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Conserved domains on  [gi|489957726|ref|WP_003861033|]
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MULTISPECIES: LacI family DNA-binding transcriptional regulator [Enterobacter]

Protein Classification

LacI family DNA-binding transcriptional regulator( domain architecture ID 11446715)

LacI family DNA-binding transcriptional regulator functions as an activator or repressor by binding a specific effector ligand that either decreases (induction) or increases DNA-binding affinity (co-repression)

CATH:  3.40.50.2300
Gene Ontology:  GO:0003677|GO:0003700|GO:0006355
PubMed:  8543068|12598694

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PurR COG1609
DNA-binding transcriptional regulator, LacI/PurR family [Transcription];
1-310 5.17e-51

DNA-binding transcriptional regulator, LacI/PurR family [Transcription];


:

Pssm-ID: 441217 [Multi-domain]  Cd Length: 335  Bit Score: 171.54  E-value: 5.17e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726   1 MSTINDVSRLAGVSKATVSRVLSGSRGVKEASRQAVLKAVDELNYRPNVIAQSLLSQSTGCIGVICAQENINQTTGYLYA 80
Cdd:COG1609    3 RVTIKDVARLAGVSVATVSRVLNGPPRVSEETRERVLAAAEELGYRPNAAARSLRTGRTRTIGVVVPDLSNPFFAELLRG 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726  81 LEKHLSQHQKHLLLRFAHTKTEV-MNALEELSCGLCDDILVIGARFPLDV--DMDN----VILVDC-MEADNANSIQFDH 152
Cdd:COG1609   83 IEEAARERGYQLLLANSDEDPEReREALRLLLSRRVDGLILAGSRLDDARleRLAEagipVVLIDRpLPDPGVPSVGVDN 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 153 AFAAETACNYLTSQGRRQIALIH-PHGSGFADQVLLGYKHALEKNFLPFNRNLVF---MDATSSSVALQELLnnASTLNF 228
Cdd:COG1609  163 RAGARLATEHLIELGHRRIAFIGgPADSSSARERLAGYREALAEAGLPPDPELVVegdFSAESGYEAARRLL--ARGPRP 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 229 NALLVADEQEAQRVIPQLQAFNKSVPEDIMVFSLGGSLHLPGI-PVIPAIEYSMDAMAARIVSWLTE----KTQMLGSYV 303
Cdd:COG1609  241 TAIFCANDLMALGALRALREAGLRVPEDVSVVGFDDIPLARYLtPPLTTVRQPIEEMGRRAAELLLDriegPDAPPERVL 320


                 ....*..
gi 489957726 304 LRGDLII 310
Cdd:COG1609  321 LPPELVV 327
 
Name Accession Description Interval E-value
PurR COG1609
DNA-binding transcriptional regulator, LacI/PurR family [Transcription];
1-310 5.17e-51

DNA-binding transcriptional regulator, LacI/PurR family [Transcription];


Pssm-ID: 441217 [Multi-domain]  Cd Length: 335  Bit Score: 171.54  E-value: 5.17e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726   1 MSTINDVSRLAGVSKATVSRVLSGSRGVKEASRQAVLKAVDELNYRPNVIAQSLLSQSTGCIGVICAQENINQTTGYLYA 80
Cdd:COG1609    3 RVTIKDVARLAGVSVATVSRVLNGPPRVSEETRERVLAAAEELGYRPNAAARSLRTGRTRTIGVVVPDLSNPFFAELLRG 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726  81 LEKHLSQHQKHLLLRFAHTKTEV-MNALEELSCGLCDDILVIGARFPLDV--DMDN----VILVDC-MEADNANSIQFDH 152
Cdd:COG1609   83 IEEAARERGYQLLLANSDEDPEReREALRLLLSRRVDGLILAGSRLDDARleRLAEagipVVLIDRpLPDPGVPSVGVDN 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 153 AFAAETACNYLTSQGRRQIALIH-PHGSGFADQVLLGYKHALEKNFLPFNRNLVF---MDATSSSVALQELLnnASTLNF 228
Cdd:COG1609  163 RAGARLATEHLIELGHRRIAFIGgPADSSSARERLAGYREALAEAGLPPDPELVVegdFSAESGYEAARRLL--ARGPRP 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 229 NALLVADEQEAQRVIPQLQAFNKSVPEDIMVFSLGGSLHLPGI-PVIPAIEYSMDAMAARIVSWLTE----KTQMLGSYV 303
Cdd:COG1609  241 TAIFCANDLMALGALRALREAGLRVPEDVSVVGFDDIPLARYLtPPLTTVRQPIEEMGRRAAELLLDriegPDAPPERVL 320


                 ....*..
gi 489957726 304 LRGDLII 310
Cdd:COG1609  321 LPPELVV 327
lacI PRK09526
lac repressor; Reviewed
 2-259 3.08e-28

lac repressor; Reviewed


Pssm-ID: 181929 [Multi-domain]  Cd Length: 342  Bit Score: 111.62  E-value: 3.08e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726   2 STINDVSRLAGVSKATVSRVLSGSRGVKEASRQAVLKAVDELNYRPNVIAQSLLSQSTGCIGVICAQENINQTTGYLYAL 81
Cdd:PRK09526   6 VTLYDVARYAGVSYQTVSRVLNQASHVSAKTREKVEAAMAELNYVPNRVAQQLAGKQSLTIGLATTSLALHAPSQIAAAI 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726  82 EKHLSQHQKHLLLRF--AHTKTEVMNALEELSCGLCDDILVigaRFPLDVDMDNVILVDC-------MEAD---NANSIQ 149
Cdd:PRK09526  86 KSRADQLGYSVVISMveRSGVEACQAAVNELLAQRVSGVII---NVPLEDADAEKIVADCadvpclfLDVSpqsPVNSVS 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 150 FDHAFAAETACNYLTSQGRRQIALIH-PHGSGFADQVLLGYKHALEKNFL-PFNrnlVF---MDATSSSVALQELLNnaS 224
Cdd:PRK09526 163 FDPEDGTRLGVEHLVELGHQRIALLAgPESSVSARLRLAGWLEYLTDYQLqPIA---VRegdWSAMSGYQQTLQMLR--E 237

                        250       260       270
                 ....*....|....*....|....*....|....*
gi 489957726 225 TLNFNALLVADEQEAQRVIPQLQAFNKSVPEDIMV 259
Cdd:PRK09526 238 GPVPSAILVANDQMALGVLRALHESGLRVPGQISV 272
HTH_LACI smart00354
helix_turn _helix lactose operon repressor;
3-65 2.47e-26

helix_turn _helix lactose operon repressor;


Pssm-ID: 197675 [Multi-domain]  Cd Length: 70  Bit Score: 98.81  E-value: 2.47e-26
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489957726     3 TINDVSRLAGVSKATVSRVLSGSRGVKEASRQAVLKAVDELNYRPNVIAQSLLSQSTGCIGVI 65
Cdd:smart00354   2 TIKDVARLAGVSKATVSRVLNGKGRVSEETREKVLAAMEELGYIPNRVARSLKGKKTKTIGLI 64
HTH_LacI cd01392
Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; ...
 6-54 1.24e-19

Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repressor binds its ligand, it undergoes a conformational change which affects the DNA-binding affinity of the repressor. In Escherichia coli, LacI represses transcription by binding with high affinity to the lac operon at a specific operator DNA sequence until it interacts with the physiological inducer allolactose or a non-degradable analog IPTG (isopropyl-beta-D-thiogalactopyranoside). Induction of the repressor lowers its affinity for the operator sequence, thereby allowing transcription of the lac operon structural genes (lacZ, lacY, and LacA). The lac repressor occurs as a tetramer made up of two functional dimers. Thus, two DNA binding domains of a dimer are required to bind the inverted repeat sequences of the operator DNA binding sites.


Pssm-ID: 143331 [Multi-domain]  Cd Length: 52  Bit Score: 80.53  E-value: 1.24e-19
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 489957726   6 DVSRLAGVSKATVSRVLSGSRGVKEASRQAVLKAVDELNYRPNVIAQSL 54
Cdd:cd01392    2 DIARAAGVSVATVSRVLNGKPRVSEETRERVLAAAEELGYRPNAAARSL 50
LacI pfam00356
Bacterial regulatory proteins, lacI family;
3-48 7.08e-18

Bacterial regulatory proteins, lacI family;


Pssm-ID: 306791 [Multi-domain]  Cd Length: 46  Bit Score: 75.75  E-value: 7.08e-18
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 489957726    3 TINDVSRLAGVSKATVSRVLSGSRGVKEASRQAVLKAVDELNYRPN 48
Cdd:pfam00356   1 TIKDVARLAGVSKSTVSRVLNNPGRVSEETRERVEAAMEELNYIPN 46
 
Name Accession Description Interval E-value
PurR COG1609
DNA-binding transcriptional regulator, LacI/PurR family [Transcription];
1-310 5.17e-51

DNA-binding transcriptional regulator, LacI/PurR family [Transcription];


Pssm-ID: 441217 [Multi-domain]  Cd Length: 335  Bit Score: 171.54  E-value: 5.17e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726   1 MSTINDVSRLAGVSKATVSRVLSGSRGVKEASRQAVLKAVDELNYRPNVIAQSLLSQSTGCIGVICAQENINQTTGYLYA 80
Cdd:COG1609    3 RVTIKDVARLAGVSVATVSRVLNGPPRVSEETRERVLAAAEELGYRPNAAARSLRTGRTRTIGVVVPDLSNPFFAELLRG 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726  81 LEKHLSQHQKHLLLRFAHTKTEV-MNALEELSCGLCDDILVIGARFPLDV--DMDN----VILVDC-MEADNANSIQFDH 152
Cdd:COG1609   83 IEEAARERGYQLLLANSDEDPEReREALRLLLSRRVDGLILAGSRLDDARleRLAEagipVVLIDRpLPDPGVPSVGVDN 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 153 AFAAETACNYLTSQGRRQIALIH-PHGSGFADQVLLGYKHALEKNFLPFNRNLVF---MDATSSSVALQELLnnASTLNF 228
Cdd:COG1609  163 RAGARLATEHLIELGHRRIAFIGgPADSSSARERLAGYREALAEAGLPPDPELVVegdFSAESGYEAARRLL--ARGPRP 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 229 NALLVADEQEAQRVIPQLQAFNKSVPEDIMVFSLGGSLHLPGI-PVIPAIEYSMDAMAARIVSWLTE----KTQMLGSYV 303
Cdd:COG1609  241 TAIFCANDLMALGALRALREAGLRVPEDVSVVGFDDIPLARYLtPPLTTVRQPIEEMGRRAAELLLDriegPDAPPERVL 320


                 ....*..
gi 489957726 304 LRGDLII 310
Cdd:COG1609  321 LPPELVV 327
lacI PRK09526
lac repressor; Reviewed
 2-259 3.08e-28

lac repressor; Reviewed


Pssm-ID: 181929 [Multi-domain]  Cd Length: 342  Bit Score: 111.62  E-value: 3.08e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726   2 STINDVSRLAGVSKATVSRVLSGSRGVKEASRQAVLKAVDELNYRPNVIAQSLLSQSTGCIGVICAQENINQTTGYLYAL 81
Cdd:PRK09526   6 VTLYDVARYAGVSYQTVSRVLNQASHVSAKTREKVEAAMAELNYVPNRVAQQLAGKQSLTIGLATTSLALHAPSQIAAAI 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726  82 EKHLSQHQKHLLLRF--AHTKTEVMNALEELSCGLCDDILVigaRFPLDVDMDNVILVDC-------MEAD---NANSIQ 149
Cdd:PRK09526  86 KSRADQLGYSVVISMveRSGVEACQAAVNELLAQRVSGVII---NVPLEDADAEKIVADCadvpclfLDVSpqsPVNSVS 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 150 FDHAFAAETACNYLTSQGRRQIALIH-PHGSGFADQVLLGYKHALEKNFL-PFNrnlVF---MDATSSSVALQELLNnaS 224
Cdd:PRK09526 163 FDPEDGTRLGVEHLVELGHQRIALLAgPESSVSARLRLAGWLEYLTDYQLqPIA---VRegdWSAMSGYQQTLQMLR--E 237

                        250       260       270
                 ....*....|....*....|....*....|....*
gi 489957726 225 TLNFNALLVADEQEAQRVIPQLQAFNKSVPEDIMV 259
Cdd:PRK09526 238 GPVPSAILVANDQMALGVLRALHESGLRVPGQISV 272
HTH_LACI smart00354
helix_turn _helix lactose operon repressor;
3-65 2.47e-26

helix_turn _helix lactose operon repressor;


Pssm-ID: 197675 [Multi-domain]  Cd Length: 70  Bit Score: 98.81  E-value: 2.47e-26
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489957726     3 TINDVSRLAGVSKATVSRVLSGSRGVKEASRQAVLKAVDELNYRPNVIAQSLLSQSTGCIGVI 65
Cdd:smart00354   2 TIKDVARLAGVSKATVSRVLNGKGRVSEETREKVLAAMEELGYIPNRVARSLKGKKTKTIGLI 64
PRK10703 PRK10703
HTH-type transcriptional repressor PurR;
1-221 1.20e-21

HTH-type transcriptional repressor PurR;


Pssm-ID: 236739 [Multi-domain]  Cd Length: 341  Bit Score: 93.25  E-value: 1.20e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726   1 MSTINDVSRLAGVSKATVSRVLSGSRGVKEASRQAVLKAVDELNYRPNVIAQSLLSQSTGCIGVICAQENINQTTGYLYA 80
Cdd:PRK10703   1 MATIKDVAKRAGVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPSAVARSLKVNHTKSIGLLATSSEAPYFAEIIEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726  81 LEKHLSQHQKHLLLRFAHTKTE-VMNALEELSCGLCDDILVIGARFPLDV-----DMDNVILV--DCMEADNA--NSIQf 150
Cdd:PRK10703  81 VEKNCYQKGYTLILCNAWNNLEkQRAYLSMLAQKRVDGLLVMCSEYPEPLlamleEYRHIPMVvmDWGEAKADftDAII- 159

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489957726 151 DHAFA-AETACNYLTSQGRRQIALIH-PHGSGFADQVLLGYKHALEKNFLPFNRNLV---FMDATSSSVALQELLN 221
Cdd:PRK10703 160 DNAFEgGYLAGRYLIERGHRDIGVIPgPLERNTGAGRLAGFMKAMEEANIKVPEEWIvqgDFEPESGYEAMQQILS 235
PRK10727 PRK10727
HTH-type transcriptional regulator GalR;
1-257 3.49e-21

HTH-type transcriptional regulator GalR;


Pssm-ID: 182681 [Multi-domain]  Cd Length: 343  Bit Score: 92.13  E-value: 3.49e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726   1 MSTINDVSRLAGVSKATVSRVLSGSRGVKEASRQAVLKAVDELNYRPNVIAQSLLSQSTGCIGVICAQENINQTTGYLYA 80
Cdd:PRK10727   1 MATIKDVARLAGVSVATVSRVINNSPKASEASRLAVHSAMESLSYHPNANARALAQQSTETVGLVVGDVSDPFFGAMVKA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726  81 LEKhLSQHQKHLLL--RFAHTKTEVMNALEELSCGLCdDILVIGARFPLDVDM--------DNVILVDCMEADNANSIQF 150
Cdd:PRK10727  81 VEQ-VAYHTGNFLLigNGYHNEQKERQAIEQLIRHRC-AALVVHAKMIPDAELaslmkqipGMVLINRILPGFENRCIAL 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 151 DHAFAAETACNYLTSQGRRQIALI-HPHGSGFADQVLLGYKHALEKNFLPFNRNLVFM---DATSSSVALQELLNNAStl 226
Cdd:PRK10727 159 DDRYGAWLATRHLIQQGHTRIGYLcSNHSISDAEDRLQGYYDALAESGIPANDRLVTFgepDESGGEQAMTELLGRGR-- 236

                        250       260       270
                 ....*....|....*....|....*....|.
gi 489957726 227 NFNALLVADEQEAQRVIPQLQAFNKSVPEDI 257
Cdd:PRK10727 237 NFTAVACYNDSMAAGAMGVLNDNGIDVPGEI 267
PRK10401 PRK10401
HTH-type transcriptional regulator GalS;
1-194 1.34e-20

HTH-type transcriptional regulator GalS;


Pssm-ID: 236681 [Multi-domain]  Cd Length: 346  Bit Score: 90.61  E-value: 1.34e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726   1 MSTINDVSRLAGVSKATVSRVLSGSRGVKEASRQAVLKAVDELNYRPNVIAQSLLSQSTGCIGVICaqenINQTTGYLYA 80
Cdd:PRK10401   1 MITIRDVARQAGVSVATVSRVLNNSALVSADTREAVMKAVSELGYRPNANAQALATQVSDTIGVVV----MDVSDAFFGA 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726  81 LEKHL----SQHQKHLLLRFAHTKT-------EVM-----NALEELSCGLCDDILvigARFpldvdMDNV---ILVDCME 141
Cdd:PRK10401  77 LVKAVdlvaQQHQKYVLIGNSYHEAekerhaiEVLirqrcNALIVHSKALSDDEL---AQF-----MDQIpgmVLINRVV 148

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 489957726 142 ADNANS-IQFDHAFAAETACNYLTSQGRRQIA-LIHPHGSGFADQVLLGYKHALE 194
Cdd:PRK10401 149 PGYAHRcVCLDNVSGARMATRMLLNNGHQRIGyLSSSHGIEDDAMRRAGWMSALK 203
HTH_LacI cd01392
Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; ...
 6-54 1.24e-19

Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repressor binds its ligand, it undergoes a conformational change which affects the DNA-binding affinity of the repressor. In Escherichia coli, LacI represses transcription by binding with high affinity to the lac operon at a specific operator DNA sequence until it interacts with the physiological inducer allolactose or a non-degradable analog IPTG (isopropyl-beta-D-thiogalactopyranoside). Induction of the repressor lowers its affinity for the operator sequence, thereby allowing transcription of the lac operon structural genes (lacZ, lacY, and LacA). The lac repressor occurs as a tetramer made up of two functional dimers. Thus, two DNA binding domains of a dimer are required to bind the inverted repeat sequences of the operator DNA binding sites.


Pssm-ID: 143331 [Multi-domain]  Cd Length: 52  Bit Score: 80.53  E-value: 1.24e-19
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 489957726   6 DVSRLAGVSKATVSRVLSGSRGVKEASRQAVLKAVDELNYRPNVIAQSL 54
Cdd:cd01392    2 DIARAAGVSVATVSRVLNGKPRVSEETRERVLAAAEELGYRPNAAARSL 50
LacI pfam00356
Bacterial regulatory proteins, lacI family;
3-48 7.08e-18

Bacterial regulatory proteins, lacI family;


Pssm-ID: 306791 [Multi-domain]  Cd Length: 46  Bit Score: 75.75  E-value: 7.08e-18
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 489957726    3 TINDVSRLAGVSKATVSRVLSGSRGVKEASRQAVLKAVDELNYRPN 48
Cdd:pfam00356   1 TIKDVARLAGVSKSTVSRVLNNPGRVSEETRERVEAAMEELNYIPN 46
PBP1_LacI_sugar_binding-like cd06267
ligand binding domain of the LacI transcriptional regulator family belonging to the type 1 ...
 78-259 6.39e-17

ligand binding domain of the LacI transcriptional regulator family belonging to the type 1 periplasmic-binding fold protein superfamily; Ligand binding domain of the LacI transcriptional regulator family belonging to the type 1 periplasmic-binding fold protein superfamily. In most cases, ligands are monosaccharide including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the domain sugar binding changes the DNA binding activity of the repressor domain.


Pssm-ID: 380491 [Multi-domain]  Cd Length: 264  Bit Score: 78.71  E-value: 6.39e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726  78 LYALEKHLSQHQKHLLLRFAHTKTE-VMNALEELSCGLCDDILVIGARFPLDVDMDN------VILVDC-MEADNANSIQ 149
Cdd:cd06267   18 LRGIEDAARERGYSLLLCNTDEDPErEREYLRLLLSRRVDGIILAPSSLDDELLEELlaagipVVLIDRrLDGLGVDSVV 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 150 FDHAFAAETACNYLTSQGRRQIALIH-PHGSGFADQVLLGYKHALEKNFLPFNRNLVFMDATSSS---VALQELLNNAST 225
Cdd:cd06267   98 VDNYAGAYLATEHLIELGHRRIAFIGgPLDLSTSRERLEGYRDALAEAGLPVDPELVVEGDFSEEsgyEAARELLALPPR 177

                        170       180       190
                 ....*....|....*....|....*....|....
gi 489957726 226 lnFNALLVADEQEAQRVIPQLQAFNKSVPEDIMV 259
Cdd:cd06267  178 --PTAIFAANDLMAIGALRALRELGLRVPEDISV 209
PRK10423 PRK10423
transcriptional repressor RbsR; Provisional
 6-199 1.11e-15

transcriptional repressor RbsR; Provisional


Pssm-ID: 182448 [Multi-domain]  Cd Length: 327  Bit Score: 76.28  E-value: 1.11e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726   6 DVSRLAGVSKATVSRVLSGSRGVKEASRQAVLKAVDELNYRPNVIAQSLLSQSTGCIGVIcaqenINQTTGYLYA----- 80
Cdd:PRK10423   3 DVARLAGVSTSTVSHVINKDRFVSEAITAKVEAAIKELNYAPSALARSLKLNQTRTIGML-----ITASTNPFYSelvrg 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726  81 LEKHLSQHQKHLLLRFAHTKTEVMN-ALEELSCGLCDDILV-----------IGARFPLdVDMdnvILVDCMEADNANSI 148
Cdd:PRK10423  78 VERSCFERGYSLVLCNTEGDEQRMNrNLETLMQKRVDGLLLlctethqpsreIMQRYPS-VPT---VMMDWAPFDGDSDL 153

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 489957726 149 QFDHAF-AAETACNYLTSQGRRQIALIH-PHGSGFADQVLLGYKHALEKNFLP 199
Cdd:PRK10423 154 IQDNSLlGGDLATQYLIDKGYTRIACITgPLDKTPARLRLEGYRAAMKRAGLN 206
PRK10014 PRK10014
DNA-binding transcriptional repressor MalI; Provisional
 3-200 1.71e-14

DNA-binding transcriptional repressor MalI; Provisional


Pssm-ID: 182193 [Multi-domain]  Cd Length: 342  Bit Score: 72.82  E-value: 1.71e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726   3 TINDVSRLAGVSKATVSRVLSGSRGVKEASRQAVLKAVDELNYRPNVIAQSLLSQSTGCIGVI----CAQENINQTTGYL 78
Cdd:PRK10014   8 TIHDVALAAGVSVSTVSLVLSGKGRISTATGERVNQAIEELGFVRNRQASALRGGQSGVIGLIvrdlSAPFYAELTAGLT 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726  79 YALEKhlsQHQKHLLLRFAHTKTEVMNALEELSCGLCDDILVIGARFPLDVDMD-----NVILVDCMEA---DNANSIQF 150
Cdd:PRK10014  88 EALEA---QGRMVFLLQGGKDGEQLAQRFSTLLNQGVDGVVIAGAAGSSDDLREmaeekGIPVVFASRAsylDDVDTVRP 164

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|..
gi 489957726 151 DHAFAAETACNYLTSQGRRQIALIHPHGSGF--ADQVlLGYKHALEKNFLPF 200
Cdd:PRK10014 165 DNMQAAQLLTEHLIRNGHQRIAWLGGQSSSLtrAERV-GGYCATLLKFGLPF 215
PBP1_GalS-like cd06270
ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory ...
 78-310 6.34e-14

ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism; Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalS is a dimeric protein like GalR,and its major role is in regulating expression of the high-affinity galactose transporter encoded by the mgl operon, whereas GalR is the exclusive regulator of galactose permease, the low-affinity galactose transporter. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type 1 periplasmic binding protein-like fold. Hence, they are homologous to the periplasmic sugar binding of ABC-type transport systems.


Pssm-ID: 380494 [Multi-domain]  Cd Length: 266  Bit Score: 70.24  E-value: 6.34e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726  78 LYALEKHLSQHQKHLLLRFAH-TKTEVMNALEELSCGLCDDILVIgARFPLDVD-------MDNVILVD-CMEADNANSI 148
Cdd:cd06270   18 LKGAERVARAHGKQLLITSGHhDAEEEREAIEFLLDRRCDAIILH-SRALSDEEliliaekIPPLVVINrYIPGLADRCV 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 149 QFDHAFAAETACNYLTSQGRRQIALIH-PHGSGFADQVLLGYKHALEKNFLPFNRNLVF---MDATSSSVALQELLnnAS 224
Cdd:cd06270   97 WLDNEQGGRLAAEHLLDLGHRRIACITgPLDIPDARERLAGYRDALAEAGIPLDPSLIIegdFTIEGGYAAAKQLL--AR 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 225 TLNFNALLVADEQEAQRVIPQLQAFNKSVPEDIMVFS-----LGGSLHlpgiPVIPAIEYSMDAMAARIVSW---LTEKT 296
Cdd:cd06270  175 GLPFTALFAYNDDMAIGALAALHEAGIKVPEDVSVIGfddvpLARYLS----PKLTTVHYPIEEMAQAAAELalnLAYGE 250

                        250
                 ....*....|....
gi 489957726 297 QMLGSYVLRGDLII 310
Cdd:cd06270  251 PLPISHEFTPTLIE 264
PBP1_LacI-like cd06290
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
 62-259 2.60e-11

ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380513 [Multi-domain]  Cd Length: 267  Bit Score: 63.02  E-value: 2.60e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726  62 IGVIcaqenINQTTGYLY-----ALEKHLSQHQKHLLLRFAHTKTEV-MNALEELSCGLCDDILVIGARFPLDVDMDN-- 133
Cdd:cd06290    2 IGVL-----VPDIDSPFYseilnGIEEVLAESGYTLIVSTSHWNADReLEILRLLLARKVDGIIVVGGFGDEELLKLLae 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 134 ---VILVDC-MEADNANSIQFDHAFAAETACNYLTSQGRRQIALIH-PHGSGFADQVLLGYKHALEKNFLPFNRNLV--- 205
Cdd:cd06290   77 gipVVLVDReLEGLNLPVVNVDNEQGGYNATNHLIDLGHRRIVHISgPEDHPDAQERYAGYRRALEDAGLEVDPRLIveg 156

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 489957726 206 -FMDaTSSSVALQELLnnASTLNFNALLVADEQEAqrvIPQLQAFNK---SVPEDIMV 259
Cdd:cd06290  157 dFTE-ESGYEAMKKLL--KRGGPFTAIFAANDLMA---LGAMKALREagiRVPDDVSV 208
Peripla_BP_3 pfam13377
Periplasmic binding protein-like domain; This domain is found in a variety of transcriptional ...
 162-294 8.22e-11

Periplasmic binding protein-like domain; This domain is found in a variety of transcriptional regulatory proteins. It is related to bacterial periplasmic binding proteins, although this domain is unlikely to be found in the periplasm. This domain acts as a sensor binding small molecule ligands that the DNA-binding domain responds to. This domain recognizes Sugars, sugar phosphates, sugar acids and purines (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 433159 [Multi-domain]  Cd Length: 160  Bit Score: 59.66  E-value: 8.22e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726  162 YLTSQGRRQIALI---HPHGSGFADQVLLGYKHALEKNFLPFNRNLVFMDATSSSVALQELLNNASTLNfNALLVADEQE 238
Cdd:pfam13377   1 HLAELGHRRIALIgpeGDRDDPYSDLRERGFREAARELGLDVEPTLYAGDDEAEAAAARERLRWLGALP-TAVFVANDEV 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726  239 AQRVIPQLQAFNKSVPEDIMVFSLGGS----LHLPGipvIPAIEYSMDAMAARIVSWLTE 294
Cdd:pfam13377  80 ALGVLQALREAGLRVPEDLSVIGFDDSplaaLVSPP---LTTVRVDAEELGRAAAELLLD 136
PBP1_AglR_RafR-like cd06292
Ligand-binding domain of uncharacterized DNA transcription repressors highly similar to that ...
 62-313 5.20e-10

Ligand-binding domain of uncharacterized DNA transcription repressors highly similar to that of the repressors specific raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators; This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins highly similar to DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR). Members of this group belong to the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380515 [Multi-domain]  Cd Length: 273  Bit Score: 59.20  E-value: 5.20e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726  62 IGVICAQENINQT----TGYLYALEKHLSQHQKHLLLrFAHTK--TEVMNALEELSCGLCDDILVIG-------ARFPLD 128
Cdd:cd06292    2 IGYVVPELPGGFSdpffDEFLAALGHAAAARGYDVLL-FTASGdeDEIDYYRDLVRSRRVDGFVLAStrhddprVRYLHE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 129 VDMDNVILVDCMEADNANSIQFDHAFAAETACNYLTSQGRRQIALI-HPHGSGFADQVLLGYKHALEKNFLPFNRNLVFM 207
Cdd:cd06292   81 AGVPFVAFGRANPDLDFPWVDVDGAAGMRQAVRHLIALGHRRIGLIgGPEGSVPSDDRLAGYRAALEEAGLPFDPGLVVE 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 208 ---DATSSSVALQELLNNASTlnFNALLVADEQEAQRVIPQLQAFNKSVPEDIMVFSLGGSlhlPGIPVI-PA---IEYS 280
Cdd:cd06292  161 genTEEGGYAAAARLLDLGPP--PTAIVCVSDLLALGAMRAARERGLRVGRDVSVVGFDDS---PLAAFThPPlttVRQP 235

                        250       260       270
                 ....*....|....*....|....*....|...
gi 489957726 281 MDAMAARIVSWLTEKTQMLGSYVlRGDLIIPDV 313
Cdd:cd06292  236 IDEIGRAVVDLLLAAIEGNPSEP-REILLQPEL 267
PBP1_MalR-like cd06294
ligand-binding domain of maltose transcription regulator MalR which is a member of the ...
 83-261 1.58e-09

ligand-binding domain of maltose transcription regulator MalR which is a member of the LacI-GalR family repressors; This group includes the ligand-binding domain of maltose transcription regulator MalR which is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380517 [Multi-domain]  Cd Length: 269  Bit Score: 57.59  E-value: 1.58e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726  83 KHLSQHQKHLLLRFAHTKTEVMNALEEL-SCGLCDDILVIGAR-------FPLDVDMDNVILVDCMEADNANSIQFDHAF 154
Cdd:cd06294   28 QVANENGYSLLLATGNTEEELLEEVKRMvRGRRVDGFILLYSKeddplieYLKEEGFPFVVIGKPLDDNDVLYVDNDNVQ 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 155 AAETACNYLTSQGRRQIALIhphgSGFADQV-----LLGYKHALEKNFLPFNRNLVFMD---ATSSSVALQELLNNasTL 226
Cdd:cd06294  108 AGYEATEYLIDKGHKRIAFI----GGDKNLVvsidrLQGYKQALKEAGLPLDDDYILLLdfsEEDGYDALQELLSK--PP 181

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 489957726 227 NFNALLVADEQEAQRVIPQLQAFNKSVPEDIMVFS 261
Cdd:cd06294  182 PPTAIVATDDLLALGVLRYLQELGLRVPEDVSIIS 216
PBP1_LacI-like cd06284
ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus ...
 107-260 6.25e-09

ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria; This group includes the ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group belongs to the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.


Pssm-ID: 380507 [Multi-domain]  Cd Length: 267  Bit Score: 56.01  E-value: 6.25e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 107 LEELSCGLCDDILVIGARFPLDVDMD---NVILVDCMEAD---NANSIQFDHAFAAETACNYLTSQGRRQIALI-HPHGS 179
Cdd:cd06284   48 LDMLRSRRVDGVILLSGRLDAELLSElskRYPIVQCCEYIpdsGVPSVSIDNEAAAYDATEYLISLGHRRIAHInGPLDN 127

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 180 GFADQVLLGYKHALEKNFLPFNRNLVFM---DATSSSVALQELLNNAStlNFNALLVADEQEAQRVIPQLQAFNKSVPED 256
Cdd:cd06284  128 VYARERLEGYRRALAEAGLPVDEDLIIEgdfSFEAGYAAARALLALPE--RPTAIFCASDELAIGAIKALRRAGLRVPED 205


                 ....
gi 489957726 257 IMVF 260
Cdd:cd06284  206 VSVI 209
PRK11303 PRK11303
catabolite repressor/activator;
3-65 4.47e-08

catabolite repressor/activator;


Pssm-ID: 236897 [Multi-domain]  Cd Length: 328  Bit Score: 53.73  E-value: 4.47e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489957726   3 TINDVSRLAGVSKATVSRVLSG---SRGVKEASRQAVLKAVDELNYRPNVIAQSLLSQSTGCIGVI 65
Cdd:PRK11303   2 KLDEIARLAGVSRTTASYVINGkakQYRVSDKTVEKVMAVVREHNYHPNAVAAGLRAGRTRSIGLI 67
PBP1_GalR cd01544
ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory ...
 77-261 1.30e-07

ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory proteins involved in galactose transport and metabolism; Ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalR is a dimeric protein like GalS and is exclusively involved in the regulation of galactose permease, the low-affinity galactose transporter. GalS is involved in regulating expression of the high-affinity galactose transporter encoded by the mgl operon. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type 1 periplasmic binding protein-like fold. Hence, they are structurally homologous to the periplasmic sugar binding of ABC-type transport systems.


Pssm-ID: 380486 [Multi-domain]  Cd Length: 269  Bit Score: 51.75  E-value: 1.30e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726  77 YLY---ALEKHLSQHQKHLllRFAHTKTEVMNALEELscglCDDILVIGaRF-PLDVD-----MDNVILVD-CMEADNAN 146
Cdd:cd01544   19 YLSirlGIEKEAKKLGYEI--KTIFRDDEDLESLLEK----VDGIIAIG-KFsKEEIEklkklNPNIVFVDsNPDPDGFD 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 147 SIQFDHAFAAETACNYLTSQGRRQIALI------HPHGSGFADQVLLGYKHALEKNFLpFNRNLVF---MDATSSSVALQ 217
Cdd:cd01544   92 SVVPDFEQAVRQALDYLIELGHRRIGFIggkeytSDDGEEIEDPRLRAFREYMKEKGL-YNEEYIYigeFSVESGYEAMK 170

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 489957726 218 ELLNNASTlnFNALLVADEQEAQRVIPQLQAFNKSVPEDIMVFS 261
Cdd:cd01544  171 ELLKEGDL--PTAFFVASDPMAIGALRALQEAGIKVPEDISIIS 212
PBP1_EndR-like cd19977
periplasmic ligand-binding domain of putative repressor of the endoglucanase operon and its ...
 119-309 1.38e-07

periplasmic ligand-binding domain of putative repressor of the endoglucanase operon and its close homologs; This group includes the ligand-binding domain of putative repressor of the endoglucanase operon from Paenibacillus polymyxa and its close homologs from other bacteria. This group belongs to the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.


Pssm-ID: 380632 [Multi-domain]  Cd Length: 264  Bit Score: 51.76  E-value: 1.38e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 119 LVIGARFPLDVDMDNVILvdcmeaDNAnsiqfdhaFAAETACNYLTSQGRRQIALIhphgsGFADQV------LLGYKHA 192
Cdd:cd19977   81 VVFVDRYIPGLDVDTVVV------DNF--------KGAYQATEHLIELGHKRIAFI-----TYPLELstrqerLEGYKAA 141

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 193 LEKNFLPFNRNLVFMDATSSSV--ALQELLNNASTlnFNALLVADEQEAQRVIPQLQAFNKSVPEDImvfSLGG------ 264
Cdd:cd19977  142 LADHGLPVDEELIKHVDRQDDVrkAISELLKLEKP--PDAIFAANNLITLEVLKAIKELGLRIPDDI---ALIGfddipw 216

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 489957726 265 -SLHLPGIPVI--PAIEysmdaMAARIVSWLTEKTQMLGS-----YVLRGDLI 309
Cdd:cd19977  217 aDLFNPPLTVIaqPTYE-----IGRKAAELLLDRIENKPKgpprqIVLPTELI 264
PBP1_LacI-like cd06281
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
 134-295 1.45e-07

ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380504 [Multi-domain]  Cd Length: 270  Bit Score: 51.86  E-value: 1.45e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 134 VILVDCMEADNANSIQFDHAFAAETACNYLTSQGRRQIALIHPH-GSGFADQVLLGYKHALEKNFLPFNRNLVFMDATSS 212
Cdd:cd06281   82 VVLIDRDLPGDIDSVLVDHRSGVRQATEYLLSLGHRRIALLTGGpDIRPGRERIAGFKAAFAAAGLPPDPDLVRLGSFSA 161

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 213 SVA---LQELLNNAS--TlnfnALLVADEQEAQRVIPQLQAFNKSVPEDIMVFSLGGS----LHLPGIPVipaIEYSMDA 283
Cdd:cd06281  162 DSGfreAMALLRQPRppT----AIIALGTQLLAGVLRAVRAAGLRIPGDLSVVSIGDSdlaeLHDPPITA---IRWDLDA 234

                        170
                 ....*....|..
gi 489957726 284 MAARIVSWLTEK 295
Cdd:cd06281  235 VGRAAAELLLDR 246
PRK14987 PRK14987
HTH-type transcriptional regulator GntR;
4-311 1.52e-07

HTH-type transcriptional regulator GntR;


Pssm-ID: 184949 [Multi-domain]  Cd Length: 331  Bit Score: 51.95  E-value: 1.52e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726   4 INDVSRLAGVSKATVSRVLSGSRGVKEASRQAVLKAVDELNYRPNVIAQSLLSQSTGCIGVICAQENINQTTGYLYALEK 83
Cdd:PRK14987   8 LQDVADRVGVTKMTVSRFLRNPEQVSVALRGKIAAALDELGYIPNRAPDILSNATSRAIGVLLPSLTNQVFAEVLRGIES 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726  84 HLSQHQKHLLLRFAHTKTEVMNALEE--LSCGLCDDILVIGARFPLDVDMDNVILVDCMEADNANS------IQFDHAFA 155
Cdd:PRK14987  88 VTDAHGYQTMLAHYGYKPEMEQERLEsmLSWNIDGLILTERTHTPRTLKMIEVAGIPVVELMDSQSpcldiaVGFDNFEA 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 156 AETACNYLTSQGRRQIALIhphGSGFADQVLL---GYKHA-LEKNFLPFNrnlVFMDATSSSVALQELLNNA--STLNFN 229
Cdd:PRK14987 168 ARQMTTAIIARGHRHIAYL---GARLDERTIIkqkGYEQAmLDAGLVPYS---VMVEQSSSYSSGIELIRQArrEYPQLD 241

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 230 ALLVADEQEAQRVIPQLQAFNKSVPEDIMVFSLGGslHLPGipvipaieysmDAMAARIVSWLTEKTQM--LGSYVL--- 304
Cdd:PRK14987 242 GVFCTNDDLAVGAAFECQRLGLKVPDDMAIAGFHG--HDIG-----------QVMEPRLASVLTPRERMgsIGAERLlar 308


                 ....*...
gi 489957726 305 -RGDLIIP 311
Cdd:PRK14987 309 iRGESVTP 316
PBP1_CcpB-like cd06286
ligand-binding domain of a novel transcription factor implicated in catabolite repression in ...
 78-289 1.68e-07

ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species; This group includes the ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species. Catabolite control protein B (CcpB) is 30% identical in sequence to CcpA which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. Like CcpA, the DNA-binding protein CcpB exerts its catabolite-repressing effect by a mechanism dependent on the presence of HPr(Ser-P), the small phosphocarrier proteins of the phosphoenolpyruvate-sugar phosphotransferase system, but with a less significant degree.


Pssm-ID: 380509 [Multi-domain]  Cd Length: 262  Bit Score: 51.39  E-value: 1.68e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726  78 LYALEKHLSQHQKHLLLRFAHTKTEV-MNALEELSCGLCDDILVIGARFPLDVDMDNV---ILVDCMEADNAN--SIQFD 151
Cdd:cd06286   18 INGIAEAAFKKGYQVLLLQTNYDKEKeLRALELLKTKQIDGLIITSRENDWEVIEPYAkygPIVLCEETDSPDipSVYID 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 152 HAFAAETACNYLTSQGRRQIALIH---PHGSGFADQVLLGYKHALEKNFLPFNRNLVFMDATS---SSVALQELLNNAST 225
Cdd:cd06286   98 RYEAYLEALEYLKEKGHRKIGYCLgrpESSSASTQARLKAYQDVLGEHGLSLREEWIFTNCHTiedGYKLAKKLLALKER 177

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489957726 226 lnFNALLVADEQEAQRVIPQLQAFNKSVPEDIMVFSLgGSLHLPGIPVIPAIEYSMDAMAARIV 289
Cdd:cd06286  178 --PDAIFTNSDEVAAGIIAEAQKNGIRVPEDLAVIGF-DNQPISELLNLTTIDQPLEEMGKEAF 238
PBP1_CcpA-like cd19975
ligand-binding domain of putative DNA transcription regulators highly similar to that of the ...
 134-259 1.99e-07

ligand-binding domain of putative DNA transcription regulators highly similar to that of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation; This group includes the ligand-binding domain of uncharacterized DNA transcription repressors highly similar to that of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. In gram-positive bacteria, CCR is controlled by HPr, a phosphoenolpyruvate:sugar phsophotrasnferase system (PTS) and a transcriptional regulator CcpA. Moreover, CcpA can regulate sporulation and antibiotic resistance as well as play a role in virulence development of certain pathogens such as the group A streptococcus. The ligand binding domain of CcpA is a member of the LacI-GalR family of bacterial transcription regulators.


Pssm-ID: 380630 [Multi-domain]  Cd Length: 269  Bit Score: 51.40  E-value: 1.99e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 134 VILVDCM-EADNANSIQFDHAFAAETACNYLTSQGRRQIALI------HPHGSgfadQVLLGYKHALEKNFLPFNRNLVF 206
Cdd:cd19975   81 VVLVSTEsEDPDIPSVKIDDYQAAYDATNYLIKKGHRKIAMIsgplddPNAGY----PRYEGYKKALKDAGLPIKENLIV 156

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 489957726 207 ---MDATSSSVALQELLNNASTlnFNALLVADEQEAQRVIPQLQAFNKSVPEDIMV 259
Cdd:cd19975  157 egdFSFKSGYQAMKRLLKNKKL--PTAVFAASDEMALGVISAAYDHGIRVPEDISV 210
PBP1_sucrose_transcription_regulator cd06288
ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members ...
 126-261 2.16e-07

ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors; This group includes the ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380511 [Multi-domain]  Cd Length: 268  Bit Score: 51.39  E-value: 2.16e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 126 PLDVDMDNVILVDCMEADNAN-SIQFDHAFAAETACNYLTSQGRRQIALIHPHGSGFA-DQVLLGYKHALEKNFLPFNRN 203
Cdd:cd06288   73 PPELTDIPLVLLNCFDDDPSLpSVVPDDEQGGYLATRHLIEAGHRRIAFIGGPEDSLAtRLRLAGYRAALAEAGIPYDPS 152

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489957726 204 LVFMDATSSS---VALQELLnnASTLNFNALLVADEQEAQRVIPQLQAFNKSVPEDIMVFS 261
Cdd:cd06288  153 LVVHGDWGREsgyEAAKRLL--SAPDRPTAIFCGNDRMAMGVYQAAAELGLRVPEDLSVVG 211
PBP1_DegA_Like cd19976
ligand-binding domain of putative DNA transcription regulators highly similar to that of the ...
 134-259 3.41e-07

ligand-binding domain of putative DNA transcription regulators highly similar to that of the transcription regulator DegA; This group includes the ligand-binding domain of uncharacterized DNA transcription repressors highly similar to that of the transcription regulator DegA, which is involved in the control of degradation of Bacillus subtilis amidophosphoribosyltransferase (purF). This group belongs to the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.


Pssm-ID: 380631 [Multi-domain]  Cd Length: 268  Bit Score: 50.71  E-value: 3.41e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 134 VILVD-CMEADNANSIQFDHAFAAETACNYLTSQGRRQIALIH-PHGSGFADQVLLGYKHALEKNFLPFNRNLVFMDATS 211
Cdd:cd19976   82 VVVLDrYIEDNDSDSVGVDDYRGGYEATKYLIELGHTRIGCIVgPPSTYNEHERIEGYKNALQDHNLPIDESWIYSGESS 161

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 489957726 212 SS---VALQELLNNAstlNFNALLVADEQEAQRVIPQLQAFNKSVPEDIMV 259
Cdd:cd19976  162 LEggyKAAEELLKSK---NPTAIFAGNDLIAMGVYRAALELGLKIPEDLSV 209
PRK10339 PRK10339
DNA-binding transcriptional repressor EbgR; Provisional
 1-262 1.31e-06

DNA-binding transcriptional repressor EbgR; Provisional


Pssm-ID: 182389 [Multi-domain]  Cd Length: 327  Bit Score: 49.37  E-value: 1.31e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726   1 MSTINDVSRLAGVSKATVSRVLSG--SRGVKEASRQAVLKAVDELNYRP--------------NVIAQSLLSQSTGC--- 61
Cdd:PRK10339   1 MATLKDIAIEAGVSLATVSRVLNDdpTLNVKEETKHRILEIAEKLEYKTssarklqtgavnqhHILAIYSYQQELEIndp 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726  62 --------IGVICAQENINQTTGYLYALEKHLSQHQKHLLLrfAHTKTEVMNALEELScglcddilvigarfpldvdmDN 133
Cdd:PRK10339  81 yylairhgIETQCEKLGIELTNCYEHSGLPDIKNVTGILIV--GKPTPALRAAASALT--------------------DN 138

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 134 VILVDCMEAD-NANSIQFDHAFAAETACNYLTSQGRRQIALI----HPHGSGFADQVLLGY---KHALEKNflpfnrNLV 205
Cdd:PRK10339 139 ICFIDFHEPGsGYDAVDIDLARISKEIIDFYINQGVNRIGFIggedEPGKADIREVAFAEYgrlKQVVREE------DIW 212

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 206 FMDATSSS---VAlQELLnnASTLNFNALLVADEQEAQRVIPQLQAFNKSVPEDIMVFSL 262
Cdd:PRK10339 213 RGGFSSSSgyeLA-KQML--AREDYPKALFVASDSIAIGVLRAIHERGLNIPQDISLISV 269
PBP1_LacI-like cd06299
ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum ...
 143-294 2.38e-06

ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum produces significant amounts of L-glutamate directly from cheap sugar and ammonia; This group includes the ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This regulatory protein is a member of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380522 [Multi-domain]  Cd Length: 268  Bit Score: 48.04  E-value: 2.38e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 143 DNANSIQFDHAFAAETACNYLTSQGRRQIALIH-PHGSGFADQVLLGYKHALEKNFLPFNRNLVF---MDATSSSVALQE 218
Cdd:cd06299   92 GGVPVVTSDNRPGAREAVEYLVSLGHRRIGYISgPLSTSTGRERLAAFRAALTAAGIPIDEELVAfgdFRQDSGAAAAHR 171

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 219 LLNNASTLnfNALLVADEQEAQRVIPQLQAFNKSVPEDIMV--------FSLGGslhlpgiPVIPAIEYSMDAMAARIVS 290
Cdd:cd06299  172 LLSRGDPP--TALIAGDSLMALGAIQALRELGLRIGDDVSLisfddvpwFELLS-------PPLTVIAQPVERIGRRAVE 242


                 ....
gi 489957726 291 WLTE 294
Cdd:cd06299  243 LLLA 246
PBP1_AraR cd01541
ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a ...
 144-310 2.66e-06

ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators; Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of AraR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type 1 periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type 1 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380483 [Multi-domain]  Cd Length: 274  Bit Score: 47.94  E-value: 2.66e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 144 NANSIQFDHAFAAETACNYLTSQGRRQIALIHPHGSGFADQVLLGYKHALEKNFLPFNRNLVFM----DATSSSVA--LQ 217
Cdd:cd01541   97 DAPSVSLDDEKGGYLATKHLIDLGHRRIAGIFKSDDLQGVERYQGFIKALREAGLPIDDDRILWysteDLEDRFFAeeLR 176

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 218 ELLNnaSTLNFNALLVADEQEAQRVIPQLQAFNKSVPEDIMVFSLGGS-LHLPGIPVIPAIE---YSMDAMAARIVswlt 293
Cdd:cd01541  177 EFLR--RLSRCTAIVCYNDEIALRLIQALREAGLRVPEDLSVVGFDDSyLASLSEPPLTSVVhpkEELGRKAAELL---- 250

                        170       180
                 ....*....|....*....|...
gi 489957726 294 ekTQML------GSYVLRGDLII 310
Cdd:cd01541  251 --LRMIeegrkpESVIFPPELIE 271
PBP1_GntR cd01575
ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of ...
 150-265 7.74e-06

ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators; This group represents the ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of GntR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type 1 periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type 1 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding, which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380489 [Multi-domain]  Cd Length: 269  Bit Score: 46.33  E-value: 7.74e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 150 FDHAFAAETACNYLTSQGRRQIALI--HPHGSGFADQVLLGYKHALEKNFLPfnRNLVFMDATSSSV-----ALQELLNN 222
Cdd:cd01575   98 FSNFAAGRAMARHLIERGYRRIAFVgaRLDGDSRARQRLEGFRDALAEAGLP--LPLVLLVELPSSFalgreALAELLAR 175

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 489957726 223 ASTLnfNALLVADEQEAQRVIPQLQAFNKSVPEDIMVFSLGGS 265
Cdd:cd01575  176 HPDL--DAIFCSNDDLALGALFECQRRGIRVPGDIAIAGFGDL 216
PBP1_LacI cd01574
ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of ...
 134-259 2.73e-05

ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators; Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of LacI is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type 1 periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type 1 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380488 [Multi-domain]  Cd Length: 265  Bit Score: 44.88  E-value: 2.73e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 134 VILVDCMEADNANSIQFDHAFAAETACNYLTSQGRRQIALIH-PHGSGFADQVLLGYKHALEKNFLPfNRNLVFMD--AT 210
Cdd:cd01574   82 VVIVGSGPSPGVPTVSIDQEEGARLATRHLLELGHRRIAHIAgPLDWVDARARLRGWREALEEAGLP-PPPVVEGDwsAA 160

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 489957726 211 SSSVALQELLNnasTLNFNALLVADEQEAQRVIPQLQAFNKSVPEDIMV 259
Cdd:cd01574  161 SGYRAGRRLLD---DGPVTAVFAANDQMALGALRALHERGLRVPEDVSV 206
PBP1_Qymf-like cd06291
ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing ...
 78-290 2.86e-05

ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs; This group includes the ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus metalliredigens (strain Qymf) and its close homologs. Qymf is a strict anaerobe that could be grown in the presence of borax and its cells are straight rods that produce endospores. This group is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380514 [Multi-domain]  Cd Length: 264  Bit Score: 44.82  E-value: 2.86e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726  78 LYALEKHLSQHQKHLLL-RFAHTKTEVMNALEELSCGLCDDILVIGARFPLDVDMDN---VILVDCMEADNANSIQFDHA 153
Cdd:cd06291   18 AKYIEKELFKKGYKMILcNSNEDEEKEKEYLEMLKRNKVDGIILGSHSLDIEEYKKLnipIVSIDRYLSEGIPSVSSDNY 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 154 FAAETACNYLTSQGRRQIALI-HPHGSGFADQVLLGYKHALEKNFLPFNRNLVFMDATSSS---VALQELLNNasTLNFN 229
Cdd:cd06291   98 QGGRLAAEHLIEKGCKKILHIgGPSNNSPANERYRGFEDALKEAGIEYEIIEIDENDFSEEdayELAKELLEK--YPDID 175

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489957726 230 ALLVADEQEAQRVIPQLQAFNKSVPEDIMVFSLGGS-LHLPGIPVIPAIEYSMDAMAARIVS 290
Cdd:cd06291  176 GIFASNDLLAIGVLKALQKLGIRVPEDVQIIGFDGIeISELLYPELTTIRQPIEEMAKEAVE 237
PBP1_CcpA cd06298
ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major ...
 134-261 3.80e-05

ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation; Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. In gram-positive bacteria, CCR is controlled by HPr, a phosphoenolpyruvate:sugar phsophotrasnferase system (PTS) and a transcriptional regulator CcpA. Moreover, CcpA can regulate sporulation and antibiotic resistance as well as play a role in virulence development of certain pathogens such as the group A streptococcus. The ligand binding domain of CcpA is a member of the LacI-GalR family of bacterial transcription regulators.


Pssm-ID: 380521 [Multi-domain]  Cd Length: 268  Bit Score: 44.59  E-value: 3.80e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 134 VILVDCMEADNA-NSIQFDHAFAAETACNYLTSQGRRQIALIhphGSGFADQV-----LLGYKHALEKNFLPFNRNLVFM 207
Cdd:cd06298   81 VVLAGTVDSDHEiPSVNIDYEQAAYDATKSLIDKGHKKIAFV---SGPLKEYInndkkLQGYKRALEEAGLEFNEPLIFE 157

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 489957726 208 ---DATSSSVALQELLNNASTlnfNALLVADEQEAQRVIPQLQAFNKSVPEDIMVFS 261
Cdd:cd06298  158 gdyDYDSGYELYEELLESGEP---DAAIVVRDEIAVGLLNAAQDRGLKVPEDLEIIG 211
PBP1_LacI-like cd19974
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
 62-310 4.93e-05

ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380629 [Multi-domain]  Cd Length: 270  Bit Score: 44.08  E-value: 4.93e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726  62 IGVICAqENINQTTGY----LYALEKHLSQHQKHLLLrfahtktEVMNALEELSCGL--------CDDILVIGaRFPLD- 128
Cdd:cd19974    2 IAVLIP-ERFFGDNSFygkiYQGIEKELSELGYNLVL-------EIISDEDEEELNLpsiiseekVDGIIILG-EISKEy 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 129 -------------VDM-DNVILVDCMEADNansiqFDHAFaaeTACNYLTSQGRRQIALIHP--HGSGFADQvLLGYKHA 192
Cdd:cd19974   73 leklkelgipvvlVDHyDEELNADSVLSDN-----YYGAY---KLTSYLIEKGHKKIGFVGDinYTSSFMDR-YLGYRKA 143

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 193 LEKNFLPFNRNLVFMDATSSSVALQELLNNASTLNF-NALLVADEQEAQRVIPQLQAFNKSVPEDIMVFSLGGSLHL-PG 270
Cdd:cd19974  144 LLEAGLPPEKEEWLLEDRDDGYGLTEEIELPLKLMLpTAFVCANDSIAIQLIKALKEKGYRVPEDISVVGFDNIELAeLS 223

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....
gi 489957726 271 IPVIPAIEYSMDAMAARIVSWLTEKTQM----LGSYVLRGDLII 310
Cdd:cd19974  224 TPPLTTVEVDKEAMGRRAVEQLLWRIENpdrpFEKILVSGKLIE 267
PBP1_LacI-like cd06280
ligand-binding domain of an uncharacterized transcription regulator from Staphylococcus ...
 137-279 6.83e-05

ligand-binding domain of an uncharacterized transcription regulator from Staphylococcus saprophyticus and its close homologs from other bacteria; This group includes the ligand-binding domain of an uncharacterized transcription regulator from Staphylococcus saprophyticus and its close homologs from other bacteria. This group belongs to the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.


Pssm-ID: 380503 [Multi-domain]  Cd Length: 266  Bit Score: 43.79  E-value: 6.83e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 137 VDCMEADnanSIQFDHAFAAETACNYLTSQGRRQIALIH-PHGSGFADQVLLGYKHALEKNFLPFNRNLVF-----MDAT 210
Cdd:cd06280   88 VEGLELD---LVAGDNREGAYKAVKHLIELGHRRIGLITgPLEISTTRERLAGYREALAEAGIPVDESLIFegdstIEGG 164

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489957726 211 SSSValQELL--NNASTlnfnALLVADEQEAQRVIPQLQAFNKSVPEDIMVFSLGG----SLHLPGIPVI--PAIEY 279
Cdd:cd06280  165 YEAV--KALLdlPPRPT----AIFATNNLMAVGALRALRERGLEIPQDISVVGFDDsdwfEIVDPPLTVVaqPAYEI 235
PBP1_PurR cd06275
ligand-binding domain of purine repressor, PurR, which functions as the master regulatory ...
 134-259 6.87e-05

ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli; Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. This dimeric PurR belongs to the LacI-GalR family of transcription regulators and is activated to bind to DNA operator sites by initially binding either of high affinity corepressors, hypoxanthine or guanine. PurR is composed of two functional domains: aan N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the purine transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380499 [Multi-domain]  Cd Length: 269  Bit Score: 43.78  E-value: 6.87e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 134 VILVDC-MEADNANSIQFDHAFAAETACNYLTSQGRRQIALI-HPHGSGFADQVLLGYKHALEKNFLPFNRNLVFM---D 208
Cdd:cd06275   82 VVVLDReIAGDNADAVLDDSFQGGYLATRHLIELGHRRIGCItGPLEHSVSRERLAGFRRALAEAGIEVPPSWIVEgdfE 161

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 489957726 209 ATSSSVALQELLNNAStlNFNALLVADEQEAQRVIPQLQAFNKSVPEDIMV 259
Cdd:cd06275  162 PEGGYEAMQRLLSQPP--RPTAVFACNDMMALGALRAAQEQGLRVPQDISI 210
PBP1_hexuronate_repressor-like cd06272
ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon ...
 146-305 1.33e-04

ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and close homologs, all members of the LacI-GalR family of bacterial transcription regulators; Ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and its close homologs from other bacteria, all of which are members of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380496 [Multi-domain]  Cd Length: 266  Bit Score: 42.75  E-value: 1.33e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 146 NSIQFDHAFAAETACNYLTSQGRRQIALIHPHGSGFADQV-LLGYKHALEKNFLPFNRNLVFMDATSSSV---ALQELLN 221
Cdd:cd06272   93 STVNVDNEKAGRLAVLLLIQKGHKSIAYIGNPNSNRNQTLrGKGFIETCEKHGIHLSDSIIDSRGLSIEGgdnAAKKLLK 172

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 222 NaSTLNfNALLVADEQEAQRVIPQLQAFNKSVPEDIMVFSLGgslHLP----GIPVIPAIEYSMDAMAARIVSWLTE--- 294
Cdd:cd06272  173 K-KTLP-KAIFCNSDDIALGVLRVLKENGISIPEDISIVSYD---NIPqearSDPPLTVVGVPIEKIAEESLRLILKlie 247

                        170
                 ....*....|....*..
gi 489957726 295 ------KTQMLGSYVLR 305
Cdd:cd06272  248 greneiQQLILYPELIF 264
PBP1_CcpA_TTHA0807 cd06297
ligand-binding domain of TTHA0807, a CcpA regulator, from Thermus thermophilus HB8 and its ...
 134-259 5.65e-04

ligand-binding domain of TTHA0807, a CcpA regulator, from Thermus thermophilus HB8 and its close homologs; Ligand-binding domain of the uncharacterized transcription regulator TTHA0807 from the extremely thermophilic organism Thermus thermophilus HB8 and close homologs from other bacteria. Although its exact biological function is not known, the TTHA0807 belongs to the catabolite control protein A (CcpA)family of regulatory proteins. The CcpA functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. In gram-positive bacteria, CCR is controlled by HPr, a phosphoenolpyruvate:sugar phsophotrasnferase system (PTS) and a transcriptional regulator CcpA. Moreover, CcpA can regulate sporulation and antibiotic resistance as well as play a role in virulence development of certain pathogens such as the group A streptococcus. The ligand binding domain of CcpA is a member of the LacI-GalR family of bacterial transcription regulators.


Pssm-ID: 380520 [Multi-domain]  Cd Length: 268  Bit Score: 40.91  E-value: 5.65e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 134 VILVDcMEADNANSIQFDHAFAAETACNYLTSQGRRQIALI-----HPHGSGFADQVLLGYKHALEKNFLPFNRNLVF-- 206
Cdd:cd06297   81 VVLID-ANSMGYDCVYVDNVKGGFMATEYLAGLGEREYVFFgieedTVFTETVFREREQGFLEALNKAGRPISSSRMFri 159

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 489957726 207 -MDATSSSVALQELLNNAStlNFNALLVADEQEAQRVIPQLQAFNKSVPEDIMV 259
Cdd:cd06297  160 dNSSKKAECLARELLKKAD--NPAAFFAAADLVALGLIRAAQSLGLRVGEDVAV 211
PBP1_LacI-like cd06273
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
 147-310 9.48e-04

ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380497 [Multi-domain]  Cd Length: 268  Bit Score: 40.18  E-value: 9.48e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 147 SIQFDHAFAAETACNYLTSQGRRQIALIHP--HGSGFADQVLLGYKHALEKNFLPFNRNLVF---MDATSSSVALQELLn 221
Cdd:cd06273   95 SIGFDNRAAAARAAQHLLDLGHRRIAVISGptAGNDRARARLAGIRDALAERGLELPEERVVeapYSIEEGREALRRLL- 173

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 222 nASTLNFNALLVADEQEAQRVIPQLQAFNKSVPEDIMVF---SLGGSLHL-PGIPVI--PAIEysMDAMAAR-IVSWLTE 294
Cdd:cd06273  174 -ARPPRPTAIICGNDVLALGALAECRRLGISVPEDLSITgfdDLELAAHLsPPLTTVrvPARE--IGELAARyLLALLEG 250

                        170
                 ....*....|....*.
gi 489957726 295 KtQMLGSYVLRGDLII 310
Cdd:cd06273  251 G-PPPKSVELETELIV 265
PBP1_LacI-like cd06277
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
 75-260 1.03e-03

ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380500 [Multi-domain]  Cd Length: 275  Bit Score: 39.92  E-value: 1.03e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726  75 TGYLYALEKHLSQHQKHLLLRFAHTKTEVMNALEELSCGLCDDILVIGARFPLDvDMD-------NVILVD-CMEADNAN 146
Cdd:cd06277   22 SELIDGIEREARKYGYNLLISSVDIGDDFDEILKELTDDQSSGIILLGTELEEK-QIKlfqdvsiPVVVVDnYFEDLNFD 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 147 SIQFDHAFAAETACNYLTSQGRRQIALIHPHG--SGFADQVLlGYKHALEKNFLPFNRNLVFM---DATSSSVALQELLN 221
Cdd:cd06277  101 CVVIDNEDGAYEAVKYLVELGHTRIGYLASSYriKNFEERRR-GFRKAMRELGLSEDPEPEFVvsvGPEGAYKDMKALLD 179

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 489957726 222 NASTLNfNALLVADEQEAQRVIPQLQAFNKSVPEDIMVF 260
Cdd:cd06277  180 TGPKLP-TAFFAENDIIALGCIKALQEAGIRVPEDVSVI 217
PBP1_AglR-like cd20010
Ligand-binding domain of DNA transcription repressor specific for alpha-glucosides (AglR) and ...
 150-289 1.44e-03

Ligand-binding domain of DNA transcription repressor specific for alpha-glucosides (AglR) and similar proteins; Ligand-binding domain of DNA transcription repressor specific for alpha-glucosides (AglR) which is a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380665 [Multi-domain]  Cd Length: 269  Bit Score: 39.46  E-value: 1.44e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 150 FDHAFAAETACNYLTSQGRRQIALIH-PHGSGFADQVLLGYKHALEKNFLPFNRNLVF---MDATSSSVALQELL--NNA 223
Cdd:cd20010  102 IDNEGAFRRATRRLLALGHRRIALLNgPEELNFAHQRRDGYRAALAEAGLPVDPALVRegpLTEEGGYQAARRLLalPPP 181

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489957726 224 STlnfnALLVADEQEAQRVIPQLQAFNKSVPEDIMVFSLGGSLHLPGI--PVIPAIEYSMDAMAARIV 289
Cdd:cd20010  182 PT----AIVCGSDLLALGAYRALREAGLSPGKDVSVIGHDDLLPALEYfsPPLTTTRSSLRDAGRRLA 245
PBP1_repressor_sugar_binding-like cd01537
Ligand-binding domain of the LacI-GalR family of transcription regulators and the ...
 142-260 2.46e-03

Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems; Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems, all of which contain the type 1 periplasmic binding protein-like fold. Their specific ligands include lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor; in general the sugar binding domain in this family binds a sugar, which in turn changes the DNA binding activity of the repressor domain. The core structure of the periplasmic binding proteins is classified into two types and they differ in number and order of beta strands in each domain: type 1, which has six beta strands, and type 2, which has five beta strands. These two distinct structural arrangements may have originated from a common ancestor.


Pssm-ID: 380479 [Multi-domain]  Cd Length: 265  Bit Score: 38.77  E-value: 2.46e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 142 ADNANSIQFDHAFAAETACNYLTSQGRRQIALIH-PHGSGFADQVLLGYKHALEKNFL---PFNRNLVFMDATSSSVALQ 217
Cdd:cd01537   92 YDKAYYVITDSKEGGIIQGDLLAKHGHIQIVLLKgPLGHPDAEARLAGVIKELNDKGIkteQLQLDTGDWDTASGKDKMD 171

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 489957726 218 ELLNNASTLnfNALLVADEQEAQRVIPQLQAFNKSVPEDIMVF 260
Cdd:cd01537  172 QWLSGPNKP--TAVIANNDAMAMGAVEALKEHGLRVPSDISVF 212
PBP1_AglR_RafR-like cd06271
ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and ...
 150-292 5.05e-03

ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators; Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380495 [Multi-domain]  Cd Length: 264  Bit Score: 37.79  E-value: 5.05e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 150 FDHAFAAETACNYLTSQGRRQIALI-HPHGSGFADQVLLGYKHALEKNFLPfnRNLVFMDATSSS--VALQELLnnASTL 226
Cdd:cd06271  100 IDNEAGAYEAVERLAGLGHRRIAFIvPPARYSPHDRRLQGYVRA*RDAGLT--GYPLDADTTLEAgrAAAQRLL--ALSP 175

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489957726 227 NFNALLVADEQEAQRVIPQLQAFNKSVPEDIMVFSLGGS--LHLPGIPVIPAIEYSMDAMAARIVSWL 292
Cdd:cd06271  176 RPTAIVTMNDSATIGLVAGLQAAGLKIGEDVSIIGKDSApfLGAMITPPLTTVHAPIAEAGRELAKAL 243
PBP1_CelR cd06295
ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly ...
 85-259 6.07e-03

ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators; This group includes the ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators. The binding of CelR to the celE promoter is inhibited specifically by cellobiose. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380518 [Multi-domain]  Cd Length: 273  Bit Score: 37.62  E-value: 6.07e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726  85 LSQHQKHLLLRFAHTKTevMNALEELSCGLCDDILVIG-----ARFPlDVDMDNVILVDCMEADNAN---SIQFDHAFAA 156
Cdd:cd06295   36 LTDRGYDMLLSTQDEDA--NQLARLLDSGRADGLIVLGqgldhDALR-ELAQQGLPMVVWGAPEDGQsycSVGSDNVKGG 112

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489957726 157 ETACNYLTSQGRRQIALI-HPHGSGFADQvLLGYKHALEKNFLPFNRNLVFMDATSSS---VALQELLnnASTLNFNALL 232
Cdd:cd06295  113 ALATEHLIEIGRRRIAFLgDPPHPEVADR-LQGYRDALAEAGLEADPSLLLSCDFTEEsgyAAMRALL--DSGTAFDAIF 189

                        170       180
                 ....*....|....*....|....*..
gi 489957726 233 VADEQEAQRVIPQLQAFNKSVPEDIMV 259
Cdd:cd06295  190 AASDLIAMGAIRALRERGISVPGDVAV 216
 
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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