHLLKNTNYSISDIASSTGFSSQSYFTQIFRKNFNMTPVKYR 270
Cdd:COG2207   172 EELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSEYR 251


                  ....*.
gi 1731510250 271 QEHAKN 276
Cdd:COG2207   252 KRLRAR 257
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 178-274 6.73e-22

Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH domain [Transcription];


Pssm-ID: 444002 [Multi-domain]  Cd Length: 318  Bit Score: 92.91  E-value: 6.73e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250 178 EYLDSNYAEHITLDTLTGLTHMnkyymvhS-------FTKYAGLSPIQYLNQTRLKRAQHLLKNTNYSISDIASSTGFSS 250
Cdd:COG4977   217 AWMEANLEEPLSVDELARRAGM-------SprtlerrFRAATGTTPARYLQRLRLERARRLLETTDLSIEEIAAACGFGS 289

                          90       100
                  ....*....|....*....|....
gi 1731510250 251 QSYFTQIFRKNFNMTPVKYRQEHA 274
Cdd:COG4977   290 ASHFRRAFRRRFGVSPSAYRRRFR 313
HTH_18 pfam12833
Helix-turn-helix domain;
197-271 3.59e-20

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 82.25  E-value: 3.59e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1731510250 197 THMNKYYMVHSFTKYAGLSPIQYLNQTRLKRAQHLL-KNTNYSISDIASSTGFSSQSYFTQIFRKNFNMTPVKYRQ 271
Cdd:pfam12833   5 LGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLlEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
155-270 4.36e-13

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 67.69  E-value: 4.36e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250 155 RSQQLIPVSINSI---RMTKECaqikEYLDSNYAEHITLDTLTGLTHMNKYYMVHSFTKYAGLSPIQYLNQTRLKRAQHL 231
Cdd:PRK10572  168 RCMEAIPESLHPPmdpRVREAC----QYISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWREDQRISRAKLL 243

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1731510250 232 LKNTNYSISDIASSTGFSSQSYFTQIFRKNFNMTPVKYR 270
Cdd:PRK10572  244 LQTTRMPIATIGRNVGYDDQLYFSRVFKKCTGASPSEFR 282
PRK13500 PRK13500
HTH-type transcriptional activator RhaR;
37-275 2.29e-12

HTH-type transcriptional activator RhaR;


Pssm-ID: 184091 [Multi-domain]  Cd Length: 312  Bit Score: 65.89  E-value: 2.29e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250  37 HTHHFTELLFVVSGEGSFSFNQEQSPLRRGDLVIIPPYTEHTERSSQNHPLEYYVL-------------GIDGISFLSQK 103
Cdd:PRK13500   64 HTHDFCELVIVWRGNGLHVLNDRPYRITRGDLFYIHADDKHSYASVNDLVLQNIIYcperlklnldwqgAIPGFSASAGQ 143

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250 104 DR---------ECAQVFCNFEHDPSIHELFRQMLYEIRTAQYgSQTICQHLLEililkiirSQQLIPVSINSIrMTKECA 174
Cdd:PRK13500  144 PHwrlgsvgmaQARQVIGQLEHESSQHVPFANEMAELLFGQL-VMLLNRHRYT--------SDSLPPTSSETL-LDKLIT 213

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250 175 QIKEYLDSNYAehitLDTLTGLTHMNKYYMVHSFTKYAGLSPIQYLNQTRLKRAQHLLKNTNYSISDIASSTGFSSQSYF 254
Cdd:PRK13500  214 RLAASLKSPFA----LDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQHSRLLISDISTECGFEDSNYF 289

                         250       260
                  ....*....|....*....|.
gi 1731510250 255 TQIFRKNFNMTPVKYRQEHAK 275
Cdd:PRK13500  290 SVVFTRETGMTPSQWRHLNSQ 310
AraC_binding pfam02311
AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization ...
 31-128 3.21e-10

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: 57.06  E-value: 3.21e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250  31 DWKSIMHTHHFTELLFVVSGEGSFSFNQEQSPLRRGDLVIIPPYTEHTERSSQNHPLEYYVLGIDGISFLSQKDR--ECA 108
Cdd:pfam02311  13 GHSFPPHVHDFYVIGYIERGVGRFRLNGRTYHLGPGDLFLLPPGEPHDYEPESEDGWRYRWLYFEPELLERILADisILA 92

                          90       100
                  ....*....|....*....|
gi 1731510250 109 QVFCNFEHDPSIHELFRQML 128
Cdd:pfam02311  93 GGPLPLLRDPELAALLRALF 112
cupin_MmsR-like_N cd06986
AraC/XylS family transcriptional regulators similar to MmsR, N-terminal cupin domain; This ...
 37-97 1.28e-09

AraC/XylS family transcriptional regulators similar to MmsR, N-terminal cupin domain; This family contains bacterial proteins containing an AraC/XylS family helix-turn-helix (HTH) DNA-binding domain C-terminal to a cupin domain, and may be possible transcriptional regulators. Included is MmsR, a bacterial transcriptional regulator thought to positively regulate the expression of the mmsAB operon. The mmsAB operon contains two structural genes involved in valine metabolism: mmsA which encodes methylmalonate-semialdehyde dehydrogenase, and mmsB which encodes 3-hydroxyisobutyrate dehydrogenase. The cupin domain of members of this subfamily does not contain a metal binding site.


Pssm-ID: 380391 [Multi-domain]  Cd Length: 84  Bit Score: 53.64  E-value: 1.28e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1731510250  37 HTHHFTE-----LLFVVSGEGSFSFNQEQSPLRRGDLVIIPPYTEHTERSSQNHPLEYYVLGIDGI 97
Cdd:cd06986    19 HSYGPAVrdyyiLHYVLSGKGTFSVNGKTYHLKAGQGFLIPPGEPHSYGADEDDPWTYYWIGFSGS 84
Cupin_1 smart00835
Cupin; This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' ...
 36-95 7.19e-06

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: 214845 [Multi-domain]  Cd Length: 146  Bit Score: 44.96  E-value: 7.19e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1731510250   36 MHTH-HFTELLFVVSGEGSFSF-----NQEQ-SPLRRGDLVIIPPYTEHTERSSQNHPLEYYVLGID 95
Cdd:smart00835  45 PHYHpRATELLYVVRGEGRVGVvdpngNKVYdARLREGDVFVVPQGHPHFQVNSGDENLEFVAFNTN 111
 
Name Accession Description Interval E-value
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
188-270 7.16e-26

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 97.24  E-value: 7.16e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250  188 ITLDTLTGLTHMNKYYMVHSFTKYAGLSPIQYLNQTRLKRAQHLLKNTNYSISDIASSTGFSSQSYFTQIFRKNFNMTPV 267
Cdd:smart00342   2 LTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTPS 81


                   ...
gi 1731510250  268 KYR 270
Cdd:smart00342  82 EYR 84
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
31-276 1.54e-24

AraC-type DNA-binding domain and AraC-containing proteins [Transcription];


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 99.08  E-value: 1.54e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250  31 DWKSIMHTHHFTELLFVVSGEGSFSFNQEQSPLRRGDLVIIPPYTEHTERSSQNHPLEYYVLGIDGISFLSQKDRECAQV 110
Cdd:COG2207    12 LLLALLLLLLLLLLLLILLLLALVLLLLLLALLLLLLLLLGLLGGLLLLLLLLLLLGLLLLLLLLLLGLLLLALLALLLL 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250 111 FCNFEHDPSIHELFRQMLYEIRTAQYGSQTICQHLLEILILKIIRSQQLIPVSINSIRMTKECAQIKEYLDSNYAEHITL 190
Cdd:COG2207    92 VGLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTL 171

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250 191 DTLTGLTHMNKYYMVHSFTKYAGLSPIQYLNQTRLKRAQHLLKNTNYSISDIASSTGFSSQSYFTQIFRKNFNMTPVKYR 270
Cdd:COG2207   172 EELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSEYR 251


                  ....*.
gi 1731510250 271 QEHAKN 276
Cdd:COG2207   252 KRLRAR 257
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 178-274 6.73e-22

Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH domain [Transcription];


Pssm-ID: 444002 [Multi-domain]  Cd Length: 318  Bit Score: 92.91  E-value: 6.73e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250 178 EYLDSNYAEHITLDTLTGLTHMnkyymvhS-------FTKYAGLSPIQYLNQTRLKRAQHLLKNTNYSISDIASSTGFSS 250
Cdd:COG4977   217 AWMEANLEEPLSVDELARRAGM-------SprtlerrFRAATGTTPARYLQRLRLERARRLLETTDLSIEEIAAACGFGS 289

                          90       100
                  ....*....|....*....|....
gi 1731510250 251 QSYFTQIFRKNFNMTPVKYRQEHA 274
Cdd:COG4977   290 ASHFRRAFRRRFGVSPSAYRRRFR 313
HTH_18 pfam12833
Helix-turn-helix domain;
197-271 3.59e-20

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 82.25  E-value: 3.59e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1731510250 197 THMNKYYMVHSFTKYAGLSPIQYLNQTRLKRAQHLL-KNTNYSISDIASSTGFSSQSYFTQIFRKNFNMTPVKYRQ 271
Cdd:pfam12833   5 LGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLlEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 174-274 5.86e-19

Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), contains Zn-binding and two AraC-type DNA-binding domains [Replication, recombination and repair];


Pssm-ID: 441772 [Multi-domain]  Cd Length: 358  Bit Score: 85.11  E-value: 5.86e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250 174 AQIKEYLDSNYAEHITLDTLTGLTHMNKYYMVHSFTKYAGLSPIQYLNQTRLKRAQHLLKnTNYSISDIASSTGFSSQSY 253
Cdd:COG2169    87 ARACRLIEAGAEDRPSLEDLAARLGLSPRHLRRLFKAHTGVTPKAYARARRLLRARQLLQ-TGLSVTDAAYAAGFGSLSR 165

                          90       100
                  ....*....|....*....|.
gi 1731510250 254 FTQIFRKNFNMTPVKYRQEHA 274
Cdd:COG2169   166 FYEAFKKLLGMTPSAYRRGGA 186
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
155-270 4.36e-13

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 67.69  E-value: 4.36e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250 155 RSQQLIPVSINSI---RMTKECaqikEYLDSNYAEHITLDTLTGLTHMNKYYMVHSFTKYAGLSPIQYLNQTRLKRAQHL 231
Cdd:PRK10572  168 RCMEAIPESLHPPmdpRVREAC----QYISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWREDQRISRAKLL 243

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1731510250 232 LKNTNYSISDIASSTGFSSQSYFTQIFRKNFNMTPVKYR 270
Cdd:PRK10572  244 LQTTRMPIATIGRNVGYDDQLYFSRVFKKCTGASPSEFR 282
PRK13500 PRK13500
HTH-type transcriptional activator RhaR;
37-275 2.29e-12

HTH-type transcriptional activator RhaR;


Pssm-ID: 184091 [Multi-domain]  Cd Length: 312  Bit Score: 65.89  E-value: 2.29e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250  37 HTHHFTELLFVVSGEGSFSFNQEQSPLRRGDLVIIPPYTEHTERSSQNHPLEYYVL-------------GIDGISFLSQK 103
Cdd:PRK13500   64 HTHDFCELVIVWRGNGLHVLNDRPYRITRGDLFYIHADDKHSYASVNDLVLQNIIYcperlklnldwqgAIPGFSASAGQ 143

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250 104 DR---------ECAQVFCNFEHDPSIHELFRQMLYEIRTAQYgSQTICQHLLEililkiirSQQLIPVSINSIrMTKECA 174
Cdd:PRK13500  144 PHwrlgsvgmaQARQVIGQLEHESSQHVPFANEMAELLFGQL-VMLLNRHRYT--------SDSLPPTSSETL-LDKLIT 213

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250 175 QIKEYLDSNYAehitLDTLTGLTHMNKYYMVHSFTKYAGLSPIQYLNQTRLKRAQHLLKNTNYSISDIASSTGFSSQSYF 254
Cdd:PRK13500  214 RLAASLKSPFA----LDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQHSRLLISDISTECGFEDSNYF 289

                         250       260
                  ....*....|....*....|.
gi 1731510250 255 TQIFRKNFNMTPVKYRQEHAK 275
Cdd:PRK13500  290 SVVFTRETGMTPSQWRHLNSQ 310
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
175-273 3.94e-12

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 64.70  E-value: 3.94e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250 175 QIKEYLDSNYAEHITLDTLT-----GLTHMNKYYMVHSftkyaGLSPIQYLNQTRLKRAQHLLKNTNYSISDIASSTGFS 249
Cdd:PRK13503  175 QLLAWLEDHFAEEVNWEALAdqfslSLRTLHRQLKQQT-----GLTPQRYLNRLRLLKARHLLRHSDASVTDIAYRCGFG 249

                          90       100
                  ....*....|....*....|....
gi 1731510250 250 SQSYFTQIFRKNFNMTPVKYRQEH 273
Cdd:PRK13503  250 DSNHFSTLFRREFSWSPRDIRQGR 273
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
37-271 2.03e-11

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 62.76  E-value: 2.03e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250  37 HTHHFTELLFVVSGEGSFSFNQEQSPLRRGDLVIIPPYTEHT----------------ERSSQNHPLEYYVLGIDGISFL 100
Cdd:PRK13502   34 HTHEFCELVMVWRGNGLHVLNERPYRITRGDLFYIRAEDKHSytsvndlvlqniiycpERLKLNVNWQAMIPGFQGAQWH 113

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250 101 ------SQKDRECAQVFCNFEH-----DPSIHE----LFRQMLYEIRTAQYGSQTIcqhlleililkiirsqqliPVSIN 165
Cdd:PRK13502  114 phwrlgSMGMNQARQVINQLEHesngrDPLANEmaelLFGQLVMTLKRHRYATDDL-------------------PATSR 174

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250 166 SIRMTKECAQIKEYLDSNYAehitLDTLTGLTHMNKYYMVHSFTKYAGLSPIQYLNQTRLKRAQHLLKNTNYSISDIASS 245
Cdd:PRK13502  175 ETLLDKLITALANSLECPFA----LDAFCQQEQCSERVLRQQFRAQTGMTINQYLRQVRICHAQYLLQHSPLMISEISMQ 250

                         250       260
                  ....*....|....*....|....*.
gi 1731510250 246 TGFSSQSYFTQIFRKNFNMTPVKYRQ 271
Cdd:PRK13502  251 CGFEDSNYFSVVFTRETGMTPSQWRH 276
PRK10371 PRK10371
transcriptional regulator MelR;
175-271 1.07e-10

transcriptional regulator MelR;


Pssm-ID: 182416 [Multi-domain]  Cd Length: 302  Bit Score: 60.99  E-value: 1.07e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250 175 QIKEYLDSNYAEHITLDTLTGLTHMNKYYMVHSFTKYAGLSPIQYLNQTRLKRAQHLLKNTNYSISDIASSTGFSSQSYF 254
Cdd:PRK10371  195 QMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQRVMQLTMKQYITAMRINHVRALLSDTDKSILDIALTAGFRSSSRF 274

                          90
                  ....*....|....*..
gi 1731510250 255 TQIFRKNFNMTPVKYRQ 271
Cdd:PRK10371  275 YSTFGKYVGMSPQQYRK 291
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
206-272 1.15e-10

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 60.69  E-value: 1.15e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1731510250 206 HSFTKYAGLSPIQYLNQTRLKRAQHLLKNTNYSISDIASSTGFSSQSYFTQIFRKNFNMTPVKYRQE 272
Cdd:PRK13501  211 QLFRQQTGMSISHYLRQIRLCHAKCLLRGSEHRISDIAARCGFEDSNYFSAVFTREAGMTPRDYRQR 277
AraC_binding pfam02311
AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization ...
 31-128 3.21e-10

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: 57.06  E-value: 3.21e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250  31 DWKSIMHTHHFTELLFVVSGEGSFSFNQEQSPLRRGDLVIIPPYTEHTERSSQNHPLEYYVLGIDGISFLSQKDR--ECA 108
Cdd:pfam02311  13 GHSFPPHVHDFYVIGYIERGVGRFRLNGRTYHLGPGDLFLLPPGEPHDYEPESEDGWRYRWLYFEPELLERILADisILA 92

                          90       100
                  ....*....|....*....|
gi 1731510250 109 QVFCNFEHDPSIHELFRQML 128
Cdd:pfam02311  93 GGPLPLLRDPELAALLRALF 112
ftrA PRK09393
transcriptional activator FtrA; Provisional
 174-270 6.37e-10

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 58.82  E-value: 6.37e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250 174 AQIKEYLDSNYAEHITLDTLTGLTHMNKYYMVHSFTKYAGLSPIQYLNQTRLKRAQHLLKNTNYSISDIASSTGFSSQSY 253
Cdd:PRK09393  221 GPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLARARDLLESSALSIDQIAERAGFGSEES 300

                          90
                  ....*....|....*..
gi 1731510250 254 FTQIFRKNFNMTPVKYR 270
Cdd:PRK09393  301 LRHHFRRRAATSPAAYR 317
cupin_MmsR-like_N cd06986
AraC/XylS family transcriptional regulators similar to MmsR, N-terminal cupin domain; This ...
 37-97 1.28e-09

AraC/XylS family transcriptional regulators similar to MmsR, N-terminal cupin domain; This family contains bacterial proteins containing an AraC/XylS family helix-turn-helix (HTH) DNA-binding domain C-terminal to a cupin domain, and may be possible transcriptional regulators. Included is MmsR, a bacterial transcriptional regulator thought to positively regulate the expression of the mmsAB operon. The mmsAB operon contains two structural genes involved in valine metabolism: mmsA which encodes methylmalonate-semialdehyde dehydrogenase, and mmsB which encodes 3-hydroxyisobutyrate dehydrogenase. The cupin domain of members of this subfamily does not contain a metal binding site.


Pssm-ID: 380391 [Multi-domain]  Cd Length: 84  Bit Score: 53.64  E-value: 1.28e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1731510250  37 HTHHFTE-----LLFVVSGEGSFSFNQEQSPLRRGDLVIIPPYTEHTERSSQNHPLEYYVLGIDGI 97
Cdd:cd06986    19 HSYGPAVrdyyiLHYVLSGKGTFSVNGKTYHLKAGQGFLIPPGEPHSYGADEDDPWTYYWIGFSGS 84
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
36-92 1.31e-09

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


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 54.08  E-value: 1.31e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1731510250  36 MHTHHFTELLFVVSGEGSFSFNQEQSPLRRGDLVIIPPYTEHTERSSQNHPLEYYVL 92
Cdd:COG1917    38 WHSHPGEELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFRNLGDEPAVLLVV 94
PRK10219 PRK10219
superoxide response transcriptional regulator SoxS;
178-271 1.66e-09

superoxide response transcriptional regulator SoxS;


Pssm-ID: 182314 [Multi-domain]  Cd Length: 107  Bit Score: 54.16  E-value: 1.66e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250 178 EYLDSNYAEHITLDTLTGLTHMNKYYMVHSFTKYAGLSPIQYLNQTRLKRAQHLLKNTNYSISDIASSTGFSSQSYFTQI 257
Cdd:PRK10219   12 AWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLLAAVELRTTERPIFDIAMDLGYVSQQTFSRV 91

                          90
                  ....*....|....
gi 1731510250 258 FRKNFNMTPVKYRQ 271
Cdd:PRK10219   92 FRRQFDRTPSDYRH 105
ManC COG0662
Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism];
36-91 4.82e-09

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


Pssm-ID: 440426 [Multi-domain]  Cd Length: 114  Bit Score: 53.22  E-value: 4.82e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1731510250  36 MHTH-HFTELLFVVSGEGSFSFNQEQSPLRRGDLVIIPPYTEHTERSSQNHPLEYYV 91
Cdd:COG0662    42 LHVHpHRDEFFYVLEGTGEVTIGDEEVELKAGDSVYIPAGVPHRLRNPGDEPLELLE 98
PRK10296 PRK10296
DNA-binding transcriptional regulator ChbR; Provisional
 182-271 1.15e-08

DNA-binding transcriptional regulator ChbR; Provisional


Pssm-ID: 182362 [Multi-domain]  Cd Length: 278  Bit Score: 54.76  E-value: 1.15e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250 182 SNYAEHiTLDTLTGLTHMNKYYMVHSFTKYAGLSPIQYLNQTRLKRAQHLLKNTNYSISDIASSTGFSSQSYFTQIFRKN 261
Cdd:PRK10296  184 EQFSES-ALENMVRLSGKSQEYLTRATRRYYGKTPMQIINEIRINFAKKQLEMTNYSVTDIAFEAGYSSPSLFIKTFKKL 262

                          90
                  ....*....|
gi 1731510250 262 FNMTPVKYRQ 271
Cdd:PRK10296  263 TSFTPGSYRK 272
cupin_DddK cd06988
Dimethylsulfoniopropionate lyase DddK and related proteins, cupin domain; This family includes ...
 37-92 2.04e-08

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: 50.31  E-value: 2.04e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1731510250  37 HTHHFTELLFVVSGEGSFSFNQEQSPLRRGDLVIIPPYTEHTERSSQNHPLEYYVL 92
Cdd:cd06988    18 HSHHEYEIFIVISGKGIVVVDGEREPVKAGDVVYIPPGTEHYVKNDGDEDFEFYSI 73
PRK09978 PRK09978
DNA-binding transcriptional regulator GadX; Provisional
 157-275 4.51e-08

DNA-binding transcriptional regulator GadX; Provisional


Pssm-ID: 137624 [Multi-domain]  Cd Length: 274  Bit Score: 53.01  E-value: 4.51e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250 157 QQLIPVSINSIR---MTKECAQIkeylDSNYAEHITLDTLTGLTHMNKYYMVHSFtKYAGLSPIQYLNQTRLKRAQHLLK 233
Cdd:PRK09978  129 EHFIPLLLNVLQpnmRTRVCTVI----NNNIAHEWTLARIASELLMSPSLLKKKL-REEETSYSQLLTECRMQRALQLIV 203

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1731510250 234 NTNYSISDIASSTGFSSQSYFTQIFRKNFNMTPVKYRQEHAK 275
Cdd:PRK09978  204 IHGFSIKRVAVSCGYHSVSYFIYVFRNYYGMTPTEYQERSAQ 245
PRK09685 PRK09685
DNA-binding transcriptional activator FeaR; Provisional
 213-274 1.12e-07

DNA-binding transcriptional activator FeaR; Provisional


Pssm-ID: 236612 [Multi-domain]  Cd Length: 302  Bit Score: 51.96  E-value: 1.12e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1731510250 213 GLSPIQYLNQTRLKR-AQHL---LKNTnySISDIASSTGFSSQSYFTQIFRKNFNMTPVKYRQEHA 274
Cdd:PRK09685  239 GLVVAQYIRNRRLDRcADDLrpaADDE--KITSIAYKWGFSDSSHFSTAFKQRFGVSPGEYRRKFR 302
cupin_RmlC-like cd02208
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 37-91 2.11e-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: 47.48  E-value: 2.11e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1731510250  37 HTHHF-TELLFVVSGEGSFSFN-QEQSPLRRGDLVIIPPYTEHTERSSQNHPLEYYV 91
Cdd:cd02208    15 HWHPEqDEIFYVLSGEGELTLDdGETVELKAGDIVLIPPGVPHSFVNTSDEPAVFLV 71
PRK11511 PRK11511
MDR efflux pump AcrAB transcriptional activator MarA;
176-270 8.47e-07

MDR efflux pump AcrAB transcriptional activator MarA;


Pssm-ID: 236920 [Multi-domain]  Cd Length: 127  Bit Score: 47.02  E-value: 8.47e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250 176 IKEYLDSNYAEHITLDTLTGLTHMNKYYMVHSFTKYAGLSPIQYLNQTRLKRAQHLLKNTNYSISDIASSTGFSSQSYFT 255
Cdd:PRK11511   14 ILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEPILYLAERYGFESQQTLT 93

                          90
                  ....*....|....*
gi 1731510250 256 QIFRKNFNMTPVKYR 270
Cdd:PRK11511   94 RTFKNYFDVPPHKYR 108
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 33-93 1.71e-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: 44.56  E-value: 1.71e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1731510250  33 KSIMHTHHF-TELLFVVSGEGSFSFNQEQSPLRRGDLVIIPPYTEHTERSSQNHPLEYYVLG 93
Cdd:pfam07883  10 SSPPHRHPGeDEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPHRFRNTGDEPARLLDVY 71
PRK15186 PRK15186
AraC family transcriptional regulator; Provisional
 219-269 4.20e-06

AraC family transcriptional regulator; Provisional


Pssm-ID: 185108 [Multi-domain]  Cd Length: 291  Bit Score: 46.98  E-value: 4.20e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1731510250 219 YLNqTRLKRAQHLLKNTNYSISDIASSTGFSSQSYFTQIFRKNFNMTPVKY 269
Cdd:PRK15186  229 YLN-ARMNKATKLLRNSEYNITRVAYMCGYDSASYFTCVFKKHFKTTPSEF 278
Cupin_1 smart00835
Cupin; This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' ...
 36-95 7.19e-06

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: 214845 [Multi-domain]  Cd Length: 146  Bit Score: 44.96  E-value: 7.19e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1731510250   36 MHTH-HFTELLFVVSGEGSFSF-----NQEQ-SPLRRGDLVIIPPYTEHTERSSQNHPLEYYVLGID 95
Cdd:smart00835  45 PHYHpRATELLYVVRGEGRVGVvdpngNKVYdARLREGDVFVVPQGHPHFQVNSGDENLEFVAFNTN 111
PRK15121 PRK15121
MDR efflux pump AcrAB transcriptional activator RobA;
179-270 7.60e-06

MDR efflux pump AcrAB transcriptional activator RobA;


Pssm-ID: 185076 [Multi-domain]  Cd Length: 289  Bit Score: 46.15  E-value: 7.60e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250 179 YLDSNYAEHITLDTLTGLTHMNKYYMVHSFTKYAGLSPIQYLNQTRLKRAQHLLKNTNYSISDIASSTGFSSQSYFTQIF 258
Cdd:PRK15121   13 WLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGHAIGAYIRARRLSKAAVALRLTSRPILDIALQYRFDSQQTFTRAF 92

                          90
                  ....*....|..
gi 1731510250 259 RKNFNMTPVKYR 270
Cdd:PRK15121   93 KKQFAQTPALYR 104
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 235-271 1.33e-05

Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the N-terminal arm of AraC binds to the DNA binding domain (pfam00165) and helps to hold the two DNA binding domains in a relative orientation that favours DNA looping. In the presence of arabinose, the arms bind over the arabinose on the dimerization domain, thus freeing the DNA-binding domains. The freed DNA-binding domains are then able to assume a conformation suitable for binding to the adjacent DNA sites that are utilized when AraC activates transcription, and hence AraC ceases looping the DNA when arabinose is added.


Pssm-ID: 425497 [Multi-domain]  Cd Length: 42  Bit Score: 41.37  E-value: 1.33e-05
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1731510250 235 TNYSISDIASSTGFSsQSYFTQIFRKNFNMTPVKYRQ 271
Cdd:pfam00165   7 TNLTIADIADELGFS-RSYFSRLFKKYTGVTPSQYRH 42
cupin_Pac13-like cd20295
monomeric dehydratase Pac13 and related proteins, cupin domain; This family includes a small ...
 37-77 4.03e-05

monomeric dehydratase Pac13 and related proteins, cupin domain; This family includes a small monomeric dehydratase Pac13 that mediates the formation of the 3'-deoxynucleotide of pacidamycins, which are uradyl peptide antibiotics (UPAs). Pac13 is involved in the formation of the unique 3'-deoxyuridine moiety found in these UPAs; it catalyzes the dehydration of uridine-5'-aldehyde. The similarity of the 3'-deoxy pacidamycin moiety with synthetic anti-retrovirals, offers a potential opportunity for the utilization of Pac13 in the biocatalytic generation of antiviral compounds. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380429 [Multi-domain]  Cd Length: 101  Bit Score: 41.82  E-value: 4.03e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1731510250  37 HTHHF----TELLFVVSGEGSFSFNQEQSPLRRGDLVIIPPYTEH 77
Cdd:cd20295    33 HEEHYhkksTEIYYVLEGEGIFELDGEAVPVKPGDLVLIPPGTRH 77
cupin_MJ1618 cd02214
Methanocaldococcus jannaschii MJ1618 and related proteins, cupin domain; This family includes ...
 7-77 4.35e-05

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: 41.35  E-value: 4.35e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1731510250   7 LINSEDLQNLNaklLSIAFSKDEGDWKSIMHTH-HFTELLFVVSGEGSFSFNQEQSPLRRGDLVIIPPYTEH 77
Cdd:cd02214     8 LLHPDNDGDPR---YSLAHARVPPGESTLPHRLkGSEEVYYILEGEGTMEIDGEPREVGPGDAVLIPPGAVQ 76
PRK15185 PRK15185
transcriptional regulator HilD; Provisional
 224-266 4.46e-05

transcriptional regulator HilD; Provisional


Pssm-ID: 185107 [Multi-domain]  Cd Length: 309  Bit Score: 44.22  E-value: 4.46e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1731510250 224 RLKRAQHLLKNTNYSISDIASSTGFSSQSYFTQIFRKNFNMTP 266
Cdd:PRK15185  258 RMNQAAKLLRIGNHNVNAVALKCGYDSTSYFIQCFKKYFKTTP 300
cupin_HNL-like cd02233
Granulicella tundricola hydroxynitrile lyase (GtHNL) and related proteins, cupin domain; This ...
 37-77 5.09e-05

Granulicella tundricola hydroxynitrile lyase (GtHNL) and related proteins, cupin domain; This family includes archaeal, eukaryotic, and bacterial proteins homologous to hydroxynitrile lyase from Granulicella tundricola (GtHNL), a novel class of HNLs that does not show any sequence or structural similarity to any other HNL and does not contain conserved motifs typical of HNLs. HNLs comprise a diverse group of enzymes that vary in terms of their substrate specificity, enantioselectivity and the need for a co-factor. In plants, they catalyze the reversible cleavage of cyanohydrins, yielding HCN and aldehydes or ketones. Also included in this family is TM1010 from Thermotoga maritima, a protein of unknown function. Some but not all members of this family have N- or C-terminal carboxymuconolactone decarboxylase domains in addition to the cupin domain. Members of this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380361 [Multi-domain]  Cd Length: 106  Bit Score: 41.38  E-value: 5.09e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1731510250  37 HTHHFTELLFVVSGEGsfsFNQEQ----SPLRRGDLVIIPPYTEH 77
Cdd:cd02233    35 HTHPGGQILIVTSGVG---WVQEEggppQELRPGDVVWIPPGVKH 76
cupin_TM1459-like cd02222
Thermotoga maritima TM1459 and related proteins, cupin domain; This family includes bacterial ...
 36-77 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: 39.74  E-value: 1.36e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1731510250  36 MHTHHFTELLFVVSGEGSFSFNQEQSPLRRGDLVIIPPYTEH 77
Cdd:cd02222    32 LHTHPWEHEVYVLRGKGVVVIGGEEYPVKPGDVVYIPPNEPH 73
cupin_MAE_RS03005 cd06987
Microcystis aeruginosa MAE_RS03005 and related proteins, cupin domain; This family includes ...
 37-77 1.58e-04

Microcystis aeruginosa MAE_RS03005 and related proteins, cupin domain; This family includes bacterial and some eukaryotic proteins homologous to MAE_RS03005, a Microcystis aeruginosa 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: 380392 [Multi-domain]  Cd Length: 122  Bit Score: 40.33  E-value: 1.58e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1731510250  37 HTHHF-TELLFVVSGEGSFSFNQEQSPLRRGDLVIIPPYTEH 77
Cdd:cd06987    44 NTHPAaHEMFFVLAGEGRAYCDGQRVPLRPGDALVVPPGSEH 85
cupin_HP0902-like cd02230
Helicobacter pylori HP0902 and related proteins, cupin domain; This family includes ...
 13-77 3.26e-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: 38.64  E-value: 3.26e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1731510250  13 LQNLNAKLLSIAFSKDEGdwksiM--HTHHFTELLFVVSGEGSFSFNQEQSPLRRGDLVIIPPYTEH 77
Cdd:cd02230     6 VQDDGLRVTLFAFDAGQE-----LseHTAPGDATVQVLEGEAEFTIGGETVTLKAGELIVMPANVPH 67
cupin_XcTcmJ-like cd07006
Xanthomonas campestris XcTcmJ and related proteins, cupin domain; This family includes ...
 45-88 7.31e-04

Xanthomonas campestris XcTcmJ and related proteins, cupin domain; This family includes bacterial and archaeal proteins homologous to plant pathogen Xanthomonas campestris tetracenomycin polyketide synthesis protein XcTcmJ, a protein encoded by the tcmJ gene. XcTcmJ is annotated as being involved in tetracenomycin polyketide biosynthesis. Also included is Xc5357 from a different strain of X. campestris. Structure studies show that binding of zinc induces conformational changes and serves a functional role in this cupin protein. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380409 [Multi-domain]  Cd Length: 89  Bit Score: 37.73  E-value: 7.31e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1731510250  45 LFVVSGEGSFSFNQEQSPLRRGDLVIIPPYTEHTERSSQNHPLE 88
Cdd:cd07006    37 LYVVSGSGEAIVEGERVALKPGSLLLIEAGETHEIRNTGDEPLK 80
cupin_YobQ-like_N cd07003
Bacillus subtilis YobQ and related proteins, N-terminal cupin domain; This family includes ...
 34-84 8.56e-04

Bacillus subtilis YobQ and related proteins, N-terminal cupin domain; This family includes bacterial proteins homologous to Bacillus subtilis YobQ and Photobacterium leiognathi LumQ, both uncharacterized proteins thought to be DNA-binding proteins that may function as AraC/XylS family transcriptional regulators. YobQ has an N-terminal cupin beta barrel domain (represented by this alignment model) and a C-terminal AraC/XylS family helix-turn-helix (HTH) DNA-binding domain. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380407 [Multi-domain]  Cd Length: 66  Bit Score: 36.99  E-value: 8.56e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1731510250  34 SIMHTHHFTELLFVVSGEGSFSFNQEQSPLRRGDLVIIPPYTEHTERSSQN 84
Cdd:cd07003     7 QSSHSHEHAQLVLPLSGSLELEVEGRGSRVKPDIGLYIPPNAEHRFAGSSD 57
cupin_TM1287-like cd02221
Thermotoga maritima TM1287 decarboxylase, cupin domain; This family includes bacterial ...
 4-89 9.44e-04

Thermotoga maritima TM1287 decarboxylase, cupin domain; This family includes bacterial proteins homologous to TM1287 decarboxylase, a Thermotoga maritima manganese-containing cupin thought to catalyze the conversion of oxalate to formate and carbon dioxide, due to its similarity to oxalate decarboxylase (OXDC) from Bacillus subtilis. TM1287 shows a cupin fold with a conserved "jelly roll-like" beta-barrel fold and forms a homodimer.


Pssm-ID: 380350 [Multi-domain]  Cd Length: 93  Bit Score: 37.45  E-value: 9.44e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731510250   4 RHYLINSEDLQNlNAKLlsiaFSK---DEGDwkSI-MHTHHF-TELLFVVSGEGSFSFNQEQSPLRRGDLVIIPPYTEHT 78
Cdd:cd02221     5 VYHLLTPEELKG-KGRL----FARvtlPPGS--SIgYHQHEGeFEIYYILSGEGLYTDNGKEYEVKAGDVTFTRDGESHG 77

                          90
                  ....*....|.
gi 1731510250  79 ERSSQNHPLEY 89
Cdd:cd02221    78 IENTGDEDLVF 88
cupin_RhaR_RhaS-like_N cd06977
HTH-type transcriptional activator RhaR and RhaS and related proteins, N-terminal cupin domain; ...
 36-84 1.20e-03

HTH-type transcriptional activator RhaR and RhaS and related proteins, N-terminal cupin domain; Members of this family contain an N-terminal cupin domain and a C-terminal AraC/XylS family helix-turn-helix (HTH) DNA-binding domain, including the HTH-type transcription activators RhaS and RhaR. RhaS and RhaR respond to the availability of L-rhamnose and activate transcription of the operons in the Escherichia coli L-rhamnose catabolic regulon. The E. coli RhaR protein activates expression of the rhaSR operon in the presence of its effector, L-rhamnose. The resulting RhaS protein (plus L-rhamnose) activates expression of the L-rhamnose catabolic operon rhaBAD as well as the transport operon rhaT. These proteins bind DNA as dimers, via their HTH motifs. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380382 [Multi-domain]  Cd Length: 147  Bit Score: 38.40  E-value: 1.20e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1731510250  36 MHTHHFTELLFVVSGEGSFSFNQEQSPLRRGDLVIIPPYTEHTERSSQN 84
Cdd:cd06977    17 EHTHDFHEIVIVTKGSGIHVLNGHPYRITAGDVFYIRPDDRHSYESVDD 65
cupin_SPO2919-like cd02224
Silicibacter pomeroyi SPO2919 and related proteins, uncharacterized sugar phosphate isomerase ...
 30-93 2.14e-03

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: 36.70  E-value: 2.14e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1731510250  30 GDWKSIMHTHHFT-ELLFVVSGEGSFSFNQEQSPLRRGDLVIIPPYTE--HTERSSQNHPLEYYVLG 93
Cdd:cd02224    27 GARSSPRHWHSAEeEFVYVLSGEGTLRLDGEEVLPRPGDFVGFPAGTGvaHQLINRSDEPLVYLVVG 93
cupin_ARD cd02232
acireductone dioxygenase (ARD), cupin domain; Acireductone dioxygenase (ARD; also known as 1, ...
 37-77 2.58e-03

acireductone dioxygenase (ARD), cupin domain; Acireductone dioxygenase (ARD; also known as 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase) catalyzes the oxidation of 1,2-dihydroxy-3-keto-5-methylthiopentene to yield two different products depending on which active site metal is present (Fe2+ or Ni2+) as part of the methionine salvage pathway. The ARD apo-enzyme, obtained after the metal is removed, is catalytically inactive. The Fe(II)-ARD reaction yields an alpha-keto acid and formic acid, while Ni(II)-ARD instead catalyzes a shunt out of the methionine salvage pathway, yielding methylthiocarboxylic acid, formic acid, and CO. ARD belongs to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization


Pssm-ID: 380360  Cd Length: 134  Bit Score: 37.14  E-value: 2.58e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1731510250  37 HTHHFTELLFVVSGEGSFSFNQEQSP-----LRRGDLVIIPPYTEH 77
Cdd:cd02232    65 HLHEDDEVRFILDGSGYFDVRDKDDEwirilVEKGDLIVVPAGIYH 110
cupin_GDO-like_N cd02216
gentisate 1,2-dioxygenase, 1-hydroxy-2-naphthoate dioxygenase, and salicylate 1,2-dioxygenase, ...
 37-77 2.59e-03

gentisate 1,2-dioxygenase, 1-hydroxy-2-naphthoate dioxygenase, and salicylate 1,2-dioxygenase, N-terminal cupin domain; This family includes the N-terminal cupin domains of three closely related bicupin aromatic ring-cleaving dioxygenases: gentisate 1,2-dioxygenase (GDO), salicylate 1,2-dioxygenase (SDO), and 1-hydroxy-2-naphthoate dioxygenase (NDO). GDO catalyzes the cleavage of the gentisate (2,5-dihydroxybenzoate) aromatic ring, a key step in the gentisate degradation pathway allowing soil bacteria to utilize 2,5-xylenol, 3,5-xylenol, and m-cresol as sole carbon and energy sources. NDO catalyzes the cleavage of 1-hydroxy-2-naphthoate as part of the bacterial phenanthrene degradation pathway. SDO is a ring cleavage dioxygenase from Pseudaminobacter salicylatoxidans that oxidizes salicylate to 2-oxohepta-3,5-dienedioic acid via a novel ring fission mechanism. SDO differs from other known GDOs and NDOs in its unique ability to oxidatively cleave many different salicylate, gentisate and 1-hydroxy-2-naphthoate substrates with high catalytic efficiency. The active site of these enzymes is located in the N-terminal domain but could be influenced by changes in the C-terminal domain, which lacks the strictly conserved metal-binding residues found in other cupin domains and is thought to be an inactive vestigial remnant.


Pssm-ID: 380346 [Multi-domain]  Cd Length: 108  Bit Score: 36.77  E-value: 2.59e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1731510250  37 HTHHFTELLFVVSGEGSFSF-NQEQSPLRRGDLVIIPPYTEH 77
Cdd:cd02216    37 HRHTPNALRFVLEGPGAYTTvDGERCDMEPGDLILTPPGTWH 78
OxdD COG2140
Oxalate decarboxylase/archaeal phosphoglucose isomerase, cupin superfamily [Carbohydrate ...
 36-90 3.82e-03

Oxalate decarboxylase/archaeal phosphoglucose isomerase, cupin superfamily [Carbohydrate transport and metabolism]; Oxalate decarboxylase/archaeal phosphoglucose isomerase, cupin superfamily is part of the Pathway/BioSystem: Glycolysis


Pssm-ID: 441743 [Multi-domain]  Cd Length: 115  Bit Score: 36.48  E-value: 3.82e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1731510250  36 MHTH-HFTELLFVVSGEGSFSF-----NQEQSPLRRGDLVIIPPYTEHTERSSQNHPLEYY 90
Cdd:COG2140    18 EHWHpNAAEWYYVLSGEARMTVqdppgRARTVDVGPGDVVYVPPGYGHYIINTGDEPLVFL 78
cupin_KdgF cd02238
pectin degradation protein KdgF and related proteins, cupin domain; This family includes ...
 36-77 4.95e-03

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: 35.91  E-value: 4.95e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1731510250  36 MHTHHFTELLFVVSGEGSFSFNQEQSPLRRGDLVIIPPYTEH 77
Cdd:cd02238    42 LHSHPHEQIGYVLSGRFEFTIGGETRILKPGDSYYIPPNVPH 83
ChrR COG3806
Anti-sigma factor ChrR, cupin superfamily [Signal transduction mechanisms];
36-78 8.14e-03

Anti-sigma factor ChrR, cupin superfamily [Signal transduction mechanisms];


Pssm-ID: 443019  Cd Length: 157  Bit Score: 36.07  E-value: 8.14e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1731510250  36 MHTHHFTELLFVVSGegsfSFNQEQSPLRRGDLVIIPPYTEHT 78
Cdd:COG3806    82 EHTHRGGEETLVLEG----AFSDEHGDYGAGDFIRADPGSEHQ 120
cupin_Bh2720-like cd02223
Bacillus halodurans Bh2720 and related proteins, cupin domain; This family includes bacterial, ...
 38-92 8.55e-03

Bacillus halodurans Bh2720 and related proteins, cupin domain; This family includes bacterial, archaeal, and eukaryotic proteins similar to Bh2720, a Bacillus halodurans protein of unknown function with a cupin beta-barrel fold.


Pssm-ID: 380352 [Multi-domain]  Cd Length: 98  Bit Score: 34.83  E-value: 8.55e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1731510250  38 THHFTE-LLFVVSGEGSFSFNQEQSPLRRGDLVIIPPYTEHTERSSQNHPLEYYVL 92
Cdd:cd02223    28 VHDDVDqFLRIEEGEGKAIMGGFESEVKDGDAIIVPAGTWHNVINTGNEPLKLYTI 83
PRK09940 PRK09940
transcriptional regulator YdeO; Provisional
 218-273 8.71e-03

transcriptional regulator YdeO; Provisional


Pssm-ID: 182157 [Multi-domain]  Cd Length: 253  Bit Score: 36.99  E-value: 8.71e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1731510250 218 QYLNQTRLKRAQHLLKnTNYSISDIASSTGFSSQSYFTQIFRKNFNMTPVKYRQEH 273
Cdd:PRK09940  180 QILLDARMQHAKNLIR-VEGSVNKIAEQCGYASTSYFIYAFRKHFGNSPKRVSKEY 234
 
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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