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Conserved domains on  [gi|1586794395|gb|TCB63277|]
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LysR family transcriptional regulator [Rhizobium leguminosarum bv. viciae]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
chol_sulf_TF super family cl33209
putative choline sulfate-utilization transcription factor; Members of this protein family are ...
 6-296 2.10e-109

putative choline sulfate-utilization transcription factor; Members of this protein family are transcription factors of the LysR family. Their genes typically are divergently transcribed from choline-sulfatase genes. That enzyme makes choline, a precursor to the osmoprotectant glycine-betaine, available by hydrolysis of choline sulfate.


The actual alignment was detected with superfamily member TIGR03418:

Pssm-ID: 188320 [Multi-domain]  Cd Length: 291  Bit Score: 318.99  E-value: 2.10e-109
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395   6 PELGWMRIFAEVARLGSFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQHRGVELTAEGERLFQVAAKTVGDIDALAR 85
Cdd:TIGR03418   1 LSLQWLRVFESAARLASFTAAARELGSTQPAVSQQIKRLEEELGVPLFERKHRGVELTEDGQRLFEAVRRGLDTIDAATA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395  86 SFRTEAQRPVVRLRTDYAFSALWLIPRMHGFRLLHPEADIQIVATQRLEPGFRDDADVVVVFGTRAEFGAIGSLLLQEKV 165
Cdd:TIGR03418  81 ALRARRRRETLTLATDFAFATYWLMPRLHRFKAAMPDVDVSIVTSQDSHDGQRDDIDVAILFGDGRWPGGEAVRLFPEEV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395 166 VPVCTKGFLDRNGPFDDPQLLAKAVLIHLDSPTPPPWFDWRSYLAEFSVTRdlHAGRGDVSFNTYSLVVQAALSEQGVAI 245
Cdd:TIGR03418 161 TPVCSPALRAGLPDPLSAADLLRLPLLHLEPTQPARWFDWAGWFRALGLER--PPAPGGLRFNNYTLVIQAAIAGQGVAL 238

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1586794395 246 GWMGLVDTLLSTHMLVEAGPPLEAPDRGYWLIPPRSANIDS--ERLSTWLVDE 296
Cdd:TIGR03418 239 GWAPLVDELLAAGQLVRLGDEPVVTERGYYLVRPPRKPRDAavEAFRDWLLDE 291
 
Name Accession Description Interval E-value
chol_sulf_TF TIGR03418
putative choline sulfate-utilization transcription factor; Members of this protein family are ...
 6-296 2.10e-109

putative choline sulfate-utilization transcription factor; Members of this protein family are transcription factors of the LysR family. Their genes typically are divergently transcribed from choline-sulfatase genes. That enzyme makes choline, a precursor to the osmoprotectant glycine-betaine, available by hydrolysis of choline sulfate.


Pssm-ID: 188320 [Multi-domain]  Cd Length: 291  Bit Score: 318.99  E-value: 2.10e-109
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395   6 PELGWMRIFAEVARLGSFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQHRGVELTAEGERLFQVAAKTVGDIDALAR 85
Cdd:TIGR03418   1 LSLQWLRVFESAARLASFTAAARELGSTQPAVSQQIKRLEEELGVPLFERKHRGVELTEDGQRLFEAVRRGLDTIDAATA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395  86 SFRTEAQRPVVRLRTDYAFSALWLIPRMHGFRLLHPEADIQIVATQRLEPGFRDDADVVVVFGTRAEFGAIGSLLLQEKV 165
Cdd:TIGR03418  81 ALRARRRRETLTLATDFAFATYWLMPRLHRFKAAMPDVDVSIVTSQDSHDGQRDDIDVAILFGDGRWPGGEAVRLFPEEV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395 166 VPVCTKGFLDRNGPFDDPQLLAKAVLIHLDSPTPPPWFDWRSYLAEFSVTRdlHAGRGDVSFNTYSLVVQAALSEQGVAI 245
Cdd:TIGR03418 161 TPVCSPALRAGLPDPLSAADLLRLPLLHLEPTQPARWFDWAGWFRALGLER--PPAPGGLRFNNYTLVIQAAIAGQGVAL 238

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1586794395 246 GWMGLVDTLLSTHMLVEAGPPLEAPDRGYWLIPPRSANIDS--ERLSTWLVDE 296
Cdd:TIGR03418 239 GWAPLVDELLAAGQLVRLGDEPVVTERGYYLVRPPRKPRDAavEAFRDWLLDE 291
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 1-300 5.18e-48

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 162.32  E-value: 5.18e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395   1 MPDRPPELGWMRIFAEVARLGSFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQHRGVELTAEGERLFQvaakTVGDI 80
Cdd:PRK11139    1 MSRRLPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFL----DIREI 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395  81 -DALA---RSFRTEAQRPVVRLRTDYAFSALWLIPRMHGFRLLHPEADIQIVATQRLEPGFRDDADVVVVFGT------R 150
Cdd:PRK11139   77 fDQLAeatRKLRARSAKGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRgnwpglR 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395 151 AEfgaigsLLLQEKVVPVCTKGFLDRNGPFDDPQLLAKAVLIHLDSPTpppwfDWRSYLAEFSVTrDLHAGRGdVSFNTY 230
Cdd:PRK11139  157 VE------KLLDEYLLPVCSPALLNGGKPLKTPEDLARHTLLHDDSRE-----DWRAWFRAAGLD-DLNVQQG-PIFSHS 223

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1586794395 231 SLVVQAALSEQGVAIGWMGLVDTLLSTHMLVEAGP-PLEAPdRGYWLIPPRSANiDSERLST---WLVDEVGRT 300
Cdd:PRK11139  224 SMALQAAIHGQGVALGNRVLAQPEIEAGRLVCPFDtVLPSP-NAFYLVCPDSQA-ELPKVAAfrqWLLAEAAQE 295
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-299 1.31e-40

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 141.54  E-value: 1.31e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395   7 ELGWMRIFAEVARLGSFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQHRGVELTAEGERLFQVAAKTVGDIDALARS 86
Cdd:COG0583     2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395  87 FRTEAQRP--VVRLRTDYAFSALWLIPRMHGFRLLHPEADIQIVA--TQRLEPGFRD-DADVVVVFgtraefgaigslll 161
Cdd:COG0583    82 LRALRGGPrgTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREgnSDRLVDALLEgELDLAIRL-------------- 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395 162 qekvvpvctkgfldrnGPFDDPQLLAKavlihldsptppPWFDWRSYLAefsVTRDLHAGRGDVSFNTYSLVVQAALSEQ 241
Cdd:COG0583   148 ----------------GPPPDPGLVAR------------PLGEERLVLV---ASPDHPLARRAPLVNSLEALLAAVAAGL 196

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395 242 GVAIGWMGLVDTLLSTHMLVEAGPPLEAPDRGYWLIPPRSANIDS--ERLSTWLVDEVGR 299
Cdd:COG0583   197 GIALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPavRAFLDFLREALAE 256
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 95-282 4.47e-32

The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate domain of LysR-type transcriptional regulators involved in controlling the expression of glutaryl-CoA dehydrogenase (GcdH), S-adenosyl-L-homocysteine hydrolase, cell division protein FtsW, tryptophan synthase, and beta-lactamase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176123 [Multi-domain]  Cd Length: 194  Bit Score: 117.68  E-value: 4.47e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395  95 VVRLRTDYAFSALWLIPRMHGFRLLHPEADIQIVATQRLEPGFRDDADVVVVFGTRAEFGAIGSLLLQEKVVPVCTKGFL 174
Cdd:cd08432     1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPALL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395 175 DRNGPfDDPQLLAKAVLIH-LDSPTPPPWFDWRSYLAEFSVTRDLHagrgdvsFNTYSLVVQAALSEQGVAIGWMGLVDT 253
Cdd:cd08432    81 AGLPL-LSPADLARHTLLHdATRPEAWQWWLWAAGVADVDARRGPR-------FDDSSLALQAAVAGLGVALAPRALVAD 152

                         170       180
                  ....*....|....*....|....*....
gi 1586794395 254 LLSTHMLVEAGPPLEAPDRGYWLIPPRSA 282
Cdd:cd08432   153 DLAAGRLVRPFDLPLPSGGAYYLVYPPGR 181
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
8-67 2.83e-24

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 92.83  E-value: 2.83e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395   8 LGWMRIFAEVARLGSFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQHRGVELTAEGE 67
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 13-173 2.41e-18

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


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 83.05  E-value: 2.41e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395  13 IFAEVARLGSFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQHRGVELTAEGERLFQVAAKTVGDIDALARSFRTEAQ 92
Cdd:NF040786    8 AFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEFDRYGK 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395  93 RPVVRLRTdyAFS---ALWLIPRM-HGFRLLHPEADIQIVAT------QRLEPGfrdDADVVVVfGTRAEFGAIGSL-LL 161
Cdd:NF040786   88 ESKGVLRI--GAStipGQYLLPELlKKFKEKYPNVRFKLMISdsikviELLLEG---EVDIGFT-GTKLEKKRLVYTpFY 161

                         170
                  ....*....|..
gi 1586794395 162 QEKVVPVCTKGF 173
Cdd:NF040786  162 KDRLVLITPNGT 173
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 7-262 4.00e-09

multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, including founding member GSU2202 from Geobacter sulfurreducens PCA, are LysR family transcriptional regulators found regularly in the vicinity of multiheme cytochromes such as GSU2203, a decaheme c-type cytochrome.


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 56.67  E-value: 4.00e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395   7 ELGWMRIFAEVARLGSFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQHRGVELTAEGERLFQVAAKTVGDIDALARS 86
Cdd:NF041036    2 ETRYLKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMDE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395  87 FRTEAQRPVVRLRTDYAFSALWLiPRMhgfrllhpeadiqivaTQRLEPGFRDDADVVVVFGTRAEfgAIGSLLLQE--- 163
Cdd:NF041036   82 LKSFKGRQRLSICCTPTFGMAHL-PGV----------------LNRFMLRNADVVDLKFLFHSPAQ--ALEGIQNKEfdl 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395 164 KVVPVCTKGFLDRNGPFDDPQllakAVLIHLDSPT---PPPWFDWRSYLAEFSVTR-------------------DLHAG 221
Cdd:NF041036  143 AIIEHCADLDLGRFHTYPLPQ----DELVFVSAPSlglPTPNVTLERLLELCLITRrdgcssrdllrrnlaeqgrDLDDF 218

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 1586794395 222 RGDVSFNTYSLVVQAALSEQGVAIGWMGLVDTLLSTHMLVE 262
Cdd:NF041036  219 RRVVVSDDLRLTIQTVLDGGGISFVSRSLVCEYLKNGQLRE 259
 
Name Accession Description Interval E-value
chol_sulf_TF TIGR03418
putative choline sulfate-utilization transcription factor; Members of this protein family are ...
 6-296 2.10e-109

putative choline sulfate-utilization transcription factor; Members of this protein family are transcription factors of the LysR family. Their genes typically are divergently transcribed from choline-sulfatase genes. That enzyme makes choline, a precursor to the osmoprotectant glycine-betaine, available by hydrolysis of choline sulfate.


Pssm-ID: 188320 [Multi-domain]  Cd Length: 291  Bit Score: 318.99  E-value: 2.10e-109
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395   6 PELGWMRIFAEVARLGSFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQHRGVELTAEGERLFQVAAKTVGDIDALAR 85
Cdd:TIGR03418   1 LSLQWLRVFESAARLASFTAAARELGSTQPAVSQQIKRLEEELGVPLFERKHRGVELTEDGQRLFEAVRRGLDTIDAATA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395  86 SFRTEAQRPVVRLRTDYAFSALWLIPRMHGFRLLHPEADIQIVATQRLEPGFRDDADVVVVFGTRAEFGAIGSLLLQEKV 165
Cdd:TIGR03418  81 ALRARRRRETLTLATDFAFATYWLMPRLHRFKAAMPDVDVSIVTSQDSHDGQRDDIDVAILFGDGRWPGGEAVRLFPEEV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395 166 VPVCTKGFLDRNGPFDDPQLLAKAVLIHLDSPTPPPWFDWRSYLAEFSVTRdlHAGRGDVSFNTYSLVVQAALSEQGVAI 245
Cdd:TIGR03418 161 TPVCSPALRAGLPDPLSAADLLRLPLLHLEPTQPARWFDWAGWFRALGLER--PPAPGGLRFNNYTLVIQAAIAGQGVAL 238

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1586794395 246 GWMGLVDTLLSTHMLVEAGPPLEAPDRGYWLIPPRSANIDS--ERLSTWLVDE 296
Cdd:TIGR03418 239 GWAPLVDELLAAGQLVRLGDEPVVTERGYYLVRPPRKPRDAavEAFRDWLLDE 291
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 1-300 5.18e-48

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 162.32  E-value: 5.18e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395   1 MPDRPPELGWMRIFAEVARLGSFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQHRGVELTAEGERLFQvaakTVGDI 80
Cdd:PRK11139    1 MSRRLPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFL----DIREI 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395  81 -DALA---RSFRTEAQRPVVRLRTDYAFSALWLIPRMHGFRLLHPEADIQIVATQRLEPGFRDDADVVVVFGT------R 150
Cdd:PRK11139   77 fDQLAeatRKLRARSAKGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRgnwpglR 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395 151 AEfgaigsLLLQEKVVPVCTKGFLDRNGPFDDPQLLAKAVLIHLDSPTpppwfDWRSYLAEFSVTrDLHAGRGdVSFNTY 230
Cdd:PRK11139  157 VE------KLLDEYLLPVCSPALLNGGKPLKTPEDLARHTLLHDDSRE-----DWRAWFRAAGLD-DLNVQQG-PIFSHS 223

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1586794395 231 SLVVQAALSEQGVAIGWMGLVDTLLSTHMLVEAGP-PLEAPdRGYWLIPPRSANiDSERLST---WLVDEVGRT 300
Cdd:PRK11139  224 SMALQAAIHGQGVALGNRVLAQPEIEAGRLVCPFDtVLPSP-NAFYLVCPDSQA-ELPKVAAfrqWLLAEAAQE 295
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-299 1.31e-40

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 141.54  E-value: 1.31e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395   7 ELGWMRIFAEVARLGSFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQHRGVELTAEGERLFQVAAKTVGDIDALARS 86
Cdd:COG0583     2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395  87 FRTEAQRP--VVRLRTDYAFSALWLIPRMHGFRLLHPEADIQIVA--TQRLEPGFRD-DADVVVVFgtraefgaigslll 161
Cdd:COG0583    82 LRALRGGPrgTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREgnSDRLVDALLEgELDLAIRL-------------- 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395 162 qekvvpvctkgfldrnGPFDDPQLLAKavlihldsptppPWFDWRSYLAefsVTRDLHAGRGDVSFNTYSLVVQAALSEQ 241
Cdd:COG0583   148 ----------------GPPPDPGLVAR------------PLGEERLVLV---ASPDHPLARRAPLVNSLEALLAAVAAGL 196

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395 242 GVAIGWMGLVDTLLSTHMLVEAGPPLEAPDRGYWLIPPRSANIDS--ERLSTWLVDEVGR 299
Cdd:COG0583   197 GIALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPavRAFLDFLREALAE 256
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
8-300 3.96e-33

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 123.57  E-value: 3.96e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395   8 LGWMRIFAEVARLGSFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQHRGVELTAEGERLFQVAAKTVGDIDALARSF 87
Cdd:PRK10086   16 LSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQEILDI 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395  88 RTeaQRPVVRLrTDYA---FSALWLIPRMHGFRLLHPEADIQIVATQRLEPGFRDDADVVVVFGTRAEFGAIGSLLLQEK 164
Cdd:PRK10086   96 KN--QELSGTL-TVYSrpsIAQCWLVPRLADFTRRYPSISLTILTGNENVNFQRAGIDLAIYFDDAPSAQLTHHFLMDEE 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395 165 VVPVCTKGFLDRNGPFDDPQLLAKAVLIH------LDSPTPppwfDWRSYLAEFSVTrdLHAGRGDVSFNTYSLVVQAAL 238
Cdd:PRK10086  173 ILPVCSPEYAERHALTGNPDNLRHCTLLHdrqawsNDSGTD----EWHSWAQHFGVN--LLPPSSGIGFDRSDLAVIAAM 246

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1586794395 239 SEQGVAIGWMGLVDTLLSTHMLVEAGPPLEAP-DRGYWLI-PPRSANIDSERLSTWLVDEVGRT 300
Cdd:PRK10086  247 NHIGVAMGRKRLVQKRLASGELVAPFGDMEVKcHQHYYVTtLPGRQWPKIEAFIDWLKEQVKTT 310
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 95-282 4.47e-32

The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate domain of LysR-type transcriptional regulators involved in controlling the expression of glutaryl-CoA dehydrogenase (GcdH), S-adenosyl-L-homocysteine hydrolase, cell division protein FtsW, tryptophan synthase, and beta-lactamase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176123 [Multi-domain]  Cd Length: 194  Bit Score: 117.68  E-value: 4.47e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395  95 VVRLRTDYAFSALWLIPRMHGFRLLHPEADIQIVATQRLEPGFRDDADVVVVFGTRAEFGAIGSLLLQEKVVPVCTKGFL 174
Cdd:cd08432     1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPALL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395 175 DRNGPfDDPQLLAKAVLIH-LDSPTPPPWFDWRSYLAEFSVTRDLHagrgdvsFNTYSLVVQAALSEQGVAIGWMGLVDT 253
Cdd:cd08432    81 AGLPL-LSPADLARHTLLHdATRPEAWQWWLWAAGVADVDARRGPR-------FDDSSLALQAAVAGLGVALAPRALVAD 152

                         170       180
                  ....*....|....*....|....*....
gi 1586794395 254 LLSTHMLVEAGPPLEAPDRGYWLIPPRSA 282
Cdd:cd08432   153 DLAAGRLVRPFDLPLPSGGAYYLVYPPGR 181
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
8-67 2.83e-24

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 92.83  E-value: 2.83e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395   8 LGWMRIFAEVARLGSFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQHRGVELTAEGE 67
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 13-173 2.41e-18

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


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 83.05  E-value: 2.41e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395  13 IFAEVARLGSFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQHRGVELTAEGERLFQVAAKTVGDIDALARSFRTEAQ 92
Cdd:NF040786    8 AFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEFDRYGK 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395  93 RPVVRLRTdyAFS---ALWLIPRM-HGFRLLHPEADIQIVAT------QRLEPGfrdDADVVVVfGTRAEFGAIGSL-LL 161
Cdd:NF040786   88 ESKGVLRI--GAStipGQYLLPELlKKFKEKYPNVRFKLMISdsikviELLLEG---EVDIGFT-GTKLEKKRLVYTpFY 161

                         170
                  ....*....|..
gi 1586794395 162 QEKVVPVCTKGF 173
Cdd:NF040786  162 KDRLVLITPNGT 173
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 104-283 8.66e-16

The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold; GcdR is involved in the glutaconate/glutarate-specific activation of the Pg promoter driving expression of a glutaryl-CoA dehydrogenase-encoding gene (gcdH). The GcdH protein is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. The structural topology of this substrate-binding domain is most similar to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176170 [Multi-domain]  Cd Length: 194  Bit Score: 74.25  E-value: 8.66e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395 104 FSALWLIPRMHGFRLLHPEADIQIVAtqRLEPgF---RDDADVVVVFGTRAEFGAIGSLLLQEKVVPVCTKGFLDRNGPf 180
Cdd:cd08481    10 FGTRWLIPRLPDFLARHPDITVNLVT--RDEP-FdfsQGSFDAAIHFGDPVWPGAESEYLMDEEVVPVCSPALLAGRAL- 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395 181 DDPQLLAKAVLIHLdSPTPPPWFDWrsyLAEFSVTRDlHAGRGdVSFNTYSLVVQAALSEQGVAIGWMGLVDTLLSTHML 260
Cdd:cd08481    86 AAPADLAHLPLLQQ-TTRPEAWRDW---FEEVGLEVP-TAYRG-MRFEQFSMLAQAAVAGLGVALLPRFLIEEELARGRL 159

                         170       180
                  ....*....|....*....|....
gi 1586794395 261 VEA-GPPLEAPDRGYWLIPPRSAN 283
Cdd:cd08481   160 VVPfNLPLTSDKAYYLVYPEDKAE 183
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 7-143 5.93e-15

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 73.65  E-value: 5.93e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395   7 ELGWMRIFAEVARLGSFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQHRGVELTAEGERLFQVAAKTVGDID---AL 83
Cdd:PRK09906    2 ELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEkakLR 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1586794395  84 ARSFRTEAQrpvvRLRTDYAFSA-LWLIPR-MHGFRLLHPEADIQIVA---TQRLEPGFRDDADV 143
Cdd:PRK09906   82 ARKIVQEDR----QLTIGFVPSAeVNLLPKvLPMFRLRHPDTLIELVSlitTQQEEKLRRGELDV 142
PRK10341 PRK10341
transcriptional regulator TdcA;
13-164 6.97e-14

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 70.66  E-value: 6.97e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395  13 IFAEVARLGSFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQHRGVELTAEGERLFQVAAKTVGDIDALARSFRTEAQ 92
Cdd:PRK10341   14 VFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEINGMSS 93

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1586794395  93 RPVVRLrtDYAFSAL---WLIPRM-HGFRLLHPEADIQIVATQ--RLEPGFRDDadvvvvfgtRAEFgAIGSLLLQEK 164
Cdd:PRK10341   94 EAVVDV--SFGFPSLigfTFMSDMiNKFKEVFPKAQVSMYEAQlsSFLPAIRDG---------RLDF-AIGTLSNEMK 159
rbcR CHL00180
LysR transcriptional regulator; Provisional
 3-127 8.89e-14

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 70.43  E-value: 8.89e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395   3 DRPPELGWMRIFAEVARLGSFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQHRGVELTAEGERLFQVAAKtvgdIDA 82
Cdd:CHL00180    2 DLPFTLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNR----ILA 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1586794395  83 LARsfrtEAQRPVVRLRTDYAFSAL---------WLIPRMHG-FRLLHPEADIQI 127
Cdd:CHL00180   78 LCE----ETCRALEDLKNLQRGTLIigasqttgtYLMPRLIGlFRQRYPQINVQL 128
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 17-67 1.42e-13

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 69.59  E-value: 1.42e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1586794395  17 VARLGSFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQHRGVELTAEGE 67
Cdd:PRK11074   13 VARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGE 63
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
11-83 1.31e-12

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 66.75  E-value: 1.31e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1586794395  11 MRIFAEVARLGSFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQHRGVELTAEGERLFQVAAKTVGDIDAL 83
Cdd:PRK10094    7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESM 79
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 12-147 4.57e-12

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 65.36  E-value: 4.57e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395  12 RIFAEVARLGSFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQHRGVELTAEGERLFQVAAKTVGDIDALARSFR--T 89
Cdd:PRK11242    7 RYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHdvA 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1586794395  90 EAQRPVVRLRTDYAFSALWLIPRMHGFRLLHP--EADIQIVATQRLEPGFRDDA-DVVVVF 147
Cdd:PRK11242   87 DLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPgiTLTIREMSQERIEALLADDElDVGIAF 147
PBP2_TrpI cd08482
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ...
 104-293 9.43e-12

The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is involved in control of tryptophan synthesis, contains type 2 periplasmic binding fold; TrpI and indoleglycerol phosphate (InGP), are required to activate transcription of the trpBA, the genes for tryptophan synthase. The trpBA is induced by the InGp substrate, rather than by tryptophan, but the exact mechanism of the activation event is not known. This substrate-binding domain of TrpI shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176171 [Multi-domain]  Cd Length: 195  Bit Score: 62.80  E-value: 9.43e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395 104 FSALWLIPRMHGFRLLHPEADIQIVATQRLEPGFRDDADVVVVFGTRA-EFGAIGSLLLQEKVVPVCTKGFLDRNGPFDD 182
Cdd:cd08482    10 LLMRWLIPRLPAFQAALPDIDLQLSASDGPVDSLRDGIDAAIRFNDAPwPAGMQVIELFPERVGPVCSPSLAPTVPLRQA 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395 183 P-QLLAKAVLIHLDSpTPPPWFDWrsylAEFSVTRDLHAGRGdVSFNTYSLVVQAALSEQGVAIGWMGLVDTLLSTHMLV 261
Cdd:cd08482    90 PaAALLGAPLLHTRS-RPQAWPDW----AAAQGLAPEKLGTG-QSFEHFYYLLEAAVAGLGVAIAPWPLVRDDLASGRLV 163

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1586794395 262 EAGPPLEAPDRGYWLIPPRSANIDSERLSTWL 293
Cdd:cd08482   164 APWGFIETGSHYVLLRPARLRDSRAGALADWL 195
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
14-69 4.21e-11

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 62.34  E-value: 4.21e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1586794395  14 FAEVARLGSFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQHRGVELTAEGERL 69
Cdd:PRK03601    9 FLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERL 64
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 10-76 4.28e-11

transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity. [Cellular processes, Toxin production and resistance, DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 62.24  E-value: 4.28e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1586794395  10 WMRIFAEVARLGSFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQhRGVELTAEGERLFQVAAKT 76
Cdd:TIGR03298   5 QLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVRT-QPCRATEAGQRLLRHARQV 70
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
14-71 4.42e-11

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 62.30  E-value: 4.42e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1586794395  14 FAEVARLGSFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQhRGVELTAEGERLFQ 71
Cdd:PRK13348   10 LAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG-RPCRPTPAGQRLLR 66
PRK09801 PRK09801
LysR family transcriptional regulator;
11-186 7.58e-11

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 61.59  E-value: 7.58e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395  11 MRIFAEVARLGSFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQHRGVELTAEGERLFQVAAKTVGDIDALARSFRTE 90
Cdd:PRK09801   11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQI 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395  91 AQRP--VVRLRTDYAFSALWLIPRMHGFRLLHPEADIQIVATQRLEPGFRDDADVVVVFGTRAEFGAIGSLLLQEKVVPV 168
Cdd:PRK09801   91 KTRPegMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDYYIAHLLTKNKRILC 170

                         170
                  ....*....|....*...
gi 1586794395 169 CTKGFLDRngpFDDPQLL 186
Cdd:PRK09801  171 AAPEYLQK---YPQPQSL 185
PRK09986 PRK09986
LysR family transcriptional regulator;
8-126 8.68e-11

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 61.28  E-value: 8.68e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395   8 LGWMRIFAEVARLGSFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQHRGVELT-------AEGERLFQVAAKTVGDI 80
Cdd:PRK09986    9 LKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLThagkilmEESRRLLDNAEQSLARV 88

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1586794395  81 DALARSfrtEAQrpvvRLRTDYAFSALW--LIPRMHGFRLLHPEADIQ 126
Cdd:PRK09986   89 EQIGRG---EAG----RIEIGIVGTALWgrLRPAMRHFLKENPNVEWL 129
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
10-76 1.01e-10

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 61.33  E-value: 1.01e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1586794395  10 WMRIFAEVARLGSFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRqHRGVELTAEGERLFQVAAKT 76
Cdd:PRK03635    6 QLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARQV 71
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
7-135 4.88e-10

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 59.26  E-value: 4.88e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395   7 ELGWMRIFAEVARLGSFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQHRGVELTAEGERLFQVAAKTVGDIdALARS 86
Cdd:PRK15421    3 EVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQI-SQALQ 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1586794395  87 FRTEAQRPVVRLRTDYAFSALWLIPRMHGFRLLHPEADIQIVATQRLEP 135
Cdd:PRK15421   82 ACNEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDP 130
PRK09791 PRK09791
LysR family transcriptional regulator;
11-74 5.48e-10

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 59.01  E-value: 5.48e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1586794395  11 MRIFAEVARLGSFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQHRGVELTAEGERLFQVAA 74
Cdd:PRK09791   10 IRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHAS 73
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 7-262 4.00e-09

multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, including founding member GSU2202 from Geobacter sulfurreducens PCA, are LysR family transcriptional regulators found regularly in the vicinity of multiheme cytochromes such as GSU2203, a decaheme c-type cytochrome.


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 56.67  E-value: 4.00e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395   7 ELGWMRIFAEVARLGSFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQHRGVELTAEGERLFQVAAKTVGDIDALARS 86
Cdd:NF041036    2 ETRYLKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMDE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395  87 FRTEAQRPVVRLRTDYAFSALWLiPRMhgfrllhpeadiqivaTQRLEPGFRDDADVVVVFGTRAEfgAIGSLLLQE--- 163
Cdd:NF041036   82 LKSFKGRQRLSICCTPTFGMAHL-PGV----------------LNRFMLRNADVVDLKFLFHSPAQ--ALEGIQNKEfdl 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395 164 KVVPVCTKGFLDRNGPFDDPQllakAVLIHLDSPT---PPPWFDWRSYLAEFSVTR-------------------DLHAG 221
Cdd:NF041036  143 AIIEHCADLDLGRFHTYPLPQ----DELVFVSAPSlglPTPNVTLERLLELCLITRrdgcssrdllrrnlaeqgrDLDDF 218

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 1586794395 222 RGDVSFNTYSLVVQAALSEQGVAIGWMGLVDTLLSTHMLVE 262
Cdd:NF041036  219 RRVVVSDDLRLTIQTVLDGGGISFVSRSLVCEYLKNGQLRE 259
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 7-75 8.05e-09

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 55.80  E-value: 8.05e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1586794395   7 ELGWMRIFAEVARLGSFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQHRGVELTAEGERLFQVAAK 75
Cdd:PRK15092   12 DLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARK 80
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
11-85 1.35e-08

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 54.98  E-value: 1.35e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1586794395  11 MRIFAEVARLG-SFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQ-HRGVELTAEGERLFQVAAKTVGDIDALAR 85
Cdd:PRK12684    6 LRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHgKRLRGLTEPGRIILASVERILQEVENLKR 82
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 93-277 2.17e-08

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


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 53.45  E-value: 2.17e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395  93 RPVVRLRTDYAFSALWLIPRMHGFRLLHPEADIQIVA--TQRLEPGFRD-DADVVVVFGTRAEFGAIGSLLLQEKVVPVC 169
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEgnSEELLDLLLEgELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395 170 TKGFLDRNGPFDDPQLLAKAVLIHLDSPTPPPWFdWRSYLAEFSVTRdlhagRGDVSFNTYSLVVQAALSEQGVAIGWMG 249
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDL-LDRALRAAGLRP-----RVVLEVNSLEALLQLVAAGLGIALLPRS 154

                         170       180
                  ....*....|....*....|....*...
gi 1586794395 250 LVDTLLSTHMLVEAGPPLEAPDRGYWLI 277
Cdd:pfam03466 155 AVARELADGRLVALPLPEPPLPRELYLV 182
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
7-71 8.57e-08

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 52.46  E-value: 8.57e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1586794395   7 ELGWMRIFAEVARLGSFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQHRGVELTAEGERLFQ 71
Cdd:PRK10632    3 RLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQ 67
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
36-92 7.54e-07

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 49.43  E-value: 7.54e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1586794395  36 AVSYQIRRLEEQFGVALLRRQHRGVELTAEGERLFQVAAKTVGDIDALARSFRTEAQ 92
Cdd:PRK11716    7 TLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGP 63
nhaR PRK11062
transcriptional activator NhaR; Provisional
 10-75 1.12e-06

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 49.24  E-value: 1.12e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1586794395  10 WMrifaeVARLGSFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQHRGVELTAEGERLFQVAAK 75
Cdd:PRK11062   13 WM-----VCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYADK 73
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 104-245 1.86e-06

The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an activator of S-adenosyl-L-homocysteine hydrolase expression, contains the type 2 periplasmic binding fold; The transcriptional regulator HvrB of the LysR family is required for the light-dependent activation of both ahcY, which encoding the enzyme S-adenosyl-L-homocysteine hydrolase (AdoHcyase) that responsible for the reversible hydrolysis of AdoHcy to adenosine and homocysteine, and orf5, a gene of unknown. The topology of this C-terminal domain of HvrB is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176172 [Multi-domain]  Cd Length: 190  Bit Score: 47.34  E-value: 1.86e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395 104 FSALWLIPRMHGFRLLHPEADIQIVATQRLEPGFRDDADVVVVFGTRAEFGAIGSLLLQEKVVPVCtkgfldRNGPFDDP 183
Cdd:cd08483    10 FASNWLMPRLGSFWAKHPEIELSLLPSADLVDLRPDGIDVAIRYGNGDWPGLESEPLTAAPFVVVA------APGLLGDR 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1586794395 184 QLLAKAVLIHLdsptppPWF------DWRSYLAEFSVTRDLHAGrgdVSFNTYSLVVQAALSEQGVAI 245
Cdd:cd08483    84 KVDSLADLAGL------PWLqergtnEQRVWLASMGVVPDLERG---VTFLPGQLVLEAARAGLGLSI 142
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 95-280 3.29e-06

The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176114 [Multi-domain]  Cd Length: 197  Bit Score: 46.66  E-value: 3.29e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395  95 VVRLRTDYAFSALWLIPRMHGFRLLHPEADIQIVATQRLEPGFRDDADVVVVFGTRAEFGAIGSLLLQEKVVPVCTKGFL 174
Cdd:cd08422     2 RLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAYL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395 175 DRNGPFDDPQLLAK-AVLIHLDSPTPPPWfdwrsylaEFSVTRDLH--AGRGDVSFNTYSLVVQAALSEQGVAIGWMGLV 251
Cdd:cd08422    82 ARHGTPQTPEDLARhRCLGYRLPGRPLRW--------RFRRGGGEVevRVRGRLVVNDGEALRAAALAGLGIALLPDFLV 153

                         170       180       190
                  ....*....|....*....|....*....|
gi 1586794395 252 DTLLSTHMLVEAGPPLEAPDRGYWLI-PPR 280
Cdd:cd08422   154 AEDLASGRLVRVLPDWRPPPLPIYAVyPSR 183
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 11-145 4.66e-06

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 47.29  E-value: 4.66e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395  11 MRIFAEVARLG-SFSAAAAGLGLTQPAVSYQIRRLEEQFGVALL-RRQHRGVELTAEGERLFQVAAKT---VGDIDALAR 85
Cdd:PRK12682    6 LRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFiRHGKRLKGLTEPGKAVLDVIERIlreVGNIKRIGD 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395  86 SF-------------RTEAQ----RPVVRLRTDYAFSALWL-------IPRMhgfrLLHPEADIQIvATQRLEpgfrDDA 141
Cdd:PRK12682   86 DFsnqdsgtltiattHTQARyvlpRVVAAFRKRYPKVNLSLhqgspdeIARM----VISGEADIGI-ATESLA----DDP 156


                  ....
gi 1586794395 142 DVVV 145
Cdd:PRK12682  157 DLAT 160
PRK12680 PRK12680
LysR family transcriptional regulator;
26-200 6.95e-06

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 46.92  E-value: 6.95e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395  26 AAAGLGLTQPAVSYQIRRLEEQFGVALLRRQHRGVE-LTAEGERLFQVAAKT---VGDIDALARSFRTEAQRPVVrLRTD 101
Cdd:PRK12680   22 AAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVlseANNIRTYAANQRRESQGQLT-LTTT 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395 102 YAFSALWLIPRMHGFRLLHPEADIQI------VATQRLEPGfrdDADVVVVFGTRAEFGA-IGSLLLQEKVVPVCTKGF- 173
Cdd:PRK12680  101 HTQARFVLPPAVAQIKQAYPQVSVHLqqaaesAALDLLGQG---DADIAIVSTAGGEPSAgIAVPLYRWRRLVVVPRGHa 177

                         170       180
                  ....*....|....*....|....*..
gi 1586794395 174 LDRNGPFDDPQLLAKAVLIHLDSPTPP 200
Cdd:PRK12680  178 LDTPRRAPDMAALAEHPLISYESSTRP 204
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
7-67 1.07e-05

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 46.20  E-value: 1.07e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1586794395   7 ELGWMRIFAEVARLGSFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQHRGVELTAEGE 67
Cdd:PRK10082   12 ETKWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGK 72
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 11-134 1.51e-05

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 45.80  E-value: 1.51e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395  11 MRIFAEVARLG-SFSAAAAGLGLTQPAVSYQIRRLEEQFGVALL-RRQHRGVELTAEGERLFQVAAKTVGD---IDALAR 85
Cdd:PRK12683    6 LRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFiRRGKRLTGLTEPGKELLQIVERMLLDaenLRRLAE 85

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1586794395  86 SFR-------------TEAQR---PVVRlrtdyAFSALWliPRMH-----------GFRLLHPEADIQIvATQRLE 134
Cdd:PRK12683   86 QFAdrdsghltvatthTQARYalpKVVR-----QFKEVF--PKVHlalrqgspqeiAEMLLNGEADIGI-ATEALD 153
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 23-77 1.78e-05

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 45.41  E-value: 1.78e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1586794395  23 FSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQHRGVELTAEGERLFQvAAKTV 77
Cdd:PRK11151   18 FRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVD-QARTV 71
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 14-132 1.95e-05

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 45.37  E-value: 1.95e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395  14 FAEVARLGSFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQHRGVELTAEGERLFQVAAKTVGDIDALARSFRTEAQR 93
Cdd:PRK14997   10 FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQVE 89

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1586794395  94 P--VVRLRTDYAFSALWLIPRMHGFRLLHPEADIQIVATQR 132
Cdd:PRK14997   90 PrgIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNR 130
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 13-55 1.89e-04

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 42.37  E-value: 1.89e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1586794395  13 IFAEVARLGSFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRR 55
Cdd:PRK10837   10 VFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDR 52
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
 104-276 2.04e-04

The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which involved in control of the beta-lactamase gene expression; contains the type 2 periplasmic binding fold; This CD represents the C-terminal substrate binding domain of LysR-type transcriptional regulator, BlaA, that involved in control of the expression of beta-lactamase genes, blaA and blaB. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. The blaA gene is located just upstream of blaB in the opposite direction and regulates the expression of the blaB. BlaA also negatively auto-regulates the expression of its own gene, blaA. BlaA (a constitutive class A penicllinase) belongs to the LysR family of transcriptional regulators, whereas BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin binding protein but it does not act as a beta-lactamase. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176176 [Multi-domain]  Cd Length: 189  Bit Score: 41.38  E-value: 2.04e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395 104 FSALWLIPRMHGFRLLHPEADIQIVATQRLEPGFRDDADVVVVFGTRAEFGAIGSLLLQEKVVPVCTKgflDRNGPFDDP 183
Cdd:cd08487    10 FAVGWLLPRLAEFRQLHPFIELRLRTNNNVVDLATEGLDFAIRFGEGLWPATHNERLLDAPLSVLCSP---EIAKRLSHP 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395 184 QLLAKAVLihLDSPTPPPWFDWRSyLAEFSVTRdlhaGRGDVsFNTYSLVVQAALSEQGVAIGWMGLVDTLLSTHMLVEa 263
Cdd:cd08487    87 ADLINETL--LRSYRTDEWLQWFE-AANMPPIK----IRGPV-FDSSRLMVEAAMQGAGVALAPAKMFSREIENGQLVQ- 157

                         170
                  ....*....|....*
gi 1586794395 264 gpPLEAPDRG--YWL 276
Cdd:cd08487   158 --PFKIEVETgsYWL 170
leuO PRK09508
leucine transcriptional activator; Reviewed
 26-70 4.46e-04

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 41.16  E-value: 4.46e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1586794395  26 AAAGLGLTQPAVSYQIRRLEEQFGVALLRRQHRGVELTAEGERLF 70
Cdd:PRK09508   42 AAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGIQPTARARQLF 86
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 13-129 6.22e-04

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 40.75  E-value: 6.22e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395  13 IFAEVARLGSFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQHRGVELTAEGERLF-QVAAKTVG--DIDALARSFRT 89
Cdd:PRK11013   11 IFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFeEVQRSYYGldRIVSAAESLRE 90

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1586794395  90 --EAQRPVVRLRtdyAFSALWLIPRMHGFRLLHPEADIQIVA 129
Cdd:PRK11013   91 frQGQLSIACLP---VFSQSLLPGLCQPFLARYPDVSLNIVP 129
HTH_ARSR cd00090
Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric ...
 11-72 8.38e-04

Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.


Pssm-ID: 238042 [Multi-domain]  Cd Length: 78  Bit Score: 37.28  E-value: 8.38e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1586794395  11 MRIFAEVARLG-SFSAAAAGLGLTQPAVSYQIRRLEEQfGVALLRRQHRGVEL-TAEGERLFQV 72
Cdd:cd00090    10 LRILRLLLEGPlTVSELAERLGLSQSTVSRHLKKLEEA-GLVESRREGRRVYYsLTDAERLLAL 72
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
 104-281 1.41e-03

The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase genes, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators, BlaA and AmpR, that are involved in control of the expression of beta-lactamase genes. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. BlaA (a constitutive class A penicillinase) belongs to the LysR family of transcriptional regulators, while BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin-binding protein, but it does not act as a beta-lactamase. AmpR regulates the expression of beta-lactamases in many enterobacterial strains and many other gram-negative bacilli. In contrast to BlaA, AmpR acts an activator only in the presence of the beta-lactam inducer. In the absence of the inducer, AmpR acts as a repressor. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176173 [Multi-domain]  Cd Length: 189  Bit Score: 38.89  E-value: 1.41e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395 104 FSALWLIPRMHGFRLLHPEADIQIVATQRLEPGFRDDADVVVVFGTRAEFGAIGSLLLQEKVVPVCTKGFLDRngpFDDP 183
Cdd:cd08484    10 FAVGWLLPRLAEFRQLHPFIDLRLSTNNNRVDIAAEGLDFAIRFGEGAWPGTDATRLFEAPLSPLCTPELARR---LSEP 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395 184 QLLAKAVLIH---LDsptpppwfDWRSYLAEFSVTRDLHAGrgdVSFNTYSLVVQAALSEQGVAIGWMGLVDTLLSTHML 260
Cdd:cd08484    87 ADLANETLLRsyrAD--------EWPQWFEAAGVPPPPING---PVFDSSLLMVEAALQGAGVALAPPSMFSRELASGAL 155

                         170       180
                  ....*....|....*....|.
gi 1586794395 261 VEAGPPlEAPDRGYWLIPPRS 281
Cdd:cd08484   156 VQPFKI-TVSTGSYWLTRLKS 175
PBP2_AmpR cd08488
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ...
 104-276 1.94e-03

The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in control of the expression of beta-lactamase gene ampC, contains the type 2 periplasmic binding fold; AmpR acts as a transcriptional activator by binding to a DNA region immediately upstream of the ampC promoter. In the absence of a beta-lactam inducer, AmpR represses the synthesis of beta-lactamase, whereas expression is induced in the presence of a beta-lactam inducer. The AmpD, AmpG, and AmpR proteins are involved in the induction of AmpC-type beta-lactamase (class C) which produced by enterobacterial strains and many other gram-negative bacilli. The activation of ampC by AmpR requires ampG for induction or high-level expression of AmpC. It is probable that the AmpD and AmpG work together to modulate the ability of AmpR to activate ampC expression. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176177 [Multi-domain]  Cd Length: 191  Bit Score: 38.67  E-value: 1.94e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395 104 FSALWLIPRMHGFRLLHPEADIQI-VATQRLEPGfRDDADVVVVFGTRAEFGAIGSLLLQEKVVPVCTKGFLDRngpFDD 182
Cdd:cd08488    10 FAVGWLLPRLADFQNRHPFIDLRLsTNNNRVDIA-AEGLDYAIRFGSGAWHGIDATRLFEAPLSPLCTPELARQ---LRE 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395 183 PQLLAKAVLIH---LDsptpppwfDWRSYLAEFSVTRDLHAGRGdVSFNTYSLVVQAALSEQGVAIGWMGLVDTLLSTHM 259
Cdd:cd08488    86 PADLARHTLLRsyrAD--------EWPQWFEAAGVGHPCGLPNS-IMFDSSLGMMEAALQGLGVALAPPSMFSRQLASGA 156

                         170
                  ....*....|....*..
gi 1586794395 260 LVEAGPPLEAPDrGYWL 276
Cdd:cd08488   157 LVQPFATTLSTG-SYWL 172
cbl PRK12679
HTH-type transcriptional regulator Cbl;
11-128 2.69e-03

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 39.02  E-value: 2.69e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395  11 MRIFAEVARLG-SFSAAAAGLGLTQPAVSYQIRRLEEQFGVAL-LRRQHRGVELTAEGERLFQVAAKTV---GDIDALAR 85
Cdd:PRK12679    6 LKIIREAARQDyNLTEVANMLFTSQSGVSRHIRELEDELGIEIfIRRGKRLLGMTEPGKALLVIAERILneaSNVRRLAD 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1586794395  86 SFRTEAqRPVVRLRTDYAFSALWLIPRMHGFRLLHPEADIQIV 128
Cdd:PRK12679   86 LFTNDT-SGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELI 127
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
11-93 2.96e-03

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 37.26  E-value: 2.96e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395  11 MRIFAEVARLG--SFSAAAAGLGLTQPAVSYQIRRLEEQfgvALLRRQH-------RGVELTAEGERLFQVAAKTVGDID 81
Cdd:COG1846    41 FRVLAALAEAGglTQSELAERLGLTKSTVSRLLDRLEEK---GLVEREPdpedrraVLVRLTEKGRALLEEARPALEALL 117

                          90
                  ....*....|..
gi 1586794395  82 ALARSFRTEAQR 93
Cdd:COG1846   118 AELLAGLSEEEL 129
PRK11050 PRK11050
manganese-binding transcriptional regulator MntR;
27-73 4.73e-03

manganese-binding transcriptional regulator MntR;


Pssm-ID: 182927 [Multi-domain]  Cd Length: 152  Bit Score: 36.91  E-value: 4.73e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1586794395  27 AAGLGLTQPAVSYQIRRLEEQfGVALlRRQHRGVELTAEGERLFQVA 73
Cdd:PRK11050   58 AARLGVSQPTVAKMLKRLARD-GLVE-MRPYRGVFLTPEGEKLAQES 102
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 11-70 5.56e-03

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 37.74  E-value: 5.56e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395  11 MRIFAEVARLGSFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQHRGVELTAEGERLF 70
Cdd:PRK11233    6 LKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILY 65
MntR COG1321
Mn-dependent transcriptional regulator MntR, DtxR family [Transcription];
27-69 5.72e-03

Mn-dependent transcriptional regulator MntR, DtxR family [Transcription];


Pssm-ID: 440932 [Multi-domain]  Cd Length: 135  Bit Score: 36.33  E-value: 5.72e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1586794395  27 AAGLGLTQPAVSYQIRRLEEQfGvaLLRRQH-RGVELTAEGERL 69
Cdd:COG1321    31 AERLGVSPPSVTEMLKKLEEK-G--LVEYEPyGGITLTEEGREL 71
cysB PRK12681
HTH-type transcriptional regulator CysB;
11-92 9.63e-03

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 37.18  E-value: 9.63e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794395  11 MRIFAEVARLG-SFSAAAAGLGLTQPAVSYQIRRLEEQFGVALLRRQHRGV-ELTAEGERLFQVAAK---TVGDIDALAR 85
Cdd:PRK12681    6 LRYIVEVVNHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLtQVTPAGEEIIRIAREilsKVESIKSVAG 85


                  ....*..
gi 1586794395  86 SFRTEAQ 92
Cdd:PRK12681   86 EHTWPDK 92
 
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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