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Conserved domains on  [gi|2456453452|ref|WP_275539308|]
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helix-turn-helix domain-containing protein [Gemmiger sp. An50]

Protein Classification

PocR and AraC domain-containing protein( domain architecture ID 11696725)

PocR and AraC domain-containing protein

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;
251-334 1.06e-32

helix_turn_helix, arabinose operon control protein;


:

Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 116.88  E-value: 1.06e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452  251 KVTLEQLAERVFLSPAYLSRVFKEETGTAFNDYLNRVRITKARQLLLHEELRIIDVASAVGFEDQSYFTKVFRRVTGMTP 330
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 2456453452  331 LRYR 334
Cdd:smart00342  81 SEYR 84
PRK13503 super family cl32884
HTH-type transcriptional activator RhaS;
168-330 7.28e-18

HTH-type transcriptional activator RhaS;


The actual alignment was detected with superfamily member PRK13503:

Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 82.42  E-value: 7.28e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452 168 AIQGQINSYILQLKQ-EERPSPYPFAT-EKAFLR---SIRRAEREEAG----RLLNELLGYIllasvfcyvdvrhahtih 238
Cdd:PRK13503  119 SVLQQVRQLVAQMEQqEESNDLEAIASrEILFMQllvLLRKSSLQENGensdARLNQLLAWL------------------ 180

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452 239 lcmqyiETHYHEKVTLEQLAERVFLSPAYLSRVFKEETGTAFNDYLNRVRITKARQLLLHEELRIIDVASAVGFEDQSYF 318
Cdd:PRK13503  181 ------EDHFAEEVNWEALADQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRHSDASVTDIAYRCGFGDSNHF 254

                         170
                  ....*....|..
gi 2456453452 319 TKVFRRVTGMTP 330
Cdd:PRK13503  255 STLFRREFSWSP 266
PocR super family cl47367
Ligand-binding sensor domain [Signal transduction mechanisms];
12-217 7.53e-15

Ligand-binding sensor domain [Signal transduction mechanisms];


The actual alignment was detected with superfamily member COG4936:

Pssm-ID: 443963 [Multi-domain]  Cd Length: 415  Bit Score: 74.83  E-value: 7.53e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452  12 STGLGCVVSNKQGDALAEYGYGCASCRV--CTLAGREKlqCVRAQNYSTAEAERFGGRYIYYCPMGLTCFVSPILGENES 89
Cdd:COG4936    20 ATGLAAVIVDPEGNPLTKPSNFQDFCRLirSTPEGRKR--CRESDARGGLEAAKTGKPYIYRCHAGLVDFAVPIIVEGEH 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452  90 AAHITAGPFLMVE-REDYIDCELTCLEKEqRTGIVRELESVPVVHTATVNQMSTLLFMAVGFLNKvSATERMRKVQSADA 168
Cdd:COG4936    98 LGNILGGQVLLEEpDEEEFRKIARELGFD-EEELLEALEEVPVVSEEKVQAAAELLFVIANYISE-LGYSNLEEELELLL 175

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 2456453452 169 IQGQINSYILQLKQEERPSPYPFATEKAFLRSIRRAEREEAGRLLNELL 217
Cdd:COG4936   176 QQSEKEEEEEERKELEALSSELSLLLLELLLVLVSLLLILLALKILLLL 224
 
Name Accession Description Interval E-value
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
251-334 1.06e-32

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 116.88  E-value: 1.06e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452  251 KVTLEQLAERVFLSPAYLSRVFKEETGTAFNDYLNRVRITKARQLLLHEELRIIDVASAVGFEDQSYFTKVFRRVTGMTP 330
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 2456453452  331 LRYR 334
Cdd:smart00342  81 SEYR 84
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
244-339 1.60e-31

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 119.11  E-value: 1.60e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452 244 IETHYHEKVTLEQLAERVFLSPAYLSRVFKEETGTAFNDYLNRVRITKARQLLLHEELRIIDVASAVGFEDQSYFTKVFR 323
Cdd:COG2207   161 LLLLLLLLLTLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFK 240

                          90
                  ....*....|....*.
gi 2456453452 324 RVTGMTPLRYRARYTQ 339
Cdd:COG2207   241 KRFGVTPSEYRKRLRA 256
HTH_18 pfam12833
Helix-turn-helix domain;
257-336 8.24e-27

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 101.13  E-value: 8.24e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452 257 LAERVFLSPAYLSRVFKEETGTAFNDYLNRVRITKARQLLLHE-ELRIIDVASAVGFEDQSYFTKVFRRVTGMTPLRYRA 335
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLEDtGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80


                  .
gi 2456453452 336 R 336
Cdd:pfam12833  81 R 81
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
209-338 4.80e-23

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 96.97  E-value: 4.80e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452 209 AGRLLNELLGYILLASVF--CY----VDVRHA--HTIHLCMQYIETHYHEKVTLEQLAERVFLSPAYLSRVFKEETGTAF 280
Cdd:PRK10572  149 SEGRYSELLAMNLLERLLlrCMeaipESLHPPmdPRVREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLGISV 228

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2456453452 281 NDYLNRVRITKARQLLLHEELRIIDVASAVGFEDQSYFTKVFRRVTGMTPLRYRARYT 338
Cdd:PRK10572  229 LRWREDQRISRAKLLLQTTRMPIATIGRNVGYDDQLYFSRVFKKCTGASPSEFRARCE 286
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
168-330 7.28e-18

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 82.42  E-value: 7.28e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452 168 AIQGQINSYILQLKQ-EERPSPYPFAT-EKAFLR---SIRRAEREEAG----RLLNELLGYIllasvfcyvdvrhahtih 238
Cdd:PRK13503  119 SVLQQVRQLVAQMEQqEESNDLEAIASrEILFMQllvLLRKSSLQENGensdARLNQLLAWL------------------ 180

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452 239 lcmqyiETHYHEKVTLEQLAERVFLSPAYLSRVFKEETGTAFNDYLNRVRITKARQLLLHEELRIIDVASAVGFEDQSYF 318
Cdd:PRK13503  181 ------EDHFAEEVNWEALADQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRHSDASVTDIAYRCGFGDSNHF 254

                         170
                  ....*....|..
gi 2456453452 319 TKVFRRVTGMTP 330
Cdd:PRK13503  255 STLFRREFSWSP 266
PocR COG4936
Ligand-binding sensor domain [Signal transduction mechanisms];
12-217 7.53e-15

Ligand-binding sensor domain [Signal transduction mechanisms];


Pssm-ID: 443963 [Multi-domain]  Cd Length: 415  Bit Score: 74.83  E-value: 7.53e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452  12 STGLGCVVSNKQGDALAEYGYGCASCRV--CTLAGREKlqCVRAQNYSTAEAERFGGRYIYYCPMGLTCFVSPILGENES 89
Cdd:COG4936    20 ATGLAAVIVDPEGNPLTKPSNFQDFCRLirSTPEGRKR--CRESDARGGLEAAKTGKPYIYRCHAGLVDFAVPIIVEGEH 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452  90 AAHITAGPFLMVE-REDYIDCELTCLEKEqRTGIVRELESVPVVHTATVNQMSTLLFMAVGFLNKvSATERMRKVQSADA 168
Cdd:COG4936    98 LGNILGGQVLLEEpDEEEFRKIARELGFD-EEELLEALEEVPVVSEEKVQAAAELLFVIANYISE-LGYSNLEEELELLL 175

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 2456453452 169 IQGQINSYILQLKQEERPSPYPFATEKAFLRSIRRAEREEAGRLLNELL 217
Cdd:COG4936   176 QQSEKEEEEEERKELEALSSELSLLLLELLLVLVSLLLILLALKILLLL 224
PocR pfam10114
Sensory domain found in PocR; PocR, a ligand binding domain, has a novel variant of the ...
 12-151 6.42e-13

Sensory domain found in PocR; PocR, a ligand binding domain, has a novel variant of the PAS-like Fold. Evidence suggests that it binds small hydrocarbon derivatives such as 1,3-propanediol. In (Natural history of sensor domains in bacterial signaling systems by Aravind L, LM Iyer, Anantharaman V, from 'Sensory Mechanisms in Bacteria: Molecular Aspects of Signal Recognition.' Caister Academic Press. 2010) - see (http://de.scribd.com/doc/28576661/Bacterial-Signaling-Chapter)


Pssm-ID: 462959  Cd Length: 155  Bit Score: 65.68  E-value: 6.42e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452  12 STGLGCVVSNKQGDALAEYGYGCASCRVC--TLAGREKlqCVRAQNYSTAEAERFGGRYIYYCPMGLTCFVSPILGENES 89
Cdd:pfam10114  12 ATGLAIVIVDLDGNPLTEPSNFTDFCKFIrsTPEGRKR--CRESDARGGREAAKPGEPYIYRCHAGLVDFAAPIIVEGEH 89

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2456453452  90 AAHITAGPFLMVE-REDYIDcELTCLEKEQRTGIVRELESVPVVHTATVNQMSTLLFMAVGFL 151
Cdd:pfam10114  90 IGNIICGQVLLEDpDEEEFR-EQAREIGFDEEEYLEALEKVPVLSEEKVRAAAELLFILANYI 151
 
Name Accession Description Interval E-value
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
251-334 1.06e-32

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 116.88  E-value: 1.06e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452  251 KVTLEQLAERVFLSPAYLSRVFKEETGTAFNDYLNRVRITKARQLLLHEELRIIDVASAVGFEDQSYFTKVFRRVTGMTP 330
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 2456453452  331 LRYR 334
Cdd:smart00342  81 SEYR 84
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
244-339 1.60e-31

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 119.11  E-value: 1.60e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452 244 IETHYHEKVTLEQLAERVFLSPAYLSRVFKEETGTAFNDYLNRVRITKARQLLLHEELRIIDVASAVGFEDQSYFTKVFR 323
Cdd:COG2207   161 LLLLLLLLLTLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFK 240

                          90
                  ....*....|....*.
gi 2456453452 324 RVTGMTPLRYRARYTQ 339
Cdd:COG2207   241 KRFGVTPSEYRKRLRA 256
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 233-337 2.86e-31

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: 119.88  E-value: 2.86e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452 233 HAH-TIHLCMQYIETHYHEKVTLEQLAERVFLSPAYLSRVFKEETGTAFNDYLNRVRITKARQLLLHEELRIIDVASAVG 311
Cdd:COG4977   207 HRDpRLARAQAWMEANLEEPLSVDELARRAGMSPRTLERRFRAATGTTPARYLQRLRLERARRLLETTDLSIEEIAAACG 286

                          90       100
                  ....*....|....*....|....*.
gi 2456453452 312 FEDQSYFTKVFRRVTGMTPLRYRARY 337
Cdd:COG4977   287 FGSASHFRRAFRRRFGVSPSAYRRRF 312
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 232-336 3.71e-27

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: 109.37  E-value: 3.71e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452 232 RHAHTIHLCMQYIETHYHEKVTLEQLAERVFLSPAYLSRVFKEETGTAFNDYLNRVRITKARQlLLHEELRIIDVASAVG 311
Cdd:COG2169    81 PRADLVARACRLIEAGAEDRPSLEDLAARLGLSPRHLRRLFKAHTGVTPKAYARARRLLRARQ-LLQTGLSVTDAAYAAG 159

                          90       100
                  ....*....|....*....|....*
gi 2456453452 312 FEDQSYFTKVFRRVTGMTPLRYRAR 336
Cdd:COG2169   160 FGSLSRFYEAFKKLLGMTPSAYRRG 184
HTH_18 pfam12833
Helix-turn-helix domain;
257-336 8.24e-27

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 101.13  E-value: 8.24e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452 257 LAERVFLSPAYLSRVFKEETGTAFNDYLNRVRITKARQLLLHE-ELRIIDVASAVGFEDQSYFTKVFRRVTGMTPLRYRA 335
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLEDtGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80


                  .
gi 2456453452 336 R 336
Cdd:pfam12833  81 R 81
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
209-338 4.80e-23

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 96.97  E-value: 4.80e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452 209 AGRLLNELLGYILLASVF--CY----VDVRHA--HTIHLCMQYIETHYHEKVTLEQLAERVFLSPAYLSRVFKEETGTAF 280
Cdd:PRK10572  149 SEGRYSELLAMNLLERLLlrCMeaipESLHPPmdPRVREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLGISV 228

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2456453452 281 NDYLNRVRITKARQLLLHEELRIIDVASAVGFEDQSYFTKVFRRVTGMTPLRYRARYT 338
Cdd:PRK10572  229 LRWREDQRISRAKLLLQTTRMPIATIGRNVGYDDQLYFSRVFKKCTGASPSEFRARCE 286
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
168-330 7.28e-18

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 82.42  E-value: 7.28e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452 168 AIQGQINSYILQLKQ-EERPSPYPFAT-EKAFLR---SIRRAEREEAG----RLLNELLGYIllasvfcyvdvrhahtih 238
Cdd:PRK13503  119 SVLQQVRQLVAQMEQqEESNDLEAIASrEILFMQllvLLRKSSLQENGensdARLNQLLAWL------------------ 180

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452 239 lcmqyiETHYHEKVTLEQLAERVFLSPAYLSRVFKEETGTAFNDYLNRVRITKARQLLLHEELRIIDVASAVGFEDQSYF 318
Cdd:PRK13503  181 ------EDHFAEEVNWEALADQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRHSDASVTDIAYRCGFGDSNHF 254

                         170
                  ....*....|..
gi 2456453452 319 TKVFRRVTGMTP 330
Cdd:PRK13503  255 STLFRREFSWSP 266
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
177-339 3.05e-16

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 78.02  E-value: 3.05e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452 177 ILQLKQEERPSPyPFA---TEKAFLRSI----RRAEREEAGRLLNE-----LLGYILLASVFCYVDVRHahtihLCMQYi 244
Cdd:PRK13501  130 IQQLAQESRKTD-SWSiqlTEVLLLQLAivlkRHRYRAEQAHLLPDgeqldLIMSALQQSLGAYFDMAD-----FCHKN- 202

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452 245 ethyhekvtleQLAERVflspayLSRVFKEETGTAFNDYLNRVRITKARQLLLHEELRIIDVASAVGFEDQSYFTKVFRR 324
Cdd:PRK13501  203 -----------QLVERS------LKQLFRQQTGMSISHYLRQIRLCHAKCLLRGSEHRISDIAARCGFEDSNYFSAVFTR 265

                         170
                  ....*....|....*
gi 2456453452 325 VTGMTPLRYRARYTQ 339
Cdd:PRK13501  266 EAGMTPRDYRQRFIR 280
PocR COG4936
Ligand-binding sensor domain [Signal transduction mechanisms];
12-217 7.53e-15

Ligand-binding sensor domain [Signal transduction mechanisms];


Pssm-ID: 443963 [Multi-domain]  Cd Length: 415  Bit Score: 74.83  E-value: 7.53e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452  12 STGLGCVVSNKQGDALAEYGYGCASCRV--CTLAGREKlqCVRAQNYSTAEAERFGGRYIYYCPMGLTCFVSPILGENES 89
Cdd:COG4936    20 ATGLAAVIVDPEGNPLTKPSNFQDFCRLirSTPEGRKR--CRESDARGGLEAAKTGKPYIYRCHAGLVDFAVPIIVEGEH 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452  90 AAHITAGPFLMVE-REDYIDCELTCLEKEqRTGIVRELESVPVVHTATVNQMSTLLFMAVGFLNKvSATERMRKVQSADA 168
Cdd:COG4936    98 LGNILGGQVLLEEpDEEEFRKIARELGFD-EEELLEALEEVPVVSEEKVQAAAELLFVIANYISE-LGYSNLEEELELLL 175

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 2456453452 169 IQGQINSYILQLKQEERPSPYPFATEKAFLRSIRRAEREEAGRLLNELL 217
Cdd:COG4936   176 QQSEKEEEEEERKELEALSSELSLLLLELLLVLVSLLLILLALKILLLL 224
PRK10371 PRK10371
transcriptional regulator MelR;
232-340 7.95e-15

transcriptional regulator MelR;


Pssm-ID: 182416 [Multi-domain]  Cd Length: 302  Bit Score: 74.09  E-value: 7.95e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452 232 RHAHT-IHLCMQYIETHYHEKVTLEQLAERVFLSPAYLSRVFKEETGTAFNDYLNRVRITKARQLLLHEELRIIDVASAV 310
Cdd:PRK10371  187 RHAQFyVSQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQRVMQLTMKQYITAMRINHVRALLSDTDKSILDIALTA 266

                          90       100       110
                  ....*....|....*....|....*....|
gi 2456453452 311 GFEDQSYFTKVFRRVTGMTPLRYRARYTQG 340
Cdd:PRK10371  267 GFRSSSRFYSTFGKYVGMSPQQYRKLSQQR 296
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
255-334 3.02e-14

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 72.01  E-value: 3.02e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452 255 EQLAERVflspayLSRVFKEETGTAFNDYLNRVRITKARQLLLHEELRIIDVASAVGFEDQSYFTKVFRRVTGMTPLRYR 334
Cdd:PRK13502  202 EQCSERV------LRQQFRAQTGMTINQYLRQVRICHAQYLLQHSPLMISEISMQCGFEDSNYFSVVFTRETGMTPSQWR 275
PRK13500 PRK13500
HTH-type transcriptional activator RhaR;
254-339 5.45e-14

HTH-type transcriptional activator RhaR;


Pssm-ID: 184091 [Multi-domain]  Cd Length: 312  Bit Score: 71.67  E-value: 5.45e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452 254 LEQLAERVFLSPAYLSRVFKEETGTAFNDYLNRVRITKARQLLLHEELRIIDVASAVGFEDQSYFTKVFRRVTGMTPLRY 333
Cdd:PRK13500  225 LDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQHSRLLISDISTECGFEDSNYFSVVFTRETGMTPSQW 304


                  ....*.
gi 2456453452 334 RARYTQ 339
Cdd:PRK13500  305 RHLNSQ 310
ftrA PRK09393
transcriptional activator FtrA; Provisional
 241-337 2.43e-13

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 69.61  E-value: 2.43e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452 241 MQYIETHYHEKVTLEQLAERVFLSPAYLSRVFKEETGTAFNDYLNRVRITKARQLLLHEELRIIDVASAVGFEDQSYFTK 320
Cdd:PRK09393  224 IDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLARARDLLESSALSIDQIAERAGFGSEESLRH 303

                          90
                  ....*....|....*..
gi 2456453452 321 VFRRVTGMTPLRYRARY 337
Cdd:PRK09393  304 HFRRRAATSPAAYRKRF 320
PocR pfam10114
Sensory domain found in PocR; PocR, a ligand binding domain, has a novel variant of the ...
 12-151 6.42e-13

Sensory domain found in PocR; PocR, a ligand binding domain, has a novel variant of the PAS-like Fold. Evidence suggests that it binds small hydrocarbon derivatives such as 1,3-propanediol. In (Natural history of sensor domains in bacterial signaling systems by Aravind L, LM Iyer, Anantharaman V, from 'Sensory Mechanisms in Bacteria: Molecular Aspects of Signal Recognition.' Caister Academic Press. 2010) - see (http://de.scribd.com/doc/28576661/Bacterial-Signaling-Chapter)


Pssm-ID: 462959  Cd Length: 155  Bit Score: 65.68  E-value: 6.42e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452  12 STGLGCVVSNKQGDALAEYGYGCASCRVC--TLAGREKlqCVRAQNYSTAEAERFGGRYIYYCPMGLTCFVSPILGENES 89
Cdd:pfam10114  12 ATGLAIVIVDLDGNPLTEPSNFTDFCKFIrsTPEGRKR--CRESDARGGREAAKPGEPYIYRCHAGLVDFAAPIIVEGEH 89

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2456453452  90 AAHITAGPFLMVE-REDYIDcELTCLEKEQRTGIVRELESVPVVHTATVNQMSTLLFMAVGFL 151
Cdd:pfam10114  90 IGNIICGQVLLEDpDEEEFR-EQAREIGFDEEEYLEALEKVPVLSEEKVRAAAELLFILANYI 151
PRK11511 PRK11511
MDR efflux pump AcrAB transcriptional activator MarA;
234-340 1.23e-12

MDR efflux pump AcrAB transcriptional activator MarA;


Pssm-ID: 236920 [Multi-domain]  Cd Length: 127  Bit Score: 63.97  E-value: 1.23e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452 234 AHTIHLCMQYIETHYHEKVTLEQLAERVFLSPAYLSRVFKEETGTAFNDYLNRVRITKARQLLLHEELRIIDVASAVGFE 313
Cdd:PRK11511    8 AITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEPILYLAERYGFE 87

                          90       100
                  ....*....|....*....|....*..
gi 2456453452 314 DQSYFTKVFRRVTGMTPLRYRARYTQG 340
Cdd:PRK11511   88 SQQTLTRTFKNYFDVPPHKYRMTNMQG 114
PRK10219 PRK10219
superoxide response transcriptional regulator SoxS;
233-336 2.01e-12

superoxide response transcriptional regulator SoxS;


Pssm-ID: 182314 [Multi-domain]  Cd Length: 107  Bit Score: 63.02  E-value: 2.01e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452 233 HAHTIHLCMQYIETHYHEKVTLEQLAERVFLSPAYLSRVFKEETGTAFNDYLNRVRITKARQLLLHEELRIIDVASAVGF 312
Cdd:PRK10219    3 HQKIIQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLLAAVELRTTERPIFDIAMDLGY 82

                          90       100
                  ....*....|....*....|....
gi 2456453452 313 EDQSYFTKVFRRVTGMTPLRYRAR 336
Cdd:PRK10219   83 VSQQTFSRVFRRQFDRTPSDYRHR 106
PRK09978 PRK09978
DNA-binding transcriptional regulator GadX; Provisional
 253-342 5.38e-10

DNA-binding transcriptional regulator GadX; Provisional


Pssm-ID: 137624 [Multi-domain]  Cd Length: 274  Bit Score: 59.17  E-value: 5.38e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452 253 TLEQLAERVFLSPAYLSRVFKEEtGTAFNDYLNRVRITKARQLLLHEELRIIDVASAVGFEDQSYFTKVFRRVTGMTPLR 332
Cdd:PRK09978  160 TLARIASELLMSPSLLKKKLREE-ETSYSQLLTECRMQRALQLIVIHGFSIKRVAVSCGYHSVSYFIYVFRNYYGMTPTE 238

                          90
                  ....*....|
gi 2456453452 333 YRARYTQGTD 342
Cdd:PRK09978  239 YQERSAQGLP 248
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 297-334 4.21e-09

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: 51.39  E-value: 4.21e-09
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 2456453452 297 LHEELRIIDVASAVGFeDQSYFTKVFRRVTGMTPLRYR 334
Cdd:pfam00165   5 LSTNLTIADIADELGF-SRSYFSRLFKKYTGVTPSQYR 41
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 244-285 9.84e-08

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: 47.53  E-value: 9.84e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2456453452 244 IETHYHEKVTLEQLAERVFLSPAYLSRVFKEETGTAFNDYLN 285
Cdd:pfam00165   1 LRENLSTNLTIADIADELGFSRSYFSRLFKKYTGVTPSQYRH 42
PRK15186 PRK15186
AraC family transcriptional regulator; Provisional
 251-335 5.56e-07

AraC family transcriptional regulator; Provisional


Pssm-ID: 185108 [Multi-domain]  Cd Length: 291  Bit Score: 50.45  E-value: 5.56e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452 251 KVTLEQLAERVFLSPAYLSRVFKEETgTAFND-YLNrVRITKARQLLLHEELRIIDVASAVGFEDQSYFTKVFRRVTGMT 329
Cdd:PRK15186  197 KWALKDISDSLYMSCSTLKRKLKQEN-TSFSEvYLN-ARMNKATKLLRNSEYNITRVAYMCGYDSASYFTCVFKKHFKTT 274


                  ....*.
gi 2456453452 330 PLRYRA 335
Cdd:PRK15186  275 PSEFLA 280
PRK09685 PRK09685
DNA-binding transcriptional activator FeaR; Provisional
 242-338 1.69e-06

DNA-binding transcriptional activator FeaR; Provisional


Pssm-ID: 236612 [Multi-domain]  Cd Length: 302  Bit Score: 48.87  E-value: 1.69e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452 242 QYIETHYH-EKVTLEQLAERVFLSPAYLSRVFkEETGTAFNDYLNRVRITKARQLL--LHEELRIIDVASAVGFEDQSYF 318
Cdd:PRK09685  204 ALIDQSIQeEILRPEWIAGELGISVRSLYRLF-AEQGLVVAQYIRNRRLDRCADDLrpAADDEKITSIAYKWGFSDSSHF 282

                          90       100
                  ....*....|....*....|
gi 2456453452 319 TKVFRRVTGMTPLRYRARYT 338
Cdd:PRK09685  283 STAFKQRFGVSPGEYRRKFR 302
PRK15435 PRK15435
bifunctional DNA-binding transcriptional regulator/O6-methylguanine-DNA methyltransferase Ada;
252-334 3.19e-06

bifunctional DNA-binding transcriptional regulator/O6-methylguanine-DNA methyltransferase Ada;


Pssm-ID: 185333 [Multi-domain]  Cd Length: 353  Bit Score: 48.25  E-value: 3.19e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452 252 VTLEQLAERVFLSPAYLSRVFKEETGTAFNDYLNRVRITKARQLLLHEElRIIDVASAVGFEDQSYFTKVFRRVTGMTPL 331
Cdd:PRK15435  100 VTLEALADQVAMSPFHLHRLFKATTGMTPKAWQQAWRARRLREALAKGE-SVTTSILNAGFPDSSSYYRKADETLGMTAK 178


                  ...
gi 2456453452 332 RYR 334
Cdd:PRK15435  179 QFR 181
PRK15121 PRK15121
MDR efflux pump AcrAB transcriptional activator RobA;
234-334 8.90e-06

MDR efflux pump AcrAB transcriptional activator RobA;


Pssm-ID: 185076 [Multi-domain]  Cd Length: 289  Bit Score: 46.54  E-value: 8.90e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2456453452 234 AHTIHLCMQYIETHYHEKVTLEQLAERVFLSPAYLSRVFKEETGTAFNDYLNRVRITKARQLLLHEELRIIDVASAVGFE 313
Cdd:PRK15121    4 AGIIRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGHAIGAYIRARRLSKAAVALRLTSRPILDIALQYRFD 83

                          90       100
                  ....*....|....*....|.
gi 2456453452 314 DQSYFTKVFRRVTGMTPLRYR 334
Cdd:PRK15121   84 SQQTFTRAFKKQFAQTPALYR 104
PRK15185 PRK15185
transcriptional regulator HilD; Provisional
 254-330 3.78e-05

transcriptional regulator HilD; Provisional


Pssm-ID: 185107 [Multi-domain]  Cd Length: 309  Bit Score: 44.99  E-value: 3.78e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2456453452 254 LEQLAERVFLSPAYLSRVFKEEtGTAFNDYLNRVRITKARQLLLHEELRIIDVASAVGFEDQSYFTKVFRRVTGMTP 330
Cdd:PRK15185  225 LTDVADHIFMSTSTLKRKLAEE-GTSFSDIYLSARMNQAAKLLRIGNHNVNAVALKCGYDSTSYFIQCFKKYFKTTP 300
PRK10296 PRK10296
DNA-binding transcriptional regulator ChbR; Provisional
 264-339 1.63e-03

DNA-binding transcriptional regulator ChbR; Provisional


Pssm-ID: 182362 [Multi-domain]  Cd Length: 278  Bit Score: 39.74  E-value: 1.63e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2456453452 264 SPAYLSRVFKEETGTAFNDYLNRVRITKARQLLLHEELRIIDVASAVGFEDQSYFTKVFRRVTGMTPLRYRARYTQ 339
Cdd:PRK10296  201 SQEYLTRATRRYYGKTPMQIINEIRINFAKKQLEMTNYSVTDIAFEAGYSSPSLFIKTFKKLTSFTPGSYRKKLTE 276
PRK15044 PRK15044
transcriptional regulator SirC; Provisional
 256-333 7.13e-03

transcriptional regulator SirC; Provisional


Pssm-ID: 185004 [Multi-domain]  Cd Length: 295  Bit Score: 37.71  E-value: 7.13e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2456453452 256 QLAERVFLSPAYLSRVFKEETGTAFNDYLNrVRITKARQLLLHEELRIIDVASAVGFEDQSYFTKVFRRVTGMTPLRY 333
Cdd:PRK15044  213 EVAGKLFMSVSSLKRKLAAEEVSFSKIYLD-ARMNQAIKLLRMGAGNISQVATMCGYDTPSYFIAIFKRHFKITPLSF 289
 
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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