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Conserved domains on  [gi|2582484231|ref|WP_311508976|]
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LysR family transcriptional regulator, partial [uncultured Corynebacterium sp.]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

LysR family transcriptional regulator containing an N-terminal HTH (helix-turn-helix) DNA-binding domain and a C-terminal substrate binding domain, which is structurally homologous to the type 2 periplasmic-binding (PBP2) fold proteins

CATH:  3.40.190.10
Gene Ontology:  GO:0003700|GO:0003677|GO:0006355
PubMed:  19047729|8257110|15808743
SCOP:  4000316

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
9-163 5.36e-46

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 150.79  E-value: 5.36e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231   9 TLPQLRAFVAIADTGHFGQAAARLGISQPSLSQALSTLEQGLGVQLVERSTRRVLVTPLGRGLIPYARQASEIVDEIVAR 88
Cdd:COG0583     2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2582484231  89 ASGRTDDLSGPLSIGVIPTVAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAIMALPSDVPSFE 163
Cdd:COG0583    82 LRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLV 156
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
9-163 5.36e-46

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 150.79  E-value: 5.36e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231   9 TLPQLRAFVAIADTGHFGQAAARLGISQPSLSQALSTLEQGLGVQLVERSTRRVLVTPLGRGLIPYARQASEIVDEIVAR 88
Cdd:COG0583     2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2582484231  89 ASGRTDDLSGPLSIGVIPTVAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAIMALPSDVPSFE 163
Cdd:COG0583    82 LRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLV 156
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 17-164 2.91e-32

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 116.67  E-value: 2.91e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231  17 VAIADTGHFGQAAARLGISQPSLSQALSTLEQGLGVQLVERSTRRVLVTPLGRGLIPYARQASEIVDEIVARASGRTDDL 96
Cdd:PRK11151   10 VALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKEMASQQGETM 89

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2582484231  97 SGPLSIGVIPTVAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAIMALPSD------VPSFEE 164
Cdd:PRK11151   90 SGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALVKEseafieVPLFDE 163
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 98-164 5.25e-26

The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily; OxyR senses hydrogen peroxide and is activated through the formation of an intramolecular disulfide bond. The OxyR activation induces the transcription of genes necessary for the bacterial defense against oxidative stress. The OxyR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The C-terminal domain also contains the redox-active cysteines that mediate the redox-dependent conformational switch. Thus, the interaction between the OxyR-tetramer and DNA is notably different between the oxidized and reduced forms. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176103 [Multi-domain]  Cd Length: 200  Bit Score: 97.60  E-value: 5.25e-26
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2582484231  98 GPLSIGVIPTVAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAIMALPSDVPSFEE 164
Cdd:cd08411     1 GPLRLGVIPTIAPYLLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEE 67
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 10-152 5.61e-25

selenium metabolism-associated LysR family transcriptional regulator; LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations.


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 97.30  E-value: 5.61e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231  10 LPQLRAFVAIADTGHFGQAAARLGISQPSLSQALSTLEQGLGVQLVERSTRRVLVTPLGRGLIPYARQASEIVDEIVARA 89
Cdd:NF040786    3 LKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEF 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2582484231  90 SGRTDDLSGPLSIGVIPTVAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAI 152
Cdd:NF040786   83 DRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGF 145
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
12-69 3.05e-22

Bacterial regulatory helix-turn-helix protein, lysR family;


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 83.97  E-value: 3.05e-22
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2582484231  12 QLRAFVAIADTGHFGQAAARLGISQPSLSQALSTLEQGLGVQLVERSTRRVLVTPLGR 69
Cdd:pfam00126   3 QLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
9-163 5.36e-46

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 150.79  E-value: 5.36e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231   9 TLPQLRAFVAIADTGHFGQAAARLGISQPSLSQALSTLEQGLGVQLVERSTRRVLVTPLGRGLIPYARQASEIVDEIVAR 88
Cdd:COG0583     2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2582484231  89 ASGRTDDLSGPLSIGVIPTVAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAIMALPSDVPSFE 163
Cdd:COG0583    82 LRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLV 156
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 17-164 2.91e-32

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 116.67  E-value: 2.91e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231  17 VAIADTGHFGQAAARLGISQPSLSQALSTLEQGLGVQLVERSTRRVLVTPLGRGLIPYARQASEIVDEIVARASGRTDDL 96
Cdd:PRK11151   10 VALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKEMASQQGETM 89

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2582484231  97 SGPLSIGVIPTVAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAIMALPSD------VPSFEE 164
Cdd:PRK11151   90 SGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALVKEseafieVPLFDE 163
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 98-164 5.25e-26

The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily; OxyR senses hydrogen peroxide and is activated through the formation of an intramolecular disulfide bond. The OxyR activation induces the transcription of genes necessary for the bacterial defense against oxidative stress. The OxyR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The C-terminal domain also contains the redox-active cysteines that mediate the redox-dependent conformational switch. Thus, the interaction between the OxyR-tetramer and DNA is notably different between the oxidized and reduced forms. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176103 [Multi-domain]  Cd Length: 200  Bit Score: 97.60  E-value: 5.25e-26
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2582484231  98 GPLSIGVIPTVAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAIMALPSDVPSFEE 164
Cdd:cd08411     1 GPLRLGVIPTIAPYLLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEE 67
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 10-152 5.61e-25

selenium metabolism-associated LysR family transcriptional regulator; LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations.


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 97.30  E-value: 5.61e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231  10 LPQLRAFVAIADTGHFGQAAARLGISQPSLSQALSTLEQGLGVQLVERSTRRVLVTPLGRGLIPYARQASEIVDEIVARA 89
Cdd:NF040786    3 LKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEF 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2582484231  90 SGRTDDLSGPLSIGVIPTVAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAI 152
Cdd:NF040786   83 DRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGF 145
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
12-69 3.05e-22

Bacterial regulatory helix-turn-helix protein, lysR family;


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 83.97  E-value: 3.05e-22
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2582484231  12 QLRAFVAIADTGHFGQAAARLGISQPSLSQALSTLEQGLGVQLVERSTRRVLVTPLGR 69
Cdd:pfam00126   3 QLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK09986 PRK09986
LysR family transcriptional regulator;
3-162 8.45e-20

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 83.62  E-value: 8.45e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231   3 NRDYRPTLPQLRAFVAIADTGHFGQAAARLGISQPSLSQALSTLEQGLGVQLVERSTRRVLVTPLG-------RGLIPYA 75
Cdd:PRK09986    2 ERLYRIDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGkilmeesRRLLDNA 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231  76 RQASEIVDEIVARASGRtddlsgpLSIGVIPTVAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAI--M 153
Cdd:PRK09986   82 EQSLARVEQIGRGEAGR-------IEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIwrM 154


                  ....*....
gi 2582484231 154 ALPSDVPSF 162
Cdd:PRK09986  155 ADLEPNPGF 163
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 10-161 2.18e-19

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 82.51  E-value: 2.18e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231  10 LPQLRAFVAIADTGHFGQAAARLGISQPSLSQALSTLEQGLGVQLVERSTRRVLVTPLGRGLIPYARQASEIVDEIVARA 89
Cdd:PRK09906    3 LRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLRA 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2582484231  90 SgRTDDLSGPLSIGVIPT----VAPYVLPNFlqlvRDELPDLKPRIVEEPTERLIESLRSGTIDAAIMALPSDVPS 161
Cdd:PRK09906   83 R-KIVQEDRQLTIGFVPSaevnLLPKVLPMF----RLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDE 153
rbcR CHL00180
LysR transcriptional regulator; Provisional
 9-152 9.70e-19

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 80.83  E-value: 9.70e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231   9 TLPQLRAFVAIADTGHFGQAAARLGISQPSLSQALSTLEQGLGVQLVERSTRRVLVTPLGRGLIPYARQASEIVDEiVAR 88
Cdd:CHL00180    6 TLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEE-TCR 84

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2582484231  89 AsgrTDDL----SGPLSIGVIPTVAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAI 152
Cdd:CHL00180   85 A---LEDLknlqRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAI 149
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 10-152 2.55e-18

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 79.62  E-value: 2.55e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231  10 LPQLRAFVAIADTGHFGQAAARLGISQPSLSQALSTLEQGLGVQLVERSTRRVLVTPLGRGLIPYARQASEIVDEiVARA 89
Cdd:PRK11242    3 LRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEA-GRRA 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2582484231  90 SGRTDDLS-GPLSIGVIPTVAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAI 152
Cdd:PRK11242   82 IHDVADLSrGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGI 145
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 10-153 3.85e-16

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 73.56  E-value: 3.85e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231  10 LPQLRAFVAIADTGHFGQAAARLGISQPSLSQALSTLEQGLGVQLVERSTRRVLVTPLGRGLIPYAR-------QASEIV 82
Cdd:PRK11233    3 FRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARailrqceQAQLAV 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2582484231  83 DeivarASGRTddLSGPLSIGVIP-TVAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAIM 153
Cdd:PRK11233   83 H-----NVGQA--LSGQVSIGLAPgTAASSLTMPLLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAVI 147
PRK09791 PRK09791
LysR family transcriptional regulator;
10-152 4.80e-16

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 73.26  E-value: 4.80e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231  10 LPQLRAFVAIADTGHFGQAAARLGISQPSLSQALSTLEQGLGVQLVERSTRRVLVTPLGRGlipYARQASEIVDEI-VAR 88
Cdd:PRK09791    7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGES---FYQHASLILEELrAAQ 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2582484231  89 AS--GRTDDLSGPLSIGVIPTVAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAI 152
Cdd:PRK09791   84 EDirQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTI 149
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 9-127 5.53e-16

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 73.18  E-value: 5.53e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231   9 TLPQLRAFVAIADTGHFGQAAARLGISQPSLSQALSTLEQGLGVQLVERSTRRVLVTPLGRGLIPYAR----QASEIvdE 84
Cdd:PRK10837    4 TLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALalleQAVEI--E 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2582484231  85 IVARASgrtddlSGPLSIGVIPTVAPYVLPNFLQLVRDELPDL 127
Cdd:PRK10837   82 QLFRED------NGALRIYASSTIGNYILPAMIARYRRDYPQL 118
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 13-162 2.37e-15

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 71.60  E-value: 2.37e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231  13 LRAFVAIADTGHFGQAAARLGISQPSLSQALSTLEQGLGVQLVERSTRRVLVTPLGRGLIPYARQASEIVDEivARASGR 92
Cdd:PRK15092   16 LRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDE--ACSSLM 93

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2582484231  93 TDDLSGPLSIGVIPTVAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAI-MALPSDVPSF 162
Cdd:PRK15092   94 YSNLQGVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAVtTHRPSSFPAL 164
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
11-77 6.97e-13

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 64.61  E-value: 6.97e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2582484231  11 PQLRAFVAIADTGHFGQAAARLGISQPSLSQALSTLEQGLGVQLVERsTRRVLVTPLGRGLIPYARQ 77
Cdd:PRK13348    5 KQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQ 70
PRK12680 PRK12680
LysR family transcriptional regulator;
9-161 7.30e-13

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 64.64  E-value: 7.30e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231   9 TLPQLRAFVAIADTG-HFGQAAARLGISQPSLSQALSTLEQGLGVQLVERSTRRV-LVTPLGRGLIPYARQASEIVDEIV 86
Cdd:PRK12680    2 TLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNIR 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2582484231  87 ARASGRTDDLSGPLSIGVIPTVAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAIMALPSDVPS 161
Cdd:PRK12680   82 TYAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEPS 156
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 100-163 3.57e-12

The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, oxidative stress responses, nodule formation of nitrogen-fixing bacteria, synthesis of virulence factors, toxin production, attachment and secretion, to name a few. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 61.46  E-value: 3.57e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2582484231 100 LSIGVIPTVAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAIMALPSDVPSFE 163
Cdd:cd05466     2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLE 65
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
13-77 1.75e-11

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 60.59  E-value: 1.75e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2582484231  13 LRAFVAIADTGHFGQAAARLGISQPSLSQALSTLEQGLGVQLVERSTRRVLVTPLGRGLIPYARQ 77
Cdd:PRK10094    7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARD 71
PRK10341 PRK10341
transcriptional regulator TdcA;
8-158 3.68e-11

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 59.88  E-value: 3.68e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231   8 PTLPQLRAFVAIADTGHFGQAAARLGISQPSLSQALSTLEQGLGVQLVERSTRRVLVTPLGRGLIPYARQASEIVDEIVA 87
Cdd:PRK10341    7 PKTQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVN 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2582484231  88 RASGRTDDLSGPLSIGVIPTVAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAIMALPSD 158
Cdd:PRK10341   87 EINGMSSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSNE 157
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 99-159 2.65e-10

The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily; This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (LTTRs) are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of N2 fixing bacteria, and synthesis of virulence factors, to a name a few. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176104 [Multi-domain]  Cd Length: 198  Bit Score: 56.40  E-value: 2.65e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2582484231  99 PLSIGVIPTVAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAIM---ALPSDV 159
Cdd:cd08412     1 TLRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTydlDLPEDI 64
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
11-160 2.81e-10

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 57.09  E-value: 2.81e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231  11 PQLRAFVAIADTGHFGQAAARLGISQPSLSQALSTLEQGLGVQLVERsTRRVLVTPLGRGLIPYARQ----ASEIVDEIV 86
Cdd:PRK03635    5 KQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARQvrllEAELLGELP 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231  87 ARASGRTddlsgPLSIGV---------IPTVAPYV--LPNFLQLVRDElpdlkprivEEPTerlIESLRSGTIDAAIMAL 155
Cdd:PRK03635   84 ALDGTPL-----TLSIAVnadslatwfLPALAPVLarSGVLLDLVVED---------QDHT---AELLRRGEVVGAVTTE 146


                  ....*
gi 2582484231 156 PSDVP 160
Cdd:PRK03635  147 PQPVQ 151
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 97-163 3.65e-10

LysR substrate binding domain; The structure of this domain is known and is similar to the periplasmic binding proteins. This domain binds a variety of ligands that caries in size and structure, such as amino acids, sugar phosphates, organic acids, metal cations, flavonoids, C6-ring carboxylic acids, H2O2, HOCl, homocysteine, NADPH, ATP, sulphate, muropeptides, acetate, salicylate, citrate, phenol- and quinolone derivatives, acetylserines, fatty acid CoA, shikimate, chorismate, homocysteine, indole-3-acetic acid, Na(I), c-di-GMP, ppGpp and hydrogen peroxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 56.14  E-value: 3.65e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2582484231  97 SGPLSIGVIPTVAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAIMALPSDVPSFE 163
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLE 67
cysB PRK12681
HTH-type transcriptional regulator CysB;
10-152 8.82e-10

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 56.06  E-value: 8.82e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231  10 LPQLRAFVAIADTG-HFGQAAARLGISQPSLSQALSTLEQGLGVQLVERS----TRrvlVTPLGRGLIPYARQASEIVDE 84
Cdd:PRK12681    3 LQQLRYIVEVVNHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSgkhlTQ---VTPAGEEIIRIAREILSKVES 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2582484231  85 IVARASGRTDDLSGPLSIGVIPTVAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAI 152
Cdd:PRK12681   80 IKSVAGEHTWPDKGSLYIATTHTQARYALPPVIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADFAI 147
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 8-152 5.71e-09

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 53.31  E-value: 5.71e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231   8 PTLPQLRAFVAIADTGHFGQAAARLGISQPSLSQALSTLEQGLGVQLVERSTRRVLVTPLGRGlipYARQASEIVDEIVA 87
Cdd:PRK11139    6 PPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQR---YFLDIREIFDQLAE 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2582484231  88 -----RASGRTddlsGPLSIGVIPTVA-----PYvLPNFLQLVrdelPDLKPRIVEepTERLIESLRSGtIDAAI 152
Cdd:PRK11139   83 atrklRARSAK----GALTVSLLPSFAiqwlvPR-LSSFNEAH----PDIDVRLKA--VDRLEDFLRDD-VDVAI 145
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 27-152 9.17e-09

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 53.07  E-value: 9.17e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231  27 QAAARLGISQPSLSQALSTLEQGLGVQLVERSTRRVL-VTPLGRGLIPYARQASEIVDEIVARASGRTDDLSGPLSIGVI 105
Cdd:PRK12682   21 EAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILREVGNIKRIGDDFSNQDSGTLTIATT 100

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2582484231 106 PTVAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAI 152
Cdd:PRK12682  101 HTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGI 147
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 100-163 1.91e-08

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LTTRs involved in degradation of aromatic compounds, such as CbnR, BenM, CatM, ClcR and TfdR, as well as that of other transcriptional regulators clustered together in phylogenetic trees, including XapR, HcaR, MprR, IlvR, BudR, AlsR, LysR, and OccR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176106 [Multi-domain]  Cd Length: 197  Bit Score: 51.35  E-value: 1.91e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2582484231 100 LSIGVIPTVAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAIMALPSDVPSFE 163
Cdd:cd08414     2 LRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLA 65
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
10-109 2.13e-08

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 51.93  E-value: 2.13e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231  10 LPQLRAFVAIADTGHFGQAAARLGISQPSLSQALSTLEQGLGVQLVERSTRRVLVTPLG-RGLIPYARQASEIVDEIVAR 88
Cdd:PRK10086   16 LSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGkRVFWALKSSLDTLNQEILDI 95

                          90       100
                  ....*....|....*....|.
gi 2582484231  89 ASGRtddLSGPLSIGVIPTVA 109
Cdd:PRK10086   96 KNQE---LSGTLTVYSRPSIA 113
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 99-158 2.05e-07

The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold; Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE. The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction system. In the presence of an inducing sugar such as L-arabinose, D-fucose, or D-galactose, GbpR activates chvE expression, while in the absence of an inducing sugar, GbpR represses expression. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176126 [Multi-domain]  Cd Length: 201  Bit Score: 48.42  E-value: 2.05e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231  99 PLSIGVIPTVAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAIMALPSD 158
Cdd:cd08435     1 TVRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIGRLADD 60
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
10-132 2.40e-07

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 48.99  E-value: 2.40e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231  10 LPQLRAFVAIADTGHFGQAAARLGISQPSLSQALSTLEQGLGVQLVERSTRRVLVTPLGRGLIPYARQASEIVDEIVARA 89
Cdd:PRK10632    4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQL 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2582484231  90 SGRTDDLSGPLSIGVIPTVAPYVLPNFLQLVRDELPDLKPRIV 132
Cdd:PRK10632   84 YAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLV 126
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
10-152 3.33e-07

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 48.43  E-value: 3.33e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231  10 LPQLRAFVAIADTG-HFGQAAARLGISQPSLSQALSTLEQGLGVQLVERSTRRVL-VTPLGRGLIPYARQASEIVDEIVA 87
Cdd:PRK12684    3 LHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERILQEVENLKR 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2582484231  88 RASGRTDDLSGPLSIGVIPTVAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAI 152
Cdd:PRK12684   83 VGKEFAAQDQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAI 147
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 9-143 4.07e-07

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 48.06  E-value: 4.07e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231   9 TLPQLRAFVAIADTGHFGQAAARLGISQPSLSQALSTLEQGLGVQLVERSTRRVLVTPLGRGLIPYARQASEIVDEIVAR 88
Cdd:PRK11013    5 SLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRSYYGLDRIVSA 84

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2582484231  89 ASGRTDDLSGPLSIGVIPTVAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESL 143
Cdd:PRK11013   85 AESLREFRQGQLSIACLPVFSQSLLPGLCQPFLARYPDVSLNIVPQESPLLEEWL 139
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
34-161 8.16e-07

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 47.12  E-value: 8.16e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231  34 ISQPSLSQALSTLEQGLGVQLVERSTRRVLVTPLGRGLIPYARQASEIVDEIVARASGRTDDLSGPLSIGVIPTVAPYVL 113
Cdd:PRK11716    3 VSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLFCSVTAAYSHL 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2582484231 114 PNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAIMALPSDVPS 161
Cdd:PRK11716   83 PPILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAAKPETLPA 130
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 12-152 1.37e-06

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 46.57  E-value: 1.37e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231  12 QLRAFVAIADTG-HFGQAAARLGISQPSLSQALSTLEQGLGVQLVERSTRRVL-VTPLGRGLIPyarqaseIVDEIVARA 89
Cdd:PRK12683    5 QLRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQ-------IVERMLLDA 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2582484231  90 ----------SGRTddlSGPLSIGVIPTVAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAI 152
Cdd:PRK12683   78 enlrrlaeqfADRD---SGHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGI 147
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
13-75 3.33e-06

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 45.39  E-value: 3.33e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2582484231  13 LRAFVAIADTGHFGQAAARLGISQPSLSQALSTLEQGLGVQLVERSTRRVLVTPLGRGLIPYA 75
Cdd:PRK03601    6 LKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYA 68
cbl PRK12679
HTH-type transcriptional regulator Cbl;
27-152 7.70e-06

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 44.42  E-value: 7.70e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231  27 QAAARLGISQPSLSQALSTLEQGLGVQLVERSTRRVL-VTPLGRGLIPYARQaseIVDEI--VAR-ASGRTDDLSGPLSI 102
Cdd:PRK12679   21 EVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLgMTEPGKALLVIAER---ILNEAsnVRRlADLFTNDTSGVLTI 97

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 2582484231 103 GVIPTVAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAI 152
Cdd:PRK12679   98 ATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGI 147
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 100-163 1.67e-05

TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176131 [Multi-domain]  Cd Length: 197  Bit Score: 42.90  E-value: 1.67e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2582484231 100 LSIGVIPTVAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAIMALPSDVPSFE 163
Cdd:cd08440     2 VRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLE 65
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 99-161 1.83e-05

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 42.97  E-value: 1.83e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2582484231  99 PLSIGVIPTVAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAIMALPSDVPS 161
Cdd:cd08436     1 RLAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPERRPP 63
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
13-116 2.05e-05

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 43.12  E-value: 2.05e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231  13 LRAFVAIADTGHFGQAAARLGISQPSLSQALSTLEQGLGVQLVERSTRRVLVTPLGRGLIPYARQASEIVDEIVARASGR 92
Cdd:PRK10082   16 LYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELRGG 95

                          90       100       110
                  ....*....|....*....|....*....|..
gi 2582484231  93 TD--------DLSGPLSIGVIPTVAPYVLPNF 116
Cdd:PRK10082   96 SDyaqrkikiAAAHSLSLGLLPSIISQMPPLF 127
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
10-77 4.01e-05

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 42.31  E-value: 4.01e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2582484231  10 LPQLRAFVAIADTGHFGQAAARLGISQPSLSQALSTLEQGLGVQLVERSTRRVLVTPLGRGLIPYARQ 77
Cdd:PRK15421    4 VKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQ 71
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 7-69 4.16e-05

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 42.28  E-value: 4.16e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2582484231   7 RPTLPQLRAFVAIADTGHFGQAAARLGISQPSLSQALSTLEQGLGVQLVERSTRRVLVTPLGR 69
Cdd:PRK14997    1 KTDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQ 63
PRK09801 PRK09801
LysR family transcriptional regulator;
8-85 5.90e-05

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 41.94  E-value: 5.90e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231   8 PTLPQLRAFVAIADTGHFGQAAARLGISQPSLSQALSTLEQGLGVQLVERSTRRVLVTPLGRGLIPYA----RQASEIVD 83
Cdd:PRK09801    6 PLAKDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHAleilTQYQRLVD 85


                  ..
gi 2582484231  84 EI 85
Cdd:PRK09801   86 DV 87
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 99-157 6.76e-05

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 41.41  E-value: 6.76e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2582484231  99 PLSIGVIPTVAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAIMALPS 157
Cdd:cd08427     1 RLRLGAIATVLTGLLPRALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVVEPP 59
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 18-154 2.23e-04

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 40.31  E-value: 2.23e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231  18 AIADTGHFGQAAARLGISQPSLSQALSTLEQGLGVQLVERSTRRVLVTPLGRGLIPYARQASEIVDEIVARASGRTDDLS 97
Cdd:PRK11074   12 AVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQVANGWR 91

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231  98 GPLSIGVIPTVAPYVLpnfLQLVRD---ELPDLKPRIVEEPTERLIESLRSGTIDAAIMA 154
Cdd:PRK11074   92 GQLSIAVDNIVRPDRT---RQLIVDfyrHFDDVELIIRQEVFNGVWDALADGRVDIAIGA 148
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
4-89 3.70e-04

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 38.80  E-value: 3.70e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231   4 RDYRPTLPQLRAFVAIADTG--HFGQAAARLGISQPSLSQALSTLEQGlgvQLVERST-----RRVLV--TPLGRGLIpy 74
Cdd:COG1846    32 AELGLTPAQFRVLAALAEAGglTQSELAERLGLTKSTVSRLLDRLEEK---GLVEREPdpedrRAVLVrlTEKGRALL-- 106

                          90
                  ....*....|....*
gi 2582484231  75 aRQASEIVDEIVARA 89
Cdd:COG1846   107 -EEARPALEALLAEL 120
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 99-152 5.64e-04

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 38.73  E-value: 5.64e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2582484231  99 PLSIGVIPTVAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAI 152
Cdd:cd08423     1 TLRVGAFPTAAAALLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAV 54
PBP2_DntR_NahR_LinR_like cd08459
The C-terminal substrate binding domain of LysR-type transcriptional regulators that are ...
 111-162 7.68e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate of the oxidative degradation of the aromatic ring in soil bacteria. LinR positively regulates expression of the genes (linD and linE) encoding enzymes for gamma-hexachlorocyclohexane (a haloorganic insecticide) degradation. Expression of linD and linE are induced by their substrates, 2,5-dichlorohydroquinone (2,5-DCHQ) and chlorohydroquinone (CHQ). The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176148 [Multi-domain]  Cd Length: 201  Bit Score: 38.33  E-value: 7.68e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2582484231 111 YVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAIMALPSDVPSF 162
Cdd:cd08459    13 YFLPRLLAALREVAPGVRIETVRLPVDELEEALESGEIDLAIGYLPDLGAGF 64
ModE COG2005
DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];
18-96 9.29e-04

DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];


Pssm-ID: 441608 [Multi-domain]  Cd Length: 118  Bit Score: 37.11  E-value: 9.29e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2582484231  18 AIADTGHFGQAAARLGISQPSLSQALSTLEQGLGVQLVERST--RR---VLVTPLGRGLIPYARQASEIVDEIVARASGR 92
Cdd:COG2005    29 AIDETGSISAAAKAMGMSYKRAWDLIDAMNNLLGEPLVERQTggKGgggARLTPEGRRLLALYRRLEAEAQRALAALFEE 108


                  ....
gi 2582484231  93 TDDL 96
Cdd:COG2005   109 LFAL 112
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 112-161 9.67e-04

The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of BudR regulator, which is responsible for induction of the butanediol formation pathway under fermentative growth conditions. Three enzymes are involved in the production of 1 mol of 2,3 butanediol from the condensation of 2 mol of pyruvate with acetolactate and acetoin as intermediates: acetolactate synthetase, acetolactate decarboxylase, and acetoin reductase. In Klebsiella terrigena, BudR regulates the expression of the budABC operon genes, encoding these three enzymes of the butanediol pathway. In many bacterial species, the use of this pathway can prevent intracellular acidification by diverting metabolism from acid production to the formation of neutral compounds (acetoin and butanediol). This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176142 [Multi-domain]  Cd Length: 199  Bit Score: 37.93  E-value: 9.67e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2582484231 112 VLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAIMALPSDVPS 161
Cdd:cd08451    15 LVPGLIRRFREAYPDVELTLEEANTAELLEALREGRLDAAFVRPPVARSD 64
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 100-152 1.12e-03

C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; CysL, also known as YwfK, is a regular of sulfur metabolism in Bacillus subtilis. Sulfur is required for the synthesis of proteins and essential cofactors in all living organism. Sulfur can be assimilated either from inorganic sources (sulfate and thiosulfate), or from organic sources (sulfate esters, sulfamates, and sulfonates). CysL activates the transcription of the cysJI operon encoding sulfite reductase, which reduces sulfite to sulfide. Both cysL mutant and cysJI mutant are unable to grow using sulfate or sulfite as the sulfur source. Like other LysR-type regulators, CysL also negatively regulates its own transcription. In Escherichia coli, three LysR-type activators are involved in the regulation of sulfur metabolism: CysB, Cbl and MetR. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176112 [Multi-domain]  Cd Length: 201  Bit Score: 37.86  E-value: 1.12e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2582484231 100 LSIGVIPTVAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAI 152
Cdd:cd08420     2 LRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGL 54
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 99-163 2.01e-03

The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; The NAC is a LysR-type transcription regulator that activates expression of operons such as hut (histidine utilization) and ure (urea utilization), allowing use of non-preferred (poor) nitrogen sources, and represses expression of operons, such as glutamate dehydrogenase (gdh), allowing assimilation of the preferred nitrogen source. The expression of the nac gene is fully dependent on the nitrogen regulatory system (NTR) and the sigma54-containing RNA polymerase (sigma54-RNAP). In response to nitrogen starvation, NTR system activates the expression of nac, and NAC activates the expression of hut, ure, and put (proline utilization). NAC is not involved in the transcription of Sigma70-RNAP operons such as glnA, which directly respond by the NTR system, but activates the transcription of sigma70-RNAP dependent operons such as hut. Hence, NAC allows the coupling of sigma70-RNAP dependent operons to the sigma54-RNAP dependent NTR system. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176124  Cd Length: 198  Bit Score: 37.19  E-value: 2.01e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2582484231  99 PLSIGVIPTVAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAIMALPSDVPSFE 163
Cdd:cd08433     1 RVSVGLPPSAASVLAVPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLS 65
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 108-163 2.64e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176109 [Multi-domain]  Cd Length: 200  Bit Score: 36.81  E-value: 2.64e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2582484231 108 VAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAIMALPSDVPSFE 163
Cdd:cd08417    10 LEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLR 65
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 100-161 4.43e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in involved in 3-phenylpropionic acid catabolism, contains the type2 periplasmic binding fold; HcaR, a member of the LysR family of transcriptional regulators, controls the expression of the hcA1, A2, B, C, and D operon, encoding for the 3-phenylpropionate dioxygenase complex and 3-phenylpropionate-2',3'-dihydrodiol dehydrogenase, that oxidizes 3-phenylpropionate to 3-(2,3-dihydroxyphenyl) propionate. Dioxygenases play an important role in protecting the cell against the toxic effects of dioxygen. The expression of hcaR is negatively auto-regulated, as for other members of the LysR family, and is strongly repressed in the presence of glucose. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176141 [Multi-domain]  Cd Length: 196  Bit Score: 36.20  E-value: 4.43e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2582484231 100 LSIGVIPTVAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAIMALPSDVPS 161
Cdd:cd08450     2 LTIGFLPGAEVQWLPEVLPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFMRPEIQSDG 63
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 100-163 4.49e-03

The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176129 [Multi-domain]  Cd Length: 197  Bit Score: 36.00  E-value: 4.49e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2582484231 100 LSIGVIPTVAPYVLPNFLQLVRDELPDLKPRIVEEPTERLIESLRSGTIDAAIMALPSDVPSFE 163
Cdd:cd08438     2 LRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFD 65
 
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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