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Conserved domains on  [gi|489526565|ref|WP_003431317|]
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helix-turn-helix domain-containing protein [Clostridioides difficile]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 13297893)

helix-turn-helix domain-containing protein such as an AraC family transcriptional regulator, which controls the expression of genes with diverse biological functions including metabolism, stress response, and virulence

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;
198-281 2.15e-25

helix_turn_helix, arabinose operon control protein;


:

Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 96.47  E-value: 2.15e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489526565   198 PIKLEDVSYEVGFSVYYFTKFFKKNTGKTFITFLNEYRLEKAKWILLNNNISIVDLVEEVGFGSTKTFYRVFKEKIGVSP 277
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 489526565   278 LEFK 281
Cdd:smart00342  81 SEYR 84
PRK10371 super family cl32508
transcriptional regulator MelR;
26-282 4.44e-12

transcriptional regulator MelR;


The actual alignment was detected with superfamily member PRK10371:

Pssm-ID: 182416 [Multi-domain]  Cd Length: 302  Bit Score: 65.23  E-value: 4.44e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489526565  26 LTTPHWHKEIEILLITEGVVNLFINDKPMQLKKGEIVIIKGGDIHYiLPSPGSER--LVFQFDISFFNDLILlneeKESL 103
Cdd:PRK10371  38 MPTSHWHGQVEVNVPFDGDVEYLINNEKVQINQGHITLFWACTPHQ-LTDPGNCRsmAIFNLPMHLFLSWPL----DKDL 112

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489526565 104 IN--LFSSIKKCSrdwsAKIRKSVFDIL-----IDIYNEDLYKIEGYSYAIKGKMYNL---IPILYRQiPREIEENTVey 173
Cdd:PRK10371 113 INhvTHGMVIKSL----ATQQLSPFEVRrwqqeLNSPNEQIRQLAIDEIGLMLKRFSLsgwEPILVNK-TSRTHKNSV-- 185

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489526565 174 einSKEILERLNNIFKYVEKNYKQPIKLEDVSYEVGFSVYYFTKFFKKNTGKTFITFLNEYRLEKAKWILLNNNISIVDL 253
Cdd:PRK10371 186 ---SRHAQFYVSQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQRVMQLTMKQYITAMRINHVRALLSDTDKSILDI 262

                        250       260
                 ....*....|....*....|....*....
gi 489526565 254 VEEVGFGSTKTFYRVFKEKIGVSPLEFKK 282
Cdd:PRK10371 263 ALTAGFRSSSRFYSTFGKYVGMSPQQYRK 291
 
Name Accession Description Interval E-value
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
198-281 2.15e-25

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 96.47  E-value: 2.15e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489526565   198 PIKLEDVSYEVGFSVYYFTKFFKKNTGKTFITFLNEYRLEKAKWILLNNNISIVDLVEEVGFGSTKTFYRVFKEKIGVSP 277
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 489526565   278 LEFK 281
Cdd:smart00342  81 SEYR 84
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
199-288 1.53e-24

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 99.47  E-value: 1.53e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489526565 199 IKLEDVSYEVGFSVYYFTKFFKKNTGKTFITFLNEYRLEKAKWILLNNNISIVDLVEEVGFGSTKTFYRVFKEKIGVSPL 278
Cdd:COG2207  169 LTLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPS 248

                         90
                 ....*....|
gi 489526565 279 EFKKRYNSLE 288
Cdd:COG2207  249 EYRKRLRARA 258
HTH_18 pfam12833
Helix-turn-helix domain;
207-283 1.20e-18

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 78.40  E-value: 1.20e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489526565  207 EVGFSVYYFTKFFKKNTGKTFITFLNEYRLEKAKWILLNN-NISIVDLVEEVGFGSTKTFYRVFKEKIGVSPLEFKKR 283
Cdd:pfam12833   4 ALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLEDtGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRRR 81
PRK10371 PRK10371
transcriptional regulator MelR;
26-282 4.44e-12

transcriptional regulator MelR;


Pssm-ID: 182416 [Multi-domain]  Cd Length: 302  Bit Score: 65.23  E-value: 4.44e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489526565  26 LTTPHWHKEIEILLITEGVVNLFINDKPMQLKKGEIVIIKGGDIHYiLPSPGSER--LVFQFDISFFNDLILlneeKESL 103
Cdd:PRK10371  38 MPTSHWHGQVEVNVPFDGDVEYLINNEKVQINQGHITLFWACTPHQ-LTDPGNCRsmAIFNLPMHLFLSWPL----DKDL 112

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489526565 104 IN--LFSSIKKCSrdwsAKIRKSVFDIL-----IDIYNEDLYKIEGYSYAIKGKMYNL---IPILYRQiPREIEENTVey 173
Cdd:PRK10371 113 INhvTHGMVIKSL----ATQQLSPFEVRrwqqeLNSPNEQIRQLAIDEIGLMLKRFSLsgwEPILVNK-TSRTHKNSV-- 185

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489526565 174 einSKEILERLNNIFKYVEKNYKQPIKLEDVSYEVGFSVYYFTKFFKKNTGKTFITFLNEYRLEKAKWILLNNNISIVDL 253
Cdd:PRK10371 186 ---SRHAQFYVSQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQRVMQLTMKQYITAMRINHVRALLSDTDKSILDI 262

                        250       260
                 ....*....|....*....|....*....
gi 489526565 254 VEEVGFGSTKTFYRVFKEKIGVSPLEFKK 282
Cdd:PRK10371 263 ALTAGFRSSSRFYSTFGKYVGMSPQQYRK 291
PRK11511 PRK11511
MDR efflux pump AcrAB transcriptional activator MarA;
184-281 5.79e-11

MDR efflux pump AcrAB transcriptional activator MarA;


Pssm-ID: 236920 [Multi-domain]  Cd Length: 127  Bit Score: 58.96  E-value: 5.79e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489526565 184 LNNIFKYVEKNYKQPIKLEDVSYEVGFSVYYFTKFFKKNTGKTFITFLNEYRLEKAKWILLNNNISIVDLVEEVGFGSTK 263
Cdd:PRK11511  11 IHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEPILYLAERYGFESQQ 90

                         90
                 ....*....|....*...
gi 489526565 264 TFYRVFKEKIGVSPLEFK 281
Cdd:PRK11511  91 TLTRTFKNYFDVPPHKYR 108
AraC_binding pfam02311
AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization ...
 29-77 1.44e-07

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: 49.74  E-value: 1.44e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 489526565   29 PHWHKEIEILLITEGVVNLFINDKPMQLKKGEIVIIKGGDIHYILPSPG 77
Cdd:pfam02311  18 PHVHDFYVIGYIERGVGRFRLNGRTYHLGPGDLFLLPPGEPHDYEPESE 66
cupin_MJ1618 cd02214
Methanocaldococcus jannaschii MJ1618 and related proteins, cupin domain; This family includes ...
 27-83 2.79e-07

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: 47.90  E-value: 2.79e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 489526565  27 TTPHWHKEI-EILLITEGVVNLFINDKPMQLKKGEIVIIKGGDIHYIlPSPGSERLVF 83
Cdd:cd02214   32 TLPHRLKGSeEVYYILEGEGTMEIDGEPREVGPGDAVLIPPGAVQRI-ENTGEEDLVF 88
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
27-72 5.01e-07

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


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 47.15  E-value: 5.01e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 489526565  27 TTPHWHKEIEILLITEGVVNLFINDKPMQLKKGEIVIIKGGDIHYI 72
Cdd:COG1917   36 TPWHSHPGEELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAF 81
 
Name Accession Description Interval E-value
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
198-281 2.15e-25

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 96.47  E-value: 2.15e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489526565   198 PIKLEDVSYEVGFSVYYFTKFFKKNTGKTFITFLNEYRLEKAKWILLNNNISIVDLVEEVGFGSTKTFYRVFKEKIGVSP 277
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 489526565   278 LEFK 281
Cdd:smart00342  81 SEYR 84
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
199-288 1.53e-24

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 99.47  E-value: 1.53e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489526565 199 IKLEDVSYEVGFSVYYFTKFFKKNTGKTFITFLNEYRLEKAKWILLNNNISIVDLVEEVGFGSTKTFYRVFKEKIGVSPL 278
Cdd:COG2207  169 LTLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPS 248

                         90
                 ....*....|
gi 489526565 279 EFKKRYNSLE 288
Cdd:COG2207  249 EYRKRLRARA 258
HTH_18 pfam12833
Helix-turn-helix domain;
207-283 1.20e-18

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 78.40  E-value: 1.20e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489526565  207 EVGFSVYYFTKFFKKNTGKTFITFLNEYRLEKAKWILLNN-NISIVDLVEEVGFGSTKTFYRVFKEKIGVSPLEFKKR 283
Cdd:pfam12833   4 ALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLEDtGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRRR 81
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 189-283 1.62e-16

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: 78.56  E-value: 1.62e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489526565 189 KYVEKNYKQPIKLEDVSYEVGFSVYYFTKFFKKNTGKTFITFLNEYRLEKAKwILLNNNISIVDLVEEVGFGSTKTFYRV 268
Cdd:COG2169   91 RLIEAGAEDRPSLEDLAARLGLSPRHLRRLFKAHTGVTPKAYARARRLLRAR-QLLQTGLSVTDAAYAAGFGSLSRFYEA 169

                         90
                 ....*....|....*
gi 489526565 269 FKEKIGVSPLEFKKR 283
Cdd:COG2169  170 FKKLLGMTPSAYRRG 184
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 182-286 1.88e-16

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: 77.89  E-value: 1.88e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489526565 182 ERLNNIFKYVEKNYKQPIKLEDVSYEVGFSVYYFTKFFKKNTGKTFITFLNEYRLEKAKWILLNNNISIVDLVEEVGFGS 261
Cdd:COG4977  210 PRLARAQAWMEANLEEPLSVDELARRAGMSPRTLERRFRAATGTTPARYLQRLRLERARRLLETTDLSIEEIAAACGFGS 289

                         90       100
                 ....*....|....*....|....*
gi 489526565 262 TKTFYRVFKEKIGVSPLEFKKRYNS 286
Cdd:COG4977  290 ASHFRRAFRRRFGVSPSAYRRRFRA 314
PRK10371 PRK10371
transcriptional regulator MelR;
26-282 4.44e-12

transcriptional regulator MelR;


Pssm-ID: 182416 [Multi-domain]  Cd Length: 302  Bit Score: 65.23  E-value: 4.44e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489526565  26 LTTPHWHKEIEILLITEGVVNLFINDKPMQLKKGEIVIIKGGDIHYiLPSPGSER--LVFQFDISFFNDLILlneeKESL 103
Cdd:PRK10371  38 MPTSHWHGQVEVNVPFDGDVEYLINNEKVQINQGHITLFWACTPHQ-LTDPGNCRsmAIFNLPMHLFLSWPL----DKDL 112

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489526565 104 IN--LFSSIKKCSrdwsAKIRKSVFDIL-----IDIYNEDLYKIEGYSYAIKGKMYNL---IPILYRQiPREIEENTVey 173
Cdd:PRK10371 113 INhvTHGMVIKSL----ATQQLSPFEVRrwqqeLNSPNEQIRQLAIDEIGLMLKRFSLsgwEPILVNK-TSRTHKNSV-- 185

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489526565 174 einSKEILERLNNIFKYVEKNYKQPIKLEDVSYEVGFSVYYFTKFFKKNTGKTFITFLNEYRLEKAKWILLNNNISIVDL 253
Cdd:PRK10371 186 ---SRHAQFYVSQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQRVMQLTMKQYITAMRINHVRALLSDTDKSILDI 262

                        250       260
                 ....*....|....*....|....*....
gi 489526565 254 VEEVGFGSTKTFYRVFKEKIGVSPLEFKK 282
Cdd:PRK10371 263 ALTAGFRSSSRFYSTFGKYVGMSPQQYRK 291
PRK11511 PRK11511
MDR efflux pump AcrAB transcriptional activator MarA;
184-281 5.79e-11

MDR efflux pump AcrAB transcriptional activator MarA;


Pssm-ID: 236920 [Multi-domain]  Cd Length: 127  Bit Score: 58.96  E-value: 5.79e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489526565 184 LNNIFKYVEKNYKQPIKLEDVSYEVGFSVYYFTKFFKKNTGKTFITFLNEYRLEKAKWILLNNNISIVDLVEEVGFGSTK 263
Cdd:PRK11511  11 IHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEPILYLAERYGFESQQ 90

                         90
                 ....*....|....*...
gi 489526565 264 TFYRVFKEKIGVSPLEFK 281
Cdd:PRK11511  91 TLTRTFKNYFDVPPHKYR 108
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
183-284 7.69e-10

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 58.45  E-value: 7.69e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489526565 183 RLNNIFKYVEKNYKQPIKLEDVSYEVGFSVYYFTKFFKKNTGKTFITFLNEYRLEKAKWILLNNNISIVDLVEEVGFGST 262
Cdd:PRK10572 184 RVREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWREDQRISRAKLLLQTTRMPIATIGRNVGYDDQ 263

                         90       100
                 ....*....|....*....|..
gi 489526565 263 KTFYRVFKEKIGVSPLEFKKRY 284
Cdd:PRK10572 264 LYFSRVFKKCTGASPSEFRARC 285
PRK10219 PRK10219
superoxide response transcriptional regulator SoxS;
182-283 6.82e-09

superoxide response transcriptional regulator SoxS;


Pssm-ID: 182314 [Multi-domain]  Cd Length: 107  Bit Score: 52.62  E-value: 6.82e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489526565 182 ERLNNIFKYVEKNYKQPIKLEDVSYEVGFSVYYFTKFFKKNTGKTFITFLNEYRLEKAKWILLNNNISIVDLVEEVGFGS 261
Cdd:PRK10219   5 KIIQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLLAAVELRTTERPIFDIAMDLGYVS 84

                         90       100
                 ....*....|....*....|..
gi 489526565 262 TKTFYRVFKEKIGVSPLEFKKR 283
Cdd:PRK10219  85 QQTFSRVFRRQFDRTPSDYRHR 106
ftrA PRK09393
transcriptional activator FtrA; Provisional
 183-284 8.78e-08

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 52.66  E-value: 8.78e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489526565 183 RLNNIFKYVEKNYKQPIKLEDVSYEVGFSVYYFTKFFKKNTGKTFITFLNEYRLEKAKWILLNNNISIVDLVEEVGFGST 262
Cdd:PRK09393 219 RLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLARARDLLESSALSIDQIAERAGFGSE 298

                         90       100
                 ....*....|....*....|..
gi 489526565 263 KTFYRVFKEKIGVSPLEFKKRY 284
Cdd:PRK09393 299 ESLRHHFRRRAATSPAAYRKRF 320
AraC_binding pfam02311
AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization ...
 29-77 1.44e-07

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: 49.74  E-value: 1.44e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 489526565   29 PHWHKEIEILLITEGVVNLFINDKPMQLKKGEIVIIKGGDIHYILPSPG 77
Cdd:pfam02311  18 PHVHDFYVIGYIERGVGRFRLNGRTYHLGPGDLFLLPPGEPHDYEPESE 66
cupin_MJ1618 cd02214
Methanocaldococcus jannaschii MJ1618 and related proteins, cupin domain; This family includes ...
 27-83 2.79e-07

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: 47.90  E-value: 2.79e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 489526565  27 TTPHWHKEI-EILLITEGVVNLFINDKPMQLKKGEIVIIKGGDIHYIlPSPGSERLVF 83
Cdd:cd02214   32 TLPHRLKGSeEVYYILEGEGTMEIDGEPREVGPGDAVLIPPGAVQRI-ENTGEEDLVF 88
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
27-72 5.01e-07

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


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 47.15  E-value: 5.01e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 489526565  27 TTPHWHKEIEILLITEGVVNLFINDKPMQLKKGEIVIIKGGDIHYI 72
Cdd:COG1917   36 TPWHSHPGEELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAF 81
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 191-232 2.15e-06

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: 43.68  E-value: 2.15e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 489526565  191 VEKNYKQPIKLEDVSYEVGFSVYYFTKFFKKNTGKTFITFLN 232
Cdd:pfam00165   1 LRENLSTNLTIADIADELGFSRSYFSRLFKKYTGVTPSQYRH 42
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
30-281 2.44e-06

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 48.13  E-value: 2.44e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489526565  30 HWHKEIEILLITEGVVNLFINDKPMQLKKGEIVIIKGGDIHyilPSPGSERLVFQfDISFFNDLILLNEEKESLINLFSS 109
Cdd:PRK13502  34 HTHEFCELVMVWRGNGLHVLNERPYRITRGDLFYIRAEDKH---SYTSVNDLVLQ-NIIYCPERLKLNVNWQAMIPGFQG 109

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489526565 110 IKKCSRdWSakirksVFDILIDIYNEDLYKIEGYSYAIKGKMYNLIPILYRQIPREIEEN---TVEYEINSKEILerLNN 186
Cdd:PRK13502 110 AQWHPH-WR------LGSMGMNQARQVINQLEHESNGRDPLANEMAELLFGQLVMTLKRHryaTDDLPATSRETL--LDK 180

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489526565 187 IFKYVEKNYKQPIKLEDVSYEVGFSVYYFTKFFKKNTGKTFITFLNEYRLEKAKWILLNNNISIVDLVEEVGFGSTKTFY 266
Cdd:PRK13502 181 LITALANSLECPFALDAFCQQEQCSERVLRQQFRAQTGMTINQYLRQVRICHAQYLLQHSPLMISEISMQCGFEDSNYFS 260

                        250
                 ....*....|....*
gi 489526565 267 RVFKEKIGVSPLEFK 281
Cdd:PRK13502 261 VVFTRETGMTPSQWR 275
cupin_DddK cd06988
Dimethylsulfoniopropionate lyase DddK and related proteins, cupin domain; This family includes ...
 27-83 3.89e-06

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: 44.15  E-value: 3.89e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 489526565  27 TTPHWHKEIEILLITEGVVNLFINDKPMQLKKGEIVIIKGGDIHYILpSPGSERLVF 83
Cdd:cd06988   15 STPHSHHEYEIFIVISGKGIVVVDGEREPVKAGDVVYIPPGTEHYVK-NDGDEDFEF 70
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
182-279 1.64e-05

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 45.44  E-value: 1.64e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489526565 182 ERLNNIFKYVEKNYKQPIKLEDVSYEVGFSVYYFTKFFKKNTGKTFITFLNEYRLEKAKWILLNNNISIVDLVEEVGFGS 261
Cdd:PRK13503 171 ARLNQLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRHSDASVTDIAYRCGFGD 250

                         90
                 ....*....|....*...
gi 489526565 262 TKTFYRVFKEKIGVSPLE 279
Cdd:PRK13503 251 SNHFSTLFRREFSWSPRD 268
ManC COG0662
Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism];
27-83 3.99e-05

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


Pssm-ID: 440426 [Multi-domain]  Cd Length: 114  Bit Score: 42.05  E-value: 3.99e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 489526565  27 TTPHWHKEI-EILLITEGVVNLFINDKPMQLKKGEIVIIKGGDIHYILpSPGSERLVF 83
Cdd:COG0662   40 LSLHVHPHRdEFFYVLEGTGEVTIGDEEVELKAGDSVYIPAGVPHRLR-NPGDEPLEL 96
cupin_MelR-like_N cd06997
AraC/XylS family transcriptional regulators similar to Escherichia coli MelR, N-terminal cupin ...
 25-70 6.07e-05

AraC/XylS family transcriptional regulators similar to Escherichia coli MelR, 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, including Escherichia coli MelR, a transcription factor that controls melibiose utilization. MelR is encoded by the melR gene and is essential for melibiose-dependent triggering of the melAB operon that encodes products needed for melibiose catabolism and transport. Expression of melR is autoregulated by MelR, which represses the melR promoter by binding to a target that overlaps the transcript start. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380401  Cd Length: 78  Bit Score: 40.82  E-value: 6.07e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 489526565  25 VLTTPHWHKEIEILLITEGVVNLFINDKPMQLKKGEIVIIKGGDIH 70
Cdd:cd06997   10 IMPTPHWHGQVEVNIPFDGDVEYLINEHAVSLNAGHIGLFWGGLPH 55
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 29-83 9.25e-05

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: 39.93  E-value: 9.25e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 489526565   29 PHWHK-EIEILLITEGVVNLFINDKPMQLKKGEIVIIKGGDIHYILpSPGSERLVF 83
Cdd:pfam07883  13 PHRHPgEDEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPHRFR-NTGDEPARL 67
PRK15121 PRK15121
MDR efflux pump AcrAB transcriptional activator RobA;
190-277 5.35e-04

MDR efflux pump AcrAB transcriptional activator RobA;


Pssm-ID: 185076 [Multi-domain]  Cd Length: 289  Bit Score: 40.76  E-value: 5.35e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489526565 190 YVEKNYKQPIKLEDVSYEVGFSVYYFTKFFKKNTGKTFITFLNEYRLEKAKWILLNNNISIVDLVEEVGFGSTKTFYRVF 269
Cdd:PRK15121  13 WLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGHAIGAYIRARRLSKAAVALRLTSRPILDIALQYRFDSQQTFTRAF 92


                 ....*...
gi 489526565 270 KEKIGVSP 277
Cdd:PRK15121  93 KKQFAQTP 100
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 244-280 1.24e-03

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: 35.98  E-value: 1.24e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 489526565  244 LNNNISIVDLVEEVGFgSTKTFYRVFKEKIGVSPLEF 280
Cdd:pfam00165   5 LSTNLTIADIADELGF-SRSYFSRLFKKYTGVTPSQY 40
PRK10296 PRK10296
DNA-binding transcriptional regulator ChbR; Provisional
 214-286 5.11e-03

DNA-binding transcriptional regulator ChbR; Provisional


Pssm-ID: 182362 [Multi-domain]  Cd Length: 278  Bit Score: 37.81  E-value: 5.11e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489526565 214 YFTKFFKKNTGKTFITFLNEYRLEKAKWILLNNNISIVDLVEEVGFGSTKTFYRVFKEKIGVSPLEFKKRYNS 286
Cdd:PRK10296 204 YLTRATRRYYGKTPMQIINEIRINFAKKQLEMTNYSVTDIAFEAGYSSPSLFIKTFKKLTSFTPGSYRKKLTE 276
 
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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